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