HierDq: Calculating hierarchical diversity based on Hill numbers

In xinghuq/HierDmap: Visualizing the geo-biodiversity profiles and the hierarchical structure of biodiversity

Calculating hierarchical diversity based on Hill numbers

Description

Calculating hierarchical diversity based on Hill numbers.When q=0, it is richness, when q=1, it is diversity of Shannon (exponential of shannon entropy), when q=2, it is diversity of Simpson.

Usage

HierDq(x, q, nreg, r, ncode)

Arguments

x	Genotype file, current version accepts genepop format.
q	The order of Hill numbers
nreg	number of regions
r	The population arrangement or the hierarchy in the region
ncode	The genotype coding type

Details

The function calculates diversity at ecosystem level, regional level, and local population level based on HierDpart package (Qin, X.2019).

Value

Diversity at ecosystem level, regional level, and local population level.

Author(s)

[e-mail]

References

Qin, X. (2019). HierDpart: partitioning hierarchical diversity and differentiation across metrics and scales, from genes to ecosystems. R package version 0.5. 0 https://cran. r-project. org/package= HierDpart.

Examples

f <- system.file('extdata',package='HierDpart')
infile <- file.path(f, "Island.gen")
file =  diveRsity::readGenepop(infile, gp=2, bootstrap = FALSE)
HierDisland=HierDq(infile,q=2,ncode=3,nreg = 4,r=c(7,4,2,3))

xinghuq/HierDmap documentation built on July 2, 2023, 10:46 a.m.