CRAN requires the check problems on this package to be fixed before 2026-07-30 or it will be archived.

PLNmodels

1.2.2

Poisson Lognormal Models

0packages depend

6.6Kdownloads / year

86.4%test coverage

6/13checks pass

Overview

About

Maintained by Julien ChiquetFirst published 2019-05-1719 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

4WARNING3NOTE6OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
WARNING r-devel-linux-x86_64-debian-gcc
NOTE r-devel-linux-x86_64-fedora-clang
WARNING r-devel-linux-x86_64-fedora-gcc
NOTE r-devel-windows-x86_64
WARNING r-patched-linux-x86_64
WARNING r-release-linux-x86_64

Slowest check: 26.1 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.36

86.4%

Coverage · measured lines

96%

Documentation · exports

Dependencies · direct

Check history

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
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

Show 2 earlier snapshots

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: 75%
Documented parameters: 99%
Return-value docs: 100%
References docs: 8%

Downloads

6.6K

CRAN downloads in the past year

Rank #8,766 · ~18/day · ~553/mo

Releases R versions

Daily download trend is not available in this view yet.

35930 days

1.3K90 days

6.6K1 year

Compare downloads with other packages →

Also on574 r2u35 autocran5.5K conda_forge

Repository

GitHub ↗ pln-team/plnmodels

59Stars

17Forks

4Open issues

0Open PRs

21Releases

2,028Commits

12Contributors

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

License GPL-3.0 · 2,028 commits · Last activity 2026-07-20

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 2026-07-19.

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)

Dependencies

Declared dependencies

27 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1.0

Imports (26)

cli corrplot dplyr future future.apply ggplot2 glassoFastgrDevicesgridgridExtra igraph magrittrMASSMatrixmethodsnloptrparallelpscl purrr R6 Rcpp rlang scalesstatstidyr torch

LinkingTo (3)

nloptr Rcpp RcppArmadillo

Suggests (5)

factoextra knitr rmarkdown spelling 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

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
1.2.2Latest
2025-03-21 · current release · 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 ↗
0.11.7
2022-08-25 · diff ↗

Show 13 earlier events

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: 19 / 7 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 4.1.0
Bundled data: 1.0 MB / 5 files
Download size: 3.2 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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