R Observatory: Metrics for seqHMM version 2.2.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

seqHMM

2.2.0Package record

Mixture Hidden Markov Models for Social Sequence Data and Other Multivariate, Multichannel Categorical Time Series

1packages dependsuggested by 4

8Kdownloads / year

60.5%test coverage

13/13flavors OK

Overview

About

Maintained by Jouni HelskeCRAN page ↗GitHub ↗Issues ↗

Designed for estimating variants of hidden (latent) Markov models (HMMs), mixture HMMs, and non-homogeneous HMMs (NHMMs) for social sequence data and other categorical time series. Special cases include feedback-augmented NHMMs, Markov models without latent layer, mixture Markov models, and latent class models. The package supports models for one or multiple subjects with one or multiple parallel sequences (channels). External covariates can be added to explain cluster membership in mixture models as well as initial, transition and emission probabilities in NHMMs. The package provides functions for evaluating and comparing models, as well as functions for visualizing of multichannel sequence data and HMMs. For NHMMs, methods for computing average causal effects and marginal state and emission probabilities are available. Models are estimated using maximum likelihood via the EM algorithm or direct numerical maximization with analytical gradients. Documentation is available via several vignettes, and Helske and Helske (2019, doi:10.18637/jss.v088.i03). For methodology behind the NHMMs, see Helske (2025, doi:10.48550/arXiv.2503.16014).

Changes in 2.2.0

EM algorithm for NHMMs now supports SQUAREM acceleration

(Varadhan and Roland, 2008).

Exposed argument save_all_solutions in estimate_nhmm and

estimate_mnhmm for saving solutions from all restarts.

Changed the options of the plots argument options of

stacked_sequence_plot to observations and hidden states.

Added an argument ids for get_*_probs functions.
estimate_nhmm and estimate_mnhmm now set init_sd=0 if restart=0 and

user has provided initial values.

Added default values for id and time for stslist_to_data.
Fixed the forward weighting in get_marginals.
Improved the performance of posterior_probs.

Show all changes in 2.2.0Hide the rest of the changes in 2.2.0

Improved the performance of summary_mnhmm and computation of posterior

cluster probabilities in general.

Improved the performance of creating the design matrices in model building.
Fixed a bug in coef.mnhmm which resulted an error on extracting

confidence intervals for emission probabilities.

Fixed mnhmm example in estimate_mnhmm documentation.
Fixed a memory leak in the M-step of initial probabilities of NHMMs.

From NEWS.md in the release

Install

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

install.packages("seqHMM", 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("helske/seqHMM")

Development version from helske/seqHMM. 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-seqhmm

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-seqHMM

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-seqHMM

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: 26.4 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK13 OK2026-05-02

Show 4 earlier changesHide 4 earlier changes

ERROR11 OK, 1 ERROR2026-04-25
NOTE12 OK, 2 NOTE2026-04-22
ERROR11 OK, 2 NOTE, 1 ERROR2026-04-18
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.2.0

READMEYes · 264 wordsVignettesYes · 4 · dynamicNEWSYes · 33% structured · mentions 2.2.0Citation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Cites a JSS article

Help pages: 65 (1 internal)includes a package overview page
Examples that run: 100%30 run in a plain check
Exported functions with examples: 49%
Documented parameters: 99%
Return-value docs: 63%
Help pages citing references: 12%

Vignettes (4)

How these are measured

Downloads

8K

CRAN downloads in the past year

Rank #4,518 · ~22/day · ~663/mo

Releases R versions

Daily download trend is not available in this view yet.

63130 days

1.9K90 days

8K1 year

Compare downloads with other packages →

Also on443 r2u2 autocran

How downloads are counted

Repository

helske/seqhmm ↗Account: helske

106Stars

31Forks

11Open issues

0Open PRs

4Releases

1,213Commits

15Commit identities

hidden-markov-modelsmixture-markov-modelsem-algorithmhmmrcategorical-datatime-series

1,213 commits · Last activity 2026-10-23 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 94
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-05-24 · 1002026-08-14 · 106

How these are measured

PracticesBeta

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

Checks run against github.com/helske/seqhmm on 2026-10-21.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Coverage (2)

Coverage reporting (Codecov).covrignore

Reproducibility and dev environment (1)

data-raw/

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

Dependencies

Declared dependencies

24 external dependencies (excludes base and recommended)

Installing seqHMM adds 84 packages (46 with compiled code, 66 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

Depends (1)

R >= 4.1.0

Imports (25)

checkmate cli collapse data.table future.apply ggplot2 ggseqplotgraphicsgrDevicesgridgridBase igraph lhsMatrixmethodsnloptr numDeriv patchwork progressr Rcpp RcppHungarian rlangstatsTraMineRutils

LinkingTo (3)

nloptr Rcpp RcppArmadillo

Suggests (5)

covr knitrMASSnnettestthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

Imports 1

Suggested by 4

Depends, Imports or LinkingTo, most downloaded first

DBHC

Suggests, most downloaded first

tna eyeprocess clickb gp3sequences

How these are counted

Code & Tests

Datasets

People & History

People (2)

Jouni Helske

Author, Maintainer since 1.0.2-1 (2015)

Satu Helske

Author

Releases (27)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
2.2.0Latest
record
2026-03-16 · current release · diff ↗
2.1.0
record
2025-09-25 · diff ↗ ·
added 1 export
permute_states
2.0.0
record
2025-05-17 · diff ↗ ·
removed 4 exports
estimate_coef, fit_hmm, fit_mhmm, trim_hmm

added 16 exports
bootstrap_coefs, data_to_stslist, estimate_mnhmm, estimate_nhmm, get_cluster_probs, get_emission_probs, get_initial_probs, get_marginals, get_transition_probs, most_probable_cluster, posterior_cluster_probabilities, simulate_mnhmm, simulate_nhmm, sort_sequences, stacked_sequence_plot, stslist_to_data
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.2.6
record
2023-07-06 · diff ↗
1.2.5
record
2023-06-12 · diff ↗ ·
added 4 exports
cluster_names<-, state_names<-, cluster_names, state_names
R
R 4.3.0 released · 2023-04-21
1.2.4
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2023-01-09 · diff ↗
1.2.3
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2022-12-12 · diff ↗
1.2.2
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2022-11-30 · diff ↗
1.2.1-1
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2022-05-25 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.2.0
record
2021-10-18 · diff ↗
1.1.1
record
2021-08-13 · diff ↗

Show 23 earlier eventsHide 23 earlier events

1.1.0
record
2021-06-18 · diff ↗
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
1.0.14
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2019-10-22 · diff ↗
1.0.13
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2019-06-17 · diff ↗
R
R 3.6.0 released · 2019-04-26
1.0.12
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2019-04-11 · diff ↗
1.0.11
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2019-04-09 · diff ↗
1.0.10
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2019-01-26 · diff ↗
1.0.9
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2018-11-06 · diff ↗
1.0.8-1
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2018-05-10 · diff ↗
R
R 3.5.0 released · 2018-04-23
1.0.8
record
2017-11-08 · diff ↗
R
R 3.4.0 released · 2017-04-21
1.0.7
record
2017-04-04 · diff ↗
1.0.6
record
2016-08-01 · diff ↗ ·
added 1 export
estimate_coef
R
R 3.3.0 released · 2016-05-03
1.0.5
record
2016-02-24 · diff ↗
1.0.4
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2016-01-14 · diff ↗
1.0.3-1
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2015-12-30 · diff ↗
1.0.3
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2015-12-23 · diff ↗
1.0.2-1
record
2015-12-19
R
R 3.2.0 released · 2015-04-16

Package metadata

First published: 2015-12-19
Total releases: 27 / 11 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 4.1.0
Bundled data: 408 KB / 8 files
Download size: 1.4 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("seqHMM")

The package provides a citation file that builds its entry when R runs it. Run citation() to see it.

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 seqHMM version 2.2.0 [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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