Re: [Treebase-devel] NeXML and R

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

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
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