Re: [Treebase-devel] treebase r package available on cran

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

Hi Rutger,

Thanks.  Overall the API has been great - I still need to add a few of the
recent prism additions to the phylo-ws side, I'm doing most of the meta-data
over OAI-MPH.

I think the primary thing I noticed was that I couldn't identify if a tree
had branch-length information without downloading the actual data file.  If
there's a way to do this from the metadata it could be very helpful.
 (Ideally identify as well whether or not the branch lengths were in units
of time; i.e. a time-calibrated chronogram vs an example where branch
lengths are still in mutational steps.

Also, I love how treebase has the methods encoded for creating the trees;
e.g. which software was used; but I didn't see how to pull that out with the
API?  My apologies if I overlooked something.

Cheers,

Carl

On Thu, Oct 27, 2011 at 6:56 AM, Rutger Vos <R....@re...> wrote:

> Hi Carl,
>
> very cool - great to see the TreeBASE API being built upon. I'd be
> interested to hear about any bugs/idiosyncrasies you've encountered.
>
> Best wishes,
>
> Rutger
>
> On Wed, Oct 26, 2011 at 3:14 AM, Carl Boettiger <cbo...@gm...>
> wrote:
> > Hi list,
> > I have created a simple R package for accessing phylogenetic trees in
> > treebase from the R interface, which is now on cran.  I've posted a few
> > examples of how to do simple queries, replicate published examples, and
> > create automatically updating meta-analyses here.  (Also included in R's
> > demo() package function).
> > Hope this is useful, I'd welcome bug reports or feature requests.
> > Cheers,
> > Carl
> > --
> > Carl Boettiger
> > UC Davis
> > http://www.carlboettiger.info/
> >
> >
> >
> ------------------------------------------------------------------------------
> > The demand for IT networking professionals continues to grow, and the
> > demand for specialized networking skills is growing even more rapidly.
> > Take a complimentary Learning@Cisco Self-Assessment and learn
> > about Cisco certifications, training, and career opportunities.
> > http://p.sf.net/sfu/cisco-dev2dev
> > _______________________________________________
> > Treebase-devel mailing list
> > Tre...@li...
> > https://lists.sourceforge.net/lists/listinfo/treebase-devel
> >
> >
>
>
>
> --
> Dr. Rutger A. Vos
> School of Biological Sciences
> Philip Lyle Building, Level 4
> University of Reading
> Reading, RG6 6BX, United Kingdom
> Tel: +44 (0) 118 378 7535
> http://rutgervos.blogspot.com
>



-- 
Carl Boettiger
UC Davis
http://www.carlboettiger.info/