Question: Cannot specify probability function for extraTrees model in caret package
0
gravatar for liuy12
3.9 years ago by
liuy120
United States
liuy120 wrote:

Hello ,everyone, 

Recently, I have been using extraTrees model in caret package. However, I noticed that the probability function for extraTrees model is set to NULL by using the following scripts:

    extratrees_para <- getModelInfo('extraTrees', regex = F)[[1]]

    extratrees_para$prob

I noticed that in the original package of extraTress, it can be used to generate probability prediction for classification problems. So I'd like to specify the prob function for extratrees_para. 

    extratrees_para$prob <- function(modelFit, newdata, submodels = NULL){
    as.data.frame(predict(modelFit, newdata, probability = TRUE))
    }
    extratrees_para$type <- 'Classification'

Then I construct train function to build the model

extratreesGrid <- expand.grid(.mtry=1:2,
                              .numRandomCuts=1)

modelfit_extratrees <- train(outcome~., data=training_scaled_sel,
                             method = extratrees_para,
                             metric = "ROC",
                             trControl = trainControl(method = 'repeatedcv',
                                                      repeats=1,
                                                      classProb = T,
                                                      summaryFunction = twoClassSummary),
                             ntree = 3000, 
                             tuneGrid = extratreesGrid) 

However, I keep getting this error message which is not very informative 

"Error in train.default(x, y, weights = w, ...) : 
  final tuning parameters could not be determined
In addition: Warning messages:
1: In nominalTrainWorkflow(x = x, y = y, wts = weights, info = trainInfo,  :
  There were missing values in resampled performance measures.
2: In train.default(x, y, weights = w, ...) :
  missing values found in aggregated results"

Below is my session information. I would be really appreciated if anyone can help me with this. Thanks!

sessioninfo()

R version 3.1.2 (2014-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] DMwR_0.4.1           BiocInstaller_1.16.5 caret_6.0-41        
[4] ggplot2_1.0.0        lattice_0.20-29      extraTrees_1.0.5    
[7] rJava_0.9-6         

loaded via a namespace (and not attached):
 [1] abind_1.4-3         bitops_1.0-6        BradleyTerry2_1.0-5
 [4] brglm_0.5-9         car_2.0-24          caTools_1.17.1     
 [7] class_7.3-11        codetools_0.2-9     colorspace_1.2-4   
[10] compiler_3.1.2      digest_0.6.8        e1071_1.6-4        
[13] foreach_1.4.2       gdata_2.16.1        gplots_2.17.0      
[16] gtable_0.1.2        gtools_3.4.1        iterators_1.0.7    
[19] KernSmooth_2.23-13  lme4_1.1-7          MASS_7.3-35        
[22] Matrix_1.1-4        mgcv_1.8-3          minqa_1.2.4        
[25] munsell_0.4.2       nlme_3.1-118        nloptr_1.0.4       
[28] nnet_7.3-8          parallel_3.1.2      pbkrtest_0.4-2     
[31] plyr_1.8.1          pROC_1.8            proto_0.3-10       
[34] quantmod_0.4-4      quantreg_5.11       Rcpp_0.11.4        
[37] reshape2_1.4.1      ROCR_1.0-7          rpart_4.1-8        
[40] scales_0.2.4        SparseM_1.6         splines_3.1.2      
[43] stringr_0.6.2       tools_3.1.2         TTR_0.22-0         
[46] xts_0.9-7           zoo_1.7-12      

 

 

 

 

ADD COMMENTlink modified 3.9 years ago • written 3.9 years ago by liuy120
Answer: Cannot specify probability function for extraTrees model in caret package
1
gravatar for liuy12
3.9 years ago by
liuy120
United States
liuy120 wrote:

Turns out that I have a older version of caret and extraTrees. I updated the packages and everything works fine now! 

ADD COMMENTlink written 3.9 years ago by liuy120
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