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401_survival_curves.do
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401_survival_curves.do
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********************************************************************************
*
* Do-file: 202_cox_models.do
*
* Programmed by: John & Alex
*
* Data used: None
*
* Data created: None
*
* Other output: None
*
********************************************************************************
*
* Purpose:
*
* Note:
********************************************************************************
clear
do `c(pwd)'/analysis/global.do
global group `1'
use $outdir/matched_cohort_$group.dta, replace
cap log close
log using $outdir/survcurves_$group, replace t
foreach v in stroke dvt pe {
preserve
* In hosp
noi di "Starting analysis for $group: `v' Outcome ..."
noi di "$group: stset in hospital"
local a = "in_hosp"
stset `v'_in_hosp_end_date , id(patient_id) failure(`v'_in_hosp) enter(hospitalised_expo_date) origin(hospitalised_expo_date)
* Label setting
cap drop flag
gen flag = "$group"
replace flag = proper(flag)
local graphLab = flag[1]
* Crude cox
stcox i.case
* Survival curve
#delimit ;
stcurv, surv at1(case=0) at2(case=1)
title("")
legend(
order(1 "`graphLab'" 2 "Covid-19")
rows(1)
symxsize(*0.4)
size(small)
)
ylabel(,angle(horizontal))
plotregion(color(white))
graphregion(color(white))
ytitle("Survival Probability" )
xtitle("Time (Days)" )
;
#delimit cr
graph export $tabfigdir/survcurv_`a'_`v'_$group.svg , as(svg) replace
forvalues s = 0/1 {
* Survival curve
stcox i.case hist_`v'
#delimit ;
stcurv, surv at1(case=0 hist_`v'=`s') at2(case=1 hist_`v'=`s')
title("")
legend(
order(1 "`graphLab'" 2 "Covid-19")
rows(1)
symxsize(*0.4)
size(small)
)
ylabel(,angle(horizontal))
plotregion(color(white))
graphregion(color(white))
ytitle("Survival Probability" )
xtitle("Time (Days)" )
;
#delimit cr
graph export $tabfigdir/survcurv_`a'_`v'_history_`s'_$group.svg , as(svg) replace
}
* DROP Patients who have the event in hospital
drop if `v'_in_hosp == 1
drop if died_date_ons_date <= discharged_expo_date
* post-hosp
foreach a in post_hosp post_hosp_gp {
noi di "$group: stset in `a'"
stset `v'_`a'_end_date , id(patient_id) failure(`v'_`a') enter(discharged_expo_date) origin(discharged_expo_date)
* Label setting
cap drop flag
gen flag = "$group"
replace flag = proper(flag)
local graphLab = flag[1]
* Crude cox
stcox i.case
* Survival curve
#delimit ;
stcurv, surv at1(case=0) at2(case=1)
title("")
legend(
order(1 "`graphLab'" 2 "Covid-19")
rows(1)
symxsize(*0.4)
size(small)
)
ylabel(,angle(horizontal))
plotregion(color(white))
graphregion(color(white))
ytitle("Survival Probability" )
xtitle("Time (Days)" )
;
#delimit cr
graph export $tabfigdir/survcurv_`a'_`v'_$group.svg , as(svg) replace
forvalues s = 0/1 {
* Survival curve
stcox i.case hist_`v'
#delimit ;
stcurv, surv at1(case=0 hist_`v'=`s') at2(case=1 hist_`v'=`s')
title("")
legend(
order(1 "`graphLab'" 2 "Covid-19")
rows(1)
symxsize(*0.4)
size(small)
)
ylabel(,angle(horizontal))
plotregion(color(white))
graphregion(color(white))
ytitle("Survival Probability" )
xtitle("Time (Days)" )
;
#delimit cr
graph export $tabfigdir/survcurv_`a'_`v'_history_`s'_$group.svg , as(svg) replace
}
}
restore
}
log close