Re: [Treebase-devel] NeXML and R

[Mark H. <mth...@gm...>]

Hi Carl,
	Brian O'Meara was also a lead on phylobase's interaction with NCL, so he'd be a good contact.

	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.

all the best,
mark


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/
>> 
>> 
>> ------------------------------------------------------------------------------
>> 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
>> 
> 
> 
> 
> -- 
> 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