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cox_ukrr_untreated.do
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cox_ukrr_untreated.do
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********************************************************************************
*
* Do-file: cox.do
*
* Project: sotrovimab-and-molnupiravir
*
* Programmed by: Bang Zheng
*
* Data used: output/main.dta
*
* Output: logs/cox.log output/phtest.svg output/phtest_psw.svg
*
********************************************************************************
*
* Purpose: This do-file implements stratified Cox regression, propensity score
* weighted Cox, and subgroup analyses.
*
********************************************************************************
* Open a log file
cap log close
log using ./logs/cox_ukrr_untreated, replace t
clear
use ./output/ukrr/main_ukrr_untreated.dta
*follow-up time and events*
stset end_date , origin(covid_test_positive_date) failure(failure==1) id(patient_id)
keep if _st==1
tab _t drug if failure==1,m col
tab failure drug,m col
*time-varying Cox*
stsplit timeband, at(0) after(time=start_date)
replace drug=-1 if _t0==0&covid_test_positive_date<start_date
replace drug=2 if drug==-1
tab drug,m
drop age_spline* calendar_day_spline*
mkspline age_spline = age, cubic nknots(4)
mkspline calendar_day_spline = day_after_campaign, cubic nknots(4)
*un-stratified Cox, missing values as a separate category*
stcox b2.drug age i.sex i.region_nhs , vce(r)
stcox b2.drug age i.sex i.region_nhs solid_cancer_new haema_disease i.years_since_rrt_missing i.rrt_mod_Tx imid immunosupression_new solid_organ_new , vce(r)
stcox b2.drug age i.sex i.region_nhs solid_cancer_new haema_disease i.years_since_rrt_missing i.rrt_mod_Tx imid immunosupression_new solid_organ_new b1.White_with_missing b5.imd_with_missing i.vaccination_3 calendar_day_spline* ,vce(r)
stcox b2.drug age i.sex i.region_nhs solid_cancer_new haema_disease i.years_since_rrt_missing i.rrt_mod_Tx imid immunosupression_new solid_organ_new b1.White_with_missing b5.imd_with_missing i.vaccination_3 calendar_day_spline* b1.bmi_g3_with_missing diabetes chronic_cardiac_disease hypertension chronic_respiratory_disease ,vce(r)
*age: 5-year band*
stcox b2.drug b7.age_5y_band i.sex i.region_nhs , vce(r)
stcox b2.drug b7.age_5y_band i.sex i.region_nhs solid_cancer_new haema_disease i.years_since_rrt_missing i.rrt_mod_Tx imid immunosupression_new solid_organ_new , vce(r)
stcox b2.drug b7.age_5y_band i.sex i.region_nhs solid_cancer_new haema_disease i.years_since_rrt_missing i.rrt_mod_Tx imid immunosupression_new solid_organ_new b1.White_with_missing b5.imd_with_missing i.vaccination_3 calendar_day_spline* ,vce(r)
stcox b2.drug b7.age_5y_band i.sex i.region_nhs solid_cancer_new haema_disease i.years_since_rrt_missing i.rrt_mod_Tx imid immunosupression_new solid_organ_new b1.White_with_missing b5.imd_with_missing i.vaccination_3 calendar_day_spline* b1.bmi_g3_with_missing diabetes chronic_cardiac_disease hypertension chronic_respiratory_disease, vce(r)
*age: Restricted cubic spline*
stcox b2.drug age_spline* i.sex i.region_nhs , vce(r)
stcox b2.drug age_spline* i.sex i.region_nhs solid_cancer_new haema_disease i.years_since_rrt_missing i.rrt_mod_Tx imid immunosupression_new solid_organ_new , vce(r)
stcox b2.drug age_spline* i.sex i.region_nhs solid_cancer_new haema_disease i.years_since_rrt_missing i.rrt_mod_Tx imid immunosupression_new solid_organ_new b1.White_with_missing b5.imd_with_missing i.vaccination_3 calendar_day_spline* , vce(r)
stcox b2.drug age_spline* i.sex i.region_nhs solid_cancer_new haema_disease i.years_since_rrt_missing i.rrt_mod_Tx imid immunosupression_new solid_organ_new b1.White_with_missing b5.imd_with_missing i.vaccination_3 calendar_day_spline* b1.bmi_g3_with_missing diabetes chronic_cardiac_disease hypertension chronic_respiratory_disease, vce(r)
*stratified Cox, missing values as a separate category*
stcox b2.drug age i.sex , strata(region_nhs) vce(r)
stcox b2.drug age i.sex solid_cancer_new haema_disease i.years_since_rrt_missing i.rrt_mod_Tx imid immunosupression_new solid_organ_new , strata(region_nhs) vce(r)
stcox b2.drug age i.sex solid_cancer_new haema_disease i.years_since_rrt_missing i.rrt_mod_Tx imid immunosupression_new solid_organ_new b1.White_with_missing b5.imd_with_missing i.vaccination_3 calendar_day_spline*, strata(region_nhs) vce(r)
stcox b2.drug age i.sex solid_cancer_new haema_disease i.years_since_rrt_missing i.rrt_mod_Tx imid immunosupression_new solid_organ_new b1.White_with_missing b5.imd_with_missing i.vaccination_3 calendar_day_spline* b1.bmi_g3_with_missing diabetes chronic_cardiac_disease hypertension chronic_respiratory_disease, strata(region_nhs) vce(r)
*age: 5-year band*
stcox b2.drug b7.age_5y_band i.sex , strata(region_nhs) vce(r)
stcox b2.drug b7.age_5y_band i.sex solid_cancer_new haema_disease i.years_since_rrt_missing i.rrt_mod_Tx imid immunosupression_new solid_organ_new , strata(region_nhs) vce(r)
stcox b2.drug b7.age_5y_band i.sex solid_cancer_new haema_disease i.years_since_rrt_missing i.rrt_mod_Tx imid immunosupression_new solid_organ_new b1.White_with_missing b5.imd_with_missing i.vaccination_3 calendar_day_spline*, strata(region_nhs) vce(r)
stcox b2.drug b7.age_5y_band i.sex solid_cancer_new haema_disease i.years_since_rrt_missing i.rrt_mod_Tx imid immunosupression_new solid_organ_new b1.White_with_missing b5.imd_with_missing i.vaccination_3 calendar_day_spline* b1.bmi_g3_with_missing diabetes chronic_cardiac_disease hypertension chronic_respiratory_disease, strata(region_nhs) vce(r)
*age: Restricted cubic spline*
stcox b2.drug age_spline* i.sex , strata(region_nhs) vce(r)
stcox b2.drug age_spline* i.sex solid_cancer_new haema_disease i.years_since_rrt_missing i.rrt_mod_Tx imid immunosupression_new solid_organ_new , strata(region_nhs) vce(r)
stcox b2.drug age_spline* i.sex solid_cancer_new haema_disease i.years_since_rrt_missing i.rrt_mod_Tx imid immunosupression_new solid_organ_new b1.White_with_missing b5.imd_with_missing i.vaccination_3 calendar_day_spline*, strata(region_nhs) vce(r)
stcox b2.drug age_spline* i.sex solid_cancer_new haema_disease i.years_since_rrt_missing i.rrt_mod_Tx imid immunosupression_new solid_organ_new b1.White_with_missing b5.imd_with_missing i.vaccination_3 calendar_day_spline* i.b1.bmi_g3_with_missing diabetes chronic_cardiac_disease hypertension chronic_respiratory_disease, strata(region_nhs) vce(r)
estat phtest,de
*by rrt_mod_Tx*
by rrt_mod_Tx, sort: stcox b2.drug age i.sex solid_cancer_new haema_disease i.years_since_rrt_missing imid immunosupression_new solid_organ_new b1.White_with_missing b5.imd_with_missing i.vaccination_3 calendar_day_spline* b1.bmi_g3_with_missing diabetes chronic_cardiac_disease hypertension chronic_respiratory_disease, strata(region_nhs) vce(r)
clear
use ./output/ukrr/main_ukrr_untreated.dta
*secondary outcomes*
*all-cause hosp/death*
*follow-up time and events*
stset end_date_allcause , origin(covid_test_positive_date) failure(failure_allcause==1) id(patient_id)
keep if _st==1
tab _t drug if failure_allcause==1,m col
tab failure_allcause drug,m col
*time-varying Cox*
stsplit timeband, at(0) after(time=start_date)
replace drug=-1 if _t0==0&covid_test_positive_date<start_date
replace drug=2 if drug==-1
tab drug,m
drop age_spline* calendar_day_spline*
mkspline age_spline = age, cubic nknots(4)
mkspline calendar_day_spline = day_after_campaign, cubic nknots(4)
*stratified Cox, missing values as a separate category*
stcox b2.drug age i.sex, strata(region_nhs) vce(r)
stcox b2.drug age i.sex solid_cancer_new haema_disease i.years_since_rrt_missing i.rrt_mod_Tx imid immunosupression_new solid_organ_new , strata(region_nhs) vce(r)
stcox b2.drug age i.sex solid_cancer_new haema_disease i.years_since_rrt_missing i.rrt_mod_Tx imid immunosupression_new solid_organ_new b1.White_with_missing b5.imd_with_missing i.vaccination_3 calendar_day_spline*, strata(region_nhs) vce(r)
stcox b2.drug age i.sex solid_cancer_new haema_disease i.years_since_rrt_missing i.rrt_mod_Tx imid immunosupression_new solid_organ_new b1.White_with_missing b5.imd_with_missing i.vaccination_3 calendar_day_spline* b1.bmi_g3_with_missing diabetes chronic_cardiac_disease hypertension chronic_respiratory_disease, strata(region_nhs) vce(r)
stcox b2.drug b7.age_5y_band i.sex, strata(region_nhs) vce(r)
stcox b2.drug b7.age_5y_band i.sex solid_cancer_new haema_disease i.years_since_rrt_missing i.rrt_mod_Tx imid immunosupression_new solid_organ_new , strata(region_nhs) vce(r)
stcox b2.drug b7.age_5y_band i.sex solid_cancer_new haema_disease i.years_since_rrt_missing i.rrt_mod_Tx imid immunosupression_new solid_organ_new b1.White_with_missing b5.imd_with_missing i.vaccination_3 calendar_day_spline*, strata(region_nhs) vce(r)
stcox b2.drug b7.age_5y_band i.sex solid_cancer_new haema_disease i.years_since_rrt_missing i.rrt_mod_Tx imid immunosupression_new solid_organ_new b1.White_with_missing b5.imd_with_missing i.vaccination_3 calendar_day_spline* b1.bmi_g3_with_missing diabetes chronic_cardiac_disease hypertension chronic_respiratory_disease, strata(region_nhs) vce(r)
stcox b2.drug age_spline* i.sex, strata(region_nhs) vce(r)
stcox b2.drug age_spline* i.sex solid_cancer_new haema_disease i.years_since_rrt_missing i.rrt_mod_Tx imid immunosupression_new solid_organ_new , strata(region_nhs) vce(r)
stcox b2.drug age_spline* i.sex solid_cancer_new haema_disease i.years_since_rrt_missing i.rrt_mod_Tx imid immunosupression_new solid_organ_new b1.White_with_missing b5.imd_with_missing i.vaccination_3 calendar_day_spline*, strata(region_nhs) vce(r)
stcox b2.drug age_spline* i.sex solid_cancer_new haema_disease i.years_since_rrt_missing i.rrt_mod_Tx imid immunosupression_new solid_organ_new b1.White_with_missing b5.imd_with_missing i.vaccination_3 calendar_day_spline* b1.bmi_g3_with_missing diabetes chronic_cardiac_disease hypertension chronic_respiratory_disease, strata(region_nhs) vce(r)
*by rrt_mod_Tx*
by rrt_mod_Tx, sort: stcox b2.drug age i.sex solid_cancer_new haema_disease i.years_since_rrt_missing imid immunosupression_new solid_organ_new b1.White_with_missing b5.imd_with_missing i.vaccination_3 calendar_day_spline* b1.bmi_g3_with_missing diabetes chronic_cardiac_disease hypertension chronic_respiratory_disease, strata(region_nhs) vce(r)
log close