Bernd Gruber, Peter Unmack, Olly Berry and Arthur Georges

Package {dartR} is an R package for (a) loading DArTâ„¢ SNP and SilicoDArT data generated from the commercial service provided by Diversity Arrays Technology Pty Ltd; (b) applying filters to those data based on locus metadata such as call rate, information content or reproducibility; (c) assigning individuals to populations and selecting subsets of individuals or populations; (d) visualization using Principal Coordinates Analysis (PCoA); and (e) providing a conduit to a range of standard data formats and R packages for analysis.

In most cases, the scripts in {dartR} are simple wrappers for scripts included in other already available packages, to provide transparent access to these packages for analyzing DArT data, and to provide some enhanced output diagnostics. Relatively few scripts provide novel analyses. We make no apologies for this, as the objective of {dartR} is to provide fundamental tools for accessing and manipulating DArT datafiles in preparation for analysis by the vast suite of packages available in R through the CRAN repository.

A summary of the capabilities of {dartR} is as follows:

The package is currently under development and available as a beta release on https://github.com/green-striped-gecko/dartR. There you will find installation instructions and other guidance. The package dartR (version 1.05) is now available on CRAN.

The package dartR has recently been announced in Molecular Ecology Resources.

Additional Notes:

dart_support_for_population_assignment.pdf

dartR_support_for_admixture_analysis.pdf

dartR_support_for_phylogenetic_analysis.pdf

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