hmmTMB

1.1.2

Fit Hidden Markov Models using Template Model Builder

0packages depend

5.2Kdownloads / year

41.0%test coverage

12/13checks pass

Overview

About

Maintained by Theo MichelotFirst published 2023-01-116 releasesCRAN page ↗GitHub ↗

Fitting hidden Markov models using automatic differentiation and Laplace approximation, allowing for fast inference and flexible covariate effects (including random effects and smoothing splines) on model parameters. The package is described by Michelot (2025) doi:10.18637/jss.v114.i05.

Install

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

install.packages("hmmTMB", 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("TheoMichelot/hmmTMB")

Development version from TheoMichelot/hmmTMB. 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-hmmtmb

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

# 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-hmmTMB

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

1ERROR12OK

Failing flavors

ERROR r-release-macos-x86_64

Slowest check: 10.2 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.09

41.0%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

ERROR2026-04-25
11 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 546 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 33%
References docs: 0%

Downloads

5.2K

CRAN downloads in the past year

Rank #10,180 · ~14/day · ~429/mo

Releases R versions

Daily download trend is not available in this view yet.

43230 days

1K90 days

5.2K1 year

Compare downloads with other packages →

Also on437 r2u36 autocran

Repository

GitHub ↗ theomichelot/hmmtmb

68Stars

12Forks

3Open issues

0Open PRs

0Releases

833Commits

7Contributors

hidden-markov-modelhmmmixed-effects-modelsr-packagerandom-effectssmoothing-splinestime-series-analysis

833 commits · Last activity 2026-04-13

Repository practices

Upstream repositoryBeta

Checks run against github.com/theomichelot/hmmtmb on 2026-07-19.

No development-tooling practices detected in the upstream repository.

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

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Depends (4)

R6mgcvTMB ggplot2

Imports (5)

MatrixstringrMASStmbstanmethods

LinkingTo (2)

TMB RcppEigen

Suggests (8)

rstan testthat knitr rmarkdown moveHMM scico MSwM unmarked

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (2)

Maintainer (1)

Theo Michelot

Author, Maintainer

Authors (2)

Theo Michelot

Author, Maintainer

Richard Glennie

Author, Contributor

Contributors (1)

Richard Glennie

Author, Contributor

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
1.1.2Latest
2025-11-05 · current release · diff ↗
1.1.1
2025-09-11 · diff ↗
1.1.0
2025-06-24 · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.0.2
2023-10-24 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.0.1
2023-01-13 · diff ↗
1.0.0
2023-01-11
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2023-01-11
Total releases: 6 / 3 yrs
License: GPL-3 OSI
Download size: 230 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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