TreeTools: RenumberTips – R documentation

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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 class 'phylo'
RenumberTips(tree, tipOrder)

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

## S3 method for class 'list'
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.

Author(s)

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))

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