tests/testthat/test-util.R

In icd: Comorbidity Calculations and Tools for ICD-9 and ICD-10 Codes

context("util")


test_that("strim", {
  # strim (trim a single string)
  expect_equal(strim(NA_character_), NA_character_)
  expect_equal(strim("jack"), "jack")
  expect_equal(strim("jack "), "jack")
  expect_equal(strim(" jack "), "jack")
  expect_equal(strim(" jack"), "jack")
  expect_equal(strim("jack\t"), "jack")
  expect_equal(strim("\tjack\t"), "jack")
  expect_equal(strim("\tjack"), "jack")
  expect_equal(strim("ja ck"), "ja ck")
  expect_equal(strim("ja ck "), "ja ck")
  expect_equal(strim(" ja ck "), "ja ck")
  expect_equal(strim(" ja ck"), "ja ck")
  # is this what I want?
  expect_error(strim(c("jack", " an other ")))
  # strim and strimCpp should do the same thing, for non-NA input
  expect_identical(strim(" a s d f "), strimCpp(" a s d f "))
})

test_that("get visit name from a matrix should fail", {
  expect_error(regexp = NA, get_visit_name(matrix(c(1, 2, 3, 4), nrow = 2)))
  expect_error(get_visit_name(matrix(c(TRUE, TRUE, TRUE, TRUE), nrow = 2)))
})

test_that("get visit name works for this failure case", {
  nms <- c(
    "id", "newborn", "age", "dx01", "dx02", "dx03", "dx04", "dx05",
    "dx06", "dx07", "dx08", "dx09", "dx10", "dx11", "dx12", "dx13",
    "dx14", "dx15", "pc01", "pc02", "pc03", "pc04", "pc05", "pc06",
    "pc07", "pc08", "dx_adm", "emergency"
  )
  df <- as.data.frame(matrix(nrow = 2, ncol = length(nms)))
  names(df) <- nms
  expect_equal(get_visit_name(df), "id")
})

test_that("logical to binary for a matrix works", {
  expect_identical(
    logical_to_binary(matrix(c(T, F, T, F), nrow = 2)),
    matrix(c(1L, 0L, 1L, 0L), nrow = 2)
  )
})

context("heuristics for determining the field names of an input data frame")

test_that("well structured data frame, ICD & visit guessed", {
  expect_equal(get_visit_name(simple_poa_pts), "visit_id")
  expect_equal(get_icd_name(simple_poa_pts), "code")
  expect_equal(get_visit_name(complex_poa_pts), "visit_id")
  expect_equal(get_icd_name(complex_poa_pts), "icd9")
  expect_equal(get_visit_name(test_twenty), "visit_id")
  expect_equal(get_icd_name(test_twenty), "icd9Code")
})

test_that("icd name heuristic works for various", {
  guesses <- c(
    "icd.?(9|10)", "icd.?(9|10).?Code", "icd",
    "diagnos", "diag.?code", "diag", "i(9|10)", "code"
  )
  x <- simple_pts
  for (n in c(
    "icd-10", "icd9", "diag", "diag1",
    "DIAGCODE", "i9code", "code", "diagnosis"
  )) {
    names(x)[2] <- n
    expect_equal(get_icd_name(x), n)
  }
})

test_that("error if an unnamed data frame is used to guess field", {
  x <- unname(simple_pts)
  expect_error(get_visit_name(x))
  expect_error(get_icd_name(x))
})

test_that("icd9 field guessed from data if name fails, any order", {
  x <- simple_poa_pts
  x10 <- x
  x10[[2]] <- icd10_each_ahrq_cmb[1:4]
  names(x)[2] <- "not_helpful"
  names(x10)[2] <- "not_helpful"
  expect_equal(get_icd_dx_name(x), "not_helpful")
  perms <- matrix(ncol = 3, byrow = TRUE, data = c(
    1, 2, 3,
    1, 3, 2,
    2, 1, 3,
    2, 3, 1,
    3, 1, 2,
    3, 2, 1
  ))
  for (i in nrow(perms)) {
    expect_equal(get_icd_name(x[perms[i, ]]), "not_helpful",
      info = paste(perms[i, ], collapse = ", ")
    )
    expect_equal(get_icd_name(x10[perms[i, ]]), "not_helpful",
      info = paste(perms[i, ], collapse = ", ")
    )
  }
})

test_that("get_icd_name: icd field not present at all", {
  x <- simple_pts
  x[2] <- NULL
  expect_equal(get_icd_name(x), names(simple_pts)[1])
  names(x)[2] <- "icd"
  expect_error(get_icd_name(x))
  x[[2]] <- as.icd9(x[[2]])
  expect_error(get_icd_name(x))
})