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/
