That seems like it would be OK, at least if you think it is OK for nonphylogenetic PCA. An alternative is to simulate data along your phylogeny, analyze it the same way, do it a couple thousand times, then make an empirical null distribution of, say, the eigenvalues when the data have no correlation on average but increased variance in the values of correlations caused by the phylogenetic hierarchy. This is discussed in our very old PHYLOGR package. However, you will need to make some decisions about the "branch lengths" to use for your individuals within species, represented by a bunch of mini-star phylogenies.
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 Experimental Evolution: Concepts, Methods, and Applications of Selection Experiments. 2009. Edited by Theodore Garland, Jr. and Michael R. Rose http://www.ucpress.edu/book.php?isbn=9780520261808 (PDFs of chapters are available from me or from the individual authors) ________________________________________ From: r-sig-phylo-boun...@r-project.org [r-sig-phylo-boun...@r-project.org] on behalf of Franck Stefani [fopstef...@gmail.com] Sent: Wednesday, August 22, 2012 3:50 PM To: r-sig-phylo@r-project.org Subject: [R-sig-phylo] pPCA - global and local components Hi, Among the graphical outputs of the pPCA, there is the scree plot showing the global and local components. I would like to know what are the criteria to define the number of GPC or LPC to interpret ? Can we use a broken stick model? Cheers, Franck [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo _______________________________________________ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
