Ensemble Platform for Species Distribution Modeling


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Documentation for package ‘biomod2’ version 4.2-5-2

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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.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_RangeSize-method Analyze the range size differences between projections of species distribution models
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_CalculateStat 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_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_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

-- 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()')
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()')
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 --

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' 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 --

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

-- S --

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()')