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 < > email@example.com> > *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 <firstname.lastname@example.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 > --- > You received this message because you are subscribed to the Google Groups > "MORPHMET" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to morphmet+unsubscr...@morphometrics.org. > > -- > MORPHMET may be accessed via its webpage at http://www.morphometrics.org > --- > You received this message because you are subscribed to the Google Groups > "MORPHMET" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to morphmet+unsubscr...@morphometrics.org. > > > > > > -- > > 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 --- You received this message because you are subscribed to the Google Groups "MORPHMET" group. To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org.