R Observatory: Metrics for biomod2 version 4.3-4-8

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

biomod2

4.3-4-8Package record

Ensemble Platform for Species Distribution Modeling

3packages dependsuggested by 2

75.7Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Maya GuéguenCRAN page ↗GitHub ↗Website ↗Issues ↗

Functions for species distribution modelling, to calibrate, evaluate, and project species-environment relationships across space and time using multiple modelling algorithms and ensemble forecasting. It accommodates diverse ecological data types (presence-only, presence-absence, counts, multi-class abundance, or relative/absolute abundance) within a unified modelling workflow which includes cross-validation schemes, pseudo-absence selection strategies, expanded model parametrization options, a dozen of algorithms, and tools for exploring and visualizing outputs.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("biomod2", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("biomodhub/biomod2")

Development version from biomodhub/biomod2. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-biomod2

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-biomod2

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-biomod2

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 12.5 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-10-14
NOTE12 OK, 1 NOTE2026-07-11
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK12 OK2026-04-27

Show 1 earlier changeHide 1 earlier change

ERROR13 OK, 1 ERROR2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 4.3-4-8

READMEYes · 847 wordsVignettesYes · 12 · staticNEWSNoCitation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 79 (27 internal)
Examples that run: 100%40 run in a plain check
Exported functions with examples: 84%
Documented parameters: 95%
Return-value docs: 91%
Help pages citing references: 8%

Vignettes (12)

Show 2 moreHide 2 vignettes

Videos - biomod2 HTML
Videos - ENM 2020 HTML

How these are measured

Downloads

75.7K

CRAN downloads in the past year

Rank #1,493 · ~208/day · ~6.3K/mo

Releases R versions

Daily download trend is not available in this view yet.

6.6K30 days

16.8K90 days

75.7K1 year

Compare downloads with other packages →

Also on2.3K r2u38 autocran3.2K conda_forge174 c2d4u

How downloads are counted

Repository

biomodhub/biomod2 ↗Organization: biomodhub

129Stars

32Forks

21Open issues

1Open PRs

11Releases

1,279Commits

14Commit identities

1,279 commits · Last activity 2026-10-21 · +1.6% stars, 30d · Discussions: 20 posts

Responsiveness

How these are sampled

PRs merged (all time): 83%
Median days to close, 50 most recently updated closed issues: 125
Median days to close, 50 most recently updated closed PRs: 1

Stars over time

2025-10-23 · 1042026-10-19 · 129

How these are measured

PracticesBeta

5 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/biomodhub/biomod2 on 2026-10-22.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Governance and community (1)

Issue templates

Docs source (2)

pkgdown

GitHub Pages site last deployed 2026-10-21

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

41 external dependencies (excludes base and recommended)

Installing biomod2 adds 39 packages (20 with compiled code, 37 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, sp 4.3 MB.

Depends (1)

R >= 4.1

Imports (18)

statsutilsmethodsterra sp reshape reshape2 abind foreach ggplot2 gbmrpartMASSpROC PresenceAbsence dplyr rlang scales

LinkingTo (0)

none

Suggests (30)

Hmisc gammgcvearth maxnet mdannetrandomForest xgboost cito torch car caret dismo ENMeval doParallel raster ggpubr testthat knitr markdown rmarkdown tidyterra ggtext patchwork kableExtra DT R.utils paletteer viridis

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

3direct

4indirect

Imports 3

Suggested by 2

Depends, Imports or LinkingTo, most downloaded first

ecospat RRgeo gecko

Suggests, most downloaded first

blockCV caretSDM

How these are counted

Code & Tests

Datasets

People & History

People (4)

Maya Guéguen

Author, Maintainer · added in 4.3-4-3

Hélène Blancheteau

Author · added in 4.3-4-3

Rémi Lemaire-Patin

Author · added in 4.3-4-3

Wilfried Thuiller

Author

Maintainer since 4.1-2 (2022), previously Damien Georges (1.3.1 to 3.5.1)

Listed in earlier versions (7)

Show 7 peopleHide 7 people

Robin Engler

no longer listed · 2.15.2 to 4.2-6-2

Damien Georges

no longer listed · 2.15.2 to 4.2-6-2

Frank Breiner

no longer listed · 3.3-7 to 4.2-6-2

Maya Gueguen

no longer listed · 3.5.1 to 4.2-6-2

Bruno Lafourcade

no longer listed · 4.1-2 to 4.2-6-2

Remi Patin

no longer listed · 4.1-2 to 4.2-6-2

Helene Blancheteau

no longer listed · 4.2-5 to 4.2-6-2

Releases (28)

Pick two releases to compare their code metrics.

4.3-4-8Latest
record
2026-10-08 · current release · diff ↗
4.3-4-7
record
2026-10-08 · diff ↗
4.3-4-6
record
2026-05-23 · diff ↗
R
R 4.6.0 released · 2026-04-24
4.3-4-5
record
2026-01-30 · diff ↗
4.3-4-4
record
2026-01-26 · diff ↗
4.3-4-3
record
2025-12-22 · diff ↗ ·
removed 1 export
bm_CalculateStat

added 6 exports
BIOMOD_Report, bm_CalculateStatAbun, bm_CalculateStatBin, bm_ModelAnalysis, bm_RangeSize, set_new_dirname
R
R 4.5.0 released · 2025-04-11
4.2-6-2
record
2025-01-24 · diff ↗ ·
added 1 export
BIOMOD_ModelingOptions
4.2-5-2
record
2024-06-14 · diff ↗
4.2-5
record
2024-05-02 · diff ↗ ·
removed 13 exports
.transform.outputs.array, BIOMOD_ConvertOldRun, BIOMOD_ModelingOptions, BIOMOD_cv, BIOMOD_presenceonly, BIOMOD_tuning, CustomIndexMaker, FilteringTransformation, Print_Default_ModelingOptions, bm_CVnnet, bm_DefaultModelingOptions, response.plot, update_objects

added 2 exports
bm_ModelingOptions, bm_Tuning
R
R 4.4.0 released · 2024-04-24
4.2-4
record
2023-06-16 · diff ↗
4.2-3
record
2023-05-11 · diff ↗ ·
added 7 exports
bm_CrossValidation, bm_CrossValidation_block, bm_CrossValidation_env, bm_CrossValidation_kfold, bm_CrossValidation_random, bm_CrossValidation_strat, bm_CrossValidation_user.defined
R
R 4.3.0 released · 2023-04-21
4.2-2
record
2023-01-16 · diff ↗ ·
added 1 export
.transform_model.as.col

Show 27 earlier eventsHide 27 earlier events

4.1-2
record
2022-10-25 · diff ↗ ·
removed 35 exports
free, plot, predict, show, get_built_models, get_evaluations, get_calib_lines, get_formal_data, get_formal_model, get_kept_models, get_needed_models, get_options, get_predictions, get_projected_models, get_scaling_model, get_variables_importance, DF_to_ARRAY, evaluate, full_suffling, level.plot, LIST_to_ARRAY, multiple.plot, randomise_data, .create.maxent.bg.dir, disk.pseudo.abs.selection, Projection, random.pseudo.abs.selection, sre.pseudo.abs.selection, user.defined.pseudo.abs.selection, .Models.prepare.data and 5 more

added 27 exports
.transform.outputs.array, BIOMOD_CrossValidation, BIOMOD_PresenceOnly, BIOMOD_Tuning, bm_BinaryTransformation, bm_CVnnet, bm_CalculateStat, bm_DefaultModelingOptions, bm_FindOptimStat, bm_MakeFormula, bm_PlotEvalBoxplot, bm_PlotEvalMean, bm_PlotRangeSize, bm_PlotResponseCurves, bm_PlotVarImpBoxplot, bm_PseudoAbsences, bm_PseudoAbsences_disk, bm_PseudoAbsences_random, bm_PseudoAbsences_sre, bm_PseudoAbsences_user.defined, bm_RunModel, bm_RunModelsLoop, bm_SRE, bm_SampleBinaryVector, bm_SampleFactorLevels, bm_VariablesImportance, get_optim_value
R
R 4.2.0 released · 2022-04-22
3.5.1
record
2021-06-11 · diff ↗ ·
added 1 export
zzz_bm
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
3.4.6
record
2020-02-26 · diff ↗ ·
removed 1 export
RemoveProperly

added 9 exports
.transform.outputs.list, disk.pseudo.abs.selection, load_stored_object, Projection, random.pseudo.abs.selection, sre.pseudo.abs.selection, user.defined.pseudo.abs.selection, .Models.prepare.data, .Projection.do.proj
R
R 3.6.0 released · 2019-04-26
3.3-7.1
record
2019-03-08 · diff ↗
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03
3.3-7
record
2016-03-01 · diff ↗ ·
added 5 exports
.create.maxent.bg.dir, BIOMOD_cv, BIOMOD_presenceonly, BIOMOD_tuning, sample.factor.levels
R
R 3.2.0 released · 2015-04-16
3.1-64
record
2014-12-10 · diff ↗ ·
added 2 exports
get_calib_lines, models_scores_graph
3.1-48
record
2014-07-07 · diff ↗
R
R 3.1.0 released · 2014-04-10
3.1-25
record
2013-12-02 · diff ↗
3.1-24
record
2013-11-25 · diff ↗
3.1-18
record
2013-10-25 · diff ↗ ·
removed 1 export
pattern:^[[:alpha:]]+

added 50 exports
BinaryTransformation, BIOMOD_RangeSize, FilteringTransformation, free, plot, predict, RemoveProperly, show, get_built_models, get_evaluations, get_formal_data, get_formal_model, get_kept_models, get_needed_models, get_options, get_predictions, get_projected_models, get_scaling_model, get_variables_importance, BIOMOD_ConvertOldRun, BIOMOD_EnsembleForecasting, BIOMOD_EnsembleModeling, BIOMOD_FormatingData, BIOMOD_LoadModels, BIOMOD_Modeling, BIOMOD_ModelingOptions, BIOMOD_Projection, calculate.stat, DF_to_ARRAY, evaluate and 20 more
R
R 3.0.0 released · 2013-04-03
2.15.2
record
2012-09-14 · diff ↗ ·
added 50 exports
BinaryTransformation, BIOMOD_RangeSize, FilteringTransformation, free, plot, predict, RemoveProperly, show, get_built_models, get_evaluations, get_formal_data, get_formal_model, get_kept_models, get_needed_models, get_options, get_predictions, get_projected_models, get_scaling_model, get_variables_importance, BIOMOD_ConvertOldRun, BIOMOD_EnsembleForecasting, BIOMOD_EnsembleModeling, BIOMOD_FormatingData, BIOMOD_LoadModels, BIOMOD_Modeling, BIOMOD_ModelingOptions, BIOMOD_Projection, calculate.stat, DF_to_ARRAY, evaluate and 20 more
2.1.15
record
2013-03-14 · diff ↗
2.1.7
record
2013-02-25 · diff ↗
2.0.0
record
2013-02-02 · diff ↗
1.3.5
record
2012-11-14 · diff ↗
1.3.1
record
2012-11-09
R
R 2.15.0 released · 2012-03-30

Package metadata

First published: 2012-09-14
Total releases: 28 / 14 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.1
Bundled data: 299 KB / 7 files
Download size: 4.1 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("biomod2")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1002/ecog.08588.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for biomod2 version 4.3-4-8 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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