TreeTools (version 0.1.3)

CollapseNode: Collapse nodes on a phylogenetic tree

Description

Collapses specified nodes or edges on a phylogenetic tree, resulting in polytomies.

Usage

CollapseNode(tree, nodes)
CollapseEdge(tree, edges)

Arguments

tree

A tree of class phylo.

nodes, edges

Integer vector specifying the nodes or edges in the tree to be dropped. (Use nodelabels or edgelabels to view numbers on a plotted tree.)

Value

CollapseNode and CollapseEdge return a tree of class phylo, corresponding to tree with the specified nodes or edges collapsed. The length of each dropped edge will (naively) be added to each descendant edge.

Examples

# NOT RUN {
library(ape)
set.seed(1)
oldPar <- par(mfrow=c(2, 1), mar=rep(0.5, 4))

tree <- rtree(7)
plot(tree)
nodelabels()
edgelabels(round(tree$edge.length, 2), cex=0.6, frame='n', adj=c(1, -1))

newTree <- CollapseNode(tree, c(12, 13))
plot(newTree)
nodelabels()
edgelabels(round(newTree$edge.length, 2), cex=0.6, frame='n', adj=c(1, -1))

par(oldPar)

# }