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Renumber a tree's tips

Source: R/tree_numbering.R
RenumberTips.Rd

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 class 'phylo'
RenumberTips(tree, tipOrder)

# S3 method for class 'multiPhylo'
RenumberTips(tree, tipOrder)

# S3 method for class 'list'
RenumberTips(tree, tipOrder)

# S3 method for class '`NULL`'
RenumberTips(tree, 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.

Value

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

See also

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

Author

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

Examples

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