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303_competing_events_time_stratified.do
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303_competing_events_time_stratified.do
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********************************************************************************
*
* Do-file: 302_competing_events.do
*
* Programmed by: John
*
* Data used: None
*
* Data created: None
*
* Other output: None
*
********************************************************************************
*
* Purpose:
*
* Note:
********************************************************************************
clear
do `c(pwd)'/analysis/global.do
cap log close
log using $outdir/competing_events_time_strat.txt, replace t
tempname measures
postfile `measures' ///
str20(comparator) str20(outcome) str25(analysis) str10(adjustment) str10(time) hr lc uc ///
using $tabfigdir/fine_gray_summary_time_strat, replace
foreach an in pneumonia gen_population {
*foreach an in pneumonia {
use $outdir/combined_covid_`an'.dta, replace
drop patient_id
gen new_patient_id = _n
global crude i.case
global age_sex i.case i.male age1 age2 age3
global full i.case i.male age1 age2 age3 i.stp i.ethnicity i.imd i.obese4cat_withmiss ///
i.smoke htdiag chronic_respiratory_disease i.asthmacat chronic_cardiac_disease ///
i.diabcat i.cancer_exhaem_cat i.cancer_haem_cat i.reduced_kidney_function_cat2 ///
i.chronic_liver_disease i.dementia i.other_neuro i.organ_transplant i.spleen ///
i.ra_sle_psoriasis i.other_immunosuppression i.hist_dvt i.hist_pe i.hist_stroke i.hist_mi i.hist_aki i.hist_heart_failure
foreach v in stroke dvt pe heart_failure mi aki t2dm {
noi di "Starting analysis for `v' Outcome ..."
preserve
local out `v'_cens_gp
local end_date `v'_cens_gp_end_date
* Apply exclusion for AKI and diabetes outcomes
if "`v'" == "t2dm" {
drop if previous_diabetes == 1
local out `v'
local end_date `v'_end_date
}
if "`v'" == "aki" {
drop if aki_exclusion_flag == 1
local out `v'_cens_gp
local end_date `v'_cens_gp_end_date
}
noi di "$group: stset in `a'"
/* Replace outcome = 2 if censoring is non-outcome death
gen act_end_date = `end_date' - 1
replace `out' = 2 if (`out' == 0) & (died_date_ons_date == act_end_date)
stset `end_date', id(new_patient_id) enter(indexdate) origin(indexdate) failure(`out'==1) */
gen act_end_date = `end_date' - 1
gen `end_date'2= `end_date'
replace `end_date'2 = td(01/02/2021) if case == 1 & act_end_date == died_date_ons_date & died_date_ons_date!= `v'_ons
replace `end_date'2 = td(01/02/2020) if case == 0 & act_end_date == died_date_ons_date & died_date_ons_date!= `v'_ons
format %td `end_date'2
gen `out'2 = `out'
replace `out'2 = 2 if (`out' == 0) & (died_date_ons_date == act_end_date) & (died_date_ons_date!= `v'_ons)
stset `end_date'2, id(new_patient_id) enter(indexdate) origin(indexdate) failure(`out')
* STSPLIT
stsplit time , at(30(30)120)
foreach adjust in full {
if "`adjust'" == "full" & "`v'" == "t2dm" {
* remove diabetes
global full i.case i.male age1 age2 age3 i.stp i.ethnicity i.imd i.obese4cat_withmiss ///
i.smoke htdiag chronic_respiratory_disease i.asthmacat chronic_cardiac_disease ///
i.cancer_exhaem_cat i.cancer_haem_cat i.reduced_kidney_function_cat2 ///
i.chronic_liver_disease i.dementia i.other_neuro i.organ_transplant i.spleen ///
i.ra_sle_psoriasis i.other_immunosuppression i.hist_dvt i.hist_pe i.hist_stroke i.hist_mi i.hist_aki i.hist_heart_failure
}
forvalues t = 0(30)120 {
stcox $`adjust' if time == `t' , vce(robust)
matrix b = r(table)
local hr= b[1,2]
local lc = b[5,2]
local uc = b[6,2]
estat phtest, detail
post `measures' ("`an'") ("`v'") ("`out'") ("`adjust'") ("`t'") ///
(`hr') (`lc') (`uc')
}
}
restore
}
}
postclose `measures'
* Change postfiles to csv
use $tabfigdir/fine_gray_summary_time_strat, replace
export delimited using $tabfigdir/fine_gray_summary_time_strat.csv, replace
log close