dartR.base: Analysing 'SNP' and 'Silicodart' Data - Basic Functions

Facilitates 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.base' is the 'base' package of the 'dartRverse' suits of packages. To install the other packages, we recommend to install the 'dartRverse' package, that supports the installation of all packages in the 'dartRverse'. If you want to cite 'dartR', you find the information by typing citation('dartR.base') in the console.

Version: 0.65
Depends: R (≥ 3.5), adegenet (≥ 2.0.0), ggplot2, dplyr, dartR.data
Imports: ape, crayon, data.table, foreach, gridExtra, methods, patchwork, plyr, reshape2, SNPRelate, StAMPP, stats, stringr, tidyr, utils, MASS
Suggests: boot, devtools, directlabels, dismo, doParallel, expm, gdistance, 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, purrr, qvalue, RColorBrewer, Rcpp, rgl, rmarkdown, rrBLUP, scales, seqinr, sf, shinyBS, shinyjs, shinythemes, shinyWidgets, SIBER, snpStats, stringi, terra, tibble, vcfR, zoo, viridis, fields, testthat (≥ 3.0.0), ggtern
Published: 2023-11-17
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.base citation info
CRAN checks: dartR.base results

Documentation:

Reference manual: dartR.base.pdf

Downloads:

Package source: dartR.base_0.65.tar.gz
Windows binaries: r-prerel: dartR.base_0.65.zip, r-release: dartR.base_0.65.zip, r-oldrel: dartR.base_0.65.zip
macOS binaries: r-prerel (arm64): dartR.base_0.65.tgz, r-release (arm64): dartR.base_0.65.tgz, r-oldrel (arm64): dartR.base_0.65.tgz, r-prerel (x86_64): dartR.base_0.65.tgz, r-release (x86_64): dartR.base_0.65.tgz
Old sources: dartR.base archive

Reverse dependencies:

Reverse depends: dartR.captive, dartR.popgen, dartR.sim, dartR.spatial, dartRverse

Linking:

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