pegas (version 0.10)

theta.s: Population Parameter THETA using Segregating Sites

Description

This function computes the population parameter THETA using the number of segregating sites \(s\) in a sample of \(n\) DNA sequences.

Usage

theta.s(x, ...)
# S3 method for DNAbin
theta.s(x, variance = FALSE, ...)
# S3 method for default
theta.s(x, n, variance = FALSE, ...)

Arguments

x

a numeric giving the number of segregating sites.

n

a numeric giving the number of sequences.

variance

a logical indicating whether the variance of the estimated THETA should be returned (TRUE), the default being FALSE.

…

arguments passed to methods.

Value

A numeric vector of length one with the estimated theta (the default), or of length two if the standard error is returned (variance = TRUE).

References

Watterson, G. A. (1975) On the number of segragating sites in genetical models without recombination. Theoretical Population Biology, 7, 256--276.

Tajima, F. (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 123, 585--595.

See Also

theta.h, theta.k, seg.sites, nuc.div, theta.tree

Examples

# NOT RUN {
data(woodmouse)
theta.s(woodmouse)
theta.s(woodmouse, variance = TRUE)
## using the default:
s <- length(seg.sites(woodmouse))
n <- nrow(woodmouse)
theta.s(s, n)
# }