Package: PLNmodels
Title: Poisson Lognormal Models
Version: 1.2.2
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, future, future.apply, ggplot2,
        glassoFast, grDevices, grid, gridExtra, igraph, magrittr, MASS,
        Matrix, methods, nloptr, parallel, pscl, purrr, R6, Rcpp,
        rlang, scales, stats, tidyr, torch
Suggests: factoextra, knitr, rmarkdown, spelling, testthat
LinkingTo: nloptr, Rcpp, RcppArmadillo
VignetteBuilder: knitr
biocViews:
Encoding: UTF-8
Language: en-US
LazyData: true
RoxygenNote: 7.3.2
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' 'mollusk.R' 'oaks.R' 'plot_utils.R' 'scRNA.R'
        'trichoptera.R' 'utils-pipe.R' 'utils-zipln.R' 'utils.R'
        'zzz.R'
NeedsCompilation: yes
Packaged: 2025-03-21 11:05:39 UTC; jchiquet
Author: Julien Chiquet [aut, cre] (<https://orcid.org/0000-0002-3629-3429>),
  Mahendra Mariadassou [aut] (<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>
Repository: CRAN
Date/Publication: 2025-03-21 17:40:06 UTC
Built: R 4.6.0; x86_64-apple-darwin20; 2026-04-26 00:11:36 UTC; unix
Archs: PLNmodels.so.dSYM
