R Observatory: Metrics for DBHC version 0.0.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

DBHC

0.0.4Package record

Sequence Clustering with Discrete-Output HMMs

0packages depend

2.4Kdownloads / year

24.4%test coverage

13/13flavors OK

Overview

About

Maintained by Gabriel BudelCRAN page ↗GitHub ↗Issues ↗

Provides an implementation of a mixture of hidden Markov models (HMMs) for discrete sequence data in the Discrete Bayesian HMM Clustering (DBHC) algorithm. The DBHC algorithm is an HMM Clustering algorithm that finds a mixture of discrete-output HMMs while using heuristics based on Bayesian Information Criterion (BIC) to search for the optimal number of HMM states and the optimal number of clusters.

Changes in 0.0.4

Bug fixes

cluster.bic() passes its eps argument on to count.parameters(), it always used the default threshold before
hmm.clust() passes its smoothing argument on to assign.clusters(), cluster assignment always smoothed with the default before
smooth.probabilities() returns a uniform distribution for a set of probabilities that are all zero, which used to stay zero and is then rejected by build_hmm()
smooth.probabilities() no longer returns negative probabilities. Absolute discounting assumes the smoothing parameter is smaller than the smallest non-zero probability, and the amount discounted is now lowered to respect that. A probability below the parameter used to be discounted to a negative value, which survived because the row still sums to one, and grew more negative every time the model was smoothed again. Estimates for data with sparse emissions change, see below

Show all changes in 0.0.4Hide the rest of the changes in 0.0.4

select.seeds() stops with a message when too few sequences are left to fill a seed, it used to select NA ids
Loops over sequences and cluster models use seq_along(), they could run an iteration on an empty set

Changes

Sequences are evaluated against a cluster model all at once in assign.clusters() and select.seeds() instead of one at a time, which makes the algorithm about five times faster on 1000 sequences and leaves all results unchanged
hmm.clust() has an argument max.iter and size.search() has an argument max.states to bound the search for cluster memberships and hidden states
An infeasible HMM raises a warning instead of printing one
The smaller Swiss Household example is fast enough to run on test again
Both Swiss Household examples are wrapped in \donttest instead of \dontrun, they are slow rather than impossible to run
Results for data with sparse emission probabilities change slightly because of the fix to smooth.probabilities() above. On the simulation study of the accompanying paper nothing changes but the BIC, by 0.0001 percent. On the full Swiss Household data the cluster models and a small number of cluster memberships change, the number of clusters and their sizes do not

Maintenance

Replaced Author and Maintainer with Authors@R
Dropped LazyData, the package has no data directory
Requires seqHMM (>= 2.0.0), the version this release is tested against
Heatmaps refer to their data with the .data pronoun, which silences the deprecation warnings from ggplot2

From NEWS.md in the release

Install

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

install.packages("DBHC", 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("gabybudel/DBHC")

Development version from gabybudel/DBHC. 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-dbhc

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-DBHC

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-DBHC

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: 3.4 min · r-release-macos-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-07-29
NOTE11 OK, 2 NOTE2026-06-09
ERROR11 OK, 1 NOTE, 1 ERROR2026-06-08

Show 1 earlier changeHide 1 earlier change

NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.0.4

READMEYes · 123 wordsVignettesNoNEWSYes · 100% structured · mentions 0.0.4Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 13
Examples that run: 100%1 run in a plain check
Exported functions with examples: 8%
Documented parameters: 100%
Return-value docs: 85%
Help pages citing references: 0%

How these are measured

Downloads

2.4K

CRAN downloads in the past year

Rank #16,231 · ~7/day · ~201/mo

Releases R versions

Daily download trend is not available in this view yet.

25230 days

77590 days

2.4K1 year

Compare downloads with other packages →

Also on82 r2u4 autocran

How downloads are counted

Repository

gabybudel/dbhc ↗Account: gabybudel

1Stars

1Forks

1Open issues

0Open PRs

0Releases

51Commits

1Commit identities

51 commits · Last activity 2026-08-07 · Default branch at 0.0.5, ahead of CRAN 0.0.4 (checked 2026-10-21)

Responsiveness

not measured

Forks over time

2021-10-22 · 12026-07-07 · 1

How these are measured

PracticesBeta

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

Checks run against github.com/gabybudel/dbhc on 2026-10-21.

Continuous integration (1)

Travis CI (config file)

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Installing DBHC adds 87 packages (49 with compiled code, 67 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

Depends (0)

none

Imports (6)

seqHMM TraMineR reshape2 ggplot2 rlangmethods

LinkingTo (0)

none

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 (2)

Gabriel Budel

Author, Maintainer since 0.0.2 (2018)

Flavius Frasincar

Author

Releases (3)

Pick two releases to compare their code metrics.

0.0.4Latest
record
2026-07-24 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
unarchivedReturned to CRAN
2022-12-22
0.0.3
record
2022-12-22 · diff ↗
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
archivedRemoved from CRAN
2020-04-03
check problems were not corrected in time Errors in '\donttest' parts of examples
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
0.0.2
record
2018-04-13
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2018-04-13
Total releases: 3 / 8 yrs
License: GPL (>= 3) OSI
Download size: 19 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("DBHC")

Format

Budel, G., & Frasincar, F. (2026). DBHC: Sequence Clustering with Discrete-Output HMMs (Version 0.0.4) [Computer software]. https://doi.org/10.32614/CRAN.package.DBHC

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 DBHC version 0.0.4 [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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