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biomod2 (version 3.1-48)

Ensemble platform for species distribution modeling

Description

Functions for species distribution modeling, calibration and evaluation, ensemble of models.

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Version

Install

install.packages('biomod2')

Monthly Downloads

3,423

Version

3.1-48

License

GPL-2

Maintainer

Damien Georges

Last Published

July 7th, 2014

Functions in biomod2 (3.1-48)

BIOMOD_Modeling

Run a range of species distribution models
BIOMOD.stored.objects-class

BIOMOD.stored.xxx objects class
biomod2.inner-method

biomod2 internal functions
full_suffling

data set shuffling tool
BIOMOD.projection.out-method

BIOMOD.projection.out getters
BIOMOD.formated.data-class

BIOMOD_FormatingData() outputs objects class
calculate.stat

Calculate evaluation metrics based on a misclassification table
getStatOptimValue

get the optimal score of evaluation statistical metrics
BIOMOD_ConvertOldRun

Convert objects and outputs from BIOMOD.xx into biomod2.xx objects and outputs
SampleMat2

Sample binary vector
BIOMOD_ModelingOptions

Configure the modeling options for each selected model
Find.Optim.Stat

Find the threshold driving to the best evaluation score
biomod2-package

Species Distribution Modeling within an Ensemble Forecasting framework
biomod2.deprecated.functions

biomod2 deprecated functions
BIOMOD_RangeSize

Analysis of the range size changes
biomod2_model-class

biomod2 models objects class and functions
makeFormula

Standardized formula maker
randomise_data

data set shuffling tool
BIOMOD.models.out-class

BIOMOD_modelling() outputs objects class
BIOMOD.EnsembleModeling.out-method

BIOMOD.EnsembleModeling.out getters
ProbDensFunc

Probability Density Function
update_objects

update biomod2 objects
sre

Surface Range Envelope
BIOMOD_FormatingData

Initialise the datasets for usage in biomod2
BIOMOD_LoadModels

Load models built within BIOMOD_Modeling function
Print_Default_ModelingOptions

Get default values of BIOMOD inner models' options
BIOMOD_EnsembleForecasting

Ensemble projections of species over space and time
FilteringTransformation

Convert species' probability of occurrence into binary presence-absence data using a predefined threshold
response.plot2

Function for for plotting predicted responses from species distribution models in 2 or 3 dimensions
BIOMOD_EnsembleModeling

Create and evaluate an ensemble set of models and predictions
BIOMOD.projection.out-class

BIOMOD_Projection() outputs objects class
BinaryTransformation

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
level.plot

Plot 2-dimensional data for visualizing distribution of species or environment
BIOMOD_Projection

Project the calibrated models within biomod2 into new space or time
BIOMOD.EnsembleModeling.out-class

BIOMOD_EnsembleModeling() outputs objects class
response.plot

Analysis of the response curves of a model within Biomod
BIOMOD.models.out-RemoveProperly

remove properly BIOMOD_Modeling outputs
variables_importance

Variables importance calculation
BIOMOD.models.out-methods

BIOMOD.models.out getters
multiple.plot

Plot and compare prediction maps within BIOMOD
CustomIndexMaker

Replace default package Index help file by a custom one.
BIOMOD.Model.Options-class

BIOMOD_ModelingOptions() outputs objects class
BIOMOD.stored.objects-methods

BIOMOD.stored.objects functions
evaluate

biomod2 modelling outputs evaluation