View source: R/ratesHistogram.R
ratesHistogram | R Documentation |
BAMM
rate frequenciesPlots a histogram of the frequency of rate values across the phylogeny.
ratesHistogram(
phylorates,
plotBrks = TRUE,
xlab = "speciation rate",
ylab = "density",
lwd = 0.2,
lty = 1,
brksCol = "black",
...
)
phylorates |
A saved |
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 |
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.
Pascal Title
plot.bammdata
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')
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.