R Observatory: Metrics for hmmTMB version 1.1.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

hmmTMB

1.1.2Package record

Fit Hidden Markov Models using Template Model Builder

0packages depend

4.6Kdownloads / year

41.0%test coverage

12/13flavors OK

Overview

About

Maintained by Theo MichelotCRAN 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.

Changes in 1.1.2

Add hurdle negative binomial distribution
Fix bug in HMM$fit_stan()
Fix bug in HMM$pseudores()

From NEWS.md in the release

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)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. 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-hmmTMB

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-hmmTMB

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

1ERROR12OK

Check messages

ERRORwhether package can be installedr-release-macos-x86_64

Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.6/hmmTMB.Rcheck/00install.out’ for details.

CRAN check page ↗

Slowest check: 10.1 min · r-oldrel-macos-x86_64

Status changes

ERROR12 OK, 1 ERRORNow
ERROR11 OK, 1 ERROR2026-04-25
NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1.2

READMEYes · 546 wordsVignettesYes · 1 · staticNEWSYes · 100% structured · mentions 1.1.2Citation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Cites a JSS article

Help pages: 32 (1 internal)includes a package overview page
Examples that run: 100%5 run in a plain check
Exported functions with examples: 27%
Documented parameters: 100%
Return-value docs: 33%
Help pages citing references: 0%

Vignettes (1)

Online resources for hmmTMB

How these are measured

Downloads

4.6K

CRAN downloads in the past year

Rank #6,854 · ~13/day · ~385/mo

Releases R versions

Daily download trend is not available in this view yet.

38630 days

1.3K90 days

4.6K1 year

Compare downloads with other packages →

Also on385 r2u4 autocran

How downloads are counted

Repository

theomichelot/hmmtmb ↗Account: TheoMichelot

68Stars

14Forks

3Open issues

0Open PRs

0Releases

871Commits

9Commit identities

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

871 commits · Last activity 2026-10-21 · Discussions: 14 posts

Responsiveness

How these are sampled

PRs merged (all time): 82%
Median days to close, 50 most recently updated closed issues: 4
Median days to close, 50 most recently updated closed PRs: 1

Forks over time

2026-07-14 · 122026-10-12 · 14

How these are measured

PracticesBeta

Checks run against github.com/theomichelot/hmmtmb on 2026-10-21.

No development-tooling practices detected in the upstream repository.

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

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Installing hmmTMB adds 51 packages (25 with compiled code, 55 MB of source tarballs). Heaviest: BH 14 MB, stringi 11 MB, ggplot2 6.0 MB.

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.

How these are counted

Code & Tests

People & History

People (2)

Theo Michelot

Author, Maintainer since 1.0.0 (2023)

Richard Glennie

Author, Contributor

Releases (6)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.1.2Latest
record
2025-11-05 · current release · diff ↗
1.1.1
record
2025-09-11 · diff ↗
1.1.0
record
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
record
2023-10-24 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.0.1
record
2023-01-13 · diff ↗
1.0.0
record
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

Cite

Cite this package

Run in R for the authors' entry:

citation("hmmTMB")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.18637/jss.v114.i05.

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 hmmTMB version 1.1.2 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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