pegas (version 0.8-2)

theta.k: Population Parameter THETA using Expected Number of Alleles

Description

This function computes the population parameter THETA using the expected number of alleles.

Usage

theta.k(x, n = NULL, k = NULL)

Arguments

x

a vector or a factor.

n

a numeric giving the sample size.

k

a numeric giving the number of alleles.

Value

• A numeric vector of length one with the estimated theta.

Details

This function can be used in two ways: either with a vector giving the individual genotypes from which the sample size and number of alleles are derived (e.g., theta.k(x)), or giving directly these two quantities (e.g., theta.k(n = 50, k = 5)).

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.

Both arguments n and k must be single numeric values.

References

Ewens, W. J. (1972) The sampling theory of selectively neutral alleles. Theoretical Population Biology, 3, 87--112.

See Also

theta.h, theta.s, theta.tree

Examples

data(jaguar)
## convert the data and compute frequencies:
S <- summary(jaguar)
## compute THETA for all loci:
sapply(S, function(x) theta.k(x$allele))