You can run in OUwie if you set the root.age (we should probably make that automatic, but haven't yet). See https://www.rdocumentation.org/packages/OUwie/versions/1.50/topics/OUwie. I believe the past issue with non-ultrametric trees comes from functions that handles the creation of the VCV matrix inappropriately by assuming an ultrametric tree. Using non-ultrametric trees may be possible in other OU packages (ouch, slouch, phylolm, MVmorph, etc.) but I don't know for sure.
It's also worth checking for why your tree is non-ultrametric. If it has a mixture of extinct and modern taxa, that's cool. If it's because you think that the branch lengths reflect the amount of change that'd drive the continuous character change (i.e., they mean number of generations for taxa with different generation times, so they don't have the same root to tip length) that's ok, too. If it's just that those are raw branch lengths (parsimony, likelihood) without making the tree a chronogram, that's bad -- the main thing OU/BM models are doing is effectively stretching and smooshing branch lengths (for OU, also adjusting the expected means) so if the starting branch lengths don't mean something that's relevant, the parameters you get from stretching also don't mean anything. [I imagine you're doing it well, just a teachable moment for new students on the list]. Best, Brian _______________________________________________________________________ Brian O'Meara, http://www.brianomeara.info, especially Calendar <http://brianomeara.info/calendars/omeara/>, CV <http://brianomeara.info/cv/>, and Feedback <http://brianomeara.info/teaching/feedback/> Associate Professor, Dept. of Ecology & Evolutionary Biology, UT Knoxville Associate Head, Dept. of Ecology & Evolutionary Biology, UT Knoxville On Thu, Dec 6, 2018 at 7:35 AM Danielle Miller <danimiller...@gmail.com> wrote: > Hi all, > > I have a non-rooted non-ultrametric tree and a corresponding set of a > single trait values for each one of the tips. > I’m interested whether it follows a BM model or an OU. > > Reading previous comments in the archive, I understood that running an OU > process is inadequate in a case of non-ultrametric trees, however I did not > fully understand why. > As I use ouch package, what are the consequences of running an unrooted > tree? And a non-ultrametric one? > > What would be the best way assessing this issue? Diversitree should be > more reliable? > > I will appreciate any explanation and help, > Danielle Miller > _______________________________________________ > 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/
