Ensemble platform for species distribution modeling


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Documentation for package ‘biomod2’ version 1.1.18

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biomod2-package 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
sre Surface Range Envelope
Print_Default_ModelingOptions Get default values of BIOMOD inner models' options
level.plot Plot 2-dimensional data for visualizing distribution of species or environment
multiple.plot Plot and compare prediction maps within BIOMOD
response.plot Analysis of the response curves of a model within Biomod
response.plot2 Analysis of the 2D or 3D response curves of a model within biomod2
BinaryTransformation 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
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 into array

-- getters & setteurs --

getEMalgos BIOMOD.EnsembleModeling.out getters
getEMalgos-method BIOMOD.EnsembleModeling.out getters
getEMbuiltModels BIOMOD.EnsembleModeling.out getters
getEMbuiltModels-method BIOMOD.EnsembleModeling.out getters
getEMeval BIOMOD.EnsembleModeling.out getters
getEMeval-method BIOMOD.EnsembleModeling.out getters
getEMkeptModels BIOMOD.EnsembleModeling.out getters
getEMkeptModels-method BIOMOD.EnsembleModeling.out getters
getModelsBuiltModels BIOMOD.models.out getters
getModelsBuiltModels-method BIOMOD.models.out getters
getModelsEvaluations BIOMOD.models.out getters
getModelsEvaluations-method BIOMOD.models.out getters
getModelsInputData BIOMOD.models.out getters
getModelsInputData-method BIOMOD.models.out getters
getModelsOptions BIOMOD.models.out getters
getModelsOptions-method BIOMOD.models.out getters
getModelsPrediction BIOMOD.models.out getters
getModelsPrediction-method BIOMOD.models.out getters
getModelsPredictionEval BIOMOD.models.out getters
getModelsPredictionEval-method BIOMOD.models.out getters
getModelsVarImport BIOMOD.models.out getters
getModelsVarImport-method BIOMOD.models.out getters
getProjection BIOMOD.projection.out getters
getProjection-method BIOMOD.projection.out getters

-- biomod2 objects --

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.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
maxent_model-class biomod2 MAXENT models objects class and functions