Dear all, I am running a GLS under the Ornstein-Uhlenbeck model (nlme package) but don't get any other p value than p=0. I changes value=1 but the p value stays zero. If I use the same with the Brownian motion model (corBrownian) it works fine but the better fitting model is OU.
There is apparently already an entry here in this mailing list dealing with the same problem but I am too new to R to understand how to fix the problem. https://stat.ethz.ch/pipermail/r-sig-phylo/2013-August/002962.html Can anybody help me to get it right? The tree I am using it class "phylo" and the data is a data.frame with numerical variables (which are log transformed continuous trait measurements like body size and skull length). I am following the method in Paradis 2012, pp221-223. My input: > library(caper) > library(geiger) > library(nlme) > oucor<-corMartins(1,phy=Tree) > trait1vstrait2.pgls<-gls(logtrait1~logtrait2, correlation=oucor, data=Data) > summary(trait1vstrait2.pgls) ...and the output: Generalized least squares fit by REML Model: logtrait1 ~ logtrait Data: Data AIC BIC logLik -163.6027 -155.3609 85.80133 Correlation Structure: corMartins Formula: ~1 Parameter estimate(s): alpha 69.93246 Coefficients: Value Std.Error t-value p-value (Intercept) -2.959326 0.2493182 -11.86967 0 Logtait1 3.510275 0.1860799 18.86434 0 Correlation: (Intr) Logtrait1 -0.999 Standardized residuals: Min Q1 Med Q3 Max -2.6395786 -0.5084116 0.2064092 0.7374675 2.9782702 Residual standard error: 0.06052139 Degrees of freedom: 60 total; 58 residual Thanks a lot! * * * * * * * * * * * Dr. Anna Bastian Postdoc, NRF Fellow [http://ruthprowse.co.za/media/47607/logo_biological_sciences_uct_alexandra_perold.jpg] University of Cape Town Animal Evolution and Systematics Group Department of Biological Sciences Room 3.32 Tel: +27 (0)21 6502405 Fax: +27 (0)21 6502718 Email: anna.bast...@uct.ac.za<mailto:anna.bast...@uct.ac.za> or anna0bast...@gmail.com<mailto:anna0bast...@gmail.com> ________________________________ UNIVERSITY OF CAPE TOWN This e-mail is subject to the UCT ICT policies and e-mail disclaimer published on our website at http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable from +27 21 650 9111. This e-mail is intended only for the person(s) to whom it is addressed. If the e-mail has reached you in error, please notify the author. If you are not the intended recipient of the e-mail you may not use, disclose, copy, redirect or print the content. If this e-mail is not related to the business of UCT it is sent by the sender in the sender's individual capacity.
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