CHMM

0.1.1

Coupled Hidden Markov Models

0packages depend

2.5Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Julie AubertFirst published 2017-04-192 releasesCRAN page ↗GitHub ↗

An exact and a variational inference for coupled Hidden Markov Models applied to the joint detection of copy number variations.

Install

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

install.packages("CHMM", 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("julieaubert/CHMM")

Development version from julieaubert/CHMM. 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-chmm

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-CHMM

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-CHMM

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

Health

CRAN checks

13OK

Slowest check: 1.2 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

None

Vignettes

README

Dependencies · direct

Check history

OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Downloads

2.5K

CRAN downloads in the past year

Rank #17,427 · ~7/day · ~206/mo

Releases R versions

Daily download trend is not available in this view yet.

27530 days

66590 days

2.5K1 year

Compare downloads with other packages →

Also on401 r2u17 autocran

Repository

GitHub ↗ julieaubert/chmm

7Stars

4Forks

0Open issues

0Open PRs

0Releases

10Commits

10 commits · +16.7% stars, 30d

Stars over time

2024-09-20 · 62026-07-07 · 7

Dependencies

Declared dependencies

1 external dependency (excludes base and recommended)

Depends (1)

R >= 3.1.0

Imports (1)

mclust

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Code Composition

R 841 (51%)Rd 443 (27%)C 367 (22%)

Code characteristics

Cyclomatic complexity: 2.5 median / 27 max
Documented parameters: 100%

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

29 11 exported

Complexity

5.2 avg / 27 max

Call network

29 nodes / 33 edges

Test coverage has not been measured for this package yet; nodes fall back to a neutral fill.

Call graph

Open call graph →

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Lowest coverage

Per-function coverage is not measured for this package yet.

People & History

People (2)

Maintainer (1)

Julie Aubert

Author, Maintainer

Authors (2)

Julie Aubert

Author, Maintainer

Xiaoqiang Wang

Author

Release timeline

2 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
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
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
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
0.1.1Latest
2017-09-29 · current release · diff ↗
R
R 3.4.0 released · 2017-04-21
0.1.0
2017-04-19
R
R 3.3.0 released · 2016-05-03

Package metadata

First published: 2017-04-19
Total releases: 2 / 9 yrs
License: GPL-2 OSI
Minimum R: ≥ 3.1.0
Bundled data: 38 KB / 1 file
Download size: 52 KB
Installed size: not tracked yet
With dependencies: not tracked yet