requireNamespaceQuietStop causing errors in custom summaryFunction caret

Question

I 'updated' the twoClassSummary function in caret to include both the negative and positive predictive values using caret functions:

testfun <- function (data, lev = NULL, model = NULL) 
{
  lvls <- levels(data$obs)
  if (length(lvls) > 2) 
    stop(paste("Your outcome has", length(lvls), "levels. The 
twoClassSummary() function isn't appropriate."))
  requireNamespaceQuietStop("ModelMetrics")
  if (!all(levels(data[, "pred"]) == lvls)) 
    stop("levels of observed and predicted data do not match")
  data$y = as.numeric(data$obs == lvls[2])
  rocAUC <- ModelMetrics::auc(ifelse(data$obs == lev[2], 0, 
                                     1), data[, lvls[1]])
  out <- c(rocAUC, sensitivity(data[, "pred"], data[, "obs"], lev[1]), 
                   specificity(data[, "pred"], data[, "obs"], lev[2]),
                   # next 3 lines are my additions and modifications
                   negPredValue(data[, "obs"], data[, "pred"], lev[2]),
                   posPredValue(data[, "obs"], data[, "pred"], lev[1]))
  names(out) <- c("ROC", "Sens", "Spec", "NPV", "PPV")
  out
}

And then my trainControl function:

train_control <- trainControl(method = 'repeatedcv', 
                              number = 10, repeats = 3,
                              summaryFunction = testfun,
                              classProbs = T,
                              savePredictions = T)

and then my model function:

modelSvm <- train(target ~ ., data = twoClassData, trControl = train_control, method = 'svmRadial')

The problem is when I run this function, I get the error Error in ctrl$summaryFunction(testOutput, lev, method) : could not find function "requireNamespaceQuietStop"

even though I haven't change that part of the function.

if I type

twoClassSummary

in the console,

environment: namespace:caret

appears (between < > signs) at the end after the function definition and I believe this is the source of my problems.

1) How do I direct R to this environment in the function? and 2) accuracy is not a predefined caret function, any suggestions on how to work accuracy into this code?

Thanks in advance....

topepo topepo · Accepted Answer · 2017-07-04T16:36:06

That function is not exported by caret, so use caret::: requireNamespaceQuietStop instead (or use used library).

requireNamespaceQuietStop causing errors in custom summaryFunction caret

1 Answers