From 43e37e19fed04efbd9253019685318977d3a33e0 Mon Sep 17 00:00:00 2001
From: rsetienne <rampaletienne@gmail.om>
Date: Wed, 23 Oct 2024 16:38:08 +0200
Subject: [PATCH] Make DAISIE_ML1 flexible to allow another loglik function to
 be optimized.

---
 R/DAISIE_ML1.R | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/R/DAISIE_ML1.R b/R/DAISIE_ML1.R
index 2fb1edb9..3bc01e1c 100644
--- a/R/DAISIE_ML1.R
+++ b/R/DAISIE_ML1.R
@@ -107,7 +107,8 @@ DAISIE_ML1 <- function(
   tolint = c(1E-16, 1E-10),
   island_ontogeny = NA,
   jitter = 0,
-  num_cycles = 1) {
+  num_cycles = 1,
+  function_to_optimize = DAISIE_loglik_all_choosepar) {
   # 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
@@ -288,7 +289,7 @@ DAISIE_ML1 <- function(
   )
 
   optimpars <- c(tol, maxiter)
-  initloglik <- DAISIE_loglik_all_choosepar(
+  initloglik <- function_to_optimize(
     trparsopt = trparsopt,
     trparsfix = trparsfix,
     idparsopt = idparsopt,