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:[email protected]]
Sent: Tuesday, January 23, 2018 9:34 PM
To: MORPHMET <[email protected]>
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:
[email protected]<mailto:[email protected]>;
[email protected]<mailto:[email protected]>
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
[email protected]<mailto:[email protected]>.
--
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 [email protected].
