[R] R and DBSCAN

Tue Jun 7 10:37:53 CEST 2011

Hello Christian

Thanks for answering. Yes, I have tried dbscan from fpc but I'm still 
stuck on the memory problem. Regarding your answer, I'm not sure which 
memory parameter should I look at. Following is the code I tried with 
dbscan parameters, maybe you can see if there is any mistake.

sstdat=read.csv("sst.dat",sep=";",header=F,col.names=c("lon","lat","sst"))

library(fpc)
sst1=subset(sstdat, sst<50)
sst2=subset(sst1, lon>-6)
sst2=subset(sst2, lon<40)
sst2=subset(sst2, lat<46)

 > dbscan(sst2$sst, 0.1, MinPts = 5, scale = FALSE, method = 
c("hybrid"), seeds = FALSE, showplot = FALSE, countmode = NULL)
Error: no se puede ubicar un vector de tamaño  858.2 Mb
 > head(sst2)
              lon   lat   sst
1257 35.18 24.98 26.78
1258 35.22 24.98 26.78
1259 35.27 24.98 26.78
1260 35.31 24.98 26.78
1261 35.35 24.98 26.78
1262 35.40 24.98 26.85

In this example I only apply dbscan to temperature values, not lon/lat, 
so eps parameter is 0.1. As it is a gridded data set any point is 
surrounded by eight data points, then I thought that at least 5 of the 
surrounding points should be within the reachability distance. But I'm 
not sure I'm getting the right approach by only considering temperature 
value, maybe then I'm missing spatial information. How should I deal 
with longitude and latitude data?

dimensions of sst2 are: 152243 rows x 3 columns

Thanks again

El 03/06/2011 18:24, Christian Hennig escribió:
> Have you considered the dbscan function in library fpc, or was it 
> another one?
> dbscan in fpc doesn't have a "distance" parameter but several options, 
> one
> of which may resolve your memory problem (look up the documentation of 
> the "memory" parameter).
>
> Using a distance matrix for hundreds of thousands of points is a 
> recipe for disaster (memory-wise). I'm not sure whether the function 
> that you used did that, but dbscan in fpc can avoid it.
>
> It is true that dbscan requires tuning constants that the user has to 
> provide. There is unfortunately no general rule how to do this; it 
> would be necessary to understand the method and the meaning of the 
> constants, and how this translates into the requirements of your 
> application.
>
> You may try several different choices and do some cluster validation 
> to see what works, but I can't explain this in general terms easily 
> via email.
>
> Hope this helps at least a bit.
>
> Best regards,
> Christian
>
>
> On Fri, 3 Jun 2011, Paco Pastor wrote:
>
>> Hello everyone,
>>
>> When looking for information about clustering of spatial data in R I 
>> was directed towards DBSCAN. I've read some docs about it and theb 
>> new questions have arisen.
>>
>> DBSCAN requires some parameters, one of them is "distance". As my 
>> data are three dimensional, longitude, latitude and temperature, 
>> which "distance" should I use? which dimension is related to that 
>> distance? I suposse it should be temperature. How do I find such 
>> minimum distance with R?
>>
>> Another parameter is the minimum number of points neded to form a 
>> cluster. Is there any method to find that number? Unfortunately I 
>> haven't found.
>>
>> Searching thorugh Google I could not find an R example for using 
>> dbscan in a dataset similar to mine, do you know any website with 
>> such kind of examples? So I can read and try to adapt to my case.
>>
>> The last question is that my first R attempt with DBSCAN (without a 
>> proper answer to the prior questions) resulted in a memory problem. R 
>> says it can not allocate vector. I start with a 4 km spaced grid with 
>> 779191 points that ends in approximately 300000 rows x 3 columns 
>> (latitude, longitude and temperature) when removing not valid SST 
>> points. Any hint to address this memory problem. Does it depend on my 
>> computer or in DBSCAN itself?
>>
>> Thanks for the patience to read a long and probably boring message 
>> and for your help.
>>
>> -- 
>> -----------
>> Francisco Pastor
>> Meteorology department, Instituto Universitario CEAM-UMH
>> http://www.ceam.es
>> -----------
>> mail: paco en ceam.es
>> skype: paco.pastor.guzman
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>
> *** --- ***
> Christian Hennig
> University College London, Department of Statistical Science
> Gower St., London WC1E 6BT, phone +44 207 679 1698
> chrish en stats.ucl.ac.uk, www.homepages.ucl.ac.uk/~ucakche

-- 
-----------
Francisco Pastor
Meteorology department, Instituto Universitario CEAM-UMH
http://www.ceam.es
-----------
mail: paco en ceam.es
skype: paco.pastor.guzman
Researcher ID: http://www.researcherid.com/rid/B-8331-2008
Cosis profile: http://www.cosis.net/profile/francisco.pastor
-----------
Parque Tecnologico, C/ Charles R. Darwin, 14
46980 PATERNA (Valencia), Spain
Tlf. 96 131 82 27 - Fax. 96 131 81 90

---------------------------------------------------------------------
Este mensaje y los ficheros anexos son confidenciales. Los mismos contienen información reservada de la empresa que no puede ser difundida. Si usted ha recibido este correo por error, tenga la amabilidad de eliminarlo de su sistema y avisar al remitente mediante reenvío a su dirección electrónica; no deberá copiar el mensaje ni divulgar su contenido a ninguna persona.

Su dirección de correo electrónico junto a sus datos personales forman parte de un fichero titularidad de la Fundación de la Comunidad Valenciana Centro de Estudios Ambientales del Mediterráneo - CEAM, con CIF: G-46957213, cuya finalidad es la de mantener el contacto con Ud. De acuerdo con la Ley Orgánica 15/1999, usted puede ejercitar sus derechos de acceso, rectificación, cancelación y, en su caso, oposición enviando una solicitud por escrito, acompañada de una fotocopia de su DNI dirigida a: Fundación de la Comunidad Valenciana Centro de Estudios Ambientales del Mediterráneo - CEAM. C/ Charles R. Darwin, 14. Parque Tecnológico.46980 PATERNA (Valencia).

This message and the attached files are confidential. They contain reserved information belonging to our centre and are not to be broadcast. If you have received this email by mistake, please delete it from your system and alert the sender by returning it to his/her email address. You must not copy or divulge the contents of the message to anyone.

Your email address and personal data are included in a file belonging to the Fundación de la Comunidad Valenciana Centro de Estudios Ambientales del Mediterráneo - CEAM, con CIF: G-46957213. The purpose of this file is to allow us to keep in contact with you. In accordance with Organic Law 15/1999, you are permitted to access, rectify, cancel or oppose the contents of this file by submitting a written request, accompanied by a photocopy of your DNI, to: Fundación de la Comunidad Valenciana Centro de Estudios Ambientales del Mediterráneo - CEAM. C/ Charles R. Darwin, 14. Parque Tecnológico.46980 PATERNA (Valencia).