R Observatory: Metrics for jSDM version 0.2.7

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

jSDM

0.2.7Package record

Joint Species Distribution Models

0packages depend

4Kdownloads / year

90.2%test coverage

11/13flavors OK

Overview

About

Maintained by Ghislain VieilledentCRAN page ↗GitHub ↗Website ↗Issues ↗Declared funder: CIRAD

Fits joint species distribution models ('jSDM') in a hierarchical Bayesian framework (Warton and al. 2015 doi:10.1016/j.tree.2015.09.007). The Gibbs sampler is written in 'C++'. It uses 'Rcpp', 'Armadillo' and 'GSL' to maximize computation efficiency.

Changes in 0.2.7

Changing maintainer to Ghislain Vieilledent <ghislain.vieilledent@cirad.fr>.

From NEWS.md in the release

Install

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

install.packages("jSDM", 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("ghislainv/jSDM")

Development version from ghislainv/jSDM. 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-jsdm

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-jSDM

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-jSDM

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

2NOTE11OK

Check messages

NOTERd contentsr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Rd files without \usage:
  ‘jSDM_binomial_probit_sp_constrained.Rd’
\arguments should not be documented without \usage.

CRAN check page ↗

Slowest check: 25.1 min · r-oldrel-windows-x86_64

Status changes

NOTE11 OK, 2 NOTENow
NOTE12 OK, 1 NOTE2026-07-11
OK12 OK2026-04-25
NOTE11 OK, 3 NOTE2026-04-22
ERROR10 OK, 3 NOTE, 1 ERROR2026-04-18
NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.2.7

READMEYes · 256 wordsVignettesYes · 2 · dynamicNEWSYes · 100% structured · mentions 0.2.7Citation fileNoWebsiteYes · pkgdown

Help pages: 22includes a package overview page
Examples that run: 100%21 run in a plain check
Exported functions with examples: 100%
Documented parameters: 99%
Return-value docs: 100%
Help pages citing references: 59%

Vignettes (2)

How these are measured

Downloads

4K

CRAN downloads in the past year

Rank #10,838 · ~11/day · ~330/mo

Releases R versions

Daily download trend is not available in this view yet.

39730 days

95690 days

4K1 year

Compare downloads with other packages →

Also on362 r2u10 autocran

How downloads are counted

Repository

ghislainv/jsdm ↗Account: ghislainv

15Stars

7Forks

7Open issues

0Open PRs

6Releases

547Commits

3Commit identities

547 commits · Last activity 2025-11-03 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 86
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-08-28 · 122026-09-08 · 15

How these are measured

PracticesBeta

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

Checks run against github.com/ghislainv/jsdm on 2026-10-11.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2025-11-03 · The repository has a site deploy workflow

pkgdown site last built 2025-11-03

Coverage (1)

Coverage reporting (Codecov)

CRAN release process (1)

cran-comments.md

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

22 external dependencies (excludes base and recommended)

Installing jSDM adds 9 packages (4 with compiled code, 18 MB of source tarballs). Heaviest: stringi 11 MB, corrplot 3.6 MB, Rcpp 1.8 MB.

Depends (1)

R >= 3.5.0

Imports (11)

Rcppgraphicsstatscoda corrplot stringiMASSparalleldoParallel foreachmethods

LinkingTo (3)

Rcpp RcppArmadillo RcppGSL

Suggests (13)

knitr kableExtra terra dplyr rmarkdown bookdown testthat boral Hmsc ggplot2 covr ape gstat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (4)

Ghislain Vieilledent

Author, Maintainer since 0.2.7 (2025)

Jeanne Clément

Author

Frédéric Gosselin

Contributor · added in 0.2.0

CIRAD

Copyright holder, Funder

Previously maintained by Jeanne Clément (0.2.0 to 0.2.6) and Ghislain Vieilledent (0.1.0).

Releases (6)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
0.2.7Latest
record
2025-11-03 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
unarchivedReturned to CRAN
2023-07-22
0.2.6
record
2023-07-22 · diff ↗
R
R 4.3.0 released · 2023-04-21
archivedRemoved from CRAN
2023-03-17
issues were not corrected in time
0.2.2
record
2023-03-02 · diff ↗ ·
added 1 export
jSDM_gaussian
R
R 4.2.0 released · 2022-04-22
0.2.1
record
2022-03-21 · diff ↗
0.2.0
record
2022-03-08 · diff ↗ ·
removed 3 exports
jSDM_binomial, jSDM_probit_block, predict.jSDM

added 7 exports
get_enviro_cor, jSDM_binomial_logit, jSDM_binomial_probit, jSDM_binomial_probit_long_format, jSDM_binomial_probit_sp_constrained, jSDM_poisson_log, plot_associations
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
0.1.0
record
2019-07-02
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2019-07-02
Total releases: 6 / 7 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5.0
Bundled data: 66 KB / 8 files
Download size: 4.8 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("jSDM")

Format

Vieilledent, G., CIRAD, Clément, J., & Gosselin, F. (2025). jSDM: Joint Species Distribution Models (Version 0.2.7) [Computer software]. https://doi.org/10.32614/CRAN.package.jSDM

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 jSDM version 0.2.7 [Data set]. HJJB, LLC. Data release v2026-10-19. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-19, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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