[R-sig-phylo] pPCA - global and local components
Dear Theodore, Thanks for your reply but I fear I am not skilled enough in stats for considering your alternative... I have a look at the paper published by Jombart et al. (2010, Putting phylogeny into the analysis of biological traits: a methodological approach. J Theor Biol 264: 693) and it seems they have only considered the first global and/or first local components and this even if the second global or local components seemed to explain a certain amount of the total variance. Franck 2012/8/23 Theodore Garland Jr theodore.garl...@ucr.edu 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=enuser=iSSbrhwJ 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 [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] pPCA - global and local components
Dear Franck, we faced that same issue in an analysis of snail shell morphologies. We decided to use randomizations of trait vectors over the phylogeny, so that they remained correlated but lost the phylogenetic pattern. We were mainly interested in the pattern of covariation with phylogenetic distance. Our procedure and results are described in: Webster et al. 2012. Mol. Phyl. Evol. 63: 625-638. Cheers, Tom tomvandooren.eu ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] pPCA - global and local components
Hello, this problem is recurrent throughout multivariate analysis, and I know of no universally satisfying solution. In spatially/phylogenetically constrained methods, the idea is that a relevant structure should exhibit both strong variance and autocorrelation. I think the simulation approaches suggested by Ted and Tom are the way to go if you seek a less descriptive approach. Cheers Thibaut From: r-sig-phylo-boun...@r-project.org [r-sig-phylo-boun...@r-project.org] on behalf of Franck Stefani [fopstef...@gmail.com] Sent: 23 August 2012 11:54 To: r-sig-phylo@r-project.org Subject: [R-sig-phylo] pPCA - global and local components Dear Theodore, Thanks for your reply but I fear I am not skilled enough in stats for considering your alternative... I have a look at the paper published by Jombart et al. (2010, Putting phylogeny into the analysis of biological traits: a methodological approach. J Theor Biol 264: 693) and it seems they have only considered the first global and/or first local components and this even if the second global or local components seemed to explain a certain amount of the total variance. Franck 2012/8/23 Theodore Garland Jr theodore.garl...@ucr.edu 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=enuser=iSSbrhwJ 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 [[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
Re: [R-sig-phylo] pPCA - global and local components
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=enuser=iSSbrhwJ 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
