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 >> --- >> 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/> > -- 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.
