Hi, Rafael. It applies for the simple OU model. Relevant code in OUwie:
if (model == "OU1"){ np=2 index<-matrix(TRUE,2,k) index.mat[1,1:k]<-1 index.mat[2,1:k]<-2 if(root.station==TRUE){ param.count<-np+1 } if(root.station==FALSE){ param.count<-np+2 } bool=root.station } If root stationarity is assumed, there are three parameters: alpha and sigma.sq (the np=2 cost) and theta (the +1 for param.count); if not assumed, there is +2 for the param.count for theta at root and theta elsewhere. For BM1, np is 1 (sigma.sq) and param.count is 2 (root state, though the MLE for this does not require optimization as there's an equation for it), so they should be comparable. Best, Brian _______________________________________________________________________ Brian O'Meara, http://brianomeara.info, especially Calendar <http://brianomeara.info/calendar.html>, CV <http://brianomeara.info/cv.html>, and Feedback <http://brianomeara.info/feedback.html> Professor, Dept. of Ecology & Evolutionary Biology, UT Knoxville Associate Head, Dept. of Ecology & Evolutionary Biology, UT Knoxville He/Him/His On Tue, Aug 27, 2019 at 12:24 PM Rafael S Marcondes <raf.marcon...@gmail.com> wrote: > Hi all, > > I'm trying to understand the number of parameters in simple BM and OU > models in OUwie. $param.count in the fitted results gives 2 for BM and 3 > for OU. I know that the 2 BM params are sigma and the trait value at the > root, but I'm a little confused about the OU params. I expected there to be > 4 of them: sigma, alpha, theta and the trait value at the root. > > Digging a little deeper, the OUwie documentation explains that under the > default settings (which I used), the value at the root is dropped from the > model and drawn from the stationary distribution of the OU process. But the > documentation only says that explicitly for the more complex OUMV and OUMVA > models. So I just wanted to make sure that that is also applied to the > simple OU model. > > I'm also wondering about the implications of this for comparing the fits of > OU and BM, if for one (BM) the root value is estimated and for the other > (OU) it is not... > > Thanks in advance, > > > *--* > *Rafael Sobral Marcondes* > PhD Candidate (Systematics, Ecology and Evolution/Ornithology) > > Museum of Natural Science <http://www.lsu.edu/mns/> > Louisiana State University > 119 Foster Hall > Baton Rouge, LA 70803, USA > > <http://goog_27804804> > www.rafaelmarcondes.com > > [[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/ > [[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/