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, hierarchical exponential Shannon entropy (true diversity of order q=1), hierarchical heterozygosity and genetic differentiation (Jaccard dissimilarity, Delta D, Fst and Jost's D). In addition,a new approach to identify population structure based on the homogeneity of multivariate variances of Shannon differentiation is presented. This package allows users 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. In summary,it implements the analyses of true diversity profiles (q=0, 1, 2), hierarchical diversities and differentiation decomposition, visualization of population structure, as well as the estimation of correlation between geographic distance and genetic differentiation.
| Version: |
1.5.0 |
| Depends: |
R (≥ 3.0) |
| Imports: |
GGally, adegenet, diveRsity, entropart, mmod, ggplot2, hierfstat, reshape2, tibble, ade4, vegan, ape, pegas, permute |
| Suggests: |
knitr, testthat, rmarkdown |
| Published: |
2021-03-31 |
| 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 |
| CRAN checks: |
HierDpart results |
Documentation:
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