Ensemble Platform for Species Distribution Modeling


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Documentation for package ‘biomod2’ version 3.5.1

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A B C D E F G L M N P R S U V Z misc

biomod2-package Species Distribution Modeling within an Ensemble Forecasting framework

-- A --

ANN_biomod2_model biomod2 models objects class and functions
ANN_biomod2_model-class biomod2 models objects class and functions
array-method Convert species' probability of occurrence into binary presence-absence data using a predefined threshold

-- B --

BinaryTransformation Convert species' probability of occurrence into binary presence-absence data using a predefined threshold
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
BIOMOD.EnsembleModeling.out BIOMOD_EnsembleModeling() outputs objects class
BIOMOD.EnsembleModeling.out-class BIOMOD_EnsembleModeling() outputs objects class
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_ModelingOptions outputs objects class
BIOMOD.models.out-class BIOMOD_modelling() outputs objects class
BIOMOD.projection.out BIOMOD_Projection() outputs objects class
BIOMOD.projection.out-class BIOMOD_Projection() outputs objects class
BIOMOD.stored.array BIOMOD.stored.xxx objects class
BIOMOD.stored.array-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.data.frame BIOMOD.stored.xxx objects class
BIOMOD.stored.data.frame-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
biomod2 Species Distribution Modeling within an Ensemble Forecasting framework
biomod2_ensemble_model biomod2 models objects class and functions
biomod2_ensemble_model-class biomod2 models objects class and functions
biomod2_model biomod2 models objects class and functions
biomod2_model-class biomod2 models objects class and functions
BIOMOD_ConvertOldRun Convert objects and outputs from BIOMOD.xx into biomod2.xx objects and outputs
BIOMOD_cv Custom models cross-validation procedure
BIOMOD_EnsembleForecasting Ensemble projections of species over space and time
BIOMOD_EnsembleModeling Create and evaluate an ensemble set of models and predictions
BIOMOD_FormatingData Initialize the datasets for usage in 'biomod2'
BIOMOD_LoadModels Load models built within BIOMOD_Modeling function
BIOMOD_Modeling Run a range of species distribution models
BIOMOD_ModelingOptions Configure the modeling options for each selected model
BIOMOD_presenceonly evaluate models with presences only metrics
BIOMOD_Projection Project the calibrated models within 'biomod2' into new space or time
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
BIOMOD_tuning Tune models parameters

-- C --

calculate.stat Calculate evaluation metrics based on a misclassification table
check_data_range 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
CustomIndexMaker Replace default package Index help file by a custom one.

-- D --

data.frame-method Convert species' probability of occurrence into binary presence-absence data using a predefined threshold
DF_to_ARRAY Convert a biomod2 data.frame (or list) into array
disk.pseudo.abs.selection biomod2 internal functions
disk.pseudo.abs.selection-method biomod2 internal functions

-- E --

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
evaluate biomod2 modelling outputs evaluation

-- F --

FDA_biomod2_model biomod2 models objects class and functions
FDA_biomod2_model-class biomod2 models objects class and functions
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
Find.Optim.Stat Calculate the best score according to a given evaluation method
free BIOMOD.projection.out getters
free-method BIOMOD.projection.out getters
full_suffling data set shuffling tool

-- G --

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
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
getStatOptimValue get the optimal score of evaluation statistical metrics
get_built_models BIOMOD.models.out getters
get_built_models-method BIOMOD.models.out getters
get_calib_lines BIOMOD.models.out getters
get_calib_lines-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
get_var_range biomod2 models objects class and functions
get_var_type 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

-- L --

level.plot Plot 2-dimensional data for visualizing distribution of species or environment
LIST_to_ARRAY Convert a biomod2 data.frame (or list) into array
load_stored_object BIOMOD.stored.objects functions
load_stored_object-method BIOMOD.stored.objects functions

-- M --

makeFormula Standardized formula maker
MARS_biomod2_model biomod2 models objects class and functions
MARS_biomod2_model-class biomod2 models objects class and functions
matrix-method Convert species' probability of occurrence into binary presence-absence data using a predefined threshold
MAXENT.Phillips.2_biomod2_model biomod2 models objects class and functions
MAXENT.Phillips.2_biomod2_model-class biomod2 models objects class and functions
MAXENT.Phillips_biomod2_model biomod2 models objects class and functions
MAXENT.Phillips_biomod2_model-class biomod2 models objects class and functions
models_scores_graph Produce models evaluation bi-dimensional graph
multiple.plot Plot and compare prediction maps within BIOMOD

-- N --

numeric-method Convert species' probability of occurrence into binary presence-absence data using a predefined threshold

-- P --

plot-method BIOMOD_FormatingData() outputs objects class
plot-method BIOMOD_Projection() outputs objects class
predict-method biomod2 models objects class and functions
Print_Default_ModelingOptions Get default values of BIOMOD inner models' options
ProbDensFunc Probability Density Function
Projection biomod2 internal functions
Projection-method biomod2 internal functions

-- R --

random.pseudo.abs.selection biomod2 internal functions
random.pseudo.abs.selection-method biomod2 internal functions
randomise_data data set shuffling tool
RasterBrick-method Convert species' probability of occurrence into binary presence-absence data using a predefined threshold
RasterLayer-method Convert species' probability of occurrence into binary presence-absence data using a predefined threshold
RasterStack-method Convert species' probability of occurrence into binary presence-absence data using a predefined threshold
response.plot Analysis of the response curves of a model within Biomod
response.plot2 Function for for plotting predicted responses from species distribution models in 2 or 3 dimensions
RF_biomod2_model biomod2 models objects class and functions
RF_biomod2_model-class biomod2 models objects class and functions

-- S --

sample.factor.levels Tool to ensure the sampling of all levels of a factorial variable
SampleMat2 Sample binary vector
show-method BIOMOD_EnsembleModeling() outputs objects class
show-method BIOMOD_ModelingOptions outputs objects class
show-method BIOMOD_FormatingData() outputs objects class
show-method BIOMOD_modelling() outputs objects class
show-method BIOMOD_Projection() outputs objects class
show-method biomod2 models objects class and functions
sre Surface Range Envelope
sre.pseudo.abs.selection biomod2 internal functions
sre.pseudo.abs.selection-method biomod2 internal functions
SRE_biomod2_model biomod2 models objects class and functions
SRE_biomod2_model-class biomod2 models objects class and functions

-- U --

update_objects update biomod2 objects
user.defined.pseudo.abs.selection biomod2 internal functions
user.defined.pseudo.abs.selection-method biomod2 internal functions

-- V --

variables_importance Variables importance calculation

-- Z --

zzz_bm Dummy function to clean working directory after package checks

-- misc --

.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.array Reshape biomod2 objects
.transform.outputs.list Reshape biomod2 objects