[Phylobase-devl] labeling order

[Ben Bolker]

  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 (!) ...

  cheers
    Ben


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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-- 
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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