tbea (version 1.6.1)

summaryBrlen: summaryBrlen: Summarise branch lengths on trees with identical topology

Description

summaryBrlen: Summarise branch lengths on trees with identical topology

Usage

summaryBrlen(mphy, method)

Value

A tree of class phylo with summary branch lengths in tree$edge.length.

Arguments

mphy

An list of objects of class multiPhylo. If a single object in this argument is of class multiPhylo, it is first enclosed in a list.

method

A character with the function name for the summary to be applied

Details

This function can be used on the output of topofreq from the $trees element in order to summarise the branch length on each topology set so that we have a single tree summarising both topology and branch lengths. Useful for depicting posterior tree density. Alternatively, it can be used with a single element provided that it is first enclosed in a list

Examples

# \donttest{
set.seed(1)
library(ape)
trl <- ape::rmtree(10, 4)
tpf <- topoFreq(unroot(trl), output="trees")
sumtrees <- summaryBrlen(tpf$trees, method = "median")
oldpar <- par(no.readonly = TRUE)
par(mfrow=c(1,3))
plot(sumtrees[[1]], type="unrooted", show.node.label=FALSE, cex=1.5)
plot(sumtrees[[2]], type="unrooted", show.node.label=FALSE, cex=1.5)
plot(sumtrees[[3]], type="unrooted", show.node.label=FALSE, cex=1.5)
par(oldpar)
# }