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

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')

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
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Type 'license()' or 'licence()' for distribution details.

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'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(BAMMtools)
Loading required package: ape
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/BAMMtools/ratesHistogram.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ratesHistogram
> ### Title: Histogram of 'BAMM' rate frequencies
> ### Aliases: ratesHistogram
> 
> ### ** Examples
> 
> data(primates, events.primates)
> ed <- getEventData(primates, events.primates, burnin=0.25, nsamples=500,
+                    type = 'trait')
Processing event data from data.frame

Discarded as burnin: GENERATIONS <  4990000
Analyzing  500  samples from posterior

Setting recursive sequence on tree...

Done with recursive sequence

> 
> # 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')
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>