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) . Mijangos et al. (2022) .


Reference manual

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install.packages("dartR.popgen")

1.2.2 by Bernd Gruber, 8 months ago


https://green-striped-gecko.github.io/dartR/


Report a bug at https://groups.google.com/g/dartr?pli=1


Browse source code at https://github.com/cran/dartR.popgen


Authors: 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] , Ching Ching Lau [ctb]


Documentation:   PDF Manual  


GPL (>= 3) license


Imports methods, adegenet, utils, MASS, dplyr, patchwork, crayon, ggplot2, data.table, stringr, furrr, future, ggdendro, LEA, pillar, plyr, terra, purrr, ggpmisc, R.utils, ape

Depends on dartR.base, dartR.data

Suggests SIBER, expm, fields, gplots, gridExtra, igraph, iterpc, label.switching, leaflet, proxy, qvalue, raster, reshape2, scales, snpStats, tidyr, viridis, zoo, gsubfn, sp


Depended on by dartR.sim.

Suggested by dartRverse.


See at CRAN