-------- Original Message --------
Subject: RE: variance in shape
Date: Mon, 2 Jun 2008 22:58:56 -0700 (PDT)
From: andrea cardini <[EMAIL PROTECTED]>
To: [email protected]
Dear Chris,
besides what Rohlf and Philipp wrote you, and on which I fully agree, I
would like to add a couple of quick comments.
If your aim is to test for differences in shape between the two
populations, either MANOVA/DA or a permutation test would do. On what is
implied by doing MANOVA/DA on shape coordinates I suggest you to read
Klingenberg & Monteiro 2005 (Syst. Biol. 54(4):678688).
Permutation tests can be easily done in TPSRegr for 2D data and Morpheus
or NTSYS for 2D/3D data. Morpheus Beta version has commands for this
that you can ask Dennis Slice or I can tell you if you need. The
permutation test MANOVA available in Morpheus is concisely described in
Fontaneto et al.2004 (Italian Journal of Zoology, 71: 63-72). Pairwise
permutation tests for mean shape differences are used in several studies
including, I believe, quite a few by Philipp and colleagues, O'Higgins
and coauthors etc.
However, if you want to see whether variance is larger within a
population compared to another one, as one would do for instance to test
for a reduction in variance in an island population, this is something
that you can possibly do with a Levene's test. An example is described
in a paper of mine (below) and another one (or more), if I remember
well, can be found in studies by Hallgrimsson and colleagues.
To get the Procrustes distances to the mean you can simply use TPSSmall
for both 2D and 3D data. Tests can then be done in any statistical
software but to have also permutations it might take a little more
effort unless you're using NTSYS.
I am pretty sure that most of these tests (certainly MANOVA/DA but
possibly also tests for variances - check the disparity module) are also
available in the IMP series, where you generally have options for doing
resampling stats too.
Good luck
Andrea
Cardini A, Thorington Jr. R. W., P. D. Polly, 2007 - Evolutionary
acceleration in the most endangered mammal of Canada: phylogenetic signal
and cranial divergence in the Vancouver Island marmot (Rodentia,
Sciuridae). Journal of Evolutionary Biology, 20: 1833-1846.
"The Levenes test requires calculating the absolute value of
the deviation of each individual from the sample mean
(Van Valen, 1978), which is satisfied by using absolute
differences to the mean size or Procrustes distances to the
mean shape. These deviations are then compared by
ANOVA ANOVA. Although this test is generally considered relatively
robust to departures from normality, we chose to
perform a randomization version of the test that compares
the observed F-statistic with the distribution
obtained by randomly reassigning deviations from sample
means to the samples."
At 12:24 02/06/2008 -0400, you wrote:
-------- Original Message --------
Subject: RE: variance in shape
Date: Mon, 2 Jun 2008 09:01:33 -0700 (PDT)
From: Chris Harrod <[EMAIL PROTECTED]>
To: [email protected] <[email protected]>
References: <[EMAIL PROTECTED]>
Folks
Thanks for all the replies both on and off list...
All the best
Chris
-----Original Message-----
From: morphmet [mailto:[EMAIL PROTECTED]
Sent: 02 June 2008 16:46
To: morphmet
Subject: Re: variance in shape
-------- Original Message --------
Subject: Re: variance in shape
Date: Mon, 2 Jun 2008 08:11:03 -0700 (PDT)
From: Philipp Mitteroecker <[EMAIL PROTECTED]>
To: [email protected]
References: <[EMAIL PROTECTED]>
Dear Chris,
CVA standardizes the within-group covariance structure to a spherical
distribution with unit variances along each axis. It would thus be
greatly misleading to compare variances of CVA scores.
Use the original Procrustes coordinates (or PCA scores or PW scores) to
compute variances. There are two common ways to produce a single summary
of variation in a multivariate data set: (1) the trace of the covariance
matrix (sometimes called total variance), which equals the sum of all
univariate variances or the sum of all eigenvalues, (2) the determinant
of the covariance matrix (generalized variance), which equals the
product of all eigenvalues. The latter one relates to the "volume" of
the point cloud, requiring a full rank covariance matrix. In an earlier
comment on morphmet Jim Rohlf gave more details on that.
Best,
Philipp
On Mo, 2.06.2008, 14:58, morphmet wrote:
-------- Original Message --------
Subject: variance in shape
Date: Sun, 1 Jun 2008 16:41:20 -0700 (PDT)
From: Chris Harrod <[EMAIL PROTECTED]>
To: [email protected] <[email protected]>
Dear all out there in morpholand.
I want to examine variance in shape between fish found in allopatry and
those found in sympatry with a putative competitor.
Can I simply compare the variance in DF/CVA scores (based on the normal
landmark analyses) between different populations, or am I being horribly
simplistic?
thanks in advance
Chris
<> ><> ><> ><> ><> ><> ><> ><> ><> ><> ><> ><> ><> ><>
Dr Chris Harrod
Lecturer in Fish and Aquatic Ecology
Ecology and Evolutionary Biology
Queen's University Belfast
School of Biological Sciences
Medical Biology Centre
97 Lisburn Road
Belfast BT9 7BL
UK
[EMAIL PROTECTED]
Tel: +44 (0) 28 90972271
Mob: +44 (0) 79 77419314
Fax: +44 (0) 28 90975877
http://www.qub.ac.uk/schools/SchoolofBiologicalSciences/Staff/DrCHarrod/
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Dr. Philipp Mitteröcker
Konrad Lorenz Institute for Evolution and Cognition Research, Austria
Department of Anthropology, University of Vienna, Austria
http://www.virtual-anthropology.com/Members/philippm
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Dr. Andrea Cardini
Lecturer in Animal Biology
Museo di Paleobiologia e dell'Orto Botanico, Universitá di Modena e Reggio
Emilia
via Università 4, 41100, Modena, Italy
tel: 0039 059 2056532; fax: 0039 059 2056535
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
E-mail address: [EMAIL PROTECTED], [EMAIL PROTECTED],
[EMAIL PROTECTED]
http://hyms.fme.googlepages.com/drandreacardini
http://ads.ahds.ac.uk/catalogue/archive/cerco_lt_2007/overview.cfm#metadata
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