ape (version 5.8)

delta.plot: Delta Plots

Description

This function makes a \(\delta\) plot following Holland et al. (2002).

Usage

delta.plot(X, k = 20, plot = TRUE, which = 1:2)

Value

This function returns invisibly a named list with two components:

• counts: the counts for the histogram of \(\delta_q\) values

• delta.bar: the mean \(\delta\) value for each observation

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 \(\delta\) plot (the default).

which

a numeric vector indicating which plots are done; 1: the histogram of the \(\delta_q\) values, 2: the plot of the individual \(\bar{\delta}\) values. By default, both plots are done.

Author

Emmanuel Paradis

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 (\(O(n^4)\)), so calculations may be very long with only a slight increase in sample size.

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

dist.dna

Examples

data(woodmouse)
d <- dist.dna(woodmouse)
delta.plot(d)
layout(1)
delta.plot(d, 40, which = 1)