# nuc.div

##### Nucleotide Diversity

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

##### Usage

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

.

##### References

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

##### See Also

##### Examples

```
# NOT RUN {
data(woodmouse)
nuc.div(woodmouse)
nuc.div(woodmouse, TRUE)
nuc.div(woodmouse, FALSE, TRUE)
# }
```

*Documentation reproduced from package pegas, version 0.12, License: GPL (>= 2)*