Hi Alastair.
If I understand this correctly, you should be able to compute the
Strahler number for the tree (and all the nodes) with one post-order
tree traversal - which is easy if you reorder the tree "pruningwise"
using the ape function reorder.phylo.
I have written a function that I think does this - I posted it to my
blog here:
http://blog.phytools.org/2013/04/computing-strahler-numbers-for-nodes-on.html.
Check it out and let us know if this does what it is supposed to.
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 4/19/2013 3:06 PM, Alastair Potts wrote:
Hi all,
Can anyone suggest an easy way of determining Strahler numbers of nodes on
a given phylogenetic tree (see http://en.wikipedia.org/wiki/Strahler_number for
details).
I have been trying this out (manually plotting the numbers) with another
set of metrics for estimating branching complexity across a range of
different trees, and I am actually quite happy with it. It is very
intuitive and often makes a lot of sense, both highlighting common groups
and oddities (for example when a node Strahler number 2 joins with a
Strahler number of, say 10, this usually indicates an odd group that is
fairly ancient that has not undergone any radiation, or experienced high
extinction rates).
I am sure that the key is using the mrca() function, and I have been
playing around with this for a few days now, but all of my solutions seem
to have little bugs in them. As my coding is exceptionally clumsy, I'll try
provide an example if no-one sees a obvious and easy way to do this.
Thanks very much in advance,
Cheers,
Alastair
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