Thanks to everyone for the quick replies! My main question was about the phylogenetic PCA.
Ryan: yes my data are landmark configurations after Procrustes superimposition. I understand allometry still has an effect after Procrustes, so I have regressed centroid size on shape and used the residuals. I have assumed all my specimens are adults so I suppose this is correction for static allometry? I didn't mention I'm using MorphoJ recommended by my supervisor. I will definitely try the morphometrics R packages if I have more analysis. MorphoJ is a little user-friendlier but cumbersome for some of what I'm doing. Many thanks! On Saturday, 28 March 2015 09:14:12 UTC, ryanfelice wrote: > > Hi Alex, > > I'm assuming that your shape data are landmark configurations that > have been subjected to a Procrustes superimposition. is that correct? > If so, I dont think the regression you described is really necessary- > Procrustes analysis will remove the effects of size, orientation, and > position. > > What software are you using for your analysis? you might find it > easier/more streamlined to use the phyl.pca function in the phytools R > package. If you use that function, make sure that you are using the > original shape data and not the independent contrasts of shape data. > > Good luck! > > -Ryan > Ryan N. Felice, PhD > Ohio University Department of Biological Sciences > 107 Irvine Hall > Athens, OH 45701 > www.rnfelice.com > ryanf...@gmail.com <javascript:> > (201)981-8642 > > > > On Fri, Mar 27, 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.
