A similar question was asked , however, the link in the answer points to a random example of a forest, it does not seem to work in my case.
Here is an example of what I'm trying to do:
gbmGrid <- expand.grid(interaction.depth = c(5, 9),
n.trees = (1:3)*200,
shrinkage = c(0.05, 0.1))
fitControl <- trainControl(
method = "cv",
number = 3,
classProbs = TRUE)
gbmFit <- train(strong~.-Id-PlayerName, data = train[1:10000,],
method = "gbm",
trControl = fitControl,
verbose = TRUE,
tuneGrid = gbmGrid)
gbmFit
Everything is going well, I get the best options. Now, if I make a prediction:
predictStrong = predict(gbmFit, newdata=train[11000:50000,])
I get a binary forecast vector, which is good:
[1] 0 1 0 0 1 0 0 0 0 0 0 0 1 1 0 0 1 1 1 0 0 0 1 ...
However, when I try to get the probabilities, I get the error message:
predictStrong = predict(gbmFit, newdata=train[11000:50000,], type="prob")
Error in `[.data.frame`(out, , obsLevels, drop = FALSE) :
undefined columns selected
Where is the problem apparently?
Additional Information:
traceback()
5: stop("undefined columns selected")
4: `[.data.frame`(out, , obsLevels, drop = FALSE)
3: out[, obsLevels, drop = FALSE]
2: predict.train(gbmFit, newdata = train[11000:50000, ], type = "prob")
1: predict(gbmFit, newdata = train[11000:50000, ], type = "prob")
Versions:
R version 3.1.0 (2014-04-10) -- "Spring Dance"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
caret version: 6.0-29
EDIT: I saw this section , and I do not receive a message about variable names, although I have a couple of variable names with underscores, which I consider valid as I use make.namesand get the same names as the original.
colnames(train) == make.names(colnames(train))
[1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE