Re: [MORPHMET] How can I test the project for identification of unknown crania?

2018-04-02 Thread K. James Soda 
Dear Dr. Ibrahim,

As you note, standard LDA does not usually permit nested groupings.  In
this scenario, you would either need to have one LDA for sex and one LDA
for ancestry OR you could have one LDA that classifies into compound
sex-ancestry groups (i.e., male-Malay, female-Malay, male-Chinese,
female-Chinese, male-Indian, and female-Indian). Obviously, the latter
option doubles the number of groups, which could have set backs depending
on the smallest sample size of any sex-ancestry combination.

If you are feeling adventurous, my advisor, a collaborator, and I have had
some success in classification problems with GM data that use two
sequential discriminate function analyses (see this paper:
https://onlinelibrary.wiley.com/doi/full/10.1002/jmor.20626, which uses a
comparable procedure to this paper:
http://digitallibrary.amnh.org/bitstream/handle/2246/4942/N3109.pdf?sequence=1).
We did this to decide whether a specimen had enough information content to
classify it to species, but a similar procedure could apply here. You would
need three LDAs: one that classifies the specimen to sex, one that
classifies male specimens to ancestry, and one that classifies female
specimens to ancestry. To classify a test specimen, you would classify the
individual to sex using the first LDA, then, based on this classification,
you would classify to ancestry using the appropriate sex-specific LDA.

Hope something in my ramblings helps you out,

James

On Mon, Apr 2, 2018 at 12:41 PM, Dr.Abdelnasser Ibrahim <
dr.nasse...@gmail.com> wrote:

> Dear Dr. Murat Maga,
>
> Thank you very much for your cooperation. It was very helpful.
>
> You already have 400 cases that you know the ancestry and sex, and you
> want to use this database to infer ancestry of two skulls, for which you
> already know the sex. All 400 cases, as well as your two unknown, specimens
> have associated landmark data that were landmarked in using identical
> protocols. Does that sum it up accurately? yes, this is right.
>
> I will derive LDA for sexual dimorphism but how can I derive it
> for ancestry? as there are three ancestries; Malay, Chinese and Indian.
>
> Regards,
> Abdelnasser
>
> On Mon, Apr 2, 2018 at 1:21 PM, Murat Maga  wrote:
>
>> We need to clarify a few things:
>>
>>
>>
>> You already have 400 cases that you know the ancestry and sex, and you
>> want to use this database to infer ancestry of two skulls, for which you
>> already know the sex. All 400 cases, as well as your two unknown, specimens
>> have associated landmark data that were landmarked in using identical
>> protocols. Does that sum it up accurately?
>>
>>
>>
>> If that’s the case, one solution would be to use derive a linear
>> discriminant function, and see how well it accurately identifies your
>> ‘known’ data. You can use all your landmark coordinates, your full (or
>> partial) PCA results to derive the LDA. At this point your goal would be to
>> validate the model. You have a large sample size and you can split half to
>> derive the LD function, and the remaining to test the LD (i.e., treat them
>> as unknowns). Once you a find a model and a parameter set that give you
>> good predictions, than you can plug in your two samples, and get your
>> results.
>>
>>
>>
>> In my opinion this kind of analysis is simpler in R than any of the
>> programs you mentioned below, since it requires frequent revising of the
>> GPA fit (scale or not scale), use allometric regression (or not), use all
>> derived coordinates (or not), etc… to get the best ‘tuned’ model for your
>> existing data.
>>
>>
>>
>> There are other ways than LD to do this, but the structure of the problem
>> is more or less the same: Derive a model, test it, if it results in
>> sensible predictions, then apply to your unknowns.
>>
>>
>>
>> Hope this helps some…
>>
>> M
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> *From:* Dr.Abdelnasser Ibrahim 
>> *Sent:* Monday, April 2, 2018 4:11 AM
>> *To:* morphmet@morphometrics.org
>> *Subject:* [MORPHMET] How can I test the project for identification of
>> unknown crania?
>>
>>
>>
>> Dear all,
>>
>>
>>
>> I'm a Ph.D. student and I'm working with 3D CT scan geometric
>> morphometric analysis for classification of known Malaysian crania to
>> different sexes and ancestries.
>>
>>
>>
>> I collected the landmarks using Stratovan software and did Principal
>> component, canonical variate, procrustes ANOVA, and DF analysis using
>> MorphoJ and SPSS. and did visualization using IDAV Landmark Editor software
>> and did cluster analysis using PAST software and used SPSS for reliability
>> tests.
>>
>>
>>
>> I need to classify unknown crania. How can I test the project for
>> identification of unknown crania?
>>
>> I did CT scan for known 2 crania one male and another female and known
>> ancestries. Then I collected the landmarks on the tested crania using the
>> same protocol. Then I added the collected coordinates to the whole
>> previously collected coordinates

Re: [MORPHMET] How can I test the project for identification of unknown crania?

2018-04-02 Thread Dr.Abdelnasser Ibrahim 
Dear Dr. Murat Maga,

Thank you very much for your cooperation. It was very helpful.

You already have 400 cases that you know the ancestry and sex, and you want
to use this database to infer ancestry of two skulls, for which you already
know the sex. All 400 cases, as well as your two unknown, specimens have
associated landmark data that were landmarked in using identical protocols.
Does that sum it up accurately? yes, this is right.

I will derive LDA for sexual dimorphism but how can I derive it
for ancestry? as there are three ancestries; Malay, Chinese and Indian.

Regards,
Abdelnasser

On Mon, Apr 2, 2018 at 1:21 PM, Murat Maga  wrote:

> We need to clarify a few things:
>
>
>
> You already have 400 cases that you know the ancestry and sex, and you
> want to use this database to infer ancestry of two skulls, for which you
> already know the sex. All 400 cases, as well as your two unknown, specimens
> have associated landmark data that were landmarked in using identical
> protocols. Does that sum it up accurately?
>
>
>
> If that’s the case, one solution would be to use derive a linear
> discriminant function, and see how well it accurately identifies your
> ‘known’ data. You can use all your landmark coordinates, your full (or
> partial) PCA results to derive the LDA. At this point your goal would be to
> validate the model. You have a large sample size and you can split half to
> derive the LD function, and the remaining to test the LD (i.e., treat them
> as unknowns). Once you a find a model and a parameter set that give you
> good predictions, than you can plug in your two samples, and get your
> results.
>
>
>
> In my opinion this kind of analysis is simpler in R than any of the
> programs you mentioned below, since it requires frequent revising of the
> GPA fit (scale or not scale), use allometric regression (or not), use all
> derived coordinates (or not), etc… to get the best ‘tuned’ model for your
> existing data.
>
>
>
> There are other ways than LD to do this, but the structure of the problem
> is more or less the same: Derive a model, test it, if it results in
> sensible predictions, then apply to your unknowns.
>
>
>
> Hope this helps some…
>
> M
>
>
>
>
>
>
>
>
>
>
>
> *From:* Dr.Abdelnasser Ibrahim 
> *Sent:* Monday, April 2, 2018 4:11 AM
> *To:* morphmet@morphometrics.org
> *Subject:* [MORPHMET] How can I test the project for identification of
> unknown crania?
>
>
>
> Dear all,
>
>
>
> I'm a Ph.D. student and I'm working with 3D CT scan geometric morphometric
> analysis for classification of known Malaysian crania to different sexes
> and ancestries.
>
>
>
> I collected the landmarks using Stratovan software and did Principal
> component, canonical variate, procrustes ANOVA, and DF analysis using
> MorphoJ and SPSS. and did visualization using IDAV Landmark Editor software
> and did cluster analysis using PAST software and used SPSS for reliability
> tests.
>
>
>
> I need to classify unknown crania. How can I test the project for
> identification of unknown crania?
>
> I did CT scan for known 2 crania one male and another female and known
> ancestries. Then I collected the landmarks on the tested crania using the
> same protocol. Then I added the collected coordinates to the whole
> previously collected coordinates of 400 cases using Notepad ++ then run PCA
> and CVA on MorphoJ. then the tested crania were classified to the groups
> which already known from the archive before.
>
>  Is this method true for testing the unknown case? or I need to use
> another method?
>
>
>
> Regards,
>
> Abdelnasser Ibrahim
>
> Ph.D. student in Pathology department (Forensic Anthropology)
>
> Hospital UKM, Cheras, Malaysia.
>
> --
> MORPHMET may be accessed via its webpage at http://www.morphometrics.org
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RE: [MORPHMET] How can I test the project for identification of unknown crania?

2018-04-02 Thread Murat Maga 
We need to clarify a few things:

You already have 400 cases that you know the ancestry and sex, and you want to 
use this database to infer ancestry of two skulls, for which you already know 
the sex. All 400 cases, as well as your two unknown, specimens have associated 
landmark data that were landmarked in using identical protocols. Does that sum 
it up accurately?

If that’s the case, one solution would be to use derive a linear discriminant 
function, and see how well it accurately identifies your ‘known’ data. You can 
use all your landmark coordinates, your full (or partial) PCA results to derive 
the LDA. At this point your goal would be to validate the model. You have a 
large sample size and you can split half to derive the LD function, and the 
remaining to test the LD (i.e., treat them as unknowns). Once you a find a 
model and a parameter set that give you good predictions, than you can plug in 
your two samples, and get your results.

In my opinion this kind of analysis is simpler in R than any of the programs 
you mentioned below, since it requires frequent revising of the GPA fit (scale 
or not scale), use allometric regression (or not), use all derived coordinates 
(or not), etc… to get the best ‘tuned’ model for your existing data.

There are other ways than LD to do this, but the structure of the problem is 
more or less the same: Derive a model, test it, if it results in sensible 
predictions, then apply to your unknowns.

Hope this helps some…
M





From: Dr.Abdelnasser Ibrahim 
Sent: Monday, April 2, 2018 4:11 AM
To: morphmet@morphometrics.org
Subject: [MORPHMET] How can I test the project for identification of unknown 
crania?

Dear all,

I'm a Ph.D. student and I'm working with 3D CT scan geometric morphometric 
analysis for classification of known Malaysian crania to different sexes and 
ancestries.

I collected the landmarks using Stratovan software and did Principal component, 
canonical variate, procrustes ANOVA, and DF analysis using MorphoJ and SPSS. 
and did visualization using IDAV Landmark Editor software and did cluster 
analysis using PAST software and used SPSS for reliability tests.

I need to classify unknown crania. How can I test the project for 
identification of unknown crania?
I did CT scan for known 2 crania one male and another female and known 
ancestries. Then I collected the landmarks on the tested crania using the same 
protocol. Then I added the collected coordinates to the whole previously 
collected coordinates of 400 cases using Notepad ++ then run PCA and CVA on 
MorphoJ. then the tested crania were classified to the groups which already 
known from the archive before.
 Is this method true for testing the unknown case? or I need to use another 
method?

Regards,
Abdelnasser Ibrahim
Ph.D. student in Pathology department (Forensic Anthropology)
Hospital UKM, Cheras, 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 
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