R Observatory: Metrics for Hmsc version 3.3-7

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

Hmsc

3.3-7Package record

Hierarchical Model of Species Communities

0packages dependsuggested by 2

27.9Kdownloads / year

29.8%test coverage

8/13flavors OK

Overview

About

Maintained by Otso OvaskainenCRAN page ↗GitHub ↗Website ↗Issues ↗

Hierarchical Modelling of Species Communities (HMSC) is a model-based approach for analyzing community ecological data. This package implements it in the Bayesian framework with Gibbs Markov chain Monte Carlo (MCMC) sampling (Tikhonov et al. (2020) doi:10.1111/2041-210X.13345).

Changes in 3.3-7

New Features

Added a set of utilities to facilitate Common to Rare Transfer Learning (CORAL).
Added integration with Hmsc-HPC add-on for delegating MCMC to TensorFlow.
Added function computeSAIR for shared and idiosyncratic responses to measured and latent predictors.
Failed updaters are only recorded during sampling. Failed updates can be detected in more cases (V, Z).

Bug Fixes

Legend for plotVariancePartitioning had two entries for Random when there were no random levels.

Show all changes in 3.3-7Hide the rest of the changes in 3.3-7

predict could fail when there were no random levels.

From inst/NEWS.md in the release

Install

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

install.packages("Hmsc", 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("hmsc-r/HMSC")

Development version from hmsc-r/HMSC. 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-hmsc

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-Hmsc

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-Hmsc

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

5NOTE8OK

Check messages

NOTEfor differences from example reference outputr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64

r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Comparing ‘Hmsc-Ex.Rout’ to ‘Hmsc-Ex.Rout.save’:
227,6626d226
< Warning in Beta[sel, j] :
<   length of dimension 1 is not a multiple of logical subscript length
< Warning in cM[sel, sel] :
<   length of dimension 1 is not a multiple of logical subscript length
< Warning in cM[sel, sel] :
<   length of dimension 2 is not a multiple of logical subscript length
< Warning in Beta[sel, j] :
<   length of dimension 1 is not a multiple of logical subscript length
< Warning in Beta[sel, j] :
<   length of dimension 1 is not a multiple of logical subscript length
< Warning in cM[sel, sel] :
<   length of dimension 1 is not a multiple of logical subscript length
< Warning in cM[sel, sel] :
<   length of dimension 2 is not a multiple of logical subscript length
< Warning in Beta[sel, j] :
<   length of dimension 1 is not a multiple of logical subscript length
< Warning in Beta[sel, j] :
<   length of dimension 1 is not a multiple of logical subscript length
< Warning in cM[sel, sel] :
<   length
...[truncated]...

< Warning in cM[sel, sel] :
<   length of dimension 2 is not a multiple of logical subscript length
< Warning in Beta[sel, j] :
<   length of dimension 1 is not a multiple of logical subscript length
< Warning in Beta[sel, j] :
<   length of dimension 1 is not a multiple of logical subscript length
< Warning in cM[sel, sel] :
<   length of dimension 1 is not a multiple of logical subscript length
< Warning in cM[sel, sel] :
<   length of dimension 2 is not a multiple of logical subscript length
< Warning in Beta[sel, j] :
<   length of dimension 1 is not a multiple of logical subscript length
< Warning in Beta[sel, j] :
<   length of dimension 1 is not a multiple of logical subscript length
< Warning in cM[sel, sel] :
<   length of dimension 1 is not a multiple of logical subscript length
< Warning in cM[sel, sel] :
<   length of dimension 2 is not a multiple of logical subscript length
< Warning in Beta[sel, j] :
<   length of dimension 1 is not a multiple of logical subscript length

r-devel-windows-x86_64

Comparing 'Hmsc-Ex.Rout' to 'Hmsc-Ex.Rout.save':
227,6626d226
< Warning in Beta[sel, j] :
<   length of dimension 1 is not a multiple of logical subscript length
< Warning in cM[sel, sel] :
<   length of dimension 1 is not a multiple of logical subscript length
< Warning in cM[sel, sel] :
<   length of dimension 2 is not a multiple of logical subscript length
< Warning in Beta[sel, j] :
<   length of dimension 1 is not a multiple of logical subscript length
< Warning in Beta[sel, j] :
<   length of dimension 1 is not a multiple of logical subscript length
< Warning in cM[sel, sel] :
<   length of dimension 1 is not a multiple of logical subscript length
< Warning in cM[sel, sel] :
<   length of dimension 2 is not a multiple of logical subscript length
< Warning in Beta[sel, j] :
<   length of dimension 1 is not a multiple of logical subscript length
< Warning in Beta[sel, j] :
<   length of dimension 1 is not a multiple of logical subscript length
< Warning in cM[sel, sel] :
<   length
...[truncated]...

< Warning in cM[sel, sel] :
<   length of dimension 2 is not a multiple of logical subscript length
< Warning in Beta[sel, j] :
<   length of dimension 1 is not a multiple of logical subscript length
< Warning in Beta[sel, j] :
<   length of dimension 1 is not a multiple of logical subscript length
< Warning in cM[sel, sel] :
<   length of dimension 1 is not a multiple of logical subscript length
< Warning in cM[sel, sel] :
<   length of dimension 2 is not a multiple of logical subscript length
< Warning in Beta[sel, j] :
<   length of dimension 1 is not a multiple of logical subscript length
< Warning in Beta[sel, j] :
<   length of dimension 1 is not a multiple of logical subscript length
< Warning in cM[sel, sel] :
<   length of dimension 1 is not a multiple of logical subscript length
< Warning in cM[sel, sel] :
<   length of dimension 2 is not a multiple of logical subscript length
< Warning in Beta[sel, j] :
<   length of dimension 1 is not a multiple of logical subscript length

CRAN check page ↗

Slowest check: 4.3 min · r-oldrel-windows-x86_64

Status changes

NOTE8 OK, 5 NOTENow
NOTE12 OK, 1 NOTE2026-09-13
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 3.3-7

READMEYes · 522 wordsVignettesYes · 10 · staticNEWSYes · 100% structured · mentions 3.3-7Citation fileNoWebsiteYes

Help pages: 42 (1 internal)includes a package overview page
Examples that run: 100%24 run in a plain check
Exported functions with examples: 68%
Documented parameters: 98%
Return-value docs: 85%
Help pages citing references: 0%

Vignettes (10)

How these are measured

Downloads

27.9K

CRAN downloads in the past year

Rank #3,259 · ~76/day · ~2.3K/mo

Releases R versions

Daily download trend is not available in this view yet.

1.4K30 days

3.5K90 days

27.9K1 year

Compare downloads with other packages →

Also on161 r2u4 autocran1.7K conda_forge68 c2d4u

How downloads are counted

Repository

hmsc-r/hmsc ↗Organization: hmsc-r

121Stars

40Forks

128Open issues

2Open PRs

6Releases

1,060Commits

17Commit identities

License file reads as GPL-3.0 · 1,060 commits · Last activity 2026-06-26 · +0.8% stars, 30d · Default branch at 3.4-1, ahead of CRAN 3.3-7 (checked 2026-10-22)

Responsiveness

How these are sampled

PRs merged (all time): 71%
Median days to close, 50 most recently updated closed issues: 6
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2026-07-14 · 1192026-09-28 · 121

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/hmsc-r/hmsc on 2026-10-22.

Continuous integration (3)

GitHub ActionsR CMD check workflowTravis CI (config file)

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

Reproducibility and dev environment (1)

data-raw/

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

18 external dependencies (excludes base and recommended)

Installing Hmsc adds 39 packages (25 with compiled code, 36 MB of source tarballs). Heaviest: ggplot2 6.0 MB, sp 4.3 MB, fields 3.9 MB.

Depends (2)

R >= 3.0.2coda

Imports (19)

abind ape BayesLogit fields FNN ggplot2MASSMatrixmatrixStats MCMCpackmethodsnnetrlangparallelpracma pROC sp statmod truncnorm

LinkingTo (0)

none

Suggests (3)

R.rsp testthat corrplot

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Suggested by 2

Suggests, most downloaded first

cotram jSDM

How these are counted

Code & Tests

Datasets

People & History

People (6)

Otso Ovaskainen

Author, Maintainer since 3.0-2 (2019)

Author

Author

Author

Author

Author

Listed in earlier versions (1)

Melinda

no longer listed · 3.0-2 to 3.3-7

Releases (7)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
3.3-7Latest
record
2025-08-29 · current release · diff ↗ ·
added 10 exports
computeSAIR, coralCombine, coralGetRareSpeciesPriors, coralGetXDataExt, coralPlotBeta, coralPredict, coralPreprocess, coralSplitToBatches, coralTrain, importPosteriorFromHPC
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
3.0-13
record
2022-08-11 · diff ↗ ·
added 1 export
pcomputePredictedValues
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
3.0-11
record
2021-02-24 · diff ↗
3.0-9
record
2020-10-29 · diff ↗
R
R 4.0.0 released · 2020-04-24
3.0-6
record
2020-03-19 · diff ↗
3.0-4
record
2019-12-16 · diff ↗
3.0-2
record
2019-10-13
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2019-10-13
Total releases: 7 / 7 yrs
License: GPL-3 | file LICENSE OSI
Minimum R: ≥ 3.0.2
Bundled data: 294 KB / 1 file
Download size: 2.4 MB

Appears in task views

Analysis of Ecological and Environmental Data

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("Hmsc")

Format

Ovaskainen, O., Dallas, T., Oksanen, J., Opedal, O., Tikhonov, G., & de Jonge, M. (2025). Hmsc: Hierarchical Model of Species Communities (Version 3.3-7) [Computer software]. https://doi.org/10.32614/CRAN.package.Hmsc

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 Hmsc version 3.3-7 [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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