-------- Original Message --------
Subject: Re: 3d data analysis in R
Date: Mon, 1 Jun 2009 09:53:35 -0700 (PDT)
From: Michael Coquerelle <[email protected]>
To: <[email protected]>
References: <[email protected]>
Dear Dean,
Actually, my data were slit ;) (I use Edgewarp). The two inverted points
(right for left) was just a matter of how I stored my data before
proceeding with my analyses in R. I just reassigned the correct
coordinates to each and the problem was solved with procGPA.
Otherwise, I would have realized this two points were inverted while
sliding because you can not miss that in Edgewarp.The set of chords for
the curve semilandmarks and the normals to the surface for each surface
semilandmarks would have been completely messy in the vicinity of the
two landmarks. You directly see that in the 3D view of this software.
Best regards,
Michael
Michael Coquerelle
University of Vienna,
Department of Anthropology
Althanstrasse, 14
A-1090 Vienna
Austria
----- Original Message -----
From: "morphmet" <[email protected]>
To: "morphmet" <[email protected]>
Sent: Monday, June 01, 2009 5:52 PM
Subject: 3d data analysis in R
-------- Original Message --------
Subject: 3d data analysis in R
Date: Fri, 29 May 2009 12:42:53 -0700 (PDT)
From: Dean Adams <[email protected]>
To: [email protected]
References: <[email protected]>
Michael,
For the data you described, one would need to let the 3D semilandmarks
slide along their tangent directions (either along curves or surfaces)
during the GPA procedure to obtain correct estimates of shape. When such
points are not allowed to slide during GPA, some interesting shape
distortions can be introduced (for illustrative examples, see Figs 1-4
in Gunz et al. 2005. Semilandmarks in three dimensions).
Unfortunately, I believe the procGPA routine in the package 'shapes'
does not allow landmarks to slide in this fashion, but rather treats all
landmarks as 'fixed' points. Thus, if semilandmarks are included in the
sample of 3D points, such distortions may be a part of the estimates of
shape and shape variation obtained.
We have recently developed an R routine for a general GPA that allows
the superimposition of either 2D or 3D landmark data. The landmarks can
represent the locations of anatomical points, semilandmarks on curves,
and semilandmarks on surfaces. Our routine is currently in the testing
stages.
We hope to have it available soon.
Best,
Dean
Dr. Dean C. Adams
Associate Professor
Department of Ecology, Evolution, and Organismal Biology
Department of Statistics
Iowa State University
Ames, Iowa
50011
At 03:47 PM 5/28/2009, you wrote:
-------- Original Message --------
Subject: Re: svd in shapes[R]
Date: Thu, 28 May 2009 11:37:01 -0700 (PDT)
From: Michael Coquerelle <[email protected]>
To: <[email protected]>
References: <[email protected]>
Hi Fabio,
I got the same message several months ago. With my data set, 151
specimens and 415 (semi)landmarks in 3d, I never had a problem while
using procgpa from the library shapes. But when I started to analyze just
a subset of the data, let say 200 (semi)landmarks, I got this message. So
I subdivided my sample by the half, one half worked the other not. So I
tried to find out what was wrong with this second half. I did several GPA
with this wrong subsample minus 1 specimen. After several GPA impossible
to run untill the end with the same error mesage, there was one GPA
completed. I checked out the specimen I erased from that GPA and this
specimen had one pair of landmarks inverted. So your problem might be
similar, two landmarks can be inverted in one specimen of your sample.
I hope that will help you.
Cheers,
Michael
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