Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

biomod2

Ensemble Platform for Species Distribution Modeling

Functions for species distribution modeling, calibration and evaluation, ensemble of models, ensemble forecasting and visualization. The package permits to run consistently up to 10 single models on a presence/absences (resp presences/pseudo-absences) dataset and to combine them in ensemble models and ensemble projections. Some bench of other evaluation and visualisation tools are also available within the package.

Functions (51)

BIOMOD.EnsembleModeling.out-methods

BIOMOD.EnsembleModeling.out getters

BIOMOD.EnsembleModeling.out-objects

BIOMOD_EnsembleModeling() outputs objects class

BIOMOD.Model.Options-objects

BIOMOD_ModelingOptions outputs objects class

BIOMOD.formated.data-class

BIOMOD_FormatingData() outputs objects class

BIOMOD.models.out-class

BIOMOD_modelling() outputs objects class

BIOMOD.models.out-methods

BIOMOD.models.out getters

BIOMOD.projection.out-class

BIOMOD_Projection() outputs objects class

BIOMOD.projection.out-methods

BIOMOD.projection.out getters

BIOMOD.stored.objects-class

BIOMOD.stored.xxx objects class

BIOMOD.stored.objects-methods

BIOMOD.stored.objects 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

Initialize 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_cv

Custom models cross-validation procedure

BIOMOD_presenceonly

evaluate models with presences only metrics

BIOMOD_tuning

Tune models parameters

BinaryTransformation-methods

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.

DF_to_ARRAY

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

FilteringTransformation

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

Find.Optim.Stat

Calculate the best score according to a given evaluation method

Print_Default_ModelingOptions

Get default values of BIOMOD inner models' options

ProbDensFunc

Probability Density Function

SampleMat2

Sample binary vector

biomod2-package

Species Distribution Modeling within an Ensemble Forecasting framework

biomod2.inner-methods

biomod2 internal functions

biomod2_model-class

biomod2 models objects class and functions

calculate.stat

Calculate evaluation metrics based on a misclassification table

deprecated_functions

biomod2 deprecated functions

dot-transform.outputs.array

Reshape biomod2 objects

dot-transform.outputs.list

Reshape biomod2 objects

evaluate

biomod2 modelling outputs evaluation

full_shuffling

data set shuffling tool

getStatOptimValue

get the optimal score of evaluation statistical metrics

level.plot

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

makeFormula

Standardized formula maker

models_scores_graph

Produce models evaluation bi-dimensional graph

multiple.plot

Plot and compare prediction maps within BIOMOD

randomise_data

data set shuffling tool

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

sample.factor.levels

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

sre

Surface Range Envelope

update_objects

update biomod2 objects

variables_importance

Variables importance calculation

biomod2

Ensemble Platform for Species Distribution Modeling

v3.4.6

GPL-2

Authors

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

Initial release

2020-02-24

biomod2

Functions (51)

biomod2

We don't support your browser anymore