delta.plot {ape} | R Documentation |
This function makes a delta plot following Holland et al. (2002).
delta.plot(X, k = 20, plot = TRUE, which = 1:2)
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 delta.bar values. By default, both plots are done. |
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.
This function returns invisibly a named list with two components:
countsthe counts for the histogram of delta_q values
delta.barthe mean delta value for each observation
Emmanuel Paradis
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.
data(woodmouse) d <- dist.dna(woodmouse) delta.plot(d) layout(1) delta.plot(d, 40, which = 1)