tests/testthat/test-hcc.R

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

context("test hcc")

test_that("can recreate the package data", {
  if (!dir.exists(system.file("data-raw", "icd_hcc_rawdata",
    package = "icd",
    mustWork = FALSE
  ))) {
    skip("HCC raw data not available")
  }
  expect_identical(
    .parse_cc_hierarchy(save_pkg_data = FALSE),
    icd_map_cc_hcc
  )
  expect_identical(
    .parse_icd9cm_cc(save_pkg_data = FALSE),
    icd9_map_cc
  )
  expect_identical(
    .parse_icd10cm_cc(save_pkg_data = FALSE),
    icd10_map_cc
  )
})

# Typical use case
# Data as expected. Multiple visits (different patients encounters)
# One of the patients with multiple visit dates, all valid ICDs
# Returns a unique HCC for each visit/date combination
# Only returns matches for valid ICDs in CC crosswalk
test_that("simple hcc 4 patients, different dates, each single HCC assigned", {
  res <- comorbid_hcc(hcc_test_simple9)
  expect_equal(dim(res), c(4, 3))
  expect_true(setequal(c("visit_id", "date", "hcc"), names(res)))
})

# Data as expected but only a single record
test_that("hcc one patient, single visit should have a single HCC assigned", {
  res <- comorbid_hcc(hcc_test_single)
  expect_equal(dim(res), c(1, 3))
  expect_true(setequal(c("visit", "date", "hcc"), names(res)))
})

# Mix of valid and invalid ICDs, some patients dont have any valid ICDs
# Only returns matches for valid ICDs in CC crosswalk
# should return 2 rows, 2 different patients
test_that("hcc 2 pt/visit combos each should have a single HCC assigned", {
  res <- comorbid_hcc(hcc_test_invalid)
  expect_equal(dim(res), c(2, 3))
  expect_true(setequal(c("patient", "date", "hcc"), names(res)))
})

test_that("github 153", {
  hcc_github153_df <- structure(
    list(
      date = structure(c(16855, 17123, 17008, NA), class = "Date"),
      visit_id = c(
        "1.98433805210381e-310", "6.92092372368813e-311",
        "7.85012017519427e-311", NA
      ),
      icd_code = c("F1020", "G4733", "M1712", NA)
    ),
    row.names = c("1", "2", "3", "NA"),
    class = c("icd_long_data", "data.frame")
  )
  expect_error(regexp = NA, comorbid_hcc(hcc_github153_df))
})

test_that("hcc icd10 codes", {
  res <- icd10_comorbid_hcc(hcc_test_simple10)
  expect_true(nrow(res) > 0)
})

test_that("hcc works with non-standard column names", {
  d2 <- hcc_test_simple9
  names(d2) <- c("a", "b", "c")
  expect_equivalent(
    comorbid_hcc(hcc_test_simple9),
    comorbid_hcc(d2,
      date_name = "c",
      visit_name = "a", icd_name = "b"
    )
  )
})