[Mesquitelist] [R-sig-phylo] functions in Mesquite of interest to R users?

[Yanis Bouchenak-Khelladi]

Hello,

Indeed, this would be a great improvement as both R (picante, ape and
apTreeshape packages) and Mesquite are tools that we, systematists,
use on a standard basis. If Mesquite is calling R, I think that:

-"shift.test" implemented in apTreeshape would be very useful as it
caluclates shifts in topological diversification (as in Chan and
Moore, 2005)
-other models of evolution
-"compar.gee" implemented in ape would allow to test for traits
association between continuous and binary characters using a Browninan
motion
-community phylogenetic functions implemented in picante (as in
phylocom, Cam Webb)

Anyways, thanks for all your great work developing Mesquite,

All the best,
Yanis




On 30/03/2009, Birgit Lemcke <birgit.lemcke at systbot.uzh.ch> wrote:
> Hello Wayne!
>
> First of all I have to thank you for your ongoing effort in
> development of Mesquite.
>
> In general I would think it would be useful to use R functions, that
> are not implemented in Mesquite.
> For example more evolutionary models for ancestral state
> reconstruction or using methodes although having a sample of several
> Bayesian trees (needs perhaps also improvement in R).
> Another usage could be to give more options for plotting trees or
> charts.
> Indeed it would be an improvement if Mesquite could be used to switch
> between the different R packages, that mostly all need a special class
> of trees.
>
> HTH
>
> Birgit
>
> Am 30.03.2009 um 00:34 schrieb Wayne Maddison:
>
>> Hilmar Lapp and I have explored the possibility of communication
>> between R and Mesquite, and have a prototype of a system that allows
>> Mesquite to call functions in R, and R to call Mesquite as if an R
>> package.  We'd like to know what the user community might see as the
>> highest priorities for such work.
>>
>> If R is calling Mesquite, what Mesquite functions would you most
>> like to see available to R?  These could be some basic calculations
>> (reconstructing ancestral states, tree simulation, etc.) or user
>> interface functions (editing trees for R, tracing character
>> evolution, etc.).
>>
>> If Mesquite is calling R, what R functions would you most like to
>> see available in Mesquite?  These could be functions in
>> phylogenetics packages such as ape, or in other R packages.
>>
>> thanks for your feedback.
>>
>> Wayne
>> --
>> --------------------------------------------------------
>> Wayne Maddison
>> Professor and Canada Research Chair
>>         Depts. of Zoology and Botany and
>>         Biodiversity Research Centre
>> & Director
>>         Beaty Biodiversity Museum
>> 6270 University Boulevard
>> University of British Columbia
>> Vancouver, BC  V6T 1Z4   Canada
>>
>> email: wmaddisn at interchange.ubc.ca   FAX: +1 604 822-2416
>>
>> Mesquite: http://mesquiteproject.org
>> MacClade: http://macclade.org
>> Salticidae:  http://salticidae.org
>> Tree of Life: http://tolweb.org
>> Beaty Biodiversity Museum: http://beatymuseum.ubc.ca
>> Home page: http://salticidae.org/wpm/home.html
>>
>> _______________________________________________
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>
> =============================
> Birgit Lemcke
> Institut of Systematic Botany
> University of Zurich
> Zollikerstrasse 107
> CH-8008 Zürich
> Switzerland
> Ph: +41 (0)44 634 8416		
> mail: birgit.lemcke at systbot.uzh.ch	
> =============================
>
>
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>
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-- 
Dr Yanis Bouchenak-Khelladi
-Smuts Postdoctoral Fellow-
 University of Cape Town
  Department of Botany
   Rondebosch 7701
      South Africa
E-mail: boucheny at tcd.ie
Phone: +(27) 21 650 3772
Fax: +(27) 21 650 4041