R: Mismatch Distribution

MMD {pegas} | R Documentation

## Mismatch Distribution

### Description

This function draws a histogram of the frequencies of pairwise distances from a set of DNA sequences.

### Usage

    MMD(x, xlab = "Distance", main = "", rug = TRUE, legend = TRUE,
        lcol = c("blue", "red"), lty = c(1, 1), bw = 2, ...)

### Arguments

`x` | a set of DNA sequences (object of class `"DNAbin"`).
`xlab` | the label for the x-axis.
`main` | the title (none by default).
`rug` | a logical specifying whether to add a rug of the pairwise distances on the horizontal axis (see `rug`).
`legend` | a logical specifying whether to draw a legend.
`lcol` | the colours used for the curves.
`lty` | the line types for the curves
`bw` | the bandwidth used for the empirical density curve (passed to `density`).
`...` | further arguments passed to `hist`.

### Details

The histogram shows the observed distribution of pairwise distances. The lines show an empirical density estimate (in blue) and the expected distribution under stable population (Rogers and Harpending 1992).

### Author(s)

Emmanuel Paradis and David Winter

### References

Rogers, A. R. and Harpending, H. (1992) Population growth makes waves in the distribution of pairwise genetic-differences. Molecular Biology and Evolution, 9, 552–569.

### Examples

    data(woodmouse)
    MMD(woodmouse, col = "grey")
    MMD(woodmouse, breaks = 20, legend = FALSE)
    MMD(woodmouse, lty = 1:2, lcol = rep("black", 2), col = "lightgrey")

[Package pegas version 1.1 Index]