R Observatory: Metrics for bamm version 0.6.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

bamm

0.6.2

Species Distribution Models as a Function of Biotic, Abiotic and Movement Factors (BAM)

0packages depend

3.7Kdownloads / year

82.9%test coverage

13/13checks pass

Overview

About

Maintained by Luis Osorio-OlveraFirst published 2022-12-205 releasesCRAN page ↗GitHub ↗

Species Distribution Modeling (SDM) is a practical methodology that aims to estimate the area of distribution of a species. However, most of the work has focused on estimating static expressions of the correlation between environmental variables. The outputs of correlative species distribution models can be interpreted as maps of the suitable environment for a species but not generally as maps of its actual distribution. Soberón and Peterson (2005) doi:10.17161/bi.v2i0.4 presented the BAM scheme, a heuristic framework that states that the occupied area of a species occurs on sites that have been accessible through dispersal (M) and have both favorable biotic (B) and abiotic conditions (A). The 'bamm' package implements classes and functions to operate on each element of the BAM and by using a cellular automata model where the occupied area of a species at time t is estimated by the multiplication of three binary matrices: one matrix represents movements (M), another abiotic -niche- tolerances (A), and a third, biotic interactions (B). The theoretical background of the package can be found in Soberón and Osorio-Olvera (2023) doi:10.1111/jbi.14587.

Install

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

install.packages("bamm", 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("luismurao/bamm")

Development version from luismurao/bamm. 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-bamm

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

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-bamm

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-bamm

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 13.7 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.24

82.9%

Coverage · measured lines

100%

Documentation · exports

19

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-22
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 2 earlier snapshots

ERROR2026-04-18
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 362 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 65%
Documented parameters: 100%
Return-value docs: 100%
References docs: 40%

Downloads

3.7K

CRAN downloads in the past year

Rank #10,374 · ~10/day · ~304/mo

Releases R versions

Daily download trend is not available in this view yet.

27630 days

92390 days

3.7K1 year

Compare downloads with other packages →

Also on431 r2u68 autocran

Repository

GitHub ↗ luismurao/bamm

2Stars

0Forks

1Open issues

0Open PRs

0Releases

287Commits

1Contributors

287 commits · Last activity 2026-04-14 · 0% stars, 30d

Stars over time

2023-01-31 · 12026-07-07 · 2

Repository practices

Upstream repositoryBeta

5 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/luismurao/bamm on 2026-08-16.

Continuous integration (1)

GitHub Actions

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (1)

RStudio project

Coverage (1)

Codecov

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

21 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (19)

animation dplyr furrr futuregraphicsgrDevicesigraph leaflet (>= 2.0)magrittrMatrixmethodspurrr raster Rcpp Rdpack RSpectra spstatsutils

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (6)

knitr rmarkdown testthat crosstalk plotly spelling

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (3)

Maintainer (1)

Luis Osorio-Olvera

Author, Maintainer

Authors (2)

Luis Osorio-Olvera

Author, Maintainer

Jorge Soberón

Author

Contributors (1)

Rusby G. Contreras-Díaz

Contributor · added in 0.5.0

Package Timeline

5 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.6.2Latest
2026-02-17 · current release · diff ↗
0.6.1
2026-02-17 · diff ↗
0.6.0
2026-02-03 · diff ↗
R
R 4.5.0 released · 2025-04-11
0.5.0
2024-07-06 · diff ↗
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
0.4.3
2022-12-20
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2022-12-20
Total releases: 5 / 4 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 3.5.0
Download size: 720 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("bamm")

Format

Osorio-Olvera, L., Contreras-Díaz, R. G., & Soberón, J. (2026). bamm: Species Distribution Models as a Function of Biotic, Abiotic and Movement Factors (BAM) (Version 0.6.2) [Computer software]. https://doi.org/10.32614/CRAN.package.bamm

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 bamm version 0.6.2 [Data set]. HJJB, LLC. Data release v2026-08-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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