removing files that have moved to pegas

[ape.git] / man / heterozygosity.Rd

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-\name{heterozygosity}
-\alias{heterozygosity}
-\alias{H}
-\title{Heterozygosity at a Locus Using Gene Frequencies}
-\usage{
-heterozygosity(x, variance = FALSE)
-H(x, variance = FALSE)
-}
-\arguments{
-  \item{x}{a vector or a factor.}
-  \item{variance}{a logical indicating whether the variance of the 
-    estimated heterozygosity should be returned (\code{TRUE}), the
-    default being \code{FALSE}.}
-}
-\description{
-  This function computes the mean heterozygosity from gene frequencies,
-  and returns optionally the associated variance.
-}
-\value{
-  a numeric vector of length one with the estimated mean heterozygosity
-  (the default), or of length two if the variance is returned
-  \code{variance = TRUE}.
-}
-\details{
-  The argument \code{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:
-
-  \deqn{\hat{H} = \frac{n}{n-1} \left(1 - \sum_{i=1}^k p_i^2 \right)}{%
-    H = n(1 - SUM (FROM i=1 TO k) p_i^2)/(n - 1)}
-
-  where \eqn{n} is the number of genes in the sample, \eqn{k} is the
-  number of alleles, and \eqn{p_i} is the observed (relative) frequency
-  of the allele \eqn{i}.
-}
-\references{
-  Nei, M. (1987) \emph{Molecular evolutionary genetics}. New York:
-  Columbia University Press.
-}
-\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}}
-\seealso{
-  \code{\link{theta.s}}
-}
-\keyword{manip}
-\keyword{univar}