-------------------------------------------------------------------------------------------------------------------------------------------------------------- Measuring mortality due to HIV-associated TB Results from the Lesedi Kamoso study Codebook & labels -------------------------------------------------------------------------------------------------------------------------------------------------------------- id Participant ID -------------------------------------------------------------------------------------------------------------------------------------------------------------- type: numeric (float) range: [1,259] units: 1 unique values: 259 missing .: 0/259 mean: 130 std. dev: 74.9111 percentiles: 10% 25% 50% 75% 90% 26 65 130 195 234 -------------------------------------------------------------------------------------------------------------------------------------------------------------- Dem_prevtb Ever treated for TB? -------------------------------------------------------------------------------------------------------------------------------------------------------------- type: numeric (byte) label: YesNo range: [0,1] units: 1 unique values: 2 missing .: 0/259 tabulation: Freq. Numeric Label 213 0 No 46 1 Yes -------------------------------------------------------------------------------------------------------------------------------------------------------------- Dem_study Parent study -------------------------------------------------------------------------------------------------------------------------------------------------------------- type: numeric (float) label: study range: [1,2] units: 1 unique values: 2 missing .: 0/259 tabulation: Freq. Numeric Label 212 1 TB Fast Track 47 2 XPHACTOR -------------------------------------------------------------------------------------------------------------------------------------------------------------- Dem_sex Gender -------------------------------------------------------------------------------------------------------------------------------------------------------------- type: numeric (byte) label: gender_lab range: [1,2] units: 1 unique values: 2 missing .: 0/259 tabulation: Freq. Numeric Label 112 1 Male 147 2 Female -------------------------------------------------------------------------------------------------------------------------------------------------------------- Dem_agedeath Age at death -------------------------------------------------------------------------------------------------------------------------------------------------------------- type: numeric (float) range: [21.385353,65.826149] units: 1.000e-06 unique values: 256 missing .: 0/259 mean: 40.7129 std. dev: 10.1659 percentiles: 10% 25% 50% 75% 90% 28.4079 33.1472 39.3374 47.3237 55.6468 -------------------------------------------------------------------------------------------------------------------------------------------------------------- Dem_enrtod Time from enrolment to death -------------------------------------------------------------------------------------------------------------------------------------------------------------- type: numeric (float) range: [-8,667] units: 1 unique values: 174 missing .: 0/259 mean: 134.097 std. dev: 133.241 percentiles: 10% 25% 50% 75% 90% 16 39 83 184 344 -------------------------------------------------------------------------------------------------------------------------------------------------------------- Dem_dtova Time from death to VA -------------------------------------------------------------------------------------------------------------------------------------------------------------- type: numeric (float) range: [0,606] units: 1 unique values: 189 missing .: 0/259 mean: 192.896 std. dev: 132.497 percentiles: 10% 25% 50% 75% 90% 43 84 157 294 386 -------------------------------------------------------------------------------------------------------------------------------------------------------------- Dem_sacitizen South African citizen? -------------------------------------------------------------------------------------------------------------------------------------------------------------- type: numeric (float) label: YesNo range: [0,1] units: 1 unique values: 2 missing .: 0/259 tabulation: Freq. Numeric Label 11 0 No 248 1 Yes -------------------------------------------------------------------------------------------------------------------------------------------------------------- Dem_black Black African? -------------------------------------------------------------------------------------------------------------------------------------------------------------- type: numeric (float) label: YesNo range: [0,1] units: 1 unique values: 2 missing .: 0/259 tabulation: Freq. Numeric Label 2 0 No 257 1 Yes -------------------------------------------------------------------------------------------------------------------------------------------------------------- Dem_urban Enrolled in urban area? -------------------------------------------------------------------------------------------------------------------------------------------------------------- type: numeric (float) label: YesNo range: [0,1] units: 1 unique values: 2 missing .: 0/259 tabulation: Freq. Numeric Label 56 0 No 203 1 Yes -------------------------------------------------------------------------------------------------------------------------------------------------------------- Dem_educ Highest education completed -------------------------------------------------------------------------------------------------------------------------------------------------------------- type: numeric (byte) label: education range: [1,7] units: 1 unique values: 7 missing .: 0/259 tabulation: Freq. Numeric Label 7 1 None/Pre-school 11 2 Grd 1-3 40 3 Grd 4-7 116 4 Grd 8-11 72 5 Grd 12 12 6 Matric/Dip 1 7 BA -------------------------------------------------------------------------------------------------------------------------------------------------------------- Dem_cd4 Most recent CD4 count -------------------------------------------------------------------------------------------------------------------------------------------------------------- type: numeric (float) range: [0,904] units: .01 unique values: 131 missing .: 2/259 mean: 83.9984 std. dev: 116.452 percentiles: 10% 25% 50% 75% 90% 7 22 51 102 144 -------------------------------------------------------------------------------------------------------------------------------------------------------------- Dem_mia MIA conducted? -------------------------------------------------------------------------------------------------------------------------------------------------------------- type: numeric (float) label: YesNo range: [0,1] units: 1 unique values: 2 missing .: 0/259 tabulation: Freq. Numeric Label 225 0 No 34 1 Yes -------------------------------------------------------------------------------------------------------------------------------------------------------------- Dem_married Marital status -------------------------------------------------------------------------------------------------------------------------------------------------------------- type: numeric (byte) label: marital range: [1,6] units: 1 unique values: 6 missing .: 0/259 tabulation: Freq. Numeric Label 165 1 Single 51 2 Married 2 3 Married-separated 14 4 Cohabitating 7 5 Divorced 20 6 Widowed -------------------------------------------------------------------------------------------------------------------------------------------------------------- Dem_hincom Household monthly income -------------------------------------------------------------------------------------------------------------------------------------------------------------- type: numeric (byte) label: averagehouseincome range: [1,7] units: 1 unique values: 6 missing .: 0/259 tabulation: Freq. Numeric Label 25 1 R4000 57 7 Dont Know -------------------------------------------------------------------------------------------------------------------------------------------------------------- Dem_artenrol Taking ART at enrolment? -------------------------------------------------------------------------------------------------------------------------------------------------------------- type: numeric (byte) label: YesNo range: [0,1] units: 1 unique values: 2 missing .: 0/259 tabulation: Freq. Numeric Label 227 0 No 32 1 Yes -------------------------------------------------------------------------------------------------------------------------------------------------------------- va_resp VA respondent -------------------------------------------------------------------------------------------------------------------------------------------------------------- type: numeric (float) label: rel2 range: [10,20] units: 1 unique values: 11 missing .: 0/259 examples: 11 Parent 13 Sibling 13 Sibling 18 Partner -------------------------------------------------------------------------------------------------------------------------------------------------------------- L3_icd L3 CoD - ICD-10 category -------------------------------------------------------------------------------------------------------------------------------------------------------------- type: numeric (float) label: icdcat2 range: [1,6] units: 1 unique values: 2 missing .: 225/259 tabulation: Freq. Numeric Label 33 1 HIV/AIDS 1 6 External/traumatic or pregnancy-related 225 . -------------------------------------------------------------------------------------------------------------------------------------------------------------- L3_sd L3 CoD - study-defined -------------------------------------------------------------------------------------------------------------------------------------------------------------- type: numeric (float) label: lk2 range: [1,6] units: 1 unique values: 4 missing .: 225/259 tabulation: Freq. Numeric Label 14 1 TB in an HIV-positive adult 15 2 HIV-associated cause, other than TB 1 3 Non-AIDS, non-HIV-associated cause in an HIV-positive adult 4 6 Indeterminate cause 225 . -------------------------------------------------------------------------------------------------------------------------------------------------------------- L2_sd L2 coD - study-defined -------------------------------------------------------------------------------------------------------------------------------------------------------------- type: numeric (float) label: lk2 range: [1,6] units: 1 unique values: 4 missing .: 0/259 tabulation: Freq. Numeric Label 70 1 TB in an HIV-positive adult 99 2 HIV-associated cause, other than TB 21 3 Non-AIDS, non-HIV-associated cause in an HIV-positive adult 69 6 Indeterminate cause -------------------------------------------------------------------------------------------------------------------------------------------------------------- L2_icd L2 CoD - ICD-10 category -------------------------------------------------------------------------------------------------------------------------------------------------------------- type: numeric (float) label: icdcat2 range: [1,7] units: 1 unique values: 6 missing .: 0/259 tabulation: Freq. Numeric Label 183 1 HIV/AIDS 2 3 Other infectious 8 4 Malignancy 7 5 Other NCD 3 6 External/traumatic or pregnancy-related 56 7 Indeterminate -------------------------------------------------------------------------------------------------------------------------------------------------------------- PCVA_sd PCVA CoD - study-defined -------------------------------------------------------------------------------------------------------------------------------------------------------------- type: numeric (float) label: lk2 range: [1,5] units: 1 unique values: 5 missing .: 0/259 tabulation: Freq. Numeric Label 105 1 TB in an HIV-positive adult 111 2 HIV-associated cause, other than TB 20 3 Non-AIDS, non-HIV-associated cause in an HIV-positive adult 2 4 TB in an HIV-negative adult 21 5 Non-TB cause in an HIV-negative adult -------------------------------------------------------------------------------------------------------------------------------------------------------------- PCVA_icd PCVA CoD - ICD-10 category -------------------------------------------------------------------------------------------------------------------------------------------------------------- type: numeric (float) label: icdcat2 range: [1,6] units: 1 unique values: 6 missing .: 0/259 tabulation: Freq. Numeric Label 206 1 HIV/AIDS 1 2 PTB 17 3 Other infectious 7 4 Malignancy 21 5 Other NCD 7 6 External/traumatic or pregnancy-related -------------------------------------------------------------------------------------------------------------------------------------------------------------- IVA_icd InterVA-4 CoD - ICD-10 category -------------------------------------------------------------------------------------------------------------------------------------------------------------- type: numeric (float) label: icdcat2 range: [1,6] units: 1 unique values: 6 missing .: 0/259 tabulation: Freq. Numeric Label 129 1 HIV/AIDS 41 2 PTB 25 3 Other infectious 37 4 Malignancy 23 5 Other NCD 4 6 External/traumatic or pregnancy-related -------------------------------------------------------------------------------------------------------------------------------------------------------------- IVA_causen InterVA-4 CoD 1 -------------------------------------------------------------------------------------------------------------------------------------------------------------- type: numeric (float) label: causen range: [11,63] units: 1 unique values: 27 missing .: 0/259 examples: 12 01.03 HIV/AIDS related death 12 01.03 HIV/AIDS related death 18 01.09 Pulmonary tuberculosis 23 02.02 Digestive neoplasms -------------------------------------------------------------------------------------------------------------------------------------------------------------- IVA_lik1 InterVA-4 - likelihood 1 -------------------------------------------------------------------------------------------------------------------------------------------------------------- type: numeric (byte) range: [41,100] units: 1 unique values: 40 missing .: 0/259 mean: 92.1892 std. dev: 13.4247 percentiles: 10% 25% 50% 75% 90% 71 90 99 100 100 -------------------------------------------------------------------------------------------------------------------------------------------------------------- IVA_causen2 InterVA-4 CoD 2 -------------------------------------------------------------------------------------------------------------------------------------------------------------- type: numeric (float) label: causen, but 1 nonmissing value is not labeled range: [0,31] units: 1 unique values: 7 missing .: 0/259 tabulation: Freq. Numeric Label 242 0 5 11 01.02 Acute resp infect, incl pneumonia 4 12 01.03 HIV/AIDS related death 3 18 01.09 Pulmonary tuberculosis 3 23 02.02 Digestive neoplasms 1 24 02.03 Respiratory neoplasms 1 31 04.01 Acute cardiac dx -------------------------------------------------------------------------------------------------------------------------------------------------------------- IVA_lik2 InterVA-4 - likelihood 2 -------------------------------------------------------------------------------------------------------------------------------------------------------------- type: numeric (byte) range: [0,49] units: 1 unique values: 10 missing .: 0/259 mean: 2.57915 std. dev: 9.87384 percentiles: 10% 25% 50% 75% 90% 0 0 0 0 0 -------------------------------------------------------------------------------------------------------------------------------------------------------------- IVA_causen3 InterVA-4 CoD 3 -------------------------------------------------------------------------------------------------------------------------------------------------------------- type: numeric (float) label: causen, but 1 nonmissing value is not labeled range: [0,11] units: 1 unique values: 2 missing .: 0/259 tabulation: Freq. Numeric Label 258 0 1 11 01.02 Acute resp infect, incl pneumonia -------------------------------------------------------------------------------------------------------------------------------------------------------------- IVA_lik3 InterVA-4 - likelihood 3 -------------------------------------------------------------------------------------------------------------------------------------------------------------- type: numeric (byte) range: [0,26] units: 1 unique values: 2 missing .: 0/259 tabulation: Freq. Value 258 0 1 26 -------------------------------------------------------------------------------------------------------------------------------------------------------------- SmartVA_icd SmartVA-Analyze CoD - ICD-10 category -------------------------------------------------------------------------------------------------------------------------------------------------------------- type: numeric (float) label: icdcat2 range: [1,7] units: 1 unique values: 7 missing .: 0/259 tabulation: Freq. Numeric Label 75 1 HIV/AIDS 5 2 PTB 26 3 Other infectious 58 4 Malignancy 34 5 Other NCD 1 6 External/traumatic or pregnancy-related 60 7 Indeterminate -------------------------------------------------------------------------------------------------------------------------------------------------------------- -------------------------------------------------------------------------------------------------------------------------------------------------------------- LABEL LIST lk2: 1 TB in an HIV-positive adult 2 HIV-associated cause, other than TB 3 Non-AIDS, non-HIV-associated cause in an HIV-positive adult 4 TB in an HIV-negative adult 5 Non-TB cause in an HIV-negative adult 6 Indeterminate cause study: 1 TB Fast Track 2 XPHACTOR _merge: 1 master only (1) 2 using only (2) 3 matched (3) 4 missing updated (4) 5 nonmissing conflict (5) rel2: 10 Grandparent 11 Parent 12 Child 13 Sibling 14 Other relative (older gen) 15 Other relative (same gen) 16 Other relative (younger gen) 17 Other relative (unspecified) 18 Partner 19 Friend 20 Caregiver 21 Other yesno: 0 No 1 Yes YesNo: 0 No 1 Yes 7 NA 9 Dont Know averagehouseincome: 1 R4000 7 Dont Know education: 1 None/Pre-school 2 Grd 1-3 3 Grd 4-7 4 Grd 8-11 5 Grd 12 6 Matric/Dip 7 BA 8 MS/PhD 9 Other marital: 1 Single 2 Married 3 Married-separated 4 Cohabitating 5 Divorced 6 Widowed gender_lab: 1 Male 2 Female causen: 10 01.01 Sepsis (non-obstetric) 11 01.02 Acute resp infect, incl pneumonia 12 01.03 HIV/AIDS related death 13 01.04 Diarrhoeal diseases 14 01.05 Malaria 15 01.06 Measles 16 01.07 Meningitis and encephalitis 17 01.08, 10.05 Tetanus 18 01.09 Pulmonary tuberculosis 19 01.10 Pertussis 20 01.11 Haemorrhagic fever 21 01.99 Other and unspecified infect dx 22 02.01 Oral neoplasms 23 02.02 Digestive neoplasms 24 02.03 Respiratory neoplasms 25 02.04 Breast neoplasms 26 02.05, 02.06 Reproductive neoplasms M,F 27 02.99 Other and unspecified neoplasms 28 03.01 Severe anaemia 29 03.02 Severe malnutrition 30 03.03 Diabetes mellitus 31 04.01 Acute cardiac dx 32 04.02 Stroke 33 04.03 Sickle cell with crisis 34 04.99 Other and unspecified cardiac dx 35 05.01 Chronic obstructive pulmonary dx 36 05.02 Asthma 37 06.01 Acute abdomen 38 06.02 Liver cirrhosis 39 07.01 Renal failure 40 08.01 Epilepsy 41 98 Other and unspecified NCD 42 10.06 Congenital malformation 43 10.01 Prematurity 44 10.02 Birth asphyxia 45 10.03 Neonatal pneumonia 46 10.04 Neonatal sepsis 47 10.99 Other and unspecified neonatal CoD 48 11.01 Fresh stillbirth 49 11.02 Macerated stillbirth 50 12.01 Road traffic accident 51 12.02 Other transport accident 52 12.03 Accid fall 53 12.04 Accid drowning and submersion 54 12.05 Accid expos to smoke, fire & flame 55 12.06 Contact with venomous plant/animal 56 12.10 Exposure to force of nature 57 12.07 Accid poisoning and noxious substances 58 12.08 Intentional self-harm 59 12.09 Assault 60 12.99 Other and unspecified external CoD 61 09.01 Ectopic pregnancy 62 09.02 Abortion-related death 63 09.03 Pregnancy-induced hypertension 64 09.04 Obstetric haemorrhage 65 09.05 Obstructed labour 66 09.06 Pregnancy-related sepsis 67 09.07 Anaemia of pregnancy 68 09.08 Ruptured uterus 69 09.99 Other and unspecified maternal CoD 70 99 Indeterminate icdcat2: 1 HIV/AIDS 2 PTB 3 Other infectious 4 Malignancy 5 Other NCD 6 External/traumatic or pregnancy-related 7 Indeterminate --------------------------------------------------------------------------------------------------------------------------------------------------------------