[MORPHMET] Sliding Semilandmarks

[Ariadne Schulz]

Hello all,

I'm having a bit of a semilandmark problem. I'm working on 3D surfaces with
semilandmarks. (Profuse thank yous to Emma for writing the scripts for
that.) The issue I'm having I think is occurring in the sliding. When I do
populations alone everything seems normal. The semilandmarks do not appear
to be going off the surface defined for them, but if I try to do more than
one population at once several of the semilandmarks slide off the surface
so my PCs get rather distorted. Based on the few individuals from different
populations I've looked at I think I do have interpopulation variation but
I wouldn't expect that to influence the sliding of semilandmarks. Has
anyone else encountered an issue like this with either 2D or 3D
semilandmarks? As with all things R I expect the answer will be something
like me omitting a comma somewhere so any suggestions you might have are
welcome.

Best,
Ari

-- 
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.

Re: [MORPHMET] Sliding Semilandmarks

[Collyer, Michael]

Ari,

If you are using geomorph, you might want to update it via GitHub.  Just a few 
days ago we updated the software with some bug fixes for surface points (one 
bug fix was for assuring non-arbitrary directions in PC planes for tangents of 
surface points).  If you are unsure how to do that, look at the post by Dean 
Adams on 15 February 2016.

Beyond that, you are asking for assistance without defining (1) how you are 
sliding your landmarks (minimizing Procrustes Distance or Bending Energy) or 
(2) other specifics that might be important (package within R, maybe other 
inputs that might be important, such as the relative numbers of fixed landmarks 
and semilandmarks, etc.).

Contrary to your logic, subsetting your sample could have an effect.  Your mean 
configuration would change in each of the subsamples, from the mean of your 
original sample, thus changing the reference configuration used in the separate 
GPAs performed.  The reference configuration has a prominent role in the 
sliding of landmarks.

With the information you provided, t is not possible to discern among user 
error, program error, or analytical artifact.

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

On Feb 18, 2016, at 9:43 AM, Ariadne Schulz 
> wrote:

Hello all,

I'm having a bit of a semilandmark problem. I'm working on 3D surfaces with 
semilandmarks. (Profuse thank yous to Emma for writing the scripts for that.) 
The issue I'm having I think is occurring in the sliding. When I do populations 
alone everything seems normal. The semilandmarks do not appear to be going off 
the surface defined for them, but if I try to do more than one population at 
once several of the semilandmarks slide off the surface so my PCs get rather 
distorted. Based on the few individuals from different populations I've looked 
at I think I do have interpopulation variation but I wouldn't expect that to 
influence the sliding of semilandmarks. Has anyone else encountered an issue 
like this with either 2D or 3D semilandmarks? As with all things R I expect the 
answer will be something like me omitting a comma somewhere so any suggestions 
you might have are welcome.

Best,
Ari

--
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.

-- 
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.

Re: [MORPHMET] Sliding Semilandmarks

[andrea cardini]

Mike, does this mean that, in general, the 
position of the semilandmarks is strongly sample 
dependent, which would mean that also the shape 
distances might change remarkably despite the 
fact one has the same number of points on exactly the same surface?
Say that I have two samples, A and B. I first (1) 
superimpose (and slide) within A. Then I do the 
same with both A and B together (2). Could I get 
appreciable differences between A1 and A2 just because of the sliding?


All Procrustes shape distances depend on the 
sample composition. However, in my experience, 
differences between A1 and A2 tend to be 
negligible with 'standard' landmarks. Is this 
different with semilandmarks? Are there 
sensitivity analyses that explore the issue (if it's an issue)?


Thanks in advance.
Cheers

Andrea

At 17:06 18/02/2016, Collyer, Michael wrote:
Contrary to your logic, subsetting your sample 
could have an effect.  Your mean configuration 
would change in each of the subsamples, from the 
mean of your original sample, thus changing the 
reference configuration used in the separate 
GPAs performed.  The reference configuration has 
a prominent role in the sliding of landmarks.



Dr. Andrea Cardini
Researcher, Dipartimento di Scienze Chimiche e 
Geologiche, Università di Modena e Reggio Emilia, 
Via Campi, 103 - 41125 Modena - Italy

tel. 0039 059 2058472

Adjunct Associate Professor, Centre for Forensic 
Science , The University of Western Australia, 35 
Stirling Highway, Crawley WA 6009, Australia


E-mail address: alcard...@gmail.com, andrea.card...@unimore.it
WEBPAGE: https://sites.google.com/site/alcardini/home/main


FREE Yellow BOOK on Geometric Morphometrics: 
http://www.italian-journal-of-mammalogy.it/issue/view/405
or full volume at: 
http://www.italian-journal-of-mammalogy.it/public/journals/3/issue_241_complete_100.pdf


Editorial board for:
Zoomorphology: 
http://www.springer.com/life+sciences/animal+sciences/journal/435
Journal of Zoological Systematics and 
Evolutionary Research: http://www.wiley.com/bw/journal.asp?ref=0947-5745=1
Hystrix, the Italian Journal of 
Mammalogy: http://www.italian-journal-of-mammalogy.it/ 


--
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.

Re: [MORPHMET] Sliding Semilandmarks

[Ariadne Schulz]

Will update and try again. That sounds - without being too hopeful - like
it might solve my problem. If not, I'll come back with better details.

I would also like the clarification on the point Andrea has asked about.
That sounds like a concerning issue for what I'm trying to do with this.

Thanks!
Ari

On Thu, Feb 18, 2016 at 4:06 PM, Collyer, Michael 
wrote:

> Ari,
>
> If you are using geomorph, you might want to update it via GitHub.  Just a
> few days ago we updated the software with some bug fixes for surface points
> (one bug fix was for assuring non-arbitrary directions in PC planes for
> tangents of surface points).  If you are unsure how to do that, look at the
> post by Dean Adams on 15 February 2016.
>
> Beyond that, you are asking for assistance without defining (1) how you
> are sliding your landmarks (minimizing Procrustes Distance or Bending
> Energy) or (2) other specifics that might be important (package within R,
> maybe other inputs that might be important, such as the relative numbers of
> fixed landmarks and semilandmarks, etc.).
>
> Contrary to your logic, subsetting your sample could have an effect.  Your
> mean configuration would change in each of the subsamples, from the mean of
> your original sample, thus changing the reference configuration used in the
> separate GPAs performed.  The reference configuration has a prominent role
> in the sliding of landmarks.
>
> With the information you provided, t is not possible to discern among user
> error, program error, or analytical artifact.
>
> 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
>
> On Feb 18, 2016, at 9:43 AM, Ariadne Schulz 
> wrote:
>
> Hello all,
>
> I'm having a bit of a semilandmark problem. I'm working on 3D surfaces
> with semilandmarks. (Profuse thank yous to Emma for writing the scripts for
> that.) The issue I'm having I think is occurring in the sliding. When I do
> populations alone everything seems normal. The semilandmarks do not appear
> to be going off the surface defined for them, but if I try to do more than
> one population at once several of the semilandmarks slide off the surface
> so my PCs get rather distorted. Based on the few individuals from different
> populations I've looked at I think I do have interpopulation variation but
> I wouldn't expect that to influence the sliding of semilandmarks. Has
> anyone else encountered an issue like this with either 2D or 3D
> semilandmarks? As with all things R I expect the answer will be something
> like me omitting a comma somewhere so any suggestions you might have are
> welcome.
>
> Best,
> Ari
>
> --
> 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.
>
>
>

-- 
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.

Re: [MORPHMET] Sliding Semilandmarks

[Collyer, Michael]

Andrea,

I like to think of semilandmark sliding as iteratively finding fitted 
(predicted) values for the generalized linear model fit described by Gunz et 
al. (2005) (equation 4), and updating coordinates by these values until there 
is no more meaningful change (with regard to an acceptable criterion).  If 
Bending energy is not used, the bending energy matrix is replaced by an 
identity matrix (i.e., independence), which produces the minimized Procrustes 
distance version of the sliding algorithm.  (This is is the same as ordinary 
least squares being a simplification of generalized least squares by using an 
identity matrix for the covariance matrix in GLS estimation of parameters.)  
Calculating the bending energy matrix requires using the reference 
configuration.  The hat matrix calculated in the process is typically 
post-multiplied by the target coordinates centered by the reference 
configuration.  Changing the reference should, therefore, change the solution.  
Also, let’s not forget that with surface points, if we follow the Gunz et al. 
(2005) recommendation, 5 nearest neighbors are used to estimate the principal 
components for defining a tangent plane.  One could use more nearest neighbors, 
which would change the tangent planes.  One could also choose to project points 
after sliding back onto the surface (by finding the nearest neighbor) or not.  
One could choose to recursively update the reference configuration as the 
Procrustes average in each iteration, or use a constant reference.  One could 
also choose different convergence criteria, depending on how precise the 
finished product should be.  This is all to say that there are several - 
perhaps arbitrary - choices that can be made that will affect the results.

Whether these nuances have an appreciable empirical effect, I’m not sure.  I 
doubt that shape distances would change “remarkably” (depending on one’s 
definition of remarkable), but I think one cannot expect that subsampling will 
produce the same Procrustes residuals that would be found from using one 
inclusive sample.

As you have indicated, the same thing happens with GPA performed on “fixed” 
landmarks.  The extent to which surface semilandmarks would be similar or more 
susceptible to change is hard to argue without considering whether bending 
energy is used, how many nearest neighbors are used, the relative density of 
surface points, etc. This is probably a question to answer empirically with 
specific data.  (Get Procrustes residuals from the full data, do it again with 
subsetted data, and maybe do a two-block PLS analysis between two sets of 
matching specimens to see if there is any appreciable change.)

I would be curious to know what others think.  I have been thinking about this 
topic a lot, especially after dealing with the programming in geomorph.  I’m 
sure there are other perspectives.

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

On Feb 18, 2016, at 11:03 AM, andrea cardini 
> wrote:

Mike, does this mean that, in general, the position of the semilandmarks is 
strongly sample dependent, which would mean that also the shape distances might 
change remarkably despite the fact one has the same number of points on exactly 
the same surface?
Say that I have two samples, A and B. I first (1) superimpose (and slide) 
within A. Then I do the same with both A and B together (2). Could I get 
appreciable differences between A1 and A2 just because of the sliding?

All Procrustes shape distances depend on the sample composition. However, in my 
experience, differences between A1 and A2 tend to be negligible with 'standard' 
landmarks. Is this different with semilandmarks? Are there sensitivity analyses 
that explore the issue (if it's an issue)?

Thanks in advance.
Cheers

Andrea

At 17:06 18/02/2016, Collyer, Michael wrote:
Contrary to your logic, subsetting your sample could have an effect.  Your mean 
configuration would change in each of the subsamples, from the mean of your 
original sample, thus changing the reference configuration used in the separate 
GPAs performed.  The reference configuration has a prominent role in the 
sliding of landmarks.


Dr. Andrea Cardini
Researcher, Dipartimento di Scienze Chimiche e Geologiche, Università di Modena 
e Reggio Emilia, Via Campi, 103 - 41125 Modena - Italy
tel. 0039 059 2058472

Adjunct Associate Professor, Centre for Forensic Science , The University of 
Western Australia, 35 Stirling Highway, Crawley WA 6009, Australia

E-mail address: alcard...@gmail.com, 
andrea.card...@unimore.it
WEBPAGE: https://sites.google.com/site/alcardini/home/main


FREE Yellow BOOK on Geometric 

Re: [MORPHMET] Sliding Semilandmarks

[Carmelo Fruciano]

Ariadne Schulz  ha scritto:


Hello all,

I'm having a bit of a semilandmark problem. I'm working on 3D surfaces with
semilandmarks. (Profuse thank yous to Emma for writing the scripts for
that.) The issue I'm having I think is occurring in the sliding. When I do
populations alone everything seems normal. The semilandmarks do not appear
to be going off the surface defined for them, but if I try to do more than
one population at once several of the semilandmarks slide off the surface
so my PCs get rather distorted. Based on the few individuals from different
populations I've looked at I think I do have interpopulation variation but
I wouldn't expect that to influence the sliding of semilandmarks. Has
anyone else encountered an issue like this with either 2D or 3D
semilandmarks? As with all things R I expect the answer will be something
like me omitting a comma somewhere so any suggestions you might have are
welcome.


Dear Ari,
to elaborate on what others have written, perhaps you also want to try  
and see how/if changing the criterion for sliding (minimizing bending  
energy vs minimizing Procrustes distance) and the number of iterations  
changes the results of your superimposition.


A post/discussion that may be interesting to you can be found at  
Stephan Schlager's blog:

http://zarquon42b.github.io/2014/11/07/ProcDSliding/

Best,
Carmelo




--
Carmelo Fruciano
Postdoctoral Fellow - Queensland University of Technology - Brisbane,  
Australia

Honorary Fellow - University of Catania - Catania, Italy
e-mail c.fruci...@unict.it
http://www.fruciano.it/research/

--
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.