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

Question

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.

Answer 1

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.