TreeTools (version 1.10.0)

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)

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.

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.)

Author

Martin R. Smith

See Also

Other tree manipulation: AddTip(), ConsensusWithout(), DropTip(), EnforceOutgroup(), ImposeConstraint(), KeptPaths(), KeptVerts(), LeafLabelInterchange(), MakeTreeBinary(), RenumberTips(), RenumberTree(), Renumber(), RootTree(), SortTree(), Subtree(), TipTimedTree(), TrivialTree

Examples

oldPar <- par(mfrow = c(3, 1), mar = rep(0.5, 4))

tree <- as.phylo(898, 7)
tree$edge.length <- 11:22
plot(tree)
nodelabels()
edgelabels()
edgelabels(round(tree$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)