I read Christy's question a little differently, and requiring some
clarification.

First, Dean, doesn't Dean & Felice fix the angle between jaw and cranium so
that you can subject a craniomandibular dataset to a common GPA, which at
the PLS step has the benefit of preserving relative size relationships
between the two structures? On the other hand, it's not clear if Christy
obtained landmarks in a way that allows her to do this as easily. For
instance, her sample may have had crania and mandibles dissected out and
landmarked separately, in which case she subject the cranium and mandible
to separate GPAs. Christy?

If GPA was performed separately for the cranium and mandible, then couldn't
Christy's issue simply be that cranium and mandible have differently
oriented principal axes (as determined by gpagen)?

Also, Christy, are you using the "plot.pls" function (warpgrids=TRUE) for
plotting? If so, then I think one option would be to make shapes=TRUE in
that function. This will give you an output that includes the coordinates
of the extreme shapes (I assume as *p**3 matrices). After that, you just
have to choose which two columns from crania extremes and which two columns
from mandible extremes provide you with common cranial and mandibular
views. You can then make 2D plots your landmarks using the base R plotting
functions. Unfortunately, you won't have warpgrids. But you can overlay two
(e.g., mandible) configurations to show the difference between extremes. Or
you can plot one extreme as the ball-and-stick wireframe and the change to
the other extreme as displacement vectors emanating from the wireframe.

David

On Wed, Jan 24, 2018 at 10:15 AM, Adams, Dean [EEOBS] <dcad...@iastate.edu>
wrote:

> Christy,
>
>
>
> That data example contained variation in relative jaw position among
> specimens, which could affect shape estimates, as well as down-stream shape
> analyses.  Several approaches have been proposed for dealing with such
> rotational variation (see Adams 1999; also Bookstein’s Orange book). One
> approach is to rotate one subset of landmarks so the angle between subsets
> is invariant across specimens. The geomorph function ‘fixed.angle’ performs
> this operation for 2D landmark datasets.
>
>
>
> As to your comment on whether or not such positional variation makes a
> difference, yes it can. PLS examines the degree of covariation between
> blocks of variables and estimates of the between block covariation will
> differ if one set of variables is rotated relative to the other. Whether
> this results in a large or small difference in r-PLS values is
> data-dependent, but the values will not be the same.
>
>
>
> For this reason, prior to any PLS analysis for evaluating integration and
> covariation patterns, one must first carefully consider what type of
> variables are being utilized, how they were generated, and whether it even
> makes sense to interpret the results biologically.
>
>
>
> Dean
>
>
>
> Dr. Dean C. Adams
>
> Professor
>
> Department of Ecology, Evolution, and Organismal Biology
>
>        Department of Statistics
>
> Iowa State University
>
> www.public.iastate.edu/~dcadams/
>
> phone: 515-294-3834 <(515)%20294-3834>
>
>
>
> *From:* Christy Anna Hipsley [mailto:chips...@unimelb.edu.au]
> *Sent:* Tuesday, January 23, 2018 9:34 PM
> *To:* MORPHMET <morphmet@morphometrics.org>
> *Subject:* [MORPHMET] relative positions of landmark partitions in
> integration tests - how important?
>
>
>
> Hi all,
>
>
>
> I'm trying to run an integration test in geomorph, or rather
> phylo.integration on 2 sets of Procrustes aligned coordinates for cranium
> and jaws of lizards, landmarked on both sides. When I plot the results I
> get graphs of the landmarks for the positive and negative extremes of
> PLS1&2, but for the cranium they are in lateral view while for the
> mandibles they are in frontal view.
>
> I'm wondering if this is an issue for the estimation of r-PLS, since in
> Adams & Felice 2004 (PLoS ONE: Assessing Trait Covariation and
> Morphological Integration on Phylogenies Using Evolutionary Covariance
> Matrices), they write "the position of the jaw was standardized relative to
> the skull by rotating the jaw to a common articulation angle among
> specimens".
>
>
>
> If it is an issue, how do I rotate the position of one of the partitions
> to be in the same orientation as the other?
>
>
>
> Thanks for any advice!
>
> Christy
>
>
>
> *Dr Christy Anna Hipsley | ARC DECRA Fellow *
>
> School of BioSciences, University of Melbourne/
>
> Museums Victoria
>
> GPO Box 666
>
> Melbourne, Victoria 3001 Australia
>
> *T:* +61 3 8341 7423 <+61%203%208341%207423> *E:*
> christy.hips...@unimelb.edu.au; chips...@museum.vic.gov.au
>
> http://blogs.unimelb.edu.au/hipsleylab/
>
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-- 
David C. Katz, Ph.D.
Postdoctoral Fellow
Benedikt Hallgrimsson Lab
University of Calgary

Research Associate
Department of Anthropology
University of California, Davis

ResearchGate profile <https://www.researchgate.net/profile/David_Katz29>
Personal webpage
<https://davidckatz.wordpress.com/>

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