From 8eaa32463998687870728aa09538f8b6e0fcfd31 Mon Sep 17 00:00:00 2001
From: MayaGueguen <maya.gueguen@gmail.com>
Date: Thu, 6 Jun 2024 16:04:46 +0200
Subject: [PATCH] Correct BIOMOD_EnsembleModeling when multiple PA datasets
 (obs and fit not matching when calling bm_FindOptimStat)

---
 R/BIOMOD_EnsembleModeling.R |  3 ++-
 docs/articles/news.html     | 11 +++++++++--
 vignettes/news.Rmd          |  4 +++-
 3 files changed, 14 insertions(+), 4 deletions(-)

diff --git a/R/BIOMOD_EnsembleModeling.R b/R/BIOMOD_EnsembleModeling.R
index fa1f162a..4cf969a3 100644
--- a/R/BIOMOD_EnsembleModeling.R
+++ b/R/BIOMOD_EnsembleModeling.R
@@ -666,7 +666,8 @@ BIOMOD_EnsembleModeling <- function(bm.mod,
                     if (all(!eval.lines)) { eval.lines <- !eval.lines }
                   }
                 } else {
-                  eval.lines <- rep(TRUE, length(pred.bm))
+                  eval.lines <- rep(FALSE, length(obs))
+                  eval.lines[as.numeric(rownames(pred.newdata))] <- TRUE
                 }
                 
                 
diff --git a/docs/articles/news.html b/docs/articles/news.html
index d72469b9..945f6212 100644
--- a/docs/articles/news.html
+++ b/docs/articles/news.html
@@ -151,10 +151,17 @@ <h3 id="section">
 <h5 id="bugfix">Bugfix<a class="anchor" aria-label="anchor" href="#bugfix"></a>
 </h5>
 <ul>
-<li>4.2-5-2 : always keep same order for variable names for
-<code>new.env</code> in <code>BIOMOD_Projection</code> and
+<li>4.2-5-2 :
+<ul>
+<li>fixed <code>BIOMOD_EnsembleModeling</code> when multiple PA datasets
+(<code>obs</code> and <code>fit</code> not matching when calling
+<code>bm_FindOptimStat</code>)</li>
+<li>always keep same order for variable names for <code>new.env</code>
+in <code>BIOMOD_Projection</code> and
 <code>BIOMOD_EnsembleForecasting</code>
 </li>
+</ul>
+</li>
 <li>4.2-5-1 :
 <ul>
 <li>removed <code>tests/</code> folder (unused)</li>
diff --git a/vignettes/news.Rmd b/vignettes/news.Rmd
index 259b1678..edaaba18 100644
--- a/vignettes/news.Rmd
+++ b/vignettes/news.Rmd
@@ -17,7 +17,9 @@ vignette: >
 
 ##### Bugfix
 
-- 4.2-5-2 : always keep same order for variable names for `new.env` in `BIOMOD_Projection` and `BIOMOD_EnsembleForecasting`
+- 4.2-5-2 :
+  + fixed `BIOMOD_EnsembleModeling` when multiple PA datasets (`obs` and `fit` not matching when calling `bm_FindOptimStat`)
+  + always keep same order for variable names for `new.env` in `BIOMOD_Projection` and `BIOMOD_EnsembleForecasting`
 - 4.2-5-1 :
   + removed `tests/` folder (unused)
   + fixed check for variable names for `new.env` in `BIOMOD_Projection` and `BIOMOD_EnsembleForecasting`