R: Nucleotide Diversity

nuc.div {pegas} | R Documentation

## Nucleotide Diversity

### Description

This function computes the nucleotide diversity from a sample of DNA sequences or a set of haplotypes.

### Usage

    nuc.div(x, ...)
    ## S3 method for class 'DNAbin'
    nuc.div(x, variance = FALSE, pairwise.deletion = FALSE, ...)
    ## S3 method for class 'haplotype'
    nuc.div(x, variance = FALSE, pairwise.deletion = FALSE, ...)

### Arguments

`x` | a matrix or a list which contains the DNA sequences.
`variance` | a logical indicating whether to compute the variance of the estimated nucleotide diversity.
`pairwise.deletion` | a logical indicating whether to delete the sites with missing data in a pairwise way. The default is to delete the sites with at least one missing data for all sequences.
`...` | further arguments to be passed.

### Details

This is a generic function with methods for classes `"DNAbin"` and `"haplotype"`. The first method uses the sum of the number of differences between pairs of sequences divided by the number of comparisons (i.e. n(n - 1)/2, where n is the number of sequences). The second method uses haplotype frequencies. It could be that both methods give (slightly) different results because of missing or ambiguous nucleotides: this is generally solved by setting `pairwise.deletion = TRUE`.

The variance of the estimated diversity uses formula (10.9) from Nei (1987). This applies only if all sequences are of the same lengths, and cannot be used if `pairwise.deletion = TRUE`. A bootstrap estimate may be in order if you insist on using the latter option.

### Value

A numeric vector with one or two values if `variance = TRUE`.

### Author(s)

Emmanuel Paradis

### References

Nei, M. (1987) Molecular evolutionary genetics. New York: Columbia University Press.

### See Also

`base.freq`, `GC.content`, `theta.s`, `seg.sites`

### Examples

    data(woodmouse)
    nuc.div(woodmouse)
    nuc.div(woodmouse, TRUE)
    nuc.div(woodmouse, FALSE, TRUE)

[Package pegas version 1.1 Index]