Re: [R] BreastCancer Dataset for Classification in kknn

From: Joris Meys <jorismeys_at_gmail.com>
Date: Tue, 01 Jun 2010 18:50:28 +0200

Hi Nitin,

It can be solved by splitting your data a bit different. You need more training data than you have evaluation data, eg : i1 = 1:400
i2=401:d

Then it works on my computer. No clue as to where the error originates from though.

Cheers
Joris

On Tue, Jun 1, 2010 at 4:27 PM, Nitin <nitin29_at_gmail.com> wrote:

> Dear All,
>
> I'm getting a error while trying to apply the BreastCancer dataset
> (package=mlbench) to kknn (package=kknn) that I don't understand as I'm new
> to R.
> The codes are as follow:
>
> rm = (list = ls())
> library(mlbench)
> data(BreastCancer)
> library(kknn)
>
> BCancer = na.omit(BreastCancer)
> d = dim(BCancer)[1]
> i1 = seq(1, d, 2)
> i2 = seq(2, d, 2)
>
> t1 = BCancer[i1, ]
> t2 = BCancer[i2, ]
> y2 = BCancer[i2, 11]
>
> x = 10
> k = array(1:x, dim = c(x,1))
> ker = array(c( "rectangular", "triangular", "epanechnikov", "biweight",
> "triweight", "cos", "inv", "gaussian"), dim = c(8,1))
>
> f = function(x, ker){
>
> BreastCancer.kknn <- kknn(Class~., train = t1, test = t2, k = x,
> kernel = ker, distance = 1)
> fit = fitted(BreastCancer.kknn)
>
> z <- (fit==y2)
> z.e <- (100 - (length(y2)-length(z[!z]))/length(y2)*100 )
> }
>
> err.k = function(ker){
> error.BreastCancer = apply(k,1,function(y) f(y, ker))
> }
>
> err.ker = apply(ker, 1, err.k)
> colnames(err.ker) = c("rectangular", "triangular", "epanechnikov",
> "biweight",
> "triweight", "cos", "inv", "gaussian")
> print(err.ker)
>
> It throws a error: Error in as.matrix(learn[, ind == i]) :
> (subscript) logical subscript too long
> In addition: Warning messages:
> 1: In model.matrix.default(mt, mf) : variable 'Id' converted to a factor
> 2: In model.matrix.default(mt, test) : variable 'Id' converted to a factor
>
> I tried the codes with other datasets in mlbench package and most of them
> working. That is the mistake here for this particular dataset and how can I
> solve it?
>
> Thanks
> Nitin
>
> [[alternative HTML version deleted]]
>
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>

-- 
Joris Meys
Statistical Consultant

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

Coupure Links 653
B-9000 Gent

tel : +32 9 264 59 87
Joris.Meys_at_Ugent.be
-------------------------------
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Received on Tue 01 Jun 2010 - 16:53:30 GMT

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