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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