Error in ConfusionMatrix the data and reference factors must have the same number of levels

Question

I\'ve trained a tree model with R caret. I\'m now trying to generate a confusion matrix and keep getting the following error:

Error in confusionMatrix

Answer 1

Might be there are missing values in the testdata, Add the following line before "predictionsTree <- predict(treeFit, testdata)" to remove NAs. I had the same error and now it works for me.

testdata <- testdata[complete.cases(testdata),]

Answer 2

Maybe your model is not predicting a certain factor. Use the table() function instead of confusionMatrix() to see if that is the problem.

Answer 3

Change them into a data frame and then use them in confusionMatrix function:

pridicted <- factor(predict(treeFit, testdata))
real <- factor(testdata$catgeory)

my_data1 <- data.frame(data = pridicted, type = "prediction")
my_data2 <- data.frame(data = real, type = "real")
my_data3 <- rbind(my_data1,my_data2)

# Check if the levels are identical
identical(levels(my_data3[my_data3$type == "prediction",1]) , levels(my_data3[my_data3$type == "real",1]))

confusionMatrix(my_data3[my_data3$type == "prediction",1], my_data3[my_data3$type == "real",1],  dnn = c("Prediction", "Reference"))