tests/testthat/test-validate_prevalence_table.R

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

test_that("prev_table: One parameter is non-numeric", {
  P <- 10
  Q <- "Twenty"
  R <- 30
  S <- 40
  nexp <- 50
  nref <- 100

  expect_identical(
    validate_prevalence_table(P, Q, R, S, nexp, nref)[[1]],
    FALSE
  )

  expect_identical(
    validate_prevalence_table(P, Q, R, S, nexp, nref)[[2]],
    "Error: table parameter(s) are not of type 'numeric'."
  )

  expect_identical(
    validate_prevalence_table(P, Q, R, S, nexp, nref)[[3]],
    "NA: prevalence table incomplete."
  )
})

test_that("prev_table: Missing nref", {
  P <- 10
  Q <- NA
  R <- 30
  S <- NA
  nexp <- 50
  nref <- NA

  expect_identical(
    validate_prevalence_table(P, Q, R, S, nexp, nref)[[1]],
    FALSE
  )

  expect_identical(
    validate_prevalence_table(P, Q, R, S, nexp, nref)[[2]],
    "Error: missing group totals."
  )

  expect_identical(
    validate_prevalence_table(P, Q, R, S, nexp, nref)[[3]],
    "NA: prevalence table incomplete."
  )
})

test_that("prev_table: Missing P", {
  P <- NA
  Q <- 20
  R <- 30
  S <- 40
  nexp <- 50
  nref <- 100

  expect_identical(
    validate_prevalence_table(P, Q, R, S, nexp, nref)[[1]],
    TRUE
  )

  expect_identical(
    validate_prevalence_table(P, Q, R, S, nexp, nref)[[2]],
    "OK: parameters pass checks for prevalence table."
  )

  expect_identical(
    validate_prevalence_table(P, Q, R, S, nexp, nref)[[3]],
    "prev_table_neg_tot"
  )
})

test_that("prev_table: Missing Q", {
  P <- 10
  Q <- NA
  R <- 30
  S <- 40
  nexp <- 50
  nref <- 100

  expect_identical(
    validate_prevalence_table(P, Q, R, S, nexp, nref)[[1]],
    TRUE
  )

  expect_identical(
    validate_prevalence_table(P, Q, R, S, nexp, nref)[[2]],
    "OK: parameters pass checks for prevalence table."
  )

  expect_identical(
    validate_prevalence_table(P, Q, R, S, nexp, nref)[[3]],
    "prev_table_pos_tot"
  )
})

test_that("prev_table: Missing P and R", {
  P <- NA
  Q <- 20
  R <- NA
  S <- 40
  nexp <- 50
  nref <- 100

  expect_identical(
    validate_prevalence_table(P, Q, R, S, nexp, nref)[[1]],
    TRUE
  )

  expect_identical(
    validate_prevalence_table(P, Q, R, S, nexp, nref)[[2]],
    "OK: parameters pass checks for prevalence table."
  )

  expect_identical(
    validate_prevalence_table(P, Q, R, S, nexp, nref)[[3]],
    "prev_table_neg_tot"
  )
})

test_that("prev_table: Missing P and Q", {
  P <- NA
  Q <- NA
  R <- 30
  S <- 40
  nexp <- 50
  nref <- 100

  expect_identical(
    validate_prevalence_table(P, Q, R, S, nexp, nref)[[1]],
    FALSE
  )

  expect_identical(
    validate_prevalence_table(P, Q, R, S, nexp, nref)[[2]],
    "Error: could not determine table type."
  )

  expect_identical(
    validate_prevalence_table(P, Q, R, S, nexp, nref)[[3]],
    "NA: could not determine table type."
  )
})

test_that("prev_table: Good pos total", {
  P <- 10
  Q <- NA
  R <- 30
  S <- NA
  nexp <- 50
  nref <- 100

  expect_identical(
    validate_prevalence_table(P, Q, R, S, nexp, nref)[[1]],
    TRUE
  )

  expect_identical(
    validate_prevalence_table(P, Q, R, S, nexp, nref)[[2]],
    "OK: parameters pass checks for prevalence table."
  )

  expect_identical(
    validate_prevalence_table(P, Q, R, S, nexp, nref)[[3]],
    "prev_table_pos_tot"
  )
})

test_that("prev_table: Good neg total", {
  P <- NA
  Q <- 20
  R <- NA
  S <- 40
  nexp <- 50
  nref <- 100

  expect_identical(
    validate_prevalence_table(P, Q, R, S, nexp, nref)[[1]],
    TRUE
  )

  expect_identical(
    validate_prevalence_table(P, Q, R, S, nexp, nref)[[2]],
    "OK: parameters pass checks for prevalence table."
  )

  expect_identical(
    validate_prevalence_table(P, Q, R, S, nexp, nref)[[3]],
    "prev_table_neg_tot"
  )
})

test_that("prev_table: Good full table", {
  P <- 10
  Q <- 20
  R <- 30
  S <- 40
  nexp <- 50
  nref <- 100

  expect_identical(
    validate_prevalence_table(P, Q, R, S, nexp, nref)[[1]],
    TRUE
  )

  expect_identical(
    validate_prevalence_table(P, Q, R, S, nexp, nref)[[2]],
    "OK: parameters pass checks for prevalence table."
  )

  expect_identical(
    validate_prevalence_table(P, Q, R, S, nexp, nref)[[3]],
    "prev_table_pos_tot"
  )
})