Hi! Liam, Tony, Sam, thank you for the answers! They forced me to think on type of model I've chosen.
I forgot to mention previously that I have used only one input tree. I choose the model ARD, because it was the best model (among SYM and ER) according to fitDiscrete (geiger). Installation of the new phytools did not change the results. As well increasing nsim (from 1000 to 5000) did not change rates qualitevly. I still have two peaks of Q-rates. What is interesting these happened only for transition state1 -> state 2 and backward (state 2 -> state 1). So I decided to check SYM model in make.simmap. The result is more convenient – one peak rates' distributions, although distribution of Q-rates were asymmetrical with long right tail. Make.simmap Q-rates with ER model looked much more gaussian. All of the analyzes were simulated with nsim=1000, Q=”mcmc”,pi=”estimated” with one input tree. The other question is which model to choose – ARD or SYM, or ER? I decided to average the log likelihood estimates of the output simulations. Is it correct to choose the model which have the maximum mean logL? Mean.logL.ARD = -84; Mean.logL.ER = -82; Mean.logL.SYM = -77 Thank you! Maria --- Original message --- From: "Tony Gamble UMN" <gambl...@umn.edu> Date: 27 January 2015, 18:13:53 > Hi Maria, > In addition to Liam and Sam’s comments you may want to look at some of your > trees individually. It is possible you have conflicting topologies that fit > quite different transition rate matrices. Examining the transition rates from > individual trees will let you determine if they fit one or the other local > optima. > Tony > > --------- > Tony Gamble, Ph.D. > Postdoctoral Researcher > Department of Genetics, Cell Biology and Development > University of Minnesota > 6-160 Jackson Hall > 321 Church St SE > Minneapolis MN 55455 > USA > Phone: 612-626-4259 > E-mail: gambl...@umn.edu > Web: www.tc.umn.edu/~gambl007 > Twitter: @tony_gamble1 > > On Jan 27, 2015, at 9:26 AM, Liam J. Revell <liam.rev...@umb.edu> wrote: > > > Hi Maria. > > > > To make sure this is not an error of the software, I highly recommend you > > install the latest version of phytools (or at least the latest version on > > CRAN). The current CRAN version is 0.4-31. I know in some earlier version > > of phytools there was an issue with make.simmap if your data had more than > > two states, but this should be fixed in the current CRAN version. > > > > Having updated phytools (and if the result persists) you might also compare > > your result to one obtained using Q="empirical" (the default). If you do > > this then the function will use the single most likelihood value for the > > transition matrix. This could tell you if the result you have found is > > being influenced by the prior (although the mean of the prior in > > make.simmap is 'hyper-parameterized' by the ML value of Q, so this seems > > somewhat unlikely). > > > > All the best, Liam > > > > Liam J. Revell, Assistant Professor of Biology > > University of Massachusetts Boston > > web: http://faculty.umb.edu/liam.revell/ > > email: liam.rev...@umb.edu > > blog: http://blog.phytools.org > > > > On 1/27/2015 9:28 AM, Maria Ghazali wrote: > >> Hi! > >> I am using phytools 0-3.10. I am trying to do ancestral reconstruction > >> with make.simmap for 3-state discrete character with Q="mcmc", nsim=1000, > >> and default priors (alpha=beta=1). In the result I have transition rates, > >> Q-matrix, for each of 1000 trees. The function proposes mean Q-matrix. But > >> I've looked at the histograms of the between-state transition rates (i.e. > >> state1 to state2, or state2 to state3, etc.). Some of the transitions have > >> bimodal distribution - with 2 maximums. Some are unimodal. > >> > >> Is that wrong? Is that a sign of bad model? > >> Сould I use medians to present the results? To show which transitions are > >> more frequent. > >> > >> Thank you, > >> Maria > >> > >> _______________________________________________ > >> 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/ _______________________________________________ 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/
