Re: [Treebase-devel] NeXML and R

[Rutger V. <rut...@gm...>]

>         2 sounds difficult (because NCL is complex), but I agree with Rutger that it is ideal. Doing that would enable NeXML reading in GARLI and RevBayes.  If someone goes that route, I'm happy to answer questions and help when I can. I'm afraid that I'm a bit overcommitted right now, so I can't pledge much coding time.

I'm happy to answer questions too but I don't know C++ so it would be
on the NeXML end. Well, perhaps I can say useful things about what did
and did not work for APIs in other languages.

> On Aug 14, 2012, at 6:41 AM, Rutger Vos wrote:
>
>> Hi Carl,
>>
>> thanks for writing in! Yes, it would be great if there was NeXML
>> support in R. I'm not actually an R programmer - though I'd like to
>> somehow absorb that ability over time, and would be willing to
>> advice/help out - but it is evident that there is a need.
>>
>> Ideally it would expose NeXML data in a way that is reasonably
>> compatible with the different phylogenetics packages for R (ape? ouch?
>> phylobase? treebase? I don't know the landscape that well). To me it
>> seems that there are the following possibilities:
>>
>> 1. a new, simple API just for reading and writing NeXML, which other
>> package authors can import
>>
>> 2. NeXML I/O in NCL (C++) is completed, package authors build on that,
>> perhaps by way of phylobase?
>>
>> 3. anarchy, different authors build their own NeXML parsers, each with
>> their own bugs (instead of all bugs in one place).
>>
>> The ideal scenario, I think, would be 2, but it would be harder than
>> 1. I vote against 3. By the way, Brian O'Meara does a lot in R, it
>> would be a good idea to solicit his opinion as well, especially in
>> relation to the DateLife R webservice he's nurturing.
>>
>> Best wishes,
>>
>> Rutger
>>
>> On Tue, Aug 14, 2012 at 2:10 AM, Carl Boettiger <cbo...@gm...> wrote:
>>> Dear TreeBASE developers,
>>>
>>> It appears that the NeXML format isn't currently supported in the R
>>> environment, but offers much richer information than the old nexus format,
>>> as exemplified by the treebase files under each.  As I've mentioned before
>>> on this list, I've written a little R package for accessing TreeBASE, which
>>> relies on nexus formats for compatibility with existing R packages.  I think
>>> this would be a great opportunity to introduce a NeXML format reader into R,
>>> and am trying to figure out where the best place is to start.  I think
>>> there's considerable NeXML expertise on this list, and was wondering if I
>>> might find anyone else interested in helping with this effort, or give some
>>> input to get me jump-started?
>>>
>>> I see that NeXML has C++, Java, PERL, Python, javascript and ruby
>>> implementations already, and I'm wondering if the best thing to do would be
>>> to wrap something like the C++ library, or start from scratch since R has a
>>> pretty solid XML library already.  Phylogenies in R are represented using a
>>> few different and mostly very crude data structures, and we could benefit a
>>> lot as R developers from a richer object -- but there's also a large
>>> community of legacy formats and software relying on those formats to
>>> support.  I could hack something together that worked, but I think I need a
>>> bit more community input to do this right.  Anyone interested?
>>>
>>> Carl
>>>
>>>
>>>
>>> --
>>> Carl Boettiger
>>> UC Davis
>>> http://www.carlboettiger.info/
>>>
>>>
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>>
>>
>>
>> --
>> Dr. Rutger A. Vos
>> Bioinformaticist
>> NCB Naturalis
>> Visiting address: Office A109, Einsteinweg 2, 2333 CC, Leiden, the Netherlands
>> Mailing address: Postbus 9517, 2300 RA, Leiden, the Netherlands
>> http://rutgervos.blogspot.com
>>
>> ------------------------------------------------------------------------------
>> Live Security Virtual Conference
>> Exclusive live event will cover all the ways today's security and
>> threat landscape has changed and how IT managers can respond. Discussions
>> will include endpoint security, mobile security and the latest in malware
>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>> _______________________________________________
>> Treebase-devel mailing list
>> Tre...@li...
>> https://lists.sourceforge.net/lists/listinfo/treebase-devel
>
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> Treebase-devel mailing list
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> https://lists.sourceforge.net/lists/listinfo/treebase-devel



-- 
Dr. Rutger A. Vos
Bioinformaticist
NCB Naturalis
Visiting address: Office A109, Einsteinweg 2, 2333 CC, Leiden, the Netherlands
Mailing address: Postbus 9517, 2300 RA, Leiden, the Netherlands
http://rutgervos.blogspot.com