A coordinate method to use for plotting. Options are
"phylogram" or "polar".
pal
A color palette to use with plot.bammdata.
shiftColor
Color to use for shift points.
spex
A character string indicating what type of macroevolutionary
rates should be plotted. "s" (default) indicates speciation rates, "e"
indicates extinction rates, and "netdiv" indicates net diversification
rates. Ignored if ephy$type = "trait".
add.freq.text
A logical indicating whether to add the posterior
frequency of each shift configuration to the plotting region.
use.plot.bammdata
A logical indicating whether to use
plot.bammdata (TRUE) or plot.phylo
(FALSE).
border
A logical indicating whether to frame the plotting region.
legend
A logical indicating whether to plot a legend.
send2pdf
A logical indicating whether to print the figure to a PDF
file.
logcolor
A logical indicating whether the rates should be
log-transformed.
breaksmethod
Method used for determining color breaks. See help
file for assignColorBreaks.
color.interval
Min and max value for the mapping of rates. One of
the two values can be NA. See details in
plot.bammdata for further details.
JenksSubset
If breaksmethod = "jenks", the number of
regularly spaced samples to subset from the full rates vector. Only
relevant for large datasets. See help file for
assignColorBreaks.
...
Further arguments to pass to plot.bammdata.
Details
This produces phylorate plots for the plotmax
most-probable shift configurations sampled with BAMM. Shift
configurations are plotted in a single graphics window. The posterior
probability (frequency) of each rate shift configuration in the
posterior is shown (omitted with argument add.freq.text = FALSE).
Points are added to the branches subtending the nodes of each rate
configuration. The size of the point is proportional to the marginal
probability that a shift occurs on a specific branch.
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.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'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/plot.credibleshiftset.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plot.credibleshiftset
> ### Title: Plot credible set of rate shift configurations from 'BAMM'
> ### analysis
> ### Aliases: plot.credibleshiftset
>
> ### ** Examples
>
> data(events.whales)
> data(whales)
> ed <- getEventData(whales, events.whales, nsamples=500)
Processing event data from data.frame
Discarded as burnin: GENERATIONS < 0
Analyzing 500 samples from posterior
Setting recursive sequence on tree...
Done with recursive sequence
> cset <- credibleShiftSet(ed, expectedNumberOfShifts = 1, threshold = 5)
> plot(cset)
Omitted 0 plots
>
>
>
>
>
> dev.off()
null device
1
>