using kohonen package in knime

[fab]

dear all.,

i want to use the power of Kohonen package in knime. I used the iris data for example . for learner node i used this code

library(kohonen)
DF <- data.frame(a=R[1:4],stringsAsFactors = TRUE)
x<-as.matrix(DF)
set.seed(10)
R<-xyf(data = x,Y=classvec2classmat(R$"class"),grid=somgrid(5,4,"hexagonal"))

for a predictor

library(kohonen)
R<-cbind(RDATA, predict(RMODEL, type="class")

but i found this error

package 'kohonen' was built under R version 2.13.2
> R<-cbind(RDATA, predict(RMODEL, type="class")
+ write.csv(R, "E:/tempknime/R-outDataTempFile-4552160382749656245.csv", row.names = TRUE);
Error: unexpected symbol in:
"R<-cbind(RDATA, predict(RMODEL, type="class")
write.csv"

Can anyone help me?

thanks
Execution halted

[Iris]

hm, there is a bracket missing.

R<-cbind(RDATA, predict(RMODEL, type="class"))

[fab]

thanks ,

but i found this new error

Error in data.frame(prediction = c("Iris-setosa", "Iris-setosa", "Iris-setosa",  :
  arguments imply differing number of rows: 150, 20
Calls: cbind ... as.data.frame -> as.data.frame.list -> eval -> eval -> data.frame
Execution halted

i need to post the simple workflow or anyone found and overcome this error ?

thanks in adance for any help

[dawid]

Hi,

there are two issues in your code:

First, you use diferent data for training the model and for making prediction, this is the same problem as described here:

http://tech.knime.org/forum/r-statistics-nodes-and-integration/serious-bug-in-r-predictor-always-predicts-training-set-not

Second, the R Predictor expects as output a vector of predicted values. The predict() method from kohonen package returns a more complicated object, which R Predictor cannot cast into vector. You have to extract predicted values by yourself.

The correct code for your R Predictor is:

library(kohonen)
DF <- data.frame(a=RDATA[1:4],stringsAsFactors = TRUE)
x<-as.matrix(DF)
R<-predict(RMODEL,x)$prediction

 

This should work.

Best,

Dawid

[fab]

dear dawid,

Thanks for your help, but i found the errors in my code . and for overcome what you noted i partitioned the set in 50% train and test.

For the code :

In the learner

library(kohonen)

x<-as.matrix(R[1:4])
y<-factor(R[[5]])
set.seed(20)
model <- xyf(scale(x),y,grid = somgrid(5, 5, "rectangular"),rlen=300)
R<-model

Is extremly important to set factor,

for the predictor

library(kohonen)
R<-cbind(RDATA, predict(RMODEL,trainY=class));

this wokrs good, and the scorer node is about 93% of accurancy.

In my hand the R learner/predicrtor nodes works well. maybe you forgot to set the path for exe.

 

thnaks for your help