pegas (version 0.1)

MMD: 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 = "blue", ...)

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 distances on the horizontal axis (see rug).

legend

a logical specifying whether to draw a legend.

lcol

the colour used for the empirical density curve.

...

further arguments passed to hist.

Details

Currently only the observed distribution of pairwise distances are plotted, as well as an empirical density estimate. Rogers and Harpending (1992) give formulae to compute the expected curves under some demographic models.

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)