Dear Jesse. The most logical explanation is that in the fitted ARD model the rate of transition away from the rare state is >> than the fitted transition rates to it (or even that the ML value of these rates is zero). Conditioning on this fitted model make it highly probably that the root is in the rare state (and that the state is rare among extant taxa of the tree). Is this consistent with the parameter values of the fitted Mk model for your data?
Another option that is available in make.simmap is Q="mcmc". This samples values for the transition matrix Q (given a model, such as model="ARD") in proportion to their posterior probability using MCMC and then stochastic histories according to their probability given the sampled value of Q. In theory this should make the result less dependent on the specific fitted value of Q. To dig any deeper I would need to have your data & tree. All the best, Liam Liam J. Revell Associate Professor, University of Massachusetts Boston Profesor Asistente, Universidad Católica de la Ssma Concepción web: http://faculty.umb.edu/liam.revell/, http://www.phytools.org On 12/21/2018 4:41 PM, Jesse Delia wrote: > Hello all, > > I have, what I think is, a strange result from make.simmap (phytools V > 0.6.44). Using an ARD model, I'm getting a high probability for the > rarest state in my dataset. Based on trait distribution, this seems like > a red flag but I cant figure out whether there is an issue. > > If anyone can have a look, I reproduced my dataset and tree, but its a > bit long and will post upon request. In the meantime, just wondering > whether this result is cause for concern? I pasted the plotted results > below, not sure if it will post to the board. > > Thanks for all your help! > > Jesse > > Rplot.jpg > > _______________________________________________ > 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/
