I have a tree with no node labels and I am running ACE many times. I
would like to somehow get ACE data, specifically reconstruction$ace
out of R. I can create node labels for my tree using function
makenodelabel, but these don't correspond to the node labels within
the phylo data structure that
Morgan-
The node labels from ace() are the ID numbers used in the edge matrix
(you can see that with tree$edge, where 'tree' is your phylogeny
object), and the are numbered from (Ntip(tree)+1) to
(Ntip(tree)+Ntip(tree)-1). Thus, to give your tree the IDs from the
edge matrix as node labels, just
This is implemented in my phytools package. This is not yet on CRAN,
but can be downloaded from
http://anolis.oeb.harvard.edu/~liam/R-phylogenetics/. The function is
ltt(). It is slow, but seems to work. Please let me know if you have
success with this.
- Liam
--
Liam J. Revell
Hi Liam Rob,
You may try using dist.nodes() for this:
x - dist.nodes(phy)
n - Ntip(phy)
ROOT - n + 1
x[ROOT, ]
The last command returns the distance from the root to all nodes and
tips which are ordered in the usual way. So you may create a vector with
+1 for the nodes, -1 for the tips, and
