Package: dartR
Type: Package
Title: Importing and Analysing SNP and Silicodart Data Generated by
        Genome-Wide Restriction Fragment Analysis
Version: 2.0.4
Date: 2022-06-03
Authors@R: c(
            person("Bernd", "Gruber", email="bernd.gruber@canberra.edu.au", role=c("aut","cre")), 
            person("Arthur", "Georges", email="georges@aerg.edu.au", role="aut"),
            person("Jose L.", "Mijangos", email="Luis.MijangosAraujo@canberra.edu.au", role="aut"), 
            person("Carlo", "Pacioni",email="carlo.pacioni@delwp.vic.gov.au",role="aut"),
            person("Peter J.", "Unmack", email="peter.mail2@unmack.net", role="ctb"),
            person("Oliver", "Berry", email="oliver.berry@csiro.au", role="ctb" ),
            person("Lindsay V.", "Clark", email="lvclark@illinois.edu", role="ctb"),
            person("Floriaan", "Devloo-Delva",email="Floriaan.Devloo-Delva@csiro.au", role="ctb"),
            person("Eric","Archer", email="eric.archer@noaa.gov", role="ctb")
            )
Description: Functions are provided that facilitate the import and analysis of
    SNP (single nucleotide polymorphism) and silicodart (presence/absence) data. 
    The main focus is on data generated by DarT (Diversity Arrays Technology). 
    However, once SNP or related fragment presence/absence data from any source 
    is imported into a genlight object many of the functions can be used. 
    Functions are available for input and output of SNP and silicodart data, for
    reporting on and filtering on various criteria (e.g. CallRate,
    Heterozygosity, Reproducibility, maximum allele frequency). Advanced 
    filtering is based on Linkage Disequilibrium and HWE (Hardy-Weinberg 
    equilibrium). Other functions are available for visualization after PCoA 
    (Principle Coordinate Analysis), or to facilitate transfer of data between 
    genlight/genind objects and newhybrids, related, phylip, structure,
    faststructure packages.
VignetteBuilder: knitr
Encoding: UTF-8
Depends: R (>= 3.5), adegenet (>= 2.0.0), ggplot2, dplyr
biocViews:
Imports:
        ape,crayon,data.table,fields,foreach,gridExtra,MASS,methods,patchwork,plyr,PopGenReport,raster,reshape2,shiny,SNPRelate,sp,StAMPP,stats,stringr,tidyr,utils,vegan
Suggests: boot, devtools, directlabels, dismo, doParallel, expm,
        gdistance, gganimate, ggrepel, ggtern, ggthemes, gplots,
        HardyWeinberg, hierfstat, igraph, iterpc, knitr,
        label.switching, leaflet, leaflet.minicharts, markdown, mmod,
        networkD3, parallel, pca3d, pegas, pheatmap, plotly, poppr,
        proxy, purrr, qvalue, RColorBrewer, Rcpp, rgl, rmarkdown,
        rrBLUP, scales, seqinr, shinyBS, shinyjs, shinythemes,
        shinyWidgets, SIBER, snpStats, stringi, terra, tibble,
        tidyverse, vcfR
License: GPL (>= 3)
LazyData: true
RoxygenNote: 7.1.2
NeedsCompilation: no
Packaged: 2022-06-03 13:48:24 UTC; s425824
Author: Bernd Gruber [aut, cre],
  Arthur Georges [aut],
  Jose L. Mijangos [aut],
  Carlo Pacioni [aut],
  Peter J. Unmack [ctb],
  Oliver Berry [ctb],
  Lindsay V. Clark [ctb],
  Floriaan Devloo-Delva [ctb],
  Eric Archer [ctb]
Maintainer: Bernd Gruber <bernd.gruber@canberra.edu.au>
Repository: CRAN
Date/Publication: 2022-06-05 16:00:02 UTC
Built: R 4.1.3; ; 2022-06-05 18:35:15 UTC; unix
