DESCRIPTION

Package: PLNmodels
Title: Poisson Lognormal Models
Version: 1.2.1
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 (>= 3.6)
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
Roxygen: list(markdown = 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'