diff --git a/DESCRIPTION b/DESCRIPTION index 455fe1af..7e6cdf4a 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Package: biomod2 Type: Package Title: Ensemble Platform for Species Distribution Modeling Version: 4.2-5 -Date: 2024-04-04 +Date: 2024-04-30 Authors@R: c(person("Wilfried", "Thuiller", role = c("aut") , email = "wilfried.thuiller@univ-grenoble-alpes.fr"), person("Damien", "Georges", role = c("aut")), @@ -75,7 +75,7 @@ Suggests: tidyterra, ggtext License: GPL-3 -RoxygenNote: 7.2.3 +RoxygenNote: 7.3.1 Encoding: UTF-8 VignetteBuilder: knitr Collate: diff --git a/R/biomod2_globalVariables.R b/R/biomod2_globalVariables.R index 79b268c5..ef9a7aa9 100644 --- a/R/biomod2_globalVariables.R +++ b/R/biomod2_globalVariables.R @@ -6,7 +6,7 @@ utils::globalVariables(names = c("i.dim1", "sub.i")) ## biomod2_classes_0 ------------ -utils::globalVariables(names = c("expected_CVnames")) +utils::globalVariables(names = c("expected_CVnames", "OptionsBigboss")) ## biomod2_classes_1 ------------ utils::globalVariables(names = c("this_PA", diff --git a/R/bm_Tuning.R b/R/bm_Tuning.R index 0912ba56..8da027c1 100644 --- a/R/bm_Tuning.R +++ b/R/bm_Tuning.R @@ -70,6 +70,7 @@ ##' \item{ANN}{\code{size}, \code{decay}, \code{bag}} ##' \item{CTA}{\code{maxdepth}} ##' \item{FDA}{\code{degree}, \code{nprune}} +##' \item{GAM.gam}{\code{span}, \code{degree}} ##' \item{GAM.mgcv}{\code{select}, \code{method}} ##' \item{GBM}{\code{n.trees}, \code{interaction.depth}, \code{shrinkage}, \code{n.minobsinnode}} ##' \item{MARS}{\code{degree}, \code{nprune}} @@ -86,7 +87,7 @@ ##' ##' @note ##' \itemize{ -##' \item No tuning for \code{GAM.gam}, \code{GLM} and \code{MAXNET} +##' \item No tuning for \code{GLM} and \code{MAXNET} ##' \item \code{MAXENT} is tuned through \code{\link[ENMeval]{ENMevaluate}} function which is ##' calling either : ##' \itemize{ @@ -161,7 +162,7 @@ ##' # tune parameters for Random Forest model ##' tuned.rf <- bm_Tuning(model = 'RF', ##' tuning.fun = 'rf', ## see in ModelsTable -##' do.formula = TRUE, +##' do.formula = FALSE, ##' bm.options = opt.d@options$RF.binary.randomForest.randomForest, ##' bm.format = myBiomodData) ##' tuned.rf @@ -207,7 +208,7 @@ bm_Tuning <- function(model, FDA.nprune = 2:38, GAM.select = c(TRUE, FALSE), GAM.method = c('GCV.Cp', 'GACV.Cp', 'REML', 'P-REML', 'ML', 'P-ML'), - GAM.span = c(0.3,0.5,0.7), + GAM.span = c(0.3, 0.5, 0.7), GAM.degree = 1, GBM.n.trees = c(500, 1000, 2500), GBM.interaction.depth = seq(2, 8, by = 3), @@ -592,7 +593,7 @@ bm_Tuning <- function(model, FDA.nprune = 2:38, GAM.select = c(TRUE, FALSE), GAM.method = c('GCV.Cp', 'GACV.Cp', 'REML', 'P-REML', 'ML', 'P-ML'), - GAM.span = c(0.3,0.5,0.7), + GAM.span = c(0.3, 0.5, 0.7), GAM.degree = 1, GBM.n.trees = c(500, 1000, 2500), GBM.interaction.depth = seq(2, 8, by = 3), @@ -651,9 +652,9 @@ bm_Tuning <- function(model, params.train = params.train[grep(model, names(params.train))] .fun_testIfIn(TRUE, "names(params.train)", names(params.train), paste0(model, ".", train.params$params)) } else if (tuning.fun == "gamLoess"){ - params.train = params.train[c('GAM.span',"GAM.degree")] + params.train = params.train[c('GAM.span', "GAM.degree")] } else { - params.train = params.train[c('GAM.select','GAM.method')] + params.train = params.train[c('GAM.select', 'GAM.method')] } names(params.train) = sub(model, "", names(params.train)) tuning.grid <- do.call(expand.grid, params.train) diff --git a/docs/404.html b/docs/404.html index fcd127dd..1de76174 100644 --- a/docs/404.html +++ b/docs/404.html @@ -6,7 +6,7 @@ Page not found (404) • biomod2 - + @@ -143,7 +143,7 @@

Page not found (404)

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/docs/articles/examples_1_mainFunctions.html b/docs/articles/examples_1_mainFunctions.html index 73cbb616..6dec230c 100644 --- a/docs/articles/examples_1_mainFunctions.html +++ b/docs/articles/examples_1_mainFunctions.html @@ -6,7 +6,7 @@ Main functions • biomod2 - + @@ -146,7 +146,7 @@

variables 

-library(biomod2)
+library(biomod2)
 library(terra)
 
 # Load species occurrences (6 species available)
@@ -471,7 +471,7 @@ 

 
 

   

-
Site built with pkgdown 2.0.7.

+
Site built with pkgdown 2.0.9.

 

 
       
diff --git a/docs/articles/examples_2_secundaryFunctions.html b/docs/articles/examples_2_secundaryFunctions.html
index 68857d39..038c0d76 100644
--- a/docs/articles/examples_2_secundaryFunctions.html
+++ b/docs/articles/examples_2_secundaryFunctions.html
@@ -6,7 +6,7 @@
 
 
 Secundary functions • biomod2
-
+
 
 
 
@@ -186,7 +186,7 @@ 

 variables
 

 
 
 ## Create simple simulated data ---------------------------------------------------------
@@ -590,7 +590,7 @@ 

 
 

   

-
Site built with pkgdown 2.0.7.

+
Site built with pkgdown 2.0.9.

 

 
       
diff --git a/docs/articles/index.html b/docs/articles/index.html
index 11b89189..81f988ea 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -1,5 +1,5 @@
 
-Articles • biomod2Articles • biomod2
@@ -130,7 +130,7 @@ 
All vignettes

 

 
 

-  
Site built with pkgdown 2.0.7.

+  
Site built with pkgdown 2.0.9.
diff --git a/docs/articles/news.html b/docs/articles/news.html index fd872f8e..7e8c7ef7 100644 --- a/docs/articles/news.html +++ b/docs/articles/news.html @@ -6,7 +6,7 @@ News • biomod2 - + @@ -75,6 +75,12 @@
  • Pseudo-absences
    • +
  • + Cross-validation +
    • +
  • + Modeling options +
  • Variability in results
    • @@ -1243,12 +1249,12 @@

    1.x.x diff --git a/docs/articles/vignette_crossValidation.html b/docs/articles/vignette_crossValidation.html index 51741341..f666ab76 100644 --- a/docs/articles/vignette_crossValidation.html +++ b/docs/articles/vignette_crossValidation.html @@ -6,7 +6,7 @@ Cross-validation • biomod2 - + @@ -443,7 +443,7 @@

    ✖ References

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.0.9.

    diff --git a/docs/articles/vignette_dataPreparation.html b/docs/articles/vignette_dataPreparation.html index 8a9691b5..d02e532d 100644 --- a/docs/articles/vignette_dataPreparation.html +++ b/docs/articles/vignette_dataPreparation.html @@ -6,7 +6,7 @@ Data preparation • biomod2 - + @@ -324,7 +324,7 @@

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.0.9.

    diff --git a/docs/articles/vignette_modelingOptions.html b/docs/articles/vignette_modelingOptions.html index 0ef21897..3db6a75a 100644 --- a/docs/articles/vignette_modelingOptions.html +++ b/docs/articles/vignette_modelingOptions.html @@ -6,7 +6,7 @@ Modeling Options • biomod2 - + @@ -429,7 +429,7 @@

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.0.9.

    diff --git a/docs/articles/vignette_pseudoAbsences.html b/docs/articles/vignette_pseudoAbsences.html index d325897b..8fd840cf 100644 --- a/docs/articles/vignette_pseudoAbsences.html +++ b/docs/articles/vignette_pseudoAbsences.html @@ -6,7 +6,7 @@ Pseudo-absences • biomod2 - + @@ -282,7 +282,7 @@

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.0.9.

    diff --git a/docs/articles/vignette_variability.html b/docs/articles/vignette_variability.html index dfe03be0..48926ace 100644 --- a/docs/articles/vignette_variability.html +++ b/docs/articles/vignette_variability.html @@ -6,7 +6,7 @@ Variability in results • biomod2 - + @@ -237,7 +237,7 @@

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.0.9.

    diff --git a/docs/articles/vignette_videos.html b/docs/articles/vignette_videos.html index 0e0550cc..954f7951 100644 --- a/docs/articles/vignette_videos.html +++ b/docs/articles/vignette_videos.html @@ -6,7 +6,7 @@ Videos • biomod2 - + @@ -186,7 +186,7 @@

    Interface (package ShinyBiomod

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.0.9.

    diff --git a/docs/authors.html b/docs/authors.html index e2a131f7..2038258a 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -1,5 +1,5 @@ -Authors and Citation • biomod2Authors and Citation • biomod2 @@ -96,7 +96,7 @@
    -

    Authors

    +

    Authors and Citation

    @@ -164,7 +164,7 @@

    Citation

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.0.9.

    diff --git a/docs/index.html b/docs/index.html index 62860173..3b42a477 100644 --- a/docs/index.html +++ b/docs/index.html @@ -6,17 +6,13 @@ Ensemble Platform for Species Distribution Modeling • biomod2 - + - + BIOMOD_EnsembleModeling() output object class — BIOMOD.ensemble.models.out • biomod2BIOMOD_EnsembleModeling() output object class — BIOMOD.ensemble.models.out • biomod2BIOMOD_FormatingData() output object class (with pseudo-absences) — BIOMOD.formated.data.PA • biomod2BIOMOD_FormatingData() output object class (with pseudo-absences) — BIOMOD.formated.data.PA • biomod2BIOMOD_FormatingData() output object class — BIOMOD.formated.data • biomod2BIOMOD_FormatingData() output object class — BIOMOD.formated.data • biomod2bm_ModelingOptions output object class — BIOMOD.models.options • biomod2bm_ModelingOptions output object class — BIOMOD.models.options • biomod2BIOMOD_Modeling() output object class — BIOMOD.models.out • biomod2BIOMOD_Modeling() output object class — BIOMOD.models.out • biomod2bm_ModelingOptions output object class — BIOMOD.options.dataset • biomod2bm_ModelingOptions output object class — BIOMOD.options.dataset • biomod2bm_ModelingOptions output object class — BIOMOD.options.default • biomod2bm_ModelingOptions output object class — BIOMOD.options.default • biomod2BIOMOD_Projection() output object class — BIOMOD.projection.out • biomod2BIOMOD_Projection() output object class — BIOMOD.projection.out • biomod2BIOMOD_Modeling and BIOMOD_EnsembleModeling -output object class — BIOMOD.stored.data • biomod2BIOMOD_Modeling and BIOMOD_EnsembleModeling output object class — BIOMOD.stored.data • biomod2BIOMOD_CrossValidation — BIOMOD_CrossValidation-deprecated • biomod2BIOMOD_CrossValidation — BIOMOD_CrossValidation-deprecated • biomod2Project ensemble species distribution models onto new environment — BIOMOD_EnsembleForecasting • biomod2Project ensemble species distribution models onto new environment — BIOMOD_EnsembleForecasting • biomod2Create and evaluate an ensemble set of models and predictions — BIOMOD_EnsembleModeling • biomod2Create and evaluate an ensemble set of models and predictions — BIOMOD_EnsembleModeling • biomod2 -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.0.9.

    diff --git a/docs/reference/BIOMOD_FormatingData.html b/docs/reference/BIOMOD_FormatingData.html index d5b2dd44..05764463 100644 --- a/docs/reference/BIOMOD_FormatingData.html +++ b/docs/reference/BIOMOD_FormatingData.html @@ -1,5 +1,5 @@ -Format input data, and select pseudo-absences if wanted, for usage in biomod2 — BIOMOD_FormatingData • biomod2Format input data, and select pseudo-absences if wanted, for usage in biomod2 — BIOMOD_FormatingData • biomod2Load species distribution models built with biomod2 — BIOMOD_LoadModels • biomod2Load species distribution models built with biomod2 — BIOMOD_LoadModels • biomod2Run a range of species distribution models — BIOMOD_Modeling • biomod2Run a range of species distribution models — BIOMOD_Modeling • biomod2BIOMOD_PresenceOnly — BIOMOD_PresenceOnly-deprecated • biomod2BIOMOD_PresenceOnly — BIOMOD_PresenceOnly-deprecated • biomod2Project a range of calibrated species distribution models onto new environment — BIOMOD_Projection • biomod2Project a range of calibrated species distribution models onto new environment — BIOMOD_Projection • biomod2Analyze the range size differences between projections of species distribution models — BIOMOD_RangeSize • biomod2Analyze the range size differences between projections of species distribution models — BIOMOD_RangeSize • biomod2BIOMOD_Tuning — BIOMOD_tuning-deprecated • biomod2BIOMOD_Tuning — BIOMOD_tuning-deprecated • biomod2BinaryTransformation — BinaryTransformation-deprecated • biomod2BinaryTransformation — BinaryTransformation-deprecated • biomod2Presence-Absence data to build test SDM — DataSpecies • biomod2Presence-Absence data to build test SDM — DataSpecies • biomod2Find.Optim.Stat — Find.Optim.Stat-deprecated • biomod2Find.Optim.Stat — Find.Optim.Stat-deprecated • biomod2Single models package and functions — ModelsTable • biomod2Single models package and functions — ModelsTable • biomod2Bigboss pre-defined parameter values for single models — OptionsBigboss • biomod2Bigboss pre-defined parameter values for single models — OptionsBigboss • biomod2ProbDensFunc — ProbDensFunc-deprecated • biomod2ProbDensFunc — ProbDensFunc-deprecated • biomod2Bioclimatic variables for SDM based on current condition — bioclim_current • biomod2Bioclimatic variables for SDM based on current condition — bioclim_current • biomod2Bioclimatic variables for SDM based on future condition — bioclim_future • biomod2Bioclimatic variables for SDM based on future condition — bioclim_future • biomod2Deprecated functions in package biomod2. — biomod2-deprecated • biomod2Ensemble model output object class (when running BIOMOD_EnsembleModeling()) — biomod2_ensemble_model • biomod2Ensemble model output object class (when running BIOMOD_EnsembleModeling()) — biomod2_ensemble_model • biomod2 @@ -190,8 +190,8 @@

    See also

    biomod2_model, BIOMOD_EnsembleModeling

    Other Toolbox objects: BIOMOD.ensemble.models.out, -BIOMOD.formated.data.PA, BIOMOD.formated.data, +BIOMOD.formated.data.PA, BIOMOD.models.options, BIOMOD.models.out, BIOMOD.options.dataset, @@ -230,7 +230,7 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.0.9.

    diff --git a/docs/reference/biomod2_model.html b/docs/reference/biomod2_model.html index cd704a07..9c3b4518 100644 --- a/docs/reference/biomod2_model.html +++ b/docs/reference/biomod2_model.html @@ -1,5 +1,5 @@ -Single model output object class (when running BIOMOD_Modeling()) — biomod2_model • biomod2Single model output object class (when running BIOMOD_Modeling()) — biomod2_model • biomod2 @@ -190,8 +190,8 @@

    See also

    BIOMOD_Modeling, bm_RunModel

    Other Toolbox objects: BIOMOD.ensemble.models.out, -BIOMOD.formated.data.PA, BIOMOD.formated.data, +BIOMOD.formated.data.PA, BIOMOD.models.options, BIOMOD.models.out, BIOMOD.options.dataset, @@ -234,7 +234,7 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.0.9.

    diff --git a/docs/reference/bm_BinaryTransformation.html b/docs/reference/bm_BinaryTransformation.html index 35d8a12d..dcb14c72 100644 --- a/docs/reference/bm_BinaryTransformation.html +++ b/docs/reference/bm_BinaryTransformation.html @@ -1,5 +1,5 @@ -Convert probability values into binary values using a predefined threshold — bm_BinaryTransformation • biomod2Convert probability values into binary values using a predefined threshold — bm_BinaryTransformation • biomod2Build cross-validation table — bm_CrossValidation • biomod2Build cross-validation table — bm_CrossValidation • biomod2Calculate the best score according to a given evaluation method — bm_FindOptimStat • biomod2Calculate the best score according to a given evaluation method — bm_FindOptimStat • biomod2Standardized formula maker — bm_MakeFormula • biomod2Standardized formula maker — bm_MakeFormula • biomod2Configure the modeling options for each selected model — bm_ModelingOptions • biomod2Configure the modeling options for each selected model — bm_ModelingOptions • biomod2 @@ -387,7 +387,7 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.0.9.

    diff --git a/docs/reference/bm_PlotEvalBoxplot.html b/docs/reference/bm_PlotEvalBoxplot.html index 4b944ad6..8559471c 100644 --- a/docs/reference/bm_PlotEvalBoxplot.html +++ b/docs/reference/bm_PlotEvalBoxplot.html @@ -1,5 +1,5 @@ -Plot boxplot of evaluation scores — bm_PlotEvalBoxplot • biomod2Plot boxplot of evaluation scores — bm_PlotEvalBoxplot • biomod2 -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.0.9.

    diff --git a/docs/reference/bm_PlotEvalMean.html b/docs/reference/bm_PlotEvalMean.html index 00fd2a99..a1afdfe7 100644 --- a/docs/reference/bm_PlotEvalMean.html +++ b/docs/reference/bm_PlotEvalMean.html @@ -1,5 +1,5 @@ -Plot mean evaluation scores — bm_PlotEvalMean • biomod2Plot mean evaluation scores — bm_PlotEvalMean • biomod2 -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.0.9.

    diff --git a/docs/reference/bm_PlotRangeSize.html b/docs/reference/bm_PlotRangeSize.html index bc05f50c..248c173f 100644 --- a/docs/reference/bm_PlotRangeSize.html +++ b/docs/reference/bm_PlotRangeSize.html @@ -1,5 +1,5 @@ -Plot species range change — bm_PlotRangeSize • biomod2Plot species range change — bm_PlotRangeSize • biomod2Plot response curves — bm_PlotResponseCurves • biomod2Plot response curves — bm_PlotResponseCurves • biomod2 -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.0.9.

    diff --git a/docs/reference/bm_PlotVarImpBoxplot.html b/docs/reference/bm_PlotVarImpBoxplot.html index cb025a4c..ff16914e 100644 --- a/docs/reference/bm_PlotVarImpBoxplot.html +++ b/docs/reference/bm_PlotVarImpBoxplot.html @@ -1,5 +1,5 @@ -Plot boxplot of variables importance — bm_PlotVarImpBoxplot • biomod2Plot boxplot of variables importance — bm_PlotVarImpBoxplot • biomod2 -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.0.9.

    diff --git a/docs/reference/bm_PseudoAbsences.html b/docs/reference/bm_PseudoAbsences.html index 121573fd..94c13132 100644 --- a/docs/reference/bm_PseudoAbsences.html +++ b/docs/reference/bm_PseudoAbsences.html @@ -1,5 +1,5 @@ -Select pseudo-absences — bm_PseudoAbsences • biomod2Select pseudo-absences — bm_PseudoAbsences • biomod2Loop to compute all single species distribution models — bm_RunModelsLoop • biomod2Loop to compute all single species distribution models — bm_RunModelsLoop • biomod2Surface Range Envelope — bm_SRE • biomod2Surface Range Envelope — bm_SRE • biomod2Sample binary vector — bm_SampleBinaryVector • biomod2Sample binary vector — bm_SampleBinaryVector • biomod2Sample all levels of a factorial variable — bm_SampleFactorLevels • biomod2Sample all levels of a factorial variable — bm_SampleFactorLevels • biomod2Tune models parameters — bm_Tuning • biomod2Tune models parameters — bm_Tuning • biomod2Variables' importance calculation — bm_VariablesImportance • biomod2Variables' importance calculation — bm_VariablesImportance • biomod2calculate.stat — calculate.stat-deprecated • biomod2calculate.stat — calculate.stat-deprecated • biomod2Check duplicated cells — check_duplicated_cells • biomod2Check duplicated cells — check_duplicated_cells • biomod2Transform categorical into numeric variables — .categorical2numeric • biomod2Transform categorical into numeric variables — .categorical2numeric • biomod2Get categorical variable names — .get_categorical_names • biomod2Get categorical variable names — .get_categorical_names • biomod2 @@ -56,6 +56,12 @@
  • Pseudo-absences
    • +
  • + Cross-validation +
    • +
  • + Modeling options +
  • Variability in results
    • @@ -123,11 +129,11 @@

    Value

    diff --git a/docs/reference/dot-get_env_class.html b/docs/reference/dot-get_env_class.html index a151ecf3..66607106 100644 --- a/docs/reference/dot-get_env_class.html +++ b/docs/reference/dot-get_env_class.html @@ -1,5 +1,5 @@ -Get class of environmental data provided — .get_env_class • biomod2Get class of environmental data provided — .get_env_class • biomod2 @@ -56,6 +56,12 @@
  • Pseudo-absences
    • +
  • + Cross-validation +
    • +
  • + Modeling options +
  • Variability in results
    • @@ -123,11 +129,11 @@

    Value

    diff --git a/docs/reference/dot-load_gam_namespace.html b/docs/reference/dot-load_gam_namespace.html index b286af1f..5811bc8b 100644 --- a/docs/reference/dot-load_gam_namespace.html +++ b/docs/reference/dot-load_gam_namespace.html @@ -1,5 +1,5 @@ -Load library for GAM models — .load_gam_namespace • biomod2Load library for GAM models — .load_gam_namespace • biomod2.transform.outputs.list — .transform.outputs.list-deprecated • biomod2.transform.outputs.list — .transform.outputs.list-deprecated • biomod2Transform predictions data.frame from long to wide with models as columns — .transform_model.as.col • biomod2Transform predictions data.frame from long to wide with models as columns — .transform_model.as.col • biomod2Pseudo-absences +
  • + Cross-validation +
    • +
  • + Modeling options +
  • Variability in results
    • @@ -140,11 +146,11 @@

    Author

    diff --git a/docs/reference/getStatOptimValue-deprecated.html b/docs/reference/getStatOptimValue-deprecated.html index 45612549..2a2074c1 100644 --- a/docs/reference/getStatOptimValue-deprecated.html +++ b/docs/reference/getStatOptimValue-deprecated.html @@ -1,5 +1,5 @@ -getStatOptimValue — getStatOptimValue-deprecated • biomod2getStatOptimValue — getStatOptimValue-deprecated • biomod2Functions to extract informations from biomod2_model objects — getters.bm • biomod2Functions to extract informations from biomod2_model objects — getters.bm • biomod2Functions to extract informations from BIOMOD.models.out, -BIOMOD.projection.out or BIOMOD.ensemble.models.out objects — getters.out • biomod2Functions to extract informations from BIOMOD.models.out, BIOMOD.projection.out or BIOMOD.ensemble.models.out objects — getters.out • biomod2Function reference • biomod2Function reference • biomod2 @@ -225,28 +225,27 @@

    Objects

    plot(<BIOMOD.formated.data>,<missing>)

    -

    plot method for BIOMOD.formated.data object class

    +

    plot method for BIOMOD.formated.data object class

    summary(<BIOMOD.formated.data>)

    -

    summary method for BIOMOD.formated.data object class

    +

    summary method for BIOMOD.formated.data object class

    BIOMOD.options.default(<character>,<character>)

    -

    bm_ModelingOptions output object class

    +

    bm_ModelingOptions output object class

    BIOMOD.options.dataset(<character>) show(<BIOMOD.options.dataset>) print(<BIOMOD.options.dataset>)

    -

    bm_ModelingOptions output object class

    +

    bm_ModelingOptions output object class

    show(<BIOMOD.models.options>) print(<BIOMOD.models.options>)

    -

    bm_ModelingOptions output object class

    +

    bm_ModelingOptions output object class

    BIOMOD.stored.data BIOMOD.stored.data-class BIOMOD.stored.data.frame-class BIOMOD.stored.SpatRaster-class BIOMOD.stored.files-class BIOMOD.stored.formated.data-class BIOMOD.stored.options-class BIOMOD.stored.models.out-class

    -

    BIOMOD_Modeling and BIOMOD_EnsembleModeling -output object class

    +

    BIOMOD_Modeling and BIOMOD_EnsembleModeling output object class

    show(<biomod2_model>)

    @@ -274,24 +273,23 @@

    Getters

    load_stored_object()

    -

    Functions to load BIOMOD.stored.data objects

    +

    Functions to load BIOMOD.stored.data objects

    get_formal_model(<biomod2_model>) get_scaling_model(<biomod2_model>)

    -

    Functions to extract informations from biomod2_model objects

    +

    Functions to extract informations from biomod2_model objects

    get_species_data(<BIOMOD.formated.data>) get_species_data(<BIOMOD.formated.data.PA>) get_eval_data(<BIOMOD.formated.data>) get_options(<BIOMOD.models.out>) get_calib_lines(<BIOMOD.models.out>) get_formal_data(<BIOMOD.models.out>) get_predictions(<BIOMOD.models.out>) get_built_models(<BIOMOD.models.out>) get_evaluations(<BIOMOD.models.out>) get_variables_importance(<BIOMOD.models.out>) get_projected_models(<BIOMOD.projection.out>) free(<BIOMOD.projection.out>) get_predictions(<BIOMOD.projection.out>) get_formal_data(<BIOMOD.ensemble.models.out>) get_built_models(<BIOMOD.ensemble.models.out>) get_kept_models(<BIOMOD.ensemble.models.out>) get_predictions(<BIOMOD.ensemble.models.out>) get_evaluations(<BIOMOD.ensemble.models.out>) get_variables_importance(<BIOMOD.ensemble.models.out>)

    -

    Functions to extract informations from BIOMOD.models.out, -BIOMOD.projection.out or BIOMOD.ensemble.models.out objects

    +

    Functions to extract informations from BIOMOD.models.out, BIOMOD.projection.out or BIOMOD.ensemble.models.out objects

    predict(<biomod2_model>)

    -

    Functions to get predictions from biomod2_model objects

    +

    Functions to get predictions from biomod2_model objects

    predict.em

    -

    Functions to get predictions from biomod2_ensemble_model objects

    +

    Functions to get predictions from biomod2_ensemble_model objects

    Data

    @@ -341,7 +339,7 @@

    Environmental data
    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.0.9.

    diff --git a/docs/reference/load_stored_object.html b/docs/reference/load_stored_object.html index e2a7f634..6431dde6 100644 --- a/docs/reference/load_stored_object.html +++ b/docs/reference/load_stored_object.html @@ -1,5 +1,5 @@ -Functions to load BIOMOD.stored.data objects — load_stored_object • biomod2Functions to load BIOMOD.stored.data objects — load_stored_object • biomod2makeFormula — makeFormula-deprecated • biomod2makeFormula — makeFormula-deprecated • biomod2models_scores_graph — models_scores_graph-deprecated • biomod2models_scores_graph — models_scores_graph-deprecated • biomod2plot method for BIOMOD.formated.data object class — plot,BIOMOD.formated.data,missing-method • biomod2plot method for BIOMOD.formated.data object class — plot,BIOMOD.formated.data,missing-method • biomod2Functions to get predictions from biomod2_model objects — predict.bm • biomod2Functions to get predictions from biomod2_model objects — predict.bm • biomod2Functions to get predictions from biomod2_ensemble_model objects — predict.em • biomod2Functions to get predictions from biomod2_ensemble_model objects — predict.em • biomod2Functions to get predictions from biomod2_model objects — predict2.bm • biomod2Functions to get predictions from biomod2_model objects — predict2.bm • biomod2Pseudo-absences +
  • + Cross-validation +
    • +
  • + Modeling options +
  • Variability in results
    • @@ -103,7 +109,7 @@

    Functions to get predictions from biomod2 biomod2_model on (new) explanatory variables. predict2 was introduced to allow a signature with two arguments : object, a type of biomod2_model and newdata, either a -SpatRaster or a data.frame.

    +SpatRaster or a data.frame.

    @@ -196,7 +202,7 @@

    Arguments

    newdata

    a data.frame or -SpatRaster object containing data for new +SpatRaster object containing data for new predictions

    @@ -240,11 +246,11 @@

    Author

    diff --git a/docs/reference/predict2.em.html b/docs/reference/predict2.em.html index 1dcbf6cb..db7e05b7 100644 --- a/docs/reference/predict2.em.html +++ b/docs/reference/predict2.em.html @@ -1,5 +1,5 @@ -Functions to get predictions from biomod2_ensemble_model objects — predict2.em • biomod2Functions to get predictions from biomod2_ensemble_model objects — predict2.em • biomod2Check whether SpatRaster is an empty rast() — rast.has.values • biomod2Check whether SpatRaster is an empty rast() — rast.has.values • biomod2 @@ -56,6 +56,12 @@
  • Pseudo-absences
    • +
  • + Cross-validation +
    • +
  • + Modeling options +
  • Variability in results
    • @@ -95,7 +101,7 @@

    Check whether SpatRaster is an empty rast()

    -

    Check whether SpatRaster is an empty rast()

    +

    Check whether SpatRaster is an empty rast()

    @@ -123,11 +129,11 @@

    Value

    diff --git a/docs/reference/response.plot2-deprecated.html b/docs/reference/response.plot2-deprecated.html index 296e91a3..1aedddee 100644 --- a/docs/reference/response.plot2-deprecated.html +++ b/docs/reference/response.plot2-deprecated.html @@ -1,5 +1,5 @@ -response.plot2 — response.plot2-deprecated • biomod2response.plot2 — response.plot2-deprecated • biomod2sample.factor.levels — sample.factor.levels-deprecated • biomod2sample.factor.levels — sample.factor.levels-deprecated • biomod2sre — sre-deprecated • biomod2sre — sre-deprecated • biomod2summary method for BIOMOD.formated.data object class — summary,BIOMOD.formated.data-method • biomod2summary method for BIOMOD.formated.data object class — summary,BIOMOD.formated.data-method • biomod2variables_importance — variables_importance-deprecated • biomod2variables_importance — variables_importance-deprecated • biomod2Dummy function to clean working directory after package checks — zzz_bm • biomod2Dummy function to clean working directory after package checks — zzz_bm • biomod2