[Treebase-devel] NeXML and R

[Carl B. <cbo...@gm...>]

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 <http://nexml.org> 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/