# theta.k: Population Parameter THETA using Expected Number of Alleles In pegas: Population and Evolutionary Genetics Analysis System

 theta.k 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.

### References

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

`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))
```

pegas documentation built on March 7, 2023, 7:21 p.m.