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]
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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