getMeanBranchLengthTree: Compute phylogeny with branch lengths equal to corresponding...

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

Compute phylogeny with branch lengths equal to corresponding macroevolutionary rate estimates

Description

Takes a bammdata object and computes a phylogenetic tree where branch lengths are equal to the mean of the marginal distributions of rates on each branch. This tree can be plotted to visualize rate variation across a phylogeny.

Usage

getMeanBranchLengthTree(ephy, rate = "speciation")

Arguments

ephy	An object of class bammdata.
rate	The type of rate-tree to be computed. Options: "speciation" (default), "extinction", "ndr" (net diversification), and "trait".

Value

A list with the following components:

• phy: A phylogenetic tree, topologically identical to the model tree, but with branch lengths replaced by the mean (marginal) rates on each branch as estimated from the posterior samples in the bammdata object.

• mean: The mean rate over all branches.

• median: the median rate over all branches.

Author(s)

Dan Rabosky

References

http://bamm-project.org/

See Also

plot.bammdata

Examples

data(whales)
data(events.whales)
ed <- getEventData(whales, events.whales, burnin=0.1, nsamples=500)
ed2 <- subsetEventData(ed, index = 1:20)
ratetree <- getMeanBranchLengthTree(ed2, rate='speciation')
plot(ratetree$phy, show.tip.label=FALSE)

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