Collapse nodes on a phylogenetic tree
Collapses specified nodes or edges on a phylogenetic tree, resulting in polytomies.
CollapseNode(tree, nodes) ## S3 method for class 'phylo' CollapseNode(tree, nodes) CollapseEdge(tree, edges)
tree |
A tree of class |
nodes, edges |
Integer vector specifying the nodes or edges in the tree
to be dropped.
(Use |
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.
Martin R. Smith
Other tree manipulation:
AddTip(),
ConsensusWithout(),
DropTip(),
EnforceOutgroup(),
LeafLabelInterchange(),
MakeTreeBinary(),
RenumberTips(),
RenumberTree(),
Renumber(),
RootTree(),
SingleTaxonTree(),
SortTree(),
Subtree()
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)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.