TreeTools: RootTree – R documentation

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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`, or a list of trees of class `list` or `multiPhylo`.
`outgroupTips`	Vector of type character, integer or logical, specifying the names or indices of the tips to include in the outgroup. If `outgroupTips` is a of type character, and a tree contains multiple tips with a matching label, the first will be used.
`node`	integer specifying node (internal or tip) to set as the root.
`resolveRoot`	logical specifying whether to resolve the root node.

Details

Note: Edge lengths are not (yet) supported. Contact the maintainer or file a GitHub issue if you would find this useful.

Value

RootTree() returns a tree of class phylo, rooted on the smallest clade that contains the specified tips, with edges and nodes numbered in preorder.

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

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

Author(s)

Martin R. Smith (martin.smith@durham.ac.uk)

Examples

tree <- PectinateTree(8)
plot(tree)
ape::nodelabels()

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

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

TreeTools

Create, Modify and Analyse Phylogenetic Trees

v1.4.4

GPL (>= 3)

Authors

Martin R. Smith [aut, cre, cph] (<https://orcid.org/0000-0001-5660-1727>), Emmanuel Paradis [cph] (<https://orcid.org/0000-0003-3092-2199>)

Initial release