R Caret Random Forest view miss-classified

R Caret Random Forest view miss-classified

By : aatif
Date : November 17 2020, 11:52 AM
I hope this helps you . Hopefully this helps. The names are all generic, but if you provide some example code and data I can clarify things.
code :
prediction <- predict(your_rf, testdata, type = "response")
location <- prediction == testdata$target

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R programming, Random forest through caret

R programming, Random forest through caret

By : Carl Weathers
Date : March 29 2020, 07:55 AM
it helps some times Most packages contain a manual, and many also include vignettes.
A quick look at the CRAN page for caret http://cran.r-project.org/web/packages/caret/index.html shows that this packages is particularly well documented.
Random Forest - Caret - Time Series

Random Forest - Caret - Time Series

By : sai mageshvar
Date : March 29 2020, 07:55 AM
Hope that helps Right now, you can't pass other options to the underlying predict method. There is a proposed change that might enable this though.
In your case, you should give the predict function a data frame that has the appropriate predictors for the next few observations.
training random forest using caret package

training random forest using caret package

By : Saritha Sreekumar
Date : March 29 2020, 07:55 AM
this will help One or more of the columns in the trainvals data frame is not a factor type, hence the error you are getting. You can convert all columns to factor using the following:
code :
trainvals[] <- lapply(trainvals, factor)
Confusion matrix for random forest in R Caret

Confusion matrix for random forest in R Caret

By : Leonce
Date : November 04 2020, 03:01 PM
this will help As I understand you would like to obtain the confusion matrix for cross validation in caret.
For this you need to specify savePredictions in trainControl. If it is set to "final" predictions for the best model are saved. By specifying classProbs = T probabilities for each class will be also saved.
code :
iris_2 <- iris[iris$Species != "setosa",] #make a two class problem
iris_2$Species <- factor(iris_2$Species) #drop levels

model_rf  <- train(Species~., tuneLength = 3, data = iris_2, method = 
                       "rf", importance = TRUE,
                   trControl = trainControl(method = "cv",
                                            number = 5,
                                            savePredictions = "final",
                                            classProbs = T))
confusionMatrix(model_rf$pred[order(model_rf$pred$rowIndex),2], iris_2$Species)
Confusion Matrix and Statistics

Prediction   versicolor virginica
  versicolor         46         6
  virginica           4        44

               Accuracy : 0.9            
                 95% CI : (0.8238, 0.951)
    No Information Rate : 0.5            
    P-Value [Acc > NIR] : <2e-16         

                  Kappa : 0.8            
 Mcnemar's Test P-Value : 0.7518         

            Sensitivity : 0.9200         
            Specificity : 0.8800         
         Pos Pred Value : 0.8846         
         Neg Pred Value : 0.9167         
             Prevalence : 0.5000         
         Detection Rate : 0.4600         
   Detection Prevalence : 0.5200         
      Balanced Accuracy : 0.9000         

       'Positive' Class : versicolor 
sapply(1:40/40, function(x){
  versicolor <- model_rf$pred[order(model_rf$pred$rowIndex),4]
  class <- ifelse(versicolor >=x, "versicolor", "virginica")
  mat <- confusionMatrix(class, iris_2$Species)
  kappa <- mat$overall[2]
  res <- data.frame(prob = x, kappa = kappa)
R Caret Random Forest AUC too good to be true?

R Caret Random Forest AUC too good to be true?

By : Cynthia
Date : March 29 2020, 07:55 AM
I think the issue was by ths following , I'll post as an answer my comment, even if this might be migrated.
I really think that you're overfitting, because you have balanced on the whole dataset. Instead you should balance only the train set.
code :
train.SMOTE <- SMOTE(graduate_4_yrs ~ ., data=grad4yr_processed_transformed,
perc.over=600, perc.under=100)
train.SMOTE <- SMOTE(graduate_4_yrs ~ ., data=trainSet, # use only the train set
perc.over=600, perc.under=100)
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