CODEWITHSUNDEEP
rr-caret
user4143385
user4143385

Reputation: 51

R caret Error: Something is wrong; all the Accuracy metric values are missing:

I'm trying to apply stacking on my dataset but here I am.

# Load library
library(DJL)
library(caret)
library(caretEnsemble)

# Load data and format the target attribute to avoid clutters
df <- dataset.engine.2015[, -c(1, 2)]
levels(df$Type) <- list(NA.D = "NA-D", NA.P = "NA-P", SC.P = "SC-P", TC.D = "TC-D", TC.P = "TC-P")

# Run
st.methods <- c("lda", "rpart", "glm", "knn", "svmRadial")
st.control <- trainControl(method = "repeatedcv", number = 5, repeats = 3, 
                           savePredictions = T, classProbs = T)
st.models  <- caretList(Type ~., data = df, trControl = st.control, methodList = st.methods)

Then I get this:

Something is wrong; all the Accuracy metric values are missing:
    Accuracy       Kappa    
 Min.   : NA   Min.   : NA  
 1st Qu.: NA   1st Qu.: NA  
 Median : NA   Median : NA  
 Mean   :NaN   Mean   :NaN  
 3rd Qu.: NA   3rd Qu.: NA  
 Max.   : NA   Max.   : NA  
 NA's   :1     NA's   :1    
Error: Stopping
In addition: There were 18 warnings (use warnings() to see them)

Can anyone help me to fix this error?

Upvotes: 3

Views: 5770

Answers (1)

Marco Sandri
Marco Sandri

Reputation: 24272

The glm model cannot be used for predicting categorical dependent variables with more than two categories. Try to delete glm from st.methods or substitute glm with, for example, multinom, gbm, randomForest.

Here are two useful experiment. In the first we consider only glm:

rm(list=ls())
library(DJL)
library(caret)
library(caretEnsemble)  
df <- dataset.engine.2015[, -c(1, 2)]
levels(df$Type) <- list(NA.D = "NA-D", NA.P = "NA-P", SC.P = "SC-P", TC.D = "TC-D", TC.P = "TC-P")

st.control <- trainControl(method = "repeatedcv", number = 5, repeats = 3, 
                           savePredictions = T, classProbs = T)

st.methods <- c("glm")
st.models  <- caretList(Type ~., data = df, trControl = st.control, methodList = st.methods)

Here is the error message:

Something is wrong; all the Accuracy metric values are missing:
    Accuracy       Kappa    
 Min.   : NA   Min.   : NA  
 1st Qu.: NA   1st Qu.: NA  
 Median : NA   Median : NA  
 Mean   :NaN   Mean   :NaN  
 3rd Qu.: NA   3rd Qu.: NA  
 Max.   : NA   Max.   : NA  
 NA's   :1     NA's   :1    
Error in train.default(x, y, weights = w, ...) : Stopping
Inoltre: There were 18 warnings (use warnings() to see them)

Now we substitute glm with multinom:

st.methods <- c("multinom")
st.models  <- caretList(Type ~., data = df, trControl = st.control, methodList = st.methods)
print(st.models)

The output is:

$multinom
Penalized Multinomial Regression 

1206 samples
   5 predictor
   5 classes: 'NA.D', 'NA.P', 'SC.P', 'TC.D', 'TC.P' 

No pre-processing
Resampling: Cross-Validated (5 fold, repeated 3 times) 
Summary of sample sizes: 964, 965, 965, 965, 965, 964, ... 
Resampling results across tuning parameters:

  decay  Accuracy   Kappa    
  0e+00  0.9306411  0.8518294
  1e-04  0.9300901  0.8506964
  1e-01  0.9328507  0.8564466

Accuracy was used to select the optimal model using  the largest value.
The final value used for the model was decay = 0.1.

Upvotes: 3

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