tests/testthat/tests_endpoint.R

In USGS-R/toxEval: Exploring Biological Relevance of Environmental Chemistry Observations

context("Endpoint tests")

# This has some CAS's that are not in toxCast:
CAS <- c(
  "3380-34-5", "106-44-5", "80-05-7", "121-00-6", "136-85-6",
  "84852-15-3", "599-64-4", "140-66-9", "1806-26-4", "20427-84-3",
  "104-35-8", "2315-61-9", "2315-67-5", "84-65-1", "13674-87-8",
  "126-73-8", "78-51-3", "5436-43-1", "119-61-9", "21145-77-7",
  "120-72-9", "124-76-5", "5989-27-5", "119-65-3", "76-22-2",
  "83-34-1", "1222-05-5", "90-12-0", "91-57-6", "581-42-0",
  "98-82-8", "1912-24-9", "314-40-9", "57837-19-1", "1610-18-0",
  "51218-45-2", "87-86-5", "102-36-3", "58-08-2", "486-56-6",
  "89-78-1", "333-41-5", "63-25-2", "62-73-7", "134-62-3",
  "2921-88-2", "86-74-8", "119-36-8", "106-46-7", "75-25-2",
  "91-20-3", "129-00-0", "206-44-0", "85-01-8", "120-12-7",
  "50-32-8", "115-86-6", "84-66-2", "115-96-8", "78-59-1",
  "127-18-4", "83-46-5", "57-88-5", "360-68-9", "19466-47-8"
)

test_that("Getting ACC values", {
  testthat::skip_on_cran()

  ACC <- get_ACC(CAS)
  expect_true(all(names(ACC) %in% c("CAS", "chnm", "flags", "endPoint", "ACC", "ACC_value", "MlWt")))

  expect_type(ACC$ACC_value, "double")
  expect_type(ACC$endPoint, "character")
  expect_type(ACC$CAS, "character")

  expect_lt(length(unique(ACC$CAS)), length(CAS))
  expect_gt(length(unique(ACC$endPoint)), length(CAS))
})

test_that("Removing flags", {
  testthat::skip_on_cran()

  ACC <- get_ACC(CAS)
  ACC_noFlags <- remove_flags(ACC,
    flagsShort = c(
      "Borderline",
      "OnlyHighest",
      "OneAbove",
      "Noisy",
      "HitCall",
      "GainAC50",
      "Biochemical",
      "ACCLessThan",
      "LessThan50",
      "GNLSmodel"
    )
  )
  expect_lt(nrow(ACC_noFlags), nrow(ACC))
  expect_true(all(is.na(ACC_noFlags$flags)))
})

test_that("Cleaning up endpoints", {
  testthat::skip_on_cran()
  # This function rejiggers some intended target family and sub-family
  # based on first paper:
  cleaned_ep <- clean_endPoint_info(end_point_info)
  expect_equal(names(cleaned_ep), names(end_point_info))
  expect_lt(nrow(cleaned_ep), nrow(end_point_info))

  cleanedNames <- c(
    "Nuclear Receptor", "Cell Cycle", "Cell Morphology",
    "DNA Binding", "Background Measurement", "Growth Factor",
    "Cell Adhesion Molecules", "Cytokine", "GPCR",
    "Kinase", "Protease", "Misc Protein",
    "Protease Inhibitor", "CYP", "Esterase",
    "Phosphatase", "Hydrolase", "Oxidoreductase",
    "Lyase", "Methyltransferase", "Ion Channel",
    "Transporter", "Channel 1", "Channel 2",
    "Steroid Hormone", "Oxidase", "Apolipoprotein",
    "Catalase", "Membrane Protein", "Cytokine Receptor",
    "Mutagenicity Response", "Ligase", "Transferase",
    "Filaments", "Microrna", "Zebrafish",
    "Malformation", "Metabolite", "Immunoglobulin",
    "Neurodevelopment", "Enzyme", "Deiodinase",
    "Apoptosis", "Growth Factor Receptor", "Mitochondria",
    "Stress Response", "Epigenetic Enzyme", "Cardiomyocyte Function",
    "Dehalogenase", "Transcription Factor", "Neuroactivity"
  )

  expect_true(all(cleanedNames %in% cleaned_ep$intended_target_family))
  expect_false(all(cleanedNames %in% end_point_info$intended_target_family))
})

test_that("Filtering endpoints", {
  testthat::skip_on_cran()

  cleaned_ep <- clean_endPoint_info(end_point_info)

  assays <- c("ATG", "NVS", "OT")
  groups <- c("Background Measurement", "Undefined", "Cell Cycle")

  filtered_ep <- filter_groups(cleaned_ep,
    groupCol = "intended_target_family",
    assays = assays,
    remove_groups = groups
  )

  expect_true(all(unique(filtered_ep$assaysFull) %in% assays))
  expect_true(!(any(unique(filtered_ep$groupCol) %in% groups)))
})