R Observatory: Metrics for hhsmm version 0.4.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

hhsmm

0.4.2Package record

Hidden Hybrid Markov/Semi-Markov Model Fitting

0packages depend

3.7Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Morteza AminiCRAN page ↗GitHub ↗Issues ↗

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. 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-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). 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: 4.0 min · r-devel-windows-x86_64

Status changes

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

Show 2 earlier changesHide 2 earlier changes

ERROR11 OK, 1 ERROR2026-04-25
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.4.2

READMENoVignettesNoNEWSNoCitation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 38
Examples that run: 97%35 run in a plain check · 1 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 94%
Documented parameters: 92%
Return-value docs: 100%
Help pages citing references: 32% with Rdpack citation macros

How these are measured

Downloads

3.7K

CRAN downloads in the past year

Rank #8,567 · ~10/day · ~309/mo

Releases R versions

Daily download trend is not available in this view yet.

42330 days

1.1K90 days

3.7K1 year

Compare downloads with other packages →

Also on363 r2u5 autocran47 c2d4u

How downloads are counted

Repository

mortamini/hhsmm ↗Account: mortamini

3Stars

1Forks

0Open issues

0Open PRs

0Releases

5Commits

1Commit identities

License file reads as GPL-3.0 · 5 commits · Last activity 2022-08-27 · The default branch showed an older version (0.2.5) than CRAN on 2026-10-21

Responsiveness

How these are sampled

PRs merged (all time): not measured
Median days to close, 50 most recently updated closed issues: 15
Median days to close, 50 most recently updated closed PRs: not measured

Stars over time

2025-01-09 · 32026-07-07 · 3

How these are measured

PracticesBeta

Checks run against github.com/mortamini/hhsmm 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

10 external dependencies (excludes base and recommended)

Installing hhsmm adds 59 packages (35 with compiled code, 48 MB of source tarballs). Heaviest: stringi 11 MB, CMAPSS 5.1 MB, lme4 4.3 MB.

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.

How these are counted

Code & Tests

People & History

People (3)

Morteza Amini

Afarin Bayat

Author

Reza Salehian

Author · added in 0.2.4

Releases (19)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
0.4.2Latest
record
2024-09-04 · current release · diff ↗
0.4.1
record
2024-09-03 · diff ↗
0.4.0
record
2024-05-08 · diff ↗ ·
added 2 exports
drobust, robust_mstep
0.3.7
record
2024-05-01 · diff ↗
R
R 4.4.0 released · 2024-04-24
0.3.6
record
2023-08-08 · diff ↗
R
R 4.3.0 released · 2023-04-21
0.3.5
record
2023-03-06 · diff ↗ ·
added 3 exports
dmultinomial.hhsmm, mstep.multinomial, rmultinomial.hhsmm
0.3.4
record
2023-01-07 · diff ↗
0.3.3
record
2022-08-05 · diff ↗
0.3.2
record
2022-05-29 · diff ↗ ·
added 1 export
addreg_hhsmm_predict
R
R 4.2.0 released · 2022-04-22
0.3.1
record
2022-02-28 · diff ↗ ·
added 3 exports
additive_reg_mstep, dnorm_additive_reg, raddreg
0.2.5
record
2022-02-08 · diff ↗

Show 11 earlier eventsHide 11 earlier events

0.2.4
record
2022-01-10 · diff ↗ ·
added 3 exports
dnonpar, nonpar_mstep, score
0.2.3
record
2021-12-01 · diff ↗ ·
added 2 exports
lagdata, rmixar
0.2.2
record
2021-11-23 · diff ↗ ·
added 4 exports
dmixlm, ltr_reg_clus, mixlm_mstep, rmixlm
0.2.1
record
2021-10-18 · diff ↗
0.2.0
record
2021-10-13 · diff ↗ ·
added 2 exports
cov.miss.mix.wt, miss_mixmvnorm_mstep
0.1.3
record
2021-09-13 · diff ↗ ·
removed 19 exports
.add.states, .build_d, .check.hhsmmspec, .dlog, .dnbinom.hhsmm, .dpois.hhsmm, .gammafit, .ginv, .lnormfit, .logdistrfit, .ltr_clus2, .nbinomfit, .plog, .progress, .rlog, .rnbinom.hhsmm, .rpois.hhsmm, .simulate_markov, .weibullfit

added 1 export
mixdiagmvnorm_mstep
unarchivedReturned to CRAN
2021-06-16
0.1.2
record
2021-06-16 · diff ↗
archivedRemoved from CRAN
2021-06-14
check problems were not corrected in time
0.1
record
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

Appears in task views

Missing Data

Cite

Cite this package

Run in R for the authors' entry:

citation("hhsmm")

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

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 v2026-10-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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