diveRsity: An R package for the estimation and exploration of population genetics parameters and their associated errors

TLDR

We present diveRsity, an R package for calculating a range of diversity and population differentiation statistics. The package computes these estimators with bootstrapped confidence intervals at loci, pairwise, and global levels, offers plotting tools for visual assessment, includes features to evaluate the validity of traditional F‑statistics—especially for highly polymorphic microsatellites—and supports other co‑dominant markers, with detailed examples and a GUI web app. Examples illustrate effective strategies for exploring data and interpreting results generated by diveRsity.

Abstract

Summary We present a new R package, diveRsity , for the calculation of various diversity statistics, including common diversity partitioning statistics (θ, G ST ) and population differentiation statistics ( D Jost , , χ 2 test for population heterogeneity), among others. The package calculates these estimators along with their respective bootstrapped confidence intervals for loci, sample population pairwise and global levels. Various plotting tools are also provided for a visual evaluation of estimated values, allowing users to critically assess the validity and significance of statistical tests from a biological perspective. diveRsity has a set of unique features, which facilitate the use of an informed framework for assessing the validity of the use of traditional F ‐statistics for the inference of demography, with reference to specific marker types, particularly focusing on highly polymorphic microsatellite loci. However, the package can be readily used for other co‐dominant marker types (e.g. allozymes, SNP s). Detailed examples of usage and descriptions of package capabilities are provided. The examples demonstrate useful strategies for the exploration of data and interpretation of results generated by diveRsity . Additional online resources for the package are also described, including a GUI web app version intended for those with more limited experience using R for statistical analysis.