Perhaps, but wouldn't significant off-diagonal elements in the sigma matrix likewise have an interesting interpretation?
A. On Wed, May 6, 2015 at 9:51 AM, Julien Clavel <[email protected]> wrote: > Hi Cody, > > Maybe in your case you are rather interested in testing whether there is > significant interaction in the "selection" strength (i.e. you constrain the > alpha matrix but not the sigma matrix) than testing for significant > correlations between traits? > > e.g. > > mvOU(tree, data, model="OU1", param=list(decomp="diagonal")) > > vs. > > mvOU(tree, data, model="OU1", param=list(decomp="symmetricPositive")) > > Best, > > Julien > > > Date: Wed, 6 May 2015 08:41:04 -0400 > > From: [email protected] > > To: [email protected] > > CC: [email protected] > > Subject: Re: [R-sig-phylo] Off-diagonal elements in multivariate OU > evolution > > > > > Hi Aaron and Julien, > > > > Thanks for the responses. I will try different methods for computing the > > log-likelihood and will report back on the list (they take a while to > > run...). > > > > The traits are a continuous plumage ornamentation score for male and > female > > passerines. They way they are calculated is a bit complicated, but they > > have approximately the same mean and variances, and both have a maximum > > value of 100. > > > > A scatterplot fills in most of the space above the 1:1 line (i.e. males > are > > almost always more ornamented than females, but all other combinations > are > > possible albeit with different densities) and there is a correlation in > the > > raw data of R2 ~ 0.28 > > > > My goal is to test whether there are cross-sex genetic constraints that > > limit the independent evolution of male and female ornamentation, and > then > > in other analyses look at sex-specific responses to different ecological > > factors. It seems obvious to me that there is co-evolution of male and > > female ornamentation given the correlation between the sexes (in the raw > > data) and my knowledge of the system, but it would be nice to show this > > statistically. > > > > Cody > > > > > > > > __________________________________________________________________ > > > > Cody Dey > > [email protected] > > > > On Wed, May 6, 2015 at 7:00 AM, Aaron King <[email protected]> wrote: > > > > > 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]/ > -- 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]/
