Man pages for biomod2
Ensemble Platform for Species Distribution Modeling

BinaryTransformation-deprecatedBinaryTransformation
bioclim_currentBioclimatic variables for SDM based on current condition
bioclim_futureBioclimatic variables for SDM based on future condition
biomod2-deprecatedDeprecated functions in package 'biomod2'.
biomod2_ensemble_modelEnsemble model output object class (when running...
biomod2_modelSingle model output object class (when running...
BIOMOD_ConvertOldRun-deprecatedBIOMOD_ConvertOldRun
BIOMOD_CrossValidation-deprecatedBIOMOD_CrossValidation
BIOMOD_cv-deprecatedBIOMOD_cv
BIOMOD_EnsembleForecastingProject ensemble species distribution models onto new...
BIOMOD_EnsembleModelingCreate and evaluate an ensemble set of models and predictions
BIOMOD.ensemble.models.out'BIOMOD_EnsembleModeling()' output object class
BIOMOD.formated.data'BIOMOD_FormatingData()' output object class
BIOMOD.formated.data.PA'BIOMOD_FormatingData()' output object class (with...
BIOMOD_FormatingDataFormat input data, and select pseudo-absences if wanted, for...
BIOMOD_LoadModelsLoad species distribution models built with 'biomod2'
BIOMOD_ModelingRun a range of species distribution models
BIOMOD_ModelingOptionsConfigure the modeling options for each selected model
BIOMOD.models.options'BIOMOD_ModelingOptions()' output object class
BIOMOD.models.out'BIOMOD_Modeling()' output object class
BIOMOD_PresenceOnlyEvaluate models with presence-only metrics
BIOMOD_presenceonly-deprecatedBIOMOD_presenceonly
BIOMOD_ProjectionProject a range of calibrated species distribution models...
BIOMOD.projection.out'BIOMOD_Projection()' output object class
BIOMOD_RangeSizeAnalyze the range size differences between projections of...
BIOMOD.stored.data'BIOMOD_EnsembleModeling()' output object class
BIOMOD_TuningTune models parameters
BIOMOD_tuning-deprecatedBIOMOD_tuning
bm_BinaryTransformationConvert probability values into binary values using a...
bm_CrossValidationBuild cross-validation table
bm_CVnnetCross-validation for Neural Networks
bm_FindOptimStatCalculate the best score according to a given evaluation...
bm_MakeFormulaStandardized formula maker
bm_PlotEvalBoxplotPlot boxplot of evaluation scores
bm_PlotEvalMeanPlot mean evaluation scores
bm_PlotRangeSizePlot species range change
bm_PlotResponseCurvesPlot response curves
bm_PlotVarImpBoxplotPlot boxplot of variables importance
bm_PseudoAbsencesSelect pseudo-absences
bm_RunModelsLoopLoop to compute all single species distribution models
bm_SampleBinaryVectorSample binary vector
bm_SampleFactorLevelsTool to ensure the sampling of all levels of a factorial...
bm_SRESurface Range Envelope
bm_VariablesImportanceVariables' importance calculation
calculate.stat-deprecatedcalculate.stat
check_duplicated_cellsCheck duplicated cells
CustomIndexMaker-deprecatedCustomIndexMaker
DataSpeciesPresence-Absence data to build test SDM
dot-categorical2numericTransform categorical into numeric variables
dot-check_bytes_formatCheck bytes formatting
dot-get_categorical_namesGet categorical variable names
dot-get_env_classGet class of environmental data provided
dot-load_gam_namespaceLoad library for GAM models
dot-transform_model.as.colTransform predictions data.frame from long to wide with...
dot-transform.outputs.array-deprecated.transform.outputs.array
dot-transform.outputs.list-deprecated.transform.outputs.list
FilteringTransformation-deprecatedFilteringTransformation
Find.Optim.Stat-deprecatedFind.Optim.Stat
getStatOptimValue-deprecatedgetStatOptimValue
getters.bmFunctions to extract informations from 'biomod2_model'...
getters.outFunctions to extract informations from 'BIOMOD.models.out',...
load_stored_objectFunctions to load 'BIOMOD.stored.data' objects
makeFormula-deprecatedmakeFormula
models_scores_graph-deprecatedmodels_scores_graph
plot'plot' method for 'BIOMOD.formated.data' object class
predict2.bmFunctions to get predictions from 'biomod2_model' objects
predict2.emFunctions to get predictions from 'biomod2_ensemble_model'...
predict.bmFunctions to get predictions from 'biomod2_model' objects
predict.emFunctions to get predictions from 'biomod2_ensemble_model'...
Print_Default_ModelingOptions-deprecatedPrint_Default_ModelingOptions
ProbDensFunc-deprecatedProbDensFunc
rast.has.valuesCheck whether SpatRaster is an empty 'rast()'
response.plot2-deprecatedresponse.plot2
response.plot-deprecatedresponse.plot
sample.factor.levels-deprecatedsample.factor.levels
sre-deprecatedsre
summary'summary' method for 'BIOMOD.formated.data' object class
update_objects-deprecatedupdate_objects
variables_importance-deprecatedvariables_importance
zzz_bmDummy function to clean working directory after package...
biomod2 documentation built on July 9, 2023, 6:05 p.m.