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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 'Splits'
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, an object (perhaps of class phylo or Splits) with tip labels, or a numeric specifying the desired order.

Value

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

See also

Other tree manipulation: AddTip(), CollapseNode(), ConsensusWithout(), DropTip(), 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))