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

Miscellaneous R functions for calculating and decomposing hierarchical diversity metrics, including hierarchical allele richness (q=0), hierarchical exponential Shannon entropy (q=1), hierarchical heterozygosity (q=2) and genetic differentiation (Fst and Delta D). This package allows you to analyse spatial structured genetic data or species data under a unifying framework (Gaggiotti, O. E. et al, 2018, Evol Appl, 11:1176-1193; <doi:10.1111/eva.12593>), which partitions diversity and differentiation into any hierarchical levels. It helps you easily structure and format your data. It produces diversity profiles (q=0,1,2), hierarchical diversities and differentiation, as well as the the correlation between geographic distance and genetic differentiation.

Version: 0.3.5
Depends: R (≥ 3.0)
Imports: GGally, adegenet, diveRsity, dplyr, entropart, ggplot2, hierfstat, reshape2, tibble, ade4, vegan, ape, pegas, permute
Suggests: knitr, testthat, rmarkdown
Published: 2019-02-13
Author: Xinghu Qin
Maintainer: Xinghu Qin <qinxinghu at gmail.com>
BugReports: https://github.com/xinghuq/HierDpart/issues
License: GPL (≥ 3)
URL: https://github.com/xinghuq/HierDpart
NeedsCompilation: no
SystemRequirements: GNU make
Materials: README
CRAN checks: HierDpart results


Reference manual: HierDpart.pdf
Vignettes: Instruction to Package HierDpart
Package source: HierDpart_0.3.5.tar.gz
Windows binaries: r-devel: HierDpart_0.3.5.zip, r-release: HierDpart_0.3.5.zip, r-oldrel: HierDpart_0.3.5.zip
OS X binaries: r-release: HierDpart_0.3.5.tgz, r-oldrel: HierDpart_0.3.5.tgz
Old sources: HierDpart archive


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