Thank you both, Ted and Joe, My first (or second) option would be doing what Ted suggested, but it will require a bit more coding than just using already existing functions. I will try to do that anyway, and compare the results to those from the cross-validation on the independent contrasts.
Best, Diego On Fri, May 16, 2014 at 2:10 PM, Joe Felsenstein <j...@gs.washington.edu>wrote: > Diego Bilski -- > > > I'm wondering if it would be statistically/philosophically correct to use > > n-fold cross-validation to evaluate a linear regression with independent > > contrasts. My doubt comes from the fact that when simply dividing the IC > > dataset in, lets say, 10 folds, some folds will remove the contrasts of > > internal nodes without necessarily removing an entire clade above that > > point, producing what can be viewed as two independent clades (a > graphical > > example would be, in Felsenstein's seminal paper, fig. 8, remove the > > contrast at node 13, while keeping those at nodes 9 and/or 10). > > and Ted Garland wrote: > > Couldn't you also just do this back at the level of the original tree and > > tip data, creating subsets by pruning the tree before you compute > contrasts? > > > > Under the model of multivariate normality with Brownian Motion > change along the phylogeny, the contrasts are i.i.d. so of course > one can use them as points for cross-validation. But of course, > unless the regression is nonlinear, there is already a parametric > framework for distributions of regression coefficients (and other > associated phenomena) in that i.i.d. MVN framework. > > The issue of what entities should be sampled in cross-validation > depends on how, at what level, you expect the model to depart from > multivariate normality with Brownian Motion. Diego and Ted seem to > have some such expectation but I can't see what that alternative > model would be. > > Joe > ---- > Joe Felsenstein j...@gs.washington.edu > Department of Genome Sciences and Department of Biology, > University of Washington, Box 355065, Seattle, WA 98195-5065 USA > > [[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/ > [[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/
