-------- Original Message --------
Subject: RE: CVA and MANOVA
Date: Thu, 28 Feb 2008 14:44:40 -0800 (PST)
From: andrea cardini <[EMAIL PROTECTED]>
To: [email protected]
I suspect that the last bit (visualization of shapes along a given CV)
can be done also in Morphologika (for both 2D or 3D data) and this can
be done using all PCs (RWs) or selecting the same subset included in the
CVA (if this was done using only the first whatever PCs).
If PCs used in the CVA accurately summarized variance, predicted shapes
on CV axes will probably be almost identical independently of whether
one uses all PCs or PWs (as in TPSRegr) or just the first PCs which were
included in the CVA.
The CV axis should be saved in Morphologika as labelvalues, if I
remember well. This option is (Paul can comment on this) still a beta
version.
Please, check that you get the right outcome (e.g., compare multivariate
tests and deformation grids with those from other software).
Cheers
Andrea
At 18:20 27/02/2008 -0500, you wrote:
-------- Original Message --------
Subject: RE: CVA and MANOVA
Date: Wed, 27 Feb 2008 15:09:24 -0800 (PST)
From: F. James Rohlf <[EMAIL PROTECTED]>
Reply-To: <[EMAIL PROTECTED]>
Organization: Stony Brook University
To: <[email protected]>
References: <[EMAIL PROTECTED]>
Statistically (and geometrically) a matrix of relative warp scores is
just a matrix of principal component scores. If you keep all of the
dimensions for which the eigenvalues are > 0 then you are just doing a
rigid rotation of a multivariate space so ordination analyses,
probabilities computed in a MANOVA, etc. must be unchanged. If you
only use a few dimensions then you are projecting into a lower
dimensional space and thus losing information so subsequent analyses
can give different results. Difficult to predict in advance what the
consequences will be (it could be that dimensions that account for
relatively little of the overall variance just happen to be good at
distinguishing groups - that would be lost if you happened to have
discarded those dimensions.
If you use relative warps as your variables then to be able to
construct shapes you will have to back transform to coordinates. This
can be done (this operation is built into tpsRelw). For other
analyses, such as CVA based on relative warps you can use the trick of
using the tpsRegr program to regress shapes (your original tps file)
onto each vector of CVA scores. If you use all of the relative warp
dimensions then the CVA scores should be identical to those based on
the original matrix of partial warp scores or a matrix of GPA
coordinates after the invariant dimensions have been removed.
=========================
F. James Rohlf
Distinguished Professor, Stony Brook University
http://life.bio.sunysb.edu/ee/rohlf
-----Original Message-----
From: morphmet [mailto:[EMAIL PROTECTED]
Sent: Wednesday, February 27, 2008 5:39 PM
To: morphmet
Subject: Re: CVA and MANOVA
-------- Original Message --------
Subject: Re: CVA and MANOVA
Date: Wed, 27 Feb 2008 08:02:38 -0800 (PST)
From: Cristian Correa <[EMAIL PROTECTED]>
To: <[email protected]>
References: <[EMAIL PROTECTED]>
Hi Amelia,
Comments from another beginner: I think you can use RW to reduce
dimensionality before conducting MANOVA. I don't see the problem,
unless
you're severely violating assumptions (in which case you can do
NPMANOVA). It may (or may not) be more difficult to visualize the
results of your analyses (depending on the RW obtained and kept)
because
you will be moving in the more integrated and distorted space of RW
compared to the more shape-comprehensive space of PW (using all PW).
You could use a few RW (e.g. the first two, if they account for much
of
the variance) in a MANOVA for statistic test. Then do a CVA to
visualize
significant differences between groups and get centroids for each
group.
It is very likely that each CV axis will pick up a different RW more
heavily. In this case it is easy to interpret morphological
differences
in each of the CV axes; you just have to move along the RW plots. I
don't think you can directly predict shape from the CVA using RW.
Can you?
In summary, I would go for RW if I really need to reduce
dimensionality,
otherwise I'd choose using the full set of PWs. But I'm a novice as
well
and I'd love to see the answers of experts.
Buena suerte!
Cristian
----- Original Message -----
*From:* morphmet <mailto:[EMAIL PROTECTED]>
*To:* morphmet <mailto:[email protected]>
*Sent:* Wednesday, February 27, 2008 9:11 AM
*Subject:* CVA and MANOVA
-------- Original Message --------
Subject: CVA and MANOVA
Date: Wed, 27 Feb 2008 05:15:56 -0800 (PST)
From: M. Amelia Chemisquy <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>>
To: [email protected]
<mailto:[email protected]>
Hi!
I'm using geometric morphometry for analyzing orchid seeds, and
since I
am quite new at this (and at statistics two) I have a few
questions. I
want to perform a CVA and a MANOVA with my morphometric
results, and I
want to know if I can use the relative warps scores for doing
this, or
it can only be done with the partial warps. What if I don´t
fulfill the
number of samples (4 times the number of variables) needed, may
I use
the relative warps in this case?
Besides, is there any way to obtain the deformation grids for
the CVA
using any of the the tps software?
Thanks a lot!
Amelia
--
Lic. Amelia Chemisquy
Instituto de Botánica Darwinion
Casilla de Correo 22
B1642HYD, San Isidro
Argentina
Tel. (54 11) 4743 4800/4742 8534
[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
www.darwin.edu.ar <http://www.darwin.edu.ar>
--
Replies will be sent to the list.
For more information visit http://www.morphometrics.org
--
Replies will be sent to the list.
For more information visit http://www.morphometrics.org
--
Replies will be sent to the list.
For more information visit http://www.morphometrics.org
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
--
Replies will be sent to the list.
For more information visit http://www.morphometrics.org
