xinghuq/HierDpart: Partitioning Diversity and Differentiation Across Metrics and Scales, from Genes to Ecosystems

Miscellaneous R functions for calculating and decomposing diversity profiles (H^q, D^q), including allele richness, exponential Shannon entropy (true diversity of order q=1), heterozygosity (also inverse Simpson index) and genetic differentiation (Jaccard dissimilarity, Delta D, Fst and Jost's D) in a hierarchy (Qin, X. & Gaggiotti, O. E. 2022, Mol. Ecol. Resour., 22(6), 2183-2195; <DOI:10.1111/1755-0998.13606>). This package allows users to analyse spatial structured genetic data or species data under a unifying framework that partitions diversity and differentiation into any hierarchical levels. It helps you easily structure and format your data. In summary,it implements the analyses of true diversity profiles (q=0, 1, 2), diversities and differentiation decomposition, visualization of population structure, as well as the estimation of correlation between geographic distance and genetic differentiation.

install.packages("remotes")
remotes::install_github("xinghuq/HierDpart")