diff --git a/DESCRIPTION b/DESCRIPTION index 67cec58b..2f7c13f3 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: biomod2 Type: Package Title: Ensemble Platform for Species Distribution Modeling -Version: 4.2-5 +Version: 4.2-5-1 Date: 2024-05-30 Authors@R: c(person("Wilfried", "Thuiller", role = c("aut") , email = "wilfried.thuiller@univ-grenoble-alpes.fr"), diff --git a/README.md b/README.md index c7852434..dea8cbbb 100644 --- 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-blue.svg)](https://github.com/biomodhub/biomod2) +[![Github Version](https://img.shields.io/badge/devel%20version-4.2--5--1-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)
-- **Development version** [![v](https://img.shields.io/badge/devel%20version-4.2--5-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--1-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 index 10f488de..9b40b52b 100644 --- a/docs/404.html +++ b/docs/404.html @@ -32,7 +32,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/articles/examples_1_mainFunctions.html b/docs/articles/examples_1_mainFunctions.html index 1d2b396c..0b94e29f 100644 --- a/docs/articles/examples_1_mainFunctions.html +++ b/docs/articles/examples_1_mainFunctions.html @@ -33,7 +33,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/articles/examples_2_secundaryFunctions.html b/docs/articles/examples_2_secundaryFunctions.html index 6537c9fb..ceb31a29 100644 --- a/docs/articles/examples_2_secundaryFunctions.html +++ b/docs/articles/examples_2_secundaryFunctions.html @@ -33,7 +33,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/articles/index.html b/docs/articles/index.html index 18237893..b4a4ae67 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -17,7 +17,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/articles/news.html b/docs/articles/news.html index a6209288..248261e6 100644 --- a/docs/articles/news.html +++ b/docs/articles/news.html @@ -33,7 +33,7 @@ biomod2 - 4.2-5 + 4.2-5-1 @@ -147,6 +147,22 @@

2024

+
+
Bugfix +
+ +

4.2-5 Modeling options and Tuning (2024-05-02)

@@ -196,7 +212,7 @@
Minor Changes -
Bugfix +
Bugfix
-
Bugfix +
Bugfix
-
Bugfix +
Bugfix
-
Bugfix +
Bugfix
-
Bugfix +
Bugfix
-
Bugfix +
Bugfix
-
Bugfix +
Bugfix
diff --git a/docs/articles/vignette_modelingOptions.html b/docs/articles/vignette_modelingOptions.html index 32085fbb..d1e1837c 100644 --- a/docs/articles/vignette_modelingOptions.html +++ b/docs/articles/vignette_modelingOptions.html @@ -33,7 +33,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/articles/vignette_presentation.html b/docs/articles/vignette_presentation.html index d93051e1..0f02e12b 100644 --- a/docs/articles/vignette_presentation.html +++ b/docs/articles/vignette_presentation.html @@ -33,7 +33,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/articles/vignette_pseudoAbsences.html b/docs/articles/vignette_pseudoAbsences.html index 00f45ad9..0f339351 100644 --- a/docs/articles/vignette_pseudoAbsences.html +++ b/docs/articles/vignette_pseudoAbsences.html @@ -33,7 +33,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/articles/vignette_variability.html b/docs/articles/vignette_variability.html index ac13c15d..1b10a2c8 100644 --- a/docs/articles/vignette_variability.html +++ b/docs/articles/vignette_variability.html @@ -33,7 +33,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/articles/vignette_videos.html b/docs/articles/vignette_videos.html index a4148702..1fc718aa 100644 --- a/docs/articles/vignette_videos.html +++ b/docs/articles/vignette_videos.html @@ -33,7 +33,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/authors.html b/docs/authors.html index 11e1e3db..1b268607 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -17,7 +17,7 @@ biomod2 - 4.2-5 + 4.2-5-1 @@ -150,13 +150,13 @@

Citation

Thuiller W, Georges D, Gueguen M, Engler R, Breiner F, Lafourcade B, Patin R, Blancheteau H (2024). biomod2: Ensemble Platform for Species Distribution Modeling. -R package version 4.2-5, https://biomodhub.github.io/biomod2/. +R package version 4.2-5-1, https://biomodhub.github.io/biomod2/. 

@Manual{,
   title = {biomod2: Ensemble Platform for Species Distribution Modeling},
   author = {Wilfried Thuiller and Damien Georges and Maya Gueguen and Robin Engler and Frank Breiner and Bruno Lafourcade and Remi Patin and Helene Blancheteau},
   year = {2024},
-  note = {R package version 4.2-5},
+  note = {R package version 4.2-5-1},
   url = {https://biomodhub.github.io/biomod2/},
 }
diff --git a/docs/index.html b/docs/index.html index 9df4cbca..2a89ce83 100644 --- a/docs/index.html +++ b/docs/index.html @@ -33,7 +33,7 @@ biomod2 - 4.2-5 + 4.2-5-1 @@ -166,7 +166,7 @@ 


 library(devtools)
@@ -324,7 +324,7 @@ 
Developers

 
Dev status

 
    
 
  • Cran Version
    • 
-
  • Github Version
    • 
+
  • Github Version
    • 
 
  • Last Commit
    • 
 
  • R-CMD-check
    • 
 

diff --git a/docs/reference/BIOMOD.ensemble.models.out.html b/docs/reference/BIOMOD.ensemble.models.out.html
index 1b12f3b5..ec9677d0 100644
--- a/docs/reference/BIOMOD.ensemble.models.out.html
+++ b/docs/reference/BIOMOD.ensemble.models.out.html
@@ -19,7 +19,7 @@
       
       
         biomod2
-        4.2-5
+        4.2-5-1
diff --git a/docs/reference/BIOMOD.formated.data.PA.html b/docs/reference/BIOMOD.formated.data.PA.html index f12eb797..8dc9fbe0 100644 --- a/docs/reference/BIOMOD.formated.data.PA.html +++ b/docs/reference/BIOMOD.formated.data.PA.html @@ -19,7 +19,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/BIOMOD.formated.data.html b/docs/reference/BIOMOD.formated.data.html index edcbaf85..8fa6e459 100644 --- a/docs/reference/BIOMOD.formated.data.html +++ b/docs/reference/BIOMOD.formated.data.html @@ -19,7 +19,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/BIOMOD.models.options.html b/docs/reference/BIOMOD.models.options.html index 67c2c1ad..065f5bed 100644 --- a/docs/reference/BIOMOD.models.options.html +++ b/docs/reference/BIOMOD.models.options.html @@ -18,7 +18,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/BIOMOD.models.out.html b/docs/reference/BIOMOD.models.out.html index 2c0c3d8d..77a3be9e 100644 --- a/docs/reference/BIOMOD.models.out.html +++ b/docs/reference/BIOMOD.models.out.html @@ -19,7 +19,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/BIOMOD.options.dataset.html b/docs/reference/BIOMOD.options.dataset.html index 2ad17612..09b0f67f 100644 --- a/docs/reference/BIOMOD.options.dataset.html +++ b/docs/reference/BIOMOD.options.dataset.html @@ -19,7 +19,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/BIOMOD.options.default.html b/docs/reference/BIOMOD.options.default.html index 3bf222b4..5410e066 100644 --- a/docs/reference/BIOMOD.options.default.html +++ b/docs/reference/BIOMOD.options.default.html @@ -19,7 +19,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/BIOMOD.projection.out.html b/docs/reference/BIOMOD.projection.out.html index 0cd3c3b7..0227c96a 100644 --- a/docs/reference/BIOMOD.projection.out.html +++ b/docs/reference/BIOMOD.projection.out.html @@ -18,7 +18,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/BIOMOD.stored.data.html b/docs/reference/BIOMOD.stored.data.html index 6801a47f..4b18e476 100644 --- a/docs/reference/BIOMOD.stored.data.html +++ b/docs/reference/BIOMOD.stored.data.html @@ -19,7 +19,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/BIOMOD_CrossValidation-deprecated.html b/docs/reference/BIOMOD_CrossValidation-deprecated.html index a3d9d1dd..d70eb963 100644 --- a/docs/reference/BIOMOD_CrossValidation-deprecated.html +++ b/docs/reference/BIOMOD_CrossValidation-deprecated.html @@ -18,7 +18,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/BIOMOD_EnsembleForecasting.html b/docs/reference/BIOMOD_EnsembleForecasting.html index f626b0c7..44670e3e 100644 --- a/docs/reference/BIOMOD_EnsembleForecasting.html +++ b/docs/reference/BIOMOD_EnsembleForecasting.html @@ -19,7 +19,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/BIOMOD_EnsembleModeling.html b/docs/reference/BIOMOD_EnsembleModeling.html index 0d9e9499..4b689bc3 100644 --- a/docs/reference/BIOMOD_EnsembleModeling.html +++ b/docs/reference/BIOMOD_EnsembleModeling.html @@ -21,7 +21,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/BIOMOD_FormatingData.html b/docs/reference/BIOMOD_FormatingData.html index 181e3d44..54086129 100644 --- a/docs/reference/BIOMOD_FormatingData.html +++ b/docs/reference/BIOMOD_FormatingData.html @@ -20,7 +20,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/BIOMOD_LoadModels.html b/docs/reference/BIOMOD_LoadModels.html index 3641c303..93de53c1 100644 --- a/docs/reference/BIOMOD_LoadModels.html +++ b/docs/reference/BIOMOD_LoadModels.html @@ -18,7 +18,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/BIOMOD_Modeling.html b/docs/reference/BIOMOD_Modeling.html index 74038c18..03a3ea2b 100644 --- a/docs/reference/BIOMOD_Modeling.html +++ b/docs/reference/BIOMOD_Modeling.html @@ -20,7 +20,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/BIOMOD_PresenceOnly-deprecated.html b/docs/reference/BIOMOD_PresenceOnly-deprecated.html index f7b6c232..7c92dfd2 100644 --- a/docs/reference/BIOMOD_PresenceOnly-deprecated.html +++ b/docs/reference/BIOMOD_PresenceOnly-deprecated.html @@ -18,7 +18,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/BIOMOD_Projection.html b/docs/reference/BIOMOD_Projection.html index b537954a..27746da3 100644 --- a/docs/reference/BIOMOD_Projection.html +++ b/docs/reference/BIOMOD_Projection.html @@ -19,7 +19,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/BIOMOD_RangeSize.html b/docs/reference/BIOMOD_RangeSize.html index 8a6b9ad3..60613a8d 100644 --- a/docs/reference/BIOMOD_RangeSize.html +++ b/docs/reference/BIOMOD_RangeSize.html @@ -20,7 +20,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/BIOMOD_tuning-deprecated.html b/docs/reference/BIOMOD_tuning-deprecated.html index 7cb7d1af..30dcd1e3 100644 --- a/docs/reference/BIOMOD_tuning-deprecated.html +++ b/docs/reference/BIOMOD_tuning-deprecated.html @@ -18,7 +18,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/BinaryTransformation-deprecated.html b/docs/reference/BinaryTransformation-deprecated.html index 3aa8f599..9e577605 100644 --- a/docs/reference/BinaryTransformation-deprecated.html +++ b/docs/reference/BinaryTransformation-deprecated.html @@ -18,7 +18,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/DataSpecies.html b/docs/reference/DataSpecies.html index 7366db99..1ed9308b 100644 --- a/docs/reference/DataSpecies.html +++ b/docs/reference/DataSpecies.html @@ -19,7 +19,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/Find.Optim.Stat-deprecated.html b/docs/reference/Find.Optim.Stat-deprecated.html index a84ef4a3..b4fd3b31 100644 --- a/docs/reference/Find.Optim.Stat-deprecated.html +++ b/docs/reference/Find.Optim.Stat-deprecated.html @@ -18,7 +18,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/ModelsTable.html b/docs/reference/ModelsTable.html index b7930f27..5743ec65 100644 --- a/docs/reference/ModelsTable.html +++ b/docs/reference/ModelsTable.html @@ -18,7 +18,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/OptionsBigboss.html b/docs/reference/OptionsBigboss.html index 12488e0e..059d7fc7 100644 --- a/docs/reference/OptionsBigboss.html +++ b/docs/reference/OptionsBigboss.html @@ -18,7 +18,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/ProbDensFunc-deprecated.html b/docs/reference/ProbDensFunc-deprecated.html index b178b29b..3b79a4b0 100644 --- a/docs/reference/ProbDensFunc-deprecated.html +++ b/docs/reference/ProbDensFunc-deprecated.html @@ -18,7 +18,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/bioclim_current.html b/docs/reference/bioclim_current.html index 62112c14..0b5ee8ec 100644 --- a/docs/reference/bioclim_current.html +++ b/docs/reference/bioclim_current.html @@ -19,7 +19,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/bioclim_future.html b/docs/reference/bioclim_future.html index 81f0f3a1..8df0d2fd 100644 --- a/docs/reference/bioclim_future.html +++ b/docs/reference/bioclim_future.html @@ -19,7 +19,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/biomod2-deprecated.html b/docs/reference/biomod2-deprecated.html index 662e00db..0458d357 100644 --- a/docs/reference/biomod2-deprecated.html +++ b/docs/reference/biomod2-deprecated.html @@ -20,7 +20,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/biomod2_ensemble_model.html b/docs/reference/biomod2_ensemble_model.html index 9e1246e1..7d955291 100644 --- a/docs/reference/biomod2_ensemble_model.html +++ b/docs/reference/biomod2_ensemble_model.html @@ -17,7 +17,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/biomod2_model.html b/docs/reference/biomod2_model.html index 29dcff36..939d3718 100644 --- a/docs/reference/biomod2_model.html +++ b/docs/reference/biomod2_model.html @@ -17,7 +17,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/bm_BinaryTransformation.html b/docs/reference/bm_BinaryTransformation.html index 8e5a4893..7cbe450a 100644 --- a/docs/reference/bm_BinaryTransformation.html +++ b/docs/reference/bm_BinaryTransformation.html @@ -19,7 +19,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/bm_CrossValidation.html b/docs/reference/bm_CrossValidation.html index c71fe159..a2f6dd31 100644 --- a/docs/reference/bm_CrossValidation.html +++ b/docs/reference/bm_CrossValidation.html @@ -19,7 +19,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/bm_FindOptimStat.html b/docs/reference/bm_FindOptimStat.html index 7b89ce8a..634f18d6 100644 --- a/docs/reference/bm_FindOptimStat.html +++ b/docs/reference/bm_FindOptimStat.html @@ -19,7 +19,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/bm_MakeFormula.html b/docs/reference/bm_MakeFormula.html index 02bb5f64..e5ea05bd 100644 --- a/docs/reference/bm_MakeFormula.html +++ b/docs/reference/bm_MakeFormula.html @@ -18,7 +18,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/bm_ModelingOptions.html b/docs/reference/bm_ModelingOptions.html index 940ac95a..676b5c0b 100644 --- a/docs/reference/bm_ModelingOptions.html +++ b/docs/reference/bm_ModelingOptions.html @@ -17,7 +17,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/bm_PlotEvalBoxplot.html b/docs/reference/bm_PlotEvalBoxplot.html index 233756d4..28b63047 100644 --- a/docs/reference/bm_PlotEvalBoxplot.html +++ b/docs/reference/bm_PlotEvalBoxplot.html @@ -21,7 +21,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/bm_PlotEvalMean.html b/docs/reference/bm_PlotEvalMean.html index ab1ab5e9..43e51565 100644 --- a/docs/reference/bm_PlotEvalMean.html +++ b/docs/reference/bm_PlotEvalMean.html @@ -22,7 +22,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/bm_PlotRangeSize.html b/docs/reference/bm_PlotRangeSize.html index 16586119..2ec21f23 100644 --- a/docs/reference/bm_PlotRangeSize.html +++ b/docs/reference/bm_PlotRangeSize.html @@ -19,7 +19,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/bm_PlotResponseCurves.html b/docs/reference/bm_PlotResponseCurves.html index a865b184..569a6a6a 100644 --- a/docs/reference/bm_PlotResponseCurves.html +++ b/docs/reference/bm_PlotResponseCurves.html @@ -21,7 +21,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/bm_PlotVarImpBoxplot.html b/docs/reference/bm_PlotVarImpBoxplot.html index c3c9a3d2..b0c1c9b6 100644 --- a/docs/reference/bm_PlotVarImpBoxplot.html +++ b/docs/reference/bm_PlotVarImpBoxplot.html @@ -21,7 +21,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/bm_PseudoAbsences.html b/docs/reference/bm_PseudoAbsences.html index 37a106ad..825e2d27 100644 --- a/docs/reference/bm_PseudoAbsences.html +++ b/docs/reference/bm_PseudoAbsences.html @@ -18,7 +18,7 @@ biomod2 - 4.2-5 + 4.2-5-1 @@ -176,14 +176,14 @@

Select pseudo-absences

Arguments

resp.var
-

a vector, SpatialPoints or -SpatialPointsDataFrame object containing binary data (0 : absence, +

a vector, SpatialPoints or +SpatialPointsDataFrame object containing binary data (0 : absence, 1 : presence, NA : indeterminate) for a single species that will be used to find the pseudo-absences

expl.var
-

a matrix, data.frame, SpatialPointsDataFrame +

a matrix, data.frame, SpatialPointsDataFrame or SpatRaster object containing the explanatory variables (in columns or layers) that will be used to find the pseudo-absences

diff --git a/docs/reference/bm_RunModelsLoop.html b/docs/reference/bm_RunModelsLoop.html index adf27e8d..3c7c1690 100644 --- a/docs/reference/bm_RunModelsLoop.html +++ b/docs/reference/bm_RunModelsLoop.html @@ -18,7 +18,7 @@ biomod2 - 4.2-5 + 4.2-5-1
diff --git a/docs/reference/bm_SRE.html b/docs/reference/bm_SRE.html index 203c5e5e..94148860 100644 --- a/docs/reference/bm_SRE.html +++ b/docs/reference/bm_SRE.html @@ -20,7 +20,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/bm_SampleBinaryVector.html b/docs/reference/bm_SampleBinaryVector.html index 2841e364..781bf474 100644 --- a/docs/reference/bm_SampleBinaryVector.html +++ b/docs/reference/bm_SampleBinaryVector.html @@ -18,7 +18,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/bm_SampleFactorLevels.html b/docs/reference/bm_SampleFactorLevels.html index c3af729d..7c8afa35 100644 --- a/docs/reference/bm_SampleFactorLevels.html +++ b/docs/reference/bm_SampleFactorLevels.html @@ -19,7 +19,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/bm_Tuning.html b/docs/reference/bm_Tuning.html index ec0fad7d..612c88df 100644 --- a/docs/reference/bm_Tuning.html +++ b/docs/reference/bm_Tuning.html @@ -18,7 +18,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/bm_VariablesImportance.html b/docs/reference/bm_VariablesImportance.html index 88e6389f..bcedea07 100644 --- a/docs/reference/bm_VariablesImportance.html +++ b/docs/reference/bm_VariablesImportance.html @@ -18,7 +18,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/calculate.stat-deprecated.html b/docs/reference/calculate.stat-deprecated.html index 0cab958a..8749d944 100644 --- a/docs/reference/calculate.stat-deprecated.html +++ b/docs/reference/calculate.stat-deprecated.html @@ -18,7 +18,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/check_duplicated_cells.html b/docs/reference/check_duplicated_cells.html index cf2c4308..2fb16447 100644 --- a/docs/reference/check_duplicated_cells.html +++ b/docs/reference/check_duplicated_cells.html @@ -18,7 +18,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/dot-categorical2numeric.html b/docs/reference/dot-categorical2numeric.html index dbbf52c2..c5d1249b 100644 --- a/docs/reference/dot-categorical2numeric.html +++ b/docs/reference/dot-categorical2numeric.html @@ -19,7 +19,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/dot-get_categorical_names.html b/docs/reference/dot-get_categorical_names.html index 90c33ad7..5dada1e8 100644 --- a/docs/reference/dot-get_categorical_names.html +++ b/docs/reference/dot-get_categorical_names.html @@ -17,7 +17,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/dot-get_env_class.html b/docs/reference/dot-get_env_class.html index 0b1c6c2b..d5bcfe5b 100644 --- a/docs/reference/dot-get_env_class.html +++ b/docs/reference/dot-get_env_class.html @@ -17,7 +17,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/dot-load_gam_namespace.html b/docs/reference/dot-load_gam_namespace.html index 42e22868..b0db67c7 100644 --- a/docs/reference/dot-load_gam_namespace.html +++ b/docs/reference/dot-load_gam_namespace.html @@ -18,7 +18,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/dot-transform.outputs.list-deprecated.html b/docs/reference/dot-transform.outputs.list-deprecated.html index fe3116f4..0eca6ab2 100644 --- a/docs/reference/dot-transform.outputs.list-deprecated.html +++ b/docs/reference/dot-transform.outputs.list-deprecated.html @@ -18,7 +18,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/dot-transform_model.as.col.html b/docs/reference/dot-transform_model.as.col.html index 8ce179d0..19afc20d 100644 --- a/docs/reference/dot-transform_model.as.col.html +++ b/docs/reference/dot-transform_model.as.col.html @@ -22,7 +22,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/getStatOptimValue-deprecated.html b/docs/reference/getStatOptimValue-deprecated.html index 717f52db..da07121d 100644 --- a/docs/reference/getStatOptimValue-deprecated.html +++ b/docs/reference/getStatOptimValue-deprecated.html @@ -18,7 +18,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/getters.bm.html b/docs/reference/getters.bm.html index cfc59945..bded2b99 100644 --- a/docs/reference/getters.bm.html +++ b/docs/reference/getters.bm.html @@ -18,7 +18,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/getters.out.html b/docs/reference/getters.out.html index 816ed973..83b38392 100644 --- a/docs/reference/getters.out.html +++ b/docs/reference/getters.out.html @@ -19,7 +19,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/index.html b/docs/reference/index.html index bc5bc04b..3afd6b3c 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -17,7 +17,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/load_stored_object.html b/docs/reference/load_stored_object.html index c762b604..f0d50036 100644 --- a/docs/reference/load_stored_object.html +++ b/docs/reference/load_stored_object.html @@ -18,7 +18,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/makeFormula-deprecated.html b/docs/reference/makeFormula-deprecated.html index e104cbdf..10047dce 100644 --- a/docs/reference/makeFormula-deprecated.html +++ b/docs/reference/makeFormula-deprecated.html @@ -18,7 +18,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/models_scores_graph-deprecated.html b/docs/reference/models_scores_graph-deprecated.html index a11ed5fe..c2a12cca 100644 --- a/docs/reference/models_scores_graph-deprecated.html +++ b/docs/reference/models_scores_graph-deprecated.html @@ -18,7 +18,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/plot.html b/docs/reference/plot.html index 6a3a9169..fa8c6652 100644 --- a/docs/reference/plot.html +++ b/docs/reference/plot.html @@ -20,7 +20,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/predict.bm.html b/docs/reference/predict.bm.html index 78eabf9b..8449c5ea 100644 --- a/docs/reference/predict.bm.html +++ b/docs/reference/predict.bm.html @@ -18,7 +18,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/predict.em.html b/docs/reference/predict.em.html index 94a13eef..c41e7f8b 100644 --- a/docs/reference/predict.em.html +++ b/docs/reference/predict.em.html @@ -18,7 +18,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/predict2.bm.html b/docs/reference/predict2.bm.html index 24d36dfc..0b931c3b 100644 --- a/docs/reference/predict2.bm.html +++ b/docs/reference/predict2.bm.html @@ -21,7 +21,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/predict2.em.html b/docs/reference/predict2.em.html index 5f401260..0d9ac476 100644 --- a/docs/reference/predict2.em.html +++ b/docs/reference/predict2.em.html @@ -18,7 +18,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/rast.has.values.html b/docs/reference/rast.has.values.html index 0d41f1e5..6f550cfe 100644 --- a/docs/reference/rast.has.values.html +++ b/docs/reference/rast.has.values.html @@ -17,7 +17,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/response.plot2-deprecated.html b/docs/reference/response.plot2-deprecated.html index b582e1c9..c0ef0f96 100644 --- a/docs/reference/response.plot2-deprecated.html +++ b/docs/reference/response.plot2-deprecated.html @@ -18,7 +18,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/sample.factor.levels-deprecated.html b/docs/reference/sample.factor.levels-deprecated.html index e062b206..e58f43a1 100644 --- a/docs/reference/sample.factor.levels-deprecated.html +++ b/docs/reference/sample.factor.levels-deprecated.html @@ -18,7 +18,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/sre-deprecated.html b/docs/reference/sre-deprecated.html index 2e6d488a..df5c9d3b 100644 --- a/docs/reference/sre-deprecated.html +++ b/docs/reference/sre-deprecated.html @@ -18,7 +18,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/summary.html b/docs/reference/summary.html index 2206632c..3404dc21 100644 --- a/docs/reference/summary.html +++ b/docs/reference/summary.html @@ -19,7 +19,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/variables_importance-deprecated.html b/docs/reference/variables_importance-deprecated.html index 70881fcb..a442aaf0 100644 --- a/docs/reference/variables_importance-deprecated.html +++ b/docs/reference/variables_importance-deprecated.html @@ -18,7 +18,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/docs/reference/zzz_bm.html b/docs/reference/zzz_bm.html index e6e47b63..170a40a3 100644 --- a/docs/reference/zzz_bm.html +++ b/docs/reference/zzz_bm.html @@ -19,7 +19,7 @@ biomod2 - 4.2-5 + 4.2-5-1 diff --git a/vignettes/news.Rmd b/vignettes/news.Rmd index 3bea68e7..5c419208 100644 --- a/vignettes/news.Rmd +++ b/vignettes/news.Rmd @@ -15,6 +15,13 @@ vignette: > ### 2024 +##### Bugfix + +- 4.2-5-1 : + + removed `tests/` folder (unused) + + fixed check for variable names for `new.env` in `BIOMOD_Projection` and `BIOMOD_EnsembleForecasting` + + fixed connexion issue with MAXENT tuning + #### 4.2-5 Modeling options and Tuning (2024-05-02) - Submitted on CRAN diff --git a/vignettes/pictures/biomod2_presentation.workflow_05_2024.pdf b/vignettes/pictures/biomod2_presentation.workflow_05_2024.pdf index 14cd8016..f0720ea5 100644 Binary files a/vignettes/pictures/biomod2_presentation.workflow_05_2024.pdf and b/vignettes/pictures/biomod2_presentation.workflow_05_2024.pdf differ