theta.k: Population Parameter THETA using Expected Number of Alleles
In dwinter/Pegas: Population and Evolutionary Genetics Analysis System

Description Usage Arguments Details Value Note Author(s) References See Also Examples

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

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

`x`	a vector or a factor.
`n`	a numeric giving the sample size.
`k`	a numeric giving the number of alleles.

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.

A numeric vector of length one with the estimated theta.

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

Emmanuel Paradis

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

theta.h, theta.s, theta.tree

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