With respect to your crankiness, is this the paper by Hansen that you are referring to?:
Bartoszek, K., Pienaar, J., Mostad, P., Andersson, S., & Hansen, T. F. (2012). A phylogenetic comparative method for studying multivariate adaptation. Journal of Theoretical Biology, 314(0), 204-215. I wrote Bartoszek to see if I could get his R code to try the method mentioned in there. If I can figure out how to apply it to my data, that will be great. I agree that it is clearly a mistake to assume one variable is responding evolutionarily only to the current value of the other (predictor variables). Regarding your comments: > If the "regressions" are being done in a model which implies > that the two variables are multivariate normal, then we can > simply estimate the parameters of that joint distribution, > which are of course the two means and the three elements of the > covariance matrix. > > If we then test whether Cov(X,Y) is different from zero, that > should be equivalent to a test of significance of either > regression. I'm not clear on what you are suggesting I do here. Isn't PGLS essentially testing Cov(X,Y) taking the phylogeny into account? And are you saying there is a way to show that my variables are significantly associated with each other even though PGLS shows different things depending on which way I run the associations? -Tom On Jul 11, 2013, at 5:46 PM, Joe Felsenstein <j...@gs.washington.edu> wrote: > > If the "regressions" are being done in a model which implies > that the two variables are multivariate normal, then we can > simply estimate the parameters of that joint distribution, > which are of course the two means and the three elements of the > covariance matrix. > > If we then test whether Cov(X,Y) is different from zero, that > should be equivalent to a test of significance of either > regression. > > /* crankiness on */ > Note of course that most "phylogenetic" regressions are being > done wrong: if they assume that Y responds to the current value > of X, but when the value of Y may actually be the result of > optimum selection which is affected by past values of X which > we do not observe directly. > > I've complained about this here in the past, to no avail, > Thomas Hansen, in a recent paper, made the same point, with > evidence too. > /* crankiness off */ > > J.F. > ---- > Joe Felsenstein j...@gs.washington.edu > Department of Genome Sciences and Department of Biology, > University of Washington, Box 355065, Seattle, WA 98195-5065 USA _________________________________________________ P. Thomas Schoenemann Associate Professor Department of Anthropology Cognitive Science Program Indiana University Bloomington, IN 47405 Phone: 812-855-8800 E-mail: t...@indiana.edu Open Research Scan Archive (ORSA) Co-Director Consulting Scholar Museum of Archaeology and Anthropology University of Pennsylvania http://www.indiana.edu/~brainevo [[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/
