tests/testthat/test-elixhausers_acc_2_Quan_article.R
In gforge/comorbidities.icd10: Calculates Comorbidity Indices Based on ICD-9/10
elixhausers_codes_2_check = list()
#Congestive heart failure
elixhausers_codes_2_check[['CHF']] = list(
icd9_basic = c('39891', '40211',
'40291', '40411', '40413',
'40491', '40493', '4283'),
icd9 = c('39891', '40201', '40211',
'40291', '40401', '4283'),
icd9_SE = c('3980', '4020', '4021',
'4029', '4040', '4283'),
icd10 = c('I099', 'I110', 'I130', 'I132',
'I255', 'I420', 'I425', 'I4256', 'I426', 'I427', 'I429', 'I4344',
'I5023',
'P290'))
# Cardiac arrhythmias
elixhausers_codes_2_check[['ARRHYTHMIA']] = list(
icd9_basic = c('42610', '42611', '42613','42627', '42660', '42689',
'4270', '4272', '42731',
'42760', '4279', '7850',
'V450', 'V533'),
icd9 = c('4260', '4267', '4269',
'4270', '4271', '4272', '4273', '4274',
'4276', '4277', '4278', '4279', '7850',
'V450', 'V533'),
icd10 = c('I441', 'I442', 'I443', 'I456', 'I459',
'I47', 'I489', 'I49', 'R000',
'R001', 'R008', 'T821',
'Z450', 'Z950'))
# Valvular disease
elixhausers_codes_2_check[['VALVE']] = list(
icd9_basic = c('0932', '394', '3955', '396', '397', '4242',
'7463', '7464', '7465', '7466', 'V422', 'V433'),
icd9 = c('0932', '394', '3955', '396', '397', '4242',
'7463', '7464', '7465', '7466', 'V422', 'V433'),
icd10 = c('A520', 'I053', 'I06', 'I07', 'I08x', 'I091',
'I098', 'I34', 'I35', 'I36', 'I377', 'I38', 'I39x',
'Q230', 'Q231', 'Q232', 'Q233', 'Z952', 'Z953', 'Z954'))
# Pulmonary circulation disorders
elixhausers_codes_2_check[['PULM.CIRC']] = list(
icd9_basic = c('4160', '4162', '4179'),
icd9 = c('4150', '4151', '416x', '4170',
'4178', '4179'),
icd10 = c('I263', 'I272', 'I280', 'I288',
'I289'))
# Peripheral vascular disorders
elixhausers_codes_2_check[['PVD']] = list(
icd9_basic = c('4402', '4414',
'4431', '4432', '4433', '4434',
'4435', '4436', '4437', '4438', '4439', '4471', '5571',
'5579', 'V434'),
icd9 = c('0930', '4373', '4402', '4414',
'4431', '4432', '4433', '4434', '4435', '4436', '4437', '4438', '4439', '4471', '5571',
'5579', 'V434'),
icd10 = c('I704', 'I716', 'I731', 'I738',
'I739', 'I771', 'I790',
'I792', 'K551', 'K558',
'K559', 'Z958', 'Z959'))
# Hypertension, uncomplicated
elixhausers_codes_2_check[['HTN.UNCOMP']] = list(
icd9_basic = c('4011', '4019'),
icd9 = c('4013'),
icd10 = c('I104'))
# Hypertension, complicated
elixhausers_codes_2_check[['HTN.COMP']] = list(
icd9_basic = c('40210', '40290',
'40410', '40490',
'40591','40599'),
icd9 = c('4022', '4034', '404', '4058'),
icd10 = c('I11', 'I123', 'I135', 'I159'))
# Paralysis
elixhausers_codes_2_check[['PARALYSIS']] = list(
icd9_basic = c('3420', '34212', '3435',
'3440', '3441', '3442',
'3443', '3444', '3445', '3446', '3449'),
icd9 = c('3341', '3423', '3435',
'3440', '3441', '3442', '3443', '3444', '3445', '3446', '3449'),
icd10 = c('G041', 'G114', 'G801',
'G802', 'G816', 'G824',
'G830', 'G831', 'G832', 'G833', 'G834', 'G839'))
# Other neurological disorders
# NEUR => OthND
elixhausers_codes_2_check[['NEURO.OTHER']] = list(
icd9_basic = c('3319', '3320', '3334',
'3335', '334', '3343', '3353',
'340', '3414', '3454',
'3481', '3483', '7803', '7843'),
icd9 = c('3319', '3320', '3321', '3334',
'3335', '334', '3343', '3353',
'3362', '3403', '3414', '3454',
'3481', '3483', '7803', '7843'),
icd10 = c('G10', 'G119', 'G122', 'G138', 'G202', 'G212', 'G215',
'G223', 'G254', 'G255',
'G312', 'G318', 'G319',
'G32x', 'G352', 'G363', 'G366', 'G372',
'G402', 'G415', 'G931',
'G934', 'R470', 'R564'))
# Chronic pulmonary disease
elixhausers_codes_2_check[['CHRONIC.PULM']] = list(
icd9_basic = c('490', '4902', '4912', '492', '4934',
'494', '496', '497', '498', '4999',
'5002', '5012', '5023', '503', '5045', '5059',
'5064'),
icd9 = c('4168', '4169', '490', '4902', '4912', '492', '4934',
'4942', '4945', '496', '497', '498', '4999',
'5002', '5012', '5023', '503', '5045', '5059',
'5064', '5081', '5088'),
icd10 = c('I278', 'I279', 'J402', 'J412',
'J42', 'J433', 'J449', 'J45', 'J46', 'J472',
'J602', 'J61', 'J623', 'J639', 'J64', 'J655', 'J666', 'J672', 'J684',
'J701', 'J703'))
# Diabetes, uncomplicated
elixhausers_codes_2_check[['DM.UNCOMP']] = list(
icd9_basic = c('2500', '2501', '2502', '2503'),
icd9 = c('2500', '2501', '2502', '2503'),
icd10 = c('E100', 'E101', 'E109',
'E110', 'E111', 'E119',
'E120', 'E121', 'E129',
'E130', 'E131', 'E139',
'E140', 'E141', 'E149'))
# Diabetes, complicated
elixhausers_codes_2_check[['DM.COMP']] = list(
icd9_basic = c('2504', '2505', '2506', '25073', '2509'),
icd9 = c('2504', '2505', '2506', '2507', '2508', '2509'),
icd10 = c('E102', 'E103', 'E104', 'E105', 'E106', 'E107', 'E108',
'E112', 'E113', 'E114', 'E115', 'E116', 'E117', 'E118', 'E122', 'E123', 'E124', 'E125', 'E126', 'E127', 'E128',
'E132', 'E133', 'E134', 'E135', 'E136', 'E137', 'E138',
'E142', 'E143', 'E144', 'E145', 'E146', 'E147', 'E148'))
# Hypothyroidism
elixhausers_codes_2_check[['HYPOTHYROID']] = list(
icd9_basic = c('2431', '2442', '2448', '2449'),
icd9 = c('2409', '2431', '2443', '2461', '2468'),
icd10 = c('E002', 'E003', 'E004', 'E012', 'E022', 'E033', 'E890'))
# Renal failure
elixhausers_codes_2_check[['RENAL']] = list(
icd9_basic = c('40311', '40391',
'40492', '585', '586',
'V420', 'V451', 'V560'),
icd9_SE = c('4030', '4031', '4039',
'4040', '4041', '4041',
'4049', '5854', '5863',
'5880', 'V420', 'V451', 'V564'),
icd9 = c('40301', '40311', '40391',
'40402', '40413', '40412',
'40492', '5854', '5863',
'5880', 'V420', 'V451', 'V564'),
icd10 = c('I120', 'I131', 'N182',
'N192', 'N250', 'Z490', 'Z491', 'Z492', 'Z940', 'Z992'))
# Liver disease
elixhausers_codes_2_check[['LIVER']] = list(
icd9_basic = c('07032', '07033',
'07054', '4560', '4561', '4562',
'5713', '5723', '5728', 'V427'),
icd9_SE = c('0702', '0703',
'0704', '0705',
'4560', '4561', '4562', '5702', '5713',
'5722', '5723', '5724', '5725', '5726', '5727', '5728', '5733', '5734',
'5738', '5739', 'V427'),
icd9 = c('07022', '07032',
'07044', '07054',
'4560', '4561', '4562', '5702', '5713',
'5722', '5723', '5724', '5725', '5726', '5727', '5728', '5733', '5734',
'5738', '5739', 'V427'),
icd10 = c('B18x', 'I85x', 'I864', 'I982',
'K70x', 'K711',
'K713', 'K714', 'K715', 'K717',
'K723', 'K733', 'K749', 'K760',
'K762', 'K763', 'K764', 'K765', 'K766', 'K767', 'K768', 'K769', 'Z944'))
# Peptic ulcer disease excluding bleeding
elixhausers_codes_2_check[['PUD']] = list(
icd9_basic = c('5317', '5319', '5327',
'5329', '5337', '5339',
'5347', '5349'),
icd9 = c('5317', '5319', '5327',
'5329', '5337', '5339',
'5347', '5349'),
icd10 = c('K257', 'K259', 'K267', 'K269',
'K277', 'K279', 'K287',
'K289'))
# AIDS/HIV
elixhausers_codes_2_check[['HIV']] = list(
icd9_basic = c('0422', '0439', '0441'),
icd9 = c('0422', '0439', '0441'),
icd10 = c('B201', 'B212', 'B229', 'B243'))
# Lymphoma
# LYMPH => Lymp
elixhausers_codes_2_check[['LYMPHOMA']] = list(
icd9_basic = c('2002', '2012', '2029', '2030', '2386'),
icd9 = c('2002', '2012', '2029', '2030', '2386'),
icd10 = c('C812', 'C823', 'C839',
'C841', 'C844', 'C853',
'C881', 'C961',
'C900', 'C902'))
# Metastatic cancer
elixhausers_codes_2_check[['METS']] = list(
icd9_basic = c('1967', '1977', '1991'),
icd9 = c('1967', '1977', '1998'),
icd10 = c('C771', 'C782', 'C799', 'C801'))
# Solid tumor without metastasis
# CANCER => Tumor
elixhausers_codes_2_check[['SOLID.TUMOR']] = list(
icd9_basic = c('1402', '1412', '1438', '1444', '1459', '1461', '1477', '1489', '1491',
'1501', '1511', '1521', '1539', '1543', '1557', '1561', '1572', '1580', '1599',
'1601', '1619', '1621', '1637', '1644', '1652', '1666', '1671', '1688', '1691',
'1707', '1712', '1723', '1743', '1755', '1790',
'1808', '1810', '1820', '1831', '1844', '1852', '1867', '1871', '1880', '1894',
'1905', '1913', '1921', '1939', '1945', '1951'),
icd9 = c('1402', '1412', '1438', '1444', '1459', '1461', '1477', '1489', '1491',
'1501', '1511', '1521', '1539', '1543', '1557', '1561', '1572', '1580', '1599',
'1601', '1619', '1621', '1637', '1644', '1652', '1666', '1671', '1688', '1691',
'1707', '1712', '1723', '1743', '1755', '1761', '1777', '1789', '1790',
'1808', '1810', '1820', '1831', '1844', '1852', '1867', '1871', '1880', '1894',
'1905', '1913', '1921', '1939', '1945', '1951'),
icd10 = c('C001', 'C010', 'C024', 'C035', 'C045', 'C055', 'C066', 'C076', 'C088', 'C092',
'C102', 'C111', 'C121', 'C130', 'C142', 'C155', 'C163', 'C178', 'C184', 'C191',
'C201', 'C217', 'C229', 'C234', 'C249', 'C251', 'C263',
'C302', 'C310', 'C323', 'C334', 'C346',
'C372', 'C380', 'C391',
'C401', 'C412', 'C433', 'C453', 'C467', 'C479', 'C481', 'C490',
'C507', 'C517', 'C525', 'C531', 'C546', 'C551', 'C561', 'C574', 'C583',
'C602', 'C619', 'C629', 'C636', 'C645', 'C673', 'C681', 'C697',
'C708', 'C718', 'C724', 'C735', 'C744', 'C752', 'C762',
'C972'))
# Rheumatoid arthritis/collagen vascular diseases
# Rheum => Rheum_A
elixhausers_codes_2_check[['RHEUM']] = list(
icd9_basic = c('7010', '7100', '7101', '7102', '7103', '7104', '7108', '7109',
'7148', '7203', '725'),
icd9_SE = c('4462', '7010', '7100', '7101', '7102', '7103', '7104', '7108', '7109',
'7112', '7148', '7193',
'7203', '7258', '7285',
'7288', '7293'),
icd9 = c('4462', '7010', '7100', '7101', '7102', '7103', '7104', '7108', '7109',
'7112', '7148', '7193',
'7203', '7258', '7285',
'72889', '72930'),
icd10 = c('L940', 'L941', 'L943', 'M051',
'M062', 'M083', 'M120', 'M123',
'M303', 'M310', 'M311', 'M312', 'M313',
'M322', 'M333', 'M346', 'M359',
'M45x', 'M461', 'M468',
'M469'))
# Coagulopathy
elixhausers_codes_2_check[['COAG']] = list(
icd9_basic = c('2860', '2864', '2871', '2873', '2874', '2875'),
icd9 = c('286x', '2871', '2873', '2874', '2875'),
icd10 = c('D65', 'D66', 'D67', 'D682', 'D691',
'D693', 'D694', 'D695', 'D696'))
# Obesity
elixhausers_codes_2_check[['OBESITY']] = list(
icd9_basic = c('2780'),
icd9 = c('2780'),
icd10 = c('E662'))
# Weight loss
# WGHT_LOSS => WL
elixhausers_codes_2_check[['WT.LOSS']] = list(
icd9_basic = c('2602', '2603', '2612', '2623', '2637'),
icd9 = c('2602', '2603', '2612', '2623', '2637',
'7832', '7994'),
icd10 = c('E402', 'E403', 'E412', 'E424', 'E434', 'E449',
'E451', 'E461', 'R634', 'R64'))
# Fluid and electrolyte disorders
elixhausers_codes_2_check[['LYTES']] = list(
icd9_basic = c('2760', '2762', '2769'),
icd9 = c('2536', '2762'),
icd10 = c('E222', 'E863', 'E879'))
# Blood loss anemia
elixhausers_codes_2_check[['ANEMIA.LOSS']] = list(
icd9_basic = c('2800'),
icd9 = c('2800'),
icd10 = c('D500'))
# Deficiency anemia
# ANEMIA => DA
elixhausers_codes_2_check[['ANEMIA.DEF']] = list(
icd9_basic = c('2801', '2802', '2803', '2804', '2805',
'2806', '2807', '2808', '2809', '2813'),
icd9 = c('2801', '2802', '2803', '2804', '2805',
'2806', '2807', '2808', '2809', '2813'),
icd10 = c('D508', 'D509', 'D512', 'D523', 'D539'))
# Alcohol abuse
elixhausers_codes_2_check[['ETOH']] = list(
icd9_basic = c('2911', '2912',
'2915', '2918', '2919',
'3039', '3050',
'V113'),
icd9 = c('2652', '2911', '2912', '2913',
'2915', '2916', '2917', '2918', '2919', '3030',
'3039', '3050', '3575',
'4255', '5353',
'5710', '5711', '5712', '5713', '9802', 'V113'),
icd10 = c('F10', 'E52', 'G621', 'I426',
'K292', 'K700', 'K703',
'K709', 'T511', 'Z502',
'Z714', 'Z721'))
# Drug abuse
# DR_ABUSE => Drug
elixhausers_codes_2_check[['DRUGS']] = list(
icd9_basic = c('2920', '29282', '3049', '3052', '3053', '3054',
'3055', '3056', '3057', '3058', '3059'),
icd9 = c('2922', '3049', '3052', '3053', '3054', '3055', '3056',
'3057', '3058', '3059', 'V6542'),
icd10 = c('F112', 'F129', 'F134', 'F151', 'F160', 'F189', 'F196',
'Z715', 'Z722'))
# Psychoses
elixhausers_codes_2_check[['PSYCHOSES']] = list(
icd9_basic = c('2952', '29604',
'2960', '2968',
'2978', '2983'),
icd9_SE = c('2938', '2952', '29604',
'2960', '2968',
'2978', '2983'),
icd9 = c('2938', '2952', '29604',
'29614', '29644',
'2978', '2983'),
icd10 = c('F202', 'F222', 'F232', 'F249', 'F257', 'F281',
'F292', 'F302', 'F312', 'F315'))
# Depression
elixhausers_codes_2_check[['DEPRESSION']] = list(
icd9_basic = c('3004', '3091', '311'),
icd9_SE = c('2961', '2963', '2965',
'3004', '3092', '311'),
icd9 = c('2962', '2963', '2965',
'3004', '3092', '311'),
icd10 = c('F204', 'F313', 'F314', 'F315', 'F322',
'F339', 'F341', 'F412', 'F432'))
context("Numeric functions")
test_that("Check Elixhausers matches or the basic elixhauser() function",{
for (n in names(elixhausers_codes_2_check)){
if ("icd9_basic" %in% names(elixhausers_codes_2_check[[n]])){
codes <- elixhausers_codes_2_check[[n]]$icd9_basic
test_df <- data.frame(Codes=codes)
out <- elixhauser(test_df)
found_codes <- out$COMORBIDITIES[,n] == 1
expect_true(all(found_codes),
info=sprintf("The script fails to properly identify from '%s' the codes '%s'",
n,
paste(codes[!found_codes],
collapse="', '")))
}
}
})
test_that("Check elixhauser count score",{
t1 <- data.frame(icd1=elixhausers_codes_2_check$CHF$icd9_basic[1],
icd2=elixhausers_codes_2_check$VALVE$icd9_basic[1],
icd3=elixhausers_codes_2_check$WT.LOSS$icd9_basic[1])
out <- elixhauser(t1)
expect_equal(out$COMORBIDITY.CT, 1+1+1,
label="3 code groups counted")
t2 <- data.frame(icd1=elixhausers_codes_2_check$HTN.COMP$icd9_basic[1],
icd2=elixhausers_codes_2_check$DRUGS$icd9_basic[1],
icd3=elixhausers_codes_2_check$DM.COMP$icd9_basic[1],
icd4=elixhausers_codes_2_check$ANEMIA.LOSS$icd9_basic[1])
out <- elixhauser(t2)
expect_equal(out$COMORBIDITY.CT, 1+1+1+1,
label="4 code groups counted")
t3 <- data.frame(icd1=elixhausers_codes_2_check$HTN.COMP$icd9_basic[1],
icd2=elixhausers_codes_2_check$DRUGS$icd9_basic[1],
icd3=NA,
icd4=elixhausers_codes_2_check$ANEMIA.LOSS$icd9_basic[1])
out <- elixhauser(t3)
expect_equal(out$COMORBIDITY.CT, 1+1+0+1,
label="3 code groups and one missing counted")
})
neg.icd9_codes <-
as.character(
c(128.9, # HELMINTH INFECTION UNSPECIFIED
136.21, # SPECIFIC INFECTION DUE TO ACANTHAMOEBA
136.29, # OTHER SPECIFIC INFECTIONS BY FREE-LIVING AMEBAE
288.04, # NEUTROPENIA DUE TO INFECTION
323.41, # OTHER ENCEPHALITIS AND ENCEPHALOMYELITIS DUE TO OTHER INFECTIONS CLASSIFIED ELSEWHERE
323.42, # OTHER MYELITIS DUE TO OTHER INFECTIONS CLASSIFIED ELSEWHERE
326, # LATE EFFECTS OF INTRACRANIAL ABSCESS OR PYOGENIC INFECTION
379.60, # INFLAMMATION (INFECTION) OF POSTPROCEDURAL BLEB, UNSPECIFIED
379.61, # INFLAMMATION (INFECTION) OF POSTPROCEDURAL BLEB, STAGE 1
379.62, # INFLAMMATION (INFECTION) OF POSTPROCEDURAL BLEB, STAGE 2
379.63, # INFLAMMATION (INFECTION) OF POSTPROCEDURAL BLEB, STAGE 3
380.11, # ACUTE INFECTION OF PINNA
380.13, # OTHER ACUTE INFECTIONS OF EXTERNAL EAR
465.8, # ACUTE UPPER RESPIRATORY INFECTIONS OF OTHER MULTIPLE SITES
465.9, # ACUTE UPPER RESPIRATORY INFECTIONS OF UNSPECIFIED SITE
519.01, # INFECTION OF TRACHEOSTOMY
733.93, # STRESS FRACTURE OF TIBIA OR FIBULA
733.94, # STRESS FRACTURE OF THE METATARSALS
733.95, # STRESS FRACTURE OF OTHER BONE
733.96, # STRESS FRACTURE OF FEMORAL NECK
806.9, # OPEN FRACTURE OF UNSPECIFIED VERTEBRA WITH SPINAL CORD INJURY
807.00, # CLOSED FRACTURE OF RIB(S) UNSPECIFIED
807.01, # CLOSED FRACTURE OF ONE RIB
807.02, # CLOSED FRACTURE OF TWO RIBS
807.03, # CLOSED FRACTURE OF THREE RIBS
807.04, # CLOSED FRACTURE OF FOUR RIBS
808.43, # MULTIPLE CLOSED PELVIC FRACTURES WITH DISRUPTION OF PELVIC CIRCLE
808.44, # MULTIPLE CLOSED PELVIC FRACTURES WITHOUT DISRUPTION OF PELVIC CIRCLE
808.49, # CLOSED FRACTURE OF OTHER SPECIFIED PART OF PELVIS
808.51, # OPEN FRACTURE OF ILIUM
808.52, # OPEN FRACTURE OF ISCHIUM
808.53, # MULTIPLE OPEN PELVIC FRACTURES WITH DISRUPTION OF PELVIC CIRCLE
808.54, # MULTIPLE OPEN PELVIC FRACTURES WITHOUT DISRUPTION OF PELVIC CIRCLE
808.59, # OPEN FRACTURE OF OTHER SPECIFIED PART OF PELVIS
808.8, # UNSPECIFIED CLOSED FRACTURE OF PELVIS
808.9, # UNSPECIFIED OPEN FRACTURE OF PELVIS
809.0, # FRACTURE OF BONES OF TRUNK CLOSED
809.1, # FRACTURE OF BONES OF TRUNK OPEN
810.00, # CLOSED FRACTURE OF CLAVICLE UNSPECIFIED PART
810.01, # CLOSED FRACTURE OF STERNAL END OF CLAVICLE
810.02, # CLOSED FRACTURE OF SHAFT OF CLAVICLE
812.10, # FRACTURE OF UNSPECIFIED PART OF UPPER END OF HUMERUS OPEN
812.11, # FRACTURE OF SURGICAL NECK OF HUMERUS OPEN
812.12, # FRACTURE OF ANATOMICAL NECK OF HUMERUS OPEN
812.13, # FRACTURE OF GREATER TUBEROSITY OF HUMERUS OPEN
812.19, # OTHER OPEN FRACTURE OF UPPER END OF HUMERUS
812.20, # FRACTURE OF UNSPECIFIED PART OF HUMERUS CLOSED
812.21, # FRACTURE OF SHAFT OF HUMERUS CLOSED
812.30, # FRACTURE OF UNSPECIFIED PART OF HUMERUS OPEN
812.31, # FRACTURE OF SHAFT OF HUMERUS OPEN
715.96, # Osteoarthrosis, unspecified whether generalized or localized, lower leg
NA))
test_that("Check elixhauser handling of negative scores",{
test_df <- data.frame(Codes=neg.icd9_codes)
out <- elixhauser(test_df)
expect_true(all(out$COMORBIDITY.CT == 0),
label="Identified comorbidities that should be negative",
info=sprintf("Comorbity code(s) identified: %s",
paste(neg.icd9_codes[rowSums(out$COMORBIDITIES) > 0],
collapse=",")))
})
context("Regular expression functions")
test_that("Check Elixhausers matches to the regular expression Quan version",{
for (n in names(elixhausers_codes_2_check)){
for (icd_ver in names(elixhausers_codes_2_check[[n]])){
if (icd_ver == "icd9_basic") {next;} # Only for the numerical version
# There are a few Swedish adaptations that have a different match
if (grepl("_SE", icd_ver)) {
country_code = "SE"
}else{
country_code = "US"
}
codes <- elixhausers_codes_2_check[[n]][[icd_ver]]
out <- t(sapply(codes,
function(code)
cmrbdt.finder.regex.elixhauser_Quan2005(icd_codes=code,
country_code=country_code,
icd_ver=gsub("[^0-9]", "", icd_ver))))
found_codes <- out[,n]
expect_true(all(found_codes),
info=sprintf("The script fails to properly identify ICD-%s from '%s' the codes '%s'",
gsub("[^0-9]", "", icd_ver),
n,
paste(codes[!found_codes],
collapse="', '")))
# # HTN.COMP overlaps and others - skip this check
# falsely_found_codes <- apply(out[,-grep(n, colnames(out))], 1, any)
# expect_true(all(!falsely_found_codes),
# info=sprintf("The script fails to properly not identify ICD-%s from '%s' the codes '%s'",
# substring(icd_ver, nchar(icd_ver)),
# n,
# paste(codes[falsely_found_codes],
# collapse="', '")))
}
}
})
gforge/comorbidities.icd10 documentation built on May 17, 2019, 2:12 a.m.
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elixhausers_codes_2_check = list()
#Congestive heart failure
elixhausers_codes_2_check[['CHF']] = list(
icd9_basic = c('39891', '40211',
'40291', '40411', '40413',
'40491', '40493', '4283'),
icd9 = c('39891', '40201', '40211',
'40291', '40401', '4283'),
icd9_SE = c('3980', '4020', '4021',
'4029', '4040', '4283'),
icd10 = c('I099', 'I110', 'I130', 'I132',
'I255', 'I420', 'I425', 'I4256', 'I426', 'I427', 'I429', 'I4344',
'I5023',
'P290'))
# Cardiac arrhythmias
elixhausers_codes_2_check[['ARRHYTHMIA']] = list(
icd9_basic = c('42610', '42611', '42613','42627', '42660', '42689',
'4270', '4272', '42731',
'42760', '4279', '7850',
'V450', 'V533'),
icd9 = c('4260', '4267', '4269',
'4270', '4271', '4272', '4273', '4274',
'4276', '4277', '4278', '4279', '7850',
'V450', 'V533'),
icd10 = c('I441', 'I442', 'I443', 'I456', 'I459',
'I47', 'I489', 'I49', 'R000',
'R001', 'R008', 'T821',
'Z450', 'Z950'))
# Valvular disease
elixhausers_codes_2_check[['VALVE']] = list(
icd9_basic = c('0932', '394', '3955', '396', '397', '4242',
'7463', '7464', '7465', '7466', 'V422', 'V433'),
icd9 = c('0932', '394', '3955', '396', '397', '4242',
'7463', '7464', '7465', '7466', 'V422', 'V433'),
icd10 = c('A520', 'I053', 'I06', 'I07', 'I08x', 'I091',
'I098', 'I34', 'I35', 'I36', 'I377', 'I38', 'I39x',
'Q230', 'Q231', 'Q232', 'Q233', 'Z952', 'Z953', 'Z954'))
# Pulmonary circulation disorders
elixhausers_codes_2_check[['PULM.CIRC']] = list(
icd9_basic = c('4160', '4162', '4179'),
icd9 = c('4150', '4151', '416x', '4170',
'4178', '4179'),
icd10 = c('I263', 'I272', 'I280', 'I288',
'I289'))
# Peripheral vascular disorders
elixhausers_codes_2_check[['PVD']] = list(
icd9_basic = c('4402', '4414',
'4431', '4432', '4433', '4434',
'4435', '4436', '4437', '4438', '4439', '4471', '5571',
'5579', 'V434'),
icd9 = c('0930', '4373', '4402', '4414',
'4431', '4432', '4433', '4434', '4435', '4436', '4437', '4438', '4439', '4471', '5571',
'5579', 'V434'),
icd10 = c('I704', 'I716', 'I731', 'I738',
'I739', 'I771', 'I790',
'I792', 'K551', 'K558',
'K559', 'Z958', 'Z959'))
# Hypertension, uncomplicated
elixhausers_codes_2_check[['HTN.UNCOMP']] = list(
icd9_basic = c('4011', '4019'),
icd9 = c('4013'),
icd10 = c('I104'))
# Hypertension, complicated
elixhausers_codes_2_check[['HTN.COMP']] = list(
icd9_basic = c('40210', '40290',
'40410', '40490',
'40591','40599'),
icd9 = c('4022', '4034', '404', '4058'),
icd10 = c('I11', 'I123', 'I135', 'I159'))
# Paralysis
elixhausers_codes_2_check[['PARALYSIS']] = list(
icd9_basic = c('3420', '34212', '3435',
'3440', '3441', '3442',
'3443', '3444', '3445', '3446', '3449'),
icd9 = c('3341', '3423', '3435',
'3440', '3441', '3442', '3443', '3444', '3445', '3446', '3449'),
icd10 = c('G041', 'G114', 'G801',
'G802', 'G816', 'G824',
'G830', 'G831', 'G832', 'G833', 'G834', 'G839'))
# Other neurological disorders
# NEUR => OthND
elixhausers_codes_2_check[['NEURO.OTHER']] = list(
icd9_basic = c('3319', '3320', '3334',
'3335', '334', '3343', '3353',
'340', '3414', '3454',
'3481', '3483', '7803', '7843'),
icd9 = c('3319', '3320', '3321', '3334',
'3335', '334', '3343', '3353',
'3362', '3403', '3414', '3454',
'3481', '3483', '7803', '7843'),
icd10 = c('G10', 'G119', 'G122', 'G138', 'G202', 'G212', 'G215',
'G223', 'G254', 'G255',
'G312', 'G318', 'G319',
'G32x', 'G352', 'G363', 'G366', 'G372',
'G402', 'G415', 'G931',
'G934', 'R470', 'R564'))
# Chronic pulmonary disease
elixhausers_codes_2_check[['CHRONIC.PULM']] = list(
icd9_basic = c('490', '4902', '4912', '492', '4934',
'494', '496', '497', '498', '4999',
'5002', '5012', '5023', '503', '5045', '5059',
'5064'),
icd9 = c('4168', '4169', '490', '4902', '4912', '492', '4934',
'4942', '4945', '496', '497', '498', '4999',
'5002', '5012', '5023', '503', '5045', '5059',
'5064', '5081', '5088'),
icd10 = c('I278', 'I279', 'J402', 'J412',
'J42', 'J433', 'J449', 'J45', 'J46', 'J472',
'J602', 'J61', 'J623', 'J639', 'J64', 'J655', 'J666', 'J672', 'J684',
'J701', 'J703'))
# Diabetes, uncomplicated
elixhausers_codes_2_check[['DM.UNCOMP']] = list(
icd9_basic = c('2500', '2501', '2502', '2503'),
icd9 = c('2500', '2501', '2502', '2503'),
icd10 = c('E100', 'E101', 'E109',
'E110', 'E111', 'E119',
'E120', 'E121', 'E129',
'E130', 'E131', 'E139',
'E140', 'E141', 'E149'))
# Diabetes, complicated
elixhausers_codes_2_check[['DM.COMP']] = list(
icd9_basic = c('2504', '2505', '2506', '25073', '2509'),
icd9 = c('2504', '2505', '2506', '2507', '2508', '2509'),
icd10 = c('E102', 'E103', 'E104', 'E105', 'E106', 'E107', 'E108',
'E112', 'E113', 'E114', 'E115', 'E116', 'E117', 'E118', 'E122', 'E123', 'E124', 'E125', 'E126', 'E127', 'E128',
'E132', 'E133', 'E134', 'E135', 'E136', 'E137', 'E138',
'E142', 'E143', 'E144', 'E145', 'E146', 'E147', 'E148'))
# Hypothyroidism
elixhausers_codes_2_check[['HYPOTHYROID']] = list(
icd9_basic = c('2431', '2442', '2448', '2449'),
icd9 = c('2409', '2431', '2443', '2461', '2468'),
icd10 = c('E002', 'E003', 'E004', 'E012', 'E022', 'E033', 'E890'))
# Renal failure
elixhausers_codes_2_check[['RENAL']] = list(
icd9_basic = c('40311', '40391',
'40492', '585', '586',
'V420', 'V451', 'V560'),
icd9_SE = c('4030', '4031', '4039',
'4040', '4041', '4041',
'4049', '5854', '5863',
'5880', 'V420', 'V451', 'V564'),
icd9 = c('40301', '40311', '40391',
'40402', '40413', '40412',
'40492', '5854', '5863',
'5880', 'V420', 'V451', 'V564'),
icd10 = c('I120', 'I131', 'N182',
'N192', 'N250', 'Z490', 'Z491', 'Z492', 'Z940', 'Z992'))
# Liver disease
elixhausers_codes_2_check[['LIVER']] = list(
icd9_basic = c('07032', '07033',
'07054', '4560', '4561', '4562',
'5713', '5723', '5728', 'V427'),
icd9_SE = c('0702', '0703',
'0704', '0705',
'4560', '4561', '4562', '5702', '5713',
'5722', '5723', '5724', '5725', '5726', '5727', '5728', '5733', '5734',
'5738', '5739', 'V427'),
icd9 = c('07022', '07032',
'07044', '07054',
'4560', '4561', '4562', '5702', '5713',
'5722', '5723', '5724', '5725', '5726', '5727', '5728', '5733', '5734',
'5738', '5739', 'V427'),
icd10 = c('B18x', 'I85x', 'I864', 'I982',
'K70x', 'K711',
'K713', 'K714', 'K715', 'K717',
'K723', 'K733', 'K749', 'K760',
'K762', 'K763', 'K764', 'K765', 'K766', 'K767', 'K768', 'K769', 'Z944'))
# Peptic ulcer disease excluding bleeding
elixhausers_codes_2_check[['PUD']] = list(
icd9_basic = c('5317', '5319', '5327',
'5329', '5337', '5339',
'5347', '5349'),
icd9 = c('5317', '5319', '5327',
'5329', '5337', '5339',
'5347', '5349'),
icd10 = c('K257', 'K259', 'K267', 'K269',
'K277', 'K279', 'K287',
'K289'))
# AIDS/HIV
elixhausers_codes_2_check[['HIV']] = list(
icd9_basic = c('0422', '0439', '0441'),
icd9 = c('0422', '0439', '0441'),
icd10 = c('B201', 'B212', 'B229', 'B243'))
# Lymphoma
# LYMPH => Lymp
elixhausers_codes_2_check[['LYMPHOMA']] = list(
icd9_basic = c('2002', '2012', '2029', '2030', '2386'),
icd9 = c('2002', '2012', '2029', '2030', '2386'),
icd10 = c('C812', 'C823', 'C839',
'C841', 'C844', 'C853',
'C881', 'C961',
'C900', 'C902'))
# Metastatic cancer
elixhausers_codes_2_check[['METS']] = list(
icd9_basic = c('1967', '1977', '1991'),
icd9 = c('1967', '1977', '1998'),
icd10 = c('C771', 'C782', 'C799', 'C801'))
# Solid tumor without metastasis
# CANCER => Tumor
elixhausers_codes_2_check[['SOLID.TUMOR']] = list(
icd9_basic = c('1402', '1412', '1438', '1444', '1459', '1461', '1477', '1489', '1491',
'1501', '1511', '1521', '1539', '1543', '1557', '1561', '1572', '1580', '1599',
'1601', '1619', '1621', '1637', '1644', '1652', '1666', '1671', '1688', '1691',
'1707', '1712', '1723', '1743', '1755', '1790',
'1808', '1810', '1820', '1831', '1844', '1852', '1867', '1871', '1880', '1894',
'1905', '1913', '1921', '1939', '1945', '1951'),
icd9 = c('1402', '1412', '1438', '1444', '1459', '1461', '1477', '1489', '1491',
'1501', '1511', '1521', '1539', '1543', '1557', '1561', '1572', '1580', '1599',
'1601', '1619', '1621', '1637', '1644', '1652', '1666', '1671', '1688', '1691',
'1707', '1712', '1723', '1743', '1755', '1761', '1777', '1789', '1790',
'1808', '1810', '1820', '1831', '1844', '1852', '1867', '1871', '1880', '1894',
'1905', '1913', '1921', '1939', '1945', '1951'),
icd10 = c('C001', 'C010', 'C024', 'C035', 'C045', 'C055', 'C066', 'C076', 'C088', 'C092',
'C102', 'C111', 'C121', 'C130', 'C142', 'C155', 'C163', 'C178', 'C184', 'C191',
'C201', 'C217', 'C229', 'C234', 'C249', 'C251', 'C263',
'C302', 'C310', 'C323', 'C334', 'C346',
'C372', 'C380', 'C391',
'C401', 'C412', 'C433', 'C453', 'C467', 'C479', 'C481', 'C490',
'C507', 'C517', 'C525', 'C531', 'C546', 'C551', 'C561', 'C574', 'C583',
'C602', 'C619', 'C629', 'C636', 'C645', 'C673', 'C681', 'C697',
'C708', 'C718', 'C724', 'C735', 'C744', 'C752', 'C762',
'C972'))
# Rheumatoid arthritis/collagen vascular diseases
# Rheum => Rheum_A
elixhausers_codes_2_check[['RHEUM']] = list(
icd9_basic = c('7010', '7100', '7101', '7102', '7103', '7104', '7108', '7109',
'7148', '7203', '725'),
icd9_SE = c('4462', '7010', '7100', '7101', '7102', '7103', '7104', '7108', '7109',
'7112', '7148', '7193',
'7203', '7258', '7285',
'7288', '7293'),
icd9 = c('4462', '7010', '7100', '7101', '7102', '7103', '7104', '7108', '7109',
'7112', '7148', '7193',
'7203', '7258', '7285',
'72889', '72930'),
icd10 = c('L940', 'L941', 'L943', 'M051',
'M062', 'M083', 'M120', 'M123',
'M303', 'M310', 'M311', 'M312', 'M313',
'M322', 'M333', 'M346', 'M359',
'M45x', 'M461', 'M468',
'M469'))
# Coagulopathy
elixhausers_codes_2_check[['COAG']] = list(
icd9_basic = c('2860', '2864', '2871', '2873', '2874', '2875'),
icd9 = c('286x', '2871', '2873', '2874', '2875'),
icd10 = c('D65', 'D66', 'D67', 'D682', 'D691',
'D693', 'D694', 'D695', 'D696'))
# Obesity
elixhausers_codes_2_check[['OBESITY']] = list(
icd9_basic = c('2780'),
icd9 = c('2780'),
icd10 = c('E662'))
# Weight loss
# WGHT_LOSS => WL
elixhausers_codes_2_check[['WT.LOSS']] = list(
icd9_basic = c('2602', '2603', '2612', '2623', '2637'),
icd9 = c('2602', '2603', '2612', '2623', '2637',
'7832', '7994'),
icd10 = c('E402', 'E403', 'E412', 'E424', 'E434', 'E449',
'E451', 'E461', 'R634', 'R64'))
# Fluid and electrolyte disorders
elixhausers_codes_2_check[['LYTES']] = list(
icd9_basic = c('2760', '2762', '2769'),
icd9 = c('2536', '2762'),
icd10 = c('E222', 'E863', 'E879'))
# Blood loss anemia
elixhausers_codes_2_check[['ANEMIA.LOSS']] = list(
icd9_basic = c('2800'),
icd9 = c('2800'),
icd10 = c('D500'))
# Deficiency anemia
# ANEMIA => DA
elixhausers_codes_2_check[['ANEMIA.DEF']] = list(
icd9_basic = c('2801', '2802', '2803', '2804', '2805',
'2806', '2807', '2808', '2809', '2813'),
icd9 = c('2801', '2802', '2803', '2804', '2805',
'2806', '2807', '2808', '2809', '2813'),
icd10 = c('D508', 'D509', 'D512', 'D523', 'D539'))
# Alcohol abuse
elixhausers_codes_2_check[['ETOH']] = list(
icd9_basic = c('2911', '2912',
'2915', '2918', '2919',
'3039', '3050',
'V113'),
icd9 = c('2652', '2911', '2912', '2913',
'2915', '2916', '2917', '2918', '2919', '3030',
'3039', '3050', '3575',
'4255', '5353',
'5710', '5711', '5712', '5713', '9802', 'V113'),
icd10 = c('F10', 'E52', 'G621', 'I426',
'K292', 'K700', 'K703',
'K709', 'T511', 'Z502',
'Z714', 'Z721'))
# Drug abuse
# DR_ABUSE => Drug
elixhausers_codes_2_check[['DRUGS']] = list(
icd9_basic = c('2920', '29282', '3049', '3052', '3053', '3054',
'3055', '3056', '3057', '3058', '3059'),
icd9 = c('2922', '3049', '3052', '3053', '3054', '3055', '3056',
'3057', '3058', '3059', 'V6542'),
icd10 = c('F112', 'F129', 'F134', 'F151', 'F160', 'F189', 'F196',
'Z715', 'Z722'))
# Psychoses
elixhausers_codes_2_check[['PSYCHOSES']] = list(
icd9_basic = c('2952', '29604',
'2960', '2968',
'2978', '2983'),
icd9_SE = c('2938', '2952', '29604',
'2960', '2968',
'2978', '2983'),
icd9 = c('2938', '2952', '29604',
'29614', '29644',
'2978', '2983'),
icd10 = c('F202', 'F222', 'F232', 'F249', 'F257', 'F281',
'F292', 'F302', 'F312', 'F315'))
# Depression
elixhausers_codes_2_check[['DEPRESSION']] = list(
icd9_basic = c('3004', '3091', '311'),
icd9_SE = c('2961', '2963', '2965',
'3004', '3092', '311'),
icd9 = c('2962', '2963', '2965',
'3004', '3092', '311'),
icd10 = c('F204', 'F313', 'F314', 'F315', 'F322',
'F339', 'F341', 'F412', 'F432'))
context("Numeric functions")
test_that("Check Elixhausers matches or the basic elixhauser() function",{
for (n in names(elixhausers_codes_2_check)){
if ("icd9_basic" %in% names(elixhausers_codes_2_check[[n]])){
codes <- elixhausers_codes_2_check[[n]]$icd9_basic
test_df <- data.frame(Codes=codes)
out <- elixhauser(test_df)
found_codes <- out$COMORBIDITIES[,n] == 1
expect_true(all(found_codes),
info=sprintf("The script fails to properly identify from '%s' the codes '%s'",
n,
paste(codes[!found_codes],
collapse="', '")))
}
}
})
test_that("Check elixhauser count score",{
t1 <- data.frame(icd1=elixhausers_codes_2_check$CHF$icd9_basic[1],
icd2=elixhausers_codes_2_check$VALVE$icd9_basic[1],
icd3=elixhausers_codes_2_check$WT.LOSS$icd9_basic[1])
out <- elixhauser(t1)
expect_equal(out$COMORBIDITY.CT, 1+1+1,
label="3 code groups counted")
t2 <- data.frame(icd1=elixhausers_codes_2_check$HTN.COMP$icd9_basic[1],
icd2=elixhausers_codes_2_check$DRUGS$icd9_basic[1],
icd3=elixhausers_codes_2_check$DM.COMP$icd9_basic[1],
icd4=elixhausers_codes_2_check$ANEMIA.LOSS$icd9_basic[1])
out <- elixhauser(t2)
expect_equal(out$COMORBIDITY.CT, 1+1+1+1,
label="4 code groups counted")
t3 <- data.frame(icd1=elixhausers_codes_2_check$HTN.COMP$icd9_basic[1],
icd2=elixhausers_codes_2_check$DRUGS$icd9_basic[1],
icd3=NA,
icd4=elixhausers_codes_2_check$ANEMIA.LOSS$icd9_basic[1])
out <- elixhauser(t3)
expect_equal(out$COMORBIDITY.CT, 1+1+0+1,
label="3 code groups and one missing counted")
})
neg.icd9_codes <-
as.character(
c(128.9, # HELMINTH INFECTION UNSPECIFIED
136.21, # SPECIFIC INFECTION DUE TO ACANTHAMOEBA
136.29, # OTHER SPECIFIC INFECTIONS BY FREE-LIVING AMEBAE
288.04, # NEUTROPENIA DUE TO INFECTION
323.41, # OTHER ENCEPHALITIS AND ENCEPHALOMYELITIS DUE TO OTHER INFECTIONS CLASSIFIED ELSEWHERE
323.42, # OTHER MYELITIS DUE TO OTHER INFECTIONS CLASSIFIED ELSEWHERE
326, # LATE EFFECTS OF INTRACRANIAL ABSCESS OR PYOGENIC INFECTION
379.60, # INFLAMMATION (INFECTION) OF POSTPROCEDURAL BLEB, UNSPECIFIED
379.61, # INFLAMMATION (INFECTION) OF POSTPROCEDURAL BLEB, STAGE 1
379.62, # INFLAMMATION (INFECTION) OF POSTPROCEDURAL BLEB, STAGE 2
379.63, # INFLAMMATION (INFECTION) OF POSTPROCEDURAL BLEB, STAGE 3
380.11, # ACUTE INFECTION OF PINNA
380.13, # OTHER ACUTE INFECTIONS OF EXTERNAL EAR
465.8, # ACUTE UPPER RESPIRATORY INFECTIONS OF OTHER MULTIPLE SITES
465.9, # ACUTE UPPER RESPIRATORY INFECTIONS OF UNSPECIFIED SITE
519.01, # INFECTION OF TRACHEOSTOMY
733.93, # STRESS FRACTURE OF TIBIA OR FIBULA
733.94, # STRESS FRACTURE OF THE METATARSALS
733.95, # STRESS FRACTURE OF OTHER BONE
733.96, # STRESS FRACTURE OF FEMORAL NECK
806.9, # OPEN FRACTURE OF UNSPECIFIED VERTEBRA WITH SPINAL CORD INJURY
807.00, # CLOSED FRACTURE OF RIB(S) UNSPECIFIED
807.01, # CLOSED FRACTURE OF ONE RIB
807.02, # CLOSED FRACTURE OF TWO RIBS
807.03, # CLOSED FRACTURE OF THREE RIBS
807.04, # CLOSED FRACTURE OF FOUR RIBS
808.43, # MULTIPLE CLOSED PELVIC FRACTURES WITH DISRUPTION OF PELVIC CIRCLE
808.44, # MULTIPLE CLOSED PELVIC FRACTURES WITHOUT DISRUPTION OF PELVIC CIRCLE
808.49, # CLOSED FRACTURE OF OTHER SPECIFIED PART OF PELVIS
808.51, # OPEN FRACTURE OF ILIUM
808.52, # OPEN FRACTURE OF ISCHIUM
808.53, # MULTIPLE OPEN PELVIC FRACTURES WITH DISRUPTION OF PELVIC CIRCLE
808.54, # MULTIPLE OPEN PELVIC FRACTURES WITHOUT DISRUPTION OF PELVIC CIRCLE
808.59, # OPEN FRACTURE OF OTHER SPECIFIED PART OF PELVIS
808.8, # UNSPECIFIED CLOSED FRACTURE OF PELVIS
808.9, # UNSPECIFIED OPEN FRACTURE OF PELVIS
809.0, # FRACTURE OF BONES OF TRUNK CLOSED
809.1, # FRACTURE OF BONES OF TRUNK OPEN
810.00, # CLOSED FRACTURE OF CLAVICLE UNSPECIFIED PART
810.01, # CLOSED FRACTURE OF STERNAL END OF CLAVICLE
810.02, # CLOSED FRACTURE OF SHAFT OF CLAVICLE
812.10, # FRACTURE OF UNSPECIFIED PART OF UPPER END OF HUMERUS OPEN
812.11, # FRACTURE OF SURGICAL NECK OF HUMERUS OPEN
812.12, # FRACTURE OF ANATOMICAL NECK OF HUMERUS OPEN
812.13, # FRACTURE OF GREATER TUBEROSITY OF HUMERUS OPEN
812.19, # OTHER OPEN FRACTURE OF UPPER END OF HUMERUS
812.20, # FRACTURE OF UNSPECIFIED PART OF HUMERUS CLOSED
812.21, # FRACTURE OF SHAFT OF HUMERUS CLOSED
812.30, # FRACTURE OF UNSPECIFIED PART OF HUMERUS OPEN
812.31, # FRACTURE OF SHAFT OF HUMERUS OPEN
715.96, # Osteoarthrosis, unspecified whether generalized or localized, lower leg
NA))
test_that("Check elixhauser handling of negative scores",{
test_df <- data.frame(Codes=neg.icd9_codes)
out <- elixhauser(test_df)
expect_true(all(out$COMORBIDITY.CT == 0),
label="Identified comorbidities that should be negative",
info=sprintf("Comorbity code(s) identified: %s",
paste(neg.icd9_codes[rowSums(out$COMORBIDITIES) > 0],
collapse=",")))
})
context("Regular expression functions")
test_that("Check Elixhausers matches to the regular expression Quan version",{
for (n in names(elixhausers_codes_2_check)){
for (icd_ver in names(elixhausers_codes_2_check[[n]])){
if (icd_ver == "icd9_basic") {next;} # Only for the numerical version
# There are a few Swedish adaptations that have a different match
if (grepl("_SE", icd_ver)) {
country_code = "SE"
}else{
country_code = "US"
}
codes <- elixhausers_codes_2_check[[n]][[icd_ver]]
out <- t(sapply(codes,
function(code)
cmrbdt.finder.regex.elixhauser_Quan2005(icd_codes=code,
country_code=country_code,
icd_ver=gsub("[^0-9]", "", icd_ver))))
found_codes <- out[,n]
expect_true(all(found_codes),
info=sprintf("The script fails to properly identify ICD-%s from '%s' the codes '%s'",
gsub("[^0-9]", "", icd_ver),
n,
paste(codes[!found_codes],
collapse="', '")))
# # HTN.COMP overlaps and others - skip this check
# falsely_found_codes <- apply(out[,-grep(n, colnames(out))], 1, any)
# expect_true(all(!falsely_found_codes),
# info=sprintf("The script fails to properly not identify ICD-%s from '%s' the codes '%s'",
# substring(icd_ver, nchar(icd_ver)),
# n,
# paste(codes[falsely_found_codes],
# collapse="', '")))
}
}
})
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