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/<http://www.public.iastate.edu/~dcadams/> phone: 515-294-3834 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 E: christy.hips...@unimelb.edu.au<mailto:christy.hips...@unimelb.edu.au>; chips...@museum.vic.gov.au<mailto: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<mailto: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.