----- Forwarded message from [email protected] ----- Date: Mon, 08 Oct 2012 11:22:36 -0700 From: [email protected] Reply-To: [email protected] Subject: Re: MorphoJ question To: [email protected]
----- Forwarded message from al cardini ----- Date: Mon, 8 Oct 2012 02:25:49 -0400 From: al cardini Reply-To: al cardini Subject: Re: MorphoJ question To: [email protected] Fully agreed with Chris. My understanding was, Daniela, that you had measured additional skulls using just one side to be faster. If that was the case, then you could try what I suggested to analyse both the original (both sides) and new (one side only) data. If you run a PCA on shape coordinates, keep only PCs with non-zero eigenvalues, and then use those for statistical analyses in other programs, which might not be able to see the redundancy in your data, you should be able to do the analyses and get the right df in parametric tests. Good luck. Cheers Andrea On 8 October 2012 01:07, <[email protected]> wrote: > > ----- Forwarded message from [email protected] ----- > > Date: Sat, 06 Oct 2012 15:55:43 -0700 > From: [email protected] > Reply-To: [email protected] > Subject: Re: MorphoJ question > To: [email protected] > > > ----- Forwarded message from Chris Klingenberg ----- > > Date: Fri, 5 Oct 2012 18:35:34 -0400 > From: Chris Klingenberg > Reply-To: Chris Klingenberg > Subject: Re: MorphoJ question > To: [email protected] > > Dear Daniela > > I'm afraid, omitting one half of the skulls is not going to increase the > sample size. If you include the landmarks in the median plane (and average > over reflected and relabeled copies of each specimen), using those and the > paired landmarks of one side is going to be exactly the same as using the > symmetric component from the analysis with object symmetry. The reason for > this is that the paired landmarks on one side perfectly predict what their > matches on the other side are doing... > > The dimensionality of the symmetric component of variation is roughly > (exactly for 2D applications) that of the total variation (or an analysis > ignoring the symmetry of the skulls). So it is pretty much the same as > omitting half the skull, except for the fact that it does not just ignore > the other half. In particular, the dimensionality of just one side plus > median landmarks (after Procrustes fit for object symmetry, averaged over > reflections) is the same as that of the symmetric component with all > landmarks. (If you don't do the averaging over reflections, the > dimensionality of one side plus median landmarks will be larger than that of > the symmetric component.) > > There is only a difference if you use software that does not deal with > singular covariance matrices well. All standard morphometrics programs > should do reasonably well, because ill-conditioned or singular covariance > matrices are very frequent. Programs like SAS and the likes will also handle > this similarly. > > So, on second thought, throwing out the paired landmarks from one side won't > help. Because it only creates additional trouble (with visualizing shape > changes, etc.), it;'s better not to do it. > > I hope this clarifies the issue. > > Best wishes, > Chris > > > > On 05/10/2012 20:13, [email protected] wrote: > > > ----- Forwarded message from Daniela Sanfelice ----- > > Date: Thu, 4 Oct 2012 10:54:42 -0400 > From: Daniela Sanfelice > Reply-To: Daniela Sanfelice > Subject: MorphoJ question > To: [email protected] > > Hey dear morphometricians! > > To improve my samples size, I will recalculate all my projects and results > about morphological integration in pinnipeds skulls using just one skull > side. > > So... no more object symmetry! However, superposition was done considering > object symmetry... > > Can I just exclude the landmarks anyway, and after include the new specimens > (with only the left side information)? > > I suppose not... but if I can´t do this way, how can I do it? > > Should I exclude the landmarks from all the raw data file by hand or there > is another easier way? > > Many thanks for your help and contributions! > > Cheers, Daniela Sanfelice. > > > > ----- End forwarded message ----- > > > > > -- > > *********************************** > Christian Peter Klingenberg > Faculty of Life Sciences > University of Manchester > Michael Smith Building > Oxford Road > Manchester M13 9PT > United Kingdom > > E-mail: [email protected] > Phone: +44 161 2753899 > Skype: chris_klingenberg > *********************************** > > > > ----- End forwarded message ----- > > > > > > ----- End forwarded message ----- > > > -- Dr. Andrea Cardini Researcher in Animal Biology Dipartimento di Scienze Chimiche e Geologiche, Università di Modena e Reggio Emilia, l.go S. Eufemia 19, 41121 Modena, Italy Honorary Fellow Functional Morphology and Evolution Unit, Hull York Medical School University of Hull, Cottingham Road, Hull, HU6 7RX, UK University of York, Heslington, York YO10 5DD, UK Adjunct Associate Professor Centre for Forensic Science , The University of Western Australia 35 Stirling Highway, Crawley WA 6009, Australia E-mail address: [email protected], [email protected], [email protected], [email protected] Webpage: http://sites.google.com/site/hymsfme/drandreacardini Datasets: http://ads.ahds.ac.uk/catalogue/archive/cerco_lt_2007/overview.cfm#metadata Editorial board for: Zoomorphology: http://www.springer.com/life+sciences/animal+sciences/journal/435 Journal of Zoological Systematics and Evolutionary Research: http://www.wiley.com/bw/journal.asp?ref=0947-5745&site=1 Hystrix, the Italian Journal of Mammalogy: http://www.italian-journal-of-mammalogy.it/ ----- End forwarded message ----- ----- End forwarded message -----
