# delta.plot

##### Delta Plots

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

- Keywords
- hplot

##### 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 \(\delta\) 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.

##### 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.

##### Value

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

##### 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

```
# NOT RUN {
data(woodmouse)
d <- dist.dna(woodmouse)
delta.plot(d)
layout(1)
delta.plot(d, 40, which = 1)
# }
```

*Documentation reproduced from package ape, version 5.4-1, License: GPL-2 | GPL-3*