R: Delta Plots

delta.plot {ape} | R Documentation

## 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)

### 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 delta.bar 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

### 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

`dist.dna`

### Examples

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

[Package ape version 4.1 Index]