I use tpsRelw for align my data and I din't have ID lost in my matrix.
Trait export the aligned file like a *tps. Respect to the size, I never
has been "residuals of size" in there, and I think that you have a
problem there, because the value should be "0" or nearly "0" (because
the size was remove it). Cardini suggest: "
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."
but in my experience that funtion doesn`t work correctly with
semilandmarks matrix, It creates a kind of loop for some landmarks. My
suggestion is: save the aligned as *tps; and for the CS, I think a good
option is import it to MorphoJ as a covariable, at least until the
problem of "loops" is solved in tpsRelw.
On 22/06/17 07:16, andrea cardini wrote:
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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