I had been imagining that precipitation was a dependent variable, not that it matters. In any case, you have the need for a lower limit of zero and probably an upper limit that is somewhat above the greatest recorded values. I can't see why you would want an OU model for precipitation, though. As Liam wrote, we all need more info about what you are doing. And we need to get the hell off the computer on a holiday!
Cheers, Ted From: Liam J. Revell [liam.rev...@umb.edu] Sent: Thursday, November 28, 2013 12:16 PM To: Theodore Garland Jr; Anna Rice; r-sig-phylo@r-project.org Subject: Re: [R-sig-phylo] Transforming data for OU model Hi Ted & Anna. phytools indeed includes a function for simulating Brownian evolution within bounds. This is in the function fastBM. It is also possible to simulate with a trend in fastBM, or under OU (as of the latest non-CRAN phytools, http://www.phytools.org) - but combining a trend or bounds with OU is not permitted. One question I have is what do you mean when you are saying you are "running an OU model" on precipitation data? Are you fitting a linear regression using GLS with a phylogenetic error structure based on the OU model in which precipitation is a predictor? If so, then it may not matter because multivariate normality of the predictors is not, strictly speaking, an assumption of GLS. Hope that may be helpful. All the best, Liam Liam J. Revell, Assistant Professor of Biology University of Massachusetts Boston web: http://faculty.umb.edu/liam.revell/ email: liam.rev...@umb.edu blog: http://blog.phytools.org On 11/28/2013 1:52 PM, Theodore Garland Jr wrote: > Given the nature of precipitation data, I don't think a log transform makes > sense biologically. It is very different from, say, body mass. > I think you need to simulate with limits, as described originally here: > > 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. > > Limits can be implemented with or without other things, such as OU and/or a > trend. > > Our programs are in DOS (What's DOS? The last operating system that worked > ...). > However, I think you can also do this in R somewhere, maybe phytools? Liam > Revell, want to jump in here? > > Happy thanksgiving, > Ted > > Theodore Garland, Jr., Professor > Department of Biology > University of California, Riverside > Riverside, CA 92521 > Office Phone: (951) 827-3524 > Wet Lab Phone: (951) 827-5724 > Dry Lab Phone: (951) 827-4026 > Home Phone: (951) 328-0820 > Skype: theodoregarland > Facsimile: (951) 827-4286 = Dept. office (not confidential) > Email: tgarl...@ucr.edu > http://www.biology.ucr.edu/people/faculty/Garland.html > http://scholar.google.com/citations?hl=en&user=iSSbrhwAAAAJ > > Inquiry-based Middle School Lesson Plan: > "Born to Run: Artificial Selection Lab" > http://www.indiana.edu/~ensiweb/lessons/BornToRun.html > > Fail Lab: Episode One > http://testtube.com/faillab/zoochosis-episode-one-evolution > http://www.youtube.com/watch?v=c0msBWyTzU0 > > ________________________________________ > From: r-sig-phylo-boun...@r-project.org [r-sig-phylo-boun...@r-project.org] > on behalf of Anna Rice [annarice...@gmail.com] > Sent: Thursday, November 28, 2013 6:47 AM > To: r-sig-phylo@r-project.org > Subject: [R-sig-phylo] Transforming data for OU model > > Hi all, > > I am running an OU model on data that is constrained by zero (precipitation > values). Therefore I thought to log transform the data. However I still > have some issues with the transformation: > > 1. When all values in the data are larger than 1.0, the log transformation > will still result in all values being positive. > 2. In case I have a value of zero, log transforming it will give -Inf. > > I would greatly appreciate any advice regarding the best way of > transforming and dealing with this kind of data. > > Thanks you, > Anna > > [[alternative HTML version deleted]] > > _______________________________________________ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ > > _______________________________________________ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ > _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
