Hmsc

3.3-7

Hierarchical Model of Species Communities

2packages depend

33.1Kdownloads / year

29.8%test coverage

13/13checks pass

Overview

About

Maintained by Otso OvaskainenFirst published 2019-10-137 releasesCRAN page ↗GitHub ↗

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).

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.

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).

Health

CRAN checks

13OK

Slowest check: 5.2 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.15

29.8%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 522 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 98%
Return-value docs: 85%
References docs: 0%

Downloads

33.1K

CRAN downloads in the past year

Rank #2,822 · ~91/day · ~2.8K/mo

Releases R versions

Daily download trend is not available in this view yet.

1.1K30 days

6.1K90 days

33.1K1 year

Compare downloads with other packages →

Also on146 r2u10 autocran2K conda_forge26 c2d4u

Repository

GitHub ↗ hmsc-r/hmsc

119Stars

40Forks

127Open issues

2Open PRs

6Releases

1,060Commits

17Contributors

License GPL-3.0 · 1,060 commits · Last activity 2026-06-26

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/hmsc-r/hmsc on 2026-07-19.

Continuous integration (2)

GitHub ActionsTravis CI

Reproducibility and dev environment (1)

data-raw/

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

18 external dependencies (excludes base and recommended)

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

2direct

0indirect

cotram jSDM

Code & Tests

People & History

People (6)

Maintainer (1)

Otso Ovaskainen

Author, Maintainer

Authors (6)

Author, Maintainer

Author

Author

Author

Author

Author

Listed in earlier versions (1)

Melinda

no longer listed · 3.0-2 to 3.3-7

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
3.3-7Latest
2025-08-29 · current release · diff ↗
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
2022-08-11 · diff ↗
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
3.0-11
2021-02-24 · diff ↗
3.0-9
2020-10-29 · diff ↗
R
R 4.0.0 released · 2020-04-24
3.0-6
2020-03-19 · diff ↗
3.0-4
2019-12-16 · diff ↗
3.0-2
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
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Analysis of Ecological and Environmental Data

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