R Observatory: Metrics for hhsmm version 0.4.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

hhsmm

0.4.2

Hidden Hybrid Markov/Semi-Markov Model Fitting

0packages depend

3.3Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Morteza AminiFirst published 2021-05-3119 releasesCRAN page ↗GitHub ↗

Develops algorithms for fitting, prediction, simulation and initialization of the following models (1)- hidden hybrid Markov/semi-Markov model, introduced by Guedon (2005) doi:10.1016/j.csda.2004.05.033, (2)- nonparametric mixture of B-splines emissions (Langrock et al., 2015 doi:10.1111/biom.12282), (3)- regime switching regression model (Kim et al., 2008 doi:10.1016/j.jeconom.2007.10.002) and auto-regressive hidden hybrid Markov/semi-Markov model, (4)- spline-based nonparametric estimation of additive state-switching models (Langrock et al., 2018 doi:10.1111/stan.12133) (5)- robust emission model proposed by Qin et al, 2024 doi:10.1007/s10479-024-05989-4 (6)- several emission distributions, including mixture of multivariate normal (which can also handle missing data using EM algorithm) and multi-nomial emission (for modeling polymer or DNA sequences) (7)- tools for prediction of future state sequence, computing the score of a new sequence, splitting the samples and sequences to train and test sets, computing the information measures of the models, computing the residual useful lifetime (reliability) and many other useful tools ... (read for more description: Amini et al., 2022 doi:10.1007/s00180-022-01248-x and its arxiv version: doi:10.48550/arXiv.2109.12489).

Install

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

install.packages("hhsmm", 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("mortamini/hhsmm")

Development version from mortamini/hhsmm. 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-hhsmm

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

# 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-hhsmm

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-hhsmm

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

Health

CRAN checks

13OK

Slowest check: 4.4 min · r-devel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

9

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-02
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 2 earlier snapshots

ERROR2026-04-25
11 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 97%
Documented parameters: 92%
Return-value docs: 100%
References docs: 32%

Downloads

3.3K

CRAN downloads in the past year

Rank #11,253 · ~9/day · ~278/mo

Releases R versions

Daily download trend is not available in this view yet.

16930 days

87290 days

3.3K1 year

Compare downloads with other packages →

Also on392 r2u15 autocran22 c2d4u

Repository

GitHub ↗ mortamini/hhsmm

3Stars

1Forks

0Open issues

0Open PRs

0Releases

5Commits

1Contributors

License GPL-3.0 · 5 commits · Last activity 2022-08-27

Stars over time

2025-01-09 · 32026-07-07 · 3

Repository practices

Upstream repositoryBeta

Checks run against github.com/mortamini/hhsmm on 2026-08-16.

No development-tooling practices detected in the upstream repository.

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

Dependencies

Declared dependencies

10 external dependencies (excludes base and recommended)

Depends (3)

R >= 4.3.0CMAPSS mvtnorm

Imports (7)

Rcpp RdpackMASSmice progress magic splines2

LinkingTo (1)

Rcpp

Suggests (1)

testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (3)

Maintainer (1)

Morteza Amini

Author, Maintainer, Copyright holder

Authors (3)

Morteza Amini

Author, Maintainer, Copyright holder

Afarin Bayat

Author

Reza Salehian

Author · added in 0.2.4

Copyright holders (1)

Morteza Amini

Author, Maintainer, Copyright holder

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
0.4.2Latest
2024-09-04 · current release · diff ↗
0.4.1
2024-09-03 · diff ↗
0.4.0
2024-05-08 · diff ↗
0.3.7
2024-05-01 · diff ↗
R
R 4.4.0 released · 2024-04-24
0.3.6
2023-08-08 · diff ↗
R
R 4.3.0 released · 2023-04-21
0.3.5
2023-03-06 · diff ↗
0.3.4
2023-01-07 · diff ↗
0.3.3
2022-08-05 · diff ↗
0.3.2
2022-05-29 · diff ↗
R
R 4.2.0 released · 2022-04-22
0.3.1
2022-02-28 · diff ↗
0.2.5
2022-02-08 · diff ↗

Show 11 earlier events

0.2.4
2022-01-10 · diff ↗
0.2.3
2021-12-01 · diff ↗
0.2.2
2021-11-23 · diff ↗
0.2.1
2021-10-18 · diff ↗
0.2.0
2021-10-13 · diff ↗
0.1.3
2021-09-13 · diff ↗
0.1.2
2021-06-16 · diff ↗
unarchivedReturned to CRAN
2021-06-16
archivedRemoved from CRAN
2021-06-14
check problems were not corrected in time
0.1
2021-05-31
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2021-05-31
Total releases: 19 / 5 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.3.0
Download size: 66 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Missing Data

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("hhsmm")

Format

Amini, M., Bayat, A., & Salehian, R. (2024). hhsmm: Hidden Hybrid Markov/Semi-Markov Model Fitting (Version 0.4.2) [Computer software]. https://doi.org/10.32614/CRAN.package.hhsmm

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 hhsmm version 0.4.2 [Data set]. HJJB, LLC. Data release v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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