Euclidean Distance Matrix Analysis (EDMA) in R?

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Euclidean Distance Matrix Analysis (EDMA) in R?

gokhanocakoglu
I am studying on statistical shape analysis,  I wonder is there any way or package available that I can perform Euclidean Distance Matrix Analysis (EDMA I or EDMA II) in R...

thanks

Gokhan
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Re: Euclidean Distance Matrix Analysis (EDMA) in R?

Tal Galili
Isn't this what
?dist
Does ?

Tal

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On Thu, Jun 24, 2010 at 2:40 PM, gokhanocakoglu <[hidden email]>wrote:

> EDMA

        [[alternative HTML version deleted]]

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Re: Euclidean Distance Matrix Analysis (EDMA) in R?

Kjetil Halvorsen
¿Is'nt this just another name for multidimensional scaling?

Kjetil

On Thu, Jun 24, 2010 at 9:15 AM, Tal Galili <[hidden email]> wrote:

> Isn't this what
> ?dist
> Does ?
>
> Tal
>
> ----------------Contact
> Details:-------------------------------------------------------
> Contact me: [hidden email] |  972-52-7275845
> Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) |
> www.r-statistics.com (English)
> ----------------------------------------------------------------------------------------------
>
>
>
>
> On Thu, Jun 24, 2010 at 2:40 PM, gokhanocakoglu <[hidden email]>wrote:
>
>> EDMA
>
>        [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

______________________________________________
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Re: Euclidean Distance Matrix Analysis (EDMA) in R?

gokhanocakoglu
In fact, Euclidean Distance Matrix Analysis (EDMA) of form is a coordinate free approach to the analysis of form using landmark data which was developed by  Subhash Lele and Joan Richstmeier. They also developed a computer program (http://www.getahead.psu.edu/comment/edma.asp) that allow to perform several techniques including EDMA I-II but I wonder is there a package or code available in R to perform EDMA...

thanks
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Re: Euclidean Distance Matrix Analysis (EDMA) in R?

Joris FA Meys
I've been looking around myself, but I couldn't find any. Maybe
somebody will chime in to direct you to the correct places. I also
checked the papers, and it seems not too hard to implement. If I find
some time, I'll take a look at it next week.

For the other two gentlemen, check:

http://www.getahead.psu.edu/PDF/EuclideanDistanceMatrixAnalysis.pdf
http://www.getahead.psu.edu/PDF/no.1.pdf

Cheers
Joris

On Fri, Jun 25, 2010 at 8:30 AM, gokhanocakoglu <[hidden email]> wrote:

>
> In fact, Euclidean Distance Matrix Analysis (EDMA) of form is a coordinate
> free approach to the analysis of form using landmark data which was
> developed by  Subhash Lele and Joan Richstmeier. They also developed a
> computer program (http://www.getahead.psu.edu/comment/edma.asp) that allow
> to perform several techniques including EDMA I-II but I wonder is there a
> package or code available in R to perform EDMA...
>
> thanks
> --
> View this message in context: http://r.789695.n4.nabble.com/Euclidean-Distance-Matrix-Analysis-EDMA-in-R-tp2266797p2268018.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>



--
Joris Meys
Statistical consultant

Ghent University
Faculty of Bioscience Engineering
Department of Applied mathematics, biometrics and process control

tel : +32 9 264 59 87
[hidden email]
-------------------------------
Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php

______________________________________________
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Re: Euclidean Distance Matrix Analysis (EDMA) in R?

gokhanocakoglu
thanks for your interests Joris



Gokhan OCAKOGLU
Uludag University
Faculty of Medicine
Department of Biostatistics
http://www20.uludag.edu.tr/~biostat/ocakoglui.htm
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Re: Euclidean Distance Matrix Analysis (EDMA) in R?

Kjetil Halvorsen
There is a freely downloadable and very relevant (& readable) book at
https://ccrma.stanford.edu/~dattorro/mybook.html
"Convex Optimization and Euclidean Distance geometry", and it indeed names EDMA
as a form of multidimensional scaling (or maybe in the oposite way).
You should have a look
at the codes for multidimensional scaling in R.

Kjetil

On Fri, Jun 25, 2010 at 6:25 AM, gokhanocakoglu <[hidden email]> wrote:

>
> thanks for your interests Joris
>
>
>
> Gokhan OCAKOGLU
> Uludag University
> Faculty of Medicine
> Department of Biostatistics
> http://www20.uludag.edu.tr/~biostat/ocakoglui.htm
>
> --
> View this message in context: http://r.789695.n4.nabble.com/Euclidean-Distance-Matrix-Analysis-EDMA-in-R-tp2266797p2268257.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

______________________________________________
[hidden email] mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: Euclidean Distance Matrix Analysis (EDMA) in R?

Joris FA Meys
Thanks for the link, very interesting book. Yet, I couldn't find the
part about EDMA. It would have surprised me anyway, as the input of
multidimensional scaling is one matrix with euclidean distances
between your observations, whereas in EDMA the data consist of a
number of distance matrices.

Quite a different thing if you ask me. Neither cmdscale nor isoMDS or
its derivated functions (eg metaMDS in the vegan package) are going to
be of any help.

Now I come to think of it, vegan has a procrustes function, but I'm
not sure if it is generalized to be of use in EDMA.

Cheers
Joris

On Fri, Jun 25, 2010 at 7:42 PM, Kjetil Halvorsen
<[hidden email]> wrote:

> There is a freely downloadable and very relevant (& readable) book at
> https://ccrma.stanford.edu/~dattorro/mybook.html
> "Convex Optimization and Euclidean Distance geometry", and it indeed names EDMA
> as a form of multidimensional scaling (or maybe in the oposite way).
> You should have a look
> at the codes for multidimensional scaling in R.
>
> Kjetil
>
> On Fri, Jun 25, 2010 at 6:25 AM, gokhanocakoglu <[hidden email]> wrote:
>>
>> thanks for your interests Joris
>>
>>
>>
>> Gokhan OCAKOGLU
>> Uludag University
>> Faculty of Medicine
>> Department of Biostatistics
>> http://www20.uludag.edu.tr/~biostat/ocakoglui.htm
>>
>> --
>> View this message in context: http://r.789695.n4.nabble.com/Euclidean-Distance-Matrix-Analysis-EDMA-in-R-tp2266797p2268257.html
>> Sent from the R help mailing list archive at Nabble.com.
>>
>> ______________________________________________
>> [hidden email] mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>



--
Joris Meys
Statistical consultant

Ghent University
Faculty of Bioscience Engineering
Department of Applied mathematics, biometrics and process control

tel : +32 9 264 59 87
[hidden email]
-------------------------------
Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php

______________________________________________
[hidden email] mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
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and provide commented, minimal, self-contained, reproducible code.
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Re: Euclidean Distance Matrix Analysis (EDMA) in R?

gokhanocakoglu
I am using EDMA for comparing the interlandmark distances of two forms. Actually there is a software called EDMA of course developed by Lele and Richstmeier but main point is I am trying to solve quite different problem on the same data set using R and EDMA so data entry format of EDMA software is different than R format, every trial(for every different data set) I have to set the data entry format according to EDMA.
Now I am checking Julien Claud's book named Morphometrics with R (http://www.springer.com/statistics/life+sciences,+medicine+%26+health/book/978-0-387-77789-4)
there is a section about EDMA and hopefully I am trying the reach same results with EDMA using EDMA software...
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Re: Euclidean Distance Matrix Analysis (EDMA) in R?

Corey Sparks
I think the hardest thing about true EDMA (meaning the Richtsmeier and Lele version) is the bootstrapping to get significance.  Have you tried their software?
http://www.getahead.psu.edu/resource_new.html
Corey Sparks, PhD
Associate Professor
Department of Demography
University of Texas at San Antonio
501 West César E. Chávez  Blvd
Monterey Building 2.270C
San Antonio, TX 78207
210-458-3166
corey.sparks 'at' utsa.edu
coreysparks.weebly.com
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Re: Euclidean Distance Matrix Analysis (EDMA) in R?

gokhanocakoglu
I am using EDMA software and I have couple of papers about statistical shape analysis and you are right about bootstrapping.
Wish R has an EDMA package and we could see how the results compatible with EDMA software.
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Re: Euclidean Distance Matrix Analysis (EDMA) in R?

Corey Sparks
I agree, i've seen procrustes in R, but not EDMA, R has natural  
support for bootstrapping via the boot() library, i'm sure others  
would  be grateful if you wanted to write some functions..
CS

Corey Sparks
Assistant Professor
Department of Demography and Organization Studies
College of Public Policy
501 West Durango Blvd
Monterrey Building 2.270C
San Antonio, TX 78207
corey.sparks 'at' utsa.edu
210 458 3166

On Jun 27, 2010, at 2:46 AM, gokhanocakoglu [via R] wrote:

> I am using EDMA software and I have couple of papers about  
> statistical shape analysis and you are right about bootstrapping.
> Wish R has an EDMA package and we could see how the results  
> compatible with EDMA software.
>
> View message @ http://r.789695.n4.nabble.com/Euclidean-Distance-Matrix-Analysis-EDMA-in-R-tp2266797p2269845.html
> To unsubscribe from Re: Euclidean Distance Matrix Analysis (EDMA) in  
> R?, click here.
>


Corey Sparks, PhD
Associate Professor
Department of Demography
University of Texas at San Antonio
501 West César E. Chávez  Blvd
Monterey Building 2.270C
San Antonio, TX 78207
210-458-3166
corey.sparks 'at' utsa.edu
coreysparks.weebly.com
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Re: Euclidean Distance Matrix Analysis (EDMA) in R?

gokhanocakoglu
basicly I am using standart shape package in R, no need additional code for analysis

http://cran.r-project.org/web/packages/shapes/index.html
http://cran.r-project.org/web/packages/shapes/shapes.pdf

anf the main reference is Statistical Shape Analysis (http://www.amazon.com/Statistical-Shape-Analysis-I-Dryden/dp/0471958166)