R carriages and gbm cannot find input

Question

I am trying to train gbm with caret package in R. At first I got the following error and thought it was due to lack of input, so I created gbmGrid , but I still get the same error message.

 sub4Collect1 <- data.frame(testing$row_id) > > cl <- makeCluster(10, type = "SOCK") > registerDoSNOW(cl) > ptm <- proc.time() > > for(i in 2:7){ + trainClass <- postPrior1[,i] + testClass <- postTest1[,i] + gbmGrid <- expand.grid(.interaction.depth = (1:5) * 2, .n.trees = (1:5)*50, .shrinkage = .1) + bootControl <- trainControl(number = 1) + set.seed(2) + gbmFit <- train(prePrior1[,-c(2,60,61,161)], trainClass, method = "gbm", tuneLength = 5, + trControl = bootControl + ##, scaled = FALSE + , tuneGrid = gbmGrid + ) + pred1 <- predict(gbmFit$finalModel, newdata = preTest1[,-c(2,60,61,161)]) + sub4Collect1 <- cbind(sub4Collect1, pred1) + print(i) + flush.console() + } Iter TrainDeviance ValidDeviance StepSize Improve 1 0.0000 -nan 0.1000 0.0000 2 0.0000 -nan 0.1000 0.0000 3 0.0000 -nan 0.1000 0.0000 4 0.0000 -nan 0.1000 0.0000 5 0.0000 -nan 0.1000 0.0000 6 0.0000 -nan 0.1000 0.0000 7 0.0000 -nan 0.1000 0.0000 8 0.0000 -nan 0.1000 0.0000 9 0.0000 -nan 0.1000 0.0000 10 0.0000 -nan 0.1000 0.0000 50 0.0000 -nan 0.1000 0.0000 Error in n.trees[n.trees > object$n.trees] <- object$n.trees : argument "n.trees" is missing, with no default > stopCluster(cl) > timee4 <- proc.time() - ptm > timee4 user system elapsed 3.563 0.306 14.472 

Any suggestions?

Answer 1

The correct code for the pred () function requires manually submitting the .n.trees parameter from the finalmodel gbmFit $ object as such:

  pred1 <- predict(gbmFit$finalModel, newdata = preTest1[,-c(2,60,61,161)], n.trees=gbmFit1$bestTune$.n.trees) 

Answer 2

If this does not work:

 pred1 <- predict(gbmFit$finalModel, newdata = preTest1[,-c(2,60,61,161)], n.trees=gbmFit1$bestTune$.n.trees) 

you can use this:

 pred1 <- predict(gbmFit, newdata = preTest1[,-c(2,60,61,161)], n.trees=gbmFit1$n.trees) 

Answer 3

I don’t think you need to pass both tuneLength and tuneGrid . Try only one or the other and see if the problem goes away.