[R] Help with this error "kernlab class probability calculations failed; returning NAs"

[Brian Feeny]

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