TreeTools (version 1.0.0)

RootTree: Root or unroot a phylogenetic tree

Description

RootTree() roots a tree on the smallest clade containing the specified tips; RootOnNode() roots a tree on a specified internal node; UnrootTree() collapses a root node, without the undefined behaviour encountered when using ape::unroot() on trees in preorder.

Usage

RootTree(tree, outgroupTips)
RootOnNode(tree, node, resolveRoot = FALSE)
UnrootTree(tree)

Arguments

tree

A tree of class phylo.

outgroupTips

Vector of type character, integer or logical, specifying the names or indices of the tips to include in the outgroup.

node

integer specifying node (internal or tip) to set as the root.

resolveRoot

logical specifying whether to resolve the root node.

Value

RootTree() returns a tree of class phylo, rooted on the smallest clade that contains the specified tips.

RootOnNode() returns a tree of class phylo, rooted on the requested node and ordered in Preorder.

UnrootTree() returns a tree of class phylo, in preorder, having collapsed the first child of the root node.

See Also

• ape::root()

• EnforceOutgroup()

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

Examples

# NOT RUN {
tree <- PectinateTree(8)
plot(tree)
ape::nodelabels()

plot(RootTree(tree, c('t6', 't7')))

plot(RootOnNode(tree, 12))
plot(RootOnNode(tree, 2))

# }