Package: PLNmodels
Title: Poisson Lognormal Models
Version: 1.2.0
Authors@R: c(
  person("Julien", "Chiquet", role = c("aut", "cre"), email = "julien.chiquet@inrae.fr",
      comment = c(ORCID = "0000-0002-3629-3429")),
  person("Mahendra", "Mariadassou", role = "aut", email = "mahendra.mariadassou@inrae.fr", 
      comment = c(ORCID = "0000-0003-2986-354X")),
  person("Stéphane", "Robin", role ="aut", email = "stephane.robin@inrae.fr"),
  person("François", "Gindraud", role = "aut", email = "francois.gindraud@gmail.com"),
  person("Julie", "Aubert", role = "ctb", email = "julie.aubert@inrae.fr"),
  person("Bastien", "Batardière", role = "ctb", email = "bastien.batardiere@inrae.fr"),
  person("Giovanni", "Poggiato", role = "ctb", email = "giov.poggiato@gmail.com"),
  person("Cole", "Trapnell", role = "ctb", email = "coletrap@uw.edu"),
  person("Maddy", "Duran", role = "ctb", email = "duran@uw.edu")
  )
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)
Encoding: UTF-8
RoxygenNote: 7.3.1
Depends: R (>= 3.4)
LazyData: true
biocViews:
Imports: methods, stats, MASS, future, future.apply, R6, glassoFast,
        pscl, Matrix, Rcpp, nloptr, igraph, grid, gridExtra, dplyr,
        tidyr, purrr, ggplot2, corrplot, magrittr, torch, rlang
Suggests: knitr, rmarkdown, testthat, pkgdown, spelling, factoextra
LinkingTo: Rcpp, RcppArmadillo, nloptr
VignetteBuilder: knitr
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'
Language: en-US
NeedsCompilation: yes
Packaged: 2024-03-05 15:19:47 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: 2024-03-05 15:50:03 UTC
Built: R 4.2.3; x86_64-w64-mingw32; 2024-04-24 03:12:59 UTC; windows
ExperimentalWindowsRuntime: ucrt
Archs: x64
