R help - Jun 2010 - Finding distance matrix for categorical data

All,

How can we find a distance matrix for categorical data 

ie.  given a csv below 

                   var1         var2    var3    var4
element1-1   yes            x         a         k
element1-2   no             y         b         l
element1-3   maybe       y         c          m

how can i compute the distance matrix between all the elements 

Actually i need it to create clusters on top of it 

Thanks & Regards
Kapil 


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see ?daisy in the library cluster

Cheers
Joris

On Thu, Jun 10, 2010 at 6:12 PM, kapil mahant <kapil_mahant at yahoo.com>
wrote:
> All,
>
> How can we find a distance matrix for categorical data
>
> ie. ?given a csv below
>
> ? ? ? ? ? ? ? ? ? var1 ? ? ? ? var2 ? ?var3 ? ?var4
> element1-1 ? yes ? ? ? ? ? ?x ? ? ? ? a ? ? ? ? k
> element1-2 ? no ? ? ? ? ? ? y ? ? ? ? b ? ? ? ? l
> element1-3 ? maybe ? ? ? y ? ? ? ? c ? ? ? ? ?m
>
> how can i compute the distance matrix between all the elements
>
> Actually i need it to create clusters on top of it
>
> Thanks & Regards
> Kapil
>
>
> ? ? ? ?[[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org 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
Joris.Meys at Ugent.be
-------------------------------
Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php

correction.
See ?daisy in the PACKAGE cluster. *slaps head*
cheers
Joris

On Thu, Jun 10, 2010 at 7:02 PM, Joris Meys <jorismeys at gmail.com>
wrote:
> see ?daisy in the library cluster
>
> Cheers
> Joris
>
> On Thu, Jun 10, 2010 at 6:12 PM, kapil mahant <kapil_mahant at
yahoo.com> wrote:
>> All,
>>
>> How can we find a distance matrix for categorical data
>>
>> ie. ?given a csv below
>>
>> ? ? ? ? ? ? ? ? ? var1 ? ? ? ? var2 ? ?var3 ? ?var4
>> element1-1 ? yes ? ? ? ? ? ?x ? ? ? ? a ? ? ? ? k
>> element1-2 ? no ? ? ? ? ? ? y ? ? ? ? b ? ? ? ? l
>> element1-3 ? maybe ? ? ? y ? ? ? ? c ? ? ? ? ?m
>>
>> how can i compute the distance matrix between all the elements
>>
>> Actually i need it to create clusters on top of it
>>
>> Thanks & Regards
>> Kapil
>>
>>
>> ? ? ? ?[[alternative HTML version deleted]]
>>
>> ______________________________________________
>> R-help at r-project.org 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
> Joris.Meys at Ugent.be
> -------------------------------
> Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php
>


-- 
Joris Meys
Statistical consultant

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

tel : +32 9 264 59 87
Joris.Meys at Ugent.be
-------------------------------
Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php

Thanks Guys , 
I am able to generate the distance matrix for mixed column values ( categorical
and ordinal ) using daisy function

But can anyone tell me how to generate clusters out of it , The point being i
dont know the number of cluster beforehand

Let me give an overview of the problem i am trying to solve is 

Given a dataset , something like below 


                    var1         var2       var3             Size
element1-1   yes            x         present          100
element1-2   no             y         absent            294
element1-3   maybe       x         absent            45


The first 3 variables being categorical and last one being ordinal 

I need to do the following 
1 )  Generate clusters out of it  ( let say they are "training
clusters" )
             I am able to compute distance matrix ( using daisy ) , but not sure
how to create unknown numbers of clusters ,  dbscan work on a distance matrix
2 )  Once that is done i want to spread some new data points in the above plot
space ( lets say these are "test points" )
3)   Find out which "test points" are lying within a boundary  of any
above discovered training clusters

If anyone know how to get this done then please let me know 
Its for an academic project and i am unable to make any progress 

Thanks and Regards
K



________________________________
From: Ingmar Visser <i.visser@uva.nl>

Sent: Fri, 11 June, 2010 2:19:33 PM
Subject: Re: [R] Finding distance matrix for categorical data

latent class analysis may be more appropriate depending on your hypotheses,
best, Ingmar



e:

All,
>
>>How can we find a distance matrix for categorical data
>
>>ie.  given a csv below
>
>>                   var1         var2    var3    var4
>>element1-1   yes            x         a         k
>>element1-2   no             y         b         l
>>element1-3   maybe       y         c          m
>
>>how can i compute the distance matrix between all the elements
>
>>Actually i need it to create clusters on top of it
>
>>Thanks & Regards
>>Kapil
>
>
>>        [[alternative HTML version deleted]]
>
>>______________________________________________
>R-help@r-project.org 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.
>


	[[alternative HTML version deleted]]