addBAMMshifts: Add 'BAMM'-inferred rate shifts to a phylogeny plot

In BAMMtools: Analysis and Visualization of Macroevolutionary Dynamics on Phylogenetic Trees

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 bammdata.
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 NULL, an object of class phylo where each branch length is equal to the marginal probability of a shift occurring on that branch. Plotted points corresponding to shifts will be sized by these probabilities.
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 points.

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)	
}

BAMMtools documentation built on Sept. 13, 2024, 1:10 a.m.