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 <mxk...@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 <bfe...@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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