[R] caret package, how can I deal with RFE+SVM wrong message?

bbslover dluthm at yeah.net
Tue Mar 23 09:42:00 CET 2010

I am learning caret package, and I want to use the RFE to reduce the
feature. I want to use RFE coupled Random Forest (RFE+FR) to complete this
task. As we know, there are a number of pre-defined sets of functions, like
random Forest(rfFuncs), however,I want to tune the parameters (mtr) when
RFE, and then I write code below, but there is something wrong message, How
can I deal with it?  
> rfGrid<-expand.grid(.mtry=c(1:2))
> rfectrl<-rfeControl(functions=caretFuncs,method="cv",verbose=F,returnResamp="final",number=10)
> subsets<-c(3,4)
> set.seed(2)
> rf.RFE<-rfe(trx,try,sizes=subsets,rfeControl=rfectrl,method="rf",tuneGrid=rfGrid)
Loading required package: class

Attaching package: 'class'

        The following object(s) are masked from package:reshape :


Fitting: mtry=1 
Fitting: mtry=2 
Error in varImp.randomForest(object$finalModel, ...) : 
  subscript out of bounds
In addition: Warning message:
package 'e1071' was built under R version 2.10.1 

At the same time, If I want to  use RFE+SVM,  RFE+nnet, and so on ,how can I
do? I have try RFE+SVM, also wrong message:> set.seed(1)
> svmProfile<-rfe(trx,try,sizes=c(1:3),
+             rfeControl=rfeControl(functions=caretFuncs,method="cv",
+             verbose=F,returnResamp="final",number=10),
+             method="svmRadial",tuneLength=5)
Fitting: sigma=0.009246713, C=0.1 
Fitting: sigma=0.009246713, C=1 
Fitting: sigma=0.009246713, C=10 
Fitting: sigma=0.009246713, C=100 
Fitting: sigma=0.009246713, C=1000 
Error in rfeControl$functions$rank(fitObject, .x, y) : 
  need importance columns for each class

thank you!
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