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

make sure you installed the package with all its dependencies:

install.packages('caret', dependencies = TRUE)

confusionMatrix( table(prediction, true_value) )

Answer 2

Try use:

confusionMatrix(table(Argument 1, Argument 2)) 

Thats worked for me.

Answer 3

The length problem you're running into is probably due to the presence of NAs in the training set -- either drop the cases that are not complete, or impute so that you do not have missing values.

Answer 4

If your data contains NAs then sometimes it will be considered as a factor level,So omit these NAs initially

DF = na.omit(DF)

Then,if your model fit is predicting some incorrect level,then it is better to use tables

confusionMatrix(table(Arg1, Arg2))

Answer 5

I had same issue but went ahead and changed it after reading data file like so..

data = na.omit(data)

Thanks all for pointer!

Answer 6

Try specifying na.pass for the na.action option:

predictionsTree <- predict(treeFit, testdata,na.action = na.pass)