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: | 1.0.0 |
| Depends: | R (≥ 3.5), adegenet (≥ 2.0.0), dartR.base, dartR.data |
| Imports: | methods, utils, MASS, dplyr, patchwork, crayon, ggplot2, data.table, stringr, furrr, future, ggdendro |
| 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: | 2024-06-27 |
| DOI: | 10.32614/CRAN.package.dartR.popgen |
| 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 |
| Reference manual: | dartR.popgen.pdf |
| Package source: | dartR.popgen_1.0.0.tar.gz |
| Windows binaries: | r-devel: dartR.popgen_1.0.0.zip, r-release: dartR.popgen_1.0.0.zip, r-oldrel: dartR.popgen_1.0.0.zip |
| macOS binaries: | r-devel (arm64): dartR.popgen_1.0.0.tgz, r-release (arm64): dartR.popgen_1.0.0.tgz, r-oldrel (arm64): dartR.popgen_1.0.0.tgz, r-devel (x86_64): dartR.popgen_1.0.0.tgz, r-release (x86_64): dartR.popgen_1.0.0.tgz, r-oldrel (x86_64): dartR.popgen_1.0.0.tgz |
| Old sources: | dartR.popgen archive |
| Reverse suggests: | dartRverse |
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