heterozygosity {ape}R Documentation

Heterozygosity at a Locus Using Gene Frequencies

Description

This function computes the mean heterozygosity from gene frequencies, and returns optionally the associated variance.

Usage

heterozygosity(x, variance = FALSE)
H(x, variance = FALSE)

Arguments

x a vector or a factor.
variance a logical indicating whether the variance of the estimated heterozygosity should be returned (TRUE), the default being FALSE.

Details

The argument x can be either a factor or a vector. If it is a factor, then it is taken to give the individual alleles in the population. If it is a numeric vector, then its values are taken to be the numbers of each allele in the population. If it is a non-numeric vector, it is a coerced as a factor.

The mean heterozygosity is estimated with:

H = n(1 - SUM (FROM i=1 TO k) p_i^2)/(n - 1)

where n is the number of genes in the sample, k is the number of alleles, and p_i is the observed (relative) frequency of the allele i.

Value

a numeric vector of length one with the estimated mean heterozygosity (the default), or of length two if the variance is returned variance = TRUE.

Author(s)

Emmanuel Paradis paradis@isem.univ-montp2.fr

References

Nei, M. (1987) Molecular Evolutionary Genetics. New York: Columbia University Press.

See Also

theta.s


[Package ape version 1.7 Index]