Package: PLNmodels
Title: Poisson Lognormal Models
Version: 1.3.0
Authors@R: c(
    person("Julien", "Chiquet", , "julien.chiquet@inrae.fr", role = c("aut", "cre"),
           comment = c(ORCID = "0000-0002-3629-3429")),
    person("Mahendra", "Mariadassou", , "mahendra.mariadassou@inrae.fr", role = "aut",
           comment = c(ORCID = "0000-0003-2986-354X")),
    person("Stéphane", "Robin", , "stephane.robin@inrae.fr", role = "aut"),
    person("François", "Gindraud", , "francois.gindraud@gmail.com", role = "aut"),
    person("Julie", "Aubert", , "julie.aubert@inrae.fr", role = "ctb"),
    person("Bastien", "Batardière", , "bastien.batardiere@inrae.fr", role = "ctb"),
    person("Giovanni", "Poggiato", , "giov.poggiato@gmail.com", role = "ctb"),
    person("Cole", "Trapnell", , "coletrap@uw.edu", role = "ctb"),
    person("Maddy", "Duran", , "duran@uw.edu", role = "ctb")
  )
Description: 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.
URL: https://pln-team.github.io/PLNmodels/
BugReports: https://github.com/pln-team/PLNmodels/issues
License: GPL (>= 3)
Depends: R (>= 4.1.0)
Imports: cli, corrplot, dplyr, ggplot2, glassoFast, grDevices, grid,
        gridExtra, igraph, magrittr, MASS, Matrix, methods, nloptr,
        parallel, purrr, R6, Rcpp, rlang, stats, tidyr, torch
Suggests: factoextra, knitr, pheatmap, rmarkdown, spelling, quarto,
        testthat
LinkingTo: nloptr, Rcpp, RcppArmadillo
VignetteBuilder: knitr
biocViews:
Encoding: UTF-8
Language: en-US
LazyData: true
Roxygen: list(markdown = TRUE)
Collate: 'PLNfit-class.R' 'PLN.R' 'PLNLDA.R' 'PLNLDAfit-S3methods.R'
        'PLNLDAfit-class.R' 'PLNPCA.R' 'PLNPCAfamily-S3methods.R'
        'PLNfamily-class.R' 'PLNPCAfamily-class.R'
        'PLNPCAfit-S3methods.R' 'PLNPCAfit-class.R'
        'PLNfamily-S3methods.R' 'PLNfit-S3methods.R' 'PLNmixture.R'
        'PLNmixturefamily-S3methods.R' 'PLNmixturefamily-class.R'
        'PLNmixturefit-S3methods.R' 'PLNmixturefit-class.R'
        'PLNmodels-package.R' 'PLNnetwork.R'
        'PLNnetworkfamily-S3methods.R' 'PLNnetworkfamily-class.R'
        'PLNnetworkfit-S3methods.R' 'PLNnetworkfit-class.R'
        'RcppExports.R' 'ZIPLNfit-class.R' 'ZIPLN.R'
        'ZIPLNfit-S3methods.R' 'ZIPLNnetwork.R' 'barents.R'
        'import_utils.R' 'microcosm.R' 'mollusk.R' 'oaks.R'
        'plot_utils.R' 'scRNA.R' 'trichoptera.R' 'utils-pipe.R'
        'utils-zipln.R' 'utils.R' 'zzz.R'
Config/roxygen2/version: 8.0.0
Config/pak/sysreqs: cmake libglpk-dev libicu-dev libxml2-dev
Repository: https://pln-team.r-universe.dev
Date/Publication: 2026-07-03 16:29:06 UTC
RemoteUrl: https://github.com/pln-team/plnmodels
RemoteRef: HEAD
RemoteSha: bd801b7e0380b8372a28d5f053d123d45b8eb1ee
NeedsCompilation: yes
Packaged: 2026-07-03 17:29:32 UTC; root
Author: Julien Chiquet [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-3629-3429>),
  Mahendra Mariadassou [aut] (ORCID:
    <https://orcid.org/0000-0003-2986-354X>),
  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@inrae.fr>