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: 1.2.0
Depends: R (≥ 3.4)
Imports: methods, stats, MASS, future, future.apply, R6, glassoFast, pscl, Matrix, Rcpp, nloptr, igraph, grid, gridExtra, dplyr, tidyr, purrr, ggplot2, corrplot, magrittr, torch, rlang
LinkingTo: Rcpp, RcppArmadillo, nloptr
Suggests: knitr, rmarkdown, testthat, pkgdown, spelling, factoextra
Published: 2024-03-05
DOI: NA
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
Analyzing multivariate count data with the Poisson log-normal model
Supervized classification of multivariate count table with the Poisson discriminant Analysis
Dimension reduction of multivariate count data with PLN-PCA
Clustering of multivariate count data with PLN-mixture
Sparse structure estimation for multivariate count data with PLN-network
Description of the Trichoptera data set

Downloads:

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

Linking:

Please use the canonical form https://CRAN.R-project.org/package=PLNmodels to link to this page.