adegenet (version 2.1.10)

Hs: Expected heterozygosity (Hs)

Description

This function computes the expected heterozygosity (Hs) within populations of a genpop object. This function is available for codominant markers (@type="codom") only. Hs is commonly used for measuring within population genetic diversity (and as such, it still has sense when computed from haploid data).

Usage

Hs(x, pop = NULL)

Value

a vector of Hs values (one value per population)

Arguments

x

a genind or genpop object.

pop

only used if x is a genind; an optional factor to be used as population; if not provided, pop(x) is used.

Author

Thibaut Jombart

Details

Let m(k) be the number of alleles of locus k, with a total of K loci. We note \(f_i\) the allele frequency of allele i in a given population. Then, \(Hs\) is given for a given population by:

\(\frac{1}{K} \sum_{k=1}^K (1 - \sum_{i=1}^{m(k)} f_i^2)\)

See Also

Hs.test to test differences in Hs between two groups

Examples

if (FALSE) {
data(nancycats)
Hs(genind2genpop(nancycats))
}