test-manip.R
In icd: Comorbidity Calculations and Tools for ICD-9 and ICD-10 Codes

context("basic ICD-9 manipulations")

test_that("zero pad decimal - bad input", {
  expect_equal(
    icd9_add_leading_zeroes(short_code = FALSE, character()),
    character()
  )
  expect_equal(
    icd9_add_leading_zeroes(short_code = FALSE, NA_character_),
    NA_character_
  )
})

test_that("zero pad decimal, numeric only", {
  expect_equal(icd9_add_leading_zeroes(short_code = FALSE, "1"), "001")
  expect_equal(icd9_add_leading_zeroes(short_code = FALSE, "01"), "001")
  expect_equal(icd9_add_leading_zeroes(short_code = FALSE, " 01 "), "001")
  expect_equal(icd9_add_leading_zeroes(short_code = FALSE, "1.1"), "001.1")
  expect_equal(icd9_add_leading_zeroes(short_code = FALSE, "1.99"), "001.99")
  expect_equal(icd9_add_leading_zeroes(short_code = FALSE, "22"), "022")
  expect_equal(icd9_add_leading_zeroes(short_code = FALSE, " 22.34 "), "022.34")

  expect_equal(icd9_add_leading_zeroes(short_code = FALSE, "333"), "333")
  expect_equal(icd9_add_leading_zeroes(short_code = FALSE, "333.99"), "333.99")
  expect_equal(icd9_add_leading_zeroes(short_code = FALSE, "333.1 "), "333.1")
  expect_equal(
    icd9_add_leading_zeroes(
      short_code = FALSE,
      c("01", "1.99 ", "22.34", "333", "999.00")
    ),
    c("001", "001.99", "022.34", "333", "999.00")
  )
})

test_that("zero pad decimel V and E codes", {
  expect_equal(icd9_add_leading_zeroes(short_code = FALSE, "V1"), "V01")
  expect_equal(icd9_add_leading_zeroes(short_code = FALSE, " V1 "), "V01")
  expect_equal(icd9_add_leading_zeroes(short_code = FALSE, "V1.1"), "V01.1")
  expect_equal(icd9_add_leading_zeroes(short_code = FALSE, "V1.99"), "V01.99")
  expect_equal(icd9_add_leading_zeroes(short_code = FALSE, "V22"), "V22")
  expect_equal(icd9_add_leading_zeroes(short_code = FALSE, " V22.34 "), "V22.34")
  expect_equal(icd9_add_leading_zeroes(short_code = FALSE, "V1"), "V01")
  expect_equal(icd9_add_leading_zeroes(short_code = FALSE, " V1 "), "V01")
  expect_equal(icd9_add_leading_zeroes(short_code = FALSE, "V1.1"), "V01.1")
  expect_equal(icd9_add_leading_zeroes(short_code = FALSE, "V1.99"), "V01.99")
  expect_equal(icd9_add_leading_zeroes(short_code = FALSE, "V22"), "V22")
  expect_equal(
    icd9_add_leading_zeroes(short_code = FALSE, " V22.34 "),
    "V22.34"
  )
})

test_that("zero pad short invalid codes", {
  expect_equal(
    icd9_add_leading_zeroes(short_code = TRUE, character()),
    character()
  )
  expect_equal(
    icd9_add_leading_zeroes(short_code = TRUE, "anything"),
    NA_character_
  )
  expect_equal(
    icd9_add_leading_zeroes(short_code = TRUE, "anything"),
    NA_character_
  )
  expect_equal(
    icd9_add_leading_zeroes(short_code = TRUE, NA_character_),
    NA_character_
  )
  # this is just re-checking the validation code...
  expect_equal(icd9_add_leading_zeroes(short_code = TRUE, "V012"), "V012")
  expect_equal(icd9_add_leading_zeroes(short_code = TRUE, "V199"), "V199")
})

test_that("zero pad short", {
  expect_equal(icd9_add_leading_zeroes(short_code = TRUE, "1"), "001")
  expect_equal(icd9_add_leading_zeroes(short_code = TRUE, "01"), "001")
  expect_equal(icd9_add_leading_zeroes(short_code = TRUE, "22"), "022")
  expect_equal(icd9_add_leading_zeroes(short_code = TRUE, " 01 "), "001")
  expect_equal(icd9_add_leading_zeroes(short_code = TRUE, "199"), "199")
  expect_equal(icd9_add_leading_zeroes(short_code = TRUE, " 02234 "), "02234")
  expect_equal(icd9_add_leading_zeroes(short_code = TRUE, "V1"), "V01")
  expect_equal(icd9_add_leading_zeroes(short_code = TRUE, " V1 "), "V01")
  expect_equal(icd9_add_leading_zeroes(short_code = TRUE, "V1"), "V01")
  expect_equal(icd9_add_leading_zeroes(short_code = TRUE, " V1 "), "V01")
  expect_equal(icd9_add_leading_zeroes(short_code = TRUE, "V11"), "V11")
  expect_equal(icd9_add_leading_zeroes(short_code = TRUE, " V11 "), "V11")
  expect_equal(icd9_add_leading_zeroes(short_code = TRUE, "V11"), "V11")
  expect_equal(icd9_add_leading_zeroes(short_code = TRUE, " V11 "), "V11")
  expect_equal(icd9_add_leading_zeroes(short_code = TRUE, " V2234 "), "V2234")
  expect_equal(icd9_add_leading_zeroes(short_code = TRUE, "3331 "), "3331")
  expect_equal(
    icd9_add_leading_zeroes(
      short_code = TRUE,
      c("9", "01", "0199 ", "02234", "333", "99900")
    ),
    c("009", "001", "0199", "02234", "333", "99900")
  )
  expect_equal(
    icd9_add_leading_zeroes(short_code = TRUE, NA_character_),
    NA_character_
  )
  expect_equal(
    icd9_add_leading_zeroes(short_code = TRUE, "V12.34"),
    NA_character_
  )
})

test_that("icd9 parts to short form numeric input", {
  expect_equal(icd9_add_leading_zeroes_major(1L), "001")
  expect_equal(icd9_add_leading_zeroes_major(10L), "010")
  expect_equal(icd9_add_leading_zeroes_major(999L), "999")
  expect_equal(icd9_add_leading_zeroes_major(10.1), NA_character_)
})

test_that("add leading zeroes to V (and E) majors", {
  expect_equal(icd9_add_leading_zeroes_major("V1"), "V01")
  expect_equal(icd9_add_leading_zeroes_major("V2"), "V02")
  expect_equal(icd9_add_leading_zeroes_major("V03"), "V03")
  expect_equal(
    icd9_add_leading_zeroes_major(c("10", "V05")),
    c("010", "V05")
  )
  expect_equal(icd9_add_leading_zeroes_major("E915"), "E915")
})

test_that("add leading zeroes to majors, invalid input", {
  expect_equal(icd9_add_leading_zeroes_major("E9"), "E009")
  # should be minimally valid code
  expect_equal(icd9_add_leading_zeroes_major("E"), NA_character_)
  expect_equal(icd9_add_leading_zeroes_major("V"), NA_character_)
  expect_equal(icd9_add_leading_zeroes_major("jasmine"), NA_character_)
  # error if validating
  expect_equal(icd9_add_leading_zeroes_major("E"), NA_character_)
  expect_equal(icd9_add_leading_zeroes_major("V"), NA_character_)
  expect_equal(icd9_add_leading_zeroes_major("jasmine"), NA_character_)
  expect_equal(icd9_add_leading_zeroes_major("E9"), "E009")
})

test_that("add leading zeroes to a factor", {
  expect_equal(
    icd9_add_leading_zeroes(factor(c("02", "300.4"))),
    factor(c("002", "300.4"))
  )
})

test_that("extracting alphabetic and numeric parts from ICD-9 codes works", {
  expect_equal(
    icd9_extract_alpha_numeric("V12"),
    matrix(data = c("V", "12"), ncol = 2)
  )
  expect_equal(
    icd9_extract_alpha_numeric(c("V12", 34)),
    t(matrix(data = c("V", "12", "", "34"), ncol = 2))
  )
})

test_that("strip leading zeroes: errors", {
  expect_equal(
    icd9_drop_leading_zeroes(short_code = FALSE, NA_character_),
    NA_character_
  )
  # no guaranteed behaviour when code is invalid: it may or may not match the
  # regex. If the user wants to get the valid codes first, they can do that.
})

test_that("strip leading zero from decimal numeric only", {
  expect_equal(icd9_drop_leading_zeroes(short_code = FALSE, "1"), "1")
  expect_equal(icd9_drop_leading_zeroes(short_code = FALSE, "01"), "1")
  expect_equal(icd9_drop_leading_zeroes(short_code = FALSE, "001"), "1")
  expect_equal(icd9_drop_leading_zeroes(short_code = FALSE, "1."), "1.")
  expect_equal(icd9_drop_leading_zeroes(short_code = FALSE, "01."), "1.")
  expect_equal(icd9_drop_leading_zeroes(short_code = FALSE, "001."), "1.")
  expect_equal(icd9_drop_leading_zeroes(short_code = FALSE, "12"), "12")
  expect_equal(icd9_drop_leading_zeroes(short_code = FALSE, "012"), "12")
  expect_equal(icd9_drop_leading_zeroes(short_code = FALSE, "12."), "12.")
  expect_equal(icd9_drop_leading_zeroes(short_code = FALSE, "012."), "12.")
  expect_equal(icd9_drop_leading_zeroes(short_code = FALSE, "123"), "123")
  expect_equal(icd9_drop_leading_zeroes(short_code = FALSE, "123."), "123.")
  expect_equal(icd9_drop_leading_zeroes(short_code = FALSE, "1.2"), "1.2")
  expect_equal(icd9_drop_leading_zeroes(short_code = FALSE, "01.2"), "1.2")
  expect_equal(icd9_drop_leading_zeroes(short_code = FALSE, "001.2"), "1.2")
  expect_equal(icd9_drop_leading_zeroes(short_code = FALSE, "12.4"), "12.4")
  expect_equal(icd9_drop_leading_zeroes(short_code = FALSE, "012.4"), "12.4")
  expect_equal(icd9_drop_leading_zeroes(short_code = FALSE, "12.78"), "12.78")
  expect_equal(icd9_drop_leading_zeroes(short_code = FALSE, "012.78"), "12.78")
  expect_equal(icd9_drop_leading_zeroes(short_code = FALSE, "123.9"), "123.9")
  expect_equal(icd9_drop_leading_zeroes(short_code = FALSE, "123.87"), "123.87")
  # just double check we can do this the other way:
  expect_equal(icd9_drop_leading_zeroes("012.78", short_code = FALSE), "12.78")
})

test_that("strip leading zero from decimal V and E", {
  expect_equal(icd9_drop_leading_zeroes(short_code = FALSE, "V1"), "V1")
  expect_equal(icd9_drop_leading_zeroes(short_code = FALSE, "V01"), "V1")
  expect_equal(icd9_drop_leading_zeroes(short_code = FALSE, "V1."), "V1.")
  expect_equal(icd9_drop_leading_zeroes(short_code = FALSE, "V01."), "V1.")
  expect_equal(icd9_drop_leading_zeroes(short_code = FALSE, "V12"), "V12")
  expect_equal(icd9_drop_leading_zeroes(short_code = FALSE, "V12.3"), "V12.3")
  expect_equal(icd9_drop_leading_zeroes(short_code = FALSE, "V1.2"), "V1.2")
  expect_equal(icd9_drop_leading_zeroes(short_code = FALSE, "V01.2"), "V1.2")
  expect_equal(icd9_drop_leading_zeroes(short_code = FALSE, "V12.78"), "V12.78")
  expect_equal(icd9_drop_leading_zeroes(short_code = FALSE, "E912"), "E912")
  expect_equal(icd9_drop_leading_zeroes(short_code = FALSE, "E912."), "E912.")
  expect_equal(icd9_drop_leading_zeroes(short_code = FALSE, "E912.7"), "E912.7")
  expect_equal(
    icd9_drop_leading_zeroes(c("V12.78", " E898.", "02", "034.5"),
      short_code = FALSE
    ),
    c("V12.78", "E898.", "2", "34.5")
  )
})

test_that("strip leading zero from short numeric only", {
  expect_equal(
    icd9_drop_leading_zeroes(short_code = TRUE, NA_character_),
    NA_character_
  )
  expect_equal(icd9_drop_leading_zeroes(short_code = TRUE, "010"), "10")
  expect_equal(icd9_drop_leading_zeroes(short_code = TRUE, "009"), "9")
  # must have zero to be valid (001.2)
  expect_equal(icd9_drop_leading_zeroes(short_code = TRUE, "0012"), "0012")
  # must have zero to be valid (001.23)
  expect_equal(icd9_drop_leading_zeroes(short_code = TRUE, "00123"), "00123")
  expect_equal(icd9_drop_leading_zeroes(short_code = TRUE, "0124"), "0124")
  expect_equal(icd9_drop_leading_zeroes(short_code = TRUE, "01278"), "01278")
  expect_equal(icd9_drop_leading_zeroes(short_code = TRUE, "1239"), "1239")
  expect_equal(icd9_drop_leading_zeroes(short_code = TRUE, "12387"), "12387")
  # check other way
  expect_equal(
    unclass(res <- icd9_drop_leading_zeroes("1239", short_code = TRUE)),
    "1239"
  )
  # not sure whether I should test for short code or icd9 classes, too.
})

test_that("strip leading zero from decimal V and E", {
  expect_equal(icd9_drop_leading_zeroes(short_code = TRUE, "V1"), "V1")
  expect_equal(icd9_drop_leading_zeroes(short_code = TRUE, "V12"), "V12")
  expect_equal(icd9_drop_leading_zeroes(short_code = TRUE, "V123"), "V123")
  # cannot drop zero and be the same code. This is an important test!
  expect_equal(icd9_drop_leading_zeroes(short_code = TRUE, "V012"), "V012")
  expect_equal(icd9_drop_leading_zeroes(short_code = TRUE, "V1278"), "V1278")
  expect_equal(icd9_drop_leading_zeroes(short_code = TRUE, "E912"), "E912")
  expect_equal(icd9_drop_leading_zeroes(short_code = TRUE, "E9127"), "E9127")
  test_that("mixed vector drop leading zero short", {
    expect_equal(
      icd9_drop_leading_zeroes(c("V1278", " E898", "02", "0345"),
        short_code = TRUE
      ),
      c("V1278", "E898", "2", "0345")
    )
  })
})

test_that("drop leading zeroes from majors: invalid input", {
  # this is a little dangerous. dropping zeroes from a major is only valid for
  # short codes if the minor is empty, but this function is unaware of this.
  expect_equal(icd9_drop_leading_zeroes_major(""), "")
  expect_equal(length(icd9_drop_leading_zeroes_major(NA_character_)), 1L)
  expect_equal(length(icd9_drop_leading_zeroes_major(NA)), 1L)
  # dropping leading zeroes from an invalid code is undefined, so no tests.
})

test_that("drop leading zeroes from majors: numeric input", {
  expect_equal(icd9_drop_leading_zeroes_major(1), "1")
  expect_equal(icd9_drop_leading_zeroes_major(20), "20")
  expect_equal(icd9_drop_leading_zeroes_major(333), "333")
  expect_equal(icd9_drop_leading_zeroes_major("1"), "1")
  expect_equal(icd9_drop_leading_zeroes_major("20"), "20")
  expect_equal(icd9_drop_leading_zeroes_major("333"), "333")
  expect_equal(icd9_drop_leading_zeroes_major("01"), "1")
  expect_equal(icd9_drop_leading_zeroes_major(" 01 "), "1")
  expect_equal(icd9_drop_leading_zeroes_major("001"), "1")
  expect_equal(icd9_drop_leading_zeroes_major("020"), "20")
})

test_that("drop leading zeroes from majors: V codes", {
  expect_equal(icd9_drop_leading_zeroes_major("V1"), "V1")
  expect_equal(icd9_drop_leading_zeroes_major("V01"), "V1")
  expect_equal(icd9_drop_leading_zeroes_major(" V12"), "V12")
})

test_that("drop leading zeroes from majors: V codes preserves lower case v", {
  # no strong reason to force this, but seems reasonable
  expect_equal(icd9_drop_leading_zeroes_major(" v01 "), "v1")
  expect_equal(icd9_drop_leading_zeroes_major(" v9 "), "v9")
})

test_that("drop leading zeroes from majors: E codes", {
  expect_equal(icd9_drop_leading_zeroes_major("E800"), "E800")
  expect_equal(icd9_drop_leading_zeroes_major(" e812 "), "e812")
})