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TreeTools (version 1.12.0)

RenumberTips: Renumber a tree's tips

Description

RenumberTips(tree, tipOrder) sorts the tips of a phylogenetic tree tree such that the indices in tree[["edge"]][, 2] correspond to the order of leaves given in tipOrder.

Usage

RenumberTips(tree, tipOrder)

# S3 method for phylo RenumberTips(tree, tipOrder)

# S3 method for multiPhylo RenumberTips(tree, tipOrder)

# S3 method for list RenumberTips(tree, tipOrder)

# S3 method for `NULL` RenumberTips(tree, tipOrder)

Value

RenumberTips() returns tree, with the tips' internal representation numbered to match tipOrder.

Arguments

tree

A tree of class phylo.

tipOrder

A character vector containing the values of tree[["tip.label"]] in the desired sort order, or an object (perhaps of class phylo or Splits) with tip labels.

See Also

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

Examples

Run this code
data("Lobo") # Loads the phyDat object Lobo.phy
tree <- RandomTree(Lobo.phy)
tree <- RenumberTips(tree, names(Lobo.phy))

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