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.gonza...@ebd.csic.es>
Subject: Re: [R-sig-phylo] Dealing with Bounded Trait Measures
To: <tgarl...@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, <tgarl...@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: tgarl...@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.reze...@uab.cat>
Subject: Re: [R-sig-phylo] Dealing with Bounded Trait Measures
To: David Bapst <dwba...@uchicago.edu>
Cc: R Sig Phylo Listserv <r-sig-phylo@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.reze...@uab.cat
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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.gonza...@ebd.csic.es
Web page: https://docs.google.com/View?id=dfs328dh_14gwwqsxcg
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