Thanks for the reference Professor Polly, very helpful. Alex Marshall MSci Student University College London alexander....@ucl.ac.uk
On Saturday, 28 March 2015 09:13:51 UTC, pdpolly wrote: > > Phylogenetic PCA has many unusual properties, and does not remove the > effects of phylogeny. Yes, it is the case that the variance of the scores > on the first phylogenetic principal component can be higher than the second > PC. We recently had a paper in the Hystrix morphometrics volumes about the > properties of pPCA and what it does and does not do. > > Polly, P. D., A. M. Lawing, A.-C. Fabre, and A. Goswami. 2013. > Phylogenetic principal components analysis and geometric morphometrics. > *Hystrix*, 24: 1-9 > > Paper is available open access from the publisher or from here: > http://mypage.iu.edu/~pdpolly/Publications.html > > P. David Polly > Geological Sciences > Adjunct, Anthropology and Biology > Indiana University > 1001 E. 10th Street > Bloomington, IN 47405-1405 > pdp...@indiana.edu <javascript:> > +1 (812) 855-7994 > http://mypage.iu.edu/~pdpolly/ > > On 27 Mar 2015, at 7:49 AM, Alex Marshall <alpm...@googlemail.com > <javascript:>> wrote: > > Hello everyone, > I'm a MSci student new to morphometrics and this group. I'm studying > morphological integration in squamate crania and one of the things I'd like > to do is an Evolutionary PCA of all my species, accounting for phylogeny > and allometry. > > I think I do this correctly but in the PCA results the PCs are not ranked > by proportion of variance e.g. PC5 has greater % variance that PCs 3 & 4. > Is this normal? > > To conduct the evolutionary PCA I created independant contrasts of all my > shape data, regressed centroid size on shape and conducted PCA on the > residuals. After this I applied the resultant PC scores to another PCA of > my original data. > > Would anyone kindly confirm if this is the right way to do it? > > Many thanks, > > Alex Marshall > MSci Student > University College London > alexander....@ucl.ac.uk <javascript:> > > -- > MORPHMET may be accessed via its webpage at http://www.morphometrics.org > > To unsubscribe from this group and stop receiving emails from it, send an > email to morphmet+u...@morphometrics.org <javascript:>. > > > -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org.
