Hi Alex, If you want to remove the effect of size on shape that is caused by ontogenetic allometry (differences in shape due to age/size per-say) you can regress the Procrustes coordinates of your samples on the centroid size and then use the residuals.
Hope this helps, Oliver Hooker PR~Statistics On 28 March 2015, F. James Rohlf <[email protected]> wrote: > Procrustes superimposition only removes isometric size variation. Shape > changes that are a function of size (allometry) are not removed so a > regression of some sort is needed. > > ____________________________________________ > F. James Rohlf, Distinguished Professor, Emeritus. Ecology & Evolution > Research Professor, Anthropology > Stony Brook University > > -----Original Message----- > From: Ryan Felice [mailto:<[email protected]>] > Sent: Friday, March 27, 2015 7:34 AM > To: Alex Marshall > Cc: <[email protected]> > Subject: Re: [MORPHMET] PC Ranks in Evolutionary PCA > > 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 > <http://www.rnfelice.com> > <[email protected]> > (201)981-8642 > > > > On Fri, Mar 27, 2015 at 7:49 AM, Alex Marshall <<[email protected]>> > 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 > > <[email protected]> > > > > -- > > 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 <[email protected]>. > > > -- > 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 <[email protected]>. > > -- > 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 <[email protected]>. > -- 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 [email protected].
