R: Population Parameter THETA using Expected Number of Alleles

theta.k {pegas} | R Documentation

## 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))

[Package pegas version 0.13 Index]