| reorder.phylo {ape} | R Documentation |
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.
## S3 method for class 'phylo' reorder(x, order = "cladewise", ...)
x |
an object of class |
order |
a character string: either |
... |
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