TreeTools (version 1.4.1)

CollapseNode: Collapse nodes on a phylogenetic tree

Description

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

Usage

CollapseNode(tree, nodes)
# S3 method for phylo
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.

See Also

Other tree manipulation: AddTip(), ConsensusWithout(), DropTip(), EnforceOutgroup(), LeafLabelInterchange(), MakeTreeBinary(), RenumberTips(), RenumberTree(), Renumber(), RootTree(), SingleTaxonTree(), SortTree(), Subtree()

Examples

# NOT RUN {
set.seed(1)
oldPar <- par(mfrow=c(3, 1), mar=rep(0.5, 4))

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

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

# Collapse by edge number
newTree <- CollapseEdge(tree, c(2, 4))
plot(newTree)

par(oldPar)

# }