DESCRIPTION

Package: snpR
Type: Package
Title: Whole-Genome Analysis Tools for Use with Single Nucleotide Polymorphism Data
Version: 1.2.4
Authors@R: c(person("William", "Hemstrom", email = "hemstrow@gmail.com",
  role = c("aut", "cre")),
  person("Melissa", "Jones", email = "mlyjones@ucdavis.edu", role = c("aut", "ctb")),
  person("Avani", "Chitre", email = "aachitre@ucdavis.edu", role = "ctb"),
  person("Keming", "Su", email = "kmsu@ucdavis.edu", role = "ctb"),
  person("Francis", "Roy", role = "cph", comment = "Holder of pophelper license"))
Description: A toolkit for analyzing Single Nucleotide Polymorphism whole-genome data in a user-friendly way,
    allowing for the data to be automatically split and calculated across multiple metadata categories simultaneously.
    This includes functions to get most summary statistics and smooth them, map pairwise linkage disequilibrium, 
    determine the significance of smoothed statistics via bootstrapping, do association testing, plot many
    kinds of results, convert to many common output formats, 
    and filter raw data. 
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
Imports:
    doParallel,
    dplyr,
    matrixStats,
    methods,
    ggplot2,
    parallel,
    plyr,
    purrr,
    rbibutils,
    reshape2,
    rlang,
    stats
Depends:
    data.table,
    foreach,
    R (>= 3.6.0)
Suggests:
    ade4,
    adegenet,
    AGHmatrix,
    ape,
    BGLR,
    bigmemory,
    bigtabulate,
    BiocManager,
    genepop,
    genio,
    geosphere,
    ggrepel,
    GMMAT,
    knitr,
    LEA,
    markdown,
    missMDA,
    mmtsne,
    openxlsx,
    ranger,
    rmarkdown,
    readr,
    remotes,
    Rtsne,
    shiny,
    umap,
    vcfR,
    viridis,
    testthat,
    covr
VignetteBuilder: knitr
RoxygenNote: 7.2.1
Collate: 
    'NeEstimator_interface.R'
    'association_functions.R'
    'bootstrapping_functions.R'
    'colony_interface.R'
    'dataset_documentation.R'
    'import_functions.R'
    'import_wrappers.R'
    'internals.R'
    'plotting_functions.R'
    'pophelper_redistribution.R'
    'sequoia_interface.R'
    'sfs_functions.R'
    'smoothing_functions.R'
    'snpRdata.R'
    'snpRdata_methods.R'
    'stat_functions.R'
    'utility_functions.R'