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biomod2 (version 3.1-25)

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

4,513

Version

3.1-25

License

GPL-2

Maintainer

Damien Georges

Last Published

December 2nd, 2013

Functions in biomod2 (3.1-25)

BIOMOD_FormatingData

Initialise the datasets for usage in biomod2

BIOMOD_ModelingOptions

Configure the modeling options for each selected model

BIOMOD.EnsembleModeling.out-method

BIOMOD.EnsembleModeling.out getters

BIOMOD.models.out-class

BIOMOD_modelling() outputs objects class

FilteringTransformation

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

variables_importance

Variables importance calculation

BIOMOD_ConvertOldRun

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

evaluate

biomod2 modelling outputs evaluation

response.plot

Analysis of the response curves of a model within Biomod

update_objects

update biomod2 objects

makeFormula

Standardized formula maker

BIOMOD_LoadModels

Load models built within BIOMOD_Modeling function

multiple.plot

Plot and compare prediction maps within BIOMOD

response.plot2

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

biomod2-package

Species Distribution Modeling within an Ensemble Forecasting framework

BIOMOD_EnsembleForecasting

Ensemble projections of species over space and time

Print_Default_ModelingOptions

Get default values of BIOMOD inner models' options

CustomIndexMaker

Replace default package Index help file by a custom one.

getStatOptimValue

get the optimal score of evaluation statistical metrics

level.plot

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

BIOMOD.stored.objects-class

BIOMOD.stored.xxx objects class

full_suffling

data set shuffling tool

BIOMOD.models.out-methods

BIOMOD.models.out getters

calculate.stat

Calculate evaluation metrics based on a misclassification table

BIOMOD.projection.out-method

BIOMOD.projection.out getters

BIOMOD.Model.Options-class

BIOMOD_ModelingOptions() outputs objects class

SampleMat2

Sample binary vector

BIOMOD.formated.data-class

BIOMOD_FormatingData() outputs objects class

BIOMOD.models.out-RemoveProperly

remove properly BIOMOD_Modeling outputs

BIOMOD_RangeSize

Analysis of the range size changes

BIOMOD.projection.out-class

BIOMOD_Projection() outputs objects class

biomod2.deprecated.functions

biomod2 deprecated functions

BIOMOD_EnsembleModeling

Create and evaluate an ensemble set of models and predictions

BIOMOD.stored.objects-methods

BIOMOD.stored.objects functions

randomise_data

data set shuffling tool

BIOMOD.EnsembleModeling.out-class

BIOMOD_EnsembleModeling() outputs objects class

BIOMOD_Modeling

Run a range of species distribution models

biomod2_model-class

biomod2 models objects class and functions

BinaryTransformation

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

ProbDensFunc

Probability Density Function

Find.Optim.Stat

Find the threshold driving to the best evaluation score

biomod2.inner-method

biomod2 internal functions

DF_to_ARRAY

Convert a biomod2 data.frame (or list) into array

sre

Surface Range Envelope

BIOMOD_Projection

Project the calibrated models within biomod2 into new space or time