R: Ensemble Platform for Species Distribution Modeling

# Ensemble Platform for Species Distribution Modeling

## Documentation for package ‘biomod2’ version 4.3-4-6

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

A B C D E F G L M O P R S X

## -- A --

ANN_biomod2_model-class | Single model output object class (when running 'BIOMOD_Modeling()')

## -- B --

bioclim_current | Bioclimatic variables for SDM based on current condition
bioclim_future | Bioclimatic variables for SDM based on future condition
BIOMOD.ensemble.models.out | 'BIOMOD_EnsembleModeling()' output object class
BIOMOD.ensemble.models.out-class | 'BIOMOD_EnsembleModeling()' output object class
BIOMOD.formated.data | 'BIOMOD_FormatingData()' output object class
BIOMOD.formated.data-class | 'BIOMOD_FormatingData()' output object class
BIOMOD.formated.data-method | 'BIOMOD_FormatingData()' output object class
BIOMOD.formated.data.PA | 'BIOMOD_FormatingData()' output object class (with pseudo-absences)
BIOMOD.formated.data.PA-class | 'BIOMOD_FormatingData()' output object class (with pseudo-absences)
BIOMOD.formated.data.PA-method | 'BIOMOD_FormatingData()' output object class (with pseudo-absences)
BIOMOD.models.options | 'bm_ModelingOptions' output object class
BIOMOD.models.options-class | 'bm_ModelingOptions' output object class
BIOMOD.models.out | 'BIOMOD_Modeling()' output object class
BIOMOD.models.out-class | 'BIOMOD_Modeling()' output object class
BIOMOD.options.dataset | 'bm_ModelingOptions' output object class
BIOMOD.options.dataset-class | 'bm_ModelingOptions' output object class
BIOMOD.options.dataset-method | 'bm_ModelingOptions' output object class
BIOMOD.options.default | 'bm_ModelingOptions' output object class
BIOMOD.options.default-class | 'bm_ModelingOptions' output object class
BIOMOD.options.default-method | 'bm_ModelingOptions' output object class
BIOMOD.projection.out | 'BIOMOD_Projection()' output object class
BIOMOD.projection.out-class | 'BIOMOD_Projection()' output object class
BIOMOD.rangesize.out | 'BIOMOD_RangeSize()' output object class
BIOMOD.rangesize.out-class | 'BIOMOD_RangeSize()' output object class
BIOMOD.stored.data | 'BIOMOD_Modeling' and 'BIOMOD_EnsembleModeling' output object class
BIOMOD.stored.data-class | 'BIOMOD_Modeling' and 'BIOMOD_EnsembleModeling' output object class
BIOMOD.stored.data.frame-class | 'BIOMOD_Modeling' and 'BIOMOD_EnsembleModeling' output object class
BIOMOD.stored.files-class | 'BIOMOD_Modeling' and 'BIOMOD_EnsembleModeling' output object class
BIOMOD.stored.formated.data-class | 'BIOMOD_Modeling' and 'BIOMOD_EnsembleModeling' output object class
BIOMOD.stored.models.out-class | 'BIOMOD_Modeling' and 'BIOMOD_EnsembleModeling' output object class
BIOMOD.stored.options-class | 'BIOMOD_Modeling' and 'BIOMOD_EnsembleModeling' output object class
BIOMOD.stored.SpatRaster-class | 'BIOMOD_Modeling' and 'BIOMOD_EnsembleModeling' output object class
biomod2_ensemble_model | Ensemble model output object class (when running 'BIOMOD_EnsembleModeling()')
biomod2_ensemble_model-class | Ensemble model output object class (when running 'BIOMOD_EnsembleModeling()')
biomod2_model | Single model output object class (when running 'BIOMOD_Modeling()')
biomod2_model-class | Single model output object class (when running 'BIOMOD_Modeling()')
BIOMOD_EnsembleForecasting | Project ensemble species distribution models onto new environment
BIOMOD_EnsembleModeling | Create and evaluate an ensemble set of models and predictions
BIOMOD_FormatingData | Format input data, and select pseudo-absences if wanted, for usage in 'biomod2'
BIOMOD_LoadModels | Load species distribution models built with 'biomod2'
BIOMOD_Modeling | Run a range of species distribution models
BIOMOD_Projection | Project a range of calibrated species distribution models onto new environment
BIOMOD_RangeSize | Analyze the range size differences between projections of species distribution models
BIOMOD_Report | Produce summary outputs from a simulation folder
bm_BinaryTransformation | Convert probability values into binary values using a predefined threshold
bm_BinaryTransformation-method | Convert probability values into binary values using a predefined threshold
bm_CalculateStatAbun | Calculate the best score according to a given evaluation method
bm_CalculateStatAbund | Calculate the best score according to a given evaluation method
bm_CalculateStatBin | Calculate the best score according to a given evaluation method
bm_CrossValidation | Build cross-validation table
bm_CrossValidation_block | Build cross-validation table
bm_CrossValidation_block-method | Build cross-validation table
bm_CrossValidation_env | Build cross-validation table
bm_CrossValidation_env-method | Build cross-validation table
bm_CrossValidation_kfold | Build cross-validation table
bm_CrossValidation_kfold-method | Build cross-validation table
bm_CrossValidation_random | Build cross-validation table
bm_CrossValidation_random-method | Build cross-validation table
bm_CrossValidation_strat | Build cross-validation table
bm_CrossValidation_strat-method | Build cross-validation table
bm_CrossValidation_user.defined | Build cross-validation table
bm_CrossValidation_user.defined-method | Build cross-validation table
bm_FindOptimStat | Calculate the best score according to a given evaluation method
bm_MakeFormula | Standardized formula maker
bm_ModelAnalysis | Analyze the residuals of the single models
bm_ModelingOptions | Configure the modeling options for each selected model
bm_PlotEvalBoxplot | Plot boxplot of evaluation scores
bm_PlotEvalMean | Plot mean evaluation scores
bm_PlotRangeSize | Plot species range change
bm_PlotResponseCurves | Plot response curves
bm_PlotVarImpBoxplot | Plot boxplot of variables importance
bm_PseudoAbsences | Select pseudo-absences
bm_PseudoAbsences_disk | Select pseudo-absences
bm_PseudoAbsences_disk-method | Select pseudo-absences
bm_PseudoAbsences_random | Select pseudo-absences
bm_PseudoAbsences_random-method | Select pseudo-absences
bm_PseudoAbsences_sre | Select pseudo-absences
bm_PseudoAbsences_sre-method | Select pseudo-absences
bm_PseudoAbsences_user.defined | Select pseudo-absences
bm_PseudoAbsences_user.defined-method | Select pseudo-absences
bm_RangeSize | Analyze the range size differences between projections of species distribution models
bm_RangeSize-method | Analyze the range size differences between projections of species distribution models
bm_RunModel | Loop to compute all single species distribution models
bm_RunModelsLoop | Loop to compute all single species distribution models
bm_SampleBinaryVector | Sample binary vector
bm_SampleFactorLevels | Sample all levels of a factorial variable
bm_SampleFactorLevels.data.frame | Sample all levels of a factorial variable
bm_SampleFactorLevels.raster | Sample all levels of a factorial variable
bm_SRE | Surface Range Envelope
bm_Tuning | Tune models parameters
bm_VariablesImportance | Variables' importance calculation

## -- C --

CTA_biomod2_model-class | Single model output object class (when running 'BIOMOD_Modeling()')

## -- D --

DataSpecies | Presence-Absence data to build test SDM
DataSTOC | Abundance to build test SDM
DNN_biomod2_model-class | Single model output object class (when running 'BIOMOD_Modeling()')

## -- E --

EMca_biomod2_model-class | Ensemble model output object class (when running 'BIOMOD_EnsembleModeling()')
EMci_biomod2_model-class | Ensemble model output object class (when running 'BIOMOD_EnsembleModeling()')
EMcv_biomod2_model-class | Ensemble model output object class (when running 'BIOMOD_EnsembleModeling()')
EMfreq_biomod2_model-class | Ensemble model output object class (when running 'BIOMOD_EnsembleModeling()')
EMmean_biomod2_model-class | Ensemble model output object class (when running 'BIOMOD_EnsembleModeling()')
EMmedian_biomod2_model-class | Ensemble model output object class (when running 'BIOMOD_EnsembleModeling()')
EMmode_biomod2_model-class | Ensemble model output object class (when running 'BIOMOD_EnsembleModeling()')
EMwmean_biomod2_model-class | Ensemble model output object class (when running 'BIOMOD_EnsembleModeling()')

## -- F --

FDA_biomod2_model-class | Single model output object class (when running 'BIOMOD_Modeling()')
free | Functions to extract informations from 'BIOMOD.models.out', 'BIOMOD.projection.out' or 'BIOMOD.ensemble.models.out' objects
free-method | Functions to extract informations from 'BIOMOD.models.out', 'BIOMOD.projection.out' or 'BIOMOD.ensemble.models.out' objects

## -- G --

GAM_biomod2_model-class | Single model output object class (when running 'BIOMOD_Modeling()')
GBM_biomod2_model-class | Single model output object class (when running 'BIOMOD_Modeling()')
getters.bm | Functions to extract informations from 'biomod2_model' objects
getters.out | Functions to extract informations from 'BIOMOD.models.out', 'BIOMOD.projection.out' or 'BIOMOD.ensemble.models.out' objects
get_built_models | Functions to extract informations from 'BIOMOD.models.out', 'BIOMOD.projection.out' or 'BIOMOD.ensemble.models.out' objects
get_built_models-method | Functions to extract informations from 'BIOMOD.models.out', 'BIOMOD.projection.out' or 'BIOMOD.ensemble.models.out' objects
get_calib_lines | Functions to extract informations from 'BIOMOD.models.out', 'BIOMOD.projection.out' or 'BIOMOD.ensemble.models.out' objects
get_calib_lines-method | Functions to extract informations from 'BIOMOD.models.out', 'BIOMOD.projection.out' or 'BIOMOD.ensemble.models.out' objects
get_evaluations | Functions to extract informations from 'BIOMOD.models.out', 'BIOMOD.projection.out' or 'BIOMOD.ensemble.models.out' objects
get_evaluations-method | Functions to extract informations from 'BIOMOD.models.out', 'BIOMOD.projection.out' or 'BIOMOD.ensemble.models.out' objects
get_eval_data | Functions to extract informations from 'BIOMOD.models.out', 'BIOMOD.projection.out' or 'BIOMOD.ensemble.models.out' objects
get_eval_data-method | Functions to extract informations from 'BIOMOD.models.out', 'BIOMOD.projection.out' or 'BIOMOD.ensemble.models.out' objects
get_formal_data | Functions to extract informations from 'BIOMOD.models.out', 'BIOMOD.projection.out' or 'BIOMOD.ensemble.models.out' objects
get_formal_data-method | Functions to extract informations from 'BIOMOD.models.out', 'BIOMOD.projection.out' or 'BIOMOD.ensemble.models.out' objects
get_formal_model | Functions to extract informations from 'biomod2_model' objects
get_formal_model-method | Functions to extract informations from 'biomod2_model' objects
get_kept_models | Functions to extract informations from 'BIOMOD.models.out', 'BIOMOD.projection.out' or 'BIOMOD.ensemble.models.out' objects
get_kept_models-method | Functions to extract informations from 'BIOMOD.models.out', 'BIOMOD.projection.out' or 'BIOMOD.ensemble.models.out' objects
get_optim_value | Calculate the best score according to a given evaluation method
get_options | Functions to extract informations from 'BIOMOD.models.out', 'BIOMOD.projection.out' or 'BIOMOD.ensemble.models.out' objects
get_options-method | Functions to extract informations from 'BIOMOD.models.out', 'BIOMOD.projection.out' or 'BIOMOD.ensemble.models.out' objects
get_predictions | Functions to extract informations from 'BIOMOD.models.out', 'BIOMOD.projection.out' or 'BIOMOD.ensemble.models.out' objects
get_predictions-method | Functions to extract informations from 'BIOMOD.models.out', 'BIOMOD.projection.out' or 'BIOMOD.ensemble.models.out' objects
get_projected_models | Functions to extract informations from 'BIOMOD.models.out', 'BIOMOD.projection.out' or 'BIOMOD.ensemble.models.out' objects
get_projected_models-method | Functions to extract informations from 'BIOMOD.models.out', 'BIOMOD.projection.out' or 'BIOMOD.ensemble.models.out' objects
get_scaling_model | Functions to extract informations from 'biomod2_model' objects
get_scaling_model-method | Functions to extract informations from 'biomod2_model' objects
get_species_data | Functions to extract informations from 'BIOMOD.models.out', 'BIOMOD.projection.out' or 'BIOMOD.ensemble.models.out' objects
get_species_data-method | Functions to extract informations from 'BIOMOD.models.out', 'BIOMOD.projection.out' or 'BIOMOD.ensemble.models.out' objects
get_variables_importance | Functions to extract informations from 'BIOMOD.models.out', 'BIOMOD.projection.out' or 'BIOMOD.ensemble.models.out' objects
get_variables_importance-method | Functions to extract informations from 'BIOMOD.models.out', 'BIOMOD.projection.out' or 'BIOMOD.ensemble.models.out' objects
GLM_biomod2_model-class | Single model output object class (when running 'BIOMOD_Modeling()')

## -- L --

load_stored_object | Functions to load 'BIOMOD.stored.data' objects
load_stored_object-method | Functions to load 'BIOMOD.stored.data' objects

## -- M --

MARS_biomod2_model-class | Single model output object class (when running 'BIOMOD_Modeling()')
MAXENT_biomod2_model-class | Single model output object class (when running 'BIOMOD_Modeling()')
MAXNET_biomod2_model-class | Single model output object class (when running 'BIOMOD_Modeling()')
ModelsTable | Single models package and functions

## -- O --

ODMAP | ODMAP empty table
OptionsBigboss | Bigboss pre-defined parameter values for single models

## -- P --

plot-method | 'BIOMOD_Projection()' output object class
plot-method | 'plot' method for 'BIOMOD.formated.data' and 'BIOMOD.formated.data.PA' object class
predict-method | Functions to get predictions from 'biomod2_model' objects
predict.biomod2_model | Functions to get predictions from 'biomod2_model' objects
predict.bm | Functions to get predictions from 'biomod2_model' objects
predict.em | Functions to get predictions from 'biomod2_ensemble_model' objects
print-method | 'bm_ModelingOptions' output object class
print-method | 'bm_ModelingOptions' output object class

## -- R --

RFd_biomod2_model-class | Single model output object class (when running 'BIOMOD_Modeling()')
RF_biomod2_model-class | Single model output object class (when running 'BIOMOD_Modeling()')

## -- S --

setters | Functions to change the place of the different biomod2 objects
set_new_dirname | Functions to change the place of the different biomod2 objects
set_new_dirname-method | Functions to change the place of the different biomod2 objects
show-method | 'BIOMOD_EnsembleModeling()' output object class
show-method | 'BIOMOD_FormatingData()' output object class
show-method | 'bm_ModelingOptions' output object class
show-method | 'BIOMOD_Modeling()' output object class
show-method | 'bm_ModelingOptions' output object class
show-method | 'BIOMOD_Projection()' output object class
show-method | Ensemble model output object class (when running 'BIOMOD_EnsembleModeling()')
show-method | Single model output object class (when running 'BIOMOD_Modeling()')
SRE_biomod2_model-class | Single model output object class (when running 'BIOMOD_Modeling()')
summary-method | 'summary' method for 'BIOMOD.formated.data' object class

## -- X --

XGBOOST_biomod2_model-class | Single model output object class (when running 'BIOMOD_Modeling()')