addBAMMshifts {BAMMtools} | R Documentation |
Add BAMM
-inferred rate shifts to a phylogeny plot
Description
Adds symbols to a plotted tree to mark the location(s) where there is a shift in the macroevolutionary dynamics of diversification or trait evolution.
Usage
addBAMMshifts(
ephy,
index = 1,
method = "phylogram",
cex = 1,
pch = 21,
col = 1,
bg = 2,
msp = NULL,
shiftnodes = NULL,
par.reset = TRUE,
...
)
Arguments
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. |
... |
additional arguments to be passed to |
Details
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
.
Note
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.
Author(s)
Mike Grundler
See Also
getShiftNodesFromIndex
, plot.bammdata
Examples
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)
}