-------- Original Message --------
Subject: errata corrige
Date: Thu, 1 Dec 2011 11:08:51 -0500
From: andrea cardini <[email protected]>
To: Jordan Mallon <[email protected]>, [email protected],
PAST <[email protected]>
The reference from my own work on BG-PCA is Seetah et al.:
http://www.sciencedirect.com/science/article/pii/S0305440311003645
The reference to Mitteroecker & Bookstein's work is in there.
Kovarovic et al.
(http://www.sciencedirect.com/science/article/pii/S0305440311002263) is the
paper we did to stress some of the issues with DA but it did not have the
BG-PCA in it.
My apologies for mis-citing ... my own work.
If they're not already there, I'll try to have pdfs asap in my publications
webpage.
Cheers
Andrea
Dear Jordan,
this is not an answer to your specific question. It's more of a general
comment.
The hierarchical nature of variation may have some other consequences: your
observations are not independent because of phylogeny. Comparative methods
try to address this issue in statistical analysis but I've never seen any
application to DA/CVA.
DA/CVA ordinations are done in a statistical space which maximize between
to within group differences. This has some interesting implications and
with small samples and large number of variables you can get a perfect
discrimination of random numbers split in arbitrary groups. I'd be very
careful with interpretations of those plots.
For ordinations, a few people (including a recent paper by Mitteroecker &
Bookstein and another one by Kovarovic, myself et al. - should be in my
webpage and in the paper you'll find the ref. to M&B and other refs) have
suggested between group PCA as an alternative for ordinations which
maximize group differences without distortions of the original morphometric
space of your data.
Good luck.
Cheers
Andrea
At 19:34 30/11/2011 -0700, Jordan Mallon wrote:
Dear all,
I've reached a bit of a dilemma with my morphometrics studies lately,
stemming from the hierarchical nature of variation. I've been studying
ecomorphology and how it varies within and between three dinosaur
families (each family contains two subfamilies). I've been using
canonical variates analysis to examine which variables best
discriminate the various taxa. The three families are perfectly
discriminated in CVA space.
Next, I would like to examine how the subfamilies differ, particularly
those that belong within the same family (i.e., looking at
intra-family variation). As far as I can tell, I have two options:
1) Place all six subfamilies into a single CVA and look for
intra-family clustering. The problem I see here is that most of the
variance captured by the CV axes will comprise inter-family
differences, rather than intra-family differences, because the
families are much more separate in space than sister subfamilies. In
other words, if families A and C are well-separated along axis 2, and
subfamilies Ai and Aii are only slightly separated along the same
axis, the loadings on that axis will tell me more about the separation
of families A and C than about subfamilies Ai and Aii. Right?
Hopefully I'm making myself clear.
2) Just run separate discriminant function analyses on all sister
subfamilies. I suppose this negates the problem above, but it
otherwise involves more work.
Has anyone run into a similar problem before? If so, how have you dealt
with it?
Thanks,
Jordan
Dr. Andrea Cardini
Researcher in Animal Biology
Dipartimento di Biologia, Universitá di Modena e Reggio Emilia, via Campi
213, 41100, Modena, Italy
tel: 0039 059 2055017 ; fax: 0039 059 2055548
Honorary Fellow
Functional Morphology and Evolution Unit, Hull York Medical School
University of Hull, Cottingham Road, Hull, HU6 7RX, UK
University of York, Heslington, York YO10 5DD, UK
Adjunct Associate Professor
Centre for Forensic Science , The University of Western Australia
35 Stirling Highway, Crawley WA 6009, Australia
E-mail address: [email protected], [email protected],
[email protected], [email protected]
Webpage: http://sites.google.com/site/hymsfme/drandreacardini
Datasets:
http://ads.ahds.ac.uk/catalogue/archive/cerco_lt_2007/overview.cfm#metadata
Editorial board for:
Zoomorphology:
http://www.springer.com/life+sciences/animal+sciences/journal/435
Journal of Zoological Systematics and Evolutionary Research:
http://www.wiley.com/bw/journal.asp?ref=0947-5745&site=1
Hystrix, the Italian Journal of Mammalogy:
http://www.italian-journal-of-mammalogy.it/
