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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: 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
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.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.