tests/testthat/test-elixhausers_according_2_SAS_code.R

In gforge/comorbidities.icd10: Calculates Comorbidity Indices Based on ICD-9/10

# Taken from http://www.chaps.ucalgary.ca/sas
# http://chaps.ucalgary.ca/files/chaps/ICD10_Elix.txt

elixhausers_icd10_testcodes = list()

# Congestive Heart Failure
elixhausers_icd10_testcodes[['CHF']] <- c('I099', 'I110', 'I130', 'I132', 'I255', 'I420', 'I425', 'I426', 'I427', 'I428', 'I429', 'I43', 'I50', 'P290')

# Caridiac Arrhythmia
elixhausers_icd10_testcodes[['Arrhy']] <- c('I441', 'I442', 'I443', 'I456', 'I459', 'I47', 'I48', 'I49', 'R000', 'R001', 'R008', 'T821', 'Z450', 'Z950')

# Valvular Disease
elixhausers_icd10_testcodes[['VD']] <- c('A520', 'I05', 'I06', 'I07', 'I08', 'I091', 'I098', 'I34', 'I35', 'I36', 'I37', 'I38', 'I39', 'Q230', 'Q231', 'Q232', 'Q233', 'Z952', 'Z953', 'Z954')

# Pulmonary Circulation Disorders
elixhausers_icd10_testcodes[['PCD']] <- c('I26', 'I27', 'I280', 'I288', 'I289')

# Peripheral Vascular Disorders
elixhausers_icd10_testcodes[['PVD']] <- c('I70', 'I71', 'I731', 'I738', 'I739', 'I771', 'I790', 'I792', 'K551', 'K558', 'K559', 'Z958', 'Z959')

# Hypertension Uncomlicated
elixhausers_icd10_testcodes[['HPTN_UC']] <- c('I10')

# Hypertension comlicated
elixhausers_icd10_testcodes[['HPTN_C']] <- c('I11', 'I12', 'I13', 'I15')

# Paralysis
elixhausers_icd10_testcodes[['Para']] <- c('G041', 'G114', 'G801', 'G802', 'G81', 'G82', 'G830', 'G831', 'G832', 'G833', 'G834', 'G839')

#  Other Neurological Disorders
elixhausers_icd10_testcodes[['OthND']] <- c('G10', 'G11', 'G12', 'G13', 'G20', 'G21', 'G22', 'G254', 'G255', 'G312', 'G318', 'G319', 'G32', 'G35', 'G36', 'G37', 'G40', 'G41', 'G931', 'G934', 'R470', 'R56')

# Chronic Pulmonary Disease
elixhausers_icd10_testcodes[['COPD']] <- c('I278', 'I279', 'J40', 'J41', 'J42', 'J43', 'J44', 'J45', 'J46', 'J47', 'J60', 'J61', 'J62', 'J63', 'J64', 'J65', 'J66', 'J67', 'J684', 'J701', 'J703')

# Diabetes Uncomplicated
elixhausers_icd10_testcodes[['Diab_UC']] <- c('E100', 'E101', 'E109', 'E110', 'E111', 'E119', 'E120', 'E121', 'E129', 'E130', 'E131', 'E139', 'E140', 'E141', 'E149')

# Diabetes Complicated
elixhausers_icd10_testcodes[['Diab_C']] <- 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_icd10_testcodes[['Hptothy']] <- c('E00', 'E01', 'E02', 'E03', 'E890')

# Renal Failure
elixhausers_icd10_testcodes[['RF']] <- c('I120', 'I131', 'N18', 'N19', 'N250', 'Z490', 'Z491', 'Z492', 'Z940', 'Z992')

# Liver Disease
elixhausers_icd10_testcodes[['LD']] <- c('B18', 'I85', 'I864', 'I982', 'K70', 'K711', 'K713', 'K714', 'K715', 'K717', 'K72', 'K73', 'K74', 'K760', 'K762', 'K763', 'K764', 'K765', 'K766', 'K767', 'K768', 'K769', 'Z944')

# Peptic Ulcer Disease excluding bleeding
elixhausers_icd10_testcodes[['PUD_NB']] <- c('K257', 'K259', 'K267', 'K269', 'K277', 'K279', 'K287', 'K289')

# AIDS/HIV
elixhausers_icd10_testcodes[['HIV']] <- c('B20', 'B21', 'B22', 'B24')

# Lymphoma
elixhausers_icd10_testcodes[['Lymp']] <- c('C81', 'C82', 'C83', 'C84', 'C85', 'C88', 'C96', 'C900', 'C902')

# Metastatic Cancer
elixhausers_icd10_testcodes[['METS']] <- c('C77', 'C78', 'C79', 'C80')

# Solid Tumor without Metastasis
elixhausers_icd10_testcodes[['Tumor']] <- c('C00', 'C01', 'C02', 'C03', 'C04', 'C05', 'C06', 'C07', 'C08', 'C09', 'C10', 'C11', 'C12', 'C13', 'C14', 'C15', 'C16', 'C17', 'C18', 'C19', 'C20', 'C21', 'C22', 'C23', 'C24', 'C25', 'C26', 'C30', 'C31', 'C32', 'C33', 'C34', 'C37', 'C38', 'C39', 'C40', 'C41', 'C43', 'C45', 'C46', 'C47', 'C48', 'C49', 'C50', 'C51', 'C52', 'C53', 'C54', 'C55', 'C56', 'C57', 'C58', 'C60', 'C61', 'C62', 'C63', 'C64', 'C65', 'C66', 'C67', 'C68', 'C69', 'C70', 'C71', 'C72', 'C73', 'C74', 'C75', 'C76', 'C97')

# Rheumatoid Arthsitis/collagen
elixhausers_icd10_testcodes[['Rheum_A']] <- c('L940', 'L941', 'L943', 'M05', 'M06', 'M08', 'M120', 'M123', 'M30', 'M310', 'M311', 'M312', 'M313', 'M32', 'M33', 'M34', 'M35', 'M45', 'M461', 'M468', 'M469')

# Coagulopathy
elixhausers_icd10_testcodes[['Coag']] <- c('D65', 'D66', 'D67', 'D68', 'D691', 'D693', 'D694', 'D695', 'D696')

# Obesity
elixhausers_icd10_testcodes[['Obesity']] <- c('E66')

# Weight Loss
elixhausers_icd10_testcodes[['WL']] <- c('E40', 'E41', 'E42', 'E43', 'E44', 'E45', 'E46', 'R634', 'R64')

# Fluid and Ecletrolyte Disorders
elixhausers_icd10_testcodes[['Fluid']] <- c('E222', 'E86', 'E87')

# Blood Loss Anemia
elixhausers_icd10_testcodes[['BLA']] <- c('D500')

# Deficiency Anemia
elixhausers_icd10_testcodes[['DA']] <- c('D508', 'D509', 'D51', 'D52', 'D53')

# Alcohol Abuse
elixhausers_icd10_testcodes[['Alcohol']] <- c('F10', 'E52', 'G621', 'I426', 'K292', 'K700', 'K703', 'K709', 'T51', 'Z502', 'Z714', 'Z721')

# Drug Abuse
elixhausers_icd10_testcodes[['Drug']] <- c('F11', 'F12', 'F13', 'F14', 'F15', 'F16', 'F18', 'F19', 'Z715', 'Z722')

# Psychoses
elixhausers_icd10_testcodes[['Psycho']] <- c('F20', 'F22', 'F23', 'F24', 'F25', 'F28', 'F29', 'F302', 'F312', 'F315')

# Depression
elixhausers_icd10_testcodes[['Dep']] <- c('F204', 'F313', 'F314', 'F315', 'F32', 'F33', 'F341', 'F412', 'F432')

# The icd 9 codes from the homepage
elixhausers_icd9_testcodes <- list()

# Congestive Heart Failure
# ['39891', '40201', '40211', '40291', '40401', '40403', '40411', '40413', '40491', '40493', '4254', '4255', '4257', '4258', '4259', '428']
# Changes in Swedish version
elixhausers_icd9_testcodes[['CHF']] <- c('3980', '402', '4040', '4254', '4255', '4257', '4258', '4259', '428')

# Caridiac Arrhythmia
elixhausers_icd9_testcodes[['Arrhy']] <- c('4260', '42613', '4267', '4269', '42610', '42612', '4270', '4271', '4272', '4273', '4274', '4276', '4278', '4279', '7850', '99601', '99604', 'V450', 'V533')

# Valvular Disease
elixhausers_icd9_testcodes[['VD']] <- c('0932', '394', '395', '396', '397', '424', '7463', '7464', '7465', '7466', 'V422', 'V433')

# Pulmonary Circulation Disorders
elixhausers_icd9_testcodes[['PCD']] <- c('4150', '4151', '416', '4170', '4178', '4179')

# Peripheral Vascular Disorders
elixhausers_icd9_testcodes[['PVD']] <- c('0930', '4373', '440', '441', '4431', '4432', '4438', '4439', '4471', '5571', '5579', 'V434')

# Hypertension Uncomlicated
elixhausers_icd9_testcodes[['HPTN_UC']] <- c('401')

# Hypertension comlicated
elixhausers_icd9_testcodes[['HPTN_C']] <- c('402', '403', '404', '405')

# Paralysis
elixhausers_icd9_testcodes[['Para']] <- c('3341', '342', '343', '3440', '3441', '3442', '3443', '3444', '3445', '3446', '3449')

#  Other Neurological Disorders
elixhausers_icd9_testcodes[['OthND']] <- c('3319', '3320', '3321', '3334', '3335', '33392', '334', '335', '3362', '340', '341', '345', '3481', '3483', '7803', '7843')

# Chronic Pulmonary Disease
elixhausers_icd9_testcodes[['COPD']] <- c('4168', '4169', '490', '491', '492', '493', '494', '495', '496', '500', '501', '502', '503', '504', '505', '5064', '5081', '5088')

# Diabetes Uncomplicated
elixhausers_icd9_testcodes[['Diab_UC']] <- c('2500', '2501', '2502', '2503')

# Diabetes Complicated
elixhausers_icd9_testcodes[['Diab_C']] <- c('2504', '2505', '2506', '2507', '2508', '2509')

# Hypothyroidism
elixhausers_icd9_testcodes[['Hptothy']] <- c('2409', '243', '244', '2461', '2468')

# Renal Failure
#['40301', '40311', '40391', '40402', '40403', '40412', '40413', '40492', '40493', '585', '586', '5880', 'V420', 'V451', 'V56']
# Swedish version
elixhausers_icd9_testcodes[['RF']] <- c('403', '585', '586', '5880', 'V420', 'V451', 'V56')

# Liver Disease
elixhausers_icd9_testcodes[['LD']] <- c('07022', '07023', '07032', '07033', '07044', '07054', '0706', '0709', '4560', '4561', '4562', '570', '571', '5722', '5723', '5724', '5728', '5733', '5734', '5738', '5739', 'V427')

# Peptic Ulcer Disease excluding bleeding
elixhausers_icd9_testcodes[['PUD_NB']] <- c('5317', '5319', '5327', '5329', '5337', '5339', '5347', '5349')

# AIDS/HIV
elixhausers_icd9_testcodes[['HIV']] <- c('042', '043', '044')

# Lymphoma
elixhausers_icd9_testcodes[['Lymp']] <- c('200', '201', '202', '2030', '2386')

# Metastatic Cancer
elixhausers_icd9_testcodes[['METS']] <- c('196', '197', '198', '199')

# Solid Tumor without Metastasis
elixhausers_icd9_testcodes[['Tumor']] <- c('140', '141', '142', '143', '144', '145',
                                           '146', '147', '148', '149', '150', '151',
                                           '152', '153', '154', '155', '156', '157',
                                           '158', '159', '160', '161', '162', '163',
                                           '164', '165', '166', '167', '168', '169', 
                                           '170', '171', '172', '174', '175', '176', 
                                           '177', '178', '179', '180', '181', '182',
                                           '183', '184', '185', '186', '187', '188',
                                           '189', '190', '191', '192', '193', '194', 
                                           '195')

# Rheumatoid Arthsitis/collagen
# org elixhausers_icd9_testcodes[['Rheum_A']] <- c('446', '7010', '7100', '7101', '7102', '7103', '7104', '7108', '7109', '7112', '714', '7193', '720', '725', '7285', '72889', '72930')
elixhausers_icd9_testcodes[['Rheum_A']] <- c('446', '7010', '7100', '7101', '7102', '7103', '7104', '7108', '7109', '7112', '714', '7193', '720', '725', '7288', '72930')
# Coagulopathy
elixhausers_icd9_testcodes[['Coag']] <- c('286', '2871', '2873', '2874', '2875')

# Obesity
elixhausers_icd9_testcodes[['Obesity']] <- c('2780')

# Weight Loss
elixhausers_icd9_testcodes[['WL']] <- c('260', '261', '262', '263', '7832', '7994')

# Fluid and Ecletrolyte Disorders
elixhausers_icd9_testcodes[['Fluid']] <- c('2536', '276')

# Blood Loss Anemia
elixhausers_icd9_testcodes[['BLA']] <- c('2800')

# Deficiency Anemia
elixhausers_icd9_testcodes[['DA']] <- c('2801', '2808', '2809', '281')

# Alcohol Abuse
elixhausers_icd9_testcodes[['Alcohol']] <- c('2652', '2911', '2912', '2913', '2915', '2918', '2919', '3030', '3039', '3050', '3575', '4255', '5353', '5710', '5711', '5712', '5713', '980', 'V113')

# Drug Abuse
#elixhausers_icd9_testcodes[['Drug']] <- c('292', '304', '3052', '3053', '3054', '3055', '3056', '3057', '3058', '3059', 'V6542')
elixhausers_icd9_testcodes[['Drug']] <- c('292', '304', '3059', 'V6542')

# Psychoses
#elixhausers_icd9_testcodes[['Psycho']] <- c('2938', '295', '29604', '29614', '29644', '29654', '297', '298')
elixhausers_icd9_testcodes[['Psycho']] <- c('2938', '295', '2960', '297', '298')
# 296A Unipolar affektiv psykos, mani

# Depression
#elixhausers_icd9_testcodes[['Dep']] <- c('2962', '2963', '2965', '3004', '309', '311')
elixhausers_icd9_testcodes[['Dep']] <- c('2961', '2963', '2965', '3004', '309', '311')
#??? elixhausers_icd9_testcodes[['Dep']] <- c('2961', '2963', '3004', '309', '311')
# 296B Unipolar affektiv psykos, melankoli


# TODO: Previously tested but should probably be implementet for R as well