The newest version of diveRsity has just been uploaded to CRAN. The major change in this version is the addition of a new function 'bigDivPart' which allows the efficient calculation of diversity partitioning and differentiation statistics for very large data sets (e.g. RAD-seq derived SNP loci). This new function uses memory efficient programming to allow the analysis of data sets containing more than 100,000 loci, on most modern laptops (e.g. I tested the function on my laptop with 6Gb RAM with a data file containing 268 individuals across 9 population samples, genotyped at 55,000 loci. The entire analysis took just over 3min and my RAM usage reached a maximum of about 3.5Gb). All detail regarding function usage can be found in the updated user manual.
About the authors
Kevin Keenan is currently working towards a PhD in population and evolutionary genetics.