adegenet: Hs – R documentation

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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)

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.

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} ∑_{k=1}^K (1 - ∑_{i=1}^{m(k)} f_i^2)

Value

a vector of Hs values (one value per population)

Author(s)

Thibaut Jombart t.jombart@imperial.ac.uk

Examples

## Not run: 
data(nancycats)
Hs(genind2genpop(nancycats))

## End(Not run)

adegenet

Exploratory Analysis of Genetic and Genomic Data

v2.1.3

GPL (>= 2)

Authors

Thibaut Jombart [aut] (<https://orcid.org/0000-0003-2226-8692>), Zhian N. Kamvar [aut, cre] (<https://orcid.org/0000-0003-1458-7108>), Caitlin Collins [ctb], Roman Lustrik [ctb], Marie-Pauline Beugin [ctb], Brian J. Knaus [ctb], Peter Solymos [ctb], Vladimir Mikryukov [ctb], Klaus Schliep [ctb], Tiago Maié [ctb], Libor Morkovsky [ctb], Ismail Ahmed [ctb], Anne Cori [ctb], Federico Calboli [ctb], RJ Ewing [ctb], Frédéric Michaud [ctb], Rebecca DeCamp [ctb], Alexandre Courtiol [ctb] (<https://orcid.org/0000-0003-0637-2959>)

Initial release

Hs