Package: adegenet
Title: Exploratory Analysis of Genetic and Genomic Data
Version: 2.1.11
Authors@R: 
    c(person(given = "Thibaut",
             family = "Jombart",
             role = "aut",
             comment = c(ORCID = "0000-0003-2226-8692")),
      person(given = "Zhian N.",
             family = "Kamvar",
             role = c("aut", "cre"),
             email = "zkamvar@gmail.com",
             comment = c(ORCID = "0000-0003-1458-7108")),
      person(given = "Caitlin",
             family = "Collins",
             role = "ctb"),
      person(given = "Roman",
             family = "Lustrik",
             role = "ctb"),
      person(given = "Marie-Pauline",
             family = "Beugin",
             role = "ctb"),
      person(given = "Brian J.",
             family = "Knaus",
             role = "ctb"),
      person(given = "Peter",
             family = "Solymos",
             role = "ctb"),
      person(given = "Vladimir",
             family = "Mikryukov",
             role = "ctb"),
      person(given = "Klaus",
             family = "Schliep",
             role = "ctb"),
      person(given = "Tiago",
             family = "Maié",
             role = "ctb"),
      person(given = "Libor",
             family = "Morkovsky",
             role = "ctb"),
      person(given = "Ismail",
             family = "Ahmed",
             role = "ctb"),
      person(given = "Anne",
             family = "Cori",
             role = "ctb"),
      person(given = "Federico",
             family = "Calboli",
             role = "ctb"),
      person(given = "RJ",
             family = "Ewing",
             role = "ctb"),
      person(given = "Frédéric",
             family = "Michaud",
             role = "ctb"),
      person(given = "Rebecca",
             family = "DeCamp",
             role = "ctb"),
      person(given = "Alexandre",
             family = "Courtiol",
             role = "ctb",
             comment = c(ORCID = "0000-0003-0637-2959")),
      person(given = "Lindsay V.",
             family = "Clark",
             role = "ctb",
             comment = c(ORCID = "0000-0002-3881-9252")),
       person(given = "Pavel",
              family = "Dimens",
              role = "ctb",
              comment = c(ORCID = "0000-0003-3823-0373")),
       person(given = "Max",
              family = "Coulter",
              role = "ctb"),
       person(given = "Ivan",
              family = "Krylov",
              role = "ctb")
       )
Description: Toolset for the exploration of genetic and genomic data.
        Adegenet provides formal (S4) classes for storing and handling
        various genetic data, including genetic markers with varying
        ploidy and hierarchical population structure ('genind' class),
        alleles counts by populations ('genpop'), and genome-wide SNP
        data ('genlight'). It also implements original multivariate
        methods (DAPC, sPCA), graphics, statistical tests, simulation
        tools, distance and similarity measures, and several spatial
        methods. A range of both empirical and simulated datasets is
        also provided to illustrate various methods.
License: GPL (>=2)
URL: https://github.com/thibautjombart/adegenet
Depends: R (>= 2.14), methods, ade4
Imports: utils, stats, grDevices, MASS, igraph, ape, shiny, ggplot2,
        seqinr, parallel, boot, reshape2, dplyr (>= 0.4.1), vegan
Suggests: adespatial, pegas, hierfstat, maps, spdep, interp, splancs,
        poppr, testthat
Encoding: UTF-8
LazyLoad: yes
RoxygenNote: 7.3.2
Collate: 'adegenet.package.R' 'datasets.R' 'dist.genlight.R'
        'orthobasis.R' 'classes.R' 'constructors.R' 'accessors.R'
        'basicMethods.R' 'handling.R' 'auxil.R' 'minorAllele.R'
        'setAs.R' 'SNPbin.R' 'strataMethods.R' 'hierarchyMethods.R'
        'glHandle.R' 'glFunctions.R' 'glSim.R' 'find.clust.R'
        'hybridize.R' 'scale.R' 'fstat.R' 'import.R' 'seqTrack.R'
        'chooseCN.R' 'genind2genpop.R' 'loadingplot.R' 'sequences.R'
        'gstat.randtest.R' 'makefreq.R' 'colorplot.R' 'monmonier.R'
        'spca.R' 'coords.monmonier.R' 'haploGen.R' 'old2new.R'
        'global_local_tests.R' 'dapc.R' 'compoplot.R' 'xvalDapc.R'
        'haploPop.R' 'PCtest.R' 'dist.genpop.R' 'Hs.R' 'propShared.R'
        'export.R' 'HWE.R' 'propTyped.R' 'inbreeding.R' 'glPlot.R'
        'gengraph.R' 'simOutbreak.R' 'mutations.R' 'snpposi.R'
        'snpzip.R' 'pairDist.R' 'snapclust.R' 'AIC.snapclust.R'
        'AICc.snapclust.R' 'BIC.snapclust.R' 'KIC.snapclust.R'
        'snapclust.choose.k.R' 'servers.R' 'showmekittens.R'
        'spca_randtest.R' 'export_to_mvmapper.R' 'doc_C_routines.R'
        'zzz.R'
Config/pak/sysreqs: cmake libglpk-dev make libicu-dev libuv1-dev
        libxml2-dev zlib1g-dev
Repository: https://thibautjombart.r-universe.dev
Date/Publication: 2025-02-07 17:03:06 UTC
RemoteUrl: https://github.com/thibautjombart/adegenet
RemoteRef: HEAD
RemoteSha: 9f24e97759c13e0edb1c700ca1e406d8dffcb1fd
NeedsCompilation: yes
Packaged: 2026-06-24 11:57:08 UTC; root
Author: Thibaut Jombart [aut] (ORCID: <https://orcid.org/0000-0003-2226-8692>),
  Zhian N. Kamvar [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-1458-7108>),
  Caitlin Collins [ctb],
  Roman Lustrik [ctb],
  Marie-Pauline Beugin [ctb],
  Brian J. Knaus [ctb],
  Peter Solymos [ctb],
  Vladimir Mikryukov [ctb],
  Klaus Schliep [ctb],
  Tiago Maié [ctb],
  Libor Morkovsky [ctb],
  Ismail Ahmed [ctb],
  Anne Cori [ctb],
  Federico Calboli [ctb],
  RJ Ewing [ctb],
  Frédéric Michaud [ctb],
  Rebecca DeCamp [ctb],
  Alexandre Courtiol [ctb] (ORCID:
    <https://orcid.org/0000-0003-0637-2959>),
  Lindsay V. Clark [ctb] (ORCID: <https://orcid.org/0000-0002-3881-9252>),
  Pavel Dimens [ctb] (ORCID: <https://orcid.org/0000-0003-3823-0373>),
  Max Coulter [ctb],
  Ivan Krylov [ctb]
Maintainer: Zhian N. Kamvar <zkamvar@gmail.com>