From 93134aef3d89e2104211ebedd9df20bc06f2fbb3 Mon Sep 17 00:00:00 2001
From: rsetienne <rampaletienne@gmail.com>
Date: Mon, 1 Jul 2024 11:56:28 +0000
Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20rsetienn?=
 =?UTF-8?q?e/DAISIE@413db4fad09a4ab8d60c99ba3c57592ee143a398=20?=
 =?UTF-8?q?=F0=9F=9A=80?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 404.html                                      |  14 +--
 CONTRIBUTING.html                             |   8 +-
 LICENSE-text.html                             |   8 +-
 articles/demo_CSvsIW.html                     |  14 +--
 articles/demo_optimize.html                   |  14 +--
 articles/demo_sim.html                        |  14 +--
 articles/index.html                           |  10 +-
 articles/stac_key.html                        |  14 +--
 authors.html                                  |  19 ++--
 deps/bootstrap-5.3.1/bootstrap.bundle.min.js  |   7 ++
 .../bootstrap.bundle.min.js.map               |   1 +
 deps/bootstrap-5.3.1/bootstrap.min.css        |   5 +
 deps/data-deps.txt                            |   4 +-
 index.html                                    |  22 ++--
 news/index.html                               |   8 +-
 pkgdown.js                                    |   8 +-
 pkgdown.yml                                   |   6 +-
 reference/Bats_GreaterAntilles.html           |   8 +-
 reference/Biwa_datalist.html                  |   8 +-
 reference/DAISIE-package.html                 |   8 +-
 reference/DAISIE_CS_max_steps.html            |   8 +-
 reference/DAISIE_ExpEIN.html                  |   8 +-
 reference/DAISIE_IC.html                      |   8 +-
 reference/DAISIE_IW_num_threads.html          |   8 +-
 reference/DAISIE_ML.html                      |  13 +--
 reference/DAISIE_ML1.html                     |   8 +-
 reference/DAISIE_ML2.html                     |   8 +-
 reference/DAISIE_ML4.html                     |  13 +--
 reference/DAISIE_ML_IW.html                   |  13 +--
 reference/DAISIE_MW_ML.html                   |  16 +--
 reference/DAISIE_ONEcolonist.html             |   8 +-
 reference/DAISIE_SR_ML.html                   |  13 +--
 reference/DAISIE_SR_loglik_CS.html            |  16 +--
 reference/DAISIE_SR_sim_core.html             |   8 +-
 reference/DAISIE_abm_factor.html              |   8 +-
 reference/DAISIE_convertprobdist.html         |  13 +--
 reference/DAISIE_count_species.html           |   8 +-
 reference/DAISIE_create_island.html           |   8 +-
 reference/DAISIE_dataprep.html                |   8 +-
 reference/DAISIE_extract_stt_median.html      |   8 +-
 reference/DAISIE_format_CS.html               |  13 +--
 reference/DAISIE_format_CS_full_stt.html      |  13 +--
 reference/DAISIE_format_CS_sampled_stt.html   |  13 +--
 reference/DAISIE_format_GW.html               |  13 +--
 reference/DAISIE_format_IW_full_stt.html      |  13 +--
 reference/DAISIE_format_IW_sampled_stt.html   |  13 +--
 reference/DAISIE_loglik_CS.html               |  13 +--
 reference/DAISIE_loglik_IW.html               |  13 +--
 reference/DAISIE_loglik_integrand.html        |  13 +--
 reference/DAISIE_loglik_integrate.html        |  13 +--
 reference/DAISIE_make_archipelago.html        |   8 +-
 reference/DAISIE_make_global.html             |   8 +-
 reference/DAISIE_margprobdist.html            |  13 +--
 reference/DAISIE_numcol.html                  |  13 +--
 reference/DAISIE_plot_age_diversity.html      |   8 +-
 reference/DAISIE_plot_area.html               |   8 +-
 reference/DAISIE_plot_cladogenesis.html       |   8 +-
 reference/DAISIE_plot_extinction.html         |   8 +-
 reference/DAISIE_plot_immigration.html        |   8 +-
 reference/DAISIE_plot_input-1.png             | Bin 36205 -> 36239 bytes
 reference/DAISIE_plot_input.html              |  41 +------
 reference/DAISIE_plot_island.html             |   8 +-
 reference/DAISIE_plot_pc_rates.html           |   8 +-
 reference/DAISIE_plot_sims.html               |   8 +-
 reference/DAISIE_plot_stt.html                |  13 +--
 reference/DAISIE_probdist.html                |   8 +-
 reference/DAISIE_sample_event_cr.html         |   8 +-
 reference/DAISIE_sample_event_time_dep.html   |   8 +-
 reference/DAISIE_sample_event_trait_dep.html  |   8 +-
 reference/DAISIE_sim.html                     |  13 +--
 reference/DAISIE_sim_MW.html                  |  13 +--
 reference/DAISIE_sim_core_cr.html             |   8 +-
 reference/DAISIE_sim_core_cr_shift.html       |   8 +-
 reference/DAISIE_sim_core_time_dep.html       |   8 +-
 reference/DAISIE_sim_core_trait_dep.html      |   8 +-
 reference/DAISIE_sim_cr_cs.html               |  13 +--
 reference/DAISIE_sim_cr_gw.html               |  13 +--
 reference/DAISIE_sim_cr_iw.html               |  13 +--
 reference/DAISIE_sim_cr_shift.html            |  13 +--
 reference/DAISIE_sim_min_type2.html           |   8 +-
 reference/DAISIE_sim_relaxed_rate.html        |  13 +--
 reference/DAISIE_sim_time_dep.html            |  13 +--
 reference/DAISIE_sim_time_dep_cs.html         |  13 +--
 reference/DAISIE_sim_time_dep_gw.html         |  13 +--
 reference/DAISIE_sim_time_dep_iw.html         |  13 +--
 reference/DAISIE_sim_trait_dep.html           |   8 +-
 reference/DAISIE_sim_trait_dep_2K.html        |   8 +-
 reference/DAISIE_sim_update_state_cr.html     |   8 +-
 .../DAISIE_sim_update_state_time_dep.html     |   8 +-
 .../DAISIE_sim_update_state_trait_dep.html    |   8 +-
 reference/Galapagos_datalist.html             |  13 +--
 reference/Galapagos_datalist_2types.html      |  13 +--
 reference/Galapagos_datatable.html            |  13 +--
 reference/Macaronesia_datalist.html           |  16 +--
 reference/NewZealand_birds_datalist.html      |   8 +-
 reference/add_column_to_dataframe.html        |   8 +-
 reference/archipelago_data.html               |   8 +-
 reference/archipelagos41.html                 |  13 +--
 reference/are_rates.html                      |   8 +-
 reference/calc_Abeta.html                     |   8 +-
 reference/calc_next_timeval.html              |   8 +-
 reference/calc_next_timeval_shift.html        |   8 +-
 reference/calc_peak.html                      |   8 +-
 reference/countspecies.html                   |   8 +-
 reference/create_CS_version.html              |   8 +-
 reference/create_area_pars.html               |   8 +-
 reference/create_full_CS_stt.html             |   8 +-
 reference/create_hyper_pars.html              |   8 +-
 reference/create_pars.html                    |   8 +-
 reference/create_trait_pars.html              |   8 +-
 reference/create_trait_pars_2K.html           |   8 +-
 reference/cum_rho.html                        |   8 +-
 reference/daisie_odeint_cs.html               |   8 +-
 reference/daisie_odeint_iw.html               |   8 +-
 reference/default_params_doc.html             |   8 +-
 reference/frogs_datalist.html                 |   8 +-
 reference/frogs_datatable.html                |  13 +--
 reference/get_ana_rate.html                   |   8 +-
 reference/get_clado_rate.html                 |   8 +-
 reference/get_ext_rate.html                   |   8 +-
 reference/get_immig_rate.html                 |   8 +-
 reference/get_trans_rate.html                 |   8 +-
 reference/index.html                          | 104 ++++++------------
 reference/integral_peak.html                  |  13 +--
 reference/island_area.html                    |   8 +-
 reference/island_area_vector.html             |   8 +-
 reference/islands_10reps_RAW.html             |  13 +--
 reference/islands_1type_1000reps.html         |  13 +--
 reference/islands_2types_1000reps.html        |  13 +--
 reference/remove_empty_elements.html          |   8 +-
 reference/rho.html                            |   8 +-
 reference/sample_relaxed_rate.html            |   8 +-
 reference/stac_table.html                     |   8 +-
 reference/transform_gamma_pars.html           |   8 +-
 reference/update_max_rates.html               |   8 +-
 reference/update_rates.html                   |   8 +-
 search.json                                   |   2 +-
 137 files changed, 634 insertions(+), 831 deletions(-)
 create mode 100644 deps/bootstrap-5.3.1/bootstrap.bundle.min.js
 create mode 100644 deps/bootstrap-5.3.1/bootstrap.bundle.min.js.map
 create mode 100644 deps/bootstrap-5.3.1/bootstrap.min.css

diff --git a/404.html b/404.html
index fcb921ae..23d2eb28 100644
--- a/404.html
+++ b/404.html
@@ -7,10 +7,10 @@
 <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
 <title>Page not found (404) • DAISIE</title>
 <script src="https://rsetienne.github.io/DAISIE/deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
-<link href="https://rsetienne.github.io/DAISIE/deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet">
-<script src="https://rsetienne.github.io/DAISIE/deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
+<link href="https://rsetienne.github.io/DAISIE/deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="https://rsetienne.github.io/DAISIE/deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
 <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
-<!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="https://rsetienne.github.io/DAISIE/pkgdown.js"></script><meta property="og:title" content="Page not found (404)">
+<!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="https://rsetienne.github.io/DAISIE/pkgdown.js"></script><meta property="og:title" content="Page not found (404)">
 <!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -20,7 +20,7 @@
     <a href="https://rsetienne.github.io/DAISIE/#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="https://rsetienne.github.io/DAISIE/index.html">DAISIE</a>
 
@@ -79,13 +79,11 @@
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p>
-<p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer>
diff --git a/CONTRIBUTING.html b/CONTRIBUTING.html
index bbc42761..a3764965 100644
--- a/CONTRIBUTING.html
+++ b/CONTRIBUTING.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>DAISIE Contributing Guidelines • DAISIE</title><script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="DAISIE Contributing Guidelines"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>DAISIE Contributing Guidelines • DAISIE</title><script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="DAISIE Contributing Guidelines"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="index.html">DAISIE</a>
 
@@ -98,11 +98,11 @@ <h2 id="vignette">Vignette<a class="anchor" aria-label="anchor" href="#vignette"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/LICENSE-text.html b/LICENSE-text.html
index 0c0d0f69..c0f798fe 100644
--- a/LICENSE-text.html
+++ b/LICENSE-text.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>License • DAISIE</title><script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="License"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>License • DAISIE</title><script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="License"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="index.html">DAISIE</a>
 
@@ -733,11 +733,11 @@
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/articles/demo_CSvsIW.html b/articles/demo_CSvsIW.html
index a4fa8c78..98073e4c 100644
--- a/articles/demo_CSvsIW.html
+++ b/articles/demo_CSvsIW.html
@@ -8,10 +8,10 @@
 <meta name="description" content="DAISIE">
 <title>Demo: Fitting clade-specific and island-wide diversity-dependence models in DAISIE • DAISIE</title>
 <script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
-<link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet">
-<script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
 <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
-<!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Demo: Fitting clade-specific and island-wide diversity-dependence models in DAISIE">
+<!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Demo: Fitting clade-specific and island-wide diversity-dependence models in DAISIE">
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 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -906,13 +906,11 @@ <h4 id="plot-the-species-through-time-plots-resulting-from-the-simulations-">3.2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p>
-<p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
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diff --git a/articles/demo_optimize.html b/articles/demo_optimize.html
index 8c211212..8c514751 100644
--- a/articles/demo_optimize.html
+++ b/articles/demo_optimize.html
@@ -8,10 +8,10 @@
 <meta name="description" content="DAISIE">
 <title>Demo optimizing parameters • DAISIE</title>
 <script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
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+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
 <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
-<!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Demo optimizing parameters">
+<!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Demo optimizing parameters">
 <meta property="og:description" content="DAISIE">
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 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -22,7 +22,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -438,13 +438,11 @@ <h4 id="example-5-optimizing-a-model-with-no-diversity-dependence-but-allowing-d
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p>
-<p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
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diff --git a/articles/demo_sim.html b/articles/demo_sim.html
index 58fe72de..f35bf5e4 100644
--- a/articles/demo_sim.html
+++ b/articles/demo_sim.html
@@ -8,10 +8,10 @@
 <meta name="description" content="DAISIE">
 <title>Demo simulating islands • DAISIE</title>
 <script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
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+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
 <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
-<!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Demo simulating islands">
+<!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Demo simulating islands">
 <meta property="og:description" content="DAISIE">
 <!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -22,7 +22,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -222,13 +222,11 @@ <h4 id="example-5-3-simulating-10-islands-allowing-darwins-finches-to-have-a-hig
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p>
-<p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer>
diff --git a/articles/index.html b/articles/index.html
index 775fdf39..8fe12095 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Articles • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Articles"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Articles • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Articles"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -54,7 +54,7 @@
 
     <div class="section ">
       <h3>All vignettes</h3>
-      <p class="section-desc"></p>
+      <div class="section-desc"></div>
 
       <dl><dt><a href="demo_CSvsIW.html">Demo: Fitting clade-specific and island-wide diversity-dependence models in DAISIE</a></dt>
         <dd>
@@ -69,11 +69,11 @@ <h3>All vignettes</h3>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/articles/stac_key.html b/articles/stac_key.html
index 86e7a364..e185dd2c 100644
--- a/articles/stac_key.html
+++ b/articles/stac_key.html
@@ -8,10 +8,10 @@
 <meta name="description" content="DAISIE">
 <title>DAISIE `stac` values • DAISIE</title>
 <script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
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-<script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
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-<!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="DAISIE `stac` values">
+<!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="DAISIE `stac` values">
 <meta property="og:description" content="DAISIE">
 <!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -22,7 +22,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -200,13 +200,11 @@ <h4 id="key-for-the-different-values-of-stac-that-can-be-used-in-daisie-objects-
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p>
-<p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer>
diff --git a/authors.html b/authors.html
index 3cccc8c8..53fe5e0f 100644
--- a/authors.html
+++ b/authors.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Authors and Citation • DAISIE</title><script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="Authors and Citation"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Authors and Citation • DAISIE</title><script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="Authors and Citation"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="index.html">DAISIE</a>
 
@@ -113,17 +113,18 @@ <h2>Authors</h2>
       <h2 id="citation">Citation</h2>
       <p><small class="dont-index">Source: <a href="https://github.com/rsetienne/DAISIE/blob/HEAD/DESCRIPTION" class="external-link"><code>DESCRIPTION</code></a></small></p>
 
-      <p>Etienne R, Valente L, Phillimore A, Haegeman B, Lambert J, Santos Neves P, Xie S, Bilderbeek R, Hildenbrandt H (2023).
+      <p>Etienne R, Valente L, Phillimore A, Haegeman B, Lambert J, Santos Neves P, Xie S, Bilderbeek R, Hildenbrandt H (2024).
 <em>DAISIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction</em>.
-https://github.com/rsetienne/DAISIE,
-https://rsetienne.github.io/DAISIE/. 
+R package version 4.4.1, 
+https://rsetienne.github.io/DAISIE/, <a href="https://github.com/rsetienne/DAISIE" class="external-link">https://github.com/rsetienne/DAISIE</a>. 
 </p>
       <pre>@Manual{,
   title = {DAISIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction},
   author = {Rampal S. Etienne and Luis Valente and Albert B. Phillimore and Bart Haegeman and Joshua W. Lambert and Pedro {Santos Neves} and Shu Xie and Richèl J.C. Bilderbeek and Hanno Hildenbrandt},
-  year = {2023},
-  note = {https://github.com/rsetienne/DAISIE,
+  year = {2024},
+  note = {R package version 4.4.1, 
 https://rsetienne.github.io/DAISIE/},
+  url = {https://github.com/rsetienne/DAISIE},
 }</pre>
     </div>
   </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
@@ -131,11 +132,11 @@ <h2 id="citation">Citation</h2>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/deps/bootstrap-5.3.1/bootstrap.bundle.min.js b/deps/bootstrap-5.3.1/bootstrap.bundle.min.js
new file mode 100644
index 00000000..e8f21f70
--- /dev/null
+++ b/deps/bootstrap-5.3.1/bootstrap.bundle.min.js
@@ -0,0 +1,7 @@
+/*!
+  * Bootstrap v5.3.1 (https://getbootstrap.com/)
+  * Copyright 2011-2023 The Bootstrap Authors (https://github.com/twbs/bootstrap/graphs/contributors)
+  * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)
+  */
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s(t){i.add(t.name),[].concat(t.requires||[],t.requiresIfExists||[]).forEach((function(t){if(!i.has(t)){var n=e.get(t);n&&s(n)}})),n.push(t)}return t.forEach((function(t){e.set(t.name,t)})),t.forEach((function(t){i.has(t.name)||s(t)})),n}var fi={placement:"bottom",modifiers:[],strategy:"absolute"};function pi(){for(var t=arguments.length,e=new Array(t),i=0;i<t;i++)e[i]=arguments[i];return!e.some((function(t){return!(t&&"function"==typeof t.getBoundingClientRect)}))}function mi(t){void 0===t&&(t={});var e=t,i=e.defaultModifiers,n=void 0===i?[]:i,s=e.defaultOptions,o=void 0===s?fi:s;return function(t,e,i){void 0===i&&(i=o);var s,r,a={placement:"bottom",orderedModifiers:[],options:Object.assign({},fi,o),modifiersData:{},elements:{reference:t,popper:e},attributes:{},styles:{}},l=[],c=!1,h={state:a,setOptions:function(i){var s="function"==typeof 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vi=Object.freeze(Object.defineProperty({__proto__:null,afterMain:ae,afterRead:se,afterWrite:he,applyStyles:_e,arrow:je,auto:Kt,basePlacements:Qt,beforeMain:oe,beforeRead:ie,beforeWrite:le,bottom:Rt,clippingParents:Ut,computeStyles:Be,createPopper:bi,createPopperBase:gi,createPopperLite:_i,detectOverflow:ii,end:Yt,eventListeners:Re,flip:si,hide:ai,left:Vt,main:re,modifierPhases:de,offset:li,placements:ee,popper:Jt,popperGenerator:mi,popperOffsets:ci,preventOverflow:hi,read:ne,reference:Zt,right:qt,start:Xt,top:zt,variationPlacements:te,viewport:Gt,write:ce},Symbol.toStringTag,{value:"Module"})),yi="dropdown",wi=".bs.dropdown",Ai=".data-api",Ei="ArrowUp",Ti="ArrowDown",Ci=`hide${wi}`,Oi=`hidden${wi}`,xi=`show${wi}`,ki=`shown${wi}`,Li=`click${wi}${Ai}`,Si=`keydown${wi}${Ai}`,Di=`keyup${wi}${Ai}`,$i="show",Ii='[data-bs-toggle="dropdown"]:not(.disabled):not(:disabled)',Ni=`${Ii}.${$i}`,Pi=".dropdown-menu",Mi=p()?"top-end":"top-start",ji=p()?"top-start":"top-end",Fi=p()?"bottom-end":"bottom-start",Hi=p()?"bottom-start":"bottom-end",Wi=p()?"left-start":"right-start",Bi=p()?"right-start":"left-start",zi={autoClose:!0,boundary:"clippingParents",display:"dynamic",offset:[0,2],popperConfig:null,reference:"toggle"},Ri={autoClose:"(boolean|string)",boundary:"(string|element)",display:"string",offset:"(array|string|function)",popperConfig:"(null|object|function)",reference:"(string|element|object)"};class qi extends W{constructor(t,e){super(t,e),this._popper=null,this._parent=this._element.parentNode,this._menu=z.next(this._element,Pi)[0]||z.prev(this._element,Pi)[0]||z.findOne(Pi,this._parent),this._inNavbar=this._detectNavbar()}static get Default(){return zi}static get DefaultType(){return Ri}static get NAME(){return yi}toggle(){return this._isShown()?this.hide():this.show()}show(){if(l(this._element)||this._isShown())return;const t={relatedTarget:this._element};if(!N.trigger(this._element,xi,t).defaultPrevented){if(this._createPopper(),"ontouchstart"in document.documentElement&&!this._parent.closest(".navbar-nav"))for(const t of[].concat(...document.body.children))N.on(t,"mouseover",h);this._element.focus(),this._element.setAttribute("aria-expanded",!0),this._menu.classList.add($i),this._element.classList.add($i),N.trigger(this._element,ki,t)}}hide(){if(l(this._element)||!this._isShown())return;const t={relatedTarget:this._element};this._completeHide(t)}dispose(){this._popper&&this._popper.destroy(),super.dispose()}update(){this._inNavbar=this._detectNavbar(),this._popper&&this._popper.update()}_completeHide(t){if(!N.trigger(this._element,Ci,t).defaultPrevented){if("ontouchstart"in document.documentElement)for(const t of[].concat(...document.body.children))N.off(t,"mouseover",h);this._popper&&this._popper.destroy(),this._menu.classList.remove($i),this._element.classList.remove($i),this._element.setAttribute("aria-expanded","false"),F.removeDataAttribute(this._menu,"popper"),N.trigger(this._element,Oi,t)}}_getConfig(t){if("object"==typeof(t=super._getConfig(t)).reference&&!o(t.reference)&&"function"!=typeof t.reference.getBoundingClientRect)throw new TypeError(`${yi.toUpperCase()}: Option "reference" provided type "object" without a required "getBoundingClientRect" method.`);return t}_createPopper(){if(void 0===vi)throw new TypeError("Bootstrap's dropdowns require Popper (https://popper.js.org)");let t=this._element;"parent"===this._config.reference?t=this._parent:o(this._config.reference)?t=r(this._config.reference):"object"==typeof this._config.reference&&(t=this._config.reference);const e=this._getPopperConfig();this._popper=bi(t,this._menu,e)}_isShown(){return this._menu.classList.contains($i)}_getPlacement(){const t=this._parent;if(t.classList.contains("dropend"))return Wi;if(t.classList.contains("dropstart"))return Bi;if(t.classList.contains("dropup-center"))return"top";if(t.classList.contains("dropdown-center"))return"bottom";const e="end"===getComputedStyle(this._menu).getPropertyValue("--bs-position").trim();return t.classList.contains("dropup")?e?ji:Mi:e?Hi:Fi}_detectNavbar(){return null!==this._element.closest(".navbar")}_getOffset(){const{offset:t}=this._config;return"string"==typeof t?t.split(",").map((t=>Number.parseInt(t,10))):"function"==typeof t?e=>t(e,this._element):t}_getPopperConfig(){const t={placement:this._getPlacement(),modifiers:[{name:"preventOverflow",options:{boundary:this._config.boundary}},{name:"offset",options:{offset:this._getOffset()}}]};return(this._inNavbar||"static"===this._config.display)&&(F.setDataAttribute(this._menu,"popper","static"),t.modifiers=[{name:"applyStyles",enabled:!1}]),{...t,...g(this._config.popperConfig,[t])}}_selectMenuItem({key:t,target:e}){const i=z.find(".dropdown-menu .dropdown-item:not(.disabled):not(:disabled)",this._menu).filter((t=>a(t)));i.length&&b(i,e,t===Ti,!i.includes(e)).focus()}static jQueryInterface(t){return this.each((function(){const e=qi.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===e[t])throw new TypeError(`No method named "${t}"`);e[t]()}}))}static clearMenus(t){if(2===t.button||"keyup"===t.type&&"Tab"!==t.key)return;const e=z.find(Ni);for(const i of e){const e=qi.getInstance(i);if(!e||!1===e._config.autoClose)continue;const n=t.composedPath(),s=n.includes(e._menu);if(n.includes(e._element)||"inside"===e._config.autoClose&&!s||"outside"===e._config.autoClose&&s)continue;if(e._menu.contains(t.target)&&("keyup"===t.type&&"Tab"===t.key||/input|select|option|textarea|form/i.test(t.target.tagName)))continue;const o={relatedTarget:e._element};"click"===t.type&&(o.clickEvent=t),e._completeHide(o)}}static dataApiKeydownHandler(t){const e=/input|textarea/i.test(t.target.tagName),i="Escape"===t.key,n=[Ei,Ti].includes(t.key);if(!n&&!i)return;if(e&&!i)return;t.preventDefault();const s=this.matches(Ii)?this:z.prev(this,Ii)[0]||z.next(this,Ii)[0]||z.findOne(Ii,t.delegateTarget.parentNode),o=qi.getOrCreateInstance(s);if(n)return t.stopPropagation(),o.show(),void o._selectMenuItem(t);o._isShown()&&(t.stopPropagation(),o.hide(),s.focus())}}N.on(document,Si,Ii,qi.dataApiKeydownHandler),N.on(document,Si,Pi,qi.dataApiKeydownHandler),N.on(document,Li,qi.clearMenus),N.on(document,Di,qi.clearMenus),N.on(document,Li,Ii,(function(t){t.preventDefault(),qi.getOrCreateInstance(this).toggle()})),m(qi);const Vi="backdrop",Ki="show",Qi=`mousedown.bs.${Vi}`,Xi={className:"modal-backdrop",clickCallback:null,isAnimated:!1,isVisible:!0,rootElement:"body"},Yi={className:"string",clickCallback:"(function|null)",isAnimated:"boolean",isVisible:"boolean",rootElement:"(element|string)"};class Ui extends H{constructor(t){super(),this._config=this._getConfig(t),this._isAppended=!1,this._element=null}static get Default(){return Xi}static get DefaultType(){return Yi}static get NAME(){return Vi}show(t){if(!this._config.isVisible)return void g(t);this._append();const e=this._getElement();this._config.isAnimated&&d(e),e.classList.add(Ki),this._emulateAnimation((()=>{g(t)}))}hide(t){this._config.isVisible?(this._getElement().classList.remove(Ki),this._emulateAnimation((()=>{this.dispose(),g(t)}))):g(t)}dispose(){this._isAppended&&(N.off(this._element,Qi),this._element.remove(),this._isAppended=!1)}_getElement(){if(!this._element){const t=document.createElement("div");t.className=this._config.className,this._config.isAnimated&&t.classList.add("fade"),this._element=t}return this._element}_configAfterMerge(t){return t.rootElement=r(t.rootElement),t}_append(){if(this._isAppended)return;const t=this._getElement();this._config.rootElement.append(t),N.on(t,Qi,(()=>{g(this._config.clickCallback)})),this._isAppended=!0}_emulateAnimation(t){_(t,this._getElement(),this._config.isAnimated)}}const Gi=".bs.focustrap",Ji=`focusin${Gi}`,Zi=`keydown.tab${Gi}`,tn="backward",en={autofocus:!0,trapElement:null},nn={autofocus:"boolean",trapElement:"element"};class sn extends H{constructor(t){super(),this._config=this._getConfig(t),this._isActive=!1,this._lastTabNavDirection=null}static get Default(){return en}static get DefaultType(){return nn}static get NAME(){return"focustrap"}activate(){this._isActive||(this._config.autofocus&&this._config.trapElement.focus(),N.off(document,Gi),N.on(document,Ji,(t=>this._handleFocusin(t))),N.on(document,Zi,(t=>this._handleKeydown(t))),this._isActive=!0)}deactivate(){this._isActive&&(this._isActive=!1,N.off(document,Gi))}_handleFocusin(t){const{trapElement:e}=this._config;if(t.target===document||t.target===e||e.contains(t.target))return;const i=z.focusableChildren(e);0===i.length?e.focus():this._lastTabNavDirection===tn?i[i.length-1].focus():i[0].focus()}_handleKeydown(t){"Tab"===t.key&&(this._lastTabNavDirection=t.shiftKey?tn:"forward")}}const on=".fixed-top, .fixed-bottom, .is-fixed, .sticky-top",rn=".sticky-top",an="padding-right",ln="margin-right";class cn{constructor(){this._element=document.body}getWidth(){const t=document.documentElement.clientWidth;return Math.abs(window.innerWidth-t)}hide(){const t=this.getWidth();this._disableOverFlow(),this._setElementAttributes(this._element,an,(e=>e+t)),this._setElementAttributes(on,an,(e=>e+t)),this._setElementAttributes(rn,ln,(e=>e-t))}reset(){this._resetElementAttributes(this._element,"overflow"),this._resetElementAttributes(this._element,an),this._resetElementAttributes(on,an),this._resetElementAttributes(rn,ln)}isOverflowing(){return this.getWidth()>0}_disableOverFlow(){this._saveInitialAttribute(this._element,"overflow"),this._element.style.overflow="hidden"}_setElementAttributes(t,e,i){const n=this.getWidth();this._applyManipulationCallback(t,(t=>{if(t!==this._element&&window.innerWidth>t.clientWidth+n)return;this._saveInitialAttribute(t,e);const s=window.getComputedStyle(t).getPropertyValue(e);t.style.setProperty(e,`${i(Number.parseFloat(s))}px`)}))}_saveInitialAttribute(t,e){const i=t.style.getPropertyValue(e);i&&F.setDataAttribute(t,e,i)}_resetElementAttributes(t,e){this._applyManipulationCallback(t,(t=>{const i=F.getDataAttribute(t,e);null!==i?(F.removeDataAttribute(t,e),t.style.setProperty(e,i)):t.style.removeProperty(e)}))}_applyManipulationCallback(t,e){if(o(t))e(t);else for(const i of z.find(t,this._element))e(i)}}const hn=".bs.modal",dn=`hide${hn}`,un=`hidePrevented${hn}`,fn=`hidden${hn}`,pn=`show${hn}`,mn=`shown${hn}`,gn=`resize${hn}`,_n=`click.dismiss${hn}`,bn=`mousedown.dismiss${hn}`,vn=`keydown.dismiss${hn}`,yn=`click${hn}.data-api`,wn="modal-open",An="show",En="modal-static",Tn={backdrop:!0,focus:!0,keyboard:!0},Cn={backdrop:"(boolean|string)",focus:"boolean",keyboard:"boolean"};class On extends W{constructor(t,e){super(t,e),this._dialog=z.findOne(".modal-dialog",this._element),this._backdrop=this._initializeBackDrop(),this._focustrap=this._initializeFocusTrap(),this._isShown=!1,this._isTransitioning=!1,this._scrollBar=new cn,this._addEventListeners()}static get Default(){return Tn}static get DefaultType(){return Cn}static get NAME(){return"modal"}toggle(t){return this._isShown?this.hide():this.show(t)}show(t){this._isShown||this._isTransitioning||N.trigger(this._element,pn,{relatedTarget:t}).defaultPrevented||(this._isShown=!0,this._isTransitioning=!0,this._scrollBar.hide(),document.body.classList.add(wn),this._adjustDialog(),this._backdrop.show((()=>this._showElement(t))))}hide(){this._isShown&&!this._isTransitioning&&(N.trigger(this._element,dn).defaultPrevented||(this._isShown=!1,this._isTransitioning=!0,this._focustrap.deactivate(),this._element.classList.remove(An),this._queueCallback((()=>this._hideModal()),this._element,this._isAnimated())))}dispose(){N.off(window,hn),N.off(this._dialog,hn),this._backdrop.dispose(),this._focustrap.deactivate(),super.dispose()}handleUpdate(){this._adjustDialog()}_initializeBackDrop(){return new Ui({isVisible:Boolean(this._config.backdrop),isAnimated:this._isAnimated()})}_initializeFocusTrap(){return new sn({trapElement:this._element})}_showElement(t){document.body.contains(this._element)||document.body.append(this._element),this._element.style.display="block",this._element.removeAttribute("aria-hidden"),this._element.setAttribute("aria-modal",!0),this._element.setAttribute("role","dialog"),this._element.scrollTop=0;const e=z.findOne(".modal-body",this._dialog);e&&(e.scrollTop=0),d(this._element),this._element.classList.add(An),this._queueCallback((()=>{this._config.focus&&this._focustrap.activate(),this._isTransitioning=!1,N.trigger(this._element,mn,{relatedTarget:t})}),this._dialog,this._isAnimated())}_addEventListeners(){N.on(this._element,vn,(t=>{"Escape"===t.key&&(this._config.keyboard?this.hide():this._triggerBackdropTransition())})),N.on(window,gn,(()=>{this._isShown&&!this._isTransitioning&&this._adjustDialog()})),N.on(this._element,bn,(t=>{N.one(this._element,_n,(e=>{this._element===t.target&&this._element===e.target&&("static"!==this._config.backdrop?this._config.backdrop&&this.hide():this._triggerBackdropTransition())}))}))}_hideModal(){this._element.style.display="none",this._element.setAttribute("aria-hidden",!0),this._element.removeAttribute("aria-modal"),this._element.removeAttribute("role"),this._isTransitioning=!1,this._backdrop.hide((()=>{document.body.classList.remove(wn),this._resetAdjustments(),this._scrollBar.reset(),N.trigger(this._element,fn)}))}_isAnimated(){return this._element.classList.contains("fade")}_triggerBackdropTransition(){if(N.trigger(this._element,un).defaultPrevented)return;const t=this._element.scrollHeight>document.documentElement.clientHeight,e=this._element.style.overflowY;"hidden"===e||this._element.classList.contains(En)||(t||(this._element.style.overflowY="hidden"),this._element.classList.add(En),this._queueCallback((()=>{this._element.classList.remove(En),this._queueCallback((()=>{this._element.style.overflowY=e}),this._dialog)}),this._dialog),this._element.focus())}_adjustDialog(){const t=this._element.scrollHeight>document.documentElement.clientHeight,e=this._scrollBar.getWidth(),i=e>0;if(i&&!t){const t=p()?"paddingLeft":"paddingRight";this._element.style[t]=`${e}px`}if(!i&&t){const t=p()?"paddingRight":"paddingLeft";this._element.style[t]=`${e}px`}}_resetAdjustments(){this._element.style.paddingLeft="",this._element.style.paddingRight=""}static jQueryInterface(t,e){return this.each((function(){const i=On.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===i[t])throw new TypeError(`No method named "${t}"`);i[t](e)}}))}}N.on(document,yn,'[data-bs-toggle="modal"]',(function(t){const e=z.getElementFromSelector(this);["A","AREA"].includes(this.tagName)&&t.preventDefault(),N.one(e,pn,(t=>{t.defaultPrevented||N.one(e,fn,(()=>{a(this)&&this.focus()}))}));const i=z.findOne(".modal.show");i&&On.getInstance(i).hide(),On.getOrCreateInstance(e).toggle(this)})),R(On),m(On);const xn=".bs.offcanvas",kn=".data-api",Ln=`load${xn}${kn}`,Sn="show",Dn="showing",$n="hiding",In=".offcanvas.show",Nn=`show${xn}`,Pn=`shown${xn}`,Mn=`hide${xn}`,jn=`hidePrevented${xn}`,Fn=`hidden${xn}`,Hn=`resize${xn}`,Wn=`click${xn}${kn}`,Bn=`keydown.dismiss${xn}`,zn={backdrop:!0,keyboard:!0,scroll:!1},Rn={backdrop:"(boolean|string)",keyboard:"boolean",scroll:"boolean"};class qn extends W{constructor(t,e){super(t,e),this._isShown=!1,this._backdrop=this._initializeBackDrop(),this._focustrap=this._initializeFocusTrap(),this._addEventListeners()}static get Default(){return zn}static get DefaultType(){return Rn}static get NAME(){return"offcanvas"}toggle(t){return this._isShown?this.hide():this.show(t)}show(t){this._isShown||N.trigger(this._element,Nn,{relatedTarget:t}).defaultPrevented||(this._isShown=!0,this._backdrop.show(),this._config.scroll||(new cn).hide(),this._element.setAttribute("aria-modal",!0),this._element.setAttribute("role","dialog"),this._element.classList.add(Dn),this._queueCallback((()=>{this._config.scroll&&!this._config.backdrop||this._focustrap.activate(),this._element.classList.add(Sn),this._element.classList.remove(Dn),N.trigger(this._element,Pn,{relatedTarget:t})}),this._element,!0))}hide(){this._isShown&&(N.trigger(this._element,Mn).defaultPrevented||(this._focustrap.deactivate(),this._element.blur(),this._isShown=!1,this._element.classList.add($n),this._backdrop.hide(),this._queueCallback((()=>{this._element.classList.remove(Sn,$n),this._element.removeAttribute("aria-modal"),this._element.removeAttribute("role"),this._config.scroll||(new cn).reset(),N.trigger(this._element,Fn)}),this._element,!0)))}dispose(){this._backdrop.dispose(),this._focustrap.deactivate(),super.dispose()}_initializeBackDrop(){const t=Boolean(this._config.backdrop);return new Ui({className:"offcanvas-backdrop",isVisible:t,isAnimated:!0,rootElement:this._element.parentNode,clickCallback:t?()=>{"static"!==this._config.backdrop?this.hide():N.trigger(this._element,jn)}:null})}_initializeFocusTrap(){return new sn({trapElement:this._element})}_addEventListeners(){N.on(this._element,Bn,(t=>{"Escape"===t.key&&(this._config.keyboard?this.hide():N.trigger(this._element,jn))}))}static jQueryInterface(t){return this.each((function(){const e=qn.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===e[t]||t.startsWith("_")||"constructor"===t)throw new TypeError(`No method named "${t}"`);e[t](this)}}))}}N.on(document,Wn,'[data-bs-toggle="offcanvas"]',(function(t){const e=z.getElementFromSelector(this);if(["A","AREA"].includes(this.tagName)&&t.preventDefault(),l(this))return;N.one(e,Fn,(()=>{a(this)&&this.focus()}));const i=z.findOne(In);i&&i!==e&&qn.getInstance(i).hide(),qn.getOrCreateInstance(e).toggle(this)})),N.on(window,Ln,(()=>{for(const t of z.find(In))qn.getOrCreateInstance(t).show()})),N.on(window,Hn,(()=>{for(const t of z.find("[aria-modal][class*=show][class*=offcanvas-]"))"fixed"!==getComputedStyle(t).position&&qn.getOrCreateInstance(t).hide()})),R(qn),m(qn);const Vn={"*":["class","dir","id","lang","role",/^aria-[\w-]*$/i],a:["target","href","title","rel"],area:[],b:[],br:[],col:[],code:[],div:[],em:[],hr:[],h1:[],h2:[],h3:[],h4:[],h5:[],h6:[],i:[],img:["src","srcset","alt","title","width","height"],li:[],ol:[],p:[],pre:[],s:[],small:[],span:[],sub:[],sup:[],strong:[],u:[],ul:[]},Kn=new Set(["background","cite","href","itemtype","longdesc","poster","src","xlink:href"]),Qn=/^(?!javascript:)(?:[a-z0-9+.-]+:|[^&:/?#]*(?:[/?#]|$))/i,Xn=(t,e)=>{const i=t.nodeName.toLowerCase();return e.includes(i)?!Kn.has(i)||Boolean(Qn.test(t.nodeValue)):e.filter((t=>t instanceof RegExp)).some((t=>t.test(i)))},Yn={allowList:Vn,content:{},extraClass:"",html:!1,sanitize:!0,sanitizeFn:null,template:"<div></div>"},Un={allowList:"object",content:"object",extraClass:"(string|function)",html:"boolean",sanitize:"boolean",sanitizeFn:"(null|function)",template:"string"},Gn={entry:"(string|element|function|null)",selector:"(string|element)"};class Jn extends H{constructor(t){super(),this._config=this._getConfig(t)}static get Default(){return Yn}static get DefaultType(){return Un}static get NAME(){return"TemplateFactory"}getContent(){return Object.values(this._config.content).map((t=>this._resolvePossibleFunction(t))).filter(Boolean)}hasContent(){return this.getContent().length>0}changeContent(t){return this._checkContent(t),this._config.content={...this._config.content,...t},this}toHtml(){const t=document.createElement("div");t.innerHTML=this._maybeSanitize(this._config.template);for(const[e,i]of Object.entries(this._config.content))this._setContent(t,i,e);const e=t.children[0],i=this._resolvePossibleFunction(this._config.extraClass);return i&&e.classList.add(...i.split(" ")),e}_typeCheckConfig(t){super._typeCheckConfig(t),this._checkContent(t.content)}_checkContent(t){for(const[e,i]of Object.entries(t))super._typeCheckConfig({selector:e,entry:i},Gn)}_setContent(t,e,i){const n=z.findOne(i,t);n&&((e=this._resolvePossibleFunction(e))?o(e)?this._putElementInTemplate(r(e),n):this._config.html?n.innerHTML=this._maybeSanitize(e):n.textContent=e:n.remove())}_maybeSanitize(t){return this._config.sanitize?function(t,e,i){if(!t.length)return t;if(i&&"function"==typeof i)return i(t);const n=(new window.DOMParser).parseFromString(t,"text/html"),s=[].concat(...n.body.querySelectorAll("*"));for(const t of s){const i=t.nodeName.toLowerCase();if(!Object.keys(e).includes(i)){t.remove();continue}const n=[].concat(...t.attributes),s=[].concat(e["*"]||[],e[i]||[]);for(const e of n)Xn(e,s)||t.removeAttribute(e.nodeName)}return n.body.innerHTML}(t,this._config.allowList,this._config.sanitizeFn):t}_resolvePossibleFunction(t){return g(t,[this])}_putElementInTemplate(t,e){if(this._config.html)return e.innerHTML="",void e.append(t);e.textContent=t.textContent}}const Zn=new Set(["sanitize","allowList","sanitizeFn"]),ts="fade",es="show",is=".modal",ns="hide.bs.modal",ss="hover",os="focus",rs={AUTO:"auto",TOP:"top",RIGHT:p()?"left":"right",BOTTOM:"bottom",LEFT:p()?"right":"left"},as={allowList:Vn,animation:!0,boundary:"clippingParents",container:!1,customClass:"",delay:0,fallbackPlacements:["top","right","bottom","left"],html:!1,offset:[0,6],placement:"top",popperConfig:null,sanitize:!0,sanitizeFn:null,selector:!1,template:'<div class="tooltip" role="tooltip"><div class="tooltip-arrow"></div><div class="tooltip-inner"></div></div>',title:"",trigger:"hover focus"},ls={allowList:"object",animation:"boolean",boundary:"(string|element)",container:"(string|element|boolean)",customClass:"(string|function)",delay:"(number|object)",fallbackPlacements:"array",html:"boolean",offset:"(array|string|function)",placement:"(string|function)",popperConfig:"(null|object|function)",sanitize:"boolean",sanitizeFn:"(null|function)",selector:"(string|boolean)",template:"string",title:"(string|element|function)",trigger:"string"};class cs extends W{constructor(t,e){if(void 0===vi)throw new TypeError("Bootstrap's tooltips require Popper (https://popper.js.org)");super(t,e),this._isEnabled=!0,this._timeout=0,this._isHovered=null,this._activeTrigger={},this._popper=null,this._templateFactory=null,this._newContent=null,this.tip=null,this._setListeners(),this._config.selector||this._fixTitle()}static get Default(){return as}static get DefaultType(){return ls}static get NAME(){return"tooltip"}enable(){this._isEnabled=!0}disable(){this._isEnabled=!1}toggleEnabled(){this._isEnabled=!this._isEnabled}toggle(){this._isEnabled&&(this._activeTrigger.click=!this._activeTrigger.click,this._isShown()?this._leave():this._enter())}dispose(){clearTimeout(this._timeout),N.off(this._element.closest(is),ns,this._hideModalHandler),this._element.getAttribute("data-bs-original-title")&&this._element.setAttribute("title",this._element.getAttribute("data-bs-original-title")),this._disposePopper(),super.dispose()}show(){if("none"===this._element.style.display)throw new Error("Please use show on visible elements");if(!this._isWithContent()||!this._isEnabled)return;const t=N.trigger(this._element,this.constructor.eventName("show")),e=(c(this._element)||this._element.ownerDocument.documentElement).contains(this._element);if(t.defaultPrevented||!e)return;this._disposePopper();const i=this._getTipElement();this._element.setAttribute("aria-describedby",i.getAttribute("id"));const{container:n}=this._config;if(this._element.ownerDocument.documentElement.contains(this.tip)||(n.append(i),N.trigger(this._element,this.constructor.eventName("inserted"))),this._popper=this._createPopper(i),i.classList.add(es),"ontouchstart"in document.documentElement)for(const t of[].concat(...document.body.children))N.on(t,"mouseover",h);this._queueCallback((()=>{N.trigger(this._element,this.constructor.eventName("shown")),!1===this._isHovered&&this._leave(),this._isHovered=!1}),this.tip,this._isAnimated())}hide(){if(this._isShown()&&!N.trigger(this._element,this.constructor.eventName("hide")).defaultPrevented){if(this._getTipElement().classList.remove(es),"ontouchstart"in document.documentElement)for(const t of[].concat(...document.body.children))N.off(t,"mouseover",h);this._activeTrigger.click=!1,this._activeTrigger[os]=!1,this._activeTrigger[ss]=!1,this._isHovered=null,this._queueCallback((()=>{this._isWithActiveTrigger()||(this._isHovered||this._disposePopper(),this._element.removeAttribute("aria-describedby"),N.trigger(this._element,this.constructor.eventName("hidden")))}),this.tip,this._isAnimated())}}update(){this._popper&&this._popper.update()}_isWithContent(){return Boolean(this._getTitle())}_getTipElement(){return this.tip||(this.tip=this._createTipElement(this._newContent||this._getContentForTemplate())),this.tip}_createTipElement(t){const e=this._getTemplateFactory(t).toHtml();if(!e)return null;e.classList.remove(ts,es),e.classList.add(`bs-${this.constructor.NAME}-auto`);const i=(t=>{do{t+=Math.floor(1e6*Math.random())}while(document.getElementById(t));return t})(this.constructor.NAME).toString();return 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object[0] : object\n  }\n\n  if (typeof object === 'string' && object.length > 0) {\n    return document.querySelector(parseSelector(object))\n  }\n\n  return null\n}\n\nconst isVisible = element => {\n  if (!isElement(element) || element.getClientRects().length === 0) {\n    return false\n  }\n\n  const elementIsVisible = getComputedStyle(element).getPropertyValue('visibility') === 'visible'\n  // Handle `details` element as its content may falsie appear visible when it is closed\n  const closedDetails = element.closest('details:not([open])')\n\n  if (!closedDetails) {\n    return elementIsVisible\n  }\n\n  if (closedDetails !== element) {\n    const summary = element.closest('summary')\n    if (summary && summary.parentNode !== closedDetails) {\n      return false\n    }\n\n    if (summary === null) {\n      return false\n    }\n  }\n\n  return elementIsVisible\n}\n\nconst isDisabled = element => {\n  if (!element || element.nodeType !== Node.ELEMENT_NODE) {\n    return true\n  }\n\n  if (element.classList.contains('disabled')) {\n    return true\n  }\n\n  if (typeof element.disabled !== 'undefined') {\n    return element.disabled\n  }\n\n  return element.hasAttribute('disabled') && element.getAttribute('disabled') !== 'false'\n}\n\nconst findShadowRoot = element => {\n  if (!document.documentElement.attachShadow) {\n    return null\n  }\n\n  // Can find the shadow root otherwise it'll return the document\n  if (typeof element.getRootNode === 'function') {\n    const root = element.getRootNode()\n    return root instanceof ShadowRoot ? root : null\n  }\n\n  if (element instanceof ShadowRoot) {\n    return element\n  }\n\n  // when we don't find a shadow root\n  if (!element.parentNode) {\n    return null\n  }\n\n  return findShadowRoot(element.parentNode)\n}\n\nconst noop = () => {}\n\n/**\n * Trick to restart an element's animation\n *\n * @param {HTMLElement} element\n * @return void\n *\n * @see https://www.charistheo.io/blog/2021/02/restart-a-css-animation-with-javascript/#restarting-a-css-animation\n */\nconst reflow = element => {\n  element.offsetHeight // eslint-disable-line no-unused-expressions\n}\n\nconst getjQuery = () => {\n  if (window.jQuery && !document.body.hasAttribute('data-bs-no-jquery')) {\n    return window.jQuery\n  }\n\n  return null\n}\n\nconst DOMContentLoadedCallbacks = []\n\nconst onDOMContentLoaded = callback => {\n  if (document.readyState === 'loading') {\n    // add listener on the first call when the document is in loading state\n    if (!DOMContentLoadedCallbacks.length) {\n      document.addEventListener('DOMContentLoaded', () => {\n        for (const callback of DOMContentLoadedCallbacks) {\n          callback()\n        }\n      })\n    }\n\n    DOMContentLoadedCallbacks.push(callback)\n  } else {\n    callback()\n  }\n}\n\nconst isRTL = () => document.documentElement.dir === 'rtl'\n\nconst defineJQueryPlugin = plugin => {\n  onDOMContentLoaded(() => {\n    const $ = getjQuery()\n    /* istanbul ignore if */\n    if ($) {\n      const name = plugin.NAME\n      const JQUERY_NO_CONFLICT = $.fn[name]\n      $.fn[name] = plugin.jQueryInterface\n      $.fn[name].Constructor = plugin\n      $.fn[name].noConflict = () => {\n        $.fn[name] = JQUERY_NO_CONFLICT\n        return plugin.jQueryInterface\n      }\n    }\n  })\n}\n\nconst execute = (possibleCallback, args = [], defaultValue = possibleCallback) => {\n  return typeof possibleCallback === 'function' ? possibleCallback(...args) : defaultValue\n}\n\nconst executeAfterTransition = (callback, transitionElement, waitForTransition = true) => {\n  if (!waitForTransition) {\n    execute(callback)\n    return\n  }\n\n  const durationPadding = 5\n  const emulatedDuration = getTransitionDurationFromElement(transitionElement) + durationPadding\n\n  let called = false\n\n  const handler = ({ target }) => {\n    if (target !== transitionElement) {\n      return\n    }\n\n    called = true\n    transitionElement.removeEventListener(TRANSITION_END, handler)\n    execute(callback)\n  }\n\n  transitionElement.addEventListener(TRANSITION_END, handler)\n  setTimeout(() => {\n    if (!called) {\n      triggerTransitionEnd(transitionElement)\n    }\n  }, emulatedDuration)\n}\n\n/**\n * Return the previous/next element of a list.\n *\n * @param {array} list    The list of elements\n * @param activeElement   The active element\n * @param shouldGetNext   Choose to get next or previous element\n * @param isCycleAllowed\n * @return {Element|elem} The proper element\n */\nconst getNextActiveElement = (list, activeElement, shouldGetNext, isCycleAllowed) => {\n  const listLength = list.length\n  let index = list.indexOf(activeElement)\n\n  // if the element does not exist in the list return an element\n  // depending on the direction and if cycle is allowed\n  if (index === -1) {\n    return !shouldGetNext && isCycleAllowed ? list[listLength - 1] : list[0]\n  }\n\n  index += shouldGetNext ? 1 : -1\n\n  if (isCycleAllowed) {\n    index = (index + listLength) % listLength\n  }\n\n  return list[Math.max(0, Math.min(index, listLength - 1))]\n}\n\nexport {\n  defineJQueryPlugin,\n  execute,\n  executeAfterTransition,\n  findShadowRoot,\n  getElement,\n  getjQuery,\n  getNextActiveElement,\n  getTransitionDurationFromElement,\n  getUID,\n  isDisabled,\n  isElement,\n  isRTL,\n  isVisible,\n  noop,\n  onDOMContentLoaded,\n  parseSelector,\n  reflow,\n  triggerTransitionEnd,\n  toType\n}\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap dom/event-handler.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport { getjQuery } from '../util/index.js'\n\n/**\n * Constants\n */\n\nconst namespaceRegex = /[^.]*(?=\\..*)\\.|.*/\nconst stripNameRegex = /\\..*/\nconst stripUidRegex = /::\\d+$/\nconst eventRegistry = {} // Events storage\nlet uidEvent = 1\nconst customEvents = {\n  mouseenter: 'mouseover',\n  mouseleave: 'mouseout'\n}\n\nconst nativeEvents = new Set([\n  'click',\n  'dblclick',\n  'mouseup',\n  'mousedown',\n  'contextmenu',\n  'mousewheel',\n  'DOMMouseScroll',\n  'mouseover',\n  'mouseout',\n  'mousemove',\n  'selectstart',\n  'selectend',\n  'keydown',\n  'keypress',\n  'keyup',\n  'orientationchange',\n  'touchstart',\n  'touchmove',\n  'touchend',\n  'touchcancel',\n  'pointerdown',\n  'pointermove',\n  'pointerup',\n  'pointerleave',\n  'pointercancel',\n  'gesturestart',\n  'gesturechange',\n  'gestureend',\n  'focus',\n  'blur',\n  'change',\n  'reset',\n  'select',\n  'submit',\n  'focusin',\n  'focusout',\n  'load',\n  'unload',\n  'beforeunload',\n  'resize',\n  'move',\n  'DOMContentLoaded',\n  'readystatechange',\n  'error',\n  'abort',\n  'scroll'\n])\n\n/**\n * Private methods\n */\n\nfunction makeEventUid(element, uid) {\n  return (uid && `${uid}::${uidEvent++}`) || element.uidEvent || uidEvent++\n}\n\nfunction getElementEvents(element) {\n  const uid = makeEventUid(element)\n\n  element.uidEvent = uid\n  eventRegistry[uid] = eventRegistry[uid] || {}\n\n  return eventRegistry[uid]\n}\n\nfunction bootstrapHandler(element, fn) {\n  return function handler(event) {\n    hydrateObj(event, { delegateTarget: element })\n\n    if (handler.oneOff) {\n      EventHandler.off(element, event.type, fn)\n    }\n\n    return fn.apply(element, [event])\n  }\n}\n\nfunction bootstrapDelegationHandler(element, selector, fn) {\n  return function handler(event) {\n    const domElements = element.querySelectorAll(selector)\n\n    for (let { target } = event; target && target !== this; target = target.parentNode) {\n      for (const domElement of domElements) {\n        if (domElement !== target) {\n          continue\n        }\n\n        hydrateObj(event, { delegateTarget: target })\n\n        if (handler.oneOff) {\n          EventHandler.off(element, event.type, selector, fn)\n        }\n\n        return fn.apply(target, [event])\n      }\n    }\n  }\n}\n\nfunction findHandler(events, callable, delegationSelector = null) {\n  return Object.values(events)\n    .find(event => event.callable === callable && event.delegationSelector === delegationSelector)\n}\n\nfunction normalizeParameters(originalTypeEvent, handler, delegationFunction) {\n  const isDelegated = typeof handler === 'string'\n  // TODO: tooltip passes `false` instead of selector, so we need to check\n  const callable = isDelegated ? delegationFunction : (handler || delegationFunction)\n  let typeEvent = getTypeEvent(originalTypeEvent)\n\n  if (!nativeEvents.has(typeEvent)) {\n    typeEvent = originalTypeEvent\n  }\n\n  return [isDelegated, callable, typeEvent]\n}\n\nfunction addHandler(element, originalTypeEvent, handler, delegationFunction, oneOff) {\n  if (typeof originalTypeEvent !== 'string' || !element) {\n    return\n  }\n\n  let [isDelegated, callable, typeEvent] = normalizeParameters(originalTypeEvent, handler, delegationFunction)\n\n  // in case of mouseenter or mouseleave wrap the handler within a function that checks for its DOM position\n  // this prevents the handler from being dispatched the same way as mouseover or mouseout does\n  if (originalTypeEvent in customEvents) {\n    const wrapFunction = fn => {\n      return function (event) {\n        if (!event.relatedTarget || (event.relatedTarget !== event.delegateTarget && !event.delegateTarget.contains(event.relatedTarget))) {\n          return fn.call(this, event)\n        }\n      }\n    }\n\n    callable = wrapFunction(callable)\n  }\n\n  const events = getElementEvents(element)\n  const handlers = events[typeEvent] || (events[typeEvent] = {})\n  const previousFunction = findHandler(handlers, callable, isDelegated ? handler : null)\n\n  if (previousFunction) {\n    previousFunction.oneOff = previousFunction.oneOff && oneOff\n\n    return\n  }\n\n  const uid = makeEventUid(callable, originalTypeEvent.replace(namespaceRegex, ''))\n  const fn = isDelegated ?\n    bootstrapDelegationHandler(element, handler, callable) :\n    bootstrapHandler(element, callable)\n\n  fn.delegationSelector = isDelegated ? handler : null\n  fn.callable = callable\n  fn.oneOff = oneOff\n  fn.uidEvent = uid\n  handlers[uid] = fn\n\n  element.addEventListener(typeEvent, fn, isDelegated)\n}\n\nfunction removeHandler(element, events, typeEvent, handler, delegationSelector) {\n  const fn = findHandler(events[typeEvent], handler, delegationSelector)\n\n  if (!fn) {\n    return\n  }\n\n  element.removeEventListener(typeEvent, fn, Boolean(delegationSelector))\n  delete events[typeEvent][fn.uidEvent]\n}\n\nfunction removeNamespacedHandlers(element, events, typeEvent, namespace) {\n  const storeElementEvent = events[typeEvent] || {}\n\n  for (const [handlerKey, event] of Object.entries(storeElementEvent)) {\n    if (handlerKey.includes(namespace)) {\n      removeHandler(element, events, typeEvent, event.callable, event.delegationSelector)\n    }\n  }\n}\n\nfunction getTypeEvent(event) {\n  // allow to get the native events from namespaced events ('click.bs.button' --> 'click')\n  event = event.replace(stripNameRegex, '')\n  return customEvents[event] || event\n}\n\nconst EventHandler = {\n  on(element, event, handler, delegationFunction) {\n    addHandler(element, event, handler, delegationFunction, false)\n  },\n\n  one(element, event, handler, delegationFunction) {\n    addHandler(element, event, handler, delegationFunction, true)\n  },\n\n  off(element, originalTypeEvent, handler, delegationFunction) {\n    if (typeof originalTypeEvent !== 'string' || !element) {\n      return\n    }\n\n    const [isDelegated, callable, typeEvent] = normalizeParameters(originalTypeEvent, handler, delegationFunction)\n    const inNamespace = typeEvent !== originalTypeEvent\n    const events = getElementEvents(element)\n    const storeElementEvent = events[typeEvent] || {}\n    const isNamespace = originalTypeEvent.startsWith('.')\n\n    if (typeof callable !== 'undefined') {\n      // Simplest case: handler is passed, remove that listener ONLY.\n      if (!Object.keys(storeElementEvent).length) {\n        return\n      }\n\n      removeHandler(element, events, typeEvent, callable, isDelegated ? handler : null)\n      return\n    }\n\n    if (isNamespace) {\n      for (const elementEvent of Object.keys(events)) {\n        removeNamespacedHandlers(element, events, elementEvent, originalTypeEvent.slice(1))\n      }\n    }\n\n    for (const [keyHandlers, event] of Object.entries(storeElementEvent)) {\n      const handlerKey = keyHandlers.replace(stripUidRegex, '')\n\n      if (!inNamespace || originalTypeEvent.includes(handlerKey)) {\n        removeHandler(element, events, typeEvent, event.callable, event.delegationSelector)\n      }\n    }\n  },\n\n  trigger(element, event, args) {\n    if (typeof event !== 'string' || !element) {\n      return null\n    }\n\n    const $ = getjQuery()\n    const typeEvent = getTypeEvent(event)\n    const inNamespace = event !== typeEvent\n\n    let jQueryEvent = null\n    let bubbles = true\n    let nativeDispatch = true\n    let defaultPrevented = false\n\n    if (inNamespace && $) {\n      jQueryEvent = $.Event(event, args)\n\n      $(element).trigger(jQueryEvent)\n      bubbles = !jQueryEvent.isPropagationStopped()\n      nativeDispatch = !jQueryEvent.isImmediatePropagationStopped()\n      defaultPrevented = jQueryEvent.isDefaultPrevented()\n    }\n\n    const evt = hydrateObj(new Event(event, { bubbles, cancelable: true }), args)\n\n    if (defaultPrevented) {\n      evt.preventDefault()\n    }\n\n    if (nativeDispatch) {\n      element.dispatchEvent(evt)\n    }\n\n    if (evt.defaultPrevented && jQueryEvent) {\n      jQueryEvent.preventDefault()\n    }\n\n    return evt\n  }\n}\n\nfunction hydrateObj(obj, meta = {}) {\n  for (const [key, value] of Object.entries(meta)) {\n    try {\n      obj[key] = value\n    } catch {\n      Object.defineProperty(obj, key, {\n        configurable: true,\n        get() {\n          return value\n        }\n      })\n    }\n  }\n\n  return obj\n}\n\nexport default EventHandler\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap dom/manipulator.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nfunction normalizeData(value) {\n  if (value === 'true') {\n    return true\n  }\n\n  if (value === 'false') {\n    return false\n  }\n\n  if (value === Number(value).toString()) {\n    return Number(value)\n  }\n\n  if (value === '' || value === 'null') {\n    return null\n  }\n\n  if (typeof value !== 'string') {\n    return value\n  }\n\n  try {\n    return JSON.parse(decodeURIComponent(value))\n  } catch {\n    return value\n  }\n}\n\nfunction normalizeDataKey(key) {\n  return key.replace(/[A-Z]/g, chr => `-${chr.toLowerCase()}`)\n}\n\nconst Manipulator = {\n  setDataAttribute(element, key, value) {\n    element.setAttribute(`data-bs-${normalizeDataKey(key)}`, value)\n  },\n\n  removeDataAttribute(element, key) {\n    element.removeAttribute(`data-bs-${normalizeDataKey(key)}`)\n  },\n\n  getDataAttributes(element) {\n    if (!element) {\n      return {}\n    }\n\n    const attributes = {}\n    const bsKeys = Object.keys(element.dataset).filter(key => key.startsWith('bs') && !key.startsWith('bsConfig'))\n\n    for (const key of bsKeys) {\n      let pureKey = key.replace(/^bs/, '')\n      pureKey = pureKey.charAt(0).toLowerCase() + pureKey.slice(1, pureKey.length)\n      attributes[pureKey] = normalizeData(element.dataset[key])\n    }\n\n    return attributes\n  },\n\n  getDataAttribute(element, key) {\n    return normalizeData(element.getAttribute(`data-bs-${normalizeDataKey(key)}`))\n  }\n}\n\nexport default Manipulator\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap util/config.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport Manipulator from '../dom/manipulator.js'\nimport { isElement, toType } from './index.js'\n\n/**\n * Class definition\n */\n\nclass Config {\n  // Getters\n  static get Default() {\n    return {}\n  }\n\n  static get DefaultType() {\n    return {}\n  }\n\n  static get NAME() {\n    throw new Error('You have to implement the static method \"NAME\", for each component!')\n  }\n\n  _getConfig(config) {\n    config = this._mergeConfigObj(config)\n    config = this._configAfterMerge(config)\n    this._typeCheckConfig(config)\n    return config\n  }\n\n  _configAfterMerge(config) {\n    return config\n  }\n\n  _mergeConfigObj(config, element) {\n    const jsonConfig = isElement(element) ? Manipulator.getDataAttribute(element, 'config') : {} // try to parse\n\n    return {\n      ...this.constructor.Default,\n      ...(typeof jsonConfig === 'object' ? jsonConfig : {}),\n      ...(isElement(element) ? Manipulator.getDataAttributes(element) : {}),\n      ...(typeof config === 'object' ? config : {})\n    }\n  }\n\n  _typeCheckConfig(config, configTypes = this.constructor.DefaultType) {\n    for (const [property, expectedTypes] of Object.entries(configTypes)) {\n      const value = config[property]\n      const valueType = isElement(value) ? 'element' : toType(value)\n\n      if (!new RegExp(expectedTypes).test(valueType)) {\n        throw new TypeError(\n          `${this.constructor.NAME.toUpperCase()}: Option \"${property}\" provided type \"${valueType}\" but expected type \"${expectedTypes}\".`\n        )\n      }\n    }\n  }\n}\n\nexport default Config\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap base-component.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport Data from './dom/data.js'\nimport EventHandler from './dom/event-handler.js'\nimport Config from './util/config.js'\nimport { executeAfterTransition, getElement } from './util/index.js'\n\n/**\n * Constants\n */\n\nconst VERSION = '5.3.1'\n\n/**\n * Class definition\n */\n\nclass BaseComponent extends Config {\n  constructor(element, config) {\n    super()\n\n    element = getElement(element)\n    if (!element) {\n      return\n    }\n\n    this._element = element\n    this._config = this._getConfig(config)\n\n    Data.set(this._element, this.constructor.DATA_KEY, this)\n  }\n\n  // Public\n  dispose() {\n    Data.remove(this._element, this.constructor.DATA_KEY)\n    EventHandler.off(this._element, this.constructor.EVENT_KEY)\n\n    for (const propertyName of Object.getOwnPropertyNames(this)) {\n      this[propertyName] = null\n    }\n  }\n\n  _queueCallback(callback, element, isAnimated = true) {\n    executeAfterTransition(callback, element, isAnimated)\n  }\n\n  _getConfig(config) {\n    config = this._mergeConfigObj(config, this._element)\n    config = this._configAfterMerge(config)\n    this._typeCheckConfig(config)\n    return config\n  }\n\n  // Static\n  static getInstance(element) {\n    return Data.get(getElement(element), this.DATA_KEY)\n  }\n\n  static getOrCreateInstance(element, config = {}) {\n    return this.getInstance(element) || new this(element, typeof config === 'object' ? config : null)\n  }\n\n  static get VERSION() {\n    return VERSION\n  }\n\n  static get DATA_KEY() {\n    return `bs.${this.NAME}`\n  }\n\n  static get EVENT_KEY() {\n    return `.${this.DATA_KEY}`\n  }\n\n  static eventName(name) {\n    return `${name}${this.EVENT_KEY}`\n  }\n}\n\nexport default BaseComponent\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap dom/selector-engine.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport { isDisabled, isVisible, parseSelector } from '../util/index.js'\n\nconst getSelector = element => {\n  let selector = element.getAttribute('data-bs-target')\n\n  if (!selector || selector === '#') {\n    let hrefAttribute = element.getAttribute('href')\n\n    // The only valid content that could double as a selector are IDs or classes,\n    // so everything starting with `#` or `.`. If a \"real\" URL is used as the selector,\n    // `document.querySelector` will rightfully complain it is invalid.\n    // See https://github.com/twbs/bootstrap/issues/32273\n    if (!hrefAttribute || (!hrefAttribute.includes('#') && !hrefAttribute.startsWith('.'))) {\n      return null\n    }\n\n    // Just in case some CMS puts out a full URL with the anchor appended\n    if (hrefAttribute.includes('#') && !hrefAttribute.startsWith('#')) {\n      hrefAttribute = `#${hrefAttribute.split('#')[1]}`\n    }\n\n    selector = hrefAttribute && hrefAttribute !== '#' ? hrefAttribute.trim() : null\n  }\n\n  return parseSelector(selector)\n}\n\nconst SelectorEngine = {\n  find(selector, element = document.documentElement) {\n    return [].concat(...Element.prototype.querySelectorAll.call(element, selector))\n  },\n\n  findOne(selector, element = document.documentElement) {\n    return Element.prototype.querySelector.call(element, selector)\n  },\n\n  children(element, selector) {\n    return [].concat(...element.children).filter(child => child.matches(selector))\n  },\n\n  parents(element, selector) {\n    const parents = []\n    let ancestor = element.parentNode.closest(selector)\n\n    while (ancestor) {\n      parents.push(ancestor)\n      ancestor = ancestor.parentNode.closest(selector)\n    }\n\n    return parents\n  },\n\n  prev(element, selector) {\n    let previous = element.previousElementSibling\n\n    while (previous) {\n      if (previous.matches(selector)) {\n        return [previous]\n      }\n\n      previous = previous.previousElementSibling\n    }\n\n    return []\n  },\n  // TODO: this is now unused; remove later along with prev()\n  next(element, selector) {\n    let next = element.nextElementSibling\n\n    while (next) {\n      if (next.matches(selector)) {\n        return [next]\n      }\n\n      next = next.nextElementSibling\n    }\n\n    return []\n  },\n\n  focusableChildren(element) {\n    const focusables = [\n      'a',\n      'button',\n      'input',\n      'textarea',\n      'select',\n      'details',\n      '[tabindex]',\n      '[contenteditable=\"true\"]'\n    ].map(selector => `${selector}:not([tabindex^=\"-\"])`).join(',')\n\n    return this.find(focusables, element).filter(el => !isDisabled(el) && isVisible(el))\n  },\n\n  getSelectorFromElement(element) {\n    const selector = getSelector(element)\n\n    if (selector) {\n      return SelectorEngine.findOne(selector) ? selector : null\n    }\n\n    return null\n  },\n\n  getElementFromSelector(element) {\n    const selector = getSelector(element)\n\n    return selector ? SelectorEngine.findOne(selector) : null\n  },\n\n  getMultipleElementsFromSelector(element) {\n    const selector = getSelector(element)\n\n    return selector ? SelectorEngine.find(selector) : []\n  }\n}\n\nexport default SelectorEngine\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap util/component-functions.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport EventHandler from '../dom/event-handler.js'\nimport SelectorEngine from '../dom/selector-engine.js'\nimport { isDisabled } from './index.js'\n\nconst enableDismissTrigger = (component, method = 'hide') => {\n  const clickEvent = `click.dismiss${component.EVENT_KEY}`\n  const name = component.NAME\n\n  EventHandler.on(document, clickEvent, `[data-bs-dismiss=\"${name}\"]`, function (event) {\n    if (['A', 'AREA'].includes(this.tagName)) {\n      event.preventDefault()\n    }\n\n    if (isDisabled(this)) {\n      return\n    }\n\n    const target = SelectorEngine.getElementFromSelector(this) || this.closest(`.${name}`)\n    const instance = component.getOrCreateInstance(target)\n\n    // Method argument is left, for Alert and only, as it doesn't implement the 'hide' method\n    instance[method]()\n  })\n}\n\nexport {\n  enableDismissTrigger\n}\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap alert.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport BaseComponent from './base-component.js'\nimport EventHandler from './dom/event-handler.js'\nimport { enableDismissTrigger } from './util/component-functions.js'\nimport { defineJQueryPlugin } from './util/index.js'\n\n/**\n * Constants\n */\n\nconst NAME = 'alert'\nconst DATA_KEY = 'bs.alert'\nconst EVENT_KEY = `.${DATA_KEY}`\n\nconst EVENT_CLOSE = `close${EVENT_KEY}`\nconst EVENT_CLOSED = `closed${EVENT_KEY}`\nconst CLASS_NAME_FADE = 'fade'\nconst CLASS_NAME_SHOW = 'show'\n\n/**\n * Class definition\n */\n\nclass Alert extends BaseComponent {\n  // Getters\n  static get NAME() {\n    return NAME\n  }\n\n  // Public\n  close() {\n    const closeEvent = EventHandler.trigger(this._element, EVENT_CLOSE)\n\n    if (closeEvent.defaultPrevented) {\n      return\n    }\n\n    this._element.classList.remove(CLASS_NAME_SHOW)\n\n    const isAnimated = this._element.classList.contains(CLASS_NAME_FADE)\n    this._queueCallback(() => this._destroyElement(), this._element, isAnimated)\n  }\n\n  // Private\n  _destroyElement() {\n    this._element.remove()\n    EventHandler.trigger(this._element, EVENT_CLOSED)\n    this.dispose()\n  }\n\n  // Static\n  static jQueryInterface(config) {\n    return this.each(function () {\n      const data = Alert.getOrCreateInstance(this)\n\n      if (typeof config !== 'string') {\n        return\n      }\n\n      if (data[config] === undefined || config.startsWith('_') || config === 'constructor') {\n        throw new TypeError(`No method named \"${config}\"`)\n      }\n\n      data[config](this)\n    })\n  }\n}\n\n/**\n * Data API implementation\n */\n\nenableDismissTrigger(Alert, 'close')\n\n/**\n * jQuery\n */\n\ndefineJQueryPlugin(Alert)\n\nexport default Alert\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap button.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport BaseComponent from './base-component.js'\nimport EventHandler from './dom/event-handler.js'\nimport { defineJQueryPlugin } from './util/index.js'\n\n/**\n * Constants\n */\n\nconst NAME = 'button'\nconst DATA_KEY = 'bs.button'\nconst EVENT_KEY = `.${DATA_KEY}`\nconst DATA_API_KEY = '.data-api'\n\nconst CLASS_NAME_ACTIVE = 'active'\nconst SELECTOR_DATA_TOGGLE = '[data-bs-toggle=\"button\"]'\nconst EVENT_CLICK_DATA_API = `click${EVENT_KEY}${DATA_API_KEY}`\n\n/**\n * Class definition\n */\n\nclass Button extends BaseComponent {\n  // Getters\n  static get NAME() {\n    return NAME\n  }\n\n  // Public\n  toggle() {\n    // Toggle class and sync the `aria-pressed` attribute with the return value of the `.toggle()` method\n    this._element.setAttribute('aria-pressed', this._element.classList.toggle(CLASS_NAME_ACTIVE))\n  }\n\n  // Static\n  static jQueryInterface(config) {\n    return this.each(function () {\n      const data = Button.getOrCreateInstance(this)\n\n      if (config === 'toggle') {\n        data[config]()\n      }\n    })\n  }\n}\n\n/**\n * Data API implementation\n */\n\nEventHandler.on(document, EVENT_CLICK_DATA_API, SELECTOR_DATA_TOGGLE, event => {\n  event.preventDefault()\n\n  const button = event.target.closest(SELECTOR_DATA_TOGGLE)\n  const data = Button.getOrCreateInstance(button)\n\n  data.toggle()\n})\n\n/**\n * jQuery\n */\n\ndefineJQueryPlugin(Button)\n\nexport default Button\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap util/swipe.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport EventHandler from '../dom/event-handler.js'\nimport Config from './config.js'\nimport { execute } from './index.js'\n\n/**\n * Constants\n */\n\nconst NAME = 'swipe'\nconst EVENT_KEY = '.bs.swipe'\nconst EVENT_TOUCHSTART = `touchstart${EVENT_KEY}`\nconst EVENT_TOUCHMOVE = `touchmove${EVENT_KEY}`\nconst EVENT_TOUCHEND = `touchend${EVENT_KEY}`\nconst EVENT_POINTERDOWN = `pointerdown${EVENT_KEY}`\nconst EVENT_POINTERUP = `pointerup${EVENT_KEY}`\nconst POINTER_TYPE_TOUCH = 'touch'\nconst POINTER_TYPE_PEN = 'pen'\nconst CLASS_NAME_POINTER_EVENT = 'pointer-event'\nconst SWIPE_THRESHOLD = 40\n\nconst Default = {\n  endCallback: null,\n  leftCallback: null,\n  rightCallback: null\n}\n\nconst DefaultType = {\n  endCallback: '(function|null)',\n  leftCallback: '(function|null)',\n  rightCallback: '(function|null)'\n}\n\n/**\n * Class definition\n */\n\nclass Swipe extends Config {\n  constructor(element, config) {\n    super()\n    this._element = element\n\n    if (!element || !Swipe.isSupported()) {\n      return\n    }\n\n    this._config = this._getConfig(config)\n    this._deltaX = 0\n    this._supportPointerEvents = Boolean(window.PointerEvent)\n    this._initEvents()\n  }\n\n  // Getters\n  static get Default() {\n    return Default\n  }\n\n  static get DefaultType() {\n    return DefaultType\n  }\n\n  static get NAME() {\n    return NAME\n  }\n\n  // Public\n  dispose() {\n    EventHandler.off(this._element, EVENT_KEY)\n  }\n\n  // Private\n  _start(event) {\n    if (!this._supportPointerEvents) {\n      this._deltaX = event.touches[0].clientX\n\n      return\n    }\n\n    if (this._eventIsPointerPenTouch(event)) {\n      this._deltaX = event.clientX\n    }\n  }\n\n  _end(event) {\n    if (this._eventIsPointerPenTouch(event)) {\n      this._deltaX = event.clientX - this._deltaX\n    }\n\n    this._handleSwipe()\n    execute(this._config.endCallback)\n  }\n\n  _move(event) {\n    this._deltaX = event.touches && event.touches.length > 1 ?\n      0 :\n      event.touches[0].clientX - this._deltaX\n  }\n\n  _handleSwipe() {\n    const absDeltaX = Math.abs(this._deltaX)\n\n    if (absDeltaX <= SWIPE_THRESHOLD) {\n      return\n    }\n\n    const direction = absDeltaX / this._deltaX\n\n    this._deltaX = 0\n\n    if (!direction) {\n      return\n    }\n\n    execute(direction > 0 ? this._config.rightCallback : this._config.leftCallback)\n  }\n\n  _initEvents() {\n    if (this._supportPointerEvents) {\n      EventHandler.on(this._element, EVENT_POINTERDOWN, event => this._start(event))\n      EventHandler.on(this._element, EVENT_POINTERUP, event => this._end(event))\n\n      this._element.classList.add(CLASS_NAME_POINTER_EVENT)\n    } else {\n      EventHandler.on(this._element, EVENT_TOUCHSTART, event => this._start(event))\n      EventHandler.on(this._element, EVENT_TOUCHMOVE, event => this._move(event))\n      EventHandler.on(this._element, EVENT_TOUCHEND, event => this._end(event))\n    }\n  }\n\n  _eventIsPointerPenTouch(event) {\n    return this._supportPointerEvents && (event.pointerType === POINTER_TYPE_PEN || event.pointerType === POINTER_TYPE_TOUCH)\n  }\n\n  // Static\n  static isSupported() {\n    return 'ontouchstart' in document.documentElement || navigator.maxTouchPoints > 0\n  }\n}\n\nexport default Swipe\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap carousel.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport BaseComponent from './base-component.js'\nimport EventHandler from './dom/event-handler.js'\nimport Manipulator from './dom/manipulator.js'\nimport SelectorEngine from './dom/selector-engine.js'\nimport {\n  defineJQueryPlugin,\n  getNextActiveElement,\n  isRTL,\n  isVisible,\n  reflow,\n  triggerTransitionEnd\n} from './util/index.js'\nimport Swipe from './util/swipe.js'\n\n/**\n * Constants\n */\n\nconst NAME = 'carousel'\nconst DATA_KEY = 'bs.carousel'\nconst EVENT_KEY = `.${DATA_KEY}`\nconst DATA_API_KEY = '.data-api'\n\nconst ARROW_LEFT_KEY = 'ArrowLeft'\nconst ARROW_RIGHT_KEY = 'ArrowRight'\nconst TOUCHEVENT_COMPAT_WAIT = 500 // Time for mouse compat events to fire after touch\n\nconst ORDER_NEXT = 'next'\nconst ORDER_PREV = 'prev'\nconst DIRECTION_LEFT = 'left'\nconst DIRECTION_RIGHT = 'right'\n\nconst EVENT_SLIDE = `slide${EVENT_KEY}`\nconst EVENT_SLID = `slid${EVENT_KEY}`\nconst EVENT_KEYDOWN = `keydown${EVENT_KEY}`\nconst EVENT_MOUSEENTER = `mouseenter${EVENT_KEY}`\nconst EVENT_MOUSELEAVE = `mouseleave${EVENT_KEY}`\nconst EVENT_DRAG_START = `dragstart${EVENT_KEY}`\nconst EVENT_LOAD_DATA_API = `load${EVENT_KEY}${DATA_API_KEY}`\nconst EVENT_CLICK_DATA_API = `click${EVENT_KEY}${DATA_API_KEY}`\n\nconst CLASS_NAME_CAROUSEL = 'carousel'\nconst CLASS_NAME_ACTIVE = 'active'\nconst CLASS_NAME_SLIDE = 'slide'\nconst CLASS_NAME_END = 'carousel-item-end'\nconst CLASS_NAME_START = 'carousel-item-start'\nconst CLASS_NAME_NEXT = 'carousel-item-next'\nconst CLASS_NAME_PREV = 'carousel-item-prev'\n\nconst SELECTOR_ACTIVE = '.active'\nconst SELECTOR_ITEM = '.carousel-item'\nconst SELECTOR_ACTIVE_ITEM = SELECTOR_ACTIVE + SELECTOR_ITEM\nconst SELECTOR_ITEM_IMG = '.carousel-item img'\nconst SELECTOR_INDICATORS = '.carousel-indicators'\nconst SELECTOR_DATA_SLIDE = '[data-bs-slide], [data-bs-slide-to]'\nconst SELECTOR_DATA_RIDE = '[data-bs-ride=\"carousel\"]'\n\nconst KEY_TO_DIRECTION = {\n  [ARROW_LEFT_KEY]: DIRECTION_RIGHT,\n  [ARROW_RIGHT_KEY]: DIRECTION_LEFT\n}\n\nconst Default = {\n  interval: 5000,\n  keyboard: true,\n  pause: 'hover',\n  ride: false,\n  touch: true,\n  wrap: true\n}\n\nconst DefaultType = {\n  interval: '(number|boolean)', // TODO:v6 remove boolean support\n  keyboard: 'boolean',\n  pause: '(string|boolean)',\n  ride: '(boolean|string)',\n  touch: 'boolean',\n  wrap: 'boolean'\n}\n\n/**\n * Class definition\n */\n\nclass Carousel extends BaseComponent {\n  constructor(element, config) {\n    super(element, config)\n\n    this._interval = null\n    this._activeElement = null\n    this._isSliding = false\n    this.touchTimeout = null\n    this._swipeHelper = null\n\n    this._indicatorsElement = SelectorEngine.findOne(SELECTOR_INDICATORS, this._element)\n    this._addEventListeners()\n\n    if (this._config.ride === CLASS_NAME_CAROUSEL) {\n      this.cycle()\n    }\n  }\n\n  // Getters\n  static get Default() {\n    return Default\n  }\n\n  static get DefaultType() {\n    return DefaultType\n  }\n\n  static get NAME() {\n    return NAME\n  }\n\n  // Public\n  next() {\n    this._slide(ORDER_NEXT)\n  }\n\n  nextWhenVisible() {\n    // FIXME TODO use `document.visibilityState`\n    // Don't call next when the page isn't visible\n    // or the carousel or its parent isn't visible\n    if (!document.hidden && isVisible(this._element)) {\n      this.next()\n    }\n  }\n\n  prev() {\n    this._slide(ORDER_PREV)\n  }\n\n  pause() {\n    if (this._isSliding) {\n      triggerTransitionEnd(this._element)\n    }\n\n    this._clearInterval()\n  }\n\n  cycle() {\n    this._clearInterval()\n    this._updateInterval()\n\n    this._interval = setInterval(() => this.nextWhenVisible(), this._config.interval)\n  }\n\n  _maybeEnableCycle() {\n    if (!this._config.ride) {\n      return\n    }\n\n    if (this._isSliding) {\n      EventHandler.one(this._element, EVENT_SLID, () => this.cycle())\n      return\n    }\n\n    this.cycle()\n  }\n\n  to(index) {\n    const items = this._getItems()\n    if (index > items.length - 1 || index < 0) {\n      return\n    }\n\n    if (this._isSliding) {\n      EventHandler.one(this._element, EVENT_SLID, () => this.to(index))\n      return\n    }\n\n    const activeIndex = this._getItemIndex(this._getActive())\n    if (activeIndex === index) {\n      return\n    }\n\n    const order = index > activeIndex ? ORDER_NEXT : ORDER_PREV\n\n    this._slide(order, items[index])\n  }\n\n  dispose() {\n    if (this._swipeHelper) {\n      this._swipeHelper.dispose()\n    }\n\n    super.dispose()\n  }\n\n  // Private\n  _configAfterMerge(config) {\n    config.defaultInterval = config.interval\n    return config\n  }\n\n  _addEventListeners() {\n    if (this._config.keyboard) {\n      EventHandler.on(this._element, EVENT_KEYDOWN, event => this._keydown(event))\n    }\n\n    if (this._config.pause === 'hover') {\n      EventHandler.on(this._element, EVENT_MOUSEENTER, () => this.pause())\n      EventHandler.on(this._element, EVENT_MOUSELEAVE, () => this._maybeEnableCycle())\n    }\n\n    if (this._config.touch && Swipe.isSupported()) {\n      this._addTouchEventListeners()\n    }\n  }\n\n  _addTouchEventListeners() {\n    for (const img of SelectorEngine.find(SELECTOR_ITEM_IMG, this._element)) {\n      EventHandler.on(img, EVENT_DRAG_START, event => event.preventDefault())\n    }\n\n    const endCallBack = () => {\n      if (this._config.pause !== 'hover') {\n        return\n      }\n\n      // If it's a touch-enabled device, mouseenter/leave are fired as\n      // part of the mouse compatibility events on first tap - the carousel\n      // would stop cycling until user tapped out of it;\n      // here, we listen for touchend, explicitly pause the carousel\n      // (as if it's the second time we tap on it, mouseenter compat event\n      // is NOT fired) and after a timeout (to allow for mouse compatibility\n      // events to fire) we explicitly restart cycling\n\n      this.pause()\n      if (this.touchTimeout) {\n        clearTimeout(this.touchTimeout)\n      }\n\n      this.touchTimeout = setTimeout(() => this._maybeEnableCycle(), TOUCHEVENT_COMPAT_WAIT + this._config.interval)\n    }\n\n    const swipeConfig = {\n      leftCallback: () => this._slide(this._directionToOrder(DIRECTION_LEFT)),\n      rightCallback: () => this._slide(this._directionToOrder(DIRECTION_RIGHT)),\n      endCallback: endCallBack\n    }\n\n    this._swipeHelper = new Swipe(this._element, swipeConfig)\n  }\n\n  _keydown(event) {\n    if (/input|textarea/i.test(event.target.tagName)) {\n      return\n    }\n\n    const direction = KEY_TO_DIRECTION[event.key]\n    if (direction) {\n      event.preventDefault()\n      this._slide(this._directionToOrder(direction))\n    }\n  }\n\n  _getItemIndex(element) {\n    return this._getItems().indexOf(element)\n  }\n\n  _setActiveIndicatorElement(index) {\n    if (!this._indicatorsElement) {\n      return\n    }\n\n    const activeIndicator = SelectorEngine.findOne(SELECTOR_ACTIVE, this._indicatorsElement)\n\n    activeIndicator.classList.remove(CLASS_NAME_ACTIVE)\n    activeIndicator.removeAttribute('aria-current')\n\n    const newActiveIndicator = SelectorEngine.findOne(`[data-bs-slide-to=\"${index}\"]`, this._indicatorsElement)\n\n    if (newActiveIndicator) {\n      newActiveIndicator.classList.add(CLASS_NAME_ACTIVE)\n      newActiveIndicator.setAttribute('aria-current', 'true')\n    }\n  }\n\n  _updateInterval() {\n    const element = this._activeElement || this._getActive()\n\n    if (!element) {\n      return\n    }\n\n    const elementInterval = Number.parseInt(element.getAttribute('data-bs-interval'), 10)\n\n    this._config.interval = elementInterval || this._config.defaultInterval\n  }\n\n  _slide(order, element = null) {\n    if (this._isSliding) {\n      return\n    }\n\n    const activeElement = this._getActive()\n    const isNext = order === ORDER_NEXT\n    const nextElement = element || getNextActiveElement(this._getItems(), activeElement, isNext, this._config.wrap)\n\n    if (nextElement === activeElement) {\n      return\n    }\n\n    const nextElementIndex = this._getItemIndex(nextElement)\n\n    const triggerEvent = eventName => {\n      return EventHandler.trigger(this._element, eventName, {\n        relatedTarget: nextElement,\n        direction: this._orderToDirection(order),\n        from: this._getItemIndex(activeElement),\n        to: nextElementIndex\n      })\n    }\n\n    const slideEvent = triggerEvent(EVENT_SLIDE)\n\n    if (slideEvent.defaultPrevented) {\n      return\n    }\n\n    if (!activeElement || !nextElement) {\n      // Some weirdness is happening, so we bail\n      // TODO: change tests that use empty divs to avoid this check\n      return\n    }\n\n    const isCycling = Boolean(this._interval)\n    this.pause()\n\n    this._isSliding = true\n\n    this._setActiveIndicatorElement(nextElementIndex)\n    this._activeElement = nextElement\n\n    const directionalClassName = isNext ? CLASS_NAME_START : CLASS_NAME_END\n    const orderClassName = isNext ? CLASS_NAME_NEXT : CLASS_NAME_PREV\n\n    nextElement.classList.add(orderClassName)\n\n    reflow(nextElement)\n\n    activeElement.classList.add(directionalClassName)\n    nextElement.classList.add(directionalClassName)\n\n    const completeCallBack = () => {\n      nextElement.classList.remove(directionalClassName, orderClassName)\n      nextElement.classList.add(CLASS_NAME_ACTIVE)\n\n      activeElement.classList.remove(CLASS_NAME_ACTIVE, orderClassName, directionalClassName)\n\n      this._isSliding = false\n\n      triggerEvent(EVENT_SLID)\n    }\n\n    this._queueCallback(completeCallBack, activeElement, this._isAnimated())\n\n    if (isCycling) {\n      this.cycle()\n    }\n  }\n\n  _isAnimated() {\n    return this._element.classList.contains(CLASS_NAME_SLIDE)\n  }\n\n  _getActive() {\n    return SelectorEngine.findOne(SELECTOR_ACTIVE_ITEM, this._element)\n  }\n\n  _getItems() {\n    return SelectorEngine.find(SELECTOR_ITEM, this._element)\n  }\n\n  _clearInterval() {\n    if (this._interval) {\n      clearInterval(this._interval)\n      this._interval = null\n    }\n  }\n\n  _directionToOrder(direction) {\n    if (isRTL()) {\n      return direction === DIRECTION_LEFT ? ORDER_PREV : ORDER_NEXT\n    }\n\n    return direction === DIRECTION_LEFT ? ORDER_NEXT : ORDER_PREV\n  }\n\n  _orderToDirection(order) {\n    if (isRTL()) {\n      return order === ORDER_PREV ? DIRECTION_LEFT : DIRECTION_RIGHT\n    }\n\n    return order === ORDER_PREV ? DIRECTION_RIGHT : DIRECTION_LEFT\n  }\n\n  // Static\n  static jQueryInterface(config) {\n    return this.each(function () {\n      const data = Carousel.getOrCreateInstance(this, config)\n\n      if (typeof config === 'number') {\n        data.to(config)\n        return\n      }\n\n      if (typeof config === 'string') {\n        if (data[config] === undefined || config.startsWith('_') || config === 'constructor') {\n          throw new TypeError(`No method named \"${config}\"`)\n        }\n\n        data[config]()\n      }\n    })\n  }\n}\n\n/**\n * Data API implementation\n */\n\nEventHandler.on(document, EVENT_CLICK_DATA_API, SELECTOR_DATA_SLIDE, function (event) {\n  const target = SelectorEngine.getElementFromSelector(this)\n\n  if (!target || !target.classList.contains(CLASS_NAME_CAROUSEL)) {\n    return\n  }\n\n  event.preventDefault()\n\n  const carousel = Carousel.getOrCreateInstance(target)\n  const slideIndex = this.getAttribute('data-bs-slide-to')\n\n  if (slideIndex) {\n    carousel.to(slideIndex)\n    carousel._maybeEnableCycle()\n    return\n  }\n\n  if (Manipulator.getDataAttribute(this, 'slide') === 'next') {\n    carousel.next()\n    carousel._maybeEnableCycle()\n    return\n  }\n\n  carousel.prev()\n  carousel._maybeEnableCycle()\n})\n\nEventHandler.on(window, EVENT_LOAD_DATA_API, () => {\n  const carousels = SelectorEngine.find(SELECTOR_DATA_RIDE)\n\n  for (const carousel of carousels) {\n    Carousel.getOrCreateInstance(carousel)\n  }\n})\n\n/**\n * jQuery\n */\n\ndefineJQueryPlugin(Carousel)\n\nexport default Carousel\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap collapse.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport BaseComponent from './base-component.js'\nimport EventHandler from './dom/event-handler.js'\nimport SelectorEngine from './dom/selector-engine.js'\nimport {\n  defineJQueryPlugin,\n  getElement,\n  reflow\n} from './util/index.js'\n\n/**\n * Constants\n */\n\nconst NAME = 'collapse'\nconst DATA_KEY = 'bs.collapse'\nconst EVENT_KEY = `.${DATA_KEY}`\nconst DATA_API_KEY = '.data-api'\n\nconst EVENT_SHOW = `show${EVENT_KEY}`\nconst EVENT_SHOWN = `shown${EVENT_KEY}`\nconst EVENT_HIDE = `hide${EVENT_KEY}`\nconst EVENT_HIDDEN = `hidden${EVENT_KEY}`\nconst EVENT_CLICK_DATA_API = `click${EVENT_KEY}${DATA_API_KEY}`\n\nconst CLASS_NAME_SHOW = 'show'\nconst CLASS_NAME_COLLAPSE = 'collapse'\nconst CLASS_NAME_COLLAPSING = 'collapsing'\nconst CLASS_NAME_COLLAPSED = 'collapsed'\nconst CLASS_NAME_DEEPER_CHILDREN = `:scope .${CLASS_NAME_COLLAPSE} .${CLASS_NAME_COLLAPSE}`\nconst CLASS_NAME_HORIZONTAL = 'collapse-horizontal'\n\nconst WIDTH = 'width'\nconst HEIGHT = 'height'\n\nconst SELECTOR_ACTIVES = '.collapse.show, .collapse.collapsing'\nconst SELECTOR_DATA_TOGGLE = '[data-bs-toggle=\"collapse\"]'\n\nconst Default = {\n  parent: null,\n  toggle: true\n}\n\nconst DefaultType = {\n  parent: '(null|element)',\n  toggle: 'boolean'\n}\n\n/**\n * Class definition\n */\n\nclass Collapse extends BaseComponent {\n  constructor(element, config) {\n    super(element, config)\n\n    this._isTransitioning = false\n    this._triggerArray = []\n\n    const toggleList = SelectorEngine.find(SELECTOR_DATA_TOGGLE)\n\n    for (const elem of toggleList) {\n      const selector = SelectorEngine.getSelectorFromElement(elem)\n      const filterElement = SelectorEngine.find(selector)\n        .filter(foundElement => foundElement === this._element)\n\n      if (selector !== null && filterElement.length) {\n        this._triggerArray.push(elem)\n      }\n    }\n\n    this._initializeChildren()\n\n    if (!this._config.parent) {\n      this._addAriaAndCollapsedClass(this._triggerArray, this._isShown())\n    }\n\n    if (this._config.toggle) {\n      this.toggle()\n    }\n  }\n\n  // Getters\n  static get Default() {\n    return Default\n  }\n\n  static get DefaultType() {\n    return DefaultType\n  }\n\n  static get NAME() {\n    return NAME\n  }\n\n  // Public\n  toggle() {\n    if (this._isShown()) {\n      this.hide()\n    } else {\n      this.show()\n    }\n  }\n\n  show() {\n    if (this._isTransitioning || this._isShown()) {\n      return\n    }\n\n    let activeChildren = []\n\n    // find active children\n    if (this._config.parent) {\n      activeChildren = this._getFirstLevelChildren(SELECTOR_ACTIVES)\n        .filter(element => element !== this._element)\n        .map(element => Collapse.getOrCreateInstance(element, { toggle: false }))\n    }\n\n    if (activeChildren.length && activeChildren[0]._isTransitioning) {\n      return\n    }\n\n    const startEvent = EventHandler.trigger(this._element, EVENT_SHOW)\n    if (startEvent.defaultPrevented) {\n      return\n    }\n\n    for (const activeInstance of activeChildren) {\n      activeInstance.hide()\n    }\n\n    const dimension = this._getDimension()\n\n    this._element.classList.remove(CLASS_NAME_COLLAPSE)\n    this._element.classList.add(CLASS_NAME_COLLAPSING)\n\n    this._element.style[dimension] = 0\n\n    this._addAriaAndCollapsedClass(this._triggerArray, true)\n    this._isTransitioning = true\n\n    const complete = () => {\n      this._isTransitioning = false\n\n      this._element.classList.remove(CLASS_NAME_COLLAPSING)\n      this._element.classList.add(CLASS_NAME_COLLAPSE, CLASS_NAME_SHOW)\n\n      this._element.style[dimension] = ''\n\n      EventHandler.trigger(this._element, EVENT_SHOWN)\n    }\n\n    const capitalizedDimension = dimension[0].toUpperCase() + dimension.slice(1)\n    const scrollSize = `scroll${capitalizedDimension}`\n\n    this._queueCallback(complete, this._element, true)\n    this._element.style[dimension] = `${this._element[scrollSize]}px`\n  }\n\n  hide() {\n    if (this._isTransitioning || !this._isShown()) {\n      return\n    }\n\n    const startEvent = EventHandler.trigger(this._element, EVENT_HIDE)\n    if (startEvent.defaultPrevented) {\n      return\n    }\n\n    const dimension = this._getDimension()\n\n    this._element.style[dimension] = `${this._element.getBoundingClientRect()[dimension]}px`\n\n    reflow(this._element)\n\n    this._element.classList.add(CLASS_NAME_COLLAPSING)\n    this._element.classList.remove(CLASS_NAME_COLLAPSE, CLASS_NAME_SHOW)\n\n    for (const trigger of this._triggerArray) {\n      const element = SelectorEngine.getElementFromSelector(trigger)\n\n      if (element && !this._isShown(element)) {\n        this._addAriaAndCollapsedClass([trigger], false)\n      }\n    }\n\n    this._isTransitioning = true\n\n    const complete = () => {\n      this._isTransitioning = false\n      this._element.classList.remove(CLASS_NAME_COLLAPSING)\n      this._element.classList.add(CLASS_NAME_COLLAPSE)\n      EventHandler.trigger(this._element, EVENT_HIDDEN)\n    }\n\n    this._element.style[dimension] = ''\n\n    this._queueCallback(complete, this._element, true)\n  }\n\n  _isShown(element = this._element) {\n    return element.classList.contains(CLASS_NAME_SHOW)\n  }\n\n  // Private\n  _configAfterMerge(config) {\n    config.toggle = Boolean(config.toggle) // Coerce string values\n    config.parent = getElement(config.parent)\n    return config\n  }\n\n  _getDimension() {\n    return this._element.classList.contains(CLASS_NAME_HORIZONTAL) ? WIDTH : HEIGHT\n  }\n\n  _initializeChildren() {\n    if (!this._config.parent) {\n      return\n    }\n\n    const children = this._getFirstLevelChildren(SELECTOR_DATA_TOGGLE)\n\n    for (const element of children) {\n      const selected = SelectorEngine.getElementFromSelector(element)\n\n      if (selected) {\n        this._addAriaAndCollapsedClass([element], this._isShown(selected))\n      }\n    }\n  }\n\n  _getFirstLevelChildren(selector) {\n    const children = SelectorEngine.find(CLASS_NAME_DEEPER_CHILDREN, this._config.parent)\n    // remove children if greater depth\n    return SelectorEngine.find(selector, this._config.parent).filter(element => !children.includes(element))\n  }\n\n  _addAriaAndCollapsedClass(triggerArray, isOpen) {\n    if (!triggerArray.length) {\n      return\n    }\n\n    for (const element of triggerArray) {\n      element.classList.toggle(CLASS_NAME_COLLAPSED, !isOpen)\n      element.setAttribute('aria-expanded', isOpen)\n    }\n  }\n\n  // Static\n  static jQueryInterface(config) {\n    const _config = {}\n    if (typeof config === 'string' && /show|hide/.test(config)) {\n      _config.toggle = false\n    }\n\n    return this.each(function () {\n      const data = Collapse.getOrCreateInstance(this, _config)\n\n      if (typeof config === 'string') {\n        if (typeof data[config] === 'undefined') {\n          throw new TypeError(`No method named \"${config}\"`)\n        }\n\n        data[config]()\n      }\n    })\n  }\n}\n\n/**\n * Data API implementation\n */\n\nEventHandler.on(document, EVENT_CLICK_DATA_API, SELECTOR_DATA_TOGGLE, function (event) {\n  // preventDefault only for <a> elements (which change the URL) not inside the collapsible element\n  if (event.target.tagName === 'A' || (event.delegateTarget && event.delegateTarget.tagName === 'A')) {\n    event.preventDefault()\n  }\n\n  for (const element of SelectorEngine.getMultipleElementsFromSelector(this)) {\n    Collapse.getOrCreateInstance(element, { toggle: false }).toggle()\n  }\n})\n\n/**\n * jQuery\n */\n\ndefineJQueryPlugin(Collapse)\n\nexport default Collapse\n","export var top = 'top';\nexport var bottom = 'bottom';\nexport var right = 'right';\nexport var left = 'left';\nexport var auto = 'auto';\nexport var basePlacements = [top, bottom, right, left];\nexport var start = 'start';\nexport var end = 'end';\nexport var clippingParents = 'clippingParents';\nexport var viewport = 'viewport';\nexport var popper = 'popper';\nexport var reference = 'reference';\nexport var variationPlacements = /*#__PURE__*/basePlacements.reduce(function (acc, placement) {\n  return acc.concat([placement + \"-\" + start, placement + \"-\" + end]);\n}, []);\nexport var placements = /*#__PURE__*/[].concat(basePlacements, [auto]).reduce(function (acc, placement) {\n  return acc.concat([placement, placement + \"-\" + start, placement + \"-\" + end]);\n}, []); // modifiers that need to read the DOM\n\nexport var beforeRead = 'beforeRead';\nexport var read = 'read';\nexport var afterRead = 'afterRead'; // pure-logic modifiers\n\nexport var beforeMain = 'beforeMain';\nexport var main = 'main';\nexport var afterMain = 'afterMain'; // modifier with the purpose to write to the DOM (or write into a framework state)\n\nexport var beforeWrite = 'beforeWrite';\nexport var write = 'write';\nexport var afterWrite = 'afterWrite';\nexport var modifierPhases = [beforeRead, read, afterRead, beforeMain, main, afterMain, beforeWrite, write, afterWrite];","export default function getNodeName(element) {\n  return element ? (element.nodeName || '').toLowerCase() : null;\n}","export default function getWindow(node) {\n  if (node == null) {\n    return window;\n  }\n\n  if (node.toString() !== '[object Window]') {\n    var ownerDocument = node.ownerDocument;\n    return ownerDocument ? ownerDocument.defaultView || window : window;\n  }\n\n  return node;\n}","import getWindow from \"./getWindow.js\";\n\nfunction isElement(node) {\n  var OwnElement = getWindow(node).Element;\n  return node instanceof OwnElement || node instanceof Element;\n}\n\nfunction isHTMLElement(node) {\n  var OwnElement = getWindow(node).HTMLElement;\n  return node instanceof OwnElement || node instanceof HTMLElement;\n}\n\nfunction isShadowRoot(node) {\n  // IE 11 has no ShadowRoot\n  if (typeof ShadowRoot === 'undefined') {\n    return false;\n  }\n\n  var OwnElement = getWindow(node).ShadowRoot;\n  return node instanceof OwnElement || node instanceof ShadowRoot;\n}\n\nexport { isElement, isHTMLElement, isShadowRoot };","import getNodeName from \"../dom-utils/getNodeName.js\";\nimport { isHTMLElement } from \"../dom-utils/instanceOf.js\"; // This modifier takes the styles prepared by the `computeStyles` modifier\n// and applies them to the HTMLElements such as popper and arrow\n\nfunction applyStyles(_ref) {\n  var state = _ref.state;\n  Object.keys(state.elements).forEach(function (name) {\n    var style = state.styles[name] || {};\n    var attributes = state.attributes[name] || {};\n    var element = state.elements[name]; // arrow is optional + virtual elements\n\n    if (!isHTMLElement(element) || !getNodeName(element)) {\n      return;\n    } // Flow doesn't support to extend this property, but it's the most\n    // effective way to apply styles to an HTMLElement\n    // $FlowFixMe[cannot-write]\n\n\n    Object.assign(element.style, style);\n    Object.keys(attributes).forEach(function (name) {\n      var value = attributes[name];\n\n      if (value === false) {\n        element.removeAttribute(name);\n      } else {\n        element.setAttribute(name, value === true ? '' : value);\n      }\n    });\n  });\n}\n\nfunction effect(_ref2) {\n  var state = _ref2.state;\n  var initialStyles = {\n    popper: {\n      position: state.options.strategy,\n      left: '0',\n      top: '0',\n      margin: '0'\n    },\n    arrow: {\n      position: 'absolute'\n    },\n    reference: {}\n  };\n  Object.assign(state.elements.popper.style, initialStyles.popper);\n  state.styles = initialStyles;\n\n  if (state.elements.arrow) {\n    Object.assign(state.elements.arrow.style, initialStyles.arrow);\n  }\n\n  return function () {\n    Object.keys(state.elements).forEach(function (name) {\n      var element = state.elements[name];\n      var attributes = state.attributes[name] || {};\n      var styleProperties = Object.keys(state.styles.hasOwnProperty(name) ? state.styles[name] : initialStyles[name]); // Set all values to an empty string to unset them\n\n      var style = styleProperties.reduce(function (style, property) {\n        style[property] = '';\n        return style;\n      }, {}); // arrow is optional + virtual elements\n\n      if (!isHTMLElement(element) || !getNodeName(element)) {\n        return;\n      }\n\n      Object.assign(element.style, style);\n      Object.keys(attributes).forEach(function (attribute) {\n        element.removeAttribute(attribute);\n      });\n    });\n  };\n} // eslint-disable-next-line import/no-unused-modules\n\n\nexport default {\n  name: 'applyStyles',\n  enabled: true,\n  phase: 'write',\n  fn: applyStyles,\n  effect: effect,\n  requires: ['computeStyles']\n};","import { auto } from \"../enums.js\";\nexport default function getBasePlacement(placement) {\n  return placement.split('-')[0];\n}","export var max = Math.max;\nexport var min = Math.min;\nexport var round = Math.round;","export default function getUAString() {\n  var uaData = navigator.userAgentData;\n\n  if (uaData != null && uaData.brands && Array.isArray(uaData.brands)) {\n    return uaData.brands.map(function (item) {\n      return item.brand + \"/\" + item.version;\n    }).join(' ');\n  }\n\n  return navigator.userAgent;\n}","import getUAString from \"../utils/userAgent.js\";\nexport default function isLayoutViewport() {\n  return !/^((?!chrome|android).)*safari/i.test(getUAString());\n}","import { isElement, isHTMLElement } from \"./instanceOf.js\";\nimport { round } from \"../utils/math.js\";\nimport getWindow from \"./getWindow.js\";\nimport isLayoutViewport from \"./isLayoutViewport.js\";\nexport default function getBoundingClientRect(element, includeScale, isFixedStrategy) {\n  if (includeScale === void 0) {\n    includeScale = false;\n  }\n\n  if (isFixedStrategy === void 0) {\n    isFixedStrategy = false;\n  }\n\n  var clientRect = element.getBoundingClientRect();\n  var scaleX = 1;\n  var scaleY = 1;\n\n  if (includeScale && isHTMLElement(element)) {\n    scaleX = element.offsetWidth > 0 ? round(clientRect.width) / element.offsetWidth || 1 : 1;\n    scaleY = element.offsetHeight > 0 ? round(clientRect.height) / element.offsetHeight || 1 : 1;\n  }\n\n  var _ref = isElement(element) ? getWindow(element) : window,\n      visualViewport = _ref.visualViewport;\n\n  var addVisualOffsets = !isLayoutViewport() && isFixedStrategy;\n  var x = (clientRect.left + (addVisualOffsets && visualViewport ? visualViewport.offsetLeft : 0)) / scaleX;\n  var y = (clientRect.top + (addVisualOffsets && visualViewport ? visualViewport.offsetTop : 0)) / scaleY;\n  var width = clientRect.width / scaleX;\n  var height = clientRect.height / scaleY;\n  return {\n    width: width,\n    height: height,\n    top: y,\n    right: x + width,\n    bottom: y + height,\n    left: x,\n    x: x,\n    y: y\n  };\n}","import getBoundingClientRect from \"./getBoundingClientRect.js\"; // Returns the layout rect of an element relative to its offsetParent. Layout\n// means it doesn't take into account transforms.\n\nexport default function getLayoutRect(element) {\n  var clientRect = getBoundingClientRect(element); // Use the clientRect sizes if it's not been transformed.\n  // Fixes https://github.com/popperjs/popper-core/issues/1223\n\n  var width = element.offsetWidth;\n  var height = element.offsetHeight;\n\n  if (Math.abs(clientRect.width - width) <= 1) {\n    width = clientRect.width;\n  }\n\n  if (Math.abs(clientRect.height - height) <= 1) {\n    height = clientRect.height;\n  }\n\n  return {\n    x: element.offsetLeft,\n    y: element.offsetTop,\n    width: width,\n    height: height\n  };\n}","import { isShadowRoot } from \"./instanceOf.js\";\nexport default function contains(parent, child) {\n  var rootNode = child.getRootNode && child.getRootNode(); // First, attempt with faster native method\n\n  if (parent.contains(child)) {\n    return true;\n  } // then fallback to custom implementation with Shadow DOM support\n  else if (rootNode && isShadowRoot(rootNode)) {\n      var next = child;\n\n      do {\n        if (next && parent.isSameNode(next)) {\n          return true;\n        } // $FlowFixMe[prop-missing]: need a better way to handle this...\n\n\n        next = next.parentNode || next.host;\n      } while (next);\n    } // Give up, the result is false\n\n\n  return false;\n}","import getWindow from \"./getWindow.js\";\nexport default function getComputedStyle(element) {\n  return getWindow(element).getComputedStyle(element);\n}","import getNodeName from \"./getNodeName.js\";\nexport default function isTableElement(element) {\n  return ['table', 'td', 'th'].indexOf(getNodeName(element)) >= 0;\n}","import { isElement } from \"./instanceOf.js\";\nexport default function getDocumentElement(element) {\n  // $FlowFixMe[incompatible-return]: assume body is always available\n  return ((isElement(element) ? element.ownerDocument : // $FlowFixMe[prop-missing]\n  element.document) || window.document).documentElement;\n}","import getNodeName from \"./getNodeName.js\";\nimport getDocumentElement from \"./getDocumentElement.js\";\nimport { isShadowRoot } from \"./instanceOf.js\";\nexport default function getParentNode(element) {\n  if (getNodeName(element) === 'html') {\n    return element;\n  }\n\n  return (// this is a quicker (but less type safe) way to save quite some bytes from the bundle\n    // $FlowFixMe[incompatible-return]\n    // $FlowFixMe[prop-missing]\n    element.assignedSlot || // step into the shadow DOM of the parent of a slotted node\n    element.parentNode || ( // DOM Element detected\n    isShadowRoot(element) ? element.host : null) || // ShadowRoot detected\n    // $FlowFixMe[incompatible-call]: HTMLElement is a Node\n    getDocumentElement(element) // fallback\n\n  );\n}","import getWindow from \"./getWindow.js\";\nimport getNodeName from \"./getNodeName.js\";\nimport getComputedStyle from \"./getComputedStyle.js\";\nimport { isHTMLElement, isShadowRoot } from \"./instanceOf.js\";\nimport isTableElement from \"./isTableElement.js\";\nimport getParentNode from \"./getParentNode.js\";\nimport getUAString from \"../utils/userAgent.js\";\n\nfunction getTrueOffsetParent(element) {\n  if (!isHTMLElement(element) || // https://github.com/popperjs/popper-core/issues/837\n  getComputedStyle(element).position === 'fixed') {\n    return null;\n  }\n\n  return element.offsetParent;\n} // `.offsetParent` reports `null` for fixed elements, while absolute elements\n// return the containing block\n\n\nfunction getContainingBlock(element) {\n  var isFirefox = /firefox/i.test(getUAString());\n  var isIE = /Trident/i.test(getUAString());\n\n  if (isIE && isHTMLElement(element)) {\n    // In IE 9, 10 and 11 fixed elements containing block is always established by the viewport\n    var elementCss = getComputedStyle(element);\n\n    if (elementCss.position === 'fixed') {\n      return null;\n    }\n  }\n\n  var currentNode = getParentNode(element);\n\n  if (isShadowRoot(currentNode)) {\n    currentNode = currentNode.host;\n  }\n\n  while (isHTMLElement(currentNode) && ['html', 'body'].indexOf(getNodeName(currentNode)) < 0) {\n    var css = getComputedStyle(currentNode); // This is non-exhaustive but covers the most common CSS properties that\n    // create a containing block.\n    // https://developer.mozilla.org/en-US/docs/Web/CSS/Containing_block#identifying_the_containing_block\n\n    if (css.transform !== 'none' || css.perspective !== 'none' || css.contain === 'paint' || ['transform', 'perspective'].indexOf(css.willChange) !== -1 || isFirefox && css.willChange === 'filter' || isFirefox && css.filter && css.filter !== 'none') {\n      return currentNode;\n    } else {\n      currentNode = currentNode.parentNode;\n    }\n  }\n\n  return null;\n} // Gets the closest ancestor positioned element. Handles some edge cases,\n// such as table ancestors and cross browser bugs.\n\n\nexport default function getOffsetParent(element) {\n  var window = getWindow(element);\n  var offsetParent = getTrueOffsetParent(element);\n\n  while (offsetParent && isTableElement(offsetParent) && getComputedStyle(offsetParent).position === 'static') {\n    offsetParent = getTrueOffsetParent(offsetParent);\n  }\n\n  if (offsetParent && (getNodeName(offsetParent) === 'html' || getNodeName(offsetParent) === 'body' && getComputedStyle(offsetParent).position === 'static')) {\n    return window;\n  }\n\n  return offsetParent || getContainingBlock(element) || window;\n}","export default function getMainAxisFromPlacement(placement) {\n  return ['top', 'bottom'].indexOf(placement) >= 0 ? 'x' : 'y';\n}","import { max as mathMax, min as mathMin } from \"./math.js\";\nexport function within(min, value, max) {\n  return mathMax(min, mathMin(value, max));\n}\nexport function withinMaxClamp(min, value, max) {\n  var v = within(min, value, max);\n  return v > max ? max : v;\n}","import getFreshSideObject from \"./getFreshSideObject.js\";\nexport default function mergePaddingObject(paddingObject) {\n  return Object.assign({}, getFreshSideObject(), paddingObject);\n}","export default function getFreshSideObject() {\n  return {\n    top: 0,\n    right: 0,\n    bottom: 0,\n    left: 0\n  };\n}","export default function expandToHashMap(value, keys) {\n  return keys.reduce(function (hashMap, key) {\n    hashMap[key] = value;\n    return hashMap;\n  }, {});\n}","import getBasePlacement from \"../utils/getBasePlacement.js\";\nimport getLayoutRect from \"../dom-utils/getLayoutRect.js\";\nimport contains from \"../dom-utils/contains.js\";\nimport getOffsetParent from \"../dom-utils/getOffsetParent.js\";\nimport getMainAxisFromPlacement from \"../utils/getMainAxisFromPlacement.js\";\nimport { within } from \"../utils/within.js\";\nimport mergePaddingObject from \"../utils/mergePaddingObject.js\";\nimport expandToHashMap from \"../utils/expandToHashMap.js\";\nimport { left, right, basePlacements, top, bottom } from \"../enums.js\"; // eslint-disable-next-line import/no-unused-modules\n\nvar toPaddingObject = function toPaddingObject(padding, state) {\n  padding = typeof padding === 'function' ? padding(Object.assign({}, state.rects, {\n    placement: state.placement\n  })) : padding;\n  return mergePaddingObject(typeof padding !== 'number' ? padding : expandToHashMap(padding, basePlacements));\n};\n\nfunction arrow(_ref) {\n  var _state$modifiersData$;\n\n  var state = _ref.state,\n      name = _ref.name,\n      options = _ref.options;\n  var arrowElement = state.elements.arrow;\n  var popperOffsets = state.modifiersData.popperOffsets;\n  var basePlacement = getBasePlacement(state.placement);\n  var axis = getMainAxisFromPlacement(basePlacement);\n  var isVertical = [left, right].indexOf(basePlacement) >= 0;\n  var len = isVertical ? 'height' : 'width';\n\n  if (!arrowElement || !popperOffsets) {\n    return;\n  }\n\n  var paddingObject = toPaddingObject(options.padding, state);\n  var arrowRect = getLayoutRect(arrowElement);\n  var minProp = axis === 'y' ? top : left;\n  var maxProp = axis === 'y' ? bottom : right;\n  var endDiff = state.rects.reference[len] + state.rects.reference[axis] - popperOffsets[axis] - state.rects.popper[len];\n  var startDiff = popperOffsets[axis] - state.rects.reference[axis];\n  var arrowOffsetParent = getOffsetParent(arrowElement);\n  var clientSize = arrowOffsetParent ? axis === 'y' ? arrowOffsetParent.clientHeight || 0 : arrowOffsetParent.clientWidth || 0 : 0;\n  var centerToReference = endDiff / 2 - startDiff / 2; // Make sure the arrow doesn't overflow the popper if the center point is\n  // outside of the popper bounds\n\n  var min = paddingObject[minProp];\n  var max = clientSize - arrowRect[len] - paddingObject[maxProp];\n  var center = clientSize / 2 - arrowRect[len] / 2 + centerToReference;\n  var offset = within(min, center, max); // Prevents breaking syntax highlighting...\n\n  var axisProp = axis;\n  state.modifiersData[name] = (_state$modifiersData$ = {}, _state$modifiersData$[axisProp] = offset, _state$modifiersData$.centerOffset = offset - center, _state$modifiersData$);\n}\n\nfunction effect(_ref2) {\n  var state = _ref2.state,\n      options = _ref2.options;\n  var _options$element = options.element,\n      arrowElement = _options$element === void 0 ? '[data-popper-arrow]' : _options$element;\n\n  if (arrowElement == null) {\n    return;\n  } // CSS selector\n\n\n  if (typeof arrowElement === 'string') {\n    arrowElement = state.elements.popper.querySelector(arrowElement);\n\n    if (!arrowElement) {\n      return;\n    }\n  }\n\n  if (!contains(state.elements.popper, arrowElement)) {\n    return;\n  }\n\n  state.elements.arrow = arrowElement;\n} // eslint-disable-next-line import/no-unused-modules\n\n\nexport default {\n  name: 'arrow',\n  enabled: true,\n  phase: 'main',\n  fn: arrow,\n  effect: effect,\n  requires: ['popperOffsets'],\n  requiresIfExists: ['preventOverflow']\n};","export default function getVariation(placement) {\n  return placement.split('-')[1];\n}","import { top, left, right, bottom, end } from \"../enums.js\";\nimport getOffsetParent from \"../dom-utils/getOffsetParent.js\";\nimport getWindow from \"../dom-utils/getWindow.js\";\nimport getDocumentElement from \"../dom-utils/getDocumentElement.js\";\nimport getComputedStyle from \"../dom-utils/getComputedStyle.js\";\nimport getBasePlacement from \"../utils/getBasePlacement.js\";\nimport getVariation from \"../utils/getVariation.js\";\nimport { round } from \"../utils/math.js\"; // eslint-disable-next-line import/no-unused-modules\n\nvar unsetSides = {\n  top: 'auto',\n  right: 'auto',\n  bottom: 'auto',\n  left: 'auto'\n}; // Round the offsets to the nearest suitable subpixel based on the DPR.\n// Zooming can change the DPR, but it seems to report a value that will\n// cleanly divide the values into the appropriate subpixels.\n\nfunction roundOffsetsByDPR(_ref, win) {\n  var x = _ref.x,\n      y = _ref.y;\n  var dpr = win.devicePixelRatio || 1;\n  return {\n    x: round(x * dpr) / dpr || 0,\n    y: round(y * dpr) / dpr || 0\n  };\n}\n\nexport function mapToStyles(_ref2) {\n  var _Object$assign2;\n\n  var popper = _ref2.popper,\n      popperRect = _ref2.popperRect,\n      placement = _ref2.placement,\n      variation = _ref2.variation,\n      offsets = _ref2.offsets,\n      position = _ref2.position,\n      gpuAcceleration = _ref2.gpuAcceleration,\n      adaptive = _ref2.adaptive,\n      roundOffsets = _ref2.roundOffsets,\n      isFixed = _ref2.isFixed;\n  var _offsets$x = offsets.x,\n      x = _offsets$x === void 0 ? 0 : _offsets$x,\n      _offsets$y = offsets.y,\n      y = _offsets$y === void 0 ? 0 : _offsets$y;\n\n  var _ref3 = typeof roundOffsets === 'function' ? roundOffsets({\n    x: x,\n    y: y\n  }) : {\n    x: x,\n    y: y\n  };\n\n  x = _ref3.x;\n  y = _ref3.y;\n  var hasX = offsets.hasOwnProperty('x');\n  var hasY = offsets.hasOwnProperty('y');\n  var sideX = left;\n  var sideY = top;\n  var win = window;\n\n  if (adaptive) {\n    var offsetParent = getOffsetParent(popper);\n    var heightProp = 'clientHeight';\n    var widthProp = 'clientWidth';\n\n    if (offsetParent === getWindow(popper)) {\n      offsetParent = getDocumentElement(popper);\n\n      if (getComputedStyle(offsetParent).position !== 'static' && position === 'absolute') {\n        heightProp = 'scrollHeight';\n        widthProp = 'scrollWidth';\n      }\n    } // $FlowFixMe[incompatible-cast]: force type refinement, we compare offsetParent with window above, but Flow doesn't detect it\n\n\n    offsetParent = offsetParent;\n\n    if (placement === top || (placement === left || placement === right) && variation === end) {\n      sideY = bottom;\n      var offsetY = isFixed && offsetParent === win && win.visualViewport ? win.visualViewport.height : // $FlowFixMe[prop-missing]\n      offsetParent[heightProp];\n      y -= offsetY - popperRect.height;\n      y *= gpuAcceleration ? 1 : -1;\n    }\n\n    if (placement === left || (placement === top || placement === bottom) && variation === end) {\n      sideX = right;\n      var offsetX = isFixed && offsetParent === win && win.visualViewport ? win.visualViewport.width : // $FlowFixMe[prop-missing]\n      offsetParent[widthProp];\n      x -= offsetX - popperRect.width;\n      x *= gpuAcceleration ? 1 : -1;\n    }\n  }\n\n  var commonStyles = Object.assign({\n    position: position\n  }, adaptive && unsetSides);\n\n  var _ref4 = roundOffsets === true ? roundOffsetsByDPR({\n    x: x,\n    y: y\n  }, getWindow(popper)) : {\n    x: x,\n    y: y\n  };\n\n  x = _ref4.x;\n  y = _ref4.y;\n\n  if (gpuAcceleration) {\n    var _Object$assign;\n\n    return Object.assign({}, commonStyles, (_Object$assign = {}, _Object$assign[sideY] = hasY ? '0' : '', _Object$assign[sideX] = hasX ? '0' : '', _Object$assign.transform = (win.devicePixelRatio || 1) <= 1 ? \"translate(\" + x + \"px, \" + y + \"px)\" : \"translate3d(\" + x + \"px, \" + y + \"px, 0)\", _Object$assign));\n  }\n\n  return Object.assign({}, commonStyles, (_Object$assign2 = {}, _Object$assign2[sideY] = hasY ? y + \"px\" : '', _Object$assign2[sideX] = hasX ? x + \"px\" : '', _Object$assign2.transform = '', _Object$assign2));\n}\n\nfunction computeStyles(_ref5) {\n  var state = _ref5.state,\n      options = _ref5.options;\n  var _options$gpuAccelerat = options.gpuAcceleration,\n      gpuAcceleration = _options$gpuAccelerat === void 0 ? true : _options$gpuAccelerat,\n      _options$adaptive = options.adaptive,\n      adaptive = _options$adaptive === void 0 ? true : _options$adaptive,\n      _options$roundOffsets = options.roundOffsets,\n      roundOffsets = _options$roundOffsets === void 0 ? true : _options$roundOffsets;\n  var commonStyles = {\n    placement: getBasePlacement(state.placement),\n    variation: getVariation(state.placement),\n    popper: state.elements.popper,\n    popperRect: state.rects.popper,\n    gpuAcceleration: gpuAcceleration,\n    isFixed: state.options.strategy === 'fixed'\n  };\n\n  if (state.modifiersData.popperOffsets != null) {\n    state.styles.popper = Object.assign({}, state.styles.popper, mapToStyles(Object.assign({}, commonStyles, {\n      offsets: state.modifiersData.popperOffsets,\n      position: state.options.strategy,\n      adaptive: adaptive,\n      roundOffsets: roundOffsets\n    })));\n  }\n\n  if (state.modifiersData.arrow != null) {\n    state.styles.arrow = Object.assign({}, state.styles.arrow, mapToStyles(Object.assign({}, commonStyles, {\n      offsets: state.modifiersData.arrow,\n      position: 'absolute',\n      adaptive: false,\n      roundOffsets: roundOffsets\n    })));\n  }\n\n  state.attributes.popper = Object.assign({}, state.attributes.popper, {\n    'data-popper-placement': state.placement\n  });\n} // eslint-disable-next-line import/no-unused-modules\n\n\nexport default {\n  name: 'computeStyles',\n  enabled: true,\n  phase: 'beforeWrite',\n  fn: computeStyles,\n  data: {}\n};","import getWindow from \"../dom-utils/getWindow.js\"; // eslint-disable-next-line import/no-unused-modules\n\nvar passive = {\n  passive: true\n};\n\nfunction effect(_ref) {\n  var state = _ref.state,\n      instance = _ref.instance,\n      options = _ref.options;\n  var _options$scroll = options.scroll,\n      scroll = _options$scroll === void 0 ? true : _options$scroll,\n      _options$resize = options.resize,\n      resize = _options$resize === void 0 ? true : _options$resize;\n  var window = getWindow(state.elements.popper);\n  var scrollParents = [].concat(state.scrollParents.reference, state.scrollParents.popper);\n\n  if (scroll) {\n    scrollParents.forEach(function (scrollParent) {\n      scrollParent.addEventListener('scroll', instance.update, passive);\n    });\n  }\n\n  if (resize) {\n    window.addEventListener('resize', instance.update, passive);\n  }\n\n  return function () {\n    if (scroll) {\n      scrollParents.forEach(function (scrollParent) {\n        scrollParent.removeEventListener('scroll', instance.update, passive);\n      });\n    }\n\n    if (resize) {\n      window.removeEventListener('resize', instance.update, passive);\n    }\n  };\n} // eslint-disable-next-line import/no-unused-modules\n\n\nexport default {\n  name: 'eventListeners',\n  enabled: true,\n  phase: 'write',\n  fn: function fn() {},\n  effect: effect,\n  data: {}\n};","var hash = {\n  left: 'right',\n  right: 'left',\n  bottom: 'top',\n  top: 'bottom'\n};\nexport default function getOppositePlacement(placement) {\n  return placement.replace(/left|right|bottom|top/g, function (matched) {\n    return hash[matched];\n  });\n}","var hash = {\n  start: 'end',\n  end: 'start'\n};\nexport default function getOppositeVariationPlacement(placement) {\n  return placement.replace(/start|end/g, function (matched) {\n    return hash[matched];\n  });\n}","import getWindow from \"./getWindow.js\";\nexport default function getWindowScroll(node) {\n  var win = getWindow(node);\n  var scrollLeft = win.pageXOffset;\n  var scrollTop = win.pageYOffset;\n  return {\n    scrollLeft: scrollLeft,\n    scrollTop: scrollTop\n  };\n}","import getBoundingClientRect from \"./getBoundingClientRect.js\";\nimport getDocumentElement from \"./getDocumentElement.js\";\nimport getWindowScroll from \"./getWindowScroll.js\";\nexport default function getWindowScrollBarX(element) {\n  // If <html> has a CSS width greater than the viewport, then this will be\n  // incorrect for RTL.\n  // Popper 1 is broken in this case and never had a bug report so let's assume\n  // it's not an issue. I don't think anyone ever specifies width on <html>\n  // anyway.\n  // Browsers where the left scrollbar doesn't cause an issue report `0` for\n  // this (e.g. Edge 2019, IE11, Safari)\n  return getBoundingClientRect(getDocumentElement(element)).left + getWindowScroll(element).scrollLeft;\n}","import getComputedStyle from \"./getComputedStyle.js\";\nexport default function isScrollParent(element) {\n  // Firefox wants us to check `-x` and `-y` variations as well\n  var _getComputedStyle = getComputedStyle(element),\n      overflow = _getComputedStyle.overflow,\n      overflowX = _getComputedStyle.overflowX,\n      overflowY = _getComputedStyle.overflowY;\n\n  return /auto|scroll|overlay|hidden/.test(overflow + overflowY + overflowX);\n}","import getParentNode from \"./getParentNode.js\";\nimport isScrollParent from \"./isScrollParent.js\";\nimport getNodeName from \"./getNodeName.js\";\nimport { isHTMLElement } from \"./instanceOf.js\";\nexport default function getScrollParent(node) {\n  if (['html', 'body', '#document'].indexOf(getNodeName(node)) >= 0) {\n    // $FlowFixMe[incompatible-return]: assume body is always available\n    return node.ownerDocument.body;\n  }\n\n  if (isHTMLElement(node) && isScrollParent(node)) {\n    return node;\n  }\n\n  return getScrollParent(getParentNode(node));\n}","import getScrollParent from \"./getScrollParent.js\";\nimport getParentNode from \"./getParentNode.js\";\nimport getWindow from \"./getWindow.js\";\nimport isScrollParent from \"./isScrollParent.js\";\n/*\ngiven a DOM element, return the list of all scroll parents, up the list of ancesors\nuntil we get to the top window object. This list is what we attach scroll listeners\nto, because if any of these parent elements scroll, we'll need to re-calculate the\nreference element's position.\n*/\n\nexport default function listScrollParents(element, list) {\n  var _element$ownerDocumen;\n\n  if (list === void 0) {\n    list = [];\n  }\n\n  var scrollParent = getScrollParent(element);\n  var isBody = scrollParent === ((_element$ownerDocumen = element.ownerDocument) == null ? void 0 : _element$ownerDocumen.body);\n  var win = getWindow(scrollParent);\n  var target = isBody ? [win].concat(win.visualViewport || [], isScrollParent(scrollParent) ? scrollParent : []) : scrollParent;\n  var updatedList = list.concat(target);\n  return isBody ? updatedList : // $FlowFixMe[incompatible-call]: isBody tells us target will be an HTMLElement here\n  updatedList.concat(listScrollParents(getParentNode(target)));\n}","export default function rectToClientRect(rect) {\n  return Object.assign({}, rect, {\n    left: rect.x,\n    top: rect.y,\n    right: rect.x + rect.width,\n    bottom: rect.y + rect.height\n  });\n}","import { viewport } from \"../enums.js\";\nimport getViewportRect from \"./getViewportRect.js\";\nimport getDocumentRect from \"./getDocumentRect.js\";\nimport listScrollParents from \"./listScrollParents.js\";\nimport getOffsetParent from \"./getOffsetParent.js\";\nimport getDocumentElement from \"./getDocumentElement.js\";\nimport getComputedStyle from \"./getComputedStyle.js\";\nimport { isElement, isHTMLElement } from \"./instanceOf.js\";\nimport getBoundingClientRect from \"./getBoundingClientRect.js\";\nimport getParentNode from \"./getParentNode.js\";\nimport contains from \"./contains.js\";\nimport getNodeName from \"./getNodeName.js\";\nimport rectToClientRect from \"../utils/rectToClientRect.js\";\nimport { max, min } from \"../utils/math.js\";\n\nfunction getInnerBoundingClientRect(element, strategy) {\n  var rect = getBoundingClientRect(element, false, strategy === 'fixed');\n  rect.top = rect.top + element.clientTop;\n  rect.left = rect.left + element.clientLeft;\n  rect.bottom = rect.top + element.clientHeight;\n  rect.right = rect.left + element.clientWidth;\n  rect.width = element.clientWidth;\n  rect.height = element.clientHeight;\n  rect.x = rect.left;\n  rect.y = rect.top;\n  return rect;\n}\n\nfunction getClientRectFromMixedType(element, clippingParent, strategy) {\n  return clippingParent === viewport ? rectToClientRect(getViewportRect(element, strategy)) : isElement(clippingParent) ? getInnerBoundingClientRect(clippingParent, strategy) : rectToClientRect(getDocumentRect(getDocumentElement(element)));\n} // A \"clipping parent\" is an overflowable container with the characteristic of\n// clipping (or hiding) overflowing elements with a position different from\n// `initial`\n\n\nfunction getClippingParents(element) {\n  var clippingParents = listScrollParents(getParentNode(element));\n  var canEscapeClipping = ['absolute', 'fixed'].indexOf(getComputedStyle(element).position) >= 0;\n  var clipperElement = canEscapeClipping && isHTMLElement(element) ? getOffsetParent(element) : element;\n\n  if (!isElement(clipperElement)) {\n    return [];\n  } // $FlowFixMe[incompatible-return]: https://github.com/facebook/flow/issues/1414\n\n\n  return clippingParents.filter(function (clippingParent) {\n    return isElement(clippingParent) && contains(clippingParent, clipperElement) && getNodeName(clippingParent) !== 'body';\n  });\n} // Gets the maximum area that the element is visible in due to any number of\n// clipping parents\n\n\nexport default function getClippingRect(element, boundary, rootBoundary, strategy) {\n  var mainClippingParents = boundary === 'clippingParents' ? getClippingParents(element) : [].concat(boundary);\n  var clippingParents = [].concat(mainClippingParents, [rootBoundary]);\n  var firstClippingParent = clippingParents[0];\n  var clippingRect = clippingParents.reduce(function (accRect, clippingParent) {\n    var rect = getClientRectFromMixedType(element, clippingParent, strategy);\n    accRect.top = max(rect.top, accRect.top);\n    accRect.right = min(rect.right, accRect.right);\n    accRect.bottom = min(rect.bottom, accRect.bottom);\n    accRect.left = max(rect.left, accRect.left);\n    return accRect;\n  }, getClientRectFromMixedType(element, firstClippingParent, strategy));\n  clippingRect.width = clippingRect.right - clippingRect.left;\n  clippingRect.height = clippingRect.bottom - clippingRect.top;\n  clippingRect.x = clippingRect.left;\n  clippingRect.y = clippingRect.top;\n  return clippingRect;\n}","import getWindow from \"./getWindow.js\";\nimport getDocumentElement from \"./getDocumentElement.js\";\nimport getWindowScrollBarX from \"./getWindowScrollBarX.js\";\nimport isLayoutViewport from \"./isLayoutViewport.js\";\nexport default function getViewportRect(element, strategy) {\n  var win = getWindow(element);\n  var html = getDocumentElement(element);\n  var visualViewport = win.visualViewport;\n  var width = html.clientWidth;\n  var height = html.clientHeight;\n  var x = 0;\n  var y = 0;\n\n  if (visualViewport) {\n    width = visualViewport.width;\n    height = visualViewport.height;\n    var layoutViewport = isLayoutViewport();\n\n    if (layoutViewport || !layoutViewport && strategy === 'fixed') {\n      x = visualViewport.offsetLeft;\n      y = visualViewport.offsetTop;\n    }\n  }\n\n  return {\n    width: width,\n    height: height,\n    x: x + getWindowScrollBarX(element),\n    y: y\n  };\n}","import getDocumentElement from \"./getDocumentElement.js\";\nimport getComputedStyle from \"./getComputedStyle.js\";\nimport getWindowScrollBarX from \"./getWindowScrollBarX.js\";\nimport getWindowScroll from \"./getWindowScroll.js\";\nimport { max } from \"../utils/math.js\"; // Gets the entire size of the scrollable document area, even extending outside\n// of the `<html>` and `<body>` rect bounds if horizontally scrollable\n\nexport default function getDocumentRect(element) {\n  var _element$ownerDocumen;\n\n  var html = getDocumentElement(element);\n  var winScroll = getWindowScroll(element);\n  var body = (_element$ownerDocumen = element.ownerDocument) == null ? void 0 : _element$ownerDocumen.body;\n  var width = max(html.scrollWidth, html.clientWidth, body ? body.scrollWidth : 0, body ? body.clientWidth : 0);\n  var height = max(html.scrollHeight, html.clientHeight, body ? body.scrollHeight : 0, body ? body.clientHeight : 0);\n  var x = -winScroll.scrollLeft + getWindowScrollBarX(element);\n  var y = -winScroll.scrollTop;\n\n  if (getComputedStyle(body || html).direction === 'rtl') {\n    x += max(html.clientWidth, body ? body.clientWidth : 0) - width;\n  }\n\n  return {\n    width: width,\n    height: height,\n    x: x,\n    y: y\n  };\n}","import getBasePlacement from \"./getBasePlacement.js\";\nimport getVariation from \"./getVariation.js\";\nimport getMainAxisFromPlacement from \"./getMainAxisFromPlacement.js\";\nimport { top, right, bottom, left, start, end } from \"../enums.js\";\nexport default function computeOffsets(_ref) {\n  var reference = _ref.reference,\n      element = _ref.element,\n      placement = _ref.placement;\n  var basePlacement = placement ? getBasePlacement(placement) : null;\n  var variation = placement ? getVariation(placement) : null;\n  var commonX = reference.x + reference.width / 2 - element.width / 2;\n  var commonY = reference.y + reference.height / 2 - element.height / 2;\n  var offsets;\n\n  switch (basePlacement) {\n    case top:\n      offsets = {\n        x: commonX,\n        y: reference.y - element.height\n      };\n      break;\n\n    case bottom:\n      offsets = {\n        x: commonX,\n        y: reference.y + reference.height\n      };\n      break;\n\n    case right:\n      offsets = {\n        x: reference.x + reference.width,\n        y: commonY\n      };\n      break;\n\n    case left:\n      offsets = {\n        x: reference.x - element.width,\n        y: commonY\n      };\n      break;\n\n    default:\n      offsets = {\n        x: reference.x,\n        y: reference.y\n      };\n  }\n\n  var mainAxis = basePlacement ? getMainAxisFromPlacement(basePlacement) : null;\n\n  if (mainAxis != null) {\n    var len = mainAxis === 'y' ? 'height' : 'width';\n\n    switch (variation) {\n      case start:\n        offsets[mainAxis] = offsets[mainAxis] - (reference[len] / 2 - element[len] / 2);\n        break;\n\n      case end:\n        offsets[mainAxis] = offsets[mainAxis] + (reference[len] / 2 - element[len] / 2);\n        break;\n\n      default:\n    }\n  }\n\n  return offsets;\n}","import getClippingRect from \"../dom-utils/getClippingRect.js\";\nimport getDocumentElement from \"../dom-utils/getDocumentElement.js\";\nimport getBoundingClientRect from \"../dom-utils/getBoundingClientRect.js\";\nimport computeOffsets from \"./computeOffsets.js\";\nimport rectToClientRect from \"./rectToClientRect.js\";\nimport { clippingParents, reference, popper, bottom, top, right, basePlacements, viewport } from \"../enums.js\";\nimport { isElement } from \"../dom-utils/instanceOf.js\";\nimport mergePaddingObject from \"./mergePaddingObject.js\";\nimport expandToHashMap from \"./expandToHashMap.js\"; // eslint-disable-next-line import/no-unused-modules\n\nexport default function detectOverflow(state, options) {\n  if (options === void 0) {\n    options = {};\n  }\n\n  var _options = options,\n      _options$placement = _options.placement,\n      placement = _options$placement === void 0 ? state.placement : _options$placement,\n      _options$strategy = _options.strategy,\n      strategy = _options$strategy === void 0 ? state.strategy : _options$strategy,\n      _options$boundary = _options.boundary,\n      boundary = _options$boundary === void 0 ? clippingParents : _options$boundary,\n      _options$rootBoundary = _options.rootBoundary,\n      rootBoundary = _options$rootBoundary === void 0 ? viewport : _options$rootBoundary,\n      _options$elementConte = _options.elementContext,\n      elementContext = _options$elementConte === void 0 ? popper : _options$elementConte,\n      _options$altBoundary = _options.altBoundary,\n      altBoundary = _options$altBoundary === void 0 ? false : _options$altBoundary,\n      _options$padding = _options.padding,\n      padding = _options$padding === void 0 ? 0 : _options$padding;\n  var paddingObject = mergePaddingObject(typeof padding !== 'number' ? padding : expandToHashMap(padding, basePlacements));\n  var altContext = elementContext === popper ? reference : popper;\n  var popperRect = state.rects.popper;\n  var element = state.elements[altBoundary ? altContext : elementContext];\n  var clippingClientRect = getClippingRect(isElement(element) ? element : element.contextElement || getDocumentElement(state.elements.popper), boundary, rootBoundary, strategy);\n  var referenceClientRect = getBoundingClientRect(state.elements.reference);\n  var popperOffsets = computeOffsets({\n    reference: referenceClientRect,\n    element: popperRect,\n    strategy: 'absolute',\n    placement: placement\n  });\n  var popperClientRect = rectToClientRect(Object.assign({}, popperRect, popperOffsets));\n  var elementClientRect = elementContext === popper ? popperClientRect : referenceClientRect; // positive = overflowing the clipping rect\n  // 0 or negative = within the clipping rect\n\n  var overflowOffsets = {\n    top: clippingClientRect.top - elementClientRect.top + paddingObject.top,\n    bottom: elementClientRect.bottom - clippingClientRect.bottom + paddingObject.bottom,\n    left: clippingClientRect.left - elementClientRect.left + paddingObject.left,\n    right: elementClientRect.right - clippingClientRect.right + paddingObject.right\n  };\n  var offsetData = state.modifiersData.offset; // Offsets can be applied only to the popper element\n\n  if (elementContext === popper && offsetData) {\n    var offset = offsetData[placement];\n    Object.keys(overflowOffsets).forEach(function (key) {\n      var multiply = [right, bottom].indexOf(key) >= 0 ? 1 : -1;\n      var axis = [top, bottom].indexOf(key) >= 0 ? 'y' : 'x';\n      overflowOffsets[key] += offset[axis] * multiply;\n    });\n  }\n\n  return overflowOffsets;\n}","import getVariation from \"./getVariation.js\";\nimport { variationPlacements, basePlacements, placements as allPlacements } from \"../enums.js\";\nimport detectOverflow from \"./detectOverflow.js\";\nimport getBasePlacement from \"./getBasePlacement.js\";\nexport default function computeAutoPlacement(state, options) {\n  if (options === void 0) {\n    options = {};\n  }\n\n  var _options = options,\n      placement = _options.placement,\n      boundary = _options.boundary,\n      rootBoundary = _options.rootBoundary,\n      padding = _options.padding,\n      flipVariations = _options.flipVariations,\n      _options$allowedAutoP = _options.allowedAutoPlacements,\n      allowedAutoPlacements = _options$allowedAutoP === void 0 ? allPlacements : _options$allowedAutoP;\n  var variation = getVariation(placement);\n  var placements = variation ? flipVariations ? variationPlacements : variationPlacements.filter(function (placement) {\n    return getVariation(placement) === variation;\n  }) : basePlacements;\n  var allowedPlacements = placements.filter(function (placement) {\n    return allowedAutoPlacements.indexOf(placement) >= 0;\n  });\n\n  if (allowedPlacements.length === 0) {\n    allowedPlacements = placements;\n  } // $FlowFixMe[incompatible-type]: Flow seems to have problems with two array unions...\n\n\n  var overflows = allowedPlacements.reduce(function (acc, placement) {\n    acc[placement] = detectOverflow(state, {\n      placement: placement,\n      boundary: boundary,\n      rootBoundary: rootBoundary,\n      padding: padding\n    })[getBasePlacement(placement)];\n    return acc;\n  }, {});\n  return Object.keys(overflows).sort(function (a, b) {\n    return overflows[a] - overflows[b];\n  });\n}","import getOppositePlacement from \"../utils/getOppositePlacement.js\";\nimport getBasePlacement from \"../utils/getBasePlacement.js\";\nimport getOppositeVariationPlacement from \"../utils/getOppositeVariationPlacement.js\";\nimport detectOverflow from \"../utils/detectOverflow.js\";\nimport computeAutoPlacement from \"../utils/computeAutoPlacement.js\";\nimport { bottom, top, start, right, left, auto } from \"../enums.js\";\nimport getVariation from \"../utils/getVariation.js\"; // eslint-disable-next-line import/no-unused-modules\n\nfunction getExpandedFallbackPlacements(placement) {\n  if (getBasePlacement(placement) === auto) {\n    return [];\n  }\n\n  var oppositePlacement = getOppositePlacement(placement);\n  return [getOppositeVariationPlacement(placement), oppositePlacement, getOppositeVariationPlacement(oppositePlacement)];\n}\n\nfunction flip(_ref) {\n  var state = _ref.state,\n      options = _ref.options,\n      name = _ref.name;\n\n  if (state.modifiersData[name]._skip) {\n    return;\n  }\n\n  var _options$mainAxis = options.mainAxis,\n      checkMainAxis = _options$mainAxis === void 0 ? true : _options$mainAxis,\n      _options$altAxis = options.altAxis,\n      checkAltAxis = _options$altAxis === void 0 ? true : _options$altAxis,\n      specifiedFallbackPlacements = options.fallbackPlacements,\n      padding = options.padding,\n      boundary = options.boundary,\n      rootBoundary = options.rootBoundary,\n      altBoundary = options.altBoundary,\n      _options$flipVariatio = options.flipVariations,\n      flipVariations = _options$flipVariatio === void 0 ? true : _options$flipVariatio,\n      allowedAutoPlacements = options.allowedAutoPlacements;\n  var preferredPlacement = state.options.placement;\n  var basePlacement = getBasePlacement(preferredPlacement);\n  var isBasePlacement = basePlacement === preferredPlacement;\n  var fallbackPlacements = specifiedFallbackPlacements || (isBasePlacement || !flipVariations ? [getOppositePlacement(preferredPlacement)] : getExpandedFallbackPlacements(preferredPlacement));\n  var placements = [preferredPlacement].concat(fallbackPlacements).reduce(function (acc, placement) {\n    return acc.concat(getBasePlacement(placement) === auto ? computeAutoPlacement(state, {\n      placement: placement,\n      boundary: boundary,\n      rootBoundary: rootBoundary,\n      padding: padding,\n      flipVariations: flipVariations,\n      allowedAutoPlacements: allowedAutoPlacements\n    }) : placement);\n  }, []);\n  var referenceRect = state.rects.reference;\n  var popperRect = state.rects.popper;\n  var checksMap = new Map();\n  var makeFallbackChecks = true;\n  var firstFittingPlacement = placements[0];\n\n  for (var i = 0; i < placements.length; i++) {\n    var placement = placements[i];\n\n    var _basePlacement = getBasePlacement(placement);\n\n    var isStartVariation = getVariation(placement) === start;\n    var isVertical = [top, bottom].indexOf(_basePlacement) >= 0;\n    var len = isVertical ? 'width' : 'height';\n    var overflow = detectOverflow(state, {\n      placement: placement,\n      boundary: boundary,\n      rootBoundary: rootBoundary,\n      altBoundary: altBoundary,\n      padding: padding\n    });\n    var mainVariationSide = isVertical ? isStartVariation ? right : left : isStartVariation ? bottom : top;\n\n    if (referenceRect[len] > popperRect[len]) {\n      mainVariationSide = getOppositePlacement(mainVariationSide);\n    }\n\n    var altVariationSide = getOppositePlacement(mainVariationSide);\n    var checks = [];\n\n    if (checkMainAxis) {\n      checks.push(overflow[_basePlacement] <= 0);\n    }\n\n    if (checkAltAxis) {\n      checks.push(overflow[mainVariationSide] <= 0, overflow[altVariationSide] <= 0);\n    }\n\n    if (checks.every(function (check) {\n      return check;\n    })) {\n      firstFittingPlacement = placement;\n      makeFallbackChecks = false;\n      break;\n    }\n\n    checksMap.set(placement, checks);\n  }\n\n  if (makeFallbackChecks) {\n    // `2` may be desired in some cases – research later\n    var numberOfChecks = flipVariations ? 3 : 1;\n\n    var _loop = function _loop(_i) {\n      var fittingPlacement = placements.find(function (placement) {\n        var checks = checksMap.get(placement);\n\n        if (checks) {\n          return checks.slice(0, _i).every(function (check) {\n            return check;\n          });\n        }\n      });\n\n      if (fittingPlacement) {\n        firstFittingPlacement = fittingPlacement;\n        return \"break\";\n      }\n    };\n\n    for (var _i = numberOfChecks; _i > 0; _i--) {\n      var _ret = _loop(_i);\n\n      if (_ret === \"break\") break;\n    }\n  }\n\n  if (state.placement !== firstFittingPlacement) {\n    state.modifiersData[name]._skip = true;\n    state.placement = firstFittingPlacement;\n    state.reset = true;\n  }\n} // eslint-disable-next-line import/no-unused-modules\n\n\nexport default {\n  name: 'flip',\n  enabled: true,\n  phase: 'main',\n  fn: flip,\n  requiresIfExists: ['offset'],\n  data: {\n    _skip: false\n  }\n};","import { top, bottom, left, right } from \"../enums.js\";\nimport detectOverflow from \"../utils/detectOverflow.js\";\n\nfunction getSideOffsets(overflow, rect, preventedOffsets) {\n  if (preventedOffsets === void 0) {\n    preventedOffsets = {\n      x: 0,\n      y: 0\n    };\n  }\n\n  return {\n    top: overflow.top - rect.height - preventedOffsets.y,\n    right: overflow.right - rect.width + preventedOffsets.x,\n    bottom: overflow.bottom - rect.height + preventedOffsets.y,\n    left: overflow.left - rect.width - preventedOffsets.x\n  };\n}\n\nfunction isAnySideFullyClipped(overflow) {\n  return [top, right, bottom, left].some(function (side) {\n    return overflow[side] >= 0;\n  });\n}\n\nfunction hide(_ref) {\n  var state = _ref.state,\n      name = _ref.name;\n  var referenceRect = state.rects.reference;\n  var popperRect = state.rects.popper;\n  var preventedOffsets = state.modifiersData.preventOverflow;\n  var referenceOverflow = detectOverflow(state, {\n    elementContext: 'reference'\n  });\n  var popperAltOverflow = detectOverflow(state, {\n    altBoundary: true\n  });\n  var referenceClippingOffsets = getSideOffsets(referenceOverflow, referenceRect);\n  var popperEscapeOffsets = getSideOffsets(popperAltOverflow, popperRect, preventedOffsets);\n  var isReferenceHidden = isAnySideFullyClipped(referenceClippingOffsets);\n  var hasPopperEscaped = isAnySideFullyClipped(popperEscapeOffsets);\n  state.modifiersData[name] = {\n    referenceClippingOffsets: referenceClippingOffsets,\n    popperEscapeOffsets: popperEscapeOffsets,\n    isReferenceHidden: isReferenceHidden,\n    hasPopperEscaped: hasPopperEscaped\n  };\n  state.attributes.popper = Object.assign({}, state.attributes.popper, {\n    'data-popper-reference-hidden': isReferenceHidden,\n    'data-popper-escaped': hasPopperEscaped\n  });\n} // eslint-disable-next-line import/no-unused-modules\n\n\nexport default {\n  name: 'hide',\n  enabled: true,\n  phase: 'main',\n  requiresIfExists: ['preventOverflow'],\n  fn: hide\n};","import getBasePlacement from \"../utils/getBasePlacement.js\";\nimport { top, left, right, placements } from \"../enums.js\"; // eslint-disable-next-line import/no-unused-modules\n\nexport function distanceAndSkiddingToXY(placement, rects, offset) {\n  var basePlacement = getBasePlacement(placement);\n  var invertDistance = [left, top].indexOf(basePlacement) >= 0 ? -1 : 1;\n\n  var _ref = typeof offset === 'function' ? offset(Object.assign({}, rects, {\n    placement: placement\n  })) : offset,\n      skidding = _ref[0],\n      distance = _ref[1];\n\n  skidding = skidding || 0;\n  distance = (distance || 0) * invertDistance;\n  return [left, right].indexOf(basePlacement) >= 0 ? {\n    x: distance,\n    y: skidding\n  } : {\n    x: skidding,\n    y: distance\n  };\n}\n\nfunction offset(_ref2) {\n  var state = _ref2.state,\n      options = _ref2.options,\n      name = _ref2.name;\n  var _options$offset = options.offset,\n      offset = _options$offset === void 0 ? [0, 0] : _options$offset;\n  var data = placements.reduce(function (acc, placement) {\n    acc[placement] = distanceAndSkiddingToXY(placement, state.rects, offset);\n    return acc;\n  }, {});\n  var _data$state$placement = data[state.placement],\n      x = _data$state$placement.x,\n      y = _data$state$placement.y;\n\n  if (state.modifiersData.popperOffsets != null) {\n    state.modifiersData.popperOffsets.x += x;\n    state.modifiersData.popperOffsets.y += y;\n  }\n\n  state.modifiersData[name] = data;\n} // eslint-disable-next-line import/no-unused-modules\n\n\nexport default {\n  name: 'offset',\n  enabled: true,\n  phase: 'main',\n  requires: ['popperOffsets'],\n  fn: offset\n};","import computeOffsets from \"../utils/computeOffsets.js\";\n\nfunction popperOffsets(_ref) {\n  var state = _ref.state,\n      name = _ref.name;\n  // Offsets are the actual position the popper needs to have to be\n  // properly positioned near its reference element\n  // This is the most basic placement, and will be adjusted by\n  // the modifiers in the next step\n  state.modifiersData[name] = computeOffsets({\n    reference: state.rects.reference,\n    element: state.rects.popper,\n    strategy: 'absolute',\n    placement: state.placement\n  });\n} // eslint-disable-next-line import/no-unused-modules\n\n\nexport default {\n  name: 'popperOffsets',\n  enabled: true,\n  phase: 'read',\n  fn: popperOffsets,\n  data: {}\n};","import { top, left, right, bottom, start } from \"../enums.js\";\nimport getBasePlacement from \"../utils/getBasePlacement.js\";\nimport getMainAxisFromPlacement from \"../utils/getMainAxisFromPlacement.js\";\nimport getAltAxis from \"../utils/getAltAxis.js\";\nimport { within, withinMaxClamp } from \"../utils/within.js\";\nimport getLayoutRect from \"../dom-utils/getLayoutRect.js\";\nimport getOffsetParent from \"../dom-utils/getOffsetParent.js\";\nimport detectOverflow from \"../utils/detectOverflow.js\";\nimport getVariation from \"../utils/getVariation.js\";\nimport getFreshSideObject from \"../utils/getFreshSideObject.js\";\nimport { min as mathMin, max as mathMax } from \"../utils/math.js\";\n\nfunction preventOverflow(_ref) {\n  var state = _ref.state,\n      options = _ref.options,\n      name = _ref.name;\n  var _options$mainAxis = options.mainAxis,\n      checkMainAxis = _options$mainAxis === void 0 ? true : _options$mainAxis,\n      _options$altAxis = options.altAxis,\n      checkAltAxis = _options$altAxis === void 0 ? false : _options$altAxis,\n      boundary = options.boundary,\n      rootBoundary = options.rootBoundary,\n      altBoundary = options.altBoundary,\n      padding = options.padding,\n      _options$tether = options.tether,\n      tether = _options$tether === void 0 ? true : _options$tether,\n      _options$tetherOffset = options.tetherOffset,\n      tetherOffset = _options$tetherOffset === void 0 ? 0 : _options$tetherOffset;\n  var overflow = detectOverflow(state, {\n    boundary: boundary,\n    rootBoundary: rootBoundary,\n    padding: padding,\n    altBoundary: altBoundary\n  });\n  var basePlacement = getBasePlacement(state.placement);\n  var variation = getVariation(state.placement);\n  var isBasePlacement = !variation;\n  var mainAxis = getMainAxisFromPlacement(basePlacement);\n  var altAxis = getAltAxis(mainAxis);\n  var popperOffsets = state.modifiersData.popperOffsets;\n  var referenceRect = state.rects.reference;\n  var popperRect = state.rects.popper;\n  var tetherOffsetValue = typeof tetherOffset === 'function' ? tetherOffset(Object.assign({}, state.rects, {\n    placement: state.placement\n  })) : tetherOffset;\n  var normalizedTetherOffsetValue = typeof tetherOffsetValue === 'number' ? {\n    mainAxis: tetherOffsetValue,\n    altAxis: tetherOffsetValue\n  } : Object.assign({\n    mainAxis: 0,\n    altAxis: 0\n  }, tetherOffsetValue);\n  var offsetModifierState = state.modifiersData.offset ? state.modifiersData.offset[state.placement] : null;\n  var data = {\n    x: 0,\n    y: 0\n  };\n\n  if (!popperOffsets) {\n    return;\n  }\n\n  if (checkMainAxis) {\n    var _offsetModifierState$;\n\n    var mainSide = mainAxis === 'y' ? top : left;\n    var altSide = mainAxis === 'y' ? bottom : right;\n    var len = mainAxis === 'y' ? 'height' : 'width';\n    var offset = popperOffsets[mainAxis];\n    var min = offset + overflow[mainSide];\n    var max = offset - overflow[altSide];\n    var additive = tether ? -popperRect[len] / 2 : 0;\n    var minLen = variation === start ? referenceRect[len] : popperRect[len];\n    var maxLen = variation === start ? -popperRect[len] : -referenceRect[len]; // We need to include the arrow in the calculation so the arrow doesn't go\n    // outside the reference bounds\n\n    var arrowElement = state.elements.arrow;\n    var arrowRect = tether && arrowElement ? getLayoutRect(arrowElement) : {\n      width: 0,\n      height: 0\n    };\n    var arrowPaddingObject = state.modifiersData['arrow#persistent'] ? state.modifiersData['arrow#persistent'].padding : getFreshSideObject();\n    var arrowPaddingMin = arrowPaddingObject[mainSide];\n    var arrowPaddingMax = arrowPaddingObject[altSide]; // If the reference length is smaller than the arrow length, we don't want\n    // to include its full size in the calculation. If the reference is small\n    // and near the edge of a boundary, the popper can overflow even if the\n    // reference is not overflowing as well (e.g. virtual elements with no\n    // width or height)\n\n    var arrowLen = within(0, referenceRect[len], arrowRect[len]);\n    var minOffset = isBasePlacement ? referenceRect[len] / 2 - additive - arrowLen - arrowPaddingMin - normalizedTetherOffsetValue.mainAxis : minLen - arrowLen - arrowPaddingMin - normalizedTetherOffsetValue.mainAxis;\n    var maxOffset = isBasePlacement ? -referenceRect[len] / 2 + additive + arrowLen + arrowPaddingMax + normalizedTetherOffsetValue.mainAxis : maxLen + arrowLen + arrowPaddingMax + normalizedTetherOffsetValue.mainAxis;\n    var arrowOffsetParent = state.elements.arrow && getOffsetParent(state.elements.arrow);\n    var clientOffset = arrowOffsetParent ? mainAxis === 'y' ? arrowOffsetParent.clientTop || 0 : arrowOffsetParent.clientLeft || 0 : 0;\n    var offsetModifierValue = (_offsetModifierState$ = offsetModifierState == null ? void 0 : offsetModifierState[mainAxis]) != null ? _offsetModifierState$ : 0;\n    var tetherMin = offset + minOffset - offsetModifierValue - clientOffset;\n    var tetherMax = offset + maxOffset - offsetModifierValue;\n    var preventedOffset = within(tether ? mathMin(min, tetherMin) : min, offset, tether ? mathMax(max, tetherMax) : max);\n    popperOffsets[mainAxis] = preventedOffset;\n    data[mainAxis] = preventedOffset - offset;\n  }\n\n  if (checkAltAxis) {\n    var _offsetModifierState$2;\n\n    var _mainSide = mainAxis === 'x' ? top : left;\n\n    var _altSide = mainAxis === 'x' ? bottom : right;\n\n    var _offset = popperOffsets[altAxis];\n\n    var _len = altAxis === 'y' ? 'height' : 'width';\n\n    var _min = _offset + overflow[_mainSide];\n\n    var _max = _offset - overflow[_altSide];\n\n    var isOriginSide = [top, left].indexOf(basePlacement) !== -1;\n\n    var _offsetModifierValue = (_offsetModifierState$2 = offsetModifierState == null ? void 0 : offsetModifierState[altAxis]) != null ? _offsetModifierState$2 : 0;\n\n    var _tetherMin = isOriginSide ? _min : _offset - referenceRect[_len] - popperRect[_len] - _offsetModifierValue + normalizedTetherOffsetValue.altAxis;\n\n    var _tetherMax = isOriginSide ? _offset + referenceRect[_len] + popperRect[_len] - _offsetModifierValue - normalizedTetherOffsetValue.altAxis : _max;\n\n    var _preventedOffset = tether && isOriginSide ? withinMaxClamp(_tetherMin, _offset, _tetherMax) : within(tether ? _tetherMin : _min, _offset, tether ? _tetherMax : _max);\n\n    popperOffsets[altAxis] = _preventedOffset;\n    data[altAxis] = _preventedOffset - _offset;\n  }\n\n  state.modifiersData[name] = data;\n} // eslint-disable-next-line import/no-unused-modules\n\n\nexport default {\n  name: 'preventOverflow',\n  enabled: true,\n  phase: 'main',\n  fn: preventOverflow,\n  requiresIfExists: ['offset']\n};","export default function getAltAxis(axis) {\n  return axis === 'x' ? 'y' : 'x';\n}","import getBoundingClientRect from \"./getBoundingClientRect.js\";\nimport getNodeScroll from \"./getNodeScroll.js\";\nimport getNodeName from \"./getNodeName.js\";\nimport { isHTMLElement } from \"./instanceOf.js\";\nimport getWindowScrollBarX from \"./getWindowScrollBarX.js\";\nimport getDocumentElement from \"./getDocumentElement.js\";\nimport isScrollParent from \"./isScrollParent.js\";\nimport { round } from \"../utils/math.js\";\n\nfunction isElementScaled(element) {\n  var rect = element.getBoundingClientRect();\n  var scaleX = round(rect.width) / element.offsetWidth || 1;\n  var scaleY = round(rect.height) / element.offsetHeight || 1;\n  return scaleX !== 1 || scaleY !== 1;\n} // Returns the composite rect of an element relative to its offsetParent.\n// Composite means it takes into account transforms as well as layout.\n\n\nexport default function getCompositeRect(elementOrVirtualElement, offsetParent, isFixed) {\n  if (isFixed === void 0) {\n    isFixed = false;\n  }\n\n  var isOffsetParentAnElement = isHTMLElement(offsetParent);\n  var offsetParentIsScaled = isHTMLElement(offsetParent) && isElementScaled(offsetParent);\n  var documentElement = getDocumentElement(offsetParent);\n  var rect = getBoundingClientRect(elementOrVirtualElement, offsetParentIsScaled, isFixed);\n  var scroll = {\n    scrollLeft: 0,\n    scrollTop: 0\n  };\n  var offsets = {\n    x: 0,\n    y: 0\n  };\n\n  if (isOffsetParentAnElement || !isOffsetParentAnElement && !isFixed) {\n    if (getNodeName(offsetParent) !== 'body' || // https://github.com/popperjs/popper-core/issues/1078\n    isScrollParent(documentElement)) {\n      scroll = getNodeScroll(offsetParent);\n    }\n\n    if (isHTMLElement(offsetParent)) {\n      offsets = getBoundingClientRect(offsetParent, true);\n      offsets.x += offsetParent.clientLeft;\n      offsets.y += offsetParent.clientTop;\n    } else if (documentElement) {\n      offsets.x = getWindowScrollBarX(documentElement);\n    }\n  }\n\n  return {\n    x: rect.left + scroll.scrollLeft - offsets.x,\n    y: rect.top + scroll.scrollTop - offsets.y,\n    width: rect.width,\n    height: rect.height\n  };\n}","import getWindowScroll from \"./getWindowScroll.js\";\nimport getWindow from \"./getWindow.js\";\nimport { isHTMLElement } from \"./instanceOf.js\";\nimport getHTMLElementScroll from \"./getHTMLElementScroll.js\";\nexport default function getNodeScroll(node) {\n  if (node === getWindow(node) || !isHTMLElement(node)) {\n    return getWindowScroll(node);\n  } else {\n    return getHTMLElementScroll(node);\n  }\n}","export default function getHTMLElementScroll(element) {\n  return {\n    scrollLeft: element.scrollLeft,\n    scrollTop: element.scrollTop\n  };\n}","import { modifierPhases } from \"../enums.js\"; // source: https://stackoverflow.com/questions/49875255\n\nfunction order(modifiers) {\n  var map = new Map();\n  var visited = new Set();\n  var result = [];\n  modifiers.forEach(function (modifier) {\n    map.set(modifier.name, modifier);\n  }); // On visiting object, check for its dependencies and visit them recursively\n\n  function sort(modifier) {\n    visited.add(modifier.name);\n    var requires = [].concat(modifier.requires || [], modifier.requiresIfExists || []);\n    requires.forEach(function (dep) {\n      if (!visited.has(dep)) {\n        var depModifier = map.get(dep);\n\n        if (depModifier) {\n          sort(depModifier);\n        }\n      }\n    });\n    result.push(modifier);\n  }\n\n  modifiers.forEach(function (modifier) {\n    if (!visited.has(modifier.name)) {\n      // check for visited object\n      sort(modifier);\n    }\n  });\n  return result;\n}\n\nexport default function orderModifiers(modifiers) {\n  // order based on dependencies\n  var orderedModifiers = order(modifiers); // order based on phase\n\n  return modifierPhases.reduce(function (acc, phase) {\n    return acc.concat(orderedModifiers.filter(function (modifier) {\n      return modifier.phase === phase;\n    }));\n  }, []);\n}","import getCompositeRect from \"./dom-utils/getCompositeRect.js\";\nimport getLayoutRect from \"./dom-utils/getLayoutRect.js\";\nimport listScrollParents from \"./dom-utils/listScrollParents.js\";\nimport getOffsetParent from \"./dom-utils/getOffsetParent.js\";\nimport orderModifiers from \"./utils/orderModifiers.js\";\nimport debounce from \"./utils/debounce.js\";\nimport mergeByName from \"./utils/mergeByName.js\";\nimport detectOverflow from \"./utils/detectOverflow.js\";\nimport { isElement } from \"./dom-utils/instanceOf.js\";\nvar DEFAULT_OPTIONS = {\n  placement: 'bottom',\n  modifiers: [],\n  strategy: 'absolute'\n};\n\nfunction areValidElements() {\n  for (var _len = arguments.length, args = new Array(_len), _key = 0; _key < _len; _key++) {\n    args[_key] = arguments[_key];\n  }\n\n  return !args.some(function (element) {\n    return !(element && typeof element.getBoundingClientRect === 'function');\n  });\n}\n\nexport function popperGenerator(generatorOptions) {\n  if (generatorOptions === void 0) {\n    generatorOptions = {};\n  }\n\n  var _generatorOptions = generatorOptions,\n      _generatorOptions$def = _generatorOptions.defaultModifiers,\n      defaultModifiers = _generatorOptions$def === void 0 ? [] : _generatorOptions$def,\n      _generatorOptions$def2 = _generatorOptions.defaultOptions,\n      defaultOptions = _generatorOptions$def2 === void 0 ? DEFAULT_OPTIONS : _generatorOptions$def2;\n  return function createPopper(reference, popper, options) {\n    if (options === void 0) {\n      options = defaultOptions;\n    }\n\n    var state = {\n      placement: 'bottom',\n      orderedModifiers: [],\n      options: Object.assign({}, DEFAULT_OPTIONS, defaultOptions),\n      modifiersData: {},\n      elements: {\n        reference: reference,\n        popper: popper\n      },\n      attributes: {},\n      styles: {}\n    };\n    var effectCleanupFns = [];\n    var isDestroyed = false;\n    var instance = {\n      state: state,\n      setOptions: function setOptions(setOptionsAction) {\n        var options = typeof setOptionsAction === 'function' ? setOptionsAction(state.options) : setOptionsAction;\n        cleanupModifierEffects();\n        state.options = Object.assign({}, defaultOptions, state.options, options);\n        state.scrollParents = {\n          reference: isElement(reference) ? listScrollParents(reference) : reference.contextElement ? listScrollParents(reference.contextElement) : [],\n          popper: listScrollParents(popper)\n        }; // Orders the modifiers based on their dependencies and `phase`\n        // properties\n\n        var orderedModifiers = orderModifiers(mergeByName([].concat(defaultModifiers, state.options.modifiers))); // Strip out disabled modifiers\n\n        state.orderedModifiers = orderedModifiers.filter(function (m) {\n          return m.enabled;\n        });\n        runModifierEffects();\n        return instance.update();\n      },\n      // Sync update – it will always be executed, even if not necessary. This\n      // is useful for low frequency updates where sync behavior simplifies the\n      // logic.\n      // For high frequency updates (e.g. `resize` and `scroll` events), always\n      // prefer the async Popper#update method\n      forceUpdate: function forceUpdate() {\n        if (isDestroyed) {\n          return;\n        }\n\n        var _state$elements = state.elements,\n            reference = _state$elements.reference,\n            popper = _state$elements.popper; // Don't proceed if `reference` or `popper` are not valid elements\n        // anymore\n\n        if (!areValidElements(reference, popper)) {\n          return;\n        } // Store the reference and popper rects to be read by modifiers\n\n\n        state.rects = {\n          reference: getCompositeRect(reference, getOffsetParent(popper), state.options.strategy === 'fixed'),\n          popper: getLayoutRect(popper)\n        }; // Modifiers have the ability to reset the current update cycle. The\n        // most common use case for this is the `flip` modifier changing the\n        // placement, which then needs to re-run all the modifiers, because the\n        // logic was previously ran for the previous placement and is therefore\n        // stale/incorrect\n\n        state.reset = false;\n        state.placement = state.options.placement; // On each update cycle, the `modifiersData` property for each modifier\n        // is filled with the initial data specified by the modifier. This means\n        // it doesn't persist and is fresh on each update.\n        // To ensure persistent data, use `${name}#persistent`\n\n        state.orderedModifiers.forEach(function (modifier) {\n          return state.modifiersData[modifier.name] = Object.assign({}, modifier.data);\n        });\n\n        for (var index = 0; index < state.orderedModifiers.length; index++) {\n          if (state.reset === true) {\n            state.reset = false;\n            index = -1;\n            continue;\n          }\n\n          var _state$orderedModifie = state.orderedModifiers[index],\n              fn = _state$orderedModifie.fn,\n              _state$orderedModifie2 = _state$orderedModifie.options,\n              _options = _state$orderedModifie2 === void 0 ? {} : _state$orderedModifie2,\n              name = _state$orderedModifie.name;\n\n          if (typeof fn === 'function') {\n            state = fn({\n              state: state,\n              options: _options,\n              name: name,\n              instance: instance\n            }) || state;\n          }\n        }\n      },\n      // Async and optimistically optimized update – it will not be executed if\n      // not necessary (debounced to run at most once-per-tick)\n      update: debounce(function () {\n        return new Promise(function (resolve) {\n          instance.forceUpdate();\n          resolve(state);\n        });\n      }),\n      destroy: function destroy() {\n        cleanupModifierEffects();\n        isDestroyed = true;\n      }\n    };\n\n    if (!areValidElements(reference, popper)) {\n      return instance;\n    }\n\n    instance.setOptions(options).then(function (state) {\n      if (!isDestroyed && options.onFirstUpdate) {\n        options.onFirstUpdate(state);\n      }\n    }); // Modifiers have the ability to execute arbitrary code before the first\n    // update cycle runs. They will be executed in the same order as the update\n    // cycle. This is useful when a modifier adds some persistent data that\n    // other modifiers need to use, but the modifier is run after the dependent\n    // one.\n\n    function runModifierEffects() {\n      state.orderedModifiers.forEach(function (_ref) {\n        var name = _ref.name,\n            _ref$options = _ref.options,\n            options = _ref$options === void 0 ? {} : _ref$options,\n            effect = _ref.effect;\n\n        if (typeof effect === 'function') {\n          var cleanupFn = effect({\n            state: state,\n            name: name,\n            instance: instance,\n            options: options\n          });\n\n          var noopFn = function noopFn() {};\n\n          effectCleanupFns.push(cleanupFn || noopFn);\n        }\n      });\n    }\n\n    function cleanupModifierEffects() {\n      effectCleanupFns.forEach(function (fn) {\n        return fn();\n      });\n      effectCleanupFns = [];\n    }\n\n    return instance;\n  };\n}\nexport var createPopper = /*#__PURE__*/popperGenerator(); // eslint-disable-next-line import/no-unused-modules\n\nexport { detectOverflow };","export default function debounce(fn) {\n  var pending;\n  return function () {\n    if (!pending) {\n      pending = new Promise(function (resolve) {\n        Promise.resolve().then(function () {\n          pending = undefined;\n          resolve(fn());\n        });\n      });\n    }\n\n    return pending;\n  };\n}","export default function mergeByName(modifiers) {\n  var merged = modifiers.reduce(function (merged, current) {\n    var existing = merged[current.name];\n    merged[current.name] = existing ? Object.assign({}, existing, current, {\n      options: Object.assign({}, existing.options, current.options),\n      data: Object.assign({}, existing.data, current.data)\n    }) : current;\n    return merged;\n  }, {}); // IE11 does not support Object.values\n\n  return Object.keys(merged).map(function (key) {\n    return merged[key];\n  });\n}","import { popperGenerator, detectOverflow } from \"./createPopper.js\";\nimport eventListeners from \"./modifiers/eventListeners.js\";\nimport popperOffsets from \"./modifiers/popperOffsets.js\";\nimport computeStyles from \"./modifiers/computeStyles.js\";\nimport applyStyles from \"./modifiers/applyStyles.js\";\nvar defaultModifiers = [eventListeners, popperOffsets, computeStyles, applyStyles];\nvar createPopper = /*#__PURE__*/popperGenerator({\n  defaultModifiers: defaultModifiers\n}); // eslint-disable-next-line import/no-unused-modules\n\nexport { createPopper, popperGenerator, defaultModifiers, detectOverflow };","import { popperGenerator, detectOverflow } from \"./createPopper.js\";\nimport eventListeners from \"./modifiers/eventListeners.js\";\nimport popperOffsets from \"./modifiers/popperOffsets.js\";\nimport computeStyles from \"./modifiers/computeStyles.js\";\nimport applyStyles from \"./modifiers/applyStyles.js\";\nimport offset from \"./modifiers/offset.js\";\nimport flip from \"./modifiers/flip.js\";\nimport preventOverflow from \"./modifiers/preventOverflow.js\";\nimport arrow from \"./modifiers/arrow.js\";\nimport hide from \"./modifiers/hide.js\";\nvar defaultModifiers = [eventListeners, popperOffsets, computeStyles, applyStyles, offset, flip, preventOverflow, arrow, hide];\nvar createPopper = /*#__PURE__*/popperGenerator({\n  defaultModifiers: defaultModifiers\n}); // eslint-disable-next-line import/no-unused-modules\n\nexport { createPopper, popperGenerator, defaultModifiers, detectOverflow }; // eslint-disable-next-line import/no-unused-modules\n\nexport { createPopper as createPopperLite } from \"./popper-lite.js\"; // eslint-disable-next-line import/no-unused-modules\n\nexport * from \"./modifiers/index.js\";","/**\n * --------------------------------------------------------------------------\n * Bootstrap dropdown.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport * as Popper from '@popperjs/core'\nimport BaseComponent from './base-component.js'\nimport EventHandler from './dom/event-handler.js'\nimport Manipulator from './dom/manipulator.js'\nimport SelectorEngine from './dom/selector-engine.js'\nimport {\n  defineJQueryPlugin,\n  execute,\n  getElement,\n  getNextActiveElement,\n  isDisabled,\n  isElement,\n  isRTL,\n  isVisible,\n  noop\n} from './util/index.js'\n\n/**\n * Constants\n */\n\nconst NAME = 'dropdown'\nconst DATA_KEY = 'bs.dropdown'\nconst EVENT_KEY = `.${DATA_KEY}`\nconst DATA_API_KEY = '.data-api'\n\nconst ESCAPE_KEY = 'Escape'\nconst TAB_KEY = 'Tab'\nconst ARROW_UP_KEY = 'ArrowUp'\nconst ARROW_DOWN_KEY = 'ArrowDown'\nconst RIGHT_MOUSE_BUTTON = 2 // MouseEvent.button value for the secondary button, usually the right button\n\nconst EVENT_HIDE = `hide${EVENT_KEY}`\nconst EVENT_HIDDEN = `hidden${EVENT_KEY}`\nconst EVENT_SHOW = `show${EVENT_KEY}`\nconst EVENT_SHOWN = `shown${EVENT_KEY}`\nconst EVENT_CLICK_DATA_API = `click${EVENT_KEY}${DATA_API_KEY}`\nconst EVENT_KEYDOWN_DATA_API = `keydown${EVENT_KEY}${DATA_API_KEY}`\nconst EVENT_KEYUP_DATA_API = `keyup${EVENT_KEY}${DATA_API_KEY}`\n\nconst CLASS_NAME_SHOW = 'show'\nconst CLASS_NAME_DROPUP = 'dropup'\nconst CLASS_NAME_DROPEND = 'dropend'\nconst CLASS_NAME_DROPSTART = 'dropstart'\nconst CLASS_NAME_DROPUP_CENTER = 'dropup-center'\nconst CLASS_NAME_DROPDOWN_CENTER = 'dropdown-center'\n\nconst SELECTOR_DATA_TOGGLE = '[data-bs-toggle=\"dropdown\"]:not(.disabled):not(:disabled)'\nconst SELECTOR_DATA_TOGGLE_SHOWN = `${SELECTOR_DATA_TOGGLE}.${CLASS_NAME_SHOW}`\nconst SELECTOR_MENU = '.dropdown-menu'\nconst SELECTOR_NAVBAR = '.navbar'\nconst SELECTOR_NAVBAR_NAV = '.navbar-nav'\nconst SELECTOR_VISIBLE_ITEMS = '.dropdown-menu .dropdown-item:not(.disabled):not(:disabled)'\n\nconst PLACEMENT_TOP = isRTL() ? 'top-end' : 'top-start'\nconst PLACEMENT_TOPEND = isRTL() ? 'top-start' : 'top-end'\nconst PLACEMENT_BOTTOM = isRTL() ? 'bottom-end' : 'bottom-start'\nconst PLACEMENT_BOTTOMEND = isRTL() ? 'bottom-start' : 'bottom-end'\nconst PLACEMENT_RIGHT = isRTL() ? 'left-start' : 'right-start'\nconst PLACEMENT_LEFT = isRTL() ? 'right-start' : 'left-start'\nconst PLACEMENT_TOPCENTER = 'top'\nconst PLACEMENT_BOTTOMCENTER = 'bottom'\n\nconst Default = {\n  autoClose: true,\n  boundary: 'clippingParents',\n  display: 'dynamic',\n  offset: [0, 2],\n  popperConfig: null,\n  reference: 'toggle'\n}\n\nconst DefaultType = {\n  autoClose: '(boolean|string)',\n  boundary: '(string|element)',\n  display: 'string',\n  offset: '(array|string|function)',\n  popperConfig: '(null|object|function)',\n  reference: '(string|element|object)'\n}\n\n/**\n * Class definition\n */\n\nclass Dropdown extends BaseComponent {\n  constructor(element, config) {\n    super(element, config)\n\n    this._popper = null\n    this._parent = this._element.parentNode // dropdown wrapper\n    // TODO: v6 revert #37011 & change markup https://getbootstrap.com/docs/5.3/forms/input-group/\n    this._menu = SelectorEngine.next(this._element, SELECTOR_MENU)[0] ||\n      SelectorEngine.prev(this._element, SELECTOR_MENU)[0] ||\n      SelectorEngine.findOne(SELECTOR_MENU, this._parent)\n    this._inNavbar = this._detectNavbar()\n  }\n\n  // Getters\n  static get Default() {\n    return Default\n  }\n\n  static get DefaultType() {\n    return DefaultType\n  }\n\n  static get NAME() {\n    return NAME\n  }\n\n  // Public\n  toggle() {\n    return this._isShown() ? this.hide() : this.show()\n  }\n\n  show() {\n    if (isDisabled(this._element) || this._isShown()) {\n      return\n    }\n\n    const relatedTarget = {\n      relatedTarget: this._element\n    }\n\n    const showEvent = EventHandler.trigger(this._element, EVENT_SHOW, relatedTarget)\n\n    if (showEvent.defaultPrevented) {\n      return\n    }\n\n    this._createPopper()\n\n    // If this is a touch-enabled device we add extra\n    // empty mouseover listeners to the body's immediate children;\n    // only needed because of broken event delegation on iOS\n    // https://www.quirksmode.org/blog/archives/2014/02/mouse_event_bub.html\n    if ('ontouchstart' in document.documentElement && !this._parent.closest(SELECTOR_NAVBAR_NAV)) {\n      for (const element of [].concat(...document.body.children)) {\n        EventHandler.on(element, 'mouseover', noop)\n      }\n    }\n\n    this._element.focus()\n    this._element.setAttribute('aria-expanded', true)\n\n    this._menu.classList.add(CLASS_NAME_SHOW)\n    this._element.classList.add(CLASS_NAME_SHOW)\n    EventHandler.trigger(this._element, EVENT_SHOWN, relatedTarget)\n  }\n\n  hide() {\n    if (isDisabled(this._element) || !this._isShown()) {\n      return\n    }\n\n    const relatedTarget = {\n      relatedTarget: this._element\n    }\n\n    this._completeHide(relatedTarget)\n  }\n\n  dispose() {\n    if (this._popper) {\n      this._popper.destroy()\n    }\n\n    super.dispose()\n  }\n\n  update() {\n    this._inNavbar = this._detectNavbar()\n    if (this._popper) {\n      this._popper.update()\n    }\n  }\n\n  // Private\n  _completeHide(relatedTarget) {\n    const hideEvent = EventHandler.trigger(this._element, EVENT_HIDE, relatedTarget)\n    if (hideEvent.defaultPrevented) {\n      return\n    }\n\n    // If this is a touch-enabled device we remove the extra\n    // empty mouseover listeners we added for iOS support\n    if ('ontouchstart' in document.documentElement) {\n      for (const element of [].concat(...document.body.children)) {\n        EventHandler.off(element, 'mouseover', noop)\n      }\n    }\n\n    if (this._popper) {\n      this._popper.destroy()\n    }\n\n    this._menu.classList.remove(CLASS_NAME_SHOW)\n    this._element.classList.remove(CLASS_NAME_SHOW)\n    this._element.setAttribute('aria-expanded', 'false')\n    Manipulator.removeDataAttribute(this._menu, 'popper')\n    EventHandler.trigger(this._element, EVENT_HIDDEN, relatedTarget)\n  }\n\n  _getConfig(config) {\n    config = super._getConfig(config)\n\n    if (typeof config.reference === 'object' && !isElement(config.reference) &&\n      typeof config.reference.getBoundingClientRect !== 'function'\n    ) {\n      // Popper virtual elements require a getBoundingClientRect method\n      throw new TypeError(`${NAME.toUpperCase()}: Option \"reference\" provided type \"object\" without a required \"getBoundingClientRect\" method.`)\n    }\n\n    return config\n  }\n\n  _createPopper() {\n    if (typeof Popper === 'undefined') {\n      throw new TypeError('Bootstrap\\'s dropdowns require Popper (https://popper.js.org)')\n    }\n\n    let referenceElement = this._element\n\n    if (this._config.reference === 'parent') {\n      referenceElement = this._parent\n    } else if (isElement(this._config.reference)) {\n      referenceElement = getElement(this._config.reference)\n    } else if (typeof this._config.reference === 'object') {\n      referenceElement = this._config.reference\n    }\n\n    const popperConfig = this._getPopperConfig()\n    this._popper = Popper.createPopper(referenceElement, this._menu, popperConfig)\n  }\n\n  _isShown() {\n    return this._menu.classList.contains(CLASS_NAME_SHOW)\n  }\n\n  _getPlacement() {\n    const parentDropdown = this._parent\n\n    if (parentDropdown.classList.contains(CLASS_NAME_DROPEND)) {\n      return PLACEMENT_RIGHT\n    }\n\n    if (parentDropdown.classList.contains(CLASS_NAME_DROPSTART)) {\n      return PLACEMENT_LEFT\n    }\n\n    if (parentDropdown.classList.contains(CLASS_NAME_DROPUP_CENTER)) {\n      return PLACEMENT_TOPCENTER\n    }\n\n    if (parentDropdown.classList.contains(CLASS_NAME_DROPDOWN_CENTER)) {\n      return PLACEMENT_BOTTOMCENTER\n    }\n\n    // We need to trim the value because custom properties can also include spaces\n    const isEnd = getComputedStyle(this._menu).getPropertyValue('--bs-position').trim() === 'end'\n\n    if (parentDropdown.classList.contains(CLASS_NAME_DROPUP)) {\n      return isEnd ? PLACEMENT_TOPEND : PLACEMENT_TOP\n    }\n\n    return isEnd ? PLACEMENT_BOTTOMEND : PLACEMENT_BOTTOM\n  }\n\n  _detectNavbar() {\n    return this._element.closest(SELECTOR_NAVBAR) !== null\n  }\n\n  _getOffset() {\n    const { offset } = this._config\n\n    if (typeof offset === 'string') {\n      return offset.split(',').map(value => Number.parseInt(value, 10))\n    }\n\n    if (typeof offset === 'function') {\n      return popperData => offset(popperData, this._element)\n    }\n\n    return offset\n  }\n\n  _getPopperConfig() {\n    const defaultBsPopperConfig = {\n      placement: this._getPlacement(),\n      modifiers: [{\n        name: 'preventOverflow',\n        options: {\n          boundary: this._config.boundary\n        }\n      },\n      {\n        name: 'offset',\n        options: {\n          offset: this._getOffset()\n        }\n      }]\n    }\n\n    // Disable Popper if we have a static display or Dropdown is in Navbar\n    if (this._inNavbar || this._config.display === 'static') {\n      Manipulator.setDataAttribute(this._menu, 'popper', 'static') // TODO: v6 remove\n      defaultBsPopperConfig.modifiers = [{\n        name: 'applyStyles',\n        enabled: false\n      }]\n    }\n\n    return {\n      ...defaultBsPopperConfig,\n      ...execute(this._config.popperConfig, [defaultBsPopperConfig])\n    }\n  }\n\n  _selectMenuItem({ key, target }) {\n    const items = SelectorEngine.find(SELECTOR_VISIBLE_ITEMS, this._menu).filter(element => isVisible(element))\n\n    if (!items.length) {\n      return\n    }\n\n    // if target isn't included in items (e.g. when expanding the dropdown)\n    // allow cycling to get the last item in case key equals ARROW_UP_KEY\n    getNextActiveElement(items, target, key === ARROW_DOWN_KEY, !items.includes(target)).focus()\n  }\n\n  // Static\n  static jQueryInterface(config) {\n    return this.each(function () {\n      const data = Dropdown.getOrCreateInstance(this, config)\n\n      if (typeof config !== 'string') {\n        return\n      }\n\n      if (typeof data[config] === 'undefined') {\n        throw new TypeError(`No method named \"${config}\"`)\n      }\n\n      data[config]()\n    })\n  }\n\n  static clearMenus(event) {\n    if (event.button === RIGHT_MOUSE_BUTTON || (event.type === 'keyup' && event.key !== TAB_KEY)) {\n      return\n    }\n\n    const openToggles = SelectorEngine.find(SELECTOR_DATA_TOGGLE_SHOWN)\n\n    for (const toggle of openToggles) {\n      const context = Dropdown.getInstance(toggle)\n      if (!context || context._config.autoClose === false) {\n        continue\n      }\n\n      const composedPath = event.composedPath()\n      const isMenuTarget = composedPath.includes(context._menu)\n      if (\n        composedPath.includes(context._element) ||\n        (context._config.autoClose === 'inside' && !isMenuTarget) ||\n        (context._config.autoClose === 'outside' && isMenuTarget)\n      ) {\n        continue\n      }\n\n      // Tab navigation through the dropdown menu or events from contained inputs shouldn't close the menu\n      if (context._menu.contains(event.target) && ((event.type === 'keyup' && event.key === TAB_KEY) || /input|select|option|textarea|form/i.test(event.target.tagName))) {\n        continue\n      }\n\n      const relatedTarget = { relatedTarget: context._element }\n\n      if (event.type === 'click') {\n        relatedTarget.clickEvent = event\n      }\n\n      context._completeHide(relatedTarget)\n    }\n  }\n\n  static dataApiKeydownHandler(event) {\n    // If not an UP | DOWN | ESCAPE key => not a dropdown command\n    // If input/textarea && if key is other than ESCAPE => not a dropdown command\n\n    const isInput = /input|textarea/i.test(event.target.tagName)\n    const isEscapeEvent = event.key === ESCAPE_KEY\n    const isUpOrDownEvent = [ARROW_UP_KEY, ARROW_DOWN_KEY].includes(event.key)\n\n    if (!isUpOrDownEvent && !isEscapeEvent) {\n      return\n    }\n\n    if (isInput && !isEscapeEvent) {\n      return\n    }\n\n    event.preventDefault()\n\n    // TODO: v6 revert #37011 & change markup https://getbootstrap.com/docs/5.3/forms/input-group/\n    const getToggleButton = this.matches(SELECTOR_DATA_TOGGLE) ?\n      this :\n      (SelectorEngine.prev(this, SELECTOR_DATA_TOGGLE)[0] ||\n        SelectorEngine.next(this, SELECTOR_DATA_TOGGLE)[0] ||\n        SelectorEngine.findOne(SELECTOR_DATA_TOGGLE, event.delegateTarget.parentNode))\n\n    const instance = Dropdown.getOrCreateInstance(getToggleButton)\n\n    if (isUpOrDownEvent) {\n      event.stopPropagation()\n      instance.show()\n      instance._selectMenuItem(event)\n      return\n    }\n\n    if (instance._isShown()) { // else is escape and we check if it is shown\n      event.stopPropagation()\n      instance.hide()\n      getToggleButton.focus()\n    }\n  }\n}\n\n/**\n * Data API implementation\n */\n\nEventHandler.on(document, EVENT_KEYDOWN_DATA_API, SELECTOR_DATA_TOGGLE, Dropdown.dataApiKeydownHandler)\nEventHandler.on(document, EVENT_KEYDOWN_DATA_API, SELECTOR_MENU, Dropdown.dataApiKeydownHandler)\nEventHandler.on(document, EVENT_CLICK_DATA_API, Dropdown.clearMenus)\nEventHandler.on(document, EVENT_KEYUP_DATA_API, Dropdown.clearMenus)\nEventHandler.on(document, EVENT_CLICK_DATA_API, SELECTOR_DATA_TOGGLE, function (event) {\n  event.preventDefault()\n  Dropdown.getOrCreateInstance(this).toggle()\n})\n\n/**\n * jQuery\n */\n\ndefineJQueryPlugin(Dropdown)\n\nexport default Dropdown\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap util/backdrop.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport EventHandler from '../dom/event-handler.js'\nimport Config from './config.js'\nimport { execute, executeAfterTransition, getElement, reflow } from './index.js'\n\n/**\n * Constants\n */\n\nconst NAME = 'backdrop'\nconst CLASS_NAME_FADE = 'fade'\nconst CLASS_NAME_SHOW = 'show'\nconst EVENT_MOUSEDOWN = `mousedown.bs.${NAME}`\n\nconst Default = {\n  className: 'modal-backdrop',\n  clickCallback: null,\n  isAnimated: false,\n  isVisible: true, // if false, we use the backdrop helper without adding any element to the dom\n  rootElement: 'body' // give the choice to place backdrop under different elements\n}\n\nconst DefaultType = {\n  className: 'string',\n  clickCallback: '(function|null)',\n  isAnimated: 'boolean',\n  isVisible: 'boolean',\n  rootElement: '(element|string)'\n}\n\n/**\n * Class definition\n */\n\nclass Backdrop extends Config {\n  constructor(config) {\n    super()\n    this._config = this._getConfig(config)\n    this._isAppended = false\n    this._element = null\n  }\n\n  // Getters\n  static get Default() {\n    return Default\n  }\n\n  static get DefaultType() {\n    return DefaultType\n  }\n\n  static get NAME() {\n    return NAME\n  }\n\n  // Public\n  show(callback) {\n    if (!this._config.isVisible) {\n      execute(callback)\n      return\n    }\n\n    this._append()\n\n    const element = this._getElement()\n    if (this._config.isAnimated) {\n      reflow(element)\n    }\n\n    element.classList.add(CLASS_NAME_SHOW)\n\n    this._emulateAnimation(() => {\n      execute(callback)\n    })\n  }\n\n  hide(callback) {\n    if (!this._config.isVisible) {\n      execute(callback)\n      return\n    }\n\n    this._getElement().classList.remove(CLASS_NAME_SHOW)\n\n    this._emulateAnimation(() => {\n      this.dispose()\n      execute(callback)\n    })\n  }\n\n  dispose() {\n    if (!this._isAppended) {\n      return\n    }\n\n    EventHandler.off(this._element, EVENT_MOUSEDOWN)\n\n    this._element.remove()\n    this._isAppended = false\n  }\n\n  // Private\n  _getElement() {\n    if (!this._element) {\n      const backdrop = document.createElement('div')\n      backdrop.className = this._config.className\n      if (this._config.isAnimated) {\n        backdrop.classList.add(CLASS_NAME_FADE)\n      }\n\n      this._element = backdrop\n    }\n\n    return this._element\n  }\n\n  _configAfterMerge(config) {\n    // use getElement() with the default \"body\" to get a fresh Element on each instantiation\n    config.rootElement = getElement(config.rootElement)\n    return config\n  }\n\n  _append() {\n    if (this._isAppended) {\n      return\n    }\n\n    const element = this._getElement()\n    this._config.rootElement.append(element)\n\n    EventHandler.on(element, EVENT_MOUSEDOWN, () => {\n      execute(this._config.clickCallback)\n    })\n\n    this._isAppended = true\n  }\n\n  _emulateAnimation(callback) {\n    executeAfterTransition(callback, this._getElement(), this._config.isAnimated)\n  }\n}\n\nexport default Backdrop\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap util/focustrap.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport EventHandler from '../dom/event-handler.js'\nimport SelectorEngine from '../dom/selector-engine.js'\nimport Config from './config.js'\n\n/**\n * Constants\n */\n\nconst NAME = 'focustrap'\nconst DATA_KEY = 'bs.focustrap'\nconst EVENT_KEY = `.${DATA_KEY}`\nconst EVENT_FOCUSIN = `focusin${EVENT_KEY}`\nconst EVENT_KEYDOWN_TAB = `keydown.tab${EVENT_KEY}`\n\nconst TAB_KEY = 'Tab'\nconst TAB_NAV_FORWARD = 'forward'\nconst TAB_NAV_BACKWARD = 'backward'\n\nconst Default = {\n  autofocus: true,\n  trapElement: null // The element to trap focus inside of\n}\n\nconst DefaultType = {\n  autofocus: 'boolean',\n  trapElement: 'element'\n}\n\n/**\n * Class definition\n */\n\nclass FocusTrap extends Config {\n  constructor(config) {\n    super()\n    this._config = this._getConfig(config)\n    this._isActive = false\n    this._lastTabNavDirection = null\n  }\n\n  // Getters\n  static get Default() {\n    return Default\n  }\n\n  static get DefaultType() {\n    return DefaultType\n  }\n\n  static get NAME() {\n    return NAME\n  }\n\n  // Public\n  activate() {\n    if (this._isActive) {\n      return\n    }\n\n    if (this._config.autofocus) {\n      this._config.trapElement.focus()\n    }\n\n    EventHandler.off(document, EVENT_KEY) // guard against infinite focus loop\n    EventHandler.on(document, EVENT_FOCUSIN, event => this._handleFocusin(event))\n    EventHandler.on(document, EVENT_KEYDOWN_TAB, event => this._handleKeydown(event))\n\n    this._isActive = true\n  }\n\n  deactivate() {\n    if (!this._isActive) {\n      return\n    }\n\n    this._isActive = false\n    EventHandler.off(document, EVENT_KEY)\n  }\n\n  // Private\n  _handleFocusin(event) {\n    const { trapElement } = this._config\n\n    if (event.target === document || event.target === trapElement || trapElement.contains(event.target)) {\n      return\n    }\n\n    const elements = SelectorEngine.focusableChildren(trapElement)\n\n    if (elements.length === 0) {\n      trapElement.focus()\n    } else if (this._lastTabNavDirection === TAB_NAV_BACKWARD) {\n      elements[elements.length - 1].focus()\n    } else {\n      elements[0].focus()\n    }\n  }\n\n  _handleKeydown(event) {\n    if (event.key !== TAB_KEY) {\n      return\n    }\n\n    this._lastTabNavDirection = event.shiftKey ? TAB_NAV_BACKWARD : TAB_NAV_FORWARD\n  }\n}\n\nexport default FocusTrap\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap util/scrollBar.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport Manipulator from '../dom/manipulator.js'\nimport SelectorEngine from '../dom/selector-engine.js'\nimport { isElement } from './index.js'\n\n/**\n * Constants\n */\n\nconst SELECTOR_FIXED_CONTENT = '.fixed-top, .fixed-bottom, .is-fixed, .sticky-top'\nconst SELECTOR_STICKY_CONTENT = '.sticky-top'\nconst PROPERTY_PADDING = 'padding-right'\nconst PROPERTY_MARGIN = 'margin-right'\n\n/**\n * Class definition\n */\n\nclass ScrollBarHelper {\n  constructor() {\n    this._element = document.body\n  }\n\n  // Public\n  getWidth() {\n    // https://developer.mozilla.org/en-US/docs/Web/API/Window/innerWidth#usage_notes\n    const documentWidth = document.documentElement.clientWidth\n    return Math.abs(window.innerWidth - documentWidth)\n  }\n\n  hide() {\n    const width = this.getWidth()\n    this._disableOverFlow()\n    // give padding to element to balance the hidden scrollbar width\n    this._setElementAttributes(this._element, PROPERTY_PADDING, calculatedValue => calculatedValue + width)\n    // trick: We adjust positive paddingRight and negative marginRight to sticky-top elements to keep showing fullwidth\n    this._setElementAttributes(SELECTOR_FIXED_CONTENT, PROPERTY_PADDING, calculatedValue => calculatedValue + width)\n    this._setElementAttributes(SELECTOR_STICKY_CONTENT, PROPERTY_MARGIN, calculatedValue => calculatedValue - width)\n  }\n\n  reset() {\n    this._resetElementAttributes(this._element, 'overflow')\n    this._resetElementAttributes(this._element, PROPERTY_PADDING)\n    this._resetElementAttributes(SELECTOR_FIXED_CONTENT, PROPERTY_PADDING)\n    this._resetElementAttributes(SELECTOR_STICKY_CONTENT, PROPERTY_MARGIN)\n  }\n\n  isOverflowing() {\n    return this.getWidth() > 0\n  }\n\n  // Private\n  _disableOverFlow() {\n    this._saveInitialAttribute(this._element, 'overflow')\n    this._element.style.overflow = 'hidden'\n  }\n\n  _setElementAttributes(selector, styleProperty, callback) {\n    const scrollbarWidth = this.getWidth()\n    const manipulationCallBack = element => {\n      if (element !== this._element && window.innerWidth > element.clientWidth + scrollbarWidth) {\n        return\n      }\n\n      this._saveInitialAttribute(element, styleProperty)\n      const calculatedValue = window.getComputedStyle(element).getPropertyValue(styleProperty)\n      element.style.setProperty(styleProperty, `${callback(Number.parseFloat(calculatedValue))}px`)\n    }\n\n    this._applyManipulationCallback(selector, manipulationCallBack)\n  }\n\n  _saveInitialAttribute(element, styleProperty) {\n    const actualValue = element.style.getPropertyValue(styleProperty)\n    if (actualValue) {\n      Manipulator.setDataAttribute(element, styleProperty, actualValue)\n    }\n  }\n\n  _resetElementAttributes(selector, styleProperty) {\n    const manipulationCallBack = element => {\n      const value = Manipulator.getDataAttribute(element, styleProperty)\n      // We only want to remove the property if the value is `null`; the value can also be zero\n      if (value === null) {\n        element.style.removeProperty(styleProperty)\n        return\n      }\n\n      Manipulator.removeDataAttribute(element, styleProperty)\n      element.style.setProperty(styleProperty, value)\n    }\n\n    this._applyManipulationCallback(selector, manipulationCallBack)\n  }\n\n  _applyManipulationCallback(selector, callBack) {\n    if (isElement(selector)) {\n      callBack(selector)\n      return\n    }\n\n    for (const sel of SelectorEngine.find(selector, this._element)) {\n      callBack(sel)\n    }\n  }\n}\n\nexport default ScrollBarHelper\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap modal.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport BaseComponent from './base-component.js'\nimport EventHandler from './dom/event-handler.js'\nimport SelectorEngine from './dom/selector-engine.js'\nimport Backdrop from './util/backdrop.js'\nimport { enableDismissTrigger } from './util/component-functions.js'\nimport FocusTrap from './util/focustrap.js'\nimport { defineJQueryPlugin, isRTL, isVisible, reflow } from './util/index.js'\nimport ScrollBarHelper from './util/scrollbar.js'\n\n/**\n * Constants\n */\n\nconst NAME = 'modal'\nconst DATA_KEY = 'bs.modal'\nconst EVENT_KEY = `.${DATA_KEY}`\nconst DATA_API_KEY = '.data-api'\nconst ESCAPE_KEY = 'Escape'\n\nconst EVENT_HIDE = `hide${EVENT_KEY}`\nconst EVENT_HIDE_PREVENTED = `hidePrevented${EVENT_KEY}`\nconst EVENT_HIDDEN = `hidden${EVENT_KEY}`\nconst EVENT_SHOW = `show${EVENT_KEY}`\nconst EVENT_SHOWN = `shown${EVENT_KEY}`\nconst EVENT_RESIZE = `resize${EVENT_KEY}`\nconst EVENT_CLICK_DISMISS = `click.dismiss${EVENT_KEY}`\nconst EVENT_MOUSEDOWN_DISMISS = `mousedown.dismiss${EVENT_KEY}`\nconst EVENT_KEYDOWN_DISMISS = `keydown.dismiss${EVENT_KEY}`\nconst EVENT_CLICK_DATA_API = `click${EVENT_KEY}${DATA_API_KEY}`\n\nconst CLASS_NAME_OPEN = 'modal-open'\nconst CLASS_NAME_FADE = 'fade'\nconst CLASS_NAME_SHOW = 'show'\nconst CLASS_NAME_STATIC = 'modal-static'\n\nconst OPEN_SELECTOR = '.modal.show'\nconst SELECTOR_DIALOG = '.modal-dialog'\nconst SELECTOR_MODAL_BODY = '.modal-body'\nconst SELECTOR_DATA_TOGGLE = '[data-bs-toggle=\"modal\"]'\n\nconst Default = {\n  backdrop: true,\n  focus: true,\n  keyboard: true\n}\n\nconst DefaultType = {\n  backdrop: '(boolean|string)',\n  focus: 'boolean',\n  keyboard: 'boolean'\n}\n\n/**\n * Class definition\n */\n\nclass Modal extends BaseComponent {\n  constructor(element, config) {\n    super(element, config)\n\n    this._dialog = SelectorEngine.findOne(SELECTOR_DIALOG, this._element)\n    this._backdrop = this._initializeBackDrop()\n    this._focustrap = this._initializeFocusTrap()\n    this._isShown = false\n    this._isTransitioning = false\n    this._scrollBar = new ScrollBarHelper()\n\n    this._addEventListeners()\n  }\n\n  // Getters\n  static get Default() {\n    return Default\n  }\n\n  static get DefaultType() {\n    return DefaultType\n  }\n\n  static get NAME() {\n    return NAME\n  }\n\n  // Public\n  toggle(relatedTarget) {\n    return this._isShown ? this.hide() : this.show(relatedTarget)\n  }\n\n  show(relatedTarget) {\n    if (this._isShown || this._isTransitioning) {\n      return\n    }\n\n    const showEvent = EventHandler.trigger(this._element, EVENT_SHOW, {\n      relatedTarget\n    })\n\n    if (showEvent.defaultPrevented) {\n      return\n    }\n\n    this._isShown = true\n    this._isTransitioning = true\n\n    this._scrollBar.hide()\n\n    document.body.classList.add(CLASS_NAME_OPEN)\n\n    this._adjustDialog()\n\n    this._backdrop.show(() => this._showElement(relatedTarget))\n  }\n\n  hide() {\n    if (!this._isShown || this._isTransitioning) {\n      return\n    }\n\n    const hideEvent = EventHandler.trigger(this._element, EVENT_HIDE)\n\n    if (hideEvent.defaultPrevented) {\n      return\n    }\n\n    this._isShown = false\n    this._isTransitioning = true\n    this._focustrap.deactivate()\n\n    this._element.classList.remove(CLASS_NAME_SHOW)\n\n    this._queueCallback(() => this._hideModal(), this._element, this._isAnimated())\n  }\n\n  dispose() {\n    EventHandler.off(window, EVENT_KEY)\n    EventHandler.off(this._dialog, EVENT_KEY)\n\n    this._backdrop.dispose()\n    this._focustrap.deactivate()\n\n    super.dispose()\n  }\n\n  handleUpdate() {\n    this._adjustDialog()\n  }\n\n  // Private\n  _initializeBackDrop() {\n    return new Backdrop({\n      isVisible: Boolean(this._config.backdrop), // 'static' option will be translated to true, and booleans will keep their value,\n      isAnimated: this._isAnimated()\n    })\n  }\n\n  _initializeFocusTrap() {\n    return new FocusTrap({\n      trapElement: this._element\n    })\n  }\n\n  _showElement(relatedTarget) {\n    // try to append dynamic modal\n    if (!document.body.contains(this._element)) {\n      document.body.append(this._element)\n    }\n\n    this._element.style.display = 'block'\n    this._element.removeAttribute('aria-hidden')\n    this._element.setAttribute('aria-modal', true)\n    this._element.setAttribute('role', 'dialog')\n    this._element.scrollTop = 0\n\n    const modalBody = SelectorEngine.findOne(SELECTOR_MODAL_BODY, this._dialog)\n    if (modalBody) {\n      modalBody.scrollTop = 0\n    }\n\n    reflow(this._element)\n\n    this._element.classList.add(CLASS_NAME_SHOW)\n\n    const transitionComplete = () => {\n      if (this._config.focus) {\n        this._focustrap.activate()\n      }\n\n      this._isTransitioning = false\n      EventHandler.trigger(this._element, EVENT_SHOWN, {\n        relatedTarget\n      })\n    }\n\n    this._queueCallback(transitionComplete, this._dialog, this._isAnimated())\n  }\n\n  _addEventListeners() {\n    EventHandler.on(this._element, EVENT_KEYDOWN_DISMISS, event => {\n      if (event.key !== ESCAPE_KEY) {\n        return\n      }\n\n      if (this._config.keyboard) {\n        this.hide()\n        return\n      }\n\n      this._triggerBackdropTransition()\n    })\n\n    EventHandler.on(window, EVENT_RESIZE, () => {\n      if (this._isShown && !this._isTransitioning) {\n        this._adjustDialog()\n      }\n    })\n\n    EventHandler.on(this._element, EVENT_MOUSEDOWN_DISMISS, event => {\n      // a bad trick to segregate clicks that may start inside dialog but end outside, and avoid listen to scrollbar clicks\n      EventHandler.one(this._element, EVENT_CLICK_DISMISS, event2 => {\n        if (this._element !== event.target || this._element !== event2.target) {\n          return\n        }\n\n        if (this._config.backdrop === 'static') {\n          this._triggerBackdropTransition()\n          return\n        }\n\n        if (this._config.backdrop) {\n          this.hide()\n        }\n      })\n    })\n  }\n\n  _hideModal() {\n    this._element.style.display = 'none'\n    this._element.setAttribute('aria-hidden', true)\n    this._element.removeAttribute('aria-modal')\n    this._element.removeAttribute('role')\n    this._isTransitioning = false\n\n    this._backdrop.hide(() => {\n      document.body.classList.remove(CLASS_NAME_OPEN)\n      this._resetAdjustments()\n      this._scrollBar.reset()\n      EventHandler.trigger(this._element, EVENT_HIDDEN)\n    })\n  }\n\n  _isAnimated() {\n    return this._element.classList.contains(CLASS_NAME_FADE)\n  }\n\n  _triggerBackdropTransition() {\n    const hideEvent = EventHandler.trigger(this._element, EVENT_HIDE_PREVENTED)\n    if (hideEvent.defaultPrevented) {\n      return\n    }\n\n    const isModalOverflowing = this._element.scrollHeight > document.documentElement.clientHeight\n    const initialOverflowY = this._element.style.overflowY\n    // return if the following background transition hasn't yet completed\n    if (initialOverflowY === 'hidden' || this._element.classList.contains(CLASS_NAME_STATIC)) {\n      return\n    }\n\n    if (!isModalOverflowing) {\n      this._element.style.overflowY = 'hidden'\n    }\n\n    this._element.classList.add(CLASS_NAME_STATIC)\n    this._queueCallback(() => {\n      this._element.classList.remove(CLASS_NAME_STATIC)\n      this._queueCallback(() => {\n        this._element.style.overflowY = initialOverflowY\n      }, this._dialog)\n    }, this._dialog)\n\n    this._element.focus()\n  }\n\n  /**\n   * The following methods are used to handle overflowing modals\n   */\n\n  _adjustDialog() {\n    const isModalOverflowing = this._element.scrollHeight > document.documentElement.clientHeight\n    const scrollbarWidth = this._scrollBar.getWidth()\n    const isBodyOverflowing = scrollbarWidth > 0\n\n    if (isBodyOverflowing && !isModalOverflowing) {\n      const property = isRTL() ? 'paddingLeft' : 'paddingRight'\n      this._element.style[property] = `${scrollbarWidth}px`\n    }\n\n    if (!isBodyOverflowing && isModalOverflowing) {\n      const property = isRTL() ? 'paddingRight' : 'paddingLeft'\n      this._element.style[property] = `${scrollbarWidth}px`\n    }\n  }\n\n  _resetAdjustments() {\n    this._element.style.paddingLeft = ''\n    this._element.style.paddingRight = ''\n  }\n\n  // Static\n  static jQueryInterface(config, relatedTarget) {\n    return this.each(function () {\n      const data = Modal.getOrCreateInstance(this, config)\n\n      if (typeof config !== 'string') {\n        return\n      }\n\n      if (typeof data[config] === 'undefined') {\n        throw new TypeError(`No method named \"${config}\"`)\n      }\n\n      data[config](relatedTarget)\n    })\n  }\n}\n\n/**\n * Data API implementation\n */\n\nEventHandler.on(document, EVENT_CLICK_DATA_API, SELECTOR_DATA_TOGGLE, function (event) {\n  const target = SelectorEngine.getElementFromSelector(this)\n\n  if (['A', 'AREA'].includes(this.tagName)) {\n    event.preventDefault()\n  }\n\n  EventHandler.one(target, EVENT_SHOW, showEvent => {\n    if (showEvent.defaultPrevented) {\n      // only register focus restorer if modal will actually get shown\n      return\n    }\n\n    EventHandler.one(target, EVENT_HIDDEN, () => {\n      if (isVisible(this)) {\n        this.focus()\n      }\n    })\n  })\n\n  // avoid conflict when clicking modal toggler while another one is open\n  const alreadyOpen = SelectorEngine.findOne(OPEN_SELECTOR)\n  if (alreadyOpen) {\n    Modal.getInstance(alreadyOpen).hide()\n  }\n\n  const data = Modal.getOrCreateInstance(target)\n\n  data.toggle(this)\n})\n\nenableDismissTrigger(Modal)\n\n/**\n * jQuery\n */\n\ndefineJQueryPlugin(Modal)\n\nexport default Modal\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap offcanvas.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport BaseComponent from './base-component.js'\nimport EventHandler from './dom/event-handler.js'\nimport SelectorEngine from './dom/selector-engine.js'\nimport Backdrop from './util/backdrop.js'\nimport { enableDismissTrigger } from './util/component-functions.js'\nimport FocusTrap from './util/focustrap.js'\nimport {\n  defineJQueryPlugin,\n  isDisabled,\n  isVisible\n} from './util/index.js'\nimport ScrollBarHelper from './util/scrollbar.js'\n\n/**\n * Constants\n */\n\nconst NAME = 'offcanvas'\nconst DATA_KEY = 'bs.offcanvas'\nconst EVENT_KEY = `.${DATA_KEY}`\nconst DATA_API_KEY = '.data-api'\nconst EVENT_LOAD_DATA_API = `load${EVENT_KEY}${DATA_API_KEY}`\nconst ESCAPE_KEY = 'Escape'\n\nconst CLASS_NAME_SHOW = 'show'\nconst CLASS_NAME_SHOWING = 'showing'\nconst CLASS_NAME_HIDING = 'hiding'\nconst CLASS_NAME_BACKDROP = 'offcanvas-backdrop'\nconst OPEN_SELECTOR = '.offcanvas.show'\n\nconst EVENT_SHOW = `show${EVENT_KEY}`\nconst EVENT_SHOWN = `shown${EVENT_KEY}`\nconst EVENT_HIDE = `hide${EVENT_KEY}`\nconst EVENT_HIDE_PREVENTED = `hidePrevented${EVENT_KEY}`\nconst EVENT_HIDDEN = `hidden${EVENT_KEY}`\nconst EVENT_RESIZE = `resize${EVENT_KEY}`\nconst EVENT_CLICK_DATA_API = `click${EVENT_KEY}${DATA_API_KEY}`\nconst EVENT_KEYDOWN_DISMISS = `keydown.dismiss${EVENT_KEY}`\n\nconst SELECTOR_DATA_TOGGLE = '[data-bs-toggle=\"offcanvas\"]'\n\nconst Default = {\n  backdrop: true,\n  keyboard: true,\n  scroll: false\n}\n\nconst DefaultType = {\n  backdrop: '(boolean|string)',\n  keyboard: 'boolean',\n  scroll: 'boolean'\n}\n\n/**\n * Class definition\n */\n\nclass Offcanvas extends BaseComponent {\n  constructor(element, config) {\n    super(element, config)\n\n    this._isShown = false\n    this._backdrop = this._initializeBackDrop()\n    this._focustrap = this._initializeFocusTrap()\n    this._addEventListeners()\n  }\n\n  // Getters\n  static get Default() {\n    return Default\n  }\n\n  static get DefaultType() {\n    return DefaultType\n  }\n\n  static get NAME() {\n    return NAME\n  }\n\n  // Public\n  toggle(relatedTarget) {\n    return this._isShown ? this.hide() : this.show(relatedTarget)\n  }\n\n  show(relatedTarget) {\n    if (this._isShown) {\n      return\n    }\n\n    const showEvent = EventHandler.trigger(this._element, EVENT_SHOW, { relatedTarget })\n\n    if (showEvent.defaultPrevented) {\n      return\n    }\n\n    this._isShown = true\n    this._backdrop.show()\n\n    if (!this._config.scroll) {\n      new ScrollBarHelper().hide()\n    }\n\n    this._element.setAttribute('aria-modal', true)\n    this._element.setAttribute('role', 'dialog')\n    this._element.classList.add(CLASS_NAME_SHOWING)\n\n    const completeCallBack = () => {\n      if (!this._config.scroll || this._config.backdrop) {\n        this._focustrap.activate()\n      }\n\n      this._element.classList.add(CLASS_NAME_SHOW)\n      this._element.classList.remove(CLASS_NAME_SHOWING)\n      EventHandler.trigger(this._element, EVENT_SHOWN, { relatedTarget })\n    }\n\n    this._queueCallback(completeCallBack, this._element, true)\n  }\n\n  hide() {\n    if (!this._isShown) {\n      return\n    }\n\n    const hideEvent = EventHandler.trigger(this._element, EVENT_HIDE)\n\n    if (hideEvent.defaultPrevented) {\n      return\n    }\n\n    this._focustrap.deactivate()\n    this._element.blur()\n    this._isShown = false\n    this._element.classList.add(CLASS_NAME_HIDING)\n    this._backdrop.hide()\n\n    const completeCallback = () => {\n      this._element.classList.remove(CLASS_NAME_SHOW, CLASS_NAME_HIDING)\n      this._element.removeAttribute('aria-modal')\n      this._element.removeAttribute('role')\n\n      if (!this._config.scroll) {\n        new ScrollBarHelper().reset()\n      }\n\n      EventHandler.trigger(this._element, EVENT_HIDDEN)\n    }\n\n    this._queueCallback(completeCallback, this._element, true)\n  }\n\n  dispose() {\n    this._backdrop.dispose()\n    this._focustrap.deactivate()\n    super.dispose()\n  }\n\n  // Private\n  _initializeBackDrop() {\n    const clickCallback = () => {\n      if (this._config.backdrop === 'static') {\n        EventHandler.trigger(this._element, EVENT_HIDE_PREVENTED)\n        return\n      }\n\n      this.hide()\n    }\n\n    // 'static' option will be translated to true, and booleans will keep their value\n    const isVisible = Boolean(this._config.backdrop)\n\n    return new Backdrop({\n      className: CLASS_NAME_BACKDROP,\n      isVisible,\n      isAnimated: true,\n      rootElement: this._element.parentNode,\n      clickCallback: isVisible ? clickCallback : null\n    })\n  }\n\n  _initializeFocusTrap() {\n    return new FocusTrap({\n      trapElement: this._element\n    })\n  }\n\n  _addEventListeners() {\n    EventHandler.on(this._element, EVENT_KEYDOWN_DISMISS, event => {\n      if (event.key !== ESCAPE_KEY) {\n        return\n      }\n\n      if (this._config.keyboard) {\n        this.hide()\n        return\n      }\n\n      EventHandler.trigger(this._element, EVENT_HIDE_PREVENTED)\n    })\n  }\n\n  // Static\n  static jQueryInterface(config) {\n    return this.each(function () {\n      const data = Offcanvas.getOrCreateInstance(this, config)\n\n      if (typeof config !== 'string') {\n        return\n      }\n\n      if (data[config] === undefined || config.startsWith('_') || config === 'constructor') {\n        throw new TypeError(`No method named \"${config}\"`)\n      }\n\n      data[config](this)\n    })\n  }\n}\n\n/**\n * Data API implementation\n */\n\nEventHandler.on(document, EVENT_CLICK_DATA_API, SELECTOR_DATA_TOGGLE, function (event) {\n  const target = SelectorEngine.getElementFromSelector(this)\n\n  if (['A', 'AREA'].includes(this.tagName)) {\n    event.preventDefault()\n  }\n\n  if (isDisabled(this)) {\n    return\n  }\n\n  EventHandler.one(target, EVENT_HIDDEN, () => {\n    // focus on trigger when it is closed\n    if (isVisible(this)) {\n      this.focus()\n    }\n  })\n\n  // avoid conflict when clicking a toggler of an offcanvas, while another is open\n  const alreadyOpen = SelectorEngine.findOne(OPEN_SELECTOR)\n  if (alreadyOpen && alreadyOpen !== target) {\n    Offcanvas.getInstance(alreadyOpen).hide()\n  }\n\n  const data = Offcanvas.getOrCreateInstance(target)\n  data.toggle(this)\n})\n\nEventHandler.on(window, EVENT_LOAD_DATA_API, () => {\n  for (const selector of SelectorEngine.find(OPEN_SELECTOR)) {\n    Offcanvas.getOrCreateInstance(selector).show()\n  }\n})\n\nEventHandler.on(window, EVENT_RESIZE, () => {\n  for (const element of SelectorEngine.find('[aria-modal][class*=show][class*=offcanvas-]')) {\n    if (getComputedStyle(element).position !== 'fixed') {\n      Offcanvas.getOrCreateInstance(element).hide()\n    }\n  }\n})\n\nenableDismissTrigger(Offcanvas)\n\n/**\n * jQuery\n */\n\ndefineJQueryPlugin(Offcanvas)\n\nexport default Offcanvas\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap util/sanitizer.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\n// js-docs-start allow-list\nconst ARIA_ATTRIBUTE_PATTERN = /^aria-[\\w-]*$/i\n\nexport const DefaultAllowlist = {\n  // Global attributes allowed on any supplied element below.\n  '*': ['class', 'dir', 'id', 'lang', 'role', ARIA_ATTRIBUTE_PATTERN],\n  a: ['target', 'href', 'title', 'rel'],\n  area: [],\n  b: [],\n  br: [],\n  col: [],\n  code: [],\n  div: [],\n  em: [],\n  hr: [],\n  h1: [],\n  h2: [],\n  h3: [],\n  h4: [],\n  h5: [],\n  h6: [],\n  i: [],\n  img: ['src', 'srcset', 'alt', 'title', 'width', 'height'],\n  li: [],\n  ol: [],\n  p: [],\n  pre: [],\n  s: [],\n  small: [],\n  span: [],\n  sub: [],\n  sup: [],\n  strong: [],\n  u: [],\n  ul: []\n}\n// js-docs-end allow-list\n\nconst uriAttributes = new Set([\n  'background',\n  'cite',\n  'href',\n  'itemtype',\n  'longdesc',\n  'poster',\n  'src',\n  'xlink:href'\n])\n\n/**\n * A pattern that recognizes URLs that are safe wrt. XSS in URL navigation\n * contexts.\n *\n * Shout-out to Angular https://github.com/angular/angular/blob/15.2.8/packages/core/src/sanitization/url_sanitizer.ts#L38\n */\n// eslint-disable-next-line unicorn/better-regex\nconst SAFE_URL_PATTERN = /^(?!javascript:)(?:[a-z0-9+.-]+:|[^&:/?#]*(?:[/?#]|$))/i\n\nconst allowedAttribute = (attribute, allowedAttributeList) => {\n  const attributeName = attribute.nodeName.toLowerCase()\n\n  if (allowedAttributeList.includes(attributeName)) {\n    if (uriAttributes.has(attributeName)) {\n      return Boolean(SAFE_URL_PATTERN.test(attribute.nodeValue))\n    }\n\n    return true\n  }\n\n  // Check if a regular expression validates the attribute.\n  return allowedAttributeList.filter(attributeRegex => attributeRegex instanceof RegExp)\n    .some(regex => regex.test(attributeName))\n}\n\nexport function sanitizeHtml(unsafeHtml, allowList, sanitizeFunction) {\n  if (!unsafeHtml.length) {\n    return unsafeHtml\n  }\n\n  if (sanitizeFunction && typeof sanitizeFunction === 'function') {\n    return sanitizeFunction(unsafeHtml)\n  }\n\n  const domParser = new window.DOMParser()\n  const createdDocument = domParser.parseFromString(unsafeHtml, 'text/html')\n  const elements = [].concat(...createdDocument.body.querySelectorAll('*'))\n\n  for (const element of elements) {\n    const elementName = element.nodeName.toLowerCase()\n\n    if (!Object.keys(allowList).includes(elementName)) {\n      element.remove()\n      continue\n    }\n\n    const attributeList = [].concat(...element.attributes)\n    const allowedAttributes = [].concat(allowList['*'] || [], allowList[elementName] || [])\n\n    for (const attribute of attributeList) {\n      if (!allowedAttribute(attribute, allowedAttributes)) {\n        element.removeAttribute(attribute.nodeName)\n      }\n    }\n  }\n\n  return createdDocument.body.innerHTML\n}\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap util/template-factory.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport SelectorEngine from '../dom/selector-engine.js'\nimport Config from './config.js'\nimport { DefaultAllowlist, sanitizeHtml } from './sanitizer.js'\nimport { execute, getElement, isElement } from './index.js'\n\n/**\n * Constants\n */\n\nconst NAME = 'TemplateFactory'\n\nconst Default = {\n  allowList: DefaultAllowlist,\n  content: {}, // { selector : text ,  selector2 : text2 , }\n  extraClass: '',\n  html: false,\n  sanitize: true,\n  sanitizeFn: null,\n  template: '<div></div>'\n}\n\nconst DefaultType = {\n  allowList: 'object',\n  content: 'object',\n  extraClass: '(string|function)',\n  html: 'boolean',\n  sanitize: 'boolean',\n  sanitizeFn: '(null|function)',\n  template: 'string'\n}\n\nconst DefaultContentType = {\n  entry: '(string|element|function|null)',\n  selector: '(string|element)'\n}\n\n/**\n * Class definition\n */\n\nclass TemplateFactory extends Config {\n  constructor(config) {\n    super()\n    this._config = this._getConfig(config)\n  }\n\n  // Getters\n  static get Default() {\n    return Default\n  }\n\n  static get DefaultType() {\n    return DefaultType\n  }\n\n  static get NAME() {\n    return NAME\n  }\n\n  // Public\n  getContent() {\n    return Object.values(this._config.content)\n      .map(config => this._resolvePossibleFunction(config))\n      .filter(Boolean)\n  }\n\n  hasContent() {\n    return this.getContent().length > 0\n  }\n\n  changeContent(content) {\n    this._checkContent(content)\n    this._config.content = { ...this._config.content, ...content }\n    return this\n  }\n\n  toHtml() {\n    const templateWrapper = document.createElement('div')\n    templateWrapper.innerHTML = this._maybeSanitize(this._config.template)\n\n    for (const [selector, text] of Object.entries(this._config.content)) {\n      this._setContent(templateWrapper, text, selector)\n    }\n\n    const template = templateWrapper.children[0]\n    const extraClass = this._resolvePossibleFunction(this._config.extraClass)\n\n    if (extraClass) {\n      template.classList.add(...extraClass.split(' '))\n    }\n\n    return template\n  }\n\n  // Private\n  _typeCheckConfig(config) {\n    super._typeCheckConfig(config)\n    this._checkContent(config.content)\n  }\n\n  _checkContent(arg) {\n    for (const [selector, content] of Object.entries(arg)) {\n      super._typeCheckConfig({ selector, entry: content }, DefaultContentType)\n    }\n  }\n\n  _setContent(template, content, selector) {\n    const templateElement = SelectorEngine.findOne(selector, template)\n\n    if (!templateElement) {\n      return\n    }\n\n    content = this._resolvePossibleFunction(content)\n\n    if (!content) {\n      templateElement.remove()\n      return\n    }\n\n    if (isElement(content)) {\n      this._putElementInTemplate(getElement(content), templateElement)\n      return\n    }\n\n    if (this._config.html) {\n      templateElement.innerHTML = this._maybeSanitize(content)\n      return\n    }\n\n    templateElement.textContent = content\n  }\n\n  _maybeSanitize(arg) {\n    return this._config.sanitize ? sanitizeHtml(arg, this._config.allowList, this._config.sanitizeFn) : arg\n  }\n\n  _resolvePossibleFunction(arg) {\n    return execute(arg, [this])\n  }\n\n  _putElementInTemplate(element, templateElement) {\n    if (this._config.html) {\n      templateElement.innerHTML = ''\n      templateElement.append(element)\n      return\n    }\n\n    templateElement.textContent = element.textContent\n  }\n}\n\nexport default TemplateFactory\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap tooltip.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport * as Popper from '@popperjs/core'\nimport BaseComponent from './base-component.js'\nimport EventHandler from './dom/event-handler.js'\nimport Manipulator from './dom/manipulator.js'\nimport { defineJQueryPlugin, execute, findShadowRoot, getElement, getUID, isRTL, noop } from './util/index.js'\nimport { DefaultAllowlist } from './util/sanitizer.js'\nimport TemplateFactory from './util/template-factory.js'\n\n/**\n * Constants\n */\n\nconst NAME = 'tooltip'\nconst DISALLOWED_ATTRIBUTES = new Set(['sanitize', 'allowList', 'sanitizeFn'])\n\nconst CLASS_NAME_FADE = 'fade'\nconst CLASS_NAME_MODAL = 'modal'\nconst CLASS_NAME_SHOW = 'show'\n\nconst SELECTOR_TOOLTIP_INNER = '.tooltip-inner'\nconst SELECTOR_MODAL = `.${CLASS_NAME_MODAL}`\n\nconst EVENT_MODAL_HIDE = 'hide.bs.modal'\n\nconst TRIGGER_HOVER = 'hover'\nconst TRIGGER_FOCUS = 'focus'\nconst TRIGGER_CLICK = 'click'\nconst TRIGGER_MANUAL = 'manual'\n\nconst EVENT_HIDE = 'hide'\nconst EVENT_HIDDEN = 'hidden'\nconst EVENT_SHOW = 'show'\nconst EVENT_SHOWN = 'shown'\nconst EVENT_INSERTED = 'inserted'\nconst EVENT_CLICK = 'click'\nconst EVENT_FOCUSIN = 'focusin'\nconst EVENT_FOCUSOUT = 'focusout'\nconst EVENT_MOUSEENTER = 'mouseenter'\nconst EVENT_MOUSELEAVE = 'mouseleave'\n\nconst AttachmentMap = {\n  AUTO: 'auto',\n  TOP: 'top',\n  RIGHT: isRTL() ? 'left' : 'right',\n  BOTTOM: 'bottom',\n  LEFT: isRTL() ? 'right' : 'left'\n}\n\nconst Default = {\n  allowList: DefaultAllowlist,\n  animation: true,\n  boundary: 'clippingParents',\n  container: false,\n  customClass: '',\n  delay: 0,\n  fallbackPlacements: ['top', 'right', 'bottom', 'left'],\n  html: false,\n  offset: [0, 6],\n  placement: 'top',\n  popperConfig: null,\n  sanitize: true,\n  sanitizeFn: null,\n  selector: false,\n  template: '<div class=\"tooltip\" role=\"tooltip\">' +\n            '<div class=\"tooltip-arrow\"></div>' +\n            '<div class=\"tooltip-inner\"></div>' +\n            '</div>',\n  title: '',\n  trigger: 'hover focus'\n}\n\nconst DefaultType = {\n  allowList: 'object',\n  animation: 'boolean',\n  boundary: '(string|element)',\n  container: '(string|element|boolean)',\n  customClass: '(string|function)',\n  delay: '(number|object)',\n  fallbackPlacements: 'array',\n  html: 'boolean',\n  offset: '(array|string|function)',\n  placement: '(string|function)',\n  popperConfig: '(null|object|function)',\n  sanitize: 'boolean',\n  sanitizeFn: '(null|function)',\n  selector: '(string|boolean)',\n  template: 'string',\n  title: '(string|element|function)',\n  trigger: 'string'\n}\n\n/**\n * Class definition\n */\n\nclass Tooltip extends BaseComponent {\n  constructor(element, config) {\n    if (typeof Popper === 'undefined') {\n      throw new TypeError('Bootstrap\\'s tooltips require Popper (https://popper.js.org)')\n    }\n\n    super(element, config)\n\n    // Private\n    this._isEnabled = true\n    this._timeout = 0\n    this._isHovered = null\n    this._activeTrigger = {}\n    this._popper = null\n    this._templateFactory = null\n    this._newContent = null\n\n    // Protected\n    this.tip = null\n\n    this._setListeners()\n\n    if (!this._config.selector) {\n      this._fixTitle()\n    }\n  }\n\n  // Getters\n  static get Default() {\n    return Default\n  }\n\n  static get DefaultType() {\n    return DefaultType\n  }\n\n  static get NAME() {\n    return NAME\n  }\n\n  // Public\n  enable() {\n    this._isEnabled = true\n  }\n\n  disable() {\n    this._isEnabled = false\n  }\n\n  toggleEnabled() {\n    this._isEnabled = !this._isEnabled\n  }\n\n  toggle() {\n    if (!this._isEnabled) {\n      return\n    }\n\n    this._activeTrigger.click = !this._activeTrigger.click\n    if (this._isShown()) {\n      this._leave()\n      return\n    }\n\n    this._enter()\n  }\n\n  dispose() {\n    clearTimeout(this._timeout)\n\n    EventHandler.off(this._element.closest(SELECTOR_MODAL), EVENT_MODAL_HIDE, this._hideModalHandler)\n\n    if (this._element.getAttribute('data-bs-original-title')) {\n      this._element.setAttribute('title', this._element.getAttribute('data-bs-original-title'))\n    }\n\n    this._disposePopper()\n    super.dispose()\n  }\n\n  show() {\n    if (this._element.style.display === 'none') {\n      throw new Error('Please use show on visible elements')\n    }\n\n    if (!(this._isWithContent() && this._isEnabled)) {\n      return\n    }\n\n    const showEvent = EventHandler.trigger(this._element, this.constructor.eventName(EVENT_SHOW))\n    const shadowRoot = findShadowRoot(this._element)\n    const isInTheDom = (shadowRoot || this._element.ownerDocument.documentElement).contains(this._element)\n\n    if (showEvent.defaultPrevented || !isInTheDom) {\n      return\n    }\n\n    // TODO: v6 remove this or make it optional\n    this._disposePopper()\n\n    const tip = this._getTipElement()\n\n    this._element.setAttribute('aria-describedby', tip.getAttribute('id'))\n\n    const { container } = this._config\n\n    if (!this._element.ownerDocument.documentElement.contains(this.tip)) {\n      container.append(tip)\n      EventHandler.trigger(this._element, this.constructor.eventName(EVENT_INSERTED))\n    }\n\n    this._popper = this._createPopper(tip)\n\n    tip.classList.add(CLASS_NAME_SHOW)\n\n    // If this is a touch-enabled device we add extra\n    // empty mouseover listeners to the body's immediate children;\n    // only needed because of broken event delegation on iOS\n    // https://www.quirksmode.org/blog/archives/2014/02/mouse_event_bub.html\n    if ('ontouchstart' in document.documentElement) {\n      for (const element of [].concat(...document.body.children)) {\n        EventHandler.on(element, 'mouseover', noop)\n      }\n    }\n\n    const complete = () => {\n      EventHandler.trigger(this._element, this.constructor.eventName(EVENT_SHOWN))\n\n      if (this._isHovered === false) {\n        this._leave()\n      }\n\n      this._isHovered = false\n    }\n\n    this._queueCallback(complete, this.tip, this._isAnimated())\n  }\n\n  hide() {\n    if (!this._isShown()) {\n      return\n    }\n\n    const hideEvent = EventHandler.trigger(this._element, this.constructor.eventName(EVENT_HIDE))\n    if (hideEvent.defaultPrevented) {\n      return\n    }\n\n    const tip = this._getTipElement()\n    tip.classList.remove(CLASS_NAME_SHOW)\n\n    // If this is a touch-enabled device we remove the extra\n    // empty mouseover listeners we added for iOS support\n    if ('ontouchstart' in document.documentElement) {\n      for (const element of [].concat(...document.body.children)) {\n        EventHandler.off(element, 'mouseover', noop)\n      }\n    }\n\n    this._activeTrigger[TRIGGER_CLICK] = false\n    this._activeTrigger[TRIGGER_FOCUS] = false\n    this._activeTrigger[TRIGGER_HOVER] = false\n    this._isHovered = null // it is a trick to support manual triggering\n\n    const complete = () => {\n      if (this._isWithActiveTrigger()) {\n        return\n      }\n\n      if (!this._isHovered) {\n        this._disposePopper()\n      }\n\n      this._element.removeAttribute('aria-describedby')\n      EventHandler.trigger(this._element, this.constructor.eventName(EVENT_HIDDEN))\n    }\n\n    this._queueCallback(complete, this.tip, this._isAnimated())\n  }\n\n  update() {\n    if (this._popper) {\n      this._popper.update()\n    }\n  }\n\n  // Protected\n  _isWithContent() {\n    return Boolean(this._getTitle())\n  }\n\n  _getTipElement() {\n    if (!this.tip) {\n      this.tip = this._createTipElement(this._newContent || this._getContentForTemplate())\n    }\n\n    return this.tip\n  }\n\n  _createTipElement(content) {\n    const tip = this._getTemplateFactory(content).toHtml()\n\n    // TODO: remove this check in v6\n    if (!tip) {\n      return null\n    }\n\n    tip.classList.remove(CLASS_NAME_FADE, CLASS_NAME_SHOW)\n    // TODO: v6 the following can be achieved with CSS only\n    tip.classList.add(`bs-${this.constructor.NAME}-auto`)\n\n    const tipId = getUID(this.constructor.NAME).toString()\n\n    tip.setAttribute('id', tipId)\n\n    if (this._isAnimated()) {\n      tip.classList.add(CLASS_NAME_FADE)\n    }\n\n    return tip\n  }\n\n  setContent(content) {\n    this._newContent = content\n    if (this._isShown()) {\n      this._disposePopper()\n      this.show()\n    }\n  }\n\n  _getTemplateFactory(content) {\n    if (this._templateFactory) {\n      this._templateFactory.changeContent(content)\n    } else {\n      this._templateFactory = new TemplateFactory({\n        ...this._config,\n        // the `content` var has to be after `this._config`\n        // to override config.content in case of popover\n        content,\n        extraClass: this._resolvePossibleFunction(this._config.customClass)\n      })\n    }\n\n    return this._templateFactory\n  }\n\n  _getContentForTemplate() {\n    return {\n      [SELECTOR_TOOLTIP_INNER]: this._getTitle()\n    }\n  }\n\n  _getTitle() {\n    return this._resolvePossibleFunction(this._config.title) || this._element.getAttribute('data-bs-original-title')\n  }\n\n  // Private\n  _initializeOnDelegatedTarget(event) {\n    return this.constructor.getOrCreateInstance(event.delegateTarget, this._getDelegateConfig())\n  }\n\n  _isAnimated() {\n    return this._config.animation || (this.tip && this.tip.classList.contains(CLASS_NAME_FADE))\n  }\n\n  _isShown() {\n    return this.tip && this.tip.classList.contains(CLASS_NAME_SHOW)\n  }\n\n  _createPopper(tip) {\n    const placement = execute(this._config.placement, [this, tip, this._element])\n    const attachment = AttachmentMap[placement.toUpperCase()]\n    return Popper.createPopper(this._element, tip, this._getPopperConfig(attachment))\n  }\n\n  _getOffset() {\n    const { offset } = this._config\n\n    if (typeof offset === 'string') {\n      return offset.split(',').map(value => Number.parseInt(value, 10))\n    }\n\n    if (typeof offset === 'function') {\n      return popperData => offset(popperData, this._element)\n    }\n\n    return offset\n  }\n\n  _resolvePossibleFunction(arg) {\n    return execute(arg, [this._element])\n  }\n\n  _getPopperConfig(attachment) {\n    const defaultBsPopperConfig = {\n      placement: attachment,\n      modifiers: [\n        {\n          name: 'flip',\n          options: {\n            fallbackPlacements: this._config.fallbackPlacements\n          }\n        },\n        {\n          name: 'offset',\n          options: {\n            offset: this._getOffset()\n          }\n        },\n        {\n          name: 'preventOverflow',\n          options: {\n            boundary: this._config.boundary\n          }\n        },\n        {\n          name: 'arrow',\n          options: {\n            element: `.${this.constructor.NAME}-arrow`\n          }\n        },\n        {\n          name: 'preSetPlacement',\n          enabled: true,\n          phase: 'beforeMain',\n          fn: data => {\n            // Pre-set Popper's placement attribute in order to read the arrow sizes properly.\n            // Otherwise, Popper mixes up the width and height dimensions since the initial arrow style is for top placement\n            this._getTipElement().setAttribute('data-popper-placement', data.state.placement)\n          }\n        }\n      ]\n    }\n\n    return {\n      ...defaultBsPopperConfig,\n      ...execute(this._config.popperConfig, [defaultBsPopperConfig])\n    }\n  }\n\n  _setListeners() {\n    const triggers = this._config.trigger.split(' ')\n\n    for (const trigger of triggers) {\n      if (trigger === 'click') {\n        EventHandler.on(this._element, this.constructor.eventName(EVENT_CLICK), this._config.selector, event => {\n          const context = this._initializeOnDelegatedTarget(event)\n          context.toggle()\n        })\n      } else if (trigger !== TRIGGER_MANUAL) {\n        const eventIn = trigger === TRIGGER_HOVER ?\n          this.constructor.eventName(EVENT_MOUSEENTER) :\n          this.constructor.eventName(EVENT_FOCUSIN)\n        const eventOut = trigger === TRIGGER_HOVER ?\n          this.constructor.eventName(EVENT_MOUSELEAVE) :\n          this.constructor.eventName(EVENT_FOCUSOUT)\n\n        EventHandler.on(this._element, eventIn, this._config.selector, event => {\n          const context = this._initializeOnDelegatedTarget(event)\n          context._activeTrigger[event.type === 'focusin' ? TRIGGER_FOCUS : TRIGGER_HOVER] = true\n          context._enter()\n        })\n        EventHandler.on(this._element, eventOut, this._config.selector, event => {\n          const context = this._initializeOnDelegatedTarget(event)\n          context._activeTrigger[event.type === 'focusout' ? TRIGGER_FOCUS : TRIGGER_HOVER] =\n            context._element.contains(event.relatedTarget)\n\n          context._leave()\n        })\n      }\n    }\n\n    this._hideModalHandler = () => {\n      if (this._element) {\n        this.hide()\n      }\n    }\n\n    EventHandler.on(this._element.closest(SELECTOR_MODAL), EVENT_MODAL_HIDE, this._hideModalHandler)\n  }\n\n  _fixTitle() {\n    const title = this._element.getAttribute('title')\n\n    if (!title) {\n      return\n    }\n\n    if (!this._element.getAttribute('aria-label') && !this._element.textContent.trim()) {\n      this._element.setAttribute('aria-label', title)\n    }\n\n    this._element.setAttribute('data-bs-original-title', title) // DO NOT USE IT. Is only for backwards compatibility\n    this._element.removeAttribute('title')\n  }\n\n  _enter() {\n    if (this._isShown() || this._isHovered) {\n      this._isHovered = true\n      return\n    }\n\n    this._isHovered = true\n\n    this._setTimeout(() => {\n      if (this._isHovered) {\n        this.show()\n      }\n    }, this._config.delay.show)\n  }\n\n  _leave() {\n    if (this._isWithActiveTrigger()) {\n      return\n    }\n\n    this._isHovered = false\n\n    this._setTimeout(() => {\n      if (!this._isHovered) {\n        this.hide()\n      }\n    }, this._config.delay.hide)\n  }\n\n  _setTimeout(handler, timeout) {\n    clearTimeout(this._timeout)\n    this._timeout = setTimeout(handler, timeout)\n  }\n\n  _isWithActiveTrigger() {\n    return Object.values(this._activeTrigger).includes(true)\n  }\n\n  _getConfig(config) {\n    const dataAttributes = Manipulator.getDataAttributes(this._element)\n\n    for (const dataAttribute of Object.keys(dataAttributes)) {\n      if (DISALLOWED_ATTRIBUTES.has(dataAttribute)) {\n        delete dataAttributes[dataAttribute]\n      }\n    }\n\n    config = {\n      ...dataAttributes,\n      ...(typeof config === 'object' && config ? config : {})\n    }\n    config = this._mergeConfigObj(config)\n    config = this._configAfterMerge(config)\n    this._typeCheckConfig(config)\n    return config\n  }\n\n  _configAfterMerge(config) {\n    config.container = config.container === false ? document.body : getElement(config.container)\n\n    if (typeof config.delay === 'number') {\n      config.delay = {\n        show: config.delay,\n        hide: config.delay\n      }\n    }\n\n    if (typeof config.title === 'number') {\n      config.title = config.title.toString()\n    }\n\n    if (typeof config.content === 'number') {\n      config.content = config.content.toString()\n    }\n\n    return config\n  }\n\n  _getDelegateConfig() {\n    const config = {}\n\n    for (const [key, value] of Object.entries(this._config)) {\n      if (this.constructor.Default[key] !== value) {\n        config[key] = value\n      }\n    }\n\n    config.selector = false\n    config.trigger = 'manual'\n\n    // In the future can be replaced with:\n    // const keysWithDifferentValues = Object.entries(this._config).filter(entry => this.constructor.Default[entry[0]] !== this._config[entry[0]])\n    // `Object.fromEntries(keysWithDifferentValues)`\n    return config\n  }\n\n  _disposePopper() {\n    if (this._popper) {\n      this._popper.destroy()\n      this._popper = null\n    }\n\n    if (this.tip) {\n      this.tip.remove()\n      this.tip = null\n    }\n  }\n\n  // Static\n  static jQueryInterface(config) {\n    return this.each(function () {\n      const data = Tooltip.getOrCreateInstance(this, config)\n\n      if (typeof config !== 'string') {\n        return\n      }\n\n      if (typeof data[config] === 'undefined') {\n        throw new TypeError(`No method named \"${config}\"`)\n      }\n\n      data[config]()\n    })\n  }\n}\n\n/**\n * jQuery\n */\n\ndefineJQueryPlugin(Tooltip)\n\nexport default Tooltip\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap popover.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport Tooltip from './tooltip.js'\nimport { defineJQueryPlugin } from './util/index.js'\n\n/**\n * Constants\n */\n\nconst NAME = 'popover'\n\nconst SELECTOR_TITLE = '.popover-header'\nconst SELECTOR_CONTENT = '.popover-body'\n\nconst Default = {\n  ...Tooltip.Default,\n  content: '',\n  offset: [0, 8],\n  placement: 'right',\n  template: '<div class=\"popover\" role=\"tooltip\">' +\n    '<div class=\"popover-arrow\"></div>' +\n    '<h3 class=\"popover-header\"></h3>' +\n    '<div class=\"popover-body\"></div>' +\n    '</div>',\n  trigger: 'click'\n}\n\nconst DefaultType = {\n  ...Tooltip.DefaultType,\n  content: '(null|string|element|function)'\n}\n\n/**\n * Class definition\n */\n\nclass Popover extends Tooltip {\n  // Getters\n  static get Default() {\n    return Default\n  }\n\n  static get DefaultType() {\n    return DefaultType\n  }\n\n  static get NAME() {\n    return NAME\n  }\n\n  // Overrides\n  _isWithContent() {\n    return this._getTitle() || this._getContent()\n  }\n\n  // Private\n  _getContentForTemplate() {\n    return {\n      [SELECTOR_TITLE]: this._getTitle(),\n      [SELECTOR_CONTENT]: this._getContent()\n    }\n  }\n\n  _getContent() {\n    return this._resolvePossibleFunction(this._config.content)\n  }\n\n  // Static\n  static jQueryInterface(config) {\n    return this.each(function () {\n      const data = Popover.getOrCreateInstance(this, config)\n\n      if (typeof config !== 'string') {\n        return\n      }\n\n      if (typeof data[config] === 'undefined') {\n        throw new TypeError(`No method named \"${config}\"`)\n      }\n\n      data[config]()\n    })\n  }\n}\n\n/**\n * jQuery\n */\n\ndefineJQueryPlugin(Popover)\n\nexport default Popover\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap scrollspy.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport BaseComponent from './base-component.js'\nimport EventHandler from './dom/event-handler.js'\nimport SelectorEngine from './dom/selector-engine.js'\nimport { defineJQueryPlugin, getElement, isDisabled, isVisible } from './util/index.js'\n\n/**\n * Constants\n */\n\nconst NAME = 'scrollspy'\nconst DATA_KEY = 'bs.scrollspy'\nconst EVENT_KEY = `.${DATA_KEY}`\nconst DATA_API_KEY = '.data-api'\n\nconst EVENT_ACTIVATE = `activate${EVENT_KEY}`\nconst EVENT_CLICK = `click${EVENT_KEY}`\nconst EVENT_LOAD_DATA_API = `load${EVENT_KEY}${DATA_API_KEY}`\n\nconst CLASS_NAME_DROPDOWN_ITEM = 'dropdown-item'\nconst CLASS_NAME_ACTIVE = 'active'\n\nconst SELECTOR_DATA_SPY = '[data-bs-spy=\"scroll\"]'\nconst SELECTOR_TARGET_LINKS = '[href]'\nconst SELECTOR_NAV_LIST_GROUP = '.nav, .list-group'\nconst SELECTOR_NAV_LINKS = '.nav-link'\nconst SELECTOR_NAV_ITEMS = '.nav-item'\nconst SELECTOR_LIST_ITEMS = '.list-group-item'\nconst SELECTOR_LINK_ITEMS = `${SELECTOR_NAV_LINKS}, ${SELECTOR_NAV_ITEMS} > ${SELECTOR_NAV_LINKS}, ${SELECTOR_LIST_ITEMS}`\nconst SELECTOR_DROPDOWN = '.dropdown'\nconst SELECTOR_DROPDOWN_TOGGLE = '.dropdown-toggle'\n\nconst Default = {\n  offset: null, // TODO: v6 @deprecated, keep it for backwards compatibility reasons\n  rootMargin: '0px 0px -25%',\n  smoothScroll: false,\n  target: null,\n  threshold: [0.1, 0.5, 1]\n}\n\nconst DefaultType = {\n  offset: '(number|null)', // TODO v6 @deprecated, keep it for backwards compatibility reasons\n  rootMargin: 'string',\n  smoothScroll: 'boolean',\n  target: 'element',\n  threshold: 'array'\n}\n\n/**\n * Class definition\n */\n\nclass ScrollSpy extends BaseComponent {\n  constructor(element, config) {\n    super(element, config)\n\n    // this._element is the observablesContainer and config.target the menu links wrapper\n    this._targetLinks = new Map()\n    this._observableSections = new Map()\n    this._rootElement = getComputedStyle(this._element).overflowY === 'visible' ? null : this._element\n    this._activeTarget = null\n    this._observer = null\n    this._previousScrollData = {\n      visibleEntryTop: 0,\n      parentScrollTop: 0\n    }\n    this.refresh() // initialize\n  }\n\n  // Getters\n  static get Default() {\n    return Default\n  }\n\n  static get DefaultType() {\n    return DefaultType\n  }\n\n  static get NAME() {\n    return NAME\n  }\n\n  // Public\n  refresh() {\n    this._initializeTargetsAndObservables()\n    this._maybeEnableSmoothScroll()\n\n    if (this._observer) {\n      this._observer.disconnect()\n    } else {\n      this._observer = this._getNewObserver()\n    }\n\n    for (const section of this._observableSections.values()) {\n      this._observer.observe(section)\n    }\n  }\n\n  dispose() {\n    this._observer.disconnect()\n    super.dispose()\n  }\n\n  // Private\n  _configAfterMerge(config) {\n    // TODO: on v6 target should be given explicitly & remove the {target: 'ss-target'} case\n    config.target = getElement(config.target) || document.body\n\n    // TODO: v6 Only for backwards compatibility reasons. Use rootMargin only\n    config.rootMargin = config.offset ? `${config.offset}px 0px -30%` : config.rootMargin\n\n    if (typeof config.threshold === 'string') {\n      config.threshold = config.threshold.split(',').map(value => Number.parseFloat(value))\n    }\n\n    return config\n  }\n\n  _maybeEnableSmoothScroll() {\n    if (!this._config.smoothScroll) {\n      return\n    }\n\n    // unregister any previous listeners\n    EventHandler.off(this._config.target, EVENT_CLICK)\n\n    EventHandler.on(this._config.target, EVENT_CLICK, SELECTOR_TARGET_LINKS, event => {\n      const observableSection = this._observableSections.get(event.target.hash)\n      if (observableSection) {\n        event.preventDefault()\n        const root = this._rootElement || window\n        const height = observableSection.offsetTop - this._element.offsetTop\n        if (root.scrollTo) {\n          root.scrollTo({ top: height, behavior: 'smooth' })\n          return\n        }\n\n        // Chrome 60 doesn't support `scrollTo`\n        root.scrollTop = height\n      }\n    })\n  }\n\n  _getNewObserver() {\n    const options = {\n      root: this._rootElement,\n      threshold: this._config.threshold,\n      rootMargin: this._config.rootMargin\n    }\n\n    return new IntersectionObserver(entries => this._observerCallback(entries), options)\n  }\n\n  // The logic of selection\n  _observerCallback(entries) {\n    const targetElement = entry => this._targetLinks.get(`#${entry.target.id}`)\n    const activate = entry => {\n      this._previousScrollData.visibleEntryTop = entry.target.offsetTop\n      this._process(targetElement(entry))\n    }\n\n    const parentScrollTop = (this._rootElement || document.documentElement).scrollTop\n    const userScrollsDown = parentScrollTop >= this._previousScrollData.parentScrollTop\n    this._previousScrollData.parentScrollTop = parentScrollTop\n\n    for (const entry of entries) {\n      if (!entry.isIntersecting) {\n        this._activeTarget = null\n        this._clearActiveClass(targetElement(entry))\n\n        continue\n      }\n\n      const entryIsLowerThanPrevious = entry.target.offsetTop >= this._previousScrollData.visibleEntryTop\n      // if we are scrolling down, pick the bigger offsetTop\n      if (userScrollsDown && entryIsLowerThanPrevious) {\n        activate(entry)\n        // if parent isn't scrolled, let's keep the first visible item, breaking the iteration\n        if (!parentScrollTop) {\n          return\n        }\n\n        continue\n      }\n\n      // if we are scrolling up, pick the smallest offsetTop\n      if (!userScrollsDown && !entryIsLowerThanPrevious) {\n        activate(entry)\n      }\n    }\n  }\n\n  _initializeTargetsAndObservables() {\n    this._targetLinks = new Map()\n    this._observableSections = new Map()\n\n    const targetLinks = SelectorEngine.find(SELECTOR_TARGET_LINKS, this._config.target)\n\n    for (const anchor of targetLinks) {\n      // ensure that the anchor has an id and is not disabled\n      if (!anchor.hash || isDisabled(anchor)) {\n        continue\n      }\n\n      const observableSection = SelectorEngine.findOne(decodeURI(anchor.hash), this._element)\n\n      // ensure that the observableSection exists & is visible\n      if (isVisible(observableSection)) {\n        this._targetLinks.set(decodeURI(anchor.hash), anchor)\n        this._observableSections.set(anchor.hash, observableSection)\n      }\n    }\n  }\n\n  _process(target) {\n    if (this._activeTarget === target) {\n      return\n    }\n\n    this._clearActiveClass(this._config.target)\n    this._activeTarget = target\n    target.classList.add(CLASS_NAME_ACTIVE)\n    this._activateParents(target)\n\n    EventHandler.trigger(this._element, EVENT_ACTIVATE, { relatedTarget: target })\n  }\n\n  _activateParents(target) {\n    // Activate dropdown parents\n    if (target.classList.contains(CLASS_NAME_DROPDOWN_ITEM)) {\n      SelectorEngine.findOne(SELECTOR_DROPDOWN_TOGGLE, target.closest(SELECTOR_DROPDOWN))\n        .classList.add(CLASS_NAME_ACTIVE)\n      return\n    }\n\n    for (const listGroup of SelectorEngine.parents(target, SELECTOR_NAV_LIST_GROUP)) {\n      // Set triggered links parents as active\n      // With both <ul> and <nav> markup a parent is the previous sibling of any nav ancestor\n      for (const item of SelectorEngine.prev(listGroup, SELECTOR_LINK_ITEMS)) {\n        item.classList.add(CLASS_NAME_ACTIVE)\n      }\n    }\n  }\n\n  _clearActiveClass(parent) {\n    parent.classList.remove(CLASS_NAME_ACTIVE)\n\n    const activeNodes = SelectorEngine.find(`${SELECTOR_TARGET_LINKS}.${CLASS_NAME_ACTIVE}`, parent)\n    for (const node of activeNodes) {\n      node.classList.remove(CLASS_NAME_ACTIVE)\n    }\n  }\n\n  // Static\n  static jQueryInterface(config) {\n    return this.each(function () {\n      const data = ScrollSpy.getOrCreateInstance(this, config)\n\n      if (typeof config !== 'string') {\n        return\n      }\n\n      if (data[config] === undefined || config.startsWith('_') || config === 'constructor') {\n        throw new TypeError(`No method named \"${config}\"`)\n      }\n\n      data[config]()\n    })\n  }\n}\n\n/**\n * Data API implementation\n */\n\nEventHandler.on(window, EVENT_LOAD_DATA_API, () => {\n  for (const spy of SelectorEngine.find(SELECTOR_DATA_SPY)) {\n    ScrollSpy.getOrCreateInstance(spy)\n  }\n})\n\n/**\n * jQuery\n */\n\ndefineJQueryPlugin(ScrollSpy)\n\nexport default ScrollSpy\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap tab.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport BaseComponent from './base-component.js'\nimport EventHandler from './dom/event-handler.js'\nimport SelectorEngine from './dom/selector-engine.js'\nimport { defineJQueryPlugin, getNextActiveElement, isDisabled } from './util/index.js'\n\n/**\n * Constants\n */\n\nconst NAME = 'tab'\nconst DATA_KEY = 'bs.tab'\nconst EVENT_KEY = `.${DATA_KEY}`\n\nconst EVENT_HIDE = `hide${EVENT_KEY}`\nconst EVENT_HIDDEN = `hidden${EVENT_KEY}`\nconst EVENT_SHOW = `show${EVENT_KEY}`\nconst EVENT_SHOWN = `shown${EVENT_KEY}`\nconst EVENT_CLICK_DATA_API = `click${EVENT_KEY}`\nconst EVENT_KEYDOWN = `keydown${EVENT_KEY}`\nconst EVENT_LOAD_DATA_API = `load${EVENT_KEY}`\n\nconst ARROW_LEFT_KEY = 'ArrowLeft'\nconst ARROW_RIGHT_KEY = 'ArrowRight'\nconst ARROW_UP_KEY = 'ArrowUp'\nconst ARROW_DOWN_KEY = 'ArrowDown'\nconst HOME_KEY = 'Home'\nconst END_KEY = 'End'\n\nconst CLASS_NAME_ACTIVE = 'active'\nconst CLASS_NAME_FADE = 'fade'\nconst CLASS_NAME_SHOW = 'show'\nconst CLASS_DROPDOWN = 'dropdown'\n\nconst SELECTOR_DROPDOWN_TOGGLE = '.dropdown-toggle'\nconst SELECTOR_DROPDOWN_MENU = '.dropdown-menu'\nconst NOT_SELECTOR_DROPDOWN_TOGGLE = ':not(.dropdown-toggle)'\n\nconst SELECTOR_TAB_PANEL = '.list-group, .nav, [role=\"tablist\"]'\nconst SELECTOR_OUTER = '.nav-item, .list-group-item'\nconst SELECTOR_INNER = `.nav-link${NOT_SELECTOR_DROPDOWN_TOGGLE}, .list-group-item${NOT_SELECTOR_DROPDOWN_TOGGLE}, [role=\"tab\"]${NOT_SELECTOR_DROPDOWN_TOGGLE}`\nconst SELECTOR_DATA_TOGGLE = '[data-bs-toggle=\"tab\"], [data-bs-toggle=\"pill\"], [data-bs-toggle=\"list\"]' // TODO: could only be `tab` in v6\nconst SELECTOR_INNER_ELEM = `${SELECTOR_INNER}, ${SELECTOR_DATA_TOGGLE}`\n\nconst SELECTOR_DATA_TOGGLE_ACTIVE = `.${CLASS_NAME_ACTIVE}[data-bs-toggle=\"tab\"], .${CLASS_NAME_ACTIVE}[data-bs-toggle=\"pill\"], .${CLASS_NAME_ACTIVE}[data-bs-toggle=\"list\"]`\n\n/**\n * Class definition\n */\n\nclass Tab extends BaseComponent {\n  constructor(element) {\n    super(element)\n    this._parent = this._element.closest(SELECTOR_TAB_PANEL)\n\n    if (!this._parent) {\n      return\n      // TODO: should throw exception in v6\n      // throw new TypeError(`${element.outerHTML} has not a valid parent ${SELECTOR_INNER_ELEM}`)\n    }\n\n    // Set up initial aria attributes\n    this._setInitialAttributes(this._parent, this._getChildren())\n\n    EventHandler.on(this._element, EVENT_KEYDOWN, event => this._keydown(event))\n  }\n\n  // Getters\n  static get NAME() {\n    return NAME\n  }\n\n  // Public\n  show() { // Shows this elem and deactivate the active sibling if exists\n    const innerElem = this._element\n    if (this._elemIsActive(innerElem)) {\n      return\n    }\n\n    // Search for active tab on same parent to deactivate it\n    const active = this._getActiveElem()\n\n    const hideEvent = active ?\n      EventHandler.trigger(active, EVENT_HIDE, { relatedTarget: innerElem }) :\n      null\n\n    const showEvent = EventHandler.trigger(innerElem, EVENT_SHOW, { relatedTarget: active })\n\n    if (showEvent.defaultPrevented || (hideEvent && hideEvent.defaultPrevented)) {\n      return\n    }\n\n    this._deactivate(active, innerElem)\n    this._activate(innerElem, active)\n  }\n\n  // Private\n  _activate(element, relatedElem) {\n    if (!element) {\n      return\n    }\n\n    element.classList.add(CLASS_NAME_ACTIVE)\n\n    this._activate(SelectorEngine.getElementFromSelector(element)) // Search and activate/show the proper section\n\n    const complete = () => {\n      if (element.getAttribute('role') !== 'tab') {\n        element.classList.add(CLASS_NAME_SHOW)\n        return\n      }\n\n      element.removeAttribute('tabindex')\n      element.setAttribute('aria-selected', true)\n      this._toggleDropDown(element, true)\n      EventHandler.trigger(element, EVENT_SHOWN, {\n        relatedTarget: relatedElem\n      })\n    }\n\n    this._queueCallback(complete, element, element.classList.contains(CLASS_NAME_FADE))\n  }\n\n  _deactivate(element, relatedElem) {\n    if (!element) {\n      return\n    }\n\n    element.classList.remove(CLASS_NAME_ACTIVE)\n    element.blur()\n\n    this._deactivate(SelectorEngine.getElementFromSelector(element)) // Search and deactivate the shown section too\n\n    const complete = () => {\n      if (element.getAttribute('role') !== 'tab') {\n        element.classList.remove(CLASS_NAME_SHOW)\n        return\n      }\n\n      element.setAttribute('aria-selected', false)\n      element.setAttribute('tabindex', '-1')\n      this._toggleDropDown(element, false)\n      EventHandler.trigger(element, EVENT_HIDDEN, { relatedTarget: relatedElem })\n    }\n\n    this._queueCallback(complete, element, element.classList.contains(CLASS_NAME_FADE))\n  }\n\n  _keydown(event) {\n    if (!([ARROW_LEFT_KEY, ARROW_RIGHT_KEY, ARROW_UP_KEY, ARROW_DOWN_KEY, HOME_KEY, END_KEY].includes(event.key))) {\n      return\n    }\n\n    event.stopPropagation()// stopPropagation/preventDefault both added to support up/down keys without scrolling the page\n    event.preventDefault()\n\n    const children = this._getChildren().filter(element => !isDisabled(element))\n    let nextActiveElement\n\n    if ([HOME_KEY, END_KEY].includes(event.key)) {\n      nextActiveElement = children[event.key === HOME_KEY ? 0 : children.length - 1]\n    } else {\n      const isNext = [ARROW_RIGHT_KEY, ARROW_DOWN_KEY].includes(event.key)\n      nextActiveElement = getNextActiveElement(children, event.target, isNext, true)\n    }\n\n    if (nextActiveElement) {\n      nextActiveElement.focus({ preventScroll: true })\n      Tab.getOrCreateInstance(nextActiveElement).show()\n    }\n  }\n\n  _getChildren() { // collection of inner elements\n    return SelectorEngine.find(SELECTOR_INNER_ELEM, this._parent)\n  }\n\n  _getActiveElem() {\n    return this._getChildren().find(child => this._elemIsActive(child)) || null\n  }\n\n  _setInitialAttributes(parent, children) {\n    this._setAttributeIfNotExists(parent, 'role', 'tablist')\n\n    for (const child of children) {\n      this._setInitialAttributesOnChild(child)\n    }\n  }\n\n  _setInitialAttributesOnChild(child) {\n    child = this._getInnerElement(child)\n    const isActive = this._elemIsActive(child)\n    const outerElem = this._getOuterElement(child)\n    child.setAttribute('aria-selected', isActive)\n\n    if (outerElem !== child) {\n      this._setAttributeIfNotExists(outerElem, 'role', 'presentation')\n    }\n\n    if (!isActive) {\n      child.setAttribute('tabindex', '-1')\n    }\n\n    this._setAttributeIfNotExists(child, 'role', 'tab')\n\n    // set attributes to the related panel too\n    this._setInitialAttributesOnTargetPanel(child)\n  }\n\n  _setInitialAttributesOnTargetPanel(child) {\n    const target = SelectorEngine.getElementFromSelector(child)\n\n    if (!target) {\n      return\n    }\n\n    this._setAttributeIfNotExists(target, 'role', 'tabpanel')\n\n    if (child.id) {\n      this._setAttributeIfNotExists(target, 'aria-labelledby', `${child.id}`)\n    }\n  }\n\n  _toggleDropDown(element, open) {\n    const outerElem = this._getOuterElement(element)\n    if (!outerElem.classList.contains(CLASS_DROPDOWN)) {\n      return\n    }\n\n    const toggle = (selector, className) => {\n      const element = SelectorEngine.findOne(selector, outerElem)\n      if (element) {\n        element.classList.toggle(className, open)\n      }\n    }\n\n    toggle(SELECTOR_DROPDOWN_TOGGLE, CLASS_NAME_ACTIVE)\n    toggle(SELECTOR_DROPDOWN_MENU, CLASS_NAME_SHOW)\n    outerElem.setAttribute('aria-expanded', open)\n  }\n\n  _setAttributeIfNotExists(element, attribute, value) {\n    if (!element.hasAttribute(attribute)) {\n      element.setAttribute(attribute, value)\n    }\n  }\n\n  _elemIsActive(elem) {\n    return elem.classList.contains(CLASS_NAME_ACTIVE)\n  }\n\n  // Try to get the inner element (usually the .nav-link)\n  _getInnerElement(elem) {\n    return elem.matches(SELECTOR_INNER_ELEM) ? elem : SelectorEngine.findOne(SELECTOR_INNER_ELEM, elem)\n  }\n\n  // Try to get the outer element (usually the .nav-item)\n  _getOuterElement(elem) {\n    return elem.closest(SELECTOR_OUTER) || elem\n  }\n\n  // Static\n  static jQueryInterface(config) {\n    return this.each(function () {\n      const data = Tab.getOrCreateInstance(this)\n\n      if (typeof config !== 'string') {\n        return\n      }\n\n      if (data[config] === undefined || config.startsWith('_') || config === 'constructor') {\n        throw new TypeError(`No method named \"${config}\"`)\n      }\n\n      data[config]()\n    })\n  }\n}\n\n/**\n * Data API implementation\n */\n\nEventHandler.on(document, EVENT_CLICK_DATA_API, SELECTOR_DATA_TOGGLE, function (event) {\n  if (['A', 'AREA'].includes(this.tagName)) {\n    event.preventDefault()\n  }\n\n  if (isDisabled(this)) {\n    return\n  }\n\n  Tab.getOrCreateInstance(this).show()\n})\n\n/**\n * Initialize on focus\n */\nEventHandler.on(window, EVENT_LOAD_DATA_API, () => {\n  for (const element of SelectorEngine.find(SELECTOR_DATA_TOGGLE_ACTIVE)) {\n    Tab.getOrCreateInstance(element)\n  }\n})\n/**\n * jQuery\n */\n\ndefineJQueryPlugin(Tab)\n\nexport default Tab\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap toast.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport BaseComponent from './base-component.js'\nimport EventHandler from './dom/event-handler.js'\nimport { enableDismissTrigger } from './util/component-functions.js'\nimport { defineJQueryPlugin, reflow } from './util/index.js'\n\n/**\n * Constants\n */\n\nconst NAME = 'toast'\nconst DATA_KEY = 'bs.toast'\nconst EVENT_KEY = `.${DATA_KEY}`\n\nconst EVENT_MOUSEOVER = `mouseover${EVENT_KEY}`\nconst EVENT_MOUSEOUT = `mouseout${EVENT_KEY}`\nconst EVENT_FOCUSIN = `focusin${EVENT_KEY}`\nconst EVENT_FOCUSOUT = `focusout${EVENT_KEY}`\nconst EVENT_HIDE = `hide${EVENT_KEY}`\nconst EVENT_HIDDEN = `hidden${EVENT_KEY}`\nconst EVENT_SHOW = `show${EVENT_KEY}`\nconst EVENT_SHOWN = `shown${EVENT_KEY}`\n\nconst CLASS_NAME_FADE = 'fade'\nconst CLASS_NAME_HIDE = 'hide' // @deprecated - kept here only for backwards compatibility\nconst CLASS_NAME_SHOW = 'show'\nconst CLASS_NAME_SHOWING = 'showing'\n\nconst DefaultType = {\n  animation: 'boolean',\n  autohide: 'boolean',\n  delay: 'number'\n}\n\nconst Default = {\n  animation: true,\n  autohide: true,\n  delay: 5000\n}\n\n/**\n * Class definition\n */\n\nclass Toast extends BaseComponent {\n  constructor(element, config) {\n    super(element, config)\n\n    this._timeout = null\n    this._hasMouseInteraction = false\n    this._hasKeyboardInteraction = false\n    this._setListeners()\n  }\n\n  // Getters\n  static get Default() {\n    return Default\n  }\n\n  static get DefaultType() {\n    return DefaultType\n  }\n\n  static get NAME() {\n    return NAME\n  }\n\n  // Public\n  show() {\n    const showEvent = EventHandler.trigger(this._element, EVENT_SHOW)\n\n    if (showEvent.defaultPrevented) {\n      return\n    }\n\n    this._clearTimeout()\n\n    if (this._config.animation) {\n      this._element.classList.add(CLASS_NAME_FADE)\n    }\n\n    const complete = () => {\n      this._element.classList.remove(CLASS_NAME_SHOWING)\n      EventHandler.trigger(this._element, EVENT_SHOWN)\n\n      this._maybeScheduleHide()\n    }\n\n    this._element.classList.remove(CLASS_NAME_HIDE) // @deprecated\n    reflow(this._element)\n    this._element.classList.add(CLASS_NAME_SHOW, CLASS_NAME_SHOWING)\n\n    this._queueCallback(complete, this._element, this._config.animation)\n  }\n\n  hide() {\n    if (!this.isShown()) {\n      return\n    }\n\n    const hideEvent = EventHandler.trigger(this._element, EVENT_HIDE)\n\n    if (hideEvent.defaultPrevented) {\n      return\n    }\n\n    const complete = () => {\n      this._element.classList.add(CLASS_NAME_HIDE) // @deprecated\n      this._element.classList.remove(CLASS_NAME_SHOWING, CLASS_NAME_SHOW)\n      EventHandler.trigger(this._element, EVENT_HIDDEN)\n    }\n\n    this._element.classList.add(CLASS_NAME_SHOWING)\n    this._queueCallback(complete, this._element, this._config.animation)\n  }\n\n  dispose() {\n    this._clearTimeout()\n\n    if (this.isShown()) {\n      this._element.classList.remove(CLASS_NAME_SHOW)\n    }\n\n    super.dispose()\n  }\n\n  isShown() {\n    return this._element.classList.contains(CLASS_NAME_SHOW)\n  }\n\n  // Private\n\n  _maybeScheduleHide() {\n    if (!this._config.autohide) {\n      return\n    }\n\n    if (this._hasMouseInteraction || this._hasKeyboardInteraction) {\n      return\n    }\n\n    this._timeout = setTimeout(() => {\n      this.hide()\n    }, this._config.delay)\n  }\n\n  _onInteraction(event, isInteracting) {\n    switch (event.type) {\n      case 'mouseover':\n      case 'mouseout': {\n        this._hasMouseInteraction = isInteracting\n        break\n      }\n\n      case 'focusin':\n      case 'focusout': {\n        this._hasKeyboardInteraction = isInteracting\n        break\n      }\n\n      default: {\n        break\n      }\n    }\n\n    if (isInteracting) {\n      this._clearTimeout()\n      return\n    }\n\n    const nextElement = event.relatedTarget\n    if (this._element === nextElement || this._element.contains(nextElement)) {\n      return\n    }\n\n    this._maybeScheduleHide()\n  }\n\n  _setListeners() {\n    EventHandler.on(this._element, EVENT_MOUSEOVER, event => this._onInteraction(event, true))\n    EventHandler.on(this._element, EVENT_MOUSEOUT, event => this._onInteraction(event, false))\n    EventHandler.on(this._element, EVENT_FOCUSIN, event => this._onInteraction(event, true))\n    EventHandler.on(this._element, EVENT_FOCUSOUT, event => this._onInteraction(event, false))\n  }\n\n  _clearTimeout() {\n    clearTimeout(this._timeout)\n    this._timeout = null\n  }\n\n  // Static\n  static jQueryInterface(config) {\n    return this.each(function () {\n      const data = Toast.getOrCreateInstance(this, config)\n\n      if (typeof config === 'string') {\n        if (typeof data[config] === 'undefined') {\n          throw new TypeError(`No method named \"${config}\"`)\n        }\n\n        data[config](this)\n      }\n    })\n  }\n}\n\n/**\n * Data API implementation\n */\n\nenableDismissTrigger(Toast)\n\n/**\n * jQuery\n */\n\ndefineJQueryPlugin(Toast)\n\nexport default Toast\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap index.umd.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport Alert from './src/alert.js'\nimport Button from './src/button.js'\nimport Carousel from './src/carousel.js'\nimport Collapse from './src/collapse.js'\nimport Dropdown from './src/dropdown.js'\nimport Modal from './src/modal.js'\nimport Offcanvas from './src/offcanvas.js'\nimport Popover from './src/popover.js'\nimport ScrollSpy from './src/scrollspy.js'\nimport Tab from './src/tab.js'\nimport Toast from './src/toast.js'\nimport Tooltip from 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\ No newline at end of file
diff --git a/deps/bootstrap-5.3.1/bootstrap.min.css b/deps/bootstrap-5.3.1/bootstrap.min.css
new file mode 100644
index 00000000..d944a2a7
--- /dev/null
+++ b/deps/bootstrap-5.3.1/bootstrap.min.css
@@ -0,0 +1,5 @@
+:root{--bslib-bootstrap-version: 5;--bslib-preset-name: ;--bslib-preset-type: }/*!
+   * Bootstrap  v5.3.1 (https://getbootstrap.com/)
+   * Copyright 2011-2023 The Bootstrap Authors
+   * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)
+   */:root,[data-bs-theme="light"]{--bs-blue: #0d6efd;--bs-indigo: #6610f2;--bs-purple: #6f42c1;--bs-pink: #d63384;--bs-red: #dc3545;--bs-orange: #fd7e14;--bs-yellow: #ffc107;--bs-green: #198754;--bs-teal: #20c997;--bs-cyan: #0dcaf0;--bs-black: #000;--bs-white: #fff;--bs-gray: #6c757d;--bs-gray-dark: #343a40;--bs-gray-100: #f8f9fa;--bs-gray-200: #e9ecef;--bs-gray-300: #dee2e6;--bs-gray-400: #ced4da;--bs-gray-500: #adb5bd;--bs-gray-600: #6c757d;--bs-gray-700: #495057;--bs-gray-800: #343a40;--bs-gray-900: #212529;--bs-default: #dee2e6;--bs-primary: #0d6efd;--bs-secondary: #6c757d;--bs-success: #198754;--bs-info: #0dcaf0;--bs-warning: #ffc107;--bs-danger: #dc3545;--bs-light: #f8f9fa;--bs-dark: #212529;--bs-default-rgb: 222,226,230;--bs-primary-rgb: 13,110,253;--bs-secondary-rgb: 108,117,125;--bs-success-rgb: 25,135,84;--bs-info-rgb: 13,202,240;--bs-warning-rgb: 255,193,7;--bs-danger-rgb: 220,53,69;--bs-light-rgb: 248,249,250;--bs-dark-rgb: 33,37,41;--bs-primary-text-emphasis: 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#198754;--bs-btn-border-color: #198754;--bs-btn-hover-color: #fff;--bs-btn-hover-bg: #198754;--bs-btn-hover-border-color: #198754;--bs-btn-focus-shadow-rgb: 25,135,84;--bs-btn-active-color: #fff;--bs-btn-active-bg: #198754;--bs-btn-active-border-color: #198754;--bs-btn-active-shadow: inset 0 3px 5px rgba(0,0,0,0.125);--bs-btn-disabled-color: #198754;--bs-btn-disabled-bg: transparent;--bs-btn-disabled-border-color: #198754;--bs-btn-bg: transparent;--bs-gradient: none}.btn-outline-info{--bs-btn-color: #0dcaf0;--bs-btn-border-color: #0dcaf0;--bs-btn-hover-color: #000;--bs-btn-hover-bg: #0dcaf0;--bs-btn-hover-border-color: #0dcaf0;--bs-btn-focus-shadow-rgb: 13,202,240;--bs-btn-active-color: #000;--bs-btn-active-bg: #0dcaf0;--bs-btn-active-border-color: #0dcaf0;--bs-btn-active-shadow: inset 0 3px 5px rgba(0,0,0,0.125);--bs-btn-disabled-color: #0dcaf0;--bs-btn-disabled-bg: transparent;--bs-btn-disabled-border-color: #0dcaf0;--bs-btn-bg: transparent;--bs-gradient: none}.btn-outline-warning{--bs-btn-color: #ffc107;--bs-btn-border-color: #ffc107;--bs-btn-hover-color: #000;--bs-btn-hover-bg: #ffc107;--bs-btn-hover-border-color: #ffc107;--bs-btn-focus-shadow-rgb: 255,193,7;--bs-btn-active-color: #000;--bs-btn-active-bg: #ffc107;--bs-btn-active-border-color: #ffc107;--bs-btn-active-shadow: inset 0 3px 5px rgba(0,0,0,0.125);--bs-btn-disabled-color: #ffc107;--bs-btn-disabled-bg: transparent;--bs-btn-disabled-border-color: #ffc107;--bs-btn-bg: transparent;--bs-gradient: none}.btn-outline-danger{--bs-btn-color: #dc3545;--bs-btn-border-color: #dc3545;--bs-btn-hover-color: #fff;--bs-btn-hover-bg: #dc3545;--bs-btn-hover-border-color: #dc3545;--bs-btn-focus-shadow-rgb: 220,53,69;--bs-btn-active-color: #fff;--bs-btn-active-bg: #dc3545;--bs-btn-active-border-color: #dc3545;--bs-btn-active-shadow: inset 0 3px 5px rgba(0,0,0,0.125);--bs-btn-disabled-color: #dc3545;--bs-btn-disabled-bg: transparent;--bs-btn-disabled-border-color: #dc3545;--bs-btn-bg: transparent;--bs-gradient: none}.btn-outline-light{--bs-btn-color: #f8f9fa;--bs-btn-border-color: #f8f9fa;--bs-btn-hover-color: #000;--bs-btn-hover-bg: #f8f9fa;--bs-btn-hover-border-color: #f8f9fa;--bs-btn-focus-shadow-rgb: 248,249,250;--bs-btn-active-color: #000;--bs-btn-active-bg: #f8f9fa;--bs-btn-active-border-color: #f8f9fa;--bs-btn-active-shadow: inset 0 3px 5px rgba(0,0,0,0.125);--bs-btn-disabled-color: #f8f9fa;--bs-btn-disabled-bg: transparent;--bs-btn-disabled-border-color: #f8f9fa;--bs-btn-bg: transparent;--bs-gradient: none}.btn-outline-dark{--bs-btn-color: #212529;--bs-btn-border-color: #212529;--bs-btn-hover-color: #fff;--bs-btn-hover-bg: #212529;--bs-btn-hover-border-color: #212529;--bs-btn-focus-shadow-rgb: 33,37,41;--bs-btn-active-color: #fff;--bs-btn-active-bg: #212529;--bs-btn-active-border-color: #212529;--bs-btn-active-shadow: inset 0 3px 5px rgba(0,0,0,0.125);--bs-btn-disabled-color: #212529;--bs-btn-disabled-bg: transparent;--bs-btn-disabled-border-color: #212529;--bs-btn-bg: transparent;--bs-gradient: none}.btn-link{--bs-btn-font-weight: 400;--bs-btn-color: var(--bs-link-color);--bs-btn-bg: transparent;--bs-btn-border-color: transparent;--bs-btn-hover-color: var(--bs-link-hover-color);--bs-btn-hover-border-color: transparent;--bs-btn-active-color: var(--bs-link-hover-color);--bs-btn-active-border-color: transparent;--bs-btn-disabled-color: #6c757d;--bs-btn-disabled-border-color: transparent;--bs-btn-box-shadow: 0 0 0 #000;--bs-btn-focus-shadow-rgb: 49,132,253;text-decoration:underline;-webkit-text-decoration:underline;-moz-text-decoration:underline;-ms-text-decoration:underline;-o-text-decoration:underline}.btn-link:focus-visible{color:var(--bs-btn-color)}.btn-link:hover{color:var(--bs-btn-hover-color)}.btn-lg,.btn-group-lg>.btn{--bs-btn-padding-y: .5rem;--bs-btn-padding-x: 1rem;--bs-btn-font-size:1.25rem;--bs-btn-border-radius: var(--bs-border-radius-lg)}.btn-sm,.btn-group-sm>.btn{--bs-btn-padding-y: .25rem;--bs-btn-padding-x: .5rem;--bs-btn-font-size:.875rem;--bs-btn-border-radius: var(--bs-border-radius-sm)}.fade{transition:opacity 0.15s linear}@media (prefers-reduced-motion: reduce){.fade{transition:none}}.fade:not(.show){opacity:0}.collapse:not(.show){display:none}.collapsing{height:0;overflow:hidden;transition:height 0.35s ease}@media (prefers-reduced-motion: reduce){.collapsing{transition:none}}.collapsing.collapse-horizontal{width:0;height:auto;transition:width 0.35s ease}@media (prefers-reduced-motion: reduce){.collapsing.collapse-horizontal{transition:none}}.dropup,.dropend,.dropdown,.dropstart,.dropup-center,.dropdown-center{position:relative}.dropdown-toggle{white-space:nowrap}.dropdown-toggle::after{display:inline-block;margin-left:.255em;vertical-align:.255em;content:"";border-top:.3em solid;border-right:.3em solid transparent;border-bottom:0;border-left:.3em solid transparent}.dropdown-toggle:empty::after{margin-left:0}.dropdown-menu{--bs-dropdown-zindex: 1000;--bs-dropdown-min-width: 10rem;--bs-dropdown-padding-x: 0;--bs-dropdown-padding-y: .5rem;--bs-dropdown-spacer: .125rem;--bs-dropdown-font-size:1rem;--bs-dropdown-color: var(--bs-body-color);--bs-dropdown-bg: var(--bs-body-bg);--bs-dropdown-border-color: var(--bs-border-color-translucent);--bs-dropdown-border-radius: var(--bs-border-radius);--bs-dropdown-border-width: var(--bs-border-width);--bs-dropdown-inner-border-radius: calc(var(--bs-border-radius) - var(--bs-border-width));--bs-dropdown-divider-bg: var(--bs-border-color-translucent);--bs-dropdown-divider-margin-y: .5rem;--bs-dropdown-box-shadow: 0 0.5rem 1rem rgba(0,0,0,0.15);--bs-dropdown-link-color: var(--bs-body-color);--bs-dropdown-link-hover-color: var(--bs-body-color);--bs-dropdown-link-hover-bg: var(--bs-tertiary-bg);--bs-dropdown-link-active-color: #fff;--bs-dropdown-link-active-bg: #0d6efd;--bs-dropdown-link-disabled-color: var(--bs-tertiary-color);--bs-dropdown-item-padding-x: 1rem;--bs-dropdown-item-padding-y: .25rem;--bs-dropdown-header-color: #6c757d;--bs-dropdown-header-padding-x: 1rem;--bs-dropdown-header-padding-y: .5rem;position:absolute;z-index:var(--bs-dropdown-zindex);display:none;min-width:var(--bs-dropdown-min-width);padding:var(--bs-dropdown-padding-y) var(--bs-dropdown-padding-x);margin:0;font-size:var(--bs-dropdown-font-size);color:var(--bs-dropdown-color);text-align:left;list-style:none;background-color:var(--bs-dropdown-bg);background-clip:padding-box;border:var(--bs-dropdown-border-width) solid var(--bs-dropdown-border-color);border-radius:var(--bs-dropdown-border-radius)}.dropdown-menu[data-bs-popper]{top:100%;left:0;margin-top:var(--bs-dropdown-spacer)}.dropdown-menu-start{--bs-position: start}.dropdown-menu-start[data-bs-popper]{right:auto;left:0}.dropdown-menu-end{--bs-position: end}.dropdown-menu-end[data-bs-popper]{right:0;left:auto}@media (min-width: 576px){.dropdown-menu-sm-start{--bs-position: start}.dropdown-menu-sm-start[data-bs-popper]{right:auto;left:0}.dropdown-menu-sm-end{--bs-position: 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.dropdown-toggle::after{display:inline-block;margin-left:.255em;vertical-align:.255em;content:""}.dropstart .dropdown-toggle::after{display:none}.dropstart .dropdown-toggle::before{display:inline-block;margin-right:.255em;vertical-align:.255em;content:"";border-top:.3em solid transparent;border-right:.3em solid;border-bottom:.3em solid transparent}.dropstart .dropdown-toggle:empty::after{margin-left:0}.dropstart .dropdown-toggle::before{vertical-align:0}.dropdown-divider{height:0;margin:var(--bs-dropdown-divider-margin-y) 0;overflow:hidden;border-top:1px solid var(--bs-dropdown-divider-bg);opacity:1}.dropdown-item{display:block;width:100%;padding:var(--bs-dropdown-item-padding-y) 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var(--bs-dropdown-header-padding-x);margin-bottom:0;font-size:.875rem;color:var(--bs-dropdown-header-color);white-space:nowrap}.dropdown-item-text{display:block;padding:var(--bs-dropdown-item-padding-y) var(--bs-dropdown-item-padding-x);color:var(--bs-dropdown-link-color)}.dropdown-menu-dark{--bs-dropdown-color: #dee2e6;--bs-dropdown-bg: #343a40;--bs-dropdown-border-color: var(--bs-border-color-translucent);--bs-dropdown-box-shadow: ;--bs-dropdown-link-color: #dee2e6;--bs-dropdown-link-hover-color: #fff;--bs-dropdown-divider-bg: var(--bs-border-color-translucent);--bs-dropdown-link-hover-bg: rgba(255,255,255,0.15);--bs-dropdown-link-active-color: #fff;--bs-dropdown-link-active-bg: #0d6efd;--bs-dropdown-link-disabled-color: #adb5bd;--bs-dropdown-header-color: #adb5bd}.btn-group,.btn-group-vertical{position:relative;display:inline-flex;vertical-align:middle}.btn-group>.btn,.btn-group-vertical>.btn{position:relative;flex:1 1 auto;-webkit-flex:1 1 auto}.btn-group>.btn-check:checked+.btn,.btn-group>.btn-check:focus+.btn,.btn-group>.btn:hover,.btn-group>.btn:focus,.btn-group>.btn:active,.btn-group>.btn.active,.btn-group-vertical>.btn-check:checked+.btn,.btn-group-vertical>.btn-check:focus+.btn,.btn-group-vertical>.btn:hover,.btn-group-vertical>.btn:focus,.btn-group-vertical>.btn:active,.btn-group-vertical>.btn.active{z-index:1}.btn-toolbar{display:flex;display:-webkit-flex;flex-wrap:wrap;-webkit-flex-wrap:wrap;justify-content:flex-start;-webkit-justify-content:flex-start}.btn-toolbar .input-group{width:auto}.btn-group{border-radius:var(--bs-border-radius)}.btn-group>:not(.btn-check:first-child)+.btn,.btn-group>.btn-group:not(:first-child){margin-left:calc(var(--bs-border-width) * -1)}.btn-group>.btn:not(:last-child):not(.dropdown-toggle),.btn-group>.btn.dropdown-toggle-split:first-child,.btn-group>.btn-group:not(:last-child)>.btn{border-top-right-radius:0;border-bottom-right-radius:0}.btn-group>.btn:nth-child(n + 3),.btn-group>:not(.btn-check)+.btn,.btn-group>.btn-group:not(:first-child)>.btn{border-top-left-radius:0;border-bottom-left-radius:0}.dropdown-toggle-split{padding-right:.5625rem;padding-left:.5625rem}.dropdown-toggle-split::after,.dropup .dropdown-toggle-split::after,.dropend .dropdown-toggle-split::after{margin-left:0}.dropstart .dropdown-toggle-split::before{margin-right:0}.btn-sm+.dropdown-toggle-split,.btn-group-sm>.btn+.dropdown-toggle-split{padding-right:.375rem;padding-left:.375rem}.btn-lg+.dropdown-toggle-split,.btn-group-lg>.btn+.dropdown-toggle-split{padding-right:.75rem;padding-left:.75rem}.btn-group-vertical{flex-direction:column;-webkit-flex-direction:column;align-items:flex-start;-webkit-align-items:flex-start;justify-content:center;-webkit-justify-content:center}.btn-group-vertical>.btn,.btn-group-vertical>.btn-group{width:100%}.btn-group-vertical>.btn:not(:first-child),.btn-group-vertical>.btn-group:not(:first-child){margin-top:calc(var(--bs-border-width) * -1)}.btn-group-vertical>.btn:not(:last-child):not(.dropdown-toggle),.btn-group-vertical>.btn-group:not(:last-child)>.btn{border-bottom-right-radius:0;border-bottom-left-radius:0}.btn-group-vertical>.btn~.btn,.btn-group-vertical>.btn-group:not(:first-child)>.btn{border-top-left-radius:0;border-top-right-radius:0}.nav{--bs-nav-link-padding-x: 1rem;--bs-nav-link-padding-y: .5rem;--bs-nav-link-font-weight: ;--bs-nav-link-color: var(--bs-link-color);--bs-nav-link-hover-color: var(--bs-link-hover-color);--bs-nav-link-disabled-color: var(--bs-secondary-color);display:flex;display:-webkit-flex;flex-wrap:wrap;-webkit-flex-wrap:wrap;padding-left:0;margin-bottom:0;list-style:none}.nav-link{display:block;padding:var(--bs-nav-link-padding-y) var(--bs-nav-link-padding-x);font-size:var(--bs-nav-link-font-size);font-weight:var(--bs-nav-link-font-weight);color:var(--bs-nav-link-color);text-decoration:none;-webkit-text-decoration:none;-moz-text-decoration:none;-ms-text-decoration:none;-o-text-decoration:none;background:none;border:0;transition:color 0.15s ease-in-out,background-color 0.15s ease-in-out,border-color 0.15s ease-in-out}@media (prefers-reduced-motion: reduce){.nav-link{transition:none}}.nav-link:hover,.nav-link:focus{color:var(--bs-nav-link-hover-color)}.nav-link:focus-visible{outline:0;box-shadow:0 0 0 .25rem rgba(13,110,253,0.25)}.nav-link.disabled,.nav-link:disabled{color:var(--bs-nav-link-disabled-color);pointer-events:none;cursor:default}.nav-tabs{--bs-nav-tabs-border-width: var(--bs-border-width);--bs-nav-tabs-border-color: var(--bs-border-color);--bs-nav-tabs-border-radius: var(--bs-border-radius);--bs-nav-tabs-link-hover-border-color: var(--bs-secondary-bg) var(--bs-secondary-bg) var(--bs-border-color);--bs-nav-tabs-link-active-color: var(--bs-emphasis-color);--bs-nav-tabs-link-active-bg: var(--bs-body-bg);--bs-nav-tabs-link-active-border-color: var(--bs-border-color) var(--bs-border-color) var(--bs-body-bg);border-bottom:var(--bs-nav-tabs-border-width) solid var(--bs-nav-tabs-border-color)}.nav-tabs .nav-link{margin-bottom:calc(-1 * var(--bs-nav-tabs-border-width));border:var(--bs-nav-tabs-border-width) solid transparent;border-top-left-radius:var(--bs-nav-tabs-border-radius);border-top-right-radius:var(--bs-nav-tabs-border-radius)}.nav-tabs .nav-link:hover,.nav-tabs .nav-link:focus{isolation:isolate;border-color:var(--bs-nav-tabs-link-hover-border-color)}.nav-tabs .nav-link.active,.nav-tabs .nav-item.show .nav-link{color:var(--bs-nav-tabs-link-active-color);background-color:var(--bs-nav-tabs-link-active-bg);border-color:var(--bs-nav-tabs-link-active-border-color)}.nav-tabs .dropdown-menu{margin-top:calc(-1 * var(--bs-nav-tabs-border-width));border-top-left-radius:0;border-top-right-radius:0}.nav-pills{--bs-nav-pills-border-radius: var(--bs-border-radius);--bs-nav-pills-link-active-color: #fff;--bs-nav-pills-link-active-bg: #0d6efd}.nav-pills .nav-link{border-radius:var(--bs-nav-pills-border-radius)}.nav-pills .nav-link.active,.nav-pills .show>.nav-link{color:var(--bs-nav-pills-link-active-color);background-color:var(--bs-nav-pills-link-active-bg)}.nav-underline{--bs-nav-underline-gap: 1rem;--bs-nav-underline-border-width: .125rem;--bs-nav-underline-link-active-color: var(--bs-emphasis-color);gap:var(--bs-nav-underline-gap)}.nav-underline .nav-link{padding-right:0;padding-left:0;border-bottom:var(--bs-nav-underline-border-width) solid transparent}.nav-underline .nav-link:hover,.nav-underline .nav-link:focus{border-bottom-color:currentcolor}.nav-underline .nav-link.active,.nav-underline .show>.nav-link{font-weight:700;color:var(--bs-nav-underline-link-active-color);border-bottom-color:currentcolor}.nav-fill>.nav-link,.nav-fill .nav-item{flex:1 1 auto;-webkit-flex:1 1 auto;text-align:center}.nav-justified>.nav-link,.nav-justified .nav-item{flex-basis:0;-webkit-flex-basis:0;flex-grow:1;-webkit-flex-grow:1;text-align:center}.nav-fill .nav-item .nav-link,.nav-justified .nav-item .nav-link{width:100%}.tab-content>.tab-pane{display:none}.tab-content>.active{display:block}.navbar{--bs-navbar-padding-x: 0;--bs-navbar-padding-y: .5rem;--bs-navbar-color: rgba(var(--bs-emphasis-color-rgb), 0.65);--bs-navbar-hover-color: rgba(var(--bs-emphasis-color-rgb), 0.8);--bs-navbar-disabled-color: rgba(var(--bs-emphasis-color-rgb), 0.3);--bs-navbar-active-color: rgba(var(--bs-emphasis-color-rgb), 1);--bs-navbar-brand-padding-y: .3125rem;--bs-navbar-brand-margin-end: 1rem;--bs-navbar-brand-font-size: 1.25rem;--bs-navbar-brand-color: rgba(var(--bs-emphasis-color-rgb), 1);--bs-navbar-brand-hover-color: rgba(var(--bs-emphasis-color-rgb), 1);--bs-navbar-nav-link-padding-x: .5rem;--bs-navbar-toggler-padding-y: .25rem;--bs-navbar-toggler-padding-x: .75rem;--bs-navbar-toggler-font-size: 1.25rem;--bs-navbar-toggler-icon-bg: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 30 30'%3e%3cpath stroke='rgba%2833,37,41,0.75%29' stroke-linecap='round' stroke-miterlimit='10' stroke-width='2' d='M4 7h22M4 15h22M4 23h22'/%3e%3c/svg%3e");--bs-navbar-toggler-border-color: rgba(var(--bs-emphasis-color-rgb), 0.15);--bs-navbar-toggler-border-radius: var(--bs-border-radius);--bs-navbar-toggler-focus-width: .25rem;--bs-navbar-toggler-transition: box-shadow 0.15s ease-in-out;position:relative;display:flex;display:-webkit-flex;flex-wrap:wrap;-webkit-flex-wrap:wrap;align-items:center;-webkit-align-items:center;justify-content:space-between;-webkit-justify-content:space-between;padding:var(--bs-navbar-padding-y) 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992px){.navbar-expand-lg{flex-wrap:nowrap;-webkit-flex-wrap:nowrap;justify-content:flex-start;-webkit-justify-content:flex-start}.navbar-expand-lg .navbar-nav{flex-direction:row;-webkit-flex-direction:row}.navbar-expand-lg .navbar-nav .dropdown-menu{position:absolute}.navbar-expand-lg .navbar-nav .nav-link{padding-right:var(--bs-navbar-nav-link-padding-x);padding-left:var(--bs-navbar-nav-link-padding-x)}.navbar-expand-lg .navbar-nav-scroll{overflow:visible}.navbar-expand-lg .navbar-collapse{display:flex !important;display:-webkit-flex !important;flex-basis:auto;-webkit-flex-basis:auto}.navbar-expand-lg .navbar-toggler{display:none}.navbar-expand-lg .offcanvas{position:static;z-index:auto;flex-grow:1;-webkit-flex-grow:1;width:auto !important;height:auto !important;visibility:visible !important;background-color:transparent !important;border:0 !important;transform:none !important;transition:none}.navbar-expand-lg .offcanvas .offcanvas-header{display:none}.navbar-expand-lg .offcanvas 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!important;transform:none !important;transition:none}.navbar-expand-xl .offcanvas .offcanvas-header{display:none}.navbar-expand-xl .offcanvas .offcanvas-body{display:flex;display:-webkit-flex;flex-grow:0;-webkit-flex-grow:0;padding:0;overflow-y:visible}}@media (min-width: 1400px){.navbar-expand-xxl{flex-wrap:nowrap;-webkit-flex-wrap:nowrap;justify-content:flex-start;-webkit-justify-content:flex-start}.navbar-expand-xxl .navbar-nav{flex-direction:row;-webkit-flex-direction:row}.navbar-expand-xxl .navbar-nav .dropdown-menu{position:absolute}.navbar-expand-xxl .navbar-nav .nav-link{padding-right:var(--bs-navbar-nav-link-padding-x);padding-left:var(--bs-navbar-nav-link-padding-x)}.navbar-expand-xxl .navbar-nav-scroll{overflow:visible}.navbar-expand-xxl .navbar-collapse{display:flex !important;display:-webkit-flex !important;flex-basis:auto;-webkit-flex-basis:auto}.navbar-expand-xxl .navbar-toggler{display:none}.navbar-expand-xxl .offcanvas{position:static;z-index:auto;flex-grow:1;-webkit-flex-grow:1;width:auto !important;height:auto !important;visibility:visible !important;background-color:transparent !important;border:0 !important;transform:none !important;transition:none}.navbar-expand-xxl .offcanvas .offcanvas-header{display:none}.navbar-expand-xxl .offcanvas .offcanvas-body{display:flex;display:-webkit-flex;flex-grow:0;-webkit-flex-grow:0;padding:0;overflow-y:visible}}.navbar-expand{flex-wrap:nowrap;-webkit-flex-wrap:nowrap;justify-content:flex-start;-webkit-justify-content:flex-start}.navbar-expand .navbar-nav{flex-direction:row;-webkit-flex-direction:row}.navbar-expand .navbar-nav .dropdown-menu{position:absolute}.navbar-expand .navbar-nav .nav-link{padding-right:var(--bs-navbar-nav-link-padding-x);padding-left:var(--bs-navbar-nav-link-padding-x)}.navbar-expand .navbar-nav-scroll{overflow:visible}.navbar-expand .navbar-collapse{display:flex !important;display:-webkit-flex 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;--bs-card-inner-border-radius: calc(var(--bs-border-radius) - (var(--bs-border-width)));--bs-card-cap-padding-y: .5rem;--bs-card-cap-padding-x: 1rem;--bs-card-cap-bg: rgba(var(--bs-body-color-rgb), 0.03);--bs-card-cap-color: ;--bs-card-height: ;--bs-card-color: ;--bs-card-bg: var(--bs-body-bg);--bs-card-img-overlay-padding: 1rem;--bs-card-group-margin: .75rem;position:relative;display:flex;display:-webkit-flex;flex-direction:column;-webkit-flex-direction:column;min-width:0;height:var(--bs-card-height);color:var(--bs-body-color);word-wrap:break-word;background-color:var(--bs-card-bg);background-clip:border-box;border:var(--bs-card-border-width) solid 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url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%23052c65'%3e%3cpath fill-rule='evenodd' d='M1.646 4.646a.5.5 0 0 1 .708 0L8 10.293l5.646-5.647a.5.5 0 0 1 .708.708l-6 6a.5.5 0 0 1-.708 0l-6-6a.5.5 0 0 1 0-.708z'/%3e%3c/svg%3e");--bs-accordion-btn-focus-border-color: #86b7fe;--bs-accordion-btn-focus-box-shadow: 0 0 0 .25rem rgba(13,110,253,0.25);--bs-accordion-body-padding-x: 1.25rem;--bs-accordion-body-padding-y: 1rem;--bs-accordion-active-color: var(--bs-primary-text-emphasis);--bs-accordion-active-bg: var(--bs-primary-bg-subtle)}.accordion-button{position:relative;display:flex;display:-webkit-flex;align-items:center;-webkit-align-items:center;width:100%;padding:var(--bs-accordion-btn-padding-y) var(--bs-accordion-btn-padding-x);font-size:1rem;color:var(--bs-accordion-btn-color);text-align:left;background-color:var(--bs-accordion-btn-bg);border:0;border-radius:0;overflow-anchor:none;transition:var(--bs-accordion-transition)}@media (prefers-reduced-motion: reduce){.accordion-button{transition:none}}.accordion-button:not(.collapsed){color:var(--bs-accordion-active-color);background-color:var(--bs-accordion-active-bg);box-shadow:inset 0 calc(-1 * var(--bs-accordion-border-width)) 0 var(--bs-accordion-border-color)}.accordion-button:not(.collapsed)::after{background-image:var(--bs-accordion-btn-active-icon);transform:var(--bs-accordion-btn-icon-transform)}.accordion-button::after{flex-shrink:0;-webkit-flex-shrink:0;width:var(--bs-accordion-btn-icon-width);height:var(--bs-accordion-btn-icon-width);margin-left:auto;content:"";background-image:var(--bs-accordion-btn-icon);background-repeat:no-repeat;background-size:var(--bs-accordion-btn-icon-width);transition:var(--bs-accordion-btn-icon-transition)}@media (prefers-reduced-motion: reduce){.accordion-button::after{transition:none}}.accordion-button:hover{z-index:2}.accordion-button:focus{z-index:3;border-color:var(--bs-accordion-btn-focus-border-color);outline:0;box-shadow:var(--bs-accordion-btn-focus-box-shadow)}.accordion-header{margin-bottom:0}.accordion-item{color:var(--bs-accordion-color);background-color:var(--bs-accordion-bg);border:var(--bs-accordion-border-width) solid var(--bs-accordion-border-color)}.accordion-item:first-of-type{border-top-left-radius:var(--bs-accordion-border-radius);border-top-right-radius:var(--bs-accordion-border-radius)}.accordion-item:first-of-type .accordion-button{border-top-left-radius:var(--bs-accordion-inner-border-radius);border-top-right-radius:var(--bs-accordion-inner-border-radius)}.accordion-item:not(:first-of-type){border-top:0}.accordion-item:last-of-type{border-bottom-right-radius:var(--bs-accordion-border-radius);border-bottom-left-radius:var(--bs-accordion-border-radius)}.accordion-item:last-of-type .accordion-button.collapsed{border-bottom-right-radius:var(--bs-accordion-inner-border-radius);border-bottom-left-radius:var(--bs-accordion-inner-border-radius)}.accordion-item:last-of-type .accordion-collapse{border-bottom-right-radius:var(--bs-accordion-border-radius);border-bottom-left-radius:var(--bs-accordion-border-radius)}.accordion-body{padding:var(--bs-accordion-body-padding-y) var(--bs-accordion-body-padding-x)}.accordion-flush .accordion-collapse{border-width:0}.accordion-flush .accordion-item{border-right:0;border-left:0;border-radius:0}.accordion-flush .accordion-item:first-child{border-top:0}.accordion-flush .accordion-item:last-child{border-bottom:0}.accordion-flush .accordion-item .accordion-button,.accordion-flush .accordion-item .accordion-button.collapsed{border-radius:0}[data-bs-theme="dark"] .accordion-button::after{--bs-accordion-btn-icon: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%236ea8fe'%3e%3cpath fill-rule='evenodd' d='M1.646 4.646a.5.5 0 0 1 .708 0L8 10.293l5.646-5.647a.5.5 0 0 1 .708.708l-6 6a.5.5 0 0 1-.708 0l-6-6a.5.5 0 0 1 0-.708z'/%3e%3c/svg%3e");--bs-accordion-btn-active-icon: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%236ea8fe'%3e%3cpath fill-rule='evenodd' d='M1.646 4.646a.5.5 0 0 1 .708 0L8 10.293l5.646-5.647a.5.5 0 0 1 .708.708l-6 6a.5.5 0 0 1-.708 0l-6-6a.5.5 0 0 1 0-.708z'/%3e%3c/svg%3e")}.breadcrumb{--bs-breadcrumb-padding-x: 0;--bs-breadcrumb-padding-y: 0;--bs-breadcrumb-margin-bottom: 1rem;--bs-breadcrumb-bg: ;--bs-breadcrumb-border-radius: ;--bs-breadcrumb-divider-color: var(--bs-secondary-color);--bs-breadcrumb-item-padding-x: .5rem;--bs-breadcrumb-item-active-color: var(--bs-secondary-color);display:flex;display:-webkit-flex;flex-wrap:wrap;-webkit-flex-wrap:wrap;padding:var(--bs-breadcrumb-padding-y) var(--bs-breadcrumb-padding-x);margin-bottom:var(--bs-breadcrumb-margin-bottom);font-size:var(--bs-breadcrumb-font-size);list-style:none;background-color:var(--bs-breadcrumb-bg);border-radius:var(--bs-breadcrumb-border-radius)}.breadcrumb-item+.breadcrumb-item{padding-left:var(--bs-breadcrumb-item-padding-x)}.breadcrumb-item+.breadcrumb-item::before{float:left;padding-right:var(--bs-breadcrumb-item-padding-x);color:var(--bs-breadcrumb-divider-color);content:var(--bs-breadcrumb-divider, "/") /* rtl: var(--bs-breadcrumb-divider, "/") */}.breadcrumb-item.active{color:var(--bs-breadcrumb-item-active-color)}.pagination{--bs-pagination-padding-x: .75rem;--bs-pagination-padding-y: .375rem;--bs-pagination-font-size:1rem;--bs-pagination-color: var(--bs-link-color);--bs-pagination-bg: var(--bs-body-bg);--bs-pagination-border-width: var(--bs-border-width);--bs-pagination-border-color: var(--bs-border-color);--bs-pagination-border-radius: var(--bs-border-radius);--bs-pagination-hover-color: var(--bs-link-hover-color);--bs-pagination-hover-bg: var(--bs-tertiary-bg);--bs-pagination-hover-border-color: var(--bs-border-color);--bs-pagination-focus-color: var(--bs-link-hover-color);--bs-pagination-focus-bg: var(--bs-secondary-bg);--bs-pagination-focus-box-shadow: 0 0 0 .25rem rgba(13,110,253,0.25);--bs-pagination-active-color: #fff;--bs-pagination-active-bg: #0d6efd;--bs-pagination-active-border-color: #0d6efd;--bs-pagination-disabled-color: var(--bs-secondary-color);--bs-pagination-disabled-bg: var(--bs-secondary-bg);--bs-pagination-disabled-border-color: var(--bs-border-color);display:flex;display:-webkit-flex;padding-left:0;list-style:none}.page-link{position:relative;display:block;padding:var(--bs-pagination-padding-y) var(--bs-pagination-padding-x);font-size:var(--bs-pagination-font-size);color:var(--bs-pagination-color);text-decoration:none;-webkit-text-decoration:none;-moz-text-decoration:none;-ms-text-decoration:none;-o-text-decoration:none;background-color:var(--bs-pagination-bg);border:var(--bs-pagination-border-width) solid var(--bs-pagination-border-color);transition:color 0.15s ease-in-out,background-color 0.15s ease-in-out,border-color 0.15s ease-in-out,box-shadow 0.15s ease-in-out}@media (prefers-reduced-motion: reduce){.page-link{transition:none}}.page-link:hover{z-index:2;color:var(--bs-pagination-hover-color);background-color:var(--bs-pagination-hover-bg);border-color:var(--bs-pagination-hover-border-color)}.page-link:focus{z-index:3;color:var(--bs-pagination-focus-color);background-color:var(--bs-pagination-focus-bg);outline:0;box-shadow:var(--bs-pagination-focus-box-shadow)}.page-link.active,.active>.page-link{z-index:3;color:var(--bs-pagination-active-color);background-color:var(--bs-pagination-active-bg);border-color:var(--bs-pagination-active-border-color)}.page-link.disabled,.disabled>.page-link{color:var(--bs-pagination-disabled-color);pointer-events:none;background-color:var(--bs-pagination-disabled-bg);border-color:var(--bs-pagination-disabled-border-color)}.page-item:not(:first-child) .page-link{margin-left:calc(var(--bs-border-width) * -1)}.page-item:first-child .page-link{border-top-left-radius:var(--bs-pagination-border-radius);border-bottom-left-radius:var(--bs-pagination-border-radius)}.page-item:last-child .page-link{border-top-right-radius:var(--bs-pagination-border-radius);border-bottom-right-radius:var(--bs-pagination-border-radius)}.pagination-lg{--bs-pagination-padding-x: 1.5rem;--bs-pagination-padding-y: .75rem;--bs-pagination-font-size:1.25rem;--bs-pagination-border-radius: var(--bs-border-radius-lg)}.pagination-sm{--bs-pagination-padding-x: .5rem;--bs-pagination-padding-y: .25rem;--bs-pagination-font-size:.875rem;--bs-pagination-border-radius: var(--bs-border-radius-sm)}.badge{--bs-badge-padding-x: .65em;--bs-badge-padding-y: .35em;--bs-badge-font-size:.75em;--bs-badge-font-weight: 700;--bs-badge-color: #fff;--bs-badge-border-radius: var(--bs-border-radius);display:inline-block;padding:var(--bs-badge-padding-y) var(--bs-badge-padding-x);font-size:var(--bs-badge-font-size);font-weight:var(--bs-badge-font-weight);line-height:1;color:var(--bs-badge-color);text-align:center;white-space:nowrap;vertical-align:baseline;border-radius:var(--bs-badge-border-radius)}.badge:empty{display:none}.btn .badge{position:relative;top:-1px}.alert{--bs-alert-bg: transparent;--bs-alert-padding-x: 1rem;--bs-alert-padding-y: 1rem;--bs-alert-margin-bottom: 1rem;--bs-alert-color: inherit;--bs-alert-border-color: transparent;--bs-alert-border: var(--bs-border-width) solid var(--bs-alert-border-color);--bs-alert-border-radius: var(--bs-border-radius);--bs-alert-link-color: inherit;position:relative;padding:var(--bs-alert-padding-y) var(--bs-alert-padding-x);margin-bottom:var(--bs-alert-margin-bottom);color:var(--bs-alert-color);background-color:var(--bs-alert-bg);border:var(--bs-alert-border);border-radius:var(--bs-alert-border-radius)}.alert-heading{color:inherit}.alert-link{font-weight:700;color:var(--bs-alert-link-color)}.alert-dismissible{padding-right:3rem}.alert-dismissible .btn-close{position:absolute;top:0;right:0;z-index:2;padding:1.25rem 1rem}.alert-default{--bs-alert-color: var(--bs-default-text-emphasis);--bs-alert-bg: var(--bs-default-bg-subtle);--bs-alert-border-color: var(--bs-default-border-subtle);--bs-alert-link-color: var(--bs-default-text-emphasis)}.alert-primary{--bs-alert-color: var(--bs-primary-text-emphasis);--bs-alert-bg: var(--bs-primary-bg-subtle);--bs-alert-border-color: var(--bs-primary-border-subtle);--bs-alert-link-color: var(--bs-primary-text-emphasis)}.alert-secondary{--bs-alert-color: var(--bs-secondary-text-emphasis);--bs-alert-bg: var(--bs-secondary-bg-subtle);--bs-alert-border-color: var(--bs-secondary-border-subtle);--bs-alert-link-color: var(--bs-secondary-text-emphasis)}.alert-success{--bs-alert-color: var(--bs-success-text-emphasis);--bs-alert-bg: var(--bs-success-bg-subtle);--bs-alert-border-color: var(--bs-success-border-subtle);--bs-alert-link-color: var(--bs-success-text-emphasis)}.alert-info{--bs-alert-color: var(--bs-info-text-emphasis);--bs-alert-bg: var(--bs-info-bg-subtle);--bs-alert-border-color: var(--bs-info-border-subtle);--bs-alert-link-color: var(--bs-info-text-emphasis)}.alert-warning{--bs-alert-color: var(--bs-warning-text-emphasis);--bs-alert-bg: var(--bs-warning-bg-subtle);--bs-alert-border-color: var(--bs-warning-border-subtle);--bs-alert-link-color: var(--bs-warning-text-emphasis)}.alert-danger{--bs-alert-color: var(--bs-danger-text-emphasis);--bs-alert-bg: var(--bs-danger-bg-subtle);--bs-alert-border-color: var(--bs-danger-border-subtle);--bs-alert-link-color: var(--bs-danger-text-emphasis)}.alert-light{--bs-alert-color: var(--bs-light-text-emphasis);--bs-alert-bg: var(--bs-light-bg-subtle);--bs-alert-border-color: var(--bs-light-border-subtle);--bs-alert-link-color: var(--bs-light-text-emphasis)}.alert-dark{--bs-alert-color: var(--bs-dark-text-emphasis);--bs-alert-bg: var(--bs-dark-bg-subtle);--bs-alert-border-color: var(--bs-dark-border-subtle);--bs-alert-link-color: var(--bs-dark-text-emphasis)}@keyframes progress-bar-stripes{0%{background-position-x:1rem}}.progress,.progress-stacked{--bs-progress-height: 1rem;--bs-progress-font-size:.75rem;--bs-progress-bg: var(--bs-secondary-bg);--bs-progress-border-radius: var(--bs-border-radius);--bs-progress-box-shadow: var(--bs-box-shadow-inset);--bs-progress-bar-color: #fff;--bs-progress-bar-bg: #0d6efd;--bs-progress-bar-transition: width 0.6s ease;display:flex;display:-webkit-flex;height:var(--bs-progress-height);overflow:hidden;font-size:var(--bs-progress-font-size);background-color:var(--bs-progress-bg);border-radius:var(--bs-progress-border-radius)}.progress-bar{display:flex;display:-webkit-flex;flex-direction:column;-webkit-flex-direction:column;justify-content:center;-webkit-justify-content:center;overflow:hidden;color:var(--bs-progress-bar-color);text-align:center;white-space:nowrap;background-color:var(--bs-progress-bar-bg);transition:var(--bs-progress-bar-transition)}@media (prefers-reduced-motion: reduce){.progress-bar{transition:none}}.progress-bar-striped{background-image:linear-gradient(45deg, rgba(255,255,255,0.15) 25%, transparent 25%, transparent 50%, rgba(255,255,255,0.15) 50%, rgba(255,255,255,0.15) 75%, transparent 75%, transparent);background-size:var(--bs-progress-height) var(--bs-progress-height)}.progress-stacked>.progress{overflow:visible}.progress-stacked>.progress>.progress-bar{width:100%}.progress-bar-animated{animation:1s linear infinite progress-bar-stripes}@media (prefers-reduced-motion: reduce){.progress-bar-animated{animation:none}}.list-group{--bs-list-group-color: var(--bs-body-color);--bs-list-group-bg: var(--bs-body-bg);--bs-list-group-border-color: var(--bs-border-color);--bs-list-group-border-width: var(--bs-border-width);--bs-list-group-border-radius: var(--bs-border-radius);--bs-list-group-item-padding-x: 1rem;--bs-list-group-item-padding-y: .5rem;--bs-list-group-action-color: var(--bs-secondary-color);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-tertiary-bg);--bs-list-group-action-active-color: var(--bs-body-color);--bs-list-group-action-active-bg: var(--bs-secondary-bg);--bs-list-group-disabled-color: var(--bs-secondary-color);--bs-list-group-disabled-bg: var(--bs-body-bg);--bs-list-group-active-color: #fff;--bs-list-group-active-bg: #0d6efd;--bs-list-group-active-border-color: #0d6efd;display:flex;display:-webkit-flex;flex-direction:column;-webkit-flex-direction:column;padding-left:0;margin-bottom:0;border-radius:var(--bs-list-group-border-radius)}.list-group-numbered{list-style-type:none;counter-reset:section}.list-group-numbered>.list-group-item::before{content:counters(section, ".") ". ";counter-increment:section}.list-group-item-action{width:100%;color:var(--bs-list-group-action-color);text-align:inherit}.list-group-item-action:hover,.list-group-item-action:focus{z-index:1;color:var(--bs-list-group-action-hover-color);text-decoration:none;background-color:var(--bs-list-group-action-hover-bg)}.list-group-item-action:active{color:var(--bs-list-group-action-active-color);background-color:var(--bs-list-group-action-active-bg)}.list-group-item{position:relative;display:block;padding:var(--bs-list-group-item-padding-y) var(--bs-list-group-item-padding-x);color:var(--bs-list-group-color);text-decoration:none;-webkit-text-decoration:none;-moz-text-decoration:none;-ms-text-decoration:none;-o-text-decoration:none;background-color:var(--bs-list-group-bg);border:var(--bs-list-group-border-width) solid var(--bs-list-group-border-color)}.list-group-item:first-child{border-top-left-radius:inherit;border-top-right-radius:inherit}.list-group-item:last-child{border-bottom-right-radius:inherit;border-bottom-left-radius:inherit}.list-group-item.disabled,.list-group-item:disabled{color:var(--bs-list-group-disabled-color);pointer-events:none;background-color:var(--bs-list-group-disabled-bg)}.list-group-item.active{z-index:2;color:var(--bs-list-group-active-color);background-color:var(--bs-list-group-active-bg);border-color:var(--bs-list-group-active-border-color)}.list-group-item+.list-group-item{border-top-width:0}.list-group-item+.list-group-item.active{margin-top:calc(-1 * var(--bs-list-group-border-width));border-top-width:var(--bs-list-group-border-width)}.list-group-horizontal{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal>.list-group-item.active{margin-top:0}.list-group-horizontal>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}@media (min-width: 576px){.list-group-horizontal-sm{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-sm>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-sm>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-sm>.list-group-item.active{margin-top:0}.list-group-horizontal-sm>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-sm>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width: 768px){.list-group-horizontal-md{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-md>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-md>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-md>.list-group-item.active{margin-top:0}.list-group-horizontal-md>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-md>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width: 992px){.list-group-horizontal-lg{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-lg>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-lg>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-lg>.list-group-item.active{margin-top:0}.list-group-horizontal-lg>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-lg>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width: 1200px){.list-group-horizontal-xl{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-xl>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-xl>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-xl>.list-group-item.active{margin-top:0}.list-group-horizontal-xl>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-xl>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width: 1400px){.list-group-horizontal-xxl{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-xxl>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-xxl>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-xxl>.list-group-item.active{margin-top:0}.list-group-horizontal-xxl>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-xxl>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}.list-group-flush{border-radius:0}.list-group-flush>.list-group-item{border-width:0 0 var(--bs-list-group-border-width)}.list-group-flush>.list-group-item:last-child{border-bottom-width:0}.list-group-item-default{--bs-list-group-color: var(--bs-default-text-emphasis);--bs-list-group-bg: var(--bs-default-bg-subtle);--bs-list-group-border-color: var(--bs-default-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-default-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-default-border-subtle);--bs-list-group-active-color: var(--bs-default-bg-subtle);--bs-list-group-active-bg: var(--bs-default-text-emphasis);--bs-list-group-active-border-color: var(--bs-default-text-emphasis)}.list-group-item-primary{--bs-list-group-color: var(--bs-primary-text-emphasis);--bs-list-group-bg: var(--bs-primary-bg-subtle);--bs-list-group-border-color: var(--bs-primary-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-primary-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-primary-border-subtle);--bs-list-group-active-color: var(--bs-primary-bg-subtle);--bs-list-group-active-bg: var(--bs-primary-text-emphasis);--bs-list-group-active-border-color: var(--bs-primary-text-emphasis)}.list-group-item-secondary{--bs-list-group-color: var(--bs-secondary-text-emphasis);--bs-list-group-bg: var(--bs-secondary-bg-subtle);--bs-list-group-border-color: var(--bs-secondary-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-secondary-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-secondary-border-subtle);--bs-list-group-active-color: var(--bs-secondary-bg-subtle);--bs-list-group-active-bg: var(--bs-secondary-text-emphasis);--bs-list-group-active-border-color: var(--bs-secondary-text-emphasis)}.list-group-item-success{--bs-list-group-color: var(--bs-success-text-emphasis);--bs-list-group-bg: var(--bs-success-bg-subtle);--bs-list-group-border-color: var(--bs-success-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-success-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-success-border-subtle);--bs-list-group-active-color: var(--bs-success-bg-subtle);--bs-list-group-active-bg: var(--bs-success-text-emphasis);--bs-list-group-active-border-color: var(--bs-success-text-emphasis)}.list-group-item-info{--bs-list-group-color: var(--bs-info-text-emphasis);--bs-list-group-bg: var(--bs-info-bg-subtle);--bs-list-group-border-color: var(--bs-info-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-info-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-info-border-subtle);--bs-list-group-active-color: var(--bs-info-bg-subtle);--bs-list-group-active-bg: var(--bs-info-text-emphasis);--bs-list-group-active-border-color: var(--bs-info-text-emphasis)}.list-group-item-warning{--bs-list-group-color: var(--bs-warning-text-emphasis);--bs-list-group-bg: var(--bs-warning-bg-subtle);--bs-list-group-border-color: var(--bs-warning-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-warning-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-warning-border-subtle);--bs-list-group-active-color: var(--bs-warning-bg-subtle);--bs-list-group-active-bg: var(--bs-warning-text-emphasis);--bs-list-group-active-border-color: var(--bs-warning-text-emphasis)}.list-group-item-danger{--bs-list-group-color: var(--bs-danger-text-emphasis);--bs-list-group-bg: var(--bs-danger-bg-subtle);--bs-list-group-border-color: var(--bs-danger-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-danger-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-danger-border-subtle);--bs-list-group-active-color: var(--bs-danger-bg-subtle);--bs-list-group-active-bg: var(--bs-danger-text-emphasis);--bs-list-group-active-border-color: var(--bs-danger-text-emphasis)}.list-group-item-light{--bs-list-group-color: var(--bs-light-text-emphasis);--bs-list-group-bg: var(--bs-light-bg-subtle);--bs-list-group-border-color: var(--bs-light-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-light-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-light-border-subtle);--bs-list-group-active-color: var(--bs-light-bg-subtle);--bs-list-group-active-bg: var(--bs-light-text-emphasis);--bs-list-group-active-border-color: var(--bs-light-text-emphasis)}.list-group-item-dark{--bs-list-group-color: var(--bs-dark-text-emphasis);--bs-list-group-bg: var(--bs-dark-bg-subtle);--bs-list-group-border-color: var(--bs-dark-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-dark-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-dark-border-subtle);--bs-list-group-active-color: var(--bs-dark-bg-subtle);--bs-list-group-active-bg: var(--bs-dark-text-emphasis);--bs-list-group-active-border-color: var(--bs-dark-text-emphasis)}.btn-close{--bs-btn-close-color: #000;--bs-btn-close-bg: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%23000'%3e%3cpath d='M.293.293a1 1 0 0 1 1.414 0L8 6.586 14.293.293a1 1 0 1 1 1.414 1.414L9.414 8l6.293 6.293a1 1 0 0 1-1.414 1.414L8 9.414l-6.293 6.293a1 1 0 0 1-1.414-1.414L6.586 8 .293 1.707a1 1 0 0 1 0-1.414z'/%3e%3c/svg%3e");--bs-btn-close-opacity: .5;--bs-btn-close-hover-opacity: .75;--bs-btn-close-focus-shadow: 0 0 0 .25rem rgba(13,110,253,0.25);--bs-btn-close-focus-opacity: 1;--bs-btn-close-disabled-opacity: .25;--bs-btn-close-white-filter: invert(1) grayscale(100%) brightness(200%);box-sizing:content-box;width:1em;height:1em;padding:.25em .25em;color:var(--bs-btn-close-color);background:transparent var(--bs-btn-close-bg) center/1em auto no-repeat;border:0;border-radius:.375rem;opacity:var(--bs-btn-close-opacity)}.btn-close:hover{color:var(--bs-btn-close-color);text-decoration:none;opacity:var(--bs-btn-close-hover-opacity)}.btn-close:focus{outline:0;box-shadow:var(--bs-btn-close-focus-shadow);opacity:var(--bs-btn-close-focus-opacity)}.btn-close:disabled,.btn-close.disabled{pointer-events:none;user-select:none;-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;opacity:var(--bs-btn-close-disabled-opacity)}.btn-close-white{filter:var(--bs-btn-close-white-filter)}[data-bs-theme="dark"] .btn-close{filter:var(--bs-btn-close-white-filter)}.toast{--bs-toast-zindex: 1090;--bs-toast-padding-x: .75rem;--bs-toast-padding-y: .5rem;--bs-toast-spacing: 1.5rem;--bs-toast-max-width: 350px;--bs-toast-font-size:.875rem;--bs-toast-color: ;--bs-toast-bg: rgba(var(--bs-body-bg-rgb), 0.85);--bs-toast-border-width: var(--bs-border-width);--bs-toast-border-color: var(--bs-border-color-translucent);--bs-toast-border-radius: var(--bs-border-radius);--bs-toast-box-shadow: var(--bs-box-shadow);--bs-toast-header-color: var(--bs-secondary-color);--bs-toast-header-bg: rgba(var(--bs-body-bg-rgb), 0.85);--bs-toast-header-border-color: var(--bs-border-color-translucent);width:var(--bs-toast-max-width);max-width:100%;font-size:var(--bs-toast-font-size);color:var(--bs-toast-color);pointer-events:auto;background-color:var(--bs-toast-bg);background-clip:padding-box;border:var(--bs-toast-border-width) solid var(--bs-toast-border-color);box-shadow:var(--bs-toast-box-shadow);border-radius:var(--bs-toast-border-radius)}.toast.showing{opacity:0}.toast:not(.show){display:none}.toast-container{--bs-toast-zindex: 1090;position:absolute;z-index:var(--bs-toast-zindex);width:max-content;width:-webkit-max-content;width:-moz-max-content;width:-ms-max-content;width:-o-max-content;max-width:100%;pointer-events:none}.toast-container>:not(:last-child){margin-bottom:var(--bs-toast-spacing)}.toast-header{display:flex;display:-webkit-flex;align-items:center;-webkit-align-items:center;padding:var(--bs-toast-padding-y) var(--bs-toast-padding-x);color:var(--bs-toast-header-color);background-color:var(--bs-toast-header-bg);background-clip:padding-box;border-bottom:var(--bs-toast-border-width) solid var(--bs-toast-header-border-color);border-top-left-radius:calc(var(--bs-toast-border-radius) - var(--bs-toast-border-width));border-top-right-radius:calc(var(--bs-toast-border-radius) - var(--bs-toast-border-width))}.toast-header .btn-close{margin-right:calc(-.5 * var(--bs-toast-padding-x));margin-left:var(--bs-toast-padding-x)}.toast-body{padding:var(--bs-toast-padding-x);word-wrap:break-word}.modal{--bs-modal-zindex: 1055;--bs-modal-width: 500px;--bs-modal-padding: 1rem;--bs-modal-margin: .5rem;--bs-modal-color: ;--bs-modal-bg: var(--bs-body-bg);--bs-modal-border-color: var(--bs-border-color-translucent);--bs-modal-border-width: var(--bs-border-width);--bs-modal-border-radius: var(--bs-border-radius-lg);--bs-modal-box-shadow: 0 0.125rem 0.25rem rgba(0,0,0,0.075);--bs-modal-inner-border-radius: calc(var(--bs-border-radius-lg) - (var(--bs-border-width)));--bs-modal-header-padding-x: 1rem;--bs-modal-header-padding-y: 1rem;--bs-modal-header-padding: 1rem 1rem;--bs-modal-header-border-color: var(--bs-border-color);--bs-modal-header-border-width: var(--bs-border-width);--bs-modal-title-line-height: 1.5;--bs-modal-footer-gap: .5rem;--bs-modal-footer-bg: ;--bs-modal-footer-border-color: var(--bs-border-color);--bs-modal-footer-border-width: var(--bs-border-width);position:fixed;top:0;left:0;z-index:var(--bs-modal-zindex);display:none;width:100%;height:100%;overflow-x:hidden;overflow-y:auto;outline:0}.modal-dialog{position:relative;width:auto;margin:var(--bs-modal-margin);pointer-events:none}.modal.fade .modal-dialog{transition:transform 0.3s ease-out;transform:translate(0, -50px)}@media (prefers-reduced-motion: reduce){.modal.fade .modal-dialog{transition:none}}.modal.show .modal-dialog{transform:none}.modal.modal-static .modal-dialog{transform:scale(1.02)}.modal-dialog-scrollable{height:calc(100% - var(--bs-modal-margin) * 2)}.modal-dialog-scrollable .modal-content{max-height:100%;overflow:hidden}.modal-dialog-scrollable .modal-body{overflow-y:auto}.modal-dialog-centered{display:flex;display:-webkit-flex;align-items:center;-webkit-align-items:center;min-height:calc(100% - var(--bs-modal-margin) * 2)}.modal-content{position:relative;display:flex;display:-webkit-flex;flex-direction:column;-webkit-flex-direction:column;width:100%;color:var(--bs-modal-color);pointer-events:auto;background-color:var(--bs-modal-bg);background-clip:padding-box;border:var(--bs-modal-border-width) solid var(--bs-modal-border-color);border-radius:var(--bs-modal-border-radius);outline:0}.modal-backdrop{--bs-backdrop-zindex: 1050;--bs-backdrop-bg: #000;--bs-backdrop-opacity: .5;position:fixed;top:0;left:0;z-index:var(--bs-backdrop-zindex);width:100vw;height:100vh;background-color:var(--bs-backdrop-bg)}.modal-backdrop.fade{opacity:0}.modal-backdrop.show{opacity:var(--bs-backdrop-opacity)}.modal-header{display:flex;display:-webkit-flex;flex-shrink:0;-webkit-flex-shrink:0;align-items:center;-webkit-align-items:center;justify-content:space-between;-webkit-justify-content:space-between;padding:var(--bs-modal-header-padding);border-bottom:var(--bs-modal-header-border-width) solid var(--bs-modal-header-border-color);border-top-left-radius:var(--bs-modal-inner-border-radius);border-top-right-radius:var(--bs-modal-inner-border-radius)}.modal-header .btn-close{padding:calc(var(--bs-modal-header-padding-y) * .5) calc(var(--bs-modal-header-padding-x) * .5);margin:calc(-.5 * var(--bs-modal-header-padding-y)) calc(-.5 * var(--bs-modal-header-padding-x)) calc(-.5 * var(--bs-modal-header-padding-y)) auto}.modal-title{margin-bottom:0;line-height:var(--bs-modal-title-line-height)}.modal-body{position:relative;flex:1 1 auto;-webkit-flex:1 1 auto;padding:var(--bs-modal-padding)}.modal-footer{display:flex;display:-webkit-flex;flex-shrink:0;-webkit-flex-shrink:0;flex-wrap:wrap;-webkit-flex-wrap:wrap;align-items:center;-webkit-align-items:center;justify-content:flex-end;-webkit-justify-content:flex-end;padding:calc(var(--bs-modal-padding) - var(--bs-modal-footer-gap) * .5);background-color:var(--bs-modal-footer-bg);border-top:var(--bs-modal-footer-border-width) solid var(--bs-modal-footer-border-color);border-bottom-right-radius:var(--bs-modal-inner-border-radius);border-bottom-left-radius:var(--bs-modal-inner-border-radius)}.modal-footer>*{margin:calc(var(--bs-modal-footer-gap) * .5)}@media (min-width: 576px){.modal{--bs-modal-margin: 1.75rem;--bs-modal-box-shadow: 0 0.5rem 1rem rgba(0,0,0,0.15)}.modal-dialog{max-width:var(--bs-modal-width);margin-right:auto;margin-left:auto}.modal-sm{--bs-modal-width: 300px}}@media (min-width: 992px){.modal-lg,.modal-xl{--bs-modal-width: 800px}}@media (min-width: 1200px){.modal-xl{--bs-modal-width: 1140px}}.modal-fullscreen{width:100vw;max-width:none;height:100%;margin:0}.modal-fullscreen .modal-content{height:100%;border:0;border-radius:0}.modal-fullscreen .modal-header,.modal-fullscreen .modal-footer{border-radius:0}.modal-fullscreen .modal-body{overflow-y:auto}@media (max-width: 575.98px){.modal-fullscreen-sm-down{width:100vw;max-width:none;height:100%;margin:0}.modal-fullscreen-sm-down .modal-content{height:100%;border:0;border-radius:0}.modal-fullscreen-sm-down .modal-header,.modal-fullscreen-sm-down .modal-footer{border-radius:0}.modal-fullscreen-sm-down .modal-body{overflow-y:auto}}@media (max-width: 767.98px){.modal-fullscreen-md-down{width:100vw;max-width:none;height:100%;margin:0}.modal-fullscreen-md-down .modal-content{height:100%;border:0;border-radius:0}.modal-fullscreen-md-down .modal-header,.modal-fullscreen-md-down .modal-footer{border-radius:0}.modal-fullscreen-md-down .modal-body{overflow-y:auto}}@media (max-width: 991.98px){.modal-fullscreen-lg-down{width:100vw;max-width:none;height:100%;margin:0}.modal-fullscreen-lg-down .modal-content{height:100%;border:0;border-radius:0}.modal-fullscreen-lg-down .modal-header,.modal-fullscreen-lg-down .modal-footer{border-radius:0}.modal-fullscreen-lg-down .modal-body{overflow-y:auto}}@media (max-width: 1199.98px){.modal-fullscreen-xl-down{width:100vw;max-width:none;height:100%;margin:0}.modal-fullscreen-xl-down .modal-content{height:100%;border:0;border-radius:0}.modal-fullscreen-xl-down .modal-header,.modal-fullscreen-xl-down .modal-footer{border-radius:0}.modal-fullscreen-xl-down .modal-body{overflow-y:auto}}@media (max-width: 1399.98px){.modal-fullscreen-xxl-down{width:100vw;max-width:none;height:100%;margin:0}.modal-fullscreen-xxl-down .modal-content{height:100%;border:0;border-radius:0}.modal-fullscreen-xxl-down .modal-header,.modal-fullscreen-xxl-down .modal-footer{border-radius:0}.modal-fullscreen-xxl-down .modal-body{overflow-y:auto}}.tooltip{--bs-tooltip-zindex: 1080;--bs-tooltip-max-width: 200px;--bs-tooltip-padding-x: .5rem;--bs-tooltip-padding-y: .25rem;--bs-tooltip-margin: ;--bs-tooltip-font-size:.875rem;--bs-tooltip-color: var(--bs-body-bg);--bs-tooltip-bg: var(--bs-emphasis-color);--bs-tooltip-border-radius: var(--bs-border-radius);--bs-tooltip-opacity: .9;--bs-tooltip-arrow-width: .8rem;--bs-tooltip-arrow-height: .4rem;z-index:var(--bs-tooltip-zindex);display:block;margin:var(--bs-tooltip-margin);font-family:var(--bs-font-sans-serif);font-style:normal;font-weight:400;line-height:1.5;text-align:left;text-align:start;text-decoration:none;text-shadow:none;text-transform:none;letter-spacing:normal;word-break:normal;white-space:normal;word-spacing:normal;line-break:auto;font-size:var(--bs-tooltip-font-size);word-wrap:break-word;opacity:0}.tooltip.show{opacity:var(--bs-tooltip-opacity)}.tooltip .tooltip-arrow{display:block;width:var(--bs-tooltip-arrow-width);height:var(--bs-tooltip-arrow-height)}.tooltip .tooltip-arrow::before{position:absolute;content:"";border-color:transparent;border-style:solid}.bs-tooltip-top .tooltip-arrow,.bs-tooltip-auto[data-popper-placement^="top"] .tooltip-arrow{bottom:calc(-1 * var(--bs-tooltip-arrow-height))}.bs-tooltip-top .tooltip-arrow::before,.bs-tooltip-auto[data-popper-placement^="top"] .tooltip-arrow::before{top:-1px;border-width:var(--bs-tooltip-arrow-height) calc(var(--bs-tooltip-arrow-width) * .5) 0;border-top-color:var(--bs-tooltip-bg)}.bs-tooltip-end .tooltip-arrow,.bs-tooltip-auto[data-popper-placement^="right"] .tooltip-arrow{left:calc(-1 * var(--bs-tooltip-arrow-height));width:var(--bs-tooltip-arrow-height);height:var(--bs-tooltip-arrow-width)}.bs-tooltip-end .tooltip-arrow::before,.bs-tooltip-auto[data-popper-placement^="right"] .tooltip-arrow::before{right:-1px;border-width:calc(var(--bs-tooltip-arrow-width) * .5) var(--bs-tooltip-arrow-height) calc(var(--bs-tooltip-arrow-width) * .5) 0;border-right-color:var(--bs-tooltip-bg)}.bs-tooltip-bottom .tooltip-arrow,.bs-tooltip-auto[data-popper-placement^="bottom"] .tooltip-arrow{top:calc(-1 * var(--bs-tooltip-arrow-height))}.bs-tooltip-bottom .tooltip-arrow::before,.bs-tooltip-auto[data-popper-placement^="bottom"] .tooltip-arrow::before{bottom:-1px;border-width:0 calc(var(--bs-tooltip-arrow-width) * .5) var(--bs-tooltip-arrow-height);border-bottom-color:var(--bs-tooltip-bg)}.bs-tooltip-start .tooltip-arrow,.bs-tooltip-auto[data-popper-placement^="left"] .tooltip-arrow{right:calc(-1 * var(--bs-tooltip-arrow-height));width:var(--bs-tooltip-arrow-height);height:var(--bs-tooltip-arrow-width)}.bs-tooltip-start .tooltip-arrow::before,.bs-tooltip-auto[data-popper-placement^="left"] .tooltip-arrow::before{left:-1px;border-width:calc(var(--bs-tooltip-arrow-width) * .5) 0 calc(var(--bs-tooltip-arrow-width) * .5) var(--bs-tooltip-arrow-height);border-left-color:var(--bs-tooltip-bg)}.tooltip-inner{max-width:var(--bs-tooltip-max-width);padding:var(--bs-tooltip-padding-y) var(--bs-tooltip-padding-x);color:var(--bs-tooltip-color);text-align:center;background-color:var(--bs-tooltip-bg);border-radius:var(--bs-tooltip-border-radius)}.popover{--bs-popover-zindex: 1070;--bs-popover-max-width: 276px;--bs-popover-font-size:.875rem;--bs-popover-bg: var(--bs-body-bg);--bs-popover-border-width: var(--bs-border-width);--bs-popover-border-color: var(--bs-border-color-translucent);--bs-popover-border-radius: var(--bs-border-radius-lg);--bs-popover-inner-border-radius: calc(var(--bs-border-radius-lg) - var(--bs-border-width));--bs-popover-box-shadow: 0 0.5rem 1rem rgba(0,0,0,0.15);--bs-popover-header-padding-x: 1rem;--bs-popover-header-padding-y: .5rem;--bs-popover-header-font-size:1rem;--bs-popover-header-color: inherit;--bs-popover-header-bg: var(--bs-secondary-bg);--bs-popover-body-padding-x: 1rem;--bs-popover-body-padding-y: 1rem;--bs-popover-body-color: var(--bs-body-color);--bs-popover-arrow-width: 1rem;--bs-popover-arrow-height: .5rem;--bs-popover-arrow-border: 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index 21592b52..693b82d1 100644
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-    model of island biota assembly through speciation, immigration and
-    extinction. See Valente et al. (2015) &lt;doi:10.1111/ele.12461&gt;.">
+<!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="Dynamical Assembly of Islands by Speciation, Immigration and Extinction">
+<meta property="og:description" content="Simulates and computes the (maximum) likelihood of a dynamical model of island biota assembly through speciation, immigration and extinction. See Valente et al. (2015) &lt;doi:10.1111/ele.12461&gt;.">
 <!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -26,7 +22,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="index.html">DAISIE</a>
 
@@ -245,13 +241,11 @@ <h2 data-toc-skip>Developers</h2>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p>
-<p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer>
diff --git a/news/index.html b/news/index.html
index e20b8563..0b0b3433 100644
--- a/news/index.html
+++ b/news/index.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Changelog • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Changelog"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Changelog • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Changelog"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -250,11 +250,11 @@ <h2 class="pkg-version" data-toc-text="2.0" id="daisie-20">DAISIE 2.0<a class="a
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/pkgdown.js b/pkgdown.js
index 5fccd9c0..9bd6621e 100644
--- a/pkgdown.js
+++ b/pkgdown.js
@@ -30,10 +30,10 @@
   /* Clipboard --------------------------*/
 
   function changeTooltipMessage(element, msg) {
-    var tooltipOriginalTitle=element.getAttribute('data-original-title');
-    element.setAttribute('data-original-title', msg);
+    var tooltipOriginalTitle=element.getAttribute('data-bs-original-title');
+    element.setAttribute('data-bs-original-title', msg);
     $(element).tooltip('show');
-    element.setAttribute('data-original-title', tooltipOriginalTitle);
+    element.setAttribute('data-bs-original-title', tooltipOriginalTitle);
   }
 
   if(ClipboardJS.isSupported()) {
@@ -60,7 +60,7 @@
         e.clearSelection();
       });
 
-      clipboard.on('error', function() {
+      clipboard.on('error', function(e) {
         changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy');
       });
 
diff --git a/pkgdown.yml b/pkgdown.yml
index 63b86c4d..1ff2c48d 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -1,12 +1,12 @@
-pandoc: 2.19.2
-pkgdown: 2.0.7
+pandoc: 3.1.11
+pkgdown: 2.0.9
 pkgdown_sha: ~
 articles:
   demo_CSvsIW: demo_CSvsIW.html
   demo_optimize: demo_optimize.html
   demo_sim: demo_sim.html
   stac_key: stac_key.html
-last_built: 2023-10-23T07:18Z
+last_built: 2024-07-01T11:54Z
 urls:
   reference: https://rsetienne.github.io/DAISIE/reference
   article: https://rsetienne.github.io/DAISIE/articles
diff --git a/reference/Bats_GreaterAntilles.html b/reference/Bats_GreaterAntilles.html
index 76167b5a..37e82623 100644
--- a/reference/Bats_GreaterAntilles.html
+++ b/reference/Bats_GreaterAntilles.html
@@ -28,7 +28,7 @@
 that were not sampled for particular clade (only applicable for endemic
 clades) 
 $type1or2 - whether the colonist belongs to type 1 or
-type 2. In this dataset all are equal to 1. "><title>Colonization and branching times of Noctilionoid bats from the Greater Antilles. — Bats_GreaterAntilles • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Colonization and branching times of Noctilionoid bats from the Greater Antilles. — Bats_GreaterAntilles"><meta property="og:description" content="A list containing the colonization and branching times of the noctilionoid
+type 2. In this dataset all are equal to 1. "><title>Colonization and branching times of Noctilionoid bats from the Greater Antilles. — Bats_GreaterAntilles • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Colonization and branching times of Noctilionoid bats from the Greater Antilles. — Bats_GreaterAntilles"><meta property="og:description" content="A list containing the colonization and branching times of the noctilionoid
 bats of the Greater Antilles. Main dataset used in
 Valente, Etienne and Dávalos (2017) Nature Ecology and Evolution. Island age 20 Myr and
 mainland pool size of 100 species.
@@ -64,7 +64,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -159,11 +159,11 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
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     </footer></div>
diff --git a/reference/Biwa_datalist.html b/reference/Biwa_datalist.html
index d32b3c92..ca4f9460 100644
--- a/reference/Biwa_datalist.html
+++ b/reference/Biwa_datalist.html
@@ -30,7 +30,7 @@
 that were not sampled for particular clade (only applicable for endemic
 clades) 
 $type1or2 - whether the colonist belongs to type 1 or
-type 2. In this dataset all are equal to 1. "><title>Colonization and branching times of 68 fish clades. — Biwa_datalist • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Colonization and branching times of 68 fish clades. — Biwa_datalist"><meta property="og:description" content="A list containing the colonization and branching times of the fishes of
+type 2. In this dataset all are equal to 1. "><title>Colonization and branching times of 68 fish clades. — Biwa_datalist • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Colonization and branching times of 68 fish clades. — Biwa_datalist"><meta property="og:description" content="A list containing the colonization and branching times of the fishes of
 Lake Biwa (Japan). Main dataset used in Hauffe et al (2020). This list can be generated
 using the DAISIE_dataprep function,
 which converts a user-specified data table into a data object, but the
@@ -68,7 +68,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -165,11 +165,11 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/DAISIE-package.html b/reference/DAISIE-package.html
index bee7edaf..473467f2 100644
--- a/reference/DAISIE-package.html
+++ b/reference/DAISIE-package.html
@@ -3,7 +3,7 @@
 assembly is governed by immigration, extinction and speciation through cladogenesis
 and anagenesis. This likelihood-based statistical package can simulate islands and
 estimate parameters of the DAISIE model based on phylogenetic/phylogeographic data.
-Cladogenesis and immigration rates can be dependent on diversity."><title>DAISIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction — DAISIE-package • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="DAISIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction — DAISIE-package"><meta property="og:description" content="DAISIE is an island biogeography model that assumes island biota
+Cladogenesis and immigration rates can be dependent on diversity."><title>DAISIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction — DAISIE-package • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="DAISIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction — DAISIE-package"><meta property="og:description" content="DAISIE is an island biogeography model that assumes island biota
 assembly is governed by immigration, extinction and speciation through cladogenesis
 and anagenesis. This likelihood-based statistical package can simulate islands and
 estimate parameters of the DAISIE model based on phylogenetic/phylogeographic data.
@@ -14,7 +14,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -130,11 +130,11 @@ <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a><
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/DAISIE_CS_max_steps.html b/reference/DAISIE_CS_max_steps.html
index 2dbeeeeb..277fea08 100644
--- a/reference/DAISIE_CS_max_steps.html
+++ b/reference/DAISIE_CS_max_steps.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Sets or retrieves the max. number of iterations used by the odeint solver."><title>CS iteration control — DAISIE_CS_max_steps • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="CS iteration control — DAISIE_CS_max_steps"><meta property="og:description" content="Sets or retrieves the max. number of iterations used by the odeint solver."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Sets or retrieves the max. number of iterations used by the odeint solver."><title>CS iteration control — DAISIE_CS_max_steps • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="CS iteration control — DAISIE_CS_max_steps"><meta property="og:description" content="Sets or retrieves the max. number of iterations used by the odeint solver."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -81,11 +81,11 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/DAISIE_ExpEIN.html b/reference/DAISIE_ExpEIN.html
index ef18dbe7..00852f8b 100644
--- a/reference/DAISIE_ExpEIN.html
+++ b/reference/DAISIE_ExpEIN.html
@@ -1,7 +1,7 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="This function calculates the expected number of endemics, non-endemics and
 the sum of these for a given set of parameter values, a given mainland
-species pool size and a given time"><title>The expected number of endemics and non-endemics under the DAISIE model — DAISIE_ExpEIN • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="The expected number of endemics and non-endemics under the DAISIE model — DAISIE_ExpEIN"><meta property="og:description" content="This function calculates the expected number of endemics, non-endemics and
+species pool size and a given time"><title>The expected number of endemics and non-endemics under the DAISIE model — DAISIE_ExpEIN • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="The expected number of endemics and non-endemics under the DAISIE model — DAISIE_ExpEIN"><meta property="og:description" content="This function calculates the expected number of endemics, non-endemics and
 the sum of these for a given set of parameter values, a given mainland
 species pool size and a given time"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -10,7 +10,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -160,11 +160,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/DAISIE_IC.html b/reference/DAISIE_IC.html
index 7cee6dab..ac5f9c6a 100644
--- a/reference/DAISIE_IC.html
+++ b/reference/DAISIE_IC.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Calculates information criterion from DAISIE ML estimates?"><title>Calculates information criterion from DAISIE ML estimates? — DAISIE_IC • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Calculates information criterion from DAISIE ML estimates? — DAISIE_IC"><meta property="og:description" content="Calculates information criterion from DAISIE ML estimates?"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Calculates information criterion from DAISIE ML estimates?"><title>Calculates information criterion from DAISIE ML estimates? — DAISIE_IC • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Calculates information criterion from DAISIE ML estimates? — DAISIE_IC"><meta property="og:description" content="Calculates information criterion from DAISIE ML estimates?"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -172,11 +172,11 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
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diff --git a/reference/DAISIE_IW_num_threads.html b/reference/DAISIE_IW_num_threads.html
index 40baa415..85bef7e9 100644
--- a/reference/DAISIE_IW_num_threads.html
+++ b/reference/DAISIE_IW_num_threads.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Sets or retrieves the number of threads used by the odeint solver."><title>IW concurrency control — DAISIE_IW_num_threads • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="IW concurrency control — DAISIE_IW_num_threads"><meta property="og:description" content="Sets or retrieves the number of threads used by the odeint solver."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Sets or retrieves the number of threads used by the odeint solver."><title>IW concurrency control — DAISIE_IW_num_threads • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="IW concurrency control — DAISIE_IW_num_threads"><meta property="og:description" content="Sets or retrieves the number of threads used by the odeint solver."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -89,11 +89,11 @@ <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/DAISIE_ML.html b/reference/DAISIE_ML.html
index d2c2a5f4..6e8a5092 100644
--- a/reference/DAISIE_ML.html
+++ b/reference/DAISIE_ML.html
@@ -10,9 +10,7 @@
 the length of idparsfix. Including the 11th parameter (p_f) in either
 idparsopt or idparsfix (and therefore initparsopt or parsfix) is optional.
 If this parameter is not specified, then the information in the data is
-used, otherwise the information in the data is overruled."><title>Maximization of the loglikelihood under the DAISIE model with clade-specific
-diversity-dependence — DAISIE_ML • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Maximization of the loglikelihood under the DAISIE model with clade-specific
-diversity-dependence — DAISIE_ML"><meta property="og:description" content="This function computes the maximum likelihood estimates of the parameters of
+used, otherwise the information in the data is overruled."><title>Maximization of the loglikelihood under the DAISIE model with clade-specific diversity-dependence — DAISIE_ML • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Maximization of the loglikelihood under the DAISIE model with clade-specific diversity-dependence — DAISIE_ML"><meta property="og:description" content="This function computes the maximum likelihood estimates of the parameters of
 the DAISIE model with clade-specific diversity-dependence for data from
 lineages colonizing an island. It also outputs the corresponding
 loglikelihood that can be used in model comparisons.
@@ -30,7 +28,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -73,8 +71,7 @@
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Maximization of the loglikelihood under the DAISIE model with clade-specific
-diversity-dependence</h1>
+      <img src="" class="logo" alt=""><h1>Maximization of the loglikelihood under the DAISIE model with clade-specific diversity-dependence</h1>
       <small class="dont-index">Source: <a href="https://github.com/rsetienne/DAISIE/blob/HEAD/R/DAISIE_ML_CS.R" class="external-link"><code>R/DAISIE_ML_CS.R</code></a></small>
       <div class="d-none name"><code>DAISIE_ML.Rd</code></div>
     </div>
@@ -628,11 +625,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/DAISIE_ML1.html b/reference/DAISIE_ML1.html
index c8e33236..63989b45 100644
--- a/reference/DAISIE_ML1.html
+++ b/reference/DAISIE_ML1.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Computes MLE for single type species under a clade specific scenario"><title>Computes MLE for single type species under a clade specific scenario — DAISIE_ML1 • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Computes MLE for single type species under a clade specific scenario — DAISIE_ML1"><meta property="og:description" content="Computes MLE for single type species under a clade specific scenario"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Computes MLE for single type species under a clade specific scenario"><title>Computes MLE for single type species under a clade specific scenario — DAISIE_ML1 • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Computes MLE for single type species under a clade specific scenario — DAISIE_ML1"><meta property="og:description" content="Computes MLE for single type species under a clade specific scenario"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -321,11 +321,11 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/DAISIE_ML2.html b/reference/DAISIE_ML2.html
index 0d80f22a..169774e1 100644
--- a/reference/DAISIE_ML2.html
+++ b/reference/DAISIE_ML2.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Computes MLE for multiple islands under a clade specific scenario"><title>Computes MLE for multiple islands under a clade specific scenario — DAISIE_ML2 • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Computes MLE for multiple islands under a clade specific scenario — DAISIE_ML2"><meta property="og:description" content="Computes MLE for multiple islands under a clade specific scenario"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -305,11 +305,11 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/DAISIE_ML4.html b/reference/DAISIE_ML4.html
index 5aaf0939..1786c4d6 100644
--- a/reference/DAISIE_ML4.html
+++ b/reference/DAISIE_ML4.html
@@ -1,8 +1,6 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Computes MLE for single type species under a clade specific scenario where
-one parameter may vary over the clades governed by a specific distribution"><title>Computes MLE for single type species under a clade specific scenario where
-one parameter may vary over the clades governed by a specific distribution — DAISIE_ML4 • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Computes MLE for single type species under a clade specific scenario where
-one parameter may vary over the clades governed by a specific distribution — DAISIE_ML4"><meta property="og:description" content="Computes MLE for single type species under a clade specific scenario where
+one parameter may vary over the clades governed by a specific distribution"><title>Computes MLE for single type species under a clade specific scenario where one parameter may vary over the clades governed by a specific distribution — DAISIE_ML4 • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Computes MLE for single type species under a clade specific scenario where one parameter may vary over the clades governed by a specific distribution — DAISIE_ML4"><meta property="og:description" content="Computes MLE for single type species under a clade specific scenario where
 one parameter may vary over the clades governed by a specific distribution"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -10,7 +8,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -53,8 +51,7 @@
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Computes MLE for single type species under a clade specific scenario where
-one parameter may vary over the clades governed by a specific distribution</h1>
+      <img src="" class="logo" alt=""><h1>Computes MLE for single type species under a clade specific scenario where one parameter may vary over the clades governed by a specific distribution</h1>
       <small class="dont-index">Source: <a href="https://github.com/rsetienne/DAISIE/blob/HEAD/R/DAISIE_ML4.R" class="external-link"><code>R/DAISIE_ML4.R</code></a></small>
       <div class="d-none name"><code>DAISIE_ML4.Rd</code></div>
     </div>
@@ -303,11 +300,11 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/DAISIE_ML_IW.html b/reference/DAISIE_ML_IW.html
index 12fab098..b827dc88 100644
--- a/reference/DAISIE_ML_IW.html
+++ b/reference/DAISIE_ML_IW.html
@@ -2,9 +2,7 @@
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="This function computes the maximum likelihood estimates of the parameters of
 the DAISIE model with island-wide diversity-dependence for data from
 lineages colonizing an island. It also outputs the corresponding
-loglikelihood that can be used in model comparisons."><title>Maximization of the loglikelihood under the DAISIE model with island-wide
-diversity-dependence — DAISIE_ML_IW • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Maximization of the loglikelihood under the DAISIE model with island-wide
-diversity-dependence — DAISIE_ML_IW"><meta property="og:description" content="This function computes the maximum likelihood estimates of the parameters of
+loglikelihood that can be used in model comparisons."><title>Maximization of the loglikelihood under the DAISIE model with island-wide diversity-dependence — DAISIE_ML_IW • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Maximization of the loglikelihood under the DAISIE model with island-wide diversity-dependence — DAISIE_ML_IW"><meta property="og:description" content="This function computes the maximum likelihood estimates of the parameters of
 the DAISIE model with island-wide diversity-dependence for data from
 lineages colonizing an island. It also outputs the corresponding
 loglikelihood that can be used in model comparisons."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
@@ -14,7 +12,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -57,8 +55,7 @@
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Maximization of the loglikelihood under the DAISIE model with island-wide
-diversity-dependence</h1>
+      <img src="" class="logo" alt=""><h1>Maximization of the loglikelihood under the DAISIE model with island-wide diversity-dependence</h1>
       <small class="dont-index">Source: <a href="https://github.com/rsetienne/DAISIE/blob/HEAD/R/DAISIE_ML_IW.R" class="external-link"><code>R/DAISIE_ML_IW.R</code></a></small>
       <div class="d-none name"><code>DAISIE_ML_IW.Rd</code></div>
     </div>
@@ -295,11 +292,11 @@ <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a><
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/DAISIE_MW_ML.html b/reference/DAISIE_MW_ML.html
index c5fe2e05..914aee26 100644
--- a/reference/DAISIE_MW_ML.html
+++ b/reference/DAISIE_MW_ML.html
@@ -10,11 +10,7 @@
 for colonization the relationship is: k - k * (d/d0)^x/(1 + (d/d0)^x). The
 d0 parameter is the 11th parameter entered. In 'sigmoidal_col_ana',
 the 11th parameter is the d0 for colonization and the 12th is the d0 for
-anagenesis."><title>Maximization of the loglikelihood under the DAISIE model with clade-specific
-diversity-dependence and explicit dependencies on island area and isolation
-as hypothesized by MacArthur &amp; Wilson — DAISIE_MW_ML • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Maximization of the loglikelihood under the DAISIE model with clade-specific
-diversity-dependence and explicit dependencies on island area and isolation
-as hypothesized by MacArthur &amp; Wilson — DAISIE_MW_ML"><meta property="og:description" content="This function computes the maximum likelihood estimates of the parameters of
+anagenesis."><title>Maximization of the loglikelihood under the DAISIE model with clade-specific diversity-dependence and explicit dependencies on island area and isolation as hypothesized by MacArthur &amp; Wilson — DAISIE_MW_ML • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Maximization of the loglikelihood under the DAISIE model with clade-specific diversity-dependence and explicit dependencies on island area and isolation as hypothesized by MacArthur &amp; Wilson — DAISIE_MW_ML"><meta property="og:description" content="This function computes the maximum likelihood estimates of the parameters of
 the relationships between parameters of the DAISIE model (with clade-specific
 diversity-dependence) and island area and distance of the island to the
 mainland for data from lineages colonizing several
@@ -32,7 +28,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -75,9 +71,7 @@
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Maximization of the loglikelihood under the DAISIE model with clade-specific
-diversity-dependence and explicit dependencies on island area and isolation
-as hypothesized by MacArthur &amp; Wilson</h1>
+      <img src="" class="logo" alt=""><h1>Maximization of the loglikelihood under the DAISIE model with clade-specific diversity-dependence and explicit dependencies on island area and isolation as hypothesized by MacArthur &amp; Wilson</h1>
       <small class="dont-index">Source: <a href="https://github.com/rsetienne/DAISIE/blob/HEAD/R/DAISIE_MW_ML.R" class="external-link"><code>R/DAISIE_MW_ML.R</code></a></small>
       <div class="d-none name"><code>DAISIE_MW_ML.Rd</code></div>
     </div>
@@ -416,11 +410,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/DAISIE_ONEcolonist.html b/reference/DAISIE_ONEcolonist.html
index ee446dde..5fd4ebff 100644
--- a/reference/DAISIE_ONEcolonist.html
+++ b/reference/DAISIE_ONEcolonist.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Convert intermediate output to final simulation output"><title>Convert intermediate output to final simulation output — DAISIE_ONEcolonist • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Convert intermediate output to final simulation output — DAISIE_ONEcolonist"><meta property="og:description" content="Convert intermediate output to final simulation output"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Convert intermediate output to final simulation output"><title>Convert intermediate output to final simulation output — DAISIE_ONEcolonist • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Convert intermediate output to final simulation output — DAISIE_ONEcolonist"><meta property="og:description" content="Convert intermediate output to final simulation output"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -120,11 +120,11 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/DAISIE_SR_ML.html b/reference/DAISIE_SR_ML.html
index 4f98ce87..e72779d8 100644
--- a/reference/DAISIE_SR_ML.html
+++ b/reference/DAISIE_SR_ML.html
@@ -10,9 +10,7 @@
 the length of idparsfix. Including the 11th parameter (p_f) in either
 idparsopt or idparsfix (and therefore initparsopt or parsfix) is optional.
 If this parameter is not specified, then the information in the data is
-used, otherwise the information in the data is overruled."><title>Maximization of the loglikelihood under the DAISIE model with clade-specific
-diversity-dependence — DAISIE_SR_ML • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Maximization of the loglikelihood under the DAISIE model with clade-specific
-diversity-dependence — DAISIE_SR_ML"><meta property="og:description" content="This function computes the maximum likelihood estimates of the parameters of
+used, otherwise the information in the data is overruled."><title>Maximization of the loglikelihood under the DAISIE model with clade-specific diversity-dependence — DAISIE_SR_ML • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Maximization of the loglikelihood under the DAISIE model with clade-specific diversity-dependence — DAISIE_SR_ML"><meta property="og:description" content="This function computes the maximum likelihood estimates of the parameters of
 the DAISIE model with clade-specific diversity-dependence and a shift in
 parameters for data from lineages colonizing an island. It also outputs the
 corresponding loglikelihood that can be used in model comparisons.
@@ -30,7 +28,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -73,8 +71,7 @@
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Maximization of the loglikelihood under the DAISIE model with clade-specific
-diversity-dependence</h1>
+      <img src="" class="logo" alt=""><h1>Maximization of the loglikelihood under the DAISIE model with clade-specific diversity-dependence</h1>
       <small class="dont-index">Source: <a href="https://github.com/rsetienne/DAISIE/blob/HEAD/R/DAISIE_SR_ML_CS.R" class="external-link"><code>R/DAISIE_SR_ML_CS.R</code></a></small>
       <div class="d-none name"><code>DAISIE_SR_ML.Rd</code></div>
     </div>
@@ -483,11 +480,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/DAISIE_SR_loglik_CS.html b/reference/DAISIE_SR_loglik_CS.html
index 9a998bb6..4f926d45 100644
--- a/reference/DAISIE_SR_loglik_CS.html
+++ b/reference/DAISIE_SR_loglik_CS.html
@@ -1,11 +1,7 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Computes the loglikelihood of the DAISIE model with clade-specific
 diversity-dependence given colonization and branching times for lineages on
-an island, and a set of model parameters that may shift at some time"><title>Computes the loglikelihood of the DAISIE model with clade-specific
-diversity-dependence given data and a set of model parameters that may shift
-at some time — DAISIE_SR_loglik_CS • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Computes the loglikelihood of the DAISIE model with clade-specific
-diversity-dependence given data and a set of model parameters that may shift
-at some time — DAISIE_SR_loglik_CS"><meta property="og:description" content="Computes the loglikelihood of the DAISIE model with clade-specific
+an island, and a set of model parameters that may shift at some time"><title>Computes the loglikelihood of the DAISIE model with clade-specific diversity-dependence given data and a set of model parameters that may shift at some time — DAISIE_SR_loglik_CS • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Computes the loglikelihood of the DAISIE model with clade-specific diversity-dependence given data and a set of model parameters that may shift at some time — DAISIE_SR_loglik_CS"><meta property="og:description" content="Computes the loglikelihood of the DAISIE model with clade-specific
 diversity-dependence given colonization and branching times for lineages on
 an island, and a set of model parameters that may shift at some time"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -14,7 +10,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -57,9 +53,7 @@
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Computes the loglikelihood of the DAISIE model with clade-specific
-diversity-dependence given data and a set of model parameters that may shift
-at some time</h1>
+      <img src="" class="logo" alt=""><h1>Computes the loglikelihood of the DAISIE model with clade-specific diversity-dependence given data and a set of model parameters that may shift at some time</h1>
       <small class="dont-index">Source: <a href="https://github.com/rsetienne/DAISIE/blob/HEAD/R/DAISIE_SR_loglik_CS.R" class="external-link"><code>R/DAISIE_SR_loglik_CS.R</code></a></small>
       <div class="d-none name"><code>DAISIE_SR_loglik_CS.Rd</code></div>
     </div>
@@ -204,11 +198,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/DAISIE_SR_sim_core.html b/reference/DAISIE_SR_sim_core.html
index 42efea37..70c6ee07 100644
--- a/reference/DAISIE_SR_sim_core.html
+++ b/reference/DAISIE_SR_sim_core.html
@@ -1,7 +1,7 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="#' @details This function's use has been deprecated in favour
 of DAISIE_sim_cr_shift(). Please use that
-function instead."><title>DEPRECATED - Algorithm component of DAISIE_SR_sim. — DAISIE_SR_sim_core • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="DEPRECATED - Algorithm component of DAISIE_SR_sim. — DAISIE_SR_sim_core"><meta property="og:description" content="#' @details This function's use has been deprecated in favour
+function instead."><title>DEPRECATED - Algorithm component of DAISIE_SR_sim. — DAISIE_SR_sim_core • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="DEPRECATED - Algorithm component of DAISIE_SR_sim. — DAISIE_SR_sim_core"><meta property="og:description" content="#' @details This function's use has been deprecated in favour
 of DAISIE_sim_cr_shift(). Please use that
 function instead."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -10,7 +10,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -125,11 +125,11 @@ <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a><
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/DAISIE_abm_factor.html b/reference/DAISIE_abm_factor.html
index ead7f869..3c5a6fc7 100644
--- a/reference/DAISIE_abm_factor.html
+++ b/reference/DAISIE_abm_factor.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Sets or retrieves the factor to calculate the step-size used by the odeint::adams_bashforth[_moulton] solvers."><title>Sets or retrieves the factor to calculate the step-size used by the odeint::adams_bashforth[_moulton] solvers. — DAISIE_abm_factor • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Sets or retrieves the factor to calculate the step-size used by the odeint::adams_bashforth[_moulton] solvers. — DAISIE_abm_factor"><meta property="og:description" content="Sets or retrieves the factor to calculate the step-size used by the odeint::adams_bashforth[_moulton] solvers."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Sets or retrieves the factor to calculate the step-size used by the odeint::adams_bashforth[_moulton] solvers."><title>Sets or retrieves the factor to calculate the step-size used by the odeint::adams_bashforth[_moulton] solvers. — DAISIE_abm_factor • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Sets or retrieves the factor to calculate the step-size used by the odeint::adams_bashforth[_moulton] solvers. — DAISIE_abm_factor"><meta property="og:description" content="Sets or retrieves the factor to calculate the step-size used by the odeint::adams_bashforth[_moulton] solvers."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -81,11 +81,11 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
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     </footer></div>
diff --git a/reference/DAISIE_convertprobdist.html b/reference/DAISIE_convertprobdist.html
index 8f0d4848..6201b45f 100644
--- a/reference/DAISIE_convertprobdist.html
+++ b/reference/DAISIE_convertprobdist.html
@@ -1,8 +1,6 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="This function converts the joint distribution of the number of endemics and
-non-endemics from the matrix format of DAISIE_probdist to a list format"><title>Converts the joint distribution of endemics and non-endemics under the
-DAISIE model to list format — DAISIE_convertprobdist • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Converts the joint distribution of endemics and non-endemics under the
-DAISIE model to list format — DAISIE_convertprobdist"><meta property="og:description" content="This function converts the joint distribution of the number of endemics and
+non-endemics from the matrix format of DAISIE_probdist to a list format"><title>Converts the joint distribution of endemics and non-endemics under the DAISIE model to list format — DAISIE_convertprobdist • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Converts the joint distribution of endemics and non-endemics under the DAISIE model to list format — DAISIE_convertprobdist"><meta property="og:description" content="This function converts the joint distribution of the number of endemics and
 non-endemics from the matrix format of DAISIE_probdist to a list format"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -10,7 +8,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -53,8 +51,7 @@
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Converts the joint distribution of endemics and non-endemics under the
-DAISIE model to list format</h1>
+      <img src="" class="logo" alt=""><h1>Converts the joint distribution of endemics and non-endemics under the DAISIE model to list format</h1>
       <small class="dont-index">Source: <a href="https://github.com/rsetienne/DAISIE/blob/HEAD/R/DAISIE_PEI.R" class="external-link"><code>R/DAISIE_PEI.R</code></a></small>
       <div class="d-none name"><code>DAISIE_convertprobdist.Rd</code></div>
     </div>
@@ -120,11 +117,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/DAISIE_count_species.html b/reference/DAISIE_count_species.html
index 7aab8aec..b2da8830 100644
--- a/reference/DAISIE_count_species.html
+++ b/reference/DAISIE_count_species.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Calculates various island diversity metrics from island datasets."><title>Count number of species in DAISIE datalist or simulated data. — DAISIE_count_species • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Count number of species in DAISIE datalist or simulated data. — DAISIE_count_species"><meta property="og:description" content="Calculates various island diversity metrics from island datasets."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Calculates various island diversity metrics from island datasets."><title>Count number of species in DAISIE datalist or simulated data. — DAISIE_count_species • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Count number of species in DAISIE datalist or simulated data. — DAISIE_count_species"><meta property="og:description" content="Calculates various island diversity metrics from island datasets."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -139,11 +139,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
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diff --git a/reference/DAISIE_create_island.html b/reference/DAISIE_create_island.html
index 3822abcd..0aa03d9a 100644
--- a/reference/DAISIE_create_island.html
+++ b/reference/DAISIE_create_island.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Converts simulation output into island output"><title>Converts simulation output into island output — DAISIE_create_island • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Converts simulation output into island output — DAISIE_create_island"><meta property="og:description" content="Converts simulation output into island output"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Converts simulation output into island output"><title>Converts simulation output into island output — DAISIE_create_island • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Converts simulation output into island output — DAISIE_create_island"><meta property="og:description" content="Converts simulation output into island output"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -120,11 +120,11 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
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-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
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diff --git a/reference/DAISIE_dataprep.html b/reference/DAISIE_dataprep.html
index a38a5ccf..abae69b3 100644
--- a/reference/DAISIE_dataprep.html
+++ b/reference/DAISIE_dataprep.html
@@ -2,7 +2,7 @@
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="This function produces a data object that can be run in DAISIE likelihood
 computation/optimization functions. The function converts a user-specified
 table to a DAISIE-compatible format. See Galapagos_datatable.Rdata for a
-template of an input table.)"><title>Prepare colonisation and branching time data to run in DAISIE. — DAISIE_dataprep • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Prepare colonisation and branching time data to run in DAISIE. — DAISIE_dataprep"><meta property="og:description" content="This function produces a data object that can be run in DAISIE likelihood
+template of an input table.)"><title>Prepare colonisation and branching time data to run in DAISIE. — DAISIE_dataprep • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Prepare colonisation and branching time data to run in DAISIE. — DAISIE_dataprep"><meta property="og:description" content="This function produces a data object that can be run in DAISIE likelihood
 computation/optimization functions. The function converts a user-specified
 table to a DAISIE-compatible format. See Galapagos_datatable.Rdata for a
 template of an input table.)"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
@@ -12,7 +12,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -702,11 +702,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
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diff --git a/reference/DAISIE_extract_stt_median.html b/reference/DAISIE_extract_stt_median.html
index 4d3bcedb..13fec67a 100644
--- a/reference/DAISIE_extract_stt_median.html
+++ b/reference/DAISIE_extract_stt_median.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Extract the STT median from the output of DAISIE_sim functions"><title>Extract the STT median from the output of DAISIE_sim functions — DAISIE_extract_stt_median • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Extract the STT median from the output of DAISIE_sim functions — DAISIE_extract_stt_median"><meta property="og:description" content="Extract the STT median from the output of DAISIE_sim functions"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Extract the STT median from the output of DAISIE_sim functions"><title>Extract the STT median from the output of DAISIE_sim functions — DAISIE_extract_stt_median • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Extract the STT median from the output of DAISIE_sim functions — DAISIE_extract_stt_median"><meta property="og:description" content="Extract the STT median from the output of DAISIE_sim functions"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -102,11 +102,11 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/DAISIE_format_CS.html b/reference/DAISIE_format_CS.html
index 3ffeda56..3790d2f9 100644
--- a/reference/DAISIE_format_CS.html
+++ b/reference/DAISIE_format_CS.html
@@ -1,8 +1,6 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Wrapper function around for the DAISIE_format_CS_full_stt and
-DAISIE_format_CS_sampled_stt"><title>Wrapper function around for the DAISIE_format_CS_full_stt and
-DAISIE_format_CS_sampled_stt — DAISIE_format_CS • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Wrapper function around for the DAISIE_format_CS_full_stt and
-DAISIE_format_CS_sampled_stt — DAISIE_format_CS"><meta property="og:description" content="Wrapper function around for the DAISIE_format_CS_full_stt and
+DAISIE_format_CS_sampled_stt"><title>Wrapper function around for the DAISIE_format_CS_full_stt and DAISIE_format_CS_sampled_stt — DAISIE_format_CS • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Wrapper function around for the DAISIE_format_CS_full_stt and DAISIE_format_CS_sampled_stt — DAISIE_format_CS"><meta property="og:description" content="Wrapper function around for the DAISIE_format_CS_full_stt and
 DAISIE_format_CS_sampled_stt"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -10,7 +8,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -53,8 +51,7 @@
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Wrapper function around for the DAISIE_format_CS_full_stt and
-DAISIE_format_CS_sampled_stt</h1>
+      <img src="" class="logo" alt=""><h1>Wrapper function around for the DAISIE_format_CS_full_stt and DAISIE_format_CS_sampled_stt</h1>
       <small class="dont-index">Source: <a href="https://github.com/rsetienne/DAISIE/blob/HEAD/R/DAISIE_format_CS.R" class="external-link"><code>R/DAISIE_format_CS.R</code></a></small>
       <div class="d-none name"><code>DAISIE_format_CS.Rd</code></div>
     </div>
@@ -145,11 +142,11 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/DAISIE_format_CS_full_stt.html b/reference/DAISIE_format_CS_full_stt.html
index 5d358f01..d7ff05e2 100644
--- a/reference/DAISIE_format_CS_full_stt.html
+++ b/reference/DAISIE_format_CS_full_stt.html
@@ -1,8 +1,6 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Formats clade-specific simulation output into standard
-DAISIE list output with complete STT table"><title>Formats clade-specific simulation output into standard
-DAISIE list output with complete STT table — DAISIE_format_CS_full_stt • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Formats clade-specific simulation output into standard
-DAISIE list output with complete STT table — DAISIE_format_CS_full_stt"><meta property="og:description" content="Formats clade-specific simulation output into standard
+DAISIE list output with complete STT table"><title>Formats clade-specific simulation output into standard DAISIE list output with complete STT table — DAISIE_format_CS_full_stt • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Formats clade-specific simulation output into standard DAISIE list output with complete STT table — DAISIE_format_CS_full_stt"><meta property="og:description" content="Formats clade-specific simulation output into standard
 DAISIE list output with complete STT table"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -10,7 +8,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -53,8 +51,7 @@
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Formats clade-specific simulation output into standard
-DAISIE list output with complete STT table</h1>
+      <img src="" class="logo" alt=""><h1>Formats clade-specific simulation output into standard DAISIE list output with complete STT table</h1>
       <small class="dont-index">Source: <a href="https://github.com/rsetienne/DAISIE/blob/HEAD/R/DAISIE_format_CS_full_stt.R" class="external-link"><code>R/DAISIE_format_CS_full_stt.R</code></a></small>
       <div class="d-none name"><code>DAISIE_format_CS_full_stt.Rd</code></div>
     </div>
@@ -138,11 +135,11 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/DAISIE_format_CS_sampled_stt.html b/reference/DAISIE_format_CS_sampled_stt.html
index 6b4aff90..6b8853dc 100644
--- a/reference/DAISIE_format_CS_sampled_stt.html
+++ b/reference/DAISIE_format_CS_sampled_stt.html
@@ -1,8 +1,6 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Formats clade-specific simulation output into standard
-DAISIE list output"><title>Formats clade-specific simulation output into standard
-DAISIE list output — DAISIE_format_CS_sampled_stt • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Formats clade-specific simulation output into standard
-DAISIE list output — DAISIE_format_CS_sampled_stt"><meta property="og:description" content="Formats clade-specific simulation output into standard
+DAISIE list output"><title>Formats clade-specific simulation output into standard DAISIE list output — DAISIE_format_CS_sampled_stt • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Formats clade-specific simulation output into standard DAISIE list output — DAISIE_format_CS_sampled_stt"><meta property="og:description" content="Formats clade-specific simulation output into standard
 DAISIE list output"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -10,7 +8,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -53,8 +51,7 @@
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Formats clade-specific simulation output into standard
-DAISIE list output</h1>
+      <img src="" class="logo" alt=""><h1>Formats clade-specific simulation output into standard DAISIE list output</h1>
       <small class="dont-index">Source: <a href="https://github.com/rsetienne/DAISIE/blob/HEAD/R/DAISIE_format_CS_sampled_stt.R" class="external-link"><code>R/DAISIE_format_CS_sampled_stt.R</code></a></small>
       <div class="d-none name"><code>DAISIE_format_CS_sampled_stt.Rd</code></div>
     </div>
@@ -145,11 +142,11 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/DAISIE_format_GW.html b/reference/DAISIE_format_GW.html
index ef1dcfc7..273398a7 100644
--- a/reference/DAISIE_format_GW.html
+++ b/reference/DAISIE_format_GW.html
@@ -1,8 +1,6 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Formats guild-wide simulation output into standard DAISIE
-list output"><title>Formats guild-wide simulation output into standard DAISIE
-list output — DAISIE_format_GW • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Formats guild-wide simulation output into standard DAISIE
-list output — DAISIE_format_GW"><meta property="og:description" content="Formats guild-wide simulation output into standard DAISIE
+list output"><title>Formats guild-wide simulation output into standard DAISIE list output — DAISIE_format_GW • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Formats guild-wide simulation output into standard DAISIE list output — DAISIE_format_GW"><meta property="og:description" content="Formats guild-wide simulation output into standard DAISIE
 list output"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -10,7 +8,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -53,8 +51,7 @@
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Formats guild-wide simulation output into standard DAISIE
-list output</h1>
+      <img src="" class="logo" alt=""><h1>Formats guild-wide simulation output into standard DAISIE list output</h1>
       <small class="dont-index">Source: <a href="https://github.com/rsetienne/DAISIE/blob/HEAD/R/DAISIE_format_GW.R" class="external-link"><code>R/DAISIE_format_GW.R</code></a></small>
       <div class="d-none name"><code>DAISIE_format_GW.Rd</code></div>
     </div>
@@ -138,11 +135,11 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/DAISIE_format_IW_full_stt.html b/reference/DAISIE_format_IW_full_stt.html
index 0be9b01f..0924b5ef 100644
--- a/reference/DAISIE_format_IW_full_stt.html
+++ b/reference/DAISIE_format_IW_full_stt.html
@@ -1,8 +1,6 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Formats clade-specific simulation output into standard
-DAISIE list output with complete STT table"><title>Formats clade-specific simulation output into standard
-DAISIE list output with complete STT table — DAISIE_format_IW_full_stt • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Formats clade-specific simulation output into standard
-DAISIE list output with complete STT table — DAISIE_format_IW_full_stt"><meta property="og:description" content="Formats clade-specific simulation output into standard
+DAISIE list output with complete STT table"><title>Formats clade-specific simulation output into standard DAISIE list output with complete STT table — DAISIE_format_IW_full_stt • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Formats clade-specific simulation output into standard DAISIE list output with complete STT table — DAISIE_format_IW_full_stt"><meta property="og:description" content="Formats clade-specific simulation output into standard
 DAISIE list output with complete STT table"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -10,7 +8,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -53,8 +51,7 @@
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Formats clade-specific simulation output into standard
-DAISIE list output with complete STT table</h1>
+      <img src="" class="logo" alt=""><h1>Formats clade-specific simulation output into standard DAISIE list output with complete STT table</h1>
       <small class="dont-index">Source: <a href="https://github.com/rsetienne/DAISIE/blob/HEAD/R/DAISIE_format_IW_full_stt.R" class="external-link"><code>R/DAISIE_format_IW_full_stt.R</code></a></small>
       <div class="d-none name"><code>DAISIE_format_IW_full_stt.Rd</code></div>
     </div>
@@ -117,11 +114,11 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/DAISIE_format_IW_sampled_stt.html b/reference/DAISIE_format_IW_sampled_stt.html
index 047c0de2..4a1acd99 100644
--- a/reference/DAISIE_format_IW_sampled_stt.html
+++ b/reference/DAISIE_format_IW_sampled_stt.html
@@ -1,8 +1,6 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Formats island-wide simulation output into standard
-DAISIE list output"><title>Formats island-wide simulation output into standard
-DAISIE list output — DAISIE_format_IW_sampled_stt • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Formats island-wide simulation output into standard
-DAISIE list output — DAISIE_format_IW_sampled_stt"><meta property="og:description" content="Formats island-wide simulation output into standard
+DAISIE list output"><title>Formats island-wide simulation output into standard DAISIE list output — DAISIE_format_IW_sampled_stt • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Formats island-wide simulation output into standard DAISIE list output — DAISIE_format_IW_sampled_stt"><meta property="og:description" content="Formats island-wide simulation output into standard
 DAISIE list output"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -10,7 +8,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -53,8 +51,7 @@
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Formats island-wide simulation output into standard
-DAISIE list output</h1>
+      <img src="" class="logo" alt=""><h1>Formats island-wide simulation output into standard DAISIE list output</h1>
       <small class="dont-index">Source: <a href="https://github.com/rsetienne/DAISIE/blob/HEAD/R/DAISIE_format_IW_sampled_stt.R" class="external-link"><code>R/DAISIE_format_IW_sampled_stt.R</code></a></small>
       <div class="d-none name"><code>DAISIE_format_IW_sampled_stt.Rd</code></div>
     </div>
@@ -129,11 +126,11 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/DAISIE_loglik_CS.html b/reference/DAISIE_loglik_CS.html
index f43a048f..f76ba017 100644
--- a/reference/DAISIE_loglik_CS.html
+++ b/reference/DAISIE_loglik_CS.html
@@ -1,9 +1,7 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Computes the loglikelihood of the DAISIE model with clade-specific
 diversity-dependence given colonization and branching times for lineages on
-an island, and a set of model parameters. The output is a loglikelihood value"><title>Computes the loglikelihood of the DAISIE model with clade-specific
-diversity-dependence given data and a set of model parameters — DAISIE_loglik_CS • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Computes the loglikelihood of the DAISIE model with clade-specific
-diversity-dependence given data and a set of model parameters — DAISIE_loglik_CS"><meta property="og:description" content="Computes the loglikelihood of the DAISIE model with clade-specific
+an island, and a set of model parameters. The output is a loglikelihood value"><title>Computes the loglikelihood of the DAISIE model with clade-specific diversity-dependence given data and a set of model parameters — DAISIE_loglik_CS • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Computes the loglikelihood of the DAISIE model with clade-specific diversity-dependence given data and a set of model parameters — DAISIE_loglik_CS"><meta property="og:description" content="Computes the loglikelihood of the DAISIE model with clade-specific
 diversity-dependence given colonization and branching times for lineages on
 an island, and a set of model parameters. The output is a loglikelihood value"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -12,7 +10,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -55,8 +53,7 @@
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Computes the loglikelihood of the DAISIE model with clade-specific
-diversity-dependence given data and a set of model parameters</h1>
+      <img src="" class="logo" alt=""><h1>Computes the loglikelihood of the DAISIE model with clade-specific diversity-dependence given data and a set of model parameters</h1>
       <small class="dont-index">Source: <a href="https://github.com/rsetienne/DAISIE/blob/HEAD/R/DAISIE_loglik_CS.R" class="external-link"><code>R/DAISIE_loglik_CS.R</code></a></small>
       <div class="d-none name"><code>DAISIE_loglik_CS.Rd</code></div>
     </div>
@@ -202,11 +199,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
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diff --git a/reference/DAISIE_loglik_IW.html b/reference/DAISIE_loglik_IW.html
index ea5a64d1..6985a071 100644
--- a/reference/DAISIE_loglik_IW.html
+++ b/reference/DAISIE_loglik_IW.html
@@ -1,9 +1,7 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Computes the loglikelihood of the DAISIE model given colonization and
 branching times for lineages on an island, and a set of model parameters for
-the DAISIE model with island-wide diversity-dependence"><title>Computes the loglikelihood of the DAISIE model with island-wide
-diversity-dependence given data and a set of model parameters — DAISIE_loglik_IW • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Computes the loglikelihood of the DAISIE model with island-wide
-diversity-dependence given data and a set of model parameters — DAISIE_loglik_IW"><meta property="og:description" content="Computes the loglikelihood of the DAISIE model given colonization and
+the DAISIE model with island-wide diversity-dependence"><title>Computes the loglikelihood of the DAISIE model with island-wide diversity-dependence given data and a set of model parameters — DAISIE_loglik_IW • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Computes the loglikelihood of the DAISIE model with island-wide diversity-dependence given data and a set of model parameters — DAISIE_loglik_IW"><meta property="og:description" content="Computes the loglikelihood of the DAISIE model given colonization and
 branching times for lineages on an island, and a set of model parameters for
 the DAISIE model with island-wide diversity-dependence"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -12,7 +10,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -55,8 +53,7 @@
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Computes the loglikelihood of the DAISIE model with island-wide
-diversity-dependence given data and a set of model parameters</h1>
+      <img src="" class="logo" alt=""><h1>Computes the loglikelihood of the DAISIE model with island-wide diversity-dependence given data and a set of model parameters</h1>
       <small class="dont-index">Source: <a href="https://github.com/rsetienne/DAISIE/blob/HEAD/R/DAISIE_loglik_IW.R" class="external-link"><code>R/DAISIE_loglik_IW.R</code></a></small>
       <div class="d-none name"><code>DAISIE_loglik_IW.Rd</code></div>
     </div>
@@ -185,11 +182,11 @@ <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a><
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/DAISIE_loglik_integrand.html b/reference/DAISIE_loglik_integrand.html
index 5d03ff88..2f5e2164 100644
--- a/reference/DAISIE_loglik_integrand.html
+++ b/reference/DAISIE_loglik_integrand.html
@@ -1,8 +1,6 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Integrand to be integrated to calculate the log likelihood for the relaxed
-rate model."><title>Integrand to be integrated to calculate the log likelihood for the relaxed
-rate model. — DAISIE_loglik_integrand • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Integrand to be integrated to calculate the log likelihood for the relaxed
-rate model. — DAISIE_loglik_integrand"><meta property="og:description" content="Integrand to be integrated to calculate the log likelihood for the relaxed
+rate model."><title>Integrand to be integrated to calculate the log likelihood for the relaxed rate model. — DAISIE_loglik_integrand • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Integrand to be integrated to calculate the log likelihood for the relaxed rate model. — DAISIE_loglik_integrand"><meta property="og:description" content="Integrand to be integrated to calculate the log likelihood for the relaxed
 rate model."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -10,7 +8,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -53,8 +51,7 @@
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Integrand to be integrated to calculate the log likelihood for the relaxed
-rate model.</h1>
+      <img src="" class="logo" alt=""><h1>Integrand to be integrated to calculate the log likelihood for the relaxed rate model.</h1>
       <small class="dont-index">Source: <a href="https://github.com/rsetienne/DAISIE/blob/HEAD/R/DAISIE_loglik_integrate.R" class="external-link"><code>R/DAISIE_loglik_integrate.R</code></a></small>
       <div class="d-none name"><code>DAISIE_loglik_integrand.Rd</code></div>
     </div>
@@ -171,11 +168,11 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/DAISIE_loglik_integrate.html b/reference/DAISIE_loglik_integrate.html
index c7b30f9f..f837fdc1 100644
--- a/reference/DAISIE_loglik_integrate.html
+++ b/reference/DAISIE_loglik_integrate.html
@@ -1,8 +1,6 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Integrates the loglikelihood of a single clade across a parameter weighted
-by a given distribution"><title>Integrates the loglikelihood of a single clade across a parameter weighted
-by a given distribution — DAISIE_loglik_integrate • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Integrates the loglikelihood of a single clade across a parameter weighted
-by a given distribution — DAISIE_loglik_integrate"><meta property="og:description" content="Integrates the loglikelihood of a single clade across a parameter weighted
+by a given distribution"><title>Integrates the loglikelihood of a single clade across a parameter weighted by a given distribution — DAISIE_loglik_integrate • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Integrates the loglikelihood of a single clade across a parameter weighted by a given distribution — DAISIE_loglik_integrate"><meta property="og:description" content="Integrates the loglikelihood of a single clade across a parameter weighted
 by a given distribution"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -10,7 +8,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -53,8 +51,7 @@
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Integrates the loglikelihood of a single clade across a parameter weighted
-by a given distribution</h1>
+      <img src="" class="logo" alt=""><h1>Integrates the loglikelihood of a single clade across a parameter weighted by a given distribution</h1>
       <small class="dont-index">Source: <a href="https://github.com/rsetienne/DAISIE/blob/HEAD/R/DAISIE_loglik_integrate.R" class="external-link"><code>R/DAISIE_loglik_integrate.R</code></a></small>
       <div class="d-none name"><code>DAISIE_loglik_integrate.Rd</code></div>
     </div>
@@ -169,11 +166,11 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/DAISIE_make_archipelago.html b/reference/DAISIE_make_archipelago.html
index 7d05e9df..11fe83a6 100644
--- a/reference/DAISIE_make_archipelago.html
+++ b/reference/DAISIE_make_archipelago.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Does some things"><title>Does some things — DAISIE_make_archipelago • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Does some things — DAISIE_make_archipelago"><meta property="og:description" content="Does some things"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -94,11 +94,11 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
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diff --git a/reference/DAISIE_make_global.html b/reference/DAISIE_make_global.html
index 7500bd50..bb3e8615 100644
--- a/reference/DAISIE_make_global.html
+++ b/reference/DAISIE_make_global.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Does something"><title>Does something — DAISIE_make_global • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Does something — DAISIE_make_global"><meta property="og:description" content="Does something"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Does something"><title>Does something — DAISIE_make_global • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Does something — DAISIE_make_global"><meta property="og:description" content="Does something"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -93,11 +93,11 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/DAISIE_margprobdist.html b/reference/DAISIE_margprobdist.html
index 9ab8fd8a..72102505 100644
--- a/reference/DAISIE_margprobdist.html
+++ b/reference/DAISIE_margprobdist.html
@@ -1,9 +1,7 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="This function calculates the marginal distribution of the number of endemics
 and non-endemics and their sum for a given set of parameter values, a given
-mainland species pool size and a given set of times"><title>The marginal distribution of endemics and non-endemics under the DAISIE
-model — DAISIE_margprobdist • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="The marginal distribution of endemics and non-endemics under the DAISIE
-model — DAISIE_margprobdist"><meta property="og:description" content="This function calculates the marginal distribution of the number of endemics
+mainland species pool size and a given set of times"><title>The marginal distribution of endemics and non-endemics under the DAISIE model — DAISIE_margprobdist • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="The marginal distribution of endemics and non-endemics under the DAISIE model — DAISIE_margprobdist"><meta property="og:description" content="This function calculates the marginal distribution of the number of endemics
 and non-endemics and their sum for a given set of parameter values, a given
 mainland species pool size and a given set of times"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -12,7 +10,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -55,8 +53,7 @@
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>The marginal distribution of endemics and non-endemics under the DAISIE
-model</h1>
+      <img src="" class="logo" alt=""><h1>The marginal distribution of endemics and non-endemics under the DAISIE model</h1>
       <small class="dont-index">Source: <a href="https://github.com/rsetienne/DAISIE/blob/HEAD/R/DAISIE_PEI.R" class="external-link"><code>R/DAISIE_PEI.R</code></a></small>
       <div class="d-none name"><code>DAISIE_margprobdist.Rd</code></div>
     </div>
@@ -165,11 +162,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/DAISIE_numcol.html b/reference/DAISIE_numcol.html
index cdf71c53..e8e3b40e 100644
--- a/reference/DAISIE_numcol.html
+++ b/reference/DAISIE_numcol.html
@@ -1,9 +1,7 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="This function calculates expectation and marginal distribution of the number
 of colonizations (lineages) for a given set of parameter values, a given
-mainland species pool size and a given set of times"><title>The expectation and marginal distribution of the number of colonizations
-(lineages) under the DAISIE model — DAISIE_numcol • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="The expectation and marginal distribution of the number of colonizations
-(lineages) under the DAISIE model — DAISIE_numcol"><meta property="og:description" content="This function calculates expectation and marginal distribution of the number
+mainland species pool size and a given set of times"><title>The expectation and marginal distribution of the number of colonizations (lineages) under the DAISIE model — DAISIE_numcol • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="The expectation and marginal distribution of the number of colonizations (lineages) under the DAISIE model — DAISIE_numcol"><meta property="og:description" content="This function calculates expectation and marginal distribution of the number
 of colonizations (lineages) for a given set of parameter values, a given
 mainland species pool size and a given set of times"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -12,7 +10,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -55,8 +53,7 @@
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>The expectation and marginal distribution of the number of colonizations
-(lineages) under the DAISIE model</h1>
+      <img src="" class="logo" alt=""><h1>The expectation and marginal distribution of the number of colonizations (lineages) under the DAISIE model</h1>
       <small class="dont-index">Source: <a href="https://github.com/rsetienne/DAISIE/blob/HEAD/R/DAISIE_PEI.R" class="external-link"><code>R/DAISIE_PEI.R</code></a></small>
       <div class="d-none name"><code>DAISIE_numcol.Rd</code></div>
     </div>
@@ -145,11 +142,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/DAISIE_plot_age_diversity.html b/reference/DAISIE_plot_age_diversity.html
index 2eec1c69..73747a9a 100644
--- a/reference/DAISIE_plot_age_diversity.html
+++ b/reference/DAISIE_plot_age_diversity.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Plots clade age against clade diversity for all clades for which
-colonisation time is known."><title>Plot clade age against clade diversity. — DAISIE_plot_age_diversity • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Plot clade age against clade diversity. — DAISIE_plot_age_diversity"><meta property="og:description" content="Plots clade age against clade diversity for all clades for which
+colonisation time is known."><title>Plot clade age against clade diversity. — DAISIE_plot_age_diversity • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Plot clade age against clade diversity. — DAISIE_plot_age_diversity"><meta property="og:description" content="Plots clade age against clade diversity for all clades for which
 colonisation time is known."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -8,7 +8,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -139,11 +139,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/DAISIE_plot_area.html b/reference/DAISIE_plot_area.html
index 7eaab395..3b94706b 100644
--- a/reference/DAISIE_plot_area.html
+++ b/reference/DAISIE_plot_area.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Plots island area function through time"><title>Plots island area function through time — DAISIE_plot_area • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Plots island area function through time — DAISIE_plot_area"><meta property="og:description" content="Plots island area function through time"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Plots island area function through time"><title>Plots island area function through time — DAISIE_plot_area • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Plots island area function through time — DAISIE_plot_area"><meta property="og:description" content="Plots island area function through time"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -145,11 +145,11 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/DAISIE_plot_cladogenesis.html b/reference/DAISIE_plot_cladogenesis.html
index 66c0fe8a..c66e1f03 100644
--- a/reference/DAISIE_plot_cladogenesis.html
+++ b/reference/DAISIE_plot_cladogenesis.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Plot cladogenesis rate through time"><title>Plot cladogenesis rate through time — DAISIE_plot_cladogenesis • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Plot cladogenesis rate through time — DAISIE_plot_cladogenesis"><meta property="og:description" content="Plot cladogenesis rate through time"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -164,11 +164,11 @@ <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a><
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
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     </footer></div>
diff --git a/reference/DAISIE_plot_extinction.html b/reference/DAISIE_plot_extinction.html
index 4e080e51..f1f546ae 100644
--- a/reference/DAISIE_plot_extinction.html
+++ b/reference/DAISIE_plot_extinction.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Plots extinction rate function through time"><title>Plots extinction rate function through time — DAISIE_plot_extinction • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Plots extinction rate function through time — DAISIE_plot_extinction"><meta property="og:description" content="Plots extinction rate function through time"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Plots extinction rate function through time"><title>Plots extinction rate function through time — DAISIE_plot_extinction • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Plots extinction rate function through time — DAISIE_plot_extinction"><meta property="og:description" content="Plots extinction rate function through time"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -165,11 +165,11 @@ <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a><
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/DAISIE_plot_immigration.html b/reference/DAISIE_plot_immigration.html
index bbcfd132..c6880c17 100644
--- a/reference/DAISIE_plot_immigration.html
+++ b/reference/DAISIE_plot_immigration.html
@@ -1,12 +1,12 @@
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-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Plot immigration rate through time"><title>Plot immigration rate through time — DAISIE_plot_immigration • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Plot immigration rate through time — DAISIE_plot_immigration"><meta property="og:description" content="Plot immigration rate through time"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -173,11 +173,11 @@ <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a><
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
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-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
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diff --git a/reference/DAISIE_plot_input-1.png b/reference/DAISIE_plot_input-1.png
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diff --git a/reference/DAISIE_plot_input.html b/reference/DAISIE_plot_input.html
index aafd13b5..924dcfdd 100644
--- a/reference/DAISIE_plot_input.html
+++ b/reference/DAISIE_plot_input.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Shows the phylogenies of the multiple clades present on the island"><title>DAISIE tree plot — DAISIE_plot_input • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="DAISIE tree plot — DAISIE_plot_input"><meta property="og:description" content="Shows the phylogenies of the multiple clades present on the island"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Shows the phylogenies of the multiple clades present on the island"><title>DAISIE tree plot — DAISIE_plot_input • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="DAISIE tree plot — DAISIE_plot_input"><meta property="og:description" content="Shows the phylogenies of the multiple clades present on the island"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -161,40 +161,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span> <span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">p</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> Registered S3 methods overwritten by 'treeio':</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>   method              from    </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>   MRCA.phylo          tidytree</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>   MRCA.treedata       tidytree</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>   Nnode.treedata      tidytree</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>   Ntip.treedata       tidytree</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>   ancestor.phylo      tidytree</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>   ancestor.treedata   tidytree</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>   child.phylo         tidytree</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>   child.treedata      tidytree</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>   full_join.phylo     tidytree</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>   full_join.treedata  tidytree</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>   groupClade.phylo    tidytree</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>   groupClade.treedata tidytree</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>   groupOTU.phylo      tidytree</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>   groupOTU.treedata   tidytree</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>   inner_join.phylo    tidytree</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>   inner_join.treedata tidytree</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>   is.rooted.treedata  tidytree</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>   nodeid.phylo        tidytree</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>   nodeid.treedata     tidytree</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>   nodelab.phylo       tidytree</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>   nodelab.treedata    tidytree</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>   offspring.phylo     tidytree</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>   offspring.treedata  tidytree</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>   parent.phylo        tidytree</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>   parent.treedata     tidytree</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>   root.treedata       tidytree</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>   rootnode.phylo      tidytree</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>   sibling.phylo       tidytree</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Scale for <span style="color: #00BB00;">y</span> is already present.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Adding another scale for <span style="color: #00BB00;">y</span>, which will replace the existing scale.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Joining with `by = join_by(label)`</span>
-<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Removed 1 rows containing missing values (`geom_point()`).</span>
+<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Removed 1 row containing missing values or values outside the scale range</span>
+<span class="r-wrn co"><span class="r-pr">#&gt;</span> (`geom_point()`).</span>
 <span class="r-plt img"><img src="DAISIE_plot_input-1.png" alt="" width="700" height="433"></span>
 <span class="r-in"><span></span></span>
 </code></pre></div>
@@ -204,11 +175,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
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diff --git a/reference/DAISIE_plot_island.html b/reference/DAISIE_plot_island.html
index b1bd5d5a..c31ef09b 100644
--- a/reference/DAISIE_plot_island.html
+++ b/reference/DAISIE_plot_island.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Produces an image with the times of colonisation, branching times, clade
-name and clade status for all clades found in a given dataset."><title>Plot colonisation and branching time of species found on an island dataset. — DAISIE_plot_island • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Plot colonisation and branching time of species found on an island dataset. — DAISIE_plot_island"><meta property="og:description" content="Produces an image with the times of colonisation, branching times, clade
+name and clade status for all clades found in a given dataset."><title>Plot colonisation and branching time of species found on an island dataset. — DAISIE_plot_island • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Plot colonisation and branching time of species found on an island dataset. — DAISIE_plot_island"><meta property="og:description" content="Produces an image with the times of colonisation, branching times, clade
 name and clade status for all clades found in a given dataset."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -8,7 +8,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -138,11 +138,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/DAISIE_plot_pc_rates.html b/reference/DAISIE_plot_pc_rates.html
index 4f8cce33..a1ba0ea3 100644
--- a/reference/DAISIE_plot_pc_rates.html
+++ b/reference/DAISIE_plot_pc_rates.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Plot per capita STT and per-capita rate change thourgh simulation"><title>Plot per capita STT and per-capita rate change thourgh simulation — DAISIE_plot_pc_rates • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Plot per capita STT and per-capita rate change thourgh simulation — DAISIE_plot_pc_rates"><meta property="og:description" content="Plot per capita STT and per-capita rate change thourgh simulation"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Plot per capita STT and per-capita rate change thourgh simulation"><title>Plot per capita STT and per-capita rate change thourgh simulation — DAISIE_plot_pc_rates • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Plot per capita STT and per-capita rate change thourgh simulation — DAISIE_plot_pc_rates"><meta property="og:description" content="Plot per capita STT and per-capita rate change thourgh simulation"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -188,11 +188,11 @@ <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a><
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/DAISIE_plot_sims.html b/reference/DAISIE_plot_sims.html
index b1cfb503..16edbca0 100644
--- a/reference/DAISIE_plot_sims.html
+++ b/reference/DAISIE_plot_sims.html
@@ -6,7 +6,7 @@
 R plots with number of total, endemic and non-endemic STTs for different
 types of species for the entire time span the islands were simulated.
 2.5-97.5th percentiles are plotted in light grey, 25-75th percentiles
-plotted in dark grey."><title>Plot island species-through-time (STT) plots — DAISIE_plot_sims • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Plot island species-through-time (STT) plots — DAISIE_plot_sims"><meta property="og:description" content="Produces STT plots. If only one type of species is present in
+plotted in dark grey."><title>Plot island species-through-time (STT) plots — DAISIE_plot_sims • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Plot island species-through-time (STT) plots — DAISIE_plot_sims"><meta property="og:description" content="Produces STT plots. If only one type of species is present in
 the simulated islands, STT is plotted for all species. If two types are
 present, three plots are produced: STT for all, STT for type 1 and STT
 for type 2.
@@ -20,7 +20,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -186,11 +186,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
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     </footer></div>
diff --git a/reference/DAISIE_plot_stt.html b/reference/DAISIE_plot_stt.html
index 18ea49f0..61ab1cd7 100644
--- a/reference/DAISIE_plot_stt.html
+++ b/reference/DAISIE_plot_stt.html
@@ -1,8 +1,6 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Create the Species-Through-Time plot. This is used to visualize
-the output of DAISIE_sim functions"><title>Create the Species-Through-Time plot. This is used to visualize
-the output of DAISIE_sim functions — DAISIE_plot_stt • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Create the Species-Through-Time plot. This is used to visualize
-the output of DAISIE_sim functions — DAISIE_plot_stt"><meta property="og:description" content="Create the Species-Through-Time plot. This is used to visualize
+the output of DAISIE_sim functions"><title>Create the Species-Through-Time plot. This is used to visualize the output of DAISIE_sim functions — DAISIE_plot_stt • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Create the Species-Through-Time plot. This is used to visualize the output of DAISIE_sim functions — DAISIE_plot_stt"><meta property="og:description" content="Create the Species-Through-Time plot. This is used to visualize
 the output of DAISIE_sim functions"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -10,7 +8,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -53,8 +51,7 @@
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Create the Species-Through-Time plot. This is used to visualize
-the output of DAISIE_sim functions</h1>
+      <img src="" class="logo" alt=""><h1>Create the Species-Through-Time plot. This is used to visualize the output of DAISIE_sim functions</h1>
       <small class="dont-index">Source: <a href="https://github.com/rsetienne/DAISIE/blob/HEAD/R/DAISIE_plot_stt.R" class="external-link"><code>R/DAISIE_plot_stt.R</code></a></small>
       <div class="d-none name"><code>DAISIE_plot_stt.Rd</code></div>
     </div>
@@ -106,11 +103,11 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/DAISIE_probdist.html b/reference/DAISIE_probdist.html
index 51c180a4..f6208428 100644
--- a/reference/DAISIE_probdist.html
+++ b/reference/DAISIE_probdist.html
@@ -1,7 +1,7 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="This function calculates the joint distribution of the number of endemics
 and non-endemics for a given set of parameter values, a given mainland
-species pool size and a given set of times"><title>The joint distribution of endemics and non-endemics under the DAISIE model — DAISIE_probdist • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="The joint distribution of endemics and non-endemics under the DAISIE model — DAISIE_probdist"><meta property="og:description" content="This function calculates the joint distribution of the number of endemics
+species pool size and a given set of times"><title>The joint distribution of endemics and non-endemics under the DAISIE model — DAISIE_probdist • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="The joint distribution of endemics and non-endemics under the DAISIE model — DAISIE_probdist"><meta property="og:description" content="This function calculates the joint distribution of the number of endemics
 and non-endemics for a given set of parameter values, a given mainland
 species pool size and a given set of times"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -10,7 +10,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -153,11 +153,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/DAISIE_sample_event_cr.html b/reference/DAISIE_sample_event_cr.html
index d2b5e3aa..b36280e8 100644
--- a/reference/DAISIE_sample_event_cr.html
+++ b/reference/DAISIE_sample_event_cr.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Samples what event to happen next"><title>Samples what event to happen next — DAISIE_sample_event_cr • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Samples what event to happen next — DAISIE_sample_event_cr"><meta property="og:description" content="Samples what event to happen next"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Samples what event to happen next"><title>Samples what event to happen next — DAISIE_sample_event_cr • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Samples what event to happen next — DAISIE_sample_event_cr"><meta property="og:description" content="Samples what event to happen next"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -90,11 +90,11 @@ <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a><
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/DAISIE_sample_event_time_dep.html b/reference/DAISIE_sample_event_time_dep.html
index 3314c865..914a9787 100644
--- a/reference/DAISIE_sample_event_time_dep.html
+++ b/reference/DAISIE_sample_event_time_dep.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Samples what event to happen next"><title>Samples what event to happen next — DAISIE_sample_event_time_dep • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Samples what event to happen next — DAISIE_sample_event_time_dep"><meta property="og:description" content="Samples what event to happen next"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Samples what event to happen next"><title>Samples what event to happen next — DAISIE_sample_event_time_dep • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Samples what event to happen next — DAISIE_sample_event_time_dep"><meta property="og:description" content="Samples what event to happen next"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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 <![endif]--></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -90,11 +90,11 @@ <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a><
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
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     </footer></div>
diff --git a/reference/DAISIE_sample_event_trait_dep.html b/reference/DAISIE_sample_event_trait_dep.html
index 77822319..fbd533e6 100644
--- a/reference/DAISIE_sample_event_trait_dep.html
+++ b/reference/DAISIE_sample_event_trait_dep.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Samples what event to happen next"><title>Samples what event to happen next — DAISIE_sample_event_trait_dep • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Samples what event to happen next — DAISIE_sample_event_trait_dep"><meta property="og:description" content="Samples what event to happen next"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Samples what event to happen next"><title>Samples what event to happen next — DAISIE_sample_event_trait_dep • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Samples what event to happen next — DAISIE_sample_event_trait_dep"><meta property="og:description" content="Samples what event to happen next"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -96,11 +96,11 @@ <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a><
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/DAISIE_sim.html b/reference/DAISIE_sim.html
index 8a873a4b..7e496f68 100644
--- a/reference/DAISIE_sim.html
+++ b/reference/DAISIE_sim.html
@@ -8,9 +8,7 @@
 macro-evolutionary processes operate, one applying to type 1 species and
 other to type 2 species. Further, it allows for the simulation of
 non-oceanic islands, generating islands for which the starting condition
-includes potential endemic and non-endemic species."><title>Simulate (non-)oceanic islands with given parameters under
-  time-constant rates — DAISIE_sim • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Simulate (non-)oceanic islands with given parameters under
-  time-constant rates — DAISIE_sim"><meta property="og:description" content="This function simulates islands with given cladogenesis,
+includes potential endemic and non-endemic species."><title>Simulate (non-)oceanic islands with given parameters under time-constant rates — DAISIE_sim • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Simulate (non-)oceanic islands with given parameters under time-constant rates — DAISIE_sim"><meta property="og:description" content="This function simulates islands with given cladogenesis,
 extinction, Kprime, immigration and anagenesis parameters, all of which
 modelled as time-constant parameters. If a single
 parameter set is provided (5 parameters) it simulates islands where all
@@ -26,7 +24,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -69,8 +67,7 @@
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Simulate (non-)oceanic islands with given parameters under
-  time-constant rates</h1>
+      <img src="" class="logo" alt=""><h1>Simulate (non-)oceanic islands with given parameters under time-constant rates</h1>
       <small class="dont-index">Source: <a href="https://github.com/rsetienne/DAISIE/blob/HEAD/R/DAISIE_sim_cr.R" class="external-link"><code>R/DAISIE_sim_cr.R</code></a></small>
       <div class="d-none name"><code>DAISIE_sim.Rd</code></div>
     </div>
@@ -411,11 +408,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/DAISIE_sim_MW.html b/reference/DAISIE_sim_MW.html
index 419b3c2a..293f7e79 100644
--- a/reference/DAISIE_sim_MW.html
+++ b/reference/DAISIE_sim_MW.html
@@ -7,9 +7,7 @@
 the dependency of rates on island area and isolation. Simulations are then run for each island,
 from island birth until the given island age based on the
 local parameters for each island (using the DAISIE_sim function).
-Returns R list object that contains the simulated islands."><title>Simulate multiple islands based on hyperparameters that describe relationships
-between area, isolation and local parameters — DAISIE_sim_MW • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Simulate multiple islands based on hyperparameters that describe relationships
-between area, isolation and local parameters — DAISIE_sim_MW"><meta property="og:description" content="This function simulates islands of given age, area and isolation.
+Returns R list object that contains the simulated islands."><title>Simulate multiple islands based on hyperparameters that describe relationships between area, isolation and local parameters — DAISIE_sim_MW • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Simulate multiple islands based on hyperparameters that describe relationships between area, isolation and local parameters — DAISIE_sim_MW"><meta property="og:description" content="This function simulates islands of given age, area and isolation.
 A list of islands/archipelagos with this information is provided as a data frame
 object (in the example,
 the archipelago_data from Valente et al 2020 Nature).
@@ -24,7 +22,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -67,8 +65,7 @@
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Simulate multiple islands based on hyperparameters that describe relationships
-between area, isolation and local parameters</h1>
+      <img src="" class="logo" alt=""><h1>Simulate multiple islands based on hyperparameters that describe relationships between area, isolation and local parameters</h1>
       <small class="dont-index">Source: <a href="https://github.com/rsetienne/DAISIE/blob/HEAD/R/DAISIE_sim_MW.R" class="external-link"><code>R/DAISIE_sim_MW.R</code></a></small>
       <div class="d-none name"><code>DAISIE_sim_MW.Rd</code></div>
     </div>
@@ -282,11 +279,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/DAISIE_sim_core_cr.html b/reference/DAISIE_sim_core_cr.html
index 7e9444a3..83f04635 100644
--- a/reference/DAISIE_sim_core_cr.html
+++ b/reference/DAISIE_sim_core_cr.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Internal function of the DAISIE simulation"><title>Internal function of the DAISIE simulation — DAISIE_sim_core_cr • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Internal function of the DAISIE simulation — DAISIE_sim_core_cr"><meta property="og:description" content="Internal function of the DAISIE simulation"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Internal function of the DAISIE simulation"><title>Internal function of the DAISIE simulation — DAISIE_sim_core_cr • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Internal function of the DAISIE simulation — DAISIE_sim_core_cr"><meta property="og:description" content="Internal function of the DAISIE simulation"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -145,11 +145,11 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/DAISIE_sim_core_cr_shift.html b/reference/DAISIE_sim_core_cr_shift.html
index 09bbbc4d..5891d1c4 100644
--- a/reference/DAISIE_sim_core_cr_shift.html
+++ b/reference/DAISIE_sim_core_cr_shift.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Internal function of the DAISIE simulation"><title>Internal function of the DAISIE simulation — DAISIE_sim_core_cr_shift • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Internal function of the DAISIE simulation — DAISIE_sim_core_cr_shift"><meta property="og:description" content="Internal function of the DAISIE simulation"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Internal function of the DAISIE simulation"><title>Internal function of the DAISIE simulation — DAISIE_sim_core_cr_shift • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Internal function of the DAISIE simulation — DAISIE_sim_core_cr_shift"><meta property="og:description" content="Internal function of the DAISIE simulation"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -151,11 +151,11 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/DAISIE_sim_core_time_dep.html b/reference/DAISIE_sim_core_time_dep.html
index dcd65574..1956a9a6 100644
--- a/reference/DAISIE_sim_core_time_dep.html
+++ b/reference/DAISIE_sim_core_time_dep.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Internal function of the DAISIE simulation"><title>Internal function of the DAISIE simulation — DAISIE_sim_core_time_dep • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Internal function of the DAISIE simulation — DAISIE_sim_core_time_dep"><meta property="og:description" content="Internal function of the DAISIE simulation"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -192,11 +192,11 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
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-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
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diff --git a/reference/DAISIE_sim_core_trait_dep.html b/reference/DAISIE_sim_core_trait_dep.html
index 87e5ab86..f3508b0f 100644
--- a/reference/DAISIE_sim_core_trait_dep.html
+++ b/reference/DAISIE_sim_core_trait_dep.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Internal function of the DAISIE simulation"><title>Internal function of the DAISIE simulation — DAISIE_sim_core_trait_dep • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Internal function of the DAISIE simulation — DAISIE_sim_core_trait_dep"><meta property="og:description" content="Internal function of the DAISIE simulation"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Internal function of the DAISIE simulation"><title>Internal function of the DAISIE simulation — DAISIE_sim_core_trait_dep • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Internal function of the DAISIE simulation — DAISIE_sim_core_trait_dep"><meta property="og:description" content="Internal function of the DAISIE simulation"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -180,11 +180,11 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
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-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
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diff --git a/reference/DAISIE_sim_cr_cs.html b/reference/DAISIE_sim_cr_cs.html
index 8c349900..481d128d 100644
--- a/reference/DAISIE_sim_cr_cs.html
+++ b/reference/DAISIE_sim_cr_cs.html
@@ -1,8 +1,6 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Simulates island replicates with an clade-specific (CS) diversity-dependent
-constant-rate process"><title>Simulates island replicates with an clade-specific (CS) diversity-dependent
-constant-rate process — DAISIE_sim_cr_cs • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Simulates island replicates with an clade-specific (CS) diversity-dependent
-constant-rate process — DAISIE_sim_cr_cs"><meta property="og:description" content="Simulates island replicates with an clade-specific (CS) diversity-dependent
+constant-rate process"><title>Simulates island replicates with an clade-specific (CS) diversity-dependent constant-rate process — DAISIE_sim_cr_cs • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Simulates island replicates with an clade-specific (CS) diversity-dependent constant-rate process — DAISIE_sim_cr_cs"><meta property="og:description" content="Simulates island replicates with an clade-specific (CS) diversity-dependent
 constant-rate process"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -10,7 +8,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -53,8 +51,7 @@
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Simulates island replicates with an clade-specific (CS) diversity-dependent
-constant-rate process</h1>
+      <img src="" class="logo" alt=""><h1>Simulates island replicates with an clade-specific (CS) diversity-dependent constant-rate process</h1>
       <small class="dont-index">Source: <a href="https://github.com/rsetienne/DAISIE/blob/HEAD/R/DAISIE_sim_cr_cs.R" class="external-link"><code>R/DAISIE_sim_cr_cs.R</code></a></small>
       <div class="d-none name"><code>DAISIE_sim_cr_cs.Rd</code></div>
     </div>
@@ -212,11 +209,11 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/DAISIE_sim_cr_gw.html b/reference/DAISIE_sim_cr_gw.html
index ed9e8406..d74c7858 100644
--- a/reference/DAISIE_sim_cr_gw.html
+++ b/reference/DAISIE_sim_cr_gw.html
@@ -1,8 +1,6 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Simulates island replicates with an guild-wide (GW) diversity-dependent
-process"><title>Simulates island replicates with an guild-wide (GW) diversity-dependent
-process — DAISIE_sim_cr_gw • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Simulates island replicates with an guild-wide (GW) diversity-dependent
-process — DAISIE_sim_cr_gw"><meta property="og:description" content="Simulates island replicates with an guild-wide (GW) diversity-dependent
+process"><title>Simulates island replicates with an guild-wide (GW) diversity-dependent process — DAISIE_sim_cr_gw • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Simulates island replicates with an guild-wide (GW) diversity-dependent process — DAISIE_sim_cr_gw"><meta property="og:description" content="Simulates island replicates with an guild-wide (GW) diversity-dependent
 process"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -10,7 +8,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -53,8 +51,7 @@
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Simulates island replicates with an guild-wide (GW) diversity-dependent
-process</h1>
+      <img src="" class="logo" alt=""><h1>Simulates island replicates with an guild-wide (GW) diversity-dependent process</h1>
       <small class="dont-index">Source: <a href="https://github.com/rsetienne/DAISIE/blob/HEAD/R/DAISIE_sim_cr_gw.R" class="external-link"><code>R/DAISIE_sim_cr_gw.R</code></a></small>
       <div class="d-none name"><code>DAISIE_sim_cr_gw.Rd</code></div>
     </div>
@@ -186,11 +183,11 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/DAISIE_sim_cr_iw.html b/reference/DAISIE_sim_cr_iw.html
index 05fd6ae7..28874a42 100644
--- a/reference/DAISIE_sim_cr_iw.html
+++ b/reference/DAISIE_sim_cr_iw.html
@@ -1,8 +1,6 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Simulates island replicates with an island-wide (IW) diversity-dependent
-constant-rate process"><title>Simulates island replicates with an island-wide (IW) diversity-dependent
-constant-rate process — DAISIE_sim_cr_iw • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Simulates island replicates with an island-wide (IW) diversity-dependent
-constant-rate process — DAISIE_sim_cr_iw"><meta property="og:description" content="Simulates island replicates with an island-wide (IW) diversity-dependent
+constant-rate process"><title>Simulates island replicates with an island-wide (IW) diversity-dependent constant-rate process — DAISIE_sim_cr_iw • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Simulates island replicates with an island-wide (IW) diversity-dependent constant-rate process — DAISIE_sim_cr_iw"><meta property="og:description" content="Simulates island replicates with an island-wide (IW) diversity-dependent
 constant-rate process"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -10,7 +8,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -53,8 +51,7 @@
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Simulates island replicates with an island-wide (IW) diversity-dependent
-constant-rate process</h1>
+      <img src="" class="logo" alt=""><h1>Simulates island replicates with an island-wide (IW) diversity-dependent constant-rate process</h1>
       <small class="dont-index">Source: <a href="https://github.com/rsetienne/DAISIE/blob/HEAD/R/DAISIE_sim_cr_iw.R" class="external-link"><code>R/DAISIE_sim_cr_iw.R</code></a></small>
       <div class="d-none name"><code>DAISIE_sim_cr_iw.Rd</code></div>
     </div>
@@ -187,11 +184,11 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/DAISIE_sim_cr_shift.html b/reference/DAISIE_sim_cr_shift.html
index a7bf5d6e..3dd8ed86 100644
--- a/reference/DAISIE_sim_cr_shift.html
+++ b/reference/DAISIE_sim_cr_shift.html
@@ -5,9 +5,7 @@
 diversification regime (i.e., different set of parameters) at one or more
 set times before the present. Further, it allows for the simulation of
 non-oceanic islands, generating islands for which the starting condition
-includes potential endemic and non-endemic species."><title>Simulate (non-)oceanic islands with given parameters under a
-  rate-shift regime — DAISIE_sim_cr_shift • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Simulate (non-)oceanic islands with given parameters under a
-  rate-shift regime — DAISIE_sim_cr_shift"><meta property="og:description" content="This function simulates islands with given cladogenesis,
+includes potential endemic and non-endemic species."><title>Simulate (non-)oceanic islands with given parameters under a rate-shift regime — DAISIE_sim_cr_shift • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Simulate (non-)oceanic islands with given parameters under a rate-shift regime — DAISIE_sim_cr_shift"><meta property="og:description" content="This function simulates islands with given cladogenesis,
 extinction, Kprime, immigration and anagenesis parameters, all of which
 modelled as time-constant parameters, which can be switched to a different
 diversification regime (i.e., different set of parameters) at one or more
@@ -20,7 +18,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -63,8 +61,7 @@
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Simulate (non-)oceanic islands with given parameters under a
-  rate-shift regime</h1>
+      <img src="" class="logo" alt=""><h1>Simulate (non-)oceanic islands with given parameters under a rate-shift regime</h1>
       <small class="dont-index">Source: <a href="https://github.com/rsetienne/DAISIE/blob/HEAD/R/DAISIE_sim_cr_shift.R" class="external-link"><code>R/DAISIE_sim_cr_shift.R</code></a></small>
       <div class="d-none name"><code>DAISIE_sim_cr_shift.Rd</code></div>
     </div>
@@ -290,11 +287,11 @@ <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a><
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/DAISIE_sim_min_type2.html b/reference/DAISIE_sim_min_type2.html
index 03911c6b..53b2c916 100644
--- a/reference/DAISIE_sim_min_type2.html
+++ b/reference/DAISIE_sim_min_type2.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Internal function of the DAISIE simulation"><title>Internal function of the DAISIE simulation — DAISIE_sim_min_type2 • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Internal function of the DAISIE simulation — DAISIE_sim_min_type2"><meta property="og:description" content="Internal function of the DAISIE simulation"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Internal function of the DAISIE simulation"><title>Internal function of the DAISIE simulation — DAISIE_sim_min_type2 • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Internal function of the DAISIE simulation — DAISIE_sim_min_type2"><meta property="og:description" content="Internal function of the DAISIE simulation"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -164,11 +164,11 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/DAISIE_sim_relaxed_rate.html b/reference/DAISIE_sim_relaxed_rate.html
index b782766b..9842efea 100644
--- a/reference/DAISIE_sim_relaxed_rate.html
+++ b/reference/DAISIE_sim_relaxed_rate.html
@@ -4,9 +4,7 @@
 can be modelled as time-constant parameters with variation between clades in
 one or multiple parameters. Further, it allows for the simulation of
 non-oceanic islands, generating islands for which the starting condition
-includes potential endemic and non-endemic species."><title>Simulate (non-)oceanic islands with given parameters under a
-  relaxed-rate model — DAISIE_sim_relaxed_rate • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Simulate (non-)oceanic islands with given parameters under a
-  relaxed-rate model — DAISIE_sim_relaxed_rate"><meta property="og:description" content="This function simulates islands with given cladogenesis,
+includes potential endemic and non-endemic species."><title>Simulate (non-)oceanic islands with given parameters under a relaxed-rate model — DAISIE_sim_relaxed_rate • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Simulate (non-)oceanic islands with given parameters under a relaxed-rate model — DAISIE_sim_relaxed_rate"><meta property="og:description" content="This function simulates islands with given cladogenesis,
 extinction, Kprime, immigration and anagenesis parameters, all of which
 can be modelled as time-constant parameters with variation between clades in
 one or multiple parameters. Further, it allows for the simulation of
@@ -18,7 +16,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -61,8 +59,7 @@
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Simulate (non-)oceanic islands with given parameters under a
-  relaxed-rate model</h1>
+      <img src="" class="logo" alt=""><h1>Simulate (non-)oceanic islands with given parameters under a relaxed-rate model</h1>
       <small class="dont-index">Source: <a href="https://github.com/rsetienne/DAISIE/blob/HEAD/R/DAISIE_sim_relaxed_rate.R" class="external-link"><code>R/DAISIE_sim_relaxed_rate.R</code></a></small>
       <div class="d-none name"><code>DAISIE_sim_relaxed_rate.Rd</code></div>
     </div>
@@ -299,11 +296,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/DAISIE_sim_time_dep.html b/reference/DAISIE_sim_time_dep.html
index 3844be12..53f1b087 100644
--- a/reference/DAISIE_sim_time_dep.html
+++ b/reference/DAISIE_sim_time_dep.html
@@ -11,9 +11,7 @@
 simultaneuosly.
 This function also allows for the simulation of
 non-oceanic islands, generating islands for which the starting condition
-includes potential endemic and non-endemic species."><title>Simulate (non-)oceanic islands with given parameters under a
-  time-dependent regime — DAISIE_sim_time_dep • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Simulate (non-)oceanic islands with given parameters under a
-  time-dependent regime — DAISIE_sim_time_dep"><meta property="og:description" content="This function simulates islands with given cladogenesis,
+includes potential endemic and non-endemic species."><title>Simulate (non-)oceanic islands with given parameters under a time-dependent regime — DAISIE_sim_time_dep • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Simulate (non-)oceanic islands with given parameters under a time-dependent regime — DAISIE_sim_time_dep"><meta property="og:description" content="This function simulates islands with given cladogenesis,
 extinction, Kprime, immigration and anagenesis parameters, all of which
 modelled as time-dependent parameters.
 Time dependency aims to capture the
@@ -32,7 +30,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -75,8 +73,7 @@
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Simulate (non-)oceanic islands with given parameters under a
-  time-dependent regime</h1>
+      <img src="" class="logo" alt=""><h1>Simulate (non-)oceanic islands with given parameters under a time-dependent regime</h1>
       <small class="dont-index">Source: <a href="https://github.com/rsetienne/DAISIE/blob/HEAD/R/DAISIE_sim_time_dep.R" class="external-link"><code>R/DAISIE_sim_time_dep.R</code></a></small>
       <div class="d-none name"><code>DAISIE_sim_time_dep.Rd</code></div>
     </div>
@@ -331,11 +328,11 @@ <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a><
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/DAISIE_sim_time_dep_cs.html b/reference/DAISIE_sim_time_dep_cs.html
index b45aaa87..33d6d9ae 100644
--- a/reference/DAISIE_sim_time_dep_cs.html
+++ b/reference/DAISIE_sim_time_dep_cs.html
@@ -1,8 +1,6 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Simulates island replicates with an clade-specific (CS) diversity-dependent
-time-dependent process"><title>Simulates island replicates with an clade-specific (CS) diversity-dependent
-time-dependent process — DAISIE_sim_time_dep_cs • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Simulates island replicates with an clade-specific (CS) diversity-dependent
-time-dependent process — DAISIE_sim_time_dep_cs"><meta property="og:description" content="Simulates island replicates with an clade-specific (CS) diversity-dependent
+time-dependent process"><title>Simulates island replicates with an clade-specific (CS) diversity-dependent time-dependent process — DAISIE_sim_time_dep_cs • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Simulates island replicates with an clade-specific (CS) diversity-dependent time-dependent process — DAISIE_sim_time_dep_cs"><meta property="og:description" content="Simulates island replicates with an clade-specific (CS) diversity-dependent
 time-dependent process"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -10,7 +8,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -53,8 +51,7 @@
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Simulates island replicates with an clade-specific (CS) diversity-dependent
-time-dependent process</h1>
+      <img src="" class="logo" alt=""><h1>Simulates island replicates with an clade-specific (CS) diversity-dependent time-dependent process</h1>
       <small class="dont-index">Source: <a href="https://github.com/rsetienne/DAISIE/blob/HEAD/R/DAISIE_sim_time_dep_cs.R" class="external-link"><code>R/DAISIE_sim_time_dep_cs.R</code></a></small>
       <div class="d-none name"><code>DAISIE_sim_time_dep_cs.Rd</code></div>
     </div>
@@ -234,11 +231,11 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/DAISIE_sim_time_dep_gw.html b/reference/DAISIE_sim_time_dep_gw.html
index 5ef203f6..48abeb0c 100644
--- a/reference/DAISIE_sim_time_dep_gw.html
+++ b/reference/DAISIE_sim_time_dep_gw.html
@@ -1,8 +1,6 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Simulates island replicates with an guild-wide (GW) diversity-dependent
-time-dependent process"><title>Simulates island replicates with an guild-wide (GW) diversity-dependent
-time-dependent process — DAISIE_sim_time_dep_gw • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Simulates island replicates with an guild-wide (GW) diversity-dependent
-time-dependent process — DAISIE_sim_time_dep_gw"><meta property="og:description" content="Simulates island replicates with an guild-wide (GW) diversity-dependent
+time-dependent process"><title>Simulates island replicates with an guild-wide (GW) diversity-dependent time-dependent process — DAISIE_sim_time_dep_gw • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Simulates island replicates with an guild-wide (GW) diversity-dependent time-dependent process — DAISIE_sim_time_dep_gw"><meta property="og:description" content="Simulates island replicates with an guild-wide (GW) diversity-dependent
 time-dependent process"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -10,7 +8,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -53,8 +51,7 @@
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Simulates island replicates with an guild-wide (GW) diversity-dependent
-time-dependent process</h1>
+      <img src="" class="logo" alt=""><h1>Simulates island replicates with an guild-wide (GW) diversity-dependent time-dependent process</h1>
       <small class="dont-index">Source: <a href="https://github.com/rsetienne/DAISIE/blob/HEAD/R/DAISIE_sim_time_dep_gw.R" class="external-link"><code>R/DAISIE_sim_time_dep_gw.R</code></a></small>
       <div class="d-none name"><code>DAISIE_sim_time_dep_gw.Rd</code></div>
     </div>
@@ -233,11 +230,11 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
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     </footer></div>
diff --git a/reference/DAISIE_sim_time_dep_iw.html b/reference/DAISIE_sim_time_dep_iw.html
index a348e852..f24572c4 100644
--- a/reference/DAISIE_sim_time_dep_iw.html
+++ b/reference/DAISIE_sim_time_dep_iw.html
@@ -1,8 +1,6 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Simulates island replicates with an island-wide (IW) diversity-dependent
-time-dependent process"><title>Simulates island replicates with an island-wide (IW) diversity-dependent
-time-dependent process — DAISIE_sim_time_dep_iw • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Simulates island replicates with an island-wide (IW) diversity-dependent
-time-dependent process — DAISIE_sim_time_dep_iw"><meta property="og:description" content="Simulates island replicates with an island-wide (IW) diversity-dependent
+time-dependent process"><title>Simulates island replicates with an island-wide (IW) diversity-dependent time-dependent process — DAISIE_sim_time_dep_iw • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Simulates island replicates with an island-wide (IW) diversity-dependent time-dependent process — DAISIE_sim_time_dep_iw"><meta property="og:description" content="Simulates island replicates with an island-wide (IW) diversity-dependent
 time-dependent process"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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@@ -10,7 +8,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -53,8 +51,7 @@
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Simulates island replicates with an island-wide (IW) diversity-dependent
-time-dependent process</h1>
+      <img src="" class="logo" alt=""><h1>Simulates island replicates with an island-wide (IW) diversity-dependent time-dependent process</h1>
       <small class="dont-index">Source: <a href="https://github.com/rsetienne/DAISIE/blob/HEAD/R/DAISIE_sim_time_dep_iw.R" class="external-link"><code>R/DAISIE_sim_time_dep_iw.R</code></a></small>
       <div class="d-none name"><code>DAISIE_sim_time_dep_iw.Rd</code></div>
     </div>
@@ -234,11 +231,11 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/DAISIE_sim_trait_dep.html b/reference/DAISIE_sim_trait_dep.html
index 756a195b..de357aa6 100644
--- a/reference/DAISIE_sim_trait_dep.html
+++ b/reference/DAISIE_sim_trait_dep.html
@@ -1,7 +1,7 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="This function simulates islands with given cladogenesis,
 extinction, K, immigration and anagenesis parameters for binary states.
-Returns R list object that contains the simulated islands"><title>Simulate islands with given trait-dependent parameters. — DAISIE_sim_trait_dep • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Simulate islands with given trait-dependent parameters. — DAISIE_sim_trait_dep"><meta property="og:description" content="This function simulates islands with given cladogenesis,
+Returns R list object that contains the simulated islands"><title>Simulate islands with given trait-dependent parameters. — DAISIE_sim_trait_dep • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Simulate islands with given trait-dependent parameters. — DAISIE_sim_trait_dep"><meta property="og:description" content="This function simulates islands with given cladogenesis,
 extinction, K, immigration and anagenesis parameters for binary states.
 Returns R list object that contains the simulated islands"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -10,7 +10,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -289,11 +289,11 @@ <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a><
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/DAISIE_sim_trait_dep_2K.html b/reference/DAISIE_sim_trait_dep_2K.html
index ac808783..84b73a95 100644
--- a/reference/DAISIE_sim_trait_dep_2K.html
+++ b/reference/DAISIE_sim_trait_dep_2K.html
@@ -2,7 +2,7 @@
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="This function simulates islands with given cladogenesis,
 extinction, K, immigration and anagenesis parameters. In this version,
 rates and K are both trait-dependent.
-Returns R list object that contains the simulated islands"><title>Simulate islands with given trait-dependent parameters. — DAISIE_sim_trait_dep_2K • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Simulate islands with given trait-dependent parameters. — DAISIE_sim_trait_dep_2K"><meta property="og:description" content="This function simulates islands with given cladogenesis,
+Returns R list object that contains the simulated islands"><title>Simulate islands with given trait-dependent parameters. — DAISIE_sim_trait_dep_2K • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Simulate islands with given trait-dependent parameters. — DAISIE_sim_trait_dep_2K"><meta property="og:description" content="This function simulates islands with given cladogenesis,
 extinction, K, immigration and anagenesis parameters. In this version,
 rates and K are both trait-dependent.
 Returns R list object that contains the simulated islands"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
@@ -12,7 +12,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -292,11 +292,11 @@ <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a><
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/DAISIE_sim_update_state_cr.html b/reference/DAISIE_sim_update_state_cr.html
index 279084c8..127e4be3 100644
--- a/reference/DAISIE_sim_update_state_cr.html
+++ b/reference/DAISIE_sim_update_state_cr.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Makes the event happen by updating island species matrix and species IDs.
-What event happens is determined by the sampling in the algorithm."><title>Updates state of island given sampled event for a constant rate case. — DAISIE_sim_update_state_cr • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Updates state of island given sampled event for a constant rate case. — DAISIE_sim_update_state_cr"><meta property="og:description" content="Makes the event happen by updating island species matrix and species IDs.
+What event happens is determined by the sampling in the algorithm."><title>Updates state of island given sampled event for a constant rate case. — DAISIE_sim_update_state_cr • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Updates state of island given sampled event for a constant rate case. — DAISIE_sim_update_state_cr"><meta property="og:description" content="Makes the event happen by updating island species matrix and species IDs.
 What event happens is determined by the sampling in the algorithm."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -8,7 +8,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -126,11 +126,11 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/DAISIE_sim_update_state_time_dep.html b/reference/DAISIE_sim_update_state_time_dep.html
index 1851e752..c269e76e 100644
--- a/reference/DAISIE_sim_update_state_time_dep.html
+++ b/reference/DAISIE_sim_update_state_time_dep.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Makes the event happen by updating island species matrix and species IDs.
-What event happens is determined by the sampling in the algorithm."><title>Updates state of island given sampled event — DAISIE_sim_update_state_time_dep • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Updates state of island given sampled event — DAISIE_sim_update_state_time_dep"><meta property="og:description" content="Makes the event happen by updating island species matrix and species IDs.
+What event happens is determined by the sampling in the algorithm."><title>Updates state of island given sampled event — DAISIE_sim_update_state_time_dep • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Updates state of island given sampled event — DAISIE_sim_update_state_time_dep"><meta property="og:description" content="Makes the event happen by updating island species matrix and species IDs.
 What event happens is determined by the sampling in the algorithm."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -8,7 +8,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -137,11 +137,11 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/DAISIE_sim_update_state_trait_dep.html b/reference/DAISIE_sim_update_state_trait_dep.html
index 0ee2ab73..44d47e94 100644
--- a/reference/DAISIE_sim_update_state_trait_dep.html
+++ b/reference/DAISIE_sim_update_state_trait_dep.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Makes the event happen by updating island species matrix and species IDs.
-What event happens is determined by the sampling in the algorithm."><title>Updates state of island given sampled event with two trait states. — DAISIE_sim_update_state_trait_dep • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Updates state of island given sampled event with two trait states. — DAISIE_sim_update_state_trait_dep"><meta property="og:description" content="Makes the event happen by updating island species matrix and species IDs.
+What event happens is determined by the sampling in the algorithm."><title>Updates state of island given sampled event with two trait states. — DAISIE_sim_update_state_trait_dep • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Updates state of island given sampled event with two trait states. — DAISIE_sim_update_state_trait_dep"><meta property="og:description" content="Makes the event happen by updating island species matrix and species IDs.
 What event happens is determined by the sampling in the algorithm."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -8,7 +8,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -139,11 +139,11 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/Galapagos_datalist.html b/reference/Galapagos_datalist.html
index cbf36cec..52a357c5 100644
--- a/reference/Galapagos_datalist.html
+++ b/reference/Galapagos_datalist.html
@@ -29,9 +29,7 @@
 that were not sampled for particular clade (only applicable for endemic
 clades) 
 $type1or2 - whether the colonist belongs to type 1 or
-type 2. In this dataset all are equal to 1. "><title>Colonization and branching times of 8 terrestrial avifaunal clades in list
-format, accepted by DAISIE_ML and DAISIE_loglik_all — Galapagos_datalist • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Colonization and branching times of 8 terrestrial avifaunal clades in list
-format, accepted by DAISIE_ML and DAISIE_loglik_all — Galapagos_datalist"><meta property="og:description" content="A list containing the colonization and branching times of the terrestrial
+type 2. In this dataset all are equal to 1. "><title>Colonization and branching times of 8 terrestrial avifaunal clades in list format, accepted by DAISIE_ML and DAISIE_loglik_all — Galapagos_datalist • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Colonization and branching times of 8 terrestrial avifaunal clades in list format, accepted by DAISIE_ML and DAISIE_loglik_all — Galapagos_datalist"><meta property="og:description" content="A list containing the colonization and branching times of the terrestrial
 avifauna in the Galapagos where no distinction is made between types of
 colonists. This list can be generated using the DAISIE_dataprep function,
 which converts a user-specified data table into a data object, but the
@@ -68,7 +66,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -111,8 +109,7 @@
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Colonization and branching times of 8 terrestrial avifaunal clades in list
-format, accepted by DAISIE_ML and DAISIE_loglik_all</h1>
+      <img src="" class="logo" alt=""><h1>Colonization and branching times of 8 terrestrial avifaunal clades in list format, accepted by DAISIE_ML and DAISIE_loglik_all</h1>
       <small class="dont-index">Source: <a href="https://github.com/rsetienne/DAISIE/blob/HEAD/R/DAISIE_data.R" class="external-link"><code>R/DAISIE_data.R</code></a></small>
       <div class="d-none name"><code>Galapagos_datalist.Rd</code></div>
     </div>
@@ -166,11 +163,11 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/Galapagos_datalist_2types.html b/reference/Galapagos_datalist_2types.html
index 4ef01b53..a6ae6ed0 100644
--- a/reference/Galapagos_datalist_2types.html
+++ b/reference/Galapagos_datalist_2types.html
@@ -29,9 +29,7 @@
 that were not sampled for particular clade (only applicable for endemic
 clades) 
 $type1or2 - whether the colonist belongs to type 1 or
-type 2. In this dataset only the finches are type 2 "><title>Colonization and branching times of 8 terrestrial avifaunal clades in list
-format, accepted by DAISIE_ML and DAISIE_loglik_all — Galapagos_datalist_2types • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Colonization and branching times of 8 terrestrial avifaunal clades in list
-format, accepted by DAISIE_ML and DAISIE_loglik_all — Galapagos_datalist_2types"><meta property="og:description" content="A list containing the colonization and branching times of the terrestrial
+type 2. In this dataset only the finches are type 2 "><title>Colonization and branching times of 8 terrestrial avifaunal clades in list format, accepted by DAISIE_ML and DAISIE_loglik_all — Galapagos_datalist_2types • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Colonization and branching times of 8 terrestrial avifaunal clades in list format, accepted by DAISIE_ML and DAISIE_loglik_all — Galapagos_datalist_2types"><meta property="og:description" content="A list containing the colonization and branching times of the terrestrial
 avifauna in the Galapagos. This list can be generated using the
 DAISIE_dataprep function, which converts a user-specified data table into a
 data object, but the object can of course also be entered directly. It is an
@@ -68,7 +66,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -111,8 +109,7 @@
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Colonization and branching times of 8 terrestrial avifaunal clades in list
-format, accepted by DAISIE_ML and DAISIE_loglik_all</h1>
+      <img src="" class="logo" alt=""><h1>Colonization and branching times of 8 terrestrial avifaunal clades in list format, accepted by DAISIE_ML and DAISIE_loglik_all</h1>
       <small class="dont-index">Source: <a href="https://github.com/rsetienne/DAISIE/blob/HEAD/R/DAISIE_data.R" class="external-link"><code>R/DAISIE_data.R</code></a></small>
       <div class="d-none name"><code>Galapagos_datalist_2types.Rd</code></div>
     </div>
@@ -165,11 +162,11 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/Galapagos_datatable.html b/reference/Galapagos_datatable.html
index 0c0dcc45..9568234d 100644
--- a/reference/Galapagos_datatable.html
+++ b/reference/Galapagos_datatable.html
@@ -26,9 +26,7 @@
  "Non_endemic_MaxAge" and "Endemic" species with no extant close relatives on the island.
  Set "NA" if colonisation time unknown and no upper bound is known.
 For "Endemic" cladogenetic species these should be branching times of the
-radiation, including the stem age of the radiation (colonisation time estimate).'><title>Colonization and branching times of 8 terrestrial avifaunal Galápagos clades in table
-format. — Galapagos_datatable • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Colonization and branching times of 8 terrestrial avifaunal Galápagos clades in table
-format. — Galapagos_datatable"><meta property="og:description" content='A table containing the colonization and branching times of the terrestrial
+radiation, including the stem age of the radiation (colonisation time estimate).'><title>Colonization and branching times of 8 terrestrial avifaunal Galápagos clades in table format. — Galapagos_datatable • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Colonization and branching times of 8 terrestrial avifaunal Galápagos clades in table format. — Galapagos_datatable"><meta property="og:description" content='A table containing the colonization and branching times of the terrestrial
 avifauna in the Galápagos. Each row on the table represents and independent
 colonisation event. The table has four columns.  
 $Clade_name -
@@ -62,7 +60,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -105,8 +103,7 @@
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Colonization and branching times of 8 terrestrial avifaunal Galápagos clades in table
-format.</h1>
+      <img src="" class="logo" alt=""><h1>Colonization and branching times of 8 terrestrial avifaunal Galápagos clades in table format.</h1>
       <small class="dont-index">Source: <a href="https://github.com/rsetienne/DAISIE/blob/HEAD/R/DAISIE_data.R" class="external-link"><code>R/DAISIE_data.R</code></a></small>
       <div class="d-none name"><code>Galapagos_datatable.Rd</code></div>
     </div>
@@ -160,11 +157,11 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/Macaronesia_datalist.html b/reference/Macaronesia_datalist.html
index a429a795..ab23933c 100644
--- a/reference/Macaronesia_datalist.html
+++ b/reference/Macaronesia_datalist.html
@@ -26,11 +26,7 @@
 particular clade (only applicable for endemic clades) 
 $type1or2 -
 whether the colonist belongs to type 1 or type 2. In this dataset all are
-equal to 1. "><title>Colonization and branching times of terrestrial avifaunal clades from
-Azores, Canary Islands, Cape Verde and Madeira in list format, accepted by
-DAISIE_ML and DAISIE_loglik_all — Macaronesia_datalist • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Colonization and branching times of terrestrial avifaunal clades from
-Azores, Canary Islands, Cape Verde and Madeira in list format, accepted by
-DAISIE_ML and DAISIE_loglik_all — Macaronesia_datalist"><meta property="og:description" content="A list containing the colonization and branching times of the terrestrial
+equal to 1. "><title>Colonization and branching times of terrestrial avifaunal clades from Azores, Canary Islands, Cape Verde and Madeira in list format, accepted by DAISIE_ML and DAISIE_loglik_all — Macaronesia_datalist • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Colonization and branching times of terrestrial avifaunal clades from Azores, Canary Islands, Cape Verde and Madeira in list format, accepted by DAISIE_ML and DAISIE_loglik_all — Macaronesia_datalist"><meta property="og:description" content="A list containing the colonization and branching times of the terrestrial
 avifauna in 4 archipelagos: Azores, Canary Islands, Cape Verde and Madeira.
 It is an R list object with the 4 main elements corresponding to each of the
 archipelagos (e.g. Macaronesia_datalist[[1]] calls the Azores data). Each of
@@ -64,7 +60,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -107,9 +103,7 @@
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Colonization and branching times of terrestrial avifaunal clades from
-Azores, Canary Islands, Cape Verde and Madeira in list format, accepted by
-DAISIE_ML and DAISIE_loglik_all</h1>
+      <img src="" class="logo" alt=""><h1>Colonization and branching times of terrestrial avifaunal clades from Azores, Canary Islands, Cape Verde and Madeira in list format, accepted by DAISIE_ML and DAISIE_loglik_all</h1>
       <small class="dont-index">Source: <a href="https://github.com/rsetienne/DAISIE/blob/HEAD/R/DAISIE_data.R" class="external-link"><code>R/DAISIE_data.R</code></a></small>
       <div class="d-none name"><code>Macaronesia_datalist.Rd</code></div>
     </div>
@@ -160,11 +154,11 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/NewZealand_birds_datalist.html b/reference/NewZealand_birds_datalist.html
index 91b462a0..c74f5822 100644
--- a/reference/NewZealand_birds_datalist.html
+++ b/reference/NewZealand_birds_datalist.html
@@ -28,7 +28,7 @@
 that were not sampled for particular clade (only applicable for endemic
 clades) 
 $type1or2 - whether the colonist belongs to type 1 or
-type 2. In this dataset all are equal to 1. "><title>Colonization and branching times of New Zealand birds. — NewZealand_birds_datalist • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Colonization and branching times of New Zealand birds. — NewZealand_birds_datalist"><meta property="og:description" content="A list containing the colonization and branching times of the birds of
+type 2. In this dataset all are equal to 1. "><title>Colonization and branching times of New Zealand birds. — NewZealand_birds_datalist • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Colonization and branching times of New Zealand birds. — NewZealand_birds_datalist"><meta property="og:description" content="A list containing the colonization and branching times of the birds of
 New Zealand. Main dataset used in
 Valente, Etienne, Garcia-R (2019) Current Biology. Island age 52 Myr and mainland
 pool size of 1000 species. 
@@ -64,7 +64,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -160,11 +160,11 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/add_column_to_dataframe.html b/reference/add_column_to_dataframe.html
index 49dafba3..16426185 100644
--- a/reference/add_column_to_dataframe.html
+++ b/reference/add_column_to_dataframe.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Add a column to a data frame"><title>Add a column to a data frame — add_column_to_dataframe • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Add a column to a data frame — add_column_to_dataframe"><meta property="og:description" content="Add a column to a data frame"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Add a column to a data frame"><title>Add a column to a data frame — add_column_to_dataframe • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Add a column to a data frame — add_column_to_dataframe"><meta property="og:description" content="Add a column to a data frame"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -92,11 +92,11 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/archipelago_data.html b/reference/archipelago_data.html
index cd3a588c..ae2eb565 100644
--- a/reference/archipelago_data.html
+++ b/reference/archipelago_data.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="A dataframe with in subsequent columns the name of the archipelago (Archipelago)
-the area of the archipelago (Area), the age (Age) and the distance from the mainland (Distance)"><title>Physical data on 41 archipelagos — archipelago_data • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Physical data on 41 archipelagos — archipelago_data"><meta property="og:description" content="A dataframe with in subsequent columns the name of the archipelago (Archipelago)
+the area of the archipelago (Area), the age (Age) and the distance from the mainland (Distance)"><title>Physical data on 41 archipelagos — archipelago_data • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Physical data on 41 archipelagos — archipelago_data"><meta property="og:description" content="A dataframe with in subsequent columns the name of the archipelago (Archipelago)
 the area of the archipelago (Area), the age (Age) and the distance from the mainland (Distance)"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -8,7 +8,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -78,11 +78,11 @@ <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a><
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/archipelagos41.html b/reference/archipelagos41.html
index 590c158d..4a4585e0 100644
--- a/reference/archipelagos41.html
+++ b/reference/archipelagos41.html
@@ -4,9 +4,7 @@
 number between 1 and 41. Using archipelagos41[[x]][[1]] will show just the
 top part of the archipelago item where the archipelago name and physical features
 are displayed. The structure of each of the archipelagos is the same as regular DAISIE
-datalist generated using DAISIE_dataprep."><title>DAISIE datalist object including bird phylogenetic data and
-physical data for 41 archipelagos — archipelagos41 • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="DAISIE datalist object including bird phylogenetic data and
-physical data for 41 archipelagos — archipelagos41"><meta property="og:description" content="A datalist with 41 items representing the 41 archipelagos.
+datalist generated using DAISIE_dataprep."><title>DAISIE datalist object including bird phylogenetic data and physical data for 41 archipelagos — archipelagos41 • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="DAISIE datalist object including bird phylogenetic data and physical data for 41 archipelagos — archipelagos41"><meta property="og:description" content="A datalist with 41 items representing the 41 archipelagos.
 Each archipelago can be called separately using archipelagos41[[x]] with x being a
 number between 1 and 41. Using archipelagos41[[x]][[1]] will show just the
 top part of the archipelago item where the archipelago name and physical features
@@ -18,7 +16,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -61,8 +59,7 @@
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>DAISIE datalist object including bird phylogenetic data and
-physical data for 41 archipelagos</h1>
+      <img src="" class="logo" alt=""><h1>DAISIE datalist object including bird phylogenetic data and physical data for 41 archipelagos</h1>
       <small class="dont-index">Source: <a href="https://github.com/rsetienne/DAISIE/blob/HEAD/R/DAISIE_data.R" class="external-link"><code>R/DAISIE_data.R</code></a></small>
       <div class="d-none name"><code>archipelagos41.Rd</code></div>
     </div>
@@ -96,11 +93,11 @@ <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a><
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/are_rates.html b/reference/are_rates.html
index 46db565e..2f027d27 100644
--- a/reference/are_rates.html
+++ b/reference/are_rates.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Determines if object rates are rates"><title>Determines if object rates are rates — are_rates • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Determines if object rates are rates — are_rates"><meta property="og:description" content="Determines if object rates are rates"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
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+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
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-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
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diff --git a/reference/calc_Abeta.html b/reference/calc_Abeta.html
index 09fd8639..4420e388 100644
--- a/reference/calc_Abeta.html
+++ b/reference/calc_Abeta.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Calculates the area at a point in time from a beta function"><title>Calculates the area at a point in time from a beta function — calc_Abeta • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Calculates the area at a point in time from a beta function — calc_Abeta"><meta property="og:description" content="Calculates the area at a point in time from a beta function"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Calculates the area at a point in time from a beta function"><title>Calculates the area at a point in time from a beta function — calc_Abeta • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Calculates the area at a point in time from a beta function — calc_Abeta"><meta property="og:description" content="Calculates the area at a point in time from a beta function"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -105,11 +105,11 @@ <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a><
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
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-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
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diff --git a/reference/calc_next_timeval.html b/reference/calc_next_timeval.html
index a0faa5af..ea7520dd 100644
--- a/reference/calc_next_timeval.html
+++ b/reference/calc_next_timeval.html
@@ -1,12 +1,12 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -91,11 +91,11 @@ <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a><
 
 
     <footer><div class="pkgdown-footer-left">
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+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
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+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
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diff --git a/reference/calc_next_timeval_shift.html b/reference/calc_next_timeval_shift.html
index 8a91d606..43c290cc 100644
--- a/reference/calc_next_timeval_shift.html
+++ b/reference/calc_next_timeval_shift.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Calculates when the next timestep will be, and if a shift has occured."><title>Calculates when the next timestep will be, and if a shift has occured. — calc_next_timeval_shift • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Calculates when the next timestep will be, and if a shift has occured. — calc_next_timeval_shift"><meta property="og:description" content="Calculates when the next timestep will be, and if a shift has occured."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Calculates when the next timestep will be, and if a shift has occured."><title>Calculates when the next timestep will be, and if a shift has occured. — calc_next_timeval_shift • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Calculates when the next timestep will be, and if a shift has occured. — calc_next_timeval_shift"><meta property="og:description" content="Calculates when the next timestep will be, and if a shift has occured."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -95,11 +95,11 @@ <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a><
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
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diff --git a/reference/calc_peak.html b/reference/calc_peak.html
index 80feff7d..afb100e6 100644
--- a/reference/calc_peak.html
+++ b/reference/calc_peak.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
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+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Calculates the peak of ontogeny curve (beta function)"><title>Calculates the peak of ontogeny curve (beta function) — calc_peak • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Calculates the peak of ontogeny curve (beta function) — calc_peak"><meta property="og:description" content="Calculates the peak of ontogeny curve (beta function)"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -95,11 +95,11 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
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diff --git a/reference/countspecies.html b/reference/countspecies.html
index 7a163ec4..226144e8 100644
--- a/reference/countspecies.html
+++ b/reference/countspecies.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Count the number of species"><title>Count the number of species — countspecies • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Count the number of species — countspecies"><meta property="og:description" content="Count the number of species"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Count the number of species"><title>Count the number of species — countspecies • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Count the number of species — countspecies"><meta property="og:description" content="Count the number of species"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -81,11 +81,11 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
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diff --git a/reference/create_CS_version.html b/reference/create_CS_version.html
index 85ecb61c..847cb645 100644
--- a/reference/create_CS_version.html
+++ b/reference/create_CS_version.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Creates the list object for CS_version argument in DAISIE_ML_CS"><title>Creates the list object for CS_version argument in DAISIE_ML_CS — create_CS_version • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Creates the list object for CS_version argument in DAISIE_ML_CS — create_CS_version"><meta property="og:description" content="Creates the list object for CS_version argument in DAISIE_ML_CS"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Creates the list object for CS_version argument in DAISIE_ML_CS"><title>Creates the list object for CS_version argument in DAISIE_ML_CS — create_CS_version • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Creates the list object for CS_version argument in DAISIE_ML_CS — create_CS_version"><meta property="og:description" content="Creates the list object for CS_version argument in DAISIE_ML_CS"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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 <![endif]--></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -107,11 +107,11 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/create_area_pars.html b/reference/create_area_pars.html
index ca996d29..960d6866 100644
--- a/reference/create_area_pars.html
+++ b/reference/create_area_pars.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Create named list of area parameters"><title>Create named list of area parameters — create_area_pars • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Create named list of area parameters — create_area_pars"><meta property="og:description" content="Create named list of area parameters"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Create named list of area parameters"><title>Create named list of area parameters — create_area_pars • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Create named list of area parameters — create_area_pars"><meta property="og:description" content="Create named list of area parameters"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -138,11 +138,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/create_full_CS_stt.html b/reference/create_full_CS_stt.html
index e26ab884..9d72da8e 100644
--- a/reference/create_full_CS_stt.html
+++ b/reference/create_full_CS_stt.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Unsampled CS full STT"><title>Unsampled CS full STT — create_full_CS_stt • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Unsampled CS full STT — create_full_CS_stt"><meta property="og:description" content="Unsampled CS full STT"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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diff --git a/reference/create_hyper_pars.html b/reference/create_hyper_pars.html
index f4f45d9f..c9b6b374 100644
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+++ b/reference/create_hyper_pars.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Create list of hyperparameters"><title>Create list of hyperparameters — create_hyper_pars • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Create list of hyperparameters — create_hyper_pars"><meta property="og:description" content="Create list of hyperparameters"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
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@@ -95,11 +95,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
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-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
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diff --git a/reference/create_pars.html b/reference/create_pars.html
index 64874a7c..bd5767d6 100644
--- a/reference/create_pars.html
+++ b/reference/create_pars.html
@@ -1,12 +1,12 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
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@@ -107,11 +107,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
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-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
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diff --git a/reference/create_trait_pars.html b/reference/create_trait_pars.html
index 388c7e34..1da827ff 100644
--- a/reference/create_trait_pars.html
+++ b/reference/create_trait_pars.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Create named list of trait state parameters"><title>Create named list of trait state parameters — create_trait_pars • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Create named list of trait state parameters — create_trait_pars"><meta property="og:description" content="Create named list of trait state parameters"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
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@@ -126,11 +126,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
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-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
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diff --git a/reference/create_trait_pars_2K.html b/reference/create_trait_pars_2K.html
index 7e1abec4..1574adfd 100644
--- a/reference/create_trait_pars_2K.html
+++ b/reference/create_trait_pars_2K.html
@@ -1,12 +1,12 @@
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diff --git a/reference/cum_rho.html b/reference/cum_rho.html
index eb9ea6bd..7a8c288a 100644
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@@ -1,12 +1,12 @@
 <!DOCTYPE html>
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+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
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diff --git a/reference/daisie_odeint_cs.html b/reference/daisie_odeint_cs.html
index 2076ca1a..9d6b9409 100644
--- a/reference/daisie_odeint_cs.html
+++ b/reference/daisie_odeint_cs.html
@@ -1,12 +1,12 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
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     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
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diff --git a/reference/daisie_odeint_iw.html b/reference/daisie_odeint_iw.html
index a7960211..ad920eea 100644
--- a/reference/daisie_odeint_iw.html
+++ b/reference/daisie_odeint_iw.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Driver for the boost::odeint solver for the IW model"><title>Driver for the boost::odeint solver for the IW model — daisie_odeint_iw • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Driver for the boost::odeint solver for the IW model — daisie_odeint_iw"><meta property="og:description" content="Driver for the boost::odeint solver for the IW model"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Driver for the boost::odeint solver for the IW model"><title>Driver for the boost::odeint solver for the IW model — daisie_odeint_iw • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Driver for the boost::odeint solver for the IW model — daisie_odeint_iw"><meta property="og:description" content="Driver for the boost::odeint solver for the IW model"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -64,11 +64,11 @@
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
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diff --git a/reference/default_params_doc.html b/reference/default_params_doc.html
index d07024e9..4aaa5bdd 100644
--- a/reference/default_params_doc.html
+++ b/reference/default_params_doc.html
@@ -1,12 +1,12 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -1057,11 +1057,11 @@ <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
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diff --git a/reference/frogs_datalist.html b/reference/frogs_datalist.html
index 06c99d87..32220afa 100644
--- a/reference/frogs_datalist.html
+++ b/reference/frogs_datalist.html
@@ -30,7 +30,7 @@
 that were not sampled for particular clade (only applicable for endemic
 clades) 
 $type1or2 - whether the colonist belongs to type 1 or
-type 2. In this dataset all are equal to 1. "><title>Colonization and branching times of 5 Eleutherodactylus clades from Hispaniola island. — frogs_datalist • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Colonization and branching times of 5 Eleutherodactylus clades from Hispaniola island. — frogs_datalist"><meta property="og:description" content="A list containing the colonization and branching times of the Eleutherodactylus frogs of
+type 2. In this dataset all are equal to 1. "><title>Colonization and branching times of 5 Eleutherodactylus clades from Hispaniola island. — frogs_datalist • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Colonization and branching times of 5 Eleutherodactylus clades from Hispaniola island. — frogs_datalist"><meta property="og:description" content="A list containing the colonization and branching times of the Eleutherodactylus frogs of
 Hispaniola. Main dataset used in Etienne et al. This list can be generated
 using the DAISIE_dataprep function, which converts a user-specified data table into a data object,
 but the
@@ -68,7 +68,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -165,11 +165,11 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/frogs_datatable.html b/reference/frogs_datatable.html
index 691b6520..d42f4b8e 100644
--- a/reference/frogs_datatable.html
+++ b/reference/frogs_datatable.html
@@ -19,9 +19,7 @@
 time of the first cladogenetic event is known, but the precise time of colonisation
 is not.
 * Endemic&amp;amp;Non_Endemic: when endemic clade and mainland ancestor has
-re-colonized '><title>Colonization and branching times of 5 Eleutherodactylus (frogs) clades from
-the island of Hispaniola. — frogs_datatable • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Colonization and branching times of 5 Eleutherodactylus (frogs) clades from
-the island of Hispaniola. — frogs_datatable"><meta property="og:description" content='A table containing the colonization and branching times of the Eleutherodacytlus
+re-colonized '><title>Colonization and branching times of 5 Eleutherodactylus (frogs) clades from the island of Hispaniola. — frogs_datatable • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Colonization and branching times of 5 Eleutherodactylus (frogs) clades from the island of Hispaniola. — frogs_datatable"><meta property="og:description" content='A table containing the colonization and branching times of the Eleutherodacytlus
 frogs of the island of Hispaniola (Greater Antilles). Each row on the table represents and independent
 colonisation event. The table has four columns.  
 $Clade_name -
@@ -48,7 +46,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -91,8 +89,7 @@
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Colonization and branching times of 5 Eleutherodactylus (frogs) clades from
-the island of Hispaniola.</h1>
+      <img src="" class="logo" alt=""><h1>Colonization and branching times of 5 Eleutherodactylus (frogs) clades from the island of Hispaniola.</h1>
       <small class="dont-index">Source: <a href="https://github.com/rsetienne/DAISIE/blob/HEAD/R/DAISIE_data.R" class="external-link"><code>R/DAISIE_data.R</code></a></small>
       <div class="d-none name"><code>frogs_datatable.Rd</code></div>
     </div>
@@ -135,11 +132,11 @@ <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a><
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/get_ana_rate.html b/reference/get_ana_rate.html
index e316fab3..bbd558b7 100644
--- a/reference/get_ana_rate.html
+++ b/reference/get_ana_rate.html
@@ -1,7 +1,7 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Internal function.
 Calculates the anagenesis rate given the current number of
-immigrant species and the per capita rate."><title>Calculate anagenesis rate — get_ana_rate • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Calculate anagenesis rate — get_ana_rate"><meta property="og:description" content="Internal function.
+immigrant species and the per capita rate."><title>Calculate anagenesis rate — get_ana_rate • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Calculate anagenesis rate — get_ana_rate"><meta property="og:description" content="Internal function.
 Calculates the anagenesis rate given the current number of
 immigrant species and the per capita rate."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -10,7 +10,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -119,11 +119,11 @@ <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a><
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/get_clado_rate.html b/reference/get_clado_rate.html
index 56d713e0..528319d1 100644
--- a/reference/get_clado_rate.html
+++ b/reference/get_clado_rate.html
@@ -2,7 +2,7 @@
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Internal function.
 Calculates the cladogenesis rate given the current number of
 species in the system, the carrying capacity and the per capita cladogenesis
-rate"><title>Calculate cladogenesis rate — get_clado_rate • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Calculate cladogenesis rate — get_clado_rate"><meta property="og:description" content="Internal function.
+rate"><title>Calculate cladogenesis rate — get_clado_rate • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Calculate cladogenesis rate — get_clado_rate"><meta property="og:description" content="Internal function.
 Calculates the cladogenesis rate given the current number of
 species in the system, the carrying capacity and the per capita cladogenesis
 rate"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
@@ -12,7 +12,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -134,11 +134,11 @@ <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a><
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
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diff --git a/reference/get_ext_rate.html b/reference/get_ext_rate.html
index 77e4dea2..170cf4b5 100644
--- a/reference/get_ext_rate.html
+++ b/reference/get_ext_rate.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Calculate extinction rate"><title>Calculate extinction rate — get_ext_rate • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Calculate extinction rate — get_ext_rate"><meta property="og:description" content="Calculate extinction rate"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Calculate extinction rate"><title>Calculate extinction rate — get_ext_rate • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Calculate extinction rate — get_ext_rate"><meta property="og:description" content="Calculate extinction rate"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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 <![endif]--></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -152,11 +152,11 @@ <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a><
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
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diff --git a/reference/get_immig_rate.html b/reference/get_immig_rate.html
index 4d28f610..86bbcc19 100644
--- a/reference/get_immig_rate.html
+++ b/reference/get_immig_rate.html
@@ -1,7 +1,7 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Internal function.
 Calculates the immigration rate given the current number of
-species in the system, the carrying capacity"><title>Calculate immigration rate — get_immig_rate • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Calculate immigration rate — get_immig_rate"><meta property="og:description" content="Internal function.
+species in the system, the carrying capacity"><title>Calculate immigration rate — get_immig_rate • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Calculate immigration rate — get_immig_rate"><meta property="og:description" content="Internal function.
 Calculates the immigration rate given the current number of
 species in the system, the carrying capacity"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -10,7 +10,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -148,11 +148,11 @@ <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a><
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/get_trans_rate.html b/reference/get_trans_rate.html
index 5a773e18..e49ecdf5 100644
--- a/reference/get_trans_rate.html
+++ b/reference/get_trans_rate.html
@@ -1,7 +1,7 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Internal function.
 Calculates the transition rate given the current number of
-immigrant species and the per capita rate."><title>Calculate transition rate — get_trans_rate • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Calculate transition rate — get_trans_rate"><meta property="og:description" content="Internal function.
+immigrant species and the per capita rate."><title>Calculate transition rate — get_trans_rate • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Calculate transition rate — get_trans_rate"><meta property="og:description" content="Internal function.
 Calculates the transition rate given the current number of
 immigrant species and the per capita rate."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -10,7 +10,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -94,11 +94,11 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/index.html b/reference/index.html
index 4c0f736d..55134095 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Function reference • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Function reference"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Function reference • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Function reference"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -97,34 +97,27 @@ <h2 id="all-functions">All functions<a class="anchor" aria-label="anchor" href="
           
           <code><a href="DAISIE_ML.html">DAISIE_ML_CS()</a></code> 
         </dt>
-        <dd>Maximization of the loglikelihood under the DAISIE model with clade-specific
-diversity-dependence</dd>
+        <dd>Maximization of the loglikelihood under the DAISIE model with clade-specific diversity-dependence</dd>
       </dl><dl><dt>
           
           <code><a href="DAISIE_ML_IW.html">DAISIE_ML_IW()</a></code> 
         </dt>
-        <dd>Maximization of the loglikelihood under the DAISIE model with island-wide
-diversity-dependence</dd>
+        <dd>Maximization of the loglikelihood under the DAISIE model with island-wide diversity-dependence</dd>
       </dl><dl><dt>
           
           <code><a href="DAISIE_MW_ML.html">DAISIE_MW_ML()</a></code> 
         </dt>
-        <dd>Maximization of the loglikelihood under the DAISIE model with clade-specific
-diversity-dependence and explicit dependencies on island area and isolation
-as hypothesized by MacArthur &amp; Wilson</dd>
+        <dd>Maximization of the loglikelihood under the DAISIE model with clade-specific diversity-dependence and explicit dependencies on island area and isolation as hypothesized by MacArthur &amp; Wilson</dd>
       </dl><dl><dt>
           
           <code><a href="DAISIE_SR_ML.html">DAISIE_SR_ML_CS()</a></code> 
         </dt>
-        <dd>Maximization of the loglikelihood under the DAISIE model with clade-specific
-diversity-dependence</dd>
+        <dd>Maximization of the loglikelihood under the DAISIE model with clade-specific diversity-dependence</dd>
       </dl><dl><dt>
           
           <code><a href="DAISIE_SR_loglik_CS.html">DAISIE_SR_loglik_CS()</a></code> 
         </dt>
-        <dd>Computes the loglikelihood of the DAISIE model with clade-specific
-diversity-dependence given data and a set of model parameters that may shift
-at some time</dd>
+        <dd>Computes the loglikelihood of the DAISIE model with clade-specific diversity-dependence given data and a set of model parameters that may shift at some time</dd>
       </dl><dl><dt>
           
           <code><a href="DAISIE_abm_factor.html">DAISIE_abm_factor()</a></code> 
@@ -134,8 +127,7 @@ <h2 id="all-functions">All functions<a class="anchor" aria-label="anchor" href="
           
           <code><a href="DAISIE_convertprobdist.html">DAISIE_convertprobdist()</a></code> 
         </dt>
-        <dd>Converts the joint distribution of endemics and non-endemics under the
-DAISIE model to list format</dd>
+        <dd>Converts the joint distribution of endemics and non-endemics under the DAISIE model to list format</dd>
       </dl><dl><dt>
           
           <code><a href="DAISIE_count_species.html">DAISIE_count_species()</a></code> 
@@ -150,32 +142,27 @@ <h2 id="all-functions">All functions<a class="anchor" aria-label="anchor" href="
           
           <code><a href="DAISIE_format_CS_full_stt.html">DAISIE_format_CS_full_stt()</a></code> 
         </dt>
-        <dd>Formats clade-specific simulation output into standard
-DAISIE list output with complete STT table</dd>
+        <dd>Formats clade-specific simulation output into standard DAISIE list output with complete STT table</dd>
       </dl><dl><dt>
           
           <code><a href="DAISIE_format_IW_full_stt.html">DAISIE_format_IW_full_stt()</a></code> 
         </dt>
-        <dd>Formats clade-specific simulation output into standard
-DAISIE list output with complete STT table</dd>
+        <dd>Formats clade-specific simulation output into standard DAISIE list output with complete STT table</dd>
       </dl><dl><dt>
           
           <code><a href="DAISIE_loglik_IW.html">DAISIE_loglik_IW()</a></code> 
         </dt>
-        <dd>Computes the loglikelihood of the DAISIE model with island-wide
-diversity-dependence given data and a set of model parameters</dd>
+        <dd>Computes the loglikelihood of the DAISIE model with island-wide diversity-dependence given data and a set of model parameters</dd>
       </dl><dl><dt>
           
           <code><a href="DAISIE_margprobdist.html">DAISIE_margprobdist()</a></code> 
         </dt>
-        <dd>The marginal distribution of endemics and non-endemics under the DAISIE
-model</dd>
+        <dd>The marginal distribution of endemics and non-endemics under the DAISIE model</dd>
       </dl><dl><dt>
           
           <code><a href="DAISIE_numcol.html">DAISIE_numcol()</a></code> 
         </dt>
-        <dd>The expectation and marginal distribution of the number of colonizations
-(lineages) under the DAISIE model</dd>
+        <dd>The expectation and marginal distribution of the number of colonizations (lineages) under the DAISIE model</dd>
       </dl><dl><dt>
           
           <code><a href="DAISIE_plot_age_diversity.html">DAISIE_plot_age_diversity()</a></code> 
@@ -205,68 +192,57 @@ <h2 id="all-functions">All functions<a class="anchor" aria-label="anchor" href="
           
           <code><a href="DAISIE_sim.html">DAISIE_sim_cr()</a></code> 
         </dt>
-        <dd>Simulate (non-)oceanic islands with given parameters under
-  time-constant rates</dd>
+        <dd>Simulate (non-)oceanic islands with given parameters under time-constant rates</dd>
       </dl><dl><dt>
           
           <code><a href="DAISIE_sim_MW.html">DAISIE_sim_MW()</a></code> 
         </dt>
-        <dd>Simulate multiple islands based on hyperparameters that describe relationships
-between area, isolation and local parameters</dd>
+        <dd>Simulate multiple islands based on hyperparameters that describe relationships between area, isolation and local parameters</dd>
       </dl><dl><dt>
           
           <code><a href="DAISIE_sim_cr_cs.html">DAISIE_sim_cr_cs()</a></code> 
         </dt>
-        <dd>Simulates island replicates with an clade-specific (CS) diversity-dependent
-constant-rate process</dd>
+        <dd>Simulates island replicates with an clade-specific (CS) diversity-dependent constant-rate process</dd>
       </dl><dl><dt>
           
           <code><a href="DAISIE_sim_cr_gw.html">DAISIE_sim_cr_gw()</a></code> 
         </dt>
-        <dd>Simulates island replicates with an guild-wide (GW) diversity-dependent
-process</dd>
+        <dd>Simulates island replicates with an guild-wide (GW) diversity-dependent process</dd>
       </dl><dl><dt>
           
           <code><a href="DAISIE_sim_cr_iw.html">DAISIE_sim_cr_iw()</a></code> 
         </dt>
-        <dd>Simulates island replicates with an island-wide (IW) diversity-dependent
-constant-rate process</dd>
+        <dd>Simulates island replicates with an island-wide (IW) diversity-dependent constant-rate process</dd>
       </dl><dl><dt>
           
           <code><a href="DAISIE_sim_cr_shift.html">DAISIE_sim_cr_shift()</a></code> 
         </dt>
-        <dd>Simulate (non-)oceanic islands with given parameters under a
-  rate-shift regime</dd>
+        <dd>Simulate (non-)oceanic islands with given parameters under a rate-shift regime</dd>
       </dl><dl><dt>
           
           <code><a href="DAISIE_sim_relaxed_rate.html">DAISIE_sim_relaxed_rate()</a></code> 
         </dt>
-        <dd>Simulate (non-)oceanic islands with given parameters under a
-  relaxed-rate model</dd>
+        <dd>Simulate (non-)oceanic islands with given parameters under a relaxed-rate model</dd>
       </dl><dl><dt>
           
           <code><a href="DAISIE_sim_time_dep.html">DAISIE_sim_time_dep()</a></code> 
         </dt>
-        <dd>Simulate (non-)oceanic islands with given parameters under a
-  time-dependent regime</dd>
+        <dd>Simulate (non-)oceanic islands with given parameters under a time-dependent regime</dd>
       </dl><dl><dt>
           
           <code><a href="DAISIE_sim_time_dep_cs.html">DAISIE_sim_time_dep_cs()</a></code> 
         </dt>
-        <dd>Simulates island replicates with an clade-specific (CS) diversity-dependent
-time-dependent process</dd>
+        <dd>Simulates island replicates with an clade-specific (CS) diversity-dependent time-dependent process</dd>
       </dl><dl><dt>
           
           <code><a href="DAISIE_sim_time_dep_gw.html">DAISIE_sim_time_dep_gw()</a></code> 
         </dt>
-        <dd>Simulates island replicates with an guild-wide (GW) diversity-dependent
-time-dependent process</dd>
+        <dd>Simulates island replicates with an guild-wide (GW) diversity-dependent time-dependent process</dd>
       </dl><dl><dt>
           
           <code><a href="DAISIE_sim_time_dep_iw.html">DAISIE_sim_time_dep_iw()</a></code> 
         </dt>
-        <dd>Simulates island replicates with an island-wide (IW) diversity-dependent
-time-dependent process</dd>
+        <dd>Simulates island replicates with an island-wide (IW) diversity-dependent time-dependent process</dd>
       </dl><dl><dt>
           
           <code><a href="DAISIE_sim_trait_dep.html">DAISIE_sim_trait_dep()</a></code> 
@@ -281,27 +257,22 @@ <h2 id="all-functions">All functions<a class="anchor" aria-label="anchor" href="
           
           <code><a href="Galapagos_datalist.html">Galapagos_datalist</a></code> 
         </dt>
-        <dd>Colonization and branching times of 8 terrestrial avifaunal clades in list
-format, accepted by DAISIE_ML and DAISIE_loglik_all</dd>
+        <dd>Colonization and branching times of 8 terrestrial avifaunal clades in list format, accepted by DAISIE_ML and DAISIE_loglik_all</dd>
       </dl><dl><dt>
           
           <code><a href="Galapagos_datalist_2types.html">Galapagos_datalist_2types</a></code> 
         </dt>
-        <dd>Colonization and branching times of 8 terrestrial avifaunal clades in list
-format, accepted by DAISIE_ML and DAISIE_loglik_all</dd>
+        <dd>Colonization and branching times of 8 terrestrial avifaunal clades in list format, accepted by DAISIE_ML and DAISIE_loglik_all</dd>
       </dl><dl><dt>
           
           <code><a href="Galapagos_datatable.html">Galapagos_datatable</a></code> 
         </dt>
-        <dd>Colonization and branching times of 8 terrestrial avifaunal Galápagos clades in table
-format.</dd>
+        <dd>Colonization and branching times of 8 terrestrial avifaunal Galápagos clades in table format.</dd>
       </dl><dl><dt>
           
           <code><a href="Macaronesia_datalist.html">Macaronesia_datalist</a></code> 
         </dt>
-        <dd>Colonization and branching times of terrestrial avifaunal clades from
-Azores, Canary Islands, Cape Verde and Madeira in list format, accepted by
-DAISIE_ML and DAISIE_loglik_all</dd>
+        <dd>Colonization and branching times of terrestrial avifaunal clades from Azores, Canary Islands, Cape Verde and Madeira in list format, accepted by DAISIE_ML and DAISIE_loglik_all</dd>
       </dl><dl><dt>
           
           <code><a href="NewZealand_birds_datalist.html">NewZealand_birds_datalist</a></code> 
@@ -321,8 +292,7 @@ <h2 id="all-functions">All functions<a class="anchor" aria-label="anchor" href="
           
           <code><a href="archipelagos41.html">archipelagos41</a></code> 
         </dt>
-        <dd>DAISIE datalist object including bird phylogenetic data and
-physical data for 41 archipelagos</dd>
+        <dd>DAISIE datalist object including bird phylogenetic data and physical data for 41 archipelagos</dd>
       </dl><dl><dt>
           
           <code><a href="create_CS_version.html">create_CS_version()</a></code> 
@@ -372,26 +342,22 @@ <h2 id="all-functions">All functions<a class="anchor" aria-label="anchor" href="
           
           <code><a href="frogs_datatable.html">frogs_datatable</a></code> 
         </dt>
-        <dd>Colonization and branching times of 5 Eleutherodactylus (frogs) clades from
-the island of Hispaniola.</dd>
+        <dd>Colonization and branching times of 5 Eleutherodactylus (frogs) clades from the island of Hispaniola.</dd>
       </dl><dl><dt>
           
           <code><a href="islands_10reps_RAW.html">islands_10reps_RAW</a></code> 
         </dt>
-        <dd>1000 islands in RAW format simulated with the ML parameters of the CR model
-for the Galapagos data.</dd>
+        <dd>1000 islands in RAW format simulated with the ML parameters of the CR model for the Galapagos data.</dd>
       </dl><dl><dt>
           
           <code><a href="islands_1type_1000reps.html">islands_1type_1000reps</a></code> 
         </dt>
-        <dd>1000 islands in DAISIE format simulated with the ML parameters of the CR
-model for the Galapagos data</dd>
+        <dd>1000 islands in DAISIE format simulated with the ML parameters of the CR model for the Galapagos data</dd>
       </dl><dl><dt>
           
           <code><a href="islands_2types_1000reps.html">islands_2types_1000reps</a></code> 
         </dt>
-        <dd>1000 islands in DAISIE format simulated with the ML parameters of the
-CR_lamc_mu_K model for the Galapagos data (2 types of species)</dd>
+        <dd>1000 islands in DAISIE format simulated with the ML parameters of the CR_lamc_mu_K model for the Galapagos data (2 types of species)</dd>
       </dl><dl><dt>
           
           <code><a href="stac_table.html">stac_table</a></code> 
@@ -402,11 +368,11 @@ <h2 id="all-functions">All functions<a class="anchor" aria-label="anchor" href="
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/integral_peak.html b/reference/integral_peak.html
index 408a6c0c..952a5428 100644
--- a/reference/integral_peak.html
+++ b/reference/integral_peak.html
@@ -7,9 +7,7 @@
 "exp(logfun)" can be zero or positive at zero
 "exp(logfun)" tends to zero at infinity
 
-'><title>Computes integral of a very peaked function, modified from the
-SADISA package — integral_peak • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Computes integral of a very peaked function, modified from the
-SADISA package — integral_peak"><meta property="og:description" content='computes the logarithm of the integral of exp(logfun) from 0
+'><title>Computes integral of a very peaked function, modified from the SADISA package — integral_peak • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Computes integral of a very peaked function, modified from the SADISA package — integral_peak"><meta property="og:description" content='computes the logarithm of the integral of exp(logfun) from 0
 to Inf under the following assumptions:
 "exp(logfun)" has a single, sharply peaked maximum
 "exp(logfun)" is increasing to the left of the peak and
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-      <img src="" class="logo" alt=""><h1>Computes integral of a very peaked function, modified from the
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+      <img src="" class="logo" alt=""><h1>Computes integral of a very peaked function, modified from the SADISA package</h1>
       <small class="dont-index">Source: <a href="https://github.com/rsetienne/DAISIE/blob/HEAD/R/DAISIE_loglik_integrate.R" class="external-link"><code>R/DAISIE_loglik_integrate.R</code></a></small>
       <div class="d-none name"><code>integral_peak.Rd</code></div>
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@@ -143,11 +140,11 @@ <h2 id="references">References<a class="anchor" aria-label="anchor" href="#refer
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
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diff --git a/reference/island_area.html b/reference/island_area.html
index db00de26..60b07be7 100644
--- a/reference/island_area.html
+++ b/reference/island_area.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Function to describe changes in area through time."><title>Function to describe changes in area through time. — island_area • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Function to describe changes in area through time. — island_area"><meta property="og:description" content="Function to describe changes in area through time."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Function to describe changes in area through time."><title>Function to describe changes in area through time. — island_area • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Function to describe changes in area through time. — island_area"><meta property="og:description" content="Function to describe changes in area through time."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
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diff --git a/reference/island_area_vector.html b/reference/island_area_vector.html
index f94f4135..4d14b323 100644
--- a/reference/island_area_vector.html
+++ b/reference/island_area_vector.html
@@ -1,12 +1,12 @@
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+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Computes island_area, but takes vector as argument (needed by )"><title>Computes island_area, but takes vector as argument (needed by ) — island_area_vector • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Computes island_area, but takes vector as argument (needed by ) — island_area_vector"><meta property="og:description" content="Computes island_area, but takes vector as argument (needed by )"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -120,11 +120,11 @@ <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a><
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
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diff --git a/reference/islands_10reps_RAW.html b/reference/islands_10reps_RAW.html
index 86e2908d..5490aa82 100644
--- a/reference/islands_10reps_RAW.html
+++ b/reference/islands_10reps_RAW.html
@@ -20,9 +20,7 @@
 the descendants of the mainland species (nI - number of non-endemic species;
 nA - number of anagenetic species, nC - number of cladogenetic species)
 $missing_species - number of island species that were not sampled for
-particular clade (only applicable for endemic clades) "><title>1000 islands in RAW format simulated with the ML parameters of the CR model
-for the Galapagos data. — islands_10reps_RAW • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="1000 islands in RAW format simulated with the ML parameters of the CR model
-for the Galapagos data. — islands_10reps_RAW"><meta property="og:description" content="Each simulated dataset is an element of the list, which can be called using
+particular clade (only applicable for endemic clades) "><title>1000 islands in RAW format simulated with the ML parameters of the CR model for the Galapagos data. — islands_10reps_RAW • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="1000 islands in RAW format simulated with the ML parameters of the CR model for the Galapagos data. — islands_10reps_RAW"><meta property="og:description" content="Each simulated dataset is an element of the list, which can be called using
 e.g. islands_10reps_RAW[[1]] Each of the island replicates is a list in
 itself. The first (e.g. islands_10reps_RAW[[x]][[1]]) element of that list
 has the following components:  The following elements of the RAW list
@@ -50,7 +48,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -93,8 +91,7 @@
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>1000 islands in RAW format simulated with the ML parameters of the CR model
-for the Galapagos data.</h1>
+      <img src="" class="logo" alt=""><h1>1000 islands in RAW format simulated with the ML parameters of the CR model for the Galapagos data.</h1>
       <small class="dont-index">Source: <a href="https://github.com/rsetienne/DAISIE/blob/HEAD/R/DAISIE_data.R" class="external-link"><code>R/DAISIE_data.R</code></a></small>
       <div class="d-none name"><code>islands_10reps_RAW.Rd</code></div>
     </div>
@@ -141,11 +138,11 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/islands_1type_1000reps.html b/reference/islands_1type_1000reps.html
index 41f45eec..54848ef7 100644
--- a/reference/islands_1type_1000reps.html
+++ b/reference/islands_1type_1000reps.html
@@ -22,9 +22,7 @@
 * Endemic&amp;amp;Non_Endemic: 3 
 * Non_endemic: 4 
 $missing_species - number of island species that were not sampled for
-particular clade (only applicable for endemic clades) "><title>1000 islands in DAISIE format simulated with the ML parameters of the CR
-model for the Galapagos data — islands_1type_1000reps • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="1000 islands in DAISIE format simulated with the ML parameters of the CR
-model for the Galapagos data — islands_1type_1000reps"><meta property="og:description" content="Each simulated dataset is an element of the list, which can be called using
+particular clade (only applicable for endemic clades) "><title>1000 islands in DAISIE format simulated with the ML parameters of the CR model for the Galapagos data — islands_1type_1000reps • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="1000 islands in DAISIE format simulated with the ML parameters of the CR model for the Galapagos data — islands_1type_1000reps"><meta property="og:description" content="Each simulated dataset is an element of the list, which can be called using
 e.g. islands_1type_1000reps[[1]] Each of the island replicates is a list in
 itself. The first (e.g. islands_1type_1000reps[[x]][[1]]) element of that
 list has the following components: 
@@ -54,7 +52,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -97,8 +95,7 @@
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>1000 islands in DAISIE format simulated with the ML parameters of the CR
-model for the Galapagos data</h1>
+      <img src="" class="logo" alt=""><h1>1000 islands in DAISIE format simulated with the ML parameters of the CR model for the Galapagos data</h1>
       <small class="dont-index">Source: <a href="https://github.com/rsetienne/DAISIE/blob/HEAD/R/DAISIE_data.R" class="external-link"><code>R/DAISIE_data.R</code></a></small>
       <div class="d-none name"><code>islands_1type_1000reps.Rd</code></div>
     </div>
@@ -145,11 +142,11 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/islands_2types_1000reps.html b/reference/islands_2types_1000reps.html
index 06ee6574..26ce086d 100644
--- a/reference/islands_2types_1000reps.html
+++ b/reference/islands_2types_1000reps.html
@@ -33,9 +33,7 @@
 * Non_endemic: 4 
 $missing_species - number of island species that were not sampled for
 particular clade (only applicable for endemic clades) 
-$type_1or2 - whether the colonist belongs to type 1 or type 2 "><title>1000 islands in DAISIE format simulated with the ML parameters of the
-CR_lamc_mu_K model for the Galapagos data (2 types of species) — islands_2types_1000reps • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="1000 islands in DAISIE format simulated with the ML parameters of the
-CR_lamc_mu_K model for the Galapagos data (2 types of species) — islands_2types_1000reps"><meta property="og:description" content="Each simulated dataset is an element of the list, which can be called using
+$type_1or2 - whether the colonist belongs to type 1 or type 2 "><title>1000 islands in DAISIE format simulated with the ML parameters of the CR_lamc_mu_K model for the Galapagos data (2 types of species) — islands_2types_1000reps • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="1000 islands in DAISIE format simulated with the ML parameters of the CR_lamc_mu_K model for the Galapagos data (2 types of species) — islands_2types_1000reps"><meta property="og:description" content="Each simulated dataset is an element of the list, which can be called using
 e.g. islands_2types_1000reps[[1]] Each of the island replicates is a list in
 itself. The first (e.g. islands_2types_1000reps[[x]][[1]]) element of that
 list has the following components: 
@@ -76,7 +74,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -119,8 +117,7 @@
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>1000 islands in DAISIE format simulated with the ML parameters of the
-CR_lamc_mu_K model for the Galapagos data (2 types of species)</h1>
+      <img src="" class="logo" alt=""><h1>1000 islands in DAISIE format simulated with the ML parameters of the CR_lamc_mu_K model for the Galapagos data (2 types of species)</h1>
       <small class="dont-index">Source: <a href="https://github.com/rsetienne/DAISIE/blob/HEAD/R/DAISIE_data.R" class="external-link"><code>R/DAISIE_data.R</code></a></small>
       <div class="d-none name"><code>islands_2types_1000reps.Rd</code></div>
     </div>
@@ -174,11 +171,11 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/remove_empty_elements.html b/reference/remove_empty_elements.html
index 7098003e..46698c77 100644
--- a/reference/remove_empty_elements.html
+++ b/reference/remove_empty_elements.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Remove superfluous lines in empty simulations"><title>Remove superfluous lines in empty simulations — remove_empty_elements • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Remove superfluous lines in empty simulations — remove_empty_elements"><meta property="og:description" content="Remove superfluous lines in empty simulations"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -81,11 +81,11 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
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-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
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diff --git a/reference/rho.html b/reference/rho.html
index 03dad332..8cf82917 100644
--- a/reference/rho.html
+++ b/reference/rho.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Gamma distribution density parameterised with mean and standard deviation"><title>Gamma distribution density parameterised with mean and standard deviation — rho • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Gamma distribution density parameterised with mean and standard deviation — rho"><meta property="og:description" content="Gamma distribution density parameterised with mean and standard deviation"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Gamma distribution density parameterised with mean and standard deviation"><title>Gamma distribution density parameterised with mean and standard deviation — rho • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Gamma distribution density parameterised with mean and standard deviation — rho"><meta property="og:description" content="Gamma distribution density parameterised with mean and standard deviation"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -87,11 +87,11 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
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diff --git a/reference/sample_relaxed_rate.html b/reference/sample_relaxed_rate.html
index 1449bea6..ef5efef5 100644
--- a/reference/sample_relaxed_rate.html
+++ b/reference/sample_relaxed_rate.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Samples from distribution when parameter is relaxed"><title>Samples from distribution when parameter is relaxed — sample_relaxed_rate • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Samples from distribution when parameter is relaxed — sample_relaxed_rate"><meta property="og:description" content="Samples from distribution when parameter is relaxed"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Samples from distribution when parameter is relaxed"><title>Samples from distribution when parameter is relaxed — sample_relaxed_rate • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Samples from distribution when parameter is relaxed — sample_relaxed_rate"><meta property="og:description" content="Samples from distribution when parameter is relaxed"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -85,11 +85,11 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/stac_table.html b/reference/stac_table.html
index 7a34e89e..a3008253 100644
--- a/reference/stac_table.html
+++ b/reference/stac_table.html
@@ -25,7 +25,7 @@
   explanation of what the colonisation time in the branching times vector
   of the DAISIE object (first element of the vector) means.
 
-"><title>Explanatory table on meaning and use of stac settings — stac_table • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Explanatory table on meaning and use of stac settings — stac_table"><meta property="og:description" content="A table containing the information regarding the meaning
+"><title>Explanatory table on meaning and use of stac settings — stac_table • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Explanatory table on meaning and use of stac settings — stac_table"><meta property="og:description" content="A table containing the information regarding the meaning
 of the stac codes utilised by DAISIE's ML functions. It is used to
 render the &quot;DAISIE stac values&quot; vignette.  
 stac stands for &quot;status of the clade&quot; formed by the immigrant. It is
@@ -58,7 +58,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -142,11 +142,11 @@ <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a><
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
 </div>
 
     </footer></div>
diff --git a/reference/transform_gamma_pars.html b/reference/transform_gamma_pars.html
index 6399b4e5..61c64720 100644
--- a/reference/transform_gamma_pars.html
+++ b/reference/transform_gamma_pars.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
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+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
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diff --git a/reference/update_max_rates.html b/reference/update_max_rates.html
index 56f26586..b5e9777f 100644
--- a/reference/update_max_rates.html
+++ b/reference/update_max_rates.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Internal function that updates the all the max rates at time t."><title>Calculates the maximum rates for a Gillespie simulation — update_max_rates • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Calculates the maximum rates for a Gillespie simulation — update_max_rates"><meta property="og:description" content="Internal function that updates the all the max rates at time t."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Internal function that updates the all the max rates at time t."><title>Calculates the maximum rates for a Gillespie simulation — update_max_rates • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Calculates the maximum rates for a Gillespie simulation — update_max_rates"><meta property="og:description" content="Internal function that updates the all the max rates at time t."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light" data-bs-theme="light"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
@@ -160,11 +160,11 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
 </div>
 
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-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
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diff --git a/reference/update_rates.html b/reference/update_rates.html
index 537d59b9..c2536db2 100644
--- a/reference/update_rates.html
+++ b/reference/update_rates.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Internal function that updates the all the rates and
-max extinction horizon at time t."><title>Calculates algorithm rates — update_rates • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Calculates algorithm rates — update_rates"><meta property="og:description" content="Internal function that updates the all the rates and
+max extinction horizon at time t."><title>Calculates algorithm rates — update_rates • DAISIE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Calculates algorithm rates — update_rates"><meta property="og:description" content="Internal function that updates the all the rates and
 max extinction horizon at time t."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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     <a class="navbar-brand me-2" href="../index.html">DAISIE</a>
 
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-  <p></p><p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
+  <p>Developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore, Bart Haegeman, Joshua W. Lambert, Pedro Santos Neves, Shu Xie, Richèl J.C. Bilderbeek, Hanno Hildenbrandt.</p>
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diff --git a/search.json b/search.json
index 4088eeb0..6101512c 100644
--- a/search.json
+++ b/search.json
@@ -1 +1 @@
-[{"path":"https://rsetienne.github.io/DAISIE/CONTRIBUTING.html","id":null,"dir":"","previous_headings":"","what":"DAISIE Contributing Guidelines","title":"DAISIE Contributing Guidelines","text":"Feature requests collaboration DAISIE encouraged. ensure consistency quality code many collaborators working codebase, certain conventions must followed. External pull-requests rejected changes required conditions met. happens, please aware way personal, sure appreciate interest DAISIE, rather, enforce rules ensure package readable bug-free can make .","code":""},{"path":"https://rsetienne.github.io/DAISIE/CONTRIBUTING.html","id":"naming","dir":"","previous_headings":"","what":"Naming","title":"DAISIE Contributing Guidelines","text":"Files functions file functions start prefix DAISIE_. Helper functions can go files start prefix DAISIE_ stored within DAISIE_ prefixed file owing point 1.","code":""},{"path":"https://rsetienne.github.io/DAISIE/CONTRIBUTING.html","id":"style","dir":"","previous_headings":"","what":"Style","title":"DAISIE Contributing Guidelines","text":"Code formatted according tidyverse style guide. can checked running devtools::lint(), examine DAISIE package check code line style guide give corrections error style exists.","code":""},{"path":"https://rsetienne.github.io/DAISIE/CONTRIBUTING.html","id":"coverage-and-testing","dir":"","previous_headings":"","what":"Coverage and testing","title":"DAISIE Contributing Guidelines","text":"Cover new functions unit test. Unit tests function way ensure new functions behave expected, internal form documentation. Unit tests cover things : correct type returned function called correctly, boundary cases behave expected, simple, short runs function return expected, correct output. helper function unit testing available usethis::use_test(). cursor function requiring testing, new file skeleton code testing generated. Test coverage can calculated using function devtools::test_coverage(). produce window function’s coverage across whole package. new functions must (least) 100% coverage. Integration tests encouraged. Integration tests, unlike unit tests, test functionality package unified way. Examples integration testing include testing entire ML routine. integration tests generally much slower run, request skipped local builds run Travis CI. Care still taken balance test’s speed usefulness, try make fast possible. still impossible, final option include said integration test DAISIE’s sister package DAISIEtesting, built specifically purpose.","code":""},{"path":"https://rsetienne.github.io/DAISIE/CONTRIBUTING.html","id":"documentation","dir":"","previous_headings":"","what":"Documentation","title":"DAISIE Contributing Guidelines","text":"Use R package roxygen2 document package individual functions. Use devtools::document() write NAMESPACE. functions documented using shortcut Ctrl + Alt + Shift + R cursor function name. write skeleton function documentation can write function description parameters, etc. Every function needs documentation. includes helper secondary functions. Internal functions require explicit documentation entry CRAN manual, marked @keyword Internal ensure developer documentation still accessible, preventing unnecessary clutter user manual. Parameter documentation written default_params_doc.R called function. Thus, individual function’s roxygen block NEVER @param field, instead @inheritParams default_params_doc. exported functions accompanied runnable easy read examples document possible flows code. means simulation can run IW CS modes, instance, example code provided methods. rare cases running example possible, e.g. virtually impossible make code fast, error expected, please write example anyway encapsulate \\dontthest{} \\dontrun{} tags respectively. Authorship/blame. direct indirect contributor piece code listed @author, unless specifically requested author. Similarly, code refers specific publication, please include formatted citation @references. Exported functions. mentioned , NAMESPACE handled automatically roxygen2. functions required users exported @export. example, sim_core family functions exported, sim family functions supposed .","code":""},{"path":"https://rsetienne.github.io/DAISIE/CONTRIBUTING.html","id":"git-github-and-continuous-integration","dir":"","previous_headings":"","what":"Git, GitHub and continuous integration","title":"DAISIE Contributing Guidelines","text":"DAISIE sorted collaborated via GitHub, repository. can make branch (permission maintainer Rampal, GitHub account name: @rsetienne), allow work code without disturbing existing working DAISIE (master branch). code working, can merged develop branch eventually master. Code can pushed branch using git, either command line directly RStudio. merge topic branch develop branch fails R CMD Check. can run R CMD Check locally using RStudio Ctrl + Shift + E, Windows need latest version RTools installed build check package source. Topic branches can merged develop, develop merged master. DAISIE package GitHub uses continuous integration (CI) using Travis CI. means every time push code GitHub repository built, checked errors test coverage calculated uploaded codecov.io.","code":""},{"path":"https://rsetienne.github.io/DAISIE/CONTRIBUTING.html","id":"vignette","dir":"","previous_headings":"","what":"Vignette","title":"DAISIE Contributing Guidelines","text":"vignette describes usage guides user using package. useful present capabilities package new user. Vignettes written Rmarkdown , comprise markdown formatted text regular R code ran generate vignette. Vignettes built every time package checked (meaning rebuilt Travis new pushed commit). Thus, contained code readable, concise, , fast run (replicates, high ML tolerance iteration count, etc), otherwise R CMD Check take long fail.","code":""},{"path":"https://rsetienne.github.io/DAISIE/articles/demo_CSvsIW.html","id":"load-prepare-and-visualize-data","dir":"Articles","previous_headings":"","what":"1. Load, prepare and visualize data","title":"Demo: Fitting clade-specific and island-wide diversity-dependence models in DAISIE","text":"want start directly model fitting can skip step go step 2. Load phylogenetic data Eleutherodacylus frogs island Hispaniola (used Etienne et al. 2020). dataset contains times colonization branching times species Eleutherodactylus frogs found island. data extracted dated molecular phylogeny Dugo-Cota et al 2019 (Ecology Letters 22:884–893). dataset includes 65 extant species, result five independent colonisation events island Hispaniola. can load data table/tibble format, making sure table headers match ones example. Eleutherodactylus data table","code":"data(frogs_datatable, package = \"DAISIE\")"},{"path":"https://rsetienne.github.io/DAISIE/articles/demo_CSvsIW.html","id":"the-table-contains-the-following-4-columns-column-headers-need-to-be-written-exactly-like-this","dir":"Articles","previous_headings":"1. Load, prepare and visualize data","what":"The table contains the following 4 columns (column headers need to be written exactly like this):","title":"Demo: Fitting clade-specific and island-wide diversity-dependence models in DAISIE","text":"Clade_name - Name clade/lineage island (e.g. clade code, genus name) Status - Endemicity status clade. Can following Endemic; Non_endemic; Endemic_MaxAge, Non_Endemic_MaxAge latter two options cases time colonisation believed overestimate. cases, DAISIE assume colonisation happened time colonisation time given Branching_times present, colonisation time given Branching_times age first cladogenesis event lineage (). MaxAge options can also used colonization time unknown, specifying “NA” column Branching_times, case DAISIE assume colonisation happened time age island present. Missing_species - Number extant species belong clade included phylogeny. Branching_times - First element colonisation time, subsequent elements branching times within island . e.g. c(colonisation_time, branching_time1; branching_time2). colonisation time unknown, ‘NA’ can specified. branching times unknown, replace ‘NA’ - just add corresponding number missing species column Missing_species.","code":""},{"path":"https://rsetienne.github.io/DAISIE/articles/demo_CSvsIW.html","id":"create-daisie-datalist-from-the-input-table","dir":"Articles","previous_headings":"","what":"1.1. Create DAISIE datalist from the input table","title":"Demo: Fitting clade-specific and island-wide diversity-dependence models in DAISIE","text":"case assuming island age 30 million years Hispaniola mainland pool size 300 species (number species may colonize island).","code":"frogs_datalist <- DAISIE_dataprep(         datatable = frogs_datatable,         island_age = 30,         M = 300)"},{"path":"https://rsetienne.github.io/DAISIE/articles/demo_CSvsIW.html","id":"view-daisie-datalist","dir":"Articles","previous_headings":"","what":"1.2. View DAISIE datalist","title":"Demo: Fitting clade-specific and island-wide diversity-dependence models in DAISIE","text":"Just type: DAISIE datalist includes data table frogs format DAISIE object can read subsequent maximum likelihood functions (e.g DAISIE_ML, DAISIE_ML_IW ). includes age island, number mainland species currently present island list extant independent colonisation events, including colonization branching times.","code":"frogs_datalist"},{"path":"https://rsetienne.github.io/DAISIE/articles/demo_CSvsIW.html","id":"visualise-the-data","dir":"Articles","previous_headings":"","what":"1.3. Visualise the data","title":"Demo: Fitting clade-specific and island-wide diversity-dependence models in DAISIE","text":"plot shows different colonization events, times colonization branching times (horizontal ticks). Dashed line shows age island. n=number species; m= number species missing.                    ","code":"DAISIE_plot_island(frogs_datalist)"},{"path":"https://rsetienne.github.io/DAISIE/articles/demo_CSvsIW.html","id":"plot-age-versus-diversity","dir":"Articles","previous_headings":"1.3. Visualise the data","what":"Plot age versus diversity","title":"Demo: Fitting clade-specific and island-wide diversity-dependence models in DAISIE","text":"","code":"# DAISIE_plot_age_diversity(frogs_datalist)"},{"path":"https://rsetienne.github.io/DAISIE/articles/demo_CSvsIW.html","id":"fit-daisie-models","dir":"Articles","previous_headings":"","what":"2. Fit DAISIE models","title":"Demo: Fitting clade-specific and island-wide diversity-dependence models in DAISIE","text":"skipped step 1, first load Hispaniola Eleutherodactylus datalist. _ fit five different DAISIE models phylogenetic data contained frogs_datalist: DI - diversity-independent model. Model K’ (carrying-capacity) set Inf. CS - clade-specific diversity-dependence model. CS_no_ana - clade-specific diversity-dependence model anagenesis. Equivalent CS model Etienne et al. 2020. IW - island-wide diversity-dependence model. IW_no_ana - island-wide diversity-dependence model anagenesis. Equivalent IW model Etienne et al. 2020. use DAISIE_ML DAISIE_ML_IW functions optimise likelihood. important settings specify functions: datalist - name DAISIE datalist (case frogs_datalist) Rate cladogenesis (per species island per time unit) Rate extinction (per species island per time unit) Carrying-capacity (K’) - maximum number species clade can reach island CS models; maximum number species island across clades IW models. Rate colonisation (per species mainland per time unit) Rate anagenesis (per species island per time unit) idparsopt - position parameters optimise (e.g. optimize cladogenesis anagenesis c(1,5). parsfix - parameters fixed, specify value (e.g. fixing K’ Inf fixing anagenesis 0 - c(Inf,0). idparsfix - position paratemers fixed (e.g. fix K’ anagenesis c(3,5)). ddmodel - Set 0 diversity-independent models; 11 diversity-dependent models (IW CS) cladogenesis colonisation decline linearly diversity. options. many options, check ? DAISIE_ML   IW models (IW IW_no_ana) use island-wide version DAISIE, computationally demanding. require high memory long run times. recommend run cluster. CS models can run regular computer laptop.  ","code":"data(frogs_datalist)"},{"path":"https://rsetienne.github.io/DAISIE/articles/demo_CSvsIW.html","id":"fit-di-model","dir":"Articles","previous_headings":"","what":"2.1 Fit DI model","title":"Demo: Fitting clade-specific and island-wide diversity-dependence models in DAISIE","text":"model contains 4 parameters: 1 - cladogenesis 2 - extinction 4 - colonisation 5 - anagenesis K’ fixed Inf Set ddmodel=0  ","code":"DAISIE_ML(   datalist = frogs_datalist,   initparsopt = c(0.18,0.03,0.0006,2),   idparsopt = c(1,2,4,5),   ddmodel = 0,   parsfix = Inf,   idparsfix = 3 ) #>    lambda_c         mu   K        gamma lambda_a    loglik df conv #> 1 0.1789218 0.02509053 Inf 0.0006259365  1568.88 -209.8634  4    0"},{"path":"https://rsetienne.github.io/DAISIE/articles/demo_CSvsIW.html","id":"fit-cs-model","dir":"Articles","previous_headings":"","what":"2.2 Fit CS model","title":"Demo: Fitting clade-specific and island-wide diversity-dependence models in DAISIE","text":"model contains 5 parameters: 1 - cladogenesis 2 - extinction 3 - K’ 4 - colonisation 5 - anagenesis Set ddmodel=11 Output shown .  ","code":"DAISIE_ML(   datalist = frogs_datalist,   initparsopt = c(0.44,0.11,36.44,0.0007,2),   idparsopt = c(1,2,3,4,5),   ddmodel = 11,   parsfix = NULL,   idparsfix = NULL )"},{"path":"https://rsetienne.github.io/DAISIE/articles/demo_CSvsIW.html","id":"fit-cs_no_ana-model","dir":"Articles","previous_headings":"","what":"2.3 Fit CS_no_ana model","title":"Demo: Fitting clade-specific and island-wide diversity-dependence models in DAISIE","text":"model contains 4 parameters: 1 - cladogenesis 2 - extinction 3 - K’ 4 - colonisation Set ddmodel=11 Output shown .  ","code":"DAISIE_ML(   datalist = frogs_datalist,   initparsopt = c(0.44,0.11,36.44,0.0007),   idparsopt = c(1,2,3,4),   ddmodel = 11,   parsfix = 0,   idparsfix = 5 )"},{"path":"https://rsetienne.github.io/DAISIE/articles/demo_CSvsIW.html","id":"fit-iw-model","dir":"Articles","previous_headings":"","what":"2.4 Fit IW model","title":"Demo: Fitting clade-specific and island-wide diversity-dependence models in DAISIE","text":"model contains 5 parameters: 1 - cladogenesis 2 - extinction 3 - K’ 4 - colonisation 5 - anagenesis Set ddmodel=11 Output shown (recommended run cluster).  ","code":"DAISIE_ML_IW(   datalist = frogs_datalist,   initparsopt = c(0.41, 0.17, 131.7, 0.0012, 2),   idparsopt = c(1,2,3,4,5),   ddmodel = 11,   parsfix = NULL,   idparsfix = NULL )"},{"path":"https://rsetienne.github.io/DAISIE/articles/demo_CSvsIW.html","id":"fit-iw_no_ana-model","dir":"Articles","previous_headings":"","what":"2.5 Fit IW_no_ana model","title":"Demo: Fitting clade-specific and island-wide diversity-dependence models in DAISIE","text":"model contains 4 parameters: 1 - cladogenesis 2 - extinction 3 - K’ 4 - colonisation Set ddmodel=11 Output shown (recommended run cluster).  ","code":"DAISIE_ML_IW(   datalist = frogs_datalist,   initparsopt = c(0.40, 0.17, 131.83, 0.0012),   idparsopt = c(1,2,3,4),   ddmodel = 11,   parsfix = 0,   idparsfix = 5 )"},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/articles/demo_CSvsIW.html","id":"simulate-islands-with-the-parameters-estimated-from-the-best-model-for-the-hispaniolan-eleutherodacytlus-data","dir":"Articles","previous_headings":"3. Simulate islands under given DAISIE models","what":"3.1 Simulate islands with the parameters estimated from the best model for the Hispaniolan Eleutherodacytlus data","title":"Demo: Fitting clade-specific and island-wide diversity-dependence models in DAISIE","text":"use DAISIE_sim function, simulates diversity dynamics island island birth specificied island age, based given set parameters (cladogenesis, extinction, carrying-capacity (K’), colonisation, anagenesis). important settings specify DAISIE_sim function: Rate cladogenesis Rate extinction Carrying-capacity (K’) Rate colonisation Rate anagenesis replicates - Number replicates simulate time - Time run simulation, example 20 million years M - Number species mainland pool divdepmodel - set CS clade-specific diversity-dependence; IW island-wide diversity-dependence Simulate CS model 30 million years, 100 replicates: Simulate IW model 30 million years, 100 replicates:  ","code":"set.seed(1) frog_sims_CS <- DAISIE_sim_cr(   time=30,   M=300,   pars=c(0.44,0.11,36.44,0.0007,0),   divdepmodel = \"CS\",   replicates= 100,   plot_sims = FALSE) #> Island replicate 1 #> Island replicate 2 #> Island replicate 3 #> Island replicate 4 #> Island replicate 5 #> Island replicate 6 #> Island replicate 7 #> Island replicate 8 #> Island replicate 9 #> Island replicate 10 #> Island replicate 11 #> Island replicate 12 #> Island replicate 13 #> Island replicate 14 #> Island replicate 15 #> Island replicate 16 #> Island replicate 17 #> Island replicate 18 #> Island replicate 19 #> Island replicate 20 #> Island replicate 21 #> Island replicate 22 #> Island replicate 23 #> Island replicate 24 #> Island replicate 25 #> Island replicate 26 #> Island replicate 27 #> Island replicate 28 #> Island replicate 29 #> Island replicate 30 #> Island replicate 31 #> Island replicate 32 #> Island replicate 33 #> Island replicate 34 #> Island replicate 35 #> Island replicate 36 #> Island replicate 37 #> Island replicate 38 #> Island replicate 39 #> 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Simulate islands under given DAISIE models","what":"3.2 Plot the species-through-time plots resulting from the simulations.","title":"Demo: Fitting clade-specific and island-wide diversity-dependence models in DAISIE","text":"","code":"DAISIE_plot_sims(frog_sims_CS)"},{"path":"https://rsetienne.github.io/DAISIE/articles/demo_optimize.html","id":"daisie-dynamic-assembly-of-island-biotas-through-speciation-immigration-and-extinction","dir":"Articles","previous_headings":"","what":"DAISIE – Dynamic Assembly of Island biotas through Speciation, Immigration and Extinction","title":"Demo optimizing parameters","text":"Citation: Valente LM, Phillimore AB, Etienne RS (2015) Equilibrium non- equilibrium dynamics simultaneously operate Galápagos islands. Ecology Letters, press.","code":""},{"path":"https://rsetienne.github.io/DAISIE/articles/demo_optimize.html","id":"loading-data-table","dir":"Articles","previous_headings":"DAISIE – Dynamic Assembly of Island biotas through Speciation, Immigration and Extinction","what":"Loading data table","title":"Demo optimizing parameters","text":"load package: raw dataset inputted table. Galápagos dataset table can visualized : row table represents independent colonisation event. table four columns: Clade_name: name independent colonization event. Endemic: applicable anagenetic species radiations. Non_endemic: taxon endemic island, age colonisation based phylogeny island non-island populations species sampled. Non_endemic_MaxAge: taxon endemic island, upper bound time colonisation island known. applies individuals island population species sampled, age species known. Endemic&Non_Endemic: endemic clade present mainland ancestor re-colonized. remote islands expected rare. Missing_species: Number island species sampled particular clade (applicable radiations). Branching_times – stem age population/species case Non-endemic, Non-endemic_MaxAge Endemic anagenetic species. cladogenetic species branching times radiation including stem age radiation. Note – species within radiation found island (e.g. back-colonisation) branching times species excluded, mainland species pool treated static. data can also visualized:","code":"library(DAISIE) data(Galapagos_datatable) knitr::kable(Galapagos_datatable) DAISIE::DAISIE_plot_island(Galapagos_datatable, island_age = 4) #> Colonisation time of 7.456 for Coccyzus is older than island age #> Colonisation time of 10.285 for Pyrocephalus is older than island age"},{"path":"https://rsetienne.github.io/DAISIE/articles/demo_optimize.html","id":"formatting-table-to-run-in-daisie","dir":"Articles","previous_headings":"DAISIE – Dynamic Assembly of Island biotas through Speciation, Immigration and Extinction","what":"Formatting table to run in DAISIE","title":"Demo optimizing parameters","text":"running analyses, datatable needs converted DAISIE datalist format using function DAISIE_dataprep. prepare two different datalists based Galápagos datatable. 1st datalist treat taxa equivalent. specify island age four million years (island_age=4) mainland pool size 1000 (M=1000). 2nd datalist allow Darwin’s finches form separate group rates can decoupled governing macroevolutionary process clades (number_clade_types=2 list_type2_clades = “Finches”). set proportion Darwin’s finch type species mainland pool 0.163. (prop_type2_pool=0.163). prop_type2_pool specified default given value proportion Galapagos lineages Darwin’s finches represent (1/8=0.125 case). objects Galapagos_datalist Galapagos_datalist_2types can now run directly DAISIE functions.","code":"data(Galapagos_datatable)         Galapagos_datalist <- DAISIE_dataprep(    datatable = Galapagos_datatable,    island_age = 4,    M = 1000 ) #> Colonisation time of 7.456 for Coccyzus is older than island age #> Colonisation time of 10.285 for Pyrocephalus is older than island age data(Galapagos_datatable)   Galapagos_datalist_2types <- DAISIE_dataprep(    datatable = Galapagos_datatable,    island_age = 4,    M = 1000,    number_clade_types = 2,    list_type2_clades = \"Finches\",    prop_type2_pool = 0.163 ) #> Colonisation time of 7.456 for Coccyzus is older than island age #> Colonisation time of 10.285 for Pyrocephalus is older than island age"},{"path":"https://rsetienne.github.io/DAISIE/articles/demo_optimize.html","id":"optimizing-parameters-using-maximum-likelihood","dir":"Articles","previous_headings":"DAISIE – Dynamic Assembly of Island biotas through Speciation, Immigration and Extinction","what":"Optimizing parameters using maximum likelihood","title":"Demo optimizing parameters","text":"function conducts maximum likelihood optimization DAISIE model parameters called DAISIE_ML. Different models can specified using ddmodel option DAISIE_ML: ddmodel = 0 : diversity-dependence ddmodel = 1 : linear diversity-dependence speciation rate ddmodel = 11: linear diversity-dependence speciation immigration rate ddmodel = 2 : exponential diversity-dependence speciation rate ddmodel = 21: exponential diversity-dependence speciation immigration rate Different types parameters can optimized fixed. parameters given following order: (1) cladogenesis rate, (2) extinction rate, (3) K’ carrying capacity (maximum number species clade can attain within island), (4) colonisation rate, (5) anagenesis rate. identities parameters optimized fixed specified idparsopt idparsfix within DAISIE_ML function. example, optimize parameters set idparsopt=1:5 idparsfix=NULL. optimize parameters fix rate extinction, set idparsopt=c(1,3,4,5) idparsfix=2. optimize parameters except cladogenesis anagenesis set idparsopt=c(2,3,4) idparsfix=c(1,5). values parameters used initial values optimization specified initparsopt, values fixed specified parsfix. example, want optimize parameters starting value 2 set initparsopt=c(2,2,2,2,2) parsfix=NULL. want starting rates 0.1, K’ fixed 20, use initparsopt=c(0.1,0.1,0.1,0.1) parsfix=20. running data, strongly recommend test multiple initial starting parameters model, particularly optimizing models multiple free parameters, high risk trapped local likelihood sub-optima. also suggest running two rounds optimization using optimized parameter set 1st round initial starting values 2nd round. Also note initial starting values examples tutorial may appropriate data.","code":""},{"path":"https://rsetienne.github.io/DAISIE/articles/demo_optimize.html","id":"example-1-optimizing-all-parameters-with-diversity-dependence-in-speciation-and-colonisation","dir":"Articles","previous_headings":"DAISIE – Dynamic Assembly of Island biotas through Speciation, Immigration and Extinction > Optimizing parameters using maximum likelihood","what":"Example 1: Optimizing all parameters, with diversity-dependence in speciation and colonisation","title":"Demo optimizing parameters","text":"now optimize five parameters datalist clades share parameters. set model linear diversity-dependence speciation rate immigration rate using ddmodel=11. set initial rate cladogenesis 2.5, initial rate extinction 2.7, initial K’ value 20, initial rate colonisation 0.009 initial rate anagenesis 1.01 (initparsopt = c(2.5,2.7,20,0.009,1.01)). optimize 5 parameters (idparsopt = 1:5) fix parameters (parsfix = NULL, idparsfix = NULL). take several minutes run. parameters optimized fixed well loglikelihood initial starting parameters set shown top screen output DAISIE_ML. optimization completed, program output maximum likelihood parameter estimates maximum loglikelihood value. given dataset, likelihood different DAISIE models can compared information criteria BIC AIC.","code":"data(Galapagos_datalist)   DAISIE_ML(    datalist = Galapagos_datalist,    initparsopt = c(2.5,2.7,20,0.009,1.01),    ddmodel = 11,    idparsopt = 1:5,    parsfix = NULL,    idparsfix = NULL )"},{"path":"https://rsetienne.github.io/DAISIE/articles/demo_optimize.html","id":"example-2-optimizing-model-without-diversity-dependence","dir":"Articles","previous_headings":"DAISIE – Dynamic Assembly of Island biotas through Speciation, Immigration and Extinction > Optimizing parameters using maximum likelihood","what":"Example 2: Optimizing model without diversity-dependence","title":"Demo optimizing parameters","text":"optimize parameters model diversity-dependence, use default model (ddmodel=0), fix parameter number 3 corresponds K’ infinity (Inf).","code":"data(Galapagos_datalist)   DAISIE_ML(    datalist = Galapagos_datalist,    initparsopt = c(2.5,2.7,0.009,1.01),    idparsopt = c(1,2,4,5),    parsfix = Inf,    idparsfix = 3 )"},{"path":"https://rsetienne.github.io/DAISIE/articles/demo_optimize.html","id":"example-3-optimizing-model-with-no-diversity-dependence-and-no-anagenesis","dir":"Articles","previous_headings":"DAISIE – Dynamic Assembly of Island biotas through Speciation, Immigration and Extinction > Optimizing parameters using maximum likelihood","what":"Example 3: Optimizing model with no diversity-dependence and no anagenesis","title":"Demo optimizing parameters","text":"optimize parameters model diversity-dependence anagenesis, use default model (ddmodel=0), fix parameters number 3 5, correspond, respectively K’ rate anagenesis.","code":"data(Galapagos_datalist)  DAISIE_ML(    datalist=Galapagos_datalist,    initparsopt = c(2.5,2.7,0.009),    idparsopt = c(1,2,4),    parsfix = c(Inf,0),    idparsfix = c(3,5) )"},{"path":"https://rsetienne.github.io/DAISIE/articles/demo_optimize.html","id":"example-4-optimizing-all-parameters-but-allowing-darwins-finches-to-have-a-separate-rate-of-cladogenesis-","dir":"Articles","previous_headings":"DAISIE – Dynamic Assembly of Island biotas through Speciation, Immigration and Extinction > Optimizing parameters using maximum likelihood","what":"Example 4: Optimizing all parameters, but allowing Darwin’s finches to have a separate rate of cladogenesis.","title":"Demo optimizing parameters","text":"example use datalist Darwin’s finches specified separate type: Galapagos_datalist_2types. two types species considered, parameters second type species order first set parameters, start number 6: (6) cladogenesis rate type 2 species, (7) extinction rate type 2 species, (8) K’ type 2 species, (9) colonisation rate type 2 species, (10) anagenesis rate type 2 species. also additional parameter 2 types species considered: proportion species type 2 mainland pool. parameter number 11. optimize parameters, allow finches separate rate cladogenesis. fix proportion type 2 species mainland pool 0.163 (therefore fixing parameter 11 idparsfix=11 parsfix=0.163). Note allowing rate cladogenesis Darwin’s finches vary background rate, need specify rates Darwin’s finches remain background – using idparsnoshift = c(7,8,9,10)).","code":"data(Galapagos_datalist_2types)   DAISIE_ML(    ddmodel=11,    datalist=Galapagos_datalist_2types,    initparsopt= c(0.38,0.55,20,0.004,1.1,2.28),    idparsopt = c(1,2,3,4,5,6),    parsfix = 0.163,    idparsfix = c(11),    idparsnoshift = c(7,8,9,10) )"},{"path":"https://rsetienne.github.io/DAISIE/articles/demo_optimize.html","id":"example-5-optimizing-a-model-with-no-diversity-dependence-but-allowing-darwins-finches-to-have-a-separate-rate-of-cladogenesis-and-extinction-","dir":"Articles","previous_headings":"DAISIE – Dynamic Assembly of Island biotas through Speciation, Immigration and Extinction > Optimizing parameters using maximum likelihood","what":"Example 5: Optimizing a model with no diversity-dependence, but allowing Darwin’s finches to have a separate rate of cladogenesis and extinction.","title":"Demo optimizing parameters","text":"","code":"data(Galapagos_datalist_2types)    DAISIE_ML(    ddmodel=0,    datalist=Galapagos_datalist_2types,    initparsopt = c(0.38,0.55,0.004,1.1,2.28,2),    idparsopt = c(1,2,4,5,6,7),    parsfix = c(Inf,0.163),    idparsfix = c(3,11),    idparsnoshift = c(8,9,10) )"},{"path":"https://rsetienne.github.io/DAISIE/articles/demo_sim.html","id":"daisie-dynamic-assembly-of-island-biotas-through-speciation-immigration-and-extinction","dir":"Articles","previous_headings":"","what":"DAISIE – Dynamic Assembly of Island biotas through Speciation, Immigration and Extinction","title":"Demo simulating islands","text":"Citation: Valente LM, Phillimore AB, Etienne RS (2015) Equilibrium non- equilibrium dynamics simultaneously operate Galápagos islands. Ecology Letters, 18(8), 844-852. https://doi.org/10.1111/ele.12461.","code":""},{"path":"https://rsetienne.github.io/DAISIE/articles/demo_sim.html","id":"loading","dir":"Articles","previous_headings":"DAISIE – Dynamic Assembly of Island biotas through Speciation, Immigration and Extinction","what":"Loading","title":"Demo simulating islands","text":"load package:","code":"library(DAISIE)"},{"path":"https://rsetienne.github.io/DAISIE/articles/demo_sim.html","id":"simulating-islands","dir":"Articles","previous_headings":"DAISIE – Dynamic Assembly of Island biotas through Speciation, Immigration and Extinction","what":"Simulating islands","title":"Demo simulating islands","text":"function DAISIE_sim allows simulation DAISIE models plots results. user specifies parameters simulated, number replicates, length simulation (typically island age), number species mainland pool. plot_sims option set default (TRUE) function produce species- -time plot showing accumulation total, endemic non-endemic species time, well confidence intervals total number species. shorten run-time vignette, reduce number n_replicates. increased accuracy, increase number.","code":"n_mainland_species <- 1000 island_age <- 4 n_replicates <- 10"},{"path":"https://rsetienne.github.io/DAISIE/articles/demo_sim.html","id":"example-5-1-simulating-10-islands-with-no-diversity-dependence-all-species-sharing-the-same-parameters-and-plotting-the-results","dir":"Articles","previous_headings":"DAISIE – Dynamic Assembly of Island biotas through Speciation, Immigration and Extinction > Simulating islands","what":"Example 5.1 – Simulating 10 islands with no diversity-dependence, all species sharing the same parameters, and plotting the results","title":"Demo simulating islands","text":"object island_replicates contains results simulation DAISIE format. 10 islands stored object, island replicate can viewed separately. example, type island_replicates[[1]] view first replicate. element list relating island contains table number species time, well branching time information independent colonisation event extant end simulation.","code":"set.seed(42) clado_rate <- 2.550687345 # cladogenesis rate ext_rate <- 2.683454548 # extinction rate clade_carr_cap <- Inf # clade-level carrying capacity imm_rate <- 0.00933207 # immigration rate ana_rate <- 1.010073119 # anagenesis rate  island_replicates <- DAISIE_sim_cr(    time = island_age,   M = n_mainland_species,    pars = c(clado_rate, ext_rate, clade_carr_cap, imm_rate, ana_rate),   replicates = n_replicates,   plot_sims = FALSE,   verbose = FALSE ) DAISIE_plot_sims(island_replicates = island_replicates)"},{"path":"https://rsetienne.github.io/DAISIE/articles/demo_sim.html","id":"example-5-2-simulating-10-islands-with-diversity-dependence-k10-all-species-sharing-the-same-parameters-and-plotting-the-results","dir":"Articles","previous_headings":"DAISIE – Dynamic Assembly of Island biotas through Speciation, Immigration and Extinction > Simulating islands","what":"Example 5.2 – Simulating 10 islands with diversity-dependence (K’=10), all species sharing the same parameters, and plotting the results","title":"Demo simulating islands","text":"","code":"clado_rate <- 2.550687345 # cladogenesis rate ext_rate <- 2.683454548 # extinction rate clade_carr_cap <- 10.0  # clade-level carrying capacity imm_rate <- 0.00933207 # immigration rate ana_rate <- 1.010073119 # anagenesis rate  island_replicates_K <- DAISIE_sim_cr(    time = island_age,    M = n_mainland_species,    pars = c(clado_rate, ext_rate, clade_carr_cap, imm_rate, ana_rate),   replicates = n_replicates,   plot_sims = FALSE,   verbose = FALSE )  DAISIE_plot_sims(island_replicates_K)"},{"path":"https://rsetienne.github.io/DAISIE/articles/demo_sim.html","id":"example-5-3-simulating-10-islands-allowing-darwins-finches-to-have-a-higher-rate-of-cladogenesis","dir":"Articles","previous_headings":"DAISIE – Dynamic Assembly of Island biotas through Speciation, Immigration and Extinction > Simulating islands","what":"Example 5.3 – Simulating 10 islands allowing Darwin’s finches to have a higher rate of cladogenesis:","title":"Demo simulating islands","text":"produces figure similar Fig. 2, three plots: one total number species, one species type 1 one species type 2. Accessing island replicate individually (e.g. island_replicates_2types[[15]]) shows information branching times species--time tables total, type 1 species type 2 species.","code":"clado_rate_1 <- 0.38 # cladogenesis rate ext_rate_1 <- 0.55 # extinction rate clade_carr_cap_1 <- Inf  # clade-level carrying capacity imm_rate_1 <- 0.04 # immigration rate ana_rate_1 <- 1.10 # anagenesis rate  clado_rate_2 <- 0.38 # cladogenesis rate ext_rate_2 <- ext_rate_1 # extinction rate clade_carr_cap_2 <- clade_carr_cap_1  # clade-level carrying capacity imm_rate_2 <- imm_rate_1 # immigration rate ana_rate_2 <- ana_rate_1 # anagenesis rate  island_replicates_2types <- DAISIE_sim_cr(    time = island_age,   M = n_mainland_species,    pars = c(     clado_rate_1, ext_rate_1, clade_carr_cap_1, imm_rate_1, ana_rate_1,     clado_rate_2, ext_rate_2, clade_carr_cap_2, imm_rate_2, ana_rate_2   ),   replicates = n_replicates,    prop_type2_pool = 0.163,   plot_sims = FALSE,   verbose = FALSE ) DAISIE_plot_sims(island_replicates_2types)"},{"path":"https://rsetienne.github.io/DAISIE/articles/stac_key.html","id":"key-for-the-different-values-of-stac-that-can-be-used-in-daisie-objects-and-how-they-can-be-specified-in-the-function-daisie_dataprep-","dir":"Articles","previous_headings":"","what":"Key for the different values of stac that can be used in DAISIE objects, and how they can be specified in the function DAISIE_dataprep.","title":"DAISIE `stac` values","text":"  stac stands “status clade” formed immigrant. important part DAISIE objects informs likelihood functions endemicity status type data available insular clade. colonisation event extant species island needs stac value specified.","code":""},{"path":"https://rsetienne.github.io/DAISIE/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Rampal S. Etienne. Author, maintainer. Luis Valente. Author. Albert B. Phillimore. Author. Bart Haegeman. Author. Joshua W. Lambert. Author. Pedro Santos Neves. Author. Shu Xie. Author. Richèl J.C. Bilderbeek. Author. Hanno Hildenbrandt. Author. Torsten Hauffe. Contributor. Giovanni Laudanno. Contributor. Nadiah Kristensen. Contributor. Raphael Scherrer. Contributor.","code":""},{"path":"https://rsetienne.github.io/DAISIE/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Etienne R, Valente L, Phillimore , Haegeman B, Lambert J, Santos Neves P, Xie S, Bilderbeek R, Hildenbrandt H (2023). DAISIE: Dynamical Assembly Islands Speciation, Immigration Extinction. https://github.com/rsetienne/DAISIE, https://rsetienne.github.io/DAISIE/.","code":"@Manual{,   title = {DAISIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction},   author = {Rampal S. Etienne and Luis Valente and Albert B. Phillimore and Bart Haegeman and Joshua W. Lambert and Pedro {Santos Neves} and Shu Xie and Richèl J.C. Bilderbeek and Hanno Hildenbrandt},   year = {2023},   note = {https://github.com/rsetienne/DAISIE, https://rsetienne.github.io/DAISIE/}, }"},{"path":"https://rsetienne.github.io/DAISIE/index.html","id":"daisie-dynamic-assembly-of-island-biota-through-speciation-immigration-and-extinction","dir":"","previous_headings":"","what":"Dynamical Assembly of Islands by Speciation, Immigration and Extinction","title":"Dynamical Assembly of Islands by Speciation, Immigration and Extinction","text":"DAISIE R package simulates computes (maximum) likelihood dynamical model island biota assembly speciation, immigration extinction. model can fitted empirical dated phylogenies simulated data. overview simulation functionality see . Details overview maximum likelihood inference capabilities estimate parameters see . details comparing two diversity depedence models see .","code":""},{"path":"https://rsetienne.github.io/DAISIE/index.html","id":"installing-daisie","dir":"","previous_headings":"","what":"Installing DAISIE","title":"Dynamical Assembly of Islands by Speciation, Immigration and Extinction","text":"N.B.: MacOS users may experience issues installing DAISIE, especially MacOS Big Sur. case, please see detailed installation instructions. DAISIE package stable version CRAN development version GitHub.","code":""},{"path":"https://rsetienne.github.io/DAISIE/index.html","id":"from-cran","dir":"","previous_headings":"Installing DAISIE","what":"From CRAN","title":"Dynamical Assembly of Islands by Speciation, Immigration and Extinction","text":"within R, :","code":"install.packages(\"DAISIE\")"},{"path":"https://rsetienne.github.io/DAISIE/index.html","id":"from-github","dir":"","previous_headings":"Installing DAISIE","what":"From GitHub","title":"Dynamical Assembly of Islands by Speciation, Immigration and Extinction","text":"Install DAISIE GitHub repository running:","code":"install.packages(\"remotes\") remotes::install_github(\"rsetienne/DAISIE\")"},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/index.html","id":"from-cran-1","dir":"","previous_headings":"Using DAISIE as a package dependency","what":"From CRAN","title":"Dynamical Assembly of Islands by Speciation, Immigration and Extinction","text":"DESCRIPTION file, add DAISIE normal package. package directly uses DAISIE: package uses DAISIE peripherals (e.g. vignettes tests):","code":"Imports:   DAISIE Suggests:   DAISIE"},{"path":"https://rsetienne.github.io/DAISIE/index.html","id":"from-github-1","dir":"","previous_headings":"Using DAISIE as a package dependency","what":"From GitHub","title":"Dynamical Assembly of Islands by Speciation, Immigration and Extinction","text":"","code":"Remotes:   rsetienne/DAISIE"},{"path":"https://rsetienne.github.io/DAISIE/index.html","id":"supportquestions","dir":"","previous_headings":"","what":"Support/Questions","title":"Dynamical Assembly of Islands by Speciation, Immigration and Extinction","text":"feature requests bug-reports matters, please submit issue.","code":""},{"path":"https://rsetienne.github.io/DAISIE/index.html","id":"feature-branches","dir":"","previous_headings":"","what":"Feature branches","title":"Dynamical Assembly of Islands by Speciation, Immigration and Extinction","text":"master: build always pass. @rsetienne control develop master merges. develop: merge feature branches, merge master @rsetienne iff build passes.","code":""},{"path":"https://rsetienne.github.io/DAISIE/index.html","id":"contributors","dir":"","previous_headings":"","what":"Contributors","title":"Dynamical Assembly of Islands by Speciation, Immigration and Extinction","text":"DAISIE originally developed Rampal S. Etienne, Luis Valente, Albert B. Phillimore Bart Haegeman. continuously maintained members @tece-lab, University Groningen.","code":""},{"path":"https://rsetienne.github.io/DAISIE/index.html","id":"references","dir":"","previous_headings":"","what":"References","title":"Dynamical Assembly of Islands by Speciation, Immigration and Extinction","text":"Etienne R. S., Valente, L., Phillimore, . B., Haegeman, B., Lambert, J. W., Neves, P., Xie, S., Bilderbeek, R. J. C., & Hildenbrandt, H. (2021). DAISIE: Dynamical Assembly Islands Speciation, Immigration Extinction. R package version 4.0.2. https://cran.r-project.org/package=DAISIE. https://doi.org/10.5281/zenodo.4054058 Valente, L., Etienne, R.S., & Phillimore, .B. (2014). effects island ontogeny species diversity phylogeny. Proceedings Royal Society B: Biological Sciences, 281(1784), 20133227–20133227. http://doi.org/10.1098/rspb.2013.3227 Valente, L., Phillimore, .B., & Etienne, R.S. (2015). Equilibrium non-equilibrium dynamics simultaneously operate Galápagos islands. Ecology Letters, 18(8), 844–852. http://doi.org/10.1111/ele.12461 Valente, L., Etienne, R.S., & Dávalos, L.M. (2017). Recent extinctions disturb path equilibrium diversity Caribbean bats. Nature Ecology & Evolution, 1(2), 0026. http://doi.org/10.1038/s41559-016-0026 Valente, L., Illera, J.C., Havenstein, K., Pallien, T., Etienne, R.S., & Tiedemann, R. (2017). Equilibrium Bird Species Diversity Atlantic Islands. Current Biology, 27(11), 1660-1666. https://doi.org/10.1016/j.cub.2017.04.053 Valente, L., Phillimore, .B., & Etienne, R.S. (2018). Using molecular phylogenies island biogeography: ’s time. Ecography, 1–3. http://doi.org/10.1111/ecog.03503 Valente, L., Etienne, R.S., & Garcia-R., J.C. (2019). Deep Macroevolutionary Impact Humans New Zealand’s Unique Avifauna. Current Biology 29 (15): 2563-2569.e4. https://doi.org/10.1016/j.cub.2019.06.058 Valente, L., Phillimore, .B., Melo, M., Warren, B.H., Clegg, S.M., Havenstein, K., Tiedemann, R., Illera, J.C., Thebaud, C., Aschenbach, T. & Etienne, R.S. (2020). Simple Dynamic Model Explains Diversity Island Birds Worldwide. Nature 579 (7797): 92–96. https://doi.org/10.1038/s41586-020-2022-5 Hauffe, T., Delicado, D., Etienne, R.S., & Valente, L. (2020). Lake expansion elevates equilibrium diversity via increasing colonization. Journal Biogeography 47: 1849–1860. https://doi.org/10.1111/jbi.13914 Valente, L., Kristensen, N., Phillimore, . B., & Etienne, R. S. (2021). Report programming bugs DAISIE R package: consequences correction. https://doi.org/10.32942/osf.io/w5ntf Santos Neves, P.*, Lambert, J. W.*, Valente, L., & Etienne, R. S. (2022). robustness simple dynamic model island biodiversity geological sea-level change. Journal Biogeography 49: 2091-2104. https://doi.org/10.1111/jbi.14519 Lambert, J. W., Santos Neves, P., Bilderbeek, R. L. C., Valente, L., Etienne, R. S. (2022). effect mainland dynamics data parameter estimates island biogeography. bioRxiv. https://doi.org/10.1101/2022.01.13.476210 Xie, S., Valente, L., Etienne, R. S. (2023). Can ignore trait-dependent colonization diversification island biogeography? Evolution. https://doi.org/10.1093/evolut/qpad006 Michielsen, N. M., Goodman, S. M., Soarimalala, V., van der Geer, . . E., Dávalos, L. M., Saville, G. ., Upham, N., Valente, L. (2023). macroevolutionary impact recent imminent mammal extinctions Madagascar. Nature Communications 14 (14). https://doi.org/10.1038/s41467-022-35215-3","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/Bats_GreaterAntilles.html","id":null,"dir":"Reference","previous_headings":"","what":"Colonization and branching times of Noctilionoid bats from the Greater Antilles. — Bats_GreaterAntilles","title":"Colonization and branching times of Noctilionoid bats from the Greater Antilles. — Bats_GreaterAntilles","text":"list containing colonization branching times noctilionoid bats Greater Antilles. Main dataset used Valente, Etienne Dávalos (2017) Nature Ecology Evolution. Island age 20 Myr mainland pool size 100 species. first element list two components: $island_age - island age $not_present - number mainland lineages present island  following elements list contain information single colonist lineage island 5 components:$colonist_name - name species clade colonized island $branching_times - island age followed stem age population/species case Non-endemic, Non-endemic_MaxAge species Endemic species close relatives island. endemic clades one species island (cladogenetic clades/ radiations) island age followed branching times island clade including stem age clade.$stac - status colonist  * Non_endemic_MaxAge: 1  * Endemic: 2  * Endemic&Non_Endemic: 3  * Non_endemic: 4  * Endemic_MaxAge: 5 6 $missing_species - number island species sampled particular clade (applicable endemic clades) $type1or2 - whether colonist belongs type 1 type 2. dataset equal 1.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/Bats_GreaterAntilles.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Colonization and branching times of Noctilionoid bats from the Greater Antilles. — Bats_GreaterAntilles","text":"list 17 elements, first contains 2 elements following 16 containing 5 components.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/Bats_GreaterAntilles.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Colonization and branching times of Noctilionoid bats from the Greater Antilles. — Bats_GreaterAntilles","text":"Valente L, Etienne RS, Dávalos (2017) Recent extinctions disturb path equilibrium diversity Caribbean bats. Nature Ecology Evolution, 1, 26.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/Biwa_datalist.html","id":null,"dir":"Reference","previous_headings":"","what":"Colonization and branching times of 68 fish clades. — Biwa_datalist","title":"Colonization and branching times of 68 fish clades. — Biwa_datalist","text":"list containing colonization branching times fishes Lake Biwa (Japan). Main dataset used Hauffe et al (2020). list can generated using DAISIE_dataprep function, converts user-specified data table data object, object can course also entered directly. R list object following elements. first element list two components: $island_age - island age $not_present - number mainland lineages present island  following elements list contains information single colonist lineage island 5 components:$colonist_name - name species clade colonized island $branching_times - island age followed stem age population/species case Non-endemic, Non-endemic_MaxAge species Endemic species close relatives island. endemic clades one species island (cladogenetic clades/ radiations) island age followed branching times island clade including stem age clade.$stac - status colonist  * Non_endemic_MaxAge: 1  * Endemic: 2  * Endemic&Non_Endemic: 3  * Non_endemic: 4  * Endemic_MaxAge: 5 6 $missing_species - number island species sampled particular clade (applicable endemic clades) $type1or2 - whether colonist belongs type 1 type 2. dataset equal 1.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/Biwa_datalist.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Colonization and branching times of 68 fish clades. — Biwa_datalist","text":"list 69 elements, first contains 2 elements following 68 containing 5 components.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/Biwa_datalist.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Colonization and branching times of 68 fish clades. — Biwa_datalist","text":"Hauffe, T., D. Delicado, R.S. Etienne L. Valente. Lake expansion elevates equilibrium diversity via increasing colonisation. (2020) Journal Biogeography","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE-package.html","id":null,"dir":"Reference","previous_headings":"","what":"DAISIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction — DAISIE-package","title":"DAISIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction — DAISIE-package","text":"DAISIE island biogeography model assumes island biota assembly governed immigration, extinction speciation cladogenesis anagenesis. likelihood-based statistical package can simulate islands estimate parameters DAISIE model based phylogenetic/phylogeographic data. Cladogenesis immigration rates can dependent diversity.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE-package.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"DAISIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction — DAISIE-package","text":"Valente, L. M., Etienne, R. S., & Phillimore, . B. (2014). effects island ontogeny species diversity phylogeny. Proceedings Royal Society London. Series B, Biological Sciences 281, 20133227. doi:10.1098/rspb.2013.3227 . Valente, L., .B. Phillimore & R.S. Etienne (2015). Equilibrium non-equilibrium dynamics simultaneously operate Galapagos islands. Ecology Letters 18: 844-852, doi:10.1111/ele.12461 . Valente, L., R.S. Etienne & L. Davalos (2017). Recent extinctions disturb path equilibrium diversity Caribbean bats. Nature Ecology Evolution 1: 0026. doi:10.1038/s41559-016-0026 . Valente, L., Illera, J. C., Havenstein, K., Pallien, T., Etienne, R. S., & Tiedemann, R. (2017). Equilibrium Bird Species Diversity Atlantic Islands. Current Biology 27: 1660-1666. doi:10.1016/j.cub.2017.04.053 . Valente, L., Phillimore, . B., & Etienne, R. (2018). Using molecular phylogenies island biogeography: time. Ecography 41: 1684-1686. doi:10.1111/ecog.03503 . Valente, L., Etienne, R. S., & Garcia-R, J. C. (2019). Deep macroevolutionary impact humans New Zealand's unique avifauna. Current Biology 29: 2563-2569. doi:10.1016/j.cub.2019.06.058 . Valente, L., Phillimore, . B., Melo, M., Warren, B. H., Clegg, S. M., Havenstein, K., & Etienne, R. S. (2020). simple dynamic model explains diversity island birds worldwide. Nature 579: 92-96. doi:10.1038/s41586-020-2022-5 . Hauffe, T., Delicado, D., Etienne, R.S., & Valente, L. (2020). Lake expansion elevates equilibrium diversity via increasing colonization. Journal Biogeography 47: 1849–1860. doi:10.1111/jbi.13914 . Valente, L., Kristensen, N., Phillimore, . B., & Etienne, R. S. (2021). Report programming bugs DAISIE R package: consequences correction. EcoEvoRxiv. doi:10.32942/osf.io/w5ntf . Santos Neves, P., Lambert, J. W., Valente, L., & Etienne, R. S. (2022). robustness simple dynamic model island biodiversity geological sea-level change. Journal Biogeography 49: 2091-2104. doi:10.1111/jbi.14519 . Lambert, J. W., Santos Neves, P., Bilderbeek, R. L. C., Valente, L., Etienne, R. S. (2022). effect mainland dynamics data parameter estimates island biogeography. bioRxiv. doi:10.1101/2022.01.13.476210 . Xie, S., Valente, L., Etienne, R. S. (2023). Can ignore trait-dependent colonization diversification island biogeography? Evolution. doi:10.1093/evolut/qpad006 . Michielsen, N. M., Goodman, S. M., Soarimalala, V., van der Geer, . . E., Dávalos, L. M., Saville, G. ., Upham, N., Valente, L. (2023). macroevolutionary impact recent imminent mammal extinctions Madagascar. Nature Communications 14 (14).doi:10.1038/s41467-022-35215-3 .","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"DAISIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction — DAISIE-package","text":"Maintainer: Rampal S. Etienne r.s.etienne@rug.nl (ORCID) Authors: Luis Valente luis.valente@naturalis.nl (ORCID) Albert B. Phillimore (ORCID) Bart Haegeman (ORCID) Joshua W. Lambert j.w.l.lambert@rug.nl (ORCID) Pedro Santos Neves p.m.santos.neves@rug.nl (ORCID) Shu Xie s.xie@rug.nl (ORCID) Richèl J.C. Bilderbeek richel@richelbilderbeek.nl (ORCID) Hanno Hildenbrandt h.hildenbrandt@rug.nl (ORCID) contributors: Torsten Hauffe torsten.hauffe@gmail.com (ORCID) [contributor] Giovanni Laudanno glaudanno@gmail.com (ORCID) [contributor] Nadiah Kristensen nadiah@nadiah.org (ORCID) [contributor] Raphael Scherrer r.scherrer@rug.nl (ORCID) [contributor]","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_CS_max_steps.html","id":null,"dir":"Reference","previous_headings":"","what":"CS iteration control — DAISIE_CS_max_steps","title":"CS iteration control — DAISIE_CS_max_steps","text":"Sets retrieves max. number iterations used odeint solver.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_CS_max_steps.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"CS iteration control — DAISIE_CS_max_steps","text":"","code":"DAISIE_CS_max_steps(max_steps)"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_CS_max_steps.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"CS iteration control — DAISIE_CS_max_steps","text":"max_steps max_steps: sets max. iterations max_steps.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_CS_max_steps.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"CS iteration control — DAISIE_CS_max_steps","text":"current max. iterations","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ExpEIN.html","id":null,"dir":"Reference","previous_headings":"","what":"The expected number of endemics and non-endemics under the DAISIE model — DAISIE_ExpEIN","title":"The expected number of endemics and non-endemics under the DAISIE model — DAISIE_ExpEIN","text":"function calculates expected number endemics, non-endemics sum given set parameter values, given mainland species pool size given time","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ExpEIN.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The expected number of endemics and non-endemics under the DAISIE model — DAISIE_ExpEIN","text":"","code":"DAISIE_ExpEIN(t, pars, M, initEI = c(0, 0))"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ExpEIN.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The expected number of endemics and non-endemics under the DAISIE model — DAISIE_ExpEIN","text":"t time expectations need computed. pars numeric vector containing model parameters: pars[1]: lambda^c (cladogenesis rate) pars[2]: mu (extinction rate) pars[3]: K (carrying capacity), set K=Inf diversity   independence. pars[4]: gamma (immigration rate) pars[5]: lambda^(anagenesis rate) pars[6]: lambda^c (cladogenesis rate) either type 2 species   rate set 2 rate shift model pars[7]: mu (extinction rate) either type 2 species rate   set 2 rate shift model pars[8]: K (carrying capacity) either type 2 species rate   set 2 rate shift model, set K=Inf diversity independence. pars[9]: gamma (immigration rate) either type 2 species   rate set 2 rate shift model pars[10]: lambda^(anagenesis rate) either type 2   species rate set 2 rate shift model Elements 6:10 required type 2 species included rate shift model. DAISIE_sim_relaxed_rate() pars[6] standard deviation gamma distribution relaxed parameter parameter chosen relaxed_par argument mean gamma distribution relaxed parameter. M Numeric defining size mainland pool, .e. number species can potentially colonize island. initEI initial values number endemics   non-endemics. DAISIE_probdist() DAISIE_margprobdist() either initprobs must NULL. DAISIE_numcol() NULL, assumed island   empty.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ExpEIN.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The expected number of endemics and non-endemics under the DAISIE model — DAISIE_ExpEIN","text":"output list three elements: ExpE number endemic species ExpI number non-endemic species ExpN sum number endemics non-endemics","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ExpEIN.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"The expected number of endemics and non-endemics under the DAISIE model — DAISIE_ExpEIN","text":"Valente, L.M., .B. Phillimore R.S. Etienne (2015). Equilibrium non-equilibrium dynamics simultaneously operate Galapagos islands. Ecology Letters 18: 844-852.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ExpEIN.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"The expected number of endemics and non-endemics under the DAISIE model — DAISIE_ExpEIN","text":"Rampal S. Etienne","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ExpEIN.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"The expected number of endemics and non-endemics under the DAISIE model — DAISIE_ExpEIN","text":"","code":"### Compute the expected values at t = 4, for a mainland pool size of 1000 potential # colonists and a vector of 5 parameters (cladogenesis, extinction, clade-level carrying # capacity, immigration, anagenesis)  DAISIE_ExpEIN(    t = 4,    pars = c(0.5,0.1,Inf,0.01,0.4),    M = 1000    ) #> $ExpE #> [1] 88.46714 #>  #> $ExpI #> [1] 9.726758 #>  #> $ExpN #> [1] 98.1939 #>"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_IC.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculates information criterion from DAISIE ML estimates? — DAISIE_IC","title":"Calculates information criterion from DAISIE ML estimates? — DAISIE_IC","text":"Calculates information criterion DAISIE ML estimates?","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_IC.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculates information criterion from DAISIE ML estimates? — DAISIE_IC","text":"","code":"DAISIE_IC(   datalist,   initparsopt,   idparsopt,   parsfix,   idparsfix,   endmc = 1000,   res = 100,   cond = 0,   ddmodel = 0 )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_IC.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculates information criterion from DAISIE ML estimates? — DAISIE_IC","text":"datalist Data object containing information colonisation branching times. object can generated using DAISIE_dataprep function, converts user-specified data table data object, object can course also entered directly. R list object following elements. first element list two three components: $island_age - island age  , depending whether distinction types made, :$not_present - number mainland lineages present island  :$not_present_type1 - number mainland lineages type 1 present island $not_present_type2 - number mainland lineages type 2 present island  remaining elements list contains information single colonist lineage island 5 components:$colonist_name - name species clade colonized island $branching_times - island age followed stem age population/species case Non-endemic, Non-endemic_MaxAge species Endemic species close relatives island. endemic clades one species island (cladogenetic clades/ radiations) island age followed branching times island clade including stem age clade$stac - status colonist  * Non_endemic_MaxAge: 1  * Endemic: 2  * Endemic&Non_Endemic: 3  * Non_Endemic: 4  * Endemic_Singleton_MaxAge: 5  * Endemic_Clade_MaxAge: 6  * Endemic&Non_Endemic_Clade_MaxAge: 7 $missing_species - number island species sampled particular clade (applicable endemic clades) $type1or2 - whether colonist belongs type 1 type 2 initparsopt initial values parameters must optimized, positive. idparsopt ids parameters must optimized. ids defined follows:  id = 1 corresponds lambda^c (cladogenesis rate)  id = 2 corresponds mu (extinction rate)  id = 3 corresponds K (clade-level carrying capacity)  id = 4 corresponds gamma (immigration rate)  id = 5 corresponds lambda^(anagenesis rate)  id = 6 corresponds lambda^c (cladogenesis rate) optional subset species  id = 7 corresponds mu (extinction rate) optional subset species id = 8 corresponds K (clade-level carrying capacity) optional subset species id = 9 corresponds gamma (immigration rate) optional subset species id = 10 corresponds lambda^(anagenesis rate) optional subset species id = 11 corresponds p_f (fraction mainland species belongs second subset species. parsfix values parameters optimized. idparsfix ids parameters optimized, e.g. c(1,3) lambda^c K optimized. endmc Numeric many simulations run. res Sets maximum number species probability must computed, must larger size largest clade. cond cond = 0 : conditioning island age  cond = 1 : conditioning island age non-extinction island biota . cond > 1 : conditioning island age least cond colonizations island. last option yet available IW model ddmodel Sets model diversity-dependence:  ddmodel = 0 : diversity dependence  ddmodel = 1 : linear dependence speciation rate  ddmodel = 11: linear dependence speciation rate immigration rate  ddmodel = 2 : exponential dependence speciation rate ddmodel = 21: exponential dependence speciation rate immigration rate","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_IC.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculates information criterion from DAISIE ML estimates? — DAISIE_IC","text":"List two numerics WIC AICb","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_IW_num_threads.html","id":null,"dir":"Reference","previous_headings":"","what":"IW concurrency control — DAISIE_IW_num_threads","title":"IW concurrency control — DAISIE_IW_num_threads","text":"Sets retrieves number threads used odeint solver.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_IW_num_threads.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"IW concurrency control — DAISIE_IW_num_threads","text":"","code":"DAISIE_IW_num_threads(num_threads)"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_IW_num_threads.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"IW concurrency control — DAISIE_IW_num_threads","text":"num_threads num_threads < 0 omitted: retrieves number threads. num_threads = 0: sets number threads number available cores. num_threads = 1: single-threaded execution. num_threads > 1: sets number threads num_threads.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_IW_num_threads.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"IW concurrency control — DAISIE_IW_num_threads","text":"number threads","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_IW_num_threads.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"IW concurrency control — DAISIE_IW_num_threads","text":"maximum number threads limited value C++ standard library function std::thread::hardware_concurrency(). also default number threads upon library load. Multithreading incurs overhead. Therefore, single-threaded execution might faster small systems.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ML.html","id":null,"dir":"Reference","previous_headings":"","what":"Maximization of the loglikelihood under the DAISIE model with clade-specific\ndiversity-dependence — DAISIE_ML","title":"Maximization of the loglikelihood under the DAISIE model with clade-specific\ndiversity-dependence — DAISIE_ML","text":"function computes maximum likelihood estimates parameters DAISIE model clade-specific diversity-dependence data lineages colonizing island. also outputs corresponding loglikelihood can used model comparisons. result sort(c(idparsopt, idparsfix, idparsnoshift)) identical c(1:10). , error reported input incoherent. happens length initparsopt different length idparsopt, length parsfix different length idparsfix. Including 11th parameter (p_f) either idparsopt idparsfix (therefore initparsopt parsfix) optional. parameter specified, information data used, otherwise information data overruled.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ML.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Maximization of the loglikelihood under the DAISIE model with clade-specific\ndiversity-dependence — DAISIE_ML","text":"","code":"DAISIE_ML_CS(   datalist,   datatype = \"single\",   initparsopt,   idparsopt,   parsfix,   idparsfix,   idparsnoshift = 6:10,   idparsmat = NULL,   res = 100,   ddmodel = 0,   cond = 0,   island_ontogeny = NA,   eqmodel = 0,   x_E = 0.95,   x_I = 0.98,   tol = c(1e-04, 1e-05, 1e-07),   maxiter = 1000 * round((1.25)^length(idparsopt)),   methode = \"lsodes\",   optimmethod = \"subplex\",   CS_version = 1,   verbose = 0,   tolint = c(1e-16, 1e-10),   jitter = 0,   num_cycles = 1 )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ML.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Maximization of the loglikelihood under the DAISIE model with clade-specific\ndiversity-dependence — DAISIE_ML","text":"datalist Data object containing information colonisation branching times. object can generated using DAISIE_dataprep function, converts user-specified data table data object, object can course also entered directly. R list object following elements. first element list two three components: $island_age - island age  , depending whether distinction types made, :$not_present - number mainland lineages present island  :$not_present_type1 - number mainland lineages type 1 present island $not_present_type2 - number mainland lineages type 2 present island  remaining elements list contains information single colonist lineage island 5 components:$colonist_name - name species clade colonized island $branching_times - island age followed stem age population/species case Non-endemic, Non-endemic_MaxAge species Endemic species close relatives island. endemic clades one species island (cladogenetic clades/ radiations) island age followed branching times island clade including stem age clade$stac - status colonist  * Non_endemic_MaxAge: 1  * Endemic: 2  * Endemic&Non_Endemic: 3  * Non_Endemic: 4  * Endemic_Singleton_MaxAge: 5  * Endemic_Clade_MaxAge: 6  * Endemic&Non_Endemic_Clade_MaxAge: 7 $missing_species - number island species sampled particular clade (applicable endemic clades) $type1or2 - whether colonist belongs type 1 type 2 datatype Sets type data: 'single' single island archipelago treated one, 'multiple' multiple archipelagoes potentially sharing parameters. initparsopt initial values parameters must optimized, positive. idparsopt ids parameters must optimized. ids defined follows:  id = 1 corresponds lambda^c (cladogenesis rate)  id = 2 corresponds mu (extinction rate)  id = 3 corresponds K (clade-level carrying capacity)  id = 4 corresponds gamma (immigration rate)  id = 5 corresponds lambda^(anagenesis rate)  id = 6 corresponds lambda^c (cladogenesis rate) optional subset species  id = 7 corresponds mu (extinction rate) optional subset species id = 8 corresponds K (clade-level carrying capacity) optional subset species id = 9 corresponds gamma (immigration rate) optional subset species id = 10 corresponds lambda^(anagenesis rate) optional subset species id = 11 corresponds p_f (fraction mainland species belongs second subset species. parsfix values parameters optimized. idparsfix ids parameters optimized, e.g. c(1,3) lambda^c K optimized. idparsnoshift datatype = 'single' : ids parameters different two groups species; can apply ids 6:10, e.g. idparsnoshift = c(6,7) means lambda^c mu values groups. idparsmat datatype = 'multiple' : Matrix containing ids parameters, linking initparsopt parsfix. Per island system use following order:  * lac = (initial) cladogenesis rate  * mu = extinction rate  * K = maximum number species possible clade  * gam = (initial) immigration rate  * laa = (initial) anagenesis rate  Example: idparsmat = rbind(c(1, 2, 3, 4, 5), c(1, 2, 3, 6, 7)) different rates immigration anagenesis two islands. res Sets maximum number species probability must computed, must larger size largest clade. ddmodel Sets model diversity-dependence:  ddmodel = 0 : diversity dependence  ddmodel = 1 : linear dependence speciation rate  ddmodel = 11: linear dependence speciation rate immigration rate  ddmodel = 2 : exponential dependence speciation rate ddmodel = 21: exponential dependence speciation rate immigration rate cond cond = 0 : conditioning island age  cond = 1 : conditioning island age non-extinction island biota . cond > 1 : conditioning island age least cond colonizations island. last option yet available IW model island_ontogeny DAISIE_sim_time_dep(), DAISIE_ML_CS plotting string describing type island ontogeny. Can \"const\", \"beta\" beta function describing area time.  functions numeric describing type island ontogeny. Can 0 constant, 1 beta function describing area time. ML functions island_ontogeny = NA assumes constant ontogeny. Time dependent estimation yet available development still ongoing. return error called case. eqmodel Sets equilibrium constraint can used likelihood optimization. available datatype = 'single'. eqmodel = 0 : equilibrium assumed  eqmodel = 13 : near-equilibrium assumed endemics using deterministic equation endemics immigrants. Endemics must within x_E equilibrium value eqmodel = 15 : near-equilibrium assumed endemics immigrants using deterministic equation endemics immigrants. Endemics must within x_E equilibrium value, non-endemics must within x_I equilibrium value. x_E Sets fraction equlibrium endemic diversity endemics assumed equilibrium; active eqmodel = 13 15. x_I Sets fraction equlibrium non-endemic diversity system assumed equilibrium; active eqmodel = 15. tol Sets tolerances optimization. Consists :  reltolx = relative tolerance parameter values optimization  reltolf = relative tolerance function value optimization  abstolx = absolute tolerance parameter values optimization. maxiter Sets maximum number iterations optimization. methode Method ODE-solver. Supported Boost ODEINT solvers (steppers) : \"odeint::runge_kutta_cash_karp54\" \"odeint::runge_kutta_fehlberg78\" \"odeint::runge_kutta_dopri5\" \"odeint::bulirsch_stoer\" without odeint::-prefix, deSolve{ode} method assumed. default method overall \"lsodes\" DAISIE_ML_CS() \"ode45\" ode() DAISIE_ML_IW(). optimmethod Method used likelihood optimization. Default `subplex` (see `subplex()` full details). Alternative \"simplex\" method previous versions. CS_version numeric list. Default 1 standard DAISIE model, relaxed-rate model list following elements: model: CS model run, options 1 single rate   DAISIE model, 2 multi-rate DAISIE, 0 IW test   model. relaxed_par: parameter relax (integrate ). Options \"cladogenesis\", \"extinction\", \"carrying_capacity\", \"immigration\", \"anagenesis\". verbose numeric vector length 1, simulations `DAISIEdataprep()` can `1` `0`, `1` gives intermediate output printed. ML functions numeric determining intermediate output printed. default: `0` print, `1` prints initial likelihood settings selected (parameters optimised, fixed shifted), `2` prints `1 also intermediate output parameters loglikelihood, `3` `2` prints intermediate progress likelihood computation. tolint Vector two elements containing absolute relative tolerance integration. jitter Numeric optimizer(). Jitters parameters optimized specified amount small, e.g. 1e-5. Jitter link{subplex}{subplex}() produces incorrect output due parameter transformation. num_cycles number cycles optimizer go . Default 1.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ML.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Maximization of the loglikelihood under the DAISIE model with clade-specific\ndiversity-dependence — DAISIE_ML","text":"output dataframe containing estimated parameters maximum loglikelihood. lambda_c gives maximum likelihood estimate lambda^c, rate cladogenesis mu gives maximum likelihood estimate mu, extinction rate K gives maximum likelihood estimate K, carrying-capacity gamma gives maximum likelihood estimate gamma, immigration rate lambda_a gives maximum likelihood estimate lambda^, rate anagenesis lambda_c2 gives maximum likelihood estimate lambda^c2, rate cladogenesis optional second group species mu2 gives maximum likelihood estimate mu2, extinction rate optional second group species K2 gives maximum likelihood estimate K2, carrying-capacity optional second group species gamma2 gives maximum likelihood estimate gamma2, immigration rate optional second group species lambda_a2 gives maximum likelihood estimate lambda^a2, rate anagenesis optional second group species loglik gives maximum loglikelihood df gives number estimated parameters, .e. degrees feedom conv gives message convergence optimization; conv = 0 means convergence","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ML.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Maximization of the loglikelihood under the DAISIE model with clade-specific\ndiversity-dependence — DAISIE_ML","text":"Valente, L.M., .B. Phillimore R.S. Etienne (2015). Equilibrium non-equilibrium dynamics simultaneously operate Galapagos islands. Ecology Letters 18: 844-852. <doi:10.1111/ele.12461>.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ML.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Maximization of the loglikelihood under the DAISIE model with clade-specific\ndiversity-dependence — DAISIE_ML","text":"Rampal S. Etienne","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ML.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Maximization of the loglikelihood under the DAISIE model with clade-specific\ndiversity-dependence — DAISIE_ML","text":"","code":"cat(\" ### When all species have the same rates, and we want to optimize all 5 parameters, # we use:  utils::data(Galapagos_datalist) DAISIE_ML(    datalist = Galapagos_datalist,    initparsopt = c(2.5,2.7,20,0.009,1.01),    ddmodel = 11,    idparsopt = 1:5,    parsfix = NULL,    idparsfix = NULL )  ### When all species have the same rates, and we want to optimize all parameters # except K (which we set equal to Inf), we use:  utils::data(Galapagos_datalist) DAISIE_ML(    datalist = Galapagos_datalist,    initparsopt = c(2.5,2.7,0.009,1.01),    idparsopt = c(1,2,4,5),    parsfix = Inf,    idparsfix = 3    )  ### When all species have the same rates except that the finches have a different # rate of cladogenesis, and we want to optimize all parameters except K (which we # set equal to Inf), fixing the proportion of finch-type species at 0.163, we use:  utils::data(Galapagos_datalist_2types) DAISIE_ML(    datalist = Galapagos_datalist_2types,    initparsopt = c(0.38,0.55,0.004,1.1,2.28),    idparsopt = c(1,2,4,5,6),    parsfix = c(Inf,Inf,0.163),    idparsfix = c(3,8,11),    idparsnoshift = c(7,9,10)    )  ### When all species have the same rates except that the finches have a different # rate of cladogenesis, extinction and a different K, and we want to optimize all # parameters, fixing the proportion of finch-type species at 0.163, we use:  utils::data(Galapagos_datalist_2types) DAISIE_ML(    datalist = Galapagos_datalist_2types,    ddmodel = 11,    initparsopt = c(0.19,0.09,0.002,0.87,20,8.9,15),    idparsopt = c(1,2,4,5,6,7,8),    parsfix = c(Inf,0.163),    idparsfix = c(3,11),    idparsnoshift = c(9,10)    )   ### When all species have the same rates except that the finches have a different # rate of extinction, and we want to optimize all parameters except K (which we # set equal to Inf), and we also# want to estimate the fraction of finch species # in the mainland pool. we use:  utils::data(Galapagos_datalist_2types) DAISIE_ML(    datalist = Galapagos_datalist_2types,    initparsopt = c(2.48,2.7,0.009,1.01,2.25,0.163),    idparsopt = c(1,2,4,5,7,11),    parsfix = c(Inf,Inf),    idparsfix = c(3,8),    idparsnoshift = c(6,9,10)    )  ### When we have two islands with the same rates except for immigration and anagenesis rate, # and we want to optimize all parameters, we use:  utils::data(Galapagos_datalist) DAISIE_ML(    datalist = list(Galapagos_datalist,Galapagos_datalist),    datatype = 'multiple',    initparsopt = c(2.5,2.7,20,0.009,1.01,0.009,1.01),    idparsmat = rbind(1:5,c(1:3,6,7)),    idparsopt = 1:7,    parsfix = NULL,    idparsfix = NULL )  ### When we consider the four Macaronesia archipelagoes and set all parameters the same # except for rates of cladogenesis, extinction and immigration for Canary Islands, # rate of cladogenesis is fixed to 0 for the other archipelagoes, # diversity-dependence is assumed to be absent # and we want to optimize all parameters, we use:  utils::data(Macaronesia_datalist) DAISIE_ML(    datalist = Macaronesia_datalist,    datatype = 'multiple',    initparsopt = c(1.053151832,0.052148979,0.512939011,0.133766934,0.152763179),    idparsmat = rbind(1:5,c(6,2,3,7,5),1:5,1:5),    idparsopt = c(2,4,5,6,7),    parsfix = c(0,Inf),    idparsfix = c(1,3) )  \") #>  #> ### When all species have the same rates, and we want to optimize all 5 parameters, #> # we use: #>  #> utils::data(Galapagos_datalist) #> DAISIE_ML( #>    datalist = Galapagos_datalist, #>    initparsopt = c(2.5,2.7,20,0.009,1.01), #>    ddmodel = 11, #>    idparsopt = 1:5, #>    parsfix = NULL, #>    idparsfix = NULL #> ) #>  #> ### When all species have the same rates, and we want to optimize all parameters #> # except K (which we set equal to Inf), we use: #>  #> utils::data(Galapagos_datalist) #> DAISIE_ML( #>    datalist = Galapagos_datalist, #>    initparsopt = c(2.5,2.7,0.009,1.01), #>    idparsopt = c(1,2,4,5), #>    parsfix = Inf, #>    idparsfix = 3 #>    ) #>  #> ### When all species have the same rates except that the finches have a different #> # rate of cladogenesis, and we want to optimize all parameters except K (which we #> # set equal to Inf), fixing the proportion of finch-type species at 0.163, we use: #>  #> utils::data(Galapagos_datalist_2types) #> DAISIE_ML( #>    datalist = Galapagos_datalist_2types, #>    initparsopt = c(0.38,0.55,0.004,1.1,2.28), #>    idparsopt = c(1,2,4,5,6), #>    parsfix = c(Inf,Inf,0.163), #>    idparsfix = c(3,8,11), #>    idparsnoshift = c(7,9,10) #>    ) #>  #> ### When all species have the same rates except that the finches have a different #> # rate of cladogenesis, extinction and a different K, and we want to optimize all #> # parameters, fixing the proportion of finch-type species at 0.163, we use: #>  #> utils::data(Galapagos_datalist_2types) #> DAISIE_ML( #>    datalist = Galapagos_datalist_2types, #>    ddmodel = 11, #>    initparsopt = c(0.19,0.09,0.002,0.87,20,8.9,15), #>    idparsopt = c(1,2,4,5,6,7,8), #>    parsfix = c(Inf,0.163), #>    idparsfix = c(3,11), #>    idparsnoshift = c(9,10) #>    ) #>  #>  #> ### When all species have the same rates except that the finches have a different #> # rate of extinction, and we want to optimize all parameters except K (which we #> # set equal to Inf), and we also# want to estimate the fraction of finch species #> # in the mainland pool. we use: #>  #> utils::data(Galapagos_datalist_2types) #> DAISIE_ML( #>    datalist = Galapagos_datalist_2types, #>    initparsopt = c(2.48,2.7,0.009,1.01,2.25,0.163), #>    idparsopt = c(1,2,4,5,7,11), #>    parsfix = c(Inf,Inf), #>    idparsfix = c(3,8), #>    idparsnoshift = c(6,9,10) #>    ) #>  #> ### When we have two islands with the same rates except for immigration and anagenesis rate, #> # and we want to optimize all parameters, we use: #>  #> utils::data(Galapagos_datalist) #> DAISIE_ML( #>    datalist = list(Galapagos_datalist,Galapagos_datalist), #>    datatype = 'multiple', #>    initparsopt = c(2.5,2.7,20,0.009,1.01,0.009,1.01), #>    idparsmat = rbind(1:5,c(1:3,6,7)), #>    idparsopt = 1:7, #>    parsfix = NULL, #>    idparsfix = NULL #> ) #>  #> ### When we consider the four Macaronesia archipelagoes and set all parameters the same #> # except for rates of cladogenesis, extinction and immigration for Canary Islands, #> # rate of cladogenesis is fixed to 0 for the other archipelagoes, #> # diversity-dependence is assumed to be absent #> # and we want to optimize all parameters, we use: #>  #> utils::data(Macaronesia_datalist) #> DAISIE_ML( #>    datalist = Macaronesia_datalist, #>    datatype = 'multiple', #>    initparsopt = c(1.053151832,0.052148979,0.512939011,0.133766934,0.152763179), #>    idparsmat = rbind(1:5,c(6,2,3,7,5),1:5,1:5), #>    idparsopt = c(2,4,5,6,7), #>    parsfix = c(0,Inf), #>    idparsfix = c(1,3) #> ) #>"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ML1.html","id":null,"dir":"Reference","previous_headings":"","what":"Computes MLE for single type species under a clade specific scenario — DAISIE_ML1","title":"Computes MLE for single type species under a clade specific scenario — DAISIE_ML1","text":"Computes MLE single type species clade specific scenario","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ML1.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Computes MLE for single type species under a clade specific scenario — DAISIE_ML1","text":"","code":"DAISIE_ML1(   datalist,   initparsopt,   idparsopt,   parsfix,   idparsfix,   idparsnoshift = 6:10,   res = 100,   ddmodel = 0,   cond = 0,   eqmodel = 0,   x_E = 0.95,   x_I = 0.98,   tol = c(1e-04, 1e-05, 1e-07),   maxiter = 1000 * round((1.25)^length(idparsopt)),   methode = \"lsodes\",   optimmethod = \"subplex\",   CS_version = 1,   verbose = 0,   tolint = c(1e-16, 1e-10),   island_ontogeny = NA,   jitter = 0,   num_cycles = 1 )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ML1.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Computes MLE for single type species under a clade specific scenario — DAISIE_ML1","text":"datalist Data object containing information colonisation branching times. object can generated using DAISIE_dataprep function, converts user-specified data table data object, object can course also entered directly. R list object following elements. first element list two three components: $island_age - island age  , depending whether distinction types made, :$not_present - number mainland lineages present island  :$not_present_type1 - number mainland lineages type 1 present island $not_present_type2 - number mainland lineages type 2 present island  remaining elements list contains information single colonist lineage island 5 components:$colonist_name - name species clade colonized island $branching_times - island age followed stem age population/species case Non-endemic, Non-endemic_MaxAge species Endemic species close relatives island. endemic clades one species island (cladogenetic clades/ radiations) island age followed branching times island clade including stem age clade$stac - status colonist  * Non_endemic_MaxAge: 1  * Endemic: 2  * Endemic&Non_Endemic: 3  * Non_Endemic: 4  * Endemic_Singleton_MaxAge: 5  * Endemic_Clade_MaxAge: 6  * Endemic&Non_Endemic_Clade_MaxAge: 7 $missing_species - number island species sampled particular clade (applicable endemic clades) $type1or2 - whether colonist belongs type 1 type 2 initparsopt initial values parameters must optimized, positive. idparsopt ids parameters must optimized. ids defined follows:  id = 1 corresponds lambda^c (cladogenesis rate)  id = 2 corresponds mu (extinction rate)  id = 3 corresponds K (clade-level carrying capacity)  id = 4 corresponds gamma (immigration rate)  id = 5 corresponds lambda^(anagenesis rate)  id = 6 corresponds lambda^c (cladogenesis rate) optional subset species  id = 7 corresponds mu (extinction rate) optional subset species id = 8 corresponds K (clade-level carrying capacity) optional subset species id = 9 corresponds gamma (immigration rate) optional subset species id = 10 corresponds lambda^(anagenesis rate) optional subset species id = 11 corresponds p_f (fraction mainland species belongs second subset species. parsfix values parameters optimized. idparsfix ids parameters optimized, e.g. c(1,3) lambda^c K optimized. idparsnoshift datatype = 'single' : ids parameters different two groups species; can apply ids 6:10, e.g. idparsnoshift = c(6,7) means lambda^c mu values groups. res Sets maximum number species probability must computed, must larger size largest clade. ddmodel Sets model diversity-dependence:  ddmodel = 0 : diversity dependence  ddmodel = 1 : linear dependence speciation rate  ddmodel = 11: linear dependence speciation rate immigration rate  ddmodel = 2 : exponential dependence speciation rate ddmodel = 21: exponential dependence speciation rate immigration rate cond cond = 0 : conditioning island age  cond = 1 : conditioning island age non-extinction island biota . cond > 1 : conditioning island age least cond colonizations island. last option yet available IW model eqmodel Sets equilibrium constraint can used likelihood optimization. available datatype = 'single'. eqmodel = 0 : equilibrium assumed  eqmodel = 13 : near-equilibrium assumed endemics using deterministic equation endemics immigrants. Endemics must within x_E equilibrium value eqmodel = 15 : near-equilibrium assumed endemics immigrants using deterministic equation endemics immigrants. Endemics must within x_E equilibrium value, non-endemics must within x_I equilibrium value. x_E Sets fraction equlibrium endemic diversity endemics assumed equilibrium; active eqmodel = 13 15. x_I Sets fraction equlibrium non-endemic diversity system assumed equilibrium; active eqmodel = 15. tol Sets tolerances optimization. Consists :  reltolx = relative tolerance parameter values optimization  reltolf = relative tolerance function value optimization  abstolx = absolute tolerance parameter values optimization. maxiter Sets maximum number iterations optimization. methode Method ODE-solver. Supported Boost ODEINT solvers (steppers) : \"odeint::runge_kutta_cash_karp54\" \"odeint::runge_kutta_fehlberg78\" \"odeint::runge_kutta_dopri5\" \"odeint::bulirsch_stoer\" without odeint::-prefix, deSolve{ode} method assumed. default method overall \"lsodes\" DAISIE_ML_CS() \"ode45\" ode() DAISIE_ML_IW(). optimmethod Method used likelihood optimization. Default `subplex` (see `subplex()` full details). Alternative \"simplex\" method previous versions. CS_version numeric list. Default 1 standard DAISIE model, relaxed-rate model list following elements: model: CS model run, options 1 single rate   DAISIE model, 2 multi-rate DAISIE, 0 IW test   model. relaxed_par: parameter relax (integrate ). Options \"cladogenesis\", \"extinction\", \"carrying_capacity\", \"immigration\", \"anagenesis\". verbose numeric vector length 1, simulations `DAISIEdataprep()` can `1` `0`, `1` gives intermediate output printed. ML functions numeric determining intermediate output printed. default: `0` print, `1` prints initial likelihood settings selected (parameters optimised, fixed shifted), `2` prints `1 also intermediate output parameters loglikelihood, `3` `2` prints intermediate progress likelihood computation. tolint Vector two elements containing absolute relative tolerance integration. island_ontogeny DAISIE_sim_time_dep(), DAISIE_ML_CS plotting string describing type island ontogeny. Can \"const\", \"beta\" beta function describing area time.  functions numeric describing type island ontogeny. Can 0 constant, 1 beta function describing area time. ML functions island_ontogeny = NA assumes constant ontogeny. Time dependent estimation yet available development still ongoing. return error called case. jitter Numeric optimizer(). Jitters parameters optimized specified amount small, e.g. 1e-5. Jitter link{subplex}{subplex}() produces incorrect output due parameter transformation. num_cycles number cycles optimizer go . Default 1.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ML1.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Computes MLE for single type species under a clade specific scenario — DAISIE_ML1","text":"output dataframe containing estimated parameters maximum loglikelihood. lambda_c gives maximum likelihood estimate lambda^c, rate cladogenesis mu gives maximum likelihood estimate mu, extinction rate K gives maximum likelihood estimate K, carrying-capacity gamma gives maximum likelihood estimate gamma, immigration rate lambda_a gives maximum likelihood estimate lambda^, rate anagenesis loglik gives maximum loglikelihood df gives number estimated parameters, .e. degrees feedom conv gives message convergence optimization; conv = 0 means convergence","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ML2.html","id":null,"dir":"Reference","previous_headings":"","what":"Computes MLE for multiple islands under a clade specific scenario — DAISIE_ML2","title":"Computes MLE for multiple islands under a clade specific scenario — DAISIE_ML2","text":"Computes MLE multiple islands clade specific scenario","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ML2.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Computes MLE for multiple islands under a clade specific scenario — DAISIE_ML2","text":"","code":"DAISIE_ML2(   datalist,   initparsopt,   idparsopt,   parsfix,   idparsfix,   idparsmat,   res = 100,   ddmodel = 0,   cond = 0,   island_ontogeny = NA,   tol = c(1e-04, 1e-05, 1e-07),   maxiter = 1000 * round((1.25)^length(idparsopt)),   methode = \"lsodes\",   optimmethod = \"subplex\",   verbose = 0,   tolint = c(1e-16, 1e-10),   jitter = 0,   num_cycles = 1 )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ML2.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Computes MLE for multiple islands under a clade specific scenario — DAISIE_ML2","text":"datalist Data object containing information colonisation branching times. object can generated using DAISIE_dataprep function, converts user-specified data table data object, object can course also entered directly. R list object following elements. first element list two three components: $island_age - island age  , depending whether distinction types made, :$not_present - number mainland lineages present island  :$not_present_type1 - number mainland lineages type 1 present island $not_present_type2 - number mainland lineages type 2 present island  remaining elements list contains information single colonist lineage island 5 components:$colonist_name - name species clade colonized island $branching_times - island age followed stem age population/species case Non-endemic, Non-endemic_MaxAge species Endemic species close relatives island. endemic clades one species island (cladogenetic clades/ radiations) island age followed branching times island clade including stem age clade$stac - status colonist  * Non_endemic_MaxAge: 1  * Endemic: 2  * Endemic&Non_Endemic: 3  * Non_Endemic: 4  * Endemic_Singleton_MaxAge: 5  * Endemic_Clade_MaxAge: 6  * Endemic&Non_Endemic_Clade_MaxAge: 7 $missing_species - number island species sampled particular clade (applicable endemic clades) $type1or2 - whether colonist belongs type 1 type 2 initparsopt initial values parameters must optimized, positive. idparsopt ids parameters must optimized. ids defined follows:  id = 1 corresponds lambda^c (cladogenesis rate)  id = 2 corresponds mu (extinction rate)  id = 3 corresponds K (clade-level carrying capacity)  id = 4 corresponds gamma (immigration rate)  id = 5 corresponds lambda^(anagenesis rate)  id = 6 corresponds lambda^c (cladogenesis rate) optional subset species  id = 7 corresponds mu (extinction rate) optional subset species id = 8 corresponds K (clade-level carrying capacity) optional subset species id = 9 corresponds gamma (immigration rate) optional subset species id = 10 corresponds lambda^(anagenesis rate) optional subset species id = 11 corresponds p_f (fraction mainland species belongs second subset species. parsfix values parameters optimized. idparsfix ids parameters optimized, e.g. c(1,3) lambda^c K optimized. idparsmat datatype = 'multiple' : Matrix containing ids parameters, linking initparsopt parsfix. Per island system use following order:  * lac = (initial) cladogenesis rate  * mu = extinction rate  * K = maximum number species possible clade  * gam = (initial) immigration rate  * laa = (initial) anagenesis rate  Example: idparsmat = rbind(c(1, 2, 3, 4, 5), c(1, 2, 3, 6, 7)) different rates immigration anagenesis two islands. res Sets maximum number species probability must computed, must larger size largest clade. ddmodel Sets model diversity-dependence:  ddmodel = 0 : diversity dependence  ddmodel = 1 : linear dependence speciation rate  ddmodel = 11: linear dependence speciation rate immigration rate  ddmodel = 2 : exponential dependence speciation rate ddmodel = 21: exponential dependence speciation rate immigration rate cond cond = 0 : conditioning island age  cond = 1 : conditioning island age non-extinction island biota . cond > 1 : conditioning island age least cond colonizations island. last option yet available IW model island_ontogeny DAISIE_sim_time_dep(), DAISIE_ML_CS plotting string describing type island ontogeny. Can \"const\", \"beta\" beta function describing area time.  functions numeric describing type island ontogeny. Can 0 constant, 1 beta function describing area time. ML functions island_ontogeny = NA assumes constant ontogeny. Time dependent estimation yet available development still ongoing. return error called case. tol Sets tolerances optimization. Consists :  reltolx = relative tolerance parameter values optimization  reltolf = relative tolerance function value optimization  abstolx = absolute tolerance parameter values optimization. maxiter Sets maximum number iterations optimization. methode Method ODE-solver. Supported Boost ODEINT solvers (steppers) : \"odeint::runge_kutta_cash_karp54\" \"odeint::runge_kutta_fehlberg78\" \"odeint::runge_kutta_dopri5\" \"odeint::bulirsch_stoer\" without odeint::-prefix, deSolve{ode} method assumed. default method overall \"lsodes\" DAISIE_ML_CS() \"ode45\" ode() DAISIE_ML_IW(). optimmethod Method used likelihood optimization. Default `subplex` (see `subplex()` full details). Alternative \"simplex\" method previous versions. verbose numeric vector length 1, simulations `DAISIEdataprep()` can `1` `0`, `1` gives intermediate output printed. ML functions numeric determining intermediate output printed. default: `0` print, `1` prints initial likelihood settings selected (parameters optimised, fixed shifted), `2` prints `1 also intermediate output parameters loglikelihood, `3` `2` prints intermediate progress likelihood computation. tolint Vector two elements containing absolute relative tolerance integration. jitter Numeric optimizer(). Jitters parameters optimized specified amount small, e.g. 1e-5. Jitter link{subplex}{subplex}() produces incorrect output due parameter transformation. num_cycles number cycles optimizer go . Default 1.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ML2.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Computes MLE for multiple islands under a clade specific scenario — DAISIE_ML2","text":"output dataframe containing estimated parameters maximum loglikelihood. lambda_c gives maximum likelihood estimate lambda^c, rate cladogenesis mu gives maximum likelihood estimate mu, extinction rate K gives maximum likelihood estimate K, carrying-capacity gamma gives maximum likelihood estimate gamma, immigration rate lambda_a gives maximum likelihood estimate lambda^, rate anagenesis lambda_c2 gives maximum likelihood estimate lambda^c2, rate cladogenesis second group species mu2 gives maximum likelihood estimate mu2, extinction rate second group species K2 gives maximum likelihood estimate K2, carrying-capacity  second group species gamma2 gives maximum likelihood estimate gamma2, immigration rate second group species lambda_a2 gives maximum likelihood estimate lambda^a2, rate anagenesis second group species loglik gives maximum loglikelihood df gives number estimated parameters, .e. degrees feedom conv gives message convergence optimization; conv = 0 means convergence","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ML4.html","id":null,"dir":"Reference","previous_headings":"","what":"Computes MLE for single type species under a clade specific scenario where\none parameter may vary over the clades governed by a specific distribution — DAISIE_ML4","title":"Computes MLE for single type species under a clade specific scenario where\none parameter may vary over the clades governed by a specific distribution — DAISIE_ML4","text":"Computes MLE single type species clade specific scenario one parameter may vary clades governed specific distribution","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ML4.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Computes MLE for single type species under a clade specific scenario where\none parameter may vary over the clades governed by a specific distribution — DAISIE_ML4","text":"","code":"DAISIE_ML4(   datalist,   initparsopt,   idparsopt,   parsfix,   idparsfix,   res = 100,   ddmodel = 0,   cond = 0,   tol = c(1e-04, 1e-05, 1e-07),   maxiter = 1000 * round((1.25)^length(idparsopt)),   methode = \"lsodes\",   optimmethod = \"subplex\",   CS_version = create_CS_version(model = 2, relaxed_par = \"cladogenesis\", par_sd = 0,     par_upper_bound = Inf),   verbose = 0,   tolint = c(1e-16, 1e-10),   island_ontogeny = NA,   jitter = 0,   num_cycles = 1 )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ML4.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Computes MLE for single type species under a clade specific scenario where\none parameter may vary over the clades governed by a specific distribution — DAISIE_ML4","text":"datalist Data object containing information colonisation branching times. object can generated using DAISIE_dataprep function, converts user-specified data table data object, object can course also entered directly. R list object following elements. first element list two three components: $island_age - island age  , depending whether distinction types made, :$not_present - number mainland lineages present island  :$not_present_type1 - number mainland lineages type 1 present island $not_present_type2 - number mainland lineages type 2 present island  remaining elements list contains information single colonist lineage island 5 components:$colonist_name - name species clade colonized island $branching_times - island age followed stem age population/species case Non-endemic, Non-endemic_MaxAge species Endemic species close relatives island. endemic clades one species island (cladogenetic clades/ radiations) island age followed branching times island clade including stem age clade$stac - status colonist  * Non_endemic_MaxAge: 1  * Endemic: 2  * Endemic&Non_Endemic: 3  * Non_Endemic: 4  * Endemic_Singleton_MaxAge: 5  * Endemic_Clade_MaxAge: 6  * Endemic&Non_Endemic_Clade_MaxAge: 7 $missing_species - number island species sampled particular clade (applicable endemic clades) $type1or2 - whether colonist belongs type 1 type 2 initparsopt initial values parameters must optimized, positive. idparsopt ids parameters must optimized. ids defined follows:  id = 1 corresponds lambda^c (cladogenesis rate)  id = 2 corresponds mu (extinction rate)  id = 3 corresponds K (clade-level carrying capacity)  id = 4 corresponds gamma (immigration rate)  id = 5 corresponds lambda^(anagenesis rate)  id = 6 corresponds lambda^c (cladogenesis rate) optional subset species  id = 7 corresponds mu (extinction rate) optional subset species id = 8 corresponds K (clade-level carrying capacity) optional subset species id = 9 corresponds gamma (immigration rate) optional subset species id = 10 corresponds lambda^(anagenesis rate) optional subset species id = 11 corresponds p_f (fraction mainland species belongs second subset species. parsfix values parameters optimized. idparsfix ids parameters optimized, e.g. c(1,3) lambda^c K optimized. res Sets maximum number species probability must computed, must larger size largest clade. ddmodel Sets model diversity-dependence:  ddmodel = 0 : diversity dependence  ddmodel = 1 : linear dependence speciation rate  ddmodel = 11: linear dependence speciation rate immigration rate  ddmodel = 2 : exponential dependence speciation rate ddmodel = 21: exponential dependence speciation rate immigration rate cond cond = 0 : conditioning island age  cond = 1 : conditioning island age non-extinction island biota . cond > 1 : conditioning island age least cond colonizations island. last option yet available IW model tol Sets tolerances optimization. Consists :  reltolx = relative tolerance parameter values optimization  reltolf = relative tolerance function value optimization  abstolx = absolute tolerance parameter values optimization. maxiter Sets maximum number iterations optimization. methode Method ODE-solver. Supported Boost ODEINT solvers (steppers) : \"odeint::runge_kutta_cash_karp54\" \"odeint::runge_kutta_fehlberg78\" \"odeint::runge_kutta_dopri5\" \"odeint::bulirsch_stoer\" without odeint::-prefix, deSolve{ode} method assumed. default method overall \"lsodes\" DAISIE_ML_CS() \"ode45\" ode() DAISIE_ML_IW(). optimmethod Method used likelihood optimization. Default `subplex` (see `subplex()` full details). Alternative \"simplex\" method previous versions. CS_version numeric list. Default 1 standard DAISIE model, relaxed-rate model list following elements: model: CS model run, options 1 single rate   DAISIE model, 2 multi-rate DAISIE, 0 IW test   model. relaxed_par: parameter relax (integrate ). Options \"cladogenesis\", \"extinction\", \"carrying_capacity\", \"immigration\", \"anagenesis\". verbose numeric vector length 1, simulations `DAISIEdataprep()` can `1` `0`, `1` gives intermediate output printed. ML functions numeric determining intermediate output printed. default: `0` print, `1` prints initial likelihood settings selected (parameters optimised, fixed shifted), `2` prints `1 also intermediate output parameters loglikelihood, `3` `2` prints intermediate progress likelihood computation. tolint Vector two elements containing absolute relative tolerance integration. island_ontogeny DAISIE_sim_time_dep(), DAISIE_ML_CS plotting string describing type island ontogeny. Can \"const\", \"beta\" beta function describing area time.  functions numeric describing type island ontogeny. Can 0 constant, 1 beta function describing area time. ML functions island_ontogeny = NA assumes constant ontogeny. Time dependent estimation yet available development still ongoing. return error called case. jitter Numeric optimizer(). Jitters parameters optimized specified amount small, e.g. 1e-5. Jitter link{subplex}{subplex}() produces incorrect output due parameter transformation. num_cycles number cycles optimizer go . Default 1.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ML4.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Computes MLE for single type species under a clade specific scenario where\none parameter may vary over the clades governed by a specific distribution — DAISIE_ML4","text":"output dataframe containing estimated parameters maximum loglikelihood. lambda_c gives maximum likelihood estimate lambda^c, rate cladogenesis mu gives maximum likelihood estimate mu, extinction rate K gives maximum likelihood estimate K, carrying-capacity gamma gives maximum likelihood estimate gamma, immigration rate lambda_a gives maximum likelihood estimate lambda^, rate anagenesis sd gives maximum likelihood estimate standard deviation parameter allowed vary loglik gives maximum loglikelihood df gives number estimated parameters, .e. degrees freedom conv gives message convergence optimization; conv = 0 means convergence","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ML_IW.html","id":null,"dir":"Reference","previous_headings":"","what":"Maximization of the loglikelihood under the DAISIE model with island-wide\ndiversity-dependence — DAISIE_ML_IW","title":"Maximization of the loglikelihood under the DAISIE model with island-wide\ndiversity-dependence — DAISIE_ML_IW","text":"function computes maximum likelihood estimates parameters DAISIE model island-wide diversity-dependence data lineages colonizing island. also outputs corresponding loglikelihood can used model comparisons.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ML_IW.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Maximization of the loglikelihood under the DAISIE model with island-wide\ndiversity-dependence — DAISIE_ML_IW","text":"","code":"DAISIE_ML_IW(   datalist,   initparsopt,   idparsopt,   parsfix,   idparsfix,   res = 100,   ddmodel = 11,   cond = 0,   tol = c(1e-04, 1e-05, 1e-07),   maxiter = 1000 * round((1.25)^length(idparsopt)),   methode = \"ode45\",   optimmethod = \"subplex\",   verbose = 0,   tolint = c(1e-16, 1e-14),   jitter = 0,   num_cycles = 1 )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ML_IW.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Maximization of the loglikelihood under the DAISIE model with island-wide\ndiversity-dependence — DAISIE_ML_IW","text":"datalist Data object containing information colonisation branching times. object can generated using DAISIE_dataprep function, converts user-specified data table data object, object can course also entered directly. R list object following elements. first element list two three components: $island_age - island age  , depending whether distinction types made, :$not_present - number mainland lineages present island  :$not_present_type1 - number mainland lineages type 1 present island $not_present_type2 - number mainland lineages type 2 present island  remaining elements list contains information single colonist lineage island 5 components:$colonist_name - name species clade colonized island $branching_times - island age followed stem age population/species case Non-endemic, Non-endemic_MaxAge species Endemic species close relatives island. endemic clades one species island (cladogenetic clades/ radiations) island age followed branching times island clade including stem age clade$stac - status colonist  * Non_endemic_MaxAge: 1  * Endemic: 2  * Endemic&Non_Endemic: 3  * Non_Endemic: 4  * Endemic_Singleton_MaxAge: 5  * Endemic_Clade_MaxAge: 6  * Endemic&Non_Endemic_Clade_MaxAge: 7 $missing_species - number island species sampled particular clade (applicable endemic clades) $type1or2 - whether colonist belongs type 1 type 2 initparsopt initial values parameters must optimized, positive. idparsopt ids parameters must optimized. ids defined follows:  id = 1 corresponds lambda^c (cladogenesis rate)  id = 2 corresponds mu (extinction rate)  id = 3 corresponds K (clade-level carrying capacity)  id = 4 corresponds gamma (immigration rate)  id = 5 corresponds lambda^(anagenesis rate)  id = 6 corresponds lambda^c (cladogenesis rate) optional subset species  id = 7 corresponds mu (extinction rate) optional subset species id = 8 corresponds K (clade-level carrying capacity) optional subset species id = 9 corresponds gamma (immigration rate) optional subset species id = 10 corresponds lambda^(anagenesis rate) optional subset species id = 11 corresponds p_f (fraction mainland species belongs second subset species. parsfix values parameters optimized. idparsfix ids parameters optimized, e.g. c(1,3) lambda^c K optimized. res Sets maximum number species probability must computed, must larger size largest clade. ddmodel Sets model diversity-dependence:  ddmodel = 0 : diversity dependence  ddmodel = 1 : linear dependence speciation rate  ddmodel = 11: linear dependence speciation rate immigration rate  ddmodel = 2 : exponential dependence speciation rate ddmodel = 21: exponential dependence speciation rate immigration rate cond cond = 0 : conditioning island age  cond = 1 : conditioning island age non-extinction island biota . cond > 1 : conditioning island age least cond colonizations island. last option yet available IW model tol Sets tolerances optimization. Consists :  reltolx = relative tolerance parameter values optimization  reltolf = relative tolerance function value optimization  abstolx = absolute tolerance parameter values optimization. maxiter Sets maximum number iterations optimization. methode Method ODE-solver. Supported Boost ODEINT solvers (steppers) : \"odeint::runge_kutta_cash_karp54\" \"odeint::runge_kutta_fehlberg78\" \"odeint::runge_kutta_dopri5\" \"odeint::bulirsch_stoer\" without odeint::-prefix, deSolve{ode} method assumed. default method overall \"lsodes\" DAISIE_ML_CS() \"ode45\" ode() DAISIE_ML_IW(). optimmethod Method used likelihood optimization. Default `subplex` (see `subplex()` full details). Alternative \"simplex\" method previous versions. verbose numeric vector length 1, simulations `DAISIEdataprep()` can `1` `0`, `1` gives intermediate output printed. ML functions numeric determining intermediate output printed. default: `0` print, `1` prints initial likelihood settings selected (parameters optimised, fixed shifted), `2` prints `1 also intermediate output parameters loglikelihood, `3` `2` prints intermediate progress likelihood computation. tolint Vector two elements containing absolute relative tolerance integration. jitter Numeric optimizer(). Jitters parameters optimized specified amount small, e.g. 1e-5. Jitter link{subplex}{subplex}() produces incorrect output due parameter transformation. num_cycles number cycles optimizer go . Default 1.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ML_IW.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Maximization of the loglikelihood under the DAISIE model with island-wide\ndiversity-dependence — DAISIE_ML_IW","text":"output dataframe containing estimated parameters maximum loglikelihood. lambda_c gives maximum likelihood estimate lambda^c, rate cladogenesis mu gives maximum likelihood estimate mu, extinction rate K gives maximum likelihood estimate K, carrying-capacity gamma gives maximum likelihood estimate gamma, immigration rate lambda_a gives maximum likelihood estimate lambda^, rate anagenesis loglik gives maximum loglikelihood df gives number estimated parameters, .e. degrees feedom conv gives message convergence optimization; conv = 0 means convergence","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ML_IW.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Maximization of the loglikelihood under the DAISIE model with island-wide\ndiversity-dependence — DAISIE_ML_IW","text":"result sort(c(idparsopt, idparsfix)) identical c(1:5). , error reported input incoherent. happens length initparsopt different length idparsopt, length parsfix different length idparsfix.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ML_IW.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Maximization of the loglikelihood under the DAISIE model with island-wide\ndiversity-dependence — DAISIE_ML_IW","text":"Valente, L.M., .B. Phillimore R.S. Etienne (2015). Equilibrium non-equilibrium dynamics simultaneously operate Galapagos islands. Ecology Letters 18: 844-852. <DOI:10.1111/ele.12461>.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ML_IW.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Maximization of the loglikelihood under the DAISIE model with island-wide\ndiversity-dependence — DAISIE_ML_IW","text":"Rampal S. Etienne","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_MW_ML.html","id":null,"dir":"Reference","previous_headings":"","what":"Maximization of the loglikelihood under the DAISIE model with clade-specific\ndiversity-dependence and explicit dependencies on island area and isolation\nas hypothesized by MacArthur & Wilson — DAISIE_MW_ML","title":"Maximization of the loglikelihood under the DAISIE model with clade-specific\ndiversity-dependence and explicit dependencies on island area and isolation\nas hypothesized by MacArthur & Wilson — DAISIE_MW_ML","text":"function computes maximum likelihood estimates parameters relationships parameters DAISIE model (clade-specific diversity-dependence) island area distance island mainland data lineages colonizing several islands/archipelagos. also outputs corresponding loglikelihood can used model comparisons. note sigmoidal functions used distance_dep: anagenesis cladogenesis, functional relationship k * (d/d0)^x/(1 + (d/d0)^x); colonization relationship : k - k * (d/d0)^x/(1 + (d/d0)^x). d0 parameter 11th parameter entered. 'sigmoidal_col_ana', 11th parameter d0 colonization 12th d0 anagenesis.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_MW_ML.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Maximization of the loglikelihood under the DAISIE model with clade-specific\ndiversity-dependence and explicit dependencies on island area and isolation\nas hypothesized by MacArthur & Wilson — DAISIE_MW_ML","text":"","code":"DAISIE_MW_ML(   datalist,   initparsopt,   idparsopt,   parsfix,   idparsfix,   res = 100,   ddmodel = 11,   cond = 0,   island_ontogeny = NA,   tol = c(1e-04, 1e-05, 1e-07),   maxiter = 1000 * round((1.25)^length(idparsopt)),   methode = \"lsodes\",   optimmethod = \"subplex\",   CS_version = 1,   verbose = 0,   tolint = c(1e-16, 1e-10),   distance_type = \"continent\",   distance_dep = \"power\",   parallel = \"local\",   cpus = 3,   num_cycles = 1 )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_MW_ML.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Maximization of the loglikelihood under the DAISIE model with clade-specific\ndiversity-dependence and explicit dependencies on island area and isolation\nas hypothesized by MacArthur & Wilson — DAISIE_MW_ML","text":"datalist Data object containing information colonisation branching times species several islands archipelagos, well area, isolation age islands/archipelagos. See data(archipelagos41) example. initparsopt initial values parameters must optimized; positive idparsopt ids parameters must optimized. ids defined follows (see Valente et al 2020 Supplementary Tables 1 2 better explanation models parameters):  id = 1 corresponds lambda^c0 (cladogenesis rate unit area)  id = 2 corresponds y (exponent area cladogenesis rate)  id = 3 corresponds mu0 (extinction rate unit area)  id = 4 corresponds x (exponent 1/area extinction rate)  id = 5 corresponds K0 (clade-level carrying capacity unit area)  id = 6 corresponds z (exponent area clade-level carrying capacity)  id = 7 corresponds gamma0 (immigration rate unit distance)  id = 8 corresponds alpha (exponent 1/distance immigration rate)  id = 9 corresponds lambda^a0 (anagenesis rate unit distance)  id = 10 corresponds beta (exponent 1/distance anagenesis rate)  id = 11 corresponds d0 models M15 M19, models distance_dep = 'sigmoidal_col', 'sigmoidal_ana' 'sigmoidal_clado'; d0 colonisation (specifying distance_dep = 'sigmoidal_col_ana' id = 12 corresponds d0 anagenesis specifying distance_dep = 'sigmoidal_col_ana' parsfix values parameters optimized idparsfix ids parameters optimized, e.g. c(1,3) lambda^c K optimized. res Sets maximum number species probability must computed, must larger size largest clade ddmodel Sets model diversity-dependence:  ddmodel = 0 : diversity dependence  ddmodel = 1 : linear dependence speciation rate  ddmodel = 11: linear dependence speciation rate immigration rate  ddmodel = 2 : exponential dependence speciation rate ddmodel = 21: exponential dependence speciation rate immigration rate cond cond = 0 : conditioning island age  cond = 1 : conditioning island age non-extinction island biota island_ontogeny type island ontonogeny. NA, constant ontogeny assumed tol Sets tolerances optimization. Consists :  reltolx = relative tolerance parameter values optimization  reltolf = relative tolerance function value optimization  abstolx = absolute tolerance parameter values optimization maxiter Sets maximum number iterations optimization methode Method ODE-solver. See package deSolve details. Default \"lsodes\" optimmethod Method used likelihood optimization. Default \"subplex\" (see subplex package). Alternative 'simplex' method previous versions. CS_version numeric list. Default 1 standard DAISIE model, relaxed-rate model list following elements: model: CS model run, options 1 single rate   DAISIE model, 2 multi-rate DAISIE, 0 IW test   model. relaxed_par: parameter relax (integrate ). Options \"cladogenesis\", \"extinction\", \"carrying_capacity\", \"immigration\", \"anagenesis\". verbose sets whether parameters likelihood printed (1) (0) tolint Vector two elements containing absolute relative tolerance integration distance_type Use 'continent' distance continent used, use 'nearest_big' distance nearest big landmass used, use 'biologically_realistic' distance take account biologically realism, e.g. average previous two thought contribute. distance_dep Sets type distance dependence used. Default power law, denoted 'power' (models M1-14 Valente et al 2020). Alternatives additive interactive contributions distance area rate cladogenesis (\"area_additive_clado\"; \"area_interactive_clado\", \"area_interactive_clado1\" \"area_interactive_clado2\"). alternatives  exponential relationship denoted 'exp'; sigmoids, either 'sigmoidal_col' sigmoid colonization, 'sigmoidal_ana' sigmoidal anagenesis, 'sigmoidal_clado' sigmoidal cladogenesis, 'sigmoidal_col_ana' sigmoids colonization anagenesis.  key different options distance_dep specified run models Valente et al 2020 (Supplementary Data Table 1 2) given :  * M1 M14 - 'power'  * M15 -'area_additive_clado'  * M16 M19 -'area_interactive_clado'  * M17 -'area_interactive_clado1'  * M18 - 'area_interactive_clado2'  * M20 M24 - sigmoidal_col'  * M21, M25 M28 - sigmoidal_ana'  * M22 M26 - 'sigmoidal_clado' * M23 M27 - 'sigmoidal_col_ana' parallel Sets whether parallel computation used. Use '' parallel computing used, 'cluster' parallel computing unix/linux cluster, 'local' parallel computation local machine. cpus Number cpus used parallel computing. Default 3. effect parallel = ''. num_cycles number cycles optimizer go . Default 1.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_MW_ML.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Maximization of the loglikelihood under the DAISIE model with clade-specific\ndiversity-dependence and explicit dependencies on island area and isolation\nas hypothesized by MacArthur & Wilson — DAISIE_MW_ML","text":"output dataframe containing estimated parameters maximum loglikelihood. lambda_c0 gives maximum likelihood estimate lambda^c, rate cladogenesis unit area y gives maximum likelihood estimate y, exponent area rate cladogenesis mu0 gives maximum likelihood estimate mu0, extinction rate x gives maximum likelihood estimate x, exponent 1/area extinction rate K0 gives maximum likelihood estimate K0, carrying-capacity unit area z gives maximum likelihood estimate z, exponent area carrying capacity gamma0 gives maximum likelihood estimate gamma0, immigration rate unit distance y gives maximum likelihood estimate alpha, exponent 1/distance rate colonization lambda_a0 gives maximum likelihood estimate lambda^a0, rate anagenesis unit distance beta gives maximum likelihood estimate beta, exponent 1/distance rate anagenesis loglik gives maximum loglikelihood df gives number estimated parameters, .e. degrees feedom conv gives message convergence optimization; conv = 0 means convergence","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_MW_ML.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Maximization of the loglikelihood under the DAISIE model with clade-specific\ndiversity-dependence and explicit dependencies on island area and isolation\nas hypothesized by MacArthur & Wilson — DAISIE_MW_ML","text":"Valente L, Phillimore AB, Melo M, Warren BH, Clegg SM, Havenstein K,  Tiedemann R, Illera JC, Thébaud C, Aschenbach T, Etienne RS. simple dynamic model  explains island bird diversity worldwide (2020) Nature, 579, 92-96","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_MW_ML.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Maximization of the loglikelihood under the DAISIE model with clade-specific\ndiversity-dependence and explicit dependencies on island area and isolation\nas hypothesized by MacArthur & Wilson — DAISIE_MW_ML","text":"Rampal S. Etienne & Luis Valente","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_MW_ML.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Maximization of the loglikelihood under the DAISIE model with clade-specific\ndiversity-dependence and explicit dependencies on island area and isolation\nas hypothesized by MacArthur & Wilson — DAISIE_MW_ML","text":"","code":"cat(\" ### Fit the M19 model as in Valente et al 2020, using the ML parameters as starting values (see Supplementary Tables 1 and 2).  utils::data(archipelagos41)  DAISIE_MW_ML( datalist= archipelagos41, initparsopt = c(0.040073803,  1.945656546,  0.150429656, 67.25643672,  0.293635061,  0.059096872,  0.382688527, 0.026510781), idparsopt = c(1,3,4,7,8,9,10,11), parsfix = c(0,Inf,0) , idparsfix = c(2,5,6), res = 100, ddmodel = 0, methode = 'lsodes', cpus = 4, parallel = 'local', optimmethod = 'subplex', tol = c(1E-4, 1E-5, 1E-7), distance_type = 'continent', distance_dep = 'area_interactive_clado' ) \") #>  #> ### Fit the M19 model as in Valente et al 2020, using the ML #> parameters as starting values (see Supplementary Tables 1 and 2). #>  #> utils::data(archipelagos41) #>  #> DAISIE_MW_ML( #> datalist= archipelagos41, #> initparsopt = #> c(0.040073803,\t1.945656546,\t0.150429656, #> 67.25643672,\t0.293635061,\t0.059096872,\t0.382688527, #> 0.026510781), #> idparsopt = c(1,3,4,7,8,9,10,11), #> parsfix = c(0,Inf,0) , #> idparsfix = c(2,5,6), #> res = 100, #> ddmodel = 0, #> methode = 'lsodes', #> cpus = 4, #> parallel = 'local', #> optimmethod = 'subplex', #> tol = c(1E-4, 1E-5, 1E-7), #> distance_type = 'continent', #> distance_dep = 'area_interactive_clado' #> )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ONEcolonist.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert intermediate output to final simulation output — DAISIE_ONEcolonist","title":"Convert intermediate output to final simulation output — DAISIE_ONEcolonist","text":"Convert intermediate output final simulation output","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ONEcolonist.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert intermediate output to final simulation output — DAISIE_ONEcolonist","text":"","code":"DAISIE_ONEcolonist(time, island_spec, stt_table)"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ONEcolonist.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert intermediate output to final simulation output — DAISIE_ONEcolonist","text":"time Numeric defining length simulation time units. example, island known 4 million years old, setting time = 4 simulate entire life span island; setting time = 2 stop simulation mid-life island. island_spec Matrix current state simulation containing number species. stt_table Matrix number species time step.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ONEcolonist.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert intermediate output to final simulation output — DAISIE_ONEcolonist","text":"list elements: [1]: stt_table, stt_table put . [2]: branching_times, sorted numeric vector, required     ML estimation functions. first element always refers     island age. Subsequent elements refer colonisation, speciation     recolonisation times. recent recolonisation time,     always omitted approximate simulation results mathematical     formulation likelihood functions used MLE. [3]: stac, status colonist. function can     returned either 2, 4 3. stac 2, one     independent colonisation present island extant species     endemic. stac 4, singleton endemic present     present. stac 3, recolonisation occurred, one     colonising lineage. [4]: missing_species, numeric value number     missing species, , species sampled phylogeny     present island. code runs simulation models,     missing_species always set 0. [5]:   all_colonisations, recolonising lineages . comprised     $event_times $species_type: $event_times ordered numeric vectors containing       events extant recolonising lineage. includes       colonisation branching times. vector pertains one       colonising lineage. $species_type string. Can \"\", \"C\"       \"\" depending whether extant clade anagenetic,       cladogenetic immigrant origin, respectively.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_SR_ML.html","id":null,"dir":"Reference","previous_headings":"","what":"Maximization of the loglikelihood under the DAISIE model with clade-specific\ndiversity-dependence — DAISIE_SR_ML","title":"Maximization of the loglikelihood under the DAISIE model with clade-specific\ndiversity-dependence — DAISIE_SR_ML","text":"function computes maximum likelihood estimates parameters DAISIE model clade-specific diversity-dependence shift parameters data lineages colonizing island. also outputs corresponding loglikelihood can used model comparisons. result sort(c(idparsopt, idparsfix, idparsnoshift)) identical c(1:10). , error reported input incoherent. happens length initparsopt different length idparsopt, length parsfix different length idparsfix. Including 11th parameter (p_f) either idparsopt idparsfix (therefore initparsopt parsfix) optional. parameter specified, information data used, otherwise information data overruled.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_SR_ML.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Maximization of the loglikelihood under the DAISIE model with clade-specific\ndiversity-dependence — DAISIE_SR_ML","text":"","code":"DAISIE_SR_ML_CS(   datalist,   initparsopt,   idparsopt,   parsfix,   idparsfix,   idparsnoshift = 6:10,   res = 100,   ddmodel = 0,   cond = 0,   island_ontogeny = NA,   tol = c(1e-04, 1e-05, 1e-07),   maxiter = 1000 * round((1.25)^length(idparsopt)),   methode = \"lsodes\",   optimmethod = \"subplex\",   CS_version = 1,   verbose = 0,   tolint = c(1e-16, 1e-10),   jitter = 0,   num_cycles = 1 )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_SR_ML.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Maximization of the loglikelihood under the DAISIE model with clade-specific\ndiversity-dependence — DAISIE_SR_ML","text":"datalist Data object containing information colonisation branching times. object can generated using DAISIE_dataprep function, converts user-specified data table data object, object can course also entered directly. R list object following elements. first element list two three components: $island_age - island age  , depending whether distinction types made, :$not_present - number mainland lineages present island  remaining elements list contains information single colonist lineage island 5 components:$colonist_name - name species clade colonized island $branching_times - island age stem age population/species case Non-endemic, Non-endemic_MaxAge Endemic anagenetic species. cladogenetic species island age branching times radiation including stem age radiation.$stac - status colonist  * Non_endemic_MaxAge: 1  * Endemic: 2  * Endemic&Non_Endemic: 3  * Non_endemic: 4  * Endemic_MaxAge: 5 $missing_species - number island species sampled particular clade (applicable endemic clades) initparsopt initial values parameters must optimized idparsopt ids parameters must optimized. ids defined follows:  id = 1 corresponds lambda^c (cladogenesis rate)  id = 2 corresponds mu (extinction rate)  id = 3 corresponds K (clade-level carrying capacity)  id = 4 corresponds gamma (immigration rate)  id = 5 corresponds lambda^(anagenesis rate)  id = 6 corresponds lambda^c (cladogenesis rate) shift  id = 7 corresponds mu (extinction rate) shift id = 8 corresponds K (clade-level carrying capacity) shift id = 9 corresponds gamma (immigration rate) shift id = 10 corresponds lambda^(anagenesis rate) shift id = 11 corresponds time shift parsfix values parameters optimized idparsfix ids parameters optimized, e.g. c(1,3) lambda^c K optimized. idparsnoshift ids parameters different shift. res Sets maximum number species probability must computed, must larger size largest clade ddmodel Sets model diversity-dependence:  ddmodel = 0 : diversity dependence  ddmodel = 1 : linear dependence speciation rate  ddmodel = 11: linear dependence speciation rate immigration rate  ddmodel = 2 : exponential dependence speciation rate ddmodel = 21: exponential dependence speciation rate immigration rate. cond cond = 0 : conditioning island age  cond = 1 : conditioning island age non-extinction island biota island_ontogeny type island ontonogeny. NA, constant ontogeny assumed. tol Sets tolerances optimization. Consists :  reltolx = relative tolerance parameter values optimization  reltolf = relative tolerance function value optimization  abstolx = absolute tolerance parameter values optimization. maxiter Sets maximum number iterations optimization. methode Method ODE-solver. See package deSolve details. Default \"lsodes\" optimmethod Method used likelihood optimization. Default \"subplex\" (see subplex package). Alternative 'simplex' method previous versions. CS_version numeric list. Default 1 standard DAISIE model, relaxed-rate model list following elements: model: CS model run, options 1 single rate   DAISIE model, 2 multi-rate DAISIE, 0 IW test   model. relaxed_par: parameter relax (integrate ). Options \"cladogenesis\", \"extinction\", \"carrying_capacity\", \"immigration\", \"anagenesis\". verbose sets whether parameters likelihood printed (1) (0). tolint Vector two elements containing absolute relative tolerance integration. jitter Numeric optimizer(). Jitters parameters optimized specified amount small, e.g. 1e-5. Jitter link[subplex]{subplex}() produces incorrect output due parameter transformation. num_cycles number cycles optimizer go . Default 1.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_SR_ML.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Maximization of the loglikelihood under the DAISIE model with clade-specific\ndiversity-dependence — DAISIE_SR_ML","text":"output dataframe containing estimated parameters maximum loglikelihood. lambda_c gives maximum likelihood estimate lambda^c, rate cladogenesis mu gives maximum likelihood estimate mu, extinction rate K gives maximum likelihood estimate K, carrying-capacity gamma gives maximum likelihood estimate gamma, immigration rate lambda_a gives maximum likelihood estimate lambda^, rate anagenesis lambda_c2 gives maximum likelihood estimate lambda^c2, rate cladogenesis optional second group species mu2 gives maximum likelihood estimate mu2, extinction rate optional second group species K2 gives maximum likelihood estimate K2, carrying-capacity optional second group species gamma2 gives maximum likelihood estimate gamma2, immigration rate optional second group species lambda_a2 gives maximum likelihood estimate lambda^a2, rate anagenesis optional second group species loglik gives maximum loglikelihood df gives number estimated parameters, .e. degrees feedom conv gives message convergence optimization; conv = 0 means convergence","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_SR_ML.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Maximization of the loglikelihood under the DAISIE model with clade-specific\ndiversity-dependence — DAISIE_SR_ML","text":"Valente, L.M., .B. Phillimore R.S. Etienne (2015). Equilibrium non-equilibrium dynamics simultaneously operate Galapagos islands. Ecology Letters 18: 844-852. <DOI:10.1111/ele.12461>.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_SR_ML.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Maximization of the loglikelihood under the DAISIE model with clade-specific\ndiversity-dependence — DAISIE_SR_ML","text":"Rampal S. Etienne","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_SR_ML.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Maximization of the loglikelihood under the DAISIE model with clade-specific\ndiversity-dependence — DAISIE_SR_ML","text":"","code":"# \\donttest{ ## In all following DAISIE_ML calls very high tolerances and low system size ## are used  for fast computation for this example. Use default or better ## tol, tolint an res values in actual analyses. ################## ### When all species have the same rates, and we want to optimize all 5 ### parameters, we use: utils::data(Galapagos_datalist) DAISIE_ML(    datalist = Galapagos_datalist,    initparsopt = c(2.5,2.7,20,0.009,1.01),    ddmodel = 11,    idparsopt = 1:5,    parsfix = NULL,    idparsfix = NULL,    tol = c(0.1, 0.02, 0.01),    tolint = c(1e-4, 1e-2),    res = 50 ) #>   lambda_c       mu  K gamma lambda_a    loglik df conv #> 1  2.15493 2.153129 20 0.009     1.01 -81.28596  5    0  ### When all species have the same rates, and we want to optimize all parameters # except K (which we set equal to Inf), we use:  utils::data(Galapagos_datalist) DAISIE_ML(    datalist = Galapagos_datalist,    initparsopt = c(2.5,2.7,0.009,1.01),    idparsopt = c(1,2,4,5),    parsfix = Inf,    idparsfix = 3,    tol = c(0.1, 0.02, 0.01),    tolint = c(1e-4, 1e-2),    res = 50    ) #>   lambda_c       mu   K gamma lambda_a    loglik df conv #> 1 3.180506 3.172027 Inf 0.009     1.01 -73.14958  4    0  ### When all species have the same rates except that the finches have a different # rate of cladogenesis, and we want to optimize all parameters except K (which we # set equal to Inf), fixing the proportion of finch-type species at 0.163, we use:  utils::data(Galapagos_datalist_2types) DAISIE_ML(    datalist = Galapagos_datalist_2types,    initparsopt = c(0.38,0.55,0.004,1.1,2.28),    idparsopt = c(1,2,4,5,6),    parsfix = c(Inf,Inf,0.163),    idparsfix = c(3,8,11),    idparsnoshift = c(7,9,10),    tol = c(0.1, 0.02, 0.01),    tolint = c(1e-4, 1e-2),    res = 50    ) #>    lambda_c        mu   K       gamma lambda_a lambda_c2       mu2  K2 #> 1 0.3840537 0.6146573 Inf 0.003956464 1.193755  3.079965 0.6146573 Inf #>        gamma2 lambda_a2 prop_type2    loglik df conv #> 1 0.003956464  1.193755      0.163 -69.57021  5    0  ### When all species have the same rates except that the finches have a different # rate of cladogenesis, extinction and a different K, and we want to optimize all # parameters, fixing the proportion of finch-type species at 0.163, we use:  utils::data(Galapagos_datalist_2types) DAISIE_ML(    datalist = Galapagos_datalist_2types,    ddmodel = 11,    initparsopt = c(0.19,0.09,0.002,0.87,20,8.9,15),    idparsopt = c(1,2,4,5,6,7,8),    parsfix = c(Inf,0.163),    idparsfix = c(3,11),    idparsnoshift = c(9,10),    tol = c(0.1, 0.02, 0.01),    tolint = c(1e-4, 1e-2),    res = 50    ) #>    lambda_c        mu   K       gamma lambda_a lambda_c2     mu2       K2 #> 1 0.2085388 0.1294331 Inf 0.002834096 1.115621  17.09695 6.32994 18.72603 #>        gamma2 lambda_a2 prop_type2    loglik df conv #> 1 0.002834096  1.115621      0.163 -64.80759  7    0   ### When all species have the same rates except that the finches have a different # rate of extinction, and we want to optimize all parameters except K (which we # set equal to Inf), and we also# want to estimate the fraction of finch species # in the mainland pool. we use:  utils::data(Galapagos_datalist_2types) DAISIE_ML(    datalist = Galapagos_datalist_2types,    initparsopt = c(2.48,2.7,0.009,1.01,2.25,0.163),    idparsopt = c(1,2,4,5,7,11),    parsfix = c(Inf,Inf),    idparsfix = c(3,8),    idparsnoshift = c(6,9,10),    tol = c(0.1, 0.02, 0.01),    tolint = c(1e-4, 1e-2),    res = 50    ) #>   lambda_c       mu   K       gamma lambda_a lambda_c2      mu2  K2      gamma2 #> 1  2.55745 3.239773 Inf 0.009729946 1.739499   2.55745 1.599674 Inf 0.009729946 #>   lambda_a2  prop_type2    loglik df conv #> 1  1.739499 0.001157252 -71.91278  6    0  ### When we have two islands with the same rates except for immigration and anagenesis rate, # and we want to optimize all parameters, we use:  utils::data(Galapagos_datalist) DAISIE_ML(    datalist = list(Galapagos_datalist,Galapagos_datalist),    datatype = 'multiple',    initparsopt = c(2.5,2.7,20,0.009,1.01,0.009,1.01),    idparsmat = rbind(1:5,c(1:3,6,7)),    idparsopt = 1:7,    parsfix = NULL,    idparsfix = NULL,    tol = c(0.1, 0.02, 0.01),    tolint = c(1e-4, 1e-2),    res = 50 ) #>   lambda_c       mu        K       gamma lambda_a    loglik df conv #> 1   2.3754 2.276205 12.28802 0.008006759 1.223171 -147.3063  7    0 #> 2   2.3754 2.276205 12.28802 0.006590183 1.054042 -147.3063  7    0  ### When we consider the four Macaronesia archipelagoes and set all parameters the same # except for rates of cladogenesis, extinction and immigration for Canary Islands, # rate of cladogenesis is fixed to 0 for the other archipelagoes, # diversity-dependence is assumed to be absent # and we want to optimize all parameters, we use:  utils::data(Macaronesia_datalist) DAISIE_ML(    datalist = Macaronesia_datalist,    datatype = 'multiple',    initparsopt = c(1.053151832,0.052148979,0.512939011,0.133766934,0.152763179),    idparsmat = rbind(1:5,c(6,2,3,7,5),1:5,1:5),    idparsopt = c(2,4,5,6,7),    parsfix = c(0,Inf),    idparsfix = c(1,3),    tol = c(0.1, 0.02, 0.01),    tolint = c(1e-4, 1e-2),    res = 50 ) #>     lambda_c       mu   K      gamma lambda_a    loglik df conv #> 1 0.00000000 1.053152 Inf 0.05214898 0.512939 -447.8626  5    0 #> 2 0.09497184 1.053152 Inf 0.15276318 0.512939 -447.8626  5    0 #> 3 0.00000000 1.053152 Inf 0.05214898 0.512939 -447.8626  5    0 #> 4 0.00000000 1.053152 Inf 0.05214898 0.512939 -447.8626  5    0  # }"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_SR_loglik_CS.html","id":null,"dir":"Reference","previous_headings":"","what":"Computes the loglikelihood of the DAISIE model with clade-specific\ndiversity-dependence given data and a set of model parameters that may shift\nat some time — DAISIE_SR_loglik_CS","title":"Computes the loglikelihood of the DAISIE model with clade-specific\ndiversity-dependence given data and a set of model parameters that may shift\nat some time — DAISIE_SR_loglik_CS","text":"Computes loglikelihood DAISIE model clade-specific diversity-dependence given colonization branching times lineages island, set model parameters may shift time","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_SR_loglik_CS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Computes the loglikelihood of the DAISIE model with clade-specific\ndiversity-dependence given data and a set of model parameters that may shift\nat some time — DAISIE_SR_loglik_CS","text":"","code":"DAISIE_SR_loglik_CS(   pars1,   pars2,   datalist,   methode = \"lsodes\",   CS_version = 1,   abstolint = 1e-16,   reltolint = 1e-10 )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_SR_loglik_CS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Computes the loglikelihood of the DAISIE model with clade-specific\ndiversity-dependence given data and a set of model parameters that may shift\nat some time — DAISIE_SR_loglik_CS","text":"pars1 Contains model parameters: pars1[1] corresponds lambda^c (cladogenesis rate) pars1[2] corresponds mu (extinction rate) pars1[3] corresponds K (clade-level carrying capacity) pars1[4] corresponds gamma (immigration rate) pars1[5] corresponds lambda^(anagenesis rate) pars1[6] corresponds lambda^c (cladogenesis rate) shift pars1[7] corresponds mu (extinction rate) shift pars1[8] corresponds K (clade-level carrying capacity) shift pars1[9] corresponds gamma (immigration rate) shift pars1[10] corresponds lambda^(anagenesis rate) shift pars1[11] corresponds time shift pars2 Contains model settings pars2[1] corresponds lx = length ODE variable x pars2[2] corresponds ddmodel = diversity-dependent model, model diversity-dependence, can one ddmodel = 0 : diversity dependence  ddmodel = 1 : linear dependence speciation rate  ddmodel = 11: linear dependence speciation rate immigration rate  ddmodel = 2 : exponential dependence speciation rate ddmodel = 21: exponential dependence speciation rate immigration ratepars2[3] corresponds cond = setting conditioning cond = 0 : conditioning island age  cond = 1 : conditioning island age non-extinction island biota  cond > 1 : conditioning island age least cond colonizations island pars2[4] sets whether parameters likelihood printed (1) (0) datalist Data object containing information colonisation branching times. object can generated using DAISIE_dataprep function, converts user-specified data table data object, object can course also entered directly. R list object following elements. first element list two three components: $island_age - island age  , depending whether distinction types made, :$not_present - number mainland lineages present island  remaining elements list contains information single colonist lineage island 5 components:$colonist_name - name species clade colonized island $branching_times - island age stem age population/species case Non-endemic, Non-endemic_MaxAge Endemic anagenetic species. cladogenetic species island age branching times radiation including stem age radiation.$stac - status colonist  - Non_endemic_MaxAge: 1  * Endemic: 2  - Endemic&Non_Endemic: 3  - Non_endemic: 4  - Endemic_MaxAge: 5 $missing_species - number island species sampled particular clade (applicable endemic clades) methode Method ODE-solver. See package deSolve details. Default \"lsodes\" CS_version numeric list. Default 1 standard DAISIE model, relaxed-rate model list following elements: model: CS model run, options 1 single rate   DAISIE model, 2 multi-rate DAISIE, 0 IW test   model. relaxed_par: parameter relax (integrate ). Options \"cladogenesis\", \"extinction\", \"carrying_capacity\", \"immigration\", \"anagenesis\". abstolint Absolute tolerance integration reltolint Relative tolerance integration","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_SR_loglik_CS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Computes the loglikelihood of the DAISIE model with clade-specific\ndiversity-dependence given data and a set of model parameters that may shift\nat some time — DAISIE_SR_loglik_CS","text":"loglikelihood","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_SR_loglik_CS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Computes the loglikelihood of the DAISIE model with clade-specific\ndiversity-dependence given data and a set of model parameters that may shift\nat some time — DAISIE_SR_loglik_CS","text":"output loglikelihood value","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_SR_loglik_CS.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Computes the loglikelihood of the DAISIE model with clade-specific\ndiversity-dependence given data and a set of model parameters that may shift\nat some time — DAISIE_SR_loglik_CS","text":"Valente, L.M., .B. Phillimore R.S. Etienne (2015). Equilibrium non-equilibrium dynamics simultaneously operate Galapagos islands. Ecology Letters 18: 844-852.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_SR_loglik_CS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Computes the loglikelihood of the DAISIE model with clade-specific\ndiversity-dependence given data and a set of model parameters that may shift\nat some time — DAISIE_SR_loglik_CS","text":"Rampal S. Etienne & Bart Haegeman","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_SR_loglik_CS.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Computes the loglikelihood of the DAISIE model with clade-specific\ndiversity-dependence given data and a set of model parameters that may shift\nat some time — DAISIE_SR_loglik_CS","text":"","code":"utils::data(Galapagos_datalist_2types) pars1 = c(0.195442017,0.087959583,Inf,0.002247364,0.873605049,           3755.202241,8.909285094,14.99999923,0.002247364,0.873605049,0.163) pars2 = c(100,11,0,1) DAISIE_loglik_all(pars1,pars2,Galapagos_datalist_2types) #> [1] -61.70282"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_SR_sim_core.html","id":null,"dir":"Reference","previous_headings":"","what":"DEPRECATED - Algorithm component of DAISIE_SR_sim. — DAISIE_SR_sim_core","title":"DEPRECATED - Algorithm component of DAISIE_SR_sim. — DAISIE_SR_sim_core","text":"#' @details function's use deprecated favour DAISIE_sim_cr_shift(). Please use function instead.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_SR_sim_core.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"DEPRECATED - Algorithm component of DAISIE_SR_sim. — DAISIE_SR_sim_core","text":"","code":"DAISIE_SR_sim_core(time, mainland_n, pars)"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_SR_sim_core.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"DEPRECATED - Algorithm component of DAISIE_SR_sim. — DAISIE_SR_sim_core","text":"time Length simulation time units. example, island know 4 million years old, setting time = 4 simulate entire life span island; setting time = 2 stop simulation mid-life island. mainland_n numeric stating number mainland species, number species can potentially colonize island. using clade-specific diversity dependence, value set 1. using island-wide diversity dependence, value set number mainland species. pars Contains model parameters: pars[1] corresponds lambda^c (cladogenesis rate) shift pars[2] corresponds mu (extinction rate) shift pars[3] corresponds K (clade-level carrying capacity) shift. Set K=Inf non-diversity dependence.pars[4] corresponds gamma (immigration rate) shift pars[5] corresponds lambda^(anagenesis rate) shift pars[6] corresponds lambda^c (cladogenesis rate) shift pars[7] corresponds mu (extinction rate) shift pars[8] corresponds K (clade-level carrying capacity) shift.  Set K=Inf non-diversity dependence. pars[9] corresponds gamma (immigration rate)  shift pars[10] corresponds lambda^(anagenesis rate) shift pars[11] corresponds time shift. defined time end simulation. example, setting time = 4 pars[11] = 1.5 simulate pars[1:5] 4 1.5 pars[6:10] 1.5 0.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_SR_sim_core.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"DEPRECATED - Algorithm component of DAISIE_SR_sim. — DAISIE_SR_sim_core","text":"List DAISIE simulation.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_SR_sim_core.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"DEPRECATED - Algorithm component of DAISIE_SR_sim. — DAISIE_SR_sim_core","text":"Hauffe, T., D. Delicado, R.S. Etienne L. Valente (2020). Lake expansion increases equilibrium diversity via target effect island biogeography","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_SR_sim_core.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"DEPRECATED - Algorithm component of DAISIE_SR_sim. — DAISIE_SR_sim_core","text":"Luis Valente, Albert Phillimore, Torsten Hauffe","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_abm_factor.html","id":null,"dir":"Reference","previous_headings":"","what":"Sets or retrieves the factor to calculate the step-size used by the odeint::adams_bashforth[_moulton] solvers. — DAISIE_abm_factor","title":"Sets or retrieves the factor to calculate the step-size used by the odeint::adams_bashforth[_moulton] solvers. — DAISIE_abm_factor","text":"Sets retrieves factor calculate step-size used odeint::adams_bashforth[_moulton] solvers.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_abm_factor.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sets or retrieves the factor to calculate the step-size used by the odeint::adams_bashforth[_moulton] solvers. — DAISIE_abm_factor","text":"","code":"DAISIE_abm_factor(factor)"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_abm_factor.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sets or retrieves the factor to calculate the step-size used by the odeint::adams_bashforth[_moulton] solvers. — DAISIE_abm_factor","text":"factor sets step-size factor * (t1 - t0).","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_abm_factor.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sets or retrieves the factor to calculate the step-size used by the odeint::adams_bashforth[_moulton] solvers. — DAISIE_abm_factor","text":"current factor","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_convertprobdist.html","id":null,"dir":"Reference","previous_headings":"","what":"Converts the joint distribution of endemics and non-endemics under the\nDAISIE model to list format — DAISIE_convertprobdist","title":"Converts the joint distribution of endemics and non-endemics under the\nDAISIE model to list format — DAISIE_convertprobdist","text":"function converts joint distribution number endemics non-endemics matrix format DAISIE_probdist list format","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_convertprobdist.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Converts the joint distribution of endemics and non-endemics under the\nDAISIE model to list format — DAISIE_convertprobdist","text":"","code":"DAISIE_convertprobdist(pb)"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_convertprobdist.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Converts the joint distribution of endemics and non-endemics under the\nDAISIE model to list format — DAISIE_convertprobdist","text":"pb Probability distribution matrix format output DAISIE_probdist().","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_convertprobdist.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Converts the joint distribution of endemics and non-endemics under the\nDAISIE model to list format — DAISIE_convertprobdist","text":"list length nrow(pb) containing matrices square dimensions size sqrt(ncol - 1) containing joint probabilities endemics rows non-endemics columns. last element list vector times joint probability distribution evaluated.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_convertprobdist.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Converts the joint distribution of endemics and non-endemics under the\nDAISIE model to list format — DAISIE_convertprobdist","text":"Valente, L.M., .B. Phillimore R.S. Etienne (2015). Equilibrium non-equilibrium dynamics simultaneously operate Galapagos islands. Ecology Letters 18: 844-852.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_convertprobdist.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Converts the joint distribution of endemics and non-endemics under the\nDAISIE model to list format — DAISIE_convertprobdist","text":"Rampal S. Etienne","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_convertprobdist.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Converts the joint distribution of endemics and non-endemics under the\nDAISIE model to list format — DAISIE_convertprobdist","text":"","code":"### Compute the probability distribution at t = 4 and t = 8, for a mainland pool # size of 250 potential colonists and a vector of 5 parameters (cladogenesis, extinction, # clade-level carrying capacity, immigration, anagenesis) starting from an empty # island; store in list format  pb <- DAISIE_probdist(    pars1 = c(0.3,0.35,Inf,0.75,0.012),    pars2 = c(100,250),    tvec = c(4,8),    initEI = c(0,0),    initprobs = NULL    ) prob_dists <- DAISIE_convertprobdist(pb)"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_count_species.html","id":null,"dir":"Reference","previous_headings":"","what":"Count number of species in DAISIE datalist or simulated data. — DAISIE_count_species","title":"Count number of species in DAISIE datalist or simulated data. — DAISIE_count_species","text":"Calculates various island diversity metrics island datasets.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_count_species.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count number of species in DAISIE datalist or simulated data. — DAISIE_count_species","text":"","code":"DAISIE_count_species(islands, sort_clade_sizes = TRUE)"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_count_species.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count number of species in DAISIE datalist or simulated data. — DAISIE_count_species","text":"islands Island datalist simulated data DAISIE datalist format. Can single island (empirical data) generated DAISIE_dataprep DAISIEprep. Can also simulated data generated DAISIE_sim function. sort_clade_sizes Default sort_clade_sizes = T outputs clade sizes sorted ascending order number species. sort_clade_sizes=F outputs clade sizes order appear input datalist.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_count_species.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count number of species in DAISIE datalist or simulated data. — DAISIE_count_species","text":"output list containing following items: clade_sizes_sorted List showing total number species island clade (including missing species). item [[]] list gives sizes clades single island. option sort_clade_sizes = T, clade sizes sorted increasing number species. option sort_clade_sizes = F clade sizes given order input datalist. size_largest_clade total number species largest island clade island. mean_clade_size Mean clade size (average island clades) number_colonisations total number colonisations (clades) island. total_number_species total number species island. extant species present, including missing species; case simulations, number species present island end simulation.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_count_species.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Count number of species in DAISIE datalist or simulated data. — DAISIE_count_species","text":"Luis Valente","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_count_species.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Count number of species in DAISIE datalist or simulated data. — DAISIE_count_species","text":"","code":"# Run function with clade sizes in the order they appear in the input data data(\"NewZealand_birds_datalist\") species_count <- DAISIE_count_species(NewZealand_birds_datalist)  # Run function with clade sizes in ascending order species_count_sorted <- DAISIE_count_species(   NewZealand_birds_datalist,   sort_clade_sizes = TRUE )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_create_island.html","id":null,"dir":"Reference","previous_headings":"","what":"Converts simulation output into island output — DAISIE_create_island","title":"Converts simulation output into island output — DAISIE_create_island","text":"Converts simulation output island output","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_create_island.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Converts simulation output into island output — DAISIE_create_island","text":"","code":"DAISIE_create_island(   stt_table,   total_time,   island_spec,   mainland_n,   trait_pars = NULL )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_create_island.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Converts simulation output into island output — DAISIE_create_island","text":"stt_table Matrix number species time step. total_time Numeric defining length simulation time units. island_spec Matrix current state simulation containing number species. mainland_n numeric stating number mainland species, number species can potentially colonize island. using clade-specific diversity dependence, value set 1. using island-wide diversity dependence, value set number mainland species. trait_pars named list containing diversification rates considering   two trait states created create_trait_pars: [1]:numeric per capita transition rate state1 [2]:numeric per capita immigration rate state2 [3]:numeric per capita extinction rate state2 [4]:numeric per capita anagenesis rate state2 [5]:numeric per capita cladogenesis rate state2 [6]:numeric per capita transition rate state2 [7]:numeric number species trait state 2    mainland","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_create_island.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Converts simulation output into island output — DAISIE_create_island","text":"list island information, composed stt table, branching times extant species, status species island number missing species.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_dataprep.html","id":null,"dir":"Reference","previous_headings":"","what":"Prepare colonisation and branching time data to run in DAISIE. — DAISIE_dataprep","title":"Prepare colonisation and branching time data to run in DAISIE. — DAISIE_dataprep","text":"function produces data object can run DAISIE likelihood computation/optimization functions. function converts user-specified table DAISIE-compatible format. See Galapagos_datatable.Rdata template input table.)","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_dataprep.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Prepare colonisation and branching time data to run in DAISIE. — DAISIE_dataprep","text":"","code":"DAISIE_dataprep(   datatable,   island_age,   M,   number_clade_types = 1,   list_type2_clades = NA,   prop_type2_pool = \"proportional\",   epss = 1e-05,   verbose = TRUE )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_dataprep.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Prepare colonisation and branching time data to run in DAISIE. — DAISIE_dataprep","text":"datatable Data frame (table) user-specified data. See file Galapagos_datatable.Rdata template input table. row table represents independent colonisation event. Table following four columns. $Clade_name - name independent colonization event $Status - One following categories:  * \"Non_endemic\": applies non-endemic species approximate colonisation time known  * \"Non_endemic_MaxAge\": applies non-endemic species cases colonisation time unknown  * \"Endemic\": applies endemic species endemic clades approximate colonisation time known  * \"Endemic_MaxAge\": applies endemic species endemic clades cases colonisation time unknown, user wants specify upper bound colonisation. example apply endemic species recently gone extinct anthropogenic causes, included phylogeny (\"NA\" given branching times column). also apply insular radiations long stem branches, time first cladogenetic event known, precise time colonisation .  * \"Endemic_MaxAge_MinAge\": Endemic_MaxAge also includes minimum age colonisation.  * \"Non_endemic_MaxAge_MinAge\": Non_endemic_MaxAge also includes minimum age colonisation.#'  * \"Endemic&Non_Endemic\": endemic clade present mainland ancestor re-colonized $Missing_species - Number island species sampled particular clade (applicable \"Endemic\" clades). NA given branching times column,  equal number species clade minus 1 $Branching_times  - Stem age population/species case \"Non_endemic\", \"Non_endemic_MaxAge\"  \"Endemic\" species extant close relatives island. Set \"NA\"  colonisation time unknown upper bound known. \"Endemic\" cladogenetic species branching times radiation, including stem age radiation (colonisation time estimate). island_age Age island appropriate units M size mainland pool, .e number species can potentially colonize island number_clade_types Number clade types. Default: number_clade_types = 1 species considered belong macroevolutionary process. number_clade_types = 2, two types clades distinct macroevolutionary processes. list_type2_clades number_clade_types = 2, list_type2_clades specifies names clades distinct macroevolutionary process. names must match $Clade_name column source data table (e.g. list_type2_clades = \"Finches\").  number_clade_types = 1, list_type2_clades = NA specified (default) prop_type2_pool Specifies fraction potential mainland colonists distinct macroevolutionary process. Applies number_clade_types = 2.  Default \"proportional\" sets fraction proportional number clades distinct macroevolutionary process colonised island. Alternatively, user can specify value 0 1 (e.g. mainland pool size 1000 prop_type2_pool = 0.02 number type2 species 20). epss Default= 1E-5 appropriate cases. value used set maximum age colonisation \"Non_endemic_MaxAge\" \"Endemic_MaxAge\" species age slightly younger island cases age provided species older island. new maximum age used upper bound integrate possible colonisation times. verbose Boolean. States intermediate results printed console. Defaults TRUE.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_dataprep.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Prepare colonisation and branching time data to run in DAISIE. — DAISIE_dataprep","text":"datalist R list object containing data: first element list two three components: $island_age - island age  , depending whether distinction species types made, :$not_present - number mainland lineages present island  :$not_present_type1 - number mainland lineages type 1 present island $not_present_type2 - number mainland lineages type 2 present island  following elements list contains information single colonist lineage island 5 components:$colonist_name - name species clade colonized island $branching_times - island age stem age population/species case \"Non-endemic\", \"Non-endemic_MaxAge\" \"Endemic\" anagenetic species. \"Endemic\" cladogenetic species island age branching times radiation including stem age radiation.$stac - status colonist  * Non_endemic_MaxAge: 1  * Endemic: 2  * Endemic&Non_Endemic: 3  * Non_endemic: 4  * Endemic_MaxAge: 5 (colonisation time given)  * Endemic_MaxAge: 6 (colonisation time cladogenesis times given) $missing_species - number island species sampled particular clade (applicable endemic clades) $type_1or2  - whether colonist belongs type 1 type 2","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_dataprep.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Prepare colonisation and branching time data to run in DAISIE. — DAISIE_dataprep","text":"output R list containing data formatted run DAISIE functions.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_dataprep.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Prepare colonisation and branching time data to run in DAISIE. — DAISIE_dataprep","text":"Valente, L.M., .B. Phillimore R.S. Etienne (2015). Equilibrium non-equilibrium dynamics simultaneously operate Galapagos islands. Ecology Letters 18: 844-852.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_dataprep.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Prepare colonisation and branching time data to run in DAISIE. — DAISIE_dataprep","text":"Luis M Valente","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_dataprep.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Prepare colonisation and branching time data to run in DAISIE. — DAISIE_dataprep","text":"","code":"### Create Galapagos data object where all taxa have the same macroevolutionary process  utils::data(Galapagos_datatable, package = \"DAISIE\") DAISIE_dataprep(    datatable = Galapagos_datatable,    island_age = 4,    M = 1000    ) #> Colonisation time of 7.456 for Coccyzus is older than island age #> Colonisation time of 10.285 for Pyrocephalus is older than island age #> [[1]] #> [[1]]$island_age #> [1] 4 #>  #> [[1]]$not_present #> [1] 992 #>  #>  #> [[2]] #> [[2]]$colonist_name #> [1] \"Coccyzus\" #>  #> [[2]]$branching_times #> [1] 4.00000 3.99999 #>  #> [[2]]$stac #> [1] 1 #>  #> [[2]]$missing_species #> [1] 0 #>  #> [[2]]$type1or2 #> [1] 1 #>  #>  #> [[3]] #> [[3]]$colonist_name #> [1] \"Dendroica\" #>  #> [[3]]$branching_times #> [1] 4.00 0.34 #>  #> [[3]]$stac #> [1] 4 #>  #> [[3]]$missing_species #> [1] 0 #>  #> [[3]]$type1or2 #> [1] 1 #>  #>  #> [[4]] #> [[4]]$colonist_name #> [1] \"Finches\" #>  #> [[4]]$branching_times #>  [1] 4.0000 3.0282 1.3227 0.8223 0.4286 0.3462 0.2450 0.1180 0.0808 0.0756 #> [11] 0.0527 0.0525 0.0327 0.0322 0.0221 0.0118 #>  #> [[4]]$stac #> [1] 2 #>  #> [[4]]$missing_species #> [1] 0 #>  #> [[4]]$type1or2 #> [1] 1 #>  #>  #> [[5]] #> [[5]]$colonist_name #> [1] \"Mimus\" #>  #> [[5]]$branching_times #> [1] 4.000 3.958 3.422 2.884 0.459 #>  #> [[5]]$stac #> [1] 2 #>  #> [[5]]$missing_species #> [1] 0 #>  #> [[5]]$type1or2 #> [1] 1 #>  #>  #> [[6]] #> [[6]]$colonist_name #> [1] \"Myiarchus\" #>  #> [[6]]$branching_times #> [1] 4.000 0.855 #>  #> [[6]]$stac #> [1] 2 #>  #> [[6]]$missing_species #> [1] 0 #>  #> [[6]]$type1or2 #> [1] 1 #>  #>  #> [[7]] #> [[7]]$colonist_name #> [1] \"Progne\" #>  #> [[7]]$branching_times #> [1] 4.000 0.086 #>  #> [[7]]$stac #> [1] 2 #>  #> [[7]]$missing_species #> [1] 0 #>  #> [[7]]$type1or2 #> [1] 1 #>  #>  #> [[8]] #> [[8]]$colonist_name #> [1] \"Pyrocephalus\" #>  #> [[8]]$branching_times #> [1] 4.00000 3.99999 #>  #> [[8]]$stac #> [1] 1 #>  #> [[8]]$missing_species #> [1] 0 #>  #> [[8]]$type1or2 #> [1] 1 #>  #>  #> [[9]] #> [[9]]$colonist_name #> [1] \"Zenaida\" #>  #> [[9]]$branching_times #> [1] 4.00 3.51 #>  #> [[9]]$stac #> [1] 2 #>  #> [[9]]$missing_species #> [1] 0 #>  #> [[9]]$type1or2 #> [1] 1 #>  #>   ### Create Galapagos data object with a distinct macroevolutionary processes # for the Darwin's finches. One process applies to type 1 species (all species # except for Darwin's finches) and the other applies only to type 2 species # (Darwin's finches). Set fraction of potential colonists of type 2 to be # proportional to the number of type2 clades present on the island.  utils::data(Galapagos_datatable, package = \"DAISIE\") DAISIE_dataprep(    datatable = Galapagos_datatable,    island_age = 4,    M = 1000,    number_clade_types = 2,    list_type2_clades = \"Finches\"    ) #> Colonisation time of 7.456 for Coccyzus is older than island age #> Colonisation time of 10.285 for Pyrocephalus is older than island age #> [[1]] #> [[1]]$island_age #> [1] 4 #>  #> [[1]]$not_present_type1 #> [1] 868 #>  #> [[1]]$not_present_type2 #> [1] 124 #>  #>  #> [[2]] #> [[2]]$colonist_name #> [1] \"Coccyzus\" #>  #> [[2]]$branching_times #> [1] 4.00000 3.99999 #>  #> [[2]]$stac #> [1] 1 #>  #> [[2]]$missing_species #> [1] 0 #>  #> [[2]]$type1or2 #> [1] 1 #>  #>  #> [[3]] #> [[3]]$colonist_name #> [1] \"Dendroica\" #>  #> [[3]]$branching_times #> [1] 4.00 0.34 #>  #> [[3]]$stac #> [1] 4 #>  #> [[3]]$missing_species #> [1] 0 #>  #> [[3]]$type1or2 #> [1] 1 #>  #>  #> [[4]] #> [[4]]$colonist_name #> [1] \"Finches\" #>  #> [[4]]$branching_times #>  [1] 4.0000 3.0282 1.3227 0.8223 0.4286 0.3462 0.2450 0.1180 0.0808 0.0756 #> [11] 0.0527 0.0525 0.0327 0.0322 0.0221 0.0118 #>  #> [[4]]$stac #> [1] 2 #>  #> [[4]]$missing_species #> [1] 0 #>  #> [[4]]$type1or2 #> [1] 2 #>  #>  #> [[5]] #> [[5]]$colonist_name #> [1] \"Mimus\" #>  #> [[5]]$branching_times #> [1] 4.000 3.958 3.422 2.884 0.459 #>  #> [[5]]$stac #> [1] 2 #>  #> [[5]]$missing_species #> [1] 0 #>  #> [[5]]$type1or2 #> [1] 1 #>  #>  #> [[6]] #> [[6]]$colonist_name #> [1] \"Myiarchus\" #>  #> [[6]]$branching_times #> [1] 4.000 0.855 #>  #> [[6]]$stac #> [1] 2 #>  #> [[6]]$missing_species #> [1] 0 #>  #> [[6]]$type1or2 #> [1] 1 #>  #>  #> [[7]] #> [[7]]$colonist_name #> [1] \"Progne\" #>  #> [[7]]$branching_times #> [1] 4.000 0.086 #>  #> [[7]]$stac #> [1] 2 #>  #> [[7]]$missing_species #> [1] 0 #>  #> [[7]]$type1or2 #> [1] 1 #>  #>  #> [[8]] #> [[8]]$colonist_name #> [1] \"Pyrocephalus\" #>  #> [[8]]$branching_times #> [1] 4.00000 3.99999 #>  #> [[8]]$stac #> [1] 1 #>  #> [[8]]$missing_species #> [1] 0 #>  #> [[8]]$type1or2 #> [1] 1 #>  #>  #> [[9]] #> [[9]]$colonist_name #> [1] \"Zenaida\" #>  #> [[9]]$branching_times #> [1] 4.00 3.51 #>  #> [[9]]$stac #> [1] 2 #>  #> [[9]]$missing_species #> [1] 0 #>  #> [[9]]$type1or2 #> [1] 1 #>  #>   ### Create Galapagos data object with a distinct macroevolutionary processes # for the Darwin's finches. One process applies to type 1 species (all species # except for Darwin's finches) and the other applies only to type 2 species # (Darwin's finches). Set fraction of potential colonists of type 2 to be 0.163.  utils::data(Galapagos_datatable, package = \"DAISIE\") DAISIE_dataprep(    datatable = Galapagos_datatable,    island_age = 4,    M = 1000,    number_clade_types = 2,    list_type2_clades = \"Finches\",    prop_type2_pool = 0.163    ) #> Colonisation time of 7.456 for Coccyzus is older than island age #> Colonisation time of 10.285 for Pyrocephalus is older than island age #> [[1]] #> [[1]]$island_age #> [1] 4 #>  #> [[1]]$not_present_type1 #> [1] 830 #>  #> [[1]]$not_present_type2 #> [1] 162 #>  #>  #> [[2]] #> [[2]]$colonist_name #> [1] \"Coccyzus\" #>  #> [[2]]$branching_times #> [1] 4.00000 3.99999 #>  #> [[2]]$stac #> [1] 1 #>  #> [[2]]$missing_species #> [1] 0 #>  #> [[2]]$type1or2 #> [1] 1 #>  #>  #> [[3]] #> [[3]]$colonist_name #> [1] \"Dendroica\" #>  #> [[3]]$branching_times #> [1] 4.00 0.34 #>  #> [[3]]$stac #> [1] 4 #>  #> [[3]]$missing_species #> [1] 0 #>  #> [[3]]$type1or2 #> [1] 1 #>  #>  #> [[4]] #> [[4]]$colonist_name #> [1] \"Finches\" #>  #> [[4]]$branching_times #>  [1] 4.0000 3.0282 1.3227 0.8223 0.4286 0.3462 0.2450 0.1180 0.0808 0.0756 #> [11] 0.0527 0.0525 0.0327 0.0322 0.0221 0.0118 #>  #> [[4]]$stac #> [1] 2 #>  #> [[4]]$missing_species #> [1] 0 #>  #> [[4]]$type1or2 #> [1] 2 #>  #>  #> [[5]] #> [[5]]$colonist_name #> [1] \"Mimus\" #>  #> [[5]]$branching_times #> [1] 4.000 3.958 3.422 2.884 0.459 #>  #> [[5]]$stac #> [1] 2 #>  #> [[5]]$missing_species #> [1] 0 #>  #> [[5]]$type1or2 #> [1] 1 #>  #>  #> [[6]] #> [[6]]$colonist_name #> [1] \"Myiarchus\" #>  #> [[6]]$branching_times #> [1] 4.000 0.855 #>  #> [[6]]$stac #> [1] 2 #>  #> [[6]]$missing_species #> [1] 0 #>  #> [[6]]$type1or2 #> [1] 1 #>  #>  #> [[7]] #> [[7]]$colonist_name #> [1] \"Progne\" #>  #> [[7]]$branching_times #> [1] 4.000 0.086 #>  #> [[7]]$stac #> [1] 2 #>  #> [[7]]$missing_species #> [1] 0 #>  #> [[7]]$type1or2 #> [1] 1 #>  #>  #> [[8]] #> [[8]]$colonist_name #> [1] \"Pyrocephalus\" #>  #> [[8]]$branching_times #> [1] 4.00000 3.99999 #>  #> [[8]]$stac #> [1] 1 #>  #> [[8]]$missing_species #> [1] 0 #>  #> [[8]]$type1or2 #> [1] 1 #>  #>  #> [[9]] #> [[9]]$colonist_name #> [1] \"Zenaida\" #>  #> [[9]]$branching_times #> [1] 4.00 3.51 #>  #> [[9]]$stac #> [1] 2 #>  #> [[9]]$missing_species #> [1] 0 #>  #> [[9]]$type1or2 #> [1] 1 #>  #>"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_extract_stt_median.html","id":null,"dir":"Reference","previous_headings":"","what":"Extract the STT median from the output of DAISIE_sim functions — DAISIE_extract_stt_median","title":"Extract the STT median from the output of DAISIE_sim functions — DAISIE_extract_stt_median","text":"Extract STT median output DAISIE_sim functions","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_extract_stt_median.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extract the STT median from the output of DAISIE_sim functions — DAISIE_extract_stt_median","text":"","code":"DAISIE_extract_stt_median(island_replicates, trait_pars = NULL)"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_extract_stt_median.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extract the STT median from the output of DAISIE_sim functions — DAISIE_extract_stt_median","text":"island_replicates List output DAISIE_sim_core_cr(), DAISIE_sim_core_time_dep(), DAISIE_sim_core_cr_shift() DAISIE_sim_min_type2() functions. Minimally, must list many elements replicates. element must list elements island_age, not_present stt_all. stt_all must data frame column names Time, nI, nA, nC present. trait_pars named list containing diversification rates considering   two trait states created create_trait_pars: [1]:numeric per capita transition rate state1 [2]:numeric per capita immigration rate state2 [3]:numeric per capita extinction rate state2 [4]:numeric per capita anagenesis rate state2 [5]:numeric per capita cladogenesis rate state2 [6]:numeric per capita transition rate state2 [7]:numeric number species trait state 2    mainland","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_extract_stt_median.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Extract the STT median from the output of DAISIE_sim functions — DAISIE_extract_stt_median","text":"matrix (?)","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_format_CS.html","id":null,"dir":"Reference","previous_headings":"","what":"Wrapper function around for the DAISIE_format_CS_full_stt and\nDAISIE_format_CS_sampled_stt — DAISIE_format_CS","title":"Wrapper function around for the DAISIE_format_CS_full_stt and\nDAISIE_format_CS_sampled_stt — DAISIE_format_CS","text":"Wrapper function around DAISIE_format_CS_full_stt DAISIE_format_CS_sampled_stt","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_format_CS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Wrapper function around for the DAISIE_format_CS_full_stt and\nDAISIE_format_CS_sampled_stt — DAISIE_format_CS","text":"","code":"DAISIE_format_CS(   island_replicates,   time,   M,   sample_freq = 25,   verbose = TRUE,   trait_pars = NULL )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_format_CS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Wrapper function around for the DAISIE_format_CS_full_stt and\nDAISIE_format_CS_sampled_stt — DAISIE_format_CS","text":"island_replicates List output DAISIE_sim_core_cr(), DAISIE_sim_core_time_dep(), DAISIE_sim_core_cr_shift() DAISIE_sim_min_type2() functions. Minimally, must list many elements replicates. element must list elements island_age, not_present stt_all. stt_all must data frame column names Time, nI, nA, nC present. time Numeric defining length simulation time units. example, island known 4 million years old, setting time = 4 simulate entire life span island; setting time = 2 stop simulation mid-life island. M Numeric defining size mainland pool, .e. number species can potentially colonize island. sample_freq Numeric specifing number units times divided plotting purposes. Larger values lead plots higher resolution, also run slower. verbose numeric vector length 1, simulations `DAISIEdataprep()` can `1` `0`, `1` gives intermediate output printed. ML functions numeric determining intermediate output printed. default: `0` print, `1` prints initial likelihood settings selected (parameters optimised, fixed shifted), `2` prints `1 also intermediate output parameters loglikelihood, `3` `2` prints intermediate progress likelihood computation. trait_pars named list containing diversification rates considering   two trait states created create_trait_pars: [1]:numeric per capita transition rate state1 [2]:numeric per capita immigration rate state2 [3]:numeric per capita extinction rate state2 [4]:numeric per capita anagenesis rate state2 [5]:numeric per capita cladogenesis rate state2 [6]:numeric per capita transition rate state2 [7]:numeric number species trait state 2    mainland","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_format_CS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Wrapper function around for the DAISIE_format_CS_full_stt and\nDAISIE_format_CS_sampled_stt — DAISIE_format_CS","text":"List CS DAISIE simulation output","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_format_CS_full_stt.html","id":null,"dir":"Reference","previous_headings":"","what":"Formats clade-specific simulation output into standard\nDAISIE list output with complete STT table — DAISIE_format_CS_full_stt","title":"Formats clade-specific simulation output into standard\nDAISIE list output with complete STT table — DAISIE_format_CS_full_stt","text":"Formats clade-specific simulation output standard DAISIE list output complete STT table","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_format_CS_full_stt.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Formats clade-specific simulation output into standard\nDAISIE list output with complete STT table — DAISIE_format_CS_full_stt","text":"","code":"DAISIE_format_CS_full_stt(   island_replicates,   time,   M,   verbose = TRUE,   trait_pars = NULL )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_format_CS_full_stt.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Formats clade-specific simulation output into standard\nDAISIE list output with complete STT table — DAISIE_format_CS_full_stt","text":"island_replicates List output DAISIE_sim_core_cr(), DAISIE_sim_core_time_dep(), DAISIE_sim_core_cr_shift() DAISIE_sim_min_type2() functions. Minimally, must list many elements replicates. element must list elements island_age, not_present stt_all. stt_all must data frame column names Time, nI, nA, nC present. time Numeric defining length simulation time units. example, island known 4 million years old, setting time = 4 simulate entire life span island; setting time = 2 stop simulation mid-life island. M Numeric defining size mainland pool, .e. number species can potentially colonize island. verbose numeric vector length 1, simulations `DAISIEdataprep()` can `1` `0`, `1` gives intermediate output printed. ML functions numeric determining intermediate output printed. default: `0` print, `1` prints initial likelihood settings selected (parameters optimised, fixed shifted), `2` prints `1 also intermediate output parameters loglikelihood, `3` `2` prints intermediate progress likelihood computation. trait_pars named list containing diversification rates considering   two trait states created create_trait_pars: [1]:numeric per capita transition rate state1 [2]:numeric per capita immigration rate state2 [3]:numeric per capita extinction rate state2 [4]:numeric per capita anagenesis rate state2 [5]:numeric per capita cladogenesis rate state2 [6]:numeric per capita transition rate state2 [7]:numeric number species trait state 2    mainland","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_format_CS_full_stt.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Formats clade-specific simulation output into standard\nDAISIE list output with complete STT table — DAISIE_format_CS_full_stt","text":"List CS DAISIE simulation output","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_format_CS_sampled_stt.html","id":null,"dir":"Reference","previous_headings":"","what":"Formats clade-specific simulation output into standard\nDAISIE list output — DAISIE_format_CS_sampled_stt","title":"Formats clade-specific simulation output into standard\nDAISIE list output — DAISIE_format_CS_sampled_stt","text":"Formats clade-specific simulation output standard DAISIE list output","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_format_CS_sampled_stt.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Formats clade-specific simulation output into standard\nDAISIE list output — DAISIE_format_CS_sampled_stt","text":"","code":"DAISIE_format_CS_sampled_stt(   island_replicates,   time,   M,   sample_freq,   verbose = TRUE,   trait_pars = NULL )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_format_CS_sampled_stt.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Formats clade-specific simulation output into standard\nDAISIE list output — DAISIE_format_CS_sampled_stt","text":"island_replicates List output DAISIE_sim_core_cr(), DAISIE_sim_core_time_dep(), DAISIE_sim_core_cr_shift() DAISIE_sim_min_type2() functions. Minimally, must list many elements replicates. element must list elements island_age, not_present stt_all. stt_all must data frame column names Time, nI, nA, nC present. time Numeric defining length simulation time units. example, island known 4 million years old, setting time = 4 simulate entire life span island; setting time = 2 stop simulation mid-life island. M Numeric defining size mainland pool, .e. number species can potentially colonize island. sample_freq Numeric specifing number units times divided plotting purposes. Larger values lead plots higher resolution, also run slower. verbose numeric vector length 1, simulations `DAISIEdataprep()` can `1` `0`, `1` gives intermediate output printed. ML functions numeric determining intermediate output printed. default: `0` print, `1` prints initial likelihood settings selected (parameters optimised, fixed shifted), `2` prints `1 also intermediate output parameters loglikelihood, `3` `2` prints intermediate progress likelihood computation. trait_pars named list containing diversification rates considering   two trait states created create_trait_pars: [1]:numeric per capita transition rate state1 [2]:numeric per capita immigration rate state2 [3]:numeric per capita extinction rate state2 [4]:numeric per capita anagenesis rate state2 [5]:numeric per capita cladogenesis rate state2 [6]:numeric per capita transition rate state2 [7]:numeric number species trait state 2    mainland","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_format_CS_sampled_stt.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Formats clade-specific simulation output into standard\nDAISIE list output — DAISIE_format_CS_sampled_stt","text":"List CS DAISIE simulation output","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_format_GW.html","id":null,"dir":"Reference","previous_headings":"","what":"Formats guild-wide simulation output into standard DAISIE\nlist output — DAISIE_format_GW","title":"Formats guild-wide simulation output into standard DAISIE\nlist output — DAISIE_format_GW","text":"Formats guild-wide simulation output standard DAISIE list output","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_format_GW.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Formats guild-wide simulation output into standard DAISIE\nlist output — DAISIE_format_GW","text":"","code":"DAISIE_format_GW(   island_replicates,   time,   M,   sample_freq,   num_guilds,   verbose = TRUE )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_format_GW.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Formats guild-wide simulation output into standard DAISIE\nlist output — DAISIE_format_GW","text":"island_replicates List output DAISIE_sim_core_cr(), DAISIE_sim_core_time_dep(), DAISIE_sim_core_cr_shift() DAISIE_sim_min_type2() functions. Minimally, must list many elements replicates. element must list elements island_age, not_present stt_all. stt_all must data frame column names Time, nI, nA, nC present. time Numeric defining length simulation time units. example, island known 4 million years old, setting time = 4 simulate entire life span island; setting time = 2 stop simulation mid-life island. M Numeric defining size mainland pool, .e. number species can potentially colonize island. sample_freq Numeric specifing number units times divided plotting purposes. Larger values lead plots higher resolution, also run slower. num_guilds number guilds mainland. number mainland species divided number guilds divdepmodel = \"GW\" verbose numeric vector length 1, simulations `DAISIEdataprep()` can `1` `0`, `1` gives intermediate output printed. ML functions numeric determining intermediate output printed. default: `0` print, `1` prints initial likelihood settings selected (parameters optimised, fixed shifted), `2` prints `1 also intermediate output parameters loglikelihood, `3` `2` prints intermediate progress likelihood computation.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_format_GW.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Formats guild-wide simulation output into standard DAISIE\nlist output — DAISIE_format_GW","text":"List GW DAISIE simulation output","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_format_IW_full_stt.html","id":null,"dir":"Reference","previous_headings":"","what":"Formats clade-specific simulation output into standard\nDAISIE list output with complete STT table — DAISIE_format_IW_full_stt","title":"Formats clade-specific simulation output into standard\nDAISIE list output with complete STT table — DAISIE_format_IW_full_stt","text":"Formats clade-specific simulation output standard DAISIE list output complete STT table","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_format_IW_full_stt.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Formats clade-specific simulation output into standard\nDAISIE list output with complete STT table — DAISIE_format_IW_full_stt","text":"","code":"DAISIE_format_IW_full_stt(island_replicates, total_time, M, verbose)"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_format_IW_full_stt.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Formats clade-specific simulation output into standard\nDAISIE list output with complete STT table — DAISIE_format_IW_full_stt","text":"island_replicates List output DAISIE_sim_core_cr(), DAISIE_sim_core_time_dep(), DAISIE_sim_core_cr_shift() DAISIE_sim_min_type2() functions. Minimally, must list many elements replicates. element must list elements island_age, not_present stt_all. stt_all must data frame column names Time, nI, nA, nC present. total_time Numeric defining length simulation time units. M Numeric defining size mainland pool, .e. number species can potentially colonize island. verbose numeric vector length 1, simulations `DAISIEdataprep()` can `1` `0`, `1` gives intermediate output printed. ML functions numeric determining intermediate output printed. default: `0` print, `1` prints initial likelihood settings selected (parameters optimised, fixed shifted), `2` prints `1 also intermediate output parameters loglikelihood, `3` `2` prints intermediate progress likelihood computation.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_format_IW_full_stt.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Formats clade-specific simulation output into standard\nDAISIE list output with complete STT table — DAISIE_format_IW_full_stt","text":"List IW DAISIE simulation output","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_format_IW_sampled_stt.html","id":null,"dir":"Reference","previous_headings":"","what":"Formats island-wide simulation output into standard\nDAISIE list output — DAISIE_format_IW_sampled_stt","title":"Formats island-wide simulation output into standard\nDAISIE list output — DAISIE_format_IW_sampled_stt","text":"Formats island-wide simulation output standard DAISIE list output","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_format_IW_sampled_stt.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Formats island-wide simulation output into standard\nDAISIE list output — DAISIE_format_IW_sampled_stt","text":"","code":"DAISIE_format_IW_sampled_stt(   island_replicates,   total_time,   M,   sample_freq,   verbose )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_format_IW_sampled_stt.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Formats island-wide simulation output into standard\nDAISIE list output — DAISIE_format_IW_sampled_stt","text":"island_replicates List output DAISIE_sim_core_cr(), DAISIE_sim_core_time_dep(), DAISIE_sim_core_cr_shift() DAISIE_sim_min_type2() functions. Minimally, must list many elements replicates. element must list elements island_age, not_present stt_all. stt_all must data frame column names Time, nI, nA, nC present. total_time Numeric defining length simulation time units. M Numeric defining size mainland pool, .e. number species can potentially colonize island. sample_freq Numeric specifing number units times divided plotting purposes. Larger values lead plots higher resolution, also run slower. verbose numeric vector length 1, simulations `DAISIEdataprep()` can `1` `0`, `1` gives intermediate output printed. ML functions numeric determining intermediate output printed. default: `0` print, `1` prints initial likelihood settings selected (parameters optimised, fixed shifted), `2` prints `1 also intermediate output parameters loglikelihood, `3` `2` prints intermediate progress likelihood computation.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_format_IW_sampled_stt.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Formats island-wide simulation output into standard\nDAISIE list output — DAISIE_format_IW_sampled_stt","text":"List IW DAISIE simulation output","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_loglik_CS.html","id":null,"dir":"Reference","previous_headings":"","what":"Computes the loglikelihood of the DAISIE model with clade-specific\ndiversity-dependence given data and a set of model parameters — DAISIE_loglik_CS","title":"Computes the loglikelihood of the DAISIE model with clade-specific\ndiversity-dependence given data and a set of model parameters — DAISIE_loglik_CS","text":"Computes loglikelihood DAISIE model clade-specific diversity-dependence given colonization branching times lineages island, set model parameters. output loglikelihood value","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_loglik_CS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Computes the loglikelihood of the DAISIE model with clade-specific\ndiversity-dependence given data and a set of model parameters — DAISIE_loglik_CS","text":"","code":"DAISIE_loglik_CS(   pars1,   pars2,   datalist,   methode = \"lsodes\",   CS_version = 1,   abstolint = 1e-16,   reltolint = 1e-10 )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_loglik_CS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Computes the loglikelihood of the DAISIE model with clade-specific\ndiversity-dependence given data and a set of model parameters — DAISIE_loglik_CS","text":"pars1 Contains model parameters: pars1[1] corresponds lambda^c (cladogenesis rate) pars1[2] corresponds mu (extinction rate) pars1[3] corresponds K (clade-level carrying capacity) pars1[4] corresponds gamma (immigration rate) pars1[5] corresponds lambda^(anagenesis rate) pars1[6] corresponds lambda^c (cladogenesis rate) optional subset species pars1[7] corresponds mu (extinction rate) optional subset speciespars1[8] corresponds K (clade-level carrying capacity) optional subset speciespars1[9] corresponds gamma (immigration rate) optional subset speciespars1[10] corresponds lambda^(anagenesis rate) optional subset speciespars1[11] corresponds p_f (fraction mainland species belongs second subset species elements 6:10 11 optional, , pars1 either contain 5, 10 11 elements. 10, fraction potential colonists type 2 computed data. 11, pars1[11] used, overruling information data. pars2 Contains model settings pars2[1] corresponds lx = length ODE variable x pars2[2] corresponds ddmodel = diversity-dependent model, model diversity-dependence, can one ddmodel = 0 : diversity dependence  ddmodel = 1 : linear dependence speciation rate  ddmodel = 11: linear dependence speciation rate immigration rate  ddmodel = 2 : exponential dependence speciation rate ddmodel = 21: exponential dependence speciation rate immigration ratepars2[3] corresponds cond = setting conditioning cond = 0 : conditioning island age  cond = 1 : conditioning island age non-extinction island biota  cond > 1 : conditioning island age least cond colonizations island pars2[4] sets whether parameters likelihood printed (1) (0) datalist Data object containing information colonisation branching times. object can generated using DAISIE_dataprep function, converts user-specified data table data object, object can course also entered directly. R list object following elements. first element list two three components: $island_age - island age  , depending whether distinction types made, :$not_present - number mainland lineages present island  :$not_present_type1 - number mainland lineages type 1 present island $not_present_type2 - number mainland lineages type 2 present island  remaining elements list contains information single colonist lineage island 5 components:$colonist_name - name species clade colonized island $branching_times - island age stem age population/species case Non-endemic, Non-endemic_MaxAge Endemic anagenetic species. cladogenetic species island age branching times radiation including stem age radiation.$stac - status colonist  * Non_endemic_MaxAge: 1  * Endemic: 2  * Endemic&Non_Endemic: 3  * Non_Endemic: 4  * Endemic_Singleton_MaxAge: 5  * Endemic_Clade_MaxAge: 6  * Endemic&Non_Endemic_Clade_MaxAge: 7  * Non_endemic_MaxAge_MinAge: 8  * Endemic_Singleton_MaxAge_MinAge: 9 $missing_species - number island species sampled particular clade (applicable endemic clades) $type1or2 - whether colonist belongs type 1 type 2 methode Method ODE-solver. See package deSolve details. Default \"lsodes\" CS_version numeric list. Default 1 standard DAISIE model, relaxed-rate model list following elements: model: CS model run, options 1 single rate   DAISIE model, 2 multi-rate DAISIE, 0 IW test   model. relaxed_par: parameter relax (integrate ). Options \"cladogenesis\", \"extinction\", \"carrying_capacity\", \"immigration\", \"anagenesis\". abstolint Absolute tolerance integration reltolint Relative tolerance integration","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_loglik_CS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Computes the loglikelihood of the DAISIE model with clade-specific\ndiversity-dependence given data and a set of model parameters — DAISIE_loglik_CS","text":"loglikelihood","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_loglik_CS.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Computes the loglikelihood of the DAISIE model with clade-specific\ndiversity-dependence given data and a set of model parameters — DAISIE_loglik_CS","text":"Valente, L.M., .B. Phillimore R.S. Etienne (2015). Equilibrium non-equilibrium dynamics simultaneously operate Galapagos islands. Ecology Letters 18: 844-852.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_loglik_CS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Computes the loglikelihood of the DAISIE model with clade-specific\ndiversity-dependence given data and a set of model parameters — DAISIE_loglik_CS","text":"Rampal S. Etienne & Bart Haegeman","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_loglik_CS.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Computes the loglikelihood of the DAISIE model with clade-specific\ndiversity-dependence given data and a set of model parameters — DAISIE_loglik_CS","text":"","code":"utils::data(Galapagos_datalist_2types) pars1 = c(0.195442017,0.087959583,Inf,0.002247364,0.873605049,           3755.202241,8.909285094,14.99999923,0.002247364,0.873605049,0.163) pars2 = c(100,11,0,1) DAISIE_loglik_all(pars1,pars2,Galapagos_datalist_2types) #> [1] -61.70282"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_loglik_IW.html","id":null,"dir":"Reference","previous_headings":"","what":"Computes the loglikelihood of the DAISIE model with island-wide\ndiversity-dependence given data and a set of model parameters — DAISIE_loglik_IW","title":"Computes the loglikelihood of the DAISIE model with island-wide\ndiversity-dependence given data and a set of model parameters — DAISIE_loglik_IW","text":"Computes loglikelihood DAISIE model given colonization branching times lineages island, set model parameters DAISIE model island-wide diversity-dependence","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_loglik_IW.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Computes the loglikelihood of the DAISIE model with island-wide\ndiversity-dependence given data and a set of model parameters — DAISIE_loglik_IW","text":"","code":"DAISIE_loglik_IW(   pars1,   pars2,   datalist,   methode = \"lsodes\",   abstolint = 1e-12,   reltolint = 1e-10,   verbose = FALSE )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_loglik_IW.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Computes the loglikelihood of the DAISIE model with island-wide\ndiversity-dependence given data and a set of model parameters — DAISIE_loglik_IW","text":"pars1 Contains model parameters: pars1[1] corresponds lambda^c (cladogenesis rate) pars1[2] corresponds mu (extinction rate) pars1[3] corresponds K (clade-level carrying capacity) pars1[4] corresponds gamma (immigration rate) pars1[5] corresponds lambda^(anagenesis rate) pars1[6] optional; may contain M, total number species mainland pars2 Contains model settings pars2[1] corresponds lx = length ODE variable x pars2[2] corresponds ddmodel = diversity-dependent model, model diversity-dependence, can one ddmodel = 0 : diversity dependence  ddmodel = 1 : linear dependence speciation rate  ddmodel = 11: linear dependence speciation rate immigration rate  ddmodel = 2 : exponential dependence speciation rate ddmodel = 21: exponential dependence speciation rate immigration rate ddmodel = 11 currently implemented pars2[3] corresponds cond = setting conditioning cond = 0 : conditioning island age  cond = 1 : conditioning island age non-extinction island biota pars2[4] Specifies whether intermediate output provided, computation may take long. Default 0, output. value 1 means parameters loglikelihood printed. value 2 means also intermediate progress loglikelihood computation shown. datalist Data object containing information colonisation branching times. object can generated using DAISIE_dataprep function, converts user-specified data table data object, object can course also entered directly. R list object following elements. first element list two three components: $island_age - island age  , depending whether distinction types made, :$not_present - number mainland lineages present island  remaining elements list contains information single colonist lineage island 5 components:$colonist_name - name species clade colonized island $branching_times - island age stem age population/species case Non-endemic, Non-endemic_MaxAge Endemic anagenetic species. cladogenetic species island age branching times radiation including stem age radiation.$stac - status colonist  * Non_endemic_MaxAge: 1  * Endemic: 2  * Endemic&Non_Endemic: 3  * Non_endemic: 4  * Endemic_MaxAge: 5 $missing_species - number island species sampled particular clade (applicable endemic clades) methode Method ODE-solver. Supported Boost ODEINT solvers (steppers) : 'odeint::runge_kutta_cash_karp54' 'odeint::runge_kutta_fehlberg78' [default] 'odeint::runge_kutta_dopri5' 'odeint::bulirsch_stoer' 'odeint::adams_bashforth_[1|2|3|4|5|6|7|8]} \\code{'odeint::adams_bashforth_moulton_[1|2|3|4|5|6|7|8] without odeint::-prefix, ode method assumed. abstolint Absolute tolerance integration reltolint Relative tolerance integration verbose Logical controling progress printed console.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_loglik_IW.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Computes the loglikelihood of the DAISIE model with island-wide\ndiversity-dependence given data and a set of model parameters — DAISIE_loglik_IW","text":"loglikelihood","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_loglik_IW.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Computes the loglikelihood of the DAISIE model with island-wide\ndiversity-dependence given data and a set of model parameters — DAISIE_loglik_IW","text":"output loglikelihood value","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_loglik_IW.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Computes the loglikelihood of the DAISIE model with island-wide\ndiversity-dependence given data and a set of model parameters — DAISIE_loglik_IW","text":"Valente, L.M., .B. Phillimore R.S. Etienne (2015). Equilibrium non-equilibrium dynamics simultaneously operate Galapagos islands. Ecology Letters 18: 844-852.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_loglik_IW.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Computes the loglikelihood of the DAISIE model with island-wide\ndiversity-dependence given data and a set of model parameters — DAISIE_loglik_IW","text":"Rampal S. Etienne & Bart Haegeman","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_loglik_integrand.html","id":null,"dir":"Reference","previous_headings":"","what":"Integrand to be integrated to calculate the log likelihood for the relaxed\nrate model. — DAISIE_loglik_integrand","title":"Integrand to be integrated to calculate the log likelihood for the relaxed\nrate model. — DAISIE_loglik_integrand","text":"Integrand integrated calculate log likelihood relaxed rate model.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_loglik_integrand.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Integrand to be integrated to calculate the log likelihood for the relaxed\nrate model. — DAISIE_loglik_integrand","text":"","code":"DAISIE_loglik_integrand(   DAISIE_par,   pars1,   pars2,   brts,   stac,   missnumspec,   methode,   abstolint,   reltolint,   verbose,   pick,   par_mean,   par_sd )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_loglik_integrand.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Integrand to be integrated to calculate the log likelihood for the relaxed\nrate model. — DAISIE_loglik_integrand","text":"DAISIE_par numeric parameter evaluate integral function. pars1 Vector model parameters: pars1[1] corresponds lambda^c (cladogenesis rate) pars1[2] corresponds mu (extinction rate) pars1[3] corresponds K (clade-level carrying capacity) pars1[4] corresponds gamma (immigration rate) pars1[5] corresponds lambda^(anagenesis rate). pars2 Vector settings: pars2[1] corresponds res, maximum number endemics non-endemics ODE system solved; must much larger actual number probability needs calculated.) pars2[2] corresponds M, size mainland pool, .e number species can potentially colonize island. brts Numeric vector branching times stac Numeric Endemicity status missnumspec Numeric missing species methode Method ODE-solver. Supported Boost ODEINT solvers (steppers) : \"odeint::runge_kutta_cash_karp54\" \"odeint::runge_kutta_fehlberg78\" \"odeint::runge_kutta_dopri5\" \"odeint::bulirsch_stoer\" without odeint::-prefix, deSolve{ode} method assumed. default method overall \"lsodes\" DAISIE_ML_CS() \"ode45\" ode() DAISIE_ML_IW(). abstolint Numeric absolute tolerance integration reltolint Numeric relative tolerance integration verbose numeric vector length 1, simulations `DAISIEdataprep()` can `1` `0`, `1` gives intermediate output printed. ML functions numeric determining intermediate output printed. default: `0` print, `1` prints initial likelihood settings selected (parameters optimised, fixed shifted), `2` prints `1 also intermediate output parameters loglikelihood, `3` `2` prints intermediate progress likelihood computation. pick Numeric determining parameter selected relaxed-rate model","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_loglik_integrand.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Integrand to be integrated to calculate the log likelihood for the relaxed\nrate model. — DAISIE_loglik_integrand","text":"numeric","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_loglik_integrate.html","id":null,"dir":"Reference","previous_headings":"","what":"Integrates the loglikelihood of a single clade across a parameter weighted\nby a given distribution — DAISIE_loglik_integrate","title":"Integrates the loglikelihood of a single clade across a parameter weighted\nby a given distribution — DAISIE_loglik_integrate","text":"Integrates loglikelihood single clade across parameter weighted given distribution","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_loglik_integrate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Integrates the loglikelihood of a single clade across a parameter weighted\nby a given distribution — DAISIE_loglik_integrate","text":"","code":"DAISIE_loglik_integrate(   pars1,   pars2,   brts,   stac,   missnumspec,   CS_version,   methode,   abstolint,   reltolint,   verbose )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_loglik_integrate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Integrates the loglikelihood of a single clade across a parameter weighted\nby a given distribution — DAISIE_loglik_integrate","text":"pars1 Vector model parameters: pars1[1] corresponds lambda^c (cladogenesis rate) pars1[2] corresponds mu (extinction rate) pars1[3] corresponds K (clade-level carrying capacity) pars1[4] corresponds gamma (immigration rate) pars1[5] corresponds lambda^(anagenesis rate). pars2 Vector settings: pars2[1] corresponds res, maximum number endemics non-endemics ODE system solved; must much larger actual number probability needs calculated.) pars2[2] corresponds M, size mainland pool, .e number species can potentially colonize island. brts Numeric vector branching times stac Numeric Endemicity status missnumspec Numeric missing species CS_version numeric list. Default 1 standard DAISIE model, relaxed-rate model list following elements: model: CS model run, options 1 single rate   DAISIE model, 2 multi-rate DAISIE, 0 IW test   model. relaxed_par: parameter relax (integrate ). Options \"cladogenesis\", \"extinction\", \"carrying_capacity\", \"immigration\", \"anagenesis\". methode Method ODE-solver. Supported Boost ODEINT solvers (steppers) : \"odeint::runge_kutta_cash_karp54\" \"odeint::runge_kutta_fehlberg78\" \"odeint::runge_kutta_dopri5\" \"odeint::bulirsch_stoer\" without odeint::-prefix, deSolve{ode} method assumed. default method overall \"lsodes\" DAISIE_ML_CS() \"ode45\" ode() DAISIE_ML_IW(). abstolint Numeric absolute tolerance integration reltolint Numeric relative tolerance integration verbose numeric vector length 1, simulations `DAISIEdataprep()` can `1` `0`, `1` gives intermediate output printed. ML functions numeric determining intermediate output printed. default: `0` print, `1` prints initial likelihood settings selected (parameters optimised, fixed shifted), `2` prints `1 also intermediate output parameters loglikelihood, `3` `2` prints intermediate progress likelihood computation.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_loglik_integrate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Integrates the loglikelihood of a single clade across a parameter weighted\nby a given distribution — DAISIE_loglik_integrate","text":"loglikelihood value","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_make_archipelago.html","id":null,"dir":"Reference","previous_headings":"","what":"Does some things — DAISIE_make_archipelago","title":"Does some things — DAISIE_make_archipelago","text":"things","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_make_archipelago.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Does some things — DAISIE_make_archipelago","text":"","code":"DAISIE_make_archipelago(archipelago, M, phylo_data, archipelago_data)"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_make_archipelago.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Does some things — DAISIE_make_archipelago","text":"archipelago something M Numeric defining size mainland pool, .e. number species can potentially colonize island. phylo_data something archipelago_data something","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_make_archipelago.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Does some things — DAISIE_make_archipelago","text":"something","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_make_global.html","id":null,"dir":"Reference","previous_headings":"","what":"Does something — DAISIE_make_global","title":"Does something — DAISIE_make_global","text":"something","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_make_global.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Does something — DAISIE_make_global","text":"","code":"DAISIE_make_global(archipelago_list, M, phylo_data, archipelago_data)"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_make_global.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Does something — DAISIE_make_global","text":"archipelago_list something M something phylo_data something archipelago_data something","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_make_global.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Does something — DAISIE_make_global","text":"something","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_margprobdist.html","id":null,"dir":"Reference","previous_headings":"","what":"The marginal distribution of endemics and non-endemics under the DAISIE\nmodel — DAISIE_margprobdist","title":"The marginal distribution of endemics and non-endemics under the DAISIE\nmodel — DAISIE_margprobdist","text":"function calculates marginal distribution number endemics non-endemics sum given set parameter values, given mainland species pool size given set times","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_margprobdist.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The marginal distribution of endemics and non-endemics under the DAISIE\nmodel — DAISIE_margprobdist","text":"","code":"DAISIE_margprobdist(   pars1,   pars2,   tvec,   initEI = c(0, 0),   initprobs = NULL,   pb = NULL )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_margprobdist.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The marginal distribution of endemics and non-endemics under the DAISIE\nmodel — DAISIE_margprobdist","text":"pars1 Vector model parameters: pars1[1] corresponds lambda^c (cladogenesis rate) pars1[2] corresponds mu (extinction rate) pars1[3] corresponds K (clade-level carrying capacity) pars1[4] corresponds gamma (immigration rate) pars1[5] corresponds lambda^(anagenesis rate). pars2 Vector settings: pars2[1] corresponds res, maximum number endemics non-endemics ODE system solved; must much larger actual number probability needs calculated.) pars2[2] corresponds M, size mainland pool, .e number species can potentially colonize island. tvec times probabilities need computed. initEI initial values number endemics   non-endemics. DAISIE_probdist() DAISIE_margprobdist() either initprobs must NULL. DAISIE_numcol() NULL, assumed island   empty. initprobs initial probability distribution number endemics non-endemics; either initEI must NULL. pb Probability distribution matrix format output DAISIE_probdist().","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_margprobdist.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The marginal distribution of endemics and non-endemics under the DAISIE\nmodel — DAISIE_margprobdist","text":"list three vectors: pE probability distribution number endemic species pI probability distribution number non-endemic species pN probability distribution sum number endemics non-endemics","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_margprobdist.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"The marginal distribution of endemics and non-endemics under the DAISIE\nmodel — DAISIE_margprobdist","text":"Valente, L.M., .B. Phillimore R.S. Etienne (2015). Equilibrium non-equilibrium dynamics simultaneously operate Galapagos islands. Ecology Letters 18: 844-852.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_margprobdist.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"The marginal distribution of endemics and non-endemics under the DAISIE\nmodel — DAISIE_margprobdist","text":"Rampal S. Etienne","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_margprobdist.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"The marginal distribution of endemics and non-endemics under the DAISIE\nmodel — DAISIE_margprobdist","text":"","code":"### Compute the marginal probability distributions at t = 4 and t = 8, for a mainland # pool size of 250 potential colonists and a vector of 5 parameters (cladogenesis, # extinction, clade-level carrying capacity, immigration, anagenesis) starting from # an empty island  marg_prob_dists <- DAISIE_margprobdist(    pars1 = c(0.3,0.35,Inf,0.75,0.012),    pars2 = c(100,250),    tvec = c(4,8),    initEI = c(5,1),    initprobs = NULL    )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_numcol.html","id":null,"dir":"Reference","previous_headings":"","what":"The expectation and marginal distribution of the number of colonizations\n(lineages) under the DAISIE model — DAISIE_numcol","title":"The expectation and marginal distribution of the number of colonizations\n(lineages) under the DAISIE model — DAISIE_numcol","text":"function calculates expectation marginal distribution number colonizations (lineages) given set parameter values, given mainland species pool size given set times","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_numcol.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The expectation and marginal distribution of the number of colonizations\n(lineages) under the DAISIE model — DAISIE_numcol","text":"","code":"DAISIE_numcol(pars1, pars2, tvec, initEI = NULL)"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_numcol.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The expectation and marginal distribution of the number of colonizations\n(lineages) under the DAISIE model — DAISIE_numcol","text":"pars1 Vector model parameters: pars1[1] corresponds lambda^c (cladogenesis rate) pars1[2] corresponds mu (extinction rate) pars1[3] corresponds K (clade-level carrying capacity) pars1[4] corresponds gamma (immigration rate) pars1[5] corresponds lambda^(anagenesis rate). pars2 Vector settings: pars2[1] corresponds res, maximum number endemics non-endemics ODE system solved; must much larger actual number probability needs calculated.) pars2[2] corresponds M, size mainland pool, .e number species can potentially colonize island. tvec times probabilities need computed. initEI initial values number endemics   non-endemics. DAISIE_probdist() DAISIE_margprobdist() either initprobs must NULL. DAISIE_numcol() NULL, assumed island   empty.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_numcol.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The expectation and marginal distribution of the number of colonizations\n(lineages) under the DAISIE model — DAISIE_numcol","text":"list three vectors: expC expectation number colonizations/lineages given times pC probability distribution number colonizations (lineages) given times","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_numcol.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"The expectation and marginal distribution of the number of colonizations\n(lineages) under the DAISIE model — DAISIE_numcol","text":"Valente, L.M., .B. Phillimore R.S. Etienne (2015). Equilibrium non-equilibrium dynamics simultaneously operate Galapagos islands. Ecology Letters 18: 844-852.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_numcol.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"The expectation and marginal distribution of the number of colonizations\n(lineages) under the DAISIE model — DAISIE_numcol","text":"Rampal S. Etienne","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_numcol.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"The expectation and marginal distribution of the number of colonizations\n(lineages) under the DAISIE model — DAISIE_numcol","text":"","code":"### Compute the marginal probability distributions at t = 4 and t = 8, for a mainland # pool size of 250 potential colonists and a vector of 5 parameters (cladogenesis, # extinction, clade-level carrying capacity, immigration, anagenesis) starting from # an empty island  numcol <- DAISIE_numcol(    pars1 = c(0.3,0.35,Inf,0.75,0.012),    pars2 = c(100,250),    tvec = c(4,8),    initEI = list(c(0,1),c(0,2),c(3,1))    )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_age_diversity.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot clade age against clade diversity. — DAISIE_plot_age_diversity","title":"Plot clade age against clade diversity. — DAISIE_plot_age_diversity","text":"Plots clade age clade diversity clades colonisation time known.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_age_diversity.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot clade age against clade diversity. — DAISIE_plot_age_diversity","text":"","code":"DAISIE_plot_age_diversity(   island,   title = \"Clade age vs clade diversity\",   island_age = NA )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_age_diversity.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot clade age against clade diversity. — DAISIE_plot_age_diversity","text":"island Island data object. Can DAISIE list format (see Galapagos_datalist DAISIE_data_prep examples) table format (see Galapagos_datatable example). title Title plot island_age Age island appropriate units. DAISIE_plot_age_diversity() DAISIE_plot_island() island input table format, age island must specified. island input DAISIE list format, option override island age specified island list.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_age_diversity.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot clade age against clade diversity. — DAISIE_plot_age_diversity","text":"R plot.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_age_diversity.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Plot clade age against clade diversity. — DAISIE_plot_age_diversity","text":"R plot showing clade island object time colonisation diversity clade. clades colonisation time known plotted. Blue - endemic; black - non-endemic. C = number independent colonisations island, N = number species island","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_age_diversity.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Plot clade age against clade diversity. — DAISIE_plot_age_diversity","text":"Valente, L.M., .B. Phillimore R.S. Etienne (2015). Equilibrium non-equilibrium dynamics simultaneously operate Galapagos islands. Ecology Letters 18: 844-852.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_age_diversity.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Plot clade age against clade diversity. — DAISIE_plot_age_diversity","text":"Luis Valente","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_age_diversity.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot clade age against clade diversity. — DAISIE_plot_age_diversity","text":"","code":"### Plot Galapagos age-diversity for Galapagos dataset utils::data(Galapagos_datalist) DAISIE_plot_age_diversity(Galapagos_datalist)"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_area.html","id":null,"dir":"Reference","previous_headings":"","what":"Plots island area function through time — DAISIE_plot_area","title":"Plots island area function through time — DAISIE_plot_area","text":"Plots island area function time","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_area.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plots island area function through time — DAISIE_plot_area","text":"","code":"DAISIE_plot_area(   total_time,   area_pars,   peak,   island_ontogeny = \"beta\",   resolution,   sea_level = \"const\" )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_area.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plots island area function through time — DAISIE_plot_area","text":"total_time Numeric defining length simulation time units. area_pars named list containing area sea level parameters created create_area_pars(): [1]: maximum area [2]: current area [3]: value 0 1 indicating island's history   peak area achieved [4]: total island age [5]: amplitude area fluctuation sea level [6]: frequency sine wave area change sea level [7]: angle slope island peak numeric value specifying peakiness (shaprness) ontogeny curve. Higher values imply peakier ontogeny. value internally calculated calc_peak() given area present area_pars. island_ontogeny DAISIE_sim_time_dep(), DAISIE_ML_CS plotting string describing type island ontogeny. Can \"const\", \"beta\" beta function describing area time.  functions numeric describing type island ontogeny. Can 0 constant, 1 beta function describing area time. ML functions island_ontogeny = NA assumes constant ontogeny. Time dependent estimation yet available development still ongoing. return error called case. resolution numeric indicating resolution plot. < 0. sea_level DAISIE_sim_time_dep() plotting string describing type sea level. Can \"const\" \"sine\" sine function describing area time.  functions numeric describing type sea level. Can 0 constant, 1 sine function describing area time.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_area.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plots island area function through time — DAISIE_plot_area","text":"plot area size time","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_cladogenesis.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot cladogenesis rate through time — DAISIE_plot_cladogenesis","title":"Plot cladogenesis rate through time — DAISIE_plot_cladogenesis","text":"Plot cladogenesis rate time","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_cladogenesis.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot cladogenesis rate through time — DAISIE_plot_cladogenesis","text":"","code":"DAISIE_plot_cladogenesis(   total_time,   K,   area_pars,   peak,   lac,   island_ontogeny = \"beta\",   sea_level = \"const\",   hyper_pars = NULL,   removed_timepoints,   resolution )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_cladogenesis.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot cladogenesis rate through time — DAISIE_plot_cladogenesis","text":"total_time Numeric defining length simulation time units. K numeric carrying capacity. area_pars named list containing area sea level parameters created create_area_pars(): [1]: maximum area [2]: current area [3]: value 0 1 indicating island's history   peak area achieved [4]: total island age [5]: amplitude area fluctuation sea level [6]: frequency sine wave area change sea level [7]: angle slope island peak numeric value specifying peakiness (shaprness) ontogeny curve. Higher values imply peakier ontogeny. value internally calculated calc_peak() given area present area_pars. lac numeric per capita cladogenesis rate. island_ontogeny DAISIE_sim_time_dep(), DAISIE_ML_CS plotting string describing type island ontogeny. Can \"const\", \"beta\" beta function describing area time.  functions numeric describing type island ontogeny. Can 0 constant, 1 beta function describing area time. ML functions island_ontogeny = NA assumes constant ontogeny. Time dependent estimation yet available development still ongoing. return error called case. sea_level DAISIE_sim_time_dep() plotting string describing type sea level. Can \"const\" \"sine\" sine function describing area time.  functions numeric describing type sea level. Can 0 constant, 1 sine function describing area time. hyper_pars named list numeric hyperparameters rate calculations returned create_hyper_pars(): [1]: d scaling parameter exponent calculating   cladogenesis rate [2]: x exponent calculating extinction rate removed_timepoints Positive integer number first datapoints removed rate plots (prevent Inf) resolution numeric indicating resolution plot. < 0.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_cladogenesis.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot cladogenesis rate through time — DAISIE_plot_cladogenesis","text":"plot per capita cladogenesis rate time dataframe immigration corresponding time","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_cladogenesis.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Plot cladogenesis rate through time — DAISIE_plot_cladogenesis","text":"Pedro Neves","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_extinction.html","id":null,"dir":"Reference","previous_headings":"","what":"Plots extinction rate function through time — DAISIE_plot_extinction","title":"Plots extinction rate function through time — DAISIE_plot_extinction","text":"Plots extinction rate function time","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_extinction.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plots extinction rate function through time — DAISIE_plot_extinction","text":"","code":"DAISIE_plot_extinction(   total_time,   area_pars,   peak,   mu,   hyper_pars,   island_ontogeny = \"beta\",   sea_level = \"const\",   removed_timepoints,   resolution,   extcutoff = 1000 )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_extinction.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plots extinction rate function through time — DAISIE_plot_extinction","text":"total_time Numeric defining length simulation time units. area_pars named list containing area sea level parameters created create_area_pars(): [1]: maximum area [2]: current area [3]: value 0 1 indicating island's history   peak area achieved [4]: total island age [5]: amplitude area fluctuation sea level [6]: frequency sine wave area change sea level [7]: angle slope island peak numeric value specifying peakiness (shaprness) ontogeny curve. Higher values imply peakier ontogeny. value internally calculated calc_peak() given area present area_pars. mu numeric per capita extinction rate. hyper_pars named list numeric hyperparameters rate calculations returned create_hyper_pars(): [1]: d scaling parameter exponent calculating   cladogenesis rate [2]: x exponent calculating extinction rate island_ontogeny DAISIE_sim_time_dep(), DAISIE_ML_CS plotting string describing type island ontogeny. Can \"const\", \"beta\" beta function describing area time.  functions numeric describing type island ontogeny. Can 0 constant, 1 beta function describing area time. ML functions island_ontogeny = NA assumes constant ontogeny. Time dependent estimation yet available development still ongoing. return error called case. sea_level DAISIE_sim_time_dep() plotting string describing type sea level. Can \"const\" \"sine\" sine function describing area time.  functions numeric describing type sea level. Can 0 constant, 1 sine function describing area time. removed_timepoints Positive integer number first datapoints removed rate plots (prevent Inf) resolution numeric indicating resolution plot. < 0. extcutoff numeric cutoff maximum extinction rate preventing large slowing simulation.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_extinction.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plots extinction rate function through time — DAISIE_plot_extinction","text":"per capita extinction rate time plot dataframe extinction corresponding time","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_extinction.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Plots extinction rate function through time — DAISIE_plot_extinction","text":"Pedro Neves","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_immigration.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot immigration rate through time — DAISIE_plot_immigration","title":"Plot immigration rate through time — DAISIE_plot_immigration","text":"Plot immigration rate time","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_immigration.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot immigration rate through time — DAISIE_plot_immigration","text":"","code":"DAISIE_plot_immigration(   total_time,   K,   area_pars,   gam,   peak,   mainland_n,   hyper_pars = NULL,   island_ontogeny = \"beta\",   sea_level = \"const\",   removed_timepoints,   resolution )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_immigration.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot immigration rate through time — DAISIE_plot_immigration","text":"total_time Numeric defining length simulation time units. K numeric carrying capacity. area_pars named list containing area sea level parameters created create_area_pars(): [1]: maximum area [2]: current area [3]: value 0 1 indicating island's history   peak area achieved [4]: total island age [5]: amplitude area fluctuation sea level [6]: frequency sine wave area change sea level [7]: angle slope island gam numeric per capita immigration rate. peak numeric value specifying peakiness (shaprness) ontogeny curve. Higher values imply peakier ontogeny. value internally calculated calc_peak() given area present area_pars. mainland_n numeric stating number mainland species, number species can potentially colonize island. using clade-specific diversity dependence, value set 1. using island-wide diversity dependence, value set number mainland species. hyper_pars named list numeric hyperparameters rate calculations returned create_hyper_pars(): [1]: d scaling parameter exponent calculating   cladogenesis rate [2]: x exponent calculating extinction rate island_ontogeny DAISIE_sim_time_dep(), DAISIE_ML_CS plotting string describing type island ontogeny. Can \"const\", \"beta\" beta function describing area time.  functions numeric describing type island ontogeny. Can 0 constant, 1 beta function describing area time. ML functions island_ontogeny = NA assumes constant ontogeny. Time dependent estimation yet available development still ongoing. return error called case. sea_level DAISIE_sim_time_dep() plotting string describing type sea level. Can \"const\" \"sine\" sine function describing area time.  functions numeric describing type sea level. Can 0 constant, 1 sine function describing area time. removed_timepoints Positive integer number first datapoints removed rate plots (prevent Inf) resolution numeric indicating resolution plot. < 0.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_immigration.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot immigration rate through time — DAISIE_plot_immigration","text":"plot per capita immigration rate time dataframe immigration corresponding time","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_immigration.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Plot immigration rate through time — DAISIE_plot_immigration","text":"Pedro Neves","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_input.html","id":null,"dir":"Reference","previous_headings":"","what":"DAISIE tree plot — DAISIE_plot_input","title":"DAISIE tree plot — DAISIE_plot_input","text":"Shows phylogenies multiple clades present island","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_input.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"DAISIE tree plot — DAISIE_plot_input","text":"","code":"DAISIE_plot_input(   trees,   age = NULL,   tcols = NULL,   metadata = NULL,   mapping = NULL,   xlen = 0.001,   pargs = NULL,   bckgd = \"white\" )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_input.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"DAISIE tree plot — DAISIE_plot_input","text":"trees list trees, phylo format, named respective clades age age island, scale branch lengths trees. unspecified, depth deepest stem across trees. tcols vector colonization times, one value per clade. Order must `trees`. unspecified, clades assigned age island colonization time. metadata Optional data frame clade-level metadata. One column must named \"clade\". mapping Optional aesthetic mapping apply trees, returned `ggplot2::aes` function. Mapped variables can anything columns `data` node-wise data frame associated `ggtree` plot created (e.g. node, label, clade, mrca) anything columns clade-wise `metadata`, provided (case aesthetics mapped nodes within clade). xlen Length extra tips grafted tree island age. hack scaling plot. Keep value small. pargs Optional arguments passed `geom_point` plotting points colonization events (e.g. size, shape...). bckgd Optional background color figure. use rectangles hack hide tree branches prior island colonization. Default white background.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_input.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"DAISIE tree plot — DAISIE_plot_input","text":"`ggtree` plot, also `ggplot` object. output fully customizable, `ggplot` object.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_input.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"DAISIE tree plot — DAISIE_plot_input","text":"Raphael Scherrer (github.com/rscherrer)","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_input.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"DAISIE tree plot — DAISIE_plot_input","text":"","code":"# check whether package tibble has been installed  if (!requireNamespace('tibble', quietly = TRUE)) {     cat(\"Package tibble needed for this function to work. Please install it.\")  } else {  set.seed(42)   # Random trees  t1 <- ape::rtree(10)  t1$tip.label <- gsub(\"t\", \"t1.\", t1$tip.label)  t2 <- ape::rtree(3)  t2$tip.label <- gsub(\"t\", \"t2.\", t2$tip.label)  t3 <- ape::rtree(2)  trees <- list(t1, t2, t3)  names(trees) <- c(\"A\", \"B\", \"C\")   # Toy colonization events for each clade  tcols <- c(4.5, 5, 4.6)   # Toy metadata  metadata <- tibble::tibble(    clade = names(trees),    endemic = TRUE,  # whether each clade is endemic    uncertain = FALSE  # whether colonization time is known for sure  )  metadata$endemic[3] <- FALSE  metadata$uncertain[2] <- TRUE   # Island age  age <- 5   # Make a plot  p <- DAISIE_plot_input(    trees,    age,    tcols,    metadata,    mapping = ggplot2::aes(color = endemic, linetype = uncertain),    pargs = list(size = 3)  ) p } #> Registered S3 methods overwritten by 'treeio': #>   method              from     #>   MRCA.phylo          tidytree #>   MRCA.treedata       tidytree #>   Nnode.treedata      tidytree #>   Ntip.treedata       tidytree #>   ancestor.phylo      tidytree #>   ancestor.treedata   tidytree #>   child.phylo         tidytree #>   child.treedata      tidytree #>   full_join.phylo     tidytree #>   full_join.treedata  tidytree #>   groupClade.phylo    tidytree #>   groupClade.treedata tidytree #>   groupOTU.phylo      tidytree #>   groupOTU.treedata   tidytree #>   inner_join.phylo    tidytree #>   inner_join.treedata tidytree #>   is.rooted.treedata  tidytree #>   nodeid.phylo        tidytree #>   nodeid.treedata     tidytree #>   nodelab.phylo       tidytree #>   nodelab.treedata    tidytree #>   offspring.phylo     tidytree #>   offspring.treedata  tidytree #>   parent.phylo        tidytree #>   parent.treedata     tidytree #>   root.treedata       tidytree #>   rootnode.phylo      tidytree #>   sibling.phylo       tidytree #> Scale for y is already present. #> Adding another scale for y, which will replace the existing scale. #> Joining with `by = join_by(label)` #> Warning: Removed 1 rows containing missing values (`geom_point()`)."},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_island.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot colonisation and branching time of species found on an island dataset. — DAISIE_plot_island","title":"Plot colonisation and branching time of species found on an island dataset. — DAISIE_plot_island","text":"Produces image times colonisation, branching times, clade name clade status clades found given dataset.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_island.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot colonisation and branching time of species found on an island dataset. — DAISIE_plot_island","text":"","code":"DAISIE_plot_island(island, island_age = NA)"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_island.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot colonisation and branching time of species found on an island dataset. — DAISIE_plot_island","text":"island Island data object. Can DAISIE list format (see Galapagos_datalist DAISIE_data_prep examples) table format (see Galapagos_datatable example). island_age Age island appropriate units. DAISIE_plot_age_diversity() DAISIE_plot_island() island input table format, age island must specified. island input DAISIE list format, option override island age specified island list.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_island.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot colonisation and branching time of species found on an island dataset. — DAISIE_plot_island","text":"R plot.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_island.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Plot colonisation and branching time of species found on an island dataset. — DAISIE_plot_island","text":"R plot showing clade island object: time colonisation, branching times, species status (endemic non-endemic), total number species clade (n), number species sampled (m).","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_island.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Plot colonisation and branching time of species found on an island dataset. — DAISIE_plot_island","text":"Valente, L.M., .B. Phillimore R.S. Etienne (2015). Equilibrium non-equilibrium dynamics simultaneously operate Galapagos islands. Ecology Letters 18: 844-852.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_island.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Plot colonisation and branching time of species found on an island dataset. — DAISIE_plot_island","text":"Luis Valente","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_island.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot colonisation and branching time of species found on an island dataset. — DAISIE_plot_island","text":"","code":"### Plot Galapagos islands dataset from data table (specify island age)  utils::data(Galapagos_datatable) DAISIE_plot_island(Galapagos_datatable, island_age=4) #> Colonisation time of 7.456 for Coccyzus is older than island age #> Colonisation time of 10.285 for Pyrocephalus is older than island age   ### Plot Galapagos islands dataset from datalist (no need to specify ## island age) utils::data(Galapagos_datalist) DAISIE_plot_island(Galapagos_datalist)"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_pc_rates.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot per capita STT and per-capita rate change thourgh simulation — DAISIE_plot_pc_rates","title":"Plot per capita STT and per-capita rate change thourgh simulation — DAISIE_plot_pc_rates","text":"Plot per capita STT per-capita rate change thourgh simulation","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_pc_rates.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot per capita STT and per-capita rate change thourgh simulation — DAISIE_plot_pc_rates","text":"","code":"DAISIE_plot_pc_rates(   total_time,   pars,   island_ontogeny,   sea_level = \"const\",   area_pars,   peak,   hyper_pars,   mainland_n = 1000,   resolution = 0.001,   simulation_outputs = NULL )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_pc_rates.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot per capita STT and per-capita rate change thourgh simulation — DAISIE_plot_pc_rates","text":"total_time Numeric defining length simulation time units. pars numeric vector containing model parameters: pars[1]: lambda^c (cladogenesis rate) pars[2]: mu (extinction rate) pars[3]: K (carrying capacity), set K=Inf diversity   independence. pars[4]: gamma (immigration rate) pars[5]: lambda^(anagenesis rate) pars[6]: lambda^c (cladogenesis rate) either type 2 species   rate set 2 rate shift model pars[7]: mu (extinction rate) either type 2 species rate   set 2 rate shift model pars[8]: K (carrying capacity) either type 2 species rate   set 2 rate shift model, set K=Inf diversity independence. pars[9]: gamma (immigration rate) either type 2 species   rate set 2 rate shift model pars[10]: lambda^(anagenesis rate) either type 2   species rate set 2 rate shift model Elements 6:10 required type 2 species included rate shift model. DAISIE_sim_relaxed_rate() pars[6] standard deviation gamma distribution relaxed parameter parameter chosen relaxed_par argument mean gamma distribution relaxed parameter. island_ontogeny DAISIE_sim_time_dep(), DAISIE_ML_CS plotting string describing type island ontogeny. Can \"const\", \"beta\" beta function describing area time.  functions numeric describing type island ontogeny. Can 0 constant, 1 beta function describing area time. ML functions island_ontogeny = NA assumes constant ontogeny. Time dependent estimation yet available development still ongoing. return error called case. sea_level DAISIE_sim_time_dep() plotting string describing type sea level. Can \"const\" \"sine\" sine function describing area time.  functions numeric describing type sea level. Can 0 constant, 1 sine function describing area time. area_pars named list containing area sea level parameters created create_area_pars(): [1]: maximum area [2]: current area [3]: value 0 1 indicating island's history   peak area achieved [4]: total island age [5]: amplitude area fluctuation sea level [6]: frequency sine wave area change sea level [7]: angle slope island peak numeric value specifying peakiness (shaprness) ontogeny curve. Higher values imply peakier ontogeny. value internally calculated calc_peak() given area present area_pars. hyper_pars named list numeric hyperparameters rate calculations returned create_hyper_pars(): [1]: d scaling parameter exponent calculating   cladogenesis rate [2]: x exponent calculating extinction rate mainland_n numeric stating number mainland species, number species can potentially colonize island. using clade-specific diversity dependence, value set 1. using island-wide diversity dependence, value set number mainland species. resolution numeric indicating resolution plot. < 0. simulation_outputs list matrices vectors simulation produced DAISIE_sim functions.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_pc_rates.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot per capita STT and per-capita rate change thourgh simulation — DAISIE_plot_pc_rates","text":"composite plot containing STT plot, variation area, extinction rate, cladogenesis rate immigration rate","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_pc_rates.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Plot per capita STT and per-capita rate change thourgh simulation — DAISIE_plot_pc_rates","text":"Pedro Neves","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_sims.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot island species-through-time (STT) plots — DAISIE_plot_sims","title":"Plot island species-through-time (STT) plots — DAISIE_plot_sims","text":"Produces STT plots. one type species present simulated islands, STT plotted species. two types present, three plots produced: STT , STT type 1 STT type 2. R plots number total, endemic non-endemic STTs different types species entire time span islands simulated. 2.5-97.5th percentiles plotted light grey, 25-75th percentiles plotted dark grey.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_sims.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot island species-through-time (STT) plots — DAISIE_plot_sims","text":"","code":"DAISIE_plot_sims(   island_replicates,   plot_plus_one = TRUE,   type = \"all_species\",   sample_freq = 25,   trait_pars = NULL )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_sims.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot island species-through-time (STT) plots — DAISIE_plot_sims","text":"island_replicates List output DAISIE_sim_core_cr(), DAISIE_sim_core_time_dep(), DAISIE_sim_core_cr_shift() DAISIE_sim_min_type2() functions. Minimally, must list many elements replicates. element must list elements island_age, not_present stt_all. stt_all must data frame column names Time, nI, nA, nC present. plot_plus_one Boolean indicate plot values plus one. Set TRUE default behavior. Set FALSE plot values without adding one. works one type species. type String indicate stt species possible stt plotted. Default \"all_species\", \"type1_species\" \"type2_species\" plotted. sample_freq Numeric specifing number units times divided plotting purposes. Larger values lead plots higher resolution, also run slower. trait_pars named list containing diversification rates considering   two trait states created create_trait_pars: [1]:numeric per capita transition rate state1 [2]:numeric per capita immigration rate state2 [3]:numeric per capita extinction rate state2 [4]:numeric per capita anagenesis rate state2 [5]:numeric per capita cladogenesis rate state2 [6]:numeric per capita transition rate state2 [7]:numeric number species trait state 2    mainland","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_sims.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot island species-through-time (STT) plots — DAISIE_plot_sims","text":"R plot.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_sims.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Plot island species-through-time (STT) plots — DAISIE_plot_sims","text":"Valente, L.M., .B. Phillimore R.S. Etienne (2015). Equilibrium non-equilibrium dynamics simultaneously operate Galapagos islands. Ecology Letters 18: 844-852.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_sims.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Plot island species-through-time (STT) plots — DAISIE_plot_sims","text":"Luis Valente","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_sims.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot island species-through-time (STT) plots — DAISIE_plot_sims","text":"","code":"### Plot islands with single process (only one type of species) utils::data(islands_1type_1000reps) DAISIE_plot_sims(   island_replicates = islands_1type_1000reps   )    ### Plot island with type 1 and type 2 utils::data(islands_2types_1000reps) DAISIE_plot_sims(   island_replicates = islands_2types_1000reps   )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_stt.html","id":null,"dir":"Reference","previous_headings":"","what":"Create the Species-Through-Time plot. This is used to visualize\nthe output of DAISIE_sim functions — DAISIE_plot_stt","title":"Create the Species-Through-Time plot. This is used to visualize\nthe output of DAISIE_sim functions — DAISIE_plot_stt","text":"Create Species--Time plot. used visualize output DAISIE_sim functions","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_stt.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create the Species-Through-Time plot. This is used to visualize\nthe output of DAISIE_sim functions — DAISIE_plot_stt","text":"","code":"DAISIE_plot_stt(   plot_plus_one = TRUE,   time,   plot_lists = plot_lists,   type = type )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_stt.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create the Species-Through-Time plot. This is used to visualize\nthe output of DAISIE_sim functions — DAISIE_plot_stt","text":"plot_plus_one Boolean indicate plot values plus one. Set TRUE default behavior. Set FALSE plot values without adding one. works one type species. time Numeric defining length simulation time units. example, island known 4 million years old, setting time = 4 simulate entire life span island; setting time = 2 stop simulation mid-life island. plot_lists List lists containing average quantile species time. type String indicate stt species possible stt plotted. Default \"all_species\", \"type1_species\" \"type2_species\" plotted.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_probdist.html","id":null,"dir":"Reference","previous_headings":"","what":"The joint distribution of endemics and non-endemics under the DAISIE model — DAISIE_probdist","title":"The joint distribution of endemics and non-endemics under the DAISIE model — DAISIE_probdist","text":"function calculates joint distribution number endemics non-endemics given set parameter values, given mainland species pool size given set times","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_probdist.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The joint distribution of endemics and non-endemics under the DAISIE model — DAISIE_probdist","text":"","code":"DAISIE_probdist(pars1, pars2, tvec, initEI = c(0, 0), initprobs = NULL)"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_probdist.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The joint distribution of endemics and non-endemics under the DAISIE model — DAISIE_probdist","text":"pars1 Vector model parameters: pars1[1] corresponds lambda^c (cladogenesis rate) pars1[2] corresponds mu (extinction rate) pars1[3] corresponds K (clade-level carrying capacity) pars1[4] corresponds gamma (immigration rate) pars1[5] corresponds lambda^(anagenesis rate). pars2 Vector settings: pars2[1] corresponds res, maximum number endemics non-endemics ODE system solved; must much larger actual number probability needs calculated.) pars2[2] corresponds M, size mainland pool, .e number species can potentially colonize island. tvec times probabilities need computed. initEI initial values number endemics   non-endemics. DAISIE_probdist() DAISIE_margprobdist() either initprobs must NULL. DAISIE_numcol() NULL, assumed island   empty. initprobs initial probability distribution number endemics non-endemics; either initEI must NULL.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_probdist.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The joint distribution of endemics and non-endemics under the DAISIE model — DAISIE_probdist","text":"matrix dimensions 1 + length(tvec) pars[2]^2 + 1] first column contains times probabilities evaluated columns contain joint probabilities.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_probdist.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"The joint distribution of endemics and non-endemics under the DAISIE model — DAISIE_probdist","text":"obtain matrix probabilities endemics rows non-endemics columns certain time, one can run DAISIE_convertprobdist","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_probdist.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"The joint distribution of endemics and non-endemics under the DAISIE model — DAISIE_probdist","text":"Valente, L.M., .B. Phillimore R.S. Etienne (2015). Equilibrium non-equilibrium dynamics simultaneously operate Galapagos islands. Ecology Letters 18: 844-852.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_probdist.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"The joint distribution of endemics and non-endemics under the DAISIE model — DAISIE_probdist","text":"Rampal S. Etienne","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_probdist.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"The joint distribution of endemics and non-endemics under the DAISIE model — DAISIE_probdist","text":"","code":"### Compute the probability distribution at t = 4 and t = 8, for a mainland pool # size of 250 potential colonists and a vector of 5 parameters (cladogenesis, # extinction, clade-level carrying capacity, immigration, anagenesis) starting # from an empty island  prob_dists <- DAISIE_probdist(    pars1 = c(0.3,0.35,Inf,0.75,0.012),    pars2 = c(100,250),    tvec = c(4,8),    initEI = c(0,0),    initprobs = NULL    )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sample_event_cr.html","id":null,"dir":"Reference","previous_headings":"","what":"Samples what event to happen next — DAISIE_sample_event_cr","title":"Samples what event to happen next — DAISIE_sample_event_cr","text":"Samples event happen next","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sample_event_cr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Samples what event to happen next — DAISIE_sample_event_cr","text":"","code":"DAISIE_sample_event_cr(rates)"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sample_event_cr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Samples what event to happen next — DAISIE_sample_event_cr","text":"rates named list numeric rates returned update_rates().","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sample_event_cr.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Samples what event to happen next — DAISIE_sample_event_cr","text":"numeric indicating event happen, supposed event happen timesteps ontogeny algorithm. [1]: immigration event [2]: extinction event [3]: cladogenesis event [4]: anagenesis event","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sample_event_cr.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Samples what event to happen next — DAISIE_sample_event_cr","text":"Pedro Neves","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sample_event_time_dep.html","id":null,"dir":"Reference","previous_headings":"","what":"Samples what event to happen next — DAISIE_sample_event_time_dep","title":"Samples what event to happen next — DAISIE_sample_event_time_dep","text":"Samples event happen next","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sample_event_time_dep.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Samples what event to happen next — DAISIE_sample_event_time_dep","text":"","code":"DAISIE_sample_event_time_dep(max_rates)"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sample_event_time_dep.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Samples what event to happen next — DAISIE_sample_event_time_dep","text":"max_rates named list numeric max rates returned update_max_rates().","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sample_event_time_dep.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Samples what event to happen next — DAISIE_sample_event_time_dep","text":"numeric indicating event happen, supposed event happen timesteps ontogeny algorithm. [1]: immigration event [2]: extinction event [3]: cladogenesis event [4]: anagenesis event","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sample_event_time_dep.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Samples what event to happen next — DAISIE_sample_event_time_dep","text":"Pedro Neves","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sample_event_trait_dep.html","id":null,"dir":"Reference","previous_headings":"","what":"Samples what event to happen next — DAISIE_sample_event_trait_dep","title":"Samples what event to happen next — DAISIE_sample_event_trait_dep","text":"Samples event happen next","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sample_event_trait_dep.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Samples what event to happen next — DAISIE_sample_event_trait_dep","text":"","code":"DAISIE_sample_event_trait_dep(rates)"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sample_event_trait_dep.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Samples what event to happen next — DAISIE_sample_event_trait_dep","text":"rates named list numeric rates returned update_rates().","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sample_event_trait_dep.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Samples what event to happen next — DAISIE_sample_event_trait_dep","text":"numeric indicating event happen, supposed event happen timesteps ontogeny algorithm. [1]: immigration event trait1 [2]: extinction event trait1 [3]: cladogenesis event trait1 [4]: anagenesis event trait1 [5]: transition event trait1 [6]: immigration event trait2 [7]: extinction event trait2 [8]: cladogenesis event trait2 [9]: anagenesis event trait2 [10]: transition event trait2","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sample_event_trait_dep.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Samples what event to happen next — DAISIE_sample_event_trait_dep","text":"Shu Xie","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim.html","id":null,"dir":"Reference","previous_headings":"","what":"Simulate (non-)oceanic islands with given parameters under\n  time-constant rates — DAISIE_sim","title":"Simulate (non-)oceanic islands with given parameters under\n  time-constant rates — DAISIE_sim","text":"function simulates islands given cladogenesis, extinction, Kprime, immigration anagenesis parameters, modelled time-constant parameters. single parameter set provided (5 parameters) simulates islands species macro-evolutionary process. two paramater sets (10 parameters) provided, simulates islands two different macro-evolutionary processes operate, one applying type 1 species type 2 species. , allows simulation non-oceanic islands, generating islands starting condition includes potential endemic non-endemic species.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulate (non-)oceanic islands with given parameters under\n  time-constant rates — DAISIE_sim","text":"","code":"DAISIE_sim_cr(   time,   M,   pars,   replicates,   divdepmodel = \"CS\",   nonoceanic_pars = c(0, 0),   num_guilds = NULL,   prop_type2_pool = NA,   replicates_apply_type2 = TRUE,   sample_freq = 25,   plot_sims = TRUE,   hyper_pars = create_hyper_pars(d = 0, x = 0),   area_pars = create_area_pars(max_area = 1, current_area = 1, proportional_peak_t = 0,     total_island_age = 0, sea_level_amplitude = 0, sea_level_frequency = 0,     island_gradient_angle = 0),   cond = 0,   verbose = TRUE,   ... )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulate (non-)oceanic islands with given parameters under\n  time-constant rates — DAISIE_sim","text":"time Numeric defining length simulation time units. example, island known 4 million years old, setting time = 4 simulate entire life span island; setting time = 2 stop simulation mid-life island. M Numeric defining size mainland pool, .e. number species can potentially colonize island. pars numeric vector containing model parameters: pars[1]: lambda^c (cladogenesis rate) pars[2]: mu (extinction rate) pars[3]: K (carrying capacity), set K=Inf diversity   independence. pars[4]: gamma (immigration rate) pars[5]: lambda^(anagenesis rate) pars[6]: lambda^c (cladogenesis rate) either type 2 species   rate set 2 rate shift model pars[7]: mu (extinction rate) either type 2 species rate   set 2 rate shift model pars[8]: K (carrying capacity) either type 2 species rate   set 2 rate shift model, set K=Inf diversity independence. pars[9]: gamma (immigration rate) either type 2 species   rate set 2 rate shift model pars[10]: lambda^(anagenesis rate) either type 2   species rate set 2 rate shift model Elements 6:10 required type 2 species included rate shift model. DAISIE_sim_relaxed_rate() pars[6] standard deviation gamma distribution relaxed parameter parameter chosen relaxed_par argument mean gamma distribution relaxed parameter. replicates Integer specifying number island replicates simulated. divdepmodel Option divdepmodel = 'CS' runs model clade-specific carrying capacity, diversity-dependence operates within single clades, .e. among species originating mainland colonist. Option divdepmodel = 'IW' runs model island-wide carrying capacity, diversity-dependence operates within among clades. Option divdepmodel = 'GW' runs model diversity-dependence operates within guild. nonoceanic_pars vector length two : [1]: probability sampling species mainland [2]: probability species sampled mainland   nonendemic num_guilds number guilds mainland. number mainland species divided number guilds divdepmodel = \"GW\" prop_type2_pool Fraction mainland species belongs second subset species (type 2). Applies two types species simulated (length(pars) = 10). DAISIE_dataprep() applies number_clade_types = 2.  DAISIE_dataprep() default \"proportional\" sets fraction proportional number clades distinct macroevolutionary process colonised island. replicates_apply_type2 Applies two types species simulated. Default replicates_apply_type2 = TRUE runs simulations number islands type 2 species colonised equal specified number replicates. recommended prop_type2_pool small rate immigration type two species (pars[9]) low, meaning replicates needed achieved adequate sample size islands type 2 species. Setting replicates_apply_type2 = FALSE simulates islands specified number replicates regardless whether type 2 species colonised . sample_freq Numeric specifing number units times divided plotting purposes. Larger values lead plots higher resolution, also run slower. plot_sims Default = TRUE plots species--time (STT) plots. detects many types species present. one type species present, STT plotted species. two types present, three plots produced: STT , STT type 1 STT type 2. hyper_pars named list numeric hyperparameters rate calculations returned create_hyper_pars(): [1]: d scaling parameter exponent calculating   cladogenesis rate [2]: x exponent calculating extinction rate area_pars named list containing area sea level parameters created create_area_pars(): [1]: maximum area [2]: current area [3]: value 0 1 indicating island's history   peak area achieved [4]: total island age [5]: amplitude area fluctuation sea level [6]: frequency sine wave area change sea level [7]: angle slope island cond cond = 0 : conditioning island age  cond = 1 : conditioning island age non-extinction island biota . cond > 1 : conditioning island age least cond colonizations island. last option yet available IW model verbose numeric vector length 1, simulations `DAISIEdataprep()` can `1` `0`, `1` gives intermediate output printed. ML functions numeric determining intermediate output printed. default: `0` print, `1` prints initial likelihood settings selected (parameters optimised, fixed shifted), `2` prints `1 also intermediate output parameters loglikelihood, `3` `2` prints intermediate progress likelihood computation. ... arguments pass plotting functions.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Simulate (non-)oceanic islands with given parameters under\n  time-constant rates — DAISIE_sim","text":"list. highest level least corresponds individual replciate. first element replicate composed island information containing: $island_age: numeric island age. $not_present: number mainland lineages     present island. present 1 type species     simulated. Becomes $not_present_type1: number mainland     lineages type 1 present island     $not_present_type2: number mainland lineages type 2     present island, two types simulated. $stt_all: STT table species island     (nI - number non-endemic species; nA - number anagenetic species,     nC - number cladogenetic species, present - number independent     colonisations present) $stt_stt_type1: STT table type 1 species island -     2 types species simulated (nI - number non-endemic     species; nA - number anagenetic species, nC - number cladogenetic     species, present - number independent colonisations present). $stt_stt_type2: STT table type 2 species island      - 2 types species simulated (nI - number non-endemic      species; nA - number anagenetic species, nC - number cladogenetic      species, present - number independent colonisations present ). $brts_table: simulations \"IW\". Table containing information order events data, use maximum likelihood optimization.). subsequent elements list pertaining replcate contain information single colonist lineage island 4 components: $branching_times: island age stem age     population/species case Non-endemic, Non-endemic_MaxAge     Endemic anagenetic species.    cladogenetic species     island age branching times radiation including     stem age radiation. $stac: integer ranging 1 4   indicating status colonist: Non_endemic_MaxAge Endemic Endemic&Non_Endemic Non_endemic_MaxAge $missing_species: number island species sampled particular clade (applicable endemic clades) $type_1or2: whether colonist belongs type 1 type 2","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Simulate (non-)oceanic islands with given parameters under\n  time-constant rates — DAISIE_sim","text":"Valente, L.M., .B. Phillimore R.S. Etienne (2015). Equilibrium non-equilibrium dynamics simultaneously operate Galapagos islands. Ecology Letters 18: 844-852.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Simulate (non-)oceanic islands with given parameters under\n  time-constant rates — DAISIE_sim","text":"Luis Valente, Albert Phillimore, Joshua Lambert, Shu Xie, Pedro Neves, Richèl J. C. Bilderbeek, Rampal Etienne","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Simulate (non-)oceanic islands with given parameters under\n  time-constant rates — DAISIE_sim","text":"","code":"## Simulate 2 islands for 1 million years, where all species have equal ## rates. Pool size 100.  clado_rate <- 0.5 ext_rate <- 0.2 carr_cap <- Inf immig_rate <- 0.05 ana_rate <- 1 sim_pars <- c(clado_rate, ext_rate, carr_cap, immig_rate, ana_rate) set.seed(1) island_replicates <- DAISIE_sim_cr(   time = 1,   M = 100,   pars = sim_pars,   replicates = 2,   plot_sims = FALSE,   verbose = FALSE )  ## Simulate 2 islands for 1 million years with two types of species (type1 ## and type 2). Pool size 100 ## Fraction of type 2 species in source pool is 0.15. Function will ## simulate until number of islands where type 2 species has colonised is ## equal to number specified in replicates.  clado_rate <- 0.5 ext_rate <- 0.2 carr_cap <- Inf immig_rate <- 0.005 ana_rate <- 1 sim_pars_type1 <- c(clado_rate, ext_rate, carr_cap, immig_rate, ana_rate) sim_pars_type2 <- sim_pars_type1 * 2 set.seed(1) island_replicates_2types <- DAISIE_sim_cr(   time = 1,   M = 100,   pars = c(sim_pars_type1, sim_pars_type2),   replicates = 2,   prop_type2_pool = 0.15,   plot_sims = FALSE,   verbose = FALSE ) ## Simulate two non-oceanic island for 1 million years. ## Pool size 500. Island area as a proportion ## of mainland is 0.1, proportion of native species is 0.9. clado_rate <- 0.5 ext_rate <- 0.2 carr_cap <- Inf immig_rate <- 0.005 ana_rate <- 1 sim_pars <- c(clado_rate, ext_rate, carr_cap, immig_rate, ana_rate) set.seed(1) island_replicates <- DAISIE_sim_cr(   time = 1,   M = 500,   pars = sim_pars,   replicates = 2,   nonoceanic_pars = c(0.1, 0.9),   plot_sims = FALSE,   verbose = FALSE )  ## Simulate 2 islands for 1 million years with a shift in immigration rate ## at 0.195 Ma, and plot the species-through-time plot. Pool size 296.  pars_before_shift <- c(0.079, 0.973, Inf, 0.136, 0.413) pars_after_shift <- c(0.079, 0.973, Inf, 0.652, 0.413) tshift <- 0.195 set.seed(1) island_shift_replicates <- DAISIE_sim_cr_shift(   time = 1,   M = 296,   pars = c(pars_before_shift, pars_after_shift),   replicates = 2,   shift_times = tshift,   plot_sims = FALSE,   verbose = FALSE )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_MW.html","id":null,"dir":"Reference","previous_headings":"","what":"Simulate multiple islands based on hyperparameters that describe relationships\nbetween area, isolation and local parameters — DAISIE_sim_MW","title":"Simulate multiple islands based on hyperparameters that describe relationships\nbetween area, isolation and local parameters — DAISIE_sim_MW","text":"function simulates islands given age, area isolation. list islands/archipelagos information provided data frame object (example, archipelago_data Valente et al 2020 Nature). island, local parameters first calculated based hyperparameters describing dependency rates island area isolation. Simulations run island, island birth given island age based local parameters island (using DAISIE_sim function). Returns R list object contains simulated islands.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_MW.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulate multiple islands based on hyperparameters that describe relationships\nbetween area, isolation and local parameters — DAISIE_sim_MW","text":"","code":"DAISIE_sim_MW(   archipelago_data,   M,   pars,   replicates,   divdepmodel = \"CS\",   distance_dep = \"power\",   cladogenesis_dep = \"NULL\",   sigmoidal_par = \"NULL\" )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_MW.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulate multiple islands based on hyperparameters that describe relationships\nbetween area, isolation and local parameters — DAISIE_sim_MW","text":"archipelago_data Object (data.frame) containing table columns following names: Archipelago: names archipelagos islands simulated; Area - area archipelago/island; Age: Age oldest island archipelago, age island single island. Distance - distance mainland (applicable isolation metric). example, dataset Valente et al 2020 41 archipelagos provided data(archipelago_data). M size mainland pool, .e number species can potentially colonize island(s). pars Contains model hyperparameters: pars[1] corresponds lambda^c0 (initial cladogenesis rate) pars[2] corresponds y (dependency cladogenesis area) 0 - dependency, positive value - cladogenesis increases area, negative value - cladogenesis decreases area pars[3] corresponds mu_0 (initial extinction rate) pars[4] corresponds x (dependency extinction area) 0 - dependency, positive value - extinction increases area, negative value - extinction decreases area. pars[5] corresponds K_0  (initial carrying capacity). Set K=Inf non-diversity dependence. pars[6] corresponds z (dependency K area). 0 - dependency, positive value - K increases area, negative value - K decreases area. pars[7] corresponds gamma_0 (initial immigration rate) pars[8] corresponds alpha (dependency immigration island isolation). 0 - dependency, positive value - immigration increases distance, negative value - immigration decreases distance pars[9] corresponds lambda^a_0 (initial anagenesis rate) pars[10] corresponds beta (dependency anagenesis island isolation). 0 - dependency,positive value - anagenesis increases distance, negative value - anagenesis decreases distance. pars[11] corresponds d0, parameter describes interactive/additive effect isolation area cladogenesis (power models); describes shape sigmoidal relationship isolation parameter (sigmoidal models). replicates Number island replicates simulated per island table archipelago_data. 5 islands archipelago_data, number replicates set 10, 50 islands simulated. divdepmodel Option divdepmodel = 'CS' runs model clade-specific carrying capacity, diversity-dependence operates within single clades, .e. among species originating mainland colonist. Option divdepmodel = 'IW' runs model island-wide carrying capacity, diversity-dependence operates within among clades. distance_dep Shape dependency parameter distance. Can type  'power' type  'sigmoidal'. cladogenesis_dep distance_dep = 'power' specified, cladogenesis_dep specifies type effect area isolation cladogenesis. possible options :  'NULL' (additive interactive effect area isolation, models M1-M14 Valente et al 2020)  'additive' (additive effect area isolation cladogenesis, model M15 Valente et al 2020)  'interactive' (interactive effect area isolation cladogenesis, models M16 M19 Valente et al 2020)  'interactive1' (interactive effect area isolation cladogenesis, model M17 Valente et al 2020)  'interactive2' (interactive effect area isolation cladogenesis, model M18 Valente et al 2020) sigmoidal_par distance_dep = 'sigmoidal', sigmoidal_par specifies parameter sigmoidal relationship distance applied. Options:  'cladogenesis' 'anagenesis'  'colonisation'.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_MW.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Simulate multiple islands based on hyperparameters that describe relationships\nbetween area, isolation and local parameters — DAISIE_sim_MW","text":"island listed rows archipelago_data, given number islands simulated depending number replicates specified. simulations island archipelago_data element list, can called using [[x]]. Individual replicates island can called [[x]][[x]] example object called global_sims, 1st replicate first island can called using global_sims[[1]][[1]]. 3rd replicate 4th island called global_sims[[4]][[3]] island replicates list . first (e.g. global_sims[[x]][[x]][[1]]) element list following components:  $island_age - island archipelago age $not_present - number mainland lineages present island $stt_all - STT table species archipelago/island (nI - number non-endemic species; nA - number anagenetic species, nC - number cladogenetic species, present - number independent colonisations present)  $area Area island archipelago  $distance Distance mainland  $name Name island archipelago subsequent elements list contain information single colonist lineage island 4 components: $branching_times - island age stem age population/species case Non-endemic, Non-endemic_MaxAge Endemic close extant relatives islands species. cladogenetic species island age branching times radiation including stem age radiation. $stac - status colonist  * Endemic: 2  * Endemic&Non_Endemic: 3  * Non_endemic: 4 $missing_species - number island species sampled particular clade (applicable endemic clades)","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_MW.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Simulate multiple islands based on hyperparameters that describe relationships\nbetween area, isolation and local parameters — DAISIE_sim_MW","text":"Valente, LM, Phillimore AB, Melo M, Warren B, Clegg S, Havenstein K, Tiedemann R, Illera JC, Thebaud C, Aschenbach T  Etienne RS (2020). simple dynamic model explain island bird diversity worldwide. Nature, 579, 92-96.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_MW.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Simulate multiple islands based on hyperparameters that describe relationships\nbetween area, isolation and local parameters — DAISIE_sim_MW","text":"Luis Valente, Albert Phillimore, Rampal Etienne","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_MW.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Simulate multiple islands based on hyperparameters that describe relationships\nbetween area, isolation and local parameters — DAISIE_sim_MW","text":"","code":"## Simulate 10 replicates for the each of the 41 archipelagos in the archipelago_data table, ##based on the hyperparameters of the M19 model (preferred model in Valente et al 2020) ## and the age, area and isolation values given in the archipelago_data table. ## Mainland pool size of 1000, clade-specific carrying capacity. The M19 model is a ## power model with an interactive effect of area and isolation on cladogenesis. ## ## data(archipelago_data) ## result <- DAISIE_sim_MW( ## archipelago_data = archipelago_data, ## M = 1000, ## pars = c(0.040073803,  0,  1.945656546,  0.150429656,  Inf,  0,  67.25643672, ## 0.293635061,  0.059096872,  0.382688527,  0.026510781), ## replicates = 10, ## distance_dep = 'power', ## cladogenesis_dep = 'interactive', ## sigmoidal_par = 'NULL', ## divdepmodel = 'CS')"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_core_cr.html","id":null,"dir":"Reference","previous_headings":"","what":"Internal function of the DAISIE simulation — DAISIE_sim_core_cr","title":"Internal function of the DAISIE simulation — DAISIE_sim_core_cr","text":"Internal function DAISIE simulation","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_core_cr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Internal function of the DAISIE simulation — DAISIE_sim_core_cr","text":"","code":"DAISIE_sim_core_cr(   time,   mainland_n,   pars,   nonoceanic_pars,   hyper_pars,   area_pars )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_core_cr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Internal function of the DAISIE simulation — DAISIE_sim_core_cr","text":"time Numeric defining length simulation time units. example, island known 4 million years old, setting time = 4 simulate entire life span island; setting time = 2 stop simulation mid-life island. mainland_n numeric stating number mainland species, number species can potentially colonize island. using clade-specific diversity dependence, value set 1. using island-wide diversity dependence, value set number mainland species. pars numeric vector containing model parameters: pars[1]: lambda^c (cladogenesis rate) pars[2]: mu (extinction rate) pars[3]: K (carrying capacity), set K=Inf diversity   independence. pars[4]: gamma (immigration rate) pars[5]: lambda^(anagenesis rate) pars[6]: lambda^c (cladogenesis rate) either type 2 species   rate set 2 rate shift model pars[7]: mu (extinction rate) either type 2 species rate   set 2 rate shift model pars[8]: K (carrying capacity) either type 2 species rate   set 2 rate shift model, set K=Inf diversity independence. pars[9]: gamma (immigration rate) either type 2 species   rate set 2 rate shift model pars[10]: lambda^(anagenesis rate) either type 2   species rate set 2 rate shift model Elements 6:10 required type 2 species included rate shift model. DAISIE_sim_relaxed_rate() pars[6] standard deviation gamma distribution relaxed parameter parameter chosen relaxed_par argument mean gamma distribution relaxed parameter. nonoceanic_pars vector length two : [1]: probability sampling species mainland [2]: probability species sampled mainland   nonendemic hyper_pars named list numeric hyperparameters rate calculations returned create_hyper_pars(): [1]: d scaling parameter exponent calculating   cladogenesis rate [2]: x exponent calculating extinction rate area_pars named list containing area sea level parameters created create_area_pars(): [1]: maximum area [2]: current area [3]: value 0 1 indicating island's history   peak area achieved [4]: total island age [5]: amplitude area fluctuation sea level [6]: frequency sine wave area change sea level [7]: angle slope island","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_core_cr_shift.html","id":null,"dir":"Reference","previous_headings":"","what":"Internal function of the DAISIE simulation — DAISIE_sim_core_cr_shift","title":"Internal function of the DAISIE simulation — DAISIE_sim_core_cr_shift","text":"Internal function DAISIE simulation","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_core_cr_shift.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Internal function of the DAISIE simulation — DAISIE_sim_core_cr_shift","text":"","code":"DAISIE_sim_core_cr_shift(   time,   mainland_n,   pars,   nonoceanic_pars = c(0, 0),   hyper_pars = NULL,   area_pars = NULL,   shift_times )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_core_cr_shift.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Internal function of the DAISIE simulation — DAISIE_sim_core_cr_shift","text":"time Numeric defining length simulation time units. example, island known 4 million years old, setting time = 4 simulate entire life span island; setting time = 2 stop simulation mid-life island. mainland_n numeric stating number mainland species, number species can potentially colonize island. using clade-specific diversity dependence, value set 1. using island-wide diversity dependence, value set number mainland species. pars numeric vector containing model parameters: pars[1]: lambda^c (cladogenesis rate) pars[2]: mu (extinction rate) pars[3]: K (carrying capacity), set K=Inf diversity   independence. pars[4]: gamma (immigration rate) pars[5]: lambda^(anagenesis rate) pars[6]: lambda^c (cladogenesis rate) either type 2 species   rate set 2 rate shift model pars[7]: mu (extinction rate) either type 2 species rate   set 2 rate shift model pars[8]: K (carrying capacity) either type 2 species rate   set 2 rate shift model, set K=Inf diversity independence. pars[9]: gamma (immigration rate) either type 2 species   rate set 2 rate shift model pars[10]: lambda^(anagenesis rate) either type 2   species rate set 2 rate shift model Elements 6:10 required type 2 species included rate shift model. DAISIE_sim_relaxed_rate() pars[6] standard deviation gamma distribution relaxed parameter parameter chosen relaxed_par argument mean gamma distribution relaxed parameter. nonoceanic_pars vector length two : [1]: probability sampling species mainland [2]: probability species sampled mainland   nonendemic hyper_pars named list numeric hyperparameters rate calculations returned create_hyper_pars(): [1]: d scaling parameter exponent calculating   cladogenesis rate [2]: x exponent calculating extinction rate area_pars named list containing area sea level parameters created create_area_pars(): [1]: maximum area [2]: current area [3]: value 0 1 indicating island's history   peak area achieved [4]: total island age [5]: amplitude area fluctuation sea level [6]: frequency sine wave area change sea level [7]: angle slope island shift_times numeric vector specifying rate shifts occur present.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_core_time_dep.html","id":null,"dir":"Reference","previous_headings":"","what":"Internal function of the DAISIE simulation — DAISIE_sim_core_time_dep","title":"Internal function of the DAISIE simulation — DAISIE_sim_core_time_dep","text":"Internal function DAISIE simulation","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_core_time_dep.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Internal function of the DAISIE simulation — DAISIE_sim_core_time_dep","text":"","code":"DAISIE_sim_core_time_dep(   time,   mainland_n,   pars,   nonoceanic_pars,   island_ontogeny = 0,   sea_level = 0,   hyper_pars,   area_pars,   peak,   Amax,   Amin,   extcutoff = 1000 )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_core_time_dep.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Internal function of the DAISIE simulation — DAISIE_sim_core_time_dep","text":"time Numeric defining length simulation time units. example, island known 4 million years old, setting time = 4 simulate entire life span island; setting time = 2 stop simulation mid-life island. mainland_n numeric stating number mainland species, number species can potentially colonize island. using clade-specific diversity dependence, value set 1. using island-wide diversity dependence, value set number mainland species. pars numeric vector containing model parameters: pars[1]: lambda^c (cladogenesis rate) pars[2]: mu (extinction rate) pars[3]: K (carrying capacity), set K=Inf diversity   independence. pars[4]: gamma (immigration rate) pars[5]: lambda^(anagenesis rate) pars[6]: lambda^c (cladogenesis rate) either type 2 species   rate set 2 rate shift model pars[7]: mu (extinction rate) either type 2 species rate   set 2 rate shift model pars[8]: K (carrying capacity) either type 2 species rate   set 2 rate shift model, set K=Inf diversity independence. pars[9]: gamma (immigration rate) either type 2 species   rate set 2 rate shift model pars[10]: lambda^(anagenesis rate) either type 2   species rate set 2 rate shift model Elements 6:10 required type 2 species included rate shift model. DAISIE_sim_relaxed_rate() pars[6] standard deviation gamma distribution relaxed parameter parameter chosen relaxed_par argument mean gamma distribution relaxed parameter. nonoceanic_pars vector length two : [1]: probability sampling species mainland [2]: probability species sampled mainland   nonendemic island_ontogeny DAISIE_sim_time_dep(), DAISIE_ML_CS plotting string describing type island ontogeny. Can \"const\", \"beta\" beta function describing area time.  functions numeric describing type island ontogeny. Can 0 constant, 1 beta function describing area time. ML functions island_ontogeny = NA assumes constant ontogeny. Time dependent estimation yet available development still ongoing. return error called case. sea_level DAISIE_sim_time_dep() plotting string describing type sea level. Can \"const\" \"sine\" sine function describing area time.  functions numeric describing type sea level. Can 0 constant, 1 sine function describing area time. hyper_pars named list numeric hyperparameters rate calculations returned create_hyper_pars(): [1]: d scaling parameter exponent calculating   cladogenesis rate [2]: x exponent calculating extinction rate area_pars named list containing area sea level parameters created create_area_pars(): [1]: maximum area [2]: current area [3]: value 0 1 indicating island's history   peak area achieved [4]: total island age [5]: amplitude area fluctuation sea level [6]: frequency sine wave area change sea level [7]: angle slope island peak numeric value specifying peakiness (shaprness) ontogeny curve. Higher values imply peakier ontogeny. value internally calculated calc_peak() given area present area_pars. Amax numeric value maximum island area simulation. Amin numeric value minimum island area simulation. extcutoff numeric cutoff maximum extinction rate preventing large slowing simulation.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_core_trait_dep.html","id":null,"dir":"Reference","previous_headings":"","what":"Internal function of the DAISIE simulation — DAISIE_sim_core_trait_dep","title":"Internal function of the DAISIE simulation — DAISIE_sim_core_trait_dep","text":"Internal function DAISIE simulation","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_core_trait_dep.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Internal function of the DAISIE simulation — DAISIE_sim_core_trait_dep","text":"","code":"DAISIE_sim_core_trait_dep(   time,   mainland_n,   pars,   island_ontogeny = 0,   sea_level = 0,   hyper_pars,   area_pars,   extcutoff = 1000,   trait_pars = NULL )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_core_trait_dep.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Internal function of the DAISIE simulation — DAISIE_sim_core_trait_dep","text":"time Numeric defining length simulation time units. example, island known 4 million years old, setting time = 4 simulate entire life span island; setting time = 2 stop simulation mid-life island. mainland_n numeric stating number mainland species, number species can potentially colonize island. using clade-specific diversity dependence, value set 1. using island-wide diversity dependence, value set number mainland species. pars numeric vector containing model parameters: pars[1]: lambda^c (cladogenesis rate) pars[2]: mu (extinction rate) pars[3]: K (carrying capacity), set K=Inf diversity   independence. pars[4]: gamma (immigration rate) pars[5]: lambda^(anagenesis rate) pars[6]: lambda^c (cladogenesis rate) either type 2 species   rate set 2 rate shift model pars[7]: mu (extinction rate) either type 2 species rate   set 2 rate shift model pars[8]: K (carrying capacity) either type 2 species rate   set 2 rate shift model, set K=Inf diversity independence. pars[9]: gamma (immigration rate) either type 2 species   rate set 2 rate shift model pars[10]: lambda^(anagenesis rate) either type 2   species rate set 2 rate shift model Elements 6:10 required type 2 species included rate shift model. DAISIE_sim_relaxed_rate() pars[6] standard deviation gamma distribution relaxed parameter parameter chosen relaxed_par argument mean gamma distribution relaxed parameter. island_ontogeny DAISIE_sim_time_dep(), DAISIE_ML_CS plotting string describing type island ontogeny. Can \"const\", \"beta\" beta function describing area time.  functions numeric describing type island ontogeny. Can 0 constant, 1 beta function describing area time. ML functions island_ontogeny = NA assumes constant ontogeny. Time dependent estimation yet available development still ongoing. return error called case. sea_level DAISIE_sim_time_dep() plotting string describing type sea level. Can \"const\" \"sine\" sine function describing area time.  functions numeric describing type sea level. Can 0 constant, 1 sine function describing area time. hyper_pars named list numeric hyperparameters rate calculations returned create_hyper_pars(): [1]: d scaling parameter exponent calculating   cladogenesis rate [2]: x exponent calculating extinction rate area_pars named list containing area sea level parameters created create_area_pars(): [1]: maximum area [2]: current area [3]: value 0 1 indicating island's history   peak area achieved [4]: total island age [5]: amplitude area fluctuation sea level [6]: frequency sine wave area change sea level [7]: angle slope island extcutoff numeric cutoff maximum extinction rate preventing large slowing simulation. trait_pars named list containing diversification rates considering   two trait states created create_trait_pars: [1]:numeric per capita transition rate state1 [2]:numeric per capita immigration rate state2 [3]:numeric per capita extinction rate state2 [4]:numeric per capita anagenesis rate state2 [5]:numeric per capita cladogenesis rate state2 [6]:numeric per capita transition rate state2 [7]:numeric number species trait state 2    mainland","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_cr_cs.html","id":null,"dir":"Reference","previous_headings":"","what":"Simulates island replicates with an clade-specific (CS) diversity-dependent\nconstant-rate process — DAISIE_sim_cr_cs","title":"Simulates island replicates with an clade-specific (CS) diversity-dependent\nconstant-rate process — DAISIE_sim_cr_cs","text":"Simulates island replicates clade-specific (CS) diversity-dependent constant-rate process","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_cr_cs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulates island replicates with an clade-specific (CS) diversity-dependent\nconstant-rate process — DAISIE_sim_cr_cs","text":"","code":"DAISIE_sim_cr_cs(   total_time,   M,   pars,   replicates,   nonoceanic_pars,   prop_type2_pool,   replicates_apply_type2,   sample_freq,   hyper_pars,   area_pars,   cond,   verbose )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_cr_cs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulates island replicates with an clade-specific (CS) diversity-dependent\nconstant-rate process — DAISIE_sim_cr_cs","text":"total_time Numeric defining length simulation time units. M Numeric defining size mainland pool, .e. number species can potentially colonize island. pars numeric vector containing model parameters: pars[1]: lambda^c (cladogenesis rate) pars[2]: mu (extinction rate) pars[3]: K (carrying capacity), set K=Inf diversity   independence. pars[4]: gamma (immigration rate) pars[5]: lambda^(anagenesis rate) pars[6]: lambda^c (cladogenesis rate) either type 2 species   rate set 2 rate shift model pars[7]: mu (extinction rate) either type 2 species rate   set 2 rate shift model pars[8]: K (carrying capacity) either type 2 species rate   set 2 rate shift model, set K=Inf diversity independence. pars[9]: gamma (immigration rate) either type 2 species   rate set 2 rate shift model pars[10]: lambda^(anagenesis rate) either type 2   species rate set 2 rate shift model Elements 6:10 required type 2 species included rate shift model. DAISIE_sim_relaxed_rate() pars[6] standard deviation gamma distribution relaxed parameter parameter chosen relaxed_par argument mean gamma distribution relaxed parameter. replicates Integer specifying number island replicates simulated. nonoceanic_pars vector length two : [1]: probability sampling species mainland [2]: probability species sampled mainland   nonendemic prop_type2_pool Fraction mainland species belongs second subset species (type 2). Applies two types species simulated (length(pars) = 10). DAISIE_dataprep() applies number_clade_types = 2.  DAISIE_dataprep() default \"proportional\" sets fraction proportional number clades distinct macroevolutionary process colonised island. replicates_apply_type2 Applies two types species simulated. Default replicates_apply_type2 = TRUE runs simulations number islands type 2 species colonised equal specified number replicates. recommended prop_type2_pool small rate immigration type two species (pars[9]) low, meaning replicates needed achieved adequate sample size islands type 2 species. Setting replicates_apply_type2 = FALSE simulates islands specified number replicates regardless whether type 2 species colonised . sample_freq Numeric specifing number units times divided plotting purposes. Larger values lead plots higher resolution, also run slower. hyper_pars named list numeric hyperparameters rate calculations returned create_hyper_pars(): [1]: d scaling parameter exponent calculating   cladogenesis rate [2]: x exponent calculating extinction rate area_pars named list containing area sea level parameters created create_area_pars(): [1]: maximum area [2]: current area [3]: value 0 1 indicating island's history   peak area achieved [4]: total island age [5]: amplitude area fluctuation sea level [6]: frequency sine wave area change sea level [7]: angle slope island cond cond = 0 : conditioning island age  cond = 1 : conditioning island age non-extinction island biota . cond > 1 : conditioning island age least cond colonizations island. last option yet available IW model verbose numeric vector length 1, simulations `DAISIEdataprep()` can `1` `0`, `1` gives intermediate output printed. ML functions numeric determining intermediate output printed. default: `0` print, `1` prints initial likelihood settings selected (parameters optimised, fixed shifted), `2` prints `1 also intermediate output parameters loglikelihood, `3` `2` prints intermediate progress likelihood computation.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_cr_cs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Simulates island replicates with an clade-specific (CS) diversity-dependent\nconstant-rate process — DAISIE_sim_cr_cs","text":"list. highest level least corresponds individual replicate. See return `DAISIE_sim_cr()` details.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_cr_gw.html","id":null,"dir":"Reference","previous_headings":"","what":"Simulates island replicates with an guild-wide (GW) diversity-dependent\nprocess — DAISIE_sim_cr_gw","title":"Simulates island replicates with an guild-wide (GW) diversity-dependent\nprocess — DAISIE_sim_cr_gw","text":"Simulates island replicates guild-wide (GW) diversity-dependent process","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_cr_gw.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulates island replicates with an guild-wide (GW) diversity-dependent\nprocess — DAISIE_sim_cr_gw","text":"","code":"DAISIE_sim_cr_gw(   total_time,   M,   pars,   replicates,   nonoceanic_pars,   num_guilds,   sample_freq,   hyper_pars,   area_pars,   verbose )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_cr_gw.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulates island replicates with an guild-wide (GW) diversity-dependent\nprocess — DAISIE_sim_cr_gw","text":"total_time Numeric defining length simulation time units. M Numeric defining size mainland pool, .e. number species can potentially colonize island. pars numeric vector containing model parameters: pars[1]: lambda^c (cladogenesis rate) pars[2]: mu (extinction rate) pars[3]: K (carrying capacity), set K=Inf diversity   independence. pars[4]: gamma (immigration rate) pars[5]: lambda^(anagenesis rate) pars[6]: lambda^c (cladogenesis rate) either type 2 species   rate set 2 rate shift model pars[7]: mu (extinction rate) either type 2 species rate   set 2 rate shift model pars[8]: K (carrying capacity) either type 2 species rate   set 2 rate shift model, set K=Inf diversity independence. pars[9]: gamma (immigration rate) either type 2 species   rate set 2 rate shift model pars[10]: lambda^(anagenesis rate) either type 2   species rate set 2 rate shift model Elements 6:10 required type 2 species included rate shift model. DAISIE_sim_relaxed_rate() pars[6] standard deviation gamma distribution relaxed parameter parameter chosen relaxed_par argument mean gamma distribution relaxed parameter. replicates Integer specifying number island replicates simulated. nonoceanic_pars vector length two : [1]: probability sampling species mainland [2]: probability species sampled mainland   nonendemic num_guilds number guilds mainland. number mainland species divided number guilds divdepmodel = \"GW\" sample_freq Numeric specifing number units times divided plotting purposes. Larger values lead plots higher resolution, also run slower. hyper_pars named list numeric hyperparameters rate calculations returned create_hyper_pars(): [1]: d scaling parameter exponent calculating   cladogenesis rate [2]: x exponent calculating extinction rate area_pars named list containing area sea level parameters created create_area_pars(): [1]: maximum area [2]: current area [3]: value 0 1 indicating island's history   peak area achieved [4]: total island age [5]: amplitude area fluctuation sea level [6]: frequency sine wave area change sea level [7]: angle slope island verbose numeric vector length 1, simulations `DAISIEdataprep()` can `1` `0`, `1` gives intermediate output printed. ML functions numeric determining intermediate output printed. default: `0` print, `1` prints initial likelihood settings selected (parameters optimised, fixed shifted), `2` prints `1 also intermediate output parameters loglikelihood, `3` `2` prints intermediate progress likelihood computation.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_cr_gw.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Simulates island replicates with an guild-wide (GW) diversity-dependent\nprocess — DAISIE_sim_cr_gw","text":"list. highest level least corresponds individual replciate. See return `DAISIE_sim_cr()` details.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_cr_iw.html","id":null,"dir":"Reference","previous_headings":"","what":"Simulates island replicates with an island-wide (IW) diversity-dependent\nconstant-rate process — DAISIE_sim_cr_iw","title":"Simulates island replicates with an island-wide (IW) diversity-dependent\nconstant-rate process — DAISIE_sim_cr_iw","text":"Simulates island replicates island-wide (IW) diversity-dependent constant-rate process","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_cr_iw.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulates island replicates with an island-wide (IW) diversity-dependent\nconstant-rate process — DAISIE_sim_cr_iw","text":"","code":"DAISIE_sim_cr_iw(   total_time,   M,   pars,   replicates,   nonoceanic_pars,   sample_freq,   hyper_pars,   area_pars,   cond,   verbose )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_cr_iw.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulates island replicates with an island-wide (IW) diversity-dependent\nconstant-rate process — DAISIE_sim_cr_iw","text":"total_time Numeric defining length simulation time units. M Numeric defining size mainland pool, .e. number species can potentially colonize island. pars numeric vector containing model parameters: pars[1]: lambda^c (cladogenesis rate) pars[2]: mu (extinction rate) pars[3]: K (carrying capacity), set K=Inf diversity   independence. pars[4]: gamma (immigration rate) pars[5]: lambda^(anagenesis rate) pars[6]: lambda^c (cladogenesis rate) either type 2 species   rate set 2 rate shift model pars[7]: mu (extinction rate) either type 2 species rate   set 2 rate shift model pars[8]: K (carrying capacity) either type 2 species rate   set 2 rate shift model, set K=Inf diversity independence. pars[9]: gamma (immigration rate) either type 2 species   rate set 2 rate shift model pars[10]: lambda^(anagenesis rate) either type 2   species rate set 2 rate shift model Elements 6:10 required type 2 species included rate shift model. DAISIE_sim_relaxed_rate() pars[6] standard deviation gamma distribution relaxed parameter parameter chosen relaxed_par argument mean gamma distribution relaxed parameter. replicates Integer specifying number island replicates simulated. nonoceanic_pars vector length two : [1]: probability sampling species mainland [2]: probability species sampled mainland   nonendemic sample_freq Numeric specifing number units times divided plotting purposes. Larger values lead plots higher resolution, also run slower. hyper_pars named list numeric hyperparameters rate calculations returned create_hyper_pars(): [1]: d scaling parameter exponent calculating   cladogenesis rate [2]: x exponent calculating extinction rate area_pars named list containing area sea level parameters created create_area_pars(): [1]: maximum area [2]: current area [3]: value 0 1 indicating island's history   peak area achieved [4]: total island age [5]: amplitude area fluctuation sea level [6]: frequency sine wave area change sea level [7]: angle slope island cond cond = 0 : conditioning island age  cond = 1 : conditioning island age non-extinction island biota . cond > 1 : conditioning island age least cond colonizations island. last option yet available IW model verbose numeric vector length 1, simulations `DAISIEdataprep()` can `1` `0`, `1` gives intermediate output printed. ML functions numeric determining intermediate output printed. default: `0` print, `1` prints initial likelihood settings selected (parameters optimised, fixed shifted), `2` prints `1 also intermediate output parameters loglikelihood, `3` `2` prints intermediate progress likelihood computation.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_cr_iw.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Simulates island replicates with an island-wide (IW) diversity-dependent\nconstant-rate process — DAISIE_sim_cr_iw","text":"list. highest level least corresponds individual replicate. See return `DAISIE_sim_cr()` details.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_cr_shift.html","id":null,"dir":"Reference","previous_headings":"","what":"Simulate (non-)oceanic islands with given parameters under a\n  rate-shift regime — DAISIE_sim_cr_shift","title":"Simulate (non-)oceanic islands with given parameters under a\n  rate-shift regime — DAISIE_sim_cr_shift","text":"function simulates islands given cladogenesis, extinction, Kprime, immigration anagenesis parameters, modelled time-constant parameters, can switched different diversification regime (.e., different set parameters) one set times present. , allows simulation non-oceanic islands, generating islands starting condition includes potential endemic non-endemic species.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_cr_shift.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulate (non-)oceanic islands with given parameters under a\n  rate-shift regime — DAISIE_sim_cr_shift","text":"","code":"DAISIE_sim_cr_shift(   time,   M,   pars,   replicates,   shift_times,   divdepmodel = \"CS\",   nonoceanic_pars = c(0, 0),   num_guilds = NULL,   sample_freq = 25,   plot_sims = TRUE,   hyper_pars = create_hyper_pars(d = 0, x = 0),   area_pars = DAISIE::create_area_pars(max_area = 1, current_area = 1,     proportional_peak_t = 0, total_island_age = 0, sea_level_amplitude = 0,     sea_level_frequency = 0, island_gradient_angle = 0),   cond = 0,   verbose = TRUE,   ... )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_cr_shift.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulate (non-)oceanic islands with given parameters under a\n  rate-shift regime — DAISIE_sim_cr_shift","text":"time Numeric defining length simulation time units. example, island known 4 million years old, setting time = 4 simulate entire life span island; setting time = 2 stop simulation mid-life island. M Numeric defining size mainland pool, .e. number species can potentially colonize island. pars numeric vector containing model parameters: pars[1]: lambda^c (cladogenesis rate) pars[2]: mu (extinction rate) pars[3]: K (carrying capacity), set K=Inf diversity   independence. pars[4]: gamma (immigration rate) pars[5]: lambda^(anagenesis rate) pars[6]: lambda^c (cladogenesis rate) either type 2 species   rate set 2 rate shift model pars[7]: mu (extinction rate) either type 2 species rate   set 2 rate shift model pars[8]: K (carrying capacity) either type 2 species rate   set 2 rate shift model, set K=Inf diversity independence. pars[9]: gamma (immigration rate) either type 2 species   rate set 2 rate shift model pars[10]: lambda^(anagenesis rate) either type 2   species rate set 2 rate shift model Elements 6:10 required type 2 species included rate shift model. DAISIE_sim_relaxed_rate() pars[6] standard deviation gamma distribution relaxed parameter parameter chosen relaxed_par argument mean gamma distribution relaxed parameter. replicates Integer specifying number island replicates simulated. shift_times numeric vector specifying rate shifts occur present. divdepmodel Option divdepmodel = 'CS' runs model clade-specific carrying capacity, diversity-dependence operates within single clades, .e. among species originating mainland colonist. Option divdepmodel = 'IW' runs model island-wide carrying capacity, diversity-dependence operates within among clades. Option divdepmodel = 'GW' runs model diversity-dependence operates within guild. nonoceanic_pars vector length two : [1]: probability sampling species mainland [2]: probability species sampled mainland   nonendemic num_guilds number guilds mainland. number mainland species divided number guilds divdepmodel = \"GW\" sample_freq Numeric specifing number units times divided plotting purposes. Larger values lead plots higher resolution, also run slower. plot_sims Default = TRUE plots species--time (STT) plots. detects many types species present. one type species present, STT plotted species. two types present, three plots produced: STT , STT type 1 STT type 2. hyper_pars named list numeric hyperparameters rate calculations returned create_hyper_pars(): [1]: d scaling parameter exponent calculating   cladogenesis rate [2]: x exponent calculating extinction rate area_pars named list containing area sea level parameters created create_area_pars(): [1]: maximum area [2]: current area [3]: value 0 1 indicating island's history   peak area achieved [4]: total island age [5]: amplitude area fluctuation sea level [6]: frequency sine wave area change sea level [7]: angle slope island cond cond = 0 : conditioning island age  cond = 1 : conditioning island age non-extinction island biota . cond > 1 : conditioning island age least cond colonizations island. last option yet available IW model verbose numeric vector length 1, simulations `DAISIEdataprep()` can `1` `0`, `1` gives intermediate output printed. ML functions numeric determining intermediate output printed. default: `0` print, `1` prints initial likelihood settings selected (parameters optimised, fixed shifted), `2` prints `1 also intermediate output parameters loglikelihood, `3` `2` prints intermediate progress likelihood computation. ... arguments pass plotting functions.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_cr_shift.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Simulate (non-)oceanic islands with given parameters under a\n  rate-shift regime — DAISIE_sim_cr_shift","text":"list. highest level least corresponds individual replciate. first element replicate composed island information containing: $island_age: numeric island age. $not_present: numeric number mainland lineages   present island. $stt_all: STT table species island     (nI - number non-endemic species; nA - number anagenetic species,     nC - number cladogenetic species, present - number independent     colonisations present) $brts_table: simulations \"IW\". Table containing information order events data, use maximum likelihood optimization.). subsequent elements list pertaining replcate contain information single colonist lineage island 4 components: $branching_times: island age stem age     population/species case Non-endemic, Non-endemic_MaxAge     Endemic anagenetic species. cladogenetic species     island age branching times radiation including     stem age radiation. $stac: integer ranging 1 4   indicating status colonist: Non_endemic_MaxAge Endemic Endemic&Non_Endemic Non_endemic_MaxAge $missing_species: number island species sampled particular clade (applicable endemic clades) $type_1or2: whether colonist belongs type 1 type 2","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_cr_shift.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Simulate (non-)oceanic islands with given parameters under a\n  rate-shift regime — DAISIE_sim_cr_shift","text":"Valente, L.M., .B. Phillimore R.S. Etienne (2015). Equilibrium non-equilibrium dynamics simultaneously operate Galapagos islands. Ecology Letters 18: 844-852. Hauffe, T., D. Delicado, R.S. Etienne L. Valente (2020). Lake expansion elevates equilibrium diversity via increasing colonization.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_cr_shift.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Simulate (non-)oceanic islands with given parameters under a\n  rate-shift regime — DAISIE_sim_cr_shift","text":"Luis Valente, Albert Phillimore, Torsten Hauffe","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_min_type2.html","id":null,"dir":"Reference","previous_headings":"","what":"Internal function of the DAISIE simulation — DAISIE_sim_min_type2","title":"Internal function of the DAISIE simulation — DAISIE_sim_min_type2","text":"Internal function DAISIE simulation","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_min_type2.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Internal function of the DAISIE simulation — DAISIE_sim_min_type2","text":"","code":"DAISIE_sim_min_type2(   time,   M,   pars,   replicates,   prop_type2_pool,   area_pars,   hyper_pars,   verbose = TRUE )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_min_type2.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Internal function of the DAISIE simulation — DAISIE_sim_min_type2","text":"time Numeric defining length simulation time units. example, island known 4 million years old, setting time = 4 simulate entire life span island; setting time = 2 stop simulation mid-life island. M Numeric defining size mainland pool, .e. number species can potentially colonize island. pars numeric vector containing model parameters: pars[1]: lambda^c (cladogenesis rate) pars[2]: mu (extinction rate) pars[3]: K (carrying capacity), set K=Inf diversity   independence. pars[4]: gamma (immigration rate) pars[5]: lambda^(anagenesis rate) pars[6]: lambda^c (cladogenesis rate) either type 2 species   rate set 2 rate shift model pars[7]: mu (extinction rate) either type 2 species rate   set 2 rate shift model pars[8]: K (carrying capacity) either type 2 species rate   set 2 rate shift model, set K=Inf diversity independence. pars[9]: gamma (immigration rate) either type 2 species   rate set 2 rate shift model pars[10]: lambda^(anagenesis rate) either type 2   species rate set 2 rate shift model Elements 6:10 required type 2 species included rate shift model. DAISIE_sim_relaxed_rate() pars[6] standard deviation gamma distribution relaxed parameter parameter chosen relaxed_par argument mean gamma distribution relaxed parameter. replicates Integer specifying number island replicates simulated. prop_type2_pool Fraction mainland species belongs second subset species (type 2). Applies two types species simulated (length(pars) = 10). DAISIE_dataprep() applies number_clade_types = 2.  DAISIE_dataprep() default \"proportional\" sets fraction proportional number clades distinct macroevolutionary process colonised island. area_pars named list containing area sea level parameters created create_area_pars(): [1]: maximum area [2]: current area [3]: value 0 1 indicating island's history   peak area achieved [4]: total island age [5]: amplitude area fluctuation sea level [6]: frequency sine wave area change sea level [7]: angle slope island hyper_pars named list numeric hyperparameters rate calculations returned create_hyper_pars(): [1]: d scaling parameter exponent calculating   cladogenesis rate [2]: x exponent calculating extinction rate verbose numeric vector length 1, simulations `DAISIEdataprep()` can `1` `0`, `1` gives intermediate output printed. ML functions numeric determining intermediate output printed. default: `0` print, `1` prints initial likelihood settings selected (parameters optimised, fixed shifted), `2` prints `1 also intermediate output parameters loglikelihood, `3` `2` prints intermediate progress likelihood computation.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_relaxed_rate.html","id":null,"dir":"Reference","previous_headings":"","what":"Simulate (non-)oceanic islands with given parameters under a\n  relaxed-rate model — DAISIE_sim_relaxed_rate","title":"Simulate (non-)oceanic islands with given parameters under a\n  relaxed-rate model — DAISIE_sim_relaxed_rate","text":"function simulates islands given cladogenesis, extinction, Kprime, immigration anagenesis parameters, can modelled time-constant parameters variation clades one multiple parameters. , allows simulation non-oceanic islands, generating islands starting condition includes potential endemic non-endemic species.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_relaxed_rate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulate (non-)oceanic islands with given parameters under a\n  relaxed-rate model — DAISIE_sim_relaxed_rate","text":"","code":"DAISIE_sim_relaxed_rate(   time,   M,   pars,   replicates,   relaxed_par,   nonoceanic_pars = c(0, 0),   sample_freq = 25,   plot_sims = TRUE,   hyper_pars = create_hyper_pars(d = 0, x = 0),   area_pars = create_area_pars(max_area = 1, current_area = 1, proportional_peak_t = 0,     total_island_age = 0, sea_level_amplitude = 0, sea_level_frequency = 0,     island_gradient_angle = 0),   cond = 0,   verbose = TRUE,   ... )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_relaxed_rate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulate (non-)oceanic islands with given parameters under a\n  relaxed-rate model — DAISIE_sim_relaxed_rate","text":"time Numeric defining length simulation time units. example, island known 4 million years old, setting time = 4 simulate entire life span island; setting time = 2 stop simulation mid-life island. M Numeric defining size mainland pool, .e. number species can potentially colonize island. pars numeric vector containing model parameters: pars[1]: lambda^c (cladogenesis rate) pars[2]: mu (extinction rate) pars[3]: K (carrying capacity), set K=Inf diversity   independence. pars[4]: gamma (immigration rate) pars[5]: lambda^(anagenesis rate) pars[6]: lambda^c (cladogenesis rate) either type 2 species   rate set 2 rate shift model pars[7]: mu (extinction rate) either type 2 species rate   set 2 rate shift model pars[8]: K (carrying capacity) either type 2 species rate   set 2 rate shift model, set K=Inf diversity independence. pars[9]: gamma (immigration rate) either type 2 species   rate set 2 rate shift model pars[10]: lambda^(anagenesis rate) either type 2   species rate set 2 rate shift model Elements 6:10 required type 2 species included rate shift model. DAISIE_sim_relaxed_rate() pars[6] standard deviation gamma distribution relaxed parameter parameter chosen relaxed_par argument mean gamma distribution relaxed parameter. replicates Integer specifying number island replicates simulated. relaxed_par string determining parameter relaxed relaxed rate model. nonoceanic_pars vector length two : [1]: probability sampling species mainland [2]: probability species sampled mainland   nonendemic sample_freq Numeric specifing number units times divided plotting purposes. Larger values lead plots higher resolution, also run slower. plot_sims Default = TRUE plots species--time (STT) plots. detects many types species present. one type species present, STT plotted species. two types present, three plots produced: STT , STT type 1 STT type 2. hyper_pars named list numeric hyperparameters rate calculations returned create_hyper_pars(): [1]: d scaling parameter exponent calculating   cladogenesis rate [2]: x exponent calculating extinction rate area_pars named list containing area sea level parameters created create_area_pars(): [1]: maximum area [2]: current area [3]: value 0 1 indicating island's history   peak area achieved [4]: total island age [5]: amplitude area fluctuation sea level [6]: frequency sine wave area change sea level [7]: angle slope island cond cond = 0 : conditioning island age  cond = 1 : conditioning island age non-extinction island biota . cond > 1 : conditioning island age least cond colonizations island. last option yet available IW model verbose numeric vector length 1, simulations `DAISIEdataprep()` can `1` `0`, `1` gives intermediate output printed. ML functions numeric determining intermediate output printed. default: `0` print, `1` prints initial likelihood settings selected (parameters optimised, fixed shifted), `2` prints `1 also intermediate output parameters loglikelihood, `3` `2` prints intermediate progress likelihood computation. ... arguments pass plotting functions.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_relaxed_rate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Simulate (non-)oceanic islands with given parameters under a\n  relaxed-rate model — DAISIE_sim_relaxed_rate","text":"list. highest level least corresponds individual replciate. first element replicate composed island information containing: $island_age: numeric island age. $not_present: number mainland lineages     present island. present 1 type species     simulated. Becomes $not_present_type1: number mainland     lineages type 1 present island     $not_present_type2: number mainland lineages type 2     present island, two types simulated. $stt_all: STT table species island     (nI - number non-endemic species; nA - number anagenetic species,     nC - number cladogenetic species, present - number independent     colonisations present) $stt_stt_type1: STT table type 1 species island -     2 types species simulated (nI - number non-endemic     species; nA - number anagenetic species, nC - number cladogenetic     species, present - number independent colonisations present). $stt_stt_type2: STT table type 2 species island      - 2 types species simulated (nI - number non-endemic      species; nA - number anagenetic species, nC - number cladogenetic      species, present - number independent colonisations present ). $brts_table: simulations \"IW\". Table containing information order events data, use maximum likelihood optimization.). subsequent elements list pertaining replcate contain information single colonist lineage island 4 components: $branching_times: island age stem age     population/species case Non-endemic, Non-endemic_MaxAge     Endemic anagenetic species.    cladogenetic species     island age branching times radiation including     stem age radiation. $stac: integer ranging 1 4   indicating status colonist: Non_endemic_MaxAge Endemic Endemic&Non_Endemic Non_endemic_MaxAge $missing_species: number island species sampled particular clade (applicable endemic clades) $type_1or2: whether colonist belongs type 1 type 2","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_relaxed_rate.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Simulate (non-)oceanic islands with given parameters under a\n  relaxed-rate model — DAISIE_sim_relaxed_rate","text":"Luis Valente, Albert Phillimore, Joshua Lambert, Shu Xie, Pedro Neves, Richèl J. C. Bilderbeek, Rampal Etienne","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_relaxed_rate.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Simulate (non-)oceanic islands with given parameters under a\n  relaxed-rate model — DAISIE_sim_relaxed_rate","text":"","code":"## Simulate an island for 1 million years, with a relaxed the rate of ## cladogenesis between clades. Pool size 500.  clado_rate <- 0.5 ext_rate <- 0.2 carr_cap <- Inf immig_rate <- 0.005 ana_rate <- 1 par_sd <- 1 sim_pars <- c(clado_rate, ext_rate, carr_cap, immig_rate, ana_rate, par_sd) set.seed(1) island_replicates <- DAISIE_sim_relaxed_rate(   time = 1,   M = 500,   pars = sim_pars,   replicates = 2,   relaxed_par = \"cladogenesis\",   plot_sims = FALSE,   verbose = FALSE )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_time_dep.html","id":null,"dir":"Reference","previous_headings":"","what":"Simulate (non-)oceanic islands with given parameters under a\n  time-dependent regime — DAISIE_sim_time_dep","title":"Simulate (non-)oceanic islands with given parameters under a\n  time-dependent regime — DAISIE_sim_time_dep","text":"function simulates islands given cladogenesis, extinction, Kprime, immigration anagenesis parameters, modelled time-dependent parameters. Time dependency aims capture effect area changes islands undego emergence subsidence. Thus, oceanic, volcanic island ontogeny scenarios can modelled (beta function), well effect sea level fluctuations (modelled sine function). See paramter entry area_pars details. island ontogeny sea level fluctuations allowed operate simultaneuosly. function also allows simulation non-oceanic islands, generating islands starting condition includes potential endemic non-endemic species.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_time_dep.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulate (non-)oceanic islands with given parameters under a\n  time-dependent regime — DAISIE_sim_time_dep","text":"","code":"DAISIE_sim_time_dep(   time,   M,   pars,   replicates,   area_pars,   hyper_pars,   divdepmodel = \"CS\",   nonoceanic_pars = c(0, 0),   num_guilds = NULL,   sample_freq = 25,   plot_sims = TRUE,   island_ontogeny = \"const\",   sea_level = \"const\",   extcutoff = 1000,   cond = 0,   verbose = TRUE,   ... )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_time_dep.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulate (non-)oceanic islands with given parameters under a\n  time-dependent regime — DAISIE_sim_time_dep","text":"time Numeric defining length simulation time units. example, island known 4 million years old, setting time = 4 simulate entire life span island; setting time = 2 stop simulation mid-life island. M Numeric defining size mainland pool, .e. number species can potentially colonize island. pars numeric vector containing model parameters: pars[1]: lambda^c (cladogenesis rate) pars[2]: mu (extinction rate) pars[3]: K (carrying capacity), set K=Inf diversity   independence. pars[4]: gamma (immigration rate) pars[5]: lambda^(anagenesis rate) pars[6]: lambda^c (cladogenesis rate) either type 2 species   rate set 2 rate shift model pars[7]: mu (extinction rate) either type 2 species rate   set 2 rate shift model pars[8]: K (carrying capacity) either type 2 species rate   set 2 rate shift model, set K=Inf diversity independence. pars[9]: gamma (immigration rate) either type 2 species   rate set 2 rate shift model pars[10]: lambda^(anagenesis rate) either type 2   species rate set 2 rate shift model Elements 6:10 required type 2 species included rate shift model. DAISIE_sim_relaxed_rate() pars[6] standard deviation gamma distribution relaxed parameter parameter chosen relaxed_par argument mean gamma distribution relaxed parameter. replicates Integer specifying number island replicates simulated. area_pars named list containing area sea level parameters created create_area_pars(): [1]: maximum area [2]: current area [3]: value 0 1 indicating island's history   peak area achieved [4]: total island age [5]: amplitude area fluctuation sea level [6]: frequency sine wave area change sea level [7]: angle slope island hyper_pars named list numeric hyperparameters rate calculations returned create_hyper_pars(): [1]: d scaling parameter exponent calculating   cladogenesis rate [2]: x exponent calculating extinction rate divdepmodel Option divdepmodel = 'CS' runs model clade-specific carrying capacity, diversity-dependence operates within single clades, .e. among species originating mainland colonist. Option divdepmodel = 'IW' runs model island-wide carrying capacity, diversity-dependence operates within among clades. Option divdepmodel = 'GW' runs model diversity-dependence operates within guild. nonoceanic_pars vector length two : [1]: probability sampling species mainland [2]: probability species sampled mainland   nonendemic num_guilds number guilds mainland. number mainland species divided number guilds divdepmodel = \"GW\" sample_freq Numeric specifing number units times divided plotting purposes. Larger values lead plots higher resolution, also run slower. plot_sims Default = TRUE plots species--time (STT) plots. detects many types species present. one type species present, STT plotted species. two types present, three plots produced: STT , STT type 1 STT type 2. island_ontogeny DAISIE_sim_time_dep(), DAISIE_ML_CS plotting string describing type island ontogeny. Can \"const\", \"beta\" beta function describing area time.  functions numeric describing type island ontogeny. Can 0 constant, 1 beta function describing area time. ML functions island_ontogeny = NA assumes constant ontogeny. Time dependent estimation yet available development still ongoing. return error called case. sea_level DAISIE_sim_time_dep() plotting string describing type sea level. Can \"const\" \"sine\" sine function describing area time.  functions numeric describing type sea level. Can 0 constant, 1 sine function describing area time. extcutoff numeric cutoff maximum extinction rate preventing large slowing simulation. cond cond = 0 : conditioning island age  cond = 1 : conditioning island age non-extinction island biota . cond > 1 : conditioning island age least cond colonizations island. last option yet available IW model verbose numeric vector length 1, simulations `DAISIEdataprep()` can `1` `0`, `1` gives intermediate output printed. ML functions numeric determining intermediate output printed. default: `0` print, `1` prints initial likelihood settings selected (parameters optimised, fixed shifted), `2` prints `1 also intermediate output parameters loglikelihood, `3` `2` prints intermediate progress likelihood computation. ... arguments pass plotting functions.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_time_dep.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Simulate (non-)oceanic islands with given parameters under a\n  time-dependent regime — DAISIE_sim_time_dep","text":"list. highest level least corresponds individual replciate. first element replicate composed island information containing: $island_age: numeric island age. $not_present: numeric number mainland lineages   present island. $stt_all: STT table species island     (nI - number non-endemic species; nA - number anagenetic species,     nC - number cladogenetic species, present - number independent     colonisations present) $brts_table: simulations \"IW\". Table containing information order events data, use maximum likelihood optimization.). subsequent elements list pertaining replcate contain information single colonist lineage island 4 components: $branching_times: island age stem age     population/species case Non-endemic, Non-endemic_MaxAge     Endemic anagenetic species. cladogenetic species     island age branching times radiation including     stem age radiation. $stac: integer ranging 1 4   indicating status colonist: Non_endemic_MaxAge Endemic Endemic&Non_Endemic Non_endemic_MaxAge $missing_species: number island species sampled particular clade (applicable endemic clades) $type_1or2: whether colonist belongs type 1 type 2","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_time_dep.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Simulate (non-)oceanic islands with given parameters under a\n  time-dependent regime — DAISIE_sim_time_dep","text":"Valente, L.M., .B. Phillimore R.S. Etienne (2015). Equilibrium non-equilibrium dynamics simultaneously operate Galapagos islands. Ecology Letters 18: 844-852. Valente, L.M., Etienne, R.S. Phillimore, .B. (2014). effects island ontogeny species diversity phylogeny. Proceedings Royal Society B: Biological Sciences 281(1784), p.20133227.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_time_dep.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Simulate (non-)oceanic islands with given parameters under a\n  time-dependent regime — DAISIE_sim_time_dep","text":"Luis Valente Albert Phillimore","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_time_dep_cs.html","id":null,"dir":"Reference","previous_headings":"","what":"Simulates island replicates with an clade-specific (CS) diversity-dependent\ntime-dependent process — DAISIE_sim_time_dep_cs","title":"Simulates island replicates with an clade-specific (CS) diversity-dependent\ntime-dependent process — DAISIE_sim_time_dep_cs","text":"Simulates island replicates clade-specific (CS) diversity-dependent time-dependent process","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_time_dep_cs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulates island replicates with an clade-specific (CS) diversity-dependent\ntime-dependent process — DAISIE_sim_time_dep_cs","text":"","code":"DAISIE_sim_time_dep_cs(   total_time,   M,   pars,   replicates,   area_pars,   hyper_pars,   nonoceanic_pars,   sample_freq,   island_ontogeny,   sea_level,   peak,   Amax,   Amin,   extcutoff,   cond,   verbose )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_time_dep_cs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulates island replicates with an clade-specific (CS) diversity-dependent\ntime-dependent process — DAISIE_sim_time_dep_cs","text":"total_time Numeric defining length simulation time units. M Numeric defining size mainland pool, .e. number species can potentially colonize island. pars numeric vector containing model parameters: pars[1]: lambda^c (cladogenesis rate) pars[2]: mu (extinction rate) pars[3]: K (carrying capacity), set K=Inf diversity   independence. pars[4]: gamma (immigration rate) pars[5]: lambda^(anagenesis rate) pars[6]: lambda^c (cladogenesis rate) either type 2 species   rate set 2 rate shift model pars[7]: mu (extinction rate) either type 2 species rate   set 2 rate shift model pars[8]: K (carrying capacity) either type 2 species rate   set 2 rate shift model, set K=Inf diversity independence. pars[9]: gamma (immigration rate) either type 2 species   rate set 2 rate shift model pars[10]: lambda^(anagenesis rate) either type 2   species rate set 2 rate shift model Elements 6:10 required type 2 species included rate shift model. DAISIE_sim_relaxed_rate() pars[6] standard deviation gamma distribution relaxed parameter parameter chosen relaxed_par argument mean gamma distribution relaxed parameter. replicates Integer specifying number island replicates simulated. area_pars named list containing area sea level parameters created create_area_pars(): [1]: maximum area [2]: current area [3]: value 0 1 indicating island's history   peak area achieved [4]: total island age [5]: amplitude area fluctuation sea level [6]: frequency sine wave area change sea level [7]: angle slope island hyper_pars named list numeric hyperparameters rate calculations returned create_hyper_pars(): [1]: d scaling parameter exponent calculating   cladogenesis rate [2]: x exponent calculating extinction rate nonoceanic_pars vector length two : [1]: probability sampling species mainland [2]: probability species sampled mainland   nonendemic sample_freq Numeric specifing number units times divided plotting purposes. Larger values lead plots higher resolution, also run slower. island_ontogeny DAISIE_sim_time_dep(), DAISIE_ML_CS plotting string describing type island ontogeny. Can \"const\", \"beta\" beta function describing area time.  functions numeric describing type island ontogeny. Can 0 constant, 1 beta function describing area time. ML functions island_ontogeny = NA assumes constant ontogeny. Time dependent estimation yet available development still ongoing. return error called case. sea_level DAISIE_sim_time_dep() plotting string describing type sea level. Can \"const\" \"sine\" sine function describing area time.  functions numeric describing type sea level. Can 0 constant, 1 sine function describing area time. peak numeric value specifying peakiness (shaprness) ontogeny curve. Higher values imply peakier ontogeny. value internally calculated calc_peak() given area present area_pars. Amax numeric value maximum island area simulation. Amin numeric value minimum island area simulation. extcutoff numeric cutoff maximum extinction rate preventing large slowing simulation. cond cond = 0 : conditioning island age  cond = 1 : conditioning island age non-extinction island biota . cond > 1 : conditioning island age least cond colonizations island. last option yet available IW model verbose numeric vector length 1, simulations `DAISIEdataprep()` can `1` `0`, `1` gives intermediate output printed. ML functions numeric determining intermediate output printed. default: `0` print, `1` prints initial likelihood settings selected (parameters optimised, fixed shifted), `2` prints `1 also intermediate output parameters loglikelihood, `3` `2` prints intermediate progress likelihood computation.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_time_dep_cs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Simulates island replicates with an clade-specific (CS) diversity-dependent\ntime-dependent process — DAISIE_sim_time_dep_cs","text":"list. highest level least corresponds individual replicate. See return `DAISIE_sim_time_dep()` details.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_time_dep_gw.html","id":null,"dir":"Reference","previous_headings":"","what":"Simulates island replicates with an guild-wide (GW) diversity-dependent\ntime-dependent process — DAISIE_sim_time_dep_gw","title":"Simulates island replicates with an guild-wide (GW) diversity-dependent\ntime-dependent process — DAISIE_sim_time_dep_gw","text":"Simulates island replicates guild-wide (GW) diversity-dependent time-dependent process","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_time_dep_gw.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulates island replicates with an guild-wide (GW) diversity-dependent\ntime-dependent process — DAISIE_sim_time_dep_gw","text":"","code":"DAISIE_sim_time_dep_gw(   total_time,   M,   pars,   replicates,   area_pars,   hyper_pars,   nonoceanic_pars,   num_guilds,   sample_freq,   island_ontogeny,   sea_level,   peak,   Amax,   Amin,   extcutoff,   verbose )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_time_dep_gw.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulates island replicates with an guild-wide (GW) diversity-dependent\ntime-dependent process — DAISIE_sim_time_dep_gw","text":"total_time Numeric defining length simulation time units. M Numeric defining size mainland pool, .e. number species can potentially colonize island. pars numeric vector containing model parameters: pars[1]: lambda^c (cladogenesis rate) pars[2]: mu (extinction rate) pars[3]: K (carrying capacity), set K=Inf diversity   independence. pars[4]: gamma (immigration rate) pars[5]: lambda^(anagenesis rate) pars[6]: lambda^c (cladogenesis rate) either type 2 species   rate set 2 rate shift model pars[7]: mu (extinction rate) either type 2 species rate   set 2 rate shift model pars[8]: K (carrying capacity) either type 2 species rate   set 2 rate shift model, set K=Inf diversity independence. pars[9]: gamma (immigration rate) either type 2 species   rate set 2 rate shift model pars[10]: lambda^(anagenesis rate) either type 2   species rate set 2 rate shift model Elements 6:10 required type 2 species included rate shift model. DAISIE_sim_relaxed_rate() pars[6] standard deviation gamma distribution relaxed parameter parameter chosen relaxed_par argument mean gamma distribution relaxed parameter. replicates Integer specifying number island replicates simulated. area_pars named list containing area sea level parameters created create_area_pars(): [1]: maximum area [2]: current area [3]: value 0 1 indicating island's history   peak area achieved [4]: total island age [5]: amplitude area fluctuation sea level [6]: frequency sine wave area change sea level [7]: angle slope island hyper_pars named list numeric hyperparameters rate calculations returned create_hyper_pars(): [1]: d scaling parameter exponent calculating   cladogenesis rate [2]: x exponent calculating extinction rate nonoceanic_pars vector length two : [1]: probability sampling species mainland [2]: probability species sampled mainland   nonendemic num_guilds number guilds mainland. number mainland species divided number guilds divdepmodel = \"GW\" sample_freq Numeric specifing number units times divided plotting purposes. Larger values lead plots higher resolution, also run slower. island_ontogeny DAISIE_sim_time_dep(), DAISIE_ML_CS plotting string describing type island ontogeny. Can \"const\", \"beta\" beta function describing area time.  functions numeric describing type island ontogeny. Can 0 constant, 1 beta function describing area time. ML functions island_ontogeny = NA assumes constant ontogeny. Time dependent estimation yet available development still ongoing. return error called case. sea_level DAISIE_sim_time_dep() plotting string describing type sea level. Can \"const\" \"sine\" sine function describing area time.  functions numeric describing type sea level. Can 0 constant, 1 sine function describing area time. peak numeric value specifying peakiness (shaprness) ontogeny curve. Higher values imply peakier ontogeny. value internally calculated calc_peak() given area present area_pars. Amax numeric value maximum island area simulation. Amin numeric value minimum island area simulation. extcutoff numeric cutoff maximum extinction rate preventing large slowing simulation. verbose numeric vector length 1, simulations `DAISIEdataprep()` can `1` `0`, `1` gives intermediate output printed. ML functions numeric determining intermediate output printed. default: `0` print, `1` prints initial likelihood settings selected (parameters optimised, fixed shifted), `2` prints `1 also intermediate output parameters loglikelihood, `3` `2` prints intermediate progress likelihood computation.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_time_dep_gw.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Simulates island replicates with an guild-wide (GW) diversity-dependent\ntime-dependent process — DAISIE_sim_time_dep_gw","text":"list. highest level least corresponds individual replicate. See return `DAISIE_sim_time_dep()` details.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_time_dep_iw.html","id":null,"dir":"Reference","previous_headings":"","what":"Simulates island replicates with an island-wide (IW) diversity-dependent\ntime-dependent process — DAISIE_sim_time_dep_iw","title":"Simulates island replicates with an island-wide (IW) diversity-dependent\ntime-dependent process — DAISIE_sim_time_dep_iw","text":"Simulates island replicates island-wide (IW) diversity-dependent time-dependent process","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_time_dep_iw.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulates island replicates with an island-wide (IW) diversity-dependent\ntime-dependent process — DAISIE_sim_time_dep_iw","text":"","code":"DAISIE_sim_time_dep_iw(   total_time,   M,   pars,   replicates,   area_pars,   hyper_pars,   nonoceanic_pars,   sample_freq,   island_ontogeny,   sea_level,   peak,   Amax,   Amin,   extcutoff,   cond,   verbose )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_time_dep_iw.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulates island replicates with an island-wide (IW) diversity-dependent\ntime-dependent process — DAISIE_sim_time_dep_iw","text":"total_time Numeric defining length simulation time units. M Numeric defining size mainland pool, .e. number species can potentially colonize island. pars numeric vector containing model parameters: pars[1]: lambda^c (cladogenesis rate) pars[2]: mu (extinction rate) pars[3]: K (carrying capacity), set K=Inf diversity   independence. pars[4]: gamma (immigration rate) pars[5]: lambda^(anagenesis rate) pars[6]: lambda^c (cladogenesis rate) either type 2 species   rate set 2 rate shift model pars[7]: mu (extinction rate) either type 2 species rate   set 2 rate shift model pars[8]: K (carrying capacity) either type 2 species rate   set 2 rate shift model, set K=Inf diversity independence. pars[9]: gamma (immigration rate) either type 2 species   rate set 2 rate shift model pars[10]: lambda^(anagenesis rate) either type 2   species rate set 2 rate shift model Elements 6:10 required type 2 species included rate shift model. DAISIE_sim_relaxed_rate() pars[6] standard deviation gamma distribution relaxed parameter parameter chosen relaxed_par argument mean gamma distribution relaxed parameter. replicates Integer specifying number island replicates simulated. area_pars named list containing area sea level parameters created create_area_pars(): [1]: maximum area [2]: current area [3]: value 0 1 indicating island's history   peak area achieved [4]: total island age [5]: amplitude area fluctuation sea level [6]: frequency sine wave area change sea level [7]: angle slope island hyper_pars named list numeric hyperparameters rate calculations returned create_hyper_pars(): [1]: d scaling parameter exponent calculating   cladogenesis rate [2]: x exponent calculating extinction rate nonoceanic_pars vector length two : [1]: probability sampling species mainland [2]: probability species sampled mainland   nonendemic sample_freq Numeric specifing number units times divided plotting purposes. Larger values lead plots higher resolution, also run slower. island_ontogeny DAISIE_sim_time_dep(), DAISIE_ML_CS plotting string describing type island ontogeny. Can \"const\", \"beta\" beta function describing area time.  functions numeric describing type island ontogeny. Can 0 constant, 1 beta function describing area time. ML functions island_ontogeny = NA assumes constant ontogeny. Time dependent estimation yet available development still ongoing. return error called case. sea_level DAISIE_sim_time_dep() plotting string describing type sea level. Can \"const\" \"sine\" sine function describing area time.  functions numeric describing type sea level. Can 0 constant, 1 sine function describing area time. peak numeric value specifying peakiness (shaprness) ontogeny curve. Higher values imply peakier ontogeny. value internally calculated calc_peak() given area present area_pars. Amax numeric value maximum island area simulation. Amin numeric value minimum island area simulation. extcutoff numeric cutoff maximum extinction rate preventing large slowing simulation. cond cond = 0 : conditioning island age  cond = 1 : conditioning island age non-extinction island biota . cond > 1 : conditioning island age least cond colonizations island. last option yet available IW model verbose numeric vector length 1, simulations `DAISIEdataprep()` can `1` `0`, `1` gives intermediate output printed. ML functions numeric determining intermediate output printed. default: `0` print, `1` prints initial likelihood settings selected (parameters optimised, fixed shifted), `2` prints `1 also intermediate output parameters loglikelihood, `3` `2` prints intermediate progress likelihood computation.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_time_dep_iw.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Simulates island replicates with an island-wide (IW) diversity-dependent\ntime-dependent process — DAISIE_sim_time_dep_iw","text":"list. highest level least corresponds individual replicate. See return `DAISIE_sim_time_dep()` details.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_trait_dep.html","id":null,"dir":"Reference","previous_headings":"","what":"Simulate islands with given trait-dependent parameters. — DAISIE_sim_trait_dep","title":"Simulate islands with given trait-dependent parameters. — DAISIE_sim_trait_dep","text":"function simulates islands given cladogenesis, extinction, K, immigration anagenesis parameters binary states. Returns R list object contains simulated islands","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_trait_dep.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulate islands with given trait-dependent parameters. — DAISIE_sim_trait_dep","text":"","code":"DAISIE_sim_trait_dep(   time,   M,   pars,   replicates,   divdepmodel = \"CS\",   sample_freq = 25,   plot_sims = TRUE,   island_ontogeny = \"const\",   sea_level = \"const\",   hyper_pars = create_hyper_pars(d = 0, x = 0),   area_pars = DAISIE::create_area_pars(max_area = 1, current_area = 1,     proportional_peak_t = 0, total_island_age = 0, sea_level_amplitude = 0,     sea_level_frequency = 0, island_gradient_angle = 0),   extcutoff = 1000,   cond = 0,   verbose = TRUE,   trait_pars = NULL,   ... )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_trait_dep.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulate islands with given trait-dependent parameters. — DAISIE_sim_trait_dep","text":"time Numeric defining length simulation time units. example, island known 4 million years old, setting time = 4 simulate entire life span island; setting time = 2 stop simulation mid-life island. M Numeric defining size mainland pool, .e. number species can potentially colonize island. pars numeric vector containing model parameters: pars[1]: lambda^c (cladogenesis rate) pars[2]: mu (extinction rate) pars[3]: K (carrying capacity), set K=Inf diversity   independence. pars[4]: gamma (immigration rate) pars[5]: lambda^(anagenesis rate) pars[6]: lambda^c (cladogenesis rate) either type 2 species   rate set 2 rate shift model pars[7]: mu (extinction rate) either type 2 species rate   set 2 rate shift model pars[8]: K (carrying capacity) either type 2 species rate   set 2 rate shift model, set K=Inf diversity independence. pars[9]: gamma (immigration rate) either type 2 species   rate set 2 rate shift model pars[10]: lambda^(anagenesis rate) either type 2   species rate set 2 rate shift model Elements 6:10 required type 2 species included rate shift model. DAISIE_sim_relaxed_rate() pars[6] standard deviation gamma distribution relaxed parameter parameter chosen relaxed_par argument mean gamma distribution relaxed parameter. replicates Integer specifying number island replicates simulated. divdepmodel Option divdepmodel = 'CS' runs model clade-specific carrying capacity, diversity-dependence operates within single clades, .e. among species originating mainland colonist. Option divdepmodel = 'IW' runs model island-wide carrying capacity, diversity-dependence operates within among clades. Option divdepmodel = 'GW' runs model diversity-dependence operates within guild. sample_freq Numeric specifing number units times divided plotting purposes. Larger values lead plots higher resolution, also run slower. plot_sims Default = TRUE plots species--time (STT) plots. detects many types species present. one type species present, STT plotted species. two types present, three plots produced: STT , STT type 1 STT type 2. island_ontogeny DAISIE_sim_time_dep(), DAISIE_ML_CS plotting string describing type island ontogeny. Can \"const\", \"beta\" beta function describing area time.  functions numeric describing type island ontogeny. Can 0 constant, 1 beta function describing area time. ML functions island_ontogeny = NA assumes constant ontogeny. Time dependent estimation yet available development still ongoing. return error called case. sea_level DAISIE_sim_time_dep() plotting string describing type sea level. Can \"const\" \"sine\" sine function describing area time.  functions numeric describing type sea level. Can 0 constant, 1 sine function describing area time. hyper_pars named list numeric hyperparameters rate calculations returned create_hyper_pars(): [1]: d scaling parameter exponent calculating   cladogenesis rate [2]: x exponent calculating extinction rate area_pars named list containing area sea level parameters created create_area_pars(): [1]: maximum area [2]: current area [3]: value 0 1 indicating island's history   peak area achieved [4]: total island age [5]: amplitude area fluctuation sea level [6]: frequency sine wave area change sea level [7]: angle slope island extcutoff numeric cutoff maximum extinction rate preventing large slowing simulation. cond cond = 0 : conditioning island age  cond = 1 : conditioning island age non-extinction island biota . cond > 1 : conditioning island age least cond colonizations island. last option yet available IW model verbose numeric vector length 1, simulations `DAISIEdataprep()` can `1` `0`, `1` gives intermediate output printed. ML functions numeric determining intermediate output printed. default: `0` print, `1` prints initial likelihood settings selected (parameters optimised, fixed shifted), `2` prints `1 also intermediate output parameters loglikelihood, `3` `2` prints intermediate progress likelihood computation. trait_pars named list containing diversification rates considering   two trait states created create_trait_pars: [1]:numeric per capita transition rate state1 [2]:numeric per capita immigration rate state2 [3]:numeric per capita extinction rate state2 [4]:numeric per capita anagenesis rate state2 [5]:numeric per capita cladogenesis rate state2 [6]:numeric per capita transition rate state2 [7]:numeric number species trait state 2    mainland ... arguments pass plotting functions.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_trait_dep.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Simulate islands with given trait-dependent parameters. — DAISIE_sim_trait_dep","text":"list. highest level least corresponds individual replciate. first element replicate composed island information containing: $island_age: numeric island age. $not_present: numeric number mainland lineages   present island. $stt_all: STT table species island     (nI - number non-endemic species; nA - number anagenetic species,     nC - number cladogenetic species, present - number independent     colonisations present) $brts_table: simulations \"IW\". Table containing information order events data, use maximum likelihood optimization.). subsequent elements list pertaining replcate contain information single colonist lineage island 4 components: $branching_times: island age stem age     population/species case Non-endemic, Non-endemic_MaxAge     Endemic anagenetic species. cladogenetic species     island age branching times radiation including     stem age radiation. $stac: integer ranging 1 4   indicating status colonist: $missing_species: number island species sampled particular clade (applicable endemic clades) $type_1or2: whether colonist belongs type 1 type 2","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_trait_dep.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Simulate islands with given trait-dependent parameters. — DAISIE_sim_trait_dep","text":"Valente, L.M., .B. Phillimore R.S. Etienne (2015). Equilibrium non-equilibrium dynamics simultaneously operate Galapagos islands. Ecology Letters 18: 844-852. Hauffe, T., D. Delicado, R.S. Etienne L. Valente (submitted). Lake expansion increases equilibrium diversity via target effect island biogeography.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_trait_dep.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Simulate islands with given trait-dependent parameters. — DAISIE_sim_trait_dep","text":"Luis Valente Albert Phillimore","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_trait_dep_2K.html","id":null,"dir":"Reference","previous_headings":"","what":"Simulate islands with given trait-dependent parameters. — DAISIE_sim_trait_dep_2K","title":"Simulate islands with given trait-dependent parameters. — DAISIE_sim_trait_dep_2K","text":"function simulates islands given cladogenesis, extinction, K, immigration anagenesis parameters. version, rates K trait-dependent. Returns R list object contains simulated islands","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_trait_dep_2K.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulate islands with given trait-dependent parameters. — DAISIE_sim_trait_dep_2K","text":"","code":"DAISIE_sim_trait_dep_2K(   time,   M,   pars,   replicates,   divdepmodel = \"CS\",   sample_freq = 25,   plot_sims = TRUE,   island_ontogeny = \"const\",   sea_level = \"const\",   hyper_pars = create_hyper_pars(d = 0, x = 0),   area_pars = DAISIE::create_area_pars(max_area = 1, current_area = 1,     proportional_peak_t = 0, total_island_age = 0, sea_level_amplitude = 0,     sea_level_frequency = 0, island_gradient_angle = 0),   extcutoff = 1000,   cond = 0,   verbose = TRUE,   trait_pars = NULL,   ... )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_trait_dep_2K.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulate islands with given trait-dependent parameters. — DAISIE_sim_trait_dep_2K","text":"time Numeric defining length simulation time units. example, island known 4 million years old, setting time = 4 simulate entire life span island; setting time = 2 stop simulation mid-life island. M Numeric defining size mainland pool, .e. number species can potentially colonize island. pars numeric vector containing model parameters: pars[1]: lambda^c (cladogenesis rate) pars[2]: mu (extinction rate) pars[3]: K (carrying capacity), set K=Inf diversity   independence. pars[4]: gamma (immigration rate) pars[5]: lambda^(anagenesis rate) pars[6]: lambda^c (cladogenesis rate) either type 2 species   rate set 2 rate shift model pars[7]: mu (extinction rate) either type 2 species rate   set 2 rate shift model pars[8]: K (carrying capacity) either type 2 species rate   set 2 rate shift model, set K=Inf diversity independence. pars[9]: gamma (immigration rate) either type 2 species   rate set 2 rate shift model pars[10]: lambda^(anagenesis rate) either type 2   species rate set 2 rate shift model Elements 6:10 required type 2 species included rate shift model. DAISIE_sim_relaxed_rate() pars[6] standard deviation gamma distribution relaxed parameter parameter chosen relaxed_par argument mean gamma distribution relaxed parameter. replicates Integer specifying number island replicates simulated. divdepmodel Option divdepmodel = 'CS' runs model clade-specific carrying capacity, diversity-dependence operates within single clades, .e. among species originating mainland colonist. Option divdepmodel = 'IW' runs model island-wide carrying capacity, diversity-dependence operates within among clades. Option divdepmodel = 'GW' runs model diversity-dependence operates within guild. sample_freq Numeric specifing number units times divided plotting purposes. Larger values lead plots higher resolution, also run slower. plot_sims Default = TRUE plots species--time (STT) plots. detects many types species present. one type species present, STT plotted species. two types present, three plots produced: STT , STT type 1 STT type 2. island_ontogeny DAISIE_sim_time_dep(), DAISIE_ML_CS plotting string describing type island ontogeny. Can \"const\", \"beta\" beta function describing area time.  functions numeric describing type island ontogeny. Can 0 constant, 1 beta function describing area time. ML functions island_ontogeny = NA assumes constant ontogeny. Time dependent estimation yet available development still ongoing. return error called case. sea_level DAISIE_sim_time_dep() plotting string describing type sea level. Can \"const\" \"sine\" sine function describing area time.  functions numeric describing type sea level. Can 0 constant, 1 sine function describing area time. hyper_pars named list numeric hyperparameters rate calculations returned create_hyper_pars(): [1]: d scaling parameter exponent calculating   cladogenesis rate [2]: x exponent calculating extinction rate area_pars named list containing area sea level parameters created create_area_pars(): [1]: maximum area [2]: current area [3]: value 0 1 indicating island's history   peak area achieved [4]: total island age [5]: amplitude area fluctuation sea level [6]: frequency sine wave area change sea level [7]: angle slope island extcutoff numeric cutoff maximum extinction rate preventing large slowing simulation. cond cond = 0 : conditioning island age  cond = 1 : conditioning island age non-extinction island biota . cond > 1 : conditioning island age least cond colonizations island. last option yet available IW model verbose numeric vector length 1, simulations `DAISIEdataprep()` can `1` `0`, `1` gives intermediate output printed. ML functions numeric determining intermediate output printed. default: `0` print, `1` prints initial likelihood settings selected (parameters optimised, fixed shifted), `2` prints `1 also intermediate output parameters loglikelihood, `3` `2` prints intermediate progress likelihood computation. trait_pars named list containing diversification rates considering   two trait states created create_trait_pars: [1]:numeric per capita transition rate state1 [2]:numeric per capita immigration rate state2 [3]:numeric per capita extinction rate state2 [4]:numeric per capita anagenesis rate state2 [5]:numeric per capita cladogenesis rate state2 [6]:numeric per capita transition rate state2 [7]:numeric number species trait state 2    mainland ... arguments pass plotting functions.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_trait_dep_2K.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Simulate islands with given trait-dependent parameters. — DAISIE_sim_trait_dep_2K","text":"list. highest level least corresponds individual replciate. first element replicate composed island information containing: $island_age: numeric island age. $not_present: numeric number mainland lineages   present island. $stt_all: STT table species island     (nI - number non-endemic species; nA - number anagenetic species,     nC - number cladogenetic species, present - number independent     colonisations present) $brts_table: simulations \"IW\". Table containing information order events data, use maximum likelihood optimization.). subsequent elements list pertaining replcate contain information single colonist lineage island 4 components: $branching_times: island age stem age     population/species case Non-endemic, Non-endemic_MaxAge     Endemic anagenetic species. cladogenetic species     island age branching times radiation including     stem age radiation. $stac: integer ranging 1 4   indicating status colonist: $missing_species: number island species sampled particular clade (applicable endemic clades) $type_1or2: whether colonist belongs type 1 type 2","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_trait_dep_2K.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Simulate islands with given trait-dependent parameters. — DAISIE_sim_trait_dep_2K","text":"Valente, L.M., .B. Phillimore R.S. Etienne (2015). Equilibrium non-equilibrium dynamics simultaneously operate Galapagos islands. Ecology Letters 18: 844-852. Hauffe, T., D. Delicado, R.S. Etienne L. Valente (submitted). Lake expansion increases equilibrium diversity via target effect island biogeography.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_trait_dep_2K.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Simulate islands with given trait-dependent parameters. — DAISIE_sim_trait_dep_2K","text":"Luis Valente Albert Phillimore","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_update_state_cr.html","id":null,"dir":"Reference","previous_headings":"","what":"Updates state of island given sampled event for a constant rate case. — DAISIE_sim_update_state_cr","title":"Updates state of island given sampled event for a constant rate case. — DAISIE_sim_update_state_cr","text":"Makes event happen updating island species matrix species IDs. event happens determined sampling algorithm.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_update_state_cr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Updates state of island given sampled event for a constant rate case. — DAISIE_sim_update_state_cr","text":"","code":"DAISIE_sim_update_state_cr(   timeval,   total_time,   possible_event,   maxspecID,   mainland_spec,   island_spec,   stt_table )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_update_state_cr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Updates state of island given sampled event for a constant rate case. — DAISIE_sim_update_state_cr","text":"timeval Numeric defining current time simulation. total_time Numeric defining length simulation time units. possible_event Numeric defining event happen. maxspecID Current species IDs. mainland_spec Number mainland species. island_spec Matrix current state simulation containing number species. stt_table Matrix number species time step.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_update_state_cr.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Updates state of island given sampled event for a constant rate case. — DAISIE_sim_update_state_cr","text":"updated state system, list island_spec matrix, integer maxspecID recent ID species stt_table, matrix current species time table.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_update_state_time_dep.html","id":null,"dir":"Reference","previous_headings":"","what":"Updates state of island given sampled event — DAISIE_sim_update_state_time_dep","title":"Updates state of island given sampled event — DAISIE_sim_update_state_time_dep","text":"Makes event happen updating island species matrix species IDs. event happens determined sampling algorithm.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_update_state_time_dep.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Updates state of island given sampled event — DAISIE_sim_update_state_time_dep","text":"","code":"DAISIE_sim_update_state_time_dep(   timeval,   total_time,   possible_event,   maxspecID,   mainland_spec,   island_spec,   stt_table,   rates,   max_rates )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_update_state_time_dep.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Updates state of island given sampled event — DAISIE_sim_update_state_time_dep","text":"timeval Numeric defining current time simulation. total_time Numeric defining length simulation time units. possible_event Numeric defining event happen. maxspecID Current species IDs. mainland_spec Number mainland species. island_spec Matrix current state simulation containing number species. stt_table Matrix number species time step. rates named list numeric rates returned update_rates(). max_rates named list numeric max rates returned update_max_rates().","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_update_state_time_dep.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Updates state of island given sampled event — DAISIE_sim_update_state_time_dep","text":"updated state system, list island_spec matrix, integer maxspecID recent ID species stt_table, matrix current species time table.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_update_state_trait_dep.html","id":null,"dir":"Reference","previous_headings":"","what":"Updates state of island given sampled event with two trait states. — DAISIE_sim_update_state_trait_dep","title":"Updates state of island given sampled event with two trait states. — DAISIE_sim_update_state_trait_dep","text":"Makes event happen updating island species matrix species IDs. event happens determined sampling algorithm.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_update_state_trait_dep.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Updates state of island given sampled event with two trait states. — DAISIE_sim_update_state_trait_dep","text":"","code":"DAISIE_sim_update_state_trait_dep(   timeval,   total_time,   possible_event,   maxspecID,   mainland_spec,   island_spec,   stt_table,   trait_pars )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_update_state_trait_dep.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Updates state of island given sampled event with two trait states. — DAISIE_sim_update_state_trait_dep","text":"timeval Numeric defining current time simulation. total_time Numeric defining length simulation time units. possible_event Numeric defining event happen. maxspecID Current species IDs. mainland_spec Number mainland species. island_spec Matrix current state simulation containing number species. stt_table Matrix number species time step. trait_pars named list containing diversification rates considering   two trait states created create_trait_pars: [1]:numeric per capita transition rate state1 [2]:numeric per capita immigration rate state2 [3]:numeric per capita extinction rate state2 [4]:numeric per capita anagenesis rate state2 [5]:numeric per capita cladogenesis rate state2 [6]:numeric per capita transition rate state2 [7]:numeric number species trait state 2    mainland","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_update_state_trait_dep.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Updates state of island given sampled event with two trait states. — DAISIE_sim_update_state_trait_dep","text":"updated state system, list island_spec matrix, integer maxspecID recent ID species stt_table, matrix current species time table.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/Galapagos_datalist.html","id":null,"dir":"Reference","previous_headings":"","what":"Colonization and branching times of 8 terrestrial avifaunal clades in list\nformat, accepted by DAISIE_ML and DAISIE_loglik_all — Galapagos_datalist","title":"Colonization and branching times of 8 terrestrial avifaunal clades in list\nformat, accepted by DAISIE_ML and DAISIE_loglik_all — Galapagos_datalist","text":"list containing colonization branching times terrestrial avifauna Galapagos distinction made types colonists. list can generated using DAISIE_dataprep function, converts user-specified data table data object, object can course also entered directly. R list object following elements. first element list two components: $island_age - island age $not_present - number mainland lineages present island  following 8 elements list contains information single colonist lineage island 5 components:$colonist_name - name species clade colonized island $branching_times - island age followed stem age population/species case Non-endemic, Non-endemic_MaxAge species Endemic species close relatives island. endemic clades one species island (cladogenetic clades/ radiations) island age followed branching times island cladeincluding stem age clade.$stac - status colonist  * Non_endemic_MaxAge: 1  * Endemic: 2  * Endemic&Non_Endemic: 3  * Non_endemic: 4 $missing_species - number island species sampled particular clade (applicable endemic clades) $type1or2 - whether colonist belongs type 1 type 2. dataset equal 1.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/Galapagos_datalist.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Colonization and branching times of 8 terrestrial avifaunal clades in list\nformat, accepted by DAISIE_ML and DAISIE_loglik_all — Galapagos_datalist","text":"list 9 elements first contains 2 elements following 8 containing 5 components.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/Galapagos_datalist.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Colonization and branching times of 8 terrestrial avifaunal clades in list\nformat, accepted by DAISIE_ML and DAISIE_loglik_all — Galapagos_datalist","text":"Valente, L.M., .B. Phillimore R.S. Etienne (2015). Equilibrium non-equilibrium dynamics simultaneously operate Galapagos islands. Ecology Letters 18: 844-852.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/Galapagos_datalist_2types.html","id":null,"dir":"Reference","previous_headings":"","what":"Colonization and branching times of 8 terrestrial avifaunal clades in list\nformat, accepted by DAISIE_ML and DAISIE_loglik_all — Galapagos_datalist_2types","title":"Colonization and branching times of 8 terrestrial avifaunal clades in list\nformat, accepted by DAISIE_ML and DAISIE_loglik_all — Galapagos_datalist_2types","text":"list containing colonization branching times terrestrial avifauna Galapagos. list can generated using DAISIE_dataprep function, converts user-specified data table data object, object can course also entered directly. R list object following elements. first element list three components: $island_age - island age $not_present_type1 - number mainland lineages type 1 present island $not_present_type2 - number mainland lineages type 2 present island  following 8 elements list contains information single colonist lineage island 5 components:$colonist_name - name species clade colonized island $branching_times - island age followed stem age population/species case Non-endemic, Non-endemic_MaxAge species Endemic species close relatives island. endemic clades one species island (cladogenetic clades/ radiations) island age followed branching times island cladeincluding stem age clade.$stac - status colonist  * Non_endemic_MaxAge: 1  * Endemic: 2  * Endemic&Non_Endemic: 3  * Non_endemic: 4 $missing_species - number island species sampled particular clade (applicable endemic clades) $type1or2 - whether colonist belongs type 1 type 2. dataset finches type 2","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/Galapagos_datalist_2types.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Colonization and branching times of 8 terrestrial avifaunal clades in list\nformat, accepted by DAISIE_ML and DAISIE_loglik_all — Galapagos_datalist_2types","text":"list 9 elements first contains 3 elements following 8 containing 5 components.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/Galapagos_datalist_2types.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Colonization and branching times of 8 terrestrial avifaunal clades in list\nformat, accepted by DAISIE_ML and DAISIE_loglik_all — Galapagos_datalist_2types","text":"Valente, L.M., .B. Phillimore R.S. Etienne (2015). Equilibrium non-equilibrium dynamics simultaneously operate Galapagos islands. Ecology Letters 18: 844-852.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/Galapagos_datatable.html","id":null,"dir":"Reference","previous_headings":"","what":"Colonization and branching times of 8 terrestrial avifaunal Galápagos clades in table\nformat. — Galapagos_datatable","title":"Colonization and branching times of 8 terrestrial avifaunal Galápagos clades in table\nformat. — Galapagos_datatable","text":"table containing colonization branching times terrestrial avifauna Galápagos. row table represents independent colonisation event. table four columns. $Clade_name - name independent colonization event $Status - One following categories:  * Non_endemic: non-endemic island species approximate time colonisation known  * Non_endemic_MaxAge: non-endemic island species colonisation time unknown  * Endemic: endemic species approximate colonisation time known  * \"Endemic_MaxAge\": applies endemic species endemic clades cases colonisation time unknown, user wants specify upper bound colonisation. example apply endemic species recently gone extinct anthropogenic causes, included phylogeny (\"NA\" given branching times column). also apply insular radiations long stem branches, time first cladogenetic event known, precise time colonisation . * Endemic&Non_Endemic: endemic clade mainland ancestor re-colonized $Missing_species - Number island species sampled particular clade (applicable endemic clades)$Branching_times - Stem age population/species case \"Non_endemic\",  \"Non_endemic_MaxAge\" \"Endemic\" species extant close relatives island.  Set \"NA\" colonisation time unknown upper bound known. \"Endemic\" cladogenetic species branching times radiation, including stem age radiation (colonisation time estimate).","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/Galapagos_datatable.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Colonization and branching times of 8 terrestrial avifaunal Galápagos clades in table\nformat. — Galapagos_datatable","text":"table 8 rows 4 columns.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/Galapagos_datatable.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Colonization and branching times of 8 terrestrial avifaunal Galápagos clades in table\nformat. — Galapagos_datatable","text":"Valente, L.M., .B. Phillimore R.S. Etienne (2015). Equilibrium non-equilibrium dynamics simultaneously operate Galapagos islands. Ecology Letters 18: 844-852.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/Macaronesia_datalist.html","id":null,"dir":"Reference","previous_headings":"","what":"Colonization and branching times of terrestrial avifaunal clades from\nAzores, Canary Islands, Cape Verde and Madeira in list format, accepted by\nDAISIE_ML and DAISIE_loglik_all — Macaronesia_datalist","title":"Colonization and branching times of terrestrial avifaunal clades from\nAzores, Canary Islands, Cape Verde and Madeira in list format, accepted by\nDAISIE_ML and DAISIE_loglik_all — Macaronesia_datalist","text":"list containing colonization branching times terrestrial avifauna 4 archipelagos: Azores, Canary Islands, Cape Verde Madeira. R list object 4 main elements corresponding archipelagos (e.g. Macaronesia_datalist[[1]] calls Azores data). four elements made several elemants: first element list archipelago two components: $island_age - island age $not_present - number mainland lineages present island  following elements list contains information single colonist lineage island 5 components:$colonist_name - name species clade colonized island $branching_times - island age followed stem age population/species case Non-endemic, Non-endemic_MaxAge species Endemic species close relatives island. endemic clades one species island (cladogenetic clades/ radiations) island age followed branching times island clade including stem age clade.  * Non_endemic_MaxAge: 1 * Endemic: 2  * Endemic&Non_Endemic: 3  * Non_endemic: 4  * Endemic_MaxAge: 5 $missing_species - number island species sampled particular clade (applicable endemic clades) $type1or2 - whether colonist belongs type 1 type 2. dataset equal 1.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/Macaronesia_datalist.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Colonization and branching times of terrestrial avifaunal clades from\nAzores, Canary Islands, Cape Verde and Madeira in list format, accepted by\nDAISIE_ML and DAISIE_loglik_all — Macaronesia_datalist","text":"list 4 main elements archipelago. element several sub-elements.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/Macaronesia_datalist.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Colonization and branching times of terrestrial avifaunal clades from\nAzores, Canary Islands, Cape Verde and Madeira in list format, accepted by\nDAISIE_ML and DAISIE_loglik_all — Macaronesia_datalist","text":"Valente L., Illera J.C, Havenstein K., Pallien T., Etienne R.S., Tiedemann R. Equilibrium bird species diversity Atlantic islands. 2017 Current Biology, 27, 1660-1666.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/NewZealand_birds_datalist.html","id":null,"dir":"Reference","previous_headings":"","what":"Colonization and branching times of New Zealand birds. — NewZealand_birds_datalist","title":"Colonization and branching times of New Zealand birds. — NewZealand_birds_datalist","text":"list containing colonization branching times birds New Zealand. Main dataset used Valente, Etienne, Garcia-R (2019) Current Biology. Island age 52 Myr mainland pool size 1000 species.  first element list two components: $island_age - island age $not_present - number mainland lineages present island  following elements list contain information single colonist lineage island 5 components:$colonist_name - name species clade colonized island $branching_times - island age followed stem age population/species case Non-endemic, Non-endemic_MaxAge species Endemic species close relatives island. endemic clades one species island (cladogenetic clades/ radiations) island age followed branching times island clade including stem age clade.$stac - status colonist  * Non_endemic_MaxAge: 1  * Endemic: 2  * Endemic&Non_Endemic: 3  * Non_endemic: 4  * Endemic_MaxAge: 5 6 $missing_species - number island species sampled particular clade (applicable endemic clades) $type1or2 - whether colonist belongs type 1 type 2. dataset equal 1.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/NewZealand_birds_datalist.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Colonization and branching times of New Zealand birds. — NewZealand_birds_datalist","text":"list 40 elements, first contains 2 elements following 39 containing 5 components.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/NewZealand_birds_datalist.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Colonization and branching times of New Zealand birds. — NewZealand_birds_datalist","text":"Valente L, Etienne RS, Garcia-R JC (2019) Deep Macroevolutionary Impact Humans New Zealand’s Unique Avifauna. Current Biology, 29, 2563–2569.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/add_column_to_dataframe.html","id":null,"dir":"Reference","previous_headings":"","what":"Add a column to a data frame — add_column_to_dataframe","title":"Add a column to a data frame — add_column_to_dataframe","text":"Add column data frame","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/add_column_to_dataframe.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add a column to a data frame — add_column_to_dataframe","text":"","code":"add_column_to_dataframe(df, position, column_to_insert)"},{"path":"https://rsetienne.github.io/DAISIE/reference/add_column_to_dataframe.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add a column to a data frame — add_column_to_dataframe","text":"df data frame add column position location data frame insert column. Position can also name column column_to_insert elements column insert. column name, name copied data frame. Id name, get name \"nc\".","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/add_column_to_dataframe.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add a column to a data frame — add_column_to_dataframe","text":"data frame column inserted","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/archipelago_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Physical data on 41 archipelagos — archipelago_data","title":"Physical data on 41 archipelagos — archipelago_data","text":"dataframe subsequent columns name archipelago (Archipelago) area archipelago (Area), age (Age) distance mainland (Distance)","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/archipelago_data.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Physical data on 41 archipelagos — archipelago_data","text":"dataframe containing information archipelago name, area, age distance mainland","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/archipelago_data.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Physical data on 41 archipelagos — archipelago_data","text":"Valente L, Phillimore AB, Melo M, Warren BH, Clegg SM, Havenstein K,  Tiedemann R, Illera JC, Thébaud C, Aschenbach T, Etienne RS. simple dynamic model  explains island bird diversity worldwide (2020) Nature, 579, 92-96","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/archipelagos41.html","id":null,"dir":"Reference","previous_headings":"","what":"DAISIE datalist object including bird phylogenetic data and\nphysical data for 41 archipelagos — archipelagos41","title":"DAISIE datalist object including bird phylogenetic data and\nphysical data for 41 archipelagos — archipelagos41","text":"datalist 41 items representing 41 archipelagos. archipelago can called separately using archipelagos41[[x]] x number 1 41. Using archipelagos41[[x]][[1]] show just top part archipelago item archipelago name physical features displayed. structure archipelagos regular DAISIE datalist generated using DAISIE_dataprep.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/archipelagos41.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"DAISIE datalist object including bird phylogenetic data and\nphysical data for 41 archipelagos — archipelagos41","text":"datalist containing data 41 archipelagos studied Valente et al 2020 (Main Dataset D1). Contains colonisation branching times bird species archipelagos. also contains information archipelago name, area, age distance nearest mainland.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/archipelagos41.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"DAISIE datalist object including bird phylogenetic data and\nphysical data for 41 archipelagos — archipelagos41","text":"Valente L, Phillimore AB, Melo M, Warren BH, Clegg SM, Havenstein K,  Tiedemann R, Illera JC, Thébaud C, Aschenbach T, Etienne RS. simple dynamic model  explains island bird diversity worldwide (2020) Nature, 579, 92-96","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/are_rates.html","id":null,"dir":"Reference","previous_headings":"","what":"Determines if object rates are rates — are_rates","title":"Determines if object rates are rates — are_rates","text":"Determines object rates rates","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/are_rates.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Determines if object rates are rates — are_rates","text":"","code":"are_rates(rates)"},{"path":"https://rsetienne.github.io/DAISIE/reference/are_rates.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Determines if object rates are rates — are_rates","text":"rates named list numeric rates returned update_rates().","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/are_rates.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Determines if object rates are rates — are_rates","text":"TRUE object rates list rates","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/calc_Abeta.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculates the area at a point in time from a beta function — calc_Abeta","title":"Calculates the area at a point in time from a beta function — calc_Abeta","text":"Calculates area point time beta function","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/calc_Abeta.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculates the area at a point in time from a beta function — calc_Abeta","text":"","code":"calc_Abeta(proptime, proptime_max, peak, Amax)"},{"path":"https://rsetienne.github.io/DAISIE/reference/calc_Abeta.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculates the area at a point in time from a beta function — calc_Abeta","text":"proptime numeric 0 1. proportion time elapsed simulation, relation total island age (NB: simulation time, island age). proptime_max numeric 0 1. proportional_peak_t. Indicates, proportion total island age ontogeny peak occur (.e. 0.5 means peak halfway time). peak numeric value specifying peakiness (shaprness) ontogeny curve. Higher values imply peakier ontogeny. value internally calculated calc_peak() given area present area_pars. Amax numeric value maximum island area simulation.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/calc_Abeta.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculates the area at a point in time from a beta function — calc_Abeta","text":"Numeric","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/calc_Abeta.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculates the area at a point in time from a beta function — calc_Abeta","text":"Joshua Lambert, Pedro Neves, Shu Xie","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/calc_next_timeval.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculates when the next timestep will be. — calc_next_timeval","title":"Calculates when the next timestep will be. — calc_next_timeval","text":"Calculates next timestep .","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/calc_next_timeval.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculates when the next timestep will be. — calc_next_timeval","text":"","code":"calc_next_timeval(max_rates, timeval)"},{"path":"https://rsetienne.github.io/DAISIE/reference/calc_next_timeval.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculates when the next timestep will be. — calc_next_timeval","text":"max_rates named list max rates returned update_rates. timeval current time simulation","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/calc_next_timeval.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculates when the next timestep will be. — calc_next_timeval","text":"named list numeric vector containing time next timestep change time.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/calc_next_timeval.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculates when the next timestep will be. — calc_next_timeval","text":"Joshua Lambert, Pedro Neves, Shu Xie","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/calc_next_timeval_shift.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculates when the next timestep will be, and if a shift has occured. — calc_next_timeval_shift","title":"Calculates when the next timestep will be, and if a shift has occured. — calc_next_timeval_shift","text":"Calculates next timestep , shift occured.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/calc_next_timeval_shift.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculates when the next timestep will be, and if a shift has occured. — calc_next_timeval_shift","text":"","code":"calc_next_timeval_shift(max_rates, timeval, dynamic_shift_times)"},{"path":"https://rsetienne.github.io/DAISIE/reference/calc_next_timeval_shift.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculates when the next timestep will be, and if a shift has occured. — calc_next_timeval_shift","text":"max_rates named list max rates returned update_rates. timeval current time simulation dynamic_shift_times numeric vector times rate shifts.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/calc_next_timeval_shift.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculates when the next timestep will be, and if a shift has occured. — calc_next_timeval_shift","text":"named list numeric vector containing time next timestep change time.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/calc_next_timeval_shift.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculates when the next timestep will be, and if a shift has occured. — calc_next_timeval_shift","text":"Joshua Lambert, Pedro Neves, Shu Xie","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/calc_peak.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculates the peak of ontogeny curve (beta function) — calc_peak","title":"Calculates the peak of ontogeny curve (beta function) — calc_peak","text":"Calculates peak ontogeny curve (beta function)","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/calc_peak.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculates the peak of ontogeny curve (beta function) — calc_peak","text":"","code":"calc_peak(total_time, area_pars)"},{"path":"https://rsetienne.github.io/DAISIE/reference/calc_peak.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculates the peak of ontogeny curve (beta function) — calc_peak","text":"total_time Numeric defining length simulation time units. area_pars named list containing area sea level parameters created create_area_pars(): [1]: maximum area [2]: current area [3]: value 0 1 indicating island's history   peak area achieved [4]: total island age [5]: amplitude area fluctuation sea level [6]: frequency sine wave area change sea level [7]: angle slope island","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/calc_peak.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculates the peak of ontogeny curve (beta function) — calc_peak","text":"numeric","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/countspecies.html","id":null,"dir":"Reference","previous_headings":"","what":"Count the number of species — countspecies","title":"Count the number of species — countspecies","text":"Count number species","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/countspecies.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count the number of species — countspecies","text":"","code":"countspecies(datalistelement)"},{"path":"https://rsetienne.github.io/DAISIE/reference/countspecies.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count the number of species — countspecies","text":"datalistelement something","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/countspecies.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count the number of species — countspecies","text":"numeric value","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/create_CS_version.html","id":null,"dir":"Reference","previous_headings":"","what":"Creates the list object for CS_version argument in DAISIE_ML_CS — create_CS_version","title":"Creates the list object for CS_version argument in DAISIE_ML_CS — create_CS_version","text":"Creates list object CS_version argument DAISIE_ML_CS","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/create_CS_version.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Creates the list object for CS_version argument in DAISIE_ML_CS — create_CS_version","text":"","code":"create_CS_version(   model = 1,   relaxed_par = NULL,   par_sd = 0,   par_upper_bound = Inf )"},{"path":"https://rsetienne.github.io/DAISIE/reference/create_CS_version.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Creates the list object for CS_version argument in DAISIE_ML_CS — create_CS_version","text":"model CS model run, options 1 single rate DAISIE model, 2 multi-rate DAISIE, 0 IW test model relaxed_par parameter relax (integrate ). Options \"cladogenesis\", \"extinction\", \"carrying_capacity\", \"immigration\", \"anagenesis\" par_sd standard deviation parameter relax par_upper_bound upper bound parameter relax","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/create_CS_version.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Creates the list object for CS_version argument in DAISIE_ML_CS — create_CS_version","text":"list four elements model: CS model run, options 1 single rate   DAISIE model, 2 multi-rate DAISIE, 0 IW test   model relaxed_par: parameter relax (integrate ). par_sd: standard deviation parameter relax par_upperbound: upper bound parameter relax.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/create_area_pars.html","id":null,"dir":"Reference","previous_headings":"","what":"Create named list of area parameters — create_area_pars","title":"Create named list of area parameters — create_area_pars","text":"Create named list area parameters","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/create_area_pars.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create named list of area parameters — create_area_pars","text":"","code":"create_area_pars(   max_area,   current_area,   proportional_peak_t,   total_island_age,   sea_level_amplitude,   sea_level_frequency,   island_gradient_angle )"},{"path":"https://rsetienne.github.io/DAISIE/reference/create_area_pars.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create named list of area parameters — create_area_pars","text":"max_area Numeric defining maximum area. current_area numeric current island area present (.e., end simulation). proportional_peak_t Numeric value 0 1 indicating island's history peak area achieved. total_island_age Numeric defining total island age. sea_level_amplitude Numeric defining amplitude area fluctuation sea level. sea_level_frequency Numeric defining frequency sine wave area change sea level. island_gradient_angle Numeric defining angle degrees specifying slope island.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/create_area_pars.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create named list of area parameters — create_area_pars","text":"list numerical values containing area sea level parameters island ontogeny simulation","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/create_area_pars.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Create named list of area parameters — create_area_pars","text":"Richel J.C Bilderbeek, Joshua Lambert, Pedro Neves","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/create_area_pars.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create named list of area parameters — create_area_pars","text":"","code":"area_pars <- create_area_pars(   max_area = 10,   current_area = 1,   proportional_peak_t = 0.5,   total_island_age = 5,   sea_level_amplitude = 5,   sea_level_frequency = 10,   island_gradient_angle = 0   )"},{"path":"https://rsetienne.github.io/DAISIE/reference/create_full_CS_stt.html","id":null,"dir":"Reference","previous_headings":"","what":"Unsampled CS full STT — create_full_CS_stt","title":"Unsampled CS full STT — create_full_CS_stt","text":"Unsampled CS full STT","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/create_full_CS_stt.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Unsampled CS full STT — create_full_CS_stt","text":"","code":"create_full_CS_stt(stt_list, stac_vec, total_time, trait_pars = NULL)"},{"path":"https://rsetienne.github.io/DAISIE/reference/create_full_CS_stt.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Unsampled CS full STT — create_full_CS_stt","text":"stt_list List full stt tables returned DAISIE_sim_core functions stac_vec Vector status species island. total_time Numeric double total time simulation. trait_pars named list containing diversification rates considering two trait states created create_trait_pars: [1]:numeric per capita transition rate state1 [2]:numeric per capita immigration rate state2 [3]:numeric per capita extinction rate state2 [4]:numeric per capita anagenesis rate state2 [5]:numeric per capita cladogenesis rate state2 [6]:numeric per capita transition rate state2 [7]:numeric number species trait state 2    mainland","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/create_full_CS_stt.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Unsampled CS full STT — create_full_CS_stt","text":"1 complete, unsampled STT table clades island CS model generated DAISIE_sim_core functions.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/create_full_CS_stt.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Unsampled CS full STT — create_full_CS_stt","text":"Pedro Neves, Joshua Lambert, Shu Xie, Giovanni Laudanno","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/create_hyper_pars.html","id":null,"dir":"Reference","previous_headings":"","what":"Create list of hyperparameters — create_hyper_pars","title":"Create list of hyperparameters — create_hyper_pars","text":"Create list hyperparameters","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/create_hyper_pars.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create list of hyperparameters — create_hyper_pars","text":"","code":"create_hyper_pars(d, x)"},{"path":"https://rsetienne.github.io/DAISIE/reference/create_hyper_pars.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create list of hyperparameters — create_hyper_pars","text":"d Numeric defining scaling parameter exponent calculating cladogenesis rate. x Numeric defining exponent calculating extinction rate.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/create_hyper_pars.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create list of hyperparameters — create_hyper_pars","text":"Named list hyperparameters","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/create_hyper_pars.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Create list of hyperparameters — create_hyper_pars","text":"Pedro Neves, Joshua Lambert","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/create_hyper_pars.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create list of hyperparameters — create_hyper_pars","text":"","code":"hyper_pars <- create_hyper_pars(d = 0.027, x = 0.15)"},{"path":"https://rsetienne.github.io/DAISIE/reference/create_pars.html","id":null,"dir":"Reference","previous_headings":"","what":"Create vector of model parameters — create_pars","title":"Create vector of model parameters — create_pars","text":"Create vector model parameters","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/create_pars.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create vector of model parameters — create_pars","text":"","code":"create_pars(clado_rate, ext_rate, carr_cap, immig_rate, ana_rate)"},{"path":"https://rsetienne.github.io/DAISIE/reference/create_pars.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create vector of model parameters — create_pars","text":"clado_rate Numeric rate cladogenesis ext_rate Numeric rate extinction carr_cap Numeric carrying capacity immig_rate Numeric rate immigration ana_rate Numeric rate anagenesis","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/create_pars.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create vector of model parameters — create_pars","text":"Numeric vector 5 elements","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/create_pars.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create vector of model parameters — create_pars","text":"","code":"create_pars(clado_rate = 1,             ext_rate = 1,             carr_cap = 10,             immig_rate = 0.1,             ana_rate = 1) #> [1]  1.0  1.0 10.0  0.1  1.0"},{"path":"https://rsetienne.github.io/DAISIE/reference/create_trait_pars.html","id":null,"dir":"Reference","previous_headings":"","what":"Create named list of trait state parameters — create_trait_pars","title":"Create named list of trait state parameters — create_trait_pars","text":"Create named list trait state parameters","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/create_trait_pars.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create named list of trait state parameters — create_trait_pars","text":"","code":"create_trait_pars(   trans_rate,   immig_rate2,   ext_rate2,   ana_rate2,   clado_rate2,   trans_rate2,   M2 )"},{"path":"https://rsetienne.github.io/DAISIE/reference/create_trait_pars.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create named list of trait state parameters — create_trait_pars","text":"trans_rate numeric per capita transition rate state1 immig_rate2 numeric per capita immigration rate state2 ext_rate2 numeric per capita extinction rate state2 ana_rate2 numeric per capita anagenesis rate state2 clado_rate2 numeric per capita cladogenesis rate state2 trans_rate2 numeric per capita transition rate state2 M2 numeric number species trait state 2 mainland","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/create_trait_pars.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create named list of trait state parameters — create_trait_pars","text":"list numerical values containing trait state parameters","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/create_trait_pars.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create named list of trait state parameters — create_trait_pars","text":"","code":"trait_pars <- create_trait_pars(    trans_rate = 0.5,    immig_rate2 = 0.1,    ext_rate2 = 0.2,    ana_rate2 = 0.3,    clado_rate2 = 0.4,    trans_rate2 = 0.5,    M2 = 1000  )"},{"path":"https://rsetienne.github.io/DAISIE/reference/create_trait_pars_2K.html","id":null,"dir":"Reference","previous_headings":"","what":"Create named list of trait state parameters — create_trait_pars_2K","title":"Create named list of trait state parameters — create_trait_pars_2K","text":"Create named list trait state parameters","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/create_trait_pars_2K.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create named list of trait state parameters — create_trait_pars_2K","text":"","code":"create_trait_pars_2K(   trans_rate,   immig_rate2,   ext_rate2,   ana_rate2,   clado_rate2,   trans_rate2,   M2,   K2 )"},{"path":"https://rsetienne.github.io/DAISIE/reference/create_trait_pars_2K.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create named list of trait state parameters — create_trait_pars_2K","text":"trans_rate numeric per capita transition rate state1 immig_rate2 numeric per capita immigration rate state2 ext_rate2 numeric per capita extinction rate state2 ana_rate2 numeric per capita anagenesis rate state2 clado_rate2 numeric per capita cladogenesis rate state2 trans_rate2 numeric per capita transition rate state2 M2 numeric number species trait state 2 mainland K2 numeric carrying capacity state 2","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/create_trait_pars_2K.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create named list of trait state parameters — create_trait_pars_2K","text":"list numerical values containing trait state parameters","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/cum_rho.html","id":null,"dir":"Reference","previous_headings":"","what":"Cumulative Gamma distribution parameterised with mean and standard deviation — cum_rho","title":"Cumulative Gamma distribution parameterised with mean and standard deviation — cum_rho","text":"Cumulative Gamma distribution parameterised mean standard deviation","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/cum_rho.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Cumulative Gamma distribution parameterised with mean and standard deviation — cum_rho","text":"","code":"cum_rho(par_upper_bound, DAISIE_dist_pars)"},{"path":"https://rsetienne.github.io/DAISIE/reference/cum_rho.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Cumulative Gamma distribution parameterised with mean and standard deviation — cum_rho","text":"DAISIE_dist_pars numeric vector two elements, first mean second standard deviation distribution.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/cum_rho.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Cumulative Gamma distribution parameterised with mean and standard deviation — cum_rho","text":"Numeric","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/daisie_odeint_cs.html","id":null,"dir":"Reference","previous_headings":"","what":"Driver for the boost::odeint solver for the CS model — daisie_odeint_cs","title":"Driver for the boost::odeint solver for the CS model — daisie_odeint_cs","text":"Driver boost::odeint solver CS model","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/daisie_odeint_cs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Driver for the boost::odeint solver for the CS model — daisie_odeint_cs","text":"Object type `state_type`, `vector_t`<double>, result integration depending runmod chosen.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/daisie_odeint_iw.html","id":null,"dir":"Reference","previous_headings":"","what":"Driver for the boost::odeint solver for the IW model — daisie_odeint_iw","title":"Driver for the boost::odeint solver for the IW model — daisie_odeint_iw","text":"Driver boost::odeint solver IW model","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/default_params_doc.html","id":null,"dir":"Reference","previous_headings":"","what":"Default parameter documentation — default_params_doc","title":"Default parameter documentation — default_params_doc","text":"Default parameter documentation","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/default_params_doc.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Default parameter documentation — default_params_doc","text":"","code":"default_params_doc(   time,   M,   pars,   replicates,   divdepmodel,   nonoceanic_pars,   num_guilds,   prop_type2_pool,   replicates_apply_type2,   sample_freq,   plot_sims,   verbose,   area_pars,   hyper_pars,   island_ontogeny,   sea_level,   extcutoff,   shift_times,   mainland_n,   island_replicates,   island_spec,   stt_table,   rates,   max_rates,   timeval,   total_time,   possible_event,   maxspecID,   mainland_spec,   max_area,   proportional_peak_t,   total_island_age,   sea_level_amplitude,   sea_level_frequency,   island_gradient_angle,   d,   x,   simulation_outputs,   plot_plus_one,   type,   plot_lists,   ...,   datalist,   datatype,   initparsopt,   idparsopt,   idparsfix,   parsfix,   idparsnoshift,   idparsmat,   res,   ddmodel,   cond,   eqmodel,   x_E,   x_I,   tol,   maxiter,   methode,   optimmethod,   CS_version,   tolint,   datatable,   island_age,   number_clade_types,   list_type2_clades,   epss,   t,   initEI,   data_table,   endmc,   archipelago,   phylo_data,   archipelago_data,   gam,   laa,   lac,   mu,   K,   num_spec,   num_immigrants,   global_min_area_time,   global_max_area_time,   distance_type,   distance_dep,   parallel,   cpus,   pars1,   pars2,   tvec,   initprobs,   pb,   island,   title,   plot_lists_simulations,   plot_lists_simulations_MLE,   kind_of_plot,   resolution,   resol,   removed_timepoints,   A,   Amin,   Amax,   peak,   proptime,   proptime_max,   current_area,   jitter,   num_cycles,   trait_pars,   relaxed_par,   relaxed_rate_pars,   brts,   stac,   missnumspec,   DAISIE_par,   DAISIE_dist_pars,   abstolint,   reltolint,   pick,   mean,   sd,   clado_rate,   ext_rate,   carr_cap,   immig_rate,   ana_rate,   islands,   sort_clade_sizes )"},{"path":"https://rsetienne.github.io/DAISIE/reference/default_params_doc.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Default parameter documentation — default_params_doc","text":"time Numeric defining length simulation time units. example, island known 4 million years old, setting time = 4 simulate entire life span island; setting time = 2 stop simulation mid-life island. M Numeric defining size mainland pool, .e. number species can potentially colonize island. pars numeric vector containing model parameters: pars[1]: lambda^c (cladogenesis rate) pars[2]: mu (extinction rate) pars[3]: K (carrying capacity), set K=Inf diversity   independence. pars[4]: gamma (immigration rate) pars[5]: lambda^(anagenesis rate) pars[6]: lambda^c (cladogenesis rate) either type 2 species   rate set 2 rate shift model pars[7]: mu (extinction rate) either type 2 species rate   set 2 rate shift model pars[8]: K (carrying capacity) either type 2 species rate   set 2 rate shift model, set K=Inf diversity independence. pars[9]: gamma (immigration rate) either type 2 species   rate set 2 rate shift model pars[10]: lambda^(anagenesis rate) either type 2   species rate set 2 rate shift model Elements 6:10 required type 2 species included rate shift model. DAISIE_sim_relaxed_rate() pars[6] standard deviation gamma distribution relaxed parameter parameter chosen relaxed_par argument mean gamma distribution relaxed parameter. replicates Integer specifying number island replicates simulated. divdepmodel Option divdepmodel = 'CS' runs model clade-specific carrying capacity, diversity-dependence operates within single clades, .e. among species originating mainland colonist. Option divdepmodel = 'IW' runs model island-wide carrying capacity, diversity-dependence operates within among clades. Option divdepmodel = 'GW' runs model diversity-dependence operates within guild. nonoceanic_pars vector length two : [1]: probability sampling species mainland [2]: probability species sampled mainland   nonendemic num_guilds number guilds mainland. number mainland species divided number guilds divdepmodel = \"GW\" prop_type2_pool Fraction mainland species belongs second subset species (type 2). Applies two types species simulated (length(pars) = 10). DAISIE_dataprep() applies number_clade_types = 2.  DAISIE_dataprep() default \"proportional\" sets fraction proportional number clades distinct macroevolutionary process colonised island. replicates_apply_type2 Applies two types species simulated. Default replicates_apply_type2 = TRUE runs simulations number islands type 2 species colonised equal specified number replicates. recommended prop_type2_pool small rate immigration type two species (pars[9]) low, meaning replicates needed achieved adequate sample size islands type 2 species. Setting replicates_apply_type2 = FALSE simulates islands specified number replicates regardless whether type 2 species colonised . sample_freq Numeric specifing number units times divided plotting purposes. Larger values lead plots higher resolution, also run slower. plot_sims Default = TRUE plots species--time (STT) plots. detects many types species present. one type species present, STT plotted species. two types present, three plots produced: STT , STT type 1 STT type 2. verbose numeric vector length 1, simulations `DAISIEdataprep()` can `1` `0`, `1` gives intermediate output printed. ML functions numeric determining intermediate output printed. default: `0` print, `1` prints initial likelihood settings selected (parameters optimised, fixed shifted), `2` prints `1 also intermediate output parameters loglikelihood, `3` `2` prints intermediate progress likelihood computation. area_pars named list containing area sea level parameters created create_area_pars(): [1]: maximum area [2]: current area [3]: value 0 1 indicating island's history   peak area achieved [4]: total island age [5]: amplitude area fluctuation sea level [6]: frequency sine wave area change sea level [7]: angle slope island hyper_pars named list numeric hyperparameters rate calculations returned create_hyper_pars(): [1]: d scaling parameter exponent calculating   cladogenesis rate [2]: x exponent calculating extinction rate island_ontogeny DAISIE_sim_time_dep(), DAISIE_ML_CS plotting string describing type island ontogeny. Can \"const\", \"beta\" beta function describing area time.  functions numeric describing type island ontogeny. Can 0 constant, 1 beta function describing area time. ML functions island_ontogeny = NA assumes constant ontogeny. Time dependent estimation yet available development still ongoing. return error called case. sea_level DAISIE_sim_time_dep() plotting string describing type sea level. Can \"const\" \"sine\" sine function describing area time.  functions numeric describing type sea level. Can 0 constant, 1 sine function describing area time. extcutoff numeric cutoff maximum extinction rate preventing large slowing simulation. shift_times numeric vector specifying rate shifts occur present. mainland_n numeric stating number mainland species, number species can potentially colonize island. using clade-specific diversity dependence, value set 1. using island-wide diversity dependence, value set number mainland species. island_replicates List output DAISIE_sim_core_cr(), DAISIE_sim_core_time_dep(), DAISIE_sim_core_cr_shift() DAISIE_sim_min_type2() functions. Minimally, must list many elements replicates. element must list elements island_age, not_present stt_all. stt_all must data frame column names Time, nI, nA, nC present. island_spec Matrix current state simulation containing number species. stt_table Matrix number species time step. rates named list numeric rates returned update_rates(). max_rates named list numeric max rates returned update_max_rates(). timeval Numeric defining current time simulation. total_time Numeric defining length simulation time units. possible_event Numeric defining event happen. maxspecID Current species IDs. mainland_spec Number mainland species. max_area Numeric defining maximum area. proportional_peak_t Numeric value 0 1 indicating island's history peak area achieved. total_island_age Numeric defining total island age. sea_level_amplitude Numeric defining amplitude area fluctuation sea level. sea_level_frequency Numeric defining frequency sine wave area change sea level. island_gradient_angle Numeric defining angle degrees specifying slope island. d Numeric defining scaling parameter exponent calculating cladogenesis rate. x Numeric defining exponent calculating extinction rate. simulation_outputs list matrices vectors simulation produced DAISIE_sim functions. plot_plus_one Boolean indicate plot values plus one. Set TRUE default behavior. Set FALSE plot values without adding one. works one type species. type String indicate stt species possible stt plotted. Default \"all_species\", \"type1_species\" \"type2_species\" plotted. plot_lists List lists containing average quantile species time. ... arguments pass plotting functions. datalist Data object containing information colonisation branching times. object can generated using DAISIE_dataprep function, converts user-specified data table data object, object can course also entered directly. R list object following elements. first element list two three components: $island_age - island age  , depending whether distinction types made, :$not_present - number mainland lineages present island  :$not_present_type1 - number mainland lineages type 1 present island $not_present_type2 - number mainland lineages type 2 present island  remaining elements list contains information single colonist lineage island 5 components:$colonist_name - name species clade colonized island $branching_times - island age followed stem age population/species case Non-endemic, Non-endemic_MaxAge species Endemic species close relatives island. endemic clades one species island (cladogenetic clades/ radiations) island age followed branching times island clade including stem age clade$stac - status colonist  * Non_endemic_MaxAge: 1  * Endemic: 2  * Endemic&Non_Endemic: 3  * Non_Endemic: 4  * Endemic_Singleton_MaxAge: 5  * Endemic_Clade_MaxAge: 6  * Endemic&Non_Endemic_Clade_MaxAge: 7 $missing_species - number island species sampled particular clade (applicable endemic clades) $type1or2 - whether colonist belongs type 1 type 2 datatype Sets type data: 'single' single island archipelago treated one, 'multiple' multiple archipelagoes potentially sharing parameters. initparsopt initial values parameters must optimized, positive. idparsopt ids parameters must optimized. ids defined follows:  id = 1 corresponds lambda^c (cladogenesis rate)  id = 2 corresponds mu (extinction rate)  id = 3 corresponds K (clade-level carrying capacity)  id = 4 corresponds gamma (immigration rate)  id = 5 corresponds lambda^(anagenesis rate)  id = 6 corresponds lambda^c (cladogenesis rate) optional subset species  id = 7 corresponds mu (extinction rate) optional subset species id = 8 corresponds K (clade-level carrying capacity) optional subset species id = 9 corresponds gamma (immigration rate) optional subset species id = 10 corresponds lambda^(anagenesis rate) optional subset species id = 11 corresponds p_f (fraction mainland species belongs second subset species. idparsfix ids parameters optimized, e.g. c(1,3) lambda^c K optimized. parsfix values parameters optimized. idparsnoshift datatype = 'single' : ids parameters different two groups species; can apply ids 6:10, e.g. idparsnoshift = c(6,7) means lambda^c mu values groups. idparsmat datatype = 'multiple' : Matrix containing ids parameters, linking initparsopt parsfix. Per island system use following order:  * lac = (initial) cladogenesis rate  * mu = extinction rate  * K = maximum number species possible clade  * gam = (initial) immigration rate  * laa = (initial) anagenesis rate  Example: idparsmat = rbind(c(1, 2, 3, 4, 5), c(1, 2, 3, 6, 7)) different rates immigration anagenesis two islands. res Sets maximum number species probability must computed, must larger size largest clade. ddmodel Sets model diversity-dependence:  ddmodel = 0 : diversity dependence  ddmodel = 1 : linear dependence speciation rate  ddmodel = 11: linear dependence speciation rate immigration rate  ddmodel = 2 : exponential dependence speciation rate ddmodel = 21: exponential dependence speciation rate immigration rate cond cond = 0 : conditioning island age  cond = 1 : conditioning island age non-extinction island biota . cond > 1 : conditioning island age least cond colonizations island. last option yet available IW model eqmodel Sets equilibrium constraint can used likelihood optimization. available datatype = 'single'. eqmodel = 0 : equilibrium assumed  eqmodel = 13 : near-equilibrium assumed endemics using deterministic equation endemics immigrants. Endemics must within x_E equilibrium value eqmodel = 15 : near-equilibrium assumed endemics immigrants using deterministic equation endemics immigrants. Endemics must within x_E equilibrium value, non-endemics must within x_I equilibrium value. x_E Sets fraction equlibrium endemic diversity endemics assumed equilibrium; active eqmodel = 13 15. x_I Sets fraction equlibrium non-endemic diversity system assumed equilibrium; active eqmodel = 15. tol Sets tolerances optimization. Consists :  reltolx = relative tolerance parameter values optimization  reltolf = relative tolerance function value optimization  abstolx = absolute tolerance parameter values optimization. maxiter Sets maximum number iterations optimization. methode Method ODE-solver. Supported Boost ODEINT solvers (steppers) : \"odeint::runge_kutta_cash_karp54\" \"odeint::runge_kutta_fehlberg78\" \"odeint::runge_kutta_dopri5\" \"odeint::bulirsch_stoer\" without odeint::-prefix, deSolve{ode} method assumed. default method overall \"lsodes\" DAISIE_ML_CS() \"ode45\" ode() DAISIE_ML_IW(). optimmethod Method used likelihood optimization. Default `subplex` (see `subplex()` full details). Alternative \"simplex\" method previous versions. CS_version numeric list. Default 1 standard DAISIE model, relaxed-rate model list following elements: model: CS model run, options 1 single rate   DAISIE model, 2 multi-rate DAISIE, 0 IW test   model. relaxed_par: parameter relax (integrate ). Options \"cladogenesis\", \"extinction\", \"carrying_capacity\", \"immigration\", \"anagenesis\". tolint Vector two elements containing absolute relative tolerance integration. datatable Data frame (table) user-specified data. See file Galapagos_datatable template input table. row table represents independent colonisation event. Table following four columns. $Clade_name - name independent colonization event $Status - One following categories:  * \"Non_endemic\": applies non-endemic species cases island non-island populations species sampled)  * \"Non_endemic_MaxAge\": applies non-endemic species cases island individuals species sampled age species available)  * \"Endemic\": applies endemic species applicable cladogenetic anagenetic species  * \"Endemic_MaxAge\": applies endemic species cases island individuals species sampled age species available. apply endemic species recently gone extinct antropogenic causes (evidently) modelled, DNA data available. * \"Endemic&Non_Endemic\": endemic clade present mainland ancestor re-colonized $Missing_species - Number island species sampled particular clade (applicable \"Endemic\" clades) $Branching_times - Stem age population/species case \"Non-endemic\", \"Non-endemic_MaxAge\" \"Endemic\" anagenetic species. \"Endemic\" cladogenetic species branching times radiation including stem age radiation. island_age Age island appropriate units. DAISIE_plot_age_diversity() DAISIE_plot_island() island input table format, age island must specified. island input DAISIE list format, option override island age specified island list. number_clade_types Number clade types. Default: number_clade_types = 1 species considered belong macroevolutionary process. number_clade_types = 2, two types clades distinct macroevolutionary processes. list_type2_clades number_clade_types = 2, list_type2_clades specifies names clades distinct macroevolutionary process. names must match $Clade_name column source data table (e.g. list_type2_clades = \"Finches\").  number_clade_types = 1, list_type2_clades = NA specified (default). epss Default= 1E-5 appropriate cases. value used set maximum age colonisation \"Non_endemic_MaxAge\" \"Endemic_MaxAge\" species age slightly younger island cases age provided species older island. new maximum age used upper bound integrate . t time expectations need computed. initEI initial values number endemics   non-endemics. DAISIE_probdist() DAISIE_margprobdist() either initprobs must NULL. DAISIE_numcol() NULL, assumed island   empty. data_table data table endmc Numeric many simulations run. archipelago something phylo_data something archipelago_data something gam numeric per capita immigration rate. laa numeric per capita anagenesis rate. lac numeric per capita cladogenesis rate. mu numeric per capita extinction rate. K numeric carrying capacity. num_spec numeric current number species. num_immigrants numeric current number non-endemic species (.k.non-endemic species). global_min_area_time stub global_max_area_time stub distance_type Use 'continent' distance continent used, use 'nearest_big' distance nearest big landmass used, use 'biologically_realistic' distance take account biologically realism, e.g. average previous two thought contribute. distance_dep Sets type distance dependence used. Default power law, denoted 'power'. Alternatives exponantial relationship denoted 'exp' sigmoids, either 'sigmoidal_col' sigmoid colonization, 'sigmoidal_ana' sigmoidal anagenesis, 'sigmoidal_clado' sigmoidal cladogenesis, 'sigmoidal_col_ana' signoids colonization anagenesis. parallel Sets whether parallel computation used. Use '' parallel computing used, 'cluster' parallel computing unix/linux cluster, 'local' parallel computation local machine. cpus Number cpus used parallel computing. Default 3. effect parallel = ''. pars1 Vector model parameters: pars1[1] corresponds lambda^c (cladogenesis rate) pars1[2] corresponds mu (extinction rate) pars1[3] corresponds K (clade-level carrying capacity) pars1[4] corresponds gamma (immigration rate) pars1[5] corresponds lambda^(anagenesis rate). pars2 Vector settings: pars2[1] corresponds res, maximum number endemics non-endemics ODE system solved; must much larger actual number probability needs calculated.) pars2[2] corresponds M, size mainland pool, .e number species can potentially colonize island. tvec times probabilities need computed. initprobs initial probability distribution number endemics non-endemics; either initEI must NULL. pb Probability distribution matrix format output DAISIE_probdist(). island Island data object. Can DAISIE list format (see Galapagos_datalist DAISIE_data_prep examples) table format (see Galapagos_datatable example). title Title plot plot_lists_simulations List simulation output parsing DAISIE_prepare_data_plotting. plot_lists_simulations_MLE List simulation output parsing DAISIE_prepare_data_plotting, obtained simulating MLE output. kind_of_plot Character vector stating STT plot resulting MLE based simulations plotted. Default \"line\" multiple individual lines. Can also \"shade\" 5% quantile. resolution numeric indicating resolution plot. < 0. resol numeric resolution summary stats calculation. > 1. removed_timepoints Positive integer number first datapoints removed rate plots (prevent Inf) numeric value island area given point time. Amin numeric value minimum island area simulation. Amax numeric value maximum island area simulation. peak numeric value specifying peakiness (shaprness) ontogeny curve. Higher values imply peakier ontogeny. value internally calculated calc_peak() given area present area_pars. proptime numeric 0 1. proportion time elapsed simulation, relation total island age (NB: simulation time, island age). proptime_max numeric 0 1. proportional_peak_t. Indicates, proportion total island age ontogeny peak occur (.e. 0.5 means peak halfway time). current_area numeric current island area present (.e., end simulation). jitter Numeric optimizer(). Jitters parameters optimized specified amount small, e.g. 1e-5. Jitter link{subplex}{subplex}() produces incorrect output due parameter transformation. num_cycles number cycles optimizer go . Default 1. trait_pars named list containing diversification rates considering   two trait states created create_trait_pars: [1]:numeric per capita transition rate state1 [2]:numeric per capita immigration rate state2 [3]:numeric per capita extinction rate state2 [4]:numeric per capita anagenesis rate state2 [5]:numeric per capita cladogenesis rate state2 [6]:numeric per capita transition rate state2 [7]:numeric number species trait state 2    mainland relaxed_par string determining parameter relaxed relaxed rate model. relaxed_rate_pars list two numbers, element one distribution mean, element two distribution standard deviation (sd). Currently distribution gamma distribution. list can created create_relaxed_rate_pars(). brts Numeric vector branching times stac Numeric Endemicity status missnumspec Numeric missing species DAISIE_par numeric parameter evaluate integral function. DAISIE_dist_pars numeric vector two elements, first mean second standard deviation distribution. abstolint Numeric absolute tolerance integration reltolint Numeric relative tolerance integration pick Numeric determining parameter selected relaxed-rate model mean Numeric mean distribution sd Numeric standard deviation distribution clado_rate Numeric rate cladogenesis ext_rate Numeric rate extinction carr_cap Numeric carrying capacity immig_rate Numeric rate immigration ana_rate Numeric rate anagenesis islands Island datalist simulated data DAISIE datalist format. Can single island (empirical data) generated DAISIE_dataprep DAISIEprep. Can also simulated data generated DAISIE_sim function. sort_clade_sizes Default sort_clade_sizes = T outputs clade sizes sorted ascending order number species. sort_clade_sizes=F outputs clade sizes order appear input datalist.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/default_params_doc.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Default parameter documentation — default_params_doc","text":"Nothing","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/default_params_doc.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Default parameter documentation — default_params_doc","text":"internal function, marked   @noRd. done, disallow   functions find documentation parameters","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/frogs_datalist.html","id":null,"dir":"Reference","previous_headings":"","what":"Colonization and branching times of 5 Eleutherodactylus clades from Hispaniola island. — frogs_datalist","title":"Colonization and branching times of 5 Eleutherodactylus clades from Hispaniola island. — frogs_datalist","text":"list containing colonization branching times Eleutherodactylus frogs Hispaniola. Main dataset used Etienne et al. list can generated using DAISIE_dataprep function, converts user-specified data table data object, object can course also entered directly. R list object following elements. first element list two components: $island_age - island age $not_present - number mainland lineages present island  following elements list contains information single colonist lineage island 5 components:$colonist_name - name species clade colonized island $branching_times - island age followed stem age population/species case Non-endemic, Non-endemic_MaxAge species Endemic species close relatives island. endemic clades one species island (cladogenetic clades/ radiations) island age followed branching times island clade including stem age clade.$stac - status colonist  * Non_endemic_MaxAge: 1  * Endemic: 2  * Endemic&Non_Endemic: 3  * Non_endemic: 4  * Endemic_MaxAge: 5 6 $missing_species - number island species sampled particular clade (applicable endemic clades) $type1or2 - whether colonist belongs type 1 type 2. dataset equal 1.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/frogs_datalist.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Colonization and branching times of 5 Eleutherodactylus clades from Hispaniola island. — frogs_datalist","text":"list 6 elements, first contains 2 elements following 5 elements containing 5 components.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/frogs_datalist.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Colonization and branching times of 5 Eleutherodactylus clades from Hispaniola island. — frogs_datalist","text":"Etienne RS, Haegeman B, Dugo-Cota , Vila C, Gonzalez-Voyer & Valente L.  limits ecological limits diversification.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/frogs_datatable.html","id":null,"dir":"Reference","previous_headings":"","what":"Colonization and branching times of 5 Eleutherodactylus (frogs) clades from\nthe island of Hispaniola. — frogs_datatable","title":"Colonization and branching times of 5 Eleutherodactylus (frogs) clades from\nthe island of Hispaniola. — frogs_datatable","text":"table containing colonization branching times Eleutherodacytlus frogs island Hispaniola (Greater Antilles). row table represents independent colonisation event. table four columns. $Clade_name - name independent colonization event $Status - One following categories:  * Non_endemic: non-endemic island species approximate time colonisation known  * Non_endemic_MaxAge: non-endemic island species colonisation time unknown  * Endemic: endemic species approximate colonisation time known  * \"Endemic_MaxAge\": applies endemic species endemic clades cases colonisation time unknown, user wants specify upper bound colonisation. example apply endemic species recently gone extinct anthropogenic causes, included phylogeny (\"NA\" given branching times column). also apply insular radiations long stem branches, time first cladogenetic event known, precise time colonisation . * Endemic&Non_Endemic: endemic clade mainland ancestor re-colonized","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/frogs_datatable.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Colonization and branching times of 5 Eleutherodactylus (frogs) clades from\nthe island of Hispaniola. — frogs_datatable","text":"table 5 rows 4 columns.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/frogs_datatable.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Colonization and branching times of 5 Eleutherodactylus (frogs) clades from\nthe island of Hispaniola. — frogs_datatable","text":"Etienne RS, Haegeman B, Dugo-Cota , Vila C, Gonzalez-Voyer & Valente L. limits ecological limits diversification.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/get_ana_rate.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate anagenesis rate — get_ana_rate","title":"Calculate anagenesis rate — get_ana_rate","text":"Internal function. Calculates anagenesis rate given current number immigrant species per capita rate.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/get_ana_rate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate anagenesis rate — get_ana_rate","text":"","code":"get_ana_rate(laa, num_immigrants, island_spec = NULL, trait_pars = NULL)"},{"path":"https://rsetienne.github.io/DAISIE/reference/get_ana_rate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate anagenesis rate — get_ana_rate","text":"laa numeric per capita anagenesis rate. num_immigrants numeric current number non-endemic species (.k.non-endemic species). island_spec Matrix current state simulation containing number species. trait_pars named list containing diversification rates considering   two trait states created create_trait_pars: [1]:numeric per capita transition rate state1 [2]:numeric per capita immigration rate state2 [3]:numeric per capita extinction rate state2 [4]:numeric per capita anagenesis rate state2 [5]:numeric per capita cladogenesis rate state2 [6]:numeric per capita transition rate state2 [7]:numeric number species trait state 2    mainland","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/get_ana_rate.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculate anagenesis rate — get_ana_rate","text":"Pedro Neves, Joshua Lambert, Shu Xie","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/get_clado_rate.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate cladogenesis rate — get_clado_rate","title":"Calculate cladogenesis rate — get_clado_rate","text":"Internal function. Calculates cladogenesis rate given current number species system, carrying capacity per capita cladogenesis rate","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/get_clado_rate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate cladogenesis rate — get_clado_rate","text":"","code":"get_clado_rate(   lac,   hyper_pars,   num_spec,   K,   A,   trait_pars = NULL,   island_spec = NULL )"},{"path":"https://rsetienne.github.io/DAISIE/reference/get_clado_rate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate cladogenesis rate — get_clado_rate","text":"lac numeric per capita cladogenesis rate. hyper_pars named list numeric hyperparameters rate calculations returned create_hyper_pars(): [1]: d scaling parameter exponent calculating   cladogenesis rate [2]: x exponent calculating extinction rate num_spec numeric current number species. K numeric carrying capacity. numeric value island area given point time. trait_pars named list containing diversification rates considering   two trait states created create_trait_pars: [1]:numeric per capita transition rate state1 [2]:numeric per capita immigration rate state2 [3]:numeric per capita extinction rate state2 [4]:numeric per capita anagenesis rate state2 [5]:numeric per capita cladogenesis rate state2 [6]:numeric per capita transition rate state2 [7]:numeric number species trait state 2    mainland island_spec Matrix current state simulation containing number species.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/get_clado_rate.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculate cladogenesis rate — get_clado_rate","text":"Pedro Neves, Joshua Lambert, Shu Xie","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/get_ext_rate.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate extinction rate — get_ext_rate","title":"Calculate extinction rate — get_ext_rate","text":"Calculate extinction rate","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/get_ext_rate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate extinction rate — get_ext_rate","text":"","code":"get_ext_rate(   mu,   hyper_pars,   extcutoff = 1000,   num_spec,   A = 1,   trait_pars = NULL,   island_spec = NULL )"},{"path":"https://rsetienne.github.io/DAISIE/reference/get_ext_rate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate extinction rate — get_ext_rate","text":"mu numeric per capita extinction rate. hyper_pars named list numeric hyperparameters rate calculations returned create_hyper_pars(): [1]: d scaling parameter exponent calculating   cladogenesis rate [2]: x exponent calculating extinction rate extcutoff numeric cutoff maximum extinction rate preventing large slowing simulation. num_spec numeric current number species. numeric value island area given point time. trait_pars named list containing diversification rates considering   two trait states created create_trait_pars: [1]:numeric per capita transition rate state1 [2]:numeric per capita immigration rate state2 [3]:numeric per capita extinction rate state2 [4]:numeric per capita anagenesis rate state2 [5]:numeric per capita cladogenesis rate state2 [6]:numeric per capita transition rate state2 [7]:numeric number species trait state 2    mainland island_spec Matrix current state simulation containing number species.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/get_ext_rate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate extinction rate — get_ext_rate","text":"numeric, extinction rate given base extinction rate, present, hyperparemeter x, (t) time-dependent traits running traint model.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/get_ext_rate.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Calculate extinction rate — get_ext_rate","text":"Valente, Luis M., Rampal S. Etienne, Albert B. Phillimore. \"effects island ontogeny species diversity phylogeny.\" Proceedings Royal Society London B: Biological Sciences 281.1784 (2014): 20133227.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/get_ext_rate.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculate extinction rate — get_ext_rate","text":"Pedro Neves, Joshua Lambert, Shu Xie","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/get_immig_rate.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate immigration rate — get_immig_rate","title":"Calculate immigration rate — get_immig_rate","text":"Internal function. Calculates immigration rate given current number species system, carrying capacity","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/get_immig_rate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate immigration rate — get_immig_rate","text":"","code":"get_immig_rate(   gam,   A = 1,   num_spec,   K,   mainland_n,   trait_pars = NULL,   island_spec = NULL )"},{"path":"https://rsetienne.github.io/DAISIE/reference/get_immig_rate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate immigration rate — get_immig_rate","text":"gam numeric per capita immigration rate. numeric value island area given point time. num_spec numeric current number species. K numeric carrying capacity. mainland_n numeric stating number mainland species, number species can potentially colonize island. using clade-specific diversity dependence, value set 1. using island-wide diversity dependence, value set number mainland species. trait_pars named list containing diversification rates considering   two trait states created create_trait_pars: [1]:numeric per capita transition rate state1 [2]:numeric per capita immigration rate state2 [3]:numeric per capita extinction rate state2 [4]:numeric per capita anagenesis rate state2 [5]:numeric per capita cladogenesis rate state2 [6]:numeric per capita transition rate state2 [7]:numeric number species trait state 2    mainland island_spec Matrix current state simulation containing number species.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/get_immig_rate.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Calculate immigration rate — get_immig_rate","text":"Valente, Luis M., Rampal S. Etienne, Albert B. Phillimore. \"effects island ontogeny species diversity phylogeny.\" Proceedings Royal Society London B: Biological Sciences 281.1784 (2014): 20133227.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/get_immig_rate.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculate immigration rate — get_immig_rate","text":"Pedro Neves, Joshua Lambert","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/get_trans_rate.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate transition rate — get_trans_rate","title":"Calculate transition rate — get_trans_rate","text":"Internal function. Calculates transition rate given current number immigrant species per capita rate.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/get_trans_rate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate transition rate — get_trans_rate","text":"","code":"get_trans_rate(trait_pars, island_spec)"},{"path":"https://rsetienne.github.io/DAISIE/reference/get_trans_rate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate transition rate — get_trans_rate","text":"trait_pars named list containing diversification rates considering two trait states created create_trait_pars: [1]:numeric per capita transition rate state1 [2]:numeric per capita immigration rate state2 [3]:numeric per capita extinction rate state2 [4]:numeric per capita anagenesis rate state2 [5]:numeric per capita cladogenesis rate state2 [6]:numeric per capita transition rate state2 [7]:numeric number species trait state 2 mainland island_spec Matrix current state simulation containing number species.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/integral_peak.html","id":null,"dir":"Reference","previous_headings":"","what":"Computes integral of a very peaked function, modified from the\nSADISA package — integral_peak","title":"Computes integral of a very peaked function, modified from the\nSADISA package — integral_peak","text":"computes logarithm integral exp(logfun) 0 Inf following assumptions: \"exp(logfun)\" single, sharply peaked maximum \"exp(logfun)\" increasing left peak  decreasing right peak \"exp(logfun)\" can zero positive zero \"exp(logfun)\" tends zero infinity","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/integral_peak.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Computes integral of a very peaked function, modified from the\nSADISA package — integral_peak","text":"","code":"integral_peak(   logfun,   xx = seq(-20, 20, 2),   xcutoff = 2,   ymaxthreshold = 1e-12,   pars1,   pars2,   brts,   stac,   missnumspec,   methode,   abstolint,   reltolint,   verbose,   pick,   par_mean,   par_sd,   par_upper_bound )"},{"path":"https://rsetienne.github.io/DAISIE/reference/integral_peak.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Computes integral of a very peaked function, modified from the\nSADISA package — integral_peak","text":"logfun logarithm function integrate xx initial set points evaluate function xcutoff maximum found among xx, parameter sets width interval find maximum ymaxthreshold sets deviation allowed finding maximum among xx","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/integral_peak.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Computes integral of a very peaked function, modified from the\nSADISA package — integral_peak","text":"result integration","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/integral_peak.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Computes integral of a very peaked function, modified from the\nSADISA package — integral_peak","text":"Haegeman, B. & R.S. Etienne (2017). general sampling formula community structure data. Methods Ecology & Evolution 8: 1506-1519. https://doi.org/10.1111/2041-210X.12807","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/island_area.html","id":null,"dir":"Reference","previous_headings":"","what":"Function to describe changes in area through time. — island_area","title":"Function to describe changes in area through time. — island_area","text":"Function describe changes area time.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/island_area.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function to describe changes in area through time. — island_area","text":"","code":"island_area(timeval, total_time, area_pars, peak, island_ontogeny, sea_level)"},{"path":"https://rsetienne.github.io/DAISIE/reference/island_area.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function to describe changes in area through time. — island_area","text":"timeval Numeric defining current time simulation. total_time Numeric defining length simulation time units. area_pars named list containing area sea level parameters created create_area_pars(): [1]: maximum area [2]: current area [3]: value 0 1 indicating island's history   peak area achieved [4]: total island age [5]: amplitude area fluctuation sea level [6]: frequency sine wave area change sea level [7]: angle slope island peak numeric value specifying peakiness (shaprness) ontogeny curve. Higher values imply peakier ontogeny. value internally calculated calc_peak() given area present area_pars. island_ontogeny DAISIE_sim_time_dep(), DAISIE_ML_CS plotting string describing type island ontogeny. Can \"const\", \"beta\" beta function describing area time.  functions numeric describing type island ontogeny. Can 0 constant, 1 beta function describing area time. ML functions island_ontogeny = NA assumes constant ontogeny. Time dependent estimation yet available development still ongoing. return error called case. sea_level DAISIE_sim_time_dep() plotting string describing type sea level. Can \"const\" \"sine\" sine function describing area time.  functions numeric describing type sea level. Can 0 constant, 1 sine function describing area time.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/island_area.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Function to describe changes in area through time. — island_area","text":"Valente, Luis M., Rampal S. Etienne, Albert B. Phillimore. \"effects island ontogeny species diversity phylogeny.\" Proceedings Royal Society London B: Biological Sciences 281.1784 (2014): 20133227.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/island_area.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Function to describe changes in area through time. — island_area","text":"Pedro Neves, Joshua Lambert","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/island_area_vector.html","id":null,"dir":"Reference","previous_headings":"","what":"Computes island_area, but takes vector as argument (needed by ) — island_area_vector","title":"Computes island_area, but takes vector as argument (needed by ) — island_area_vector","text":"Computes island_area, takes vector argument (needed )","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/island_area_vector.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Computes island_area, but takes vector as argument (needed by ) — island_area_vector","text":"","code":"island_area_vector(   timeval,   area_pars,   island_ontogeny,   sea_level,   total_time,   peak )"},{"path":"https://rsetienne.github.io/DAISIE/reference/island_area_vector.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Computes island_area, but takes vector as argument (needed by ) — island_area_vector","text":"timeval current time simulation area_pars vector similar list produced create_area_pars [1]: maximum area [2]: value 0 1 indicating island's history   peak area achieved [3]: total island age island_ontogeny string describing type island ontogeny. Can NULL, \"beta\" beta function describing area time. sea_level numeric describing type sea level.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/island_area_vector.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Computes island_area, but takes vector as argument (needed by ) — island_area_vector","text":"Valente, Luis M., Rampal S. Etienne, Albert B. Phillimore. \"effects island ontogeny species diversity phylogeny.\" Proceedings Royal Society London B: Biological Sciences 281.1784 (2014): 20133227.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/island_area_vector.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Computes island_area, but takes vector as argument (needed by ) — island_area_vector","text":"Pedro Neves","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/islands_10reps_RAW.html","id":null,"dir":"Reference","previous_headings":"","what":"1000 islands in RAW format simulated with the ML parameters of the CR model\nfor the Galapagos data. — islands_10reps_RAW","title":"1000 islands in RAW format simulated with the ML parameters of the CR model\nfor the Galapagos data. — islands_10reps_RAW","text":"simulated dataset element list, can called using e.g. islands_10reps_RAW[[1]] island replicates list . first (e.g. islands_10reps_RAW[[x]][[1]]) element list following components:  following elements RAW list contain information single colonist lineage island 5 components:$branching_times - island age stem age population/species case Non-endemic, Non-endemic_MaxAge Endemic anagenetic species. cladogenetic species island age branching times radiation including stem age radiation.$stac - status colonist  * Not_present: 0  * Non_endemic_MaxAge: 1  * Endemic: 2  * Endemic&Non_Endemic: 3  * Non_endemic: 4 $stt_table - Species--time table descendants mainland species (nI - number non-endemic species; nA - number anagenetic species, nC - number cladogenetic species)$missing_species - number island species sampled particular clade (applicable endemic clades)","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/islands_10reps_RAW.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"1000 islands in RAW format simulated with the ML parameters of the CR model\nfor the Galapagos data. — islands_10reps_RAW","text":"list 10 items.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/islands_10reps_RAW.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"1000 islands in RAW format simulated with the ML parameters of the CR model\nfor the Galapagos data. — islands_10reps_RAW","text":"Valente, L.M., .B. Phillimore R.S. Etienne (2015). Equilibrium non-equilibrium dynamics simultaneously operate Galapagos islands. Ecology Letters 18: 844-852.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/islands_1type_1000reps.html","id":null,"dir":"Reference","previous_headings":"","what":"1000 islands in DAISIE format simulated with the ML parameters of the CR\nmodel for the Galapagos data — islands_1type_1000reps","title":"1000 islands in DAISIE format simulated with the ML parameters of the CR\nmodel for the Galapagos data — islands_1type_1000reps","text":"simulated dataset element list, can called using e.g. islands_1type_1000reps[[1]] island replicates list . first (e.g. islands_1type_1000reps[[x]][[1]]) element list following components: $island_age - island age$not_present - number mainland lineages present island $stt_all - STT table species island (nI - number non-endemic species; nA - number anagenetic species, nC - number cladogenetic species, present - number independent colonisations present ) subsequent elements list contain information single colonist lineage island 3 components:$branching_times - island age stem age population/species case Non-endemic, Non-endemic_MaxAge Endemic anagenetic species. cladogenetic species island age branching times radiation including stem age radiation.$stac - status colonist  * Non_endemic_MaxAge: 1  * Endemic: 2  * Endemic&Non_Endemic: 3  * Non_endemic: 4 $missing_species - number island species sampled particular clade (applicable endemic clades)","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/islands_1type_1000reps.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"1000 islands in DAISIE format simulated with the ML parameters of the CR\nmodel for the Galapagos data — islands_1type_1000reps","text":"list 1000 items.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/islands_1type_1000reps.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"1000 islands in DAISIE format simulated with the ML parameters of the CR\nmodel for the Galapagos data — islands_1type_1000reps","text":"Valente, L.M., .B. Phillimore R.S. Etienne (2015). Equilibrium non-equilibrium dynamics simultaneously operate Galapagos islands. Ecology Letters 18: 844-852.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/islands_2types_1000reps.html","id":null,"dir":"Reference","previous_headings":"","what":"1000 islands in DAISIE format simulated with the ML parameters of the\nCR_lamc_mu_K model for the Galapagos data (2 types of species) — islands_2types_1000reps","title":"1000 islands in DAISIE format simulated with the ML parameters of the\nCR_lamc_mu_K model for the Galapagos data (2 types of species) — islands_2types_1000reps","text":"simulated dataset element list, can called using e.g. islands_2types_1000reps[[1]] island replicates list . first (e.g. islands_2types_1000reps[[x]][[1]]) element list following components: $island_age - island age$not_present_type1 - number mainland lineages type 1 present island $not_present_type2 - number mainland lineages type 2 present island $stt_all - STT table species island (nI - number non-endemic species; nA - number anagenetic species, nC - number cladogenetic species, present - number independent colonisations present )$stt_stt_type1 - STT table type 1 species island (nI - number non-endemic species; nA - number anagenetic species, nC - number cladogenetic species, present - number independent colonisations present )$stt_stt_type2 - STT table type 2 species island (nI - number non-endemic species; nA - number anagenetic species, nC - number cladogenetic species, present - number independent colonisations present ) subsequent elements list contain information single colonist lineage island 4 components:$branching_times - island age stem age population/species case Non-endemic, Non-endemic_MaxAge Endemic anagenetic species. cladogenetic species island age branching times radiation including stem age radiation.$stac - status colonist  * Non_endemic_MaxAge: 1  * Endemic: 2  * Endemic&Non_Endemic: 3  * Non_endemic: 4 $missing_species - number island species sampled particular clade (applicable endemic clades) $type_1or2 - whether colonist belongs type 1 type 2","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/islands_2types_1000reps.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"1000 islands in DAISIE format simulated with the ML parameters of the\nCR_lamc_mu_K model for the Galapagos data (2 types of species) — islands_2types_1000reps","text":"list 1000 items.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/islands_2types_1000reps.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"1000 islands in DAISIE format simulated with the ML parameters of the\nCR_lamc_mu_K model for the Galapagos data (2 types of species) — islands_2types_1000reps","text":"Valente, L.M., .B. Phillimore R.S. Etienne (2015). Equilibrium non-equilibrium dynamics simultaneously operate Galapagos islands. Ecology Letters 18: 844-852.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/remove_empty_elements.html","id":null,"dir":"Reference","previous_headings":"","what":"Remove superfluous lines in empty simulations — remove_empty_elements","title":"Remove superfluous lines in empty simulations — remove_empty_elements","text":"Remove superfluous lines empty simulations","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/remove_empty_elements.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Remove superfluous lines in empty simulations — remove_empty_elements","text":"","code":"remove_empty_elements(sims)"},{"path":"https://rsetienne.github.io/DAISIE/reference/remove_empty_elements.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Remove superfluous lines in empty simulations — remove_empty_elements","text":"sims List output DAISIE_sim","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/remove_empty_elements.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Remove superfluous lines in empty simulations — remove_empty_elements","text":"Output DAISIE_sim without empty elements","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/rho.html","id":null,"dir":"Reference","previous_headings":"","what":"Gamma distribution density parameterised with mean and standard deviation — rho","title":"Gamma distribution density parameterised with mean and standard deviation — rho","text":"Gamma distribution density parameterised mean standard deviation","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/rho.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Gamma distribution density parameterised with mean and standard deviation — rho","text":"","code":"rho(DAISIE_par, DAISIE_dist_pars)"},{"path":"https://rsetienne.github.io/DAISIE/reference/rho.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Gamma distribution density parameterised with mean and standard deviation — rho","text":"DAISIE_par numeric parameter evaluate integral function. DAISIE_dist_pars numeric vector two elements, first mean second standard deviation distribution.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/rho.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Gamma distribution density parameterised with mean and standard deviation — rho","text":"Numeric","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/sample_relaxed_rate.html","id":null,"dir":"Reference","previous_headings":"","what":"Samples from distribution when parameter is relaxed — sample_relaxed_rate","title":"Samples from distribution when parameter is relaxed — sample_relaxed_rate","text":"Samples distribution parameter relaxed","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/sample_relaxed_rate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Samples from distribution when parameter is relaxed — sample_relaxed_rate","text":"","code":"sample_relaxed_rate(pars, relaxed_par)"},{"path":"https://rsetienne.github.io/DAISIE/reference/sample_relaxed_rate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Samples from distribution when parameter is relaxed — sample_relaxed_rate","text":"pars vector 5 elements model parameters relaxed_par string determining parameter relaxed","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/sample_relaxed_rate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Samples from distribution when parameter is relaxed — sample_relaxed_rate","text":"vector parameters.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/stac_table.html","id":null,"dir":"Reference","previous_headings":"","what":"Explanatory table on meaning and use of stac settings — stac_table","title":"Explanatory table on meaning and use of stac settings — stac_table","text":"table containing information regarding meaning stac codes utilised DAISIE's ML functions. used render \"DAISIE stac values\" vignette. stac stands \"status clade\" formed immigrant. important part DAISIE objects informs likelihood functions endemicity status type data available insular clade. colonisation event extant species island needs stac value specified. also implications included DAISIE object \"branching_times\" vector, also described table. table composed following columns: $stac: numeric stac code 1 9. $Input DAISIE_dataprep table \"Clade_Name\": character   possibilities input DAISIE_dataprep()   clade, translated numeric stac code   $stac. $Type species clade\": character   plain English explanation different possible kinds   island lineages can considered DAISIE. $Input DAISIE_dataprep table \"Branching_times\":   character plain English explanation branching times   vector DAISIE object contain. $Colonisation times: character plain English   explanation colonisation time branching times vector   DAISIE object (first element vector) means.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/stac_table.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Explanatory table on meaning and use of stac settings — stac_table","text":"table 9 rows 5 columns.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/transform_gamma_pars.html","id":null,"dir":"Reference","previous_headings":"","what":"Transforms mean and standard deviation to shape and scale gamma parameters — transform_gamma_pars","title":"Transforms mean and standard deviation to shape and scale gamma parameters — transform_gamma_pars","text":"Transforms mean standard deviation shape scale gamma parameters","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/transform_gamma_pars.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Transforms mean and standard deviation to shape and scale gamma parameters — transform_gamma_pars","text":"","code":"transform_gamma_pars(par_mean, par_sd)"},{"path":"https://rsetienne.github.io/DAISIE/reference/transform_gamma_pars.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Transforms mean and standard deviation to shape and scale gamma parameters — transform_gamma_pars","text":"par_mean mean relaxed parameter par_sd standard deviation relaxed parameter","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/transform_gamma_pars.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Transforms mean and standard deviation to shape and scale gamma parameters — transform_gamma_pars","text":"list shape scale parameters","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/update_max_rates.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculates the maximum rates for a Gillespie simulation — update_max_rates","title":"Calculates the maximum rates for a Gillespie simulation — update_max_rates","text":"Internal function updates max rates time t.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/update_max_rates.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculates the maximum rates for a Gillespie simulation — update_max_rates","text":"","code":"update_max_rates(   gam,   laa,   lac,   mu,   hyper_pars = NULL,   extcutoff,   K,   num_spec,   num_immigrants,   mainland_n,   Amin,   Amax )"},{"path":"https://rsetienne.github.io/DAISIE/reference/update_max_rates.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculates the maximum rates for a Gillespie simulation — update_max_rates","text":"gam numeric per capita immigration rate. laa numeric per capita anagenesis rate. lac numeric per capita cladogenesis rate. mu numeric per capita extinction rate. hyper_pars named list numeric hyperparameters rate calculations returned create_hyper_pars(): [1]: d scaling parameter exponent calculating   cladogenesis rate [2]: x exponent calculating extinction rate extcutoff numeric cutoff maximum extinction rate preventing large slowing simulation. K numeric carrying capacity. num_spec numeric current number species. num_immigrants numeric current number non-endemic species (.k.non-endemic species). mainland_n numeric stating number mainland species, number species can potentially colonize island. using clade-specific diversity dependence, value set 1. using island-wide diversity dependence, value set number mainland species. Amin numeric value minimum island area simulation. Amax numeric value maximum island area simulation.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/update_max_rates.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculates the maximum rates for a Gillespie simulation — update_max_rates","text":"named list updated effective rates.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/update_rates.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculates algorithm rates — update_rates","title":"Calculates algorithm rates — update_rates","text":"Internal function updates rates max extinction horizon time t.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/update_rates.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculates algorithm rates — update_rates","text":"","code":"update_rates(   timeval,   total_time,   gam,   laa,   lac,   mu,   hyper_pars = hyper_pars,   area_pars = NULL,   peak = NULL,   island_ontogeny = NULL,   sea_level = NULL,   extcutoff,   K,   num_spec,   num_immigrants,   mainland_n,   trait_pars = NULL,   island_spec = NULL )"},{"path":"https://rsetienne.github.io/DAISIE/reference/update_rates.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculates algorithm rates — update_rates","text":"timeval Numeric defining current time simulation. total_time Numeric defining length simulation time units. gam numeric per capita immigration rate. laa numeric per capita anagenesis rate. lac numeric per capita cladogenesis rate. mu numeric per capita extinction rate. hyper_pars named list numeric hyperparameters rate calculations returned create_hyper_pars(): [1]: d scaling parameter exponent calculating   cladogenesis rate [2]: x exponent calculating extinction rate area_pars named list containing area sea level parameters created create_area_pars(): [1]: maximum area [2]: current area [3]: value 0 1 indicating island's history   peak area achieved [4]: total island age [5]: amplitude area fluctuation sea level [6]: frequency sine wave area change sea level [7]: angle slope island peak numeric value specifying peakiness (shaprness) ontogeny curve. Higher values imply peakier ontogeny. value internally calculated calc_peak() given area present area_pars. island_ontogeny DAISIE_sim_time_dep(), DAISIE_ML_CS plotting string describing type island ontogeny. Can \"const\", \"beta\" beta function describing area time.  functions numeric describing type island ontogeny. Can 0 constant, 1 beta function describing area time. ML functions island_ontogeny = NA assumes constant ontogeny. Time dependent estimation yet available development still ongoing. return error called case. sea_level DAISIE_sim_time_dep() plotting string describing type sea level. Can \"const\" \"sine\" sine function describing area time.  functions numeric describing type sea level. Can 0 constant, 1 sine function describing area time. extcutoff numeric cutoff maximum extinction rate preventing large slowing simulation. K numeric carrying capacity. num_spec numeric current number species. num_immigrants numeric current number non-endemic species (.k.non-endemic species). mainland_n numeric stating number mainland species, number species can potentially colonize island. using clade-specific diversity dependence, value set 1. using island-wide diversity dependence, value set number mainland species. trait_pars named list containing diversification rates considering   two trait states created create_trait_pars: [1]:numeric per capita transition rate state1 [2]:numeric per capita immigration rate state2 [3]:numeric per capita extinction rate state2 [4]:numeric per capita anagenesis rate state2 [5]:numeric per capita cladogenesis rate state2 [6]:numeric per capita transition rate state2 [7]:numeric number species trait state 2    mainland island_spec Matrix current state simulation containing number species.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/update_rates.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculates algorithm rates — update_rates","text":"named list updated effective rates.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/news/index.html","id":"daisie-441","dir":"Changelog","previous_headings":"","what":"DAISIE 4.4.1","title":"DAISIE 4.4.1","text":"CRAN release: 2023-10-21 Fix bug calculation shift loglikelihoods. Fix bug parameters optimized incorrectly Inf #159 #160 (@joshwlambert). DAISIE_SR_loglik_CS_M1() now DAISIE_loglik_CS_shift(). New pkgdown website. Several improvements relaxed rate code.","code":""},{"path":"https://rsetienne.github.io/DAISIE/news/index.html","id":"daisie-440","dir":"Changelog","previous_headings":"","what":"DAISIE 4.4.0","title":"DAISIE 4.4.0","text":"CRAN release: 2023-04-02 longer include patched version boost/numeric/odeint/stepper/bulirsch_stoer.hpp, address issue passing previously uninitialised variable boost::units::quantity<boost::units::si::dimensionless, double>. Document return type exported Rcpp functions. Move internal non-error printing console message() warning(). Add internal functions address . verbose variable now numeric, varying 0 3. Increasing values increase amount messages printed. Change default printing output golden rule silence verbose == 0. print , set verbose >= 1. Remove calls options(warn = -1) suppress warnings non standard way. Use suppressWarnings() appropriate. Safely restore graphics settings plot. Fix references DESCRIPTION. Remove internal (unnecessary) calls internal functions via :::. longer use roxygen2 tag internal document without index use noRd instead. are_area_pars() now internal. Replace \\dontrun examples documentation \\donttest. Speed examples. License package C++ source files BSL-1.0 (c) Hanno Hildenbrandt, FORTRAN files BSL-1.0 (c) Rampal S. Etienne. Add LICENSE.note, inst/COPYRIGHTS clarify license copyrights. Pipe files DESCRIPTION.","code":""},{"path":"https://rsetienne.github.io/DAISIE/news/index.html","id":"daisie-434","dir":"Changelog","previous_headings":"","what":"DAISIE 4.3.4","title":"DAISIE 4.3.4","text":"Require C++17 via CXX_STD flag Makevars[.win]. Add SystemRequirements: C++17 DESCRIPTION standard “Writing R Extensions” requires explicitly stated. Depends R (>= 4.2.0) due C++17 requirement Windows due Rtools 4.0, used R 4.0-4.1. Toolchain Rtools 4.0 gcc 8.3 “GCC 9.1 first release non-experimental C++17 support”. per https://gcc.gnu.org/.","code":""},{"path":"https://rsetienne.github.io/DAISIE/news/index.html","id":"daisie-433","dir":"Changelog","previous_headings":"","what":"DAISIE 4.3.3","title":"DAISIE 4.3.3","text":"Patched version boost/numeric/odeint/stepper/bulirsch_stoer.hpp. done including patched header file src/patched_bulrisch_stoer.h boost/numeric/odeint shadow boost/numeric/odeint/stepper/bulrisch_stoer.hpp issue fixed BOOST_VERSION == 1.81.0. Must check fixes upcomming boost (BH) releases. Fix tab spacing src/DAISIE_loglik_rhs_FORTRAN.f95. Re-implement clang16 -D_HAS_AUTO_PTR_ETC flag fix via Makevars[.win] comply CRAN requests force C++ standard C++14 without using SystemRequirements line DESCRIPTION, CRAN’s request. Skip plotting tests cause problems headless systems. run manually. Skip tests --now experimental steppers ODEINT rosenbrock4 adams bashfort moulton 1 slow.","code":""},{"path":"https://rsetienne.github.io/DAISIE/news/index.html","id":"daisie-432","dir":"Changelog","previous_headings":"","what":"DAISIE 4.3.2","title":"DAISIE 4.3.2","text":"Add config.h macro, checking , setting, _HAS_AUTO_PTR_ETC BOOST_NO_AUTO_PTR. Change SystemRequirements DESCRIPTION C++17 C++14. fix applied package 'DDD' version 5.2.1.","code":""},{"path":"https://rsetienne.github.io/DAISIE/news/index.html","id":"daisie-431","dir":"Changelog","previous_headings":"","what":"DAISIE 4.3.1","title":"DAISIE 4.3.1","text":"CRAN release: 2023-02-13 Fix issue prevented ‘covr’ running correctly. Depend R >= 4.1.0, C++17. Tests DAISIE_ML_*() integration tests don’t run CRAN due long runtime.","code":""},{"path":"https://rsetienne.github.io/DAISIE/news/index.html","id":"daisie-430","dir":"Changelog","previous_headings":"","what":"DAISIE 4.3.0","title":"DAISIE 4.3.0","text":"Due recent changes CRAN policy result warnings due use Rcpp related packages link libraries use sprintf (‘Rcpp’ ‘BH’), ‘DAISIE’ now requires Rcpp v(>= 1.0.10) BH v(>= 1.81.0-1). See https://github.com/RcppCore/Rcpp/pull/1236 https://github.com/eddelbuettel/bh/pull/90 respectively. Also require package ‘DDD’ v(>= 5.0.0). Add code trait-dependent simulations considering two carrying capacities trait state. Improvements relaxed rate model fitting procedure. Add DAISIE_count_species() count number species datalist simulated data. Simply printing code wrapping multiple instances print_parameters_and_loglik(). Overall documentation improvements updated references. Bug fix DAISIE_sim_cr_iw(), wrongly computed number species present. #147 Improve likelihood calculation. Fixed incorrect likelihood present type 2 case CS model inference values lambda high, C++ implementation. Overhaul GHA workflows date conservative run. Feature branches require tag [run ci] added commit message run.","code":""},{"path":"https://rsetienne.github.io/DAISIE/news/index.html","id":"daisie-421","dir":"Changelog","previous_headings":"","what":"DAISIE 4.2.1","title":"DAISIE 4.2.1","text":"Bug fixes DAISIE_loglik_CS()likelihood code continental sampling (probability initial presence island). Bug fix DAISIE_sim_cr_iw() replication works correctly.","code":""},{"path":"https://rsetienne.github.io/DAISIE/news/index.html","id":"daisie-420","dir":"Changelog","previous_headings":"","what":"DAISIE 4.2.0","title":"DAISIE 4.2.0","text":"CRAN release: 2022-06-02 divergence time unknown known occurred specific point time island’s existence. divergence time unknown known occurred specific point time island’s existence (usually known dated population level phylogenetic data available). Improve finalise continental island estimation scenario, initially species present island inception. Improve tests related two points . Remove DAISIE time dependent estimation code now ease work remaining code. Development proceed separately. Rate computations simulation first calculated per lineage, calculated per island. needed time dependent estimation later . Improve zenodo metadata. Add methode = \"odeint::adams_bashforth_moulton_X\" list available numeric integrators parameter estimation.","code":""},{"path":"https://rsetienne.github.io/DAISIE/news/index.html","id":"daisie-411","dir":"Changelog","previous_headings":"","what":"DAISIE 4.1.1","title":"DAISIE 4.1.1","text":"Correctly use .data.frame() rather class(foo) == \"data.frame\" satisfy CRAN note.","code":""},{"path":"https://rsetienne.github.io/DAISIE/news/index.html","id":"daisie-410","dir":"Changelog","previous_headings":"","what":"DAISIE 4.1.0","title":"DAISIE 4.1.0","text":"Produces full stt tables. Can run conditioning number surviving species present. Added DAISIE_CS_max_steps() manually change maximum number integration steps CS C++ integrators. Renamed reworked simulation architecture. Renamed totaltime total_time. Integrators package 'deSolve' reinstated default ODE solvers. Added stac_key vignette detailing possible statuses colonist lineages. Use LazyData.","code":""},{"path":"https://rsetienne.github.io/DAISIE/news/index.html","id":"daisie-405","dir":"Changelog","previous_headings":"","what":"DAISIE 4.0.5","title":"DAISIE 4.0.5","text":"N.B.: MacOS users may experience issues installing DAISIE, especially MacOS Big Sur. case, please see detailed installation instructions. \"odeint::runge_kutta_cash_karp54\" \"odeint::runge_kutta_fehlberg78\" [default] \"odeint::runge_kutta_dopri5\" \"odeint::bulirsch_stoer\" without odeint::-prefix, deSolve::ode method assumed. deSolve::ode using \"lsodes\" still default, . Make sure CS_version = 0 (default) use C++ ODEINT numerical integration. * Better handling number threads use DAISIE_IW_num_threads() ML estimation IW model threads available. * Fixes numerical instability conditional probability calculation IW model probability extinction close 1. * Introduce approximation log conditional likelihood computed add message triggered.","code":""},{"path":"https://rsetienne.github.io/DAISIE/news/index.html","id":"daisie-402","dir":"Changelog","previous_headings":"","what":"DAISIE 4.0.2","title":"DAISIE 4.0.2","text":"N.B.: MacOS users may experience issues installing DAISIE, especially MacOS Big Sur. case, please see detailed installation instructions. Suggest ggtree >= 3.0.0.","code":""},{"path":"https://rsetienne.github.io/DAISIE/news/index.html","id":"daisie-401","dir":"Changelog","previous_headings":"","what":"DAISIE 4.0.1","title":"DAISIE 4.0.1","text":"N.B.: MacOS users may experience issues installing DAISIE, especially MacOS Big Sur. case, please see detailed installation instructions. Fix possibility fitting CS model IW likelihood simulated data setting CS_version = 0. Improve CS_version documentation.","code":""},{"path":"https://rsetienne.github.io/DAISIE/news/index.html","id":"daisie-400","dir":"Changelog","previous_headings":"","what":"DAISIE 4.0.0","title":"DAISIE 4.0.0","text":"N.B.: MacOS users may experience issues installing DAISIE, especially MacOS Big Sur. case, please see detailed installation instructions. Fix bug calculating conditional probabilities, now correctly calculated island age present. Fix bug calculating probabilities upon migration, assumed recolonisation possible CS model. Handling recolonisation manner possible IW model, approximation now made. influence bug approximation IW model expected minimal, particularly cases colonisation rate low. cases low colonisation norm. Add num_cycles argument ML functions, allowing specify many cycles optimizer take. Defaults 1. Minor vignette corrections. Improve README.md documentation.","code":""},{"path":"https://rsetienne.github.io/DAISIE/news/index.html","id":"daisie-321","dir":"Changelog","previous_headings":"","what":"DAISIE 3.2.1","title":"DAISIE 3.2.1","text":"N.B.: MacOS users may experience issues installing DAISIE, especially MacOS Big Sur. case, please see detailed installation instructions. Minor documentation improvements.","code":""},{"path":"https://rsetienne.github.io/DAISIE/news/index.html","id":"daisie-320","dir":"Changelog","previous_headings":"","what":"DAISIE 3.2.0","title":"DAISIE 3.2.0","text":"N.B.: MacOS users may experience issues installing DAISIE, especially MacOS Big Sur. case, please see detailed installation instructions. DAISIE_loglikg_IW() now efficient numerically stable. Numerical integration now done via C++ package odeint. Add relaxed rate capabilities (inference simulations). Relaxed rate models allow parameters static, sampled specific probability distributions. Introduce MinAge data status DAISIE data objects. status containing MinAge sets lower boundary colonization situations precise colonization time unknown. interpreted DAISIE_dataprep() information passed likelihood optimization functions. See DAISIE_dataprep() help page details. back-end results new stac values 8 9. Bug fix “bug 2” bug report manuscript. bug present DAISIE_ONEcolonist() recolonization occurs. now fixed colonization branching times stored way now think best dealt likelihood code. recolonization cases, $other_clades_same_ancestor renamed $all_colonisations. #125 Fix bug occurs rarely, computing log conditional probabilities. applicable ML code running cond. Removed deprecated legacy functions. Removed functions named DAISIE_*_VERSION_NUMBER() DAISIE_calc_*_rate() funcions get_brts_mya(). #126 Made functions internal, . DAISIE_make_global() create_island() now internal. #127 @HHildenbrandt now author. Added @xieshu95’s @joshwlambert’s ORCIDs. Added NEWS.md file track changes package.","code":""},{"path":"https://rsetienne.github.io/DAISIE/news/index.html","id":"daisie-310","dir":"Changelog","previous_headings":"","what":"DAISIE 3.1.0","title":"DAISIE 3.1.0","text":"Expands possibility conditioning simulations MLE CS model number colonizing lineages. simulation ML functions, cond argument can now greater one. non-zero cond signifies ML simulation conditioned least cond colonizations island. Implements #121, sim ML level. Add BugReports, Website missing ORCID DESCRIPTION.","code":""},{"path":"https://rsetienne.github.io/DAISIE/news/index.html","id":"daisie-301","dir":"Changelog","previous_headings":"","what":"DAISIE 3.0.1","title":"DAISIE 3.0.1","text":"CRAN release: 2020-08-26 Correct @joshwlambert’s name DESCRIPTION. DAISIE_sim_relaxed_rate() input closer DAISIE_ML() input. Documentation improvements. Tweak Makevars.","code":""},{"path":"https://rsetienne.github.io/DAISIE/news/index.html","id":"daisie-300","dir":"Changelog","previous_headings":"","what":"DAISIE 3.0.0","title":"DAISIE 3.0.0","text":"CRAN release: 2020-08-14 Major revamp simulation code. Simulations now accessed using DAISIE_sim_*() syntax. Constant rate, time-dependent, trait-dependent, (multiple) split-rate available. Relaxed-rate inference available DAISIE_ML_CS(). Improved vignettes documenting CS IW cases. Full stt can returned setting sample_freq = Inf DAISIE_sim_*() functions. Optional plotting DAISIE_plot_input(). (Requires additional dependencies). Back-end architecture improvements.","code":""},{"path":"https://rsetienne.github.io/DAISIE/news/index.html","id":"daisie-201","dir":"Changelog","previous_headings":"","what":"DAISIE 2.0.1","title":"DAISIE 2.0.1","text":"Minor update v2.0: empty islands simulated output list contains one element instead two (second indicated stac = 0, .e. surviving colonization).","code":""},{"path":"https://rsetienne.github.io/DAISIE/news/index.html","id":"daisie-20","dir":"Changelog","previous_headings":"","what":"DAISIE 2.0","title":"DAISIE 2.0","text":"Contains functions used : Valente L., Etienne R.S., Garcia-R J.C. (2019) Deep macroevolutionary impact humans New Zealand’s unique avifauna. Current Biology , 29, 2563-2569.e4. https://doi.org/10.1016/j.cub.2019.06.058 Valente L., Phillimore .B., Melo M. et al. (2020) simple dynamic model explains diversity island birds worldwide. Nature , 579, 92–96. https://doi.org/10.1038/s41586-020-2022-5 Hauffe T, Delicado D, Etienne R.S. Valente L. (2020) Lake expansion elevates equilibrium diversity via increasing colonisation. Journal Biogeography. https://doi.org/10.1111/jbi.13914","code":""}]
+[{"path":"https://rsetienne.github.io/DAISIE/CONTRIBUTING.html","id":null,"dir":"","previous_headings":"","what":"DAISIE Contributing Guidelines","title":"DAISIE Contributing Guidelines","text":"Feature requests collaboration DAISIE encouraged. ensure consistency quality code many collaborators working codebase, certain conventions must followed. External pull-requests rejected changes required conditions met. happens, please aware way personal, sure appreciate interest DAISIE, rather, enforce rules ensure package readable bug-free can make .","code":""},{"path":"https://rsetienne.github.io/DAISIE/CONTRIBUTING.html","id":"naming","dir":"","previous_headings":"","what":"Naming","title":"DAISIE Contributing Guidelines","text":"Files functions file functions start prefix DAISIE_. Helper functions can go files start prefix DAISIE_ stored within DAISIE_ prefixed file owing point 1.","code":""},{"path":"https://rsetienne.github.io/DAISIE/CONTRIBUTING.html","id":"style","dir":"","previous_headings":"","what":"Style","title":"DAISIE Contributing Guidelines","text":"Code formatted according tidyverse style guide. can checked running devtools::lint(), examine DAISIE package check code line style guide give corrections error style exists.","code":""},{"path":"https://rsetienne.github.io/DAISIE/CONTRIBUTING.html","id":"coverage-and-testing","dir":"","previous_headings":"","what":"Coverage and testing","title":"DAISIE Contributing Guidelines","text":"Cover new functions unit test. Unit tests function way ensure new functions behave expected, internal form documentation. Unit tests cover things : correct type returned function called correctly, boundary cases behave expected, simple, short runs function return expected, correct output. helper function unit testing available usethis::use_test(). cursor function requiring testing, new file skeleton code testing generated. Test coverage can calculated using function devtools::test_coverage(). produce window function’s coverage across whole package. new functions must (least) 100% coverage. Integration tests encouraged. Integration tests, unlike unit tests, test functionality package unified way. Examples integration testing include testing entire ML routine. integration tests generally much slower run, request skipped local builds run Travis CI. Care still taken balance test’s speed usefulness, try make fast possible. still impossible, final option include said integration test DAISIE’s sister package DAISIEtesting, built specifically purpose.","code":""},{"path":"https://rsetienne.github.io/DAISIE/CONTRIBUTING.html","id":"documentation","dir":"","previous_headings":"","what":"Documentation","title":"DAISIE Contributing Guidelines","text":"Use R package roxygen2 document package individual functions. Use devtools::document() write NAMESPACE. functions documented using shortcut Ctrl + Alt + Shift + R cursor function name. write skeleton function documentation can write function description parameters, etc. Every function needs documentation. includes helper secondary functions. Internal functions require explicit documentation entry CRAN manual, marked @keyword Internal ensure developer documentation still accessible, preventing unnecessary clutter user manual. Parameter documentation written default_params_doc.R called function. Thus, individual function’s roxygen block NEVER @param field, instead @inheritParams default_params_doc. exported functions accompanied runnable easy read examples document possible flows code. means simulation can run IW CS modes, instance, example code provided methods. rare cases running example possible, e.g. virtually impossible make code fast, error expected, please write example anyway encapsulate \\dontthest{} \\dontrun{} tags respectively. Authorship/blame. direct indirect contributor piece code listed @author, unless specifically requested author. Similarly, code refers specific publication, please include formatted citation @references. Exported functions. mentioned , NAMESPACE handled automatically roxygen2. functions required users exported @export. example, sim_core family functions exported, sim family functions supposed .","code":""},{"path":"https://rsetienne.github.io/DAISIE/CONTRIBUTING.html","id":"git-github-and-continuous-integration","dir":"","previous_headings":"","what":"Git, GitHub and continuous integration","title":"DAISIE Contributing Guidelines","text":"DAISIE sorted collaborated via GitHub, repository. can make branch (permission maintainer Rampal, GitHub account name: @rsetienne), allow work code without disturbing existing working DAISIE (master branch). code working, can merged develop branch eventually master. Code can pushed branch using git, either command line directly RStudio. merge topic branch develop branch fails R CMD Check. can run R CMD Check locally using RStudio Ctrl + Shift + E, Windows need latest version RTools installed build check package source. Topic branches can merged develop, develop merged master. DAISIE package GitHub uses continuous integration (CI) using Travis CI. means every time push code GitHub repository built, checked errors test coverage calculated uploaded codecov.io.","code":""},{"path":"https://rsetienne.github.io/DAISIE/CONTRIBUTING.html","id":"vignette","dir":"","previous_headings":"","what":"Vignette","title":"DAISIE Contributing Guidelines","text":"vignette describes usage guides user using package. useful present capabilities package new user. Vignettes written Rmarkdown , comprise markdown formatted text regular R code ran generate vignette. Vignettes built every time package checked (meaning rebuilt Travis new pushed commit). Thus, contained code readable, concise, , fast run (replicates, high ML tolerance iteration count, etc), otherwise R CMD Check take long fail.","code":""},{"path":"https://rsetienne.github.io/DAISIE/articles/demo_CSvsIW.html","id":"load-prepare-and-visualize-data","dir":"Articles","previous_headings":"","what":"1. Load, prepare and visualize data","title":"Demo: Fitting clade-specific and island-wide diversity-dependence models in DAISIE","text":"want start directly model fitting can skip step go step 2. Load phylogenetic data Eleutherodacylus frogs island Hispaniola (used Etienne et al. 2020). dataset contains times colonization branching times species Eleutherodactylus frogs found island. data extracted dated molecular phylogeny Dugo-Cota et al 2019 (Ecology Letters 22:884–893). dataset includes 65 extant species, result five independent colonisation events island Hispaniola. can load data table/tibble format, making sure table headers match ones example. Eleutherodactylus data table","code":"data(frogs_datatable, package = \"DAISIE\")"},{"path":"https://rsetienne.github.io/DAISIE/articles/demo_CSvsIW.html","id":"the-table-contains-the-following-4-columns-column-headers-need-to-be-written-exactly-like-this","dir":"Articles","previous_headings":"1. Load, prepare and visualize data","what":"The table contains the following 4 columns (column headers need to be written exactly like this):","title":"Demo: Fitting clade-specific and island-wide diversity-dependence models in DAISIE","text":"Clade_name - Name clade/lineage island (e.g. clade code, genus name) Status - Endemicity status clade. Can following Endemic; Non_endemic; Endemic_MaxAge, Non_Endemic_MaxAge latter two options cases time colonisation believed overestimate. cases, DAISIE assume colonisation happened time colonisation time given Branching_times present, colonisation time given Branching_times age first cladogenesis event lineage (). MaxAge options can also used colonization time unknown, specifying “NA” column Branching_times, case DAISIE assume colonisation happened time age island present. Missing_species - Number extant species belong clade included phylogeny. Branching_times - First element colonisation time, subsequent elements branching times within island . e.g. c(colonisation_time, branching_time1; branching_time2). colonisation time unknown, ‘NA’ can specified. branching times unknown, replace ‘NA’ - just add corresponding number missing species column Missing_species.","code":""},{"path":"https://rsetienne.github.io/DAISIE/articles/demo_CSvsIW.html","id":"create-daisie-datalist-from-the-input-table","dir":"Articles","previous_headings":"","what":"1.1. Create DAISIE datalist from the input table","title":"Demo: Fitting clade-specific and island-wide diversity-dependence models in DAISIE","text":"case assuming island age 30 million years Hispaniola mainland pool size 300 species (number species may colonize island).","code":"frogs_datalist <- DAISIE_dataprep(         datatable = frogs_datatable,         island_age = 30,         M = 300)"},{"path":"https://rsetienne.github.io/DAISIE/articles/demo_CSvsIW.html","id":"view-daisie-datalist","dir":"Articles","previous_headings":"","what":"1.2. View DAISIE datalist","title":"Demo: Fitting clade-specific and island-wide diversity-dependence models in DAISIE","text":"Just type: DAISIE datalist includes data table frogs format DAISIE object can read subsequent maximum likelihood functions (e.g DAISIE_ML, DAISIE_ML_IW ). includes age island, number mainland species currently present island list extant independent colonisation events, including colonization branching times.","code":"frogs_datalist"},{"path":"https://rsetienne.github.io/DAISIE/articles/demo_CSvsIW.html","id":"visualise-the-data","dir":"Articles","previous_headings":"","what":"1.3. Visualise the data","title":"Demo: Fitting clade-specific and island-wide diversity-dependence models in DAISIE","text":"plot shows different colonization events, times colonization branching times (horizontal ticks). Dashed line shows age island. n=number species; m= number species missing.                    ","code":"DAISIE_plot_island(frogs_datalist)"},{"path":"https://rsetienne.github.io/DAISIE/articles/demo_CSvsIW.html","id":"plot-age-versus-diversity","dir":"Articles","previous_headings":"1.3. Visualise the data","what":"Plot age versus diversity","title":"Demo: Fitting clade-specific and island-wide diversity-dependence models in DAISIE","text":"","code":"# DAISIE_plot_age_diversity(frogs_datalist)"},{"path":"https://rsetienne.github.io/DAISIE/articles/demo_CSvsIW.html","id":"fit-daisie-models","dir":"Articles","previous_headings":"","what":"2. Fit DAISIE models","title":"Demo: Fitting clade-specific and island-wide diversity-dependence models in DAISIE","text":"skipped step 1, first load Hispaniola Eleutherodactylus datalist. _ fit five different DAISIE models phylogenetic data contained frogs_datalist: DI - diversity-independent model. Model K’ (carrying-capacity) set Inf. CS - clade-specific diversity-dependence model. CS_no_ana - clade-specific diversity-dependence model anagenesis. Equivalent CS model Etienne et al. 2020. IW - island-wide diversity-dependence model. IW_no_ana - island-wide diversity-dependence model anagenesis. Equivalent IW model Etienne et al. 2020. use DAISIE_ML DAISIE_ML_IW functions optimise likelihood. important settings specify functions: datalist - name DAISIE datalist (case frogs_datalist) Rate cladogenesis (per species island per time unit) Rate extinction (per species island per time unit) Carrying-capacity (K’) - maximum number species clade can reach island CS models; maximum number species island across clades IW models. Rate colonisation (per species mainland per time unit) Rate anagenesis (per species island per time unit) idparsopt - position parameters optimise (e.g. optimize cladogenesis anagenesis c(1,5). parsfix - parameters fixed, specify value (e.g. fixing K’ Inf fixing anagenesis 0 - c(Inf,0). idparsfix - position paratemers fixed (e.g. fix K’ anagenesis c(3,5)). ddmodel - Set 0 diversity-independent models; 11 diversity-dependent models (IW CS) cladogenesis colonisation decline linearly diversity. options. many options, check ? DAISIE_ML   IW models (IW IW_no_ana) use island-wide version DAISIE, computationally demanding. require high memory long run times. recommend run cluster. CS models can run regular computer laptop.  ","code":"data(frogs_datalist)"},{"path":"https://rsetienne.github.io/DAISIE/articles/demo_CSvsIW.html","id":"fit-di-model","dir":"Articles","previous_headings":"","what":"2.1 Fit DI model","title":"Demo: Fitting clade-specific and island-wide diversity-dependence models in DAISIE","text":"model contains 4 parameters: 1 - cladogenesis 2 - extinction 4 - colonisation 5 - anagenesis K’ fixed Inf Set ddmodel=0  ","code":"DAISIE_ML(   datalist = frogs_datalist,   initparsopt = c(0.18,0.03,0.0006,2),   idparsopt = c(1,2,4,5),   ddmodel = 0,   parsfix = Inf,   idparsfix = 3 ) #>    lambda_c         mu   K        gamma lambda_a    loglik df conv #> 1 0.1789218 0.02509053 Inf 0.0006259365  1568.88 -209.8634  4    0"},{"path":"https://rsetienne.github.io/DAISIE/articles/demo_CSvsIW.html","id":"fit-cs-model","dir":"Articles","previous_headings":"","what":"2.2 Fit CS model","title":"Demo: Fitting clade-specific and island-wide diversity-dependence models in DAISIE","text":"model contains 5 parameters: 1 - cladogenesis 2 - extinction 3 - K’ 4 - colonisation 5 - anagenesis Set ddmodel=11 Output shown .  ","code":"DAISIE_ML(   datalist = frogs_datalist,   initparsopt = c(0.44,0.11,36.44,0.0007,2),   idparsopt = c(1,2,3,4,5),   ddmodel = 11,   parsfix = NULL,   idparsfix = NULL )"},{"path":"https://rsetienne.github.io/DAISIE/articles/demo_CSvsIW.html","id":"fit-cs_no_ana-model","dir":"Articles","previous_headings":"","what":"2.3 Fit CS_no_ana model","title":"Demo: Fitting clade-specific and island-wide diversity-dependence models in DAISIE","text":"model contains 4 parameters: 1 - cladogenesis 2 - extinction 3 - K’ 4 - colonisation Set ddmodel=11 Output shown .  ","code":"DAISIE_ML(   datalist = frogs_datalist,   initparsopt = c(0.44,0.11,36.44,0.0007),   idparsopt = c(1,2,3,4),   ddmodel = 11,   parsfix = 0,   idparsfix = 5 )"},{"path":"https://rsetienne.github.io/DAISIE/articles/demo_CSvsIW.html","id":"fit-iw-model","dir":"Articles","previous_headings":"","what":"2.4 Fit IW model","title":"Demo: Fitting clade-specific and island-wide diversity-dependence models in DAISIE","text":"model contains 5 parameters: 1 - cladogenesis 2 - extinction 3 - K’ 4 - colonisation 5 - anagenesis Set ddmodel=11 Output shown (recommended run cluster).  ","code":"DAISIE_ML_IW(   datalist = frogs_datalist,   initparsopt = c(0.41, 0.17, 131.7, 0.0012, 2),   idparsopt = c(1,2,3,4,5),   ddmodel = 11,   parsfix = NULL,   idparsfix = NULL )"},{"path":"https://rsetienne.github.io/DAISIE/articles/demo_CSvsIW.html","id":"fit-iw_no_ana-model","dir":"Articles","previous_headings":"","what":"2.5 Fit IW_no_ana model","title":"Demo: Fitting clade-specific and island-wide diversity-dependence models in DAISIE","text":"model contains 4 parameters: 1 - cladogenesis 2 - extinction 3 - K’ 4 - colonisation Set ddmodel=11 Output shown (recommended run cluster).  ","code":"DAISIE_ML_IW(   datalist = frogs_datalist,   initparsopt = c(0.40, 0.17, 131.83, 0.0012),   idparsopt = c(1,2,3,4),   ddmodel = 11,   parsfix = 0,   idparsfix = 5 )"},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/articles/demo_CSvsIW.html","id":"simulate-islands-with-the-parameters-estimated-from-the-best-model-for-the-hispaniolan-eleutherodacytlus-data","dir":"Articles","previous_headings":"3. Simulate islands under given DAISIE models","what":"3.1 Simulate islands with the parameters estimated from the best model for the Hispaniolan Eleutherodacytlus data","title":"Demo: Fitting clade-specific and island-wide diversity-dependence models in DAISIE","text":"use DAISIE_sim function, simulates diversity dynamics island island birth specificied island age, based given set parameters (cladogenesis, extinction, carrying-capacity (K’), colonisation, anagenesis). important settings specify DAISIE_sim function: Rate cladogenesis Rate extinction Carrying-capacity (K’) Rate colonisation Rate anagenesis replicates - Number replicates simulate time - Time run simulation, example 20 million years M - Number species mainland pool divdepmodel - set CS clade-specific diversity-dependence; IW island-wide diversity-dependence Simulate CS model 30 million years, 100 replicates: Simulate IW model 30 million years, 100 replicates:  ","code":"set.seed(1) frog_sims_CS <- DAISIE_sim_cr(   time=30,   M=300,   pars=c(0.44,0.11,36.44,0.0007,0),   divdepmodel = \"CS\",   replicates= 100,   plot_sims = FALSE) #> Island replicate 1 #> Island replicate 2 #> Island replicate 3 #> Island replicate 4 #> Island replicate 5 #> Island replicate 6 #> Island replicate 7 #> Island replicate 8 #> Island replicate 9 #> Island replicate 10 #> Island replicate 11 #> Island replicate 12 #> Island replicate 13 #> Island replicate 14 #> Island replicate 15 #> Island replicate 16 #> Island replicate 17 #> Island replicate 18 #> Island replicate 19 #> Island replicate 20 #> Island replicate 21 #> Island replicate 22 #> Island replicate 23 #> Island replicate 24 #> Island replicate 25 #> Island replicate 26 #> Island replicate 27 #> Island replicate 28 #> Island replicate 29 #> Island replicate 30 #> Island replicate 31 #> Island replicate 32 #> Island replicate 33 #> Island replicate 34 #> Island replicate 35 #> Island replicate 36 #> Island replicate 37 #> Island replicate 38 #> Island replicate 39 #> 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replicate 2 #> Island replicate 3 #> Island replicate 4 #> Island replicate 5 #> Island replicate 6 #> Island replicate 7 #> Island replicate 8 #> Island replicate 9 #> Island replicate 10 #> Island replicate 11 #> Island replicate 12 #> Island replicate 13 #> Island replicate 14 #> Island replicate 15 #> Island replicate 16 #> Island replicate 17 #> Island replicate 18 #> Island replicate 19 #> Island replicate 20 #> Island replicate 21 #> Island replicate 22 #> Island replicate 23 #> Island replicate 24 #> Island replicate 25 #> Island replicate 26 #> Island replicate 27 #> Island replicate 28 #> Island replicate 29 #> Island replicate 30 #> Island replicate 31 #> Island replicate 32 #> Island replicate 33 #> Island replicate 34 #> Island replicate 35 #> Island replicate 36 #> Island replicate 37 #> Island replicate 38 #> Island replicate 39 #> Island replicate 40 #> Island replicate 41 #> Island replicate 42 #> Island replicate 43 #> Island replicate 44 #> Island replicate 45 #> 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Simulate islands under given DAISIE models","what":"3.2 Plot the species-through-time plots resulting from the simulations.","title":"Demo: Fitting clade-specific and island-wide diversity-dependence models in DAISIE","text":"","code":"DAISIE_plot_sims(frog_sims_CS)"},{"path":"https://rsetienne.github.io/DAISIE/articles/demo_optimize.html","id":"daisie-dynamic-assembly-of-island-biotas-through-speciation-immigration-and-extinction","dir":"Articles","previous_headings":"","what":"DAISIE – Dynamic Assembly of Island biotas through Speciation, Immigration and Extinction","title":"Demo optimizing parameters","text":"Citation: Valente LM, Phillimore AB, Etienne RS (2015) Equilibrium non- equilibrium dynamics simultaneously operate Galápagos islands. Ecology Letters, press.","code":""},{"path":"https://rsetienne.github.io/DAISIE/articles/demo_optimize.html","id":"loading-data-table","dir":"Articles","previous_headings":"DAISIE – Dynamic Assembly of Island biotas through Speciation, Immigration and Extinction","what":"Loading data table","title":"Demo optimizing parameters","text":"load package: raw dataset inputted table. Galápagos dataset table can visualized : row table represents independent colonisation event. table four columns: Clade_name: name independent colonization event. Endemic: applicable anagenetic species radiations. Non_endemic: taxon endemic island, age colonisation based phylogeny island non-island populations species sampled. Non_endemic_MaxAge: taxon endemic island, upper bound time colonisation island known. applies individuals island population species sampled, age species known. Endemic&Non_Endemic: endemic clade present mainland ancestor re-colonized. remote islands expected rare. Missing_species: Number island species sampled particular clade (applicable radiations). Branching_times – stem age population/species case Non-endemic, Non-endemic_MaxAge Endemic anagenetic species. cladogenetic species branching times radiation including stem age radiation. Note – species within radiation found island (e.g. back-colonisation) branching times species excluded, mainland species pool treated static. data can also visualized:","code":"library(DAISIE) data(Galapagos_datatable) knitr::kable(Galapagos_datatable) DAISIE::DAISIE_plot_island(Galapagos_datatable, island_age = 4) #> Colonisation time of 7.456 for Coccyzus is older than island age #> Colonisation time of 10.285 for Pyrocephalus is older than island age"},{"path":"https://rsetienne.github.io/DAISIE/articles/demo_optimize.html","id":"formatting-table-to-run-in-daisie","dir":"Articles","previous_headings":"DAISIE – Dynamic Assembly of Island biotas through Speciation, Immigration and Extinction","what":"Formatting table to run in DAISIE","title":"Demo optimizing parameters","text":"running analyses, datatable needs converted DAISIE datalist format using function DAISIE_dataprep. prepare two different datalists based Galápagos datatable. 1st datalist treat taxa equivalent. specify island age four million years (island_age=4) mainland pool size 1000 (M=1000). 2nd datalist allow Darwin’s finches form separate group rates can decoupled governing macroevolutionary process clades (number_clade_types=2 list_type2_clades = “Finches”). set proportion Darwin’s finch type species mainland pool 0.163. (prop_type2_pool=0.163). prop_type2_pool specified default given value proportion Galapagos lineages Darwin’s finches represent (1/8=0.125 case). objects Galapagos_datalist Galapagos_datalist_2types can now run directly DAISIE functions.","code":"data(Galapagos_datatable)         Galapagos_datalist <- DAISIE_dataprep(    datatable = Galapagos_datatable,    island_age = 4,    M = 1000 ) #> Colonisation time of 7.456 for Coccyzus is older than island age #> Colonisation time of 10.285 for Pyrocephalus is older than island age data(Galapagos_datatable)   Galapagos_datalist_2types <- DAISIE_dataprep(    datatable = Galapagos_datatable,    island_age = 4,    M = 1000,    number_clade_types = 2,    list_type2_clades = \"Finches\",    prop_type2_pool = 0.163 ) #> Colonisation time of 7.456 for Coccyzus is older than island age #> Colonisation time of 10.285 for Pyrocephalus is older than island age"},{"path":"https://rsetienne.github.io/DAISIE/articles/demo_optimize.html","id":"optimizing-parameters-using-maximum-likelihood","dir":"Articles","previous_headings":"DAISIE – Dynamic Assembly of Island biotas through Speciation, Immigration and Extinction","what":"Optimizing parameters using maximum likelihood","title":"Demo optimizing parameters","text":"function conducts maximum likelihood optimization DAISIE model parameters called DAISIE_ML. Different models can specified using ddmodel option DAISIE_ML: ddmodel = 0 : diversity-dependence ddmodel = 1 : linear diversity-dependence speciation rate ddmodel = 11: linear diversity-dependence speciation immigration rate ddmodel = 2 : exponential diversity-dependence speciation rate ddmodel = 21: exponential diversity-dependence speciation immigration rate Different types parameters can optimized fixed. parameters given following order: (1) cladogenesis rate, (2) extinction rate, (3) K’ carrying capacity (maximum number species clade can attain within island), (4) colonisation rate, (5) anagenesis rate. identities parameters optimized fixed specified idparsopt idparsfix within DAISIE_ML function. example, optimize parameters set idparsopt=1:5 idparsfix=NULL. optimize parameters fix rate extinction, set idparsopt=c(1,3,4,5) idparsfix=2. optimize parameters except cladogenesis anagenesis set idparsopt=c(2,3,4) idparsfix=c(1,5). values parameters used initial values optimization specified initparsopt, values fixed specified parsfix. example, want optimize parameters starting value 2 set initparsopt=c(2,2,2,2,2) parsfix=NULL. want starting rates 0.1, K’ fixed 20, use initparsopt=c(0.1,0.1,0.1,0.1) parsfix=20. running data, strongly recommend test multiple initial starting parameters model, particularly optimizing models multiple free parameters, high risk trapped local likelihood sub-optima. also suggest running two rounds optimization using optimized parameter set 1st round initial starting values 2nd round. Also note initial starting values examples tutorial may appropriate data.","code":""},{"path":"https://rsetienne.github.io/DAISIE/articles/demo_optimize.html","id":"example-1-optimizing-all-parameters-with-diversity-dependence-in-speciation-and-colonisation","dir":"Articles","previous_headings":"DAISIE – Dynamic Assembly of Island biotas through Speciation, Immigration and Extinction > Optimizing parameters using maximum likelihood","what":"Example 1: Optimizing all parameters, with diversity-dependence in speciation and colonisation","title":"Demo optimizing parameters","text":"now optimize five parameters datalist clades share parameters. set model linear diversity-dependence speciation rate immigration rate using ddmodel=11. set initial rate cladogenesis 2.5, initial rate extinction 2.7, initial K’ value 20, initial rate colonisation 0.009 initial rate anagenesis 1.01 (initparsopt = c(2.5,2.7,20,0.009,1.01)). optimize 5 parameters (idparsopt = 1:5) fix parameters (parsfix = NULL, idparsfix = NULL). take several minutes run. parameters optimized fixed well loglikelihood initial starting parameters set shown top screen output DAISIE_ML. optimization completed, program output maximum likelihood parameter estimates maximum loglikelihood value. given dataset, likelihood different DAISIE models can compared information criteria BIC AIC.","code":"data(Galapagos_datalist)   DAISIE_ML(    datalist = Galapagos_datalist,    initparsopt = c(2.5,2.7,20,0.009,1.01),    ddmodel = 11,    idparsopt = 1:5,    parsfix = NULL,    idparsfix = NULL )"},{"path":"https://rsetienne.github.io/DAISIE/articles/demo_optimize.html","id":"example-2-optimizing-model-without-diversity-dependence","dir":"Articles","previous_headings":"DAISIE – Dynamic Assembly of Island biotas through Speciation, Immigration and Extinction > Optimizing parameters using maximum likelihood","what":"Example 2: Optimizing model without diversity-dependence","title":"Demo optimizing parameters","text":"optimize parameters model diversity-dependence, use default model (ddmodel=0), fix parameter number 3 corresponds K’ infinity (Inf).","code":"data(Galapagos_datalist)   DAISIE_ML(    datalist = Galapagos_datalist,    initparsopt = c(2.5,2.7,0.009,1.01),    idparsopt = c(1,2,4,5),    parsfix = Inf,    idparsfix = 3 )"},{"path":"https://rsetienne.github.io/DAISIE/articles/demo_optimize.html","id":"example-3-optimizing-model-with-no-diversity-dependence-and-no-anagenesis","dir":"Articles","previous_headings":"DAISIE – Dynamic Assembly of Island biotas through Speciation, Immigration and Extinction > Optimizing parameters using maximum likelihood","what":"Example 3: Optimizing model with no diversity-dependence and no anagenesis","title":"Demo optimizing parameters","text":"optimize parameters model diversity-dependence anagenesis, use default model (ddmodel=0), fix parameters number 3 5, correspond, respectively K’ rate anagenesis.","code":"data(Galapagos_datalist)  DAISIE_ML(    datalist=Galapagos_datalist,    initparsopt = c(2.5,2.7,0.009),    idparsopt = c(1,2,4),    parsfix = c(Inf,0),    idparsfix = c(3,5) )"},{"path":"https://rsetienne.github.io/DAISIE/articles/demo_optimize.html","id":"example-4-optimizing-all-parameters-but-allowing-darwins-finches-to-have-a-separate-rate-of-cladogenesis-","dir":"Articles","previous_headings":"DAISIE – Dynamic Assembly of Island biotas through Speciation, Immigration and Extinction > Optimizing parameters using maximum likelihood","what":"Example 4: Optimizing all parameters, but allowing Darwin’s finches to have a separate rate of cladogenesis.","title":"Demo optimizing parameters","text":"example use datalist Darwin’s finches specified separate type: Galapagos_datalist_2types. two types species considered, parameters second type species order first set parameters, start number 6: (6) cladogenesis rate type 2 species, (7) extinction rate type 2 species, (8) K’ type 2 species, (9) colonisation rate type 2 species, (10) anagenesis rate type 2 species. also additional parameter 2 types species considered: proportion species type 2 mainland pool. parameter number 11. optimize parameters, allow finches separate rate cladogenesis. fix proportion type 2 species mainland pool 0.163 (therefore fixing parameter 11 idparsfix=11 parsfix=0.163). Note allowing rate cladogenesis Darwin’s finches vary background rate, need specify rates Darwin’s finches remain background – using idparsnoshift = c(7,8,9,10)).","code":"data(Galapagos_datalist_2types)   DAISIE_ML(    ddmodel=11,    datalist=Galapagos_datalist_2types,    initparsopt= c(0.38,0.55,20,0.004,1.1,2.28),    idparsopt = c(1,2,3,4,5,6),    parsfix = 0.163,    idparsfix = c(11),    idparsnoshift = c(7,8,9,10) )"},{"path":"https://rsetienne.github.io/DAISIE/articles/demo_optimize.html","id":"example-5-optimizing-a-model-with-no-diversity-dependence-but-allowing-darwins-finches-to-have-a-separate-rate-of-cladogenesis-and-extinction-","dir":"Articles","previous_headings":"DAISIE – Dynamic Assembly of Island biotas through Speciation, Immigration and Extinction > Optimizing parameters using maximum likelihood","what":"Example 5: Optimizing a model with no diversity-dependence, but allowing Darwin’s finches to have a separate rate of cladogenesis and extinction.","title":"Demo optimizing parameters","text":"","code":"data(Galapagos_datalist_2types)    DAISIE_ML(    ddmodel=0,    datalist=Galapagos_datalist_2types,    initparsopt = c(0.38,0.55,0.004,1.1,2.28,2),    idparsopt = c(1,2,4,5,6,7),    parsfix = c(Inf,0.163),    idparsfix = c(3,11),    idparsnoshift = c(8,9,10) )"},{"path":"https://rsetienne.github.io/DAISIE/articles/demo_sim.html","id":"daisie-dynamic-assembly-of-island-biotas-through-speciation-immigration-and-extinction","dir":"Articles","previous_headings":"","what":"DAISIE – Dynamic Assembly of Island biotas through Speciation, Immigration and Extinction","title":"Demo simulating islands","text":"Citation: Valente LM, Phillimore AB, Etienne RS (2015) Equilibrium non- equilibrium dynamics simultaneously operate Galápagos islands. Ecology Letters, 18(8), 844-852. https://doi.org/10.1111/ele.12461.","code":""},{"path":"https://rsetienne.github.io/DAISIE/articles/demo_sim.html","id":"loading","dir":"Articles","previous_headings":"DAISIE – Dynamic Assembly of Island biotas through Speciation, Immigration and Extinction","what":"Loading","title":"Demo simulating islands","text":"load package:","code":"library(DAISIE)"},{"path":"https://rsetienne.github.io/DAISIE/articles/demo_sim.html","id":"simulating-islands","dir":"Articles","previous_headings":"DAISIE – Dynamic Assembly of Island biotas through Speciation, Immigration and Extinction","what":"Simulating islands","title":"Demo simulating islands","text":"function DAISIE_sim allows simulation DAISIE models plots results. user specifies parameters simulated, number replicates, length simulation (typically island age), number species mainland pool. plot_sims option set default (TRUE) function produce species- -time plot showing accumulation total, endemic non-endemic species time, well confidence intervals total number species. shorten run-time vignette, reduce number n_replicates. increased accuracy, increase number.","code":"n_mainland_species <- 1000 island_age <- 4 n_replicates <- 10"},{"path":"https://rsetienne.github.io/DAISIE/articles/demo_sim.html","id":"example-5-1-simulating-10-islands-with-no-diversity-dependence-all-species-sharing-the-same-parameters-and-plotting-the-results","dir":"Articles","previous_headings":"DAISIE – Dynamic Assembly of Island biotas through Speciation, Immigration and Extinction > Simulating islands","what":"Example 5.1 – Simulating 10 islands with no diversity-dependence, all species sharing the same parameters, and plotting the results","title":"Demo simulating islands","text":"object island_replicates contains results simulation DAISIE format. 10 islands stored object, island replicate can viewed separately. example, type island_replicates[[1]] view first replicate. element list relating island contains table number species time, well branching time information independent colonisation event extant end simulation.","code":"set.seed(42) clado_rate <- 2.550687345 # cladogenesis rate ext_rate <- 2.683454548 # extinction rate clade_carr_cap <- Inf # clade-level carrying capacity imm_rate <- 0.00933207 # immigration rate ana_rate <- 1.010073119 # anagenesis rate  island_replicates <- DAISIE_sim_cr(    time = island_age,   M = n_mainland_species,    pars = c(clado_rate, ext_rate, clade_carr_cap, imm_rate, ana_rate),   replicates = n_replicates,   plot_sims = FALSE,   verbose = FALSE ) DAISIE_plot_sims(island_replicates = island_replicates)"},{"path":"https://rsetienne.github.io/DAISIE/articles/demo_sim.html","id":"example-5-2-simulating-10-islands-with-diversity-dependence-k10-all-species-sharing-the-same-parameters-and-plotting-the-results","dir":"Articles","previous_headings":"DAISIE – Dynamic Assembly of Island biotas through Speciation, Immigration and Extinction > Simulating islands","what":"Example 5.2 – Simulating 10 islands with diversity-dependence (K’=10), all species sharing the same parameters, and plotting the results","title":"Demo simulating islands","text":"","code":"clado_rate <- 2.550687345 # cladogenesis rate ext_rate <- 2.683454548 # extinction rate clade_carr_cap <- 10.0  # clade-level carrying capacity imm_rate <- 0.00933207 # immigration rate ana_rate <- 1.010073119 # anagenesis rate  island_replicates_K <- DAISIE_sim_cr(    time = island_age,    M = n_mainland_species,    pars = c(clado_rate, ext_rate, clade_carr_cap, imm_rate, ana_rate),   replicates = n_replicates,   plot_sims = FALSE,   verbose = FALSE )  DAISIE_plot_sims(island_replicates_K)"},{"path":"https://rsetienne.github.io/DAISIE/articles/demo_sim.html","id":"example-5-3-simulating-10-islands-allowing-darwins-finches-to-have-a-higher-rate-of-cladogenesis","dir":"Articles","previous_headings":"DAISIE – Dynamic Assembly of Island biotas through Speciation, Immigration and Extinction > Simulating islands","what":"Example 5.3 – Simulating 10 islands allowing Darwin’s finches to have a higher rate of cladogenesis:","title":"Demo simulating islands","text":"produces figure similar Fig. 2, three plots: one total number species, one species type 1 one species type 2. Accessing island replicate individually (e.g. island_replicates_2types[[15]]) shows information branching times species--time tables total, type 1 species type 2 species.","code":"clado_rate_1 <- 0.38 # cladogenesis rate ext_rate_1 <- 0.55 # extinction rate clade_carr_cap_1 <- Inf  # clade-level carrying capacity imm_rate_1 <- 0.04 # immigration rate ana_rate_1 <- 1.10 # anagenesis rate  clado_rate_2 <- 0.38 # cladogenesis rate ext_rate_2 <- ext_rate_1 # extinction rate clade_carr_cap_2 <- clade_carr_cap_1  # clade-level carrying capacity imm_rate_2 <- imm_rate_1 # immigration rate ana_rate_2 <- ana_rate_1 # anagenesis rate  island_replicates_2types <- DAISIE_sim_cr(    time = island_age,   M = n_mainland_species,    pars = c(     clado_rate_1, ext_rate_1, clade_carr_cap_1, imm_rate_1, ana_rate_1,     clado_rate_2, ext_rate_2, clade_carr_cap_2, imm_rate_2, ana_rate_2   ),   replicates = n_replicates,    prop_type2_pool = 0.163,   plot_sims = FALSE,   verbose = FALSE ) DAISIE_plot_sims(island_replicates_2types)"},{"path":"https://rsetienne.github.io/DAISIE/articles/stac_key.html","id":"key-for-the-different-values-of-stac-that-can-be-used-in-daisie-objects-and-how-they-can-be-specified-in-the-function-daisie_dataprep-","dir":"Articles","previous_headings":"","what":"Key for the different values of stac that can be used in DAISIE objects, and how they can be specified in the function DAISIE_dataprep.","title":"DAISIE `stac` values","text":"  stac stands “status clade” formed immigrant. important part DAISIE objects informs likelihood functions endemicity status type data available insular clade. colonisation event extant species island needs stac value specified.","code":""},{"path":"https://rsetienne.github.io/DAISIE/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Rampal S. Etienne. Author, maintainer. Luis Valente. Author. Albert B. Phillimore. Author. Bart Haegeman. Author. Joshua W. Lambert. Author. Pedro Santos Neves. Author. Shu Xie. Author. Richèl J.C. Bilderbeek. Author. Hanno Hildenbrandt. Author. Torsten Hauffe. Contributor. Giovanni Laudanno. Contributor. Nadiah Kristensen. Contributor. Raphael Scherrer. Contributor.","code":""},{"path":"https://rsetienne.github.io/DAISIE/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Etienne R, Valente L, Phillimore , Haegeman B, Lambert J, Santos Neves P, Xie S, Bilderbeek R, Hildenbrandt H (2024). DAISIE: Dynamical Assembly Islands Speciation, Immigration Extinction. R package version 4.4.1,  https://rsetienne.github.io/DAISIE/, https://github.com/rsetienne/DAISIE.","code":"@Manual{,   title = {DAISIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction},   author = {Rampal S. Etienne and Luis Valente and Albert B. Phillimore and Bart Haegeman and Joshua W. Lambert and Pedro {Santos Neves} and Shu Xie and Richèl J.C. Bilderbeek and Hanno Hildenbrandt},   year = {2024},   note = {R package version 4.4.1,  https://rsetienne.github.io/DAISIE/},   url = {https://github.com/rsetienne/DAISIE}, }"},{"path":"https://rsetienne.github.io/DAISIE/index.html","id":"daisie-dynamic-assembly-of-island-biota-through-speciation-immigration-and-extinction","dir":"","previous_headings":"","what":"Dynamical Assembly of Islands by Speciation, Immigration and Extinction","title":"Dynamical Assembly of Islands by Speciation, Immigration and Extinction","text":"DAISIE R package simulates computes (maximum) likelihood dynamical model island biota assembly speciation, immigration extinction. model can fitted empirical dated phylogenies simulated data. overview simulation functionality see . Details overview maximum likelihood inference capabilities estimate parameters see . details comparing two diversity depedence models see .","code":""},{"path":"https://rsetienne.github.io/DAISIE/index.html","id":"installing-daisie","dir":"","previous_headings":"","what":"Installing DAISIE","title":"Dynamical Assembly of Islands by Speciation, Immigration and Extinction","text":"N.B.: MacOS users may experience issues installing DAISIE, especially MacOS Big Sur. case, please see detailed installation instructions. DAISIE package stable version CRAN development version GitHub.","code":""},{"path":"https://rsetienne.github.io/DAISIE/index.html","id":"from-cran","dir":"","previous_headings":"Installing DAISIE","what":"From CRAN","title":"Dynamical Assembly of Islands by Speciation, Immigration and Extinction","text":"within R, :","code":"install.packages(\"DAISIE\")"},{"path":"https://rsetienne.github.io/DAISIE/index.html","id":"from-github","dir":"","previous_headings":"Installing DAISIE","what":"From GitHub","title":"Dynamical Assembly of Islands by Speciation, Immigration and Extinction","text":"Install DAISIE GitHub repository running:","code":"install.packages(\"remotes\") remotes::install_github(\"rsetienne/DAISIE\")"},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/index.html","id":"from-cran-1","dir":"","previous_headings":"Using DAISIE as a package dependency","what":"From CRAN","title":"Dynamical Assembly of Islands by Speciation, Immigration and Extinction","text":"DESCRIPTION file, add DAISIE normal package. package directly uses DAISIE: package uses DAISIE peripherals (e.g. vignettes tests):","code":"Imports:   DAISIE Suggests:   DAISIE"},{"path":"https://rsetienne.github.io/DAISIE/index.html","id":"from-github-1","dir":"","previous_headings":"Using DAISIE as a package dependency","what":"From GitHub","title":"Dynamical Assembly of Islands by Speciation, Immigration and Extinction","text":"","code":"Remotes:   rsetienne/DAISIE"},{"path":"https://rsetienne.github.io/DAISIE/index.html","id":"supportquestions","dir":"","previous_headings":"","what":"Support/Questions","title":"Dynamical Assembly of Islands by Speciation, Immigration and Extinction","text":"feature requests bug-reports matters, please submit issue.","code":""},{"path":"https://rsetienne.github.io/DAISIE/index.html","id":"feature-branches","dir":"","previous_headings":"","what":"Feature branches","title":"Dynamical Assembly of Islands by Speciation, Immigration and Extinction","text":"master: build always pass. @rsetienne control develop master merges. develop: merge feature branches, merge master @rsetienne iff build passes.","code":""},{"path":"https://rsetienne.github.io/DAISIE/index.html","id":"contributors","dir":"","previous_headings":"","what":"Contributors","title":"Dynamical Assembly of Islands by Speciation, Immigration and Extinction","text":"DAISIE originally developed Rampal S. Etienne, Luis Valente, Albert B. Phillimore Bart Haegeman. continuously maintained members @tece-lab, University Groningen.","code":""},{"path":"https://rsetienne.github.io/DAISIE/index.html","id":"references","dir":"","previous_headings":"","what":"References","title":"Dynamical Assembly of Islands by Speciation, Immigration and Extinction","text":"Etienne R. S., Valente, L., Phillimore, . B., Haegeman, B., Lambert, J. W., Neves, P., Xie, S., Bilderbeek, R. J. C., & Hildenbrandt, H. (2021). DAISIE: Dynamical Assembly Islands Speciation, Immigration Extinction. R package version 4.0.2. https://cran.r-project.org/package=DAISIE. https://doi.org/10.5281/zenodo.4054058 Valente, L., Etienne, R.S., & Phillimore, .B. (2014). effects island ontogeny species diversity phylogeny. Proceedings Royal Society B: Biological Sciences, 281(1784), 20133227–20133227. http://doi.org/10.1098/rspb.2013.3227 Valente, L., Phillimore, .B., & Etienne, R.S. (2015). Equilibrium non-equilibrium dynamics simultaneously operate Galápagos islands. Ecology Letters, 18(8), 844–852. http://doi.org/10.1111/ele.12461 Valente, L., Etienne, R.S., & Dávalos, L.M. (2017). Recent extinctions disturb path equilibrium diversity Caribbean bats. Nature Ecology & Evolution, 1(2), 0026. http://doi.org/10.1038/s41559-016-0026 Valente, L., Illera, J.C., Havenstein, K., Pallien, T., Etienne, R.S., & Tiedemann, R. (2017). Equilibrium Bird Species Diversity Atlantic Islands. Current Biology, 27(11), 1660-1666. https://doi.org/10.1016/j.cub.2017.04.053 Valente, L., Phillimore, .B., & Etienne, R.S. (2018). Using molecular phylogenies island biogeography: ’s time. Ecography, 1–3. http://doi.org/10.1111/ecog.03503 Valente, L., Etienne, R.S., & Garcia-R., J.C. (2019). Deep Macroevolutionary Impact Humans New Zealand’s Unique Avifauna. Current Biology 29 (15): 2563-2569.e4. https://doi.org/10.1016/j.cub.2019.06.058 Valente, L., Phillimore, .B., Melo, M., Warren, B.H., Clegg, S.M., Havenstein, K., Tiedemann, R., Illera, J.C., Thebaud, C., Aschenbach, T. & Etienne, R.S. (2020). Simple Dynamic Model Explains Diversity Island Birds Worldwide. Nature 579 (7797): 92–96. https://doi.org/10.1038/s41586-020-2022-5 Hauffe, T., Delicado, D., Etienne, R.S., & Valente, L. (2020). Lake expansion elevates equilibrium diversity via increasing colonization. Journal Biogeography 47: 1849–1860. https://doi.org/10.1111/jbi.13914 Valente, L., Kristensen, N., Phillimore, . B., & Etienne, R. S. (2021). Report programming bugs DAISIE R package: consequences correction. https://doi.org/10.32942/osf.io/w5ntf Santos Neves, P.*, Lambert, J. W.*, Valente, L., & Etienne, R. S. (2022). robustness simple dynamic model island biodiversity geological sea-level change. Journal Biogeography 49: 2091-2104. https://doi.org/10.1111/jbi.14519 Lambert, J. W., Santos Neves, P., Bilderbeek, R. L. C., Valente, L., Etienne, R. S. (2022). effect mainland dynamics data parameter estimates island biogeography. bioRxiv. https://doi.org/10.1101/2022.01.13.476210 Xie, S., Valente, L., Etienne, R. S. (2023). Can ignore trait-dependent colonization diversification island biogeography? Evolution. https://doi.org/10.1093/evolut/qpad006 Michielsen, N. M., Goodman, S. M., Soarimalala, V., van der Geer, . . E., Dávalos, L. M., Saville, G. ., Upham, N., Valente, L. (2023). macroevolutionary impact recent imminent mammal extinctions Madagascar. Nature Communications 14 (14). https://doi.org/10.1038/s41467-022-35215-3","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/Bats_GreaterAntilles.html","id":null,"dir":"Reference","previous_headings":"","what":"Colonization and branching times of Noctilionoid bats from the Greater Antilles. — Bats_GreaterAntilles","title":"Colonization and branching times of Noctilionoid bats from the Greater Antilles. — Bats_GreaterAntilles","text":"list containing colonization branching times noctilionoid bats Greater Antilles. Main dataset used Valente, Etienne Dávalos (2017) Nature Ecology Evolution. Island age 20 Myr mainland pool size 100 species. first element list two components: $island_age - island age $not_present - number mainland lineages present island  following elements list contain information single colonist lineage island 5 components:$colonist_name - name species clade colonized island $branching_times - island age followed stem age population/species case Non-endemic, Non-endemic_MaxAge species Endemic species close relatives island. endemic clades one species island (cladogenetic clades/ radiations) island age followed branching times island clade including stem age clade.$stac - status colonist  * Non_endemic_MaxAge: 1  * Endemic: 2  * Endemic&Non_Endemic: 3  * Non_endemic: 4  * Endemic_MaxAge: 5 6 $missing_species - number island species sampled particular clade (applicable endemic clades) $type1or2 - whether colonist belongs type 1 type 2. dataset equal 1.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/Bats_GreaterAntilles.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Colonization and branching times of Noctilionoid bats from the Greater Antilles. — Bats_GreaterAntilles","text":"list 17 elements, first contains 2 elements following 16 containing 5 components.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/Bats_GreaterAntilles.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Colonization and branching times of Noctilionoid bats from the Greater Antilles. — Bats_GreaterAntilles","text":"Valente L, Etienne RS, Dávalos (2017) Recent extinctions disturb path equilibrium diversity Caribbean bats. Nature Ecology Evolution, 1, 26.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/Biwa_datalist.html","id":null,"dir":"Reference","previous_headings":"","what":"Colonization and branching times of 68 fish clades. — Biwa_datalist","title":"Colonization and branching times of 68 fish clades. — Biwa_datalist","text":"list containing colonization branching times fishes Lake Biwa (Japan). Main dataset used Hauffe et al (2020). list can generated using DAISIE_dataprep function, converts user-specified data table data object, object can course also entered directly. R list object following elements. first element list two components: $island_age - island age $not_present - number mainland lineages present island  following elements list contains information single colonist lineage island 5 components:$colonist_name - name species clade colonized island $branching_times - island age followed stem age population/species case Non-endemic, Non-endemic_MaxAge species Endemic species close relatives island. endemic clades one species island (cladogenetic clades/ radiations) island age followed branching times island clade including stem age clade.$stac - status colonist  * Non_endemic_MaxAge: 1  * Endemic: 2  * Endemic&Non_Endemic: 3  * Non_endemic: 4  * Endemic_MaxAge: 5 6 $missing_species - number island species sampled particular clade (applicable endemic clades) $type1or2 - whether colonist belongs type 1 type 2. dataset equal 1.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/Biwa_datalist.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Colonization and branching times of 68 fish clades. — Biwa_datalist","text":"list 69 elements, first contains 2 elements following 68 containing 5 components.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/Biwa_datalist.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Colonization and branching times of 68 fish clades. — Biwa_datalist","text":"Hauffe, T., D. Delicado, R.S. Etienne L. Valente. Lake expansion elevates equilibrium diversity via increasing colonisation. (2020) Journal Biogeography","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE-package.html","id":null,"dir":"Reference","previous_headings":"","what":"DAISIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction — DAISIE-package","title":"DAISIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction — DAISIE-package","text":"DAISIE island biogeography model assumes island biota assembly governed immigration, extinction speciation cladogenesis anagenesis. likelihood-based statistical package can simulate islands estimate parameters DAISIE model based phylogenetic/phylogeographic data. Cladogenesis immigration rates can dependent diversity.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE-package.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"DAISIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction — DAISIE-package","text":"Valente, L. M., Etienne, R. S., & Phillimore, . B. (2014). effects island ontogeny species diversity phylogeny. Proceedings Royal Society London. Series B, Biological Sciences 281, 20133227. doi:10.1098/rspb.2013.3227 . Valente, L., .B. Phillimore & R.S. Etienne (2015). Equilibrium non-equilibrium dynamics simultaneously operate Galapagos islands. Ecology Letters 18: 844-852, doi:10.1111/ele.12461 . Valente, L., R.S. Etienne & L. Davalos (2017). Recent extinctions disturb path equilibrium diversity Caribbean bats. Nature Ecology Evolution 1: 0026. doi:10.1038/s41559-016-0026 . Valente, L., Illera, J. C., Havenstein, K., Pallien, T., Etienne, R. S., & Tiedemann, R. (2017). Equilibrium Bird Species Diversity Atlantic Islands. Current Biology 27: 1660-1666. doi:10.1016/j.cub.2017.04.053 . Valente, L., Phillimore, . B., & Etienne, R. (2018). Using molecular phylogenies island biogeography: time. Ecography 41: 1684-1686. doi:10.1111/ecog.03503 . Valente, L., Etienne, R. S., & Garcia-R, J. C. (2019). Deep macroevolutionary impact humans New Zealand's unique avifauna. Current Biology 29: 2563-2569. doi:10.1016/j.cub.2019.06.058 . Valente, L., Phillimore, . B., Melo, M., Warren, B. H., Clegg, S. M., Havenstein, K., & Etienne, R. S. (2020). simple dynamic model explains diversity island birds worldwide. Nature 579: 92-96. doi:10.1038/s41586-020-2022-5 . Hauffe, T., Delicado, D., Etienne, R.S., & Valente, L. (2020). Lake expansion elevates equilibrium diversity via increasing colonization. Journal Biogeography 47: 1849–1860. doi:10.1111/jbi.13914 . Valente, L., Kristensen, N., Phillimore, . B., & Etienne, R. S. (2021). Report programming bugs DAISIE R package: consequences correction. EcoEvoRxiv. doi:10.32942/osf.io/w5ntf . Santos Neves, P., Lambert, J. W., Valente, L., & Etienne, R. S. (2022). robustness simple dynamic model island biodiversity geological sea-level change. Journal Biogeography 49: 2091-2104. doi:10.1111/jbi.14519 . Lambert, J. W., Santos Neves, P., Bilderbeek, R. L. C., Valente, L., Etienne, R. S. (2022). effect mainland dynamics data parameter estimates island biogeography. bioRxiv. doi:10.1101/2022.01.13.476210 . Xie, S., Valente, L., Etienne, R. S. (2023). Can ignore trait-dependent colonization diversification island biogeography? Evolution. doi:10.1093/evolut/qpad006 . Michielsen, N. M., Goodman, S. M., Soarimalala, V., van der Geer, . . E., Dávalos, L. M., Saville, G. ., Upham, N., Valente, L. (2023). macroevolutionary impact recent imminent mammal extinctions Madagascar. Nature Communications 14 (14).doi:10.1038/s41467-022-35215-3 .","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"DAISIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction — DAISIE-package","text":"Maintainer: Rampal S. Etienne r.s.etienne@rug.nl (ORCID) Authors: Luis Valente luis.valente@naturalis.nl (ORCID) Albert B. Phillimore (ORCID) Bart Haegeman (ORCID) Joshua W. Lambert j.w.l.lambert@rug.nl (ORCID) Pedro Santos Neves p.m.santos.neves@rug.nl (ORCID) Shu Xie s.xie@rug.nl (ORCID) Richèl J.C. Bilderbeek richel@richelbilderbeek.nl (ORCID) Hanno Hildenbrandt h.hildenbrandt@rug.nl (ORCID) contributors: Torsten Hauffe torsten.hauffe@gmail.com (ORCID) [contributor] Giovanni Laudanno glaudanno@gmail.com (ORCID) [contributor] Nadiah Kristensen nadiah@nadiah.org (ORCID) [contributor] Raphael Scherrer r.scherrer@rug.nl (ORCID) [contributor]","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_CS_max_steps.html","id":null,"dir":"Reference","previous_headings":"","what":"CS iteration control — DAISIE_CS_max_steps","title":"CS iteration control — DAISIE_CS_max_steps","text":"Sets retrieves max. number iterations used odeint solver.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_CS_max_steps.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"CS iteration control — DAISIE_CS_max_steps","text":"","code":"DAISIE_CS_max_steps(max_steps)"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_CS_max_steps.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"CS iteration control — DAISIE_CS_max_steps","text":"max_steps max_steps: sets max. iterations max_steps.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_CS_max_steps.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"CS iteration control — DAISIE_CS_max_steps","text":"current max. iterations","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ExpEIN.html","id":null,"dir":"Reference","previous_headings":"","what":"The expected number of endemics and non-endemics under the DAISIE model — DAISIE_ExpEIN","title":"The expected number of endemics and non-endemics under the DAISIE model — DAISIE_ExpEIN","text":"function calculates expected number endemics, non-endemics sum given set parameter values, given mainland species pool size given time","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ExpEIN.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The expected number of endemics and non-endemics under the DAISIE model — DAISIE_ExpEIN","text":"","code":"DAISIE_ExpEIN(t, pars, M, initEI = c(0, 0))"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ExpEIN.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The expected number of endemics and non-endemics under the DAISIE model — DAISIE_ExpEIN","text":"t time expectations need computed. pars numeric vector containing model parameters: pars[1]: lambda^c (cladogenesis rate) pars[2]: mu (extinction rate) pars[3]: K (carrying capacity), set K=Inf diversity   independence. pars[4]: gamma (immigration rate) pars[5]: lambda^(anagenesis rate) pars[6]: lambda^c (cladogenesis rate) either type 2 species   rate set 2 rate shift model pars[7]: mu (extinction rate) either type 2 species rate   set 2 rate shift model pars[8]: K (carrying capacity) either type 2 species rate   set 2 rate shift model, set K=Inf diversity independence. pars[9]: gamma (immigration rate) either type 2 species   rate set 2 rate shift model pars[10]: lambda^(anagenesis rate) either type 2   species rate set 2 rate shift model Elements 6:10 required type 2 species included rate shift model. DAISIE_sim_relaxed_rate() pars[6] standard deviation gamma distribution relaxed parameter parameter chosen relaxed_par argument mean gamma distribution relaxed parameter. M Numeric defining size mainland pool, .e. number species can potentially colonize island. initEI initial values number endemics   non-endemics. DAISIE_probdist() DAISIE_margprobdist() either initprobs must NULL. DAISIE_numcol() NULL, assumed island   empty.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ExpEIN.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The expected number of endemics and non-endemics under the DAISIE model — DAISIE_ExpEIN","text":"output list three elements: ExpE number endemic species ExpI number non-endemic species ExpN sum number endemics non-endemics","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ExpEIN.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"The expected number of endemics and non-endemics under the DAISIE model — DAISIE_ExpEIN","text":"Valente, L.M., .B. Phillimore R.S. Etienne (2015). Equilibrium non-equilibrium dynamics simultaneously operate Galapagos islands. Ecology Letters 18: 844-852.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ExpEIN.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"The expected number of endemics and non-endemics under the DAISIE model — DAISIE_ExpEIN","text":"Rampal S. Etienne","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ExpEIN.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"The expected number of endemics and non-endemics under the DAISIE model — DAISIE_ExpEIN","text":"","code":"### Compute the expected values at t = 4, for a mainland pool size of 1000 potential # colonists and a vector of 5 parameters (cladogenesis, extinction, clade-level carrying # capacity, immigration, anagenesis)  DAISIE_ExpEIN(    t = 4,    pars = c(0.5,0.1,Inf,0.01,0.4),    M = 1000    ) #> $ExpE #> [1] 88.46714 #>  #> $ExpI #> [1] 9.726758 #>  #> $ExpN #> [1] 98.1939 #>"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_IC.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculates information criterion from DAISIE ML estimates? — DAISIE_IC","title":"Calculates information criterion from DAISIE ML estimates? — DAISIE_IC","text":"Calculates information criterion DAISIE ML estimates?","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_IC.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculates information criterion from DAISIE ML estimates? — DAISIE_IC","text":"","code":"DAISIE_IC(   datalist,   initparsopt,   idparsopt,   parsfix,   idparsfix,   endmc = 1000,   res = 100,   cond = 0,   ddmodel = 0 )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_IC.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculates information criterion from DAISIE ML estimates? — DAISIE_IC","text":"datalist Data object containing information colonisation branching times. object can generated using DAISIE_dataprep function, converts user-specified data table data object, object can course also entered directly. R list object following elements. first element list two three components: $island_age - island age  , depending whether distinction types made, :$not_present - number mainland lineages present island  :$not_present_type1 - number mainland lineages type 1 present island $not_present_type2 - number mainland lineages type 2 present island  remaining elements list contains information single colonist lineage island 5 components:$colonist_name - name species clade colonized island $branching_times - island age followed stem age population/species case Non-endemic, Non-endemic_MaxAge species Endemic species close relatives island. endemic clades one species island (cladogenetic clades/ radiations) island age followed branching times island clade including stem age clade$stac - status colonist  * Non_endemic_MaxAge: 1  * Endemic: 2  * Endemic&Non_Endemic: 3  * Non_Endemic: 4  * Endemic_Singleton_MaxAge: 5  * Endemic_Clade_MaxAge: 6  * Endemic&Non_Endemic_Clade_MaxAge: 7 $missing_species - number island species sampled particular clade (applicable endemic clades) $type1or2 - whether colonist belongs type 1 type 2 initparsopt initial values parameters must optimized, positive. idparsopt ids parameters must optimized. ids defined follows:  id = 1 corresponds lambda^c (cladogenesis rate)  id = 2 corresponds mu (extinction rate)  id = 3 corresponds K (clade-level carrying capacity)  id = 4 corresponds gamma (immigration rate)  id = 5 corresponds lambda^(anagenesis rate)  id = 6 corresponds lambda^c (cladogenesis rate) optional subset species  id = 7 corresponds mu (extinction rate) optional subset species id = 8 corresponds K (clade-level carrying capacity) optional subset species id = 9 corresponds gamma (immigration rate) optional subset species id = 10 corresponds lambda^(anagenesis rate) optional subset species id = 11 corresponds p_f (fraction mainland species belongs second subset species. parsfix values parameters optimized. idparsfix ids parameters optimized, e.g. c(1,3) lambda^c K optimized. endmc Numeric many simulations run. res Sets maximum number species probability must computed, must larger size largest clade. cond cond = 0 : conditioning island age  cond = 1 : conditioning island age non-extinction island biota . cond > 1 : conditioning island age least cond colonizations island. last option yet available IW model ddmodel Sets model diversity-dependence:  ddmodel = 0 : diversity dependence  ddmodel = 1 : linear dependence speciation rate  ddmodel = 11: linear dependence speciation rate immigration rate  ddmodel = 2 : exponential dependence speciation rate ddmodel = 21: exponential dependence speciation rate immigration rate","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_IC.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculates information criterion from DAISIE ML estimates? — DAISIE_IC","text":"List two numerics WIC AICb","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_IW_num_threads.html","id":null,"dir":"Reference","previous_headings":"","what":"IW concurrency control — DAISIE_IW_num_threads","title":"IW concurrency control — DAISIE_IW_num_threads","text":"Sets retrieves number threads used odeint solver.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_IW_num_threads.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"IW concurrency control — DAISIE_IW_num_threads","text":"","code":"DAISIE_IW_num_threads(num_threads)"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_IW_num_threads.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"IW concurrency control — DAISIE_IW_num_threads","text":"num_threads num_threads < 0 omitted: retrieves number threads. num_threads = 0: sets number threads number available cores. num_threads = 1: single-threaded execution. num_threads > 1: sets number threads num_threads.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_IW_num_threads.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"IW concurrency control — DAISIE_IW_num_threads","text":"number threads","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_IW_num_threads.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"IW concurrency control — DAISIE_IW_num_threads","text":"maximum number threads limited value C++ standard library function std::thread::hardware_concurrency(). also default number threads upon library load. Multithreading incurs overhead. Therefore, single-threaded execution might faster small systems.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ML.html","id":null,"dir":"Reference","previous_headings":"","what":"Maximization of the loglikelihood under the DAISIE model with clade-specific diversity-dependence — DAISIE_ML","title":"Maximization of the loglikelihood under the DAISIE model with clade-specific diversity-dependence — DAISIE_ML","text":"function computes maximum likelihood estimates parameters DAISIE model clade-specific diversity-dependence data lineages colonizing island. also outputs corresponding loglikelihood can used model comparisons. result sort(c(idparsopt, idparsfix, idparsnoshift)) identical c(1:10). , error reported input incoherent. happens length initparsopt different length idparsopt, length parsfix different length idparsfix. Including 11th parameter (p_f) either idparsopt idparsfix (therefore initparsopt parsfix) optional. parameter specified, information data used, otherwise information data overruled.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ML.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Maximization of the loglikelihood under the DAISIE model with clade-specific diversity-dependence — DAISIE_ML","text":"","code":"DAISIE_ML_CS(   datalist,   datatype = \"single\",   initparsopt,   idparsopt,   parsfix,   idparsfix,   idparsnoshift = 6:10,   idparsmat = NULL,   res = 100,   ddmodel = 0,   cond = 0,   island_ontogeny = NA,   eqmodel = 0,   x_E = 0.95,   x_I = 0.98,   tol = c(1e-04, 1e-05, 1e-07),   maxiter = 1000 * round((1.25)^length(idparsopt)),   methode = \"lsodes\",   optimmethod = \"subplex\",   CS_version = 1,   verbose = 0,   tolint = c(1e-16, 1e-10),   jitter = 0,   num_cycles = 1 )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ML.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Maximization of the loglikelihood under the DAISIE model with clade-specific diversity-dependence — DAISIE_ML","text":"datalist Data object containing information colonisation branching times. object can generated using DAISIE_dataprep function, converts user-specified data table data object, object can course also entered directly. R list object following elements. first element list two three components: $island_age - island age  , depending whether distinction types made, :$not_present - number mainland lineages present island  :$not_present_type1 - number mainland lineages type 1 present island $not_present_type2 - number mainland lineages type 2 present island  remaining elements list contains information single colonist lineage island 5 components:$colonist_name - name species clade colonized island $branching_times - island age followed stem age population/species case Non-endemic, Non-endemic_MaxAge species Endemic species close relatives island. endemic clades one species island (cladogenetic clades/ radiations) island age followed branching times island clade including stem age clade$stac - status colonist  * Non_endemic_MaxAge: 1  * Endemic: 2  * Endemic&Non_Endemic: 3  * Non_Endemic: 4  * Endemic_Singleton_MaxAge: 5  * Endemic_Clade_MaxAge: 6  * Endemic&Non_Endemic_Clade_MaxAge: 7 $missing_species - number island species sampled particular clade (applicable endemic clades) $type1or2 - whether colonist belongs type 1 type 2 datatype Sets type data: 'single' single island archipelago treated one, 'multiple' multiple archipelagoes potentially sharing parameters. initparsopt initial values parameters must optimized, positive. idparsopt ids parameters must optimized. ids defined follows:  id = 1 corresponds lambda^c (cladogenesis rate)  id = 2 corresponds mu (extinction rate)  id = 3 corresponds K (clade-level carrying capacity)  id = 4 corresponds gamma (immigration rate)  id = 5 corresponds lambda^(anagenesis rate)  id = 6 corresponds lambda^c (cladogenesis rate) optional subset species  id = 7 corresponds mu (extinction rate) optional subset species id = 8 corresponds K (clade-level carrying capacity) optional subset species id = 9 corresponds gamma (immigration rate) optional subset species id = 10 corresponds lambda^(anagenesis rate) optional subset species id = 11 corresponds p_f (fraction mainland species belongs second subset species. parsfix values parameters optimized. idparsfix ids parameters optimized, e.g. c(1,3) lambda^c K optimized. idparsnoshift datatype = 'single' : ids parameters different two groups species; can apply ids 6:10, e.g. idparsnoshift = c(6,7) means lambda^c mu values groups. idparsmat datatype = 'multiple' : Matrix containing ids parameters, linking initparsopt parsfix. Per island system use following order:  * lac = (initial) cladogenesis rate  * mu = extinction rate  * K = maximum number species possible clade  * gam = (initial) immigration rate  * laa = (initial) anagenesis rate  Example: idparsmat = rbind(c(1, 2, 3, 4, 5), c(1, 2, 3, 6, 7)) different rates immigration anagenesis two islands. res Sets maximum number species probability must computed, must larger size largest clade. ddmodel Sets model diversity-dependence:  ddmodel = 0 : diversity dependence  ddmodel = 1 : linear dependence speciation rate  ddmodel = 11: linear dependence speciation rate immigration rate  ddmodel = 2 : exponential dependence speciation rate ddmodel = 21: exponential dependence speciation rate immigration rate cond cond = 0 : conditioning island age  cond = 1 : conditioning island age non-extinction island biota . cond > 1 : conditioning island age least cond colonizations island. last option yet available IW model island_ontogeny DAISIE_sim_time_dep(), DAISIE_ML_CS plotting string describing type island ontogeny. Can \"const\", \"beta\" beta function describing area time.  functions numeric describing type island ontogeny. Can 0 constant, 1 beta function describing area time. ML functions island_ontogeny = NA assumes constant ontogeny. Time dependent estimation yet available development still ongoing. return error called case. eqmodel Sets equilibrium constraint can used likelihood optimization. available datatype = 'single'. eqmodel = 0 : equilibrium assumed  eqmodel = 13 : near-equilibrium assumed endemics using deterministic equation endemics immigrants. Endemics must within x_E equilibrium value eqmodel = 15 : near-equilibrium assumed endemics immigrants using deterministic equation endemics immigrants. Endemics must within x_E equilibrium value, non-endemics must within x_I equilibrium value. x_E Sets fraction equlibrium endemic diversity endemics assumed equilibrium; active eqmodel = 13 15. x_I Sets fraction equlibrium non-endemic diversity system assumed equilibrium; active eqmodel = 15. tol Sets tolerances optimization. Consists :  reltolx = relative tolerance parameter values optimization  reltolf = relative tolerance function value optimization  abstolx = absolute tolerance parameter values optimization. maxiter Sets maximum number iterations optimization. methode Method ODE-solver. Supported Boost ODEINT solvers (steppers) : \"odeint::runge_kutta_cash_karp54\" \"odeint::runge_kutta_fehlberg78\" \"odeint::runge_kutta_dopri5\" \"odeint::bulirsch_stoer\" without odeint::-prefix, deSolve{ode} method assumed. default method overall \"lsodes\" DAISIE_ML_CS() \"ode45\" ode() DAISIE_ML_IW(). optimmethod Method used likelihood optimization. Default `subplex` (see `subplex()` full details). Alternative \"simplex\" method previous versions. CS_version numeric list. Default 1 standard DAISIE model, relaxed-rate model list following elements: model: CS model run, options 1 single rate   DAISIE model, 2 multi-rate DAISIE, 0 IW test   model. relaxed_par: parameter relax (integrate ). Options \"cladogenesis\", \"extinction\", \"carrying_capacity\", \"immigration\", \"anagenesis\". verbose numeric vector length 1, simulations `DAISIEdataprep()` can `1` `0`, `1` gives intermediate output printed. ML functions numeric determining intermediate output printed. default: `0` print, `1` prints initial likelihood settings selected (parameters optimised, fixed shifted), `2` prints `1 also intermediate output parameters loglikelihood, `3` `2` prints intermediate progress likelihood computation. tolint Vector two elements containing absolute relative tolerance integration. jitter Numeric optimizer(). Jitters parameters optimized specified amount small, e.g. 1e-5. Jitter link{subplex}{subplex}() produces incorrect output due parameter transformation. num_cycles number cycles optimizer go . Default 1.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ML.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Maximization of the loglikelihood under the DAISIE model with clade-specific diversity-dependence — DAISIE_ML","text":"output dataframe containing estimated parameters maximum loglikelihood. lambda_c gives maximum likelihood estimate lambda^c, rate cladogenesis mu gives maximum likelihood estimate mu, extinction rate K gives maximum likelihood estimate K, carrying-capacity gamma gives maximum likelihood estimate gamma, immigration rate lambda_a gives maximum likelihood estimate lambda^, rate anagenesis lambda_c2 gives maximum likelihood estimate lambda^c2, rate cladogenesis optional second group species mu2 gives maximum likelihood estimate mu2, extinction rate optional second group species K2 gives maximum likelihood estimate K2, carrying-capacity optional second group species gamma2 gives maximum likelihood estimate gamma2, immigration rate optional second group species lambda_a2 gives maximum likelihood estimate lambda^a2, rate anagenesis optional second group species loglik gives maximum loglikelihood df gives number estimated parameters, .e. degrees feedom conv gives message convergence optimization; conv = 0 means convergence","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ML.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Maximization of the loglikelihood under the DAISIE model with clade-specific diversity-dependence — DAISIE_ML","text":"Valente, L.M., .B. Phillimore R.S. Etienne (2015). Equilibrium non-equilibrium dynamics simultaneously operate Galapagos islands. Ecology Letters 18: 844-852. <doi:10.1111/ele.12461>.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ML.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Maximization of the loglikelihood under the DAISIE model with clade-specific diversity-dependence — DAISIE_ML","text":"Rampal S. Etienne","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ML.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Maximization of the loglikelihood under the DAISIE model with clade-specific diversity-dependence — DAISIE_ML","text":"","code":"cat(\" ### When all species have the same rates, and we want to optimize all 5 parameters, # we use:  utils::data(Galapagos_datalist) DAISIE_ML(    datalist = Galapagos_datalist,    initparsopt = c(2.5,2.7,20,0.009,1.01),    ddmodel = 11,    idparsopt = 1:5,    parsfix = NULL,    idparsfix = NULL )  ### When all species have the same rates, and we want to optimize all parameters # except K (which we set equal to Inf), we use:  utils::data(Galapagos_datalist) DAISIE_ML(    datalist = Galapagos_datalist,    initparsopt = c(2.5,2.7,0.009,1.01),    idparsopt = c(1,2,4,5),    parsfix = Inf,    idparsfix = 3    )  ### When all species have the same rates except that the finches have a different # rate of cladogenesis, and we want to optimize all parameters except K (which we # set equal to Inf), fixing the proportion of finch-type species at 0.163, we use:  utils::data(Galapagos_datalist_2types) DAISIE_ML(    datalist = Galapagos_datalist_2types,    initparsopt = c(0.38,0.55,0.004,1.1,2.28),    idparsopt = c(1,2,4,5,6),    parsfix = c(Inf,Inf,0.163),    idparsfix = c(3,8,11),    idparsnoshift = c(7,9,10)    )  ### When all species have the same rates except that the finches have a different # rate of cladogenesis, extinction and a different K, and we want to optimize all # parameters, fixing the proportion of finch-type species at 0.163, we use:  utils::data(Galapagos_datalist_2types) DAISIE_ML(    datalist = Galapagos_datalist_2types,    ddmodel = 11,    initparsopt = c(0.19,0.09,0.002,0.87,20,8.9,15),    idparsopt = c(1,2,4,5,6,7,8),    parsfix = c(Inf,0.163),    idparsfix = c(3,11),    idparsnoshift = c(9,10)    )   ### When all species have the same rates except that the finches have a different # rate of extinction, and we want to optimize all parameters except K (which we # set equal to Inf), and we also# want to estimate the fraction of finch species # in the mainland pool. we use:  utils::data(Galapagos_datalist_2types) DAISIE_ML(    datalist = Galapagos_datalist_2types,    initparsopt = c(2.48,2.7,0.009,1.01,2.25,0.163),    idparsopt = c(1,2,4,5,7,11),    parsfix = c(Inf,Inf),    idparsfix = c(3,8),    idparsnoshift = c(6,9,10)    )  ### When we have two islands with the same rates except for immigration and anagenesis rate, # and we want to optimize all parameters, we use:  utils::data(Galapagos_datalist) DAISIE_ML(    datalist = list(Galapagos_datalist,Galapagos_datalist),    datatype = 'multiple',    initparsopt = c(2.5,2.7,20,0.009,1.01,0.009,1.01),    idparsmat = rbind(1:5,c(1:3,6,7)),    idparsopt = 1:7,    parsfix = NULL,    idparsfix = NULL )  ### When we consider the four Macaronesia archipelagoes and set all parameters the same # except for rates of cladogenesis, extinction and immigration for Canary Islands, # rate of cladogenesis is fixed to 0 for the other archipelagoes, # diversity-dependence is assumed to be absent # and we want to optimize all parameters, we use:  utils::data(Macaronesia_datalist) DAISIE_ML(    datalist = Macaronesia_datalist,    datatype = 'multiple',    initparsopt = c(1.053151832,0.052148979,0.512939011,0.133766934,0.152763179),    idparsmat = rbind(1:5,c(6,2,3,7,5),1:5,1:5),    idparsopt = c(2,4,5,6,7),    parsfix = c(0,Inf),    idparsfix = c(1,3) )  \") #>  #> ### When all species have the same rates, and we want to optimize all 5 parameters, #> # we use: #>  #> utils::data(Galapagos_datalist) #> DAISIE_ML( #>    datalist = Galapagos_datalist, #>    initparsopt = c(2.5,2.7,20,0.009,1.01), #>    ddmodel = 11, #>    idparsopt = 1:5, #>    parsfix = NULL, #>    idparsfix = NULL #> ) #>  #> ### When all species have the same rates, and we want to optimize all parameters #> # except K (which we set equal to Inf), we use: #>  #> utils::data(Galapagos_datalist) #> DAISIE_ML( #>    datalist = Galapagos_datalist, #>    initparsopt = c(2.5,2.7,0.009,1.01), #>    idparsopt = c(1,2,4,5), #>    parsfix = Inf, #>    idparsfix = 3 #>    ) #>  #> ### When all species have the same rates except that the finches have a different #> # rate of cladogenesis, and we want to optimize all parameters except K (which we #> # set equal to Inf), fixing the proportion of finch-type species at 0.163, we use: #>  #> utils::data(Galapagos_datalist_2types) #> DAISIE_ML( #>    datalist = Galapagos_datalist_2types, #>    initparsopt = c(0.38,0.55,0.004,1.1,2.28), #>    idparsopt = c(1,2,4,5,6), #>    parsfix = c(Inf,Inf,0.163), #>    idparsfix = c(3,8,11), #>    idparsnoshift = c(7,9,10) #>    ) #>  #> ### When all species have the same rates except that the finches have a different #> # rate of cladogenesis, extinction and a different K, and we want to optimize all #> # parameters, fixing the proportion of finch-type species at 0.163, we use: #>  #> utils::data(Galapagos_datalist_2types) #> DAISIE_ML( #>    datalist = Galapagos_datalist_2types, #>    ddmodel = 11, #>    initparsopt = c(0.19,0.09,0.002,0.87,20,8.9,15), #>    idparsopt = c(1,2,4,5,6,7,8), #>    parsfix = c(Inf,0.163), #>    idparsfix = c(3,11), #>    idparsnoshift = c(9,10) #>    ) #>  #>  #> ### When all species have the same rates except that the finches have a different #> # rate of extinction, and we want to optimize all parameters except K (which we #> # set equal to Inf), and we also# want to estimate the fraction of finch species #> # in the mainland pool. we use: #>  #> utils::data(Galapagos_datalist_2types) #> DAISIE_ML( #>    datalist = Galapagos_datalist_2types, #>    initparsopt = c(2.48,2.7,0.009,1.01,2.25,0.163), #>    idparsopt = c(1,2,4,5,7,11), #>    parsfix = c(Inf,Inf), #>    idparsfix = c(3,8), #>    idparsnoshift = c(6,9,10) #>    ) #>  #> ### When we have two islands with the same rates except for immigration and anagenesis rate, #> # and we want to optimize all parameters, we use: #>  #> utils::data(Galapagos_datalist) #> DAISIE_ML( #>    datalist = list(Galapagos_datalist,Galapagos_datalist), #>    datatype = 'multiple', #>    initparsopt = c(2.5,2.7,20,0.009,1.01,0.009,1.01), #>    idparsmat = rbind(1:5,c(1:3,6,7)), #>    idparsopt = 1:7, #>    parsfix = NULL, #>    idparsfix = NULL #> ) #>  #> ### When we consider the four Macaronesia archipelagoes and set all parameters the same #> # except for rates of cladogenesis, extinction and immigration for Canary Islands, #> # rate of cladogenesis is fixed to 0 for the other archipelagoes, #> # diversity-dependence is assumed to be absent #> # and we want to optimize all parameters, we use: #>  #> utils::data(Macaronesia_datalist) #> DAISIE_ML( #>    datalist = Macaronesia_datalist, #>    datatype = 'multiple', #>    initparsopt = c(1.053151832,0.052148979,0.512939011,0.133766934,0.152763179), #>    idparsmat = rbind(1:5,c(6,2,3,7,5),1:5,1:5), #>    idparsopt = c(2,4,5,6,7), #>    parsfix = c(0,Inf), #>    idparsfix = c(1,3) #> ) #>"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ML1.html","id":null,"dir":"Reference","previous_headings":"","what":"Computes MLE for single type species under a clade specific scenario — DAISIE_ML1","title":"Computes MLE for single type species under a clade specific scenario — DAISIE_ML1","text":"Computes MLE single type species clade specific scenario","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ML1.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Computes MLE for single type species under a clade specific scenario — DAISIE_ML1","text":"","code":"DAISIE_ML1(   datalist,   initparsopt,   idparsopt,   parsfix,   idparsfix,   idparsnoshift = 6:10,   res = 100,   ddmodel = 0,   cond = 0,   eqmodel = 0,   x_E = 0.95,   x_I = 0.98,   tol = c(1e-04, 1e-05, 1e-07),   maxiter = 1000 * round((1.25)^length(idparsopt)),   methode = \"lsodes\",   optimmethod = \"subplex\",   CS_version = 1,   verbose = 0,   tolint = c(1e-16, 1e-10),   island_ontogeny = NA,   jitter = 0,   num_cycles = 1 )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ML1.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Computes MLE for single type species under a clade specific scenario — DAISIE_ML1","text":"datalist Data object containing information colonisation branching times. object can generated using DAISIE_dataprep function, converts user-specified data table data object, object can course also entered directly. R list object following elements. first element list two three components: $island_age - island age  , depending whether distinction types made, :$not_present - number mainland lineages present island  :$not_present_type1 - number mainland lineages type 1 present island $not_present_type2 - number mainland lineages type 2 present island  remaining elements list contains information single colonist lineage island 5 components:$colonist_name - name species clade colonized island $branching_times - island age followed stem age population/species case Non-endemic, Non-endemic_MaxAge species Endemic species close relatives island. endemic clades one species island (cladogenetic clades/ radiations) island age followed branching times island clade including stem age clade$stac - status colonist  * Non_endemic_MaxAge: 1  * Endemic: 2  * Endemic&Non_Endemic: 3  * Non_Endemic: 4  * Endemic_Singleton_MaxAge: 5  * Endemic_Clade_MaxAge: 6  * Endemic&Non_Endemic_Clade_MaxAge: 7 $missing_species - number island species sampled particular clade (applicable endemic clades) $type1or2 - whether colonist belongs type 1 type 2 initparsopt initial values parameters must optimized, positive. idparsopt ids parameters must optimized. ids defined follows:  id = 1 corresponds lambda^c (cladogenesis rate)  id = 2 corresponds mu (extinction rate)  id = 3 corresponds K (clade-level carrying capacity)  id = 4 corresponds gamma (immigration rate)  id = 5 corresponds lambda^(anagenesis rate)  id = 6 corresponds lambda^c (cladogenesis rate) optional subset species  id = 7 corresponds mu (extinction rate) optional subset species id = 8 corresponds K (clade-level carrying capacity) optional subset species id = 9 corresponds gamma (immigration rate) optional subset species id = 10 corresponds lambda^(anagenesis rate) optional subset species id = 11 corresponds p_f (fraction mainland species belongs second subset species. parsfix values parameters optimized. idparsfix ids parameters optimized, e.g. c(1,3) lambda^c K optimized. idparsnoshift datatype = 'single' : ids parameters different two groups species; can apply ids 6:10, e.g. idparsnoshift = c(6,7) means lambda^c mu values groups. res Sets maximum number species probability must computed, must larger size largest clade. ddmodel Sets model diversity-dependence:  ddmodel = 0 : diversity dependence  ddmodel = 1 : linear dependence speciation rate  ddmodel = 11: linear dependence speciation rate immigration rate  ddmodel = 2 : exponential dependence speciation rate ddmodel = 21: exponential dependence speciation rate immigration rate cond cond = 0 : conditioning island age  cond = 1 : conditioning island age non-extinction island biota . cond > 1 : conditioning island age least cond colonizations island. last option yet available IW model eqmodel Sets equilibrium constraint can used likelihood optimization. available datatype = 'single'. eqmodel = 0 : equilibrium assumed  eqmodel = 13 : near-equilibrium assumed endemics using deterministic equation endemics immigrants. Endemics must within x_E equilibrium value eqmodel = 15 : near-equilibrium assumed endemics immigrants using deterministic equation endemics immigrants. Endemics must within x_E equilibrium value, non-endemics must within x_I equilibrium value. x_E Sets fraction equlibrium endemic diversity endemics assumed equilibrium; active eqmodel = 13 15. x_I Sets fraction equlibrium non-endemic diversity system assumed equilibrium; active eqmodel = 15. tol Sets tolerances optimization. Consists :  reltolx = relative tolerance parameter values optimization  reltolf = relative tolerance function value optimization  abstolx = absolute tolerance parameter values optimization. maxiter Sets maximum number iterations optimization. methode Method ODE-solver. Supported Boost ODEINT solvers (steppers) : \"odeint::runge_kutta_cash_karp54\" \"odeint::runge_kutta_fehlberg78\" \"odeint::runge_kutta_dopri5\" \"odeint::bulirsch_stoer\" without odeint::-prefix, deSolve{ode} method assumed. default method overall \"lsodes\" DAISIE_ML_CS() \"ode45\" ode() DAISIE_ML_IW(). optimmethod Method used likelihood optimization. Default `subplex` (see `subplex()` full details). Alternative \"simplex\" method previous versions. CS_version numeric list. Default 1 standard DAISIE model, relaxed-rate model list following elements: model: CS model run, options 1 single rate   DAISIE model, 2 multi-rate DAISIE, 0 IW test   model. relaxed_par: parameter relax (integrate ). Options \"cladogenesis\", \"extinction\", \"carrying_capacity\", \"immigration\", \"anagenesis\". verbose numeric vector length 1, simulations `DAISIEdataprep()` can `1` `0`, `1` gives intermediate output printed. ML functions numeric determining intermediate output printed. default: `0` print, `1` prints initial likelihood settings selected (parameters optimised, fixed shifted), `2` prints `1 also intermediate output parameters loglikelihood, `3` `2` prints intermediate progress likelihood computation. tolint Vector two elements containing absolute relative tolerance integration. island_ontogeny DAISIE_sim_time_dep(), DAISIE_ML_CS plotting string describing type island ontogeny. Can \"const\", \"beta\" beta function describing area time.  functions numeric describing type island ontogeny. Can 0 constant, 1 beta function describing area time. ML functions island_ontogeny = NA assumes constant ontogeny. Time dependent estimation yet available development still ongoing. return error called case. jitter Numeric optimizer(). Jitters parameters optimized specified amount small, e.g. 1e-5. Jitter link{subplex}{subplex}() produces incorrect output due parameter transformation. num_cycles number cycles optimizer go . Default 1.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ML1.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Computes MLE for single type species under a clade specific scenario — DAISIE_ML1","text":"output dataframe containing estimated parameters maximum loglikelihood. lambda_c gives maximum likelihood estimate lambda^c, rate cladogenesis mu gives maximum likelihood estimate mu, extinction rate K gives maximum likelihood estimate K, carrying-capacity gamma gives maximum likelihood estimate gamma, immigration rate lambda_a gives maximum likelihood estimate lambda^, rate anagenesis loglik gives maximum loglikelihood df gives number estimated parameters, .e. degrees feedom conv gives message convergence optimization; conv = 0 means convergence","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ML2.html","id":null,"dir":"Reference","previous_headings":"","what":"Computes MLE for multiple islands under a clade specific scenario — DAISIE_ML2","title":"Computes MLE for multiple islands under a clade specific scenario — DAISIE_ML2","text":"Computes MLE multiple islands clade specific scenario","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ML2.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Computes MLE for multiple islands under a clade specific scenario — DAISIE_ML2","text":"","code":"DAISIE_ML2(   datalist,   initparsopt,   idparsopt,   parsfix,   idparsfix,   idparsmat,   res = 100,   ddmodel = 0,   cond = 0,   island_ontogeny = NA,   tol = c(1e-04, 1e-05, 1e-07),   maxiter = 1000 * round((1.25)^length(idparsopt)),   methode = \"lsodes\",   optimmethod = \"subplex\",   verbose = 0,   tolint = c(1e-16, 1e-10),   jitter = 0,   num_cycles = 1 )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ML2.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Computes MLE for multiple islands under a clade specific scenario — DAISIE_ML2","text":"datalist Data object containing information colonisation branching times. object can generated using DAISIE_dataprep function, converts user-specified data table data object, object can course also entered directly. R list object following elements. first element list two three components: $island_age - island age  , depending whether distinction types made, :$not_present - number mainland lineages present island  :$not_present_type1 - number mainland lineages type 1 present island $not_present_type2 - number mainland lineages type 2 present island  remaining elements list contains information single colonist lineage island 5 components:$colonist_name - name species clade colonized island $branching_times - island age followed stem age population/species case Non-endemic, Non-endemic_MaxAge species Endemic species close relatives island. endemic clades one species island (cladogenetic clades/ radiations) island age followed branching times island clade including stem age clade$stac - status colonist  * Non_endemic_MaxAge: 1  * Endemic: 2  * Endemic&Non_Endemic: 3  * Non_Endemic: 4  * Endemic_Singleton_MaxAge: 5  * Endemic_Clade_MaxAge: 6  * Endemic&Non_Endemic_Clade_MaxAge: 7 $missing_species - number island species sampled particular clade (applicable endemic clades) $type1or2 - whether colonist belongs type 1 type 2 initparsopt initial values parameters must optimized, positive. idparsopt ids parameters must optimized. ids defined follows:  id = 1 corresponds lambda^c (cladogenesis rate)  id = 2 corresponds mu (extinction rate)  id = 3 corresponds K (clade-level carrying capacity)  id = 4 corresponds gamma (immigration rate)  id = 5 corresponds lambda^(anagenesis rate)  id = 6 corresponds lambda^c (cladogenesis rate) optional subset species  id = 7 corresponds mu (extinction rate) optional subset species id = 8 corresponds K (clade-level carrying capacity) optional subset species id = 9 corresponds gamma (immigration rate) optional subset species id = 10 corresponds lambda^(anagenesis rate) optional subset species id = 11 corresponds p_f (fraction mainland species belongs second subset species. parsfix values parameters optimized. idparsfix ids parameters optimized, e.g. c(1,3) lambda^c K optimized. idparsmat datatype = 'multiple' : Matrix containing ids parameters, linking initparsopt parsfix. Per island system use following order:  * lac = (initial) cladogenesis rate  * mu = extinction rate  * K = maximum number species possible clade  * gam = (initial) immigration rate  * laa = (initial) anagenesis rate  Example: idparsmat = rbind(c(1, 2, 3, 4, 5), c(1, 2, 3, 6, 7)) different rates immigration anagenesis two islands. res Sets maximum number species probability must computed, must larger size largest clade. ddmodel Sets model diversity-dependence:  ddmodel = 0 : diversity dependence  ddmodel = 1 : linear dependence speciation rate  ddmodel = 11: linear dependence speciation rate immigration rate  ddmodel = 2 : exponential dependence speciation rate ddmodel = 21: exponential dependence speciation rate immigration rate cond cond = 0 : conditioning island age  cond = 1 : conditioning island age non-extinction island biota . cond > 1 : conditioning island age least cond colonizations island. last option yet available IW model island_ontogeny DAISIE_sim_time_dep(), DAISIE_ML_CS plotting string describing type island ontogeny. Can \"const\", \"beta\" beta function describing area time.  functions numeric describing type island ontogeny. Can 0 constant, 1 beta function describing area time. ML functions island_ontogeny = NA assumes constant ontogeny. Time dependent estimation yet available development still ongoing. return error called case. tol Sets tolerances optimization. Consists :  reltolx = relative tolerance parameter values optimization  reltolf = relative tolerance function value optimization  abstolx = absolute tolerance parameter values optimization. maxiter Sets maximum number iterations optimization. methode Method ODE-solver. Supported Boost ODEINT solvers (steppers) : \"odeint::runge_kutta_cash_karp54\" \"odeint::runge_kutta_fehlberg78\" \"odeint::runge_kutta_dopri5\" \"odeint::bulirsch_stoer\" without odeint::-prefix, deSolve{ode} method assumed. default method overall \"lsodes\" DAISIE_ML_CS() \"ode45\" ode() DAISIE_ML_IW(). optimmethod Method used likelihood optimization. Default `subplex` (see `subplex()` full details). Alternative \"simplex\" method previous versions. verbose numeric vector length 1, simulations `DAISIEdataprep()` can `1` `0`, `1` gives intermediate output printed. ML functions numeric determining intermediate output printed. default: `0` print, `1` prints initial likelihood settings selected (parameters optimised, fixed shifted), `2` prints `1 also intermediate output parameters loglikelihood, `3` `2` prints intermediate progress likelihood computation. tolint Vector two elements containing absolute relative tolerance integration. jitter Numeric optimizer(). Jitters parameters optimized specified amount small, e.g. 1e-5. Jitter link{subplex}{subplex}() produces incorrect output due parameter transformation. num_cycles number cycles optimizer go . Default 1.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ML2.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Computes MLE for multiple islands under a clade specific scenario — DAISIE_ML2","text":"output dataframe containing estimated parameters maximum loglikelihood. lambda_c gives maximum likelihood estimate lambda^c, rate cladogenesis mu gives maximum likelihood estimate mu, extinction rate K gives maximum likelihood estimate K, carrying-capacity gamma gives maximum likelihood estimate gamma, immigration rate lambda_a gives maximum likelihood estimate lambda^, rate anagenesis lambda_c2 gives maximum likelihood estimate lambda^c2, rate cladogenesis second group species mu2 gives maximum likelihood estimate mu2, extinction rate second group species K2 gives maximum likelihood estimate K2, carrying-capacity  second group species gamma2 gives maximum likelihood estimate gamma2, immigration rate second group species lambda_a2 gives maximum likelihood estimate lambda^a2, rate anagenesis second group species loglik gives maximum loglikelihood df gives number estimated parameters, .e. degrees feedom conv gives message convergence optimization; conv = 0 means convergence","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ML4.html","id":null,"dir":"Reference","previous_headings":"","what":"Computes MLE for single type species under a clade specific scenario where one parameter may vary over the clades governed by a specific distribution — DAISIE_ML4","title":"Computes MLE for single type species under a clade specific scenario where one parameter may vary over the clades governed by a specific distribution — DAISIE_ML4","text":"Computes MLE single type species clade specific scenario one parameter may vary clades governed specific distribution","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ML4.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Computes MLE for single type species under a clade specific scenario where one parameter may vary over the clades governed by a specific distribution — DAISIE_ML4","text":"","code":"DAISIE_ML4(   datalist,   initparsopt,   idparsopt,   parsfix,   idparsfix,   res = 100,   ddmodel = 0,   cond = 0,   tol = c(1e-04, 1e-05, 1e-07),   maxiter = 1000 * round((1.25)^length(idparsopt)),   methode = \"lsodes\",   optimmethod = \"subplex\",   CS_version = create_CS_version(model = 2, relaxed_par = \"cladogenesis\", par_sd = 0,     par_upper_bound = Inf),   verbose = 0,   tolint = c(1e-16, 1e-10),   island_ontogeny = NA,   jitter = 0,   num_cycles = 1 )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ML4.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Computes MLE for single type species under a clade specific scenario where one parameter may vary over the clades governed by a specific distribution — DAISIE_ML4","text":"datalist Data object containing information colonisation branching times. object can generated using DAISIE_dataprep function, converts user-specified data table data object, object can course also entered directly. R list object following elements. first element list two three components: $island_age - island age  , depending whether distinction types made, :$not_present - number mainland lineages present island  :$not_present_type1 - number mainland lineages type 1 present island $not_present_type2 - number mainland lineages type 2 present island  remaining elements list contains information single colonist lineage island 5 components:$colonist_name - name species clade colonized island $branching_times - island age followed stem age population/species case Non-endemic, Non-endemic_MaxAge species Endemic species close relatives island. endemic clades one species island (cladogenetic clades/ radiations) island age followed branching times island clade including stem age clade$stac - status colonist  * Non_endemic_MaxAge: 1  * Endemic: 2  * Endemic&Non_Endemic: 3  * Non_Endemic: 4  * Endemic_Singleton_MaxAge: 5  * Endemic_Clade_MaxAge: 6  * Endemic&Non_Endemic_Clade_MaxAge: 7 $missing_species - number island species sampled particular clade (applicable endemic clades) $type1or2 - whether colonist belongs type 1 type 2 initparsopt initial values parameters must optimized, positive. idparsopt ids parameters must optimized. ids defined follows:  id = 1 corresponds lambda^c (cladogenesis rate)  id = 2 corresponds mu (extinction rate)  id = 3 corresponds K (clade-level carrying capacity)  id = 4 corresponds gamma (immigration rate)  id = 5 corresponds lambda^(anagenesis rate)  id = 6 corresponds lambda^c (cladogenesis rate) optional subset species  id = 7 corresponds mu (extinction rate) optional subset species id = 8 corresponds K (clade-level carrying capacity) optional subset species id = 9 corresponds gamma (immigration rate) optional subset species id = 10 corresponds lambda^(anagenesis rate) optional subset species id = 11 corresponds p_f (fraction mainland species belongs second subset species. parsfix values parameters optimized. idparsfix ids parameters optimized, e.g. c(1,3) lambda^c K optimized. res Sets maximum number species probability must computed, must larger size largest clade. ddmodel Sets model diversity-dependence:  ddmodel = 0 : diversity dependence  ddmodel = 1 : linear dependence speciation rate  ddmodel = 11: linear dependence speciation rate immigration rate  ddmodel = 2 : exponential dependence speciation rate ddmodel = 21: exponential dependence speciation rate immigration rate cond cond = 0 : conditioning island age  cond = 1 : conditioning island age non-extinction island biota . cond > 1 : conditioning island age least cond colonizations island. last option yet available IW model tol Sets tolerances optimization. Consists :  reltolx = relative tolerance parameter values optimization  reltolf = relative tolerance function value optimization  abstolx = absolute tolerance parameter values optimization. maxiter Sets maximum number iterations optimization. methode Method ODE-solver. Supported Boost ODEINT solvers (steppers) : \"odeint::runge_kutta_cash_karp54\" \"odeint::runge_kutta_fehlberg78\" \"odeint::runge_kutta_dopri5\" \"odeint::bulirsch_stoer\" without odeint::-prefix, deSolve{ode} method assumed. default method overall \"lsodes\" DAISIE_ML_CS() \"ode45\" ode() DAISIE_ML_IW(). optimmethod Method used likelihood optimization. Default `subplex` (see `subplex()` full details). Alternative \"simplex\" method previous versions. CS_version numeric list. Default 1 standard DAISIE model, relaxed-rate model list following elements: model: CS model run, options 1 single rate   DAISIE model, 2 multi-rate DAISIE, 0 IW test   model. relaxed_par: parameter relax (integrate ). Options \"cladogenesis\", \"extinction\", \"carrying_capacity\", \"immigration\", \"anagenesis\". verbose numeric vector length 1, simulations `DAISIEdataprep()` can `1` `0`, `1` gives intermediate output printed. ML functions numeric determining intermediate output printed. default: `0` print, `1` prints initial likelihood settings selected (parameters optimised, fixed shifted), `2` prints `1 also intermediate output parameters loglikelihood, `3` `2` prints intermediate progress likelihood computation. tolint Vector two elements containing absolute relative tolerance integration. island_ontogeny DAISIE_sim_time_dep(), DAISIE_ML_CS plotting string describing type island ontogeny. Can \"const\", \"beta\" beta function describing area time.  functions numeric describing type island ontogeny. Can 0 constant, 1 beta function describing area time. ML functions island_ontogeny = NA assumes constant ontogeny. Time dependent estimation yet available development still ongoing. return error called case. jitter Numeric optimizer(). Jitters parameters optimized specified amount small, e.g. 1e-5. Jitter link{subplex}{subplex}() produces incorrect output due parameter transformation. num_cycles number cycles optimizer go . Default 1.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ML4.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Computes MLE for single type species under a clade specific scenario where one parameter may vary over the clades governed by a specific distribution — DAISIE_ML4","text":"output dataframe containing estimated parameters maximum loglikelihood. lambda_c gives maximum likelihood estimate lambda^c, rate cladogenesis mu gives maximum likelihood estimate mu, extinction rate K gives maximum likelihood estimate K, carrying-capacity gamma gives maximum likelihood estimate gamma, immigration rate lambda_a gives maximum likelihood estimate lambda^, rate anagenesis sd gives maximum likelihood estimate standard deviation parameter allowed vary loglik gives maximum loglikelihood df gives number estimated parameters, .e. degrees freedom conv gives message convergence optimization; conv = 0 means convergence","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ML_IW.html","id":null,"dir":"Reference","previous_headings":"","what":"Maximization of the loglikelihood under the DAISIE model with island-wide diversity-dependence — DAISIE_ML_IW","title":"Maximization of the loglikelihood under the DAISIE model with island-wide diversity-dependence — DAISIE_ML_IW","text":"function computes maximum likelihood estimates parameters DAISIE model island-wide diversity-dependence data lineages colonizing island. also outputs corresponding loglikelihood can used model comparisons.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ML_IW.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Maximization of the loglikelihood under the DAISIE model with island-wide diversity-dependence — DAISIE_ML_IW","text":"","code":"DAISIE_ML_IW(   datalist,   initparsopt,   idparsopt,   parsfix,   idparsfix,   res = 100,   ddmodel = 11,   cond = 0,   tol = c(1e-04, 1e-05, 1e-07),   maxiter = 1000 * round((1.25)^length(idparsopt)),   methode = \"ode45\",   optimmethod = \"subplex\",   verbose = 0,   tolint = c(1e-16, 1e-14),   jitter = 0,   num_cycles = 1 )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ML_IW.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Maximization of the loglikelihood under the DAISIE model with island-wide diversity-dependence — DAISIE_ML_IW","text":"datalist Data object containing information colonisation branching times. object can generated using DAISIE_dataprep function, converts user-specified data table data object, object can course also entered directly. R list object following elements. first element list two three components: $island_age - island age  , depending whether distinction types made, :$not_present - number mainland lineages present island  :$not_present_type1 - number mainland lineages type 1 present island $not_present_type2 - number mainland lineages type 2 present island  remaining elements list contains information single colonist lineage island 5 components:$colonist_name - name species clade colonized island $branching_times - island age followed stem age population/species case Non-endemic, Non-endemic_MaxAge species Endemic species close relatives island. endemic clades one species island (cladogenetic clades/ radiations) island age followed branching times island clade including stem age clade$stac - status colonist  * Non_endemic_MaxAge: 1  * Endemic: 2  * Endemic&Non_Endemic: 3  * Non_Endemic: 4  * Endemic_Singleton_MaxAge: 5  * Endemic_Clade_MaxAge: 6  * Endemic&Non_Endemic_Clade_MaxAge: 7 $missing_species - number island species sampled particular clade (applicable endemic clades) $type1or2 - whether colonist belongs type 1 type 2 initparsopt initial values parameters must optimized, positive. idparsopt ids parameters must optimized. ids defined follows:  id = 1 corresponds lambda^c (cladogenesis rate)  id = 2 corresponds mu (extinction rate)  id = 3 corresponds K (clade-level carrying capacity)  id = 4 corresponds gamma (immigration rate)  id = 5 corresponds lambda^(anagenesis rate)  id = 6 corresponds lambda^c (cladogenesis rate) optional subset species  id = 7 corresponds mu (extinction rate) optional subset species id = 8 corresponds K (clade-level carrying capacity) optional subset species id = 9 corresponds gamma (immigration rate) optional subset species id = 10 corresponds lambda^(anagenesis rate) optional subset species id = 11 corresponds p_f (fraction mainland species belongs second subset species. parsfix values parameters optimized. idparsfix ids parameters optimized, e.g. c(1,3) lambda^c K optimized. res Sets maximum number species probability must computed, must larger size largest clade. ddmodel Sets model diversity-dependence:  ddmodel = 0 : diversity dependence  ddmodel = 1 : linear dependence speciation rate  ddmodel = 11: linear dependence speciation rate immigration rate  ddmodel = 2 : exponential dependence speciation rate ddmodel = 21: exponential dependence speciation rate immigration rate cond cond = 0 : conditioning island age  cond = 1 : conditioning island age non-extinction island biota . cond > 1 : conditioning island age least cond colonizations island. last option yet available IW model tol Sets tolerances optimization. Consists :  reltolx = relative tolerance parameter values optimization  reltolf = relative tolerance function value optimization  abstolx = absolute tolerance parameter values optimization. maxiter Sets maximum number iterations optimization. methode Method ODE-solver. Supported Boost ODEINT solvers (steppers) : \"odeint::runge_kutta_cash_karp54\" \"odeint::runge_kutta_fehlberg78\" \"odeint::runge_kutta_dopri5\" \"odeint::bulirsch_stoer\" without odeint::-prefix, deSolve{ode} method assumed. default method overall \"lsodes\" DAISIE_ML_CS() \"ode45\" ode() DAISIE_ML_IW(). optimmethod Method used likelihood optimization. Default `subplex` (see `subplex()` full details). Alternative \"simplex\" method previous versions. verbose numeric vector length 1, simulations `DAISIEdataprep()` can `1` `0`, `1` gives intermediate output printed. ML functions numeric determining intermediate output printed. default: `0` print, `1` prints initial likelihood settings selected (parameters optimised, fixed shifted), `2` prints `1 also intermediate output parameters loglikelihood, `3` `2` prints intermediate progress likelihood computation. tolint Vector two elements containing absolute relative tolerance integration. jitter Numeric optimizer(). Jitters parameters optimized specified amount small, e.g. 1e-5. Jitter link{subplex}{subplex}() produces incorrect output due parameter transformation. num_cycles number cycles optimizer go . Default 1.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ML_IW.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Maximization of the loglikelihood under the DAISIE model with island-wide diversity-dependence — DAISIE_ML_IW","text":"output dataframe containing estimated parameters maximum loglikelihood. lambda_c gives maximum likelihood estimate lambda^c, rate cladogenesis mu gives maximum likelihood estimate mu, extinction rate K gives maximum likelihood estimate K, carrying-capacity gamma gives maximum likelihood estimate gamma, immigration rate lambda_a gives maximum likelihood estimate lambda^, rate anagenesis loglik gives maximum loglikelihood df gives number estimated parameters, .e. degrees feedom conv gives message convergence optimization; conv = 0 means convergence","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ML_IW.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Maximization of the loglikelihood under the DAISIE model with island-wide diversity-dependence — DAISIE_ML_IW","text":"result sort(c(idparsopt, idparsfix)) identical c(1:5). , error reported input incoherent. happens length initparsopt different length idparsopt, length parsfix different length idparsfix.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ML_IW.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Maximization of the loglikelihood under the DAISIE model with island-wide diversity-dependence — DAISIE_ML_IW","text":"Valente, L.M., .B. Phillimore R.S. Etienne (2015). Equilibrium non-equilibrium dynamics simultaneously operate Galapagos islands. Ecology Letters 18: 844-852. <DOI:10.1111/ele.12461>.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ML_IW.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Maximization of the loglikelihood under the DAISIE model with island-wide diversity-dependence — DAISIE_ML_IW","text":"Rampal S. Etienne","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_MW_ML.html","id":null,"dir":"Reference","previous_headings":"","what":"Maximization of the loglikelihood under the DAISIE model with clade-specific diversity-dependence and explicit dependencies on island area and isolation as hypothesized by MacArthur & Wilson — DAISIE_MW_ML","title":"Maximization of the loglikelihood under the DAISIE model with clade-specific diversity-dependence and explicit dependencies on island area and isolation as hypothesized by MacArthur & Wilson — DAISIE_MW_ML","text":"function computes maximum likelihood estimates parameters relationships parameters DAISIE model (clade-specific diversity-dependence) island area distance island mainland data lineages colonizing several islands/archipelagos. also outputs corresponding loglikelihood can used model comparisons. note sigmoidal functions used distance_dep: anagenesis cladogenesis, functional relationship k * (d/d0)^x/(1 + (d/d0)^x); colonization relationship : k - k * (d/d0)^x/(1 + (d/d0)^x). d0 parameter 11th parameter entered. 'sigmoidal_col_ana', 11th parameter d0 colonization 12th d0 anagenesis.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_MW_ML.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Maximization of the loglikelihood under the DAISIE model with clade-specific diversity-dependence and explicit dependencies on island area and isolation as hypothesized by MacArthur & Wilson — DAISIE_MW_ML","text":"","code":"DAISIE_MW_ML(   datalist,   initparsopt,   idparsopt,   parsfix,   idparsfix,   res = 100,   ddmodel = 11,   cond = 0,   island_ontogeny = NA,   tol = c(1e-04, 1e-05, 1e-07),   maxiter = 1000 * round((1.25)^length(idparsopt)),   methode = \"lsodes\",   optimmethod = \"subplex\",   CS_version = 1,   verbose = 0,   tolint = c(1e-16, 1e-10),   distance_type = \"continent\",   distance_dep = \"power\",   parallel = \"local\",   cpus = 3,   num_cycles = 1 )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_MW_ML.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Maximization of the loglikelihood under the DAISIE model with clade-specific diversity-dependence and explicit dependencies on island area and isolation as hypothesized by MacArthur & Wilson — DAISIE_MW_ML","text":"datalist Data object containing information colonisation branching times species several islands archipelagos, well area, isolation age islands/archipelagos. See data(archipelagos41) example. initparsopt initial values parameters must optimized; positive idparsopt ids parameters must optimized. ids defined follows (see Valente et al 2020 Supplementary Tables 1 2 better explanation models parameters):  id = 1 corresponds lambda^c0 (cladogenesis rate unit area)  id = 2 corresponds y (exponent area cladogenesis rate)  id = 3 corresponds mu0 (extinction rate unit area)  id = 4 corresponds x (exponent 1/area extinction rate)  id = 5 corresponds K0 (clade-level carrying capacity unit area)  id = 6 corresponds z (exponent area clade-level carrying capacity)  id = 7 corresponds gamma0 (immigration rate unit distance)  id = 8 corresponds alpha (exponent 1/distance immigration rate)  id = 9 corresponds lambda^a0 (anagenesis rate unit distance)  id = 10 corresponds beta (exponent 1/distance anagenesis rate)  id = 11 corresponds d0 models M15 M19, models distance_dep = 'sigmoidal_col', 'sigmoidal_ana' 'sigmoidal_clado'; d0 colonisation (specifying distance_dep = 'sigmoidal_col_ana' id = 12 corresponds d0 anagenesis specifying distance_dep = 'sigmoidal_col_ana' parsfix values parameters optimized idparsfix ids parameters optimized, e.g. c(1,3) lambda^c K optimized. res Sets maximum number species probability must computed, must larger size largest clade ddmodel Sets model diversity-dependence:  ddmodel = 0 : diversity dependence  ddmodel = 1 : linear dependence speciation rate  ddmodel = 11: linear dependence speciation rate immigration rate  ddmodel = 2 : exponential dependence speciation rate ddmodel = 21: exponential dependence speciation rate immigration rate cond cond = 0 : conditioning island age  cond = 1 : conditioning island age non-extinction island biota island_ontogeny type island ontonogeny. NA, constant ontogeny assumed tol Sets tolerances optimization. Consists :  reltolx = relative tolerance parameter values optimization  reltolf = relative tolerance function value optimization  abstolx = absolute tolerance parameter values optimization maxiter Sets maximum number iterations optimization methode Method ODE-solver. See package deSolve details. Default \"lsodes\" optimmethod Method used likelihood optimization. Default \"subplex\" (see subplex package). Alternative 'simplex' method previous versions. CS_version numeric list. Default 1 standard DAISIE model, relaxed-rate model list following elements: model: CS model run, options 1 single rate   DAISIE model, 2 multi-rate DAISIE, 0 IW test   model. relaxed_par: parameter relax (integrate ). Options \"cladogenesis\", \"extinction\", \"carrying_capacity\", \"immigration\", \"anagenesis\". verbose sets whether parameters likelihood printed (1) (0) tolint Vector two elements containing absolute relative tolerance integration distance_type Use 'continent' distance continent used, use 'nearest_big' distance nearest big landmass used, use 'biologically_realistic' distance take account biologically realism, e.g. average previous two thought contribute. distance_dep Sets type distance dependence used. Default power law, denoted 'power' (models M1-14 Valente et al 2020). Alternatives additive interactive contributions distance area rate cladogenesis (\"area_additive_clado\"; \"area_interactive_clado\", \"area_interactive_clado1\" \"area_interactive_clado2\"). alternatives  exponential relationship denoted 'exp'; sigmoids, either 'sigmoidal_col' sigmoid colonization, 'sigmoidal_ana' sigmoidal anagenesis, 'sigmoidal_clado' sigmoidal cladogenesis, 'sigmoidal_col_ana' sigmoids colonization anagenesis.  key different options distance_dep specified run models Valente et al 2020 (Supplementary Data Table 1 2) given :  * M1 M14 - 'power'  * M15 -'area_additive_clado'  * M16 M19 -'area_interactive_clado'  * M17 -'area_interactive_clado1'  * M18 - 'area_interactive_clado2'  * M20 M24 - sigmoidal_col'  * M21, M25 M28 - sigmoidal_ana'  * M22 M26 - 'sigmoidal_clado' * M23 M27 - 'sigmoidal_col_ana' parallel Sets whether parallel computation used. Use '' parallel computing used, 'cluster' parallel computing unix/linux cluster, 'local' parallel computation local machine. cpus Number cpus used parallel computing. Default 3. effect parallel = ''. num_cycles number cycles optimizer go . Default 1.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_MW_ML.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Maximization of the loglikelihood under the DAISIE model with clade-specific diversity-dependence and explicit dependencies on island area and isolation as hypothesized by MacArthur & Wilson — DAISIE_MW_ML","text":"output dataframe containing estimated parameters maximum loglikelihood. lambda_c0 gives maximum likelihood estimate lambda^c, rate cladogenesis unit area y gives maximum likelihood estimate y, exponent area rate cladogenesis mu0 gives maximum likelihood estimate mu0, extinction rate x gives maximum likelihood estimate x, exponent 1/area extinction rate K0 gives maximum likelihood estimate K0, carrying-capacity unit area z gives maximum likelihood estimate z, exponent area carrying capacity gamma0 gives maximum likelihood estimate gamma0, immigration rate unit distance y gives maximum likelihood estimate alpha, exponent 1/distance rate colonization lambda_a0 gives maximum likelihood estimate lambda^a0, rate anagenesis unit distance beta gives maximum likelihood estimate beta, exponent 1/distance rate anagenesis loglik gives maximum loglikelihood df gives number estimated parameters, .e. degrees feedom conv gives message convergence optimization; conv = 0 means convergence","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_MW_ML.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Maximization of the loglikelihood under the DAISIE model with clade-specific diversity-dependence and explicit dependencies on island area and isolation as hypothesized by MacArthur & Wilson — DAISIE_MW_ML","text":"Valente L, Phillimore AB, Melo M, Warren BH, Clegg SM, Havenstein K,  Tiedemann R, Illera JC, Thébaud C, Aschenbach T, Etienne RS. simple dynamic model  explains island bird diversity worldwide (2020) Nature, 579, 92-96","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_MW_ML.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Maximization of the loglikelihood under the DAISIE model with clade-specific diversity-dependence and explicit dependencies on island area and isolation as hypothesized by MacArthur & Wilson — DAISIE_MW_ML","text":"Rampal S. Etienne & Luis Valente","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_MW_ML.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Maximization of the loglikelihood under the DAISIE model with clade-specific diversity-dependence and explicit dependencies on island area and isolation as hypothesized by MacArthur & Wilson — DAISIE_MW_ML","text":"","code":"cat(\" ### Fit the M19 model as in Valente et al 2020, using the ML parameters as starting values (see Supplementary Tables 1 and 2).  utils::data(archipelagos41)  DAISIE_MW_ML( datalist= archipelagos41, initparsopt = c(0.040073803,  1.945656546,  0.150429656, 67.25643672,  0.293635061,  0.059096872,  0.382688527, 0.026510781), idparsopt = c(1,3,4,7,8,9,10,11), parsfix = c(0,Inf,0) , idparsfix = c(2,5,6), res = 100, ddmodel = 0, methode = 'lsodes', cpus = 4, parallel = 'local', optimmethod = 'subplex', tol = c(1E-4, 1E-5, 1E-7), distance_type = 'continent', distance_dep = 'area_interactive_clado' ) \") #>  #> ### Fit the M19 model as in Valente et al 2020, using the ML #> parameters as starting values (see Supplementary Tables 1 and 2). #>  #> utils::data(archipelagos41) #>  #> DAISIE_MW_ML( #> datalist= archipelagos41, #> initparsopt = #> c(0.040073803,\t1.945656546,\t0.150429656, #> 67.25643672,\t0.293635061,\t0.059096872,\t0.382688527, #> 0.026510781), #> idparsopt = c(1,3,4,7,8,9,10,11), #> parsfix = c(0,Inf,0) , #> idparsfix = c(2,5,6), #> res = 100, #> ddmodel = 0, #> methode = 'lsodes', #> cpus = 4, #> parallel = 'local', #> optimmethod = 'subplex', #> tol = c(1E-4, 1E-5, 1E-7), #> distance_type = 'continent', #> distance_dep = 'area_interactive_clado' #> )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ONEcolonist.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert intermediate output to final simulation output — DAISIE_ONEcolonist","title":"Convert intermediate output to final simulation output — DAISIE_ONEcolonist","text":"Convert intermediate output final simulation output","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ONEcolonist.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert intermediate output to final simulation output — DAISIE_ONEcolonist","text":"","code":"DAISIE_ONEcolonist(time, island_spec, stt_table)"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ONEcolonist.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert intermediate output to final simulation output — DAISIE_ONEcolonist","text":"time Numeric defining length simulation time units. example, island known 4 million years old, setting time = 4 simulate entire life span island; setting time = 2 stop simulation mid-life island. island_spec Matrix current state simulation containing number species. stt_table Matrix number species time step.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_ONEcolonist.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert intermediate output to final simulation output — DAISIE_ONEcolonist","text":"list elements: [1]: stt_table, stt_table put . [2]: branching_times, sorted numeric vector, required     ML estimation functions. first element always refers     island age. Subsequent elements refer colonisation, speciation     recolonisation times. recent recolonisation time,     always omitted approximate simulation results mathematical     formulation likelihood functions used MLE. [3]: stac, status colonist. function can     returned either 2, 4 3. stac 2, one     independent colonisation present island extant species     endemic. stac 4, singleton endemic present     present. stac 3, recolonisation occurred, one     colonising lineage. [4]: missing_species, numeric value number     missing species, , species sampled phylogeny     present island. code runs simulation models,     missing_species always set 0. [5]:   all_colonisations, recolonising lineages . comprised     $event_times $species_type: $event_times ordered numeric vectors containing       events extant recolonising lineage. includes       colonisation branching times. vector pertains one       colonising lineage. $species_type string. Can \"\", \"C\"       \"\" depending whether extant clade anagenetic,       cladogenetic immigrant origin, respectively.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_SR_ML.html","id":null,"dir":"Reference","previous_headings":"","what":"Maximization of the loglikelihood under the DAISIE model with clade-specific diversity-dependence — DAISIE_SR_ML","title":"Maximization of the loglikelihood under the DAISIE model with clade-specific diversity-dependence — DAISIE_SR_ML","text":"function computes maximum likelihood estimates parameters DAISIE model clade-specific diversity-dependence shift parameters data lineages colonizing island. also outputs corresponding loglikelihood can used model comparisons. result sort(c(idparsopt, idparsfix, idparsnoshift)) identical c(1:10). , error reported input incoherent. happens length initparsopt different length idparsopt, length parsfix different length idparsfix. Including 11th parameter (p_f) either idparsopt idparsfix (therefore initparsopt parsfix) optional. parameter specified, information data used, otherwise information data overruled.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_SR_ML.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Maximization of the loglikelihood under the DAISIE model with clade-specific diversity-dependence — DAISIE_SR_ML","text":"","code":"DAISIE_SR_ML_CS(   datalist,   initparsopt,   idparsopt,   parsfix,   idparsfix,   idparsnoshift = 6:10,   res = 100,   ddmodel = 0,   cond = 0,   island_ontogeny = NA,   tol = c(1e-04, 1e-05, 1e-07),   maxiter = 1000 * round((1.25)^length(idparsopt)),   methode = \"lsodes\",   optimmethod = \"subplex\",   CS_version = 1,   verbose = 0,   tolint = c(1e-16, 1e-10),   jitter = 0,   num_cycles = 1 )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_SR_ML.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Maximization of the loglikelihood under the DAISIE model with clade-specific diversity-dependence — DAISIE_SR_ML","text":"datalist Data object containing information colonisation branching times. object can generated using DAISIE_dataprep function, converts user-specified data table data object, object can course also entered directly. R list object following elements. first element list two three components: $island_age - island age  , depending whether distinction types made, :$not_present - number mainland lineages present island  remaining elements list contains information single colonist lineage island 5 components:$colonist_name - name species clade colonized island $branching_times - island age stem age population/species case Non-endemic, Non-endemic_MaxAge Endemic anagenetic species. cladogenetic species island age branching times radiation including stem age radiation.$stac - status colonist  * Non_endemic_MaxAge: 1  * Endemic: 2  * Endemic&Non_Endemic: 3  * Non_endemic: 4  * Endemic_MaxAge: 5 $missing_species - number island species sampled particular clade (applicable endemic clades) initparsopt initial values parameters must optimized idparsopt ids parameters must optimized. ids defined follows:  id = 1 corresponds lambda^c (cladogenesis rate)  id = 2 corresponds mu (extinction rate)  id = 3 corresponds K (clade-level carrying capacity)  id = 4 corresponds gamma (immigration rate)  id = 5 corresponds lambda^(anagenesis rate)  id = 6 corresponds lambda^c (cladogenesis rate) shift  id = 7 corresponds mu (extinction rate) shift id = 8 corresponds K (clade-level carrying capacity) shift id = 9 corresponds gamma (immigration rate) shift id = 10 corresponds lambda^(anagenesis rate) shift id = 11 corresponds time shift parsfix values parameters optimized idparsfix ids parameters optimized, e.g. c(1,3) lambda^c K optimized. idparsnoshift ids parameters different shift. res Sets maximum number species probability must computed, must larger size largest clade ddmodel Sets model diversity-dependence:  ddmodel = 0 : diversity dependence  ddmodel = 1 : linear dependence speciation rate  ddmodel = 11: linear dependence speciation rate immigration rate  ddmodel = 2 : exponential dependence speciation rate ddmodel = 21: exponential dependence speciation rate immigration rate. cond cond = 0 : conditioning island age  cond = 1 : conditioning island age non-extinction island biota island_ontogeny type island ontonogeny. NA, constant ontogeny assumed. tol Sets tolerances optimization. Consists :  reltolx = relative tolerance parameter values optimization  reltolf = relative tolerance function value optimization  abstolx = absolute tolerance parameter values optimization. maxiter Sets maximum number iterations optimization. methode Method ODE-solver. See package deSolve details. Default \"lsodes\" optimmethod Method used likelihood optimization. Default \"subplex\" (see subplex package). Alternative 'simplex' method previous versions. CS_version numeric list. Default 1 standard DAISIE model, relaxed-rate model list following elements: model: CS model run, options 1 single rate   DAISIE model, 2 multi-rate DAISIE, 0 IW test   model. relaxed_par: parameter relax (integrate ). Options \"cladogenesis\", \"extinction\", \"carrying_capacity\", \"immigration\", \"anagenesis\". verbose sets whether parameters likelihood printed (1) (0). tolint Vector two elements containing absolute relative tolerance integration. jitter Numeric optimizer(). Jitters parameters optimized specified amount small, e.g. 1e-5. Jitter link[subplex]{subplex}() produces incorrect output due parameter transformation. num_cycles number cycles optimizer go . Default 1.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_SR_ML.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Maximization of the loglikelihood under the DAISIE model with clade-specific diversity-dependence — DAISIE_SR_ML","text":"output dataframe containing estimated parameters maximum loglikelihood. lambda_c gives maximum likelihood estimate lambda^c, rate cladogenesis mu gives maximum likelihood estimate mu, extinction rate K gives maximum likelihood estimate K, carrying-capacity gamma gives maximum likelihood estimate gamma, immigration rate lambda_a gives maximum likelihood estimate lambda^, rate anagenesis lambda_c2 gives maximum likelihood estimate lambda^c2, rate cladogenesis optional second group species mu2 gives maximum likelihood estimate mu2, extinction rate optional second group species K2 gives maximum likelihood estimate K2, carrying-capacity optional second group species gamma2 gives maximum likelihood estimate gamma2, immigration rate optional second group species lambda_a2 gives maximum likelihood estimate lambda^a2, rate anagenesis optional second group species loglik gives maximum loglikelihood df gives number estimated parameters, .e. degrees feedom conv gives message convergence optimization; conv = 0 means convergence","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_SR_ML.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Maximization of the loglikelihood under the DAISIE model with clade-specific diversity-dependence — DAISIE_SR_ML","text":"Valente, L.M., .B. Phillimore R.S. Etienne (2015). Equilibrium non-equilibrium dynamics simultaneously operate Galapagos islands. Ecology Letters 18: 844-852. <DOI:10.1111/ele.12461>.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_SR_ML.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Maximization of the loglikelihood under the DAISIE model with clade-specific diversity-dependence — DAISIE_SR_ML","text":"Rampal S. Etienne","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_SR_ML.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Maximization of the loglikelihood under the DAISIE model with clade-specific diversity-dependence — DAISIE_SR_ML","text":"","code":"# \\donttest{ ## In all following DAISIE_ML calls very high tolerances and low system size ## are used  for fast computation for this example. Use default or better ## tol, tolint an res values in actual analyses. ################## ### When all species have the same rates, and we want to optimize all 5 ### parameters, we use: utils::data(Galapagos_datalist) DAISIE_ML(    datalist = Galapagos_datalist,    initparsopt = c(2.5,2.7,20,0.009,1.01),    ddmodel = 11,    idparsopt = 1:5,    parsfix = NULL,    idparsfix = NULL,    tol = c(0.1, 0.02, 0.01),    tolint = c(1e-4, 1e-2),    res = 50 ) #>   lambda_c       mu  K gamma lambda_a    loglik df conv #> 1  2.15493 2.153129 20 0.009     1.01 -81.28596  5    0  ### When all species have the same rates, and we want to optimize all parameters # except K (which we set equal to Inf), we use:  utils::data(Galapagos_datalist) DAISIE_ML(    datalist = Galapagos_datalist,    initparsopt = c(2.5,2.7,0.009,1.01),    idparsopt = c(1,2,4,5),    parsfix = Inf,    idparsfix = 3,    tol = c(0.1, 0.02, 0.01),    tolint = c(1e-4, 1e-2),    res = 50    ) #>   lambda_c       mu   K gamma lambda_a    loglik df conv #> 1 3.180506 3.172027 Inf 0.009     1.01 -73.14958  4    0  ### When all species have the same rates except that the finches have a different # rate of cladogenesis, and we want to optimize all parameters except K (which we # set equal to Inf), fixing the proportion of finch-type species at 0.163, we use:  utils::data(Galapagos_datalist_2types) DAISIE_ML(    datalist = Galapagos_datalist_2types,    initparsopt = c(0.38,0.55,0.004,1.1,2.28),    idparsopt = c(1,2,4,5,6),    parsfix = c(Inf,Inf,0.163),    idparsfix = c(3,8,11),    idparsnoshift = c(7,9,10),    tol = c(0.1, 0.02, 0.01),    tolint = c(1e-4, 1e-2),    res = 50    ) #>    lambda_c        mu   K       gamma lambda_a lambda_c2       mu2  K2 #> 1 0.3840537 0.6146573 Inf 0.003956464 1.193755  3.079965 0.6146573 Inf #>        gamma2 lambda_a2 prop_type2    loglik df conv #> 1 0.003956464  1.193755      0.163 -69.57021  5    0  ### When all species have the same rates except that the finches have a different # rate of cladogenesis, extinction and a different K, and we want to optimize all # parameters, fixing the proportion of finch-type species at 0.163, we use:  utils::data(Galapagos_datalist_2types) DAISIE_ML(    datalist = Galapagos_datalist_2types,    ddmodel = 11,    initparsopt = c(0.19,0.09,0.002,0.87,20,8.9,15),    idparsopt = c(1,2,4,5,6,7,8),    parsfix = c(Inf,0.163),    idparsfix = c(3,11),    idparsnoshift = c(9,10),    tol = c(0.1, 0.02, 0.01),    tolint = c(1e-4, 1e-2),    res = 50    ) #>    lambda_c        mu   K       gamma lambda_a lambda_c2     mu2       K2 #> 1 0.2085388 0.1294331 Inf 0.002834096 1.115621  17.09695 6.32994 18.72603 #>        gamma2 lambda_a2 prop_type2    loglik df conv #> 1 0.002834096  1.115621      0.163 -64.80759  7    0   ### When all species have the same rates except that the finches have a different # rate of extinction, and we want to optimize all parameters except K (which we # set equal to Inf), and we also# want to estimate the fraction of finch species # in the mainland pool. we use:  utils::data(Galapagos_datalist_2types) DAISIE_ML(    datalist = Galapagos_datalist_2types,    initparsopt = c(2.48,2.7,0.009,1.01,2.25,0.163),    idparsopt = c(1,2,4,5,7,11),    parsfix = c(Inf,Inf),    idparsfix = c(3,8),    idparsnoshift = c(6,9,10),    tol = c(0.1, 0.02, 0.01),    tolint = c(1e-4, 1e-2),    res = 50    ) #>   lambda_c       mu   K       gamma lambda_a lambda_c2      mu2  K2      gamma2 #> 1  2.55745 3.239773 Inf 0.009729946 1.739499   2.55745 1.599674 Inf 0.009729946 #>   lambda_a2  prop_type2    loglik df conv #> 1  1.739499 0.001157252 -71.91278  6    0  ### When we have two islands with the same rates except for immigration and anagenesis rate, # and we want to optimize all parameters, we use:  utils::data(Galapagos_datalist) DAISIE_ML(    datalist = list(Galapagos_datalist,Galapagos_datalist),    datatype = 'multiple',    initparsopt = c(2.5,2.7,20,0.009,1.01,0.009,1.01),    idparsmat = rbind(1:5,c(1:3,6,7)),    idparsopt = 1:7,    parsfix = NULL,    idparsfix = NULL,    tol = c(0.1, 0.02, 0.01),    tolint = c(1e-4, 1e-2),    res = 50 ) #>   lambda_c       mu        K       gamma lambda_a    loglik df conv #> 1   2.3754 2.276205 12.28802 0.008006759 1.223171 -147.3063  7    0 #> 2   2.3754 2.276205 12.28802 0.006590183 1.054042 -147.3063  7    0  ### When we consider the four Macaronesia archipelagoes and set all parameters the same # except for rates of cladogenesis, extinction and immigration for Canary Islands, # rate of cladogenesis is fixed to 0 for the other archipelagoes, # diversity-dependence is assumed to be absent # and we want to optimize all parameters, we use:  utils::data(Macaronesia_datalist) DAISIE_ML(    datalist = Macaronesia_datalist,    datatype = 'multiple',    initparsopt = c(1.053151832,0.052148979,0.512939011,0.133766934,0.152763179),    idparsmat = rbind(1:5,c(6,2,3,7,5),1:5,1:5),    idparsopt = c(2,4,5,6,7),    parsfix = c(0,Inf),    idparsfix = c(1,3),    tol = c(0.1, 0.02, 0.01),    tolint = c(1e-4, 1e-2),    res = 50 ) #>     lambda_c       mu   K      gamma lambda_a    loglik df conv #> 1 0.00000000 1.053152 Inf 0.05214898 0.512939 -447.8626  5    0 #> 2 0.09497184 1.053152 Inf 0.15276318 0.512939 -447.8626  5    0 #> 3 0.00000000 1.053152 Inf 0.05214898 0.512939 -447.8626  5    0 #> 4 0.00000000 1.053152 Inf 0.05214898 0.512939 -447.8626  5    0  # }"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_SR_loglik_CS.html","id":null,"dir":"Reference","previous_headings":"","what":"Computes the loglikelihood of the DAISIE model with clade-specific diversity-dependence given data and a set of model parameters that may shift at some time — DAISIE_SR_loglik_CS","title":"Computes the loglikelihood of the DAISIE model with clade-specific diversity-dependence given data and a set of model parameters that may shift at some time — DAISIE_SR_loglik_CS","text":"Computes loglikelihood DAISIE model clade-specific diversity-dependence given colonization branching times lineages island, set model parameters may shift time","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_SR_loglik_CS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Computes the loglikelihood of the DAISIE model with clade-specific diversity-dependence given data and a set of model parameters that may shift at some time — DAISIE_SR_loglik_CS","text":"","code":"DAISIE_SR_loglik_CS(   pars1,   pars2,   datalist,   methode = \"lsodes\",   CS_version = 1,   abstolint = 1e-16,   reltolint = 1e-10 )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_SR_loglik_CS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Computes the loglikelihood of the DAISIE model with clade-specific diversity-dependence given data and a set of model parameters that may shift at some time — DAISIE_SR_loglik_CS","text":"pars1 Contains model parameters: pars1[1] corresponds lambda^c (cladogenesis rate) pars1[2] corresponds mu (extinction rate) pars1[3] corresponds K (clade-level carrying capacity) pars1[4] corresponds gamma (immigration rate) pars1[5] corresponds lambda^(anagenesis rate) pars1[6] corresponds lambda^c (cladogenesis rate) shift pars1[7] corresponds mu (extinction rate) shift pars1[8] corresponds K (clade-level carrying capacity) shift pars1[9] corresponds gamma (immigration rate) shift pars1[10] corresponds lambda^(anagenesis rate) shift pars1[11] corresponds time shift pars2 Contains model settings pars2[1] corresponds lx = length ODE variable x pars2[2] corresponds ddmodel = diversity-dependent model, model diversity-dependence, can one ddmodel = 0 : diversity dependence  ddmodel = 1 : linear dependence speciation rate  ddmodel = 11: linear dependence speciation rate immigration rate  ddmodel = 2 : exponential dependence speciation rate ddmodel = 21: exponential dependence speciation rate immigration ratepars2[3] corresponds cond = setting conditioning cond = 0 : conditioning island age  cond = 1 : conditioning island age non-extinction island biota  cond > 1 : conditioning island age least cond colonizations island pars2[4] sets whether parameters likelihood printed (1) (0) datalist Data object containing information colonisation branching times. object can generated using DAISIE_dataprep function, converts user-specified data table data object, object can course also entered directly. R list object following elements. first element list two three components: $island_age - island age  , depending whether distinction types made, :$not_present - number mainland lineages present island  remaining elements list contains information single colonist lineage island 5 components:$colonist_name - name species clade colonized island $branching_times - island age stem age population/species case Non-endemic, Non-endemic_MaxAge Endemic anagenetic species. cladogenetic species island age branching times radiation including stem age radiation.$stac - status colonist  - Non_endemic_MaxAge: 1  * Endemic: 2  - Endemic&Non_Endemic: 3  - Non_endemic: 4  - Endemic_MaxAge: 5 $missing_species - number island species sampled particular clade (applicable endemic clades) methode Method ODE-solver. See package deSolve details. Default \"lsodes\" CS_version numeric list. Default 1 standard DAISIE model, relaxed-rate model list following elements: model: CS model run, options 1 single rate   DAISIE model, 2 multi-rate DAISIE, 0 IW test   model. relaxed_par: parameter relax (integrate ). Options \"cladogenesis\", \"extinction\", \"carrying_capacity\", \"immigration\", \"anagenesis\". abstolint Absolute tolerance integration reltolint Relative tolerance integration","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_SR_loglik_CS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Computes the loglikelihood of the DAISIE model with clade-specific diversity-dependence given data and a set of model parameters that may shift at some time — DAISIE_SR_loglik_CS","text":"loglikelihood","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_SR_loglik_CS.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Computes the loglikelihood of the DAISIE model with clade-specific diversity-dependence given data and a set of model parameters that may shift at some time — DAISIE_SR_loglik_CS","text":"output loglikelihood value","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_SR_loglik_CS.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Computes the loglikelihood of the DAISIE model with clade-specific diversity-dependence given data and a set of model parameters that may shift at some time — DAISIE_SR_loglik_CS","text":"Valente, L.M., .B. Phillimore R.S. Etienne (2015). Equilibrium non-equilibrium dynamics simultaneously operate Galapagos islands. Ecology Letters 18: 844-852.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_SR_loglik_CS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Computes the loglikelihood of the DAISIE model with clade-specific diversity-dependence given data and a set of model parameters that may shift at some time — DAISIE_SR_loglik_CS","text":"Rampal S. Etienne & Bart Haegeman","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_SR_loglik_CS.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Computes the loglikelihood of the DAISIE model with clade-specific diversity-dependence given data and a set of model parameters that may shift at some time — DAISIE_SR_loglik_CS","text":"","code":"utils::data(Galapagos_datalist_2types) pars1 = c(0.195442017,0.087959583,Inf,0.002247364,0.873605049,           3755.202241,8.909285094,14.99999923,0.002247364,0.873605049,0.163) pars2 = c(100,11,0,1) DAISIE_loglik_all(pars1,pars2,Galapagos_datalist_2types) #> [1] -61.70282"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_SR_sim_core.html","id":null,"dir":"Reference","previous_headings":"","what":"DEPRECATED - Algorithm component of DAISIE_SR_sim. — DAISIE_SR_sim_core","title":"DEPRECATED - Algorithm component of DAISIE_SR_sim. — DAISIE_SR_sim_core","text":"#' @details function's use deprecated favour DAISIE_sim_cr_shift(). Please use function instead.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_SR_sim_core.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"DEPRECATED - Algorithm component of DAISIE_SR_sim. — DAISIE_SR_sim_core","text":"","code":"DAISIE_SR_sim_core(time, mainland_n, pars)"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_SR_sim_core.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"DEPRECATED - Algorithm component of DAISIE_SR_sim. — DAISIE_SR_sim_core","text":"time Length simulation time units. example, island know 4 million years old, setting time = 4 simulate entire life span island; setting time = 2 stop simulation mid-life island. mainland_n numeric stating number mainland species, number species can potentially colonize island. using clade-specific diversity dependence, value set 1. using island-wide diversity dependence, value set number mainland species. pars Contains model parameters: pars[1] corresponds lambda^c (cladogenesis rate) shift pars[2] corresponds mu (extinction rate) shift pars[3] corresponds K (clade-level carrying capacity) shift. Set K=Inf non-diversity dependence.pars[4] corresponds gamma (immigration rate) shift pars[5] corresponds lambda^(anagenesis rate) shift pars[6] corresponds lambda^c (cladogenesis rate) shift pars[7] corresponds mu (extinction rate) shift pars[8] corresponds K (clade-level carrying capacity) shift.  Set K=Inf non-diversity dependence. pars[9] corresponds gamma (immigration rate)  shift pars[10] corresponds lambda^(anagenesis rate) shift pars[11] corresponds time shift. defined time end simulation. example, setting time = 4 pars[11] = 1.5 simulate pars[1:5] 4 1.5 pars[6:10] 1.5 0.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_SR_sim_core.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"DEPRECATED - Algorithm component of DAISIE_SR_sim. — DAISIE_SR_sim_core","text":"List DAISIE simulation.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_SR_sim_core.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"DEPRECATED - Algorithm component of DAISIE_SR_sim. — DAISIE_SR_sim_core","text":"Hauffe, T., D. Delicado, R.S. Etienne L. Valente (2020). Lake expansion increases equilibrium diversity via target effect island biogeography","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_SR_sim_core.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"DEPRECATED - Algorithm component of DAISIE_SR_sim. — DAISIE_SR_sim_core","text":"Luis Valente, Albert Phillimore, Torsten Hauffe","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_abm_factor.html","id":null,"dir":"Reference","previous_headings":"","what":"Sets or retrieves the factor to calculate the step-size used by the odeint::adams_bashforth[_moulton] solvers. — DAISIE_abm_factor","title":"Sets or retrieves the factor to calculate the step-size used by the odeint::adams_bashforth[_moulton] solvers. — DAISIE_abm_factor","text":"Sets retrieves factor calculate step-size used odeint::adams_bashforth[_moulton] solvers.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_abm_factor.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sets or retrieves the factor to calculate the step-size used by the odeint::adams_bashforth[_moulton] solvers. — DAISIE_abm_factor","text":"","code":"DAISIE_abm_factor(factor)"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_abm_factor.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sets or retrieves the factor to calculate the step-size used by the odeint::adams_bashforth[_moulton] solvers. — DAISIE_abm_factor","text":"factor sets step-size factor * (t1 - t0).","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_abm_factor.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sets or retrieves the factor to calculate the step-size used by the odeint::adams_bashforth[_moulton] solvers. — DAISIE_abm_factor","text":"current factor","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_convertprobdist.html","id":null,"dir":"Reference","previous_headings":"","what":"Converts the joint distribution of endemics and non-endemics under the DAISIE model to list format — DAISIE_convertprobdist","title":"Converts the joint distribution of endemics and non-endemics under the DAISIE model to list format — DAISIE_convertprobdist","text":"function converts joint distribution number endemics non-endemics matrix format DAISIE_probdist list format","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_convertprobdist.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Converts the joint distribution of endemics and non-endemics under the DAISIE model to list format — DAISIE_convertprobdist","text":"","code":"DAISIE_convertprobdist(pb)"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_convertprobdist.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Converts the joint distribution of endemics and non-endemics under the DAISIE model to list format — DAISIE_convertprobdist","text":"pb Probability distribution matrix format output DAISIE_probdist().","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_convertprobdist.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Converts the joint distribution of endemics and non-endemics under the DAISIE model to list format — DAISIE_convertprobdist","text":"list length nrow(pb) containing matrices square dimensions size sqrt(ncol - 1) containing joint probabilities endemics rows non-endemics columns. last element list vector times joint probability distribution evaluated.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_convertprobdist.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Converts the joint distribution of endemics and non-endemics under the DAISIE model to list format — DAISIE_convertprobdist","text":"Valente, L.M., .B. Phillimore R.S. Etienne (2015). Equilibrium non-equilibrium dynamics simultaneously operate Galapagos islands. Ecology Letters 18: 844-852.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_convertprobdist.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Converts the joint distribution of endemics and non-endemics under the DAISIE model to list format — DAISIE_convertprobdist","text":"Rampal S. Etienne","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_convertprobdist.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Converts the joint distribution of endemics and non-endemics under the DAISIE model to list format — DAISIE_convertprobdist","text":"","code":"### Compute the probability distribution at t = 4 and t = 8, for a mainland pool # size of 250 potential colonists and a vector of 5 parameters (cladogenesis, extinction, # clade-level carrying capacity, immigration, anagenesis) starting from an empty # island; store in list format  pb <- DAISIE_probdist(    pars1 = c(0.3,0.35,Inf,0.75,0.012),    pars2 = c(100,250),    tvec = c(4,8),    initEI = c(0,0),    initprobs = NULL    ) prob_dists <- DAISIE_convertprobdist(pb)"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_count_species.html","id":null,"dir":"Reference","previous_headings":"","what":"Count number of species in DAISIE datalist or simulated data. — DAISIE_count_species","title":"Count number of species in DAISIE datalist or simulated data. — DAISIE_count_species","text":"Calculates various island diversity metrics island datasets.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_count_species.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count number of species in DAISIE datalist or simulated data. — DAISIE_count_species","text":"","code":"DAISIE_count_species(islands, sort_clade_sizes = TRUE)"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_count_species.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count number of species in DAISIE datalist or simulated data. — DAISIE_count_species","text":"islands Island datalist simulated data DAISIE datalist format. Can single island (empirical data) generated DAISIE_dataprep DAISIEprep. Can also simulated data generated DAISIE_sim function. sort_clade_sizes Default sort_clade_sizes = T outputs clade sizes sorted ascending order number species. sort_clade_sizes=F outputs clade sizes order appear input datalist.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_count_species.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count number of species in DAISIE datalist or simulated data. — DAISIE_count_species","text":"output list containing following items: clade_sizes_sorted List showing total number species island clade (including missing species). item [[]] list gives sizes clades single island. option sort_clade_sizes = T, clade sizes sorted increasing number species. option sort_clade_sizes = F clade sizes given order input datalist. size_largest_clade total number species largest island clade island. mean_clade_size Mean clade size (average island clades) number_colonisations total number colonisations (clades) island. total_number_species total number species island. extant species present, including missing species; case simulations, number species present island end simulation.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_count_species.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Count number of species in DAISIE datalist or simulated data. — DAISIE_count_species","text":"Luis Valente","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_count_species.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Count number of species in DAISIE datalist or simulated data. — DAISIE_count_species","text":"","code":"# Run function with clade sizes in the order they appear in the input data data(\"NewZealand_birds_datalist\") species_count <- DAISIE_count_species(NewZealand_birds_datalist)  # Run function with clade sizes in ascending order species_count_sorted <- DAISIE_count_species(   NewZealand_birds_datalist,   sort_clade_sizes = TRUE )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_create_island.html","id":null,"dir":"Reference","previous_headings":"","what":"Converts simulation output into island output — DAISIE_create_island","title":"Converts simulation output into island output — DAISIE_create_island","text":"Converts simulation output island output","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_create_island.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Converts simulation output into island output — DAISIE_create_island","text":"","code":"DAISIE_create_island(   stt_table,   total_time,   island_spec,   mainland_n,   trait_pars = NULL )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_create_island.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Converts simulation output into island output — DAISIE_create_island","text":"stt_table Matrix number species time step. total_time Numeric defining length simulation time units. island_spec Matrix current state simulation containing number species. mainland_n numeric stating number mainland species, number species can potentially colonize island. using clade-specific diversity dependence, value set 1. using island-wide diversity dependence, value set number mainland species. trait_pars named list containing diversification rates considering   two trait states created create_trait_pars: [1]:numeric per capita transition rate state1 [2]:numeric per capita immigration rate state2 [3]:numeric per capita extinction rate state2 [4]:numeric per capita anagenesis rate state2 [5]:numeric per capita cladogenesis rate state2 [6]:numeric per capita transition rate state2 [7]:numeric number species trait state 2    mainland","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_create_island.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Converts simulation output into island output — DAISIE_create_island","text":"list island information, composed stt table, branching times extant species, status species island number missing species.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_dataprep.html","id":null,"dir":"Reference","previous_headings":"","what":"Prepare colonisation and branching time data to run in DAISIE. — DAISIE_dataprep","title":"Prepare colonisation and branching time data to run in DAISIE. — DAISIE_dataprep","text":"function produces data object can run DAISIE likelihood computation/optimization functions. function converts user-specified table DAISIE-compatible format. See Galapagos_datatable.Rdata template input table.)","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_dataprep.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Prepare colonisation and branching time data to run in DAISIE. — DAISIE_dataprep","text":"","code":"DAISIE_dataprep(   datatable,   island_age,   M,   number_clade_types = 1,   list_type2_clades = NA,   prop_type2_pool = \"proportional\",   epss = 1e-05,   verbose = TRUE )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_dataprep.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Prepare colonisation and branching time data to run in DAISIE. — DAISIE_dataprep","text":"datatable Data frame (table) user-specified data. See file Galapagos_datatable.Rdata template input table. row table represents independent colonisation event. Table following four columns. $Clade_name - name independent colonization event $Status - One following categories:  * \"Non_endemic\": applies non-endemic species approximate colonisation time known  * \"Non_endemic_MaxAge\": applies non-endemic species cases colonisation time unknown  * \"Endemic\": applies endemic species endemic clades approximate colonisation time known  * \"Endemic_MaxAge\": applies endemic species endemic clades cases colonisation time unknown, user wants specify upper bound colonisation. example apply endemic species recently gone extinct anthropogenic causes, included phylogeny (\"NA\" given branching times column). also apply insular radiations long stem branches, time first cladogenetic event known, precise time colonisation .  * \"Endemic_MaxAge_MinAge\": Endemic_MaxAge also includes minimum age colonisation.  * \"Non_endemic_MaxAge_MinAge\": Non_endemic_MaxAge also includes minimum age colonisation.#'  * \"Endemic&Non_Endemic\": endemic clade present mainland ancestor re-colonized $Missing_species - Number island species sampled particular clade (applicable \"Endemic\" clades). NA given branching times column,  equal number species clade minus 1 $Branching_times  - Stem age population/species case \"Non_endemic\", \"Non_endemic_MaxAge\"  \"Endemic\" species extant close relatives island. Set \"NA\"  colonisation time unknown upper bound known. \"Endemic\" cladogenetic species branching times radiation, including stem age radiation (colonisation time estimate). island_age Age island appropriate units M size mainland pool, .e number species can potentially colonize island number_clade_types Number clade types. Default: number_clade_types = 1 species considered belong macroevolutionary process. number_clade_types = 2, two types clades distinct macroevolutionary processes. list_type2_clades number_clade_types = 2, list_type2_clades specifies names clades distinct macroevolutionary process. names must match $Clade_name column source data table (e.g. list_type2_clades = \"Finches\").  number_clade_types = 1, list_type2_clades = NA specified (default) prop_type2_pool Specifies fraction potential mainland colonists distinct macroevolutionary process. Applies number_clade_types = 2.  Default \"proportional\" sets fraction proportional number clades distinct macroevolutionary process colonised island. Alternatively, user can specify value 0 1 (e.g. mainland pool size 1000 prop_type2_pool = 0.02 number type2 species 20). epss Default= 1E-5 appropriate cases. value used set maximum age colonisation \"Non_endemic_MaxAge\" \"Endemic_MaxAge\" species age slightly younger island cases age provided species older island. new maximum age used upper bound integrate possible colonisation times. verbose Boolean. States intermediate results printed console. Defaults TRUE.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_dataprep.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Prepare colonisation and branching time data to run in DAISIE. — DAISIE_dataprep","text":"datalist R list object containing data: first element list two three components: $island_age - island age  , depending whether distinction species types made, :$not_present - number mainland lineages present island  :$not_present_type1 - number mainland lineages type 1 present island $not_present_type2 - number mainland lineages type 2 present island  following elements list contains information single colonist lineage island 5 components:$colonist_name - name species clade colonized island $branching_times - island age stem age population/species case \"Non-endemic\", \"Non-endemic_MaxAge\" \"Endemic\" anagenetic species. \"Endemic\" cladogenetic species island age branching times radiation including stem age radiation.$stac - status colonist  * Non_endemic_MaxAge: 1  * Endemic: 2  * Endemic&Non_Endemic: 3  * Non_endemic: 4  * Endemic_MaxAge: 5 (colonisation time given)  * Endemic_MaxAge: 6 (colonisation time cladogenesis times given) $missing_species - number island species sampled particular clade (applicable endemic clades) $type_1or2  - whether colonist belongs type 1 type 2","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_dataprep.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Prepare colonisation and branching time data to run in DAISIE. — DAISIE_dataprep","text":"output R list containing data formatted run DAISIE functions.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_dataprep.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Prepare colonisation and branching time data to run in DAISIE. — DAISIE_dataprep","text":"Valente, L.M., .B. Phillimore R.S. Etienne (2015). Equilibrium non-equilibrium dynamics simultaneously operate Galapagos islands. Ecology Letters 18: 844-852.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_dataprep.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Prepare colonisation and branching time data to run in DAISIE. — DAISIE_dataprep","text":"Luis M Valente","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_dataprep.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Prepare colonisation and branching time data to run in DAISIE. — DAISIE_dataprep","text":"","code":"### Create Galapagos data object where all taxa have the same macroevolutionary process  utils::data(Galapagos_datatable, package = \"DAISIE\") DAISIE_dataprep(    datatable = Galapagos_datatable,    island_age = 4,    M = 1000    ) #> Colonisation time of 7.456 for Coccyzus is older than island age #> Colonisation time of 10.285 for Pyrocephalus is older than island age #> [[1]] #> [[1]]$island_age #> [1] 4 #>  #> [[1]]$not_present #> [1] 992 #>  #>  #> [[2]] #> [[2]]$colonist_name #> [1] \"Coccyzus\" #>  #> [[2]]$branching_times #> [1] 4.00000 3.99999 #>  #> [[2]]$stac #> [1] 1 #>  #> [[2]]$missing_species #> [1] 0 #>  #> [[2]]$type1or2 #> [1] 1 #>  #>  #> [[3]] #> [[3]]$colonist_name #> [1] \"Dendroica\" #>  #> [[3]]$branching_times #> [1] 4.00 0.34 #>  #> [[3]]$stac #> [1] 4 #>  #> [[3]]$missing_species #> [1] 0 #>  #> [[3]]$type1or2 #> [1] 1 #>  #>  #> [[4]] #> [[4]]$colonist_name #> [1] \"Finches\" #>  #> [[4]]$branching_times #>  [1] 4.0000 3.0282 1.3227 0.8223 0.4286 0.3462 0.2450 0.1180 0.0808 0.0756 #> [11] 0.0527 0.0525 0.0327 0.0322 0.0221 0.0118 #>  #> [[4]]$stac #> [1] 2 #>  #> [[4]]$missing_species #> [1] 0 #>  #> [[4]]$type1or2 #> [1] 1 #>  #>  #> [[5]] #> [[5]]$colonist_name #> [1] \"Mimus\" #>  #> [[5]]$branching_times #> [1] 4.000 3.958 3.422 2.884 0.459 #>  #> [[5]]$stac #> [1] 2 #>  #> [[5]]$missing_species #> [1] 0 #>  #> [[5]]$type1or2 #> [1] 1 #>  #>  #> [[6]] #> [[6]]$colonist_name #> [1] \"Myiarchus\" #>  #> [[6]]$branching_times #> [1] 4.000 0.855 #>  #> [[6]]$stac #> [1] 2 #>  #> [[6]]$missing_species #> [1] 0 #>  #> [[6]]$type1or2 #> [1] 1 #>  #>  #> [[7]] #> [[7]]$colonist_name #> [1] \"Progne\" #>  #> [[7]]$branching_times #> [1] 4.000 0.086 #>  #> [[7]]$stac #> [1] 2 #>  #> [[7]]$missing_species #> [1] 0 #>  #> [[7]]$type1or2 #> [1] 1 #>  #>  #> [[8]] #> [[8]]$colonist_name #> [1] \"Pyrocephalus\" #>  #> [[8]]$branching_times #> [1] 4.00000 3.99999 #>  #> [[8]]$stac #> [1] 1 #>  #> [[8]]$missing_species #> [1] 0 #>  #> [[8]]$type1or2 #> [1] 1 #>  #>  #> [[9]] #> [[9]]$colonist_name #> [1] \"Zenaida\" #>  #> [[9]]$branching_times #> [1] 4.00 3.51 #>  #> [[9]]$stac #> [1] 2 #>  #> [[9]]$missing_species #> [1] 0 #>  #> [[9]]$type1or2 #> [1] 1 #>  #>   ### Create Galapagos data object with a distinct macroevolutionary processes # for the Darwin's finches. One process applies to type 1 species (all species # except for Darwin's finches) and the other applies only to type 2 species # (Darwin's finches). Set fraction of potential colonists of type 2 to be # proportional to the number of type2 clades present on the island.  utils::data(Galapagos_datatable, package = \"DAISIE\") DAISIE_dataprep(    datatable = Galapagos_datatable,    island_age = 4,    M = 1000,    number_clade_types = 2,    list_type2_clades = \"Finches\"    ) #> Colonisation time of 7.456 for Coccyzus is older than island age #> Colonisation time of 10.285 for Pyrocephalus is older than island age #> [[1]] #> [[1]]$island_age #> [1] 4 #>  #> [[1]]$not_present_type1 #> [1] 868 #>  #> [[1]]$not_present_type2 #> [1] 124 #>  #>  #> [[2]] #> [[2]]$colonist_name #> [1] \"Coccyzus\" #>  #> [[2]]$branching_times #> [1] 4.00000 3.99999 #>  #> [[2]]$stac #> [1] 1 #>  #> [[2]]$missing_species #> [1] 0 #>  #> [[2]]$type1or2 #> [1] 1 #>  #>  #> [[3]] #> [[3]]$colonist_name #> [1] \"Dendroica\" #>  #> [[3]]$branching_times #> [1] 4.00 0.34 #>  #> [[3]]$stac #> [1] 4 #>  #> [[3]]$missing_species #> [1] 0 #>  #> [[3]]$type1or2 #> [1] 1 #>  #>  #> [[4]] #> [[4]]$colonist_name #> [1] \"Finches\" #>  #> [[4]]$branching_times #>  [1] 4.0000 3.0282 1.3227 0.8223 0.4286 0.3462 0.2450 0.1180 0.0808 0.0756 #> [11] 0.0527 0.0525 0.0327 0.0322 0.0221 0.0118 #>  #> [[4]]$stac #> [1] 2 #>  #> [[4]]$missing_species #> [1] 0 #>  #> [[4]]$type1or2 #> [1] 2 #>  #>  #> [[5]] #> [[5]]$colonist_name #> [1] \"Mimus\" #>  #> [[5]]$branching_times #> [1] 4.000 3.958 3.422 2.884 0.459 #>  #> [[5]]$stac #> [1] 2 #>  #> [[5]]$missing_species #> [1] 0 #>  #> [[5]]$type1or2 #> [1] 1 #>  #>  #> [[6]] #> [[6]]$colonist_name #> [1] \"Myiarchus\" #>  #> [[6]]$branching_times #> [1] 4.000 0.855 #>  #> [[6]]$stac #> [1] 2 #>  #> [[6]]$missing_species #> [1] 0 #>  #> [[6]]$type1or2 #> [1] 1 #>  #>  #> [[7]] #> [[7]]$colonist_name #> [1] \"Progne\" #>  #> [[7]]$branching_times #> [1] 4.000 0.086 #>  #> [[7]]$stac #> [1] 2 #>  #> [[7]]$missing_species #> [1] 0 #>  #> [[7]]$type1or2 #> [1] 1 #>  #>  #> [[8]] #> [[8]]$colonist_name #> [1] \"Pyrocephalus\" #>  #> [[8]]$branching_times #> [1] 4.00000 3.99999 #>  #> [[8]]$stac #> [1] 1 #>  #> [[8]]$missing_species #> [1] 0 #>  #> [[8]]$type1or2 #> [1] 1 #>  #>  #> [[9]] #> [[9]]$colonist_name #> [1] \"Zenaida\" #>  #> [[9]]$branching_times #> [1] 4.00 3.51 #>  #> [[9]]$stac #> [1] 2 #>  #> [[9]]$missing_species #> [1] 0 #>  #> [[9]]$type1or2 #> [1] 1 #>  #>   ### Create Galapagos data object with a distinct macroevolutionary processes # for the Darwin's finches. One process applies to type 1 species (all species # except for Darwin's finches) and the other applies only to type 2 species # (Darwin's finches). Set fraction of potential colonists of type 2 to be 0.163.  utils::data(Galapagos_datatable, package = \"DAISIE\") DAISIE_dataprep(    datatable = Galapagos_datatable,    island_age = 4,    M = 1000,    number_clade_types = 2,    list_type2_clades = \"Finches\",    prop_type2_pool = 0.163    ) #> Colonisation time of 7.456 for Coccyzus is older than island age #> Colonisation time of 10.285 for Pyrocephalus is older than island age #> [[1]] #> [[1]]$island_age #> [1] 4 #>  #> [[1]]$not_present_type1 #> [1] 830 #>  #> [[1]]$not_present_type2 #> [1] 162 #>  #>  #> [[2]] #> [[2]]$colonist_name #> [1] \"Coccyzus\" #>  #> [[2]]$branching_times #> [1] 4.00000 3.99999 #>  #> [[2]]$stac #> [1] 1 #>  #> [[2]]$missing_species #> [1] 0 #>  #> [[2]]$type1or2 #> [1] 1 #>  #>  #> [[3]] #> [[3]]$colonist_name #> [1] \"Dendroica\" #>  #> [[3]]$branching_times #> [1] 4.00 0.34 #>  #> [[3]]$stac #> [1] 4 #>  #> [[3]]$missing_species #> [1] 0 #>  #> [[3]]$type1or2 #> [1] 1 #>  #>  #> [[4]] #> [[4]]$colonist_name #> [1] \"Finches\" #>  #> [[4]]$branching_times #>  [1] 4.0000 3.0282 1.3227 0.8223 0.4286 0.3462 0.2450 0.1180 0.0808 0.0756 #> [11] 0.0527 0.0525 0.0327 0.0322 0.0221 0.0118 #>  #> [[4]]$stac #> [1] 2 #>  #> [[4]]$missing_species #> [1] 0 #>  #> [[4]]$type1or2 #> [1] 2 #>  #>  #> [[5]] #> [[5]]$colonist_name #> [1] \"Mimus\" #>  #> [[5]]$branching_times #> [1] 4.000 3.958 3.422 2.884 0.459 #>  #> [[5]]$stac #> [1] 2 #>  #> [[5]]$missing_species #> [1] 0 #>  #> [[5]]$type1or2 #> [1] 1 #>  #>  #> [[6]] #> [[6]]$colonist_name #> [1] \"Myiarchus\" #>  #> [[6]]$branching_times #> [1] 4.000 0.855 #>  #> [[6]]$stac #> [1] 2 #>  #> [[6]]$missing_species #> [1] 0 #>  #> [[6]]$type1or2 #> [1] 1 #>  #>  #> [[7]] #> [[7]]$colonist_name #> [1] \"Progne\" #>  #> [[7]]$branching_times #> [1] 4.000 0.086 #>  #> [[7]]$stac #> [1] 2 #>  #> [[7]]$missing_species #> [1] 0 #>  #> [[7]]$type1or2 #> [1] 1 #>  #>  #> [[8]] #> [[8]]$colonist_name #> [1] \"Pyrocephalus\" #>  #> [[8]]$branching_times #> [1] 4.00000 3.99999 #>  #> [[8]]$stac #> [1] 1 #>  #> [[8]]$missing_species #> [1] 0 #>  #> [[8]]$type1or2 #> [1] 1 #>  #>  #> [[9]] #> [[9]]$colonist_name #> [1] \"Zenaida\" #>  #> [[9]]$branching_times #> [1] 4.00 3.51 #>  #> [[9]]$stac #> [1] 2 #>  #> [[9]]$missing_species #> [1] 0 #>  #> [[9]]$type1or2 #> [1] 1 #>  #>"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_extract_stt_median.html","id":null,"dir":"Reference","previous_headings":"","what":"Extract the STT median from the output of DAISIE_sim functions — DAISIE_extract_stt_median","title":"Extract the STT median from the output of DAISIE_sim functions — DAISIE_extract_stt_median","text":"Extract STT median output DAISIE_sim functions","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_extract_stt_median.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extract the STT median from the output of DAISIE_sim functions — DAISIE_extract_stt_median","text":"","code":"DAISIE_extract_stt_median(island_replicates, trait_pars = NULL)"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_extract_stt_median.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extract the STT median from the output of DAISIE_sim functions — DAISIE_extract_stt_median","text":"island_replicates List output DAISIE_sim_core_cr(), DAISIE_sim_core_time_dep(), DAISIE_sim_core_cr_shift() DAISIE_sim_min_type2() functions. Minimally, must list many elements replicates. element must list elements island_age, not_present stt_all. stt_all must data frame column names Time, nI, nA, nC present. trait_pars named list containing diversification rates considering   two trait states created create_trait_pars: [1]:numeric per capita transition rate state1 [2]:numeric per capita immigration rate state2 [3]:numeric per capita extinction rate state2 [4]:numeric per capita anagenesis rate state2 [5]:numeric per capita cladogenesis rate state2 [6]:numeric per capita transition rate state2 [7]:numeric number species trait state 2    mainland","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_extract_stt_median.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Extract the STT median from the output of DAISIE_sim functions — DAISIE_extract_stt_median","text":"matrix (?)","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_format_CS.html","id":null,"dir":"Reference","previous_headings":"","what":"Wrapper function around for the DAISIE_format_CS_full_stt and DAISIE_format_CS_sampled_stt — DAISIE_format_CS","title":"Wrapper function around for the DAISIE_format_CS_full_stt and DAISIE_format_CS_sampled_stt — DAISIE_format_CS","text":"Wrapper function around DAISIE_format_CS_full_stt DAISIE_format_CS_sampled_stt","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_format_CS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Wrapper function around for the DAISIE_format_CS_full_stt and DAISIE_format_CS_sampled_stt — DAISIE_format_CS","text":"","code":"DAISIE_format_CS(   island_replicates,   time,   M,   sample_freq = 25,   verbose = TRUE,   trait_pars = NULL )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_format_CS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Wrapper function around for the DAISIE_format_CS_full_stt and DAISIE_format_CS_sampled_stt — DAISIE_format_CS","text":"island_replicates List output DAISIE_sim_core_cr(), DAISIE_sim_core_time_dep(), DAISIE_sim_core_cr_shift() DAISIE_sim_min_type2() functions. Minimally, must list many elements replicates. element must list elements island_age, not_present stt_all. stt_all must data frame column names Time, nI, nA, nC present. time Numeric defining length simulation time units. example, island known 4 million years old, setting time = 4 simulate entire life span island; setting time = 2 stop simulation mid-life island. M Numeric defining size mainland pool, .e. number species can potentially colonize island. sample_freq Numeric specifing number units times divided plotting purposes. Larger values lead plots higher resolution, also run slower. verbose numeric vector length 1, simulations `DAISIEdataprep()` can `1` `0`, `1` gives intermediate output printed. ML functions numeric determining intermediate output printed. default: `0` print, `1` prints initial likelihood settings selected (parameters optimised, fixed shifted), `2` prints `1 also intermediate output parameters loglikelihood, `3` `2` prints intermediate progress likelihood computation. trait_pars named list containing diversification rates considering   two trait states created create_trait_pars: [1]:numeric per capita transition rate state1 [2]:numeric per capita immigration rate state2 [3]:numeric per capita extinction rate state2 [4]:numeric per capita anagenesis rate state2 [5]:numeric per capita cladogenesis rate state2 [6]:numeric per capita transition rate state2 [7]:numeric number species trait state 2    mainland","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_format_CS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Wrapper function around for the DAISIE_format_CS_full_stt and DAISIE_format_CS_sampled_stt — DAISIE_format_CS","text":"List CS DAISIE simulation output","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_format_CS_full_stt.html","id":null,"dir":"Reference","previous_headings":"","what":"Formats clade-specific simulation output into standard DAISIE list output with complete STT table — DAISIE_format_CS_full_stt","title":"Formats clade-specific simulation output into standard DAISIE list output with complete STT table — DAISIE_format_CS_full_stt","text":"Formats clade-specific simulation output standard DAISIE list output complete STT table","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_format_CS_full_stt.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Formats clade-specific simulation output into standard DAISIE list output with complete STT table — DAISIE_format_CS_full_stt","text":"","code":"DAISIE_format_CS_full_stt(   island_replicates,   time,   M,   verbose = TRUE,   trait_pars = NULL )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_format_CS_full_stt.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Formats clade-specific simulation output into standard DAISIE list output with complete STT table — DAISIE_format_CS_full_stt","text":"island_replicates List output DAISIE_sim_core_cr(), DAISIE_sim_core_time_dep(), DAISIE_sim_core_cr_shift() DAISIE_sim_min_type2() functions. Minimally, must list many elements replicates. element must list elements island_age, not_present stt_all. stt_all must data frame column names Time, nI, nA, nC present. time Numeric defining length simulation time units. example, island known 4 million years old, setting time = 4 simulate entire life span island; setting time = 2 stop simulation mid-life island. M Numeric defining size mainland pool, .e. number species can potentially colonize island. verbose numeric vector length 1, simulations `DAISIEdataprep()` can `1` `0`, `1` gives intermediate output printed. ML functions numeric determining intermediate output printed. default: `0` print, `1` prints initial likelihood settings selected (parameters optimised, fixed shifted), `2` prints `1 also intermediate output parameters loglikelihood, `3` `2` prints intermediate progress likelihood computation. trait_pars named list containing diversification rates considering   two trait states created create_trait_pars: [1]:numeric per capita transition rate state1 [2]:numeric per capita immigration rate state2 [3]:numeric per capita extinction rate state2 [4]:numeric per capita anagenesis rate state2 [5]:numeric per capita cladogenesis rate state2 [6]:numeric per capita transition rate state2 [7]:numeric number species trait state 2    mainland","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_format_CS_full_stt.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Formats clade-specific simulation output into standard DAISIE list output with complete STT table — DAISIE_format_CS_full_stt","text":"List CS DAISIE simulation output","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_format_CS_sampled_stt.html","id":null,"dir":"Reference","previous_headings":"","what":"Formats clade-specific simulation output into standard DAISIE list output — DAISIE_format_CS_sampled_stt","title":"Formats clade-specific simulation output into standard DAISIE list output — DAISIE_format_CS_sampled_stt","text":"Formats clade-specific simulation output standard DAISIE list output","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_format_CS_sampled_stt.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Formats clade-specific simulation output into standard DAISIE list output — DAISIE_format_CS_sampled_stt","text":"","code":"DAISIE_format_CS_sampled_stt(   island_replicates,   time,   M,   sample_freq,   verbose = TRUE,   trait_pars = NULL )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_format_CS_sampled_stt.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Formats clade-specific simulation output into standard DAISIE list output — DAISIE_format_CS_sampled_stt","text":"island_replicates List output DAISIE_sim_core_cr(), DAISIE_sim_core_time_dep(), DAISIE_sim_core_cr_shift() DAISIE_sim_min_type2() functions. Minimally, must list many elements replicates. element must list elements island_age, not_present stt_all. stt_all must data frame column names Time, nI, nA, nC present. time Numeric defining length simulation time units. example, island known 4 million years old, setting time = 4 simulate entire life span island; setting time = 2 stop simulation mid-life island. M Numeric defining size mainland pool, .e. number species can potentially colonize island. sample_freq Numeric specifing number units times divided plotting purposes. Larger values lead plots higher resolution, also run slower. verbose numeric vector length 1, simulations `DAISIEdataprep()` can `1` `0`, `1` gives intermediate output printed. ML functions numeric determining intermediate output printed. default: `0` print, `1` prints initial likelihood settings selected (parameters optimised, fixed shifted), `2` prints `1 also intermediate output parameters loglikelihood, `3` `2` prints intermediate progress likelihood computation. trait_pars named list containing diversification rates considering   two trait states created create_trait_pars: [1]:numeric per capita transition rate state1 [2]:numeric per capita immigration rate state2 [3]:numeric per capita extinction rate state2 [4]:numeric per capita anagenesis rate state2 [5]:numeric per capita cladogenesis rate state2 [6]:numeric per capita transition rate state2 [7]:numeric number species trait state 2    mainland","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_format_CS_sampled_stt.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Formats clade-specific simulation output into standard DAISIE list output — DAISIE_format_CS_sampled_stt","text":"List CS DAISIE simulation output","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_format_GW.html","id":null,"dir":"Reference","previous_headings":"","what":"Formats guild-wide simulation output into standard DAISIE list output — DAISIE_format_GW","title":"Formats guild-wide simulation output into standard DAISIE list output — DAISIE_format_GW","text":"Formats guild-wide simulation output standard DAISIE list output","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_format_GW.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Formats guild-wide simulation output into standard DAISIE list output — DAISIE_format_GW","text":"","code":"DAISIE_format_GW(   island_replicates,   time,   M,   sample_freq,   num_guilds,   verbose = TRUE )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_format_GW.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Formats guild-wide simulation output into standard DAISIE list output — DAISIE_format_GW","text":"island_replicates List output DAISIE_sim_core_cr(), DAISIE_sim_core_time_dep(), DAISIE_sim_core_cr_shift() DAISIE_sim_min_type2() functions. Minimally, must list many elements replicates. element must list elements island_age, not_present stt_all. stt_all must data frame column names Time, nI, nA, nC present. time Numeric defining length simulation time units. example, island known 4 million years old, setting time = 4 simulate entire life span island; setting time = 2 stop simulation mid-life island. M Numeric defining size mainland pool, .e. number species can potentially colonize island. sample_freq Numeric specifing number units times divided plotting purposes. Larger values lead plots higher resolution, also run slower. num_guilds number guilds mainland. number mainland species divided number guilds divdepmodel = \"GW\" verbose numeric vector length 1, simulations `DAISIEdataprep()` can `1` `0`, `1` gives intermediate output printed. ML functions numeric determining intermediate output printed. default: `0` print, `1` prints initial likelihood settings selected (parameters optimised, fixed shifted), `2` prints `1 also intermediate output parameters loglikelihood, `3` `2` prints intermediate progress likelihood computation.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_format_GW.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Formats guild-wide simulation output into standard DAISIE list output — DAISIE_format_GW","text":"List GW DAISIE simulation output","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_format_IW_full_stt.html","id":null,"dir":"Reference","previous_headings":"","what":"Formats clade-specific simulation output into standard DAISIE list output with complete STT table — DAISIE_format_IW_full_stt","title":"Formats clade-specific simulation output into standard DAISIE list output with complete STT table — DAISIE_format_IW_full_stt","text":"Formats clade-specific simulation output standard DAISIE list output complete STT table","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_format_IW_full_stt.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Formats clade-specific simulation output into standard DAISIE list output with complete STT table — DAISIE_format_IW_full_stt","text":"","code":"DAISIE_format_IW_full_stt(island_replicates, total_time, M, verbose)"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_format_IW_full_stt.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Formats clade-specific simulation output into standard DAISIE list output with complete STT table — DAISIE_format_IW_full_stt","text":"island_replicates List output DAISIE_sim_core_cr(), DAISIE_sim_core_time_dep(), DAISIE_sim_core_cr_shift() DAISIE_sim_min_type2() functions. Minimally, must list many elements replicates. element must list elements island_age, not_present stt_all. stt_all must data frame column names Time, nI, nA, nC present. total_time Numeric defining length simulation time units. M Numeric defining size mainland pool, .e. number species can potentially colonize island. verbose numeric vector length 1, simulations `DAISIEdataprep()` can `1` `0`, `1` gives intermediate output printed. ML functions numeric determining intermediate output printed. default: `0` print, `1` prints initial likelihood settings selected (parameters optimised, fixed shifted), `2` prints `1 also intermediate output parameters loglikelihood, `3` `2` prints intermediate progress likelihood computation.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_format_IW_full_stt.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Formats clade-specific simulation output into standard DAISIE list output with complete STT table — DAISIE_format_IW_full_stt","text":"List IW DAISIE simulation output","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_format_IW_sampled_stt.html","id":null,"dir":"Reference","previous_headings":"","what":"Formats island-wide simulation output into standard DAISIE list output — DAISIE_format_IW_sampled_stt","title":"Formats island-wide simulation output into standard DAISIE list output — DAISIE_format_IW_sampled_stt","text":"Formats island-wide simulation output standard DAISIE list output","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_format_IW_sampled_stt.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Formats island-wide simulation output into standard DAISIE list output — DAISIE_format_IW_sampled_stt","text":"","code":"DAISIE_format_IW_sampled_stt(   island_replicates,   total_time,   M,   sample_freq,   verbose )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_format_IW_sampled_stt.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Formats island-wide simulation output into standard DAISIE list output — DAISIE_format_IW_sampled_stt","text":"island_replicates List output DAISIE_sim_core_cr(), DAISIE_sim_core_time_dep(), DAISIE_sim_core_cr_shift() DAISIE_sim_min_type2() functions. Minimally, must list many elements replicates. element must list elements island_age, not_present stt_all. stt_all must data frame column names Time, nI, nA, nC present. total_time Numeric defining length simulation time units. M Numeric defining size mainland pool, .e. number species can potentially colonize island. sample_freq Numeric specifing number units times divided plotting purposes. Larger values lead plots higher resolution, also run slower. verbose numeric vector length 1, simulations `DAISIEdataprep()` can `1` `0`, `1` gives intermediate output printed. ML functions numeric determining intermediate output printed. default: `0` print, `1` prints initial likelihood settings selected (parameters optimised, fixed shifted), `2` prints `1 also intermediate output parameters loglikelihood, `3` `2` prints intermediate progress likelihood computation.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_format_IW_sampled_stt.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Formats island-wide simulation output into standard DAISIE list output — DAISIE_format_IW_sampled_stt","text":"List IW DAISIE simulation output","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_loglik_CS.html","id":null,"dir":"Reference","previous_headings":"","what":"Computes the loglikelihood of the DAISIE model with clade-specific diversity-dependence given data and a set of model parameters — DAISIE_loglik_CS","title":"Computes the loglikelihood of the DAISIE model with clade-specific diversity-dependence given data and a set of model parameters — DAISIE_loglik_CS","text":"Computes loglikelihood DAISIE model clade-specific diversity-dependence given colonization branching times lineages island, set model parameters. output loglikelihood value","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_loglik_CS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Computes the loglikelihood of the DAISIE model with clade-specific diversity-dependence given data and a set of model parameters — DAISIE_loglik_CS","text":"","code":"DAISIE_loglik_CS(   pars1,   pars2,   datalist,   methode = \"lsodes\",   CS_version = 1,   abstolint = 1e-16,   reltolint = 1e-10 )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_loglik_CS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Computes the loglikelihood of the DAISIE model with clade-specific diversity-dependence given data and a set of model parameters — DAISIE_loglik_CS","text":"pars1 Contains model parameters: pars1[1] corresponds lambda^c (cladogenesis rate) pars1[2] corresponds mu (extinction rate) pars1[3] corresponds K (clade-level carrying capacity) pars1[4] corresponds gamma (immigration rate) pars1[5] corresponds lambda^(anagenesis rate) pars1[6] corresponds lambda^c (cladogenesis rate) optional subset species pars1[7] corresponds mu (extinction rate) optional subset speciespars1[8] corresponds K (clade-level carrying capacity) optional subset speciespars1[9] corresponds gamma (immigration rate) optional subset speciespars1[10] corresponds lambda^(anagenesis rate) optional subset speciespars1[11] corresponds p_f (fraction mainland species belongs second subset species elements 6:10 11 optional, , pars1 either contain 5, 10 11 elements. 10, fraction potential colonists type 2 computed data. 11, pars1[11] used, overruling information data. pars2 Contains model settings pars2[1] corresponds lx = length ODE variable x pars2[2] corresponds ddmodel = diversity-dependent model, model diversity-dependence, can one ddmodel = 0 : diversity dependence  ddmodel = 1 : linear dependence speciation rate  ddmodel = 11: linear dependence speciation rate immigration rate  ddmodel = 2 : exponential dependence speciation rate ddmodel = 21: exponential dependence speciation rate immigration ratepars2[3] corresponds cond = setting conditioning cond = 0 : conditioning island age  cond = 1 : conditioning island age non-extinction island biota  cond > 1 : conditioning island age least cond colonizations island pars2[4] sets whether parameters likelihood printed (1) (0) datalist Data object containing information colonisation branching times. object can generated using DAISIE_dataprep function, converts user-specified data table data object, object can course also entered directly. R list object following elements. first element list two three components: $island_age - island age  , depending whether distinction types made, :$not_present - number mainland lineages present island  :$not_present_type1 - number mainland lineages type 1 present island $not_present_type2 - number mainland lineages type 2 present island  remaining elements list contains information single colonist lineage island 5 components:$colonist_name - name species clade colonized island $branching_times - island age stem age population/species case Non-endemic, Non-endemic_MaxAge Endemic anagenetic species. cladogenetic species island age branching times radiation including stem age radiation.$stac - status colonist  * Non_endemic_MaxAge: 1  * Endemic: 2  * Endemic&Non_Endemic: 3  * Non_Endemic: 4  * Endemic_Singleton_MaxAge: 5  * Endemic_Clade_MaxAge: 6  * Endemic&Non_Endemic_Clade_MaxAge: 7  * Non_endemic_MaxAge_MinAge: 8  * Endemic_Singleton_MaxAge_MinAge: 9 $missing_species - number island species sampled particular clade (applicable endemic clades) $type1or2 - whether colonist belongs type 1 type 2 methode Method ODE-solver. See package deSolve details. Default \"lsodes\" CS_version numeric list. Default 1 standard DAISIE model, relaxed-rate model list following elements: model: CS model run, options 1 single rate   DAISIE model, 2 multi-rate DAISIE, 0 IW test   model. relaxed_par: parameter relax (integrate ). Options \"cladogenesis\", \"extinction\", \"carrying_capacity\", \"immigration\", \"anagenesis\". abstolint Absolute tolerance integration reltolint Relative tolerance integration","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_loglik_CS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Computes the loglikelihood of the DAISIE model with clade-specific diversity-dependence given data and a set of model parameters — DAISIE_loglik_CS","text":"loglikelihood","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_loglik_CS.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Computes the loglikelihood of the DAISIE model with clade-specific diversity-dependence given data and a set of model parameters — DAISIE_loglik_CS","text":"Valente, L.M., .B. Phillimore R.S. Etienne (2015). Equilibrium non-equilibrium dynamics simultaneously operate Galapagos islands. Ecology Letters 18: 844-852.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_loglik_CS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Computes the loglikelihood of the DAISIE model with clade-specific diversity-dependence given data and a set of model parameters — DAISIE_loglik_CS","text":"Rampal S. Etienne & Bart Haegeman","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_loglik_CS.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Computes the loglikelihood of the DAISIE model with clade-specific diversity-dependence given data and a set of model parameters — DAISIE_loglik_CS","text":"","code":"utils::data(Galapagos_datalist_2types) pars1 = c(0.195442017,0.087959583,Inf,0.002247364,0.873605049,           3755.202241,8.909285094,14.99999923,0.002247364,0.873605049,0.163) pars2 = c(100,11,0,1) DAISIE_loglik_all(pars1,pars2,Galapagos_datalist_2types) #> [1] -61.70282"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_loglik_IW.html","id":null,"dir":"Reference","previous_headings":"","what":"Computes the loglikelihood of the DAISIE model with island-wide diversity-dependence given data and a set of model parameters — DAISIE_loglik_IW","title":"Computes the loglikelihood of the DAISIE model with island-wide diversity-dependence given data and a set of model parameters — DAISIE_loglik_IW","text":"Computes loglikelihood DAISIE model given colonization branching times lineages island, set model parameters DAISIE model island-wide diversity-dependence","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_loglik_IW.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Computes the loglikelihood of the DAISIE model with island-wide diversity-dependence given data and a set of model parameters — DAISIE_loglik_IW","text":"","code":"DAISIE_loglik_IW(   pars1,   pars2,   datalist,   methode = \"lsodes\",   abstolint = 1e-12,   reltolint = 1e-10,   verbose = FALSE )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_loglik_IW.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Computes the loglikelihood of the DAISIE model with island-wide diversity-dependence given data and a set of model parameters — DAISIE_loglik_IW","text":"pars1 Contains model parameters: pars1[1] corresponds lambda^c (cladogenesis rate) pars1[2] corresponds mu (extinction rate) pars1[3] corresponds K (clade-level carrying capacity) pars1[4] corresponds gamma (immigration rate) pars1[5] corresponds lambda^(anagenesis rate) pars1[6] optional; may contain M, total number species mainland pars2 Contains model settings pars2[1] corresponds lx = length ODE variable x pars2[2] corresponds ddmodel = diversity-dependent model, model diversity-dependence, can one ddmodel = 0 : diversity dependence  ddmodel = 1 : linear dependence speciation rate  ddmodel = 11: linear dependence speciation rate immigration rate  ddmodel = 2 : exponential dependence speciation rate ddmodel = 21: exponential dependence speciation rate immigration rate ddmodel = 11 currently implemented pars2[3] corresponds cond = setting conditioning cond = 0 : conditioning island age  cond = 1 : conditioning island age non-extinction island biota pars2[4] Specifies whether intermediate output provided, computation may take long. Default 0, output. value 1 means parameters loglikelihood printed. value 2 means also intermediate progress loglikelihood computation shown. datalist Data object containing information colonisation branching times. object can generated using DAISIE_dataprep function, converts user-specified data table data object, object can course also entered directly. R list object following elements. first element list two three components: $island_age - island age  , depending whether distinction types made, :$not_present - number mainland lineages present island  remaining elements list contains information single colonist lineage island 5 components:$colonist_name - name species clade colonized island $branching_times - island age stem age population/species case Non-endemic, Non-endemic_MaxAge Endemic anagenetic species. cladogenetic species island age branching times radiation including stem age radiation.$stac - status colonist  * Non_endemic_MaxAge: 1  * Endemic: 2  * Endemic&Non_Endemic: 3  * Non_endemic: 4  * Endemic_MaxAge: 5 $missing_species - number island species sampled particular clade (applicable endemic clades) methode Method ODE-solver. Supported Boost ODEINT solvers (steppers) : 'odeint::runge_kutta_cash_karp54' 'odeint::runge_kutta_fehlberg78' [default] 'odeint::runge_kutta_dopri5' 'odeint::bulirsch_stoer' 'odeint::adams_bashforth_[1|2|3|4|5|6|7|8]} \\code{'odeint::adams_bashforth_moulton_[1|2|3|4|5|6|7|8] without odeint::-prefix, ode method assumed. abstolint Absolute tolerance integration reltolint Relative tolerance integration verbose Logical controling progress printed console.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_loglik_IW.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Computes the loglikelihood of the DAISIE model with island-wide diversity-dependence given data and a set of model parameters — DAISIE_loglik_IW","text":"loglikelihood","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_loglik_IW.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Computes the loglikelihood of the DAISIE model with island-wide diversity-dependence given data and a set of model parameters — DAISIE_loglik_IW","text":"output loglikelihood value","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_loglik_IW.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Computes the loglikelihood of the DAISIE model with island-wide diversity-dependence given data and a set of model parameters — DAISIE_loglik_IW","text":"Valente, L.M., .B. Phillimore R.S. Etienne (2015). Equilibrium non-equilibrium dynamics simultaneously operate Galapagos islands. Ecology Letters 18: 844-852.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_loglik_IW.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Computes the loglikelihood of the DAISIE model with island-wide diversity-dependence given data and a set of model parameters — DAISIE_loglik_IW","text":"Rampal S. Etienne & Bart Haegeman","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_loglik_integrand.html","id":null,"dir":"Reference","previous_headings":"","what":"Integrand to be integrated to calculate the log likelihood for the relaxed rate model. — DAISIE_loglik_integrand","title":"Integrand to be integrated to calculate the log likelihood for the relaxed rate model. — DAISIE_loglik_integrand","text":"Integrand integrated calculate log likelihood relaxed rate model.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_loglik_integrand.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Integrand to be integrated to calculate the log likelihood for the relaxed rate model. — DAISIE_loglik_integrand","text":"","code":"DAISIE_loglik_integrand(   DAISIE_par,   pars1,   pars2,   brts,   stac,   missnumspec,   methode,   abstolint,   reltolint,   verbose,   pick,   par_mean,   par_sd )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_loglik_integrand.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Integrand to be integrated to calculate the log likelihood for the relaxed rate model. — DAISIE_loglik_integrand","text":"DAISIE_par numeric parameter evaluate integral function. pars1 Vector model parameters: pars1[1] corresponds lambda^c (cladogenesis rate) pars1[2] corresponds mu (extinction rate) pars1[3] corresponds K (clade-level carrying capacity) pars1[4] corresponds gamma (immigration rate) pars1[5] corresponds lambda^(anagenesis rate). pars2 Vector settings: pars2[1] corresponds res, maximum number endemics non-endemics ODE system solved; must much larger actual number probability needs calculated.) pars2[2] corresponds M, size mainland pool, .e number species can potentially colonize island. brts Numeric vector branching times stac Numeric Endemicity status missnumspec Numeric missing species methode Method ODE-solver. Supported Boost ODEINT solvers (steppers) : \"odeint::runge_kutta_cash_karp54\" \"odeint::runge_kutta_fehlberg78\" \"odeint::runge_kutta_dopri5\" \"odeint::bulirsch_stoer\" without odeint::-prefix, deSolve{ode} method assumed. default method overall \"lsodes\" DAISIE_ML_CS() \"ode45\" ode() DAISIE_ML_IW(). abstolint Numeric absolute tolerance integration reltolint Numeric relative tolerance integration verbose numeric vector length 1, simulations `DAISIEdataprep()` can `1` `0`, `1` gives intermediate output printed. ML functions numeric determining intermediate output printed. default: `0` print, `1` prints initial likelihood settings selected (parameters optimised, fixed shifted), `2` prints `1 also intermediate output parameters loglikelihood, `3` `2` prints intermediate progress likelihood computation. pick Numeric determining parameter selected relaxed-rate model","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_loglik_integrand.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Integrand to be integrated to calculate the log likelihood for the relaxed rate model. — DAISIE_loglik_integrand","text":"numeric","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_loglik_integrate.html","id":null,"dir":"Reference","previous_headings":"","what":"Integrates the loglikelihood of a single clade across a parameter weighted by a given distribution — DAISIE_loglik_integrate","title":"Integrates the loglikelihood of a single clade across a parameter weighted by a given distribution — DAISIE_loglik_integrate","text":"Integrates loglikelihood single clade across parameter weighted given distribution","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_loglik_integrate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Integrates the loglikelihood of a single clade across a parameter weighted by a given distribution — DAISIE_loglik_integrate","text":"","code":"DAISIE_loglik_integrate(   pars1,   pars2,   brts,   stac,   missnumspec,   CS_version,   methode,   abstolint,   reltolint,   verbose )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_loglik_integrate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Integrates the loglikelihood of a single clade across a parameter weighted by a given distribution — DAISIE_loglik_integrate","text":"pars1 Vector model parameters: pars1[1] corresponds lambda^c (cladogenesis rate) pars1[2] corresponds mu (extinction rate) pars1[3] corresponds K (clade-level carrying capacity) pars1[4] corresponds gamma (immigration rate) pars1[5] corresponds lambda^(anagenesis rate). pars2 Vector settings: pars2[1] corresponds res, maximum number endemics non-endemics ODE system solved; must much larger actual number probability needs calculated.) pars2[2] corresponds M, size mainland pool, .e number species can potentially colonize island. brts Numeric vector branching times stac Numeric Endemicity status missnumspec Numeric missing species CS_version numeric list. Default 1 standard DAISIE model, relaxed-rate model list following elements: model: CS model run, options 1 single rate   DAISIE model, 2 multi-rate DAISIE, 0 IW test   model. relaxed_par: parameter relax (integrate ). Options \"cladogenesis\", \"extinction\", \"carrying_capacity\", \"immigration\", \"anagenesis\". methode Method ODE-solver. Supported Boost ODEINT solvers (steppers) : \"odeint::runge_kutta_cash_karp54\" \"odeint::runge_kutta_fehlberg78\" \"odeint::runge_kutta_dopri5\" \"odeint::bulirsch_stoer\" without odeint::-prefix, deSolve{ode} method assumed. default method overall \"lsodes\" DAISIE_ML_CS() \"ode45\" ode() DAISIE_ML_IW(). abstolint Numeric absolute tolerance integration reltolint Numeric relative tolerance integration verbose numeric vector length 1, simulations `DAISIEdataprep()` can `1` `0`, `1` gives intermediate output printed. ML functions numeric determining intermediate output printed. default: `0` print, `1` prints initial likelihood settings selected (parameters optimised, fixed shifted), `2` prints `1 also intermediate output parameters loglikelihood, `3` `2` prints intermediate progress likelihood computation.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_loglik_integrate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Integrates the loglikelihood of a single clade across a parameter weighted by a given distribution — DAISIE_loglik_integrate","text":"loglikelihood value","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_make_archipelago.html","id":null,"dir":"Reference","previous_headings":"","what":"Does some things — DAISIE_make_archipelago","title":"Does some things — DAISIE_make_archipelago","text":"things","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_make_archipelago.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Does some things — DAISIE_make_archipelago","text":"","code":"DAISIE_make_archipelago(archipelago, M, phylo_data, archipelago_data)"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_make_archipelago.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Does some things — DAISIE_make_archipelago","text":"archipelago something M Numeric defining size mainland pool, .e. number species can potentially colonize island. phylo_data something archipelago_data something","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_make_archipelago.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Does some things — DAISIE_make_archipelago","text":"something","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_make_global.html","id":null,"dir":"Reference","previous_headings":"","what":"Does something — DAISIE_make_global","title":"Does something — DAISIE_make_global","text":"something","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_make_global.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Does something — DAISIE_make_global","text":"","code":"DAISIE_make_global(archipelago_list, M, phylo_data, archipelago_data)"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_make_global.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Does something — DAISIE_make_global","text":"archipelago_list something M something phylo_data something archipelago_data something","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_make_global.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Does something — DAISIE_make_global","text":"something","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_margprobdist.html","id":null,"dir":"Reference","previous_headings":"","what":"The marginal distribution of endemics and non-endemics under the DAISIE model — DAISIE_margprobdist","title":"The marginal distribution of endemics and non-endemics under the DAISIE model — DAISIE_margprobdist","text":"function calculates marginal distribution number endemics non-endemics sum given set parameter values, given mainland species pool size given set times","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_margprobdist.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The marginal distribution of endemics and non-endemics under the DAISIE model — DAISIE_margprobdist","text":"","code":"DAISIE_margprobdist(   pars1,   pars2,   tvec,   initEI = c(0, 0),   initprobs = NULL,   pb = NULL )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_margprobdist.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The marginal distribution of endemics and non-endemics under the DAISIE model — DAISIE_margprobdist","text":"pars1 Vector model parameters: pars1[1] corresponds lambda^c (cladogenesis rate) pars1[2] corresponds mu (extinction rate) pars1[3] corresponds K (clade-level carrying capacity) pars1[4] corresponds gamma (immigration rate) pars1[5] corresponds lambda^(anagenesis rate). pars2 Vector settings: pars2[1] corresponds res, maximum number endemics non-endemics ODE system solved; must much larger actual number probability needs calculated.) pars2[2] corresponds M, size mainland pool, .e number species can potentially colonize island. tvec times probabilities need computed. initEI initial values number endemics   non-endemics. DAISIE_probdist() DAISIE_margprobdist() either initprobs must NULL. DAISIE_numcol() NULL, assumed island   empty. initprobs initial probability distribution number endemics non-endemics; either initEI must NULL. pb Probability distribution matrix format output DAISIE_probdist().","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_margprobdist.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The marginal distribution of endemics and non-endemics under the DAISIE model — DAISIE_margprobdist","text":"list three vectors: pE probability distribution number endemic species pI probability distribution number non-endemic species pN probability distribution sum number endemics non-endemics","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_margprobdist.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"The marginal distribution of endemics and non-endemics under the DAISIE model — DAISIE_margprobdist","text":"Valente, L.M., .B. Phillimore R.S. Etienne (2015). Equilibrium non-equilibrium dynamics simultaneously operate Galapagos islands. Ecology Letters 18: 844-852.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_margprobdist.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"The marginal distribution of endemics and non-endemics under the DAISIE model — DAISIE_margprobdist","text":"Rampal S. Etienne","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_margprobdist.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"The marginal distribution of endemics and non-endemics under the DAISIE model — DAISIE_margprobdist","text":"","code":"### Compute the marginal probability distributions at t = 4 and t = 8, for a mainland # pool size of 250 potential colonists and a vector of 5 parameters (cladogenesis, # extinction, clade-level carrying capacity, immigration, anagenesis) starting from # an empty island  marg_prob_dists <- DAISIE_margprobdist(    pars1 = c(0.3,0.35,Inf,0.75,0.012),    pars2 = c(100,250),    tvec = c(4,8),    initEI = c(5,1),    initprobs = NULL    )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_numcol.html","id":null,"dir":"Reference","previous_headings":"","what":"The expectation and marginal distribution of the number of colonizations (lineages) under the DAISIE model — DAISIE_numcol","title":"The expectation and marginal distribution of the number of colonizations (lineages) under the DAISIE model — DAISIE_numcol","text":"function calculates expectation marginal distribution number colonizations (lineages) given set parameter values, given mainland species pool size given set times","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_numcol.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The expectation and marginal distribution of the number of colonizations (lineages) under the DAISIE model — DAISIE_numcol","text":"","code":"DAISIE_numcol(pars1, pars2, tvec, initEI = NULL)"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_numcol.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The expectation and marginal distribution of the number of colonizations (lineages) under the DAISIE model — DAISIE_numcol","text":"pars1 Vector model parameters: pars1[1] corresponds lambda^c (cladogenesis rate) pars1[2] corresponds mu (extinction rate) pars1[3] corresponds K (clade-level carrying capacity) pars1[4] corresponds gamma (immigration rate) pars1[5] corresponds lambda^(anagenesis rate). pars2 Vector settings: pars2[1] corresponds res, maximum number endemics non-endemics ODE system solved; must much larger actual number probability needs calculated.) pars2[2] corresponds M, size mainland pool, .e number species can potentially colonize island. tvec times probabilities need computed. initEI initial values number endemics   non-endemics. DAISIE_probdist() DAISIE_margprobdist() either initprobs must NULL. DAISIE_numcol() NULL, assumed island   empty.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_numcol.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The expectation and marginal distribution of the number of colonizations (lineages) under the DAISIE model — DAISIE_numcol","text":"list three vectors: expC expectation number colonizations/lineages given times pC probability distribution number colonizations (lineages) given times","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_numcol.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"The expectation and marginal distribution of the number of colonizations (lineages) under the DAISIE model — DAISIE_numcol","text":"Valente, L.M., .B. Phillimore R.S. Etienne (2015). Equilibrium non-equilibrium dynamics simultaneously operate Galapagos islands. Ecology Letters 18: 844-852.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_numcol.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"The expectation and marginal distribution of the number of colonizations (lineages) under the DAISIE model — DAISIE_numcol","text":"Rampal S. Etienne","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_numcol.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"The expectation and marginal distribution of the number of colonizations (lineages) under the DAISIE model — DAISIE_numcol","text":"","code":"### Compute the marginal probability distributions at t = 4 and t = 8, for a mainland # pool size of 250 potential colonists and a vector of 5 parameters (cladogenesis, # extinction, clade-level carrying capacity, immigration, anagenesis) starting from # an empty island  numcol <- DAISIE_numcol(    pars1 = c(0.3,0.35,Inf,0.75,0.012),    pars2 = c(100,250),    tvec = c(4,8),    initEI = list(c(0,1),c(0,2),c(3,1))    )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_age_diversity.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot clade age against clade diversity. — DAISIE_plot_age_diversity","title":"Plot clade age against clade diversity. — DAISIE_plot_age_diversity","text":"Plots clade age clade diversity clades colonisation time known.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_age_diversity.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot clade age against clade diversity. — DAISIE_plot_age_diversity","text":"","code":"DAISIE_plot_age_diversity(   island,   title = \"Clade age vs clade diversity\",   island_age = NA )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_age_diversity.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot clade age against clade diversity. — DAISIE_plot_age_diversity","text":"island Island data object. Can DAISIE list format (see Galapagos_datalist DAISIE_data_prep examples) table format (see Galapagos_datatable example). title Title plot island_age Age island appropriate units. DAISIE_plot_age_diversity() DAISIE_plot_island() island input table format, age island must specified. island input DAISIE list format, option override island age specified island list.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_age_diversity.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot clade age against clade diversity. — DAISIE_plot_age_diversity","text":"R plot.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_age_diversity.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Plot clade age against clade diversity. — DAISIE_plot_age_diversity","text":"R plot showing clade island object time colonisation diversity clade. clades colonisation time known plotted. Blue - endemic; black - non-endemic. C = number independent colonisations island, N = number species island","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_age_diversity.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Plot clade age against clade diversity. — DAISIE_plot_age_diversity","text":"Valente, L.M., .B. Phillimore R.S. Etienne (2015). Equilibrium non-equilibrium dynamics simultaneously operate Galapagos islands. Ecology Letters 18: 844-852.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_age_diversity.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Plot clade age against clade diversity. — DAISIE_plot_age_diversity","text":"Luis Valente","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_age_diversity.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot clade age against clade diversity. — DAISIE_plot_age_diversity","text":"","code":"### Plot Galapagos age-diversity for Galapagos dataset utils::data(Galapagos_datalist) DAISIE_plot_age_diversity(Galapagos_datalist)"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_area.html","id":null,"dir":"Reference","previous_headings":"","what":"Plots island area function through time — DAISIE_plot_area","title":"Plots island area function through time — DAISIE_plot_area","text":"Plots island area function time","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_area.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plots island area function through time — DAISIE_plot_area","text":"","code":"DAISIE_plot_area(   total_time,   area_pars,   peak,   island_ontogeny = \"beta\",   resolution,   sea_level = \"const\" )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_area.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plots island area function through time — DAISIE_plot_area","text":"total_time Numeric defining length simulation time units. area_pars named list containing area sea level parameters created create_area_pars(): [1]: maximum area [2]: current area [3]: value 0 1 indicating island's history   peak area achieved [4]: total island age [5]: amplitude area fluctuation sea level [6]: frequency sine wave area change sea level [7]: angle slope island peak numeric value specifying peakiness (shaprness) ontogeny curve. Higher values imply peakier ontogeny. value internally calculated calc_peak() given area present area_pars. island_ontogeny DAISIE_sim_time_dep(), DAISIE_ML_CS plotting string describing type island ontogeny. Can \"const\", \"beta\" beta function describing area time.  functions numeric describing type island ontogeny. Can 0 constant, 1 beta function describing area time. ML functions island_ontogeny = NA assumes constant ontogeny. Time dependent estimation yet available development still ongoing. return error called case. resolution numeric indicating resolution plot. < 0. sea_level DAISIE_sim_time_dep() plotting string describing type sea level. Can \"const\" \"sine\" sine function describing area time.  functions numeric describing type sea level. Can 0 constant, 1 sine function describing area time.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_area.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plots island area function through time — DAISIE_plot_area","text":"plot area size time","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_cladogenesis.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot cladogenesis rate through time — DAISIE_plot_cladogenesis","title":"Plot cladogenesis rate through time — DAISIE_plot_cladogenesis","text":"Plot cladogenesis rate time","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_cladogenesis.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot cladogenesis rate through time — DAISIE_plot_cladogenesis","text":"","code":"DAISIE_plot_cladogenesis(   total_time,   K,   area_pars,   peak,   lac,   island_ontogeny = \"beta\",   sea_level = \"const\",   hyper_pars = NULL,   removed_timepoints,   resolution )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_cladogenesis.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot cladogenesis rate through time — DAISIE_plot_cladogenesis","text":"total_time Numeric defining length simulation time units. K numeric carrying capacity. area_pars named list containing area sea level parameters created create_area_pars(): [1]: maximum area [2]: current area [3]: value 0 1 indicating island's history   peak area achieved [4]: total island age [5]: amplitude area fluctuation sea level [6]: frequency sine wave area change sea level [7]: angle slope island peak numeric value specifying peakiness (shaprness) ontogeny curve. Higher values imply peakier ontogeny. value internally calculated calc_peak() given area present area_pars. lac numeric per capita cladogenesis rate. island_ontogeny DAISIE_sim_time_dep(), DAISIE_ML_CS plotting string describing type island ontogeny. Can \"const\", \"beta\" beta function describing area time.  functions numeric describing type island ontogeny. Can 0 constant, 1 beta function describing area time. ML functions island_ontogeny = NA assumes constant ontogeny. Time dependent estimation yet available development still ongoing. return error called case. sea_level DAISIE_sim_time_dep() plotting string describing type sea level. Can \"const\" \"sine\" sine function describing area time.  functions numeric describing type sea level. Can 0 constant, 1 sine function describing area time. hyper_pars named list numeric hyperparameters rate calculations returned create_hyper_pars(): [1]: d scaling parameter exponent calculating   cladogenesis rate [2]: x exponent calculating extinction rate removed_timepoints Positive integer number first datapoints removed rate plots (prevent Inf) resolution numeric indicating resolution plot. < 0.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_cladogenesis.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot cladogenesis rate through time — DAISIE_plot_cladogenesis","text":"plot per capita cladogenesis rate time dataframe immigration corresponding time","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_cladogenesis.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Plot cladogenesis rate through time — DAISIE_plot_cladogenesis","text":"Pedro Neves","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_extinction.html","id":null,"dir":"Reference","previous_headings":"","what":"Plots extinction rate function through time — DAISIE_plot_extinction","title":"Plots extinction rate function through time — DAISIE_plot_extinction","text":"Plots extinction rate function time","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_extinction.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plots extinction rate function through time — DAISIE_plot_extinction","text":"","code":"DAISIE_plot_extinction(   total_time,   area_pars,   peak,   mu,   hyper_pars,   island_ontogeny = \"beta\",   sea_level = \"const\",   removed_timepoints,   resolution,   extcutoff = 1000 )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_extinction.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plots extinction rate function through time — DAISIE_plot_extinction","text":"total_time Numeric defining length simulation time units. area_pars named list containing area sea level parameters created create_area_pars(): [1]: maximum area [2]: current area [3]: value 0 1 indicating island's history   peak area achieved [4]: total island age [5]: amplitude area fluctuation sea level [6]: frequency sine wave area change sea level [7]: angle slope island peak numeric value specifying peakiness (shaprness) ontogeny curve. Higher values imply peakier ontogeny. value internally calculated calc_peak() given area present area_pars. mu numeric per capita extinction rate. hyper_pars named list numeric hyperparameters rate calculations returned create_hyper_pars(): [1]: d scaling parameter exponent calculating   cladogenesis rate [2]: x exponent calculating extinction rate island_ontogeny DAISIE_sim_time_dep(), DAISIE_ML_CS plotting string describing type island ontogeny. Can \"const\", \"beta\" beta function describing area time.  functions numeric describing type island ontogeny. Can 0 constant, 1 beta function describing area time. ML functions island_ontogeny = NA assumes constant ontogeny. Time dependent estimation yet available development still ongoing. return error called case. sea_level DAISIE_sim_time_dep() plotting string describing type sea level. Can \"const\" \"sine\" sine function describing area time.  functions numeric describing type sea level. Can 0 constant, 1 sine function describing area time. removed_timepoints Positive integer number first datapoints removed rate plots (prevent Inf) resolution numeric indicating resolution plot. < 0. extcutoff numeric cutoff maximum extinction rate preventing large slowing simulation.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_extinction.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plots extinction rate function through time — DAISIE_plot_extinction","text":"per capita extinction rate time plot dataframe extinction corresponding time","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_extinction.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Plots extinction rate function through time — DAISIE_plot_extinction","text":"Pedro Neves","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_immigration.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot immigration rate through time — DAISIE_plot_immigration","title":"Plot immigration rate through time — DAISIE_plot_immigration","text":"Plot immigration rate time","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_immigration.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot immigration rate through time — DAISIE_plot_immigration","text":"","code":"DAISIE_plot_immigration(   total_time,   K,   area_pars,   gam,   peak,   mainland_n,   hyper_pars = NULL,   island_ontogeny = \"beta\",   sea_level = \"const\",   removed_timepoints,   resolution )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_immigration.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot immigration rate through time — DAISIE_plot_immigration","text":"total_time Numeric defining length simulation time units. K numeric carrying capacity. area_pars named list containing area sea level parameters created create_area_pars(): [1]: maximum area [2]: current area [3]: value 0 1 indicating island's history   peak area achieved [4]: total island age [5]: amplitude area fluctuation sea level [6]: frequency sine wave area change sea level [7]: angle slope island gam numeric per capita immigration rate. peak numeric value specifying peakiness (shaprness) ontogeny curve. Higher values imply peakier ontogeny. value internally calculated calc_peak() given area present area_pars. mainland_n numeric stating number mainland species, number species can potentially colonize island. using clade-specific diversity dependence, value set 1. using island-wide diversity dependence, value set number mainland species. hyper_pars named list numeric hyperparameters rate calculations returned create_hyper_pars(): [1]: d scaling parameter exponent calculating   cladogenesis rate [2]: x exponent calculating extinction rate island_ontogeny DAISIE_sim_time_dep(), DAISIE_ML_CS plotting string describing type island ontogeny. Can \"const\", \"beta\" beta function describing area time.  functions numeric describing type island ontogeny. Can 0 constant, 1 beta function describing area time. ML functions island_ontogeny = NA assumes constant ontogeny. Time dependent estimation yet available development still ongoing. return error called case. sea_level DAISIE_sim_time_dep() plotting string describing type sea level. Can \"const\" \"sine\" sine function describing area time.  functions numeric describing type sea level. Can 0 constant, 1 sine function describing area time. removed_timepoints Positive integer number first datapoints removed rate plots (prevent Inf) resolution numeric indicating resolution plot. < 0.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_immigration.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot immigration rate through time — DAISIE_plot_immigration","text":"plot per capita immigration rate time dataframe immigration corresponding time","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_immigration.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Plot immigration rate through time — DAISIE_plot_immigration","text":"Pedro Neves","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_input.html","id":null,"dir":"Reference","previous_headings":"","what":"DAISIE tree plot — DAISIE_plot_input","title":"DAISIE tree plot — DAISIE_plot_input","text":"Shows phylogenies multiple clades present island","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_input.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"DAISIE tree plot — DAISIE_plot_input","text":"","code":"DAISIE_plot_input(   trees,   age = NULL,   tcols = NULL,   metadata = NULL,   mapping = NULL,   xlen = 0.001,   pargs = NULL,   bckgd = \"white\" )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_input.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"DAISIE tree plot — DAISIE_plot_input","text":"trees list trees, phylo format, named respective clades age age island, scale branch lengths trees. unspecified, depth deepest stem across trees. tcols vector colonization times, one value per clade. Order must `trees`. unspecified, clades assigned age island colonization time. metadata Optional data frame clade-level metadata. One column must named \"clade\". mapping Optional aesthetic mapping apply trees, returned `ggplot2::aes` function. Mapped variables can anything columns `data` node-wise data frame associated `ggtree` plot created (e.g. node, label, clade, mrca) anything columns clade-wise `metadata`, provided (case aesthetics mapped nodes within clade). xlen Length extra tips grafted tree island age. hack scaling plot. Keep value small. pargs Optional arguments passed `geom_point` plotting points colonization events (e.g. size, shape...). bckgd Optional background color figure. use rectangles hack hide tree branches prior island colonization. Default white background.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_input.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"DAISIE tree plot — DAISIE_plot_input","text":"`ggtree` plot, also `ggplot` object. output fully customizable, `ggplot` object.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_input.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"DAISIE tree plot — DAISIE_plot_input","text":"Raphael Scherrer (github.com/rscherrer)","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_input.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"DAISIE tree plot — DAISIE_plot_input","text":"","code":"# check whether package tibble has been installed  if (!requireNamespace('tibble', quietly = TRUE)) {     cat(\"Package tibble needed for this function to work. Please install it.\")  } else {  set.seed(42)   # Random trees  t1 <- ape::rtree(10)  t1$tip.label <- gsub(\"t\", \"t1.\", t1$tip.label)  t2 <- ape::rtree(3)  t2$tip.label <- gsub(\"t\", \"t2.\", t2$tip.label)  t3 <- ape::rtree(2)  trees <- list(t1, t2, t3)  names(trees) <- c(\"A\", \"B\", \"C\")   # Toy colonization events for each clade  tcols <- c(4.5, 5, 4.6)   # Toy metadata  metadata <- tibble::tibble(    clade = names(trees),    endemic = TRUE,  # whether each clade is endemic    uncertain = FALSE  # whether colonization time is known for sure  )  metadata$endemic[3] <- FALSE  metadata$uncertain[2] <- TRUE   # Island age  age <- 5   # Make a plot  p <- DAISIE_plot_input(    trees,    age,    tcols,    metadata,    mapping = ggplot2::aes(color = endemic, linetype = uncertain),    pargs = list(size = 3)  ) p } #> Scale for y is already present. #> Adding another scale for y, which will replace the existing scale. #> Joining with `by = join_by(label)` #> Warning: Removed 1 row containing missing values or values outside the scale range #> (`geom_point()`)."},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_island.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot colonisation and branching time of species found on an island dataset. — DAISIE_plot_island","title":"Plot colonisation and branching time of species found on an island dataset. — DAISIE_plot_island","text":"Produces image times colonisation, branching times, clade name clade status clades found given dataset.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_island.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot colonisation and branching time of species found on an island dataset. — DAISIE_plot_island","text":"","code":"DAISIE_plot_island(island, island_age = NA)"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_island.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot colonisation and branching time of species found on an island dataset. — DAISIE_plot_island","text":"island Island data object. Can DAISIE list format (see Galapagos_datalist DAISIE_data_prep examples) table format (see Galapagos_datatable example). island_age Age island appropriate units. DAISIE_plot_age_diversity() DAISIE_plot_island() island input table format, age island must specified. island input DAISIE list format, option override island age specified island list.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_island.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot colonisation and branching time of species found on an island dataset. — DAISIE_plot_island","text":"R plot.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_island.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Plot colonisation and branching time of species found on an island dataset. — DAISIE_plot_island","text":"R plot showing clade island object: time colonisation, branching times, species status (endemic non-endemic), total number species clade (n), number species sampled (m).","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_island.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Plot colonisation and branching time of species found on an island dataset. — DAISIE_plot_island","text":"Valente, L.M., .B. Phillimore R.S. Etienne (2015). Equilibrium non-equilibrium dynamics simultaneously operate Galapagos islands. Ecology Letters 18: 844-852.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_island.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Plot colonisation and branching time of species found on an island dataset. — DAISIE_plot_island","text":"Luis Valente","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_island.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot colonisation and branching time of species found on an island dataset. — DAISIE_plot_island","text":"","code":"### Plot Galapagos islands dataset from data table (specify island age)  utils::data(Galapagos_datatable) DAISIE_plot_island(Galapagos_datatable, island_age=4) #> Colonisation time of 7.456 for Coccyzus is older than island age #> Colonisation time of 10.285 for Pyrocephalus is older than island age   ### Plot Galapagos islands dataset from datalist (no need to specify ## island age) utils::data(Galapagos_datalist) DAISIE_plot_island(Galapagos_datalist)"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_pc_rates.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot per capita STT and per-capita rate change thourgh simulation — DAISIE_plot_pc_rates","title":"Plot per capita STT and per-capita rate change thourgh simulation — DAISIE_plot_pc_rates","text":"Plot per capita STT per-capita rate change thourgh simulation","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_pc_rates.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot per capita STT and per-capita rate change thourgh simulation — DAISIE_plot_pc_rates","text":"","code":"DAISIE_plot_pc_rates(   total_time,   pars,   island_ontogeny,   sea_level = \"const\",   area_pars,   peak,   hyper_pars,   mainland_n = 1000,   resolution = 0.001,   simulation_outputs = NULL )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_pc_rates.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot per capita STT and per-capita rate change thourgh simulation — DAISIE_plot_pc_rates","text":"total_time Numeric defining length simulation time units. pars numeric vector containing model parameters: pars[1]: lambda^c (cladogenesis rate) pars[2]: mu (extinction rate) pars[3]: K (carrying capacity), set K=Inf diversity   independence. pars[4]: gamma (immigration rate) pars[5]: lambda^(anagenesis rate) pars[6]: lambda^c (cladogenesis rate) either type 2 species   rate set 2 rate shift model pars[7]: mu (extinction rate) either type 2 species rate   set 2 rate shift model pars[8]: K (carrying capacity) either type 2 species rate   set 2 rate shift model, set K=Inf diversity independence. pars[9]: gamma (immigration rate) either type 2 species   rate set 2 rate shift model pars[10]: lambda^(anagenesis rate) either type 2   species rate set 2 rate shift model Elements 6:10 required type 2 species included rate shift model. DAISIE_sim_relaxed_rate() pars[6] standard deviation gamma distribution relaxed parameter parameter chosen relaxed_par argument mean gamma distribution relaxed parameter. island_ontogeny DAISIE_sim_time_dep(), DAISIE_ML_CS plotting string describing type island ontogeny. Can \"const\", \"beta\" beta function describing area time.  functions numeric describing type island ontogeny. Can 0 constant, 1 beta function describing area time. ML functions island_ontogeny = NA assumes constant ontogeny. Time dependent estimation yet available development still ongoing. return error called case. sea_level DAISIE_sim_time_dep() plotting string describing type sea level. Can \"const\" \"sine\" sine function describing area time.  functions numeric describing type sea level. Can 0 constant, 1 sine function describing area time. area_pars named list containing area sea level parameters created create_area_pars(): [1]: maximum area [2]: current area [3]: value 0 1 indicating island's history   peak area achieved [4]: total island age [5]: amplitude area fluctuation sea level [6]: frequency sine wave area change sea level [7]: angle slope island peak numeric value specifying peakiness (shaprness) ontogeny curve. Higher values imply peakier ontogeny. value internally calculated calc_peak() given area present area_pars. hyper_pars named list numeric hyperparameters rate calculations returned create_hyper_pars(): [1]: d scaling parameter exponent calculating   cladogenesis rate [2]: x exponent calculating extinction rate mainland_n numeric stating number mainland species, number species can potentially colonize island. using clade-specific diversity dependence, value set 1. using island-wide diversity dependence, value set number mainland species. resolution numeric indicating resolution plot. < 0. simulation_outputs list matrices vectors simulation produced DAISIE_sim functions.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_pc_rates.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot per capita STT and per-capita rate change thourgh simulation — DAISIE_plot_pc_rates","text":"composite plot containing STT plot, variation area, extinction rate, cladogenesis rate immigration rate","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_pc_rates.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Plot per capita STT and per-capita rate change thourgh simulation — DAISIE_plot_pc_rates","text":"Pedro Neves","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_sims.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot island species-through-time (STT) plots — DAISIE_plot_sims","title":"Plot island species-through-time (STT) plots — DAISIE_plot_sims","text":"Produces STT plots. one type species present simulated islands, STT plotted species. two types present, three plots produced: STT , STT type 1 STT type 2. R plots number total, endemic non-endemic STTs different types species entire time span islands simulated. 2.5-97.5th percentiles plotted light grey, 25-75th percentiles plotted dark grey.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_sims.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot island species-through-time (STT) plots — DAISIE_plot_sims","text":"","code":"DAISIE_plot_sims(   island_replicates,   plot_plus_one = TRUE,   type = \"all_species\",   sample_freq = 25,   trait_pars = NULL )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_sims.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot island species-through-time (STT) plots — DAISIE_plot_sims","text":"island_replicates List output DAISIE_sim_core_cr(), DAISIE_sim_core_time_dep(), DAISIE_sim_core_cr_shift() DAISIE_sim_min_type2() functions. Minimally, must list many elements replicates. element must list elements island_age, not_present stt_all. stt_all must data frame column names Time, nI, nA, nC present. plot_plus_one Boolean indicate plot values plus one. Set TRUE default behavior. Set FALSE plot values without adding one. works one type species. type String indicate stt species possible stt plotted. Default \"all_species\", \"type1_species\" \"type2_species\" plotted. sample_freq Numeric specifing number units times divided plotting purposes. Larger values lead plots higher resolution, also run slower. trait_pars named list containing diversification rates considering   two trait states created create_trait_pars: [1]:numeric per capita transition rate state1 [2]:numeric per capita immigration rate state2 [3]:numeric per capita extinction rate state2 [4]:numeric per capita anagenesis rate state2 [5]:numeric per capita cladogenesis rate state2 [6]:numeric per capita transition rate state2 [7]:numeric number species trait state 2    mainland","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_sims.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot island species-through-time (STT) plots — DAISIE_plot_sims","text":"R plot.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_sims.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Plot island species-through-time (STT) plots — DAISIE_plot_sims","text":"Valente, L.M., .B. Phillimore R.S. Etienne (2015). Equilibrium non-equilibrium dynamics simultaneously operate Galapagos islands. Ecology Letters 18: 844-852.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_sims.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Plot island species-through-time (STT) plots — DAISIE_plot_sims","text":"Luis Valente","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_sims.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot island species-through-time (STT) plots — DAISIE_plot_sims","text":"","code":"### Plot islands with single process (only one type of species) utils::data(islands_1type_1000reps) DAISIE_plot_sims(   island_replicates = islands_1type_1000reps   )    ### Plot island with type 1 and type 2 utils::data(islands_2types_1000reps) DAISIE_plot_sims(   island_replicates = islands_2types_1000reps   )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_stt.html","id":null,"dir":"Reference","previous_headings":"","what":"Create the Species-Through-Time plot. This is used to visualize the output of DAISIE_sim functions — DAISIE_plot_stt","title":"Create the Species-Through-Time plot. This is used to visualize the output of DAISIE_sim functions — DAISIE_plot_stt","text":"Create Species--Time plot. used visualize output DAISIE_sim functions","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_stt.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create the Species-Through-Time plot. This is used to visualize the output of DAISIE_sim functions — DAISIE_plot_stt","text":"","code":"DAISIE_plot_stt(   plot_plus_one = TRUE,   time,   plot_lists = plot_lists,   type = type )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_plot_stt.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create the Species-Through-Time plot. This is used to visualize the output of DAISIE_sim functions — DAISIE_plot_stt","text":"plot_plus_one Boolean indicate plot values plus one. Set TRUE default behavior. Set FALSE plot values without adding one. works one type species. time Numeric defining length simulation time units. example, island known 4 million years old, setting time = 4 simulate entire life span island; setting time = 2 stop simulation mid-life island. plot_lists List lists containing average quantile species time. type String indicate stt species possible stt plotted. Default \"all_species\", \"type1_species\" \"type2_species\" plotted.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_probdist.html","id":null,"dir":"Reference","previous_headings":"","what":"The joint distribution of endemics and non-endemics under the DAISIE model — DAISIE_probdist","title":"The joint distribution of endemics and non-endemics under the DAISIE model — DAISIE_probdist","text":"function calculates joint distribution number endemics non-endemics given set parameter values, given mainland species pool size given set times","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_probdist.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The joint distribution of endemics and non-endemics under the DAISIE model — DAISIE_probdist","text":"","code":"DAISIE_probdist(pars1, pars2, tvec, initEI = c(0, 0), initprobs = NULL)"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_probdist.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The joint distribution of endemics and non-endemics under the DAISIE model — DAISIE_probdist","text":"pars1 Vector model parameters: pars1[1] corresponds lambda^c (cladogenesis rate) pars1[2] corresponds mu (extinction rate) pars1[3] corresponds K (clade-level carrying capacity) pars1[4] corresponds gamma (immigration rate) pars1[5] corresponds lambda^(anagenesis rate). pars2 Vector settings: pars2[1] corresponds res, maximum number endemics non-endemics ODE system solved; must much larger actual number probability needs calculated.) pars2[2] corresponds M, size mainland pool, .e number species can potentially colonize island. tvec times probabilities need computed. initEI initial values number endemics   non-endemics. DAISIE_probdist() DAISIE_margprobdist() either initprobs must NULL. DAISIE_numcol() NULL, assumed island   empty. initprobs initial probability distribution number endemics non-endemics; either initEI must NULL.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_probdist.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The joint distribution of endemics and non-endemics under the DAISIE model — DAISIE_probdist","text":"matrix dimensions 1 + length(tvec) pars[2]^2 + 1] first column contains times probabilities evaluated columns contain joint probabilities.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_probdist.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"The joint distribution of endemics and non-endemics under the DAISIE model — DAISIE_probdist","text":"obtain matrix probabilities endemics rows non-endemics columns certain time, one can run DAISIE_convertprobdist","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_probdist.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"The joint distribution of endemics and non-endemics under the DAISIE model — DAISIE_probdist","text":"Valente, L.M., .B. Phillimore R.S. Etienne (2015). Equilibrium non-equilibrium dynamics simultaneously operate Galapagos islands. Ecology Letters 18: 844-852.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_probdist.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"The joint distribution of endemics and non-endemics under the DAISIE model — DAISIE_probdist","text":"Rampal S. Etienne","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_probdist.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"The joint distribution of endemics and non-endemics under the DAISIE model — DAISIE_probdist","text":"","code":"### Compute the probability distribution at t = 4 and t = 8, for a mainland pool # size of 250 potential colonists and a vector of 5 parameters (cladogenesis, # extinction, clade-level carrying capacity, immigration, anagenesis) starting # from an empty island  prob_dists <- DAISIE_probdist(    pars1 = c(0.3,0.35,Inf,0.75,0.012),    pars2 = c(100,250),    tvec = c(4,8),    initEI = c(0,0),    initprobs = NULL    )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sample_event_cr.html","id":null,"dir":"Reference","previous_headings":"","what":"Samples what event to happen next — DAISIE_sample_event_cr","title":"Samples what event to happen next — DAISIE_sample_event_cr","text":"Samples event happen next","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sample_event_cr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Samples what event to happen next — DAISIE_sample_event_cr","text":"","code":"DAISIE_sample_event_cr(rates)"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sample_event_cr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Samples what event to happen next — DAISIE_sample_event_cr","text":"rates named list numeric rates returned update_rates().","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sample_event_cr.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Samples what event to happen next — DAISIE_sample_event_cr","text":"numeric indicating event happen, supposed event happen timesteps ontogeny algorithm. [1]: immigration event [2]: extinction event [3]: cladogenesis event [4]: anagenesis event","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sample_event_cr.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Samples what event to happen next — DAISIE_sample_event_cr","text":"Pedro Neves","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sample_event_time_dep.html","id":null,"dir":"Reference","previous_headings":"","what":"Samples what event to happen next — DAISIE_sample_event_time_dep","title":"Samples what event to happen next — DAISIE_sample_event_time_dep","text":"Samples event happen next","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sample_event_time_dep.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Samples what event to happen next — DAISIE_sample_event_time_dep","text":"","code":"DAISIE_sample_event_time_dep(max_rates)"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sample_event_time_dep.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Samples what event to happen next — DAISIE_sample_event_time_dep","text":"max_rates named list numeric max rates returned update_max_rates().","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sample_event_time_dep.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Samples what event to happen next — DAISIE_sample_event_time_dep","text":"numeric indicating event happen, supposed event happen timesteps ontogeny algorithm. [1]: immigration event [2]: extinction event [3]: cladogenesis event [4]: anagenesis event","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sample_event_time_dep.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Samples what event to happen next — DAISIE_sample_event_time_dep","text":"Pedro Neves","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sample_event_trait_dep.html","id":null,"dir":"Reference","previous_headings":"","what":"Samples what event to happen next — DAISIE_sample_event_trait_dep","title":"Samples what event to happen next — DAISIE_sample_event_trait_dep","text":"Samples event happen next","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sample_event_trait_dep.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Samples what event to happen next — DAISIE_sample_event_trait_dep","text":"","code":"DAISIE_sample_event_trait_dep(rates)"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sample_event_trait_dep.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Samples what event to happen next — DAISIE_sample_event_trait_dep","text":"rates named list numeric rates returned update_rates().","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sample_event_trait_dep.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Samples what event to happen next — DAISIE_sample_event_trait_dep","text":"numeric indicating event happen, supposed event happen timesteps ontogeny algorithm. [1]: immigration event trait1 [2]: extinction event trait1 [3]: cladogenesis event trait1 [4]: anagenesis event trait1 [5]: transition event trait1 [6]: immigration event trait2 [7]: extinction event trait2 [8]: cladogenesis event trait2 [9]: anagenesis event trait2 [10]: transition event trait2","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sample_event_trait_dep.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Samples what event to happen next — DAISIE_sample_event_trait_dep","text":"Shu Xie","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim.html","id":null,"dir":"Reference","previous_headings":"","what":"Simulate (non-)oceanic islands with given parameters under time-constant rates — DAISIE_sim","title":"Simulate (non-)oceanic islands with given parameters under time-constant rates — DAISIE_sim","text":"function simulates islands given cladogenesis, extinction, Kprime, immigration anagenesis parameters, modelled time-constant parameters. single parameter set provided (5 parameters) simulates islands species macro-evolutionary process. two paramater sets (10 parameters) provided, simulates islands two different macro-evolutionary processes operate, one applying type 1 species type 2 species. , allows simulation non-oceanic islands, generating islands starting condition includes potential endemic non-endemic species.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulate (non-)oceanic islands with given parameters under time-constant rates — DAISIE_sim","text":"","code":"DAISIE_sim_cr(   time,   M,   pars,   replicates,   divdepmodel = \"CS\",   nonoceanic_pars = c(0, 0),   num_guilds = NULL,   prop_type2_pool = NA,   replicates_apply_type2 = TRUE,   sample_freq = 25,   plot_sims = TRUE,   hyper_pars = create_hyper_pars(d = 0, x = 0),   area_pars = create_area_pars(max_area = 1, current_area = 1, proportional_peak_t = 0,     total_island_age = 0, sea_level_amplitude = 0, sea_level_frequency = 0,     island_gradient_angle = 0),   cond = 0,   verbose = TRUE,   ... )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulate (non-)oceanic islands with given parameters under time-constant rates — DAISIE_sim","text":"time Numeric defining length simulation time units. example, island known 4 million years old, setting time = 4 simulate entire life span island; setting time = 2 stop simulation mid-life island. M Numeric defining size mainland pool, .e. number species can potentially colonize island. pars numeric vector containing model parameters: pars[1]: lambda^c (cladogenesis rate) pars[2]: mu (extinction rate) pars[3]: K (carrying capacity), set K=Inf diversity   independence. pars[4]: gamma (immigration rate) pars[5]: lambda^(anagenesis rate) pars[6]: lambda^c (cladogenesis rate) either type 2 species   rate set 2 rate shift model pars[7]: mu (extinction rate) either type 2 species rate   set 2 rate shift model pars[8]: K (carrying capacity) either type 2 species rate   set 2 rate shift model, set K=Inf diversity independence. pars[9]: gamma (immigration rate) either type 2 species   rate set 2 rate shift model pars[10]: lambda^(anagenesis rate) either type 2   species rate set 2 rate shift model Elements 6:10 required type 2 species included rate shift model. DAISIE_sim_relaxed_rate() pars[6] standard deviation gamma distribution relaxed parameter parameter chosen relaxed_par argument mean gamma distribution relaxed parameter. replicates Integer specifying number island replicates simulated. divdepmodel Option divdepmodel = 'CS' runs model clade-specific carrying capacity, diversity-dependence operates within single clades, .e. among species originating mainland colonist. Option divdepmodel = 'IW' runs model island-wide carrying capacity, diversity-dependence operates within among clades. Option divdepmodel = 'GW' runs model diversity-dependence operates within guild. nonoceanic_pars vector length two : [1]: probability sampling species mainland [2]: probability species sampled mainland   nonendemic num_guilds number guilds mainland. number mainland species divided number guilds divdepmodel = \"GW\" prop_type2_pool Fraction mainland species belongs second subset species (type 2). Applies two types species simulated (length(pars) = 10). DAISIE_dataprep() applies number_clade_types = 2.  DAISIE_dataprep() default \"proportional\" sets fraction proportional number clades distinct macroevolutionary process colonised island. replicates_apply_type2 Applies two types species simulated. Default replicates_apply_type2 = TRUE runs simulations number islands type 2 species colonised equal specified number replicates. recommended prop_type2_pool small rate immigration type two species (pars[9]) low, meaning replicates needed achieved adequate sample size islands type 2 species. Setting replicates_apply_type2 = FALSE simulates islands specified number replicates regardless whether type 2 species colonised . sample_freq Numeric specifing number units times divided plotting purposes. Larger values lead plots higher resolution, also run slower. plot_sims Default = TRUE plots species--time (STT) plots. detects many types species present. one type species present, STT plotted species. two types present, three plots produced: STT , STT type 1 STT type 2. hyper_pars named list numeric hyperparameters rate calculations returned create_hyper_pars(): [1]: d scaling parameter exponent calculating   cladogenesis rate [2]: x exponent calculating extinction rate area_pars named list containing area sea level parameters created create_area_pars(): [1]: maximum area [2]: current area [3]: value 0 1 indicating island's history   peak area achieved [4]: total island age [5]: amplitude area fluctuation sea level [6]: frequency sine wave area change sea level [7]: angle slope island cond cond = 0 : conditioning island age  cond = 1 : conditioning island age non-extinction island biota . cond > 1 : conditioning island age least cond colonizations island. last option yet available IW model verbose numeric vector length 1, simulations `DAISIEdataprep()` can `1` `0`, `1` gives intermediate output printed. ML functions numeric determining intermediate output printed. default: `0` print, `1` prints initial likelihood settings selected (parameters optimised, fixed shifted), `2` prints `1 also intermediate output parameters loglikelihood, `3` `2` prints intermediate progress likelihood computation. ... arguments pass plotting functions.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Simulate (non-)oceanic islands with given parameters under time-constant rates — DAISIE_sim","text":"list. highest level least corresponds individual replciate. first element replicate composed island information containing: $island_age: numeric island age. $not_present: number mainland lineages     present island. present 1 type species     simulated. Becomes $not_present_type1: number mainland     lineages type 1 present island     $not_present_type2: number mainland lineages type 2     present island, two types simulated. $stt_all: STT table species island     (nI - number non-endemic species; nA - number anagenetic species,     nC - number cladogenetic species, present - number independent     colonisations present) $stt_stt_type1: STT table type 1 species island -     2 types species simulated (nI - number non-endemic     species; nA - number anagenetic species, nC - number cladogenetic     species, present - number independent colonisations present). $stt_stt_type2: STT table type 2 species island      - 2 types species simulated (nI - number non-endemic      species; nA - number anagenetic species, nC - number cladogenetic      species, present - number independent colonisations present ). $brts_table: simulations \"IW\". Table containing information order events data, use maximum likelihood optimization.). subsequent elements list pertaining replcate contain information single colonist lineage island 4 components: $branching_times: island age stem age     population/species case Non-endemic, Non-endemic_MaxAge     Endemic anagenetic species.    cladogenetic species     island age branching times radiation including     stem age radiation. $stac: integer ranging 1 4   indicating status colonist: Non_endemic_MaxAge Endemic Endemic&Non_Endemic Non_endemic_MaxAge $missing_species: number island species sampled particular clade (applicable endemic clades) $type_1or2: whether colonist belongs type 1 type 2","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Simulate (non-)oceanic islands with given parameters under time-constant rates — DAISIE_sim","text":"Valente, L.M., .B. Phillimore R.S. Etienne (2015). Equilibrium non-equilibrium dynamics simultaneously operate Galapagos islands. Ecology Letters 18: 844-852.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Simulate (non-)oceanic islands with given parameters under time-constant rates — DAISIE_sim","text":"Luis Valente, Albert Phillimore, Joshua Lambert, Shu Xie, Pedro Neves, Richèl J. C. Bilderbeek, Rampal Etienne","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Simulate (non-)oceanic islands with given parameters under time-constant rates — DAISIE_sim","text":"","code":"## Simulate 2 islands for 1 million years, where all species have equal ## rates. Pool size 100.  clado_rate <- 0.5 ext_rate <- 0.2 carr_cap <- Inf immig_rate <- 0.05 ana_rate <- 1 sim_pars <- c(clado_rate, ext_rate, carr_cap, immig_rate, ana_rate) set.seed(1) island_replicates <- DAISIE_sim_cr(   time = 1,   M = 100,   pars = sim_pars,   replicates = 2,   plot_sims = FALSE,   verbose = FALSE )  ## Simulate 2 islands for 1 million years with two types of species (type1 ## and type 2). Pool size 100 ## Fraction of type 2 species in source pool is 0.15. Function will ## simulate until number of islands where type 2 species has colonised is ## equal to number specified in replicates.  clado_rate <- 0.5 ext_rate <- 0.2 carr_cap <- Inf immig_rate <- 0.005 ana_rate <- 1 sim_pars_type1 <- c(clado_rate, ext_rate, carr_cap, immig_rate, ana_rate) sim_pars_type2 <- sim_pars_type1 * 2 set.seed(1) island_replicates_2types <- DAISIE_sim_cr(   time = 1,   M = 100,   pars = c(sim_pars_type1, sim_pars_type2),   replicates = 2,   prop_type2_pool = 0.15,   plot_sims = FALSE,   verbose = FALSE ) ## Simulate two non-oceanic island for 1 million years. ## Pool size 500. Island area as a proportion ## of mainland is 0.1, proportion of native species is 0.9. clado_rate <- 0.5 ext_rate <- 0.2 carr_cap <- Inf immig_rate <- 0.005 ana_rate <- 1 sim_pars <- c(clado_rate, ext_rate, carr_cap, immig_rate, ana_rate) set.seed(1) island_replicates <- DAISIE_sim_cr(   time = 1,   M = 500,   pars = sim_pars,   replicates = 2,   nonoceanic_pars = c(0.1, 0.9),   plot_sims = FALSE,   verbose = FALSE )  ## Simulate 2 islands for 1 million years with a shift in immigration rate ## at 0.195 Ma, and plot the species-through-time plot. Pool size 296.  pars_before_shift <- c(0.079, 0.973, Inf, 0.136, 0.413) pars_after_shift <- c(0.079, 0.973, Inf, 0.652, 0.413) tshift <- 0.195 set.seed(1) island_shift_replicates <- DAISIE_sim_cr_shift(   time = 1,   M = 296,   pars = c(pars_before_shift, pars_after_shift),   replicates = 2,   shift_times = tshift,   plot_sims = FALSE,   verbose = FALSE )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_MW.html","id":null,"dir":"Reference","previous_headings":"","what":"Simulate multiple islands based on hyperparameters that describe relationships between area, isolation and local parameters — DAISIE_sim_MW","title":"Simulate multiple islands based on hyperparameters that describe relationships between area, isolation and local parameters — DAISIE_sim_MW","text":"function simulates islands given age, area isolation. list islands/archipelagos information provided data frame object (example, archipelago_data Valente et al 2020 Nature). island, local parameters first calculated based hyperparameters describing dependency rates island area isolation. Simulations run island, island birth given island age based local parameters island (using DAISIE_sim function). Returns R list object contains simulated islands.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_MW.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulate multiple islands based on hyperparameters that describe relationships between area, isolation and local parameters — DAISIE_sim_MW","text":"","code":"DAISIE_sim_MW(   archipelago_data,   M,   pars,   replicates,   divdepmodel = \"CS\",   distance_dep = \"power\",   cladogenesis_dep = \"NULL\",   sigmoidal_par = \"NULL\" )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_MW.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulate multiple islands based on hyperparameters that describe relationships between area, isolation and local parameters — DAISIE_sim_MW","text":"archipelago_data Object (data.frame) containing table columns following names: Archipelago: names archipelagos islands simulated; Area - area archipelago/island; Age: Age oldest island archipelago, age island single island. Distance - distance mainland (applicable isolation metric). example, dataset Valente et al 2020 41 archipelagos provided data(archipelago_data). M size mainland pool, .e number species can potentially colonize island(s). pars Contains model hyperparameters: pars[1] corresponds lambda^c0 (initial cladogenesis rate) pars[2] corresponds y (dependency cladogenesis area) 0 - dependency, positive value - cladogenesis increases area, negative value - cladogenesis decreases area pars[3] corresponds mu_0 (initial extinction rate) pars[4] corresponds x (dependency extinction area) 0 - dependency, positive value - extinction increases area, negative value - extinction decreases area. pars[5] corresponds K_0  (initial carrying capacity). Set K=Inf non-diversity dependence. pars[6] corresponds z (dependency K area). 0 - dependency, positive value - K increases area, negative value - K decreases area. pars[7] corresponds gamma_0 (initial immigration rate) pars[8] corresponds alpha (dependency immigration island isolation). 0 - dependency, positive value - immigration increases distance, negative value - immigration decreases distance pars[9] corresponds lambda^a_0 (initial anagenesis rate) pars[10] corresponds beta (dependency anagenesis island isolation). 0 - dependency,positive value - anagenesis increases distance, negative value - anagenesis decreases distance. pars[11] corresponds d0, parameter describes interactive/additive effect isolation area cladogenesis (power models); describes shape sigmoidal relationship isolation parameter (sigmoidal models). replicates Number island replicates simulated per island table archipelago_data. 5 islands archipelago_data, number replicates set 10, 50 islands simulated. divdepmodel Option divdepmodel = 'CS' runs model clade-specific carrying capacity, diversity-dependence operates within single clades, .e. among species originating mainland colonist. Option divdepmodel = 'IW' runs model island-wide carrying capacity, diversity-dependence operates within among clades. distance_dep Shape dependency parameter distance. Can type  'power' type  'sigmoidal'. cladogenesis_dep distance_dep = 'power' specified, cladogenesis_dep specifies type effect area isolation cladogenesis. possible options :  'NULL' (additive interactive effect area isolation, models M1-M14 Valente et al 2020)  'additive' (additive effect area isolation cladogenesis, model M15 Valente et al 2020)  'interactive' (interactive effect area isolation cladogenesis, models M16 M19 Valente et al 2020)  'interactive1' (interactive effect area isolation cladogenesis, model M17 Valente et al 2020)  'interactive2' (interactive effect area isolation cladogenesis, model M18 Valente et al 2020) sigmoidal_par distance_dep = 'sigmoidal', sigmoidal_par specifies parameter sigmoidal relationship distance applied. Options:  'cladogenesis' 'anagenesis'  'colonisation'.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_MW.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Simulate multiple islands based on hyperparameters that describe relationships between area, isolation and local parameters — DAISIE_sim_MW","text":"island listed rows archipelago_data, given number islands simulated depending number replicates specified. simulations island archipelago_data element list, can called using [[x]]. Individual replicates island can called [[x]][[x]] example object called global_sims, 1st replicate first island can called using global_sims[[1]][[1]]. 3rd replicate 4th island called global_sims[[4]][[3]] island replicates list . first (e.g. global_sims[[x]][[x]][[1]]) element list following components:  $island_age - island archipelago age $not_present - number mainland lineages present island $stt_all - STT table species archipelago/island (nI - number non-endemic species; nA - number anagenetic species, nC - number cladogenetic species, present - number independent colonisations present)  $area Area island archipelago  $distance Distance mainland  $name Name island archipelago subsequent elements list contain information single colonist lineage island 4 components: $branching_times - island age stem age population/species case Non-endemic, Non-endemic_MaxAge Endemic close extant relatives islands species. cladogenetic species island age branching times radiation including stem age radiation. $stac - status colonist  * Endemic: 2  * Endemic&Non_Endemic: 3  * Non_endemic: 4 $missing_species - number island species sampled particular clade (applicable endemic clades)","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_MW.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Simulate multiple islands based on hyperparameters that describe relationships between area, isolation and local parameters — DAISIE_sim_MW","text":"Valente, LM, Phillimore AB, Melo M, Warren B, Clegg S, Havenstein K, Tiedemann R, Illera JC, Thebaud C, Aschenbach T  Etienne RS (2020). simple dynamic model explain island bird diversity worldwide. Nature, 579, 92-96.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_MW.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Simulate multiple islands based on hyperparameters that describe relationships between area, isolation and local parameters — DAISIE_sim_MW","text":"Luis Valente, Albert Phillimore, Rampal Etienne","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_MW.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Simulate multiple islands based on hyperparameters that describe relationships between area, isolation and local parameters — DAISIE_sim_MW","text":"","code":"## Simulate 10 replicates for the each of the 41 archipelagos in the archipelago_data table, ##based on the hyperparameters of the M19 model (preferred model in Valente et al 2020) ## and the age, area and isolation values given in the archipelago_data table. ## Mainland pool size of 1000, clade-specific carrying capacity. The M19 model is a ## power model with an interactive effect of area and isolation on cladogenesis. ## ## data(archipelago_data) ## result <- DAISIE_sim_MW( ## archipelago_data = archipelago_data, ## M = 1000, ## pars = c(0.040073803,  0,  1.945656546,  0.150429656,  Inf,  0,  67.25643672, ## 0.293635061,  0.059096872,  0.382688527,  0.026510781), ## replicates = 10, ## distance_dep = 'power', ## cladogenesis_dep = 'interactive', ## sigmoidal_par = 'NULL', ## divdepmodel = 'CS')"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_core_cr.html","id":null,"dir":"Reference","previous_headings":"","what":"Internal function of the DAISIE simulation — DAISIE_sim_core_cr","title":"Internal function of the DAISIE simulation — DAISIE_sim_core_cr","text":"Internal function DAISIE simulation","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_core_cr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Internal function of the DAISIE simulation — DAISIE_sim_core_cr","text":"","code":"DAISIE_sim_core_cr(   time,   mainland_n,   pars,   nonoceanic_pars,   hyper_pars,   area_pars )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_core_cr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Internal function of the DAISIE simulation — DAISIE_sim_core_cr","text":"time Numeric defining length simulation time units. example, island known 4 million years old, setting time = 4 simulate entire life span island; setting time = 2 stop simulation mid-life island. mainland_n numeric stating number mainland species, number species can potentially colonize island. using clade-specific diversity dependence, value set 1. using island-wide diversity dependence, value set number mainland species. pars numeric vector containing model parameters: pars[1]: lambda^c (cladogenesis rate) pars[2]: mu (extinction rate) pars[3]: K (carrying capacity), set K=Inf diversity   independence. pars[4]: gamma (immigration rate) pars[5]: lambda^(anagenesis rate) pars[6]: lambda^c (cladogenesis rate) either type 2 species   rate set 2 rate shift model pars[7]: mu (extinction rate) either type 2 species rate   set 2 rate shift model pars[8]: K (carrying capacity) either type 2 species rate   set 2 rate shift model, set K=Inf diversity independence. pars[9]: gamma (immigration rate) either type 2 species   rate set 2 rate shift model pars[10]: lambda^(anagenesis rate) either type 2   species rate set 2 rate shift model Elements 6:10 required type 2 species included rate shift model. DAISIE_sim_relaxed_rate() pars[6] standard deviation gamma distribution relaxed parameter parameter chosen relaxed_par argument mean gamma distribution relaxed parameter. nonoceanic_pars vector length two : [1]: probability sampling species mainland [2]: probability species sampled mainland   nonendemic hyper_pars named list numeric hyperparameters rate calculations returned create_hyper_pars(): [1]: d scaling parameter exponent calculating   cladogenesis rate [2]: x exponent calculating extinction rate area_pars named list containing area sea level parameters created create_area_pars(): [1]: maximum area [2]: current area [3]: value 0 1 indicating island's history   peak area achieved [4]: total island age [5]: amplitude area fluctuation sea level [6]: frequency sine wave area change sea level [7]: angle slope island","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_core_cr_shift.html","id":null,"dir":"Reference","previous_headings":"","what":"Internal function of the DAISIE simulation — DAISIE_sim_core_cr_shift","title":"Internal function of the DAISIE simulation — DAISIE_sim_core_cr_shift","text":"Internal function DAISIE simulation","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_core_cr_shift.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Internal function of the DAISIE simulation — DAISIE_sim_core_cr_shift","text":"","code":"DAISIE_sim_core_cr_shift(   time,   mainland_n,   pars,   nonoceanic_pars = c(0, 0),   hyper_pars = NULL,   area_pars = NULL,   shift_times )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_core_cr_shift.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Internal function of the DAISIE simulation — DAISIE_sim_core_cr_shift","text":"time Numeric defining length simulation time units. example, island known 4 million years old, setting time = 4 simulate entire life span island; setting time = 2 stop simulation mid-life island. mainland_n numeric stating number mainland species, number species can potentially colonize island. using clade-specific diversity dependence, value set 1. using island-wide diversity dependence, value set number mainland species. pars numeric vector containing model parameters: pars[1]: lambda^c (cladogenesis rate) pars[2]: mu (extinction rate) pars[3]: K (carrying capacity), set K=Inf diversity   independence. pars[4]: gamma (immigration rate) pars[5]: lambda^(anagenesis rate) pars[6]: lambda^c (cladogenesis rate) either type 2 species   rate set 2 rate shift model pars[7]: mu (extinction rate) either type 2 species rate   set 2 rate shift model pars[8]: K (carrying capacity) either type 2 species rate   set 2 rate shift model, set K=Inf diversity independence. pars[9]: gamma (immigration rate) either type 2 species   rate set 2 rate shift model pars[10]: lambda^(anagenesis rate) either type 2   species rate set 2 rate shift model Elements 6:10 required type 2 species included rate shift model. DAISIE_sim_relaxed_rate() pars[6] standard deviation gamma distribution relaxed parameter parameter chosen relaxed_par argument mean gamma distribution relaxed parameter. nonoceanic_pars vector length two : [1]: probability sampling species mainland [2]: probability species sampled mainland   nonendemic hyper_pars named list numeric hyperparameters rate calculations returned create_hyper_pars(): [1]: d scaling parameter exponent calculating   cladogenesis rate [2]: x exponent calculating extinction rate area_pars named list containing area sea level parameters created create_area_pars(): [1]: maximum area [2]: current area [3]: value 0 1 indicating island's history   peak area achieved [4]: total island age [5]: amplitude area fluctuation sea level [6]: frequency sine wave area change sea level [7]: angle slope island shift_times numeric vector specifying rate shifts occur present.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_core_time_dep.html","id":null,"dir":"Reference","previous_headings":"","what":"Internal function of the DAISIE simulation — DAISIE_sim_core_time_dep","title":"Internal function of the DAISIE simulation — DAISIE_sim_core_time_dep","text":"Internal function DAISIE simulation","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_core_time_dep.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Internal function of the DAISIE simulation — DAISIE_sim_core_time_dep","text":"","code":"DAISIE_sim_core_time_dep(   time,   mainland_n,   pars,   nonoceanic_pars,   island_ontogeny = 0,   sea_level = 0,   hyper_pars,   area_pars,   peak,   Amax,   Amin,   extcutoff = 1000 )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_core_time_dep.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Internal function of the DAISIE simulation — DAISIE_sim_core_time_dep","text":"time Numeric defining length simulation time units. example, island known 4 million years old, setting time = 4 simulate entire life span island; setting time = 2 stop simulation mid-life island. mainland_n numeric stating number mainland species, number species can potentially colonize island. using clade-specific diversity dependence, value set 1. using island-wide diversity dependence, value set number mainland species. pars numeric vector containing model parameters: pars[1]: lambda^c (cladogenesis rate) pars[2]: mu (extinction rate) pars[3]: K (carrying capacity), set K=Inf diversity   independence. pars[4]: gamma (immigration rate) pars[5]: lambda^(anagenesis rate) pars[6]: lambda^c (cladogenesis rate) either type 2 species   rate set 2 rate shift model pars[7]: mu (extinction rate) either type 2 species rate   set 2 rate shift model pars[8]: K (carrying capacity) either type 2 species rate   set 2 rate shift model, set K=Inf diversity independence. pars[9]: gamma (immigration rate) either type 2 species   rate set 2 rate shift model pars[10]: lambda^(anagenesis rate) either type 2   species rate set 2 rate shift model Elements 6:10 required type 2 species included rate shift model. DAISIE_sim_relaxed_rate() pars[6] standard deviation gamma distribution relaxed parameter parameter chosen relaxed_par argument mean gamma distribution relaxed parameter. nonoceanic_pars vector length two : [1]: probability sampling species mainland [2]: probability species sampled mainland   nonendemic island_ontogeny DAISIE_sim_time_dep(), DAISIE_ML_CS plotting string describing type island ontogeny. Can \"const\", \"beta\" beta function describing area time.  functions numeric describing type island ontogeny. Can 0 constant, 1 beta function describing area time. ML functions island_ontogeny = NA assumes constant ontogeny. Time dependent estimation yet available development still ongoing. return error called case. sea_level DAISIE_sim_time_dep() plotting string describing type sea level. Can \"const\" \"sine\" sine function describing area time.  functions numeric describing type sea level. Can 0 constant, 1 sine function describing area time. hyper_pars named list numeric hyperparameters rate calculations returned create_hyper_pars(): [1]: d scaling parameter exponent calculating   cladogenesis rate [2]: x exponent calculating extinction rate area_pars named list containing area sea level parameters created create_area_pars(): [1]: maximum area [2]: current area [3]: value 0 1 indicating island's history   peak area achieved [4]: total island age [5]: amplitude area fluctuation sea level [6]: frequency sine wave area change sea level [7]: angle slope island peak numeric value specifying peakiness (shaprness) ontogeny curve. Higher values imply peakier ontogeny. value internally calculated calc_peak() given area present area_pars. Amax numeric value maximum island area simulation. Amin numeric value minimum island area simulation. extcutoff numeric cutoff maximum extinction rate preventing large slowing simulation.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_core_trait_dep.html","id":null,"dir":"Reference","previous_headings":"","what":"Internal function of the DAISIE simulation — DAISIE_sim_core_trait_dep","title":"Internal function of the DAISIE simulation — DAISIE_sim_core_trait_dep","text":"Internal function DAISIE simulation","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_core_trait_dep.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Internal function of the DAISIE simulation — DAISIE_sim_core_trait_dep","text":"","code":"DAISIE_sim_core_trait_dep(   time,   mainland_n,   pars,   island_ontogeny = 0,   sea_level = 0,   hyper_pars,   area_pars,   extcutoff = 1000,   trait_pars = NULL )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_core_trait_dep.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Internal function of the DAISIE simulation — DAISIE_sim_core_trait_dep","text":"time Numeric defining length simulation time units. example, island known 4 million years old, setting time = 4 simulate entire life span island; setting time = 2 stop simulation mid-life island. mainland_n numeric stating number mainland species, number species can potentially colonize island. using clade-specific diversity dependence, value set 1. using island-wide diversity dependence, value set number mainland species. pars numeric vector containing model parameters: pars[1]: lambda^c (cladogenesis rate) pars[2]: mu (extinction rate) pars[3]: K (carrying capacity), set K=Inf diversity   independence. pars[4]: gamma (immigration rate) pars[5]: lambda^(anagenesis rate) pars[6]: lambda^c (cladogenesis rate) either type 2 species   rate set 2 rate shift model pars[7]: mu (extinction rate) either type 2 species rate   set 2 rate shift model pars[8]: K (carrying capacity) either type 2 species rate   set 2 rate shift model, set K=Inf diversity independence. pars[9]: gamma (immigration rate) either type 2 species   rate set 2 rate shift model pars[10]: lambda^(anagenesis rate) either type 2   species rate set 2 rate shift model Elements 6:10 required type 2 species included rate shift model. DAISIE_sim_relaxed_rate() pars[6] standard deviation gamma distribution relaxed parameter parameter chosen relaxed_par argument mean gamma distribution relaxed parameter. island_ontogeny DAISIE_sim_time_dep(), DAISIE_ML_CS plotting string describing type island ontogeny. Can \"const\", \"beta\" beta function describing area time.  functions numeric describing type island ontogeny. Can 0 constant, 1 beta function describing area time. ML functions island_ontogeny = NA assumes constant ontogeny. Time dependent estimation yet available development still ongoing. return error called case. sea_level DAISIE_sim_time_dep() plotting string describing type sea level. Can \"const\" \"sine\" sine function describing area time.  functions numeric describing type sea level. Can 0 constant, 1 sine function describing area time. hyper_pars named list numeric hyperparameters rate calculations returned create_hyper_pars(): [1]: d scaling parameter exponent calculating   cladogenesis rate [2]: x exponent calculating extinction rate area_pars named list containing area sea level parameters created create_area_pars(): [1]: maximum area [2]: current area [3]: value 0 1 indicating island's history   peak area achieved [4]: total island age [5]: amplitude area fluctuation sea level [6]: frequency sine wave area change sea level [7]: angle slope island extcutoff numeric cutoff maximum extinction rate preventing large slowing simulation. trait_pars named list containing diversification rates considering   two trait states created create_trait_pars: [1]:numeric per capita transition rate state1 [2]:numeric per capita immigration rate state2 [3]:numeric per capita extinction rate state2 [4]:numeric per capita anagenesis rate state2 [5]:numeric per capita cladogenesis rate state2 [6]:numeric per capita transition rate state2 [7]:numeric number species trait state 2    mainland","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_cr_cs.html","id":null,"dir":"Reference","previous_headings":"","what":"Simulates island replicates with an clade-specific (CS) diversity-dependent constant-rate process — DAISIE_sim_cr_cs","title":"Simulates island replicates with an clade-specific (CS) diversity-dependent constant-rate process — DAISIE_sim_cr_cs","text":"Simulates island replicates clade-specific (CS) diversity-dependent constant-rate process","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_cr_cs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulates island replicates with an clade-specific (CS) diversity-dependent constant-rate process — DAISIE_sim_cr_cs","text":"","code":"DAISIE_sim_cr_cs(   total_time,   M,   pars,   replicates,   nonoceanic_pars,   prop_type2_pool,   replicates_apply_type2,   sample_freq,   hyper_pars,   area_pars,   cond,   verbose )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_cr_cs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulates island replicates with an clade-specific (CS) diversity-dependent constant-rate process — DAISIE_sim_cr_cs","text":"total_time Numeric defining length simulation time units. M Numeric defining size mainland pool, .e. number species can potentially colonize island. pars numeric vector containing model parameters: pars[1]: lambda^c (cladogenesis rate) pars[2]: mu (extinction rate) pars[3]: K (carrying capacity), set K=Inf diversity   independence. pars[4]: gamma (immigration rate) pars[5]: lambda^(anagenesis rate) pars[6]: lambda^c (cladogenesis rate) either type 2 species   rate set 2 rate shift model pars[7]: mu (extinction rate) either type 2 species rate   set 2 rate shift model pars[8]: K (carrying capacity) either type 2 species rate   set 2 rate shift model, set K=Inf diversity independence. pars[9]: gamma (immigration rate) either type 2 species   rate set 2 rate shift model pars[10]: lambda^(anagenesis rate) either type 2   species rate set 2 rate shift model Elements 6:10 required type 2 species included rate shift model. DAISIE_sim_relaxed_rate() pars[6] standard deviation gamma distribution relaxed parameter parameter chosen relaxed_par argument mean gamma distribution relaxed parameter. replicates Integer specifying number island replicates simulated. nonoceanic_pars vector length two : [1]: probability sampling species mainland [2]: probability species sampled mainland   nonendemic prop_type2_pool Fraction mainland species belongs second subset species (type 2). Applies two types species simulated (length(pars) = 10). DAISIE_dataprep() applies number_clade_types = 2.  DAISIE_dataprep() default \"proportional\" sets fraction proportional number clades distinct macroevolutionary process colonised island. replicates_apply_type2 Applies two types species simulated. Default replicates_apply_type2 = TRUE runs simulations number islands type 2 species colonised equal specified number replicates. recommended prop_type2_pool small rate immigration type two species (pars[9]) low, meaning replicates needed achieved adequate sample size islands type 2 species. Setting replicates_apply_type2 = FALSE simulates islands specified number replicates regardless whether type 2 species colonised . sample_freq Numeric specifing number units times divided plotting purposes. Larger values lead plots higher resolution, also run slower. hyper_pars named list numeric hyperparameters rate calculations returned create_hyper_pars(): [1]: d scaling parameter exponent calculating   cladogenesis rate [2]: x exponent calculating extinction rate area_pars named list containing area sea level parameters created create_area_pars(): [1]: maximum area [2]: current area [3]: value 0 1 indicating island's history   peak area achieved [4]: total island age [5]: amplitude area fluctuation sea level [6]: frequency sine wave area change sea level [7]: angle slope island cond cond = 0 : conditioning island age  cond = 1 : conditioning island age non-extinction island biota . cond > 1 : conditioning island age least cond colonizations island. last option yet available IW model verbose numeric vector length 1, simulations `DAISIEdataprep()` can `1` `0`, `1` gives intermediate output printed. ML functions numeric determining intermediate output printed. default: `0` print, `1` prints initial likelihood settings selected (parameters optimised, fixed shifted), `2` prints `1 also intermediate output parameters loglikelihood, `3` `2` prints intermediate progress likelihood computation.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_cr_cs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Simulates island replicates with an clade-specific (CS) diversity-dependent constant-rate process — DAISIE_sim_cr_cs","text":"list. highest level least corresponds individual replicate. See return `DAISIE_sim_cr()` details.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_cr_gw.html","id":null,"dir":"Reference","previous_headings":"","what":"Simulates island replicates with an guild-wide (GW) diversity-dependent process — DAISIE_sim_cr_gw","title":"Simulates island replicates with an guild-wide (GW) diversity-dependent process — DAISIE_sim_cr_gw","text":"Simulates island replicates guild-wide (GW) diversity-dependent process","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_cr_gw.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulates island replicates with an guild-wide (GW) diversity-dependent process — DAISIE_sim_cr_gw","text":"","code":"DAISIE_sim_cr_gw(   total_time,   M,   pars,   replicates,   nonoceanic_pars,   num_guilds,   sample_freq,   hyper_pars,   area_pars,   verbose )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_cr_gw.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulates island replicates with an guild-wide (GW) diversity-dependent process — DAISIE_sim_cr_gw","text":"total_time Numeric defining length simulation time units. M Numeric defining size mainland pool, .e. number species can potentially colonize island. pars numeric vector containing model parameters: pars[1]: lambda^c (cladogenesis rate) pars[2]: mu (extinction rate) pars[3]: K (carrying capacity), set K=Inf diversity   independence. pars[4]: gamma (immigration rate) pars[5]: lambda^(anagenesis rate) pars[6]: lambda^c (cladogenesis rate) either type 2 species   rate set 2 rate shift model pars[7]: mu (extinction rate) either type 2 species rate   set 2 rate shift model pars[8]: K (carrying capacity) either type 2 species rate   set 2 rate shift model, set K=Inf diversity independence. pars[9]: gamma (immigration rate) either type 2 species   rate set 2 rate shift model pars[10]: lambda^(anagenesis rate) either type 2   species rate set 2 rate shift model Elements 6:10 required type 2 species included rate shift model. DAISIE_sim_relaxed_rate() pars[6] standard deviation gamma distribution relaxed parameter parameter chosen relaxed_par argument mean gamma distribution relaxed parameter. replicates Integer specifying number island replicates simulated. nonoceanic_pars vector length two : [1]: probability sampling species mainland [2]: probability species sampled mainland   nonendemic num_guilds number guilds mainland. number mainland species divided number guilds divdepmodel = \"GW\" sample_freq Numeric specifing number units times divided plotting purposes. Larger values lead plots higher resolution, also run slower. hyper_pars named list numeric hyperparameters rate calculations returned create_hyper_pars(): [1]: d scaling parameter exponent calculating   cladogenesis rate [2]: x exponent calculating extinction rate area_pars named list containing area sea level parameters created create_area_pars(): [1]: maximum area [2]: current area [3]: value 0 1 indicating island's history   peak area achieved [4]: total island age [5]: amplitude area fluctuation sea level [6]: frequency sine wave area change sea level [7]: angle slope island verbose numeric vector length 1, simulations `DAISIEdataprep()` can `1` `0`, `1` gives intermediate output printed. ML functions numeric determining intermediate output printed. default: `0` print, `1` prints initial likelihood settings selected (parameters optimised, fixed shifted), `2` prints `1 also intermediate output parameters loglikelihood, `3` `2` prints intermediate progress likelihood computation.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_cr_gw.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Simulates island replicates with an guild-wide (GW) diversity-dependent process — DAISIE_sim_cr_gw","text":"list. highest level least corresponds individual replciate. See return `DAISIE_sim_cr()` details.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_cr_iw.html","id":null,"dir":"Reference","previous_headings":"","what":"Simulates island replicates with an island-wide (IW) diversity-dependent constant-rate process — DAISIE_sim_cr_iw","title":"Simulates island replicates with an island-wide (IW) diversity-dependent constant-rate process — DAISIE_sim_cr_iw","text":"Simulates island replicates island-wide (IW) diversity-dependent constant-rate process","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_cr_iw.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulates island replicates with an island-wide (IW) diversity-dependent constant-rate process — DAISIE_sim_cr_iw","text":"","code":"DAISIE_sim_cr_iw(   total_time,   M,   pars,   replicates,   nonoceanic_pars,   sample_freq,   hyper_pars,   area_pars,   cond,   verbose )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_cr_iw.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulates island replicates with an island-wide (IW) diversity-dependent constant-rate process — DAISIE_sim_cr_iw","text":"total_time Numeric defining length simulation time units. M Numeric defining size mainland pool, .e. number species can potentially colonize island. pars numeric vector containing model parameters: pars[1]: lambda^c (cladogenesis rate) pars[2]: mu (extinction rate) pars[3]: K (carrying capacity), set K=Inf diversity   independence. pars[4]: gamma (immigration rate) pars[5]: lambda^(anagenesis rate) pars[6]: lambda^c (cladogenesis rate) either type 2 species   rate set 2 rate shift model pars[7]: mu (extinction rate) either type 2 species rate   set 2 rate shift model pars[8]: K (carrying capacity) either type 2 species rate   set 2 rate shift model, set K=Inf diversity independence. pars[9]: gamma (immigration rate) either type 2 species   rate set 2 rate shift model pars[10]: lambda^(anagenesis rate) either type 2   species rate set 2 rate shift model Elements 6:10 required type 2 species included rate shift model. DAISIE_sim_relaxed_rate() pars[6] standard deviation gamma distribution relaxed parameter parameter chosen relaxed_par argument mean gamma distribution relaxed parameter. replicates Integer specifying number island replicates simulated. nonoceanic_pars vector length two : [1]: probability sampling species mainland [2]: probability species sampled mainland   nonendemic sample_freq Numeric specifing number units times divided plotting purposes. Larger values lead plots higher resolution, also run slower. hyper_pars named list numeric hyperparameters rate calculations returned create_hyper_pars(): [1]: d scaling parameter exponent calculating   cladogenesis rate [2]: x exponent calculating extinction rate area_pars named list containing area sea level parameters created create_area_pars(): [1]: maximum area [2]: current area [3]: value 0 1 indicating island's history   peak area achieved [4]: total island age [5]: amplitude area fluctuation sea level [6]: frequency sine wave area change sea level [7]: angle slope island cond cond = 0 : conditioning island age  cond = 1 : conditioning island age non-extinction island biota . cond > 1 : conditioning island age least cond colonizations island. last option yet available IW model verbose numeric vector length 1, simulations `DAISIEdataprep()` can `1` `0`, `1` gives intermediate output printed. ML functions numeric determining intermediate output printed. default: `0` print, `1` prints initial likelihood settings selected (parameters optimised, fixed shifted), `2` prints `1 also intermediate output parameters loglikelihood, `3` `2` prints intermediate progress likelihood computation.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_cr_iw.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Simulates island replicates with an island-wide (IW) diversity-dependent constant-rate process — DAISIE_sim_cr_iw","text":"list. highest level least corresponds individual replicate. See return `DAISIE_sim_cr()` details.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_cr_shift.html","id":null,"dir":"Reference","previous_headings":"","what":"Simulate (non-)oceanic islands with given parameters under a rate-shift regime — DAISIE_sim_cr_shift","title":"Simulate (non-)oceanic islands with given parameters under a rate-shift regime — DAISIE_sim_cr_shift","text":"function simulates islands given cladogenesis, extinction, Kprime, immigration anagenesis parameters, modelled time-constant parameters, can switched different diversification regime (.e., different set parameters) one set times present. , allows simulation non-oceanic islands, generating islands starting condition includes potential endemic non-endemic species.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_cr_shift.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulate (non-)oceanic islands with given parameters under a rate-shift regime — DAISIE_sim_cr_shift","text":"","code":"DAISIE_sim_cr_shift(   time,   M,   pars,   replicates,   shift_times,   divdepmodel = \"CS\",   nonoceanic_pars = c(0, 0),   num_guilds = NULL,   sample_freq = 25,   plot_sims = TRUE,   hyper_pars = create_hyper_pars(d = 0, x = 0),   area_pars = DAISIE::create_area_pars(max_area = 1, current_area = 1,     proportional_peak_t = 0, total_island_age = 0, sea_level_amplitude = 0,     sea_level_frequency = 0, island_gradient_angle = 0),   cond = 0,   verbose = TRUE,   ... )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_cr_shift.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulate (non-)oceanic islands with given parameters under a rate-shift regime — DAISIE_sim_cr_shift","text":"time Numeric defining length simulation time units. example, island known 4 million years old, setting time = 4 simulate entire life span island; setting time = 2 stop simulation mid-life island. M Numeric defining size mainland pool, .e. number species can potentially colonize island. pars numeric vector containing model parameters: pars[1]: lambda^c (cladogenesis rate) pars[2]: mu (extinction rate) pars[3]: K (carrying capacity), set K=Inf diversity   independence. pars[4]: gamma (immigration rate) pars[5]: lambda^(anagenesis rate) pars[6]: lambda^c (cladogenesis rate) either type 2 species   rate set 2 rate shift model pars[7]: mu (extinction rate) either type 2 species rate   set 2 rate shift model pars[8]: K (carrying capacity) either type 2 species rate   set 2 rate shift model, set K=Inf diversity independence. pars[9]: gamma (immigration rate) either type 2 species   rate set 2 rate shift model pars[10]: lambda^(anagenesis rate) either type 2   species rate set 2 rate shift model Elements 6:10 required type 2 species included rate shift model. DAISIE_sim_relaxed_rate() pars[6] standard deviation gamma distribution relaxed parameter parameter chosen relaxed_par argument mean gamma distribution relaxed parameter. replicates Integer specifying number island replicates simulated. shift_times numeric vector specifying rate shifts occur present. divdepmodel Option divdepmodel = 'CS' runs model clade-specific carrying capacity, diversity-dependence operates within single clades, .e. among species originating mainland colonist. Option divdepmodel = 'IW' runs model island-wide carrying capacity, diversity-dependence operates within among clades. Option divdepmodel = 'GW' runs model diversity-dependence operates within guild. nonoceanic_pars vector length two : [1]: probability sampling species mainland [2]: probability species sampled mainland   nonendemic num_guilds number guilds mainland. number mainland species divided number guilds divdepmodel = \"GW\" sample_freq Numeric specifing number units times divided plotting purposes. Larger values lead plots higher resolution, also run slower. plot_sims Default = TRUE plots species--time (STT) plots. detects many types species present. one type species present, STT plotted species. two types present, three plots produced: STT , STT type 1 STT type 2. hyper_pars named list numeric hyperparameters rate calculations returned create_hyper_pars(): [1]: d scaling parameter exponent calculating   cladogenesis rate [2]: x exponent calculating extinction rate area_pars named list containing area sea level parameters created create_area_pars(): [1]: maximum area [2]: current area [3]: value 0 1 indicating island's history   peak area achieved [4]: total island age [5]: amplitude area fluctuation sea level [6]: frequency sine wave area change sea level [7]: angle slope island cond cond = 0 : conditioning island age  cond = 1 : conditioning island age non-extinction island biota . cond > 1 : conditioning island age least cond colonizations island. last option yet available IW model verbose numeric vector length 1, simulations `DAISIEdataprep()` can `1` `0`, `1` gives intermediate output printed. ML functions numeric determining intermediate output printed. default: `0` print, `1` prints initial likelihood settings selected (parameters optimised, fixed shifted), `2` prints `1 also intermediate output parameters loglikelihood, `3` `2` prints intermediate progress likelihood computation. ... arguments pass plotting functions.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_cr_shift.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Simulate (non-)oceanic islands with given parameters under a rate-shift regime — DAISIE_sim_cr_shift","text":"list. highest level least corresponds individual replciate. first element replicate composed island information containing: $island_age: numeric island age. $not_present: numeric number mainland lineages   present island. $stt_all: STT table species island     (nI - number non-endemic species; nA - number anagenetic species,     nC - number cladogenetic species, present - number independent     colonisations present) $brts_table: simulations \"IW\". Table containing information order events data, use maximum likelihood optimization.). subsequent elements list pertaining replcate contain information single colonist lineage island 4 components: $branching_times: island age stem age     population/species case Non-endemic, Non-endemic_MaxAge     Endemic anagenetic species. cladogenetic species     island age branching times radiation including     stem age radiation. $stac: integer ranging 1 4   indicating status colonist: Non_endemic_MaxAge Endemic Endemic&Non_Endemic Non_endemic_MaxAge $missing_species: number island species sampled particular clade (applicable endemic clades) $type_1or2: whether colonist belongs type 1 type 2","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_cr_shift.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Simulate (non-)oceanic islands with given parameters under a rate-shift regime — DAISIE_sim_cr_shift","text":"Valente, L.M., .B. Phillimore R.S. Etienne (2015). Equilibrium non-equilibrium dynamics simultaneously operate Galapagos islands. Ecology Letters 18: 844-852. Hauffe, T., D. Delicado, R.S. Etienne L. Valente (2020). Lake expansion elevates equilibrium diversity via increasing colonization.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_cr_shift.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Simulate (non-)oceanic islands with given parameters under a rate-shift regime — DAISIE_sim_cr_shift","text":"Luis Valente, Albert Phillimore, Torsten Hauffe","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_min_type2.html","id":null,"dir":"Reference","previous_headings":"","what":"Internal function of the DAISIE simulation — DAISIE_sim_min_type2","title":"Internal function of the DAISIE simulation — DAISIE_sim_min_type2","text":"Internal function DAISIE simulation","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_min_type2.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Internal function of the DAISIE simulation — DAISIE_sim_min_type2","text":"","code":"DAISIE_sim_min_type2(   time,   M,   pars,   replicates,   prop_type2_pool,   area_pars,   hyper_pars,   verbose = TRUE )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_min_type2.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Internal function of the DAISIE simulation — DAISIE_sim_min_type2","text":"time Numeric defining length simulation time units. example, island known 4 million years old, setting time = 4 simulate entire life span island; setting time = 2 stop simulation mid-life island. M Numeric defining size mainland pool, .e. number species can potentially colonize island. pars numeric vector containing model parameters: pars[1]: lambda^c (cladogenesis rate) pars[2]: mu (extinction rate) pars[3]: K (carrying capacity), set K=Inf diversity   independence. pars[4]: gamma (immigration rate) pars[5]: lambda^(anagenesis rate) pars[6]: lambda^c (cladogenesis rate) either type 2 species   rate set 2 rate shift model pars[7]: mu (extinction rate) either type 2 species rate   set 2 rate shift model pars[8]: K (carrying capacity) either type 2 species rate   set 2 rate shift model, set K=Inf diversity independence. pars[9]: gamma (immigration rate) either type 2 species   rate set 2 rate shift model pars[10]: lambda^(anagenesis rate) either type 2   species rate set 2 rate shift model Elements 6:10 required type 2 species included rate shift model. DAISIE_sim_relaxed_rate() pars[6] standard deviation gamma distribution relaxed parameter parameter chosen relaxed_par argument mean gamma distribution relaxed parameter. replicates Integer specifying number island replicates simulated. prop_type2_pool Fraction mainland species belongs second subset species (type 2). Applies two types species simulated (length(pars) = 10). DAISIE_dataprep() applies number_clade_types = 2.  DAISIE_dataprep() default \"proportional\" sets fraction proportional number clades distinct macroevolutionary process colonised island. area_pars named list containing area sea level parameters created create_area_pars(): [1]: maximum area [2]: current area [3]: value 0 1 indicating island's history   peak area achieved [4]: total island age [5]: amplitude area fluctuation sea level [6]: frequency sine wave area change sea level [7]: angle slope island hyper_pars named list numeric hyperparameters rate calculations returned create_hyper_pars(): [1]: d scaling parameter exponent calculating   cladogenesis rate [2]: x exponent calculating extinction rate verbose numeric vector length 1, simulations `DAISIEdataprep()` can `1` `0`, `1` gives intermediate output printed. ML functions numeric determining intermediate output printed. default: `0` print, `1` prints initial likelihood settings selected (parameters optimised, fixed shifted), `2` prints `1 also intermediate output parameters loglikelihood, `3` `2` prints intermediate progress likelihood computation.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_relaxed_rate.html","id":null,"dir":"Reference","previous_headings":"","what":"Simulate (non-)oceanic islands with given parameters under a relaxed-rate model — DAISIE_sim_relaxed_rate","title":"Simulate (non-)oceanic islands with given parameters under a relaxed-rate model — DAISIE_sim_relaxed_rate","text":"function simulates islands given cladogenesis, extinction, Kprime, immigration anagenesis parameters, can modelled time-constant parameters variation clades one multiple parameters. , allows simulation non-oceanic islands, generating islands starting condition includes potential endemic non-endemic species.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_relaxed_rate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulate (non-)oceanic islands with given parameters under a relaxed-rate model — DAISIE_sim_relaxed_rate","text":"","code":"DAISIE_sim_relaxed_rate(   time,   M,   pars,   replicates,   relaxed_par,   nonoceanic_pars = c(0, 0),   sample_freq = 25,   plot_sims = TRUE,   hyper_pars = create_hyper_pars(d = 0, x = 0),   area_pars = create_area_pars(max_area = 1, current_area = 1, proportional_peak_t = 0,     total_island_age = 0, sea_level_amplitude = 0, sea_level_frequency = 0,     island_gradient_angle = 0),   cond = 0,   verbose = TRUE,   ... )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_relaxed_rate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulate (non-)oceanic islands with given parameters under a relaxed-rate model — DAISIE_sim_relaxed_rate","text":"time Numeric defining length simulation time units. example, island known 4 million years old, setting time = 4 simulate entire life span island; setting time = 2 stop simulation mid-life island. M Numeric defining size mainland pool, .e. number species can potentially colonize island. pars numeric vector containing model parameters: pars[1]: lambda^c (cladogenesis rate) pars[2]: mu (extinction rate) pars[3]: K (carrying capacity), set K=Inf diversity   independence. pars[4]: gamma (immigration rate) pars[5]: lambda^(anagenesis rate) pars[6]: lambda^c (cladogenesis rate) either type 2 species   rate set 2 rate shift model pars[7]: mu (extinction rate) either type 2 species rate   set 2 rate shift model pars[8]: K (carrying capacity) either type 2 species rate   set 2 rate shift model, set K=Inf diversity independence. pars[9]: gamma (immigration rate) either type 2 species   rate set 2 rate shift model pars[10]: lambda^(anagenesis rate) either type 2   species rate set 2 rate shift model Elements 6:10 required type 2 species included rate shift model. DAISIE_sim_relaxed_rate() pars[6] standard deviation gamma distribution relaxed parameter parameter chosen relaxed_par argument mean gamma distribution relaxed parameter. replicates Integer specifying number island replicates simulated. relaxed_par string determining parameter relaxed relaxed rate model. nonoceanic_pars vector length two : [1]: probability sampling species mainland [2]: probability species sampled mainland   nonendemic sample_freq Numeric specifing number units times divided plotting purposes. Larger values lead plots higher resolution, also run slower. plot_sims Default = TRUE plots species--time (STT) plots. detects many types species present. one type species present, STT plotted species. two types present, three plots produced: STT , STT type 1 STT type 2. hyper_pars named list numeric hyperparameters rate calculations returned create_hyper_pars(): [1]: d scaling parameter exponent calculating   cladogenesis rate [2]: x exponent calculating extinction rate area_pars named list containing area sea level parameters created create_area_pars(): [1]: maximum area [2]: current area [3]: value 0 1 indicating island's history   peak area achieved [4]: total island age [5]: amplitude area fluctuation sea level [6]: frequency sine wave area change sea level [7]: angle slope island cond cond = 0 : conditioning island age  cond = 1 : conditioning island age non-extinction island biota . cond > 1 : conditioning island age least cond colonizations island. last option yet available IW model verbose numeric vector length 1, simulations `DAISIEdataprep()` can `1` `0`, `1` gives intermediate output printed. ML functions numeric determining intermediate output printed. default: `0` print, `1` prints initial likelihood settings selected (parameters optimised, fixed shifted), `2` prints `1 also intermediate output parameters loglikelihood, `3` `2` prints intermediate progress likelihood computation. ... arguments pass plotting functions.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_relaxed_rate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Simulate (non-)oceanic islands with given parameters under a relaxed-rate model — DAISIE_sim_relaxed_rate","text":"list. highest level least corresponds individual replciate. first element replicate composed island information containing: $island_age: numeric island age. $not_present: number mainland lineages     present island. present 1 type species     simulated. Becomes $not_present_type1: number mainland     lineages type 1 present island     $not_present_type2: number mainland lineages type 2     present island, two types simulated. $stt_all: STT table species island     (nI - number non-endemic species; nA - number anagenetic species,     nC - number cladogenetic species, present - number independent     colonisations present) $stt_stt_type1: STT table type 1 species island -     2 types species simulated (nI - number non-endemic     species; nA - number anagenetic species, nC - number cladogenetic     species, present - number independent colonisations present). $stt_stt_type2: STT table type 2 species island      - 2 types species simulated (nI - number non-endemic      species; nA - number anagenetic species, nC - number cladogenetic      species, present - number independent colonisations present ). $brts_table: simulations \"IW\". Table containing information order events data, use maximum likelihood optimization.). subsequent elements list pertaining replcate contain information single colonist lineage island 4 components: $branching_times: island age stem age     population/species case Non-endemic, Non-endemic_MaxAge     Endemic anagenetic species.    cladogenetic species     island age branching times radiation including     stem age radiation. $stac: integer ranging 1 4   indicating status colonist: Non_endemic_MaxAge Endemic Endemic&Non_Endemic Non_endemic_MaxAge $missing_species: number island species sampled particular clade (applicable endemic clades) $type_1or2: whether colonist belongs type 1 type 2","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_relaxed_rate.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Simulate (non-)oceanic islands with given parameters under a relaxed-rate model — DAISIE_sim_relaxed_rate","text":"Luis Valente, Albert Phillimore, Joshua Lambert, Shu Xie, Pedro Neves, Richèl J. C. Bilderbeek, Rampal Etienne","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_relaxed_rate.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Simulate (non-)oceanic islands with given parameters under a relaxed-rate model — DAISIE_sim_relaxed_rate","text":"","code":"## Simulate an island for 1 million years, with a relaxed the rate of ## cladogenesis between clades. Pool size 500.  clado_rate <- 0.5 ext_rate <- 0.2 carr_cap <- Inf immig_rate <- 0.005 ana_rate <- 1 par_sd <- 1 sim_pars <- c(clado_rate, ext_rate, carr_cap, immig_rate, ana_rate, par_sd) set.seed(1) island_replicates <- DAISIE_sim_relaxed_rate(   time = 1,   M = 500,   pars = sim_pars,   replicates = 2,   relaxed_par = \"cladogenesis\",   plot_sims = FALSE,   verbose = FALSE )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_time_dep.html","id":null,"dir":"Reference","previous_headings":"","what":"Simulate (non-)oceanic islands with given parameters under a time-dependent regime — DAISIE_sim_time_dep","title":"Simulate (non-)oceanic islands with given parameters under a time-dependent regime — DAISIE_sim_time_dep","text":"function simulates islands given cladogenesis, extinction, Kprime, immigration anagenesis parameters, modelled time-dependent parameters. Time dependency aims capture effect area changes islands undego emergence subsidence. Thus, oceanic, volcanic island ontogeny scenarios can modelled (beta function), well effect sea level fluctuations (modelled sine function). See paramter entry area_pars details. island ontogeny sea level fluctuations allowed operate simultaneuosly. function also allows simulation non-oceanic islands, generating islands starting condition includes potential endemic non-endemic species.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_time_dep.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulate (non-)oceanic islands with given parameters under a time-dependent regime — DAISIE_sim_time_dep","text":"","code":"DAISIE_sim_time_dep(   time,   M,   pars,   replicates,   area_pars,   hyper_pars,   divdepmodel = \"CS\",   nonoceanic_pars = c(0, 0),   num_guilds = NULL,   sample_freq = 25,   plot_sims = TRUE,   island_ontogeny = \"const\",   sea_level = \"const\",   extcutoff = 1000,   cond = 0,   verbose = TRUE,   ... )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_time_dep.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulate (non-)oceanic islands with given parameters under a time-dependent regime — DAISIE_sim_time_dep","text":"time Numeric defining length simulation time units. example, island known 4 million years old, setting time = 4 simulate entire life span island; setting time = 2 stop simulation mid-life island. M Numeric defining size mainland pool, .e. number species can potentially colonize island. pars numeric vector containing model parameters: pars[1]: lambda^c (cladogenesis rate) pars[2]: mu (extinction rate) pars[3]: K (carrying capacity), set K=Inf diversity   independence. pars[4]: gamma (immigration rate) pars[5]: lambda^(anagenesis rate) pars[6]: lambda^c (cladogenesis rate) either type 2 species   rate set 2 rate shift model pars[7]: mu (extinction rate) either type 2 species rate   set 2 rate shift model pars[8]: K (carrying capacity) either type 2 species rate   set 2 rate shift model, set K=Inf diversity independence. pars[9]: gamma (immigration rate) either type 2 species   rate set 2 rate shift model pars[10]: lambda^(anagenesis rate) either type 2   species rate set 2 rate shift model Elements 6:10 required type 2 species included rate shift model. DAISIE_sim_relaxed_rate() pars[6] standard deviation gamma distribution relaxed parameter parameter chosen relaxed_par argument mean gamma distribution relaxed parameter. replicates Integer specifying number island replicates simulated. area_pars named list containing area sea level parameters created create_area_pars(): [1]: maximum area [2]: current area [3]: value 0 1 indicating island's history   peak area achieved [4]: total island age [5]: amplitude area fluctuation sea level [6]: frequency sine wave area change sea level [7]: angle slope island hyper_pars named list numeric hyperparameters rate calculations returned create_hyper_pars(): [1]: d scaling parameter exponent calculating   cladogenesis rate [2]: x exponent calculating extinction rate divdepmodel Option divdepmodel = 'CS' runs model clade-specific carrying capacity, diversity-dependence operates within single clades, .e. among species originating mainland colonist. Option divdepmodel = 'IW' runs model island-wide carrying capacity, diversity-dependence operates within among clades. Option divdepmodel = 'GW' runs model diversity-dependence operates within guild. nonoceanic_pars vector length two : [1]: probability sampling species mainland [2]: probability species sampled mainland   nonendemic num_guilds number guilds mainland. number mainland species divided number guilds divdepmodel = \"GW\" sample_freq Numeric specifing number units times divided plotting purposes. Larger values lead plots higher resolution, also run slower. plot_sims Default = TRUE plots species--time (STT) plots. detects many types species present. one type species present, STT plotted species. two types present, three plots produced: STT , STT type 1 STT type 2. island_ontogeny DAISIE_sim_time_dep(), DAISIE_ML_CS plotting string describing type island ontogeny. Can \"const\", \"beta\" beta function describing area time.  functions numeric describing type island ontogeny. Can 0 constant, 1 beta function describing area time. ML functions island_ontogeny = NA assumes constant ontogeny. Time dependent estimation yet available development still ongoing. return error called case. sea_level DAISIE_sim_time_dep() plotting string describing type sea level. Can \"const\" \"sine\" sine function describing area time.  functions numeric describing type sea level. Can 0 constant, 1 sine function describing area time. extcutoff numeric cutoff maximum extinction rate preventing large slowing simulation. cond cond = 0 : conditioning island age  cond = 1 : conditioning island age non-extinction island biota . cond > 1 : conditioning island age least cond colonizations island. last option yet available IW model verbose numeric vector length 1, simulations `DAISIEdataprep()` can `1` `0`, `1` gives intermediate output printed. ML functions numeric determining intermediate output printed. default: `0` print, `1` prints initial likelihood settings selected (parameters optimised, fixed shifted), `2` prints `1 also intermediate output parameters loglikelihood, `3` `2` prints intermediate progress likelihood computation. ... arguments pass plotting functions.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_time_dep.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Simulate (non-)oceanic islands with given parameters under a time-dependent regime — DAISIE_sim_time_dep","text":"list. highest level least corresponds individual replciate. first element replicate composed island information containing: $island_age: numeric island age. $not_present: numeric number mainland lineages   present island. $stt_all: STT table species island     (nI - number non-endemic species; nA - number anagenetic species,     nC - number cladogenetic species, present - number independent     colonisations present) $brts_table: simulations \"IW\". Table containing information order events data, use maximum likelihood optimization.). subsequent elements list pertaining replcate contain information single colonist lineage island 4 components: $branching_times: island age stem age     population/species case Non-endemic, Non-endemic_MaxAge     Endemic anagenetic species. cladogenetic species     island age branching times radiation including     stem age radiation. $stac: integer ranging 1 4   indicating status colonist: Non_endemic_MaxAge Endemic Endemic&Non_Endemic Non_endemic_MaxAge $missing_species: number island species sampled particular clade (applicable endemic clades) $type_1or2: whether colonist belongs type 1 type 2","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_time_dep.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Simulate (non-)oceanic islands with given parameters under a time-dependent regime — DAISIE_sim_time_dep","text":"Valente, L.M., .B. Phillimore R.S. Etienne (2015). Equilibrium non-equilibrium dynamics simultaneously operate Galapagos islands. Ecology Letters 18: 844-852. Valente, L.M., Etienne, R.S. Phillimore, .B. (2014). effects island ontogeny species diversity phylogeny. Proceedings Royal Society B: Biological Sciences 281(1784), p.20133227.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_time_dep.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Simulate (non-)oceanic islands with given parameters under a time-dependent regime — DAISIE_sim_time_dep","text":"Luis Valente Albert Phillimore","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_time_dep_cs.html","id":null,"dir":"Reference","previous_headings":"","what":"Simulates island replicates with an clade-specific (CS) diversity-dependent time-dependent process — DAISIE_sim_time_dep_cs","title":"Simulates island replicates with an clade-specific (CS) diversity-dependent time-dependent process — DAISIE_sim_time_dep_cs","text":"Simulates island replicates clade-specific (CS) diversity-dependent time-dependent process","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_time_dep_cs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulates island replicates with an clade-specific (CS) diversity-dependent time-dependent process — DAISIE_sim_time_dep_cs","text":"","code":"DAISIE_sim_time_dep_cs(   total_time,   M,   pars,   replicates,   area_pars,   hyper_pars,   nonoceanic_pars,   sample_freq,   island_ontogeny,   sea_level,   peak,   Amax,   Amin,   extcutoff,   cond,   verbose )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_time_dep_cs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulates island replicates with an clade-specific (CS) diversity-dependent time-dependent process — DAISIE_sim_time_dep_cs","text":"total_time Numeric defining length simulation time units. M Numeric defining size mainland pool, .e. number species can potentially colonize island. pars numeric vector containing model parameters: pars[1]: lambda^c (cladogenesis rate) pars[2]: mu (extinction rate) pars[3]: K (carrying capacity), set K=Inf diversity   independence. pars[4]: gamma (immigration rate) pars[5]: lambda^(anagenesis rate) pars[6]: lambda^c (cladogenesis rate) either type 2 species   rate set 2 rate shift model pars[7]: mu (extinction rate) either type 2 species rate   set 2 rate shift model pars[8]: K (carrying capacity) either type 2 species rate   set 2 rate shift model, set K=Inf diversity independence. pars[9]: gamma (immigration rate) either type 2 species   rate set 2 rate shift model pars[10]: lambda^(anagenesis rate) either type 2   species rate set 2 rate shift model Elements 6:10 required type 2 species included rate shift model. DAISIE_sim_relaxed_rate() pars[6] standard deviation gamma distribution relaxed parameter parameter chosen relaxed_par argument mean gamma distribution relaxed parameter. replicates Integer specifying number island replicates simulated. area_pars named list containing area sea level parameters created create_area_pars(): [1]: maximum area [2]: current area [3]: value 0 1 indicating island's history   peak area achieved [4]: total island age [5]: amplitude area fluctuation sea level [6]: frequency sine wave area change sea level [7]: angle slope island hyper_pars named list numeric hyperparameters rate calculations returned create_hyper_pars(): [1]: d scaling parameter exponent calculating   cladogenesis rate [2]: x exponent calculating extinction rate nonoceanic_pars vector length two : [1]: probability sampling species mainland [2]: probability species sampled mainland   nonendemic sample_freq Numeric specifing number units times divided plotting purposes. Larger values lead plots higher resolution, also run slower. island_ontogeny DAISIE_sim_time_dep(), DAISIE_ML_CS plotting string describing type island ontogeny. Can \"const\", \"beta\" beta function describing area time.  functions numeric describing type island ontogeny. Can 0 constant, 1 beta function describing area time. ML functions island_ontogeny = NA assumes constant ontogeny. Time dependent estimation yet available development still ongoing. return error called case. sea_level DAISIE_sim_time_dep() plotting string describing type sea level. Can \"const\" \"sine\" sine function describing area time.  functions numeric describing type sea level. Can 0 constant, 1 sine function describing area time. peak numeric value specifying peakiness (shaprness) ontogeny curve. Higher values imply peakier ontogeny. value internally calculated calc_peak() given area present area_pars. Amax numeric value maximum island area simulation. Amin numeric value minimum island area simulation. extcutoff numeric cutoff maximum extinction rate preventing large slowing simulation. cond cond = 0 : conditioning island age  cond = 1 : conditioning island age non-extinction island biota . cond > 1 : conditioning island age least cond colonizations island. last option yet available IW model verbose numeric vector length 1, simulations `DAISIEdataprep()` can `1` `0`, `1` gives intermediate output printed. ML functions numeric determining intermediate output printed. default: `0` print, `1` prints initial likelihood settings selected (parameters optimised, fixed shifted), `2` prints `1 also intermediate output parameters loglikelihood, `3` `2` prints intermediate progress likelihood computation.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_time_dep_cs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Simulates island replicates with an clade-specific (CS) diversity-dependent time-dependent process — DAISIE_sim_time_dep_cs","text":"list. highest level least corresponds individual replicate. See return `DAISIE_sim_time_dep()` details.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_time_dep_gw.html","id":null,"dir":"Reference","previous_headings":"","what":"Simulates island replicates with an guild-wide (GW) diversity-dependent time-dependent process — DAISIE_sim_time_dep_gw","title":"Simulates island replicates with an guild-wide (GW) diversity-dependent time-dependent process — DAISIE_sim_time_dep_gw","text":"Simulates island replicates guild-wide (GW) diversity-dependent time-dependent process","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_time_dep_gw.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulates island replicates with an guild-wide (GW) diversity-dependent time-dependent process — DAISIE_sim_time_dep_gw","text":"","code":"DAISIE_sim_time_dep_gw(   total_time,   M,   pars,   replicates,   area_pars,   hyper_pars,   nonoceanic_pars,   num_guilds,   sample_freq,   island_ontogeny,   sea_level,   peak,   Amax,   Amin,   extcutoff,   verbose )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_time_dep_gw.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulates island replicates with an guild-wide (GW) diversity-dependent time-dependent process — DAISIE_sim_time_dep_gw","text":"total_time Numeric defining length simulation time units. M Numeric defining size mainland pool, .e. number species can potentially colonize island. pars numeric vector containing model parameters: pars[1]: lambda^c (cladogenesis rate) pars[2]: mu (extinction rate) pars[3]: K (carrying capacity), set K=Inf diversity   independence. pars[4]: gamma (immigration rate) pars[5]: lambda^(anagenesis rate) pars[6]: lambda^c (cladogenesis rate) either type 2 species   rate set 2 rate shift model pars[7]: mu (extinction rate) either type 2 species rate   set 2 rate shift model pars[8]: K (carrying capacity) either type 2 species rate   set 2 rate shift model, set K=Inf diversity independence. pars[9]: gamma (immigration rate) either type 2 species   rate set 2 rate shift model pars[10]: lambda^(anagenesis rate) either type 2   species rate set 2 rate shift model Elements 6:10 required type 2 species included rate shift model. DAISIE_sim_relaxed_rate() pars[6] standard deviation gamma distribution relaxed parameter parameter chosen relaxed_par argument mean gamma distribution relaxed parameter. replicates Integer specifying number island replicates simulated. area_pars named list containing area sea level parameters created create_area_pars(): [1]: maximum area [2]: current area [3]: value 0 1 indicating island's history   peak area achieved [4]: total island age [5]: amplitude area fluctuation sea level [6]: frequency sine wave area change sea level [7]: angle slope island hyper_pars named list numeric hyperparameters rate calculations returned create_hyper_pars(): [1]: d scaling parameter exponent calculating   cladogenesis rate [2]: x exponent calculating extinction rate nonoceanic_pars vector length two : [1]: probability sampling species mainland [2]: probability species sampled mainland   nonendemic num_guilds number guilds mainland. number mainland species divided number guilds divdepmodel = \"GW\" sample_freq Numeric specifing number units times divided plotting purposes. Larger values lead plots higher resolution, also run slower. island_ontogeny DAISIE_sim_time_dep(), DAISIE_ML_CS plotting string describing type island ontogeny. Can \"const\", \"beta\" beta function describing area time.  functions numeric describing type island ontogeny. Can 0 constant, 1 beta function describing area time. ML functions island_ontogeny = NA assumes constant ontogeny. Time dependent estimation yet available development still ongoing. return error called case. sea_level DAISIE_sim_time_dep() plotting string describing type sea level. Can \"const\" \"sine\" sine function describing area time.  functions numeric describing type sea level. Can 0 constant, 1 sine function describing area time. peak numeric value specifying peakiness (shaprness) ontogeny curve. Higher values imply peakier ontogeny. value internally calculated calc_peak() given area present area_pars. Amax numeric value maximum island area simulation. Amin numeric value minimum island area simulation. extcutoff numeric cutoff maximum extinction rate preventing large slowing simulation. verbose numeric vector length 1, simulations `DAISIEdataprep()` can `1` `0`, `1` gives intermediate output printed. ML functions numeric determining intermediate output printed. default: `0` print, `1` prints initial likelihood settings selected (parameters optimised, fixed shifted), `2` prints `1 also intermediate output parameters loglikelihood, `3` `2` prints intermediate progress likelihood computation.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_time_dep_gw.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Simulates island replicates with an guild-wide (GW) diversity-dependent time-dependent process — DAISIE_sim_time_dep_gw","text":"list. highest level least corresponds individual replicate. See return `DAISIE_sim_time_dep()` details.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_time_dep_iw.html","id":null,"dir":"Reference","previous_headings":"","what":"Simulates island replicates with an island-wide (IW) diversity-dependent time-dependent process — DAISIE_sim_time_dep_iw","title":"Simulates island replicates with an island-wide (IW) diversity-dependent time-dependent process — DAISIE_sim_time_dep_iw","text":"Simulates island replicates island-wide (IW) diversity-dependent time-dependent process","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_time_dep_iw.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulates island replicates with an island-wide (IW) diversity-dependent time-dependent process — DAISIE_sim_time_dep_iw","text":"","code":"DAISIE_sim_time_dep_iw(   total_time,   M,   pars,   replicates,   area_pars,   hyper_pars,   nonoceanic_pars,   sample_freq,   island_ontogeny,   sea_level,   peak,   Amax,   Amin,   extcutoff,   cond,   verbose )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_time_dep_iw.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulates island replicates with an island-wide (IW) diversity-dependent time-dependent process — DAISIE_sim_time_dep_iw","text":"total_time Numeric defining length simulation time units. M Numeric defining size mainland pool, .e. number species can potentially colonize island. pars numeric vector containing model parameters: pars[1]: lambda^c (cladogenesis rate) pars[2]: mu (extinction rate) pars[3]: K (carrying capacity), set K=Inf diversity   independence. pars[4]: gamma (immigration rate) pars[5]: lambda^(anagenesis rate) pars[6]: lambda^c (cladogenesis rate) either type 2 species   rate set 2 rate shift model pars[7]: mu (extinction rate) either type 2 species rate   set 2 rate shift model pars[8]: K (carrying capacity) either type 2 species rate   set 2 rate shift model, set K=Inf diversity independence. pars[9]: gamma (immigration rate) either type 2 species   rate set 2 rate shift model pars[10]: lambda^(anagenesis rate) either type 2   species rate set 2 rate shift model Elements 6:10 required type 2 species included rate shift model. DAISIE_sim_relaxed_rate() pars[6] standard deviation gamma distribution relaxed parameter parameter chosen relaxed_par argument mean gamma distribution relaxed parameter. replicates Integer specifying number island replicates simulated. area_pars named list containing area sea level parameters created create_area_pars(): [1]: maximum area [2]: current area [3]: value 0 1 indicating island's history   peak area achieved [4]: total island age [5]: amplitude area fluctuation sea level [6]: frequency sine wave area change sea level [7]: angle slope island hyper_pars named list numeric hyperparameters rate calculations returned create_hyper_pars(): [1]: d scaling parameter exponent calculating   cladogenesis rate [2]: x exponent calculating extinction rate nonoceanic_pars vector length two : [1]: probability sampling species mainland [2]: probability species sampled mainland   nonendemic sample_freq Numeric specifing number units times divided plotting purposes. Larger values lead plots higher resolution, also run slower. island_ontogeny DAISIE_sim_time_dep(), DAISIE_ML_CS plotting string describing type island ontogeny. Can \"const\", \"beta\" beta function describing area time.  functions numeric describing type island ontogeny. Can 0 constant, 1 beta function describing area time. ML functions island_ontogeny = NA assumes constant ontogeny. Time dependent estimation yet available development still ongoing. return error called case. sea_level DAISIE_sim_time_dep() plotting string describing type sea level. Can \"const\" \"sine\" sine function describing area time.  functions numeric describing type sea level. Can 0 constant, 1 sine function describing area time. peak numeric value specifying peakiness (shaprness) ontogeny curve. Higher values imply peakier ontogeny. value internally calculated calc_peak() given area present area_pars. Amax numeric value maximum island area simulation. Amin numeric value minimum island area simulation. extcutoff numeric cutoff maximum extinction rate preventing large slowing simulation. cond cond = 0 : conditioning island age  cond = 1 : conditioning island age non-extinction island biota . cond > 1 : conditioning island age least cond colonizations island. last option yet available IW model verbose numeric vector length 1, simulations `DAISIEdataprep()` can `1` `0`, `1` gives intermediate output printed. ML functions numeric determining intermediate output printed. default: `0` print, `1` prints initial likelihood settings selected (parameters optimised, fixed shifted), `2` prints `1 also intermediate output parameters loglikelihood, `3` `2` prints intermediate progress likelihood computation.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_time_dep_iw.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Simulates island replicates with an island-wide (IW) diversity-dependent time-dependent process — DAISIE_sim_time_dep_iw","text":"list. highest level least corresponds individual replicate. See return `DAISIE_sim_time_dep()` details.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_trait_dep.html","id":null,"dir":"Reference","previous_headings":"","what":"Simulate islands with given trait-dependent parameters. — DAISIE_sim_trait_dep","title":"Simulate islands with given trait-dependent parameters. — DAISIE_sim_trait_dep","text":"function simulates islands given cladogenesis, extinction, K, immigration anagenesis parameters binary states. Returns R list object contains simulated islands","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_trait_dep.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulate islands with given trait-dependent parameters. — DAISIE_sim_trait_dep","text":"","code":"DAISIE_sim_trait_dep(   time,   M,   pars,   replicates,   divdepmodel = \"CS\",   sample_freq = 25,   plot_sims = TRUE,   island_ontogeny = \"const\",   sea_level = \"const\",   hyper_pars = create_hyper_pars(d = 0, x = 0),   area_pars = DAISIE::create_area_pars(max_area = 1, current_area = 1,     proportional_peak_t = 0, total_island_age = 0, sea_level_amplitude = 0,     sea_level_frequency = 0, island_gradient_angle = 0),   extcutoff = 1000,   cond = 0,   verbose = TRUE,   trait_pars = NULL,   ... )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_trait_dep.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulate islands with given trait-dependent parameters. — DAISIE_sim_trait_dep","text":"time Numeric defining length simulation time units. example, island known 4 million years old, setting time = 4 simulate entire life span island; setting time = 2 stop simulation mid-life island. M Numeric defining size mainland pool, .e. number species can potentially colonize island. pars numeric vector containing model parameters: pars[1]: lambda^c (cladogenesis rate) pars[2]: mu (extinction rate) pars[3]: K (carrying capacity), set K=Inf diversity   independence. pars[4]: gamma (immigration rate) pars[5]: lambda^(anagenesis rate) pars[6]: lambda^c (cladogenesis rate) either type 2 species   rate set 2 rate shift model pars[7]: mu (extinction rate) either type 2 species rate   set 2 rate shift model pars[8]: K (carrying capacity) either type 2 species rate   set 2 rate shift model, set K=Inf diversity independence. pars[9]: gamma (immigration rate) either type 2 species   rate set 2 rate shift model pars[10]: lambda^(anagenesis rate) either type 2   species rate set 2 rate shift model Elements 6:10 required type 2 species included rate shift model. DAISIE_sim_relaxed_rate() pars[6] standard deviation gamma distribution relaxed parameter parameter chosen relaxed_par argument mean gamma distribution relaxed parameter. replicates Integer specifying number island replicates simulated. divdepmodel Option divdepmodel = 'CS' runs model clade-specific carrying capacity, diversity-dependence operates within single clades, .e. among species originating mainland colonist. Option divdepmodel = 'IW' runs model island-wide carrying capacity, diversity-dependence operates within among clades. Option divdepmodel = 'GW' runs model diversity-dependence operates within guild. sample_freq Numeric specifing number units times divided plotting purposes. Larger values lead plots higher resolution, also run slower. plot_sims Default = TRUE plots species--time (STT) plots. detects many types species present. one type species present, STT plotted species. two types present, three plots produced: STT , STT type 1 STT type 2. island_ontogeny DAISIE_sim_time_dep(), DAISIE_ML_CS plotting string describing type island ontogeny. Can \"const\", \"beta\" beta function describing area time.  functions numeric describing type island ontogeny. Can 0 constant, 1 beta function describing area time. ML functions island_ontogeny = NA assumes constant ontogeny. Time dependent estimation yet available development still ongoing. return error called case. sea_level DAISIE_sim_time_dep() plotting string describing type sea level. Can \"const\" \"sine\" sine function describing area time.  functions numeric describing type sea level. Can 0 constant, 1 sine function describing area time. hyper_pars named list numeric hyperparameters rate calculations returned create_hyper_pars(): [1]: d scaling parameter exponent calculating   cladogenesis rate [2]: x exponent calculating extinction rate area_pars named list containing area sea level parameters created create_area_pars(): [1]: maximum area [2]: current area [3]: value 0 1 indicating island's history   peak area achieved [4]: total island age [5]: amplitude area fluctuation sea level [6]: frequency sine wave area change sea level [7]: angle slope island extcutoff numeric cutoff maximum extinction rate preventing large slowing simulation. cond cond = 0 : conditioning island age  cond = 1 : conditioning island age non-extinction island biota . cond > 1 : conditioning island age least cond colonizations island. last option yet available IW model verbose numeric vector length 1, simulations `DAISIEdataprep()` can `1` `0`, `1` gives intermediate output printed. ML functions numeric determining intermediate output printed. default: `0` print, `1` prints initial likelihood settings selected (parameters optimised, fixed shifted), `2` prints `1 also intermediate output parameters loglikelihood, `3` `2` prints intermediate progress likelihood computation. trait_pars named list containing diversification rates considering   two trait states created create_trait_pars: [1]:numeric per capita transition rate state1 [2]:numeric per capita immigration rate state2 [3]:numeric per capita extinction rate state2 [4]:numeric per capita anagenesis rate state2 [5]:numeric per capita cladogenesis rate state2 [6]:numeric per capita transition rate state2 [7]:numeric number species trait state 2    mainland ... arguments pass plotting functions.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_trait_dep.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Simulate islands with given trait-dependent parameters. — DAISIE_sim_trait_dep","text":"list. highest level least corresponds individual replciate. first element replicate composed island information containing: $island_age: numeric island age. $not_present: numeric number mainland lineages   present island. $stt_all: STT table species island     (nI - number non-endemic species; nA - number anagenetic species,     nC - number cladogenetic species, present - number independent     colonisations present) $brts_table: simulations \"IW\". Table containing information order events data, use maximum likelihood optimization.). subsequent elements list pertaining replcate contain information single colonist lineage island 4 components: $branching_times: island age stem age     population/species case Non-endemic, Non-endemic_MaxAge     Endemic anagenetic species. cladogenetic species     island age branching times radiation including     stem age radiation. $stac: integer ranging 1 4   indicating status colonist: $missing_species: number island species sampled particular clade (applicable endemic clades) $type_1or2: whether colonist belongs type 1 type 2","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_trait_dep.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Simulate islands with given trait-dependent parameters. — DAISIE_sim_trait_dep","text":"Valente, L.M., .B. Phillimore R.S. Etienne (2015). Equilibrium non-equilibrium dynamics simultaneously operate Galapagos islands. Ecology Letters 18: 844-852. Hauffe, T., D. Delicado, R.S. Etienne L. Valente (submitted). Lake expansion increases equilibrium diversity via target effect island biogeography.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_trait_dep.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Simulate islands with given trait-dependent parameters. — DAISIE_sim_trait_dep","text":"Luis Valente Albert Phillimore","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_trait_dep_2K.html","id":null,"dir":"Reference","previous_headings":"","what":"Simulate islands with given trait-dependent parameters. — DAISIE_sim_trait_dep_2K","title":"Simulate islands with given trait-dependent parameters. — DAISIE_sim_trait_dep_2K","text":"function simulates islands given cladogenesis, extinction, K, immigration anagenesis parameters. version, rates K trait-dependent. Returns R list object contains simulated islands","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_trait_dep_2K.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulate islands with given trait-dependent parameters. — DAISIE_sim_trait_dep_2K","text":"","code":"DAISIE_sim_trait_dep_2K(   time,   M,   pars,   replicates,   divdepmodel = \"CS\",   sample_freq = 25,   plot_sims = TRUE,   island_ontogeny = \"const\",   sea_level = \"const\",   hyper_pars = create_hyper_pars(d = 0, x = 0),   area_pars = DAISIE::create_area_pars(max_area = 1, current_area = 1,     proportional_peak_t = 0, total_island_age = 0, sea_level_amplitude = 0,     sea_level_frequency = 0, island_gradient_angle = 0),   extcutoff = 1000,   cond = 0,   verbose = TRUE,   trait_pars = NULL,   ... )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_trait_dep_2K.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulate islands with given trait-dependent parameters. — DAISIE_sim_trait_dep_2K","text":"time Numeric defining length simulation time units. example, island known 4 million years old, setting time = 4 simulate entire life span island; setting time = 2 stop simulation mid-life island. M Numeric defining size mainland pool, .e. number species can potentially colonize island. pars numeric vector containing model parameters: pars[1]: lambda^c (cladogenesis rate) pars[2]: mu (extinction rate) pars[3]: K (carrying capacity), set K=Inf diversity   independence. pars[4]: gamma (immigration rate) pars[5]: lambda^(anagenesis rate) pars[6]: lambda^c (cladogenesis rate) either type 2 species   rate set 2 rate shift model pars[7]: mu (extinction rate) either type 2 species rate   set 2 rate shift model pars[8]: K (carrying capacity) either type 2 species rate   set 2 rate shift model, set K=Inf diversity independence. pars[9]: gamma (immigration rate) either type 2 species   rate set 2 rate shift model pars[10]: lambda^(anagenesis rate) either type 2   species rate set 2 rate shift model Elements 6:10 required type 2 species included rate shift model. DAISIE_sim_relaxed_rate() pars[6] standard deviation gamma distribution relaxed parameter parameter chosen relaxed_par argument mean gamma distribution relaxed parameter. replicates Integer specifying number island replicates simulated. divdepmodel Option divdepmodel = 'CS' runs model clade-specific carrying capacity, diversity-dependence operates within single clades, .e. among species originating mainland colonist. Option divdepmodel = 'IW' runs model island-wide carrying capacity, diversity-dependence operates within among clades. Option divdepmodel = 'GW' runs model diversity-dependence operates within guild. sample_freq Numeric specifing number units times divided plotting purposes. Larger values lead plots higher resolution, also run slower. plot_sims Default = TRUE plots species--time (STT) plots. detects many types species present. one type species present, STT plotted species. two types present, three plots produced: STT , STT type 1 STT type 2. island_ontogeny DAISIE_sim_time_dep(), DAISIE_ML_CS plotting string describing type island ontogeny. Can \"const\", \"beta\" beta function describing area time.  functions numeric describing type island ontogeny. Can 0 constant, 1 beta function describing area time. ML functions island_ontogeny = NA assumes constant ontogeny. Time dependent estimation yet available development still ongoing. return error called case. sea_level DAISIE_sim_time_dep() plotting string describing type sea level. Can \"const\" \"sine\" sine function describing area time.  functions numeric describing type sea level. Can 0 constant, 1 sine function describing area time. hyper_pars named list numeric hyperparameters rate calculations returned create_hyper_pars(): [1]: d scaling parameter exponent calculating   cladogenesis rate [2]: x exponent calculating extinction rate area_pars named list containing area sea level parameters created create_area_pars(): [1]: maximum area [2]: current area [3]: value 0 1 indicating island's history   peak area achieved [4]: total island age [5]: amplitude area fluctuation sea level [6]: frequency sine wave area change sea level [7]: angle slope island extcutoff numeric cutoff maximum extinction rate preventing large slowing simulation. cond cond = 0 : conditioning island age  cond = 1 : conditioning island age non-extinction island biota . cond > 1 : conditioning island age least cond colonizations island. last option yet available IW model verbose numeric vector length 1, simulations `DAISIEdataprep()` can `1` `0`, `1` gives intermediate output printed. ML functions numeric determining intermediate output printed. default: `0` print, `1` prints initial likelihood settings selected (parameters optimised, fixed shifted), `2` prints `1 also intermediate output parameters loglikelihood, `3` `2` prints intermediate progress likelihood computation. trait_pars named list containing diversification rates considering   two trait states created create_trait_pars: [1]:numeric per capita transition rate state1 [2]:numeric per capita immigration rate state2 [3]:numeric per capita extinction rate state2 [4]:numeric per capita anagenesis rate state2 [5]:numeric per capita cladogenesis rate state2 [6]:numeric per capita transition rate state2 [7]:numeric number species trait state 2    mainland ... arguments pass plotting functions.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_trait_dep_2K.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Simulate islands with given trait-dependent parameters. — DAISIE_sim_trait_dep_2K","text":"list. highest level least corresponds individual replciate. first element replicate composed island information containing: $island_age: numeric island age. $not_present: numeric number mainland lineages   present island. $stt_all: STT table species island     (nI - number non-endemic species; nA - number anagenetic species,     nC - number cladogenetic species, present - number independent     colonisations present) $brts_table: simulations \"IW\". Table containing information order events data, use maximum likelihood optimization.). subsequent elements list pertaining replcate contain information single colonist lineage island 4 components: $branching_times: island age stem age     population/species case Non-endemic, Non-endemic_MaxAge     Endemic anagenetic species. cladogenetic species     island age branching times radiation including     stem age radiation. $stac: integer ranging 1 4   indicating status colonist: $missing_species: number island species sampled particular clade (applicable endemic clades) $type_1or2: whether colonist belongs type 1 type 2","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_trait_dep_2K.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Simulate islands with given trait-dependent parameters. — DAISIE_sim_trait_dep_2K","text":"Valente, L.M., .B. Phillimore R.S. Etienne (2015). Equilibrium non-equilibrium dynamics simultaneously operate Galapagos islands. Ecology Letters 18: 844-852. Hauffe, T., D. Delicado, R.S. Etienne L. Valente (submitted). Lake expansion increases equilibrium diversity via target effect island biogeography.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_trait_dep_2K.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Simulate islands with given trait-dependent parameters. — DAISIE_sim_trait_dep_2K","text":"Luis Valente Albert Phillimore","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_update_state_cr.html","id":null,"dir":"Reference","previous_headings":"","what":"Updates state of island given sampled event for a constant rate case. — DAISIE_sim_update_state_cr","title":"Updates state of island given sampled event for a constant rate case. — DAISIE_sim_update_state_cr","text":"Makes event happen updating island species matrix species IDs. event happens determined sampling algorithm.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_update_state_cr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Updates state of island given sampled event for a constant rate case. — DAISIE_sim_update_state_cr","text":"","code":"DAISIE_sim_update_state_cr(   timeval,   total_time,   possible_event,   maxspecID,   mainland_spec,   island_spec,   stt_table )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_update_state_cr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Updates state of island given sampled event for a constant rate case. — DAISIE_sim_update_state_cr","text":"timeval Numeric defining current time simulation. total_time Numeric defining length simulation time units. possible_event Numeric defining event happen. maxspecID Current species IDs. mainland_spec Number mainland species. island_spec Matrix current state simulation containing number species. stt_table Matrix number species time step.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_update_state_cr.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Updates state of island given sampled event for a constant rate case. — DAISIE_sim_update_state_cr","text":"updated state system, list island_spec matrix, integer maxspecID recent ID species stt_table, matrix current species time table.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_update_state_time_dep.html","id":null,"dir":"Reference","previous_headings":"","what":"Updates state of island given sampled event — DAISIE_sim_update_state_time_dep","title":"Updates state of island given sampled event — DAISIE_sim_update_state_time_dep","text":"Makes event happen updating island species matrix species IDs. event happens determined sampling algorithm.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_update_state_time_dep.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Updates state of island given sampled event — DAISIE_sim_update_state_time_dep","text":"","code":"DAISIE_sim_update_state_time_dep(   timeval,   total_time,   possible_event,   maxspecID,   mainland_spec,   island_spec,   stt_table,   rates,   max_rates )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_update_state_time_dep.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Updates state of island given sampled event — DAISIE_sim_update_state_time_dep","text":"timeval Numeric defining current time simulation. total_time Numeric defining length simulation time units. possible_event Numeric defining event happen. maxspecID Current species IDs. mainland_spec Number mainland species. island_spec Matrix current state simulation containing number species. stt_table Matrix number species time step. rates named list numeric rates returned update_rates(). max_rates named list numeric max rates returned update_max_rates().","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_update_state_time_dep.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Updates state of island given sampled event — DAISIE_sim_update_state_time_dep","text":"updated state system, list island_spec matrix, integer maxspecID recent ID species stt_table, matrix current species time table.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_update_state_trait_dep.html","id":null,"dir":"Reference","previous_headings":"","what":"Updates state of island given sampled event with two trait states. — DAISIE_sim_update_state_trait_dep","title":"Updates state of island given sampled event with two trait states. — DAISIE_sim_update_state_trait_dep","text":"Makes event happen updating island species matrix species IDs. event happens determined sampling algorithm.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_update_state_trait_dep.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Updates state of island given sampled event with two trait states. — DAISIE_sim_update_state_trait_dep","text":"","code":"DAISIE_sim_update_state_trait_dep(   timeval,   total_time,   possible_event,   maxspecID,   mainland_spec,   island_spec,   stt_table,   trait_pars )"},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_update_state_trait_dep.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Updates state of island given sampled event with two trait states. — DAISIE_sim_update_state_trait_dep","text":"timeval Numeric defining current time simulation. total_time Numeric defining length simulation time units. possible_event Numeric defining event happen. maxspecID Current species IDs. mainland_spec Number mainland species. island_spec Matrix current state simulation containing number species. stt_table Matrix number species time step. trait_pars named list containing diversification rates considering   two trait states created create_trait_pars: [1]:numeric per capita transition rate state1 [2]:numeric per capita immigration rate state2 [3]:numeric per capita extinction rate state2 [4]:numeric per capita anagenesis rate state2 [5]:numeric per capita cladogenesis rate state2 [6]:numeric per capita transition rate state2 [7]:numeric number species trait state 2    mainland","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/DAISIE_sim_update_state_trait_dep.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Updates state of island given sampled event with two trait states. — DAISIE_sim_update_state_trait_dep","text":"updated state system, list island_spec matrix, integer maxspecID recent ID species stt_table, matrix current species time table.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/Galapagos_datalist.html","id":null,"dir":"Reference","previous_headings":"","what":"Colonization and branching times of 8 terrestrial avifaunal clades in list format, accepted by DAISIE_ML and DAISIE_loglik_all — Galapagos_datalist","title":"Colonization and branching times of 8 terrestrial avifaunal clades in list format, accepted by DAISIE_ML and DAISIE_loglik_all — Galapagos_datalist","text":"list containing colonization branching times terrestrial avifauna Galapagos distinction made types colonists. list can generated using DAISIE_dataprep function, converts user-specified data table data object, object can course also entered directly. R list object following elements. first element list two components: $island_age - island age $not_present - number mainland lineages present island  following 8 elements list contains information single colonist lineage island 5 components:$colonist_name - name species clade colonized island $branching_times - island age followed stem age population/species case Non-endemic, Non-endemic_MaxAge species Endemic species close relatives island. endemic clades one species island (cladogenetic clades/ radiations) island age followed branching times island cladeincluding stem age clade.$stac - status colonist  * Non_endemic_MaxAge: 1  * Endemic: 2  * Endemic&Non_Endemic: 3  * Non_endemic: 4 $missing_species - number island species sampled particular clade (applicable endemic clades) $type1or2 - whether colonist belongs type 1 type 2. dataset equal 1.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/Galapagos_datalist.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Colonization and branching times of 8 terrestrial avifaunal clades in list format, accepted by DAISIE_ML and DAISIE_loglik_all — Galapagos_datalist","text":"list 9 elements first contains 2 elements following 8 containing 5 components.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/Galapagos_datalist.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Colonization and branching times of 8 terrestrial avifaunal clades in list format, accepted by DAISIE_ML and DAISIE_loglik_all — Galapagos_datalist","text":"Valente, L.M., .B. Phillimore R.S. Etienne (2015). Equilibrium non-equilibrium dynamics simultaneously operate Galapagos islands. Ecology Letters 18: 844-852.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/Galapagos_datalist_2types.html","id":null,"dir":"Reference","previous_headings":"","what":"Colonization and branching times of 8 terrestrial avifaunal clades in list format, accepted by DAISIE_ML and DAISIE_loglik_all — Galapagos_datalist_2types","title":"Colonization and branching times of 8 terrestrial avifaunal clades in list format, accepted by DAISIE_ML and DAISIE_loglik_all — Galapagos_datalist_2types","text":"list containing colonization branching times terrestrial avifauna Galapagos. list can generated using DAISIE_dataprep function, converts user-specified data table data object, object can course also entered directly. R list object following elements. first element list three components: $island_age - island age $not_present_type1 - number mainland lineages type 1 present island $not_present_type2 - number mainland lineages type 2 present island  following 8 elements list contains information single colonist lineage island 5 components:$colonist_name - name species clade colonized island $branching_times - island age followed stem age population/species case Non-endemic, Non-endemic_MaxAge species Endemic species close relatives island. endemic clades one species island (cladogenetic clades/ radiations) island age followed branching times island cladeincluding stem age clade.$stac - status colonist  * Non_endemic_MaxAge: 1  * Endemic: 2  * Endemic&Non_Endemic: 3  * Non_endemic: 4 $missing_species - number island species sampled particular clade (applicable endemic clades) $type1or2 - whether colonist belongs type 1 type 2. dataset finches type 2","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/Galapagos_datalist_2types.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Colonization and branching times of 8 terrestrial avifaunal clades in list format, accepted by DAISIE_ML and DAISIE_loglik_all — Galapagos_datalist_2types","text":"list 9 elements first contains 3 elements following 8 containing 5 components.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/Galapagos_datalist_2types.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Colonization and branching times of 8 terrestrial avifaunal clades in list format, accepted by DAISIE_ML and DAISIE_loglik_all — Galapagos_datalist_2types","text":"Valente, L.M., .B. Phillimore R.S. Etienne (2015). Equilibrium non-equilibrium dynamics simultaneously operate Galapagos islands. Ecology Letters 18: 844-852.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/Galapagos_datatable.html","id":null,"dir":"Reference","previous_headings":"","what":"Colonization and branching times of 8 terrestrial avifaunal Galápagos clades in table format. — Galapagos_datatable","title":"Colonization and branching times of 8 terrestrial avifaunal Galápagos clades in table format. — Galapagos_datatable","text":"table containing colonization branching times terrestrial avifauna Galápagos. row table represents independent colonisation event. table four columns. $Clade_name - name independent colonization event $Status - One following categories:  * Non_endemic: non-endemic island species approximate time colonisation known  * Non_endemic_MaxAge: non-endemic island species colonisation time unknown  * Endemic: endemic species approximate colonisation time known  * \"Endemic_MaxAge\": applies endemic species endemic clades cases colonisation time unknown, user wants specify upper bound colonisation. example apply endemic species recently gone extinct anthropogenic causes, included phylogeny (\"NA\" given branching times column). also apply insular radiations long stem branches, time first cladogenetic event known, precise time colonisation . * Endemic&Non_Endemic: endemic clade mainland ancestor re-colonized $Missing_species - Number island species sampled particular clade (applicable endemic clades)$Branching_times - Stem age population/species case \"Non_endemic\",  \"Non_endemic_MaxAge\" \"Endemic\" species extant close relatives island.  Set \"NA\" colonisation time unknown upper bound known. \"Endemic\" cladogenetic species branching times radiation, including stem age radiation (colonisation time estimate).","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/Galapagos_datatable.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Colonization and branching times of 8 terrestrial avifaunal Galápagos clades in table format. — Galapagos_datatable","text":"table 8 rows 4 columns.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/Galapagos_datatable.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Colonization and branching times of 8 terrestrial avifaunal Galápagos clades in table format. — Galapagos_datatable","text":"Valente, L.M., .B. Phillimore R.S. Etienne (2015). Equilibrium non-equilibrium dynamics simultaneously operate Galapagos islands. Ecology Letters 18: 844-852.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/Macaronesia_datalist.html","id":null,"dir":"Reference","previous_headings":"","what":"Colonization and branching times of terrestrial avifaunal clades from Azores, Canary Islands, Cape Verde and Madeira in list format, accepted by DAISIE_ML and DAISIE_loglik_all — Macaronesia_datalist","title":"Colonization and branching times of terrestrial avifaunal clades from Azores, Canary Islands, Cape Verde and Madeira in list format, accepted by DAISIE_ML and DAISIE_loglik_all — Macaronesia_datalist","text":"list containing colonization branching times terrestrial avifauna 4 archipelagos: Azores, Canary Islands, Cape Verde Madeira. R list object 4 main elements corresponding archipelagos (e.g. Macaronesia_datalist[[1]] calls Azores data). four elements made several elemants: first element list archipelago two components: $island_age - island age $not_present - number mainland lineages present island  following elements list contains information single colonist lineage island 5 components:$colonist_name - name species clade colonized island $branching_times - island age followed stem age population/species case Non-endemic, Non-endemic_MaxAge species Endemic species close relatives island. endemic clades one species island (cladogenetic clades/ radiations) island age followed branching times island clade including stem age clade.  * Non_endemic_MaxAge: 1 * Endemic: 2  * Endemic&Non_Endemic: 3  * Non_endemic: 4  * Endemic_MaxAge: 5 $missing_species - number island species sampled particular clade (applicable endemic clades) $type1or2 - whether colonist belongs type 1 type 2. dataset equal 1.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/Macaronesia_datalist.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Colonization and branching times of terrestrial avifaunal clades from Azores, Canary Islands, Cape Verde and Madeira in list format, accepted by DAISIE_ML and DAISIE_loglik_all — Macaronesia_datalist","text":"list 4 main elements archipelago. element several sub-elements.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/Macaronesia_datalist.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Colonization and branching times of terrestrial avifaunal clades from Azores, Canary Islands, Cape Verde and Madeira in list format, accepted by DAISIE_ML and DAISIE_loglik_all — Macaronesia_datalist","text":"Valente L., Illera J.C, Havenstein K., Pallien T., Etienne R.S., Tiedemann R. Equilibrium bird species diversity Atlantic islands. 2017 Current Biology, 27, 1660-1666.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/NewZealand_birds_datalist.html","id":null,"dir":"Reference","previous_headings":"","what":"Colonization and branching times of New Zealand birds. — NewZealand_birds_datalist","title":"Colonization and branching times of New Zealand birds. — NewZealand_birds_datalist","text":"list containing colonization branching times birds New Zealand. Main dataset used Valente, Etienne, Garcia-R (2019) Current Biology. Island age 52 Myr mainland pool size 1000 species.  first element list two components: $island_age - island age $not_present - number mainland lineages present island  following elements list contain information single colonist lineage island 5 components:$colonist_name - name species clade colonized island $branching_times - island age followed stem age population/species case Non-endemic, Non-endemic_MaxAge species Endemic species close relatives island. endemic clades one species island (cladogenetic clades/ radiations) island age followed branching times island clade including stem age clade.$stac - status colonist  * Non_endemic_MaxAge: 1  * Endemic: 2  * Endemic&Non_Endemic: 3  * Non_endemic: 4  * Endemic_MaxAge: 5 6 $missing_species - number island species sampled particular clade (applicable endemic clades) $type1or2 - whether colonist belongs type 1 type 2. dataset equal 1.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/NewZealand_birds_datalist.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Colonization and branching times of New Zealand birds. — NewZealand_birds_datalist","text":"list 40 elements, first contains 2 elements following 39 containing 5 components.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/NewZealand_birds_datalist.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Colonization and branching times of New Zealand birds. — NewZealand_birds_datalist","text":"Valente L, Etienne RS, Garcia-R JC (2019) Deep Macroevolutionary Impact Humans New Zealand’s Unique Avifauna. Current Biology, 29, 2563–2569.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/add_column_to_dataframe.html","id":null,"dir":"Reference","previous_headings":"","what":"Add a column to a data frame — add_column_to_dataframe","title":"Add a column to a data frame — add_column_to_dataframe","text":"Add column data frame","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/add_column_to_dataframe.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add a column to a data frame — add_column_to_dataframe","text":"","code":"add_column_to_dataframe(df, position, column_to_insert)"},{"path":"https://rsetienne.github.io/DAISIE/reference/add_column_to_dataframe.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add a column to a data frame — add_column_to_dataframe","text":"df data frame add column position location data frame insert column. Position can also name column column_to_insert elements column insert. column name, name copied data frame. Id name, get name \"nc\".","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/add_column_to_dataframe.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add a column to a data frame — add_column_to_dataframe","text":"data frame column inserted","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/archipelago_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Physical data on 41 archipelagos — archipelago_data","title":"Physical data on 41 archipelagos — archipelago_data","text":"dataframe subsequent columns name archipelago (Archipelago) area archipelago (Area), age (Age) distance mainland (Distance)","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/archipelago_data.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Physical data on 41 archipelagos — archipelago_data","text":"dataframe containing information archipelago name, area, age distance mainland","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/archipelago_data.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Physical data on 41 archipelagos — archipelago_data","text":"Valente L, Phillimore AB, Melo M, Warren BH, Clegg SM, Havenstein K,  Tiedemann R, Illera JC, Thébaud C, Aschenbach T, Etienne RS. simple dynamic model  explains island bird diversity worldwide (2020) Nature, 579, 92-96","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/archipelagos41.html","id":null,"dir":"Reference","previous_headings":"","what":"DAISIE datalist object including bird phylogenetic data and physical data for 41 archipelagos — archipelagos41","title":"DAISIE datalist object including bird phylogenetic data and physical data for 41 archipelagos — archipelagos41","text":"datalist 41 items representing 41 archipelagos. archipelago can called separately using archipelagos41[[x]] x number 1 41. Using archipelagos41[[x]][[1]] show just top part archipelago item archipelago name physical features displayed. structure archipelagos regular DAISIE datalist generated using DAISIE_dataprep.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/archipelagos41.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"DAISIE datalist object including bird phylogenetic data and physical data for 41 archipelagos — archipelagos41","text":"datalist containing data 41 archipelagos studied Valente et al 2020 (Main Dataset D1). Contains colonisation branching times bird species archipelagos. also contains information archipelago name, area, age distance nearest mainland.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/archipelagos41.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"DAISIE datalist object including bird phylogenetic data and physical data for 41 archipelagos — archipelagos41","text":"Valente L, Phillimore AB, Melo M, Warren BH, Clegg SM, Havenstein K,  Tiedemann R, Illera JC, Thébaud C, Aschenbach T, Etienne RS. simple dynamic model  explains island bird diversity worldwide (2020) Nature, 579, 92-96","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/are_rates.html","id":null,"dir":"Reference","previous_headings":"","what":"Determines if object rates are rates — are_rates","title":"Determines if object rates are rates — are_rates","text":"Determines object rates rates","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/are_rates.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Determines if object rates are rates — are_rates","text":"","code":"are_rates(rates)"},{"path":"https://rsetienne.github.io/DAISIE/reference/are_rates.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Determines if object rates are rates — are_rates","text":"rates named list numeric rates returned update_rates().","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/are_rates.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Determines if object rates are rates — are_rates","text":"TRUE object rates list rates","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/calc_Abeta.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculates the area at a point in time from a beta function — calc_Abeta","title":"Calculates the area at a point in time from a beta function — calc_Abeta","text":"Calculates area point time beta function","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/calc_Abeta.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculates the area at a point in time from a beta function — calc_Abeta","text":"","code":"calc_Abeta(proptime, proptime_max, peak, Amax)"},{"path":"https://rsetienne.github.io/DAISIE/reference/calc_Abeta.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculates the area at a point in time from a beta function — calc_Abeta","text":"proptime numeric 0 1. proportion time elapsed simulation, relation total island age (NB: simulation time, island age). proptime_max numeric 0 1. proportional_peak_t. Indicates, proportion total island age ontogeny peak occur (.e. 0.5 means peak halfway time). peak numeric value specifying peakiness (shaprness) ontogeny curve. Higher values imply peakier ontogeny. value internally calculated calc_peak() given area present area_pars. Amax numeric value maximum island area simulation.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/calc_Abeta.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculates the area at a point in time from a beta function — calc_Abeta","text":"Numeric","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/calc_Abeta.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculates the area at a point in time from a beta function — calc_Abeta","text":"Joshua Lambert, Pedro Neves, Shu Xie","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/calc_next_timeval.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculates when the next timestep will be. — calc_next_timeval","title":"Calculates when the next timestep will be. — calc_next_timeval","text":"Calculates next timestep .","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/calc_next_timeval.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculates when the next timestep will be. — calc_next_timeval","text":"","code":"calc_next_timeval(max_rates, timeval)"},{"path":"https://rsetienne.github.io/DAISIE/reference/calc_next_timeval.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculates when the next timestep will be. — calc_next_timeval","text":"max_rates named list max rates returned update_rates. timeval current time simulation","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/calc_next_timeval.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculates when the next timestep will be. — calc_next_timeval","text":"named list numeric vector containing time next timestep change time.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/calc_next_timeval.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculates when the next timestep will be. — calc_next_timeval","text":"Joshua Lambert, Pedro Neves, Shu Xie","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/calc_next_timeval_shift.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculates when the next timestep will be, and if a shift has occured. — calc_next_timeval_shift","title":"Calculates when the next timestep will be, and if a shift has occured. — calc_next_timeval_shift","text":"Calculates next timestep , shift occured.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/calc_next_timeval_shift.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculates when the next timestep will be, and if a shift has occured. — calc_next_timeval_shift","text":"","code":"calc_next_timeval_shift(max_rates, timeval, dynamic_shift_times)"},{"path":"https://rsetienne.github.io/DAISIE/reference/calc_next_timeval_shift.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculates when the next timestep will be, and if a shift has occured. — calc_next_timeval_shift","text":"max_rates named list max rates returned update_rates. timeval current time simulation dynamic_shift_times numeric vector times rate shifts.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/calc_next_timeval_shift.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculates when the next timestep will be, and if a shift has occured. — calc_next_timeval_shift","text":"named list numeric vector containing time next timestep change time.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/calc_next_timeval_shift.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculates when the next timestep will be, and if a shift has occured. — calc_next_timeval_shift","text":"Joshua Lambert, Pedro Neves, Shu Xie","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/calc_peak.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculates the peak of ontogeny curve (beta function) — calc_peak","title":"Calculates the peak of ontogeny curve (beta function) — calc_peak","text":"Calculates peak ontogeny curve (beta function)","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/calc_peak.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculates the peak of ontogeny curve (beta function) — calc_peak","text":"","code":"calc_peak(total_time, area_pars)"},{"path":"https://rsetienne.github.io/DAISIE/reference/calc_peak.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculates the peak of ontogeny curve (beta function) — calc_peak","text":"total_time Numeric defining length simulation time units. area_pars named list containing area sea level parameters created create_area_pars(): [1]: maximum area [2]: current area [3]: value 0 1 indicating island's history   peak area achieved [4]: total island age [5]: amplitude area fluctuation sea level [6]: frequency sine wave area change sea level [7]: angle slope island","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/calc_peak.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculates the peak of ontogeny curve (beta function) — calc_peak","text":"numeric","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/countspecies.html","id":null,"dir":"Reference","previous_headings":"","what":"Count the number of species — countspecies","title":"Count the number of species — countspecies","text":"Count number species","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/countspecies.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count the number of species — countspecies","text":"","code":"countspecies(datalistelement)"},{"path":"https://rsetienne.github.io/DAISIE/reference/countspecies.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count the number of species — countspecies","text":"datalistelement something","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/countspecies.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count the number of species — countspecies","text":"numeric value","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/create_CS_version.html","id":null,"dir":"Reference","previous_headings":"","what":"Creates the list object for CS_version argument in DAISIE_ML_CS — create_CS_version","title":"Creates the list object for CS_version argument in DAISIE_ML_CS — create_CS_version","text":"Creates list object CS_version argument DAISIE_ML_CS","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/create_CS_version.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Creates the list object for CS_version argument in DAISIE_ML_CS — create_CS_version","text":"","code":"create_CS_version(   model = 1,   relaxed_par = NULL,   par_sd = 0,   par_upper_bound = Inf )"},{"path":"https://rsetienne.github.io/DAISIE/reference/create_CS_version.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Creates the list object for CS_version argument in DAISIE_ML_CS — create_CS_version","text":"model CS model run, options 1 single rate DAISIE model, 2 multi-rate DAISIE, 0 IW test model relaxed_par parameter relax (integrate ). Options \"cladogenesis\", \"extinction\", \"carrying_capacity\", \"immigration\", \"anagenesis\" par_sd standard deviation parameter relax par_upper_bound upper bound parameter relax","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/create_CS_version.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Creates the list object for CS_version argument in DAISIE_ML_CS — create_CS_version","text":"list four elements model: CS model run, options 1 single rate   DAISIE model, 2 multi-rate DAISIE, 0 IW test   model relaxed_par: parameter relax (integrate ). par_sd: standard deviation parameter relax par_upperbound: upper bound parameter relax.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/create_area_pars.html","id":null,"dir":"Reference","previous_headings":"","what":"Create named list of area parameters — create_area_pars","title":"Create named list of area parameters — create_area_pars","text":"Create named list area parameters","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/create_area_pars.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create named list of area parameters — create_area_pars","text":"","code":"create_area_pars(   max_area,   current_area,   proportional_peak_t,   total_island_age,   sea_level_amplitude,   sea_level_frequency,   island_gradient_angle )"},{"path":"https://rsetienne.github.io/DAISIE/reference/create_area_pars.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create named list of area parameters — create_area_pars","text":"max_area Numeric defining maximum area. current_area numeric current island area present (.e., end simulation). proportional_peak_t Numeric value 0 1 indicating island's history peak area achieved. total_island_age Numeric defining total island age. sea_level_amplitude Numeric defining amplitude area fluctuation sea level. sea_level_frequency Numeric defining frequency sine wave area change sea level. island_gradient_angle Numeric defining angle degrees specifying slope island.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/create_area_pars.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create named list of area parameters — create_area_pars","text":"list numerical values containing area sea level parameters island ontogeny simulation","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/create_area_pars.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Create named list of area parameters — create_area_pars","text":"Richel J.C Bilderbeek, Joshua Lambert, Pedro Neves","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/create_area_pars.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create named list of area parameters — create_area_pars","text":"","code":"area_pars <- create_area_pars(   max_area = 10,   current_area = 1,   proportional_peak_t = 0.5,   total_island_age = 5,   sea_level_amplitude = 5,   sea_level_frequency = 10,   island_gradient_angle = 0   )"},{"path":"https://rsetienne.github.io/DAISIE/reference/create_full_CS_stt.html","id":null,"dir":"Reference","previous_headings":"","what":"Unsampled CS full STT — create_full_CS_stt","title":"Unsampled CS full STT — create_full_CS_stt","text":"Unsampled CS full STT","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/create_full_CS_stt.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Unsampled CS full STT — create_full_CS_stt","text":"","code":"create_full_CS_stt(stt_list, stac_vec, total_time, trait_pars = NULL)"},{"path":"https://rsetienne.github.io/DAISIE/reference/create_full_CS_stt.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Unsampled CS full STT — create_full_CS_stt","text":"stt_list List full stt tables returned DAISIE_sim_core functions stac_vec Vector status species island. total_time Numeric double total time simulation. trait_pars named list containing diversification rates considering two trait states created create_trait_pars: [1]:numeric per capita transition rate state1 [2]:numeric per capita immigration rate state2 [3]:numeric per capita extinction rate state2 [4]:numeric per capita anagenesis rate state2 [5]:numeric per capita cladogenesis rate state2 [6]:numeric per capita transition rate state2 [7]:numeric number species trait state 2    mainland","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/create_full_CS_stt.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Unsampled CS full STT — create_full_CS_stt","text":"1 complete, unsampled STT table clades island CS model generated DAISIE_sim_core functions.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/create_full_CS_stt.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Unsampled CS full STT — create_full_CS_stt","text":"Pedro Neves, Joshua Lambert, Shu Xie, Giovanni Laudanno","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/create_hyper_pars.html","id":null,"dir":"Reference","previous_headings":"","what":"Create list of hyperparameters — create_hyper_pars","title":"Create list of hyperparameters — create_hyper_pars","text":"Create list hyperparameters","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/create_hyper_pars.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create list of hyperparameters — create_hyper_pars","text":"","code":"create_hyper_pars(d, x)"},{"path":"https://rsetienne.github.io/DAISIE/reference/create_hyper_pars.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create list of hyperparameters — create_hyper_pars","text":"d Numeric defining scaling parameter exponent calculating cladogenesis rate. x Numeric defining exponent calculating extinction rate.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/create_hyper_pars.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create list of hyperparameters — create_hyper_pars","text":"Named list hyperparameters","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/create_hyper_pars.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Create list of hyperparameters — create_hyper_pars","text":"Pedro Neves, Joshua Lambert","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/create_hyper_pars.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create list of hyperparameters — create_hyper_pars","text":"","code":"hyper_pars <- create_hyper_pars(d = 0.027, x = 0.15)"},{"path":"https://rsetienne.github.io/DAISIE/reference/create_pars.html","id":null,"dir":"Reference","previous_headings":"","what":"Create vector of model parameters — create_pars","title":"Create vector of model parameters — create_pars","text":"Create vector model parameters","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/create_pars.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create vector of model parameters — create_pars","text":"","code":"create_pars(clado_rate, ext_rate, carr_cap, immig_rate, ana_rate)"},{"path":"https://rsetienne.github.io/DAISIE/reference/create_pars.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create vector of model parameters — create_pars","text":"clado_rate Numeric rate cladogenesis ext_rate Numeric rate extinction carr_cap Numeric carrying capacity immig_rate Numeric rate immigration ana_rate Numeric rate anagenesis","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/create_pars.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create vector of model parameters — create_pars","text":"Numeric vector 5 elements","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/create_pars.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create vector of model parameters — create_pars","text":"","code":"create_pars(clado_rate = 1,             ext_rate = 1,             carr_cap = 10,             immig_rate = 0.1,             ana_rate = 1) #> [1]  1.0  1.0 10.0  0.1  1.0"},{"path":"https://rsetienne.github.io/DAISIE/reference/create_trait_pars.html","id":null,"dir":"Reference","previous_headings":"","what":"Create named list of trait state parameters — create_trait_pars","title":"Create named list of trait state parameters — create_trait_pars","text":"Create named list trait state parameters","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/create_trait_pars.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create named list of trait state parameters — create_trait_pars","text":"","code":"create_trait_pars(   trans_rate,   immig_rate2,   ext_rate2,   ana_rate2,   clado_rate2,   trans_rate2,   M2 )"},{"path":"https://rsetienne.github.io/DAISIE/reference/create_trait_pars.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create named list of trait state parameters — create_trait_pars","text":"trans_rate numeric per capita transition rate state1 immig_rate2 numeric per capita immigration rate state2 ext_rate2 numeric per capita extinction rate state2 ana_rate2 numeric per capita anagenesis rate state2 clado_rate2 numeric per capita cladogenesis rate state2 trans_rate2 numeric per capita transition rate state2 M2 numeric number species trait state 2 mainland","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/create_trait_pars.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create named list of trait state parameters — create_trait_pars","text":"list numerical values containing trait state parameters","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/create_trait_pars.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create named list of trait state parameters — create_trait_pars","text":"","code":"trait_pars <- create_trait_pars(    trans_rate = 0.5,    immig_rate2 = 0.1,    ext_rate2 = 0.2,    ana_rate2 = 0.3,    clado_rate2 = 0.4,    trans_rate2 = 0.5,    M2 = 1000  )"},{"path":"https://rsetienne.github.io/DAISIE/reference/create_trait_pars_2K.html","id":null,"dir":"Reference","previous_headings":"","what":"Create named list of trait state parameters — create_trait_pars_2K","title":"Create named list of trait state parameters — create_trait_pars_2K","text":"Create named list trait state parameters","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/create_trait_pars_2K.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create named list of trait state parameters — create_trait_pars_2K","text":"","code":"create_trait_pars_2K(   trans_rate,   immig_rate2,   ext_rate2,   ana_rate2,   clado_rate2,   trans_rate2,   M2,   K2 )"},{"path":"https://rsetienne.github.io/DAISIE/reference/create_trait_pars_2K.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create named list of trait state parameters — create_trait_pars_2K","text":"trans_rate numeric per capita transition rate state1 immig_rate2 numeric per capita immigration rate state2 ext_rate2 numeric per capita extinction rate state2 ana_rate2 numeric per capita anagenesis rate state2 clado_rate2 numeric per capita cladogenesis rate state2 trans_rate2 numeric per capita transition rate state2 M2 numeric number species trait state 2 mainland K2 numeric carrying capacity state 2","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/create_trait_pars_2K.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create named list of trait state parameters — create_trait_pars_2K","text":"list numerical values containing trait state parameters","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/cum_rho.html","id":null,"dir":"Reference","previous_headings":"","what":"Cumulative Gamma distribution parameterised with mean and standard deviation — cum_rho","title":"Cumulative Gamma distribution parameterised with mean and standard deviation — cum_rho","text":"Cumulative Gamma distribution parameterised mean standard deviation","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/cum_rho.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Cumulative Gamma distribution parameterised with mean and standard deviation — cum_rho","text":"","code":"cum_rho(par_upper_bound, DAISIE_dist_pars)"},{"path":"https://rsetienne.github.io/DAISIE/reference/cum_rho.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Cumulative Gamma distribution parameterised with mean and standard deviation — cum_rho","text":"DAISIE_dist_pars numeric vector two elements, first mean second standard deviation distribution.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/cum_rho.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Cumulative Gamma distribution parameterised with mean and standard deviation — cum_rho","text":"Numeric","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/daisie_odeint_cs.html","id":null,"dir":"Reference","previous_headings":"","what":"Driver for the boost::odeint solver for the CS model — daisie_odeint_cs","title":"Driver for the boost::odeint solver for the CS model — daisie_odeint_cs","text":"Driver boost::odeint solver CS model","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/daisie_odeint_cs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Driver for the boost::odeint solver for the CS model — daisie_odeint_cs","text":"Object type `state_type`, `vector_t`<double>, result integration depending runmod chosen.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/daisie_odeint_iw.html","id":null,"dir":"Reference","previous_headings":"","what":"Driver for the boost::odeint solver for the IW model — daisie_odeint_iw","title":"Driver for the boost::odeint solver for the IW model — daisie_odeint_iw","text":"Driver boost::odeint solver IW model","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/default_params_doc.html","id":null,"dir":"Reference","previous_headings":"","what":"Default parameter documentation — default_params_doc","title":"Default parameter documentation — default_params_doc","text":"Default parameter documentation","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/default_params_doc.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Default parameter documentation — default_params_doc","text":"","code":"default_params_doc(   time,   M,   pars,   replicates,   divdepmodel,   nonoceanic_pars,   num_guilds,   prop_type2_pool,   replicates_apply_type2,   sample_freq,   plot_sims,   verbose,   area_pars,   hyper_pars,   island_ontogeny,   sea_level,   extcutoff,   shift_times,   mainland_n,   island_replicates,   island_spec,   stt_table,   rates,   max_rates,   timeval,   total_time,   possible_event,   maxspecID,   mainland_spec,   max_area,   proportional_peak_t,   total_island_age,   sea_level_amplitude,   sea_level_frequency,   island_gradient_angle,   d,   x,   simulation_outputs,   plot_plus_one,   type,   plot_lists,   ...,   datalist,   datatype,   initparsopt,   idparsopt,   idparsfix,   parsfix,   idparsnoshift,   idparsmat,   res,   ddmodel,   cond,   eqmodel,   x_E,   x_I,   tol,   maxiter,   methode,   optimmethod,   CS_version,   tolint,   datatable,   island_age,   number_clade_types,   list_type2_clades,   epss,   t,   initEI,   data_table,   endmc,   archipelago,   phylo_data,   archipelago_data,   gam,   laa,   lac,   mu,   K,   num_spec,   num_immigrants,   global_min_area_time,   global_max_area_time,   distance_type,   distance_dep,   parallel,   cpus,   pars1,   pars2,   tvec,   initprobs,   pb,   island,   title,   plot_lists_simulations,   plot_lists_simulations_MLE,   kind_of_plot,   resolution,   resol,   removed_timepoints,   A,   Amin,   Amax,   peak,   proptime,   proptime_max,   current_area,   jitter,   num_cycles,   trait_pars,   relaxed_par,   relaxed_rate_pars,   brts,   stac,   missnumspec,   DAISIE_par,   DAISIE_dist_pars,   abstolint,   reltolint,   pick,   mean,   sd,   clado_rate,   ext_rate,   carr_cap,   immig_rate,   ana_rate,   islands,   sort_clade_sizes )"},{"path":"https://rsetienne.github.io/DAISIE/reference/default_params_doc.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Default parameter documentation — default_params_doc","text":"time Numeric defining length simulation time units. example, island known 4 million years old, setting time = 4 simulate entire life span island; setting time = 2 stop simulation mid-life island. M Numeric defining size mainland pool, .e. number species can potentially colonize island. pars numeric vector containing model parameters: pars[1]: lambda^c (cladogenesis rate) pars[2]: mu (extinction rate) pars[3]: K (carrying capacity), set K=Inf diversity   independence. pars[4]: gamma (immigration rate) pars[5]: lambda^(anagenesis rate) pars[6]: lambda^c (cladogenesis rate) either type 2 species   rate set 2 rate shift model pars[7]: mu (extinction rate) either type 2 species rate   set 2 rate shift model pars[8]: K (carrying capacity) either type 2 species rate   set 2 rate shift model, set K=Inf diversity independence. pars[9]: gamma (immigration rate) either type 2 species   rate set 2 rate shift model pars[10]: lambda^(anagenesis rate) either type 2   species rate set 2 rate shift model Elements 6:10 required type 2 species included rate shift model. DAISIE_sim_relaxed_rate() pars[6] standard deviation gamma distribution relaxed parameter parameter chosen relaxed_par argument mean gamma distribution relaxed parameter. replicates Integer specifying number island replicates simulated. divdepmodel Option divdepmodel = 'CS' runs model clade-specific carrying capacity, diversity-dependence operates within single clades, .e. among species originating mainland colonist. Option divdepmodel = 'IW' runs model island-wide carrying capacity, diversity-dependence operates within among clades. Option divdepmodel = 'GW' runs model diversity-dependence operates within guild. nonoceanic_pars vector length two : [1]: probability sampling species mainland [2]: probability species sampled mainland   nonendemic num_guilds number guilds mainland. number mainland species divided number guilds divdepmodel = \"GW\" prop_type2_pool Fraction mainland species belongs second subset species (type 2). Applies two types species simulated (length(pars) = 10). DAISIE_dataprep() applies number_clade_types = 2.  DAISIE_dataprep() default \"proportional\" sets fraction proportional number clades distinct macroevolutionary process colonised island. replicates_apply_type2 Applies two types species simulated. Default replicates_apply_type2 = TRUE runs simulations number islands type 2 species colonised equal specified number replicates. recommended prop_type2_pool small rate immigration type two species (pars[9]) low, meaning replicates needed achieved adequate sample size islands type 2 species. Setting replicates_apply_type2 = FALSE simulates islands specified number replicates regardless whether type 2 species colonised . sample_freq Numeric specifing number units times divided plotting purposes. Larger values lead plots higher resolution, also run slower. plot_sims Default = TRUE plots species--time (STT) plots. detects many types species present. one type species present, STT plotted species. two types present, three plots produced: STT , STT type 1 STT type 2. verbose numeric vector length 1, simulations `DAISIEdataprep()` can `1` `0`, `1` gives intermediate output printed. ML functions numeric determining intermediate output printed. default: `0` print, `1` prints initial likelihood settings selected (parameters optimised, fixed shifted), `2` prints `1 also intermediate output parameters loglikelihood, `3` `2` prints intermediate progress likelihood computation. area_pars named list containing area sea level parameters created create_area_pars(): [1]: maximum area [2]: current area [3]: value 0 1 indicating island's history   peak area achieved [4]: total island age [5]: amplitude area fluctuation sea level [6]: frequency sine wave area change sea level [7]: angle slope island hyper_pars named list numeric hyperparameters rate calculations returned create_hyper_pars(): [1]: d scaling parameter exponent calculating   cladogenesis rate [2]: x exponent calculating extinction rate island_ontogeny DAISIE_sim_time_dep(), DAISIE_ML_CS plotting string describing type island ontogeny. Can \"const\", \"beta\" beta function describing area time.  functions numeric describing type island ontogeny. Can 0 constant, 1 beta function describing area time. ML functions island_ontogeny = NA assumes constant ontogeny. Time dependent estimation yet available development still ongoing. return error called case. sea_level DAISIE_sim_time_dep() plotting string describing type sea level. Can \"const\" \"sine\" sine function describing area time.  functions numeric describing type sea level. Can 0 constant, 1 sine function describing area time. extcutoff numeric cutoff maximum extinction rate preventing large slowing simulation. shift_times numeric vector specifying rate shifts occur present. mainland_n numeric stating number mainland species, number species can potentially colonize island. using clade-specific diversity dependence, value set 1. using island-wide diversity dependence, value set number mainland species. island_replicates List output DAISIE_sim_core_cr(), DAISIE_sim_core_time_dep(), DAISIE_sim_core_cr_shift() DAISIE_sim_min_type2() functions. Minimally, must list many elements replicates. element must list elements island_age, not_present stt_all. stt_all must data frame column names Time, nI, nA, nC present. island_spec Matrix current state simulation containing number species. stt_table Matrix number species time step. rates named list numeric rates returned update_rates(). max_rates named list numeric max rates returned update_max_rates(). timeval Numeric defining current time simulation. total_time Numeric defining length simulation time units. possible_event Numeric defining event happen. maxspecID Current species IDs. mainland_spec Number mainland species. max_area Numeric defining maximum area. proportional_peak_t Numeric value 0 1 indicating island's history peak area achieved. total_island_age Numeric defining total island age. sea_level_amplitude Numeric defining amplitude area fluctuation sea level. sea_level_frequency Numeric defining frequency sine wave area change sea level. island_gradient_angle Numeric defining angle degrees specifying slope island. d Numeric defining scaling parameter exponent calculating cladogenesis rate. x Numeric defining exponent calculating extinction rate. simulation_outputs list matrices vectors simulation produced DAISIE_sim functions. plot_plus_one Boolean indicate plot values plus one. Set TRUE default behavior. Set FALSE plot values without adding one. works one type species. type String indicate stt species possible stt plotted. Default \"all_species\", \"type1_species\" \"type2_species\" plotted. plot_lists List lists containing average quantile species time. ... arguments pass plotting functions. datalist Data object containing information colonisation branching times. object can generated using DAISIE_dataprep function, converts user-specified data table data object, object can course also entered directly. R list object following elements. first element list two three components: $island_age - island age  , depending whether distinction types made, :$not_present - number mainland lineages present island  :$not_present_type1 - number mainland lineages type 1 present island $not_present_type2 - number mainland lineages type 2 present island  remaining elements list contains information single colonist lineage island 5 components:$colonist_name - name species clade colonized island $branching_times - island age followed stem age population/species case Non-endemic, Non-endemic_MaxAge species Endemic species close relatives island. endemic clades one species island (cladogenetic clades/ radiations) island age followed branching times island clade including stem age clade$stac - status colonist  * Non_endemic_MaxAge: 1  * Endemic: 2  * Endemic&Non_Endemic: 3  * Non_Endemic: 4  * Endemic_Singleton_MaxAge: 5  * Endemic_Clade_MaxAge: 6  * Endemic&Non_Endemic_Clade_MaxAge: 7 $missing_species - number island species sampled particular clade (applicable endemic clades) $type1or2 - whether colonist belongs type 1 type 2 datatype Sets type data: 'single' single island archipelago treated one, 'multiple' multiple archipelagoes potentially sharing parameters. initparsopt initial values parameters must optimized, positive. idparsopt ids parameters must optimized. ids defined follows:  id = 1 corresponds lambda^c (cladogenesis rate)  id = 2 corresponds mu (extinction rate)  id = 3 corresponds K (clade-level carrying capacity)  id = 4 corresponds gamma (immigration rate)  id = 5 corresponds lambda^(anagenesis rate)  id = 6 corresponds lambda^c (cladogenesis rate) optional subset species  id = 7 corresponds mu (extinction rate) optional subset species id = 8 corresponds K (clade-level carrying capacity) optional subset species id = 9 corresponds gamma (immigration rate) optional subset species id = 10 corresponds lambda^(anagenesis rate) optional subset species id = 11 corresponds p_f (fraction mainland species belongs second subset species. idparsfix ids parameters optimized, e.g. c(1,3) lambda^c K optimized. parsfix values parameters optimized. idparsnoshift datatype = 'single' : ids parameters different two groups species; can apply ids 6:10, e.g. idparsnoshift = c(6,7) means lambda^c mu values groups. idparsmat datatype = 'multiple' : Matrix containing ids parameters, linking initparsopt parsfix. Per island system use following order:  * lac = (initial) cladogenesis rate  * mu = extinction rate  * K = maximum number species possible clade  * gam = (initial) immigration rate  * laa = (initial) anagenesis rate  Example: idparsmat = rbind(c(1, 2, 3, 4, 5), c(1, 2, 3, 6, 7)) different rates immigration anagenesis two islands. res Sets maximum number species probability must computed, must larger size largest clade. ddmodel Sets model diversity-dependence:  ddmodel = 0 : diversity dependence  ddmodel = 1 : linear dependence speciation rate  ddmodel = 11: linear dependence speciation rate immigration rate  ddmodel = 2 : exponential dependence speciation rate ddmodel = 21: exponential dependence speciation rate immigration rate cond cond = 0 : conditioning island age  cond = 1 : conditioning island age non-extinction island biota . cond > 1 : conditioning island age least cond colonizations island. last option yet available IW model eqmodel Sets equilibrium constraint can used likelihood optimization. available datatype = 'single'. eqmodel = 0 : equilibrium assumed  eqmodel = 13 : near-equilibrium assumed endemics using deterministic equation endemics immigrants. Endemics must within x_E equilibrium value eqmodel = 15 : near-equilibrium assumed endemics immigrants using deterministic equation endemics immigrants. Endemics must within x_E equilibrium value, non-endemics must within x_I equilibrium value. x_E Sets fraction equlibrium endemic diversity endemics assumed equilibrium; active eqmodel = 13 15. x_I Sets fraction equlibrium non-endemic diversity system assumed equilibrium; active eqmodel = 15. tol Sets tolerances optimization. Consists :  reltolx = relative tolerance parameter values optimization  reltolf = relative tolerance function value optimization  abstolx = absolute tolerance parameter values optimization. maxiter Sets maximum number iterations optimization. methode Method ODE-solver. Supported Boost ODEINT solvers (steppers) : \"odeint::runge_kutta_cash_karp54\" \"odeint::runge_kutta_fehlberg78\" \"odeint::runge_kutta_dopri5\" \"odeint::bulirsch_stoer\" without odeint::-prefix, deSolve{ode} method assumed. default method overall \"lsodes\" DAISIE_ML_CS() \"ode45\" ode() DAISIE_ML_IW(). optimmethod Method used likelihood optimization. Default `subplex` (see `subplex()` full details). Alternative \"simplex\" method previous versions. CS_version numeric list. Default 1 standard DAISIE model, relaxed-rate model list following elements: model: CS model run, options 1 single rate   DAISIE model, 2 multi-rate DAISIE, 0 IW test   model. relaxed_par: parameter relax (integrate ). Options \"cladogenesis\", \"extinction\", \"carrying_capacity\", \"immigration\", \"anagenesis\". tolint Vector two elements containing absolute relative tolerance integration. datatable Data frame (table) user-specified data. See file Galapagos_datatable template input table. row table represents independent colonisation event. Table following four columns. $Clade_name - name independent colonization event $Status - One following categories:  * \"Non_endemic\": applies non-endemic species cases island non-island populations species sampled)  * \"Non_endemic_MaxAge\": applies non-endemic species cases island individuals species sampled age species available)  * \"Endemic\": applies endemic species applicable cladogenetic anagenetic species  * \"Endemic_MaxAge\": applies endemic species cases island individuals species sampled age species available. apply endemic species recently gone extinct antropogenic causes (evidently) modelled, DNA data available. * \"Endemic&Non_Endemic\": endemic clade present mainland ancestor re-colonized $Missing_species - Number island species sampled particular clade (applicable \"Endemic\" clades) $Branching_times - Stem age population/species case \"Non-endemic\", \"Non-endemic_MaxAge\" \"Endemic\" anagenetic species. \"Endemic\" cladogenetic species branching times radiation including stem age radiation. island_age Age island appropriate units. DAISIE_plot_age_diversity() DAISIE_plot_island() island input table format, age island must specified. island input DAISIE list format, option override island age specified island list. number_clade_types Number clade types. Default: number_clade_types = 1 species considered belong macroevolutionary process. number_clade_types = 2, two types clades distinct macroevolutionary processes. list_type2_clades number_clade_types = 2, list_type2_clades specifies names clades distinct macroevolutionary process. names must match $Clade_name column source data table (e.g. list_type2_clades = \"Finches\").  number_clade_types = 1, list_type2_clades = NA specified (default). epss Default= 1E-5 appropriate cases. value used set maximum age colonisation \"Non_endemic_MaxAge\" \"Endemic_MaxAge\" species age slightly younger island cases age provided species older island. new maximum age used upper bound integrate . t time expectations need computed. initEI initial values number endemics   non-endemics. DAISIE_probdist() DAISIE_margprobdist() either initprobs must NULL. DAISIE_numcol() NULL, assumed island   empty. data_table data table endmc Numeric many simulations run. archipelago something phylo_data something archipelago_data something gam numeric per capita immigration rate. laa numeric per capita anagenesis rate. lac numeric per capita cladogenesis rate. mu numeric per capita extinction rate. K numeric carrying capacity. num_spec numeric current number species. num_immigrants numeric current number non-endemic species (.k.non-endemic species). global_min_area_time stub global_max_area_time stub distance_type Use 'continent' distance continent used, use 'nearest_big' distance nearest big landmass used, use 'biologically_realistic' distance take account biologically realism, e.g. average previous two thought contribute. distance_dep Sets type distance dependence used. Default power law, denoted 'power'. Alternatives exponantial relationship denoted 'exp' sigmoids, either 'sigmoidal_col' sigmoid colonization, 'sigmoidal_ana' sigmoidal anagenesis, 'sigmoidal_clado' sigmoidal cladogenesis, 'sigmoidal_col_ana' signoids colonization anagenesis. parallel Sets whether parallel computation used. Use '' parallel computing used, 'cluster' parallel computing unix/linux cluster, 'local' parallel computation local machine. cpus Number cpus used parallel computing. Default 3. effect parallel = ''. pars1 Vector model parameters: pars1[1] corresponds lambda^c (cladogenesis rate) pars1[2] corresponds mu (extinction rate) pars1[3] corresponds K (clade-level carrying capacity) pars1[4] corresponds gamma (immigration rate) pars1[5] corresponds lambda^(anagenesis rate). pars2 Vector settings: pars2[1] corresponds res, maximum number endemics non-endemics ODE system solved; must much larger actual number probability needs calculated.) pars2[2] corresponds M, size mainland pool, .e number species can potentially colonize island. tvec times probabilities need computed. initprobs initial probability distribution number endemics non-endemics; either initEI must NULL. pb Probability distribution matrix format output DAISIE_probdist(). island Island data object. Can DAISIE list format (see Galapagos_datalist DAISIE_data_prep examples) table format (see Galapagos_datatable example). title Title plot plot_lists_simulations List simulation output parsing DAISIE_prepare_data_plotting. plot_lists_simulations_MLE List simulation output parsing DAISIE_prepare_data_plotting, obtained simulating MLE output. kind_of_plot Character vector stating STT plot resulting MLE based simulations plotted. Default \"line\" multiple individual lines. Can also \"shade\" 5% quantile. resolution numeric indicating resolution plot. < 0. resol numeric resolution summary stats calculation. > 1. removed_timepoints Positive integer number first datapoints removed rate plots (prevent Inf) numeric value island area given point time. Amin numeric value minimum island area simulation. Amax numeric value maximum island area simulation. peak numeric value specifying peakiness (shaprness) ontogeny curve. Higher values imply peakier ontogeny. value internally calculated calc_peak() given area present area_pars. proptime numeric 0 1. proportion time elapsed simulation, relation total island age (NB: simulation time, island age). proptime_max numeric 0 1. proportional_peak_t. Indicates, proportion total island age ontogeny peak occur (.e. 0.5 means peak halfway time). current_area numeric current island area present (.e., end simulation). jitter Numeric optimizer(). Jitters parameters optimized specified amount small, e.g. 1e-5. Jitter link{subplex}{subplex}() produces incorrect output due parameter transformation. num_cycles number cycles optimizer go . Default 1. trait_pars named list containing diversification rates considering   two trait states created create_trait_pars: [1]:numeric per capita transition rate state1 [2]:numeric per capita immigration rate state2 [3]:numeric per capita extinction rate state2 [4]:numeric per capita anagenesis rate state2 [5]:numeric per capita cladogenesis rate state2 [6]:numeric per capita transition rate state2 [7]:numeric number species trait state 2    mainland relaxed_par string determining parameter relaxed relaxed rate model. relaxed_rate_pars list two numbers, element one distribution mean, element two distribution standard deviation (sd). Currently distribution gamma distribution. list can created create_relaxed_rate_pars(). brts Numeric vector branching times stac Numeric Endemicity status missnumspec Numeric missing species DAISIE_par numeric parameter evaluate integral function. DAISIE_dist_pars numeric vector two elements, first mean second standard deviation distribution. abstolint Numeric absolute tolerance integration reltolint Numeric relative tolerance integration pick Numeric determining parameter selected relaxed-rate model mean Numeric mean distribution sd Numeric standard deviation distribution clado_rate Numeric rate cladogenesis ext_rate Numeric rate extinction carr_cap Numeric carrying capacity immig_rate Numeric rate immigration ana_rate Numeric rate anagenesis islands Island datalist simulated data DAISIE datalist format. Can single island (empirical data) generated DAISIE_dataprep DAISIEprep. Can also simulated data generated DAISIE_sim function. sort_clade_sizes Default sort_clade_sizes = T outputs clade sizes sorted ascending order number species. sort_clade_sizes=F outputs clade sizes order appear input datalist.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/default_params_doc.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Default parameter documentation — default_params_doc","text":"Nothing","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/default_params_doc.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Default parameter documentation — default_params_doc","text":"internal function, marked   @noRd. done, disallow   functions find documentation parameters","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/frogs_datalist.html","id":null,"dir":"Reference","previous_headings":"","what":"Colonization and branching times of 5 Eleutherodactylus clades from Hispaniola island. — frogs_datalist","title":"Colonization and branching times of 5 Eleutherodactylus clades from Hispaniola island. — frogs_datalist","text":"list containing colonization branching times Eleutherodactylus frogs Hispaniola. Main dataset used Etienne et al. list can generated using DAISIE_dataprep function, converts user-specified data table data object, object can course also entered directly. R list object following elements. first element list two components: $island_age - island age $not_present - number mainland lineages present island  following elements list contains information single colonist lineage island 5 components:$colonist_name - name species clade colonized island $branching_times - island age followed stem age population/species case Non-endemic, Non-endemic_MaxAge species Endemic species close relatives island. endemic clades one species island (cladogenetic clades/ radiations) island age followed branching times island clade including stem age clade.$stac - status colonist  * Non_endemic_MaxAge: 1  * Endemic: 2  * Endemic&Non_Endemic: 3  * Non_endemic: 4  * Endemic_MaxAge: 5 6 $missing_species - number island species sampled particular clade (applicable endemic clades) $type1or2 - whether colonist belongs type 1 type 2. dataset equal 1.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/frogs_datalist.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Colonization and branching times of 5 Eleutherodactylus clades from Hispaniola island. — frogs_datalist","text":"list 6 elements, first contains 2 elements following 5 elements containing 5 components.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/frogs_datalist.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Colonization and branching times of 5 Eleutherodactylus clades from Hispaniola island. — frogs_datalist","text":"Etienne RS, Haegeman B, Dugo-Cota , Vila C, Gonzalez-Voyer & Valente L.  limits ecological limits diversification.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/frogs_datatable.html","id":null,"dir":"Reference","previous_headings":"","what":"Colonization and branching times of 5 Eleutherodactylus (frogs) clades from the island of Hispaniola. — frogs_datatable","title":"Colonization and branching times of 5 Eleutherodactylus (frogs) clades from the island of Hispaniola. — frogs_datatable","text":"table containing colonization branching times Eleutherodacytlus frogs island Hispaniola (Greater Antilles). row table represents independent colonisation event. table four columns. $Clade_name - name independent colonization event $Status - One following categories:  * Non_endemic: non-endemic island species approximate time colonisation known  * Non_endemic_MaxAge: non-endemic island species colonisation time unknown  * Endemic: endemic species approximate colonisation time known  * \"Endemic_MaxAge\": applies endemic species endemic clades cases colonisation time unknown, user wants specify upper bound colonisation. example apply endemic species recently gone extinct anthropogenic causes, included phylogeny (\"NA\" given branching times column). also apply insular radiations long stem branches, time first cladogenetic event known, precise time colonisation . * Endemic&Non_Endemic: endemic clade mainland ancestor re-colonized","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/frogs_datatable.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Colonization and branching times of 5 Eleutherodactylus (frogs) clades from the island of Hispaniola. — frogs_datatable","text":"table 5 rows 4 columns.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/frogs_datatable.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Colonization and branching times of 5 Eleutherodactylus (frogs) clades from the island of Hispaniola. — frogs_datatable","text":"Etienne RS, Haegeman B, Dugo-Cota , Vila C, Gonzalez-Voyer & Valente L. limits ecological limits diversification.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/get_ana_rate.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate anagenesis rate — get_ana_rate","title":"Calculate anagenesis rate — get_ana_rate","text":"Internal function. Calculates anagenesis rate given current number immigrant species per capita rate.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/get_ana_rate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate anagenesis rate — get_ana_rate","text":"","code":"get_ana_rate(laa, num_immigrants, island_spec = NULL, trait_pars = NULL)"},{"path":"https://rsetienne.github.io/DAISIE/reference/get_ana_rate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate anagenesis rate — get_ana_rate","text":"laa numeric per capita anagenesis rate. num_immigrants numeric current number non-endemic species (.k.non-endemic species). island_spec Matrix current state simulation containing number species. trait_pars named list containing diversification rates considering   two trait states created create_trait_pars: [1]:numeric per capita transition rate state1 [2]:numeric per capita immigration rate state2 [3]:numeric per capita extinction rate state2 [4]:numeric per capita anagenesis rate state2 [5]:numeric per capita cladogenesis rate state2 [6]:numeric per capita transition rate state2 [7]:numeric number species trait state 2    mainland","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/get_ana_rate.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculate anagenesis rate — get_ana_rate","text":"Pedro Neves, Joshua Lambert, Shu Xie","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/get_clado_rate.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate cladogenesis rate — get_clado_rate","title":"Calculate cladogenesis rate — get_clado_rate","text":"Internal function. Calculates cladogenesis rate given current number species system, carrying capacity per capita cladogenesis rate","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/get_clado_rate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate cladogenesis rate — get_clado_rate","text":"","code":"get_clado_rate(   lac,   hyper_pars,   num_spec,   K,   A,   trait_pars = NULL,   island_spec = NULL )"},{"path":"https://rsetienne.github.io/DAISIE/reference/get_clado_rate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate cladogenesis rate — get_clado_rate","text":"lac numeric per capita cladogenesis rate. hyper_pars named list numeric hyperparameters rate calculations returned create_hyper_pars(): [1]: d scaling parameter exponent calculating   cladogenesis rate [2]: x exponent calculating extinction rate num_spec numeric current number species. K numeric carrying capacity. numeric value island area given point time. trait_pars named list containing diversification rates considering   two trait states created create_trait_pars: [1]:numeric per capita transition rate state1 [2]:numeric per capita immigration rate state2 [3]:numeric per capita extinction rate state2 [4]:numeric per capita anagenesis rate state2 [5]:numeric per capita cladogenesis rate state2 [6]:numeric per capita transition rate state2 [7]:numeric number species trait state 2    mainland island_spec Matrix current state simulation containing number species.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/get_clado_rate.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculate cladogenesis rate — get_clado_rate","text":"Pedro Neves, Joshua Lambert, Shu Xie","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/get_ext_rate.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate extinction rate — get_ext_rate","title":"Calculate extinction rate — get_ext_rate","text":"Calculate extinction rate","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/get_ext_rate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate extinction rate — get_ext_rate","text":"","code":"get_ext_rate(   mu,   hyper_pars,   extcutoff = 1000,   num_spec,   A = 1,   trait_pars = NULL,   island_spec = NULL )"},{"path":"https://rsetienne.github.io/DAISIE/reference/get_ext_rate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate extinction rate — get_ext_rate","text":"mu numeric per capita extinction rate. hyper_pars named list numeric hyperparameters rate calculations returned create_hyper_pars(): [1]: d scaling parameter exponent calculating   cladogenesis rate [2]: x exponent calculating extinction rate extcutoff numeric cutoff maximum extinction rate preventing large slowing simulation. num_spec numeric current number species. numeric value island area given point time. trait_pars named list containing diversification rates considering   two trait states created create_trait_pars: [1]:numeric per capita transition rate state1 [2]:numeric per capita immigration rate state2 [3]:numeric per capita extinction rate state2 [4]:numeric per capita anagenesis rate state2 [5]:numeric per capita cladogenesis rate state2 [6]:numeric per capita transition rate state2 [7]:numeric number species trait state 2    mainland island_spec Matrix current state simulation containing number species.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/get_ext_rate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate extinction rate — get_ext_rate","text":"numeric, extinction rate given base extinction rate, present, hyperparemeter x, (t) time-dependent traits running traint model.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/get_ext_rate.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Calculate extinction rate — get_ext_rate","text":"Valente, Luis M., Rampal S. Etienne, Albert B. Phillimore. \"effects island ontogeny species diversity phylogeny.\" Proceedings Royal Society London B: Biological Sciences 281.1784 (2014): 20133227.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/get_ext_rate.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculate extinction rate — get_ext_rate","text":"Pedro Neves, Joshua Lambert, Shu Xie","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/get_immig_rate.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate immigration rate — get_immig_rate","title":"Calculate immigration rate — get_immig_rate","text":"Internal function. Calculates immigration rate given current number species system, carrying capacity","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/get_immig_rate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate immigration rate — get_immig_rate","text":"","code":"get_immig_rate(   gam,   A = 1,   num_spec,   K,   mainland_n,   trait_pars = NULL,   island_spec = NULL )"},{"path":"https://rsetienne.github.io/DAISIE/reference/get_immig_rate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate immigration rate — get_immig_rate","text":"gam numeric per capita immigration rate. numeric value island area given point time. num_spec numeric current number species. K numeric carrying capacity. mainland_n numeric stating number mainland species, number species can potentially colonize island. using clade-specific diversity dependence, value set 1. using island-wide diversity dependence, value set number mainland species. trait_pars named list containing diversification rates considering   two trait states created create_trait_pars: [1]:numeric per capita transition rate state1 [2]:numeric per capita immigration rate state2 [3]:numeric per capita extinction rate state2 [4]:numeric per capita anagenesis rate state2 [5]:numeric per capita cladogenesis rate state2 [6]:numeric per capita transition rate state2 [7]:numeric number species trait state 2    mainland island_spec Matrix current state simulation containing number species.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/get_immig_rate.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Calculate immigration rate — get_immig_rate","text":"Valente, Luis M., Rampal S. Etienne, Albert B. Phillimore. \"effects island ontogeny species diversity phylogeny.\" Proceedings Royal Society London B: Biological Sciences 281.1784 (2014): 20133227.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/get_immig_rate.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculate immigration rate — get_immig_rate","text":"Pedro Neves, Joshua Lambert","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/get_trans_rate.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate transition rate — get_trans_rate","title":"Calculate transition rate — get_trans_rate","text":"Internal function. Calculates transition rate given current number immigrant species per capita rate.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/get_trans_rate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate transition rate — get_trans_rate","text":"","code":"get_trans_rate(trait_pars, island_spec)"},{"path":"https://rsetienne.github.io/DAISIE/reference/get_trans_rate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate transition rate — get_trans_rate","text":"trait_pars named list containing diversification rates considering two trait states created create_trait_pars: [1]:numeric per capita transition rate state1 [2]:numeric per capita immigration rate state2 [3]:numeric per capita extinction rate state2 [4]:numeric per capita anagenesis rate state2 [5]:numeric per capita cladogenesis rate state2 [6]:numeric per capita transition rate state2 [7]:numeric number species trait state 2 mainland island_spec Matrix current state simulation containing number species.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/integral_peak.html","id":null,"dir":"Reference","previous_headings":"","what":"Computes integral of a very peaked function, modified from the SADISA package — integral_peak","title":"Computes integral of a very peaked function, modified from the SADISA package — integral_peak","text":"computes logarithm integral exp(logfun) 0 Inf following assumptions: \"exp(logfun)\" single, sharply peaked maximum \"exp(logfun)\" increasing left peak  decreasing right peak \"exp(logfun)\" can zero positive zero \"exp(logfun)\" tends zero infinity","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/integral_peak.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Computes integral of a very peaked function, modified from the SADISA package — integral_peak","text":"","code":"integral_peak(   logfun,   xx = seq(-20, 20, 2),   xcutoff = 2,   ymaxthreshold = 1e-12,   pars1,   pars2,   brts,   stac,   missnumspec,   methode,   abstolint,   reltolint,   verbose,   pick,   par_mean,   par_sd,   par_upper_bound )"},{"path":"https://rsetienne.github.io/DAISIE/reference/integral_peak.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Computes integral of a very peaked function, modified from the SADISA package — integral_peak","text":"logfun logarithm function integrate xx initial set points evaluate function xcutoff maximum found among xx, parameter sets width interval find maximum ymaxthreshold sets deviation allowed finding maximum among xx","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/integral_peak.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Computes integral of a very peaked function, modified from the SADISA package — integral_peak","text":"result integration","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/integral_peak.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Computes integral of a very peaked function, modified from the SADISA package — integral_peak","text":"Haegeman, B. & R.S. Etienne (2017). general sampling formula community structure data. Methods Ecology & Evolution 8: 1506-1519. https://doi.org/10.1111/2041-210X.12807","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/island_area.html","id":null,"dir":"Reference","previous_headings":"","what":"Function to describe changes in area through time. — island_area","title":"Function to describe changes in area through time. — island_area","text":"Function describe changes area time.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/island_area.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function to describe changes in area through time. — island_area","text":"","code":"island_area(timeval, total_time, area_pars, peak, island_ontogeny, sea_level)"},{"path":"https://rsetienne.github.io/DAISIE/reference/island_area.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function to describe changes in area through time. — island_area","text":"timeval Numeric defining current time simulation. total_time Numeric defining length simulation time units. area_pars named list containing area sea level parameters created create_area_pars(): [1]: maximum area [2]: current area [3]: value 0 1 indicating island's history   peak area achieved [4]: total island age [5]: amplitude area fluctuation sea level [6]: frequency sine wave area change sea level [7]: angle slope island peak numeric value specifying peakiness (shaprness) ontogeny curve. Higher values imply peakier ontogeny. value internally calculated calc_peak() given area present area_pars. island_ontogeny DAISIE_sim_time_dep(), DAISIE_ML_CS plotting string describing type island ontogeny. Can \"const\", \"beta\" beta function describing area time.  functions numeric describing type island ontogeny. Can 0 constant, 1 beta function describing area time. ML functions island_ontogeny = NA assumes constant ontogeny. Time dependent estimation yet available development still ongoing. return error called case. sea_level DAISIE_sim_time_dep() plotting string describing type sea level. Can \"const\" \"sine\" sine function describing area time.  functions numeric describing type sea level. Can 0 constant, 1 sine function describing area time.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/island_area.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Function to describe changes in area through time. — island_area","text":"Valente, Luis M., Rampal S. Etienne, Albert B. Phillimore. \"effects island ontogeny species diversity phylogeny.\" Proceedings Royal Society London B: Biological Sciences 281.1784 (2014): 20133227.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/island_area.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Function to describe changes in area through time. — island_area","text":"Pedro Neves, Joshua Lambert","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/island_area_vector.html","id":null,"dir":"Reference","previous_headings":"","what":"Computes island_area, but takes vector as argument (needed by ) — island_area_vector","title":"Computes island_area, but takes vector as argument (needed by ) — island_area_vector","text":"Computes island_area, takes vector argument (needed )","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/island_area_vector.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Computes island_area, but takes vector as argument (needed by ) — island_area_vector","text":"","code":"island_area_vector(   timeval,   area_pars,   island_ontogeny,   sea_level,   total_time,   peak )"},{"path":"https://rsetienne.github.io/DAISIE/reference/island_area_vector.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Computes island_area, but takes vector as argument (needed by ) — island_area_vector","text":"timeval current time simulation area_pars vector similar list produced create_area_pars [1]: maximum area [2]: value 0 1 indicating island's history   peak area achieved [3]: total island age island_ontogeny string describing type island ontogeny. Can NULL, \"beta\" beta function describing area time. sea_level numeric describing type sea level.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/island_area_vector.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Computes island_area, but takes vector as argument (needed by ) — island_area_vector","text":"Valente, Luis M., Rampal S. Etienne, Albert B. Phillimore. \"effects island ontogeny species diversity phylogeny.\" Proceedings Royal Society London B: Biological Sciences 281.1784 (2014): 20133227.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/island_area_vector.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Computes island_area, but takes vector as argument (needed by ) — island_area_vector","text":"Pedro Neves","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/islands_10reps_RAW.html","id":null,"dir":"Reference","previous_headings":"","what":"1000 islands in RAW format simulated with the ML parameters of the CR model for the Galapagos data. — islands_10reps_RAW","title":"1000 islands in RAW format simulated with the ML parameters of the CR model for the Galapagos data. — islands_10reps_RAW","text":"simulated dataset element list, can called using e.g. islands_10reps_RAW[[1]] island replicates list . first (e.g. islands_10reps_RAW[[x]][[1]]) element list following components:  following elements RAW list contain information single colonist lineage island 5 components:$branching_times - island age stem age population/species case Non-endemic, Non-endemic_MaxAge Endemic anagenetic species. cladogenetic species island age branching times radiation including stem age radiation.$stac - status colonist  * Not_present: 0  * Non_endemic_MaxAge: 1  * Endemic: 2  * Endemic&Non_Endemic: 3  * Non_endemic: 4 $stt_table - Species--time table descendants mainland species (nI - number non-endemic species; nA - number anagenetic species, nC - number cladogenetic species)$missing_species - number island species sampled particular clade (applicable endemic clades)","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/islands_10reps_RAW.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"1000 islands in RAW format simulated with the ML parameters of the CR model for the Galapagos data. — islands_10reps_RAW","text":"list 10 items.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/islands_10reps_RAW.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"1000 islands in RAW format simulated with the ML parameters of the CR model for the Galapagos data. — islands_10reps_RAW","text":"Valente, L.M., .B. Phillimore R.S. Etienne (2015). Equilibrium non-equilibrium dynamics simultaneously operate Galapagos islands. Ecology Letters 18: 844-852.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/islands_1type_1000reps.html","id":null,"dir":"Reference","previous_headings":"","what":"1000 islands in DAISIE format simulated with the ML parameters of the CR model for the Galapagos data — islands_1type_1000reps","title":"1000 islands in DAISIE format simulated with the ML parameters of the CR model for the Galapagos data — islands_1type_1000reps","text":"simulated dataset element list, can called using e.g. islands_1type_1000reps[[1]] island replicates list . first (e.g. islands_1type_1000reps[[x]][[1]]) element list following components: $island_age - island age$not_present - number mainland lineages present island $stt_all - STT table species island (nI - number non-endemic species; nA - number anagenetic species, nC - number cladogenetic species, present - number independent colonisations present ) subsequent elements list contain information single colonist lineage island 3 components:$branching_times - island age stem age population/species case Non-endemic, Non-endemic_MaxAge Endemic anagenetic species. cladogenetic species island age branching times radiation including stem age radiation.$stac - status colonist  * Non_endemic_MaxAge: 1  * Endemic: 2  * Endemic&Non_Endemic: 3  * Non_endemic: 4 $missing_species - number island species sampled particular clade (applicable endemic clades)","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/islands_1type_1000reps.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"1000 islands in DAISIE format simulated with the ML parameters of the CR model for the Galapagos data — islands_1type_1000reps","text":"list 1000 items.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/islands_1type_1000reps.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"1000 islands in DAISIE format simulated with the ML parameters of the CR model for the Galapagos data — islands_1type_1000reps","text":"Valente, L.M., .B. Phillimore R.S. Etienne (2015). Equilibrium non-equilibrium dynamics simultaneously operate Galapagos islands. Ecology Letters 18: 844-852.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/islands_2types_1000reps.html","id":null,"dir":"Reference","previous_headings":"","what":"1000 islands in DAISIE format simulated with the ML parameters of the CR_lamc_mu_K model for the Galapagos data (2 types of species) — islands_2types_1000reps","title":"1000 islands in DAISIE format simulated with the ML parameters of the CR_lamc_mu_K model for the Galapagos data (2 types of species) — islands_2types_1000reps","text":"simulated dataset element list, can called using e.g. islands_2types_1000reps[[1]] island replicates list . first (e.g. islands_2types_1000reps[[x]][[1]]) element list following components: $island_age - island age$not_present_type1 - number mainland lineages type 1 present island $not_present_type2 - number mainland lineages type 2 present island $stt_all - STT table species island (nI - number non-endemic species; nA - number anagenetic species, nC - number cladogenetic species, present - number independent colonisations present )$stt_stt_type1 - STT table type 1 species island (nI - number non-endemic species; nA - number anagenetic species, nC - number cladogenetic species, present - number independent colonisations present )$stt_stt_type2 - STT table type 2 species island (nI - number non-endemic species; nA - number anagenetic species, nC - number cladogenetic species, present - number independent colonisations present ) subsequent elements list contain information single colonist lineage island 4 components:$branching_times - island age stem age population/species case Non-endemic, Non-endemic_MaxAge Endemic anagenetic species. cladogenetic species island age branching times radiation including stem age radiation.$stac - status colonist  * Non_endemic_MaxAge: 1  * Endemic: 2  * Endemic&Non_Endemic: 3  * Non_endemic: 4 $missing_species - number island species sampled particular clade (applicable endemic clades) $type_1or2 - whether colonist belongs type 1 type 2","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/islands_2types_1000reps.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"1000 islands in DAISIE format simulated with the ML parameters of the CR_lamc_mu_K model for the Galapagos data (2 types of species) — islands_2types_1000reps","text":"list 1000 items.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/islands_2types_1000reps.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"1000 islands in DAISIE format simulated with the ML parameters of the CR_lamc_mu_K model for the Galapagos data (2 types of species) — islands_2types_1000reps","text":"Valente, L.M., .B. Phillimore R.S. Etienne (2015). Equilibrium non-equilibrium dynamics simultaneously operate Galapagos islands. Ecology Letters 18: 844-852.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/remove_empty_elements.html","id":null,"dir":"Reference","previous_headings":"","what":"Remove superfluous lines in empty simulations — remove_empty_elements","title":"Remove superfluous lines in empty simulations — remove_empty_elements","text":"Remove superfluous lines empty simulations","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/remove_empty_elements.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Remove superfluous lines in empty simulations — remove_empty_elements","text":"","code":"remove_empty_elements(sims)"},{"path":"https://rsetienne.github.io/DAISIE/reference/remove_empty_elements.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Remove superfluous lines in empty simulations — remove_empty_elements","text":"sims List output DAISIE_sim","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/remove_empty_elements.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Remove superfluous lines in empty simulations — remove_empty_elements","text":"Output DAISIE_sim without empty elements","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/rho.html","id":null,"dir":"Reference","previous_headings":"","what":"Gamma distribution density parameterised with mean and standard deviation — rho","title":"Gamma distribution density parameterised with mean and standard deviation — rho","text":"Gamma distribution density parameterised mean standard deviation","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/rho.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Gamma distribution density parameterised with mean and standard deviation — rho","text":"","code":"rho(DAISIE_par, DAISIE_dist_pars)"},{"path":"https://rsetienne.github.io/DAISIE/reference/rho.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Gamma distribution density parameterised with mean and standard deviation — rho","text":"DAISIE_par numeric parameter evaluate integral function. DAISIE_dist_pars numeric vector two elements, first mean second standard deviation distribution.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/rho.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Gamma distribution density parameterised with mean and standard deviation — rho","text":"Numeric","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/sample_relaxed_rate.html","id":null,"dir":"Reference","previous_headings":"","what":"Samples from distribution when parameter is relaxed — sample_relaxed_rate","title":"Samples from distribution when parameter is relaxed — sample_relaxed_rate","text":"Samples distribution parameter relaxed","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/sample_relaxed_rate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Samples from distribution when parameter is relaxed — sample_relaxed_rate","text":"","code":"sample_relaxed_rate(pars, relaxed_par)"},{"path":"https://rsetienne.github.io/DAISIE/reference/sample_relaxed_rate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Samples from distribution when parameter is relaxed — sample_relaxed_rate","text":"pars vector 5 elements model parameters relaxed_par string determining parameter relaxed","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/sample_relaxed_rate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Samples from distribution when parameter is relaxed — sample_relaxed_rate","text":"vector parameters.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/stac_table.html","id":null,"dir":"Reference","previous_headings":"","what":"Explanatory table on meaning and use of stac settings — stac_table","title":"Explanatory table on meaning and use of stac settings — stac_table","text":"table containing information regarding meaning stac codes utilised DAISIE's ML functions. used render \"DAISIE stac values\" vignette. stac stands \"status clade\" formed immigrant. important part DAISIE objects informs likelihood functions endemicity status type data available insular clade. colonisation event extant species island needs stac value specified. also implications included DAISIE object \"branching_times\" vector, also described table. table composed following columns: $stac: numeric stac code 1 9. $Input DAISIE_dataprep table \"Clade_Name\": character   possibilities input DAISIE_dataprep()   clade, translated numeric stac code   $stac. $Type species clade\": character   plain English explanation different possible kinds   island lineages can considered DAISIE. $Input DAISIE_dataprep table \"Branching_times\":   character plain English explanation branching times   vector DAISIE object contain. $Colonisation times: character plain English   explanation colonisation time branching times vector   DAISIE object (first element vector) means.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/stac_table.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Explanatory table on meaning and use of stac settings — stac_table","text":"table 9 rows 5 columns.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/transform_gamma_pars.html","id":null,"dir":"Reference","previous_headings":"","what":"Transforms mean and standard deviation to shape and scale gamma parameters — transform_gamma_pars","title":"Transforms mean and standard deviation to shape and scale gamma parameters — transform_gamma_pars","text":"Transforms mean standard deviation shape scale gamma parameters","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/transform_gamma_pars.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Transforms mean and standard deviation to shape and scale gamma parameters — transform_gamma_pars","text":"","code":"transform_gamma_pars(par_mean, par_sd)"},{"path":"https://rsetienne.github.io/DAISIE/reference/transform_gamma_pars.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Transforms mean and standard deviation to shape and scale gamma parameters — transform_gamma_pars","text":"par_mean mean relaxed parameter par_sd standard deviation relaxed parameter","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/transform_gamma_pars.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Transforms mean and standard deviation to shape and scale gamma parameters — transform_gamma_pars","text":"list shape scale parameters","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/update_max_rates.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculates the maximum rates for a Gillespie simulation — update_max_rates","title":"Calculates the maximum rates for a Gillespie simulation — update_max_rates","text":"Internal function updates max rates time t.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/update_max_rates.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculates the maximum rates for a Gillespie simulation — update_max_rates","text":"","code":"update_max_rates(   gam,   laa,   lac,   mu,   hyper_pars = NULL,   extcutoff,   K,   num_spec,   num_immigrants,   mainland_n,   Amin,   Amax )"},{"path":"https://rsetienne.github.io/DAISIE/reference/update_max_rates.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculates the maximum rates for a Gillespie simulation — update_max_rates","text":"gam numeric per capita immigration rate. laa numeric per capita anagenesis rate. lac numeric per capita cladogenesis rate. mu numeric per capita extinction rate. hyper_pars named list numeric hyperparameters rate calculations returned create_hyper_pars(): [1]: d scaling parameter exponent calculating   cladogenesis rate [2]: x exponent calculating extinction rate extcutoff numeric cutoff maximum extinction rate preventing large slowing simulation. K numeric carrying capacity. num_spec numeric current number species. num_immigrants numeric current number non-endemic species (.k.non-endemic species). mainland_n numeric stating number mainland species, number species can potentially colonize island. using clade-specific diversity dependence, value set 1. using island-wide diversity dependence, value set number mainland species. Amin numeric value minimum island area simulation. Amax numeric value maximum island area simulation.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/update_max_rates.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculates the maximum rates for a Gillespie simulation — update_max_rates","text":"named list updated effective rates.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/reference/update_rates.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculates algorithm rates — update_rates","title":"Calculates algorithm rates — update_rates","text":"Internal function updates rates max extinction horizon time t.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/update_rates.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculates algorithm rates — update_rates","text":"","code":"update_rates(   timeval,   total_time,   gam,   laa,   lac,   mu,   hyper_pars = hyper_pars,   area_pars = NULL,   peak = NULL,   island_ontogeny = NULL,   sea_level = NULL,   extcutoff,   K,   num_spec,   num_immigrants,   mainland_n,   trait_pars = NULL,   island_spec = NULL )"},{"path":"https://rsetienne.github.io/DAISIE/reference/update_rates.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculates algorithm rates — update_rates","text":"timeval Numeric defining current time simulation. total_time Numeric defining length simulation time units. gam numeric per capita immigration rate. laa numeric per capita anagenesis rate. lac numeric per capita cladogenesis rate. mu numeric per capita extinction rate. hyper_pars named list numeric hyperparameters rate calculations returned create_hyper_pars(): [1]: d scaling parameter exponent calculating   cladogenesis rate [2]: x exponent calculating extinction rate area_pars named list containing area sea level parameters created create_area_pars(): [1]: maximum area [2]: current area [3]: value 0 1 indicating island's history   peak area achieved [4]: total island age [5]: amplitude area fluctuation sea level [6]: frequency sine wave area change sea level [7]: angle slope island peak numeric value specifying peakiness (shaprness) ontogeny curve. Higher values imply peakier ontogeny. value internally calculated calc_peak() given area present area_pars. island_ontogeny DAISIE_sim_time_dep(), DAISIE_ML_CS plotting string describing type island ontogeny. Can \"const\", \"beta\" beta function describing area time.  functions numeric describing type island ontogeny. Can 0 constant, 1 beta function describing area time. ML functions island_ontogeny = NA assumes constant ontogeny. Time dependent estimation yet available development still ongoing. return error called case. sea_level DAISIE_sim_time_dep() plotting string describing type sea level. Can \"const\" \"sine\" sine function describing area time.  functions numeric describing type sea level. Can 0 constant, 1 sine function describing area time. extcutoff numeric cutoff maximum extinction rate preventing large slowing simulation. K numeric carrying capacity. num_spec numeric current number species. num_immigrants numeric current number non-endemic species (.k.non-endemic species). mainland_n numeric stating number mainland species, number species can potentially colonize island. using clade-specific diversity dependence, value set 1. using island-wide diversity dependence, value set number mainland species. trait_pars named list containing diversification rates considering   two trait states created create_trait_pars: [1]:numeric per capita transition rate state1 [2]:numeric per capita immigration rate state2 [3]:numeric per capita extinction rate state2 [4]:numeric per capita anagenesis rate state2 [5]:numeric per capita cladogenesis rate state2 [6]:numeric per capita transition rate state2 [7]:numeric number species trait state 2    mainland island_spec Matrix current state simulation containing number species.","code":""},{"path":"https://rsetienne.github.io/DAISIE/reference/update_rates.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculates algorithm rates — update_rates","text":"named list updated effective rates.","code":""},{"path":[]},{"path":"https://rsetienne.github.io/DAISIE/news/index.html","id":"daisie-441","dir":"Changelog","previous_headings":"","what":"DAISIE 4.4.1","title":"DAISIE 4.4.1","text":"CRAN release: 2023-10-21 Fix bug calculation shift loglikelihoods. Fix bug parameters optimized incorrectly Inf #159 #160 (@joshwlambert). DAISIE_SR_loglik_CS_M1() now DAISIE_loglik_CS_shift(). New pkgdown website. Several improvements relaxed rate code.","code":""},{"path":"https://rsetienne.github.io/DAISIE/news/index.html","id":"daisie-440","dir":"Changelog","previous_headings":"","what":"DAISIE 4.4.0","title":"DAISIE 4.4.0","text":"CRAN release: 2023-04-02 longer include patched version boost/numeric/odeint/stepper/bulirsch_stoer.hpp, address issue passing previously uninitialised variable boost::units::quantity<boost::units::si::dimensionless, double>. Document return type exported Rcpp functions. Move internal non-error printing console message() warning(). Add internal functions address . verbose variable now numeric, varying 0 3. Increasing values increase amount messages printed. Change default printing output golden rule silence verbose == 0. print , set verbose >= 1. Remove calls options(warn = -1) suppress warnings non standard way. Use suppressWarnings() appropriate. Safely restore graphics settings plot. Fix references DESCRIPTION. Remove internal (unnecessary) calls internal functions via :::. longer use roxygen2 tag internal document without index use noRd instead. are_area_pars() now internal. Replace \\dontrun examples documentation \\donttest. Speed examples. License package C++ source files BSL-1.0 (c) Hanno Hildenbrandt, FORTRAN files BSL-1.0 (c) Rampal S. Etienne. Add LICENSE.note, inst/COPYRIGHTS clarify license copyrights. Pipe files DESCRIPTION.","code":""},{"path":"https://rsetienne.github.io/DAISIE/news/index.html","id":"daisie-434","dir":"Changelog","previous_headings":"","what":"DAISIE 4.3.4","title":"DAISIE 4.3.4","text":"Require C++17 via CXX_STD flag Makevars[.win]. Add SystemRequirements: C++17 DESCRIPTION standard “Writing R Extensions” requires explicitly stated. Depends R (>= 4.2.0) due C++17 requirement Windows due Rtools 4.0, used R 4.0-4.1. Toolchain Rtools 4.0 gcc 8.3 “GCC 9.1 first release non-experimental C++17 support”. per https://gcc.gnu.org/.","code":""},{"path":"https://rsetienne.github.io/DAISIE/news/index.html","id":"daisie-433","dir":"Changelog","previous_headings":"","what":"DAISIE 4.3.3","title":"DAISIE 4.3.3","text":"Patched version boost/numeric/odeint/stepper/bulirsch_stoer.hpp. done including patched header file src/patched_bulrisch_stoer.h boost/numeric/odeint shadow boost/numeric/odeint/stepper/bulrisch_stoer.hpp issue fixed BOOST_VERSION == 1.81.0. Must check fixes upcomming boost (BH) releases. Fix tab spacing src/DAISIE_loglik_rhs_FORTRAN.f95. Re-implement clang16 -D_HAS_AUTO_PTR_ETC flag fix via Makevars[.win] comply CRAN requests force C++ standard C++14 without using SystemRequirements line DESCRIPTION, CRAN’s request. Skip plotting tests cause problems headless systems. run manually. Skip tests --now experimental steppers ODEINT rosenbrock4 adams bashfort moulton 1 slow.","code":""},{"path":"https://rsetienne.github.io/DAISIE/news/index.html","id":"daisie-432","dir":"Changelog","previous_headings":"","what":"DAISIE 4.3.2","title":"DAISIE 4.3.2","text":"Add config.h macro, checking , setting, _HAS_AUTO_PTR_ETC BOOST_NO_AUTO_PTR. Change SystemRequirements DESCRIPTION C++17 C++14. fix applied package 'DDD' version 5.2.1.","code":""},{"path":"https://rsetienne.github.io/DAISIE/news/index.html","id":"daisie-431","dir":"Changelog","previous_headings":"","what":"DAISIE 4.3.1","title":"DAISIE 4.3.1","text":"CRAN release: 2023-02-13 Fix issue prevented ‘covr’ running correctly. Depend R >= 4.1.0, C++17. Tests DAISIE_ML_*() integration tests don’t run CRAN due long runtime.","code":""},{"path":"https://rsetienne.github.io/DAISIE/news/index.html","id":"daisie-430","dir":"Changelog","previous_headings":"","what":"DAISIE 4.3.0","title":"DAISIE 4.3.0","text":"Due recent changes CRAN policy result warnings due use Rcpp related packages link libraries use sprintf (‘Rcpp’ ‘BH’), ‘DAISIE’ now requires Rcpp v(>= 1.0.10) BH v(>= 1.81.0-1). See https://github.com/RcppCore/Rcpp/pull/1236 https://github.com/eddelbuettel/bh/pull/90 respectively. Also require package ‘DDD’ v(>= 5.0.0). Add code trait-dependent simulations considering two carrying capacities trait state. Improvements relaxed rate model fitting procedure. Add DAISIE_count_species() count number species datalist simulated data. Simply printing code wrapping multiple instances print_parameters_and_loglik(). Overall documentation improvements updated references. Bug fix DAISIE_sim_cr_iw(), wrongly computed number species present. #147 Improve likelihood calculation. Fixed incorrect likelihood present type 2 case CS model inference values lambda high, C++ implementation. Overhaul GHA workflows date conservative run. Feature branches require tag [run ci] added commit message run.","code":""},{"path":"https://rsetienne.github.io/DAISIE/news/index.html","id":"daisie-421","dir":"Changelog","previous_headings":"","what":"DAISIE 4.2.1","title":"DAISIE 4.2.1","text":"Bug fixes DAISIE_loglik_CS()likelihood code continental sampling (probability initial presence island). Bug fix DAISIE_sim_cr_iw() replication works correctly.","code":""},{"path":"https://rsetienne.github.io/DAISIE/news/index.html","id":"daisie-420","dir":"Changelog","previous_headings":"","what":"DAISIE 4.2.0","title":"DAISIE 4.2.0","text":"CRAN release: 2022-06-02 divergence time unknown known occurred specific point time island’s existence. divergence time unknown known occurred specific point time island’s existence (usually known dated population level phylogenetic data available). Improve finalise continental island estimation scenario, initially species present island inception. Improve tests related two points . Remove DAISIE time dependent estimation code now ease work remaining code. Development proceed separately. Rate computations simulation first calculated per lineage, calculated per island. needed time dependent estimation later . Improve zenodo metadata. Add methode = \"odeint::adams_bashforth_moulton_X\" list available numeric integrators parameter estimation.","code":""},{"path":"https://rsetienne.github.io/DAISIE/news/index.html","id":"daisie-411","dir":"Changelog","previous_headings":"","what":"DAISIE 4.1.1","title":"DAISIE 4.1.1","text":"Correctly use .data.frame() rather class(foo) == \"data.frame\" satisfy CRAN note.","code":""},{"path":"https://rsetienne.github.io/DAISIE/news/index.html","id":"daisie-410","dir":"Changelog","previous_headings":"","what":"DAISIE 4.1.0","title":"DAISIE 4.1.0","text":"Produces full stt tables. Can run conditioning number surviving species present. Added DAISIE_CS_max_steps() manually change maximum number integration steps CS C++ integrators. Renamed reworked simulation architecture. Renamed totaltime total_time. Integrators package 'deSolve' reinstated default ODE solvers. Added stac_key vignette detailing possible statuses colonist lineages. Use LazyData.","code":""},{"path":"https://rsetienne.github.io/DAISIE/news/index.html","id":"daisie-405","dir":"Changelog","previous_headings":"","what":"DAISIE 4.0.5","title":"DAISIE 4.0.5","text":"N.B.: MacOS users may experience issues installing DAISIE, especially MacOS Big Sur. case, please see detailed installation instructions. \"odeint::runge_kutta_cash_karp54\" \"odeint::runge_kutta_fehlberg78\" [default] \"odeint::runge_kutta_dopri5\" \"odeint::bulirsch_stoer\" without odeint::-prefix, deSolve::ode method assumed. deSolve::ode using \"lsodes\" still default, . Make sure CS_version = 0 (default) use C++ ODEINT numerical integration. * Better handling number threads use DAISIE_IW_num_threads() ML estimation IW model threads available. * Fixes numerical instability conditional probability calculation IW model probability extinction close 1. * Introduce approximation log conditional likelihood computed add message triggered.","code":""},{"path":"https://rsetienne.github.io/DAISIE/news/index.html","id":"daisie-402","dir":"Changelog","previous_headings":"","what":"DAISIE 4.0.2","title":"DAISIE 4.0.2","text":"N.B.: MacOS users may experience issues installing DAISIE, especially MacOS Big Sur. case, please see detailed installation instructions. Suggest ggtree >= 3.0.0.","code":""},{"path":"https://rsetienne.github.io/DAISIE/news/index.html","id":"daisie-401","dir":"Changelog","previous_headings":"","what":"DAISIE 4.0.1","title":"DAISIE 4.0.1","text":"N.B.: MacOS users may experience issues installing DAISIE, especially MacOS Big Sur. case, please see detailed installation instructions. Fix possibility fitting CS model IW likelihood simulated data setting CS_version = 0. Improve CS_version documentation.","code":""},{"path":"https://rsetienne.github.io/DAISIE/news/index.html","id":"daisie-400","dir":"Changelog","previous_headings":"","what":"DAISIE 4.0.0","title":"DAISIE 4.0.0","text":"N.B.: MacOS users may experience issues installing DAISIE, especially MacOS Big Sur. case, please see detailed installation instructions. Fix bug calculating conditional probabilities, now correctly calculated island age present. Fix bug calculating probabilities upon migration, assumed recolonisation possible CS model. Handling recolonisation manner possible IW model, approximation now made. influence bug approximation IW model expected minimal, particularly cases colonisation rate low. cases low colonisation norm. Add num_cycles argument ML functions, allowing specify many cycles optimizer take. Defaults 1. Minor vignette corrections. Improve README.md documentation.","code":""},{"path":"https://rsetienne.github.io/DAISIE/news/index.html","id":"daisie-321","dir":"Changelog","previous_headings":"","what":"DAISIE 3.2.1","title":"DAISIE 3.2.1","text":"N.B.: MacOS users may experience issues installing DAISIE, especially MacOS Big Sur. case, please see detailed installation instructions. Minor documentation improvements.","code":""},{"path":"https://rsetienne.github.io/DAISIE/news/index.html","id":"daisie-320","dir":"Changelog","previous_headings":"","what":"DAISIE 3.2.0","title":"DAISIE 3.2.0","text":"N.B.: MacOS users may experience issues installing DAISIE, especially MacOS Big Sur. case, please see detailed installation instructions. DAISIE_loglikg_IW() now efficient numerically stable. Numerical integration now done via C++ package odeint. Add relaxed rate capabilities (inference simulations). Relaxed rate models allow parameters static, sampled specific probability distributions. Introduce MinAge data status DAISIE data objects. status containing MinAge sets lower boundary colonization situations precise colonization time unknown. interpreted DAISIE_dataprep() information passed likelihood optimization functions. See DAISIE_dataprep() help page details. back-end results new stac values 8 9. Bug fix “bug 2” bug report manuscript. bug present DAISIE_ONEcolonist() recolonization occurs. now fixed colonization branching times stored way now think best dealt likelihood code. recolonization cases, $other_clades_same_ancestor renamed $all_colonisations. #125 Fix bug occurs rarely, computing log conditional probabilities. applicable ML code running cond. Removed deprecated legacy functions. Removed functions named DAISIE_*_VERSION_NUMBER() DAISIE_calc_*_rate() funcions get_brts_mya(). #126 Made functions internal, . DAISIE_make_global() create_island() now internal. #127 @HHildenbrandt now author. Added @xieshu95’s @joshwlambert’s ORCIDs. Added NEWS.md file track changes package.","code":""},{"path":"https://rsetienne.github.io/DAISIE/news/index.html","id":"daisie-310","dir":"Changelog","previous_headings":"","what":"DAISIE 3.1.0","title":"DAISIE 3.1.0","text":"Expands possibility conditioning simulations MLE CS model number colonizing lineages. simulation ML functions, cond argument can now greater one. non-zero cond signifies ML simulation conditioned least cond colonizations island. Implements #121, sim ML level. Add BugReports, Website missing ORCID DESCRIPTION.","code":""},{"path":"https://rsetienne.github.io/DAISIE/news/index.html","id":"daisie-301","dir":"Changelog","previous_headings":"","what":"DAISIE 3.0.1","title":"DAISIE 3.0.1","text":"CRAN release: 2020-08-26 Correct @joshwlambert’s name DESCRIPTION. DAISIE_sim_relaxed_rate() input closer DAISIE_ML() input. Documentation improvements. Tweak Makevars.","code":""},{"path":"https://rsetienne.github.io/DAISIE/news/index.html","id":"daisie-300","dir":"Changelog","previous_headings":"","what":"DAISIE 3.0.0","title":"DAISIE 3.0.0","text":"CRAN release: 2020-08-14 Major revamp simulation code. Simulations now accessed using DAISIE_sim_*() syntax. Constant rate, time-dependent, trait-dependent, (multiple) split-rate available. Relaxed-rate inference available DAISIE_ML_CS(). Improved vignettes documenting CS IW cases. Full stt can returned setting sample_freq = Inf DAISIE_sim_*() functions. Optional plotting DAISIE_plot_input(). (Requires additional dependencies). Back-end architecture improvements.","code":""},{"path":"https://rsetienne.github.io/DAISIE/news/index.html","id":"daisie-201","dir":"Changelog","previous_headings":"","what":"DAISIE 2.0.1","title":"DAISIE 2.0.1","text":"Minor update v2.0: empty islands simulated output list contains one element instead two (second indicated stac = 0, .e. surviving colonization).","code":""},{"path":"https://rsetienne.github.io/DAISIE/news/index.html","id":"daisie-20","dir":"Changelog","previous_headings":"","what":"DAISIE 2.0","title":"DAISIE 2.0","text":"Contains functions used : Valente L., Etienne R.S., Garcia-R J.C. (2019) Deep macroevolutionary impact humans New Zealand’s unique avifauna. Current Biology , 29, 2563-2569.e4. https://doi.org/10.1016/j.cub.2019.06.058 Valente L., Phillimore .B., Melo M. et al. (2020) simple dynamic model explains diversity island birds worldwide. Nature , 579, 92–96. https://doi.org/10.1038/s41586-020-2022-5 Hauffe T, Delicado D, Etienne R.S. Valente L. (2020) Lake expansion elevates equilibrium diversity via increasing colonisation. Journal Biogeography. https://doi.org/10.1111/jbi.13914","code":""}]