reorder.phylo: Internal Reordering of Trees
In gjuggler/ape: Analyses of Phylogenetics and Evolution

Description Usage Arguments Details Value Author(s) See Also Examples

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.

1 2	## S3 method for class 'phylo' reorder(x, order = "cladewise", ...)

`x`	an object of class `"phylo"`.
`order`	a character string: either `"cladewise"` (the default), or `"pruningwise"`, or any unambiguous abbreviation of these.
`...`	further arguments passed to or from other methods.

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.

an object of class "phylo".

Emmanuel Paradis

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

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