Danielle, Apologies for the late comment on this, but what do you mean by non-rooted? Do you mean the tree is rooted, but has a three-way split with the outgroup at the root node? You shouldn't do OU on a tree you can't assign a root to.
I'm also just a bit curious what gave you the sense that OU was inappropriate for non-ultrametric trees. To my knowledge, this was only an issue in one case, as highlighted by Slater (2014), that one particularly (popular) algorithm for fitting evolutionary models doesn't work for OU on non-ultrametric trees. I don't think this is as much of a concern in 2018, as I think most/all packages that were doing such have fixed their code so an alternative algorithm is used when a non-ultrametric tree is given (as with a tree containing fossil taxa). Cheers, -Dave On Thu, Dec 6, 2018 at 6:35 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/ > -- David W. Bapst, PhD Asst Research Professor, Geology & Geophysics, Texas A & M University Postdoc, Ecology & Evolutionary Biology, Univ of Tenn Knoxville https://github.com/dwbapst/paleotree [[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/
