R Observatory: Metrics for sjSDM version 1.0.7

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

sjSDM

1.0.7

Scalable Joint Species Distribution Modeling

0packages depend

3.5Kdownloads / year

8.9%test coverage

13/13checks pass

Overview

About

Maintained by Maximilian PichlerFirst published 2022-01-108 releasesCRAN page ↗GitHub ↗

A scalable and fast method for estimating joint Species Distribution Models (jSDMs) for big community data, including eDNA data. The package estimates a full (i.e. non-latent) jSDM with different response distributions (including the traditional multivariate probit model). The package allows to perform variation partitioning (VP) / ANOVA on the fitted models to separate the contribution of environmental, spatial, and biotic associations. In addition, the total R-squared can be further partitioned per species and site to reveal the internal metacommunity structure, see Leibold et al., doi:10.1111/oik.08618. The internal structure can then be regressed against environmental and spatial distinctiveness, richness, and traits to analyze metacommunity assembly processes. The package includes support for accounting for spatial autocorrelation and the option to fit responses using deep neural networks instead of a standard linear predictor. As described in Pichler & Hartig (2021) doi:10.1111/2041-210X.13687, scalability is achieved by using a Monte Carlo approximation of the joint likelihood implemented via 'PyTorch' and 'reticulate', which can be run on CPUs or GPUs.

Install

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

install.packages("sjSDM", 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("TheoreticalEcology/s-jSDM")

Development version from TheoreticalEcology/s-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-sjsdm

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-sjSDM

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-sjSDM

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

Health

CRAN checks

13OK

Slowest check: 18.7 min · r-devel-windows-x86_64

Code health

Yes

Tests · ratio 0.18

8.9%

Coverage · measured lines

100%

Documentation · exports

20

Dependencies · direct

Check history

OK2026-08-04
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-05-28
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-05-20
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 35 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 0%
Documented parameters: 100%
Return-value docs: 100%
References docs: 17%

Downloads

3.5K

CRAN downloads in the past year

Rank #12,063 · ~10/day · ~291/mo

Releases R versions

Daily download trend is not available in this view yet.

21630 days

82390 days

3.5K1 year

Compare downloads with other packages →

Also on146 r2u16 autocran28 c2d4u

Repository

GitHub ↗ theoreticalecology/s-jsdm

79Stars

15Forks

56Open issues

0Open PRs

6Releases

567Commits

7Contributors

species-distribution-modellingspecies-interactionsmachine-learningdeep-learninggpu-acceleration

License GPL-3.0 · 567 commits · Last activity 2026-06-11 · 0% stars, 30d

Stars over time

2025-04-14 · 692026-07-07 · 79

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/theoreticalecology/s-jsdm on 2026-08-16.

Continuous integration (1)

GitHub Actions

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

19 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1.0

Imports (20)

reticulatestatsmvtnormutilsrstudioapi abindgraphicsgrDevicesMetricsparallelmgcvcli crayon ggplot2 checkmate mathjaxr beeswarm qgam scales viridis

LinkingTo (0)

none

Suggests (5)

testthat knitr rmarkdown iml fields

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (3)

Maintainer (1)

Maximilian Pichler

Author, Maintainer

Authors (2)

Maximilian Pichler

Author, Maintainer

Florian Hartig

Author

Contributors (1)

Wang Cai

Contributor

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
1.0.7Latest
2025-09-17 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
1.0.6
2024-08-19 · diff ↗
R
R 4.4.0 released · 2024-04-24
1.0.5
2023-06-18 · diff ↗
unarchivedReturned to CRAN
2023-06-18
archivedRemoved from CRAN
2023-05-07
requires archived package 'ggtern'
R
R 4.3.0 released · 2023-04-21
1.0.4
2023-03-30 · diff ↗
1.0.3
2022-09-14 · diff ↗
1.0.2
2022-06-24 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.0.1
2022-03-11 · diff ↗
1.0.0
2022-01-10
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2022-01-10
Total releases: 8 / 4 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.1.0
Bundled data: 72 KB / 2 files
Download size: 1.2 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Analysis of Ecological and Environmental Data

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("sjSDM")

Format

Pichler, M., Cai, W., & Hartig, F. (2026). sjSDM: Scalable Joint Species Distribution Modeling (Version 1.0.7) [Computer software]. https://doi.org/10.32614/CRAN.package.sjSDM

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 sjSDM version 1.0.7 [Data set]. HJJB, LLC. Data release v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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