tests/testthat/test-pl-multi.R

In exprso: Rapid Deployment of Machine Learning Algorithms

library(exprso)
suppressWarnings(RNGversion("3.5.0"))

###########################################################
### Test plGridMulti

if(as.numeric(gsub("\\.", "", packageVersion("e1071"))) >= 170){

  load(file.path("data.RData"))

  set.seed(1)
  splitSets <- splitStratify(arrayMulti, percent.include = 67)
  fs.inner <- ctrlFeatureSelect(func = "fsStats", top = 0, how = "t.test")
  pl <- plGridMulti(trainingSet(splitSets), testSet(splitSets), top = c(2, 3, 0), ctrlFS = fs.inner,
                    how = "buildSVM", kernel = c("linear", "radial"), gamma = c(.1, .2))

  test_that("each ExprsMachine from plGridMulti has its own fs history", {

    expect_error(
      plGridMulti(array)
    )

    expect_equal(
      as.character(class(pl@machs[[1]])),
      "ExprsModule"
    )

    expect_equal(
      as.character(class(pl@machs[[1]]@mach[[1]])),
      "ExprsMachine"
    )

    expect_equal(
      pl@machs[[1]]@mach[[1]]@preFilter[[2]],
      c("feat4", "feat1")
    )

    expect_equal(
      pl@machs[[1]]@mach[[2]]@preFilter[[2]],
      c("feat4", "feat2")
    )

    expect_equal(
      mean(pl@summary$valid.acc),
      0.9356725
    )
  })

  ss <- ctrlSplitSet(func = "splitStratify", percent.include = 67)
  fs <- ctrlFeatureSelect(func = "fsNULL", top = 0)
  gs <- ctrlGridSearch(func = "plGridMulti", how = "buildSVM", top = c(2, 3, 0), ctrlFS = fs.inner,
                       kernel = c("linear", "radial"), gamma = c(.1, .2))

  set.seed(1)
  splitSets <- splitStratify(arrayMulti, percent.include = 67)
  pl <- plGridMulti(trainingSet(splitSets), testSet(splitSets), top = c(2, 3, 0), ctrlFS = fs.inner,
                    how = "buildSVM", kernel = c("linear", "radial"), gamma = c(.1, .2))

  set.seed(1)
  pmc <- plMonteCarlo(arrayMulti, B = 1, ctrlSS = ss, ctrlFS = fs, ctrlGS = gs)

  test_that("plGridMulti works within plMonteCarlo", {

    expect_equal(
      pl@summary[, c("kernel", "gamma", "cost", "train.acc", "valid.acc")],
      pmc@summary[, c("kernel", "gamma", "cost", "train.acc", "valid.acc")]
    )
  })

  set.seed(1)
  nest <- plNested(arrayMulti, ctrlFS = fs, ctrlGS = gs, fold = 10)

  test_that("plGridMulti works within plNested", {

    expect_equal(
      round(mean(nest@summary$valid.acc), 4),
      round(0.9194444, 4)
    )
  })
}