Miscellaneous R functions for calculating and decomposing multiple hierarchical diversity metrics, including hierarchical allele richness (q=1), 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: | 0.1.2 |
Depends: | R (≥ 3.0) |
Imports: | GGally, adegenet, diveRsity, dplyr, entropart, ggplot2, hierfstat, reshape2, tibble |
Suggests: | knitr, testthat, rmarkdown |
Published: | 2018-10-26 |
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 pPackage HierDpart |
Package source: | HierDpart_0.1.2.tar.gz |
Windows binaries: | r-devel: HierDpart_0.1.2.zip, r-release: HierDpart_0.1.2.zip, r-oldrel: HierDpart_0.1.2.zip |
OS X binaries: | r-release: HierDpart_0.1.2.tgz, r-oldrel: HierDpart_0.1.2.tgz |
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