tests/testthat/test_clinical_events_to_phecodes.R

In rmgpanw/codemapper: Functions for Mapping Between Clinical Coding Systems

# SETUP ---------------------------------------------------------------

all_lkps_maps_dummy <- build_all_lkps_maps_dummy()

ALL_LKPS_MAPS_DUMMY <- all_lkps_maps_to_db(all_lkps_maps_dummy,
                                           db_path = tempfile(fileext = ".db"))

clinical_events_dummy <- dummy_clinical_events_tidy()

clinical_events_phecodes_dummy <- map_clinical_events_to_phecodes(
  clinical_events = clinical_events_dummy,
  all_lkps_maps = all_lkps_maps_dummy,
  min_date_only = FALSE
)

phecode_reverse_map_dummy <-
  make_phecode_reverse_map(
    clinical_events_phecodes = clinical_events_phecodes_dummy,
    all_lkps_maps = all_lkps_maps_dummy
  )

# TESTS -------------------------------------------------------------------

# `map_clinical_events_to_phecodes()` -------------------------------------

test_that("`map_clinical_events_to_phecodes()` works with `all_lkps_maps` as a database",
          {
            expect_true(is.data.frame(
              map_clinical_events_to_phecodes(
                clinical_events = clinical_events_dummy,
                all_lkps_maps = ALL_LKPS_MAPS_DUMMY,
                min_date_only = FALSE
              )
            ))
          })

# check:

## - Read code for hypertension maps to 3 character 'I10' icd10, which is
## undivided and therefore ends with 'X' - the 'X' should be removed from icd10
## column in final result

test_that("`map_clinical_events_to_phecodes()` returns expected output with default `col_filters`", {
  expect_equal(
    clinical_events_phecodes_dummy,
    tibble::tribble(
      ~eid, ~source, ~index, ~code, ~date, ~icd10, ~phecode,
      1, "f40001", "0_0", NA, "1917-10-08", "I10", "401.1",
      1, "f40002", "0_0", NA, "1955-02-11", "E109", "250.1",
      1, "gpc3_r3", "3", "XaIP9", "1917-10-08", "L721", "706.2",
      1, "gpc3_r3", "3", "XaIP9", "1917-10-08", "L721", "704",
      1, "gpc3_r3", "3", "XE0Uc", "1917-10-08", "I10", "401.1",
      1, "f41271", "0_0", "4019", "1910-02-19", "I10", "401.1"
    )
  )
})

# note that now Read 3 'XaIP9' (Sebaceous cyst) maps to male and female specific
# ICD10 codes (N508 Other specified disorders of male genital organs, and N948
# Other specified conditions associated with female genital organs and menstrual
# cycle)

# note that Read 2 "C10.." (Diabetes mellitus) now maps to all diabetes subtypes
test_that("`map_clinical_events_to_phecodes()` returns expected output with no `col_filters`", {
  result_no_filters <- map_clinical_events_to_phecodes(
    clinical_events = clinical_events_dummy,
    all_lkps_maps = all_lkps_maps_dummy,
    min_date_only = FALSE,
    col_filters = NULL
  )

  expect_equal(
    result_no_filters,
    tibble::tribble(
      ~eid, ~source, ~index, ~code, ~date, ~icd10, ~phecode,
      1, "f40001", "0_0", NA, "1917-10-08", "I10", "401.1",
      1, "f40002", "0_0", NA, "1955-02-11", "E109", "250.1",
      1, "gpc1_r2", "1", "C10..", "1965-08-08", "E10", "250.1",
      1, "gpc1_r2", "1", "C10..", "1965-08-08", "E100", "250.1",
      1, "gpc1_r2", "1", "C10..", "1965-08-08", "E101", "250.11",
      1, "gpc1_r2", "1", "C10..", "1965-08-08", "E102", "250.12",
      1, "gpc1_r2", "1", "C10..", "1965-08-08", "E103", "250.23",
      1, "gpc1_r2", "1", "C10..", "1965-08-08", "E103", "250.7",
      1, "gpc1_r2", "1", "C10..", "1965-08-08", "E103", "250.13",
      1, "gpc1_r2", "1", "C10..", "1965-08-08", "E104", "250.14",
      1, "gpc1_r2", "1", "C10..", "1965-08-08", "E104", "250.24",
      1, "gpc1_r2", "1", "C10..", "1965-08-08", "E105", "443.7",
      1, "gpc1_r2", "1", "C10..", "1965-08-08", "E106", "250.1",
      1, "gpc1_r2", "1", "C10..", "1965-08-08", "E107", "250.1",
      1, "gpc1_r2", "1", "C10..", "1965-08-08", "E108", "250.1",
      1, "gpc1_r2", "1", "C10..", "1965-08-08", "E109", "250.1",
      1, "gpc1_r2", "1", "C10..", "1965-08-08", "E11", "250.2",
      1, "gpc1_r2", "1", "C10..", "1965-08-08", "E110", "250.2",
      1, "gpc1_r2", "1", "C10..", "1965-08-08", "E111", "250.21",
      1, "gpc1_r2", "1", "C10..", "1965-08-08", "E112", "250.22",
      1, "gpc1_r2", "1", "C10..", "1965-08-08", "E113", "250.23",
      1, "gpc1_r2", "1", "C10..", "1965-08-08", "E114", "250.24",
      1, "gpc1_r2", "1", "C10..", "1965-08-08", "E115", "443.7",
      1, "gpc1_r2", "1", "C10..", "1965-08-08", "E116", "250.2",
      1, "gpc1_r2", "1", "C10..", "1965-08-08", "E117", "250.2",
      1, "gpc1_r2", "1", "C10..", "1965-08-08", "E118", "250.2",
      1, "gpc1_r2", "1", "C10..", "1965-08-08", "E119", "250.2",
      1, "gpc1_r2", "1", "C10..", "1965-08-08", "E121", "260.2",
      1, "gpc1_r2", "1", "C10..", "1965-08-08", "E121", "249",
      1, "gpc1_r2", "1", "C10..", "1965-08-08", "E122", "260.2",
      1, "gpc1_r2", "1", "C10..", "1965-08-08", "E122", "249",
      1, "gpc1_r2", "1", "C10..", "1965-08-08", "E123", "250.23",
      1, "gpc1_r2", "1", "C10..", "1965-08-08", "E125", "249",
      1, "gpc1_r2", "1", "C10..", "1965-08-08", "E125", "260.2",
      1, "gpc1_r2", "1", "C10..", "1965-08-08", "E127", "260.2",
      1, "gpc1_r2", "1", "C10..", "1965-08-08", "E127", "249",
      1, "gpc1_r2", "1", "C10..", "1965-08-08", "E128", "249",
      1, "gpc1_r2", "1", "C10..", "1965-08-08", "E129", "249",
      1, "gpc1_r2", "1", "C10..", "1965-08-08", "E13", "250.2",
      1, "gpc1_r2", "1", "C10..", "1965-08-08", "E131", "250.21",
      1, "gpc1_r2", "1", "C10..", "1965-08-08", "E133", "250.7",
      1, "gpc1_r2", "1", "C10..", "1965-08-08", "E134", "250.24",
      1, "gpc1_r2", "1", "C10..", "1965-08-08", "E135", "250.2",
      1, "gpc1_r2", "1", "C10..", "1965-08-08", "E136", "250.2",
      1, "gpc1_r2", "1", "C10..", "1965-08-08", "E137", "250.2",
      1, "gpc1_r2", "1", "C10..", "1965-08-08", "E138", "250.2",
      1, "gpc1_r2", "1", "C10..", "1965-08-08", "E139", "250.2",
      1, "gpc1_r2", "1", "C10..", "1965-08-08", "E145", "443.7",
      1, "gpc1_r2", "1", "C10..", "1965-08-08", "E149", "250.2",
      1, "gpc1_r2", "2", "C10..", "1917-10-08", "E10", "250.1",
      1, "gpc1_r2", "2", "C10..", "1917-10-08", "E100", "250.1",
      1, "gpc1_r2", "2", "C10..", "1917-10-08", "E101", "250.11",
      1, "gpc1_r2", "2", "C10..", "1917-10-08", "E102", "250.12",
      1, "gpc1_r2", "2", "C10..", "1917-10-08", "E103", "250.23",
      1, "gpc1_r2", "2", "C10..", "1917-10-08", "E103", "250.7",
      1, "gpc1_r2", "2", "C10..", "1917-10-08", "E103", "250.13",
      1, "gpc1_r2", "2", "C10..", "1917-10-08", "E104", "250.14",
      1, "gpc1_r2", "2", "C10..", "1917-10-08", "E104", "250.24",
      1, "gpc1_r2", "2", "C10..", "1917-10-08", "E105", "443.7",
      1, "gpc1_r2", "2", "C10..", "1917-10-08", "E106", "250.1",
      1, "gpc1_r2", "2", "C10..", "1917-10-08", "E107", "250.1",
      1, "gpc1_r2", "2", "C10..", "1917-10-08", "E108", "250.1",
      1, "gpc1_r2", "2", "C10..", "1917-10-08", "E109", "250.1",
      1, "gpc1_r2", "2", "C10..", "1917-10-08", "E11", "250.2",
      1, "gpc1_r2", "2", "C10..", "1917-10-08", "E110", "250.2",
      1, "gpc1_r2", "2", "C10..", "1917-10-08", "E111", "250.21",
      1, "gpc1_r2", "2", "C10..", "1917-10-08", "E112", "250.22",
      1, "gpc1_r2", "2", "C10..", "1917-10-08", "E113", "250.23",
      1, "gpc1_r2", "2", "C10..", "1917-10-08", "E114", "250.24",
      1, "gpc1_r2", "2", "C10..", "1917-10-08", "E115", "443.7",
      1, "gpc1_r2", "2", "C10..", "1917-10-08", "E116", "250.2",
      1, "gpc1_r2", "2", "C10..", "1917-10-08", "E117", "250.2",
      1, "gpc1_r2", "2", "C10..", "1917-10-08", "E118", "250.2",
      1, "gpc1_r2", "2", "C10..", "1917-10-08", "E119", "250.2",
      1, "gpc1_r2", "2", "C10..", "1917-10-08", "E121", "260.2",
      1, "gpc1_r2", "2", "C10..", "1917-10-08", "E121", "249",
      1, "gpc1_r2", "2", "C10..", "1917-10-08", "E122", "260.2",
      1, "gpc1_r2", "2", "C10..", "1917-10-08", "E122", "249",
      1, "gpc1_r2", "2", "C10..", "1917-10-08", "E123", "250.23",
      1, "gpc1_r2", "2", "C10..", "1917-10-08", "E125", "249",
      1, "gpc1_r2", "2", "C10..", "1917-10-08", "E125", "260.2",
      1, "gpc1_r2", "2", "C10..", "1917-10-08", "E127", "260.2",
      1, "gpc1_r2", "2", "C10..", "1917-10-08", "E127", "249",
      1, "gpc1_r2", "2", "C10..", "1917-10-08", "E128", "249",
      1, "gpc1_r2", "2", "C10..", "1917-10-08", "E129", "249",
      1, "gpc1_r2", "2", "C10..", "1917-10-08", "E13", "250.2",
      1, "gpc1_r2", "2", "C10..", "1917-10-08", "E131", "250.21",
      1, "gpc1_r2", "2", "C10..", "1917-10-08", "E133", "250.7",
      1, "gpc1_r2", "2", "C10..", "1917-10-08", "E134", "250.24",
      1, "gpc1_r2", "2", "C10..", "1917-10-08", "E135", "250.2",
      1, "gpc1_r2", "2", "C10..", "1917-10-08", "E136", "250.2",
      1, "gpc1_r2", "2", "C10..", "1917-10-08", "E137", "250.2",
      1, "gpc1_r2", "2", "C10..", "1917-10-08", "E138", "250.2",
      1, "gpc1_r2", "2", "C10..", "1917-10-08", "E139", "250.2",
      1, "gpc1_r2", "2", "C10..", "1917-10-08", "E145", "443.7",
      1, "gpc1_r2", "2", "C10..", "1917-10-08", "E149", "250.2",
      1, "gpc3_r3", "3", "XaIP9", "1917-10-08", "L721", "706.2",
      1, "gpc3_r3", "3", "XaIP9", "1917-10-08", "L721", "704",
      1, "gpc3_r3", "3", "XaIP9", "1917-10-08", "H028", "374",
      1, "gpc3_r3", "3", "XaIP9", "1917-10-08", "N508", "608",
      1, "gpc3_r3", "3", "XaIP9", "1917-10-08", "N608", "610.8",
      1, "gpc3_r3", "3", "XaIP9", "1917-10-08", "N948", "625",
      1, "gpc3_r3", "3", "XE0Uc", "1917-10-08", "I10", "401.1",
      1, "f41271", "0_0", "4019", "1910-02-19", "I10", "401.1"
    )
  )
})

# `make_phecode_reverse_map()` --------------------------------------------


test_that("`make_phecode_reverse_map()` works with `all_lkps_maps` as a database",
          {
            expect_true(is.data.frame(
              make_phecode_reverse_map(
                clinical_events_phecodes = clinical_events_phecodes_dummy,
                all_lkps_maps = ALL_LKPS_MAPS_DUMMY
              )
            ))
          })

test_that("`make_phecode_reverse_map()` returns expected results", {
  expect_equal(
    phecode_reverse_map_dummy,
    tibble::tribble(
      ~phecode, ~phecode_description, ~data_coding, ~code, ~description, ~icd10_equivalent, ~icd10_description,
      "401.1", "Essential hypertension", "icd10", "I10", "Essential (primary) hypertension", "I10", "Essential (primary) hypertension",
      "250.1", "Type 1 diabetes", "icd10", "E109", "Type 1 diabetes mellitus Without complications", "E109", "Type 1 diabetes mellitus Without complications",
      "401.1", "Essential hypertension", "icd9", "4019", "ESSENTIAL HYPERTENSION NOT SPECIFIED", "I10", "Essential (primary) hypertension",
      "706.2", "Sebaceous cyst", "read3", "XaIP9", "Sebaceous cyst", "L721", "Trichilemmal cyst",
      "704", "Diseases of hair and hair follicles", "read3", "XaIP9", "Sebaceous cyst", "L721", "Trichilemmal cyst",
      "401.1", "Essential hypertension", "read3", "XE0Uc", "Essential hypertension", "I10", "Essential (primary) hypertension"
    )
  )
})