tests/testthat/test-caretEnsemble.R

In jknowles/EWStools: Tools for automating the testing and evaluation of education early warning system models

# Test-caretEnsemble
library(caretEnsemble)
data(EWStestData)

test_that("ROCtests work for caretEnsembles", {
  skip_on_cran()
  skip_if_not_installed("MASS")
  skip_if_not_installed("klaR")
  ctrl <- trainControl(method = "repeatedcv", 
                       repeats = 3, classProbs = TRUE, savePredictions = TRUE,
                       summaryFunction = twoClassSummary)
  out <- caretList(methodList = c("knn", "glm", "nb"), 
                   trControl = ctrl, x = modeldat$traindata$preds, 
                   y = modeldat$traindata$class, tuneLength = 5)
  outEns <- caretEnsemble(out)
  res1 <- ROCtest(outEns)
  res2t <- ROCtest(outEns, testdata = modeldat$testdata)
  outEns$metric <- "ROC"
  MA1 <- modAcc(outEns, datatype = c("test", "train"), testdata = modeldat$testdata)
  testdf1 <- dfExtract(modAcc(outEns, datatype = c("test", "train"), testdata = modeldat$testdata))
  expect_is(res1, "ROCit")
  expect_is(res2t, "ROCit")
  expect_is(MA1, "list")
  expect_is(testdf1, "data.frame")
  expect_is(out, "caretList")
  expect_is(outEns, "caretEnsemble")
})

test_that("ROCtests work for caretStack", {
  skip_on_cran()
  skip_if_not_installed("MASS")
  skip_if_not_installed("klaR")
  ctrl <- trainControl(method = "repeatedcv", 
                       repeats = 3, classProbs = TRUE, savePredictions = TRUE,
                       summaryFunction = twoClassSummary)
  out <- caretList(methodList = c("knn", "glm", "nb"), 
                   trControl = ctrl, x = modeldat$traindata$preds, 
                   y = modeldat$traindata$class, tuneLength = 5)
  outStack <- caretStack(out, method = 'glm')
  res1 <- ROCtest(outStack)
  res2t <- ROCtest(outStack, testdata = modeldat$testdata)
  outStack$metric <- "ROC"
  MA1 <- modAcc(outStack, datatype = c("test", "train"), testdata = modeldat$testdata)
  testdf1 <- dfExtract(modAcc(outStack, datatype = c("test", "train"), testdata = modeldat$testdata))
  expect_is(res1, "ROCit")
  expect_is(res2t, "ROCit")
  expect_is(MA1, "list")
  expect_is(testdf1, "data.frame")
  expect_is(out, "caretList")
  expect_is(outStack, "caretStack")
})