R: Haplotype Diversity

hap.div {pegas} | R Documentation

## Haplotype Diversity

### Description

This function computes haplotype diversity from DNA sequences. This is a generic function.

### Usage

    hap.div(x, ...)
    ## S3 method for class 'haplotype'
    hap.div(x, variance = FALSE, method = "Nei", ...)
    ## S3 method for class 'DNAbin'
    hap.div(x, variance = FALSE, method = "Nei", ...)

### Arguments

`x` | an object with DNA data.
`variance` | a logical value specifying whether to calculate the variance of the estimated haplotype diversity.
`method` | (unused, see details).
`...` | further arguments passed to and from methods.

### Details

Currently, only Nei and Tajima's (1981) method is available.

### Value

a numeric vector with one or two values (if `variance = TRUE`).

### Author(s)

Emmanuel Paradis

### References

Nei, M. and Tajima, F. (1981) DNA polymorphism detectable by restriction endonuclease. Genetics, 97, 145–163.

### See Also

`nuc.div`

### Examples

    data(woodmouse)
    hap.div(woodmouse) # all haplotypes are unique

    ## neuraminidase sequences from the 2009 H1N1 data (delivered with adegenet):
    fl <- system.file("files/pdH1N1-NA.fasta", package = "adegenet")
    H1N1.NA <- read.dna(fl, "fasta")
    hap.div(H1N1.NA, TRUE)

[Package pegas version 1.1 Index]