Reference

Modeling species distributions
Main functions
BIOMOD_FormatingData()	Format input data, and select pseudo-absences if wanted, for usage in biomod2
BIOMOD_Modeling()	Run a range of species distribution models
BIOMOD_Projection()	Project a range of calibrated species distribution models onto new environment
BIOMOD_EnsembleModeling()	Create and evaluate an ensemble set of models and predictions
BIOMOD_EnsembleForecasting()	Project ensemble species distribution models onto new environment
BIOMOD_RangeSize()	Analyze the range size differences between projections of species distribution models
BIOMOD_LoadModels()	Load species distribution models built with biomod2
BIOMOD_Report()	Produce summary outputs from a simulation folder
Secundary functions
bm_MakeFormula()	Standardized formula maker
bm_SampleBinaryVector()	Sample binary vector
bm_SampleFactorLevels()	Sample all levels of a factorial variable
bm_PseudoAbsences() bm_PseudoAbsences_user.defined() bm_PseudoAbsences_random() bm_PseudoAbsences_sre() bm_PseudoAbsences_disk()	Select pseudo-absences
bm_CrossValidation() bm_CrossValidation_user.defined() bm_CrossValidation_random() bm_CrossValidation_kfold() bm_CrossValidation_block() bm_CrossValidation_strat() bm_CrossValidation_env()	Build cross-validation table
bm_ModelingOptions()	Configure the modeling options for each selected model
bm_Tuning()	Tune models parameters
bm_RunModelsLoop() bm_RunModel()	Loop to compute all single species distribution models
bm_SRE()	Surface Range Envelope
bm_FindOptimStat() get_optim_value() bm_CalculateStatBin() bm_CalculateStatAbun()	Calculate the best score according to a given evaluation method
bm_BinaryTransformation()	Convert probability values into binary values using a predefined threshold
bm_VariablesImportance()	Variables' importance calculation
bm_ModelAnalysis()	Analyze the residuals of the single models
bm_RangeSize()	Analyze the range size differences between projections of species distribution models
bm_PlotEvalMean()	Plot mean evaluation scores
bm_PlotEvalBoxplot()	Plot boxplot of evaluation scores
bm_PlotVarImpBoxplot()	Plot boxplot of variables importance
bm_PlotResponseCurves()	Plot response curves
bm_PlotRangeSize()	Plot species range change
Toolbox
Objects
BIOMOD.formated.data(<numeric>,<data.frame>) BIOMOD.formated.data(<data.frame>,<ANY>) BIOMOD.formated.data(<numeric>,<matrix>) BIOMOD.formated.data(<numeric>,<SpatRaster>) show(<BIOMOD.formated.data>)	BIOMOD_FormatingData() output object class
BIOMOD.formated.data.PA(<numeric>,<data.frame>) BIOMOD.formated.data.PA(<numeric>,<SpatRaster>)	BIOMOD_FormatingData() output object class (with pseudo-absences)
plot(<BIOMOD.formated.data>,<missing>) .plot.BIOMOD.formated.data.abundance()	plot method for BIOMOD.formated.data object class
summary(<BIOMOD.formated.data>)	summary method for BIOMOD.formated.data object class
BIOMOD.options.default(<character>,<character>)	bm_ModelingOptions output object class
BIOMOD.options.dataset(<character>) show(<BIOMOD.options.dataset>) print(<BIOMOD.options.dataset>)	bm_ModelingOptions output object class
show(<BIOMOD.models.options>) print(<BIOMOD.models.options>)	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
show(<biomod2_model>)	Single model output object class (when running BIOMOD_Modeling())
show(<biomod2_ensemble_model>)	Ensemble model output object class (when running BIOMOD_EnsembleModeling())
show(<BIOMOD.models.out>)	BIOMOD_Modeling() output object class
plot(<BIOMOD.projection.out>,<missing>) show(<BIOMOD.projection.out>)	BIOMOD_Projection() output object class
show(<BIOMOD.ensemble.models.out>)	BIOMOD_EnsembleModeling() output object class
BIOMOD.rangesize.out BIOMOD.rangesize.out-class	BIOMOD_RangeSize() output object class
Getters
load_stored_object()	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
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
set_new_dirname()	Functions to change the place of the different biomod2 objects
predict(<biomod2_model>)	Functions to get predictions from biomod2_model objects
predict.em	Functions to get predictions from biomod2_ensemble_model objects
Data
Models options
ModelsTable	Single models package and functions
OptionsBigboss	Bigboss pre-defined parameter values for single models
Species data
DataSpecies	Presence-Absence data to build test SDM
Environmental data
bioclim_current	Bioclimatic variables for SDM based on current condition
bioclim_future	Bioclimatic variables for SDM based on future condition
Reporting results
ODMAP	ODMAP empty table