[Phylobase-devl] labeling order

Ben Bolker bolker at ufl.edu
Wed Dec 24 20:55:19 CET 2008

  DON'T ADD SORT AT THE END OF nodeId(), please.
  nodeId() is the one remaining function that allows the end user
to get the actual order of the nodes (short of edge(object)[,2] etc.).
If you want to add a "sort" argument to the method (default FALSE)
that's OK with me, but we need nodeId to be able to do the
sorting-into-edge-matrix order operation (!) ...


François Michonneau wrote:
>> I'd say yes. I added sort() at the end of nodeId should I commit it (I
>> understood it was the agreement). It also fixes:
>> nodeLabels(tr) <- as.character(nodeId(tr))
> .... but it breaks the prune function which calls some APE functions.
> On Wed, 2008-12-24 at 11:21 -0500, Ben Bolker wrote:
>> Shall I go ahead and bite the bullet/move to putting & leaving
>> underlying representation (@node.label, @tip.label, etc.) in
>> node ID order?
>>   Ben
>> _______________________________________________
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>> Phylobase-devl at lists.r-forge.r-project.org
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Ben Bolker
Associate professor, Biology Dep't, Univ. of Florida
bolker at ufl.edu / www.zoology.ufl.edu/bolker
GPG key: www.zoology.ufl.edu/bolker/benbolker-publickey.asc

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