/* This is stata code for defining Cirrhosis using administrative data The algorithm is published in Tonelli et al BMC Med Inform Dec Making 2015;15:31 and based on the work in Goldberg et al Pharmacoepidemiol Drug Saf 2012;21:765-769 1) Specify the file name for the hospitalization data Define the variable names for the ICD-9 codes as hosp_icd9_codeX (X indicating the diagnosis code position) Define the maximum number of ICD-9 diagnosis code position as num_hosp_icd9 Define the variable name for ICD-10 codes as hosp_icd10_codeX (X indicating the diagnosis code position) Define the maximum number of ICD-10 diagnosis code position as num_hosp_icd10 Define the variable name of the hospitalization start date as hosp_start_date Define the variable names of the types of hospitalization as type 2) Specify the file name for the physician claims data Define the variable names for the ICD-9 codes as claim_icd9_codeX (X indicating the diagnosis code position) Define the maximum number of ICD-9 diagnosis code position as num_claim_icd9 Define the variable name of the physician claims date as claim_start_date 3) Specify the file name for the ACCS data Define the variable names for the ICD-9 codes as accs_icd9_codeX (X indicating the diagnosis code position) Define the maximum number of ICD-9 diagnosis code position as num_accs_icd9 Define the variable names for ICD-10 codes as accs_icd10_codeX (X indicating the diagnosis code position) Define the maximum number of ICD-10 diagnosis code position as num_accs_icd10 Define the variable name of the ACCS start date as accs_start_date 4) Specify the directory of the output dataset 5) Create study cohort which includes the unique patient identifier, the study start and end dates (e.g., when a patient turns 18 until they die or out-migrate) 6) hepatic_ICD.do needs to be run first */ * File name and variable names for the hospitalizations dataset global data_hosp = "G:\Open Data\ICDC 2013\ICDC Source\Constant files\hosp94_2013.dta" global hosp_icd9_code = "hosp_icd9dx_code" global num_hosp_icd9 = 16 global hosp_icd10_code = "hosp_icd10dx_code" global num_hosp_icd10 = 25 global hosp_start_date = "start_date" global type = "diag_type" * File name and variable names for the physician claims dataset global data_claim = "G:\Open Data\ICDC 2013\ICDC Source\claims_94_13.dta" global claim_icd9_code = "hlth_dx_icd9x_code_" global num_claim_icd9 = 3 global claim_start_date = "start_date" * File name and variable names for the ACCS dataset global data_accs = "G:\Open Data\ICDC 2013\ICDC Source\Constant files\accs97_2013.dta" global accs_icd9_code = "accs_icd9dx_code" global num_accs_icd9 = 6 global accs_icd10_code = "accs_icd10dx_code" global num_accs_icd10 = 10 global accs_start_date = "start_date" * Output dataset directory global out_source = "G:\Projects\Phoebe\MM30codes\kidtran" /* Sample program call ICDmm30_cirrhosis cohort akdnid study_start_date study_end_date 'cohort' is the file name of the study cohort 'id' is the unique patient identifier 'study_start_date' is the study start date 'study_end_date' is the study end date */ version 13.1 capture program drop ICDmm30_cirrhosis program ICDmm30_cirrhosis set more off gettoken cohort 0:0 gettoken id 0:0 gettoken study_start_date 0:0 gettoken study_end_date 0:0 use `cohort', clear duplicates drop sort `id', stable save cohort_cirrhosis, replace * Cirrhosis local ICD9_cirrhosis 5712 5715 5716 local ICD10_cirrhosis K703 K743 K744 K745 K746 * One hospitalization use "${data_hosp}" , clear keep `id' ${hosp_start_date} ${hosp_icd9_code}1-${hosp_icd9_code}${num_hosp_icd9} ${hosp_icd10_code}1-${hosp_icd10_code}${num_hosp_icd10} /// ${type}1- ${type}16 ${type}17- ${type}${num_hosp_icd10} recast long ${hosp_start_date}, force sort `id', stable merge n:1 `id' using cohort_cirrhosis keep if _merge==3 drop _merge keep if ${hosp_start_date}>=`study_start_date' & ${hosp_start_date}<=`study_end_date' local n=${num_hosp_icd9} forvalues nhos9=1(1)`n' { capture replace ${hosp_icd9_code}`nhos9'= subinstr(${hosp_icd9_code}`nhos9', ".", "",.) } local m=${num_hosp_icd10} forvalues nhos10=1(1)`m' { capture replace ${hosp_icd10_code}`nhos10'= subinstr(${hosp_icd10_code}`nhos10', ".", "",.) } gen type="" gen code="" local n=${num_hosp_icd9} foreach i in `ICD9_cirrhosis' { local len=strlen("`i'") forvalues dx=`n'(-1)1 { capture replace code="`i'" if substr(${hosp_icd9_code}`dx',1,`len') =="`i'" capture replace type=${type}`dx' if substr(${hosp_icd9_code}`dx',1,`len') =="`i'" } } local m=${num_hosp_icd10} foreach j in `ICD10_cirrhosis' { local len=strlen("`j'") forvalues dx=`m'(-1)1 { capture replace code = "`j'" if substr(${hosp_icd10_code}`dx',1,`len') == "`j'" capture replace type=${type}`dx' if substr(${hosp_icd10_code}`dx',1,`len')== "`j'" } } keep if code!="" gen source="hosp" keep `id' ${hosp_start_date} type code source rename ${hosp_start_date} cirrhosis_date sort `id' cirrhosis_date, stable bysort `id': keep if _n==1 save "${out_source}\ICD_cirrhosis.dta", replace * One claim use "${data_claim}",clear keep `id' ${claim_start_date} ${claim_icd9_code}1-${claim_icd9_code}${num_claim_icd9} recast long ${claim_start_date}, force sort `id', stable merge n:1 `id' using cohort_cirrhosis keep if _merge==3 drop _merge keep if ${claim_start_date}>=`study_start_date' & ${claim_start_date}<=`study_end_date' local n=${num_claim_icd9} forvalues nclaim9=1(1)`n' { capture replace ${claim_icd9_code}`nclaim9'= subinstr(${claim_icd9_code}`nclaim9', ".", "",.) } gen code="" local n=${num_claim_icd9} foreach i in `ICD9_cirrhosis' { local len=strlen("`i'") forvalues dx=`n'(-1)1 { capture replace code="`i'" if substr(${claim_icd9_code}`dx',1,`len') =="`i'" } } keep if code!="" sort `id' ${claim_start_date}, stable gen source="claim" keep `id' ${claim_start_date} code source rename ${claim_start_date} cirrhosis_date sort `id' cirrhosis_date bysort `id': keep if _n==1 * Append hospitalizations with claims append using "${out_source}\ICD_cirrhosis.dta" sort `id' cirrhosis_date, stable save "${out_source}\ICD_cirrhosis.dta", replace * One accs use "${data_accs}",clear keep `id' ${accs_start_date} ${accs_icd9_code}1-${accs_icd9_code}${num_accs_icd9} ${accs_icd10_code}1-${accs_icd10_code}${num_accs_icd10} recast long ${accs_start_date}, force sort `id', stable merge n:1 `id' using cohort_cirrhosis keep if _merge==3 drop _merge keep if ${accs_start_date}>=`study_start_date' & ${accs_start_date}<=`study_end_date' local n=${num_accs_icd9} forvalues naccs9=1(1)`n' { capture replace ${accs_icd9_code}`nclaim9'= subinstr(${accs_icd9_code}`nclaim9', ".", "",.) } local m=${num_accs_icd10} forvalues naccs10=1(1)`m' { capture replace ${accs_icd10_code}`nclaim10'= subinstr(${accs_icd10_code}`naccs10', ".", "",.) } gen code="" local n=${num_accs_icd9} foreach i in `ICD9_cirrhosis' { local len=strlen("`i'") forvalues dx=`n'(-1)1 { capture replace code="`i'" if substr(${accs_icd9_code}`dx',1,`len') =="`i'" & code=="" } } local m=${num_accs_icd10} foreach i in `ICD10_cirrhosis' { local len=strlen("`i'") forvalues dx=`m'(-1)1 { capture replace code="`i'" if substr(${accs_icd10_code}`dx',1,`len') =="`i'" & code=="" } } keep if code!="" sort `id' ${accs_start_date}, stable gen source="accs" keep `id' ${accs_start_date} code source bysort `id': keep if _n==1 rename ${accs_start_date} cirrhosis_date * Append hospitalizations and claims with accs append using "${out_source}\ICD_cirrhosis.dta" sort `id' cirrhosis_date, stable bysort `id': keep if _n==1 foreach i of varlist code type source { rename `i' `i'_cirrhosis } merge `id' using "${out_source}\ICD_hepatic.dta" keep if _merge==3 replace cirrhosis_date=hepatic_date if cirrhosis_date