[Phylobase-devl] stalled ...

Ben Bolker bolker at ufl.edu
Fri Jan 16 04:31:41 CET 2009

Steven Kembel wrote:
> Hi Ben,
>>> 2. see what we can do to detect & fix problems with unrooted trees:
>>> this includes a lot of Steve's "to do" list (sorting out nodeId,
>>> nNode, etc.)
>>  ???
> I can look at this but probably won't get a chance to do so for a week  
> if anyone else wants to tackle it. If we've settled on the nodeId/edge  
> order question it should just be a matter of checking things like  
> nNode in construction and print methods to make sure they work with  
> unrooted trees.

  You might end up doing it ...
>>> 6. with some input from Emmanuel, implement SOME form of
>>> checking/consistency rule for ordering when importing/exporting
>>> from/to ape
>>   NOT DONE. Volunteers?
> It sounded like pruningwise is maybe subtly different than preorder so  
> not sure what to do on import from ape but for export to ape can we  
> simply reorder the tree preorder?

  We could choose to allow "pruningwise" as an option (not one we
generate, but one we allow).

>>> 2. adding metadata/annotation slots, although if we know
>>> their GENERAL form it would be nice to add them to phylo4[d]
>>> objects now because adding slots later breaks backward compatibility
>>> of saved objects (but we may just have to bite the bullet and
>>> do it later).  In particular if these were slots of type list()
>>> we could be vague about what we were going to put in (at the
>>> cost of less-strong typing of the objects)
>>  Could add as list() if we can agree on names for the slots,
>> how many.
> I think a single @metadata slot should be enough, if it's a list we  
> can put whatever else we want in there in the future. An annotation  
> slot is tricky, if annotations are going to be attached to nodes/edges  
> they can be phylo4d data, but if they apply to the whole tree they can  
> be metadata, so just a @metadata slot may be enough?

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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