I'm happy that Jim made my ill written point clear. What I meant is that the two methods in my experience (with the amount of variation I find in most zoological dataset) do not make an appreciable difference.
"Data dependent", Mike, is in the sense Dean put it: "difference one finds between a full and partial Procrustes alignment is dataset dependent" and the reason I wrote it is indeed not to generalize from my own experience (limited to my own datasets). All the best Andrea On 1 November 2017 at 04:18, F. James Rohlf <[email protected]> wrote: > Note that the distinction between full and partial Procrustes is not very > important if shape variation is in fact very small. > > > > In a partial Procrustes superimposition there is an additional step that > projects the aligned specimens onto the tangent space. Without that step > the shapes are still in the curved space of GPA aligned shapes. As a > result, there will be one less eigenvalue than expected that is “exactly” > equal to zero (i.e., around 10^-16). Its size depends on the amount of > curvature of the space around the GPA consensus shape and that depends on > the amount of shape variation in the sample and thus is data dependent. > > > > However, it seems reasonable to me to apply this extra step if one is > going to use multivariate methods that assume that one has a linear space. > This was discussed in Rohlf, F. J. 1999. Shape statistics: Procrustes > superimpositions and tangent spaces. Journal of Classification, 16:197-223. > Slice 2001. Syst. Biol. 50:141–149 is also relevant. > > > > _ _ _ _ _ _ _ _ _ > > F. James Rohlf, Distinguished Prof. Emeritus > > [image: univautosig] > > Depts. of Anthropology and of Ecology & Evolution > > > > > > *From:* Mike Collyer [mailto:[email protected]] > *Sent:* Tuesday, October 31, 2017 12:29 PM > *To:* andrea cardini <[email protected]> > *Cc:* [email protected] > *Subject:* Re: [MORPHMET] Procrustes fit > > > > Andrea, > > > > I think it is worth it to do a pedantic review of your exercise for the > benefit of the community. > > > > First, the differences are not data dependent - they are method > dependent. TPSRelw uses partial Procrustes; MorphoJ uses full Procrustes > superimposition. PCA would have the exact same variance explained by > dimensions (rounding notwithstanding) if the two programs used the same > superimposition method. > > > > The results are similar because the methods are similar. Maybe what you > meant by “data dependent” is that in another case, the different methods > might lead to more disparate results, for which I agree. Again, for the > benefit of others, I think this distinction is important. > > > > Second, I think the special characters had very little to do with the > results from the analysis but might indeed cause problems for one program > compared to another. This would have more to do with each program’s > programming to identify and deal with such things. > > > > Cheers! > > Mike > > > > > > On Oct 31, 2017, at 12:05 PM, andrea cardini <[email protected]> wrote: > > > > Dear All, > yes, there are differences and they're data dependent but in Andrey's case > (as it's my experience all the times I checked with my own data) they're > very small. > I gave a very quick look and it's better to check more carefully. However, > in the screenshot one can see the % of variance explained computed in PAST > 2.17, MorphoJ and TPSRelw: they're almost identical and PC1 vs PC2 in the > three programs (not shown) look the same except for flipping one or the > other axis. > > The issue may have something to do with special characters in the TPS > file: I could run it in TPSRelw only after converting to NTS, which removed > the special characters in the image names. > > Cheers > > Andrea > > > > On 31/10/17 16:35, Adams, Dean [EEOBS] wrote: > > Andrey, > To repeat: there is no reason to expect the numbers to match identically > across software packages, particularly column by column (if that is what > you are examining). Even if two packages perform things identically in > terms of the algebra (e.g,. GPA using TpsRelw and geomorph), the numbers > may differ slightly for other reasons (post-rotation of the alignment to > the principal axes of the consensus, etc.). > What is important for downstream statistical analyses is not the > individual columns of numbers found from the GPA alignment, but rather the > relationships of specimens in the resultant shape space. That is, how > different are shapes from one another? In the case I mentioned above, if > you took the aligned specimens from TpsRelw and obtained the Procrustes > (Euclidean) distance matrix from them, and did the same with the aligned > specimens from geomorph, and then performed a matrix correlation, the > correlation would be precisely 1.0. This means the information is > identical in the two superimpositions, even if they differ slightly in how > the entire set is oriented relative to the X-Y axis. Incidentally, in the > above case one would also find a perfect correlation between distances from > the GPA-aligned specimens, those shapes rotated to their principal axes, or > differences in shape found from the thin-plate spline and uniform shape > components taken together. For an early discussion of these issues see > Rohlf 1999. > However, performing the procedure above where one set of GPA-aligned > coordinates is from MorphoJ will not produce a perfect correlation of 1.0, > as MorphoJ uses Full Procrustes superimposition. That means the perceived > relationships between shapes is not being represented in the same manner: > which of course is a known difference between full and partial Procrustes > fitting. How much of a difference one finds between a full and partial > Procrustes alignment is dataset dependent. > Dean > Dr. Dean C. Adams > Professor > Department of Ecology, Evolution, and Organismal Biology > Department of Statistics > Iowa State University > www.public.iastate.edu/~dcadams/<http://www.public.iastate.edu/~dcadams/> > phone: 515-294-3834 > *From:*Andrey Lissovsky [mailto:[email protected] <[email protected]>] > *Sent:* Tuesday, October 31, 2017 10:21 AM > *To:* MORPHMET <[email protected]> > *Cc:* [email protected]; [email protected] > *Subject:* Re: [MORPHMET] Procrustes fit > Thank you Dean, > Of course, numbers should differ. But in my case, there is no correlation > between two sets. I guess that in theory the two sets should have r at > least around 0.9? > On Tuesday, October 31, 2017 at 5:31:51 PM UTC+3, dcadams wrote: > Andrey, > It is unreasonable to expect the numbers will match perfectly > between these two software packages, as the way in which they > perform the operations differs. First, MorphoJ uses Full Procrustes > fit, whereas the TPS series, geomorph, and others use Partial > Procrustes fitting. That will make a difference. > Second, there may be additional differences in in how the > superimponsed specimens, and thus the consensus, is aligned relative > to the X-Y coordinate system. Some packages allow one to rotate the > consensus and aligned specimens to their principal axes > post-superimposition. That too could lead to differences. > Dean > Dr. Dean C. Adams > Professor > Department of Ecology, Evolution, and Organismal Biology > Department of Statistics > Iowa State University > www.public.iastate.edu/~dcadams/ > <http://www.public.iastate.edu/~dcadams/> > phone: 515-294-3834 > *From:*Andrey Lissovsky [mailto:[email protected] <javascript:>] > *Sent:* Tuesday, October 31, 2017 9:26 AM > *To:* MORPHMET <[email protected] <javascript:>> > *Cc:* [email protected] <javascript:>; [email protected] <javascript:> > *Subject:* Re: [MORPHMET] Procrustes fit > Thank you, Andrea > I understand that difference should be tiny, so something goes > wrong. I enclose one of my tps files. Usually I check dots and > commas, so the reason is probably in some different way.. > It is possible that I am mixing up menu items.. Last time I use this > software, the labels were different. > Now I use: > In MorphoJ: Preliminaries -- New Procrustes fit -- Align by > principle axes > then: Export dataset -- Procrustes coordinates > In TPS Relw: Actions -- Consensus > then: File -- Save -- Aligned specimens > Is this ok? Should these chains lead to the same results? > On Tuesday, October 31, 2017 at 5:04:56 PM UTC+3, alcardini wrote: > Andrey, the last time I checked this (last July, I believe), > differences > between MorphoJ and TPSRelw were tiny and negligible. I compared > MorphoJ > with R in the last days, and again differences were tiny. > The first thing I'd check is whether there's an issue with > commas vs > dots as decimal separators. > If you send me the tps file, I can give a quick look. > Cheers > Andrea > -- MORPHMET may be accessed via its webpage at > http://www.morphometrics.org > --- > You received this message because you are subscribed to the Google > Groups "MORPHMET" group. > To unsubscribe from this group and stop receiving emails from it, > send an email to [email protected] <javascript:>. > -- > MORPHMET may be accessed via its webpage at http://www.morphometrics.org > --- > You received this message because you are subscribed to the Google Groups > "MORPHMET" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]<mailto: > [email protected] > <[email protected]>>. > -- > MORPHMET may be accessed via its webpage at http://www.morphometrics.org > --- > You received this message because you are subscribed to the Google Groups > "MORPHMET" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]<mailto: > [email protected] > <[email protected]>>. > > > -- > > Dr. Andrea Cardini > Researcher, Dipartimento di Scienze Chimiche e Geologiche, Università di > Modena e Reggio Emilia, Via Campi, 103 - 41125 Modena - Italy > <https://maps.google.com/?q=Emilia,+Via+Campi,+103+-+41125+Modena+-+Italy&entry=gmail&source=g> > tel. 0039 059 2058472 <059%20205%208472> > > Adjunct Associate Professor, School of Anatomy, Physiology and Human > Biology, The University of Western Australia, 35 Stirling Highway, > Crawley WA 6009, Australia > <https://maps.google.com/?q=35+Stirling+Highway,+Crawley+WA+6009,+Australia&entry=gmail&source=g> > > E-mail address: [email protected], [email protected] > WEBPAGE: https://sites.google.com/site/alcardini/home/main > > FREE Yellow BOOK on Geometric Morphometrics: http://www. > italian-journal-of-mammalogy.it/public/journals/3/issue_ > 241_complete_100.pdf > > ESTIMATE YOUR GLOBAL FOOTPRINT: http://www.footprintnetwork.org/en/index. > php/GFN/page/calculators/ > > -- > MORPHMET may be accessed via its webpage at http://www.morphometrics.org > --- You received this message because you are subscribed to the Google > Groups "MORPHMET" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > <Selection_004.jpg> > > > > -- > MORPHMET may be accessed via its webpage at http://www.morphometrics.org > --- > You received this message because you are subscribed to the Google Groups > "MORPHMET" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > -- Dr. Andrea Cardini Researcher, Dipartimento di Scienze Chimiche e Geologiche, Università di Modena e Reggio Emilia, Via Campi, 103 - 41125 Modena - Italy tel. 0039 059 2058472 Adjunct Associate Professor, School of Anatomy, Physiology and Human Biology, The University of Western Australia, 35 Stirling Highway, Crawley WA 6009, Australia E-mail address: [email protected], [email protected] WEBPAGE: https://sites.google.com/site/alcardini/home/main FREE Yellow BOOK on Geometric Morphometrics: http://www.italian-journal-of-mammalogy.it/public/journals/3/issue_241_complete_100.pdf ESTIMATE YOUR GLOBAL FOOTPRINT: http://www.footprintnetwork.org/en/index.php/GFN/page/calculators/ -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org --- You received this message because you are subscribed to the Google Groups "MORPHMET" group. 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