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https://biomodhub.github.io/biomod2/

Installation

  • Stable version (3.5.1) from cran :
install.packages("biomod2", dependencies = TRUE)
library(devtools)
devtools::install_github("biomodhub/biomod2", dependencies = TRUE)

Breaking news

! biomod2 4.1 is now available !

/!\ Package fresh start... meaning some changes in function names and parameters. We apologize for the trouble >{o.o}< Sorry for the inconvenience, and please feel free to indicate if you notice some strange new behaviors !

What is changed ?

  • all code functions have been cleaned, and old / unused functions have been removed
  • function names have been standardized (BIOMOD_ for main functions, bm_ for secundary functions)
  • parameter names have been standardized (same typo, same names for similar parameters across functions)
  • all documentation and examples have been cleaned up

What is new ?

  • plot functions have been re-written with ggplot2
  • biomod2 website has been created, with proper roxygen2 documentation and help vignettes

But... why ?

  • For every minute spent on organizing, an hour is earned.” — Benjamin Franklin
    • better documentation, better formation, better help provided
    • new improvements to come (update of single models, implementation of abundance models, etc)

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Version

Install

install.packages('biomod2')

Monthly Downloads

3,423

Version

4.1-2

License

GPL-3

Maintainer

Maya Gueguen

Last Published

October 25th, 2022

Functions in biomod2 (4.1-2)

BIOMOD.ensemble.models.out

BIOMOD_EnsembleModeling() output object class
BIOMOD.stored.data

BIOMOD_EnsembleModeling() output object class
BIOMOD.models.out

BIOMOD_Modeling() output object class
BIOMOD.projection.out

BIOMOD_Projection() output object class
BIOMOD.formated.data

BIOMOD_FormatingData() output object class
BIOMOD_CrossValidation

Custom models cross-validation procedure
BIOMOD.formated.data.PA

BIOMOD_FormatingData() output object class (with pseudo-absences)
BIOMOD_EnsembleForecasting

Project ensemble species distribution models onto new environment
BIOMOD.models.options

BIOMOD_ModelingOptions() output object class
BIOMOD_ConvertOldRun-deprecated

BIOMOD_ConvertOldRun
BIOMOD_Projection

Project a range of calibrated species distribution models onto new environment
BIOMOD_LoadModels

Load species distribution models built with biomod2
BIOMOD_Tuning

Tune models parameters
BIOMOD_cv-deprecated

BIOMOD_cv
BIOMOD_Modeling

Run a range of species distribution models
BIOMOD_PresenceOnly

Evaluate models with presence-only metrics
BIOMOD_ModelingOptions

Configure the modeling options for each selected model
BIOMOD_RangeSize

Analyze the range size differences between projections of species distribution models
BIOMOD_EnsembleModeling

Create and evaluate an ensemble set of models and predictions
BIOMOD_FormatingData

Format input data, and select pseudo-absences if wanted, for usage in biomod2
biomod2_ensemble_model

Ensemble model output object class (when running BIOMOD_EnsembleModeling())
BinaryTransformation-deprecated

BinaryTransformation
CustomIndexMaker-deprecated

CustomIndexMaker
FilteringTransformation-deprecated

FilteringTransformation
Find.Optim.Stat-deprecated

Find.Optim.Stat
biomod2-deprecated

Deprecated functions in package biomod2.
BIOMOD_tuning-deprecated

BIOMOD_tuning
BIOMOD_presenceonly-deprecated

BIOMOD_presenceonly
Print_Default_ModelingOptions-deprecated

Print_Default_ModelingOptions
ProbDensFunc-deprecated

ProbDensFunc
bm_CVnnet

Cross-validation for Neural Networks
biomod2_model

Single model output object class (when running BIOMOD_Modeling())
bm_FindOptimStat

Calculate the best score according to a given evaluation method
bm_PlotVarImpBoxplot

Plot boxplot of variables importance
bm_PlotEvalBoxplot

Plot boxplot of evaluation scores
bm_BinaryTransformation

Convert probability values into binary values using a predefined threshold
bm_PlotResponseCurves

Plot response curves
bm_PlotRangeSize

Plot species range change
calculate.stat-deprecated

calculate.stat
.load_gam_namespace

Load library for GAM models
bm_PlotEvalMean

Plot mean evaluation scores
bm_MakeFormula

Standardized formula maker
bm_SampleBinaryVector

Sample binary vector
.transform.outputs.array-deprecated

.transform.outputs.array
.transform.outputs.list-deprecated

.transform.outputs.list
bm_SRE

Surface Range Envelope
bm_PseudoAbsences

Select pseudo-absences
bm_RunModelsLoop

Loop to compute all single species distribution models
predict.bm

Functions to get predictions from biomod2_model objects
predict.em

Functions to get predictions from biomod2_ensemble_model objects
makeFormula-deprecated

makeFormula
load_stored_object

Functions to load BIOMOD.stored.data objects
getters.out

Functions to extract informations from BIOMOD.models.out, BIOMOD.projection.out or BIOMOD.ensemble.models.out objects
getStatOptimValue-deprecated

getStatOptimValue
zzz_bm

Dummy function to clean working directory after package checks
sample.factor.levels-deprecated

sample.factor.levels
predict2.bm

Functions to get predictions from biomod2_model objects
models_scores_graph-deprecated

models_scores_graph
bm_SampleFactorLevels

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

Variables' importance calculation
getters.bm

Functions to extract informations from biomod2_model objects
predict2.em

Functions to get predictions from biomod2_ensemble_model objects
update_objects-deprecated

update_objects
response.plot2-deprecated

response.plot2
variables_importance-deprecated

variables_importance
response.plot-deprecated

response.plot
sre-deprecated

sre