Cody, Have you taken care to scale your data so that they have approximately the same means and variances? Sometimes numerical issues arise due to a mismatch of scales? What are your variables? If you plot one against the other, what do you see?
Regarding the interpretations: a good deal depends on just what the variables are. The conclusion: significant off-diagonal elements -> coevolution is overly simplistic, but that is the general idea, yes. Aaron On Tue, May 5, 2015 at 5:17 PM, Cody Dey <[email protected]> wrote: > Hi all, > > I have a large dataset (~6000 species) including two traits of interest. I > am hoping to test whether the extant patterns are more consistent with each > trait evolving independently under OU processes (with 1 regime per trait) > or if the traits have co-evolved in some manner (i.e. the traits influence > one another's optima). > > I have been trying to use mvMORPH and mvSLOUCH to fit two models (one of > independent evolution, and one of dependent evolution) using the code > below. My plan was then to compare AIC values from the two models. From > what I gather, the off-diagonal elements of the alpha and sigma matrix > determine whether there is co-evolution of the trait optima, and the > stochastic element of the OU processes, respectively. > > ##in mvMORPH > > independ.evolv<-mvOU(tree, data, model="OU1", > param=list(alpha="constraint", sigma="constraint")) > depend.evolv<-mvOU(tree, data, model="OU1", param=list(alpha=NULL, > sigma=NULL)) > > ##and a similar thing in mvSLOUCH > independ.evolv<-ouchModel(tree, data, regimes=NULL, Atype="Diagonal", > Syytype="Diagonal") > depend.evolv<-ouchModel(tree, data, regimes=NULL, Atype="DecomposableReal", > Syytype="UpperTri") > > My questions are: > > 1. Is my interpretation of these models correct? Specifically I am > concerned about the interpretation of the alpha matrix. I am somewhat > confused as to how the off-diagonal alpha elements influence the OU process > when I have specified 1 regime per trait. > > 2. I am frequently encountering errors during model fitting in mvMORPH of > the type"Error in loglik_mvmorph(dat, matEstim$V, matEstim$W, n, p, error = > error, : the leading minor of order 5833 is not positive definite". I > gather this has to do with a problem in the matrix decomposition, but is > there a practical solution? I have tried some of the other 'decomp' > options but this does not seem to help. > > 3. I had a few emails with Krzysztof Bartoszek (author of mvSLOUCH) and he > suggested that such a large dataset would be problematic. Would this be an > issue for mvMORPH as well? If so, is there a generally acceptable > work-around for reducing the size of comparative data sets to accommodate > models like this? > > Many thanks in advance > > > ____________________________________________________________________________ > > Cody Dey > [email protected] > McMaster University > Department of Biology > > [[alternative HTML version deleted]] > > _______________________________________________ > R-sig-phylo mailing list - [email protected] > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at > http://www.mail-archive.com/[email protected]/ > -- Aaron A. King, Ph.D. Ecology & Evolutionary Biology Mathematics Center for the Study of Complex Systems University of Michigan GPG Public Key: 0x15780975 [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/[email protected]/
