# delta.plot

From ape v2.7-3
by Emmanuel Paradis

##### 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:
- counts

delta.bar the 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

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

*Documentation reproduced from package ape, version 2.7-3, License: GPL (>= 2)*

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