MMD: Mismatch Distribution

In dwinter/Pegas: Population and Evolutionary Genetics Analysis System

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 pairwise 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.

Author(s)

Emmanuel Paradis

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)

dwinter/Pegas documentation built on May 15, 2019, 6:21 p.m.