Now if only archaeological and museum skeletal samples would stop
disarticulating and stay in anatomical position.

On Wed, Jan 24, 2018 at 11:29 AM, David Katz <dck...@ucdavis.edu> wrote:

> 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/
>>
>> --
>> MORPHMET may be accessed via its webpage at http://www.morphometrics.org
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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/>
>



-- 
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/>

-- 
MORPHMET may be accessed via its webpage at http://www.morphometrics.org
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