v4.2-5-2

Fix order for variable names for new.env in BIOMOD_Projection and BIOMOD_EnsembleForecasting
biomodhub · May 31, 2024 · 3709ae9 · 3709ae9
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Showing 93 changed files with 104 additions and 96 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: biomod2
 Type: Package
 Title: Ensemble Platform for Species Distribution Modeling
-Version: 4.2-5-1
-Date: 2024-05-30
+Version: 4.2-5-2
+Date: 2024-05-31
 Authors@R: c(person("Wilfried", "Thuiller", role = c("aut")
                     , email = "[email protected]"),
              person("Damien", "Georges", role = c("aut")),

diff --git a/R/BIOMOD_EnsembleForecasting.R b/R/BIOMOD_EnsembleForecasting.R
@@ -594,10 +594,12 @@ BIOMOD_EnsembleForecasting <- function(bm.em,
 
     if (inherits(new.env, 'SpatRaster')) {
       .fun_testIfIn(TRUE, "names(new.env)", names(new.env), bm.em@expl.var.names, exact = TRUE)
+      new.env <- new.env[[bm.em@expl.var.names]]
       new.env.mask <- .get_data_mask(new.env, value.out = 1)
       new.env <- mask(new.env, new.env.mask)
     } else {
       .fun_testIfIn(TRUE, "colnames(new.env)", colnames(new.env), bm.em@expl.var.names, exact = TRUE)
+      new.env <- new.env[ , bm.em@expl.var.names, drop = FALSE]
     }
 
     which.factor <- which(sapply(new.env, is.factor))

diff --git a/R/BIOMOD_Projection.R b/R/BIOMOD_Projection.R
@@ -530,6 +530,7 @@ BIOMOD_Projection <- function(bm.mod,
 
   if (inherits(new.env, 'SpatRaster')) {
     .fun_testIfIn(TRUE, "names(new.env)", names(new.env), bm.mod@expl.var.names, exact = TRUE)
+    new.env <- new.env[[bm.mod@expl.var.names]]
     new.env.mask <- .get_data_mask(new.env, value.out = 1)
     new.env <- mask(new.env, new.env.mask)
   } else {

diff --git a/README.md b/README.md
@@ -1,5 +1,5 @@
 [![Cran Version](https://www.r-pkg.org/badges/version/biomod2?color=yellow)](https://cran.r-project.org/package=biomod2)
-[![Github Version](https://img.shields.io/badge/devel%20version-4.2--5--1-blue.svg)](https://github.com/biomodhub/biomod2)
+[![Github Version](https://img.shields.io/badge/devel%20version-4.2--5--2-blue.svg)](https://github.com/biomodhub/biomod2)
 [![Last Commit](https://img.shields.io/github/last-commit/biomodhub/biomod2.svg)](https://github.com/biomodhub/biomod2/commits/master)
 [![R-CMD-check](https://github.com/biomodhub/biomod2/actions/workflows/R-CMD-check.yml/badge.svg)](https://github.com/biomodhub/biomod2/actions/workflows/R-CMD-check.yml)
 
@@ -49,7 +49,7 @@ install.packages("biomod2", dependencies = TRUE)
 
 <br/>
 
-- **Development version** [![v](https://img.shields.io/badge/devel%20version-4.2--5--1-blue.svg)](https://github.com/biomodhub/biomod2) from [biomodhub](https://github.com/biomodhub/biomod2) :
+- **Development version** [![v](https://img.shields.io/badge/devel%20version-4.2--5--2-blue.svg)](https://github.com/biomodhub/biomod2) from [biomodhub](https://github.com/biomodhub/biomod2) :
 
 ```R
 library(devtools)

diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/articles/examples_1_mainFunctions.html b/docs/articles/examples_1_mainFunctions.html
diff --git a/docs/articles/examples_2_secundaryFunctions.html b/docs/articles/examples_2_secundaryFunctions.html
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/articles/news.html b/docs/articles/news.html
diff --git a/docs/articles/vignette_crossValidation.html b/docs/articles/vignette_crossValidation.html
diff --git a/docs/articles/vignette_dataPreparation.html b/docs/articles/vignette_dataPreparation.html
diff --git a/docs/articles/vignette_modelingOptions.html b/docs/articles/vignette_modelingOptions.html
diff --git a/docs/articles/vignette_presentation.html b/docs/articles/vignette_presentation.html
diff --git a/docs/articles/vignette_pseudoAbsences.html b/docs/articles/vignette_pseudoAbsences.html
diff --git a/docs/articles/vignette_variability.html b/docs/articles/vignette_variability.html
diff --git a/docs/articles/vignette_videos.html b/docs/articles/vignette_videos.html
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/reference/BIOMOD.ensemble.models.out.html b/docs/reference/BIOMOD.ensemble.models.out.html
diff --git a/docs/reference/BIOMOD.formated.data.PA.html b/docs/reference/BIOMOD.formated.data.PA.html
diff --git a/docs/reference/BIOMOD.formated.data.html b/docs/reference/BIOMOD.formated.data.html
diff --git a/docs/reference/BIOMOD.models.options.html b/docs/reference/BIOMOD.models.options.html
diff --git a/docs/reference/BIOMOD.models.out.html b/docs/reference/BIOMOD.models.out.html
diff --git a/docs/reference/BIOMOD.options.dataset.html b/docs/reference/BIOMOD.options.dataset.html
diff --git a/docs/reference/BIOMOD.options.default.html b/docs/reference/BIOMOD.options.default.html
diff --git a/docs/reference/BIOMOD.projection.out.html b/docs/reference/BIOMOD.projection.out.html
diff --git a/docs/reference/BIOMOD.stored.data.html b/docs/reference/BIOMOD.stored.data.html
diff --git a/docs/reference/BIOMOD_CrossValidation-deprecated.html b/docs/reference/BIOMOD_CrossValidation-deprecated.html
diff --git a/docs/reference/BIOMOD_EnsembleForecasting.html b/docs/reference/BIOMOD_EnsembleForecasting.html
diff --git a/docs/reference/BIOMOD_EnsembleModeling.html b/docs/reference/BIOMOD_EnsembleModeling.html
diff --git a/docs/reference/BIOMOD_FormatingData.html b/docs/reference/BIOMOD_FormatingData.html
diff --git a/docs/reference/BIOMOD_LoadModels.html b/docs/reference/BIOMOD_LoadModels.html
diff --git a/docs/reference/BIOMOD_Modeling.html b/docs/reference/BIOMOD_Modeling.html
diff --git a/docs/reference/BIOMOD_PresenceOnly-deprecated.html b/docs/reference/BIOMOD_PresenceOnly-deprecated.html
diff --git a/docs/reference/BIOMOD_Projection.html b/docs/reference/BIOMOD_Projection.html
diff --git a/docs/reference/BIOMOD_RangeSize.html b/docs/reference/BIOMOD_RangeSize.html
diff --git a/docs/reference/BIOMOD_tuning-deprecated.html b/docs/reference/BIOMOD_tuning-deprecated.html
diff --git a/docs/reference/BinaryTransformation-deprecated.html b/docs/reference/BinaryTransformation-deprecated.html