View source: R/addBAMMshifts.R
addBAMMshifts | R Documentation |
BAMM
-inferred rate shifts to a phylogeny plotAdds symbols to a plotted tree to mark the location(s) where there is a shift in the macroevolutionary dynamics of diversification or trait evolution.
addBAMMshifts( ephy, index = 1, method = "phylogram", cex = 1, pch = 21, col = 1, bg = 2, msp = NULL, shiftnodes = NULL, par.reset = TRUE )
ephy |
An object of class |
index |
An integer indicating which posterior sample to use for adding shifts to the plotted tree. |
method |
A character string indicating the method used in plotting. Must be "polar" or "phylogram". |
cex |
A numeric indicating the character expansion ("size") of the plotted points. |
pch |
An integer indicating the choice of plotting symbol. |
col |
An integer or character string indicating the border color of the plotting symbol. |
bg |
An integer or character string indicating the background color of the plotting symbol. |
msp |
If not |
shiftnodes |
An optional vector of node numbers indicating the locations of shifts to plot. |
par.reset |
A logical indicating whether to reset the graphical parameters before exiting. |
Any given sample from the posterior distribution sampled using
BAMM
contains a potentially unique configuration of rate shifts
and associated parameters. There is no single "best" rate shift, but
rather a set of shift configurations (and associated parameters) -
along with their relative probabilities - sampled with MCMC. This
function enables the user to plot the locations of shifts sampled with
BAMM
for a given sample from the posterior.
If the bammdata
object contains just a single sample, these
shifts will be plotted regardless of the value of index
.
If a shiftnodes
argument is passed care should be taken to
ensure that the nodes are in the same order as in the event data for
the sample index.
Mike Grundler
getShiftNodesFromIndex
, plot.bammdata
data(whales, events.whales) ed <- getEventData(whales, events.whales, burnin=0.25, nsamples = 500) # adding shifts to tree for specific posterior samples plot(ed, method="polar") addBAMMshifts(ed, index=5, "polar") # multi-panel plotting and adding shifts par(mfrow=c(2,3),mar=c(5,1,1,1)) samples = sample(1:length(ed$eventData), 6) for (i in 1:6) { sed <- subsetEventData(ed, samples[i]) plot(sed, par.reset=FALSE) addBAMMshifts(sed,index=1,method="phylogram",par.reset=FALSE) }
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