Package: dartR
Type: Package
Title: Importing and Analysing 'SNP' and 'Silicodart' Data Generated by
        Genome-Wide Restriction Fragment Analysis
Version: 2.9.9.5
Date: 2025-03-24
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("Diana", "Robledo-Ruiz",email="diana.robledoruiz1@monash.edu",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, data from other sequencing platforms can be used once 'SNP' or related 
    fragment presence/absence data from any source is imported. Genetic datasets 
    are stored in a derived 'genlight' format (package 'adegenet'), that allows for 
    a very compact storage of data and metadata. Functions are available for 
    importing and exporting of 'SNP' and 'silicodart' data, for reporting on and 
    filtering on various criteria (e.g. 'CallRate', heterozygosity, reproducibility, 
    maximum allele frequency). Additional functions are available for visualization 
    (e.g. Principle Coordinate Analysis) and creating a spatial representation 
    using maps. 'dartR' supports also the analysis of 3rd party software package 
    such as 'newhybrid', 'structure', 'NeEstimator' and 'blast'. Since version 
    2.0.3 we also implemented simulation functions, that allow to forward simulate
    'SNP' dynamics under different population and evolutionary dynamics. 
    Comprehensive tutorials and support can be found at our 'github' repository: 
    github.com/green-striped-gecko/dartR/. If you want to cite 'dartR', you find 
    the information by typing citation('dartR') in the console.
VignetteBuilder: knitr
Encoding: UTF-8
Depends: R (>= 3.5), adegenet (>= 2.0.0), ggplot2, dplyr, dartR.data
biocViews:
Imports:
        ape,crayon,data.table,fields,foreach,gridExtra,MASS,methods,patchwork,plyr,PopGenReport,raster,reshape2,shiny,SNPRelate,sp
        (>= 1.6.1),StAMPP,stats,stringr,tidyr,utils, gsubfn, purrr
Suggests: boot, devtools, directlabels, dismo, doParallel, expm,
        gdistance, ggtern, gganimate, ggrepel, grid, gtable, ggthemes,
        gplots, HardyWeinberg, hierfstat, igraph, iterpc, knitr,
        label.switching, lattice, leaflet, leaflet.minicharts,
        markdown, mmod, networkD3, parallel, pegas, pheatmap, plotly,
        poppr, proxy, qvalue, RColorBrewer, Rcpp, rgl, rmarkdown,
        rrBLUP, scales, seqinr, shinyBS, shinyjs, shinythemes,
        shinyWidgets, SIBER, snpStats, stringi, terra, tibble, vcfR,
        zoo, viridis, vegan
License: GPL (>= 3)
LazyData: true
RoxygenNote: 7.3.2
NeedsCompilation: no
Packaged: 2025-03-25 00:35:23 UTC; s425824
Author: Bernd Gruber [aut, cre],
  Arthur Georges [aut],
  Jose L. Mijangos [aut],
  Carlo Pacioni [aut],
  Diana Robledo-Ruiz [aut],
  Peter J. Unmack [ctb],
  Oliver Berry [ctb],
  Lindsay V. Clark [ctb],
  Floriaan Devloo-Delva [ctb],
  Eric Archer [ctb]
URL: https://green-striped-gecko.github.io/dartR/,
        https://github.com/green-striped-gecko/dartR
BugReports: https://groups.google.com/g/dartr?pli=1
Maintainer: Bernd Gruber <bernd.gruber@canberra.edu.au>
Repository: CRAN
Date/Publication: 2025-03-25 09:50:02 UTC
Built: R 4.5.2; ; 2025-11-01 03:37:38 UTC; windows
