No argument here.

On Wed, Jan 24, 2018 at 11:12 AM, Adams, Dean [EEOBS] <dcad...@iastate.edu>
wrote:

> David,
>
>
>
> Yes, fixing the angle first allows for a single GPA, which then retains
> relative size information across the substructures. And yes, it puts things
> in a common orientation. Both have major advantages for downstream PLS, and
> its interpretation. Many PLS-based integration analyses in GMM examine
> covariation in substructures from a single larger object subjected to a
> single GPA.  I point to the classic paper of Bookstein et al. 2003 as an
> exemplar.
>
>
>
> I would argue that it is in such cases where integration patterns are most
> interpretable, as with a single GPA one is able to characterize covariation
> patterns among sets of variables whose spatial relationships have been
> retained throughout the analysis. This is rather important. When this isn’t
> the case, it is much more challenging to derive interpretable estimates.
> This is what I was alluding to in the last part of my previous post.
>
>
>
> 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:* katz.w...@gmail.com [mailto:katz.w...@gmail.com] *On Behalf Of *David
> Katz
> *Sent:* Wednesday, January 24, 2018 11:48 AM
> *To:* Adams, Dean [EEOBS] <dcad...@iastate.edu>
> *Cc:* Christy Anna Hipsley <chips...@unimelb.edu.au>; MORPHMET <
> morphmet@morphometrics.org>
> *Subject:* Re: [MORPHMET] relative positions of landmark partitions in
> integration tests - how important?
>
>
>
> 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/>
>



-- 
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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