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105_analysis_plots.do
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105_analysis_plots.do
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/*==============================================================================
DO FILE NAME: 105_analysis.do.do
DATE: 07/07/2023
AUTHOR: Ruth Costello (adapted from Christopher Rentsch)
DESCRIPTION OF FILE: Produce cumulative incidence plots
==============================================================================*/
adopath + ./analysis/ado
cap mkdir ./output/graphs
cap mkdir ./output/tables
* Open a log file
cap log using ./logs/analysis.log, replace
* Open file to write results to
file open tablecontent using ./output/tables/cum_incidence.txt, write text replace
file write tablecontent ("Outcome") _tab ("Exposure") _tab ("Cumulative incidence") _tab ("95% confidence interval") _n
* plot for each outcome - age and sex adjusted only
foreach outcome in hosp_any composite_any {
use ./output/an_dataset_`outcome', clear
describe
gen index_date = date("01/03/2020", "DMY")
stset stop, fail(`outcome'_flag) id(patient_id) enter(index_date) origin(index_date)
* Add cumulative incidence plots
* Not stratifying by stp as cannot use tvc and stratify
* Age and sex adjusted model
* Setting df (degrees of freedom for restricted cubic splines) as 3 as this is default
* Setting dftvc (degrees of freedom for time-dependent effects) as 1 = linear effect of log time
stpm2 udca age_tv male, tvc(udca) dftvc(1) df(3) scale(hazard) eform
summ _t
local tmax=r(max)
local tmaxplus1=r(max)+1
range days 0 `tmax' `tmaxplus1'
stpm2_standsurv if udca == 1, at1(udca 0) at2(udca 1) timevar(days) ci contrast(difference) fail
gen date = d(1/3/2020)+ days
format date %tddd_Month
for var _at1 _at2 _at1_lci _at1_uci _at2_lci _at2_uci _contrast2_1 _contrast2_1_lci _contrast2_1_uci: replace X=100*X
*cumulative mortality at last day of follow-up - write to file
file write tablecontent ("`outcome'") _tab ("No UDCA") _tab
* cumulative outcome - no UDCA
sum _at1 if days==`tmax'
file write tablecontent (r(mean)) _tab
sum _at1_lci if days==`tmax'
file write tablecontent (r(mean)) _tab
sum _at1_uci if days==`tmax'
file write tablecontent (r(mean)) _tab _n
* cumulative outcome - UDCA
file write tablecontent ("`outcome'") _tab ("UDCA") _tab
sum _at2 if days==`tmax'
file write tablecontent (r(mean)) _tab
sum _at2_lci if days==`tmax'
file write tablecontent (r(mean)) _tab
sum _at2_uci if days==`tmax'
file write tablecontent (r(mean)) _tab _n
*l date days _at1 _at1_lci _at1_uci _at2 _at2_lci _at2_uci if days<.
twoway (rarea _at1_lci _at1_uci days, color(red%25)) ///
(rarea _at2_lci _at2_uci days, color(blue%25)) ///
(line _at1 days, sort lcolor(red)) ///
(line _at2 days, sort lcolor(blue) lpattern(dash)) ///
, legend(order(1 "No UDCA" 2 "UDCA") ring(0) cols(1) pos(11) region(lwidth(none))) ///
title("Time to `outcome'", justification(left) size(med) ) ///
yscale(range(0, 1)) ///
ylabel(0 (1) 10, angle(0) format(%4.1f) labsize(small)) ///
xlabel(0 (200) 1035, labsize(small)) ///
ytitle("Cumulative outcomes (%)", size(medsmall)) ///
xtitle("Days since 1 Mar 2020", size(medsmall)) ///
graphregion(fcolor(white)) saving(adjcurv_`outcome', replace)
graph export "./output/graphs/adjcurv_`outcome'.svg", as(svg) replace
* Close window
graph close
}
use ./output/an_dataset_died_covid_any, clear
describe
gen index_date = date("01/03/2020", "DMY")
stset stop, fail(died_covid_any_flag) id(patient_id) enter(index_date) origin(index_date)
* Add cumulative incidence plots
* Not stratifying by stp as cannot use tvc and stratify
* Age and sex adjusted model
* Setting df (degrees of freedom for restricted cubic splines) as 3 as this is default
* Setting dftvc (degrees of freedom for time-dependent effects) as 1 = linear effect of log time
stpm2 udca age_tv male, tvc(udca age_tv) dftvc(1) df(3) scale(hazard) eform
summ _t
local tmax=r(max)
local tmaxplus1=r(max)+1
range days 0 `tmax' `tmaxplus1'
stpm2_standsurv if udca == 1, at1(udca 0) at2(udca 1) timevar(days) ci contrast(difference) fail
gen date = d(1/3/2020)+ days
format date %tddd_Month
for var _at1 _at2 _at1_lci _at1_uci _at2_lci _at2_uci _contrast2_1 _contrast2_1_lci _contrast2_1_uci: replace X=100*X
*cumulative mortality at last day of follow-up - write to file
file write tablecontent ("Death") _tab ("No UDCA") _tab
* cumulative outcome - no UDCA
sum _at1 if days==`tmax'
file write tablecontent (r(mean)) _tab
sum _at1_lci if days==`tmax'
file write tablecontent (r(mean)) _tab
sum _at1_uci if days==`tmax'
file write tablecontent (r(mean)) _tab _n
* cumulative outcome - UDCA
file write tablecontent ("Death") _tab ("UDCA") _tab
sum _at2 if days==`tmax'
file write tablecontent (r(mean)) _tab
sum _at2_lci if days==`tmax'
file write tablecontent (r(mean)) _tab
sum _at2_uci if days==`tmax'
file write tablecontent (r(mean)) _tab _n
*l date days _at1 _at1_lci _at1_uci _at2 _at2_lci _at2_uci if days<.
twoway (rarea _at1_lci _at1_uci days, color(red%25)) ///
(rarea _at2_lci _at2_uci days, color(blue%25)) ///
(line _at1 days, sort lcolor(red)) ///
(line _at2 days, sort lcolor(blue) lpattern(dash)) ///
, legend(order(1 "No UDCA" 2 "UDCA") ring(0) cols(1) pos(11) region(lwidth(none))) ///
title("Time to COVID-19 death", justification(left) size(med) ) ///
yscale(range(0, 1)) ///
ylabel(0 (0.2) 2, angle(0) format(%4.1f) labsize(small)) ///
xlabel(0 (200) 1035, labsize(small)) ///
ytitle("Cumulative mortality (%)", size(medsmall)) ///
xtitle("Days since 1 Mar 2020", size(medsmall)) ///
graphregion(fcolor(white)) saving(adjcurv_`outcome', replace)
graph export "./output/graphs/adjcurv_died_covid_any.svg", as(svg) replace
* Close window
graph close
* plot for each outcome - fully adjusted
foreach outcome in hosp_any composite_any {
use ./output/an_dataset_`outcome', clear
describe
gen index_date = date("01/03/2020", "DMY")
stset stop, fail(`outcome'_flag) id(patient_id) enter(index_date) origin(index_date)
* Add cumulative incidence plots
* Not stratifying by stp as cannot use tvc and stratify
* Fully adjusted model (though not including wave as not right in main model)
* Setting df (degrees of freedom for restricted cubic splines) as 3 as this is default
* Setting dftvc (degrees of freedom for time-dependent effects) as 1 = linear effect of log time
* stpm2_standsurv cannot use factor variables so creating dummy variables:
tab imd, gen(imd)
tab bmi_cat, gen(bmi_cat)
tab smoking, gen(smoking)
* Check all binary
foreach vars in udca male any_high_risk_condition eth_bin imd1 imd2 imd3 imd4 imd5 bmi_cat1 bmi_cat2 bmi_cat3 ///
bmi_cat4 bmi_cat5 smoking1 smoking2 smoking3 severe_disease covid_vacc_first liver_trans {
tab `vars', m nolabel
}
* fully adjusted model to fit
stpm2 udca male age_tv any_high_risk_condition eth_bin imd2 imd3 imd4 imd5 bmi_cat1 bmi_cat3 ///
bmi_cat4 bmi_cat5 smoking2 smoking3 severe_disease covid_vacc_first liver_trans, ///
tvc(udca severe_disease covid_vacc_first liver_trans age_tv) dftvc(1) df(1) scale(hazard) eform
summ _t
local tmax=r(max)
local tmaxplus1=r(max)+1
range days 0 `tmax' `tmaxplus1'
stpm2_standsurv if udca == 1, at1(udca 0) at2(udca 1) timevar(days) ci contrast(difference) fail
gen date = d(1/3/2020)+ days
format date %tddd_Month
for var _at1 _at2 _at1_lci _at1_uci _at2_lci _at2_uci _contrast2_1 _contrast2_1_lci _contrast2_1_uci: replace X=100*X
*cumulative mortality at last day of follow-up
list _at1* if days==`tmax', noobs
list _at2* if days==`tmax', noobs
list _contrast* if days==`tmax', noobs
*cumulative mortality at last day of follow-up - write to file
file write tablecontent ("`outcome' fully adjusted") _tab ("No UDCA") _tab
* cumulative outcome - no UDCA
sum _at1 if days==`tmax'
file write tablecontent (r(mean)) _tab
sum _at1_lci if days==`tmax'
file write tablecontent (r(mean)) _tab
sum _at1_uci if days==`tmax'
file write tablecontent (r(mean)) _tab _n
* cumulative outcome - UDCA
file write tablecontent ("`outcome'") _tab ("UDCA") _tab
sum _at2 if days==`tmax'
file write tablecontent (r(mean)) _tab
sum _at2_lci if days==`tmax'
file write tablecontent (r(mean)) _tab
sum _at2_uci if days==`tmax'
file write tablecontent (r(mean)) _tab _n
*l date days _at1 _at1_lci _at1_uci _at2 _at2_lci _at2_uci if days<.
twoway (rarea _at1_lci _at1_uci days, color(red%25)) ///
(rarea _at2_lci _at2_uci days, color(blue%25)) ///
(line _at1 days, sort lcolor(red)) ///
(line _at2 days, sort lcolor(blue) lpattern(dash)) ///
, legend(order(1 "No UDCA" 2 "UDCA") ring(0) cols(1) pos(11) region(lwidth(none))) ///
title("Time to `outcome'", justification(left) size(med) ) ///
yscale(range(0, 1)) ///
ylabel(0 (1) 10, angle(0) format(%4.1f) labsize(small)) ///
xlabel(0 (200) 1035, labsize(small)) ///
ytitle("Cumulative outcomes (%)", size(medsmall)) ///
xtitle("Days since 1 Mar 2020", size(medsmall)) ///
graphregion(fcolor(white)) saving(adjcurv_f_`outcome', replace)
graph export "./output/graphs/adjcurv_f_`outcome'.svg", as(svg) replace
* Close window
graph close
}
use ./output/an_dataset_died_covid_any, clear
describe
gen index_date = date("01/03/2020", "DMY")
stset stop, fail(died_covid_any_flag) id(patient_id) enter(index_date) origin(index_date)
* Add cumulative incidence plots
* Not stratifying by stp as cannot use tvc and stratify
* Fully adjusted model - currently not running
* Setting df (degrees of freedom for restricted cubic splines) as 3 as this is default
* Setting dftvc (degrees of freedom for time-dependent effects) as 1 = linear effect of log time
* stpm2_standsurv cannot use factor variables so creating dummy variables:
tab imd, gen(imd)
tab bmi_cat, gen(bmi_cat)
tab smoking, gen(smoking)
* Check all binary
foreach vars in udca male any_high_risk_condition eth_bin imd1 imd2 imd3 imd4 imd5 bmi_cat1 bmi_cat2 bmi_cat3 ///
bmi_cat4 bmi_cat5 smoking1 smoking2 smoking3 severe_disease covid_vacc_first liver_trans {
tab `vars', m nolabel
}
stpm2 udca male age_tv any_high_risk_condition eth_bin imd2 imd3 imd4 imd5 bmi_cat1 bmi_cat3 ///
bmi_cat4 bmi_cat5 smoking2 smoking3 severe_disease covid_vacc_first liver_trans, ///
tvc(udca severe_disease covid_vacc_first liver_trans age_tv) dftvc(1) df(1) scale(hazard) eform
summ _t
local tmax=r(max)
local tmaxplus1=r(max)+1
range days 0 `tmax' `tmaxplus1'
stpm2_standsurv if udca == 1, at1(udca 0) at2(udca 1) timevar(days) ci contrast(difference) fail
gen date = d(1/3/2020)+ days
format date %tddd_Month
for var _at1 _at2 _at1_lci _at1_uci _at2_lci _at2_uci _contrast2_1 _contrast2_1_lci _contrast2_1_uci: replace X=100*X
*cumulative mortality at last day of follow-up
list _at1* if days==`tmax', noobs
list _at2* if days==`tmax', noobs
list _contrast* if days==`tmax', noobs
*cumulative mortality at last day of follow-up - write to file
file write tablecontent ("Death fully adjusted") _tab ("No UDCA") _tab
* cumulative outcome - no UDCA
sum _at1 if days==`tmax'
file write tablecontent (r(mean)) _tab
sum _at1_lci if days==`tmax'
file write tablecontent (r(mean)) _tab
sum _at1_uci if days==`tmax'
file write tablecontent (r(mean)) _tab _n
* cumulative outcome - UDCA
file write tablecontent ("Death") _tab ("UDCA") _tab
sum _at2 if days==`tmax'
file write tablecontent (r(mean)) _tab
sum _at2_lci if days==`tmax'
file write tablecontent (r(mean)) _tab
sum _at2_uci if days==`tmax'
file write tablecontent (r(mean)) _tab _n
*l date days _at1 _at1_lci _at1_uci _at2 _at2_lci _at2_uci if days<.
twoway (rarea _at1_lci _at1_uci days, color(red%25)) ///
(rarea _at2_lci _at2_uci days, color(blue%25)) ///
(line _at1 days, sort lcolor(red)) ///
(line _at2 days, sort lcolor(blue) lpattern(dash)) ///
, legend(order(1 "No UDCA" 2 "UDCA") ring(0) cols(1) pos(11) region(lwidth(none))) ///
title("Time to `outcome'", justification(left) size(med) ) ///
yscale(range(0, 1)) ///
ylabel(0 (0.2) 2, angle(0) format(%4.1f) labsize(small)) ///
xlabel(0 (200) 1035, labsize(small)) ///
ytitle("Cumulative mortality (%)", size(medsmall)) ///
xtitle("Days since 1 Mar 2020", size(medsmall)) ///
graphregion(fcolor(white)) saving(adjcurv_`outcome', replace)
graph export "./output/graphs/adjcurv_f_died_covid_any.svg", as(svg) replace
* Close window
graph close
file close tablecontent