p.s. an absorbing boundary might be a good model for something like the disappearance of a gene or something. When it goes to such a low frequency it goes extinct. Then in order to reevolve, it needs to mutate (basically re-originate, which is a very rare event). But for "reversible" traits, absorbing boundaries don't seem like a good model to me. I have never been able to think up a good biological mechanism for a reflecting boundary.
Sorry for the extra email from the incomplete thought. M On Mar 5, 2011, at 8:50 PM, Marguerite Butler wrote: > Hi David, Liam and everyone, > > Reflecting traits at boundaries or absorbing them is something that can be > done, but I guess I'd like to encourage everyone to think carefully about the > interpretation of such simulations. What are you trying to model and what > does it mean at the end? Doing these boundary manipulations produces odd > shaped-distributions of traits at the end of the simulated process. But > probably more importantly, does this a good model for the biological process > which might be occurring? If so, then great. But I would guess not with > traits such as spine length. > > The zero issue is a hard problem. Is it a combination of a discrete trait > (presence/absence) and a continuous trait (length)? Or perhaps a better model > would be a threshold trait with underlying continuous variation but below > some boundary it will not be expressed? Has anyone developed a model that can > be used for such a scenario? In the absence of such a model, I've done things > like what Enrico suggests, with a kludge solution like adding a very small > value to all values to avoid the zero. This doesn't make much difference to > the analysis, and avoids the singularity at log(0). If you have a trait that > is a frequency, you can use the logit() function instead of log(), as we did > in Scales et al 2009. > > Scales J.A., King A.A., and Butler M.A. (2009) Running for your life or > running for your dinner: What drives fiber-type evolution in lizard locomotor > muscles? Am. Nat.173:543-553. > > Marguerite > > On Mar 5, 2011, at 11:06 AM, Liam J. Revell wrote: > >> I'm not sure that this is what Dave has in mind, but if anyone is interested >> in simulating bounded evolution in R, I just added it to my "fastBM()" >> function (code here: >> http://anolis.oeb.harvard.edu/~liam/R-phylogenetics/fastBM/v0.3/fastBM.R). >> >> In the process of evolving traits up the tree, I just bounce back any >> phenotypes that exceed the lower or upper boundary conditions specified by >> the user (by default they are -Inf and Inf). I think I did this properly. >> Feedback welcome though. >> >> - Liam >> >> -- >> Liam J. Revell >> University of Massachusetts Boston >> web: http://faculty.umb.edu/liam.revell/ >> (new) email: liam.rev...@umb.edu >> (new) blog: http://phytools.blogspot.com >> >> On 3/5/2011 12:55 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 >>>> >>>> _______________________________________________ >>>> R-sig-phylo mailing list >>>> R-sig-phylo@r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo >>> >>> _______________________________________________ >>> R-sig-phylo mailing list >>> R-sig-phylo@r-project.org >>> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo >> >> _______________________________________________ >> R-sig-phylo mailing list >> R-sig-phylo@r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > > ____________________________________________ > Marguerite A. Butler > Associate Professor > Department of Zoology > University of Hawaii > 2538 McCarthy Mall, Edmondson 259 > Honolulu, HI 96822 > > FAX: 808-956-9812 > Dept: 808-956-8617 > http://www2.hawaii.edu/~mbutler > http://www.hawaii.edu/zoology/ > > > [[alternative HTML version deleted]] > > _______________________________________________ > R-sig-phylo mailing list > R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo ____________________________________________ Marguerite A. Butler Associate Professor Department of Zoology University of Hawaii 2538 McCarthy Mall, Edmondson 259 Honolulu, HI 96822 FAX: 808-956-9812 Dept: 808-956-8617 http://www2.hawaii.edu/~mbutler http://www.hawaii.edu/zoology/ [[alternative HTML version deleted]]
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