MMD {pegas} | R Documentation |
This function draws a histogram of the frequencies of pairwise distances from a set of DNA sequences.
MMD(x, xlab = "Distance", main = "", rug = TRUE, legend = TRUE, lcol = "blue", ...)
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 . |
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.
Emmanuel Paradis
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.
data(woodmouse) MMD(woodmouse, col = "grey") MMD(woodmouse, breaks = 20, legend = FALSE)