Caret: undefined columns selected

Question

I have been trying to get the below code to run in caret but get the error. Can anyone tell me how to trouble shoot it.

Error in [.data.frame(data, , lvls[1]) : undefined columns selected

library(tidyverse)
library(caret)

mydf <- iris

mydf <- mydf %>% 
  mutate(tgt = as.factor(ifelse(Species == 'setosa','Y','N'))) %>% 
  select(everything(), -Species)

trainIndex <- createDataPartition(mydf$tgt, p = 0.75, times = 1, list = FALSE)
train <- mydf[trainIndex,]
test <- mydf[-trainIndex,]

fitControl <- trainControl(method = 'repeatedcv',
                       number = 10,
                       repeats = 10,
                       allowParallel = TRUE,
                       summaryFunction = twoClassSummary)

fit_log <- train(tgt~.,
             data = train,
             method = "glm",
             trControl = fitControl,
             family = "binomial")

Answer 1

You need to used classProbs = TRUE in your control function. The ROC curve is based on the class probabilities and the error is the summary function not finding those columns.