![caret train caret train](https://ichef.bbci.co.uk/news/1024/branded_news/B42B/production/_101932164_train3still.jpg)
With these changes, I got the same lambda values across the two methods and almost identical estimates: set. Typically, 5-10 folds is recommended ( nfolds = 5 for cv.glmnet and number=5 for caret). Second, 3 folds is too small for your CV to be reliable. So you'd be better off using more of the data as your initial training set. Another note is that for Cross Validation, you're not using the testing set at all, because the algorithm basically creates testing sets for you using the "training set". The function train() is a core function of caret. We’re gonna do that by using the train() function.
![caret train caret train](https://www.grandmasnurseryrhymes.com/images/train_Fotolia_38377026_XS.jpg)
Normally, we would want a training set that is at least comparable in size to the testing set. install.packages('caret') Creating a simple model. First, your training set is too small relative to your testing set. This will pass the NA values unmodified directly to the prediction function (this will cause prediction functions that do not support missing values to fail, for those you would. So I'm really stuck on why the two approaches are so different, while they should be quite similar? - I hope the community has some idea whats the issue here To the train function in caret, you can pass the parameter na.action na.pass, and no preprocessing (do not specify preProcess, leave it as its default value NULL). As main explanaition, I think the sampling approach for each fold might be an issue - but I use the same seeds and the results are quite different. I know that using standardize=FALSE in cv.glmnet() is not advisable, but I really want compare both methods using the same prerequisites. To summarise, the optimal lambdas are given as: TuneGrid = id(alpha = 1,lambda = seq(0.001,0.1,by = 0.001)))Ĭoef(test_class_cv_model$finalModel, test_class_cv_model$bestTune$lambda) Test_class_cv_model <- train(trainX, trainY, method = "glmnet", trControl = cctrl1,metric = "ROC", Testing <- twoClassSim(500, linearVars = 2)Ĭvob1=cv.glmnet(x=as.matrix(trainX),y=trainY,family="binomial",alpha=1, asure="auc", nfolds = 3,lambda = seq(0.001,0.1,by = 0.001),standardize=FALSE)Ĭctrl1 <- trainControl(method="cv", number=3, returnResamp="all",classProbs=TRUE,summaryFunction=twoClassSummary) Training <- twoClassSim(50, linearVars = 2) What is the proper way to use glmnet with caret?īut no answer has been given, which might be due to the reproducability of the question.įollowing the first question, I give a quite similar example but do have the same question: Why are the estimated lambdas so different? library(caret) The caret package has several functions that attempt to streamline the model building and evaluation process. There seems to be a lot of confusion in the comparison of using glmnet within caret to search for an optimal lambda and using cv.glmnet to do the same task.Ĭlassification model train.glmnet vs.