plot.beast.object {beast}

Plot function

Description

This function plots objects returned by the beast function. All output is diverted to a pdf file provided in the fileName argument.

Usage

## S3 method for class 'beast.object'
plot(x, fileName, width, height, pointsize, ylab, xlab, timeScale, myPal, boxwex, ...)

Arguments

x

An object of class beast.object, which is returned by the beast function.

fileName

Name of the output pdf file.

width

Width of pdf file. Default: 9

height

Height pdf file. Default: 6

pointsize

Pointsize. Default: 12

ylab

y-axis label. Default: x.

xlab

x-axis label. Default: t.

timeScale

A multiplicative-factor which will be used to scale the x-axis labels. For example, if time-points correspond to 10-minute periods, then setting timeScale = 1/6 will make the x-axis labels correspond to hours. Default: timeScale = 1.

myPal

Vector of colors that will be used to produce the plot with all time-series overlayed. If the distinct values of the inferred numbers of change-points is less than 10, the Set1 pallete of the RColorBrewer library is used. Otherwise, the user has to manually define the colors.

boxwex

A scale factor to be applied to all boxes. The appearance of the plot can be improved by making the boxes narrower or wider. Default: 0.2.

...

ignored.

Details

The function will produce a plot with all time-series coloured according to the corresponding number of change-points. In addition, it will generate individual plots per time-series displaying the observed data with boxplots which summarize the posterior distribution of change-points locations, conditionally on the most probable number of change-points.

Author(s)

Panagiotis Papastamoulis