From b5c2d9b4b6d02834eec0625bab2318102114cde0 Mon Sep 17 00:00:00 2001
From: rsetienne <rampaletienne@gmail.om>
Date: Wed, 23 Oct 2024 17:39:55 +0200
Subject: [PATCH] Allowing for adding approximate loglikelihood function

---
 R/DAISIE_ML1.R   | 8 +++++++-
 R/DAISIE_ML_CS.R | 6 ++++--
 2 files changed, 11 insertions(+), 3 deletions(-)

diff --git a/R/DAISIE_ML1.R b/R/DAISIE_ML1.R
index 3bc01e1c..4f602942 100644
--- a/R/DAISIE_ML1.R
+++ b/R/DAISIE_ML1.R
@@ -108,7 +108,7 @@ DAISIE_ML1 <- function(
   island_ontogeny = NA,
   jitter = 0,
   num_cycles = 1,
-  function_to_optimize = DAISIE_loglik_all_choosepar) {
+  function_to_optimize = 'DAISIE_exact') {
   # datalist = list of all data: branching times, status of clade, and numnber of missing species
   # datalist[[,]][1] = list of branching times (positive, from present to past)
   # - max(brts) = age of the island
@@ -157,6 +157,12 @@ DAISIE_ML1 <- function(
   #  . eqmodel = 4 : equilibrium is assumed on immigrants using deterministic equation for endemics and immigrants
   #  . eqmodel = 5 : equilibrium is assumed on endemics and immigrants using deterministic equation for endemics and immigrants
 
+  if(function_to_optimize == 'DAISIE_exact') {
+    function_to_optimize <- DAISIE_loglik_all_choosepar
+  } else
+  {
+    DAISIE_loglik_all_choosepar_approx
+  }
 
   out2err <- data.frame(
     lambda_c = NA,
diff --git a/R/DAISIE_ML_CS.R b/R/DAISIE_ML_CS.R
index 18b40c7c..58dfa9a8 100644
--- a/R/DAISIE_ML_CS.R
+++ b/R/DAISIE_ML_CS.R
@@ -183,7 +183,8 @@ DAISIE_ML_CS <- DAISIE_ML <- function(
   verbose = 0,
   tolint = c(1E-16, 1E-10),
   jitter = 0,
-  num_cycles = 1) {
+  num_cycles = 1,
+  function_to_optimize = 'DAISIE_exact') {
 
   if (datatype == "single") {
     if (is.na(island_ontogeny)) {
@@ -229,7 +230,8 @@ DAISIE_ML_CS <- DAISIE_ML <- function(
                           verbose = verbose,
                           tolint = tolint,
                           jitter = jitter,
-                          num_cycles = num_cycles)
+                          num_cycles = num_cycles,
+                          function_to_optimize = function_to_optimize)
       }
     } else {
         stop(