Hi Miriam - As you said, all of the pPCA axes should have a phylogenetic covariance of 0. If you construct an evolutionary vcv matrix from those variables, the matrix should have 0's for all non-diagonal elements. If you use that matrix to simulate data, the results will then be identical to the case where you simulate each PC independently.
So: it doesn't matter, both are the same! Luke On Aug 12, 2013, at 4:53 PM, Miriam Santos-Herrera <[email protected]> wrote: > Dear all, > > I am trying to compare the disparities between two clades, the empirical > values are very different so now I am wondering, is this significantly > different than a random expectation? > > to test this I performed 1,000 simulations assuming BM. However here comes > my question: my traits are size corrected variables (obtained through > "phyl.resid") which afterwards have been transformed using a phylogenetic > PCA (using "phyl.pca" with correlation matrix). If I understand well > what phyl.pca does, my axes in the pPCA present a phylogenetic covariance > 0. Therefore, does it make any sense to simulate using the vcv matrix? or > instead of that should I simulate each PC independently (each one with its > rate parameter), and then combine them to calculate the disparities in each > simulation? > > any help on this would be very appreciated. > > thank you very much. > > > Miriam. > > [[alternative HTML version deleted]] > > _______________________________________________ > R-sig-phylo mailing list - [email protected] > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at http://www.mail-archive.com/[email protected]/ Luke Harmon Associate Professor Biological Sciences University of Idaho 208-885-0346 [email protected] _______________________________________________ R-sig-phylo mailing list - [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/[email protected]/
