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

Description Usage Arguments Value Author(s) References See Also Examples

View source: R/getMeanBranchLengthTree.R

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

1
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:

Author(s)

Dan Rabosky

References

http://bamm-project.org

See Also

plot.bammdata

Examples

1
2
3
4
5
6
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 May 29, 2017, 5:47 p.m.