ratesHistogram {BAMMtools}

Histogram of BAMM rate frequencies

Description

Plots a histogram of the frequency of rate values across the phylogeny.

Usage

ratesHistogram(
  phylorates,
  plotBrks = TRUE,
  xlab = "speciation rate",
  ylab = "density",
  lwd = 0.2,
  lty = 1,
  brksCol = "black",
  ...
)

Arguments

phylorates

A saved plot.bammdata object.

plotBrks

Boolean, should breaks be plotted over the histogram.

xlab

x-axis label.

ylab

y-axis label.

lwd

Line width for breaks.

lty

Line style for breaks.

brksCol

Color of breaks lines.

...

Additional arguments passed on to mtext for axis labels.

Details

With this function, a histogram is plotted that shows the frequency of rates present in the dataset. The color scheme plotted is taken from the saved plot.bammdata object that is the main input. Therefore, the mapping of colors to rates in the histogram corresponds exactly to what is plotted in the phylorate plot. If plotBrks = TRUE, then the color breaks used for the phylorates plot are shown.

This function can be a useful tool for exploring different plot.bammdata options. Please see http://bamm-project.org/colorbreaks.html on the bamm-project website for more information on the utility of this function.

Author(s)

Pascal Title

References

http://bamm-project.org/

See Also

plot.bammdata

Examples

data(primates, events.primates)
ed <- getEventData(primates, events.primates, burnin=0.25, nsamples=500,
                   type = 'trait')

# create phylorate plot with the jenks breaks method to generate output
phylorates <- plot(ed, breaksmethod='jenks', show = FALSE)

ratesHistogram(phylorates, plotBrks = TRUE, xlab = 'trait rates')