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: 2026-06-21 08:11:14 UTC; root
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
Config/pak/sysreqs: cmake libgdal-dev gdal-bin libgeos-dev libglpk-dev
        make default-jdk libicu-dev libpng-dev libuv1-dev libxml2-dev
        libssl-dev libproj-dev libsqlite3-dev zlib1g-dev
Repository: https://green-striped-gecko.r-universe.dev
Date/Publication: 2025-03-27 23:13:38 UTC
RemoteUrl: https://github.com/green-striped-gecko/dartr
RemoteRef: HEAD
RemoteSha: 569cf287054949c61c84299afd41a3a490624703
Maintainer: Bernd Gruber <bernd.gruber@canberra.edu.au>