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biomod2: Ensemble Platform for Species Distribution Modeling

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

Installation

You can install biomod2 in R using devtools:

devel version (from biomodhub)

devtools::install_github("biomodhub/biomod2", dependencies = TRUE)

stable version (from cran)

install.packages("biomod2", dependencies = TRUE)

Development team

Wilfried Thuiller [aut, cre]
Damien Georges [aut, cre]
Robin Engler [aut]
Frank Breiner [aut]

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Version

Install

install.packages('biomod2')

Monthly Downloads

13,433

Version

3.4.6

License

GPL-2

Maintainer

Damien Georges

Last Published

February 26th, 2020

Functions in biomod2 (3.4.6)

BIOMOD.stored.objects-methods

BIOMOD.stored.objects functions

BIOMOD.Model.Options-class

BIOMOD_ModelingOptions outputs objects class

BIOMOD.formated.data-class

BIOMOD_FormatingData() outputs objects class

BIOMOD.EnsembleModeling.out-class

BIOMOD_EnsembleModeling() outputs objects class

BIOMOD.stored.objects-class

BIOMOD.stored.xxx objects class

BIOMOD.models.out-class

BIOMOD_modelling() outputs objects class

BIOMOD.projection.out-class

BIOMOD_Projection() outputs objects class

BIOMOD.EnsembleModeling.out-method

BIOMOD.EnsembleModeling.out getters

BIOMOD.models.out-methods

BIOMOD.models.out getters

BIOMOD_ModelingOptions

Configure the modeling options for each selected model

BIOMOD.projection.out-method

BIOMOD.projection.out getters

BIOMOD_Modeling

Run a range of species distribution models

Custom models cross-validation procedure

BIOMOD_RangeSize

Analysis of the range size changes

BIOMOD_LoadModels

Load models built within BIOMOD_Modeling function

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

.transform.outputs.array

Reshape biomod2 objects

BinaryTransformation

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

CustomIndexMaker

Replace default package Index help file by a custom one.

Print_Default_ModelingOptions

Get default values of BIOMOD inner models' options

Probability Density Function

.transform.outputs.list

Reshape biomod2 objects

models_scores_graph

Produce models evaluation bi-dimensional graph

BIOMOD_FormatingData

Initialize the datasets for usage in biomod2

Sample binary vector

Find.Optim.Stat

Calculate the best score according to a given evaluation method

FilteringTransformation

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

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

BIOMOD_presenceonly

evaluate models with presences only metrics

BIOMOD_EnsembleForecasting

Ensemble projections of species over space and time

data set shuffling tool

biomod2 modelling outputs evaluation

Tune models parameters

biomod2.inner-method

biomod2 internal functions

BIOMOD_ConvertOldRun

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

Plot and compare prediction maps within BIOMOD

biomod2.deprecated.functions

biomod2 deprecated functions

biomod2-package

Species Distribution Modeling within an Ensemble Forecasting framework

biomod2_model-class

biomod2 models objects class and functions

getStatOptimValue

get the optimal score of evaluation statistical metrics

update biomod2 objects

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

Standardized formula maker

sample.factor.levels

Tool to ensure the sampling of all levels of a factorial variable

data set shuffling tool

Analysis of the response curves of a model within Biomod

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

Surface Range Envelope

Calculate evaluation metrics based on a misclassification table

variables_importance

Variables importance calculation