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:

Installing dartR

CRAN version

install.packages("dartR")
library(dartR)

Latest stable version (github)

install.packages("devtools")
library(devtools)
install_github("green-striped-gecko/dartR")
library(dartR)

Help

A Q&A forum called dartR has been established on Google Groups to assist with issues as they arise. You are welcome to join.

Tutorials

Sample Data Files

dartR contains a number of small sample files (e.g. testset.gl), but in addition, you might wish to access the following files.

They can be downloaded as a zip file and unzipped into your working directory for use with the tutorials.

Reading

The package dartR was announced in Molecular Ecology Resources.


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