The point is simple: the variables called centroid size and log centroid
size in MorphoJ won't be the real size of the original structures if
they're imported without rescaling them.
They are, in my experience, about 1 and, regardless of the reason (which
I find less important), they're wrong. Of course, if one does not do
anything with size, shape data will be fine. I would not risk to be
misled, nevertheless. In fact, I might have happened to review one or
two papers when someone was testing allometry or something else
involving size, when size was about 1 for all specimens.
Cheers
Andrea
On 22/06/17 11:18, Paolo Piras wrote:
Hi folks/Andrea,
just to underline this:
Andrea,when you say
"an 'apparent size variable' which is a series of numbers virtually
equal to 1 (differences will be approximation errors)."
I think that MorphoJ "reads" the actual CS values from the aligned
coordinates saved by TPSrelw that, as you say, have lost their original
size. However, small deviations from 1 are not due to approximation
error as I *suspect* that the "aligned coordinates" saved by TPSrelw are
those projected on the tangent plane (by an orthogonal [more commonly
used] or stereographic projection) and for this reason they have
necesarily a CS larger than 1 that is the radius of the hyperspherical
Kendall's Shape Space. In order to reach the tangent plane from the
sphere one necessarily must go beyond its radius (that geometrically
*IS* the size of a configuration lying on that space) and the CS will be
inevitably larger than 1.
An indirect proof for this would be to verify that what you call
"approximation error" gives CS values always slightly larger than 1 and
never smaller.
So I think there is no error in having, for those data, CS
slightly different (=larger) from 1 as they MUST have CS larger than 1
by construction.
However,I'm not sure at 100% if TPSrelw works as I hypothesized here..
Playing a bit with TPSrelw could unveil this.
All the best
Paolo
2017-06-22 11:00 GMT+02:00 andrea cardini <alcard...@gmail.com
<mailto:alcard...@gmail.com>>:
Hi Pere,
there's plenty of work arounds this. I agree with Carmelo that the
nts format may be easier to edit manually, so that you can put back
the necessary labels.
HOWEVER, PLEASE BE CAREFUL because SIZE WILL BE MISSING from those
data. As most of the time you may want to analyse both size and
shape, instead of importing in MorphoJ the aligned specimens from
the TPSRelw slid configurations, I'd suggest to save the SCALED
ALIGNED SPECIMENS in TPSRelw. Jim added this option for this
purpose: this way you get the aligned specimens rescaled to the
original centroid size. Therefore, when you import them in MorphoJ
and redo the Procrustes fit, you will get both the aligned specimens
as well as their size.
In contrast, if you import the aligned data (not rescaled), size
won't be there but you may be easily tricked and think it is there,
because MorphoJ requires that you redo the Procrustes fit and then
you'll get an 'apparent size variable' which is a series of numbers
virtually equal to 1 (differences will be approximation errors).
Use the scaled aligned and you won't have this issue.
Cheers
Andrea
On 22/06/17 10:07, Pere Ibáñez wrote:
Hello All,
I am using TPSRelW to slide semilandmarks. Once I have the
consensus, I use Save aligned to export the aligned coordinates
(including slid semilandmarks) as a tps file, that I want to
import into MorphoJ.
The problem is that the file that is exported has the IDs of the
specimens empty, with no information. And MorphoJ doesn't import
it without that information, so I have to type it one by one on
the tps file. Does anyone know how to export that tps file from
TPSRelW without losing the ID?
Thanks!
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FREE Yellow BOOK on Geometric Morphometrics:
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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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