Hi Miguel, I have not used this package. Is d the estimated parameter for an OU model? If so, then it would seem to be paramaterized differently from most implementations.
In general, when one is using an OU model (d), Grafen's rho, Pagel's lambda, or an ACDC model (which we called g in Blomberg et al. 2003), a value of one (unity) gives the original tree, i.e., exactly the amount of signal (averaged across the tree) that you would expect under Brownian motion. A value of zero should return a star phylogeny (generally with contemporaneous tips, but I am not sure for all implementations of the above transforms). A value greater than one indicates more signal that expected under Brownian motion. You can get this in real data sets (see Blomberg et al. 2003). You can also get it in simulated data sets occasionally (rarely) by chance. Or, if you simulate under Brownian motion, and then manually add a constant to the phenotypes of all members of one or more entire clades, then you should be able to get the parameter estimate to exceed one. Note that the K statistic of Blomberg et al. (2003) behaves the same way. K = 0 indicates a star best fits the data (no phylogenetic signal), K = 1 indiucates the specified tree and a Brownian motion model fits the data well, and K > 1 indicates more signal than expected under Brownian motion. Again, one sometimes gets K values greater than one (highest we saw was 4.02). Blomberg, S. P., T. Garland, Jr., and A. R. Ives. 2003. Testing for phylogenetic signal in comparative data: behavioral traits are more labile. Evolution 57:717-745. Cheers, 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 ________________________________________ From: r-sig-phylo-boun...@r-project.org [r-sig-phylo-boun...@r-project.org] on behalf of miguel.ve...@uv.es [miguel.ve...@uv.es] Sent: Friday, May 17, 2013 8:56 AM To: r-sig-phylo@r-project.org Subject: [R-sig-phylo] Phylosignal with phylo.d Dear list: I am using phylo.d in caper package and the Estimated D is lower than 0 (D=-0.71), suggesting a phylogenetic signal greater than Brownian expectation. However, the Probability of E(D) resulting from Brownian phylogenetic structure is p=0.98. Should I interpret this p-value as non-significant? or should I interpret it as a significant p=1-0.98=0.02? I am asking this question because I have never been able to detect a significant phylosignal higher than BM even with simulated data. Estimated D : -0.7107697 Probability of E(D) resulting from no (random) phylogenetic structure : 0 Probability of E(D) resulting from Brownian phylogenetic structure : 0.98 Thanks Miguel Verdu -- ******************************************************************** Centro de Investigaciones sobre Desertificacion (CSIC-UV-GV) Carretera Moncada - Náquera, Km. 4,5 Apartado Oficial 46113 Moncada (Valencia) Spain Tel +34 96 3424204 Fax +34 96 3424160 www.uv.es/verducam _______________________________________________ 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/
