# Ensemble platform for species distribution modeling

## Documentation for package ‘biomod2’ version 3.3-7.1

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.
- Package NEWS.

## Help Pages

- main functions
- other functions
- getters, setters & cleaner
- biomod2 objects
- internal functions
- deprecated functions

biomod2-package | Species Distribution Modeling within an Ensemble Forecasting framework
biomod2 | Species Distribution Modeling within an Ensemble Forecasting framework

### -- main functions --

BIOMOD_FormatingData | Initialise the datasets for usage in 'biomod2'
BIOMOD_ModelingOptions | Configure the modeling options for each selected model
BIOMOD_Modeling | Run a range of species distribution models
BIOMOD_EnsembleModeling | Create and evaluate an ensemble set of models and predictions
BIOMOD_Projection | Project the calibrated models within 'biomod2' into new space or time
BIOMOD_EnsembleForecasting | Ensemble projections of species over space and time

### -- other functions --

BIOMOD_ConvertOldRun | Convert objects and outputs from BIOMOD.xx into biomod2.xx objects and outputs
BIOMOD_LoadModels | Load models built within BIOMOD_Modeling function
BIOMOD_RangeSize | Analysis of the range size changes
BIOMOD_RangeSize-method | Analysis of the range size changes
BIOMOD_RangeSize-methods | Analysis of the range size changes
evaluate | biomod2 modeling outputs evaluation
BIOMOD_presenceonly | evaluate models with presences only metrics
variables_importance | Variables importance calculation
sre | Surface Range Envelope
BIOMOD_tunning | Function to tune biomod single models parameters
Print_Default_ModelingOptions | Get default values of BIOMOD inner models' options
BIOMOD_cv | Custom models cross-validation procedure
level.plot | Plot 2-dimensional data for visualizing distribution of species or environment
multiple.plot | Plot and compare prediction maps within BIOMOD
response.plot2 | Analysis of the 2D or 3D response curves of a model within biomod2
models_scores_graph | Produce models evaluation bi-dimensional graph
ProbDensFunc | Probability Density Function
BinaryTransformation | Convert species' probability of occurrence into binary presence-absence data using a predefined threshold
BinaryTransformation-method | Convert species' probability of occurrence into binary presence-absence data using a predefined threshold
BinaryTransformation-methods | Convert species' probability of occurrence into binary presence-absence data using a predefined threshold
FilteringTransformation | Convert species' probability of occurrence into binary presence-absence data using a predefined threshold
FilteringTransformation-method | Convert species' probability of occurrence into binary presence-absence data using a predefined threshold
FilteringTransformation-methods | Convert species' probability of occurrence into binary presence-absence data using a predefined threshold
makeFormula | Standardized formula maker
CustomIndexMaker | Replace default package Index help file by a custom one.
Find.Optim.Stat | Find the threshold driving to the best evaluation score
calculate.stat | Calculate evaluation metrics based on a misclassification table
getStatOptimValue | get the optimal score of evaluation statistical metrics
SampleMat2 | Sample binary vector
DF_to_ARRAY | Convert a biomod2 data.frame (or list) into array
LIST_to_ARRAY | Convert a biomod2 data.frame (or list) into array
randomise_data | data set shuffling tool
full_suffling | data set shuffling tool

### -- getters , setters & cleaners --

RemoveProperly | remove properly BIOMOD_Modeling outputs
RemoveProperly-method | remove properly BIOMOD_Modeling outputs
free | BIOMOD.projection.out setter
free-method | BIOMOD.projection.out setter
get_built_models | BIOMOD.models.out getters
get_built_models-method | BIOMOD.models.out getters
get_evaluations | BIOMOD.models.out getters
get_evaluations-method | BIOMOD.models.out getters
get_formal_data | BIOMOD.models.out getters
get_formal_data-method | BIOMOD.models.out getters
get_formal_model | biomod2 models objects class and functions
get_formal_model-method | biomod2 models objects class and functions
get_kept_models | BIOMOD.EnsembleModeling.out getters
get_kept_models-method | BIOMOD.EnsembleModeling.out getters
get_needed_models | BIOMOD.EnsembleModeling.out getters
get_needed_models-method | BIOMOD.EnsembleModeling.out getters
get_options | BIOMOD.models.out getters
get_options-method | BIOMOD.models.out getters
get_predictions | BIOMOD.models.out getters
get_predictions-method | BIOMOD.models.out getters
get_projected_models | BIOMOD.projection.out getters
get_projected_models-method | BIOMOD.projection.out getters
get_scaling_model | biomod2 models objects class and functions
get_scaling_model-method | biomod2 models objects class and functions
get_variables_importance | BIOMOD.models.out getters
get_variables_importance-method | BIOMOD.models.out getters

### -- biomod2 objects --

#### main functions outputs

BIOMOD.formated.data | BIOMOD_FormatingData() outputs objects class
BIOMOD.formated.data-class | BIOMOD_FormatingData() outputs objects class
BIOMOD.formated.data-method | BIOMOD_FormatingData() outputs objects class
BIOMOD.formated.data.PA | BIOMOD_FormatingData() outputs objects class
BIOMOD.formated.data.PA-class | BIOMOD_FormatingData() outputs objects class
BIOMOD.Model.Options-class | BIOMOD_() outputs objects class
BIOMOD.models.out-class | BIOMOD_modelling() outputs objects class
biomod2_model | biomod2 models objects class and functions
biomod2_model-class | biomod2 models objects class and functions
biomod2_ensemble_model | biomod2 models objects class and functions
biomod2_ensemble_model-class | biomod2 models objects class and functions
BIOMOD.EnsembleModeling.out | BIOMOD_EnsembleModeling() outputs objects class
BIOMOD.EnsembleModeling.out-class | BIOMOD_EnsembleModeling() outputs objects class
BIOMOD.projection.out | BIOMOD_Projection() outputs objects class
BIOMOD.projection.out-class | BIOMOD_Projection() outputs objects class

#### main functions outputs prints and plots

plot-method | BIOMOD_FormatingData() outputs objects class
plot-method | BIOMOD_Projection() outputs objects class
show,BIOMOD.Model.Options | BIOMOD_ModelingOptions() outputs objects class
show-method | BIOMOD_EnsembleModeling() outputs objects class
show-method | BIOMOD_FormatingData() outputs objects class
show-method | BIOMOD_modelling() outputs objects class
show-method | BIOMOD_Projection() outputs objects class

#### biomod2 individual models

ANN_biomod2_model | biomod2 models objects class and functions
ANN_biomod2_model-class | biomod2 models objects class and functions
CTA_biomod2_model | biomod2 models objects class and functions
CTA_biomod2_model-class | biomod2 models objects class and functions
FDA_biomod2_model | biomod2 models objects class and functions
FDA_biomod2_model-class | biomod2 models objects class and functions
GAM_biomod2_model | biomod2 models objects class and functions
GAM_biomod2_model-class | biomod2 models objects class and functions
GBM_biomod2_model | biomod2 models objects class and functions
GBM_biomod2_model-class | biomod2 models objects class and functions
GLM_biomod2_model | biomod2 models objects class and functions
GLM_biomod2_model-class | biomod2 models objects class and functions
MARS_biomod2_model | biomod2 models objects class and functions
MARS_biomod2_model-class | biomod2 models objects class and functions
MAXENT_biomod2_model | biomod2 models objects class and functions
MAXENT_biomod2_model-class | biomod2 models objects class and functions
RF_biomod2_model | biomod2 models objects class and functions
RF_biomod2_model-class | biomod2 models objects class and functions
SRE_biomod2_model | biomod2 models objects class and functions
SRE_biomod2_model-class | biomod2 models objects class and functions
EMca_biomod2_model | biomod2 models objects class and functions
EMca_biomod2_model-class | biomod2 models objects class and functions
EMci_biomod2_model | biomod2 models objects class and functions
EMci_biomod2_model-class | biomod2 models objects class and functions
EMcv_biomod2_model | biomod2 models objects class and functions
EMcv_biomod2_model-class | biomod2 models objects class and functions
EMmean_biomod2_model | biomod2 models objects class and functions
EMmean_biomod2_model-class | biomod2 models objects class and functions
EMmedian_biomod2_model | biomod2 models objects class and functions
EMmedian_biomod2_model-class | biomod2 models objects class and functions
EMwmean_biomod2_model | biomod2 models objects class and functions
EMwmean_biomod2_model-class | biomod2 models objects class and functions
predict-method | biomod2 models objects class and functions
show-method | biomod2 models objects class and functions
get_var_range | biomod2 models objects class and functions
get_var_type | biomod2 models objects class and functions

#### biomod2 storing objects

BIOMOD.stored.array | BIOMOD.stored.xxx objects class
BIOMOD.stored.array-class | BIOMOD.stored.xxx objects class
BIOMOD.stored.data.frame | BIOMOD.stored.xxx objects class
BIOMOD.stored.data.frame-class | BIOMOD.stored.xxx objects class
BIOMOD.stored.data | BIOMOD.stored.xxx objects class
BIOMOD.stored.data-class | BIOMOD.stored.xxx objects class
BIOMOD.stored.files | BIOMOD.stored.xxx objects class
BIOMOD.stored.files-class | BIOMOD.stored.xxx objects class
BIOMOD.stored.formated.data | BIOMOD.stored.xxx objects class
BIOMOD.stored.formated.data-class | BIOMOD.stored.xxx objects class
BIOMOD.stored.models.options | BIOMOD.stored.xxx objects class
BIOMOD.stored.models.options-class | BIOMOD.stored.xxx objects class
BIOMOD.stored.models.out | BIOMOD.stored.xxx objects class
BIOMOD.stored.models.out-class | BIOMOD.stored.xxx objects class
BIOMOD.stored.raster.stack | BIOMOD.stored.xxx objects class
BIOMOD.stored.raster.stack-class | BIOMOD.stored.xxx objects class
load_stored_object | BIOMOD.stored.objects functions
load_stored_object-method | BIOMOD.stored.objects functions

### -- internal functions --

disk.pseudo.abs.selection | biomod2 internal functions
disk.pseudo.abs.selection-method | biomod2 internal functions
random.pseudo.abs.selection | biomod2 internal functions
random.pseudo.abs.selection-method | biomod2 internal functions
sre.pseudo.abs.selection | biomod2 internal functions
sre.pseudo.abs.selection-method | biomod2 internal functions
user.defined.pseudo.abs.selection | biomod2 internal functions
user.defined.pseudo.abs.selection-method | biomod2 internal functions
Projection | biomod2 internal functions
Projection-method | biomod2 internal functions
.Models.prepare.data | biomod2 internal functions
.Models.prepare.data-method | biomod2 internal functions
.Projection.do.proj | biomod2 internal functions
.Projection.do.proj-method | biomod2 internal functions
.transform.outputs | biomod2 internal functions
.transform.outputs-method | biomod2 internal functions
check_data_range | biomod2 models objects class and functions

### -- deprecated functions --

response.plot | Analysis of the response curves of a model within Biomod
getEMalgos | biomod2 deprecated functions
getEMalgos-method | biomod2 deprecated functions
getEMbuiltModels | biomod2 deprecated functions
getEMbuiltModels-method | biomod2 deprecated functions
getEMeval | biomod2 deprecated functions
getEMeval-method | biomod2 deprecated functions
getEMkeptModels | biomod2 deprecated functions
getEMkeptModels-method | biomod2 deprecated functions
getEM_needed_models | biomod2 deprecated functions
getEM_needed_models-method | biomod2 deprecated functions
getFormalModel | biomod2 deprecated functions
getFormalModel-method | biomod2 deprecated functions
getModelsBuiltModels | biomod2 deprecated functions
getModelsBuiltModels-method | biomod2 deprecated functions
getModelsEvaluations | biomod2 deprecated functions
getModelsEvaluations-method | biomod2 deprecated functions
getModelsInputData | biomod2 deprecated functions
getModelsInputData-method | biomod2 deprecated functions
getModelsOptions | biomod2 deprecated functions
getModelsOptions-method | biomod2 deprecated functions
getModelsPrediction | biomod2 deprecated functions
getModelsPrediction-method | biomod2 deprecated functions
getModelsPredictionEval | biomod2 deprecated functions
getModelsPredictionEval-method | biomod2 deprecated functions
getModelsVarImport | biomod2 deprecated functions
getModelsVarImport-method | biomod2 deprecated functions
getProjection | biomod2 deprecated functions
getProjection-method | biomod2 deprecated functions
getScalingModel | biomod2 deprecated functions
getScalingModel-method | biomod2 deprecated functions