CODEWITHSUNDEEP
rr-caretrocglmnet
trickymaverick
trickymaverick

Reputation: 199

Unable to specify type="response" in Caret's predict function

I am trying to plot a ROC curve for my glmnet regression model. In order to do that, I am trying to predict using type = "response" in predict function: 

 pred_glmnet_s10_2class <- predict(model_train_glmnet_s10_2class,
                                   newdata=testing_s10_2class,
                                   s = "model_train_glmnet_s10_2class$finalModel$lambdaOpt",
                                   type="response")

and I get the following error:

Error in predict.train(model_train_glmnet_s10_2class, newdata = testing_s10_2class, : type must be either "raw" or "prob"

My predictions and class labels are binary 0 and 1 and have been factored. Any help is really appreciated. Also, any ideas on how to plot AUC (Area Under ROC curve) vs number of features? Thanks!

Upvotes: 0

Views: 6879

Answers (1)

topepo
topepo

Reputation: 14331

Assuming that model_train_glmnet_s10_2class was generated by train (showing the code would be helpful)...

Using predict(model_train_glmnet_s10_2class) is using predict.train and uses the optimal lambda values determined by train automatically. If you want the probabilities, just use type = "prob".

Your syntax is consistent with predict.glmnet and not predict.train.

As said in the documentation, it is a really bad idea to use model_train_glmnet_s10_2class$finalModel directly to do the predictions

Upvotes: 2

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