R Observatory: Metrics for PLNmodels version 1.3.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

PLNmodels

1.3.0

Poisson Lognormal Models

0packages depend

6.5Kdownloads / year

84.4%test coverage

13/13checks pass

Overview

About

Maintained by Julien ChiquetFirst published 2019-05-1720 releasesCRAN page ↗GitHub ↗

The Poisson-lognormal model and variants (Chiquet, Mariadassou and Robin, 2021 doi:10.3389/fevo.2021.588292) can be used for a variety of multivariate problems when count data are at play, including principal component analysis for count data, discriminant analysis, model-based clustering and network inference. Implements variational algorithms to fit such models accompanied with a set of functions for visualization and diagnostic.

Install

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

install.packages("PLNmodels", 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("pln-team/PLNmodels")

Development version from pln-team/PLNmodels. 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-plnmodels

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

# 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-PLNmodels

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

Health

CRAN checks

13OK

Slowest check: 18.2 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.35

84.4%

Coverage · measured lines

96%

Documentation · exports

22

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-02
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
WARNING2026-07-07
11 OK · 0 NOTE · 2 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

Show 4 earlier snapshots

OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-22
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
10 OK · 3 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 77%
Documented parameters: 99%
Return-value docs: 100%
References docs: 8%

Downloads

6.5K

CRAN downloads in the past year

Rank #6,111 · ~18/day · ~542/mo

Releases R versions

Daily download trend is not available in this view yet.

44830 days

1.3K90 days

6.5K1 year

Compare downloads with other packages →

Also on575 r2u24 autocran5.6K conda_forge

Repository

GitHub ↗ pln-team/plnmodels

60Stars

17Forks

4Open issues

0Open PRs

22Releases

2,035Commits

12Contributors

poisson-lognormal-modelcount-datanetwork-inferencepcamultivariate-analysisr-package

License GPL-3.0 · 2,035 commits · Last activity 2026-07-30 · +1.7% stars, 30d

Stars over time

2026-07-14 · 592026-08-20 · 60

Repository practices

Upstream repositoryBeta

7 development-tooling and community-health practices detected across 6 families in the upstream repository

Checks run against github.com/pln-team/plnmodels on 2026-08-23.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Docs source (1)

README.qmd

Show all practices

Lint, format, editor (1)

RStudio project

Coverage (1)

Codecov

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

Development tooling

AI-assisted toolingBeta

Uses AI-assisted development tooling (declared in repo)

Earliest detected marker: claude on 2026-06-08

claude

Most recent: claude on 2026-06-08

Evidence

claude: on 2026-06-08 · evidence B, D

How this is detected·Detection ruleset v2 (updated 2026-07-29)

Dependencies

Declared dependencies

25 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1.0

Imports (22)

cli corrplot dplyr ggplot2 glassoFastgrDevicesgridgridExtra igraph magrittrMASSMatrixmethodsnloptrparallelpurrr R6 Rcpp rlangstatstidyr torch

LinkingTo (3)

nloptr Rcpp RcppArmadillo

Suggests (7)

factoextra knitr pheatmap rmarkdown spelling quarto testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (9)

Maintainer (1)

Julien Chiquet

Author, Maintainer

Authors (4)

Julien Chiquet

Author, Maintainer

François Gindraud

Author · added in 0.11.4

Mahendra Mariadassou

Author

Stéphane Robin

Author

Contributors (5)

Julie Aubert

Contributor · added in 1.1.0

Bastien Batardière

Contributor · added in 1.1.0

Maddy Duran

Contributor · added in 1.1.0

Giovanni Poggiato

Contributor · added in 0.11.7

Cole Trapnell

Contributor · added in 1.1.0

Package Timeline

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

1.3.0Latest
2026-07-27 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
1.2.2
2025-03-21 · diff ↗
unarchivedReturned to CRAN
2025-03-21
archivedRemoved from CRAN
2025-03-19
needed patch was ignored Sent by the 'nloptr' maintainer
1.2.1
2025-03-10 · diff ↗
R
R 4.4.0 released · 2024-04-24
1.2.0
2024-03-05 · diff ↗
1.1.0
2024-01-08 · diff ↗
1.0.4
2023-08-24 · diff ↗
1.0.3
2023-07-01 · diff ↗
1.0.2
2023-06-21 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.0.1
2023-02-12 · diff ↗
1.0.0
2023-01-06 · diff ↗

Show 14 earlier events

0.11.7
2022-08-25 · diff ↗
R
R 4.2.0 released · 2022-04-22
0.11.6
2022-02-01 · diff ↗
0.11.5
2022-01-20 · diff ↗
R
R 4.1.0 released · 2021-05-18
0.11.4
2021-03-16 · diff ↗
0.10.6
2020-06-22 · diff ↗
0.10.5
2020-06-16 · diff ↗
R
R 4.0.0 released · 2020-04-24
0.9.5
2020-01-27 · diff ↗
0.9.4
2020-01-14 · diff ↗
0.9.3
2019-12-05 · diff ↗
0.9.2
2019-05-17
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2019-05-17
Total releases: 20 / 7 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 4.1.0
Bundled data: 1.1 MB / 6 files
Download size: 3.6 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("PLNmodels")

Format

Chiquet, J., Aubert, J., Batardière, B., Duran, M., Gindraud, F., Mariadassou, M., Poggiato, G., Robin, S., & Trapnell, C. (2026). PLNmodels: Poisson Lognormal Models (Version 1.3.0) [Computer software]. https://doi.org/10.32614/CRAN.package.PLNmodels

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 PLNmodels version 1.3.0 [Data set]. HJJB, LLC. Data release v2026-08-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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