Mismatch Distribution
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 = c("blue", "red"), lty = c(1, 1), bw = 2, ...)x |
a set of DNA sequences (object of class |
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 |
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 |
... |
further arguments passed to |
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).
Emmanuel Paradis and David Winter
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)
MMD(woodmouse, lty = 1:2, lcol = rep("black", 2), col = "lightgrey")Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.