Hmsc: Hierarchical Model of Species Communities

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>).

Version:	3.3-7
Depends:	R (≥ 3.0.2), coda
Imports:	abind, ape, BayesLogit, fields, FNN, ggplot2, MASS, Matrix, matrixStats, MCMCpack, methods, nnet, rlang, parallel, pracma, pROC, sp, statmod, truncnorm
Suggests:	R.rsp, testthat, corrplot
Published:	2025-08-28
DOI:	10.32614/CRAN.package.Hmsc
Author:	Gleb Tikhonov [aut], Otso Ovaskainen [aut, cre], Jari Oksanen [aut], Melinda de Jonge [aut], Oystein Opedal [aut], Tad Dallas [aut]
Maintainer:	Otso Ovaskainen <otso.t.ovaskainen at jyu.fi>
BugReports:	https://github.com/hmsc-r/HMSC/issues/
License:	GPL-3 | file LICENSE
URL:	https://www.helsinki.fi/en/researchgroups/statistical-ecology/software/hmsc
NeedsCompilation:	no
Materials:	README, NEWS
In views:	Environmetrics
CRAN checks:	Hmsc results

Documentation:

Reference manual:	Hmsc.html , Hmsc.pdf
Vignettes:	Getting started with HMSC-R: univariate models (source) Getting started with HMSC-R: low-dimensional multivariate models (source) Getting started with HMSC-R: high-dimensional multivariate models (source) Getting started with HMSC-R: spatial models (source) Testing the performance of Hmsc with simulated data (source)

Downloads:

Package source:	Hmsc_3.3-7.tar.gz
Windows binaries:	r-devel: Hmsc_3.3-7.zip, r-release: Hmsc_3.3-7.zip, r-oldrel: Hmsc_3.3-7.zip
macOS binaries:	r-release (arm64): Hmsc_3.3-7.tgz, r-oldrel (arm64): Hmsc_3.3-7.tgz, r-release (x86_64): Hmsc_3.3-7.tgz, r-oldrel (x86_64): Hmsc_3.3-7.tgz
Old sources:	Hmsc archive

Reverse dependencies:

Reverse suggests:

cotram, jSDM

Linking:

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