From 38b61f197406c50be0ff9b0a4274e3254e8e96ab Mon Sep 17 00:00:00 2001
From: rsetienne <rampaletienne@gmail.om>
Date: Thu, 24 Oct 2024 12:11:59 +0200
Subject: [PATCH] Updating documentation files.

---
 man/DAISIE_ML.Rd          | 8 +++++++-
 man/DAISIE_ML1.Rd         | 8 +++++++-
 man/default_params_doc.Rd | 5 +++++
 3 files changed, 19 insertions(+), 2 deletions(-)

diff --git a/man/DAISIE_ML.Rd b/man/DAISIE_ML.Rd
index 3cf746dd..8004a6cf 100644
--- a/man/DAISIE_ML.Rd
+++ b/man/DAISIE_ML.Rd
@@ -30,7 +30,8 @@ DAISIE_ML_CS(
   verbose = 0,
   tolint = c(1e-16, 1e-10),
   jitter = 0,
-  num_cycles = 1
+  num_cycles = 1,
+  function_to_optimize = "DAISIE_exact"
 )
 }
 \arguments{
@@ -201,6 +202,11 @@ incorrect output due to parameter transformation.}
 
 \item{num_cycles}{The number of cycles the optimizer will go through.
 Default is 1.}
+
+\item{function_to_optimize}{Here one can indicate to use a function
+('DAISIE_approx') that approximates the DAISIE likelihood or the default
+value 'DAISIE_exact'). The approximate likelihood can for example be used
+in case the exact one fails.}
 }
 \value{
 The output is a dataframe containing estimated parameters and
diff --git a/man/DAISIE_ML1.Rd b/man/DAISIE_ML1.Rd
index 158de7c1..2cb61361 100644
--- a/man/DAISIE_ML1.Rd
+++ b/man/DAISIE_ML1.Rd
@@ -26,7 +26,8 @@ DAISIE_ML1(
   tolint = c(1e-16, 1e-10),
   island_ontogeny = NA,
   jitter = 0,
-  num_cycles = 1
+  num_cycles = 1,
+  function_to_optimize = "DAISIE_exact"
 )
 }
 \arguments{
@@ -184,6 +185,11 @@ incorrect output due to parameter transformation.}
 
 \item{num_cycles}{The number of cycles the optimizer will go through.
 Default is 1.}
+
+\item{function_to_optimize}{Here one can indicate to use a function
+('DAISIE_approx') that approximates the DAISIE likelihood or the default
+value 'DAISIE_exact'). The approximate likelihood can for example be used
+in case the exact one fails.}
 }
 \value{
 The output is a dataframe containing estimated parameters and
diff --git a/man/default_params_doc.Rd b/man/default_params_doc.Rd
index 5665810c..9ce49557 100644
--- a/man/default_params_doc.Rd
+++ b/man/default_params_doc.Rd
@@ -737,6 +737,11 @@ DAISIEprep. Can also be simulated data generated with DAISIE_sim function.}
 \item{sort_clade_sizes}{Default sort_clade_sizes = T outputs clade sizes
 sorted in ascending order of number of species. sort_clade_sizes=F outputs
 clade sizes in the same order as they appear in the input datalist.}
+
+\item{function_to_optimize}{Here one can indicate to use a function
+('DAISIE_approx') that approximates the DAISIE likelihood or the default
+value 'DAISIE_exact'). The approximate likelihood can for example be used
+in case the exact one fails.}
 }
 \value{
 Nothing