Ensemble platform for species distribution modeling


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Documentation for package ‘biomod2’ version 2.1.15

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A B C D F G L M P R S U 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

-- B --

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
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
biomod2 Species Distribution Modeling within an Ensemble Forecasting framework
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_EnsembleForecasting Ensemble projections of species over space and time
BIOMOD_EnsembleModeling Create and evaluate an ensemble set of models and predictions
BIOMOD_FormatingData Initialise 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_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

-- C --

calculate.stat Calculate evaluation metrics based on a misclassification table
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 --

DF_to_ARRAY Convert a biomod2 data.frame into array
disk.pseudo.abs.selection biomod2 internal functions
disk.pseudo.abs.selection-method biomod2 internal functions

-- 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 Find the threshold driving to the best evaluation score
free BIOMOD.projection.out getters
free-method BIOMOD.projection.out getters

-- 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 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
getFormalModel biomod2 models objects class and functions
getFormalModel-method biomod2 models objects class and functions
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
getScalingModel biomod2 models objects class and functions
getScalingModel-method biomod2 models objects class and functions
getStatOptimValue get the optimal score of evaluation statistical metrics
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

-- M --

makeFormula Standardized formula maker
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
multiple.plot Plot and compare prediction maps within BIOMOD

-- 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
RemoveProperly remove properly BIOMOD_Modeling outputs
RemoveProperly-method remove properly BIOMOD_Modeling outputs
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 --

SampleMat2 Sample binary vector
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
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 --

user.defined.pseudo.abs.selection biomod2 internal functions
user.defined.pseudo.abs.selection-method biomod2 internal functions

-- 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 biomod2 internal functions
.transform.outputs-method biomod2 internal functions