Re: [MORPHMET] A question regarding "target shape"

[Carmelo Fruciano]

On 05/11/2018 18:50, Diego Ardón wrote:

Captura de pantalla 2018-11-05 a la(s) 11.40.26.png


Thank you Mr. Fruciano. I had already made the DFA, but wasn't aware the 
graphical output represented both groups (it certainly makes sense). I 
have a couple of other questions regarding semi-landmarks. I probably 
should start a new topic, but I'll first try out here:



So, I was adviced to use semi-landmarks, I placed them with MakeFan8, 
saved the files as images and then used TpsDig to place all landmarks, 
however I didn't make any distinctions between landmarks and 
semi-landmarks. What unsettles me is (1) that I've recently comed across 
the term "sliding semi-landmarks", which leads me to believe 
semi-landmarks should behave in a particular way.


Well, it's a long topic, but the general idea is that, to account for 
the uncertainty in placement of a semilandmark along a curve, this is 
slid along the curve itself (or, more frequently, its approximation) so 
that ideally only variation perpendicular to the curve (reflecting the 
curvature) is retained.
In current practice, semilandmarks are slid. Various software can do 
this, the most popular for 2D data being certainly tpsRelW by F.J. Rohlf.

A good, recent and accessible treatment of this topic is:

Gunz & Mitteroecker 2013. Semilandmarks: a method for quantifying curves 
and surfaces. Hystrix



The second thing that 
unsettles me is whether "more semi-landmarks" means a better analysis.


Not necessarily.

I 
can understand that most people wouldn't use 65 landmarks+semilandmarks 
because it's a painstaking job to digitize them, however, in my recent 
reads I've comed across concepts like a "Variables to specimen ratio", 
which one paper suggested specimens should be 5 times the number of 
variables. I do have a a data set of nearly 400 specimens, but it does 
come short if indeed I should have 65*2*5 specimens!


There are two issues: 1. whether statistical procedures are defined, 2. 
whether one has enough power and/or how large is error in estimates.


The first issue is easy to deal with: certain statistical procedures 
(for instance, the ones involving matrix inversion) are not defined if 
there are many variables and relatively few cases. These procedures 
simply "don't work". However, there are other alternative procedures 
which do work (e.g., the ones based on distances) and/or workarounds 
(e.g., use of generalized inverses).


The second issue is much more complex and I doubt one can give a 
straightforward answer. In general, the more observations (specimens) 
the better (when one can get them, that is). But the idea of a certain 
number of observations relative to the number of variables is, at best, 
a rule of thumb.


Clearly, having too many variables can create problems and artifacts. An 
interesting recent example of this can be found in


Bookstein 2016 - A newly noticed formula enforces fundamental limits of 
geometric morphometric analyses. Evolutionary Biology


In your particular case, if I were you I would ask myself whether all 
those points/semilandmarks are that necessary to capture biologically 
relevant variation. That is a question that only you can answer, based 
on your knowledge of the biological problem at hand.


Statistical power and reliability of estimates is another issue, which 
is in part dataset-dependent (as well as dependent on which statistical 
procedures you intend to use). An interesting paper dealing with this is


Cardini 2007. Sample size and sampling error in geometric morphometric 
studies of size and shape. Zoomorphology


In general, as said above, it's very hard to give straightforward 
answers to your question.

I hope this still helps, though.
Carmelo


==
Carmelo Fruciano
Institute of Biology
Ecole Normale Superieure - Paris
CNRS
http://www.fruciano.it/research/


El lunes, 5 de noviembre de 2018, 2:12:20 (UTC-6), Carmelo Fruciano 
escribió:




On 03/11/2018 22:28, Diego Ardón wrote:
 > Dear Mr. Soda,
 >
 > Thank you for replying. Your statement " setting one group’s mean
shape
 > to be the starting shape and the other group’s to the target;
this will
 > lead to the most direct comparison. " pretty much describes what
I have
 > in mind to do. Which software could I use to do this? since I
believe
 > MorphoJ will not do it.

Dear Diego,
MorphoJ will actually do it. The easiest is to use what is under the
menu "Discriminant analysis". MorphoJ's user guide has a brief but very
clear description of the graphical output.
I hope this helps.
Best,
Carmelo


-- 



==
Carmelo Fruciano
Institute of Biology
Ecole Normale Superieure - Paris
CNRS
http://www.fruciano.it/research/ 


 > El miércoles, 31 de octubre de 2018, 13:51:07 (UTC-6), K. James Soda
 > escribió:
 >
 >     Dear Mr. Ardón,
 >
 >     

Re: [MORPHMET] A question regarding "target shape"

[Diego Ardón]

[image: Captura de pantalla 2018-11-05 a la(s) 11.40.26.png]


Thank you Mr. Fruciano. I had already made the DFA, but wasn't aware the 
graphical output represented both groups (it certainly makes sense). I have 
a couple of other questions regarding semi-landmarks. I probably should 
start a new topic, but I'll first try out here:


So, I was adviced to use semi-landmarks, I placed them with MakeFan8, saved 
the files as images and then used TpsDig to place all landmarks, however I 
didn't make any distinctions between landmarks and semi-landmarks. What 
unsettles me is (1) that I've recently comed across the term "sliding 
semi-landmarks", which leads me to believe semi-landmarks should behave in 
a particular way. The second thing that unsettles me is whether "more 
semi-landmarks" means a better analysis. I can understand that most people 
wouldn't use 65 landmarks+semilandmarks because it's a painstaking job to 
digitize them, however, in my recent reads I've comed across concepts like 
a "Variables to specimen ratio", which one paper suggested specimens should 
be 5 times the number of variables. I do have a a data set of nearly 400 
specimens, but it does come short if indeed I should have 65*2*5 specimens!

Well, I'll double post in case someone finds him or herself in the same 
conundrum.


El lunes, 5 de noviembre de 2018, 2:12:20 (UTC-6), Carmelo Fruciano 
escribió:
>
>
>
> On 03/11/2018 22:28, Diego Ardón wrote: 
> > Dear Mr. Soda, 
> > 
> > Thank you for replying. Your statement " setting one group’s mean shape 
> > to be the starting shape and the other group’s to the target; this will 
> > lead to the most direct comparison. " pretty much describes what I have 
> > in mind to do. Which software could I use to do this? since I believe 
> > MorphoJ will not do it. 
>
> Dear Diego, 
> MorphoJ will actually do it. The easiest is to use what is under the 
> menu "Discriminant analysis". MorphoJ's user guide has a brief but very 
> clear description of the graphical output. 
> I hope this helps. 
> Best, 
> Carmelo 
>
>
> -- 
>
>
> == 
> Carmelo Fruciano 
> Institute of Biology 
> Ecole Normale Superieure - Paris 
> CNRS 
> http://www.fruciano.it/research/ 
>
>
> > El miércoles, 31 de octubre de 2018, 13:51:07 (UTC-6), K. James Soda 
> > escribió: 
> > 
> > Dear Mr. Ardón, 
> > 
> > Good question. Whenever we make shape comparisons in GM, be that via 
> > displacement vector or deformation grid (which is what you’re 
> > doing), we can typically only compare two shapes at a time. One 
> > shape is called the reference (or starting shape, in this case). 
> > This is the shape for which the grid would look “normal”; straight, 
> > equally spaced grid lines. The second is the target, where the grid 
> > is deformed to take this second configuration. If you want to 
> > compare two geographic groups, I would suggest setting one group’s 
> > mean shape to be the starting shape and the other group’s to the 
> > target; this will lead to the most direct comparison. I am not 
> > certain how easy this is to do in MorphoJ, though. 
> > 
> > Hope this helps, 
> > 
> > James 
> > 
> > On Oct 31, 2018, at 12:01 PM, Diego Ardón  > > wrote: 
> > 
> >> Hello, my name is Diego and I'm currently undertaking a Master's 
> >> program in Mexico. One of my thesis project involves a geometric 
> >> morphometrics study on the shape of a freshwater fish which 
> >> distributes across Central America. I'm currently having trouble 
> >> with a concept that will probably be very simple to most of you, 
> >> but which I haven't found a way to get my head around. 
> >> 
> >> I'm running a CVA on MorphoJ, dividing my dataset into two 
> >> geographically distinct groups. I run the test and change the type 
> >> of graph to a "Warped Outline Drawing". So now the graph is 
> >> showing a "starting shape" which I interpret as it being the 
> >> average of all my landmark data (both geographical groupings), 
> >> however I'm not sure on how to interpret the "target shape". I was 
> >> expecting to have two "target shapes", one for each of the 
> >> geographical groupings. Could someone please help point out my 
> >> misunderstanding and offer me a way on how to interpret the 
> >> "target shape"? 
> >> 
> >> Thank you, I'll be very thankful 
> >> 
> >> Diego Ardón 
> >> 
> >> -- 
> >> MORPHMET may be accessed via its webpage at 
> >> http://www.morphometrics.org 
> >> --- 
> >> You received this message because you are subscribed to the Google 
> >> Groups "MORPHMET" group. 
> >> To unsubscribe from this group and stop receiving emails from it, 
> >> send an email to morphmet+u...@morphometrics.org . 
> > 
> > -- 
> > MORPHMET may be accessed via its webpage at http://www.morphometrics.org 
> > --- 
> > You received this message because you are 

Re: [MORPHMET] A question regarding "target shape"

[Carmelo Fruciano]

On 03/11/2018 22:28, Diego Ardón wrote:

Dear Mr. Soda,

Thank you for replying. Your statement " setting one group’s mean shape 
to be the starting shape and the other group’s to the target; this will 
lead to the most direct comparison. " pretty much describes what I have 
in mind to do. Which software could I use to do this? since I believe 
MorphoJ will not do it.


Dear Diego,
MorphoJ will actually do it. The easiest is to use what is under the 
menu "Discriminant analysis". MorphoJ's user guide has a brief but very 
clear description of the graphical output.

I hope this helps.
Best,
Carmelo


--


==
Carmelo Fruciano
Institute of Biology
Ecole Normale Superieure - Paris
CNRS
http://www.fruciano.it/research/


El miércoles, 31 de octubre de 2018, 13:51:07 (UTC-6), K. James Soda 
escribió:


Dear Mr. Ardón,

Good question. Whenever we make shape comparisons in GM, be that via
displacement vector or deformation grid (which is what you’re
doing), we can typically only compare two shapes at a time. One
shape is called the reference (or starting shape, in this case).
This is the shape for which the grid would look “normal”; straight,
equally spaced grid lines. The second is the target, where the grid
is deformed to take this second configuration. If you want to
compare two geographic groups, I would suggest setting one group’s
mean shape to be the starting shape and the other group’s to the
target; this will lead to the most direct comparison. I am not
certain how easy this is to do in MorphoJ, though.

Hope this helps,

James

On Oct 31, 2018, at 12:01 PM, Diego Ardón > wrote:


Hello, my name is Diego and I'm currently undertaking a Master's
program in Mexico. One of my thesis project involves a geometric
morphometrics study on the shape of a freshwater fish which
distributes across Central America. I'm currently having trouble
with a concept that will probably be very simple to most of you,
but which I haven't found a way to get my head around.

I'm running a CVA on MorphoJ, dividing my dataset into two
geographically distinct groups. I run the test and change the type
of graph to a "Warped Outline Drawing". So now the graph is
showing a "starting shape" which I interpret as it being the
average of all my landmark data (both geographical groupings),
however I'm not sure on how to interpret the "target shape". I was
expecting to have two "target shapes", one for each of the
geographical groupings. Could someone please help point out my
misunderstanding and offer me a way on how to interpret the
"target shape"?

Thank you, I'll be very thankful

Diego Ardón

-- 
MORPHMET may be accessed via its webpage at

http://www.morphometrics.org
---
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Groups "MORPHMET" group.
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send an email to morphmet+u...@morphometrics.org .


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.


--


==
Carmelo Fruciano
Institute of Biology
Ecole Normale Superieure - Paris
CNRS
http://www.fruciano.it/research/

--
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Re: [MORPHMET] A question regarding "target shape"

[Diego Ardón]

Dear Mr. Soda,

Thank you for replying. Your statement " setting one group’s mean shape to 
be the starting shape and the other group’s to the target; this will lead 
to the most direct comparison. " pretty much describes what I have in mind 
to do. Which software could I use to do this? since I believe MorphoJ will 
not do it.



El miércoles, 31 de octubre de 2018, 13:51:07 (UTC-6), K. James Soda 
escribió:
>
> Dear Mr. Ardón,
>
> Good question. Whenever we make shape comparisons in GM, be that via 
> displacement vector or deformation grid (which is what you’re doing), we 
> can typically only compare two shapes at a time. One shape is called the 
> reference (or starting shape, in this case). This is the shape for which 
> the grid would look “normal”; straight, equally spaced grid lines. The 
> second is the target, where the grid is deformed to take this second 
> configuration. If you want to compare two geographic groups, I would 
> suggest setting one group’s mean shape to be the starting shape and the 
> other group’s to the target; this will lead to the most direct comparison. 
> I am not certain how easy this is to do in MorphoJ, though.
>
> Hope this helps,
>
> James
>
> On Oct 31, 2018, at 12:01 PM, Diego Ardón  > wrote:
>
> Hello, my name is Diego and I'm currently undertaking a Master's program 
> in Mexico. One of my thesis project involves a geometric morphometrics 
> study on the shape of a freshwater fish which distributes across Central 
> America. I'm currently having trouble with a concept that will probably be 
> very simple to most of you, but which I haven't found a way to get my head 
> around. 
>
> I'm running a CVA on MorphoJ, dividing my dataset into two geographically 
> distinct groups. I run the test and change the type of graph to a "Warped 
> Outline Drawing". So now the graph is showing a "starting shape" which I 
> interpret as it being the average of all my landmark data (both 
> geographical groupings), however I'm not sure on how to interpret the 
> "target shape". I was expecting to have two "target shapes", one for each 
> of the geographical groupings. Could someone please help point out my 
> misunderstanding and offer me a way on how to interpret the "target shape"? 
>
> Thank you, I'll be very thankful
>
> Diego Ardón
>
> -- 
> MORPHMET may be accessed via its webpage at http://www.morphometrics.org
> --- 
> You received this message because you are subscribed to the Google Groups 
> "MORPHMET" group.
> To unsubscribe from this group and stop receiving emails from it, send an 
> email to morphmet+u...@morphometrics.org .
>
>

-- 
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Re: [MORPHMET] A question regarding "target shape"

[K. James Soda]

Dear Mr. Ardón,

Good question. Whenever we make shape comparisons in GM, be that via 
displacement vector or deformation grid (which is what you’re doing), we can 
typically only compare two shapes at a time. One shape is called the reference 
(or starting shape, in this case). This is the shape for which the grid would 
look “normal”; straight, equally spaced grid lines. The second is the target, 
where the grid is deformed to take this second configuration. If you want to 
compare two geographic groups, I would suggest setting one group’s mean shape 
to be the starting shape and the other group’s to the target; this will lead to 
the most direct comparison. I am not certain how easy this is to do in MorphoJ, 
though.

Hope this helps,

James

> On Oct 31, 2018, at 12:01 PM, Diego Ardón  wrote:
> 
> Hello, my name is Diego and I'm currently undertaking a Master's program in 
> Mexico. One of my thesis project involves a geometric morphometrics study on 
> the shape of a freshwater fish which distributes across Central America. I'm 
> currently having trouble with a concept that will probably be very simple to 
> most of you, but which I haven't found a way to get my head around. 
> 
> I'm running a CVA on MorphoJ, dividing my dataset into two geographically 
> distinct groups. I run the test and change the type of graph to a "Warped 
> Outline Drawing". So now the graph is showing a "starting shape" which I 
> interpret as it being the average of all my landmark data (both geographical 
> groupings), however I'm not sure on how to interpret the "target shape". I 
> was expecting to have two "target shapes", one for each of the geographical 
> groupings. Could someone please help point out my misunderstanding and offer 
> me a way on how to interpret the "target shape"? 
> 
> Thank you, I'll be very thankful
> 
> Diego Ardón
> -- 
> MORPHMET may be accessed via its webpage at http://www.morphometrics.org
> --- 
> You received this message because you are subscribed to the Google Groups 
> "MORPHMET" group.
> To unsubscribe from this group and stop receiving emails from it, send an 
> email to morphmet+unsubscr...@morphometrics.org.

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[MORPHMET] A question regarding "target shape"

[Diego Ardón]

Hello, my name is Diego and I'm currently undertaking a Master's program in 
Mexico. One of my thesis project involves a geometric morphometrics study 
on the shape of a freshwater fish which distributes across Central America. 
I'm currently having trouble with a concept that will probably be very 
simple to most of you, but which I haven't found a way to get my head 
around. 

I'm running a CVA on MorphoJ, dividing my dataset into two geographically 
distinct groups. I run the test and change the type of graph to a "Warped 
Outline Drawing". So now the graph is showing a "starting shape" which I 
interpret as it being the average of all my landmark data (both 
geographical groupings), however I'm not sure on how to interpret the 
"target shape". I was expecting to have two "target shapes", one for each 
of the geographical groupings. Could someone please help point out my 
misunderstanding and offer me a way on how to interpret the "target shape"? 

Thank you, I'll be very thankful

Diego Ardón

-- 
MORPHMET may be accessed via its webpage at http://www.morphometrics.org
--- 
You received this message because you are subscribed to the Google Groups 
"MORPHMET" group.
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