[R] svm plot question

[David Meyer]

Aimin:

hard to tell. IMO, without specifying defaults, it could only work with
purely numeric data since factors were wrongly processed.

David.

Aimin Yan wrote:
> thanks, I did get this plot.
> Before I have this problem, I did get a plot by my code.
> However after I change a little my code. it doesn't work.
> It is pity not saving my original code.
> 
> Now the question is the plot I get using your code is different from
> what I got before.
> Moreover I did remember I use plot(m.svm,p5.new,As~Cur)
> 
> Do you know why?
> 
> Thanks,
> 
> Aimin
> 
> At 06:32 AM 12/8/2006, David Meyer wrote:
>> Aimin:
>>
>> 1) Please do not spam the r-help list---one request per issue (and two
>> private mails to the code author) really suffice. Not all contributors
>> to the R-project are on-line 24/24, and have time to provide immediate
>> answers.
>>
>> 2) The error occurs because plot.svm() currently does not set valid
>> defaults for categorical dimensions you are conditioning on for your
>> 2D-plot (in your example: 'P' and 'Aa') which certainly is a bug. I will
>> commit a fix for the next release of e1071. For the time being, you will
>> have to explicitly specify the levels of 'P' and 'Aa':
>>
>> plot(m.svm,p5.new,As~Cur, slice = list(P = factor("821p", levels =
>> levels(P)), Aa = factor("ALA", levels = levels(Aa))))
>>
>> (Note that the defaults for the "slice" argument are completely
>> arbitrary anyway).
>>
>> Thanks for pointing this out,
>>
>> David
>>
>> Aimin Yan wrote:
>> > I have a question about svm in R
>> >
>> > I run the following code, all other is ok,
>> > but plot(m.svm,p5.new,As~Cur) is not ok
>> >
>> > Do you know why?
>> >
>> > install.packages("e1071")
>> > library(e1071)
>> > library(MASS)
>> > p5 <- read.csv("http://www.public.iastate.edu/~aiminy/data/p_5_2.csv")
>> > p5.new<-subset(p5,select=-Ms)
>> > p5.new$Y<-factor(p5.new$Y)
>> > levels(p5.new$Y) <- list(Out=c(1), In=c(0))
>> > attach(p5.new)
>> > m.svm<-svm(Y~P+Aa+As+Cur,data=p5.new)
>> > summary(m.svm)
>> > plot(m.svm,p5.new,As~Cur)
>> >
>> > Here is output:
>> >
>> >> install.packages("e1071")
>> > --- Please select a CRAN mirror for use in this session ---
>> > trying URL
>> >
>> 'http://rh-mirror.linux.iastate.edu/CRAN/bin/windows/contrib/2.4/e1071_1.5-16.zip'
>>
>> >
>> > Content type 'application/zip' length 592258 bytes
>> > opened URL
>> > downloaded 578Kb
>> >
>> > package 'e1071' successfully unpacked and MD5 sums checked
>> >
>> > The downloaded packages are in
>> >         C:\Documents and Settings\aiminy\Local
>> > Settings\Temp\RtmpY0B2qb\downloaded_packages
>> > updating HTML package descriptions
>> >> library(e1071)
>> > Loading required package: class
>> >> library(MASS)
>> >> p5 <- read.csv("http://www.public.iastate.edu/~aiminy/data/p_5_2.csv")
>> >> p5.new<-subset(p5,select=-Ms)
>> >> p5.new$Y<-factor(p5.new$Y)
>> >> levels(p5.new$Y) <- list(Out=c(1), In=c(0))
>> >> attach(p5.new)
>> >> m.svm<-svm(Y~P+Aa+As+Cur,data=p5.new)
>> >> summary(m.svm)
>> >
>> > Call:
>> > svm(formula = Y ~ P + Aa + As + Cur, data = p5.new)
>> >
>> >
>> > Parameters:
>> >    SVM-Type:  C-classification
>> >  SVM-Kernel:  radial
>> >        cost:  1
>> >       gamma:  0.04
>> >
>> > Number of Support Vectors:  758
>> >
>> >  ( 382 376 )
>> >
>> >
>> > Number of Classes:  2
>> >
>> > Levels:
>> >  Out In
>> >
>> >
>> >
>> >> plot(m.svm,p5.new,As~Cur)
>> > Error in scale(newdata[, object$scaled, drop = FALSE], center =
>> > object$x.scale$"scaled:center",  :
>> >         (subscript) logical subscript too long
>> >>
>> >>
>> >
>> >
>> >
>>
>> -- 
>> Dr. David Meyer
>> Department of Information Systems and Operations
>>
>> Vienna University of Economics and Business Administration
>> Augasse 2-6, A-1090 Wien, Austria, Europe
>> Tel: +43-1-313 36 4393
>> Fax: +43-1-313 36 90 4393
>> HP:  http://wi.wu-wien.ac.at/~meyer/
> 
> 
> 
> 

-- 
Dr. David Meyer
Department of Information Systems and Operations

Vienna University of Economics and Business Administration
Augasse 2-6, A-1090 Wien, Austria, Europe
Tel: +43-1-313 36 4393
Fax: +43-1-313 36 90 4393
HP:  http://wi.wu-wien.ac.at/~meyer/