delta.plot {ape} | R Documentation |
Delta Plots
Description
This function makes a plot following Holland et
al. (2002).
Usage
delta.plot(X, k = 20, plot = TRUE, which = 1:2)
Arguments
X |
a distance matrix, may be an object of class “dist”. |
k |
an integer giving the number of intervals in the plot. |
plot |
a logical specifying whether to draw the
|
which |
a numeric vector indicating which plots are done; 1: the
histogram of the |
Details
See Holland et al. (2002) for details and interpretation.
The computing time of this function is proportional to the fourth
power of the number of observations (), so calculations
may be very long with only a slight increase in sample size.
Value
This function returns invisibly a named list with two components:
counts: the counts for the histogram of
values
delta.bar: the mean
value for each observation
Author(s)
Emmanuel Paradis
References
Holland, B. R., Huber, K. T., Dress, A. and Moulton, V. (2002) Delta plots: a tool for analyzing phylogenetic distance data. Molecular Biology and Evolution, 12, 2051–2059.
See Also
Examples
data(woodmouse)
d <- dist.dna(woodmouse)
delta.plot(d)
layout(1)
delta.plot(d, 40, which = 1)