dartR.popgen: Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

Facilitates the analysis of SNP (single nucleotide polymorphism) and silicodart (presence/absence) data. 'dartR.popgen' provides a suit of functions to analyse such data in a population genetics context. It provides several functions to calculate population genetic metrics and to study population structure. Quite a few functions need additional software to be able to run (gl.run.structure(), gl.blast(), gl.LDNe()). You find detailed description in the help pages how to download and link the packages so the function can run the software. 'dartR.popgen' is part of the the 'dartRverse' suit of packages. Gruber et al. (2018) <doi:10.1111/1755-0998.12745>. Mijangos et al. (2022) <doi:10.1111/2041-210X.13918>.

Version: 0.32
Depends: R (≥ 3.5), adegenet (≥ 2.0.0), dartR.base, dartR.data
Imports: methods, utils, MASS, dplyr, patchwork, crayon, ggplot2, data.table, stringr
Suggests: SIBER, expm, fields, gplots, gridExtra, igraph, iterpc, label.switching, leaflet, plyr, proxy, purrr, qvalue, raster, reshape2, scales, snpStats, tidyr, viridis, zoo, gsubfn, sp
Published: 2023-11-21
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 at canberra.edu.au>
BugReports: https://groups.google.com/g/dartr?pli=1
License: GPL (≥ 3)
URL: https://green-striped-gecko.github.io/dartR/
NeedsCompilation: no
Citation: dartR.popgen citation info
CRAN checks: dartR.popgen results

Documentation:

Reference manual: dartR.popgen.pdf

Downloads:

Package source: dartR.popgen_0.32.tar.gz
Windows binaries: r-prerel: dartR.popgen_0.32.zip, r-release: dartR.popgen_0.32.zip, r-oldrel: dartR.popgen_0.32.zip
macOS binaries: r-prerel (arm64): dartR.popgen_0.32.tgz, r-release (arm64): dartR.popgen_0.32.tgz, r-oldrel (arm64): dartR.popgen_0.32.tgz, r-prerel (x86_64): dartR.popgen_0.32.tgz, r-release (x86_64): dartR.popgen_0.32.tgz

Reverse dependencies:

Reverse suggests: dartRverse

Linking:

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