Re: [Treebase-devel] R, apTreeshape, and dbtree

[Michael E. <mi...@sf...>]

Hi, 

I had a busy month or two with various admin things around here, but I plan to get back to working on NCL starting at the beginning of October.

Mick



----- Original Message -----
From: "Rutger Vos" <rut...@gm...>
To: "Todd Vision" <tj...@bi...>
Cc: tre...@li..., "Aaron J. Mackey" <ajm...@gm...>, "Mark Holder" <mth...@ku...>, "Michael Elliot" <mi...@sf...>
Sent: Friday, September 24, 2010 3:37:57 PM
Subject: Re: [Treebase-devel] R, apTreeshape, and dbtree

Interesting idea. I don't see Aaron's NeXML code in the phylobase
repository (though I may be overlooking it?). What I did see is that
it uses NCL, so perhaps this is contingent on NCL supporting NeXML.
What is the status of the latter? Has this gone completely on ice?

On Fri, Sep 24, 2010 at 7:27 PM, Todd Vision <tj...@bi...> wrote:
>
> All,
>
> An interesting thread from the R-sig-phylo list below.   I believe the only databases that dbtree formerly supported were treebase and pandit.  It might be worthwhile dusting off Aaron Mackey's code for reading NeXML in the R phylobase module and building in support for web service access to TreeBase directly.
>
> Todd
>
> Begin forwarded message:
>
>> From: Eric Durand <eri...@be...>
>> Date: September 24, 2010 12:20:15 PM EDT
>> To: Andre Levy <and...@gm...>
>> Cc: "r-s...@r-..." <r-s...@r-...>
>> Subject: Re: [R-sig-phylo] dbtrees
>>
>> Hi Andre,
>>
>> You are correct, we removed the dbtree function. This is because tree databases were changing too fast and too much, so this function was too difficult to maintain. The best way to access trees is, imo, to go online to the database web interface directly, then download the trees to a local file before reading them into R.
>>
>> Cheers,
>> Eric
>>
>> On Sep 24, 2010, at 9:16 AM, Andre Levy wrote:
>>
>>> Hi All
>>> I'm new to R and to APE. Am starting by reading and going through Paradis' book, and have already stumbled on the changes to apTreeshape. Have already found the new pdf package description (dated April 23, 2010; most recent?) and found an older one from 2007. (Also found a pdf describing Ape dated June 2010)
>>>
>>> By comparing the two pdfs of apTreeshape I gather that the "dbtrees" function is no longer incorporated. Is there another alternative for grabbing trees from a tree database?
>>>
>>> Cheers
>>> André Levy
>>>
>>> Unidade de Investigação em Eco-Etologia / Eco-Ethology Research Unit
>>> ISPA - Instituto Universitário
>>> Rua Jardim do Tabaco 34, 1149-041 LISBOA Portugal
>>> Tel: ++351 218 811 700  Fax: ++351 218 860 954
>>> http://www.ispa.pt/ui/uie/bcao/andre_levy.asp
>>>
>>> Centro de Biociências / Biosciences Center
>>> (same mailing address)
>>> http://centrodebiociencias.webnode.com/
>
>
>
>
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-- 
Dr. Rutger A. Vos
School of Biological Sciences
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University of Reading
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