R: Allelic Richness and Rarefaction Plots

allelicrichness {pegas} | R Documentation

## Allelic Richness and Rarefaction Plots

### Description

These functions analyse allelic richness.

### Usage

    allelicrichness(x, pop = NULL, method = "extrapolation")
    rarefactionplot(x, maxn = nrow(x), type = "l", xlab = "Sample size",
                    ylab = "Expected number of alleles", plot = TRUE, ...)
    rhost(x, pop = NULL, method = "extrapolation")

### Arguments

`x` | an object of class `"loci"`.
`pop` | a vector or factor giving the population assignment of each row of `x`, or a single numeric value specifying which column of `x` to use as population indicator. By default, the column labelled `"population"` is used.
`method` | a character string which should be one of “extrapolation”, “rarefaction”, “raw” or an unambiguous abbreviation of these.
`maxn` | the largest sample size used to calculate the rarefaction curve.
`type, xlab, ylab` | arguments passed to `plot`.
`plot` | a logical value specifying whether to do the rarefaction plot (`TRUE` by default).
`...` | arguments passed to and from methods.

### Details

`allelicrichness` computes for each locus in `x` the estimated allelic richness. Three methods are available: the extrapolation method (Foulley and Ollivier 2006), the rarefaction method (Hurlbert 1971), and the raw numbers of alleles.

`rarefactionplot` computes the rarefaction curves of the number of alleles with respect to sample size using the Hurlbert's (1971) method. A plot is made by default.

### Value

`allelicrichness` returns a numeric matrix.

`rarefactionplot` returns invisibly a list of matrices with the coordinates of the rarefaction plots for each locus.

`rhost` returns a numeric vector.

### Author(s)

Emmanuel Paradis

### References

El Mousadik, A. and Petit, R. J. (1996) High level of genetic differentiation for allelic richness among populations of the argan tree [Argania spinosa (L. Skeels)] endemic to Morocco. Theoretical and Applied Genetics, 92, 832–836.

Foulley, J. L. and Ollivier, L. (2006) Estimating allelic richness and its diversity. Livestock Science, 101, 150–158.

Hurlbert, S. H. (1971) The nonconcept of species diversity: a critique and alternative parameters. Ecology, 52, 577–586.

### Examples

    data(jaguar)
    rarefactionplot(jaguar)
    allelicrichness(jaguar)
    rhost(jaguar)

[Package pegas version 0.13 Index]