Hello,
for some time I am trying to figure out the most proper design for my
study and greatly appreciate any comments.
I want to study intraspecific geographic morphological variation in
mysid shrimps (Mysis relicta) and correlate/compare it with the
presumably neutral molecular variation
Do any of you have experience using CART (Classification and Regression
Trees) for shape classification and if so, do you have any opinions or
lessons learned you can share with me?
Thanx,
Kath Robinette
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Actually I have not received any direct answer. What I am going to do at
the moment is to get partial warp scores from all the specimens and
analyse these scores. Probably I could also use residuals after GPA to
test for a congruence of the results.
I have just uploaded ver. 1.33 of tpsDig to the Stony Brook
Morphometrics server. It fixes a problem with template mode when the
first point moved was to the right of the second point. Thanks to Diego
Astua de Moraes for reporting the problem.
---
F. James Rohlf
State
Dear Morphometricians,
The Web address for the Fish Bibliography was wrong!
The correct URL for the Fish Bibliography is given below:
http://igspot.ig.com.br/maurobio/en/fish_bib.html
Many thanks to Jim Rohlf for reporting the problem.
Regards,
--
+ - - - - - - - - - - - - Mauro J.
I can't open the fish file. Is the address correct? The fish_html is
suspicious, but fish.html doesn't work either.
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
Sent: Monday, February 24, 2003 7:28 AM
To: [EMAIL PROTECTED]
Subject: Fish Bibliography
Dear
Dear Morphometricians,
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Mauro's fish posting has prompted me to send out a request. I'm
assembling a similar bibliography of mollusc morphometrics
references. I'd also like to include a list of people interested in
molluscan morphometrics.
Dear Ellinor,
Here are a few more references on mollusc morphometrics.
Ackerly,SC (1990): Using growth functions to identify homologous
landmarks on mollusc shells. In: Proceedings of the Michigan
Morphometrics Workshop. (Eds: Rohlf,FJ; Bookstein,FL) (Special
Publication, Number 2.) The
Hi Ellinor,
Here are references to a couple of my papers, as well as a
few others I am aware of. Let me know if you would prefer full
journal titles.
Ackerly, S. C. 1989. Kinematics of accretionary shell growth, with
examples from brachiopods and molluscs. Paleobiology 15: 147-164.
I have just uploaded new versions of tpsSuper and tpsSplin to the Stony
Brook morphometrics website.
tpsSuper was modified by adding an option to ignore image files. This
allows
one to just do a GPA superimposition and look at landmark configurations
without loading the images.
tpsSplin was
What type of artifact? Is, for example, the fish bent due to
preservation or is it something more complicated?
RW1 is just a PC1 so the same rules apply to both.
F. James Rohlf - Dept. Ecology Evolution
SUNY, Stony Brook, NY 11794-5245
-Original Message-
From:
It has been suggested that I remind everyone that the email address of
the sender of messages to morphmet is stripped from the message. If you
want to allow direct replies to yourself, then you must include your
email address as a signature or in some other form.
Doing so will probably enhance
Indeed as Jim notes.
The positive elements of the first latent vector of a positive definite
square matrix is an artefact. This is incorporated in the
Frobenius-Perron theorem for the spectral properties of non-negative
matrices. Ref. Gantmacher, F. R. Matrizenrechnung II (1966), VEB
Deutscher
The problem with PC1 is not what I would call a mathematical artifact. I
view it as more of a statistical problem.
In traditional morphometric data, variables usually have very large
positive correlations between them. This is usually mostly due to the
effects of size. Small organisms have small
There was a problem in the upload of version tpsDig version 1.34
yesterday (the exe file for 1.31 was uploaded by mistake). It should be
fixed now. Please try again. Sorry for the inconvenience.
---
F. James Rohlf
[EMAIL PROTECTED]
3/19/03
==
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For
There are many 3D laser scanners out there, and they vary quite a bit in
price and resolution. Given the size of the objects you're looking at,
you would likely have to go for a more expensive model (eg laserdesign,
polhemus). Portability, if required, also limits your choices. You might
want to
Geez, I really did read it before I posted it (and before I approved
it). Sorry...
On Fri, 2003-03-28 at 09:34, [EMAIL PROTECTED] wrote:
to a comment centroid (anywhere, but we take the origin for
^^^ common
There are, of course, and infinite number of other approaches that
I agree with the idea of Dr. Warheit.
And also apologize for my ingorance and possibly naive statements,
nevertheless I would like to add some coments on the same theme.
I have been thinking on how to remove allometric relationships after
applying warp transformations, and probably working with
Hi Marc,
I am quite new in the morphometric field as well and like you
I have had a lots of problem understanding many of the morphometric book
that I came accross. Here some of the articles and book that were really
helpful:
Rohlf, J. F. (1990)Morphometrics. Annu. Rev. Ecol. Syst.
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Thanks, ds
--
Dennis E
Dear friends,
I understand that one of the main consecuences of applying alignment
tranformations to landmark data, such as the GLS, is the elimination of
the effects of size. In this case, I also understand that size is
assumed to be isometric. Nevertheless, I found a paper explaining that
Hmmm, guess I felt like writing...
There is a fair degree of subtlety embedded in this question. First, to
say something about size you must define how you measure size. In the
realm of superimpositions, one must also define criteria for measuring
and optimizing translation and rotation.
I would like to apply the phylogenetic generalized least-squares
analysis implemented in NTSYS. I have tried with the three species
example from Rohlf (2001, Evolution,55:2143-2160), but I am unable to
reproduce the values for the intercept (0.6698; pag 2147) and the slope
(0.0617).
I would
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SEMILANDMARKS, points that have been assigned geometric
homology along curves and that are then treated as if they
were proper landmarks in subsequent geometric morphometric
Dear morphometricians,
I'd like to have your precious advice about possible simple measures of
shape variation for a sample in a multivariate space. I discussed about
this with Prof. Rohlf about one year ago, and I know that it's hard to
find a 'good analogue' of SD in univariate analyses.
Dear Brett,
this is just a fast opinion, and I am sure of that more experienced
people in the list will be able to give you better advice. If I got it
right, do not find discriminant analysis to be the best technique for
your purposes. You will get as many groups as you enter into the
analysis.
Dear Morphometricians,
I have written a very simple program for converting files in NTSYSpc
format to the Comma-Separated Values (CSV) format compatible with
MS-Excel and other spreadsheet and statistical software. Sure, Jim
Rohlf's tpsUtil program can do that as well, but my program is quite
While it was not designed for that specific purpose and thus perhaps not
an ideal solution, I think it would be easier to use tpsDig than to have
to digitize landmarks using tpsDig, then use PAST to compute all
distances, and then select just the ones you want. TpsDig has a
measurement mode that
Dear morphmetters
There will be a symposium entitled 'Insect Morphometrics' at the next
International Congress of Entomology in Brisbane, Australia, 15-21
August 2004. This symposium will feature morphometric studies that
contribute to the understanding of insect biology -- development,
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Hi,
am in the process of exactly the same thing, I have some references,
my email address is [EMAIL PROTECTED]
Best Regards.
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
Sent: 01 October 2003 13:16
To: [EMAIL PROTECTED]
Subject: 3D Thin Plane Spline
Dear
Hi Fred,
My name is Tim Hutton, apologies for the lack of identification in the
previous post (it was my first message to this list). My email and
details are below this time.
In VTK (the visualization toolkit) there is the option of using the
r2logr kernel or the r kernel, since the class does
This summer the copies of padwin and bacwin were lost from the Stony
Brook server. I have tried to reach the author (Jean-Pierre Dujardin)
but have not yet received a response. Please contact me if you have a
recent address or have a recent copy of these programs. I would like to
restore them to
To: Kathleen M. Robinette, Ph.D.
Principal Research Anthropologist
Air Force Research Laboratory
I have to get special persmission to install any software on
my computer, so I haven't been able to download any of this
type of freeware yet. I hope to soon. I am
The following should be of interest to the list. -dslice
Dear friends and colleagues:
As you may already know, NYCEP (the New York Consortium in Evolutionary
Primatology) was recently funded by the NSF IGERT Program for 5 more
years of
With regards to the limit on number of samples in the TPS programs
I have (in conjunction with Arnar Palsson) used ~15000 samples (wings)
in both TPS RelW and PLS without any problems at all
Ian Dworkin
[EMAIL PROTECTED]
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I am looking for software that can measure the angle
between two lines WITHOUT having to identify the
vertex of the angle. Many of the angles I am
interested in are very small and I cannot plot the
vertex within the
Erin,
It seems this would be easy to do in a spreadsheet, but I use MorphoSys
since I have it. This program can project two lines to find a vertex
and then measure the angle between the lines. The program costs $250
but requires a $2000 out-of-production framegrabber that you can still
get,
account for morphmet
and the support account for the Morpheus et al. software.
For more information on how to use this mailing list see...
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Hello Morphmetters,
I would appreciate receiving information (i.e., supplier, distributer,
price, and specifications) concerning purchasing calipers (e.g.,
approximately 30 cm maximum span) that can output readings directly to a
computer.
appreciatively,
Jon
Jon Stone
McMaster University
anything in the morphmet
archives (but I'm not sure if I was using them correctly).
Thanks in advance,
C. Tristan Stayton
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Hi Jon,
I like the Mitutoyo line:
www.mitutoyo.com
Cheers,
Thom
()()(
Dr. Thomas J. DeWitt, Assistant Professor
Department of Wildlife Fisheries Sciences
Program in Bioenvironmental Sciences
Texas AM University
2258 TAMU
College Station, TX 77843-2258
Tel.
I have just uploaded ver. 1.28 of tpsUtil to the Stony Brook
morphometrics server. This implements a suggestion by Diego Astua de
Moraes that the 'build tps file' window should use checkboxes and allow
multiple selections at the same time as in the 'delete/reorder
landmarks' window. It does seem
I am doing a morphometric study about a shark, but I've got difficulties
with the interpretation of the results. I've digitalized 75 specimens
and marked 19 landmarks. I don't know whether is better to see the
visuallization plot of the partial or of the relative warps for the
interpretation of
Javier
Your question is straightforward and I can recommend the approach I
would take. With 19 landmarks you should have 34 PW's. My philosophy
says you should ignore the RWs as they are an undesigned morphospace
with respect to questions in which you are interested. I would perform
the
[EMAIL PROTECTED] wrote:
I am doing a morphometric study about a shark, but I've got
difficulties
with the interpretation of the results. I've digitalized 75 specimens
and marked 19 landmarks. I don't know whether is better to see the
visuallization plot of the partial or of the relative warps
I would just like to remind everyone, that I do some reformatting of
messages sent to morphmet. As part of the moderation process the text of
messages are transferred from one document to another. This sometimes
leads to formatting problems (especially with hard linebreaks). I go
through
I agree with most of the suggestions but there is still a role for
relative warps in such a study. They give one an overall view of the
major variation in the data. The ordination plot often allows one to
detect (and thus eliminate) any wild outliers that might be present. It
will also give one
[Minor reformatting by me - line breaks and such. -ds ]
I'd like to insert a comment into a current thread that
several of you may have already heard me state in lectures, in
previously anonymous reviews, and similar arenas. The stimulus for this
was Thom DeWitt's answer just now to
Hello all,
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I loved some of the humor I saw in Thom's message, and was impressed
that someone was able to insert some humor effectively. I am terrible
at it, and even when I don't intend it I find that my messages can read
as
One more thought.
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In a univariate anova the distinction I made in the previous note is
less clear. The division in an anova is by a scalar constant (square
root of the error mean square) so that the relative differences
terribly confused this situation. -ds]
I enjoyed seeing morphmet suddenly come to life! Sorry I was not able to
comment earlier about MANOVA, permutation tests, etc. (I was busy
preparing for a seminar).
I agree with a lot of what has been said but I will try making a few
points in my own words.
1
First of all I would like to thank the quickness and the great number of
contributions in answering my question about shark morphometrics:
although in some concret aspects there are contraditory- or perphaps
complementary- advices, in general it has clarified me lots of doubts.
I would like to
Fellow morphometricians:
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I would like to ask two questions regarding the operation of morpheus.
Firstly, what command line do I have to type in to set the translation
mode on for procrustes superimposition. Secondly, I am
Have anyone had problems with the tolerance in discriminant analysis if
the input variables for such anlaysis have previously been transformed
by Burnaby's method?
We are studing the population structure of a fish species in the North
Atlantic.
17 variables (distances between landmarks) have
I don't really remember the details of what the Burnaby scale-adjustment
does, but I think it's somewhat similar to Darroch and Mosimann's
approach to scale adjustment (someone correct me if I'm wrong). With
DM, the measurements are transformed by dividing through by some
reasonable measure of
Fax: 336-716-2870
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and the support account for the Morpheus et al. software.
For more information on how to use this mailing
Perhaps I need to expand on the implications of what I said in my
message.
Because the Burnaby method removes dimensions from a matrix, the
resulting matrix is supposed to be singular. That means that software
that does not use some form of generalized inverse will complain about
the covariance
That's right - I was perhaps a little too fast-and-loose when I
equated Darroch and Mosimann with Burnaby. It would have been more
precise to say that Darroch and Mosimann and Burnaby CAN give the same
results, depending upon how you set them up. Dividing each measurement
through by
Some comments relative to the numerous questions:
1) When alpha is not zero the uniform component must be left out. This
alone can change the relative warps.
2) Different non-zero values for alpha usually changes the relative
warps also. The change can be quite large.
3) You should apply any
Hi,
Does anyone know of a program that can digitise open curves, i.e. place
landmark and non-landmark points along an open-ended line or curve for
EES analysis? I can't get tpsdig to do this, and can't see anything
else obvious on the SB site.
Thanks
David
Hi there,
I got a newbie question. I was reading a paper on
interspecific morphological variation, and at some
point the authors say that each value of the
standardized PC1 for each species was divided by
1/sqrt(number of characters) to assess morphological
divergence from isometry.
Could
another
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The mapping of pixels described in today's email from Dr. Taylor is
substantially the same as what is offered in the 2D module of our
current Edgewarp package. Interested users should upload the 3.26
release from
I have a rather rough tool called MakeFan on my website that might be
useful for your project.
Have a look at
http://www.canisius.edu/~sheets/morphsoft.html
It produces output files in TPS format.
-Dave
Hi,
Does anyone know of a program that can digitise open curves, i.e.
place
landmark
I will be out of town for a while. Therefore, monitoring will be
temporarily disabled on morphmet.
I trust your common sense will tell you that I would not approve any
money-laundering ventures with Nigerian widows. I keep all of those for
myself and am waiting for my first big payout as soon
another
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In general, Rohlf's program tpsSuper does this sort of thing. The idea
is to:
a) GPA the landmarks associated with a number of images (e.g., two) to
create a consensus configuration.
b) and this is the non-obvious
Hello again. For those interested enough to try image unwarping by
Edgewarp, the 1994 (!) manual is on line at
ftp://brainmap.med.umich.edu/pub/edgewarp2/MANUAL
as an ascii file. (Note this is a different directory from the one
where the current release itself is actually posted.)
I guess what is meant is the fact that if you compute a normalized PC1
from a correlation matrix based on p variables for data in which PC1
represents size and growth is isometric then the loadings will all be
equal to 1/sqrt(p). That is because normalized means that the sum of
the squared
Dear morphometricians,
currently we are attempting to apply the landmark GM methods in the
investigation of population dynamics and phenotypic plasticity in
relation to experimentaly defined ecological conditions in some green
algae, where the homologous landmarks (and/or semilandmarks) can be
Since I don't see any replies to this, I will offer some comments:
a) You're algae is quite nice looking.
b) Despite the two-way symmetry of your organisms, if you are not
interested in evaluating that part of shape variation, you can proceed
(cautiously) to study it ignoring the asymmetry. Any
Stony Brook Morphometrics website update: I have just split the
directory of people interested in morphometrics into four parts because
it was getting long enough so that it was beginning to load slowly. I
have also entered all of the corrections and new entries that people
have sent me. Note that
Dear Group,
I'm making my first foray into 2-D data collection, and have run up
against a snag using tpsDig. The documentation states that if one uses
the Set Scale feature, the scale factor Also scales the coordinates
appropriately. I know that I'm in the correct mode because the Scale
Factor
That is correct, the coordinates themselves are still in pixels in order
to plot correct against the image. Computations such as centroid size,
areas, and linear distances are, however, computed with the scaled
coordinates.
---
F. James Rohlf
State University of New York,
I have just uploaded ver. 1.39 of tpsRelw to the SB Morphometrics
server.
The primary change is to change the way the program slides
semilandmarks. It provides a number of new options and also provides
additional information. One will probably want to use the new version of
the tpsSpline program
, North Carolina, USA
27157-1022
Phone: 336-716-5384
Fax: 336-716-2870
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Thanks to all for the helpful responses concerning scaling in TPSdig.
Now that I'm collecting data, I've run up against the missing data(MD)
problem. Unless TPSdig has a missing landmark option that I've
missed, I need to find some way to put a placeholder in the TPS file.
The best idea I've
The following may be of interest to list members:
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Morphometrics- Applications in Biology and Paleontology
edited by Ashraf M. T. Elewa (Minia Univ., Egypt)
Springer-Verlag (Heidelberg, Germany). 2004. XIV, 263 p., 104 illus.
For those who are interested in my book, please contact me, if you have
problems or you need more details, on:
[EMAIL PROTECTED]
--
Dr. Ashraf M. T. Elewa
Associate Professor
Geology Department
Faculty of Science
Minia
Sorry, folks, but the school upgraded their Microsoft mail server last
week and crippled my access to the morphmet account. I can do some
things, but it is a painfully difficult process. I have submitted a
request for help, but only time will tell if the result is any different
from submitting
Useful, though sometimes technical, information, critiques, and
expositions on the traditional use of ratios in morphometric analysis
can be found in:
Bookstein, F. L. 1991. Morphometric Tools for Landmark Data: Geometry
and Biology. (The Orange Book)
and
Bookstein, F. L., Chernoff, B., Elder,
You may also try looking at:
Bookstein FL (1989) 'Size and shape': a comment on semantics.
Systematic Zoology 38:173-180.
Marc Moniz
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
On Behalf Of [EMAIL PROTECTED]
Sent: Tuesday, May 18, 2004 9:51 AM
To: [EMAIL
You mention that you have many more variables than specimens. As a result,
you cannot use the various alternatives that you list. Discriminant
functions, canonical variates, etc. all require that the pooled within-group
covariance matrix be based on a sample size larger than the number of
Dear Brett and Marta,
I think the problem you are encountering may not be the size-versus-shape issue, but a
Normal distribution issue. PCA Analysis assumes multivariate normality. I know for
human beings the distribution of men and women combined is often not Multivariate
Normal. It is
--
Dennis E. Slice, Ph.D.
Department of Biomedical Engineering
Division of Radiologic Sciences
Wake Forest University School of Medicine
Winston-Salem, North Carolina, USA
27157-1022
Phone: 336-716-5384
Fax: 336-716-2870
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Dear Brett,
If the problem is separating size and shape, then, fortunately, in my edited
book titled Morphometrics- Applications in Biology and Paleontology
(Springer-Verlag, 2004) you will find a chapter that is written by
Garcia-Rodriguez et al. They used the Sheared PCA analysis and could
There is a method called common PCA which seems to overcome the problem of
non-multinormality of overall sample that includes several subsamples all
with different central momenta. The source to read is:
Flury B. 1988. Common principal components and relatÃ…d multivariate models.
NY: Wiley. 258 p.
Just a comment on this one, from a pragmatic point of view.
It is of course true that PCA is only *guaranteed* to
produce components maximizing variance if you have
multivariate normality. The theory of PCA is based on this
assumption. But in many cases, PCA is used purely as a
visualization
In my understanding to PCA, its main goal is to reduce the dimensionality of
a problem without the loss of too much information. In other words,
according to Prof. Rohlf, the purpose of PCA is to give you a low
dimensional space that accounts for as much variation as possible. However,
I agree
Don't know what happened to cause the earlier message largely void of content, but I
think the original communication was to correct the Red Book reference.
The date is 1985, not 1982. -ds
On Tue, 2004-05-18 at 14:12, [EMAIL PROTECTED] wrote:
--
Dennis E. Slice, Ph.D.
Department of
Dear collegues,
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About the above discussion on the linear measurements data for multivariate
analysis, I should state that most times my problem (and I expect the problem
of many people that wrks with it) is not of
I applaud your courage, Dr. Hammer. I hope everyone appreciates how intimidating this
list of experts can be.
I also agree with your point that PCA can be used when the data are not multivariate
normal if you are just using it to visualize information, or if you just know what it
is doing
Dr. Hammer, Please consider your courage credited. -ds
A couple of points about PCA in general:
1) PCA makes no assumptions about the distribution (multivariate normal
or otherwise) of your data. It is a procedure that simply produces the
linear combinations of variables with maximum variance
Dear Colleagues,
Nicholas Jones and I are pleased to announce that morphologika, which
is a Windows based program for 3d geometric morphometrics is available
at:
http://www.york.ac.uk/res/fme/index.htm
It can be downloaded from the resources page.
We ask that you complete details of your
1) PCA makes no assumptions about the distribution (multivariate
normal
or otherwise) of your data. It is a procedure that simply produces the
linear combinations of variables with maximum variance subject to
orthogonality to other such axes.
OK, but variance may or may not be a meaningful
Marta,
I have a pdf version of the Darroch Mosimann Biometrika paper. What
is your e-mail address so I can send it directly to you.
Marc Moniz
[EMAIL PROTECTED]
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
Sent: Thursday, May 20, 2004 11:35 AM
To: [EMAIL
While my original account problems have not been solved, they have at
least be addressed by moving to a new server. So, I now have total (much
faster than before) access to the morphmet account.
This means list moderation should be back to what passes for normal.
However, if you posted a message
G'day all,
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Thanks to everyone for your comments. They've been a great help, and I'm
glad that my question sparked a bit of discussion on the subject.
After some pondering, I've got a few more questions and some more
details
Is anyone aware of studies regarding changes in facial size or shape
over time among adult humans, independent of weight gain, significant
dental work, or disfigurement?
Thanks.
Dennis Groce
NIOSH, Morgantown WV
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