Package: dartR
Type: Package
Title: Importing and Analysing Snp and Silicodart Data Generated by
        Genome-Wide Restriction Fragment Analysis
Version: 1.0
Date: 2017-12-06
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("Peter J.", "Unmack", email="peter.mail2@unmack.net", rol="ctb"),
            person("Oliver", "Berry", email="oliver.berry@csiro.au", rol="ctb" )  )
Description: Functions are provided that facilitate the import and analysis of
    snp 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. Other functions
    are available for visualization after PCoA, or to facilitate transfer of data
    between genlight/genind objects and newhybrids, related, phylip packages etc.
VignetteBuilder: knitr
Depends: R (>= 3.1.1), adegenet (>= 2.0.0)
Imports: plyr, tidyr, reshape2, MASS, ggplot2, directlabels, quadprog,
        rgl, misc3d, pca3d, utils, Demerelate, seqinr, pegas, SNPassoc,
        methods, doParallel, stats, data.table, parallel, foreach,
        stringr, ape, vegan, SNPRelate, StAMPP, dismo, DBI, qvalue,
        plotly, sp, rgdal
Suggests: knitr, rmarkdown, mmod, PopGenReport
License: GPL-2
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-12-05 23:24:57 UTC; s425824
Author: Bernd Gruber [aut, cre],
  Arthur Georges [aut],
  Peter J. Unmack [ctb],
  Oliver Berry [ctb]
Maintainer: Bernd Gruber <bernd.gruber@canberra.edu.au>
Repository: CRAN
Date/Publication: 2017-12-06 11:25:30 UTC
Built: R 3.3.3; ; 2018-04-22 18:06:55 UTC; windows
