DESCRIPTION

Package: strataG
Title: Summaries and Population Structure Analyses of Genetic Data
Description: A toolkit for analyzing stratified population genetic data. 
  Functions are provided for summarizing and checking loci 
  (haploid, diploid, and polyploid), single stranded DNA sequences,
  calculating most population subdivision metrics, and running external programs 
  such as structure and fastsimcoal. The package is further described in 
  Archer et al (2016) <doi:10.1111/1755-0998.12559>.
Version: 2.5.01
License: GNU General Public License
Authors@R: c(
  EA = person("Eric", "Archer", email = "eric.archer@noaa.gov", role = c("aut", "cre")),
  PA = person("Paula", "Adams", email = "peadams@crimson.ua.edu", role = c("aut")),
  BS = person("Brita", "Schneiders", email = "britaschneiders@u.northwestern.edu", role = c("aut")),
  SF = person("Sarina", "Fernandez", email = "sarinafernandez5@gmail.com", role = c("aut")),
  WA = person("Warren", "Asfazadour", email = "wasfazad@hotmail.com", role = c("aut")))
URL: https://github.com/EricArcher/strataG
BugReports: https://github.com/EricArcher/strataG/issues
Depends:
    R (>= 4.0.0)
Suggests:
    knitr,
    rmarkdown,
    testthat,
    qgraph
Imports:
    Rcpp (>= 1.0.5),
    ape (>= 5.4),
    apex (>= 1.0.4),
    adegenet (>= 2.1.3),
    dplyr (>= 1.0.2),
    tibble (>= 3.0.4),
    tidyr (>= 1.1.2),
    purrr (>= 0.3.4),
    data.table (>= 1.13.6),
    copula (> 1.0),
    genepop (>= 1.1.7),
    ggplot2 (>= 3.3.3),
    graphics,
    grid (>= 4.0.3),
    gridExtra (>= 2.3),
    magrittr (>= 2.0.1),
    methods,
    pegas (>= 0.14),
    phangorn (>= 2.5.5),
    rlang (>= 0.4.10),
    rmetasim,
    sprex (>= 1.4.2),
    stats,
    stringi (>= 1.5.3),
    swfscMisc (>= 1.4),
    utils
Remotes:
    stranda/rmetasim
Collate:
    strataG-package.R
    RcppExports.R
    gtypes.class.R
    gtypes.accessors.R
    is.gtypes.R
    gtypes.initialize.R
    strataG-internal.R
    as.data.frame.gtypes.R
    alleleFreqs.R
    alleleSplit.R
    allelicRichness.R
    as.multidna.R
    dupGenotypes.R
    heterozygosity.R
    labelHaplotypes.R
    numAlleles.R
    numGenotyped.R
    numMissing.R
    permuteStrata.R
    privateAlleles.R
    propUniqueAlleles.R
    readGenData.R
    removeUnusedSequences.R
    sharedLoci.R
    strataSplit.R
    stratify.R
    summarizeLoci.R
    summarizeInds.R
    summarizeSeqs.R
    gtypes.show.R
    gtypes.summary.R
    writeGtypes.R
    df2gtypes.R
    sequence2gtypes.R
    baseFreqs.R
    createConsensus.R
    iupac.R
    expandHaplotypes.R
    trimNs.R
    fasta.R
    fixedSites.R
    variableSites.R
    nucleotideDiversity.R
    fixedDifferences.R
    lowFreqSubs.R
    sequenceLikelihoods.R
    nucleotideDivergence.R
    popGenEqns.R
    freq2GenData.R
    gtypes2genind.R
    gtypes2genlight.R
    gtypes2loci.R
    gtypes2phyDat.R
    theta.R
    maf.R
    TiTvRatio.R
    simGammaHaps.R
    mostDistantSequences.R
    mostRepresentativeSequences.R
    write.nexus.snapp.R
    mega.R
    mRatio.R
    neiDa.R
    mafft.R
    arlequin.R
    ldNe.R
    genepop.R
    hweTest.R
    jackHWE.R
    LDgenepop.R
    fsc.input.R
    fscWrite.R
    fscRun.R
    fscRead.R
    sfs.R
    structure.R
    structurePlot.R
    evanno.R
    clumpp.R
    fusFs.R
    tajimasD.R
    popStructTest.R
    gelato.R
    phase.R
    maverickRun.R
    summarizeAll.R
    landscape2gtypes.R
LazyData: TRUE
VignetteBuilder: knitr
LinkingTo: Rcpp, RcppArmadillo
Encoding: UTF-8
RoxygenNote: 7.2.3