[R-sig-phylo] Dealing with Bounded Trait Measures

Hilmar Lapp hlapp at nescent.org
Sun Mar 6 06:55:06 CET 2011


If someone were willing to mentor the R side, this might be a great  
project idea for our Summer of Code participation [1], for which we  
are pulling together the mentoring organization application right now.

	-hilmar

[1] http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2011

On Mar 5, 2011, at 2:00 PM, <tgarland at ucr.edu> <tgarland at ucr.edu> wrote:

> I have no such plans, but am happy to send the documentation for the  
> code and the original Turbo Pascal code (and compiled versions) to  
> anyone who is interested.  I'd certainly like to see this done.
>
> Cheers,
> Ted
>
>  ---- Original message ----
>
>    Date: Sat, 5 Mar 2011 19:28:26 +0100
>    From: Alejandro Gonzalez <alejandro.gonzalez at ebd.csic.es>
>    Subject: Re: [R-sig-phylo] Dealing with Bounded Trait Measures
>    To: <tgarland at ucr.edu>
>
>    Hello,
>    Is there any plans, be it short-term or in the future, to implement
>    PDSIMUL into a package for the R platform? It seems like it would
>    make for a useful addition.
>    Cheers
>    Alejandro
>    On 5, Mar 2011, at 6:55 PM, <tgarland at ucr.edu> wrote:
>
>      Hello David, Enrico, et al.,
>
>      I may have lost track of what Dave was originally trying to do,
>      and I am not familiar with all of the options presently available
>      in r for simulating continuously valued traits along a specified
>      phylogenetic tree.  However, I wanted to point out that MANY
>      possibilities, including trends, the OU process, and actual  
> limits
>      to trait evolution implemented in several ways, are available in
>      our original DOS program PDSIMUL.EXE that accompanies this paper:
>
>      Garland, T., Jr., A. W. Dickerman, C. M. Janis, and J. A. Jones.
>      1993. Phylogenetic analysis of covariance by computer simulation.
>      Systematic Biology 42:265-292.
>
>      It has been used many times to look at trends, limits, etc.,  
> e.g.,
>      in these papers:
>
>      Díaz-Uriarte, R., and T. Garland, Jr. 1996. Testing hypotheses of
>      correlated evolution using phylogenetically independent  
> contrasts:
>      sensitivity to deviations from Brownian motion. Systematic  
> Biology
>      45:27-47.
>      Laurin, M. 2010. Assessment of the relative merits of a few
>      methods to detect evolutionary trends. Syst. Biol. 59:689-704.
>
>      Cheers,
>      Ted
>
>      Theodore Garland, Jr.
>      Professor
>      Department of Biology
>      University of California, Riverside
>      Riverside, CA 92521
>      Office Phone:  (951) 827-3524
>      Lab Phone:  (951) 827-5724
>      Home Phone:  (951) 328-0820
>      Facsimile:  (951) 827-4286 = Dept. office (not confidential)
>      Email:  tgarland at ucr.edu
>
>      Main Departmental page:
>      http://www.biology.ucr.edu/people/faculty/Garland.html
>
>      List of all Publications:
>      http://www.biology.ucr.edu/people/faculty/Garland/GarlandPublications.html
>
>      Garland and Rose, 2009
>      http://www.ucpress.edu/books/pages/10604.php
>
>       ---- Original message ----
>
>         Date: Sat, 05 Mar 2011 15:36:13 +0100
>         From: Enrico Rezende <enrico.rezende at uab.cat>
>         Subject: Re: [R-sig-phylo] Dealing with Bounded Trait Measures
>         To: David Bapst <dwbapst at uchicago.edu>
>         Cc: R Sig Phylo Listserv <r-sig-phylo at r-project.org>
>
>        David,
>
>        on the top of my head, if no species measurement strictly
>
>         corresponds to
>
>        zero, you may log-transform the data. You may then simulate
>
>         Brownian
>
>        motion in log-transformed values, which will correspond to a
>
>         boundary of
>
>        zero in a linear scale (i.e., the more negative the log number,
>        the
>
>        closer the trait value is to zero - but never zero - in a  
> linear
>
>         scale).
>
>        This also explains why you can simulate the evolution of body
>        mass
>
>        employing Brownian motion in log-transformed units and no
>        species
>
>         will
>
>        ever be assigned a body mass of zero. On more speculative
>        grounds,
>
>         this
>
>        may simply reflect the fact that many biological processes and
>
>         their
>
>        regulation occur in a multiplicative, not additive, scale.
>
>        The problem with regards to this approach is that you cannot
>        really
>
>         have
>
>        any species with a trait = 0 given that the log-transformation
>        is
>
>        impossible in this case, so you might add some constant in case
>
>         this
>
>        occurs (caution because the constant would be arbitrary and
>        might
>
>         have
>
>        an impact on the outcome of analyses). Did not think about this
>        for
>
>         too
>
>        long, though.
>
>        Hope this helps,
>
>        Enrico
>
>        El 4/3/11 9:14 p.m., David Bapst escribió:
>
>          All-
>
>          As far as I understand it, the vast majority of continuous
>
>         character
>
>          analyses assume that the trait is distributed normally and
>
>         without
>
>          bounds. Is there an appropriate transformation to for
>
>         measurements of
>
>          a trait that does have one or more bounds and where some taxa
>
>         actually
>
>          are at that bound? I have several traits where the bound is
>          zero,
>
>         and
>
>          some taxa are actually at zero for this trait. (A practical
>
>         example is
>
>          'spine length', where some taxa have virtually no spine.) And
>          if
>
>         there
>
>          is no transformation applicable, is it analytically
>          appropriate
>
>         to
>
>          remove taxa that have 'zero units' for that trait? Must we
>
>         convert
>
>          these traits to discrete categories to deal with them at all?
>
>          As always, I appreciate your advice.
>
>          -Dave Bapst, UChicago
>
>        --
>
>         
> ************************************************************************
>
>        Enrico L. Rezende
>
>        Departament de Genètica i de Microbiologia
>
>        Facultat de Biociències, Edifici Cn
>
>        Universitat Autònoma de Barcelona
>
>        08193 Bellaterra (Barcelona)
>
>        SPAIN
>
>        Telephone: +34 93 581 4705
>
>        Fax: +34 93 581 2387
>
>        E-mail: enrico.rezende at uab.cat
>
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>
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>
>    __________________________________
>    Alejandro Gonzalez Voyer
>    Post-doc
>    NEW ADDRESS
>    Estación Biológica de Doñana
>    Consejo Superior de Investigaciones Científicas (CSIC)
>    Av Américo Vespucio s/n
>    41092 Sevilla
>    Spain
>    Tel: + 34 - 954 466700, ext 1749
>    E-mail: alejandro.gonzalez at ebd.csic.es
>    Web page: https://docs.google.com/View?id=dfs328dh_14gwwqsxcg
>
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: Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
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