PLNmodels: Poisson Lognormal Models

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.

Version: 1.2.1
Depends: R (≥ 4.1.0)
Imports: cli, corrplot, dplyr, future, future.apply, ggplot2, glassoFast, grDevices, grid, gridExtra, igraph, magrittr, MASS, Matrix, methods, nloptr, parallel, pscl, purrr, R6, Rcpp, rlang, scales, stats, tidyr, torch
LinkingTo: nloptr, Rcpp, RcppArmadillo
Suggests: factoextra, knitr, rmarkdown, spelling, testthat
Published: 2025-03-10
DOI: 10.32614/CRAN.package.PLNmodels
Author: Julien Chiquet ORCID iD [aut, cre], Mahendra Mariadassou ORCID iD [aut], Stéphane Robin [aut], François Gindraud [aut], Julie Aubert [ctb], Bastien Batardière [ctb], Giovanni Poggiato [ctb], Cole Trapnell [ctb], Maddy Duran [ctb]
Maintainer: Julien Chiquet <julien.chiquet at inrae.fr>
BugReports: https://github.com/pln-team/PLNmodels/issues
License: GPL (≥ 3)
URL: https://pln-team.github.io/PLNmodels/
NeedsCompilation: yes
Language: en-US
Citation: PLNmodels citation info
Materials: NEWS
CRAN checks: PLNmodels results

Documentation:

Reference manual: PLNmodels.pdf
Vignettes: import (source, R code)
Analyzing multivariate count data with the Poisson log-normal model (source, R code)
Supervized classification of multivariate count table with the Poisson discriminant Analysis (source, R code)
Dimension reduction of multivariate count data with PLN-PCA (source, R code)
Clustering of multivariate count data with PLN-mixture (source, R code)
Sparse structure estimation for multivariate count data with PLN-network (source, R code)
Description of the Trichoptera data set (source, R code)

Downloads:

Package source: PLNmodels_1.2.1.tar.gz
Windows binaries: r-devel: PLNmodels_1.2.0.zip, r-release: PLNmodels_1.2.1.zip, r-oldrel: PLNmodels_1.2.0.zip
macOS binaries: r-devel (arm64): PLNmodels_1.2.1.tgz, r-release (arm64): PLNmodels_1.2.1.tgz, r-oldrel (arm64): PLNmodels_1.2.1.tgz, r-devel (x86_64): PLNmodels_1.2.1.tgz, r-release (x86_64): PLNmodels_1.2.1.tgz, r-oldrel (x86_64): PLNmodels_1.2.1.tgz
Old sources: PLNmodels archive

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