[Phylobase-devl] a graphics challenge ...

Brian O'Meara bcomeara at nescent.org
Wed Mar 11 19:55:51 CET 2009

On Mar 11, 2009, at 12:30 AM, Peter Cowan wrote:

> As a former student myself, I'd be willing to help mentor this time  
> around.


> What types of projects would move phylobase forward?  A parser for  
> one of the xml phylogeny formats?  Metadata support?  Multi- 
> phylo4?  Tighter integration with NCL? Rewrites of performance  
> sensitive methods in C? A testing framework for the package?

Just FYI, there's a proposal on the NESCent page to add nexml parsing  
to NCL. Iff that gets accepted and completed, updating the NCL in  
phylobase would automatically bring in xml input.

> Other ideas?

There are some ideas on our features page: <http://r-forge.r- 
project.org/tracker/?atid=491&group_id=111&func=browse>. I personally  
like the idea of incorporating branch swapping algorithms (TBR, NNI)  
into phylobase (but are they around somewhere there already? --  
didn't see them). This is a basic "tree" function that isn't commonly  
available (I had to code my own in C++ a few years ago, though now  
there's a library to do it; phangorn can do NNIs in R). It has some  
chewy bits (for example, you'd want to know when you've exhausted all  
possible TBR swaps for a given topology, but how do you store this  
information?; also, what happens to information on nodes/edges, how  
do you assign initial branch lengths if relevant, etc). But I don't  
think this is a core feature in the same way that communicating with  
ape or reading nexus are. There's also the practical issue of utility  
-- who's going to use these functions? You're probably not going to  
code a tree search algorithm in R.

Another idea, though probably not for phylobase sensu strictu, is to  
finish the R-Mesquite bridge started at the hackathon.

Also, just to bubble it up again, Ben's email from Jan. on things to  
do before release is below. Anything that can be done coding-wise  
(rather than design or documentation) to get the release out would be  
helpful & appropriate.

Begin forwarded message:
> From: Ben Bolker <bolker at ufl.edu>
> Date: January 14, 2009 3:58:16 PM EST
> To: phylobase-devl at r-forge.wu-wien.ac.at
> Subject: [Phylobase-devl] stalled ...
>   So -- where are we?
>   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.
>> 5. make the naming-convention changes as recommended
>   NOT DONE.  Volunteers?  Francois wanted some plurals to
> be kept ...

[some progress has been made on this]

>> 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 propose that we DELAY:
>> 1. updating ncl to the newer version (unless Brian has this
>> all ready to go)
>> 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.
>   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 ...

> Peter
> On Mar 9, 2009, at 7:35 PM, Hilmar Lapp wrote:
>> I'd like to echo Brian's comment. You (phylobase) can have students
>> working over the summer for you; all you need to do is put up a
>> project idea and designate mentor(s).
>> I know that mentoring is also work, but the results can greatly push
>> along a project.
>> Let me know if there's anything I can help with coordinating this.
>> 	-hilmar
>> On Mar 9, 2009, at 12:05 PM, Brian O'Meara wrote:
>>> Good link, Ben. Google Summer of Code is starting up again, and  
>>> there
>>> are no R projects yet on the NESCent page (<https://www.nescent.org/
>>> wg_phyloinformatics/Phyloinformatics_Summer_of_Code_2009>).  
>>> Perhaps a
>>> way to charge the paddles?
>>> Brian
>>> On Mar 9, 2009, at 2:07 AM, Ben Bolker wrote:
>>>> http://www.stat.columbia.edu/~cook/movabletype/archives/2009/03/
>>>> more_on_display.html
>>>> Someday soon I hope to get out the defibrillator and see if we
>>>> can get phylobase going again ...
>>>> cheers
>>>>   Ben
>>>> -- 
>>>> 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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>>>> phylobase-devl
>>> ________________________________
>>> Brian O'Meara
>>> NESCent
>>> Durham, NC
>>> http://www.brianomeara.info
>>> ________________________________
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>>> phylobase-devl
>> -- 
>> ===========================================================
>> : Hilmar Lapp  -:-  Durham, NC  -:- hlapp at duke dot edu :
>> ===========================================================
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Brian O'Meara
Durham, NC

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