Thanks, Josef (and those that answered privately). Based on what you wrote, it seems to me that using sigsq as a measure of rate of evolution would make sense for BM, but the interaction between sigsq and alpha in OU would make the interpretation of sigsq as a rate measure complicated, if not unfeasible. Would you agree?
On Mon, Dec 7, 2015 at 9:49 PM, Josef C Uyeda <pseudac...@gmail.com> wrote: > Karla, > The units of sigsq are in your trait units^2 per time unit of your > phylogeny. So if your trait is in cm and your phylogeny in millions of > years, then the units of sigsq are in cm^2/my. > > Comparing BM to OU units is more complicated. Gene Hunt discussed this in > the following paper: > http://paleobiol.geoscienceworld.org/content/38/3/351.short > Long story short, they are in the same units, but it may not be > particularly meaningful to compare them between OU and BM models. For > example, you can have an extremely high sigsq in the OU model, but if alpha > is very high as well, you may end up with very slow rates of evolution when > observed over the lifetime of a phylogeny (specifically, the stationary > variance of the OU process is sigsq^2/(2*alpha), thus if alpha is high > enough the stationary variance will tend towards 0, and all the traits > across taxa will be virtually identical). > > Hope this helps. > Josef Uyeda > > > > On 12/07/2015 03:35 PM, Karla Shikev wrote: > >> Dear all, >> >> I am fitting a BM model using fitContinuous, a vector of trait values and >> a >> time-calibrated tree and then I use the sigsq parameter as my measure of >> the rate of evolution of the trait in question. My questions are: >> >> (1) what is the unit of the sigsq parameter? >> (2) to what extent is the sigsq in a BM model comparable to sigsq in an OU >> model, for instance? are they on the same units? >> >> Thanks! >> >> Karla >> >> [[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/ >> > > _______________________________________________ > 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/
