R Observatory: Metrics for mHMMbayes version 1.1.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

mHMMbayes

1.1.1Package record

Multilevel Hidden Markov Models Using Bayesian Estimation

0packages depend

3.1Kdownloads / year

70.5%test coverage

13/13flavors OK

Overview

About

Maintained by Emmeke AartsCRAN page ↗GitHub ↗Issues ↗

An implementation of the multilevel (also known as mixed or random effects) hidden Markov model using Bayesian estimation in R. The multilevel hidden Markov model (HMM) is a generalization of the well-known hidden Markov model, for the latter see Rabiner (1989) doi:10.1109/5.18626. The multilevel HMM is tailored to accommodate (intense) longitudinal data of multiple individuals simultaneously, see e.g., de Haan-Rietdijk et al. doi:10.1080/00273171.2017.1370364. Using a multilevel framework, we allow for heterogeneity in the model parameters (transition probability matrix and conditional distribution), while estimating one overall HMM. The model can be fitted on multivariate data with either a categorical, normal, or Poisson distribution, and include individual level covariates (allowing for e.g., group comparisons on model parameters). Parameters are estimated using Bayesian estimation utilizing the forward-backward recursion within a hybrid Metropolis within Gibbs sampler. Missing data (NA) in the dependent variables is accommodated assuming MAR. The package also includes various visualization options, a function to simulate data, and a function to obtain the most likely hidden state sequence for each individual using the Viterbi algorithm.

Changes in 1.1.1

Accomodating the possibility of fitting a 1-state mHMM

This version includes the possibility of running (and simulating data from) a 1-state multilevel hidden Markov model. This is mainly convenient for benchmarking purposes for model selection (e.g., how much does the AIC / AICc decrease from a 1-state to a 2-state model). To accommodate this change the following main functions are updated: mHMM() and sim_mHMM(). The following S3 methods were updated: print(), summary(), and plot(). In addition, the following post processing functions were updated: obtain_emiss(), obtain_gamma(), and vit_mHMM().

Other minor changes:

The estimation vignette is changed from a pdf output file to a html output file due to recurrent issues with GHA workflow and rendering pdf vignettes.

From NEWS.md in the release

Install

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

install.packages("mHMMbayes", 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("emmekeaarts/mHMMbayes")

Development version from emmekeaarts/mHMMbayes. 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-mhmmbayes

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-mHMMbayes

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-mHMMbayes

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

13OK

CRAN check page ↗

Slowest check: 4.6 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-04-22
ERROR13 OK, 1 ERROR2026-04-18
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1.1

READMEYes · 312 wordsVignettesYes · 2 · dynamicNEWSYes · 100% structured · mentions 1.1.1Citation fileNo

Help pages: 20 (1 internal)includes a package overview page
Examples that run: 71%12 run in a plain check · 5 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 25% with a bibliography file

Vignettes (2)

How these are measured

Downloads

3.1K

CRAN downloads in the past year

Rank #11,536 · ~9/day · ~261/mo

Releases R versions

Daily download trend is not available in this view yet.

33930 days

94090 days

3.1K1 year

Compare downloads with other packages →

Also on346 r2u6 autocran

How downloads are counted

Repository

emmekeaarts/mhmmbayes ↗Account: emmekeaarts

26Stars

12Forks

6Open issues

3Open PRs

4Releases

489Commits

3Commit identities

489 commits · Last activity 2026-04-17 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 55%
Median days to close, 50 most recently updated closed issues: 324
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-07-30 · 212026-07-07 · 26

How these are measured

PracticesBeta

9 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/emmekeaarts/mhmmbayes on 2026-10-22.

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 2026-04-17

Reproducibility and dev environment (1)

data-raw/

CRAN release process (3)

cran-comments.mdrevdep/CRAN-SUBMISSION

Show all practicesHide 1 practice

Lint, format, editor (1)

RStudio project

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

AI coding toolsBeta

An outside contributor's pull request to this repository was written with an AI coding tool.

From outside contributors

Claude Code
Pull requests: 1 from outside contributors, first on 2025-09-27, 1 from forks

How this is detected·Detection ruleset v4 (updated 2026-09-27)

Dependencies

Declared dependencies

10 external dependencies (excludes base and recommended)

Installing mHMMbayes adds 10 packages (7 with compiled code, 8.0 MB of source tarballs). Heaviest: Rcpp 1.8 MB, mcmc 1.5 MB, rbibutils 1.1 MB.

Depends (1)

R >= 3.6.0

Imports (5)

MCMCpack mvtnormstatsRdpack Rcpp

LinkingTo (1)

Rcpp

Suggests (6)

knitr rmarkdown alluvialgrDevicesRColorBrewer testthat

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 (2)

Emmeke Aarts

Author, Maintainer since 0.1.0 (2019)

Sebastian Mildiner Moraga

Author · added in 0.2.0

Releases (6)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.1.1Latest
record
2025-07-11 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.1.0
record
2024-04-01 · diff ↗ ·
added 3 exports
pd_RW_emiss_count, prior_emiss_count, var_to_logvar
1.0.0
record
2023-10-02 · diff ↗ ·
added 1 export
prior_emiss_cont
R
R 4.3.0 released · 2023-04-21
0.2.0
record
2022-08-17 · diff ↗ ·
added 6 exports
int_to_prob, pd_RW_emiss_cat, pd_RW_gamma, prior_emiss_cat, prior_gamma, prob_to_int
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
0.1.1
record
2019-10-30 · diff ↗
0.1.0
record
2019-10-25
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2019-10-25
Total releases: 6 / 7 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.6.0
Bundled data: 4.0 KB / 2 files
Download size: 2.5 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("mHMMbayes")

Format

Aarts, E., & Mildiner Moraga, S. (2025). mHMMbayes: Multilevel Hidden Markov Models Using Bayesian Estimation (Version 1.1.1) [Computer software]. https://doi.org/10.32614/CRAN.package.mHMMbayes

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 mHMMbayes version 1.1.1 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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