tests/testthat/testcall_path.R

In zoonproject/zoon: Reproducible, Accessible & Shareable Species Distribution Modelling

context("call_path")

test_that("Test call_path in a large number of variations", {
  skip_on_cran()

  CP_work <- workflow(
    occurrence = list(UKAnophelesPlumbeus, NaiveRandomPresence),
    covariate = UKAir,
    process = Background(n = 70),
    model = RandomForest,
    output = PrintMap
  )

  expect_equal(
    attr(Occurrence(CP_work)[[1]], "call_path"),
    structure(list(covariate = "UKAnophelesPlumbeus"),
              .Names = "occurrence")
  )
  expect_equal(
    attr(Occurrence(CP_work)[[2]], "call_path"),
    structure(list(covariate = "NaiveRandomPresence"),
              .Names = "occurrence")
  )
  expect_equal(
    attr(Covariate(CP_work), "call_path"),
    structure(list(covariate = "UKAir"),
              .Names = "covariate")
  )
  expect_equal(
    attr(Process(CP_work)[[1]], "call_path"),
    structure(
      list(occurrence = "UKAnophelesPlumbeus",
           covariate = "UKAir",
           process = "Background"),
      .Names = c("occurrence", "covariate", "process")
    )
  )
  expect_equal(
    attr(Process(CP_work)[[2]], "call_path"),
    structure(
      list(occurrence = "NaiveRandomPresence",
           covariate = "UKAir",
           process = "Background"),
      .Names = c("occurrence", "covariate", "process")
    )
  )
  expect_equal(
    attr(Model(CP_work)[[1]], "call_path"),
    structure(
      list(occurrence = "UKAnophelesPlumbeus",
           covariate = "UKAir",
           process = "Background",
           model = "RandomForest"),
      .Names = c("occurrence", "covariate", "process", "model")
    )
  )
  expect_equal(
    attr(Output(CP_work)[[1]], "call_path"),
    structure(
      list(occurrence = "UKAnophelesPlumbeus",
           covariate = "UKAir",
           process = "Background",
           model = "RandomForest",
           output = "PrintMap"),
      .Names = c("occurrence", "covariate", "process", "model", "output")
    )
  )
  expect_equal(
    attr(Output(CP_work)[[2]], "call_path"),
    structure(
      list(occurrence = "NaiveRandomPresence",
           covariate = "UKAir",
           process = "Background",
           model = "RandomForest",
           output = "PrintMap"),
      .Names = c("occurrence", "covariate", "process", "model", "output")
    )
  )

  CP_worka <- workflow(
    occurrence = Chain(UKAnophelesPlumbeus, NaiveRandomPresence),
    covariate = UKAir,
    process = Background(n = 70),
    model = RandomForest,
    output = PrintMap
  )

  expect_equal(
    attr(Occurrence(CP_worka), "call_path"),
    structure(list(occurrence = paste("Chain(UKAnophelesPlumbeus,",
                                      "NaiveRandomPresence)")),
              .Names = "occurrence")
  )
  expect_equal(
    attr(Process(CP_worka), "call_path"),
    structure(
      list(occurrence = paste("Chain(UKAnophelesPlumbeus,",
                              "NaiveRandomPresence)"),
           covariate = "UKAir",
           process = "Background"),
      .Names = c("occurrence", "covariate", "process")
    )
  )
  expect_equal(
    attr(Model(CP_worka), "call_path"),
    structure(
      list(occurrence = paste("Chain(UKAnophelesPlumbeus,",
                              "NaiveRandomPresence)"),
           covariate = "UKAir",
           process = "Background",
           model = "RandomForest"),
      .Names = c("occurrence", "covariate", "process", "model")
    )
  )
  expect_equal(
    attr(Output(CP_worka), "call_path"),
    structure(
      list(occurrence = paste("Chain(UKAnophelesPlumbeus,",
                              "NaiveRandomPresence)"),
           covariate = "UKAir",
           process = "Background",
           model = "RandomForest",
           output = "PrintMap"),
      .Names = c("occurrence", "covariate", "process", "model", "output")
    )
  )

  CP_work2 <- workflow(
    occurrence = UKAnophelesPlumbeus,
    covariate = list(NaiveRandomRaster, UKAir),
    process = Background(n = 70),
    model = RandomForest,
    output = PrintMap
  )

  expect_equal(
    attr(Covariate(CP_work2)[[1]], "call_path"),
    structure(list(covariate = "NaiveRandomRaster"),
              .Names = "covariate")
  )
  expect_equal(
    attr(Covariate(CP_work2)[[2]], "call_path"),
    structure(list(covariate = "UKAir"),
              .Names = "covariate")
  )
  expect_equal(
    attr(Process(CP_work2)[[1]], "call_path"),
    structure(
      list(occurrence = "UKAnophelesPlumbeus",
           covariate = "NaiveRandomRaster",
           process = "Background"),
      .Names = c("occurrence", "covariate", "process")
    )
  )
  expect_equal(
    attr(Process(CP_work2)[[2]], "call_path"),
    structure(
      list(occurrence = "UKAnophelesPlumbeus",
           covariate = "UKAir",
           process = "Background"),
      .Names = c("occurrence", "covariate", "process")
    )
  )
  expect_equal(
    attr(Model(CP_work2)[[1]], "call_path"),
    structure(
      list(occurrence = "UKAnophelesPlumbeus",
           covariate = "NaiveRandomRaster",
           process = "Background",
           model = "RandomForest"),
      .Names = c("occurrence", "covariate", "process", "model")
    )
  )
  expect_equal(
    attr(Model(CP_work2)[[2]], "call_path"),
    structure(
      list(occurrence = "UKAnophelesPlumbeus",
           covariate = "UKAir",
           process = "Background",
           model = "RandomForest"),
      .Names = c("occurrence", "covariate", "process", "model")
    )
  )
  expect_equal(
    attr(Output(CP_work2)[[1]], "call_path"),
    structure(
      list(occurrence = "UKAnophelesPlumbeus",
           covariate = "NaiveRandomRaster",
           process = "Background",
           model = "RandomForest",
           output = "PrintMap"),
      .Names = c("occurrence", "covariate", "process", "model", "output")
    )
  )
  expect_equal(
    attr(Output(CP_work2)[[2]], "call_path"),
    structure(
      list(occurrence = "UKAnophelesPlumbeus",
           covariate = "UKAir",
           process = "Background",
           model = "RandomForest",
           output = "PrintMap"),
      .Names = c("occurrence", "covariate", "process", "model", "output")
    )
  )


  CP_work2a <- workflow(
    occurrence = UKAnophelesPlumbeus,
    covariate = Chain(UKAir, UKAir),
    process = Background(n = 70),
    model = RandomForest,
    output = PrintMap
  )

  expect_equal(
    attr(Covariate(CP_work2a), "call_path"),
    structure(list(covariate = "Chain(UKAir, UKAir)"),
              .Names = "covariate")
  )
  expect_equal(
    attr(Process(CP_work2a), "call_path"),
    structure(
      list(occurrence = "UKAnophelesPlumbeus",
           covariate = "Chain(UKAir, UKAir)",
           process = "Background"),
      .Names = c("occurrence", "covariate", "process")
    )
  )
  expect_equal(
    attr(Model(CP_work2a), "call_path"),
    structure(
      list(occurrence = "UKAnophelesPlumbeus",
           covariate = "Chain(UKAir, UKAir)",
           process = "Background",
           model = "RandomForest"),
      .Names = c("occurrence", "covariate", "process", "model")
    )
  )
  expect_equal(
    attr(Output(CP_work2a), "call_path"),
    structure(
      list(occurrence = "UKAnophelesPlumbeus",
           covariate = "Chain(UKAir, UKAir)",
           process = "Background",
           model = "RandomForest",
           output = "PrintMap"),
      .Names = c("occurrence", "covariate", "process", "model", "output")
    )
  )


  CP_work1 <- workflow(
    occurrence = Chain(UKAnophelesPlumbeus, NaiveRandomPresence),
    covariate = UKAir,
    process = list(OneHundredBackground, Background(n = 70)),
    model = RandomForest,
    output = PrintMap
  )

  expect_equal(
    attr(Occurrence(CP_work1), "call_path"),
    structure(list(occurrence = paste("Chain(UKAnophelesPlumbeus,",
                                      "NaiveRandomPresence)")),
              .Names = "occurrence")
  )
  expect_equal(
    attr(Process(CP_work1)[[1]], "call_path"),
    structure(
      list(occurrence = paste("Chain(UKAnophelesPlumbeus,",
                              "NaiveRandomPresence)"),
           covariate = "UKAir",
           process = "OneHundredBackground"),
      .Names = c("occurrence", "covariate", "process")
    )
  )
  expect_equal(
    attr(Process(CP_work1)[[2]], "call_path"),
    structure(
      list(occurrence = paste("Chain(UKAnophelesPlumbeus,",
                              "NaiveRandomPresence)"),
           covariate = "UKAir",
           process = "Background"),
      .Names = c("occurrence", "covariate", "process")
    )
  )
  expect_equal(
    attr(Model(CP_work1)[[1]], "call_path"),
    structure(
      list(occurrence = paste("Chain(UKAnophelesPlumbeus,",
                              "NaiveRandomPresence)"),
           covariate = "UKAir",
           process = "OneHundredBackground",
           model = "RandomForest"),
      .Names = c("occurrence", "covariate", "process", "model")
    )
  )
  expect_equal(
    attr(Model(CP_work1)[[2]], "call_path"),
    structure(
      list(occurrence = paste("Chain(UKAnophelesPlumbeus,",
                              "NaiveRandomPresence)"),
           covariate = "UKAir",
           process = "Background",
           model = "RandomForest"),
      .Names = c("occurrence", "covariate", "process", "model")
    )
  )
  expect_equal(
    attr(Output(CP_work1)[[1]], "call_path"),
    structure(
      list(occurrence = paste("Chain(UKAnophelesPlumbeus,",
                              "NaiveRandomPresence)"),
           covariate = "UKAir",
           process = "OneHundredBackground",
           model = "RandomForest",
           output = "PrintMap"),
      .Names = c("occurrence", "covariate", "process", "model", "output")
    )
  )
  expect_equal(
    attr(Output(CP_work1)[[2]], "call_path"),
    structure(
      list(occurrence = paste("Chain(UKAnophelesPlumbeus,",
                              "NaiveRandomPresence)"),
           covariate = "UKAir",
           process = "Background",
           model = "RandomForest",
           output = "PrintMap"),
      .Names = c("occurrence", "covariate", "process", "model", "output")
    )
  )
  expect_equal(
    attr(Output(CP_work1)[[1]], "call_path"),
    structure(
      list(occurrence = paste("Chain(UKAnophelesPlumbeus,",
                              "NaiveRandomPresence)"),
           covariate = "UKAir",
           process = "OneHundredBackground",
           model = "RandomForest",
           output = "PrintMap"),
      .Names = c("occurrence", "covariate", "process", "model", "output")
    )
  )
  
  expect_equal(
    attr(Output(CP_work1)[[2]], "call_path"),
    structure(
      list(occurrence = paste("Chain(UKAnophelesPlumbeus,",
                              "NaiveRandomPresence)"),
           covariate = "UKAir",
           process = "Background",
           model = "RandomForest",
           output = "PrintMap"),
      .Names = c("occurrence", "covariate", "process", "model", "output")
    )
  )

  CP_work1a <- workflow(
    occurrence = Chain(UKAnophelesPlumbeus, NaiveRandomPresence),
    covariate = UKAir,
    process = Chain(NoProcess, Background(n = 70)),
    model = RandomForest,
    output = PrintMap
  )

  expect_equal(
    attr(Occurrence(CP_work1a), "call_path"),
    structure(list(occurrence = paste("Chain(UKAnophelesPlumbeus,",
                                      "NaiveRandomPresence)")),
              .Names = "occurrence")
  )
  expect_equal(
    attr(Process(CP_work1a), "call_path"),
    structure(
      list(occurrence = paste("Chain(UKAnophelesPlumbeus,",
                              "NaiveRandomPresence)"),
           covariate = "UKAir",
           process = "Chain(NoProcess, Background)"),
      .Names = c("occurrence", "covariate", "process")
    )
  )
  expect_equal(
    attr(Model(CP_work1a), "call_path"),
    structure(
      list(occurrence = paste("Chain(UKAnophelesPlumbeus,",
                              "NaiveRandomPresence)"),
           covariate = "UKAir",
           process = "Chain(NoProcess, Background)",
           model = "RandomForest"),
      .Names = c("occurrence", "covariate", "process", "model")
    )
  )
  expect_equal(
    attr(Output(CP_work1a), "call_path"),
    structure(
      list(occurrence = paste("Chain(UKAnophelesPlumbeus,",
                              "NaiveRandomPresence)"),
           covariate = "UKAir",
           process = "Chain(NoProcess, Background)",
           model = "RandomForest",
           output = "PrintMap"),
      .Names = c("occurrence", "covariate", "process", "model", "output")
    )
  )


  CP_work3 <- workflow(
    occurrence = Chain(UKAnophelesPlumbeus, NaiveRandomPresence),
    covariate = UKAir,
    process = Chain(NoProcess, Background(n = 70)),
    model = list(RandomForest, LogisticRegression),
    output = PrintMap
  )

  expect_equal(
    attr(Model(CP_work3)[[1]], "call_path"),
    structure(
      list(occurrence = paste("Chain(UKAnophelesPlumbeus,",
                              "NaiveRandomPresence)"),
           covariate = "UKAir",
           process = "Chain(NoProcess, Background)",
           model = "RandomForest"),
      .Names = c("occurrence", "covariate", "process", "model")
    )
  )
  expect_equal(
    attr(Model(CP_work3)[[2]], "call_path"),
    structure(
      list(occurrence = paste("Chain(UKAnophelesPlumbeus,",
                              "NaiveRandomPresence)"),
           covariate = "UKAir",
           process = "Chain(NoProcess, Background)",
           model = "LogisticRegression"),
      .Names = c("occurrence", "covariate", "process", "model")
    )
  )
  expect_equal(
    attr(Output(CP_work3)[[1]], "call_path"),
    structure(
      list(occurrence = paste("Chain(UKAnophelesPlumbeus,",
                              "NaiveRandomPresence)"),
           covariate = "UKAir",
           process = "Chain(NoProcess, Background)",
           model = "RandomForest",
           output = "PrintMap"),
      .Names = c("occurrence", "covariate", "process", "model", "output")
    )
  )
  expect_equal(
    attr(Output(CP_work3)[[2]], "call_path"),
    structure(
      list(occurrence = paste("Chain(UKAnophelesPlumbeus,",
                              "NaiveRandomPresence)"),
           covariate = "UKAir",
           process = "Chain(NoProcess, Background)",
           model = "LogisticRegression",
           output = "PrintMap"),
      .Names = c("occurrence", "covariate", "process", "model", "output")
    )
  )


  CP_work3a <- workflow(
    occurrence = UKAnophelesPlumbeus,
    covariate = UKAir,
    process = Background(n = 70),
    model = LogisticRegression,
    output = PrintMap
  )

  expect_equal(
    attr(Model(CP_work3a), "call_path"),
    structure(
      list(occurrence = "UKAnophelesPlumbeus",
           covariate = "UKAir",
           process = "Background",
           model = "LogisticRegression"),
      .Names = c("occurrence", "covariate", "process", "model")
    )
  )
  expect_equal(
    attr(Output(CP_work3a), "call_path"),
    structure(
      list(occurrence = "UKAnophelesPlumbeus",
           covariate = "UKAir",
           process = "Background",
           model = "LogisticRegression",
           output = "PrintMap"),
      .Names = c("occurrence", "covariate", "process", "model", "output")
    )
  )

  suppressWarnings({SDMTools_check <- requireNamespace('SDMTools', quietly = TRUE)})
  if(!SDMTools_check) skip('Some tests require SDMTools - install it first')
  
  CP_work4 <- workflow(
    occurrence = UKAnophelesPlumbeus,
    covariate = UKAir,
    process = Background(n = 70),
    model = LogisticRegression,
    output = list(SurfaceMap, PerformanceMeasures)
  )

  expect_null(attr(Output(CP_work4)[[1]], "call_path"))
  expect_equal(
    attr(Output(CP_work4)[[2]], "call_path"),
    structure(
      list(occurrence = "UKAnophelesPlumbeus",
           covariate = "UKAir",
           process = "Background",
           model = "LogisticRegression",
           output = "PerformanceMeasures"),
      .Names = c("occurrence", "covariate", "process", "model", "output")
    )
  )

  CP_work4b <- workflow(
    occurrence = UKAnophelesPlumbeus,
    covariate = UKAir,
    process = Background(n = 70),
    model = LogisticRegression,
    output = Chain(SurfaceMap, PerformanceMeasures)
  )
  expect_null(attr(Output(CP_work4b)[[1]], "call_path"))
  expect_equal(
    attr(Output(CP_work4b)[[2]], "call_path"),
    structure(
      list(occurrence = "UKAnophelesPlumbeus",
           covariate = "UKAir",
           process = "Background",
           model = "LogisticRegression",
           output = "PerformanceMeasures"),
      .Names = c("occurrence", "covariate", "process", "model", "output")
    )
  )

  CP_work4c <- workflow(
    occurrence = UKAnophelesPlumbeus,
    covariate = UKAir,
    process = Background(n = 70),
    model = list(LogisticRegression, RandomForest),
    output = Chain(PrintMap, PerformanceMeasures)
  )
  expect_equal(
    attr(Output(CP_work4c)[[1]], "call_path"),
    structure(
      list(
        occurrence = "UKAnophelesPlumbeus",
        covariate = "UKAir",
        process = "Background",
        model = "LogisticRegression",
        output = "PrintMap"
      ),
      .Names = c("occurrence", "covariate", "process", "model", "output")
    )
  )
  expect_equal(
    attr(Output(CP_work4c)[[2]], "call_path"),
    structure(
      list(
        occurrence = "UKAnophelesPlumbeus",
        covariate = "UKAir",
        process = "Background",
        model = "LogisticRegression",
        output = "PerformanceMeasures"
      ),
      .Names = c("occurrence", "covariate", "process", "model", "output")
    )
  )
  expect_equal(
    attr(Output(CP_work4c)[[3]], "call_path"),
    structure(
      list(
        occurrence = "UKAnophelesPlumbeus",
        covariate = "UKAir",
        process = "Background",
        model = "RandomForest",
        output = "PrintMap"
      ),
      .Names = c("occurrence", "covariate", "process", "model", "output")
    )
  )
  expect_equal(
    attr(Output(CP_work4c)[[4]], "call_path"),
    structure(
      list(
        occurrence = "UKAnophelesPlumbeus",
        covariate = "UKAir",
        process = "Background",
        model = "RandomForest",
        output = "PerformanceMeasures"
      ),
      .Names = c("occurrence", "covariate", "process", "model", "output")
    )
  )
})