Subscript out of bounds (Caret variable importance for randomForest)
I have trained a model in R:
require(caret)
require(randomForest)
myControl = trainControl(method='cv',number=5,repeats=2,returnResamp='none')
model2 = train(increaseInAssessedLevel~., data=trainData, method = 'rf', trControl=myControl)
The dataset is fairly large, but the model runs fine. I can access its parts and run commands such as:
> model2[3]
$results
mtry RMSE Rsquared RMSESD RsquaredSD
1 2 0.1901304 0.3342449 0.004586902 0.05089500
2 61 0.1080164 0.6984240 0.006195397 0.04428158
3 120 0.1084201 0.6954841 0.007119253 0.04362755
But I get the following error:
> varImp(model2)
Error in varImp[, "%IncMSE"] : subscript out of bounds
Apparently there is supposed to be a wrapper, but that does not seem to be the case: (cf:http://www.inside-r.org/packages/cran/caret/docs/varImp)
varImp.randomForest(model2)
Error: could not find function "varImp.randomForest"
But this is particularly odd:
> traceback()
No traceback available
> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-redhat-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] elasticnet_1.1 lars_1.2 klaR_0.6-9 MASS_7.3-26
[5] kernlab_0.9-18 nnet_7.3-6 randomForest_4.6-7 doMC_1.3.0
[9] iterators_1.0.6 caret_5.17-7 reshape2_1.2.2 plyr_1.8
[13] lattice_0.20-15 foreach_1.4.1 cluster_1.14.4
loaded via a namespace (and not attached):
[1] codetools_0.2-8 compiler_3.0.1 grid_3.0.1 stringr_0.6.2
[5] tools_3.0.1
Answer
In the train() statement, you need to specify the option importance=T. This will get passed to the underlying random forest call. Otherwise, importance is not calculated, giving you that error.