tests/testthat/test-validate_contingency_table.R

In iAM-AMR/sawmill: Process Queries from the CEDAR Database

test_that("con_table: One parameter is non-numeric", {
  A <- 10
  B <- "Twenty"
  C <- 30
  D <- 40
  nexp <- 50
  nref <- 100

  expect_identical(
    validate_contingency_table(A, B, C, D, nexp, nref)[[1]],
    FALSE
  )

  expect_identical(
    validate_contingency_table(A, B, C, D, nexp, nref)[[2]],
    "Error: table parameters are not of type 'numeric'."
  )

  expect_identical(
    validate_contingency_table(A, B, C, D, nexp, nref)[[3]],
    "NA: contingency table incomplete."
  )
})

test_that("con_table: Missing nref", {
  A <- 10
  B <- NA
  C <- 30
  D <- NA
  nexp <- 50
  nref <- NA

  expect_identical(
    validate_contingency_table(A, B, C, D, nexp, nref)[[1]],
    FALSE
  )

  expect_identical(
    validate_contingency_table(A, B, C, D, nexp, nref)[[2]],
    "Error: missing group totals."
  )

  expect_identical(
    validate_contingency_table(A, B, C, D, nexp, nref)[[3]],
    "NA: contingency table incomplete."
  )
})

test_that("con_table: Missing A", {
  A <- NA
  B <- 20
  C <- 30
  D <- 40
  nexp <- 50
  nref <- 100

  expect_identical(
    validate_contingency_table(A, B, C, D, nexp, nref)[[1]],
    TRUE
  )

  expect_identical(
    validate_contingency_table(A, B, C, D, nexp, nref)[[2]],
    "OK: parameters pass checks for contingency table."
  )

  expect_identical(
    validate_contingency_table(A, B, C, D, nexp, nref)[[3]],
    "con_table_pos_tot"
  )
})

test_that("con_table: Missing B", {
  A <- 10
  B <- NA
  C <- 30
  D <- 40
  nexp <- 50
  nref <- 100

  expect_identical(
    validate_contingency_table(A, B, C, D, nexp, nref)[[1]],
    TRUE
  )

  expect_identical(
    validate_contingency_table(A, B, C, D, nexp, nref)[[2]],
    "OK: parameters pass checks for contingency table."
  )

  expect_identical(
    validate_contingency_table(A, B, C, D, nexp, nref)[[3]],
    "con_table_pos_tot"
  )
})

test_that("con_table: Missing A and C", {
  A <- NA
  B <- 20
  C <- NA
  D <- 40
  nexp <- 50
  nref <- 100

  expect_identical(
    validate_contingency_table(A, B, C, D, nexp, nref)[[1]],
    TRUE
  )

  expect_identical(
    validate_contingency_table(A, B, C, D, nexp, nref)[[2]],
    "OK: parameters pass checks for contingency table."
  )

  expect_identical(
    validate_contingency_table(A, B, C, D, nexp, nref)[[3]],
    "con_table_pos_tot"
  )
})

test_that("con_table: Missing A and B", {
  A <- NA
  B <- NA
  C <- 30
  D <- 40
  nexp <- 50
  nref <- 100

  expect_identical(
    validate_contingency_table(A, B, C, D, nexp, nref)[[1]],
    FALSE
  )

  expect_identical(
    validate_contingency_table(A, B, C, D, nexp, nref)[[2]],
    "Error: could not determine table type."
  )

  expect_identical(
    validate_contingency_table(A, B, C, D, nexp, nref)[[3]],
    "NA: could not determine table type."
  )
})

test_that("con_table: Good pos total", {
  A <- 10
  B <- NA
  C <- 30
  D <- NA
  nexp <- 50
  nref <- 100

  expect_identical(
    validate_contingency_table(A, B, C, D, nexp, nref)[[1]],
    TRUE
  )

  expect_identical(
    validate_contingency_table(A, B, C, D, nexp, nref)[[2]],
    "OK: parameters pass checks for contingency table."
  )

  expect_identical(
    validate_contingency_table(A, B, C, D, nexp, nref)[[3]],
    "con_table_pos_tot"
  )
})

test_that("con_table: Good neg total", {
  A <- NA
  B <- 20
  C <- NA
  D <- 40
  nexp <- 50
  nref <- 100

  expect_identical(
    validate_contingency_table(A, B, C, D, nexp, nref)[[1]],
    TRUE
  )

  expect_identical(
    validate_contingency_table(A, B, C, D, nexp, nref)[[2]],
    "OK: parameters pass checks for contingency table."
  )

  expect_identical(
    validate_contingency_table(A, B, C, D, nexp, nref)[[3]],
    "con_table_pos_tot"
  )
})

test_that("con_table: Good full table", {
  A <- 10
  B <- 20
  C <- 30
  D <- 40
  nexp <- 50
  nref <- 100

  expect_identical(
    validate_contingency_table(A, B, C, D, nexp, nref)[[1]],
    TRUE
  )

  expect_identical(
    validate_contingency_table(A, B, C, D, nexp, nref)[[2]],
    "OK: parameters pass checks for contingency table."
  )

  expect_identical(
    validate_contingency_table(A, B, C, D, nexp, nref)[[3]],
    "con_table_pos_tot"
  )
})