theta.k {pegas}

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.

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.

Value

A numeric vector of length one with the estimated theta.

Note

For the moment, no standard-error or confidence interval is computed.

Author(s)

Emmanuel Paradis

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