Hi Christofer, Try with the package mvSLOUCH (available on CRAN). I ran my data with it without a problem. The computation time might be a burden if you have many large trees (~5 min per ~50 terminal tree and two optima). Also, if you want to test the likelihood of having multiple regimes, it is easy to convert for instance the phy$node.label vector that you would use in OUwie, into the "regimes" vector used in mvSLOUCH.
Jeremy Beaulieu also suggested log-transforming the trait values (in case that you have many negative values) before running OUwie. I hope this helps. Cheers, Santiago Santiago Sanchez-Ramirez Ecology and Evolutionary Biology, University of Toronto Natural History (Mycology), Royal Ontario Museum 100 Queen's Park Toronto, ON M5S 2C6 Canada > On Feb 17, 2014, at 6:00 AM, r-sig-phylo-requ...@r-project.org wrote: > > Send R-sig-phylo mailing list submissions to > r-sig-phylo@r-project.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > or, via email, send a message with subject or body 'help' to > r-sig-phylo-requ...@r-project.org > > You can reach the person managing the list at > r-sig-phylo-ow...@r-project.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of R-sig-phylo digest..." > > > Today's Topics: > > 1. Re: Fit BM, OU (1 theta), OU (2 theta) with the same function > (Christofer Clemente) > 2. Re: Fit BM, OU (1 theta), OU (2 theta) with the same function > (Christofer Clemente) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 16 Feb 2014 11:00:38 +0000 (UTC) > From: Christofer Clemente <c.cleme...@uq.edu.au> > To: r-sig-phylo@r-project.org > Subject: Re: [R-sig-phylo] Fit BM, OU (1 theta), OU (2 theta) with the > same function > Message-ID: <loom.20140216t115041-...@post.gmane.org> > Content-Type: text/plain; charset=us-ascii > > > > > > Hi Brian and Santiago, > > I have been trying to test models of evolution using OUwie and i ran into an > identical problem to that Santiago describes. > > I am using a phylogeny (tree) of 111 species in ape's "phylo" format. > my data frame (df) is of three columns: species, discrete trait, continuous > trait. > > bm1Output = OUwie(tree, df, model = "BM1") > is successful > > ou1Output = OUwie(pruned, df1, model = "OU1") > returns > Error in svd(m) : infinite or missing values in 'x' > > ou1Output = OUwie(pruned, df1, model = "OU1", diagn=FALSE) > similarly returns the error > Error in svd(m) : infinite or missing values in 'x' > > Any suggestions greatly appreciated > > best > > Christofer > > > > ------------------------------ > > Message: 2 > Date: Mon, 17 Feb 2014 08:55:00 +0000 (UTC) > From: Christofer Clemente <c.cleme...@uq.edu.au> > To: r-sig-phylo@r-project.org > Subject: Re: [R-sig-phylo] Fit BM, OU (1 theta), OU (2 theta) with the > same function > Message-ID: <loom.20140217t095410-...@post.gmane.org> > Content-Type: text/plain; charset=us-ascii > > i should also note i am using the latest version of OUwie '1.39' > > > > ------------------------------ > > _______________________________________________ > R-sig-phylo mailing list > R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > > > End of R-sig-phylo Digest, Vol 73, Issue 11 > ******************************************* _______________________________________________ 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/
