RE: [MORPHMET] Morphmet in the Future

2019-07-01 Thread F. James Rohlf
That is an interesting suggestion. Whatever we do next it should not depend on 
any single individual. A problem is that we do not have a morphometrics society 
or an editor of a journal that could take ownership of morphmet. 

 

Jim

_ _ _ _ _ _ _ _ _

F. James Rohlf, Distinguished Prof. Emeritus



Depts. of Anthropology and of Ecology & Evolution

 

 

From: Murat Maga  
Sent: Monday, July 1, 2019 3:03 AM
To: K. James Soda ; MORPHMET 
Subject: RE: [MORPHMET] Morphmet in the Future

 

Dear Morphmet community,

 

Couple weeks prior to his sudden demise, I suggested Dennis to consider moving 
the morphmet at some point to a modern forum platform that support markups, 
code formatting and inline images. 

 

You can check out https://discourse.slicer.org to see one in action. The main 
benefit that I see is the potential for a more community build up and 
engagement. For people who prefer to receive messages as emails (myself 
included), they can configure their accounts to subscribe to messages.

 

Discourse is open-source and free to install and to use on ones own servers.  
There are various hosted options for a small fee too, 
https://www.discourse.org/pricing. 

 

It is sad having to talk about changes so soon after Dennis’s passing, but I 
thought it is an appropriate discussion to have.

 

M 

 

 

From: K. James Soda mailto:k.jamess...@gmail.com> > 
Sent: Saturday, June 29, 2019 9:10 PM
To: MORPHMET mailto:morphmet@morphometrics.org> >
Subject: [MORPHMET] Morphmet in the Future

 

Dear Fellow Morphometricians,


I want to give a quick comment about the future of morphmet after Dennis's 
passing so that any necessary changes will not come as a surprise. Please rest 
assure that it is not a question of whether morphmet will continue but rather 
if any different procedures will be required to make or view posts. Right now, 
morphmet is linked to morphometrics.org <http://morphometrics.org> , which is a 
domain that belonged to Dennis himself. As a result, it is possible that, at 
some point in the future, morphmet may temporarily go down if the 
morphmetrics.org <http://morphmetrics.org>  domain becomes unavailable.

What does this mean for you as a member? Right now, very little. You can 
continue to post to morphmet and new members can join morphmet without 
interruption. If in the future, this ceases to be the case, you will receive an 
invitation to a near identical Google group that will function in the same 
manner as morphmet has operated since the 2014 transition. Invitations will 
likely be distributed over the course of two to three days. The invitation 
email will include instructions on any changes to the submission process, which 
will likely only include a new email address for making posts and a new web 
address for the forum.

If you have any questions or concerns, please contact me either on or off of 
the list (k.jamess...@gmail.com <mailto:k.jamess...@gmail.com> ).

Best regards,

James Soda


Interim Moderator
(Soon to be) Assistant Professor
Department of Mathematics
Quinnipiac University
Hamden, CT 06518


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RE: [MORPHMET] Re: semilandmarks in biology

2018-11-06 Thread F. James Rohlf
Perhaps, but Procrustes superimposition already adds lots of covariances also. 
It is a bit tricky (meaning that I do not know of a good solution) to preserve 
the "real" covariances and distinguish them from artifacts of fitting. GM works 
well for testing differences among means of groups but studying covariances 
among shape variables is a much more difficult problem. Some ML approaches have 
been suggested that could minimize the covariances due to superimposition but 
the ones I have looked at require some very unreasonable biological assumptions 
about their statistical properties.

Such discussions will not die until there are good solutions or else someone 
proves that no good solution is possible.  I still have hope for some clever 
idea.

_ _ _ _ _ _ _ _ _
F. James Rohlf, Distinguished Prof. Emeritus

Depts. of Anthropology and of Ecology & Evolution


-Original Message-
From: alcardini  
Sent: Tuesday, November 6, 2018 12:35 PM
To: F. James Rohlf 
Cc: mitte...@univie.ac.at; MORPHMET 
Subject: Re: [MORPHMET] Re: semilandmarks in biology

Yes, but doesn't that also add more covariance that wasn't there in the first 
place?
Neither least squares nor minimum bending energy, that we minimize for sliding, 
are biological models: they will reduce variance but will do it in ways that 
are totally biologically arbitrary.

In the examples I showed sliding led to the appearance of patterns from totally 
random data and that effect was much stronger than without sliding.
I neither advocate sliding or not sliding. Semilandmarks are different from 
landmarks and more is not necessarily better. There are definitely some 
applications where I find them very useful but many more where they seem to be 
there just to make cool pictures.

As Mike said, we've already had this discussion. Besides different views on 
what to measure and why, at that time I hadn't appreciated the problem with p/n 
and the potential strength of the patterns introduced by the covariance created 
by the superimposition (plus sliding!).

Cheers

Andrea

On 06/11/2018, F. James Rohlf  wrote:
> I agree with Philipp but I would like to add that the way I think 
> about the justification for the sliding of semilandmarks is that if 
> one were smart enough to know exactly where the most meaningful 
> locations are along some curve then one should just place the points 
> along the curve and computationally treat them as fixed landmarks. 
> However, if their exact positions are to some extend arbitrary 
> (usually the case) although still along a defined curve then sliding 
> makes sense to me as it minimizes the apparent differences among 
> specimens (the sliding minimizes your measure of how much specimens differ 
> from each other or, usually, the mean shape.
>
>
>
> _ _ _ _ _ _ _ _ _
>
> F. James Rohlf, Distinguished Prof. Emeritus
>
>
>
> Depts. of Anthropology and of Ecology & Evolution
>
>
>
>
>
> From: mitte...@univie.ac.at 
> Sent: Tuesday, November 6, 2018 9:09 AM
> To: MORPHMET 
> Subject: [MORPHMET] Re: semilandmarks in biology
>
>
>
> I agree only in part.
>
>
>
> Whether or not semilandmarks "really are needed" may be hard to say 
> beforehand. If the signal is known well enough before the study, even 
> a single linear distance or distance ratio may suffice. In fact, most 
> geometric morphometric studies are characterized by an oversampling of
> (anatomical) landmarks as an exploratory strategy: it allows for 
> unexpected findings (and nice visualizations).
>
>
>
> Furthermore, there is a fundamental difference between sliding 
> semilandmarks and other outline methods, including EFA. When 
> establishing correspondence of semilandmarks across individuals, the 
> minBE sliding algorithm takes the anatomical landmarks (and their 
> stronger biological homology) into account, while standard EFA and 
> related techniques cannot easily combine point homology with curve or 
> surface homology. Clearly, when point homology exists, it should be 
> parameterized accordingly. If smooth curves or surfaces exists, they 
> should also be parameterized, whether or not this makes the analysis slightly 
> more challenging.
>
>
>
> Anyway, different landmarks often convey different biological signals 
> and different homology criteria. For instance, Type I and Type II 
> landmarks (sensu Bookstein 1991) differ fundamentally in their notion of 
> homology.
> Whereas Type I landmarks are defined in terms of local anatomy or 
> histology, a Type II landmark is a purely geometric construct, which 
> may or may not coincide with notions of anatomical/developmental 
> homology. ANY reasonable morphometric analysis must be interpreted in 
> the light of the correspondence function employed, and the some h

RE: [MORPHMET] Re: semilandmarks in biology

2018-11-06 Thread F. James Rohlf
I agree with Philipp but I would like to add that the way I think about the 
justification for the sliding of semilandmarks is that if one were smart enough 
to know exactly where the most meaningful locations are along some curve then 
one should just place the points along the curve and computationally treat them 
as fixed landmarks. However, if their exact positions are to some extend 
arbitrary (usually the case) although still along a defined curve then sliding 
makes sense to me as it minimizes the apparent differences among specimens (the 
sliding minimizes your measure of how much specimens differ from each other or, 
usually, the mean shape. 

 

_ _ _ _ _ _ _ _ _

F. James Rohlf, Distinguished Prof. Emeritus



Depts. of Anthropology and of Ecology & Evolution

 

 

From: mitte...@univie.ac.at  
Sent: Tuesday, November 6, 2018 9:09 AM
To: MORPHMET 
Subject: [MORPHMET] Re: semilandmarks in biology

 

I agree only in part.

 

Whether or not semilandmarks "really are needed" may be hard to say beforehand. 
If the signal is known well enough before the study, even a single linear 
distance or distance ratio may suffice. In fact, most geometric morphometric 
studies are characterized by an oversampling of (anatomical) landmarks as an 
exploratory strategy: it allows for unexpected findings (and nice 
visualizations). 

 

Furthermore, there is a fundamental difference between sliding semilandmarks 
and other outline methods, including EFA. When establishing correspondence of 
semilandmarks across individuals, the minBE sliding algorithm takes the 
anatomical landmarks (and their stronger biological homology) into account, 
while standard EFA and related techniques cannot easily combine point homology 
with curve or surface homology. Clearly, when point homology exists, it should 
be parameterized accordingly. If smooth curves or surfaces exists, they should 
also be parameterized, whether or not this makes the analysis slightly more 
challenging.

 

Anyway, different landmarks often convey different biological signals and 
different homology criteria. For instance, Type I and Type II landmarks (sensu 
Bookstein 1991) differ fundamentally in their notion of homology. Whereas Type 
I landmarks are defined in terms of local anatomy or histology, a Type II 
landmark is a purely geometric construct, which may or may not coincide with 
notions of anatomical/developmental homology. ANY reasonable morphometric 
analysis must be interpreted in the light of the correspondence function 
employed, and the some holds true for semilandmarks. For this, of course, one 
needs to understand the basic properties of sliding landmarks, much as the 
basic properties of Procrustes alignment, etc.. For instance, both the sliding 
algorithm and Procrustes alignment introduce correlations between shape 
coordinates (hence their reduced degrees of freedom). This is one of the 
reasons why I have warned for many years and in many publications about the 
biological interpretation of raw correlations (e.g., summarized in Mitteroecker 
et al. 2012 Evol Biol). Interpretations in terms of morphological integration 
or modularity are even more difficult because in most studies these concepts 
are not operationalized. They are either described by vague and biologically 
trivial narratives, or they are themselves defined as patterns of correlations, 
which is circular and makes most "hypotheses" untestable.

 

The same criticism applies to the naive interpretation of PCA scree plots and 
derived statistics. An isotropic (circular) distribution of shape coordinates 
corresponds to no biological model or hypothesis whatsoever (e.g., Huttegger & 
Mitteroecker 2011, Bookstein & Mitteroecker 2014, and Bookstein 2015, all three 
in Evol Biol). Accordingly, a deviation from isometry does not itself inform 
about integration or modularity (in any reasonable biological sense).

The multivariate distribution of shape coordinates, including "dominant 
directions of variation," depend on many arbitrary factors, including the 
spacing, superimposition, and sliding of landmarks as well as on the number of 
landmarks relative to the number of cases. But all of this applies to both 
anatomical landmarks and sliding semilandmarks.

 

I don't understand how the fact that semilandmarks makes some of these issues 
more obvious is an argument against their use.

 

Best,

 

Philipp

 

 

 

 

 

 


Am Dienstag, 6. November 2018 13:28:55 UTC+1 schrieb alcardini:

As a biologist, for me, the question about whether or not to use semilandmarks 
starts with whether I really need them and what they're actually measuring.

On this, among others, Klingenberg, O'Higgins and Oxnard have written some very 
important easy-to-read papers that everyone doing morphometrics should consider 
and carefully ponder. They can be found at: 
https://preview.tinyurl.com/semilandmarks

I've included there also an older criticis

RE: [MORPHMET] How to project shape difference onto different PC

2018-05-18 Thread F. James Rohlf
Yes, the PC axes are “comparable”. I think the best way to think about what a 
PCA does is to interpret it as a projection of a multidimensional space down to 
a low dimensional space that captures as much of the overall variation as 
possible. The first axis is somewhat special because it represents the best 
1-dimensional space. Past that one should think of 1 and 2 giving the best 
2-dimensional space and 1, 2, and 3 giving the best 3-dimensional space, etc. 
The axes themselves are not of a priori interest in an application – it is the 
space that is of interest. A consequence is that plots showing projections of 
points relative to PC1, PC2,etc. must be plotted to the same scale (i.e., 
consistent with the fact that the eigenvalues give the variances along each 
axis). If, as unfortunately often the case, the axes are plotted using 
different scales then the space has been distorted and is no longer the space 
that best accounts for the overall variation in the data. That also distorts 
the impressions one gets in looking at the plot as using different scales 
changes the relative distances between points.

 

Within that reduced space one may find that particular axes can seem to be 
interpretable but one should really look at the space and decide which 
directions within the space are most interesting based on the patterns of the 
data. That is, the data need to suggest interesting direction unless one has 
some a priori groups one wishes to compares. Often the first PC is of special 
interest but that is often due to allometry and the relatively large impact of 
size variation. That is, by now, a rather boring result! The individual PC axes 
are defined based on convenient mathematical properties – not based on any 
biological models so each one should not be considered separately as things of 
special interest.

 

The above also means that one need not just visualize variation along each axis 
separately. One can, as in tpsRelw software, visualize any specified point 
within the PC space or in any direction of interest within the PC space.

 

_ _ _ _ _ _ _ _ _

F. James Rohlf, Distinguished Prof. Emeritus



Depts. of Anthropology and of Ecology & Evolution

 

 

From: Yinan Hu <yinanhu...@gmail.com> 
Sent: Friday, May 18, 2018 2:19 PM
To: MORPHMET <morphmet@morphometrics.org>
Subject: Re: [MORPHMET] How to project shape difference onto different PC

 

Dear James,

 

Thanks for the reply. Yes I have completed a PCA on a GM dataset with 11 
landmarks, and you got it exactly right that I'm trying to decompose shape 
differences onto individual PCs.  

 

The reason I was hesitating to do the vector projection is that I'm not sure if 
PC scores on different PCs are directly comparable to each other. For 
simplicity, let's say I'm only considering PC1 and PC2, which explains 80% of 
shape variation in total (60% + 20%). Group A has a mean PC1 score of 0.5, and 
PC2 score of 0.1; where as Group B has a mean PC1 score of 0.4 and PC2 score of 
0.3.  Then I'm looking at a 0.1 difference along PC1 and a 0.2 difference along 
PC2 between these two groups. 

 

Would this mean they differ twice as much along PC2 than PC1, such that in the 
80% of shape variation explained by these two PCs, 1/3 is along PC1 and 2/3 is 
along PC2?

 

But considering that PC1 explains three times more variation than PC2 (60% vs 
20%), would this mean I should weigh the PC score difference (distance along 
each PC)? i.e. although the absolute difference in mean PC1 score is 0.1, it 
should be weighed three times more than the difference along PC2 so in the 80% 
of shape variation explained by these two PCs, 3/5 is along PC1 and 2/5 is 
along PC2?

 

 

On the other hand, I agree visualizing the shape difference along each PC can 
be helpful, and I'm pretty sure the plotRefToTarget function from the R package 
geomorph can achieve this.

 

Thanks again.

Best,

 

Yinan

 


On Friday, May 18, 2018 at 12:53:32 PM UTC-4, K. James Soda wrote:

Dear Dr. Hu,

Let me begin by restating how I understand the question: You have completed a 
PCA on a morphological data set in which there are two subsets of interest. Now 
you would like to decompose the difference between the two subsets into 
differences along individual PCs. Here is my two cents on the issue:

I would say that the literal solution to this problem would probably be 
something along the lines of what you proposed. For simplicity, say that you 
summarized each subset using its mean position in the PC space. This would be 
expressed as a vector where each element is a position along a single PC. The 
difference between these two vectors would then be a decomposition of how far 
you would need to move along each PC axis to move from one mean to the other. 
You could then standardize the elements so that their absolute values sum to 
one. This would be an expression of what percentage of the distance is along 
each PC.

What I perceive as the subtext 

RE: [MORPHMET] Problem creating sliding semilandmarks with tps software

2017-12-22 Thread F. James Rohlf
Not quite the way I intended the tps software to be used. The “curves” feature 
was originally intended for curves to be shown but not actually used in any 
computations. Some now do use it to enter points intended to be semilandmarks – 
perhaps because the lines connecting them give the impression of belonging to 
cures. Appending tps curves to landmarks feature can be used but it is an extra 
complication.

 

In tpsRelw only landmark points are used. If the sliders file is input then the 
indicated landmarks will be used as sliding semilandmarks. 

 

Note: unless a curve is very complex, 40 semilandmarks to probably too many.

 

The tpsUtil program should not, of course, crash. Please provide me more 
details about the version used, the input file, and at what point the program 
crashed. I will then try to fix the problem.

 



F. James Rohlf, Distinguished Professor, Emeritus. Ecology & Evolution

Research Professor, Anthropology

Stony Brook University

 

From: Natalia Siomava [mailto:nat.siom...@gmail.com] 
Sent: Friday, December 22, 2017 12:20 PM
To: MORPHMET <morphmet@morphometrics.org>
Subject: [MORPHMET] Problem creating sliding semilandmarks with tps software

 


Hello everybody,

I am trying to add some sliding semilandmarks in my analysis but got stuck with 
defining them.
What I have done:
1) digitized normal LM (13)
2) created a curvature in tpsDig and resampled curve by length with the same 
number of LM (40) for each specimen
3) with tpsUtil “Append tps Curve to landmarks”, I transformed 40 curve points 
into LM.

At this point, the file looks fine: LM=53 (13 real LM + 40 come from the curve 
points). I can also open it in MorphoJ but I all 53 points are shown as LM, not 
semiLM. However, when I use this file in tpsUtil to "Make sliders file", I get 
an error: "Access violation at address "00449136 in module "tpsUtil.exe". Read 
of address 0008." I click several times OK and get a window with "No 
semilandmarks" I get 3 options: "Load Semi.", "Create", and "Cancel". If I 
click "Create", an .NTS file is created but it's not possible to open it with 
MorphoJ. MorphoJ gives as error "The chosen dimentionality and the number of 
data columns in the file are inconsistent".

Could you please explain me what I do wrong? I will appreciate any help and/or 
suggestions.

Thank you,
Best,
Natalia


 

 
<https://lh3.googleusercontent.com/-id2J2QGOwC4/Wj2Es42rclI/A0U/dYaVjK7IMPIY1oZsXgFWeeolNwG2wHvKwCLcBGAs/s1600/1.jpg>
  
<https://lh3.googleusercontent.com/-Q3DoSe9ZjEU/Wj2Ew86zYdI/A0Y/lbEi_I4bEXEOaIcvkVucFgUxWOLv_8q4QCLcBGAs/s1600/2.jpg>
 

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RE: [MORPHMET] Problems with loading new files into tpsDig

2017-12-20 Thread F. James Rohlf
1) Two possibilities: if the full path to the images option is not used then 
the images have to be in the same folder as the tps file (the solution is to 
copy the image files to the new location). Alternatively, if the full paths are 
used then the software will assume the images are still in the original 
location (solution is to edit the tps file using a simple editor such as 
Windows notepad and do a global search and replace to point to the new 
location. 

2) Seems a little odd. Note that just using a "reflex camera" is not enough - 
you have to also set the resolution to the desired level. By default tpsDig2 
should show the images to fill the screen. If they are in fact higher 
resolution then they should not be pixelated unless they are greatly enlarged. 
You could send me one image for me to look at to see if there is something 
special about the images.
________
F. James Rohlf, Distinguished Professor, Emeritus. Ecology & Evolution
Research Professor, Anthropology
Stony Brook University

-Original Message-
From: Lisa Krendl [mailto:lisa.maria.kre...@gmail.com] 
Sent: Tuesday, December 12, 2017 1:22 AM
To: MORPHMET <morphmet@morphometrics.org>
Subject: [MORPHMET] Problems with loading new files into tpsDig

Dear all,

I have two problems in terms of dealing with the tpsDig program:

1)
I have been using tpsDig before to set landmarks, but since I rearranged my 
files and folders I always get an error report when I am trying to upload TPS 
files into the program. 

The error meassage is: 
Image file not found: C: 
Cannot open file "C:.". The system cannot find the indicated path.

I already tried to use different versions of tpsDig. I also deleted all the 
folders with my data and after transferring it back to my computer it still did 
not work. Why could that be?

2)
Besides that, I have one more issue with the program. For initial trials I used 
a compact camera. These pictures worked, but the pictures (image size: 1,06 MB) 
are a little blurred so I decided to use a single-lens reflex camera to obtain 
the pictures. The new pictures (image size: 5,77 MB) do not stretch across the 
whole user interface of the program and when I try to zoom in they get very 
pixelated. 
For further research I want to use the reflex camera. Do you know how I could 
solve the problem?

Your help is very much appreciated. Thank you very much in advance.

Kind regards,
Lisa Krendl

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RE: [MORPHMET] Issue with sliders file data

2017-12-07 Thread F. James Rohlf
If you send me your tps and slider files (but no need to send the image files) 
then I can see if I can find the problem.

_ _ _ _ _ _ _ _ _
F. James Rohlf, Distinguished Prof. Emeritus

Depts. of Anthropology and of Ecology & Evolution


-Original Message-
From: Katherine Morucci [mailto:morucci...@gmail.com] 
Sent: Wednesday, December 6, 2017 8:16 PM
To: MORPHMET <morphmet@morphometrics.org>
Subject: [MORPHMET] Issue with sliders file data

Hi There,

I recently decided to reuse some data from an old 2D GM project on swine tooth 
morphology. When I went to rerun some of my data using my project's original 
code, I was unable to perform a general procrustes analysis using gpagen 
without receiving the error message: Error in x[s[, 3], ]: subscript out of 
bounds. I continued to receive this message after re-running all of my old 
data. I'm not sure why there would be an issue with the dimensionality of my 
data now, that did not exist before. I decided to rebuild a TPS file for 
superimposition and creation of a new sliders file. This also did not work. 


I'm not very experienced with R or the TPS suites, so it's likely that I'm 
overlooking something very simple, but after spinning my wheels on this for a 
few days I wanted to reach out for advice. Any help would be greatly 
appreciated!

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RE: [MORPHMET] Appending tps curves to landmarks

2017-11-10 Thread F. James Rohlf
Please send me a copy of the tps file you are having a problem with (I do not 
need all of the images). Should be an easy fix but I would like to check your 
file to be sure.

 

_ _ _ _ _ _ _ _ _

F. James Rohlf, Distinguished Prof. Emeritus



Depts. of Anthropology and of Ecology & Evolution

 

 

From: Candice Neves [mailto:536...@students.wits.ac.za] 
Sent: Friday, November 10, 2017 5:26 AM
To: MORPHMET <morphmet@morphometrics.org>
Subject: [MORPHMET] Appending tps curves to landmarks

 

Hi All

 

I'm currently trying to append curves to landmarks using the function in 
tpsUtil (I want to use the curve information as sliding landmarks) however any 
time I try to do this tpsUtil gives me an error message saying '0.004149' is 
not a valid floating point value.' I take this to mean that one of the points I 
made when digitizing is not "valid" and so tpsUtil cannot read the file? Is 
this right? When I was digitizing tpsDIG kept popping up error messages but I 
couldn't figure out what I was doing wrong, I was just tracing the outline 
using the 'draw curve' function. I'd delete the curve and start over, but it 
happened every time I outlined a molar so eventually I jut kept going. Did this 
mess me up? Was there a way to fix what I was doing that would have meant my 
curves would be read in tpsUtil? Is there a way I can manually append my curve 
data as landmarks that could still be read into Geomorph or Momocs as sliding 
landmarks? Could I edit the tps file manally to do this or am I going to have 
to start over redrawing the curves? I need to delete some landmarks as well, so 
I'm having the same problem with tpsUtil, I was planning on manually deleting 
the landmarks I no longer want for my specimens (or should I just tell the R 
packages I use to exclude certain landmarks? I think this might be better).

 

Any help would be greatly appreciated

Thanks

Candice Neves

MSc Candidate

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[MORPHMET] morphometrics courses

2017-10-02 Thread F. James Rohlf
The web page at http://life.bio.sunysb.edu/morph/notices.html has just been
updated to list the upcoming courses. You may find this to be a convenient
list.  This will be a busy Fall and Winter!

 

_ _ _ _ _ _ _ _ _

F. James Rohlf, Distinguished Prof. Emeritus



Depts. of Anthropology and of Ecology & Evolution

 

 

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RE: [MORPHMET] number of landmarks and sample size

2017-05-31 Thread F. James Rohlf
Another, though non-statistical, approach to judge whether one has an 
appropriate number of landmarks or perhaps too many is to use the tpsSuper 
software. 

One could start with many landmarks and confirm (one hopes) that the average 
unwarped image is clear implying that the landmarks have captured the variation 
of not only the landmarks but the structures around them. You can then remove 
landmarks and see whether the average looks fuzzier. If so, that reflects 
variation not well tracked by the chosen landmarks.  If there is little change 
then the landmarks you removed are not really necessary to track the variation 
in the sample. One could then continue the process. Clearly the issue is not 
just the number of landmarks but where they are located relative to the 
variation among the specimens. This process could be automated to try 
combinations of landmarks such that some measure of variation in pixels of the 
unwarped images are minimized. I seem to remember that Mardia made a suggestion 
like that many years ago.
_ _ _ _ _ _ _ _ _
F. James Rohlf, Distinguished Prof. Emeritus
Stony Brook University
Depts. of Anthropology and of Ecology & Evolution

-Original Message-
From: Murat Maga [mailto:m...@uw.edu] 
Sent: Wednesday, May 31, 2017 12:33 PM
To: Mike Collyer <mlcoll...@gmail.com>; Lea Wolter <leawolter...@gmail.com>
Cc: MORPHMET <morphmet@morphometrics.org>
Subject: RE: [MORPHMET] number of landmarks and sample size

I want to chime in on Mike's comment about density of landmarking changing the 
effect size. Nicolas Navarro and I did something similar in context of 
quantitative genetics of mandible shape and came to a similar conclusion using 
2D, 3D and 3D semi-landmarks sets on same dataset.

Navarro N, Maga AM. 2016. Does 3D Phenotyping Yield Substantial Insights in the 
Genetics of the Mouse Mandible Shape? G3: Genes, Genomes, Genetics 6:1153–1163.


-Original Message-
From: Mike Collyer [mailto:mlcoll...@gmail.com] 
Sent: Wednesday, May 31, 2017 7:43 AM
To: Lea Wolter <leawolter...@gmail.com>
Cc: MORPHMET <morphmet@morphometrics.org>
Subject: Re: [MORPHMET] number of landmarks and sample size

Dear Lea,

I see others have responded to your inquiry, already.  I thought I would add an 
additional perspective.

Your question about statistical significance requires asking a follow-up 
question.  What statistical methods would you intend to use to evaluate 
“significance”?  If you are worried about the number of landmarks, your concern 
suggests you might be using parametric test statistics frequently associated 
with MANOVA, like Wilks lambda or Pilai trace.  Indeed, when using these 
statistics and converting them to approximate F values, one must have many more 
specimens than landmarks (more error degrees of freedom than shape variables, 
to be more precise), if “significance” is to be inferred from probabilities 
associated with F-distributions.  Therefore, limiting the number of landmarks 
might be a goal.

When using resampling procedures to conduct ANOVA, using fewer landmarks can 
paradoxically decrease effect sizes, as an overly simplified definition of 
shape becomes implied.  We demonstrated this in our paper: Collyer, M.L., D.J. 
Sekora, and D.C. Adams. 2015. A method for analysis of phenotypic change for 
phenotypes described by high-dimensional data. Heredity. 115: 357-365.  This is 
consistent with Andrea’s comment about quality over quantity with the caveat 
that limited quantity precludes quality.  In other words, too few landmarks 
translates to limited ability to discern shape differences, because the shape 
compared is basic.  In the paper, we used two separate landmark configurations: 
one with few landmarks and the other with the same landmarks plus sliding 
semilandmarks between fixed points, on different populations of fish.  We found 
that adding the semilandmarks increased the effect size for population 
differences and sexual dimorphism.  But if we constrained our analyses to 
parametric MANOVA for our small samples, we would have to use the simpler 
landmark configurations and live with the results.

I do not wish to suggest that adding more landmarks is better.  Overkill is 
certainly a concern.  I would suggest though that statistical power would be 
for me less of a concern than a proper characterization of the shape I wish to 
compare among samples.  If I suspect curvature is important but am afraid to 
use (semi)landmarks that would allow me to assess the curvature differences 
among groups, opting instead to use just the endpoints of a structure because I 
am worried about statistical power, then I just allowed a statistical procedure 
to take me away from the biologically relevant question I sought to address.  
Andrea is correct that quality is better than quantity, but quantity can be a 
burden in either direction (too few or too many).  Additionally, statistical 
power will vary among statistical met

RE: [MORPHMET] Interpreting PCA results

2017-05-15 Thread F. James Rohlf
What is important is not the fact that one is going +/- one standard deviation 
along each axis. When shape changes are subtle one may need to go beyond the 
observed range to make it more obvious to the eye what the changes are. Exactly 
how far one goes away from the mean is arbitrary. It is a visualization – not 
statistics.

 

--

F. James Rohlf New email: f.james.ro...@stonybrook.edu

Distinguished Professor, Emeritus. Dept. of Ecol. & Evol.

& Research Professor. Dept. of Anthropology

Stony Brook University 11794-4364

WWW: http://life.bio.sunysb.edu/morph/rohlf

P Please consider the environment before printing this email 

 

From: mahendiran mylswamy [mailto:mahenr...@gmail.com] 
Sent: Monday, May 15, 2017 2:31 AM
To: f.james.ro...@stonybrook.edu
Cc: morphmet@morphometrics.org; dsbriss_dmd <orthofl...@gmail.com>; K. James 
Soda <k.jamess...@gmail.com>
Subject: RE: [MORPHMET] Interpreting PCA results

 

Dear all,

I read interesting comments and the attached manuscript as well.

I find David question us interesting.

If any one could answer David question in a simple way?

I am quoting his question below?.

"What I do not quite understand is what exactly is the purpose of applying 
standard deviation(s) to the PCA and then warping the Procrustes average shape 
to these standard deviations? "

 

 

On 15 May 2017 6:08 a.m., "F. James Rohlf" <f.james.ro...@stonybrook.edu 
<mailto:f.james.ro...@stonybrook.edu> > wrote:

I agree with these comments but would like to add another point. I prefer to 
think that the purpose of the PCA is to produce a low-dimension space that 
captures as much of the overall variation (in a least-squares sense) as 
possible. Within that space there is no need to limit the visualizations to the 
extremes of each axis – one can investigate any direction within that space if 
there is a pattern in the data that suggests an interesting direction. The 
directions of the axes are mathematical constructs and not bases on any 
biological principles. Perhaps one sees some clusters in the PCA ordination but 
the variation within or between clusters need not be parallel to one of the PC 
axes. One can then look in other directions. That is why the tpsRelw program 
allows one to visualize any point in the ordination space – not just parallel 
to the axes. That means for publication one has to decide which directions are 
of interest – not just mechanically display the extremes of the axes.

 

--

F. James Rohlf New email: f.james.ro...@stonybrook.edu 
<mailto:f.james.ro...@stonybrook.edu> 

Distinguished Professor, Emeritus. Dept. of Ecol. & Evol.

& Research Professor. Dept. of Anthropology

Stony Brook University 11794-4364

WWW: http://life.bio.sunysb.edu/morph/rohlf

P Please consider the environment before printing this email 

 

From: K. James Soda [mailto:k.jamess...@gmail.com 
<mailto:k.jamess...@gmail.com> ] 
Sent: Sunday, May 14, 2017 7:28 PM
To: dsbriss_dmd <orthofl...@gmail.com <mailto:orthofl...@gmail.com> >
Cc: MORPHMET <morphmet@morphometrics.org <mailto:morphmet@morphometrics.org> >
Subject: Re: [MORPHMET] Interpreting PCA results

 

Dear David,

Great question!  I disagree with the statement that the samples' variance in 
shape space is not biologically real or, perhaps more accurately, is less real 
than the variance in any other space.  As far as I see it, the basic strategy 
in any biostatistical study, be it GM or otherwise, is that a researcher 
represents a real biological population as an abstract statistical population.  
They then use this abstract statistical population as a proxy for the real one 
so that inferences in the statistical space have implications for the real 
world.  

For example, a PCA finds a direction in the statistical space in which the 
statistical population tends to be spread out.  This is interesting to the 
researcher because this direction has a correspondence to certain real world 
variables.  As a result, the PCA tells the researcher in what ways the real 
population tends to vary.  The key point, though, is that the researcher 
transitioned from the statistical space to the real world.

Moving from shape space to the real world is no different in principle.  We 
have a real population of specimens, whose shape are of interest to us, and we 
represent them using vectors of shape variables.  The vectors are abstractions; 
it is not as if we can hold a vector in our hands.  However, this is irrelevant 
because they are just proxies, no less real than any other quantitative 
representation.  What matters is if we can tie them back to the real world.  
This is why morphometricians implement a visualization step.  In a PCA, the PCs 
describe how our proxies vary, and we visualize in order to see how this 
variation appears in the real world.  It is infeasible to visualize every point 
along this

RE: [MORPHMET] Interpreting PCA results

2017-05-14 Thread F. James Rohlf
I agree with these comments but would like to add another point. I prefer to 
think that the purpose of the PCA is to produce a low-dimension space that 
captures as much of the overall variation (in a least-squares sense) as 
possible. Within that space there is no need to limit the visualizations to the 
extremes of each axis – one can investigate any direction within that space if 
there is a pattern in the data that suggests an interesting direction. The 
directions of the axes are mathematical constructs and not bases on any 
biological principles. Perhaps one sees some clusters in the PCA ordination but 
the variation within or between clusters need not be parallel to one of the PC 
axes. One can then look in other directions. That is why the tpsRelw program 
allows one to visualize any point in the ordination space – not just parallel 
to the axes. That means for publication one has to decide which directions are 
of interest – not just mechanically display the extremes of the axes.

 

--

F. James Rohlf New email: f.james.ro...@stonybrook.edu

Distinguished Professor, Emeritus. Dept. of Ecol. & Evol.

& Research Professor. Dept. of Anthropology

Stony Brook University 11794-4364

WWW: http://life.bio.sunysb.edu/morph/rohlf

P Please consider the environment before printing this email 

 

From: K. James Soda [mailto:k.jamess...@gmail.com] 
Sent: Sunday, May 14, 2017 7:28 PM
To: dsbriss_dmd <orthofl...@gmail.com>
Cc: MORPHMET <morphmet@morphometrics.org>
Subject: Re: [MORPHMET] Interpreting PCA results

 

Dear David,

Great question!  I disagree with the statement that the samples' variance in 
shape space is not biologically real or, perhaps more accurately, is less real 
than the variance in any other space.  As far as I see it, the basic strategy 
in any biostatistical study, be it GM or otherwise, is that a researcher 
represents a real biological population as an abstract statistical population.  
They then use this abstract statistical population as a proxy for the real one 
so that inferences in the statistical space have implications for the real 
world.  

For example, a PCA finds a direction in the statistical space in which the 
statistical population tends to be spread out.  This is interesting to the 
researcher because this direction has a correspondence to certain real world 
variables.  As a result, the PCA tells the researcher in what ways the real 
population tends to vary.  The key point, though, is that the researcher 
transitioned from the statistical space to the real world.

Moving from shape space to the real world is no different in principle.  We 
have a real population of specimens, whose shape are of interest to us, and we 
represent them using vectors of shape variables.  The vectors are abstractions; 
it is not as if we can hold a vector in our hands.  However, this is irrelevant 
because they are just proxies, no less real than any other quantitative 
representation.  What matters is if we can tie them back to the real world.  
This is why morphometricians implement a visualization step.  In a PCA, the PCs 
describe how our proxies vary, and we visualize in order to see how this 
variation appears in the real world.  It is infeasible to visualize every point 
along this axis, so we instead visualize a handful.  Since the core goal in PCA 
(at least in this context) is to describe variance, we generally describe the 
locations where a visualization occurs in units of standard deviations from the 
mean.  We could use absolute distances along an axis, but this is probably more 
arbitrary than standard deviation units.  The standard deviations come from the 
data's distribution, whereas the absolute distance is really only well-defined 
in the mathematical space.

To summarize: i) Nearly all quantitative analyses involve an abstraction to a 
mathematical space.  ii) The description of points in a mathematical space is 
useful to the researcher because the researcher is able to translate the 
abstract mathematical space into a real world interpretation.  iii) In GM, the 
shape variables are traditionally translated into the real world via 
visualization.  Ergo, morphometricians often interpret PCA results via 
visualizations along individual PCs.  To aid in interpretation, this tends to 
occur in standard deviation units because the standard deviation is more easily 
tied to the real world relative to arbitrary selecting a unit of distance.

Perhaps some of these points are up for debate, but remember that statistics is 
largely the study of VARIATION.  If the variation in shape space did not have 
any biological significance, almost no analysis after alignment would be 
possible.

Hope somewhere in this long commentary, you found something helpful,

James

 

On Tue, May 9, 2017 at 4:56 PM, dsbriss_dmd <orthofl...@gmail.com 
<mailto:orthofl...@gmail.com> > wrote:

Good afternoon all, I have a question about interpretat

RE: [MORPHMET] question about form space

2017-05-12 Thread F. James Rohlf
tpsRelw has an option (on the “Options” menu) to specify the use of form space 
when doing an analysis of relative warps (PCA).

 

--

F. James Rohlf New email: f.james.ro...@stonybrook.edu

Distinguished Professor, Emeritus. Dept. of Ecol. & Evol.

& Research Professor. Dept. of Anthropology

Stony Brook University 11794-4364

WWW: http://life.bio.sunysb.edu/morph/rohlf

P Please consider the environment before printing this email 

 

From: marcelo cardillo [mailto:marcelo.cardi...@gmail.com] 
Sent: Thursday, May 11, 2017 12:47 PM
To: MORPHMET <morphmet@morphometrics.org>
Subject: [MORPHMET] question about form space

 

Dear Colleagues,  I´m interested to work in the form space (shape plus size) 
with the ouput data of the tpsrewl. Should I use the scale aligned specimen 
matrix.?, also  which is the proper method to display this matrix (a PCA with 
the covariance matrix maybe) ?.  

 

  best!

 M

 

 




 

-- 

Dr.Marcelo Cardillo
IMHICIHU-CONICET-UBA
Saavedra 15, 5to piso cp (1083)

Teléfono: (011) 4953-8548 - Interno 212
Buenos Aires. Capital Federal. Argentina
http://conicet.academia.edu/MarceloCardillo

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[MORPHMET] tpsDig2 update

2017-03-01 Thread F. James Rohlf
I have just uploaded version 2.30 of tpsDig2 to the
http://life.bio.sunysb.edu/morph server.

 

It fixes a problem with the decimal character when reading coordinates of
curves.  Thanks to Jessica Grahn for reporting the problem.

 



F. James Rohlf, Distinguished Professor, Emeritus. Ecology & Evolution

Research Professor, Anthropology

Stony Brook University

 

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RE: [MORPHMET] tpsDig2 and closed curves

2017-02-26 Thread F. James Rohlf
Yes, that was the intended behavior. As mention on a prior posting, the closed 
curve option is only for esthetics – it displays a line to connect the first 
and last points but coordinates on the first point is not added to the end of 
the list. In GM one must avoid the chance that two points would have identical 
coordinates as a deformation in their positions would require an infinite 
amount of bending energy.  However I could change the interpolation rule if 
users request it.

 



F. James Rohlf, Distinguished Professor, Emeritus. Ecology & Evolution

Research Professor, Anthropology

Stony Brook University

 

From: J Coelho [mailto:joaopedrocoe...@gmail.com] 
Sent: Sunday, February 26, 2017 3:41 AM
To: MORPHMET <morphmet@morphometrics.org>
Subject: [MORPHMET] tpsDig2 and closed curves

 

Greetings morphometricians,

 

I noticed a strange behaviour while attempting to obtain closed curves from 
tpsDig2.

 

When I resample the curve, the first and last point remain fixed, and only 
other points get repositioned. This is the correct behaviour for open curves. 
However - to my understanding - in closed curves only one of these points (ex. 
first) should be fixed.

 

To reproduce it, follow:

 

1. Options > Close Curve

2. Modes > Draw Curve

3. Now, draw anything you wish, ex. an ellipse.

4. Right click on your closed curve > Resample Curve

4.1 Input a far bigger number of points (I know, I know, but it's easier to 
notice this way)

4.2 Chose [By Length] > Ok.

 

The distance between last and first landmark remains fixed. Again, a behaviour 
I'd only expect in open curves. Am I wrong to expect the resampling to effect 
all points except the first one in the specific case of closed curves??

 

Thanks in advance,

Best Regards,

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RE: [MORPHMET] Problems visualizing curves across versions of tpsDig

2017-02-23 Thread F. James Rohlf
This is most likely caused by not setting the decimal character (. Or ,) to 
agree with what is used in the tps file.

 



F. James Rohlf, Distinguished Professor, Emeritus. Ecology & Evolution

Research Professor, Anthropology

Stony Brook University

 

From: Luis Ruedas [mailto:rue...@pdx.edu] 
Sent: Tuesday, February 21, 2017 12:49 PM
To: morphmet@morphometrics.org
Subject: [MORPHMET] Problems visualizing curves across versions of tpsDig

 

 

I have been digitizing data from some 2D images on a computer where I had
loaded tpsDig 2.16 (yes, a long time ago, I know) then tried to work on a
laptop with tpsDig 2.29.  Initially, I was unable to see the curves I had
created.  When I changed to a high vis color, I noticed a thick line on the
bottom edge of the image in tpsDig.  The file remains unchanged, with the
original curve coordinates.

Anyone know what may be going on? Help is welcome...

All the best,

Luis

 

-- 


Luis A. Ruedas, Ph.D.
Associate Professor of Biology
Portland State University

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[MORPHMET] tpsdSuper update

2017-02-23 Thread F. James Rohlf
I have just uploaded version 2.04 of tpsSuper to the
http://life.bio.sunysb.edu/morph server.

 

It fixes a problem in saving aligned specimens that was noticed by Jennifer
Valvo.

 



F. James Rohlf, Distinguished Professor, Emeritus. Ecology & Evolution

Research Professor, Anthropology

Stony Brook University

 

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[MORPHMET] tpsUtil and tpsRelw updates

2017-02-20 Thread F. James Rohlf
I have just uploaded the following to the http://life.bio.sunysb.edu/morph
server:

 

tpsUtil version 1.74. Adds a feature suggested by Sonja Windhager. The
reorder  specimens option can now read a vector of 0 or 1 values to
indicate which specimens should be deleted or kept in a file. 

 

tpsRelw version 1.67. A number of small problems fixed. Also updated the
help file.

 

tpsSuper - still version 2.03 but recompiled with the newer version of the
compiler. 

 

The problems with the 64 bit versions (for 64 bit Windows versions) of the
tps software seem to have been fixed in the new compiler version.

 

As always, let me know of any problems or suggestions for the tps software.



F. James Rohlf, Distinguished Professor, Emeritus. Ecology & Evolution

Research Professor, Anthropology

Stony Brook University

 

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[MORPHMET] tpsUtil update - version 1.73

2017-02-07 Thread F. James Rohlf
I have updated the tpsUtil program to version 1.73 and uploaded it to the
life.bio.sunysb.edu/morph server.  At the suggestion of T.J. Slezak I have
extended the "compute area" option to also include the computation of the
length of the perimeter and a measure of circularity of the outline points.
He has also suggested that I remind users that the "complete curve" option
in tpsDig2 is just esthetic - the curve will be seen as a closed outline but
the first point will not be duplicated in the output file.

 

________

F. James Rohlf, Distinguished Professor, Emeritus. Ecology & Evolution

Research Professor, Anthropology

Stony Brook University

 

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RE: [MORPHMET] eliminating the effect of population differences

2017-01-19 Thread F. James Rohlf
Is the assumption that these are all provide estimates of the same covariance 
matrix? If so, one could test for homogeneity of covariance matrices and then 
compute a common (i.e., average) covariance matrix. The test will require 
adequate sample sizes (more samples within each population than the number of 
shape variables).

 



F. James Rohlf, Distinguished Professor, Emeritus. Ecology & Evolution

Research Professor, Anthropology

Stony Brook University

 

From: Ariadne Schulz [mailto:ariadne.sch...@gmail.com] 
Sent: Wednesday, January 18, 2017 10:27 AM
To: Elahe <ellie.parv...@gmail.com>
Cc: MORPHMET <morphmet@morphometrics.org>
Subject: Re: [MORPHMET] eliminating the effect of population differences

 

I would like to hear any responses to this as well. I did something similar and 
I wasn't sure how to approach this question. In future studies I would like to 
address precisely this issue. My inclination would be that first you would want 
to determine how much morphological variation you're getting between sites. You 
could then look at sexual dimorphism within each site and/or you could look at 
variation of only females and only males over all sites. But this is all rather 
clunky and does not eliminate any interpopulation variation. If anyone has 
already proposed or can propose a better methodology I'd be interested in it as 
well.

Best,

Ari

 

On Wed, Jan 18, 2017 at 5:29 PM, Elahe <ellie.parv...@gmail.com 
<mailto:ellie.parv...@gmail.com> > wrote:

Dear all,

 

I have pooled samples from 7 different populations of one species in order to 
study the allometric growth and sexual dimorphism in that species. As different 
populations may have subtle differences in terms of body dimensions with each 
other, I want to remove their effects. 

Can anyone suggest a way to eliminate population effects and maybe finding some 
residuals that are homogeneous and can be used for further analyses?

 

I would appreciate any helps :)

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[MORPHMET] tpsUtil update

2017-01-19 Thread F. James Rohlf
I have just uploaded version 1.71 of tpsUtil to the 

http://life.bio.sunysb.edu/morph

server. 

 

It adds better error messages to handle the cases where the decimal
separator character in the data does not match the option set in the
software.

 



F. James Rohlf, Distinguished Professor, Emeritus. Ecology & Evolution

Research Professor, Anthropology

Stony Brook University

 

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RE: [MORPHMET] the problem with CVA... or is it?

2016-11-28 Thread F. James Rohlf
While you do have more sample than variables, it is too close. One prefers to 
have many more samples than the number of variables. Another problem is that a 
CVA with 144 variables will mostly involve a covariance matrix that is close to 
being singular. One way I like to check for problems (and is provided in 
NTSYSpc) is to first project the data onto the PCA axes based on the pooled 
within-groups covariance matrix. If the CVA suggests that the PC axes with the 
smallest eigenvalues are the most important for distinguishing groups then you 
are very likely to be in trouble. In that case, apparent large differences 
between some groups may be due to rounding errors in the computations. One 
solution is to drop PCA dimensions with small eigenvalues (of course you will 
then not be able to detect any real differences in those dimensions but in most 
studies that is not likely to be a problem). That also improves the ratio of 
the number of samples relative to the number of variables.

 

It is nice to produce a CVA type plot showing the relative distances among 
group means. One could just do a PCA of the group means. However, the purpose 
of the CVA plot is to show distances that are a function of how close the means 
are statistically (in the sense of how easily they can be distinguished). 
Distances in such a plot do not correspond to the absolute amount of shape 
difference as measured by Procrustes distances. The choice of distance is 
important.

 

One could also do a PCOORD of a matrix of generalized distances but for 
visualization of shapes you will need information about the shape variables 
themselves. That can be done after a PCOORD analysis but using a CVA is more 
straight-forward. Depends of the purpose of your study. Note that if 
projections onto the PCA axes were used as variables then the results of the 
CVA will have to be back-transformed.

 

--

F. James Rohlf New email: f.james.ro...@stonybrook.edu

Distinguished Professor, Emeritus. Dept. of Ecol. & Evol.

& Research Professor. Dept. of Anthropology

Stony Brook University 11794-4364

WWW: http://life.bio.sunysb.edu/morph/rohlf

P Please consider the environment before printing this email 

 

From: Christy Hipsley [mailto:chips...@museum.vic.gov.au] 
Sent: Monday, November 28, 2016 6:04 PM
To: MORPHMET <morphmet@morphometrics.org>
Subject: [MORPHMET] the problem with CVA... or is it?

 

Dear Morphmet-ers,

 

I'm seeking advice on methods for visualizing shape features that distinguish 
multiple groups using GM. I know CVA has fallen out of favor for a number of 
reasons discussed here - e.g., more variables than groups, nonisotropic 
variation:

 

Mitteroecker, P., and Bookstein, F. 2011. Linear discrimination, ordination, 
and the visualization of selection gradients in modern morphometrics. Evol. 
Biol. 38:100–114.

Klingenberg, C. P., and Monteiro, L. R. 2005. Distances and directions in 
multidimensional shape spaces: Implications for morphometric applications. 
Syst. Biol. 54:678–688.

 

Although given these limitations, is it really expected to give completely 
false results regarding the visualization of shape changes? In my study sytem, 
I show that ecological groups have statistically different cranial shapes, 
using both Procrustes ANOVA and PGLS. Now I simply want to visualize what the 
main features are that distinguish them, preferably using warps or wireframes, 
so that those changes must be directly relateable to the original landmark 
coordinates. I did that using individual specimens instead of species means, so 
I have 161 individuals vs 144 variables (48 landmarks*3D). I also did a 
between-group PCA on the species means which shows the same pattern, so is it 
technically "wrong" to show both? 

 

Thanks for any feedback on this issue, and I would appreciate to hear any 
alternative methods that people might use. I use MorphoJ and Geomorph for 
analyses.

 

Best,

Christy

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RE: [MORPHMET] Problems with min-dsquare sliding in tpsRelw

2016-08-24 Thread F. James Rohlf
An advantage of the bending energy approach is that it minimizes the chance of 
collapsing landmarks because changes in the positions of landmarks that are 
close together requires much more bending energy. This is not usually a problem 
but it can be if the outline has a sharp corner - which seems likely for a beak.

--
F. James Rohlf New email: f.james.ro...@stonybrook.edu
Distinguished Professor, Emeritus. Dept. of Ecol. & Evol.
& Research Professor. Dept. of Anthropology
Stony Brook University 11794-4364
The much revised 4th editions of Biometry and Statistical Tables are now 
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 Please consider the environment before printing this email 

-Original Message-
From: Guillermo Navalón [mailto:guiyelm...@gmail.com] 
Sent: Monday, August 22, 2016 9:34 AM
To: MORPHMET <morphmet@morphometrics.org>
Subject: [MORPHMET] Problems with min-dsquare sliding in tpsRelw

Hi everyone,

In a very disparate sample of bird skulls I am using a configuration with both 
lnmdks and smlndmks. Specifically, to capture the lateral morphology of the 
beak (likely the most variable area) I digitized 2 curves with 15 evenly-spaced 
semilandmarks. 

The 2 curves are constrained by 3 regular lndmks forming a triangle, the 
tip-of-the-beak landmark (landmark 1) is the anterior end of both curves. 

When I slide the smlndmks in tpsRelw with min-dsquare slide method some of the 
anterior smlndmks collapse in a very narrow section in both of the 2 curves in 
the Procrustes superimposition. This effect is not affecting to the other curve 
in the configuration (midline of the neurocranium) that is apparently much less 
variable in my sample. Also, minimum bending energy slide method does not 
affect the superimposition in this way, but I want to try to use min-dsquare.

I have tried to change the slide maximum iterations and slide recursive options 
but still recover the same effect.


 Any idea what is going on here? Is it a bug of the program or is it a proper 
statistical effect? 

Thank you!

Guillermo Navalón

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[MORPHMET] RE: tpsDig2 version 2.28 available

2016-08-23 Thread F. James Rohlf
Oh, and there was another important change to tpsDig2. Some uses have
reported that the landmark labels were no longer visible. Actually they were
present but very small because their size was in terms of the size of the
pixels in the image (which would be very small if the image was very large).
There is now an option to specify the label size in terms of screen pixels
so they should remain visible even when the image is zoomed. 

 

--

F. James Rohlf New email: f.james.ro...@stonybrook.edu

Distinguished Professor, Emeritus. Dept. of Ecol. & Evol.

& Research Professor. Dept. of Anthropology

Stony Brook University 11794-4364

The much revised 4th editions of Biometry and Statistical Tables are now
available:

 <http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal>
http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal

 
<http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-ro
hlf>
http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-roh
lf

P Please consider the environment before printing this email 

 

From: F. James Rohlf [mailto:f.james.ro...@stonybrook.edu] 
Sent: Tuesday, August 23, 2016 4:59 PM
To: 'Morphmet (morphmet@morphometrics.org)' <morphmet@morphometrics.org>
Subject: tpsDig2 version 2.28 available

 

I have just uploaded version 2.28 of tpsDig2 to the
http://life.bio.sunysb.edu/morph site.

 

The new version again does a proper screen copy and save of both the image
and any landmarks or curves currently on the screen. One can also now
specify the color of the line to be used for measurement. A few other minor
things were also fixed.

 

Thanks to Mauro Cavalcanti for the suggestions.

 

------

F. James Rohlf New email: f.james.ro...@stonybrook.edu
<mailto:f.james.ro...@stonybrook.edu> 

Distinguished Professor, Emeritus. Dept. of Ecol. & Evol.

& Research Professor. Dept. of Anthropology

Stony Brook University 11794-4364

The much revised 4th editions of Biometry and Statistical Tables are now
available:

 <http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal>
http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal

 
<http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-ro
hlf>
http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-roh
lf

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[MORPHMET] tpsDig2 version 2.28 available

2016-08-23 Thread F. James Rohlf
I have just uploaded version 2.28 of tpsDig2 to the
http://life.bio.sunysb.edu/morph site.

 

The new version again does a proper screen copy and save of both the image
and any landmarks or curves currently on the screen. One can also now
specify the color of the line to be used for measurement. A few other minor
things were also fixed.

 

Thanks to Mauro Cavalcanti for the suggestions.

 

--

F. James Rohlf New email: f.james.ro...@stonybrook.edu

Distinguished Professor, Emeritus. Dept. of Ecol. & Evol.

& Research Professor. Dept. of Anthropology

Stony Brook University 11794-4364

The much revised 4th editions of Biometry and Statistical Tables are now
available:

 <http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal>
http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal

 
<http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-ro
hlf>
http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-roh
lf

P Please consider the environment before printing this email 

 

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[MORPHMET] tpsSuper update to 2.03

2016-07-07 Thread F. James Rohlf
I have just uploaded version 2.03 of the TpsSuper program to the
life.biol.sunysb.edu/morph server.

 

The only change is to add the ability to directly save all of the unwarped
images to files.  There is a new menu item for this on the plot unwarped
images window.

 

Thanks to Jennifer Valvo for suggesting this addition.

 

--

F. James Rohlf New email: f.james.ro...@stonybrook.edu

Distinguished Professor, Emeritus. Dept. of Ecol. & Evol.

& Research Professor. Dept. of Anthropology

Stony Brook University 11794-4364

The much revised 4th editions of Biometry and Statistical Tables are now
available:

 <http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal>
http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal

 
<http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-ro
hlf>
http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-roh
lf

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[MORPHMET] tpsRelw update to version 1.65

2016-06-28 Thread F. James Rohlf
I have just uploaded version 1.65 of tpsRelw to the
http://life.bio.sunysb.edu server. Several important changes were made. 

 

Problems with printing, saving, and copying the plot of the variance of
partial warp scores against bending energy were fixed. Thanks to Shibu
Vardhanan for reporting the problem. I also made a number of additions to
the help file. Some options are, perhaps, somewhat easier to understand now.

 

--

F. James Rohlf New email: f.james.ro...@stonybrook.edu

Distinguished Professor, Emeritus. Dept. of Ecol. & Evol.

& Research Professor. Dept. of Anthropology

Stony Brook University 11794-4364

The much revised 4th editions of Biometry and Statistical Tables are now
available:

 <http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal>
http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal

 
<http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-ro
hlf>
http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-roh
lf

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[MORPHMET] tpsUtil (v. 1.70) & tpsDig2 (v. 2.27) updates

2016-06-17 Thread F. James Rohlf
I have just made small but important changes in tpsUtil and tpsDig2 and
uploaded them to the http://life.bio.sunysb.edu/morph server. Again, fixing
problems with the decimal character ("," vs. "."). The most important
problem was that the scale factor could be written to the tps file by
tpsDig2 using a "," even though a "." Was used for the coordinates of the
landmarks. The tpsUtil program had a problem showing which character was to
be used for the decimal character.  Thanks to Claudia Wrozyna for pointing
out the problem. I was also just reminded about it by Katerina Papayiannis. 

 

Please keep notifying me if you find a problem using my software. I greatly
appreciate comments, suggestions, and even complaints about something not
working correctly as it helps me improve the software.

 

--

F. James Rohlf New email: f.james.ro...@stonybrook.edu

Distinguished Professor, Emeritus. Dept. of Ecol. & Evol.

& Research Professor. Dept. of Anthropology

Stony Brook University 11794-4364

The much revised 4th editions of Biometry and Statistical Tables are now
available:

 <http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal>
http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal

 
<http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-ro
hlf>
http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-roh
lf

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[MORPHMET] tpsRelw update 1.64

2016-06-08 Thread F. James Rohlf
I have just uploaded version 1.64 to the http://life.bio.sunysb.edu/morph
server. It fixes a problem in the visualization of shapes implied by
different positions in the PCA plot. The problem was than when the plot was
printed or saved to a file it did not match the correct plot shown on the
screen. 

 

Thanks to Weimin Si for reporting the problem.

 

--

F. James Rohlf New email: f.james.ro...@stonybrook.edu

Distinguished Professor, Emeritus. Dept. of Ecol. & Evol.

& Research Professor. Dept. of Anthropology

Stony Brook University 11794-4364

The much revised 4th editions of Biometry and Statistical Tables are now
available:

 <http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal>
http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal

 
<http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-ro
hlf>
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[MORPHMET] tpsRelw update

2016-05-11 Thread F. James Rohlf
I have just uploaded version 1.63. It fixes a problem reported by Carlo
Meloro. When saving aligned specimens in the .nts format the number of
columns in the matrix was set to 0 rather than twice the number of
landmarks.

 



F. James Rohlf, Distinguished Professor, Emeritus. Ecology & Evolution

Research Professor, Anthropology

Stony Brook University

 

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[MORPHMET] tpsDig2 update to version 2.26

2016-04-14 Thread F. James Rohlf
I have just uploaded version 2.26 of tpsDig2 to the
http://life.bio.sunysb.edu/morph server. This fixes some problems and
suggestions reported by Miriam Zelditch. There is now an option on the
Options menu so that the current zoom will be kept when moving from one
specimen to another. The 'go to specimen' window now allows for files with
of up to 9 specimens - I assume that will be large enough for most
users. Please let me know of other changes that would make using the program
easier.

 

Thanks again, Miriam!



F. James Rohlf, Distinguished Professor, Emeritus. Ecology & Evolution

Research Professor, Anthropology

Stony Brook University

 

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RE: [MORPHMET] replacing df with principal components for MANOVA tests

2016-04-05 Thread F. James Rohlf
Note: to give statistically reliable results it needs to do more than just 
“culls the dimensions of x to match the number of positive non-zero 
eigenvalues”. You need to have the number of degrees of freedom much larger 
than the number of dimensions of the space or else you are likely to find that 
the PC dimensions with the smallest eigenvalues apparently account for most of 
the differences among groups. Simply using randomization tests do not solve 
this problem.

 



F. James Rohlf, Distinguished Professor, Emeritus. Ecology & Evolution

Research Professor, Anthropology

Stony Brook University

 

From: Collyer, Michael [mailto:michael.coll...@wku.edu] 
Sent: Tuesday, April 5, 2016 5:29 AM
To: Brenna Hays <bkhays...@gmail.com>
Cc: MORPHMET <morphmet@morphometrics.org>
Subject: Re: [MORPHMET] replacing df with principal components for MANOVA tests

 

Brenna, 

 

The PCA you performed produces a list of objects, one of which is a matrix of 
PC scores.

 

Change AIS.PC to AISPC$x, and it should work.  In this case, $x is the matrix 
of scores.

 

The help files for the functions you use tell you the objects that are 
returned.  You can also use attributes() to see the list of objects returned.  
The $ indicate that you are going to the list and extracting the object that 
follows.  

 

Just as a cautionary note, you might make sure that the number of columns for x 
is not the same as the number of landmarks times the dimensions (2 or 3).  I 
cannot remember if R automatically culls the dimensions of x to match the 
number of positive non-zero eigenvalues.  If not, you might have to do that 
yourself.  There are also non-parametric MANOVA options that do not rely on 
degrees of freedom, which would make theses steps unnecessary, if you are 
comfortable with using randomization tests.

 

Good luck!

Mike

 

Michael Collyer

Associate Professor

Biostatistics
Department of Biology
Western Kentucky University
1906 College Heights Blvd. #11080 
Bowling Green, KY 42101-1080
Phone: 270-745-8765; Fax: 270-745-6856
Email: michael.coll...@wku.edu <mailto:michael.coll...@wku.edu> 

 

On Apr 5, 2016, at 10:16 AM, Brenna Hays <bkhays...@gmail.com 
<mailto:bkhays...@gmail.com> > wrote:

 

I have been reading up on MANOVA and come across the common complication 
requiring a large number of degrees of freedom. After performing Procrustes 
superimpositions on my landmark configurations, along with my small sample 
sizes, is not allowing me to perform MANOVA tests. 

 

I have read that one can fix this problem by replacing the coordinates with 
principal components. The coding from my information source is very vague, but 
I've been trying some different things. Below is my code - note the error 
message at the bottom. 

 

AISarray <- two.d.array(AIS.shape)

 

ID <- c(1, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3)

Depth <- c(3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5)

Region <- c(7, 8, 8, 8, 8, 8, 8, 8, 5, 5, 5)

RR <- c(2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2)

CDR <- c(2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1)

 

AISdf <- cbind(AISarray, ID, Depth, Region, RR, CDR)

 

specs <- as.factor(AISdf[,51])

depth <- as.factor(AISdf[,52])

region <- as.factor(AISdf[,53])

rr <- as.factor(AISdf[,54])

cdr <- as.factor(AISdf[,55])

 

AIS.PC <- prcomp(AISarray)

summary(manova(lm(AIS.PC~specs*region))) #NOT WORKING

Error in model.frame.default(formula = AIS.PC ~ specs * region, 
drop.unused.levels = TRUE) : 

  invalid type (list) for variable 'AIS.PC'

 

It seems MANOVA requires a data frame, but replacing the coordinates with 
principal components turns it into a list. I cannot find any other information 
on this matter. Any help would be much appreciated. 

Thanks, 

 

Brenna Hays

Research Assistant, Master's Student

Nova Southeastern University

 

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RE: [MORPHMET] Richard Reyment (1926-2016)

2016-03-31 Thread F. James Rohlf
Oh, that is a great loss. He has done very important early work in multivariate 
morphometrics. His work had a large influence on me when I was a graduate 
student.  A very enthusiastic worker on many subjects - quite impressive! I 
very much enjoyed my interactions with him especially when I visited him in 
Uppsala for two months. 


F. James Rohlf, Distinguished Professor, Emeritus. Ecology & Evolution
Research Professor, Anthropology
Stony Brook University

-Original Message-
From: Eric Delson [mailto:eric.del...@lehman.cuny.edu] 
Sent: Thursday, March 31, 2016 5:51 AM
To: morphmet@morphometrics.org
Subject: Re: [MORPHMET] Richard Reyment (1926-2016)

I also am saddened to hear of Prof. Reyment's death. He kindly aided me in 
Uppsala when I was traveling as a grad student to observe fossil primate 
specimens, and he showed me Chinese material from several sites including 
Zhoukoudian. I recall how he was complaining about the infighting between 
Stalinist and Maoist radical student groups on campus. It was only much later 
that I learned about his morphometric work through Les Marcus and others. He 
will be missed.
Eric Delson
CUNY & AMNH

On 3/31/2016 11:41 AM, Norman MacLeod wrote:
> It is with great sadness that I inform this community of the death of Richard 
> Reyment, who passed away at his home in Sollentuna, Sweden, just outside 
> Stockholm, on 30 March. A brief autobiography of Richard’s life and work is 
> available 
> at:https://urldefense.proofpoint.com/v2/url?u=http-3A__richardreyment.com_index.html=BQIFaQ=uxRm7bTqKzXs8e5WpHvdhQ=QsvmrqJR0YtjwRsCcawJg9FfJ-6mHfFhAx1IUIyo7A8=_1Nri_WOtwk2NSubYPK_nLTwqmbWMKYoFN67cslzX24=YWOQofIGSixW0D0Jq6wSq4Jj-VsjJ51nqZjcCk4LokY=
>   . I would not presume to improve on the information he has already provided 
> there other than to add that he was my good friend, a valued colleague and 
> true intellectual of unusually broad interests, abilities and 
> accomplishments. I often wince when I hear someone described as a “polymath” 
> these days as the term has become devalued through overuse. However, Richard 
> was a genuine polymath as his bibliography all too readily attests. Over a 
> career that spanned more than half a century Richard assimilated a vast body 
> of knowledge of about quantitative data analysis, morphometrics, 
> palaeontology, geology and a variety of other fields by remaining an active 
> and engaged researcher as well as a teacher, editor, author and 
> administrator. In pursuing these interests he had the good fortune to be able 
> to undertake this assimilation piece-by-piece, paper-by-paper, book-by-book 
> as these fields were developing; through their heydays at it were. Now, there 
> is simply too much information being published by too many people on too many 
> topics to allow anyone to develop the sort of synoptic understanding Richard 
> achieved for even a single speciality, much less half-a-dozen. People like 
> Richard are now passing from the scene. That is a tragedy for us all. 
> Possibly with one or two rare exceptions, we’ll not see their like again.
>
> Richard’s daughter Britt-Louse has informed me that his funeral will be held 
> in the next few weeks and will be attended only by the family.
>
> Norm MacLeod


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[MORPHMET] tpsRelw update to 1.62

2016-03-09 Thread F. James Rohlf
I have just uploaded version 1.62 of tpsRelw to the
http://life.bio.sunysb.edu/morph server. It fixes a problem with saving
aligned specimens in the .nts format. Thanks to Carlo Meloro for reporting
the problem.

 



F. James Rohlf, Distinguished Professor, Emeritus. Ecology & Evolution

Research Professor, Anthropology

Stony Brook University

 

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[MORPHMET] another tpsDig2 update

2016-03-06 Thread F. James Rohlf
I have just uploaded version 2.25 of tpsDig2 to the
http://life.bio.sunysb.edu/morph server. This fixes some problems (e.g.,
errors selecting some operations when no specimens had yet been loaded). I
also added an option to sound a "beep" when a landmark is digitized. Thanks
to Mauro Cavalcanti for bringing these to my attention.

 

____

F. James Rohlf, Distinguished Professor, Emeritus. Ecology & Evolution

Research Professor, Anthropology

Stony Brook University

 

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[MORPHMET] tpsDig2 update to version 2.24

2016-03-05 Thread F. James Rohlf
I have just uploaded version 2.24 of tpsDig2 to the
http://life.bio.sunysb.edu/morph server. This fixes a problem in the context
menu where the option to delete a landmark was not listed after on resampled
the points in a curve. Thanks to Miriam Zelditch for letting me know that
there was this problem.

 

Reminder: use just the 32 bit versions of the tps software for now.

 



F. James Rohlf, Distinguished Professor, Emeritus. Ecology & Evolution

Research Professor, Anthropology

Stony Brook University

 

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[MORPHMET] tps series - 64 bit problems

2016-02-24 Thread F. James Rohlf
It is apparent that the compiler I used to generate the 64 bit versions of
the tps software has some serious problems. If you run into any problems
using them please try switching back to the normal 32 bit versions until I
can obtain an updated version of the compiler and associated libraries. If
they work for you then they are ok to use but many experience crashes.



F. James Rohlf, Distinguished Professor, Emeritus. Ecology & Evolution

Research Professor, Anthropology

Stony Brook University

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[MORPHMET] tpsUtil update

2016-01-31 Thread F. James Rohlf
I have just uploaded version 1.68 of tpsUtil to the
http://life.bio.sunysb.edu/morph server. Small change: I just added another
error message for an inconsistency in the numbers of landmarks in a tps
file.

 



F. James Rohlf, Distinguished Professor, Emeritus. Ecology & Evolution

Research Professor, Anthropology

Stony Brook University

 

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RE: [MORPHMET] Mahalanobis distance in cluster analysis of shape variables

2016-01-30 Thread F. James Rohlf
The distinction is that Mahalanobis distance should be thought of as a 
statistical distance. For a single variable it is like a z-score (a difference 
divided by a standard deviation). It is not a measure of the absolute amount of 
difference. In the multivariate case Mahalanobis distance is relative to the 
amount of the amount of variation in the direction of the difference (that is 
what taking into account within-group covariation gives you).

 

Both Mahalanobis and Euclidean distances are valid. It depends on what you wish 
“distance” to mean. In morphometrics do you want to cluster based on how 
similar shapes are (in terms of  distance in Kendall shape space) or based on 
the degree of statistical overlap in population samples (e.g., the degree to 
which specimens from the two groups might be misidentified).

 

A practical problem with Mahalanobis distance in many morphometric studies is 
that it requires large sample sizes within groups because landmark data is 
usually high dimensional and thus very large samples are needed for reliable 
results.

 



F. James Rohlf, Distinguished Professor, Emeritus. Ecology & Evolution

Research Professor, Anthropology

Stony Brook University

 

From: Elahep [mailto:ellie.parv...@gmail.com] 
Sent: Saturday, January 30, 2016 7:14 AM
To: MORPHMET <morphmet@morphometrics.org>
Cc: ellie.parv...@gmail.com; jkunk...@une.edu
Subject: Re: [MORPHMET] Mahalanobis distance in cluster analysis of shape 
variables

 

Dear Joseph,

 

Thanks for your detailed explanation. As it is recommended by Claude in 
"morphometrics with R" (2008) it's better to use the Mahalanobis distance for 
clustering group means, because this will be scaled by the within-group 
variance-covariance. In my analysis, I calculated the mean value of relative 
warp scores for each population and then carried out a UPGMA cluster analysis 
based on the Euclidian distance and results were satisfying for me and they 
were congruent with my other results. According to the book and other articles 
I ran the same analysis but based on the Mahalanobis distance in PAST software, 
but unfortunately whenever I ran the analysis the software error "Invalid 
floating point operation" appeared!! so I couldn't see the Mahalanobis's 
cluster!! (I couldn't realize why this error happens)

Euclidian distance worked for me, but I was just curious to understand if my 
analyses is statistically meaningful!!

 

Thanks again for your answer,

Elahe

On Saturday, January 30, 2016 at 5:12:46 PM UTC+3:30, Joseph Kunkel wrote:

I can not speak directly to why it is frequently used in GM cluster analysis 
but I would like to mention how I look at Mahalanobis distance based on its 
calculation. 

Mahalanobis distance is not a pure distance metric like Euclidian or Manhattan 
distance, as you have stated it is ‘standardized’.  What doe that really mean?  
It sounds supeficially good. 

One way of computing it is to rotate the k-landmark data set to simplest form 
treating the landmarks as factors.  This way would consider all landmarks to 
have a common covariance structure in XY or XYZ in three dimensions.  That is a 
already a streetch, since not all landmarks can be assumed to have the same 
covariance structure.  In addition the landmarks have all been already centered 
about their centroid and rotated to coincide, which has eliminated a dgeree of 
freedom of variability that can have consequences.   

Furthermore not all species landmarks can be expected to have the same 
covariance structure, which is an assumption made in the ordinary Mahalanobis 
distance application to strut analysis between populations or species.  The 
assumption of similar data structure of course applies to the null hypothesis 
where there is no difference.  The typical statistical test explodes when the 
null hypothesis is falsified so just when you want the Mahalanobis distance 
metric to be accurate it starts misbehaving. 

After rotation to simplest axes one does an 1 df F-test between each of the 
landmarks.  These tests are all independent so they can be summed together to 
produce a k df F-test which is Mahalonobis D squared.So Mahalonobis D is 
the square root of the sum of independent F-tests, but those F-tests are based 
on all sorts of assumptions about the variance of the landmarks.  I immagine on 
could modify calculation of D by limiting the sum over the top 95 or 99% 
variance components of the principal components. 

Many times applications of analytical techniques are judged by whether they 
‘work’ or not.   If a clustering method works for you, use it(?).  I am of the 
opinion that I use statistics to convince myself rather than the audience.   A 
confluence on many arguments is used to make a case. 

Joe 

-·.  .· ·.  .><º>·.  .· ·.  .><º>·.  .· ·.  .><º> .··.· >=-   
=º}>< 
Joseph G. Kunkel, Re

[MORPHMET] tpsRelw update

2015-12-30 Thread F. James Rohlf
I have just uploaded version 1.62 of tpsRelw to the
http://life.bio.sunysb.edu/morph site.

 

Just one change - a problem that caused the scale factor to be ignored in
computing centroid size was fixed. (In the prior version I had tried to be a
little too clever in making the software tolerant of using the wrong decimal
separation character.) Thanks to Luciano Brambilla for discovering the
problem.

 

I hope everyone has a healthy and productive 2016!

 

--

F. James Rohlf New email: f.james.ro...@stonybrook.edu

Distinguished Professor, Emeritus. Dept. of Ecol. & Evol.

& Research Professor. Dept. of Anthropology

Stony Brook University 11794-4364

The much revised 4th editions of Biometry and Statistical Tables are now
available:

 <http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal>
http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal

 
<http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-ro
hlf>
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RE: [MORPHMET] Invalid floating point operation

2015-12-12 Thread F. James Rohlf
I can't tell unless I see the tps file but such problems are usually due to the 
setting for the decimal character: . or ,. There is an option in tpsRelw that 
allows you to set it to match what is in your tps file.

--
F. James Rohlf New email: f.james.ro...@stonybrook.edu
Distinguished Professor, Emeritus. Dept. of Ecol. & Evol.
& Research Professor. Dept. of Anthropology
Stony Brook University 11794-4364
The much revised 4th editions of Biometry and Statistical Tables are now 
available:
http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal
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 Please consider the environment before printing this email 

-Original Message-
From: Kandace Hugentobler [mailto:kandace.hugentob...@gmail.com] 
Sent: Friday, December 11, 2015 8:34 PM
To: MORPHMET <morphmet@morphometrics.org>
Subject: [MORPHMET] Invalid floating point operation

Hi,

I am currently working on a tps file and trying to do the relative warps and I 
keep getting an "Invalid floating point operation." error. I looked over the 
tps file and couldn't see errors, but I may be missing something. TpsRelw is 
working with a different tps file. I tried restarting the computer and 
redownloading tps relw. Do you have any suggestions?

Thanks,

Kandace

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[MORPHMET] tpsDig2

2015-11-13 Thread F. James Rohlf
For some reason people have not been able to download the tpsDig2 32 bit
software (a server warning). I just uploaded a fresh copy of the same
version (2.22) and it seems to download ok now.

 

--

F. James Rohlf New email: f.james.ro...@stonybrook.edu

Distinguished Professor, Emeritus. Dept. of Ecol. & Evol.

& Research Professor. Dept. of Anthropology

Stony Brook University 11794-4364

The much revised 4th editions of Biometry and Statistical Tables are now
available:

 <http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal>
http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal

 
<http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-ro
hlf>
http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-roh
lf

P Please consider the environment before printing this email 

 

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[MORPHMET] The interpretation of PCs individually

2015-10-31 Thread F. James Rohlf
I recently responded privately to a message at interpretation of individual
PCs but I thought my response might be of interest to the group.

 

The problem with highlighting and interpreting the "most important" PCs is
that it implies that the individual PCs are likely to have special
biological meaning. There is no reason for that to be true (although people
can and commonly do find interpretations of almost any pattern). One should
remember that PCA is a mathematical/statistical tool to project as much as
possible of the variation in a multivariate space down onto as few
dimensions as possible. Because it is a projection  it is essential that the
scales of the axes are the same when plotting PC1 vs. PC2, etc.). No
biological model is involved in the definition of a PCA. It is just an
elegant mathematical partitioning of the overall variance into orthogonal
(uncorrelated, not independent) components. There undoubtedly are
interesting directions in that space but for biological applications it does
not seem likely that the underlying dimensions should happen to be perfectly
uncorrelated. A user would have to justify that assumption before they
should try to interpret individual PCs. It is often done but that does not
make it correct.

 

A related thing to remember is that within the plot of the low-dimensional
space is that the interesting directions to interpret need not be parallel
to the axes. Especially true for data with samples within and among species.
The PCs may not align to either the main directions of variation within
species or among species. They will be some compromise and thus even the
first axis may not be that interpretable except for relatively homogeneous
samples. I saw an interesting example of that a few years ago in a study in
which the variation within one group of species was parallel to PC2 but
variation within the other major group of species was equally along PC1 and
PC2 (i.e., the  major dimension of variation in the 2nd group was at an
angle of about 45 degrees to the PC1 and PC2 axes.

 

 

------

F. James Rohlf New email: f.james.ro...@stonybrook.edu

Distinguished Professor, Emeritus. Dept. of Ecol. & Evol.

& Research Professor. Dept. of Anthropology

Stony Brook University 11794-4364

The much revised 4th editions of Biometry and Statistical Tables are now
available:

 <http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal>
http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal

 
<http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-ro
hlf>
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RE: [MORPHMET] Appending TPS files

2015-10-20 Thread F. James Rohlf
That option in tpsUtil will do what you wish. The trick is just that the files 
must be in the same directory. You just select the directory – not individual 
files because the program will then display a list of all the tps files in that 
directory and you can select which ones should be combined and in which order.

 

--

F. James Rohlf New email: f.james.ro...@stonybrook.edu

Distinguished Professor, Emeritus. Dept. of Ecol. & Evol.

& Research Professor. Dept. of Anthropology

Stony Brook University 11794-4364

The much revised 4th editions of Biometry and Statistical Tables are now 
available:

http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal

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P Please consider the environment before printing this email 

 

From: Daniel Svozil [mailto:dpsvo...@gmail.com] 
Sent: Tuesday, October 20, 2015 2:03 AM
To: MORPHMET <morphmet@morphometrics.org>
Subject: [MORPHMET] Appending TPS files

 

Hi All,

 

So I am facing a dilemma, where I have digitized landmarks on 90 individuals, 
for each of 11 populations. The images and the associated TPS file for each 
population is located in a separate folder (i.e. one folder per population).

 

Now, I want to combine the TPS files from each population, into one single TPS 
file. Is this possible? If so, how do I do it? 

 

I have tried clicking append, (File>Save data>Append) in TPS Dig2, as well as 
the Append files option in the drop down menu of TPS Util. In both cases, I get 
the dialog box, where it asks for an input directory and an output directory, 
however, no option to select multiple TPS files is available. 

 

It occurred to me that perhaps the separate TPS files had to be located in the 
same folder, (I did not check the "include path" option when I created each 
individual TPS file), but even so, when I repeat the Append files steps listed 
above, I am still presented with the input/output directory options and only 
the one TPS that was originally associated with that folder (i.e. pop1 TPS file 
is the only one available in the pop1 directory, even though I have copied the 
pop2 TPS file and images over, as well).

 

Any suggestions? Or will I have to start over with a TPS file containing all 
images from all the populations as one?

 

Kind regards,

 

 

Daniel.

 

 

 

 

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[MORPHMET] tpsUtil update - 1.64

2015-09-26 Thread F. James Rohlf
A new update, 1.64, has just been uploaded to the
http://life.bio.sunysb.edu/morph server.

This fixes a problem in the "Delete/reorder landmarks" option. Thanks to
Andrea Cardini for reporting the problem.

 

------

F. James Rohlf New email: f.james.ro...@stonybrook.edu

Distinguished Professor, Emeritus. Dept. of Ecol. & Evol.

& Research Professor. Dept. of Anthropology

Stony Brook University 11794-4364

The much revised 4th editions of Biometry and Statistical Tables are now
available:

 <http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal>
http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal

 
<http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-ro
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[MORPHMET] tpsDig2 update 2.20

2015-09-09 Thread F. James Rohlf
A new version of tpsDig2 has been uploaded to
http:life.bio.sunysb.edu/morph. The only changes reflect an observation made
by Ingrid Grueso that one may unknowingly click on the "M" button to
indicate a missing landmark when one intends to click on the landmark
digitizing button right next to it. I have added a new entry on the Options
menu where one can specify whether a pop-up confirmation window should be
displayed when one clicks on the "M" button. Click on "OK" to add a missing
landmark or "Cancel" to ignore and return to digitizing landmarks.

 

--

F. James Rohlf New email: f.james.ro...@stonybrook.edu

Distinguished Professor, Emeritus. Dept. of Ecol. & Evol.

& Research Professor. Dept. of Anthropology

Stony Brook University 11794-4364

The much revised 4th editions of Biometry and Statistical Tables are now
available:

 <http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal>
http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal

 
<http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-ro
hlf>
http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-roh
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[MORPHMET] tpsUtil update 1.63

2015-09-08 Thread F. James Rohlf
I have just uploaded tpsUtil 1.63 to the life.bio.sunysb.edu/morph server.
It adds a feature recently suggested by Andrea Cardini. There is now a plot
that shows which landmarks are being deleted or retained and what their new
numbers of the retained landmarks will be. 

 

Note: this module works for both 2D and 3D data though the plot only uses
the X & Y coordinates.

 

--

F. James Rohlf New email: f.james.ro...@stonybrook.edu

Distinguished Professor, Emeritus. Dept. of Ecol. & Evol.

& Research Professor. Dept. of Anthropology

Stony Brook University 11794-4364

The much revised 4th editions of Biometry and Statistical Tables are now
available:

 <http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal>
http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal

 
<http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-ro
hlf>
http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-roh
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[MORPHMET] tpsUtil again

2015-08-27 Thread F. James Rohlf
I have uploaded version 1.62 to the SBU server. It fixes a problem with
appending NTS files that contain blank lines. I have also modified the
delete/reorder specimens and the landmarks options so they allow a more
convenient (and standard) multiple selection.

 

Thanks again to Andrea Cardini for pointing out the problem and making the
suggestions. 

 

--

F. James Rohlf New email: f.james.ro...@stonybrook.edu

Distinguished Professor, Emeritus. Dept. of Ecol.  Evol.

 Research Professor. Dept. of Anthropology

Stony Brook University 11794-4364

The much revised 4th editions of Biometry and Statistical Tables are now
available:

 http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal
http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal

 
http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-ro
hlf
http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-roh
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[MORPHMET] one more update: tpsTree

2015-08-22 Thread F. James Rohlf
Version 1.22 now has 32 and 64 bit executables. Relatively minor changes to
the program (mostly fixing memory leaks) but many changes were made to the
help file. It should be more helpful now.

 

Again, the files can be downloaded from http://life.bio.sunysb.edu/morph.

 

This will be the last of the high priority updates to the tps programs. The
other programs (e.g., tpsSplin, tpsBias, tpsPower, consistency) will be
updated later - unless there is a specific request for one or more of the
other tps programs.

--

F. James Rohlf New email: f.james.ro...@stonybrook.edu

Distinguished Professor, Emeritus. Dept. of Ecol.  Evol.

 Research Professor. Dept. of Anthropology

Stony Brook University 11794-4364

The much revised 4th editions of Biometry and Statistical Tables are now
available:

 http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal
http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal

 
http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-ro
hlf
http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-roh
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[MORPHMET] tpsDig2 update to version 2.19

2015-08-20 Thread F. James Rohlf
An update to tpsDig2 has just been uploaded to the
http://life.bio.sunysb.ed/morph server. Some relatively small changes to
both the program (both 32 and 64 bit versions) and the help file. A
printable version of the help file is also included to serve as a user
manual

 

--

F. James Rohlf New email: f.james.ro...@stonybrook.edu

Distinguished Professor, Emeritus. Dept. of Ecol.  Evol.

 Research Professor. Dept. of Anthropology

Stony Brook University 11794-4364

The much revised 4th editions of Biometry and Statistical Tables are now
available:

 http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal
http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal

 
http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-ro
hlf
http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-roh
lf

P Please consider the environment before printing this email 

 

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[MORPHMET] change of email

2015-08-20 Thread F. James Rohlf
In case viewers did not notice the note below next to my name in prior
postings on morphmet, my email address is changing.

 

The new one is f.james.ro...@stonybrook.edu
mailto:f.james.ro...@stonybrook.edu 

 

The old one (ro...@life.bio.sunysb.edu mailto:ro...@life.bio.sunysb.edu )
is now being forwarded to the new address so that will also work for a while
-  but that will end in early September.

 

Sorry for any inconvenience. Now I have to find all the places where my old
address is displayed. The 

http://life.bio.sunysb.edu/morph

server will still function as before - just the email is changed. 

--

F. James Rohlf New email: f.james.ro...@stonybrook.edu

Distinguished Professor Emeritus, Dept. of Ecol.  Evol.

Research Professor, Dept. of Anthropology

Stony Brook University 11794-4364

The much revised 4th editions of Biometry and Statistical Tables are now
available:

 http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal
http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal

 
http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-ro
hlf
http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-roh
lf

P Please consider the environment before printing this email 

 

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[MORPHMET] tpsUtil update to 1.61

2015-08-17 Thread F. James Rohlf
Continuing progress: I have just uploaded version 1.61 of tpsUtil to the
Stony Brook server. Both 32 and 64 bit versions are now available.  Small
changes to the program and useful changes to the help file were made.

 

--

F. James Rohlf New email: f.james.ro...@stonybrook.edu

Distinguished Professor Emeritus, Dept. of Ecol.  Evol.

Research Professor, Dept. of Anthropology

Stony Brook University 11794-4364

The much revised 4th editions of Biometry and Statistical Tables are now
available:

 http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal
http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal

 
http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-ro
hlf
http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-roh
lf

P Please consider the environment before printing this email 

 

-- 
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[MORPHMET] More tps updates

2015-08-16 Thread F. James Rohlf
I have just uploaded to http://life.bio.sunysb.edu/morph new versions of
tpsSmall, tpsRelw, and tpsRegr for both 32 and 64 bits. tpsRegr has a
problem with the 'most recently used files' feature of the files menu fixed.
Its help file has also been updated. The other programs had just minor
tweaks.  The main change was to use a new version of the compiler and a more
automated way to create the install files - which should reduce the chance
of errors in the creation of these files.

Changes to the other programs in the tps series should be available soon.
Now is a good time to send me suggestions and/or complaints.

Note my new email address shown below. The present one should continue to
work until early September.
--

F. James Rohlf New email: f.james.ro...@stonybrook.edu
mailto:f.james.ro...@stonybrook.edu 
Distinguished Professor Emeritus, Dept. of Ecol.  Evol.
Research Professor, Dept. of Anthropology
Stony Brook University 11794-4364

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[MORPHMET] Update of tpsPLS to 1.23

2015-08-16 Thread F. James Rohlf
I have just uploaded version 1.23 of tpsPLS to the
http://life.bio.sunysb.edu/morph server. A 64 bit version is now available.
Minor changes to the program. An option to specify the decimal character is
included.  Fixed some corrupted equations in the details topic in the help
file.

 

--

F. James Rohlf New email: f.james.ro...@stonybrook.edu

Distinguished Professor Emeritus, Dept. of Ecol.  Evol.

Research Professor, Dept. of Anthropology

Stony Brook University 11794-4364

The much revised 4th editions of Biometry and Statistical Tables are now
available:

 http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal
http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal

 
http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-ro
hlf
http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-roh
lf

P Please consider the environment before printing this email 

 

 

-- 
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[MORPHMET] tpsTri update

2015-08-16 Thread F. James Rohlf
Version 1.28 of tpsTri has been uploaded to the
http://life.bio.sunysb.edu/morph server. It now includes both 32 and 64 bit
versions. The help file has been updated and minor changes to the program
itself (allows for selection of the decimal character and location of the
tpsTri.ini file.

 

--

F. James Rohlf New email: f.james.ro...@stonybrook.edu

Distinguished Professor Emeritus, Dept. of Ecol.  Evol.

Research Professor, Dept. of Anthropology

Stony Brook University 11794-4364

The much revised 4th editions of Biometry and Statistical Tables are now
available:

 http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal
http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal

 
http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-ro
hlf
http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-roh
lf

P Please consider the environment before printing this email 

 

-- 
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[MORPHMET] tpsSmall update + more soon

2015-08-11 Thread F. James Rohlf
I have just uploaded ver. 1.33 of tpsSmall. As before, there are 32 and 64
bit versions. The installations are now setup so that one can, if one
wishes, install both versions on the same computer. However, for most users
there is no real point to install 32  64 bit versions on the same computer
but handy for those who wish to test software and find problems that they
can report back to me. 

 

Note: the file names have been changed slightly so it is important that the
old version be uninstalled. I am using a new program to generate install
files and I expect it to do a better job of uninstalling. Note also that the
64 bit version does require a 64 bit version of Windows.

 

tpsSmall is the simplest program in the tps series so I have uploaded it
first. I am now using a more automatic method for building both versions and
their installation files.  If no installation problems are reported then I
will be uploading similar updates to most of the rest of the tps programs.

 

For users, this is an optional update as there are no important changes in
the computations performed by the software.

--

F. James Rohlf, Distinguished Professor Emeritus, Dept. of Ecol.  Evol.

Research Professor, Dept. of Anthropology

Stony Brook University 11794-4364

The much revised 4th editions of Biometry and Statistical Tables are now
available:

 http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal
http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal

 
http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-ro
hlf
http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-roh
lf

P Please consider the environment before printing this email 

 

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[MORPHMET] tpsDig2 update

2015-07-18 Thread F. James Rohlf
I have just uploaded version 2.19 of the tpsDig2 program to the
http://life.bio.sunysb.edu/morph server.

 

This version includes both 32 and 64 bit versions. It also fixes the INI
file storage problem (the help file also describes a way to force the
program to still use the program's folder - seems necessary on some
computers). Using the user's documents folder is more standard and also more
desirable because it enables different users of the same computer to save
different preferences.

 

There were also a number of small changes. For example, there are now
additional image enhancement options. The fit to window option is now
retained when moving from one image to the next. A printable user manual is
also included as a PDF file. It has identical information as contained in
the help file. It is just a different format that some may find more
convenient.

 

Thanks to Lucia Alarcon Rios for letting me know that at least some Windows
7 computers still require the INI file to be placed with the program. Again,
please let me know if there are problems with this latest version.

 

--

F. James Rohlf, Distinguished Professor Emeritus, Dept. of Ecol.  Evol.

Research Professor, Dept. of Anthropology

Stony Brook University 11794-4364

The much revised 4th editions of Biometry and Statistical Tables are now
available:

 http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal
http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal

 
http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-ro
hlf
http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-roh
lf

P Please consider the environment before printing this email 

 

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[MORPHMET] tpsRelw one more time!

2015-06-30 Thread F. James Rohlf
I have just uploaded version 1.58 to the life.bio.sunysb.edu server. The
only important change is that it now works with Windows XP.

 

Thanks to Mauro Cavalcanti for testing it on his WinXP computers. Also
thanks to Jesus Marugán and others for their help with passing along the
exact text of the error messages.

 

--

F. James Rohlf, Distinguished Professor Emeritus, Dept. of Ecol.  Evol.

Research Professor, Dept. of Anthropology

Stony Brook University

The much revised 4th editions of Biometry and Statistical Tables are now
available:

 http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal
http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal

 
http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-ro
hlf
http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-roh
lf

P Please consider the environment before printing this email 

 

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[MORPHMET] tpsRelw problem fixed!

2015-06-29 Thread F. James Rohlf
I just uploaded a new version (1.57) of tpsRelw to the
life.bio.sunysb.edu/morph site.  The problem with being unable to close a
window should now be fixed. As always, it is best to uninstall the old
version before installing the new one.

 

Sorry for the delay in fixing the problem but my Internet access was not
very good at the Galapagos or Machu Picchu. The rocking of the boat and then
the thin oxygen did not help either. However, they were very interesting
places to visit!

--

F. James Rohlf, Distinguished Professor Emeritus, Dept. of Ecol.  Evol.

Research Professor, Dept. of Anthropology

Stony Brook University

The much revised 4th editions of Biometry and Statistical Tables are now
available:

 http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal
http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal

 
http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-ro
hlf
http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-roh
lf

P Please consider the environment before printing this email 

 

-- 
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To unsubscribe from this group and stop receiving emails from it, send an email 
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Re: [MORPHMET] Problem with tpsRelw v1.56

2015-06-20 Thread F. James Rohlf


Sorry for the problems with tpsRelw. Unfortunately i an in Equador now and soon 
will be in Peru.  I will  probably not be able to upload a fix until i return 
on the 26th.  I would appreciate info about those computers with a problem as i 
cannot get it to fail on any of my computers using win7 or win8.1.
---F. James RohlfDistinguished Professor Emeritus,Ecology  
EvolutionResearch Professor, Anthropology Stony Brook University

 Original message 
From: Mauro Cavalcanti mauro...@gmail.com 
Date: 06/19/2015  9:20 AM  (GMT-05:00) 
To: Nico Posnien nico.posn...@gmail.com 
Cc: MORPHMET morphmet@morphometrics.org 
Subject: Re: [MORPHMET] Problem with tpsRelw v1.56 

Dear Nico  ALL,

Running the program in administrador mode does not solve the problem for me, 
under WinXP. And I insist -- this problem does *not* appear in any other 
program from Jim Rohlf's TPS Series. It affects only the latest version of 
tpsRelw.

Best regards,

2015-06-19 6:34 GMT-03:00 Nico Posnien nico.posn...@gmail.com:
Dear all, Same problem here. Same error message. For me it is not even possible 
to do any analysis. Does not seem to be a Windows XP specific problem since I 
run Windows 8.1. Is it possible to re-upload a previous version of tpsRelw? 
Thanks a lot! Cheers,Nico Von: Mauro Cavalcanti [mailto:mauro...@gmail.com] 
Gesendet: Mittwoch, 17. Juni 2015 23:28
An: MORPHMET
Betreff: [MORPHMET] Problem with tpsRelw v1.56 Dear ALL,I just installed the 
latest version of tpsRelw (v1.56) on my old (but faithful) Windows XP computer 
but stumbled upon a strange problem: Every time I attempt to close either the 
program's  main window or the About dialog box, I got the error message: 
Unable to write to C:\Documents and Settings\Mauro 
Cavalcanti\tps\tpsRelw.ini. This means that I cannot exit the program except 
by killing the running process using Windows task manager. I do not have such 
problem with any other program in the tpsSeries, installed on the same 
machine.Any hints?Best regards,

-- Dr. Mauro J. Cavalcanti
E-mail: mauro...@gmail.com
Web: http://sites.google.com/site/maurobio-- 
MORPHMET may be accessed via its webpage at http://www.morphometrics.orgTo 
unsubscribe from this group and stop receiving emails from it, send an email to 
morphmet+unsubscr...@morphometrics.org.



-- 

MORPHMET may be accessed via its webpage at http://www.morphometrics.org




To unsubscribe from this group and stop receiving emails from it, send an email 
to morphmet+unsubscr...@morphometrics.org.




-- 
Dr. Mauro J. Cavalcanti
E-mail: mauro...@gmail.com
Web: http://sites.google.com/site/maurobio




-- 

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[MORPHMET] new publication

2015-06-12 Thread F. James Rohlf
for those using my tps software, the following publication may be a convenient 
thing to site.

http://dx.doi.org/10.4404/hystrix-26.1-11264

-
F. James Rohlf, 
Distinguished Professor, Emeritus
Dept. of Ecology  Evolution
Research Professor, Dept of Anthropology
Stony Brook University

-- 
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[MORPHMET] another tpsRelw update - 1.56

2015-06-10 Thread F. James Rohlf
I have uploaded a new version of tpsRelw with several annoying problems
fixed (I hope). Please let me know if you have difficulty using this
software. Note: I may not be responsive right away because I expect to have
only intermittent Internet service for the next two weeks.

 

--

F. James Rohlf, Distinguished Professor Emeritus, Dept. of Ecol.  Evol.

Research Professor, Dept. of Anthropology

Stony Brook University

The much revised 4th editions of Biometry and Statistical Tables are now
available:

 http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal
http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal

 
http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-ro
hlf
http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-roh
lf

P Please consider the environment before printing this email 

 

-- 
MORPHMET may be accessed via its webpage at http://www.morphometrics.org

To unsubscribe from this group and stop receiving emails from it, send an email 
to morphmet+unsubscr...@morphometrics.org.


[MORPHMET] An important update for tpsRelw

2015-05-29 Thread F. James Rohlf
Version 1.55 of tpsRelw has been uploaded to the
http://life.bio.sunysb.edu/morph server.

 

This version is available for both 32-bit and 64-bit versions of Windows.
New features include Bookstein's (2015) suggestion of plotting the log of
the variance of the partial warps against the log their corresponding
bending energies (this seems quite useful and informative for my data). You
can now select subsets of landmarks. Problems with the display of equations
in prior versions has been fixed. Note: it is best to uninstall the old
version before installing the new version. Note that the executables have
the same names so both versions cannot be installed on the same computer
without some careful renaming of files.

 

Please let me know of any problems or additions that would be useful.

 

--

F. James Rohlf, Distinguished Professor Emeritus, Stony Brook University

The much revised 4th editions of Biometry and Statistical Tables are now
available:

 http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal
http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal

 
http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-ro
hlf
http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-roh
lf

P Please consider the environment before printing this email 

 

-- 
MORPHMET may be accessed via its webpage at http://www.morphometrics.org

To unsubscribe from this group and stop receiving emails from it, send an email 
to morphmet+unsubscr...@morphometrics.org.


[MORPHMET] RE: tpsDig on a Mac using wine

2015-05-19 Thread F. James Rohlf
Thanks!  Does that also work for 64 bit versions of the programs? tpsSmall is a 
simple program, would you mind testing the 64 bit version? I am also, of 
course, curious about how it works on the other emulators. I try to program in 
a very standard way for maximum compatibility with Windows.

 

--

F. James Rohlf, Distinguished Professor Emeritus, Stony Brook University

The much revised 4th editions of Biometry and Statistical Tables are now 
available:

http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal

http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-rohlf

P Please consider the environment before printing this email 

 

From: Joseph Kunkel [mailto:j...@bio.umass.edu] 
Sent: Tuesday, May 19, 2015 3:35 PM
To: ro...@life.bio.sunysb.edu; morphmet@morphometrics.org
Cc: Joe Kunkel
Subject: tpsDig on a Mac using wine

 

Dear Jim and Morphmet,

 

I just want to comment on using tpsDig on a Mac.  tps Dig is my go-to software 
for 2-D landmark digitizing of images.  To digitize I would previously have to 
use one of my PCs in my lab which was often a pain.  I was reluctant to use 
several of the PC-on-your-Mac options because they meant partitioning your disc 
or in some sense running two separate worlds on your Mac which always made me 
nervous for several security software reasons.  

Using the emulation program, wine (https://www.winehq.org/), has changed 
everything.  It works as a unix program run from your Mac Terminal console.  I 
have tested several of the tps suite of software from Rohlf and they work like 
a charm.  One trick however to get around the need for a ‘right-click’ in 
tpsDig is to redefine the right-click as something else such as a track-pad tap 
which works like a charm.

Thank you wine for allowing me to ‘go home’ and do tpsDig on my Macs!

-·.  .· ·.  .º·.  .· ·.  .º·.  .· ·.  .º .··.· =-   
=º}

Joseph G. Kunkel, Emeritus Professor

Biology Department

UMass Amherst 

Amherst MA 01003

j...@bio.umass.edu mailto:j...@bio.umass.edu 

 

 

 

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[MORPHMET] tpsSmall and tpsSuper updates - 64bit also

2015-05-19 Thread F. James Rohlf
I have just uploaded new versions of the tpsSmall and tpsSuper programs to
the life.bio.sunysb.edu/morph server.

 

These make it easier to specify the character (. or ,) that is to be used as
the decimal separator character. I have received a number of questions
lately due to mismatched decimal characters. I have also uploaded 64 bit
versions of these two programs. The 64 bit version is unlikely to make much
difference in running the tpsSmall program but can be important for the
tpsSuper program if you have a large number of large images. Similar updates
are planned for the other tps programs.

 

Including 64 bit versions is an experiment. I would appreciate feedback
about whether including 64 bit versions is useful. If not, then I will not
bother with 64 bit versions for the other tps programs as it does take a
little more effort to keep track of two versions.

 

--

F. James Rohlf, Distinguished Professor Emeritus, Stony Brook University

The much revised 4th editions of Biometry and Statistical Tables are now
available:

 http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal
http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal

 
http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-ro
hlf
http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-roh
lf

P Please consider the environment before printing this email 

 

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[MORPHMET] tpsDig2 update to 2.18

2015-03-31 Thread F. James Rohlf
I have just uploaded version 2.18 of tpsDig2 to the
life.bio.sunysb.edu/morph server.

 

At the suggestion of Dean Adams, I have added a provision for missing
landmarks. They are coded as the coordinates -1,-1 in the output file. Check
the help file for more information.  The geomorph package will have an
option that will convert them to its format. However, the other tps programs
do not yet know how to handle such missing landmarks.

 

I have also added an option so that the image will be zoomed + or - as
necessary to fit the window. Should make the usage more convenient.

 

Please keep sending me suggestions and bug reports!



F. James Rohlf, Distinguished Professor, Emeritus. Ecology  Evolution

Research Professor, Anthropology

Stony Brook University

 

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RE: [MORPHMET] PC Ranks in Evolutionary PCA

2015-03-28 Thread F. James Rohlf
Procrustes superimposition only removes isometric size variation. Shape changes 
that are a function of size (allometry) are not removed so a regression of some 
sort is needed.


F. James Rohlf, Distinguished Professor, Emeritus. Ecology  Evolution
Research Professor, Anthropology
Stony Brook University

-Original Message-
From: Ryan Felice [mailto:ryanfel...@gmail.com] 
Sent: Friday, March 27, 2015 7:34 AM
To: Alex Marshall
Cc: morphmet@morphometrics.org
Subject: Re: [MORPHMET] PC Ranks in Evolutionary PCA

Hi Alex,

I'm assuming that your shape data are landmark configurations that have been 
subjected to a Procrustes superimposition. is that correct?
If so, I dont think the regression you described is really necessary- 
Procrustes analysis will remove the effects of size, orientation, and position.

What software are you using for your analysis? you might find it easier/more 
streamlined to use the phyl.pca function in the phytools R package. If you use 
that function, make sure that you are using the original shape data and not the 
independent contrasts of shape data.

Good luck!

-Ryan
Ryan N. Felice, PhD
Ohio University Department of Biological Sciences
107 Irvine Hall
Athens, OH 45701
www.rnfelice.com
ryanfel...@gmail.com
(201)981-8642



On Fri, Mar 27, 2015 at 7:49 AM, Alex Marshall alpmar...@googlemail.com wrote:
 Hello everyone,
 I'm a MSci student new to morphometrics and this group. I'm studying 
 morphological integration in squamate crania and one of the things I'd like 
 to do is an Evolutionary PCA of all my species, accounting for phylogeny and 
 allometry.

 I think I do this correctly but in the PCA results the PCs are not ranked by 
 proportion of variance e.g. PC5 has greater % variance that PCs 3  4. Is 
 this normal?

 To conduct the evolutionary PCA I created independant contrasts of all my 
 shape data, regressed centroid size on shape and conducted PCA on the 
 residuals. After this I applied the resultant PC scores to another PCA of my 
 original data.

 Would anyone kindly confirm if this is the right way to do it?

 Many thanks,

 Alex Marshall
 MSci Student
 University College London
 alexander.marshall...@ucl.ac.uk

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[MORPHMET] tpsUtil update

2015-03-11 Thread F. James Rohlf
Another update to tpsUtil upload to the Stony Brook server. This fixed a
problem in the calculation of areas option. Thanks to Russell Minton for
pointing out the problem. New version is 1.60.

 



F. James Rohlf, Distinguished Professor, Emeritus. Ecology  Evolution

Research Professor, Anthropology

Stony Brook University

 

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[MORPHMET] tpsUtil update 1.59

2015-03-04 Thread F. James Rohlf
I have just uploaded a new version (1.59) to the Stony Brook Morphometrics
server. It enables the delete  reorder landmarks operation to be applied to
3D data.  Thanks to Andrea Cardini for noticing the problem.

 



F. James Rohlf, Distinguished Professor, Emeritus. Ecology  Evolution

Research Professor, Anthropology

Stony Brook University

 

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[MORPHMET] updates

2014-10-24 Thread F. James Rohlf
tpsPLS, tpsTri, tpsSmall, tpsRegr, and tpsRelw have been updated and are
available on the Stony Brook Morphometrics server.

 

These now include a small change prompted by Andrea Cardini to make them
more compatible with older versions of Windows (such as WinXP). As needed, I
will update some of the other tps programs.

 

--

F. James Rohlf, Distinguished Professor Emeritus, Stony Brook University

The much revised 4th editions of Biometry and Statistical Tables are now
available:

 http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal
http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal

 
http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-ro
hlf
http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-roh
lf

P Please consider the environment before printing this email 

 

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tpsDig2 update

2009-12-20 Thread F. James Rohlf
I have just uploaded ver. 2.14 to the Stony Brook Morphometrics server. This
version adds the ability to save the area and the length of a hand drawn
curve to the listing file.  Note that the length of the curve is just for
the points drawn - it is not the length of the closed curve even if the
curve is drawn as closed (I may change that in the future).

 

Thanks to Dean Adams for the suggestion.

 

--

F. James Rohlf, Distinguished Professor

Dept. Ecology and Evolution, Stony Brook University, NY 11794-5245

 



RE: Sliding semilandmarks in tpsDIG

2005-04-08 Thread F. James Rohlf
That is available in the tpsRelw program.


F. James Rohlf, Distinguished Professor,
Dept. Ecology  Evolution, Stony Brook University, Stony Brook, NY
11794-5345

 

 -Original Message-
 From: Gerard Gavin [mailto:[EMAIL PROTECTED] 
 Sent: Friday, April 08, 2005 2:59 PM
 To: morphmet@morphometrics.org
 Subject: Sliding semilandmarks in tpsDIG
 
 
 Dear morphometricians,
 
 Does anyone know if it is possable to set the sliding 
 semilandmarks to slide along a curve (outline) the tps series?
 
 
 Rohlf, F. J. 2004. tpsDig, digitize landmarks and outlines, 
 version 2.0. 
 Department of Ecology and Evolution, State University of New 
 York at Stony 
 Brook.
 
 Thanks a lot for your help.
 Gerard Gavin
 
 
 [EMAIL PROTECTED] Tel: +44 (0117) 928 5402
 Department of Earth Sciences,  Fax: +44 117 925 3385
 Wills Memorial Building,
 Queen's Road,
 Bristol BS8 1RJ
 
 http://palaeo.gly.bris.ac.uk/personnel/Gavin.html
 




RE: Tangent Space

2005-04-07 Thread F. James Rohlf
If you have saved the consensus configuration from the prior GPA, then all
you need to do is to align the new specimen with that consensus
configuration.

---
F. James Rohlf, Distinguished Professor
State University of New York, Stony Brook, NY 11794-5245
www: http://life.bio.sunysb.edu/ee/rohlf  

 -Original Message-
 From: L C Morecroft [mailto:[EMAIL PROTECTED] 
 Sent: Wednesday, April 06, 2005 11:28 AM
 To: morphmet@morphometrics.org
 Subject: Tangent Space
 
 Dear morphometricians,
 
 I have 2000 configurations of 30 landmark points in 3D space. 
 I have carried out a Generalized Procrustes Alignment (GPA) 
 on these configurations and now I have a query relating to 
 the tangent space..as I read that the points in the 
 tangent space can be related back to actual shapes in the 
 original 3D space...
 
 So, if I obtain one additional configuration of the same 30 
 landmark points, is there some method available to find out 
 where abouts in the tangent space (for the original 2000 
 configurations) this new configuration will lie, without 
 having to repeat the GPA on 2001 configurations? 
 
 If you don't want to reply to the list my e-mail address is:
 
 [EMAIL PROTECTED]
 
 Thanks in advance
 
 Lucy Morecroft
 
 Research Associate
 University of Sheffield