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multiple_imputation.do
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multiple_imputation.do
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********************************************************************************
*
* Do-file: multiple_imputation.do
*
* Project: sotrovimab-and-molnupiravir
*
* Programmed by: Bang Zheng
*
* Data used: output/main.dta
*
* Output: logs/MI.log
*
********************************************************************************
*
* Purpose: This do-file implements stratified Cox regression after multiple imputation for covariates.
*
********************************************************************************
* Open a log file
cap log close
log using ./logs/MI, replace t
clear
use ./output/main.dta
stset end_date , origin(start_date) failure(failure==1)
keep if _st==1
*MI*
*install ice package by changing ado filepath*
sysdir
sysdir set PLUS "analysis/ado"
sysdir set PERSONAL "analysis/ado"
set seed 1000
ice m.ethnicity m.bmi_group4 m.imd drug age i.sex i.stp downs_syndrome solid_cancer haema_disease renal_disease liver_disease imid immunosupression hiv_aids solid_organ rare_neuro i.vaccination_status i.week_after_campaign diabetes chronic_cardiac_disease hypertension chronic_respiratory_disease failure, m(5) saving(imputed,replace)
clear
use imputed
mi import ice, imputed(ethnicity bmi_group4 imd)
mi stset end_date , origin(start_date) failure(failure==1)
mi estimate, hr: stcox i.drug age i.sex downs_syndrome solid_cancer haema_disease renal_disease liver_disease imid immunosupression hiv_aids solid_organ rare_neuro b6.ethnicity b5.imd i.vaccination_status i.week_after_campaign,strata(stp)
mi estimate, hr: stcox i.drug age i.sex downs_syndrome solid_cancer haema_disease renal_disease liver_disease imid immunosupression hiv_aids solid_organ rare_neuro b6.ethnicity b5.imd i.vaccination_status i.week_after_campaign b1.bmi_group4 diabetes chronic_cardiac_disease hypertension chronic_respiratory_disease, strata(stp)
log close