R Observatory: Metrics for sjSDM version 1.0.7

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

sjSDM

1.0.7Package record

Scalable Joint Species Distribution Modeling

0packages depend

3.5Kdownloads / year

8.9%test coverage

11/13flavors OK

Overview

About

Maintained by Maximilian PichlerCRAN page ↗GitHub ↗Issues ↗

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.

Changes in 1.0.7

importance function was removed (deprecated)

Bug fixes

cv function, use correct indices in parallel block modus #155, thanks to @jannebor
remove ggtern dependency

From NEWS.md in the release

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. 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-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). 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

2WARNING11OK

Check messages

WARNINGS3 generic/method consistencyr-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

warning: Failed to inspect Python interpreter from search path at `/usr/sbin/pypy`
  cause: Can't use Python at `/usr/sbin/pypy`
  cause: Python executable does not support `-I` flag. Please use Python 3.6 or newer.
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.

WARNINGfor code/documentation mismatchesr-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

warning: Failed to inspect Python interpreter from search path at `/usr/sbin/pypy`
  cause: Can't use Python at `/usr/sbin/pypy`
  cause: Python executable does not support `-I` flag. Please use Python 3.6 or newer.
warning: Failed to inspect Python interpreter from search path at `/usr/sbin/pypy`
  cause: Can't use Python at `/usr/sbin/pypy`
  cause: Python executable does not support `-I` flag. Please use Python 3.6 or newer.
warning: Failed to inspect Python interpreter from search path at `/usr/sbin/pypy`
  cause: Can't use Python at `/usr/sbin/pypy`
  cause: Python executable does not support `-I` flag. Please use Python 3.6 or newer.

WARNINGfor missing documentation entriesr-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

warning: Failed to inspect Python interpreter from search path at `/usr/sbin/pypy`
  cause: Can't use Python at `/usr/sbin/pypy`
  cause: Python executable does not support `-I` flag. Please use Python 3.6 or newer.
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.

WARNINGreplacement functionsr-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

warning: Failed to inspect Python interpreter from search path at `/usr/sbin/pypy`
  cause: Can't use Python at `/usr/sbin/pypy`
  cause: Python executable does not support `-I` flag. Please use Python 3.6 or newer.
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.

NOTER code for possible problemsr-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

warning: Failed to inspect Python interpreter from search path at `/usr/sbin/pypy`
  cause: Can't use Python at `/usr/sbin/pypy`
  cause: Python executable does not support `-I` flag. Please use Python 3.6 or newer.
warning: Failed to inspect Python interpreter from search path at `/usr/sbin/pypy`
  cause: Can't use Python at `/usr/sbin/pypy`
  cause: Python executable does not support `-I` flag. Please use Python 3.6 or newer.

warning: Failed to inspect Python interpreter from search path at `/usr/sbin/pypy`
  cause: Can't use Python at `/usr/sbin/pypy`
  cause: Python executable does not support `-I` flag. Please use Python 3.6 or newer.

NOTERd \usage sectionsr-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

warning: Failed to inspect Python interpreter from search path at `/usr/sbin/pypy`
  cause: Can't use Python at `/usr/sbin/pypy`
  cause: Python executable does not support `-I` flag. Please use Python 3.6 or newer.
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.

NOTEdependencies in R coder-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

warning: Failed to inspect Python interpreter from search path at `/usr/sbin/pypy`
  cause: Can't use Python at `/usr/sbin/pypy`
  cause: Python executable does not support `-I` flag. Please use Python 3.6 or newer.

NOTEforeign function callsr-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

warning: Failed to inspect Python interpreter from search path at `/usr/sbin/pypy`
  cause: Can't use Python at `/usr/sbin/pypy`
  cause: Python executable does not support `-I` flag. Please use Python 3.6 or newer.
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.

NOTEwhether startup messages can be suppressedr-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

warning: Failed to inspect Python interpreter from search path at `/usr/sbin/pypy`
  cause: Can't use Python at `/usr/sbin/pypy`
  cause: Python executable does not support `-I` flag. Please use Python 3.6 or newer.

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.

CRAN check page ↗

Slowest check: 14.1 min · r-release-windows-x86_64

Status changes

WARNING11 OK, 2 WARNINGNow
WARNING12 OK, 1 WARNING2026-09-10
OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-05-28
ERROR12 OK, 1 ERROR2026-05-20

Show 1 earlier changeHide 1 earlier change

OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.7

READMEYes · 35 wordsVignettesYes · 1 · staticNEWSYes · 100% structured · mentions 1.0.7Citation fileYes · cites a publication

Help pages: 59includes a package overview page
Examples that run: 0%18 never run
Exported functions with examples: 28%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 17%

Vignettes (1)

sjSDM: Getting started with sjSDM - a scalable joint Species Distribution Model

How these are measured

Downloads

3.5K

CRAN downloads in the past year

Rank #8,965 · ~10/day · ~292/mo

Releases R versions

Daily download trend is not available in this view yet.

40530 days

1.1K90 days

3.5K1 year

Compare downloads with other packages →

Also on119 r2u2 autocran49 c2d4u

How downloads are counted

Repository

theoreticalecology/s-jsdm ↗Organization: TheoreticalEcology

79Stars

17Forks

57Open issues

0Open PRs

6Releases

575Commits

7Commit identities

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

License file reads as GPL-3.0 · 575 commits · Last activity 2026-10-17 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 94%
Median days to close, 50 most recently updated closed issues: 64
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-08-28 · 702026-07-07 · 79

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/theoreticalecology/s-jsdm on 2026-10-21.

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 (2)

README.Rmd

GitHub Pages site last deployed 2024-07-30

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

19 external dependencies (excludes base and recommended)

Installing sjSDM adds 62 packages (32 with compiled code, 52 MB of source tarballs). Heaviest: ggplot2 6.0 MB, bslib 5.6 MB, qgam 3.9 MB.

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.

How these are counted

Code & Tests

Datasets

People & History

People (3)

Maximilian Pichler

Author, Maintainer since 1.0.0 (2022)

Florian Hartig

Author

Wang Cai

Contributor

Releases (8)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.0.7Latest
record
2025-09-17 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
1.0.6
record
2024-08-19 · diff ↗ ·
removed 2 exports
importance, plotInternalStructure

added 2 exports
internalStructure, plotAssemblyEffects
R
R 4.4.0 released · 2024-04-24
unarchivedReturned to CRAN
2023-06-18
1.0.5
record
2023-06-18 · diff ↗
archivedRemoved from CRAN
2023-05-07
requires archived package 'ggtern'
R
R 4.3.0 released · 2023-04-21
1.0.4
record
2023-03-30 · diff ↗ ·
added 2 exports
getCor, plotInternalStructure
1.0.3
record
2022-09-14 · diff ↗
1.0.2
record
2022-06-24 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.0.1
record
2022-03-11 · diff ↗
1.0.0
record
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

Appears in task views

Analysis of Ecological and Environmental Data

Cite

Cite this package

Run in R for the authors' entry:

citation("sjSDM")

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

It points to 10.1111/2041-210x.13687.

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 v2026-10-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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