[SOLVED] Warning message: "missing values in resampled performance measures" in caret train() using rpart

Warning message: "missing values in resampled performance measures" in caret train() using rpart

I am using the caret package to train a model with "rpart" package;

tr = train(y ~ ., data = trainingDATA, method = "rpart")

Data has no missing values or NA's, but when running the command a warning message comes up;

    Warning message:
In nominalTrainWorkflow(x = x, y = y, wts = weights, info = trainInfo,  :
  There were missing values in resampled performance measures.

Does anyone know (or could point me to where to find an answer) what does this warning mean? I know it is telling me that there were missing values in resampled performance measures - but what does that exactly mean and how can a situation like that arise? BTW, the predict() function works fine with the fitted model, so it is just my curiosity.

Solution

Not definitively sure without more data.

If this is regression, the most likely case is that the tree did not find a good split and used the average of the outcome as the predictor. That's fine but you cannot calculate R^2 since the variance of the predictions is zero.

If classification, it's hard to say. You could have a resample where one of the outcome classes has zero samples so sensitivity or specificity is undefined and thus NA.