jSDM

0.2.7

Joint Species Distribution Models

0packages depend

4.1Kdownloads / year

90.2%test coverage

11/13checks pass

Overview

About

Maintained by Ghislain VieilledentFirst published 2019-07-026 releasesCRAN page ↗GitHub ↗

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.

Install

R (CRAN)pak (dev)Ubuntu (r2u)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.

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

# 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).

Health

CRAN checks

2NOTE11OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 25.2 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.79

90.2%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-07-11
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-22
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
10 OK · 3 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 256 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 99%
Return-value docs: 100%
References docs: 59%

Downloads

4.1K

CRAN downloads in the past year

Rank #13,222 · ~11/day · ~341/mo

Releases R versions

Daily download trend is not available in this view yet.

26230 days

79490 days

4.1K1 year

Compare downloads with other packages →

Also on447 r2u28 autocran

Repository

GitHub ↗ ghislainv/jsdm

14Stars

7Forks

7Open issues

0Open PRs

6Releases

547Commits

3Contributors

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

Stars over time

2024-06-18 · 112026-07-07 · 14

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/ghislainv/jsdm on 2026-07-19.

Continuous integration (1)

GitHub Actions

CRAN release process (1)

cran-comments.md

Docs source (1)

README.Rmd

Coverage (1)

Codecov

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

Dependencies

Declared dependencies

22 external dependencies (excludes base and recommended)

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.

Code & Tests

Datasets

People & History

People (4)

Maintainer (1)

Ghislain Vieilledent

Author, Maintainer

Authors (2)

Ghislain Vieilledent

Author, Maintainer

Jeanne Clément

Author

Contributors (1)

Frédéric Gosselin

Contributor · added in 0.2.0

CIRAD

Funders (1)

CIRAD

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
0.2.7Latest
2025-11-03 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
0.2.6
2023-07-22 · diff ↗
unarchivedReturned to CRAN
2023-07-22
R
R 4.3.0 released · 2023-04-21
archivedRemoved from CRAN
2023-03-17
issues were not corrected in time
0.2.2
2023-03-02 · diff ↗
R
R 4.2.0 released · 2022-04-22
0.2.1
2022-03-21 · diff ↗
0.2.0
2022-03-08 · diff ↗
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
0.1.0
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
Installed size: not tracked yet
With dependencies: not tracked yet

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