Re: [MORPHMET] Interpreting PC scores graph in MorphoJ when the first two PC's are difference due to operator input

[Helmi Hadi]

Hi Hadas,

Thank you for the reply. The test has been conducted previously before 
finalising the landmark points for other users. I suspect the raw bone data 
itself is unsatisfactory. The .obj files generated from 
PACS>MITK>MeshLab>IDAVLandmark to have problems. 

Kind regards,
Helmi

On Tuesday, October 11, 2016 at 4:50:12 AM UTC+8, Hadas L. wrote:
>
> Hi,
>
> I would consider doing a short reliability test on five specimens for each 
> individual for the single point landmarks and the curves. This shouldn't 
> take long and will give you an idea as to whether the landmarks are 
> reliable or not. Ideally this should be done before adding the landmarks to 
> the data set.
>
> Sincerely,
> Hadas
>
> On Sun, Oct 9, 2016 at 5:56 AM, Helmi Hadi  > wrote:
>
>> Dear Morphometricians, 
>>
>> I have a weird problem and I was hoping someone could help me on this. 
>>
>> I have the same CT bone (n=400) with 14 landmarks (2 Single point and 12 
>> sliding) larndmarked in IDAV Landmark by three different individuals 
>> following a figure key table. Each individual landmarked 100+ different 
>> bones. The figure key table has the shape of the bone, with the landmark 
>> locations and the order of landmarking. All users were briefed by a single 
>> person (user1) on how to extract the bone and landmark. All three 
>> individuals were present throughout the entire procedure but the bone 
>> segmentation and landmarking process was conducted individually. 
>>
>> When I combine all the data, I noticed that PC1 and PC2 graph has two 
>> clusters. The effect is about 55% (as detailed in the eigenvalues below) 
>> After further checking the classifiers in MorphoJ, the source of the 
>> clustering is one person (user1) landmarked it is slightly differently 
>> compared to the other two. I have checked the outliers tab and no glaring 
>> outliers exists. As the sample size is big, the curve seem to be quite 
>> normal. 
>>
>> Eigenvalues  % Variance Cumulative %
>>   1. 0.01603351  55.674   55.674
>>   2. 0.00496222  17.230   72.904
>>   3. 0.00224594   7.799   80.703
>>   4. 0.00121085   4.204   84.907
>>   5. 0.00076858   2.669   87.576
>> ...
>>
>> How to interpret the results for this kind of data? Things which come to 
>> my mind are:
>>
>> 1. Maybe the bones for user1 are different compared to the other two 
>> users.
>> Or 
>> 2. User1 thinks the landmark location slightly different compared to 
>> others.
>> Or
>> 3. User2 and 3 could not locate the landmark locations of user1.
>> Or
>> 4. The landmarks selected are unreliable.
>>
>> Ideally I would need few other people relandmark the entire set, but it 
>> is not possible to do it now. Can anyone help shed some light on what is 
>> the probable cause? Thank you.
>>
>>
>> Kind regards,
>>
>> Helmi Hadi, PhD
>>  School of Health Sciences, Universiti Sains Malaysia,
>> 16150 Kubang Kerian, Kelantan, MALAYSIA
>>
>>
>> -- 
>> 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] Interpreting PC scores graph in MorphoJ when the first two PC's are difference due to operator input

[Helmi Hadi]

Dear Carmelo,

Thank you. I will try to look at the at that method. Thank you also for 
giving the reference material. The landmarks chosen has been tested to be 
replicable based on prior testing before deploying to other users. The 
first person briefed and thought all the other users the landmarking 
procedure and the segmentation and cleaning of the bone in PACS (a CT 
database). I will have a look at raw ct files first and try to get it 
landmarked. Maybe some people see the semi-landmarks slightly differently. 

Kind regards,
Helmi 

On Monday, October 10, 2016 at 8:28:32 AM UTC+8, Carmelo Fruciano wrote:
>
> Dear Helmi, 
> I won't answer you in detail on your specific case as I didn't fully   
> understand the problem/design. 
>
> Ideally, if you have at least a subset of the same bones being   
> digitized by all the users/operators, you can check for your   
> hypothesis 1. 
>
> In some cases it might be possible to "remove" measurement error from   
> your data using the method presented in 
>
> Valentin AE, Penin X, Chanut JP, Sévigny JM, Rohlf FJ (2008) Arching 
> effect on fish body shape in geometric morphometric studies. Journal of 
> Fish 
> Biology 73:623–638. doi:10./j.1095-8649.2008.01961.x 
>
> That method and other approaches/issues are also discussed in my   
> recent review on the topic of measurement error 
>
> Fruciano C (2016) Measurement error in geometric morphometrics.   
> Development Genes and Evolution, 226(3):139–158. doi:   
> 10.1007/s00427-016-0537-4. 
>
> which might be useful to you to understand what's possible to do in   
> your specific case. 
>
> I hope this helps, 
> Carmelo 
>
>
>
>
>
> Helmi Hadi > ha scritto: 
>
> > Dear Morphometricians, 
> > 
> > I have a weird problem and I was hoping someone could help me on this. 
> > 
> > I have the same CT bone (n=400) with 14 landmarks (2 Single point and 12 
> > sliding) larndmarked in IDAV Landmark by three different individuals 
> > following a figure key table. Each individual landmarked 100+ different 
> > bones. The figure key table has the shape of the bone, with the landmark 
> > locations and the order of landmarking. All users were briefed by a 
> single 
> > person (user1) on how to extract the bone and landmark. All three 
> > individuals were present throughout the entire procedure but the bone 
> > segmentation and landmarking process was conducted individually. 
> > 
> > When I combine all the data, I noticed that PC1 and PC2 graph has two 
> > clusters. The effect is about 55% (as detailed in the eigenvalues below) 
> > After further checking the classifiers in MorphoJ, the source of the 
> > clustering is one person (user1) landmarked it is slightly differently 
> > compared to the other two. I have checked the outliers tab and no 
> glaring 
> > outliers exists. As the sample size is big, the curve seem to be quite 
> > normal. 
> > 
> > Eigenvalues  % Variance Cumulative % 
> >   1. 0.01603351  55.674   55.674 
> >   2. 0.00496222  17.230   72.904 
> >   3. 0.00224594   7.799   80.703 
> >   4. 0.00121085   4.204   84.907 
> >   5. 0.00076858   2.669   87.576 
> > ... 
> > 
> > How to interpret the results for this kind of data? Things which come to 
> my 
> > mind are: 
> > 
> > 1. Maybe the bones for user1 are different compared to the other two 
> users. 
> > Or 
> > 2. User1 thinks the landmark location slightly different compared to 
> others. 
> > Or 
> > 3. User2 and 3 could not locate the landmark locations of user1. 
> > Or 
> > 4. The landmarks selected are unreliable. 
> > 
> > Ideally I would need few other people relandmark the entire set, but it 
> is 
> > not possible to do it now. Can anyone help shed some light on what is 
> the 
> > probable cause? Thank you. 
> > 
> > 
> > Kind regards, 
> > 
> > Helmi Hadi, PhD 
> >  School of Health Sciences, Universiti Sains Malaysia, 
> > 16150 Kubang Kerian, Kelantan, MALAYSIA 
> > 
> > 
> > -- 
> > 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 . 
> > 
>
>
>
> -- 
> Carmelo Fruciano 
> Postdoctoral Fellow - Queensland University of Technology - Brisbane,   
> Australia 
> Honorary Fellow - University of Catania - Catania, Italy 
> e-mail c.fru...@unict.it  
> http://www.fruciano.it/research/ 
>
>

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[MORPHMET] PhD opportunity with morphometrics

[Jen Bright]

Hello all, 

I have funding for a PhD student to undertake a project which, given my own 
background, would likely involve a lot of morphometrics work. Please see ad at 
the following link: https://t.co/w3NSGAC6sw

Jen

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Re: [MORPHMET] Interpreting PC scores graph in MorphoJ when the first two PC's are difference due to operator input

[Hadas L.]

Hi,

I would consider doing a short reliability test on five specimens for each
individual for the single point landmarks and the curves. This shouldn't
take long and will give you an idea as to whether the landmarks are
reliable or not. Ideally this should be done before adding the landmarks to
the data set.

Sincerely,
Hadas

On Sun, Oct 9, 2016 at 5:56 AM, Helmi Hadi  wrote:

> Dear Morphometricians,
>
> I have a weird problem and I was hoping someone could help me on this.
>
> I have the same CT bone (n=400) with 14 landmarks (2 Single point and 12
> sliding) larndmarked in IDAV Landmark by three different individuals
> following a figure key table. Each individual landmarked 100+ different
> bones. The figure key table has the shape of the bone, with the landmark
> locations and the order of landmarking. All users were briefed by a single
> person (user1) on how to extract the bone and landmark. All three
> individuals were present throughout the entire procedure but the bone
> segmentation and landmarking process was conducted individually.
>
> When I combine all the data, I noticed that PC1 and PC2 graph has two
> clusters. The effect is about 55% (as detailed in the eigenvalues below)
> After further checking the classifiers in MorphoJ, the source of the
> clustering is one person (user1) landmarked it is slightly differently
> compared to the other two. I have checked the outliers tab and no glaring
> outliers exists. As the sample size is big, the curve seem to be quite
> normal.
>
> Eigenvalues  % Variance Cumulative %
>   1. 0.01603351  55.674   55.674
>   2. 0.00496222  17.230   72.904
>   3. 0.00224594   7.799   80.703
>   4. 0.00121085   4.204   84.907
>   5. 0.00076858   2.669   87.576
> ...
>
> How to interpret the results for this kind of data? Things which come to
> my mind are:
>
> 1. Maybe the bones for user1 are different compared to the other two users.
> Or
> 2. User1 thinks the landmark location slightly different compared to
> others.
> Or
> 3. User2 and 3 could not locate the landmark locations of user1.
> Or
> 4. The landmarks selected are unreliable.
>
> Ideally I would need few other people relandmark the entire set, but it is
> not possible to do it now. Can anyone help shed some light on what is the
> probable cause? Thank you.
>
>
> Kind regards,
>
> Helmi Hadi, PhD
>  School of Health Sciences, Universiti Sains Malaysia,
> 16150 Kubang Kerian, Kelantan, MALAYSIA
>
>
> --
> 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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RE: [MORPHMET] Question about size adjusted residuals in Geomorph

[Adams, Dean [EEOBS]]

Edgar,

If you perform a multivariate regression of shape on size (shape~size), the 
residuals from this regression represent that shape component not explained by 
size variation and the relationship between the two. In the literature, this is 
commonly referred to as size-adjusted residuals or allometry free shape.

Dean

Dr. Dean C. Adams
Professor
Department of Ecology, Evolution, and Organismal Biology
   Department of Statistics
Iowa State University
www.public.iastate.edu/~dcadams/
phone: 515-294-3834

From: Edgar Esteban Herrera Collazos [mailto:edgaresteba...@gmail.com]
Sent: Sunday, October 9, 2016 8:46 AM
To: morphmet@morphometrics.org
Subject: [MORPHMET] Question about size adjusted residuals in Geomorph

Hi everyone, I'm working in Geomorph package in R and I have a question 
regarding working with allometric effect.

What is the difference between size-adjusted residuals and allometry free 
shapes.

Thanks in advance
--
Edgar Esteban Herrera Collazos B.Sc.
Cel: 319 379 0213

Postgraduate Student at Pontificia Universidad Javeriana
Ichthyology Laboratory 108B Ed 53 - 3208320 Ext 4127
---
Estudiante de Posgrado en la Pontificia Universidad Javeriana
Laboratorio de Ictiología 108B Ed 53 - 3208320 Ext 4127


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