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>/<http://www.public.iastate.edu/~dcadams/
>>  <http://www.public.iastate.edu/~dcadams/>>
>> phone: 515-294-3834
>> *From:*Andrey Lissovsky [mailto:andlis...@gmail.com 
>> <mailto:andlis...@gmail.com>]
>> *Sent:* Tuesday, October 31, 2017 10:21 AM
>> *To:* MORPHMET <morphmet@morphometrics.org 
>> <mailto:morphmet@morphometrics.org>>
>> *Cc:* andlis...@gmail.com <mailto:andlis...@gmail.com>; volk...@yandex.ru 
>> <mailto: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/>
>>    <http://www.public.iastate.edu/~dcadams/ 
>> <http://www.public.iastate.edu/~dcadams/>>
>>    phone: 515-294-3834
>>    *From:*Andrey Lissovsky [mailto:andl...@gmail.com <http://gmail.com/> 
>> <javascript:>]
>>    *Sent:* Tuesday, October 31, 2017 9:26 AM
>>    *To:* MORPHMET <morp...@morphometrics.org <http://morphometrics.org/> 
>> <javascript:>>
>>    *Cc:* andl...@gmail.com <http://gmail.com/> <javascript:>; 
>> vol...@yandex.ru <http://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
> 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 <mailto:alcard...@gmail.com>, 
> andrea.card...@unimore.it <mailto:andrea.card...@unimore.it>
> WEBPAGE: https://sites.google.com/site/alcardini/home/main 
> <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
>  
> <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/ 
> <http://www.footprintnetwork.org/en/index.php/GFN/page/calculators/>
> 
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