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 <f.james.ro...@stonybrook.edu>
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:mlcoll...@gmail.com]
> *Sent:* Tuesday, October 31, 2017 12:29 PM
> *To:* andrea cardini <alcard...@gmail.com>
> *Cc:* morphmet@morphometrics.org
> *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 <alcard...@gmail.com> 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:andlis...@gmail.com <andlis...@gmail.com>]
> *Sent:* Tuesday, October 31, 2017 10:21 AM
> *To:* MORPHMET <morphmet@morphometrics.org>
> *Cc:* andlis...@gmail.com; volk...@yandex.ru
> *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:andl...@gmail.com <javascript:>]
>    *Sent:* Tuesday, October 31, 2017 9:26 AM
>    *To:* MORPHMET <morp...@morphometrics.org <javascript:>>
>    *Cc:* andl...@gmail.com <javascript:>; vol...@yandex.ru <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
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> Dr. Andrea Cardini
> Researcher, Dipartimento di Scienze Chimiche e Geologiche, Università di
> Modena e Reggio Emilia, Via Campi, 103 - 41125 Modena - Italy
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> WEBPAGE: https://sites.google.com/site/alcardini/home/main
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> FREE Yellow BOOK on Geometric Morphometrics: http://www.
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> 241_complete_100.pdf
>
> ESTIMATE YOUR GLOBAL FOOTPRINT: http://www.footprintnetwork.org/en/index.
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-- 

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: alcard...@gmail.com, andrea.card...@unimore.it
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/

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