

Yes I am still getting this error, here is my sessionInfo:

> sessionInfo()
R version 2.15.2 (2012-10-26)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] e1071_1.6-1     class_7.3-5     kernlab_0.9-14  caret_5.15-045  foreach_1.4.0   cluster_1.14.3 
[7] reshape_0.8.4   plyr_1.7.1      lattice_0.20-10

loaded via a namespace (and not attached):
[1] codetools_0.2-8 compiler_2.15.2 grid_2.15.2     iterators_1.0.6 tools_2.15.2   


Is there an example that shows a classProbs example, I could try to run it to replicate and see if it works on my system.

Brian

On Nov 29, 2012, at 10:10 PM, Max Kuhn <mxkuhn@gmail.com> wrote:

> You didn't provide the results of sessionInfo().
> 
> Upgrade to the version just released on cran and see if you still have the issue.
> 
> Max
> 
> 
> On Thu, Nov 29, 2012 at 6:55 PM, Brian Feeny <bfeeny@mac.com> wrote:
> I have never been able to get class probabilities to work and I am relatively new to using these tools, and I am looking for some insight as to what may be wrong.
> 
> I am using caret with kernlab/ksvm.  I will simplify my problem to a basic data set which produces the same problem.  I have read the caret vignettes as well as documentation for ?train.  I appreciate any direction you can give.  I realize this is a very small dataset, the actual data is much larger, I am just using 10 rows as an example:
> 
> trainset <- data.frame(
>   outcome=factor(c("0","1","0","1","0","1","1","1","1","0")),
>   age=c(10, 23, 5, 28, 81, 48, 82, 23, 11, 9),
>   amount=c(10.11, 22.23, 494.2, 2.0, 29.2, 39.2, 39.2, 39.0, 11.1, 12.2)
> )
> 
> > str(trainset)
> 'data.frame':   7 obs. of  3 variables:
>  $ outcome: Factor w/ 2 levels "0","1": 2 1 2 2 2 2 1
>  $ age    : num  23 5 28 48 82 11 9
>  $ amount : num  22.2 494.2 2 39.2 39.2 ...
> 
> > colSums(is.na(trainset))
> outcome     age  amount
>       0       0       0
> 
> 
> ## SAMPLING AND FORMULA
> dataset <- trainset
> index <- 1:nrow(dataset)
> testindex <- sample(index, trunc(length(index)*30/100))
> trainset <- dataset[-testindex,]
> testset <- dataset[testindex,-1]
> 
> 
> ## TUNE caret / kernlab
> set.seed(1)
> MyTrainControl=trainControl(
>   method = "repeatedcv",
>   number=10,
>   repeats=5,
>   returnResamp = "all",
>   classProbs = TRUE
> )
> 
> 
> ## MODEL
> rbfSVM <- train(outcome~., data = trainset,
>                method="svmRadial",
>                preProc = c("scale"),
>                tuneLength = 10,
>                trControl=MyTrainControl,
>                fit = FALSE
> )
> 
> There were 50 or more warnings (use warnings() to see the first 50)
> > warnings()
> Warning messages:
> 1: In train.default(x, y, weights = w, ...) :
>   At least one of the class levels are not valid R variables names; This may cause errors if class probabilities are generated because the variables names will be converted to: X0, X1
> 2:  In caret:::predictionFunction(method = method, modelFit = mod$fit,  ... :
>   kernlab class prediction calculations failed; returning NAs
> 
> ______________________________________________
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
> 
> 
> 
> -- 
> 
> Max


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