Hi Alex, Another type of allometry that is worth mentioned is the static allometry. So, if you want to remove this allometry effect (differences in shape in a same age group in adults, per example) you can use the same regression.
Cheers Carlos On Sat, Mar 28, 2015 at 8:04 PM, <oliverhoo...@prstatistics.co.uk> wrote: > 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 <ro...@life.bio.sunysb.edu> 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:<ryanfel...@gmail.com>] > > Sent: Friday, March 27, 2015 7:34 AM > > To: Alex Marshall > > Cc: <morphmet@morphometrics.org> > > 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> > > <ryanfel...@gmail.com> > > (201)981-8642 > > > > > > > > On Fri, Mar 27, 2015 at 7:49 AM, Alex Marshall << > alpmar...@googlemail.com>> 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.marshall...@ucl.ac.uk> > > > > > > -- > > > 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>. > > > > > -- > > 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>. > > > > -- > > 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>. > > > > -- > 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. > -- Carlos Eduardo R. D. Alencar - Biólogo, PhD. - Academia.edu Profile <https://ufrn.academia.edu/CaducasRochaDuarte> carlosce2...@gmail.com Grupo de Estudos em Ecologia e Fisiologia de Animais Aquáticos - GEEFAA [ www.geefaa.com] -- 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.
