reorder.phylo

0th

Percentile

Internal Reordering of Trees

This function changes the internal structure of a phylogeny stored as an object of class "phylo". The tree returned is the same than the one input, but the ordering of the edges could be different.

Keywords
manip
Usage
## S3 method for class 'phylo':
reorder(x, order = "cladewise", ...)
Details

Because in a tree coded as an object of class "phylo" each branch is represented by a row in the element `edge', there is an arbitrary choice for the ordering of these rows. reorder allows to reorder these rows according to two rules: in the "cladewise" order each clade is formed by a series of contiguous rows; this is the order returned by read.tree. In the "pruningwise" order, rows are arranged so that ``pruning'' the tree (or post-order tree traversal) can be done by descending along the rows of `edge'. The possible multichotomies and branch lengths are preserved.

Value

an object of class "phylo".

See Also

read.tree to read tree files in Newick format, reorder for the generic function

Aliases
Examples
data(bird.families)
tr <- reorder(bird.families, "p")
all.equal(bird.families, tr) # uses all.equal.phylo actually
all.equal.list(bird.families, tr) # bypasses the generic
Documentation reproduced from package ape, version 3.0-2, License: GPL (>= 2)

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