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?
Cheers, Ted Theodore Garland, Jr., Professor Department of Biology University of California, Riverside Riverside, CA 92521 Office Phone: (951) 827-3524 Facsimile: (951) 827-4286 = Dept. office (not confidential) Email: tgarl...@ucr.edu http://www.biology.ucr.edu/people/faculty/Garland.html http://scholar.google.com/citations?hl=en&user=iSSbrhwAAAAJ Director, UCR Institute for the Development of Educational Applications http://idea.ucr.edu/ Inquiry-based Middle School Lesson Plan: "Born to Run: Artificial Selection Lab" http://www.indiana.edu/~ensiweb/lessons/BornToRun.html Fail Lab: Episode One http://testtube.com/faillab/zoochosis-episode-one-evolution http://www.youtube.com/watch?v=c0msBWyTzU0 ________________________________________ From: r-sig-phylo-boun...@r-project.org [r-sig-phylo-boun...@r-project.org] on behalf of Diego Bilski [diegobil...@gmail.com] Sent: Friday, May 16, 2014 7:55 AM To: r-sig-phylo@r-project.org Subject: [R-sig-phylo] Cross-validation with independent contrasts Dear all, 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). Any thoughts? Best wishes, Diego Bilski [[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/
