[Phylobase-devl] stalled ...

Ben Bolker bolker at ufl.edu
Fri Jan 16 04:30:34 CET 2009

Peter Cowan wrote:
> On Jan 14, 2009, at 12:58 PM, Ben Bolker wrote:
>>  So -- where are we?
> At this point, I think we should make all the backwards incompatible  
> changes we've been discussing.  Everything else can be deferred as far  
> as I'm concerned.
>>  From before:
>>> 1. merge my branch (with the aforementioned controversial
>>> ordering)  {Peter, can you help with this if/when we
>>> decide to go for it?}
>>  DONE.
>>> 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.)
>>  ???
>>> 3. fix problems in node labeling on plots that stem from
>>> the change in edge matrix format (Peter may already have a fix
>>> for this but was waiting on other changes)
>>   DONE.
>>> 4.  PDC proposes that we change the NA in the root-node-row
>>> to (-1) instead; I propose that we add a "dropRoot" function
>>> (which just operates on a raw edge matrix, not on a phylo4
>>> object) to abstract the operation of dropping the appropriate
>>> row (essentially substituting for places where we have na.omit
>>> or edge[!is.na(edge[,1]),] in the code now
>>  NA to -1 switch not made.
>>  edges now has a drop.root argument (default = FALSE) that
>> should do this.
> I'd still rather have -1 than NA, there are cases when have the NA is  
> a problem but it's useful to have an nrow(edge) == nNodes().  Is there  
> a reason for keeping NA aside from inertia?

  What are the cases when the NA is a problem?  When you want to
make comparisons on the whole first column of the matrix?

>>> 5. make the naming-convention changes as recommended
>>  NOT DONE.  Volunteers?  Francois wanted some plurals to
>> be kept ...
> I think this should be a priority.  Nothing is worse than having  
> commands "disappear" when updating to a new version.  So before we  
> release an 'official' version we should pick final names.
>>> 6. with some input from Emmanuel, implement SOME form of
>>> checking/consistency rule for ordering when importing/exporting
>>> from/to ape
>>   NOT DONE. Volunteers?
> I'd be okay with deferring this.  It won't be surprising to users if  
> we make this better in the future right?

  On the other hand, it's also pretty easy to do.
>>>  I propose that we DELAY:
>>> 1. updating ncl to the newer version (unless Brian has this
>>> all ready to go)
> Also agreed
>>> 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'd be okay with deferring this as well.  This is an enhancement that  
> won't break older code right?

  This *will* break older objects (not code) if we add a slot to
the class definitions.

>>  PS: if someone wants to take a look at the "hard way" simulator
>> code in section 9 of the vignette and suggest ways that this could
>> be done more easily (possibly by adding convenience functions and/or
>> accessors that do the hard work), please feel free ...
> I can take a look at this, sometime next week probably.  We should  
> also decide how we are going to handle newlines for the vignette.  I  
> think that I've been soft wrapping and Ben has been hard wrapping,  
> which causes havoc with svn.  Do you have a preference Ben?

  Soft wrapping is fine with me.


> Cheers
> Peter
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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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