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106_analysis_models.do
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106_analysis_models.do
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/*==============================================================================
DO FILE NAME: 105_analysis_models.do.do
DATE: 07/07/2023
AUTHOR: Ruth Costello
DESCRIPTION OF FILE: Produce cox models
==============================================================================*/
adopath + ./analysis/ado
cap mkdir ./output/tables
cap mkdir ./output/graphs
cap mkdir ./output/tempdata
* Open a log file
cap log using ./logs/analysis_models.log, replace
* Open file to write results to
file open tablecontent using ./output/tables/cox_models.txt, write text replace
file write tablecontent ("Outcome") _tab ("Exposure status") _tab ("events") _tab ("total_person_mths") _tab ("Rate") _tab ("unadj_hr") _tab ///
("unadj_ci") _tab ("unadj_lci") _tab ("unadj_uci") _tab ("p_adj_hr") _tab ("p_adj_ci") _tab ("p_adj_lci") _tab ("p_adj_uci") _tab ("f_adj_hr") _tab ("f_adj_ci") _tab ("f_adj_lci") _tab ("f_adj_uci") _tab _n
* Cox models and Schoenfeld residual plots for each outcome
foreach outcome in died_covid_any hosp_any composite_any {
use ./output/an_dataset_`outcome', clear
missings report
drop if stp==""
* Open file to write results
describe
gen index_date = date("01/03/2020", "DMY")
stset stop, fail(`outcome'_flag) id(patient_id) enter(index_date) origin(index_date)
count if `outcome'_flag==1
if r(N) > 10 {
sts graph, by(udca) title("`outcome'") graphregion(fcolor(white)) ylabel(.75(.1)1)
graph export ./output/graphs/km_`outcome'.svg, as(svg) replace
* Cox model - crude
stcox udca, strata(stp) vce(robust)
estimates save "./output/tempdata/crude_`outcome'", replace
eststo model1
parmest, label eform format(estimate p lb ub) saving("./output/tempdata/surv_crude_`outcome'", replace) idstr("crude_`outcome'")
estat phtest, detail
* Plot schoenfeld residuals
estat phtest, plot(udca) ///
graphregion(fcolor(white)) ///
ylabel(, nogrid labsize(small)) ///
xlabel(, labsize(small)) ///
xtitle("Time", size(small)) ///
ytitle("Scaled Schoenfeld Residuals", size(small)) ///
msize(small) ///
mcolor(gs6) ///
msymbol(circle_hollow) ///
scheme(s1mono) ///
title ("`outcome'", position(11) size(medsmall)) ///
name(uni_plot_`outcome') ///
note("")
* Cox model - age and sex adjusted
stcox udca age_tv male, strata(stp) vce(robust)
estimates save "./output/tempdata/p_adj_model_`outcome'", replace
eststo model2
parmest, label eform format(estimate p lb ub) saving("./output/tempdata/p_surv_adj_`outcome'", replace) idstr("adj_`outcome'")
estat phtest, detail
* Cox model - fully adjusted
stcox udca age_tv male any_high_risk_condition i.eth_bin i.imd ib2.bmi_cat i.smoking severe_disease covid_vacc_first liver_trans, strata(stp) vce(robust)
estimates save "./output/tempdata/adj_model_`outcome'", replace
eststo model3
parmest, label eform format(estimate p lb ub) saving("./output/tempdata/surv_adj_`outcome'", replace) idstr("adj_`outcome'")
estat phtest, detail
* Plot Schoenfeld residuals
estat phtest, plot(udca) ///
graphregion(fcolor(white)) ///
ylabel(, nogrid labsize(small)) ///
xlabel(, labsize(small)) ///
xtitle("Time", size(small)) ///
ytitle("Scaled Schoenfeld Residuals", size(small)) ///
msize(small) ///
mcolor(gs6) ///
msymbol(circle_hollow) ///
scheme(s1mono) ///
title ("Adjusted `outcome'", position(11) size(medsmall)) ///
name(adj_plot_`outcome') ///
note("")
graph combine uni_plot_`outcome' adj_plot_`outcome'
graph export ./output/graphs/schoenplot_`outcome'.svg, as(svg) replace
* Cox model - fully adjusted with binary ethnicity variable
stcox udca age_tv male any_high_risk_condition i.ethnicity i.imd ib2.bmi_cat i.smoking severe_disease covid_vacc_first liver_trans, strata(stp) vce(robust)
* flag single row for each person
bys patient_id (start): gen number = _n==_N
tab number
* Count number unexposed at any time
bys patient_id : egen unexposed_ever = min(udca)
tab unexposed_ever if number==1
safecount if unexposed_ever==0 & number==1
local denominator = r(N)
safecount if udca == 0 & `outcome'_flag == 1
local event = round(r(N),6)
di "no udca events = " `event'
bysort udca: egen total_follow_up = total(_t) if number==1
su total_follow_up if udca==0 & number==1
local person_mth = round(r(mean),6)/30
di `person_mth'
local rate = 100000*(`event'/`person_mth')
di `rate'
if `event'>10 & `event'!=. {
file write tablecontent ("`outcome'") _tab ("No UDCA") _tab (`event') _tab %10.0f (`person_mth') _tab %3.2f (`rate') _tab
file write tablecontent ("1.00") _tab _tab ("1.00") _n
}
else {
file write tablecontent ("`outcome'") _tab ("No UDCA") _tab ("redact") _n
continue
}
* Count number exposed at any time
bys patient_id : egen exposed_ever = max(udca)
tab exposed_ever if number==1
qui safecount if exposed_ever==1 & number==1
local denominator = r(N)
qui safecount if udca == 1 & `outcome'_flag == 1
local event = round(r(N),6)
di "udca events = " `event'
qui su total_follow_up if udca==1 & number==1
local person_mth = round(r(mean),6)/30
local rate = 100000*(`event'/`person_mth')
if `event'>10 & `event'!=. {
file write tablecontent ("`outcome'") _tab ("UDCA") _tab (`event') _tab %10.0f (`person_mth') _tab %3.2f (`rate') _tab
cap estimates use "./output/tempdata/crude_`outcome'"
cap lincom udca, eform
file write tablecontent %4.2f (r(estimate)) _tab ("(") %4.2f (r(lb)) (" - ") %4.2f (r(ub)) (")") _tab %4.2f (r(lb)) _tab %4.2f (r(ub)) _tab
cap estimates clear
cap estimates use "./output/tempdata/p_adj_model_`outcome'"
cap lincom udca, eform
file write tablecontent %4.2f (r(estimate)) _tab ("(") %4.2f (r(lb)) (" - ") %4.2f (r(ub)) (")") _tab %4.2f (r(lb)) _tab %4.2f (r(ub)) _tab
cap estimates clear
cap estimates use "./output/tempdata/adj_model_`outcome'"
cap lincom udca, eform
file write tablecontent %4.2f (r(estimate)) _tab ("(") %4.2f (r(lb)) (" - ") %4.2f (r(ub)) (")") _tab %4.2f (r(lb)) _tab %4.2f (r(ub)) _tab _n
cap estimates clear
}
else {
file write tablecontent ("`outcome'") _tab ("UDCA") _tab ("redact") _n
continue
}
drop total_follow_up
}
else {
file write tablecontent ("`outcome'") _tab ("redact") _n
continue
}
}
* sensitivity analysis - 90 day exposure
file write tablecontent _n ("90 day exposure sensitivity analysis") _n
file write tablecontent ("Outcome") _tab ("Exposure status") _tab ("events") _tab ("total_person_mths") _tab ("Rate") _tab ("unadj_hr") _tab ///
("unadj_ci") _tab ("unadj_lci") _tab ("unadj_uci") _tab ("p_adj_hr") _tab ("p_adj_ci") _tab ("p_adj_lci") _tab ("p_adj_uci") _tab ("f_adj_hr") _tab ("f_adj_ci") _tab ("f_adj_lci") _tab ("f_adj_uci") _tab _n
* Cox models and Schoenfeld residual plots for each outcome
foreach outcome in died_covid_any hosp_any composite_any {
use ./output/an_dataset_90_`outcome', clear
* Open file to write results
missings report
drop if stp==""
describe
gen index_date = date("01/03/2020", "DMY")
stset stop, fail(`outcome'_flag) id(patient_id) enter(index_date) origin(index_date)
count if `outcome'_flag==1
if r(N) > 10 {
sts graph, by(udca) title("`outcome'") graphregion(fcolor(white)) ylabel(.75(.1)1)
graph export ./output/graphs/km_90_`outcome'.svg, as(svg) replace
* Cox model - crude
stcox udca, strata(stp) vce(robust)
estimates save "./output/tempdata/crude_`outcome'", replace
eststo model4
parmest, label eform format(estimate p lb ub) saving("./output/tempdata/surv_crude_90_`outcome'", replace) idstr("crude_`outcome'")
estat phtest, detail
* Plot schoenfeld residuals
estat phtest, plot(udca) ///
graphregion(fcolor(white)) ///
ylabel(, nogrid labsize(small)) ///
xlabel(, labsize(small)) ///
xtitle("Time", size(small)) ///
ytitle("Scaled Schoenfeld Residuals", size(small)) ///
msize(small) ///
mcolor(gs6) ///
msymbol(circle_hollow) ///
scheme(s1mono) ///
title ("`outcome'", position(11) size(medsmall)) ///
name(uni_plot_90_`outcome') ///
note("")
* Cox model - age and sex adjusted
stcox udca age_tv male, strata(stp) vce(robust)
estimates save "./output/tempdata/p_adj_model_`outcome'", replace
eststo model5
parmest, label eform format(estimate p lb ub) saving("./output/tempdata/p_surv_adj_90_`outcome'", replace) idstr("adj_`outcome'")
estat phtest, detail
* Cox model - fully adjusted
stcox udca age_tv male any_high_risk_condition i.eth_bin i.imd ib2.bmi_cat i.smoking severe_disease covid_vacc_first liver_trans, strata(stp) vce(robust)
estimates save "./output/tempdata/adj_model_`outcome'", replace
eststo model6
parmest, label eform format(estimate p lb ub) saving("./output/tempdata/surv_adj_90_`outcome'", replace) idstr("adj_`outcome'")
estat phtest, detail
* Plot Schoenfeld residuals
estat phtest, plot(udca) ///
graphregion(fcolor(white)) ///
ylabel(, nogrid labsize(small)) ///
xlabel(, labsize(small)) ///
xtitle("Time", size(small)) ///
ytitle("Scaled Schoenfeld Residuals", size(small)) ///
msize(small) ///
mcolor(gs6) ///
msymbol(circle_hollow) ///
scheme(s1mono) ///
title ("Adjusted `outcome'", position(11) size(medsmall)) ///
name(adj_plot_90_`outcome') ///
note("")
graph combine uni_plot_90_`outcome' adj_plot_90_`outcome'
graph export ./output/graphs/schoenplot_90_`outcome'.svg, as(svg) replace
* Cox model - fully adjusted with binary ethnicity variable
stcox udca age_tv male any_high_risk_condition i.ethnicity i.imd ib2.bmi_cat i.smoking severe_disease covid_vacc_first liver_trans, strata(stp) vce(robust)
* flag single row for each person
bys patient_id (start): gen number = _n==_N
tab number
* Count number unexposed at any time
bys patient_id : egen unexposed_ever = min(udca)
tab unexposed_ever if number==1
safecount if unexposed_ever==0 & number==1
local denominator = r(N)
safecount if udca == 0 & `outcome'_flag == 1
local event = round(r(N),6)
di "no udca events = " `event'
bysort udca: egen total_follow_up = total(_t) if number==1
su total_follow_up if udca==0 & number==1
local person_mth = round(r(mean),6)/30
di `person_mth'
local rate = 100000*(`event'/`person_mth')
di `rate'
if `event'>10 & `event'!=. {
file write tablecontent ("`outcome'") _tab ("No UDCA") _tab (`event') _tab %10.0f (`person_mth') _tab %3.2f (`rate') _tab
file write tablecontent ("1.00") _tab _tab ("1.00") _n
}
else {
file write tablecontent ("`outcome'") _tab ("No UDCA") _tab ("redact") _n
continue
}
* Count number exposed at any time
bys patient_id : egen exposed_ever = max(udca)
tab exposed_ever if number==1
qui safecount if exposed_ever==1 & number==1
local denominator = r(N)
qui safecount if udca == 1 & `outcome'_flag == 1
local event = round(r(N),6)
di "udca events = " `event'
qui su total_follow_up if udca==1 & number==1
local person_mth = round(r(mean),6)/30
local rate = 100000*(`event'/`person_mth')
if `event'>10 & `event'!=. {
file write tablecontent ("`outcome'") _tab ("UDCA") _tab (`event') _tab %10.0f (`person_mth') _tab %3.2f (`rate') _tab
cap estimates use "./output/tempdata/crude_`outcome'"
cap lincom udca, eform
file write tablecontent %4.2f (r(estimate)) _tab ("(") %4.2f (r(lb)) (" - ") %4.2f (r(ub)) (")") _tab %4.2f (r(lb)) _tab %4.2f (r(ub)) _tab
cap estimates clear
cap estimates use "./output/tempdata/p_adj_model_`outcome'"
cap lincom udca, eform
file write tablecontent %4.2f (r(estimate)) _tab ("(") %4.2f (r(lb)) (" - ") %4.2f (r(ub)) (")") _tab %4.2f (r(lb)) _tab %4.2f (r(ub)) _tab
cap estimates clear
cap estimates use "./output/tempdata/adj_model_`outcome'"
cap lincom udca, eform
file write tablecontent %4.2f (r(estimate)) _tab ("(") %4.2f (r(lb)) (" - ") %4.2f (r(ub)) (")") _tab %4.2f (r(lb)) _tab %4.2f (r(ub)) _tab _n
cap estimates clear
}
else {
file write tablecontent ("`outcome'") _tab ("UDCA") _tab ("redact") _n
continue
}
drop total_follow_up
}
else {
file write tablecontent ("`outcome'") _tab ("redact") _n
continue
}
}
* sensitivity analysis - 120 day overlap exposure
file write tablecontent _n ("120 day overlap exposure sensitivity analysis") _n
file write tablecontent ("Outcome") _tab ("Exposure status") _tab ("events") _tab ("total_person_mths") _tab ("Rate") _tab ("unadj_hr") _tab ///
("unadj_ci") _tab ("unadj_lci") _tab ("unadj_uci") _tab ("p_adj_hr") _tab ("p_adj_ci") _tab ("p_adj_lci") _tab ("p_adj_uci") _tab ("f_adj_hr") _tab ("f_adj_ci") _tab ("f_adj_lci") _tab ("f_adj_uci") _tab _n
* Cox models and Schoenfeld residual plots for each outcome
foreach outcome in died_covid_any hosp_any composite_any {
use ./output/an_dataset_overlap_120_`outcome', clear
* Open file to write results
missings report
drop if stp==""
describe
gen index_date = date("01/03/2020", "DMY")
stset stop, fail(`outcome'_flag) id(patient_id) enter(index_date) origin(index_date)
count if `outcome'_flag==1
if r(N) > 10 {
sts graph, by(udca) title("`outcome'") graphregion(fcolor(white)) ylabel(.75(.1)1)
graph export ./output/graphs/km_o_120_`outcome'.svg, as(svg) replace
* Cox model - crude
stcox udca, strata(stp) vce(robust)
estimates save "./output/tempdata/crude_`outcome'", replace
eststo model7
parmest, label eform format(estimate p lb ub) saving("./output/tempdata/surv_crude_o_120_`outcome'", replace) idstr("crude_`outcome'")
estat phtest, detail
* Plot schoenfeld residuals
estat phtest, plot(udca) ///
graphregion(fcolor(white)) ///
ylabel(, nogrid labsize(small)) ///
xlabel(, labsize(small)) ///
xtitle("Time", size(small)) ///
ytitle("Scaled Schoenfeld Residuals", size(small)) ///
msize(small) ///
mcolor(gs6) ///
msymbol(circle_hollow) ///
scheme(s1mono) ///
title ("`outcome'", position(11) size(medsmall)) ///
name(uni_plot_o_120_`outcome') ///
note("")
* Cox model - age and sex adjusted
stcox udca age_tv male, strata(stp) vce(robust)
estimates save "./output/tempdata/p_adj_model_`outcome'", replace
eststo model8
parmest, label eform format(estimate p lb ub) saving("./output/tempdata/p_surv_adj_o_120_`outcome'", replace) idstr("adj_`outcome'")
estat phtest, detail
* Cox model - fully adjusted
stcox udca age_tv male any_high_risk_condition i.eth_bin i.imd ib2.bmi_cat i.smoking severe_disease covid_vacc_first liver_trans, strata(stp) vce(robust)
estimates save "./output/tempdata/adj_model_`outcome'", replace
eststo model9
parmest, label eform format(estimate p lb ub) saving("./output/tempdata/surv_adj_o_120_`outcome'", replace) idstr("adj_`outcome'")
estat phtest, detail
* Plot Schoenfeld residuals
estat phtest, plot(udca) ///
graphregion(fcolor(white)) ///
ylabel(, nogrid labsize(small)) ///
xlabel(, labsize(small)) ///
xtitle("Time", size(small)) ///
ytitle("Scaled Schoenfeld Residuals", size(small)) ///
msize(small) ///
mcolor(gs6) ///
msymbol(circle_hollow) ///
scheme(s1mono) ///
title ("Adjusted `outcome'", position(11) size(medsmall)) ///
name(adj_plot_o_120_`outcome') ///
note("")
graph combine uni_plot_o_120_`outcome' adj_plot_o_120_`outcome'
graph export ./output/graphs/schoenplot_o_120_`outcome'.svg, as(svg) replace
* Cox model - fully adjusted with binary ethnicity variable
stcox udca age_tv male any_high_risk_condition i.ethnicity i.imd ib2.bmi_cat i.smoking severe_disease covid_vacc_first liver_trans, strata(stp) vce(robust)
* flag single row for each person
bys patient_id (start): gen number = _n==_N
tab number
* Count number unexposed at any time
bys patient_id : egen unexposed_ever = min(udca)
tab unexposed_ever if number==1
safecount if unexposed_ever==0 & number==1
local denominator = round(r(N),6)
safecount if udca == 0 & `outcome'_flag == 1
local event = round(r(N),6)
di "no udca events = " `event'
bysort udca: egen total_follow_up = total(_t) if number==1
su total_follow_up if udca==0 & number==1
local person_mth = round(r(mean),6)/30
di `person_mth'
local rate = 100000*(`event'/`person_mth')
di `rate'
if `event'>10 & `event'!=. {
file write tablecontent ("`outcome'") _tab ("No UDCA") _tab (`event') _tab %10.0f (`person_mth') _tab %3.2f (`rate') _tab
file write tablecontent ("1.00") _tab _tab ("1.00") _n
}
else {
file write tablecontent ("`outcome'") _tab ("No UDCA") _tab ("redact") _n
continue
}
* Count number exposed at any time
bys patient_id : egen exposed_ever = max(udca)
tab exposed_ever if number==1
qui safecount if exposed_ever==1 & number==1
local denominator = r(N)
qui safecount if udca == 1 & `outcome'_flag == 1
local event = round(r(N),6)
di "udca events = " `event'
qui su total_follow_up if udca==1 & number==1
local person_mth = round(r(mean),6)/30
local rate = 100000*(`event'/`person_mth')
if `event'>10 & `event'!=. {
file write tablecontent ("`outcome'") _tab ("UDCA") _tab (`event') _tab %10.0f (`person_mth') _tab %3.2f (`rate') _tab
cap estimates use "./output/tempdata/crude_`outcome'"
cap lincom udca, eform
file write tablecontent %4.2f (r(estimate)) _tab ("(") %4.2f (r(lb)) (" - ") %4.2f (r(ub)) (")") _tab %4.2f (r(lb)) _tab %4.2f (r(ub)) _tab
cap estimates clear
cap estimates use "./output/tempdata/p_adj_model_`outcome'"
cap lincom udca, eform
file write tablecontent %4.2f (r(estimate)) _tab ("(") %4.2f (r(lb)) (" - ") %4.2f (r(ub)) (")") _tab %4.2f (r(lb)) _tab %4.2f (r(ub)) _tab
cap estimates clear
cap estimates use "./output/tempdata/adj_model_`outcome'"
cap lincom udca, eform
file write tablecontent %4.2f (r(estimate)) _tab ("(") %4.2f (r(lb)) (" - ") %4.2f (r(ub)) (")") _tab %4.2f (r(lb)) _tab %4.2f (r(ub)) _tab _n
cap estimates clear
}
else {
file write tablecontent ("`outcome'") _tab ("UDCA") _tab ("redact") _n
continue
}
drop total_follow_up
}
else {
file write tablecontent ("`outcome'") _tab ("redact") _n
continue
}
}
* sensitivity analysis - stratify by PBC vs PSC
file write tablecontent _n ("PBC only sensitivity analysis") _n
file write tablecontent ("Outcome") _tab ("Exposure status") _tab ("events") _tab ("total_person_mths") _tab ("Rate") _tab ("unadj_hr") _tab ///
("unadj_ci") _tab ("unadj_lci") _tab ("unadj_uci") _tab ("p_adj_hr") _tab ("p_adj_ci") _tab ("p_adj_lci") _tab ("p_adj_uci") _tab ("f_adj_hr") _tab ("f_adj_ci") _tab ("f_adj_lci") _tab ("f_adj_uci") _tab _n
* Cox models and Schoenfeld residual plots for each outcome
foreach outcome in died_covid_any hosp_any composite_any {
use ./output/an_dataset_`outcome', clear
drop if stp==""
* Open file to write results
describe
gen index_date = date("01/03/2020", "DMY")
stset stop, fail(`outcome'_flag) id(patient_id) enter(index_date) origin(index_date)
count if `outcome'_flag==1 & has_pbc==1
if r(N) > 10 {
sts graph, by(udca) title("`outcome'") graphregion(fcolor(white)) ylabel(.75(.1)1)
graph export ./output/graphs/km_pbc_`outcome'.svg, as(svg) replace
* Cox model - crude
stcox udca if has_pbc==1, strata(stp) vce(robust)
estimates save "./output/tempdata/crude_`outcome'", replace
eststo model10
parmest, label eform format(estimate p lb ub) saving("./output/tempdata/surv_crude_pbc_`outcome'", replace) idstr("crude_`outcome'")
estat phtest, detail
* Plot schoenfeld residuals
estat phtest, plot(udca) ///
graphregion(fcolor(white)) ///
ylabel(, nogrid labsize(small)) ///
xlabel(, labsize(small)) ///
xtitle("Time", size(small)) ///
ytitle("Scaled Schoenfeld Residuals", size(small)) ///
msize(small) ///
mcolor(gs6) ///
msymbol(circle_hollow) ///
scheme(s1mono) ///
title ("`outcome'", position(11) size(medsmall)) ///
name(uni_plot_pbc_`outcome') ///
note("")
* Cox model - age and sex adjusted
stcox udca age_tv male if has_pbc==1, strata(stp) vce(robust)
estimates save "./output/tempdata/p_adj_model_`outcome'", replace
eststo model11
parmest, label eform format(estimate p lb ub) saving("./output/tempdata/p_surv_adj_pbc_`outcome'", replace) idstr("adj_`outcome'")
estat phtest, detail
* Cox model - fully adjusted
stcox udca age_tv male any_high_risk_condition i.eth_bin i.imd ib2.bmi_cat i.smoking severe_disease covid_vacc_first liver_trans if has_pbc==1, strata(stp) vce(robust)
estimates save "./output/tempdata/adj_model_`outcome'", replace
eststo model12
parmest, label eform format(estimate p lb ub) saving("./output/tempdata/surv_adj_pbc_`outcome'", replace) idstr("adj_`outcome'")
estat phtest, detail
* Plot Schoenfeld residuals
estat phtest, plot(udca) ///
graphregion(fcolor(white)) ///
ylabel(, nogrid labsize(small)) ///
xlabel(, labsize(small)) ///
xtitle("Time", size(small)) ///
ytitle("Scaled Schoenfeld Residuals", size(small)) ///
msize(small) ///
mcolor(gs6) ///
msymbol(circle_hollow) ///
scheme(s1mono) ///
title ("Adjusted `outcome'", position(11) size(medsmall)) ///
name(adj_plot_pbc_`outcome') ///
note("")
graph combine uni_plot_pbc_`outcome' adj_plot_pbc_`outcome'
graph export ./output/graphs/schoenplot_pbc_`outcome'.svg, as(svg) replace
* Cox model - fully adjusted with categorical ethnicity variable
stcox udca age_tv male any_high_risk_condition i.ethnicity i.imd ib2.bmi_cat i.smoking severe_disease covid_vacc_first liver_trans if has_pbc==1, strata(stp) vce(robust)
* flag single row for each person
bys patient_id (start): gen number = _n==_N
tab number
* Count number unexposed at any time
bys patient_id : egen unexposed_ever = min(udca)
tab unexposed_ever if number==1 & has_pbc==1
safecount if unexposed_ever==0 & has_pbc==1 & number==1
local denominator = r(N)
safecount if udca == 0 & `outcome'_flag == 1 & has_pbc==1
local event = round(r(N),6)
di "no udca events = " `event'
bysort udca: egen total_follow_up = total(_t) if number==1
su total_follow_up if udca==0 & number==1 & has_pbc==1
local person_mth = round(r(mean),6)/30
di `person_mth'
local rate = 100000*(`event'/`person_mth')
di `rate'
if `event'>10 & `event'!=. {
file write tablecontent ("`outcome'") _tab ("No UDCA") _tab (`event') _tab %10.0f (`person_mth') _tab %3.2f (`rate') _tab
file write tablecontent ("1.00") _tab _tab ("1.00") _n
}
else {
file write tablecontent ("`outcome'") _tab ("No UDCA") _tab ("redact") _n
continue
}
* Count number exposed at any time
bys patient_id : egen exposed_ever = max(udca)
tab exposed_ever if number==1 & has_pbc==1
qui safecount if exposed_ever==1 & number==1 & has_pbc==1
local denominator = r(N)
qui safecount if udca == 1 & `outcome'_flag == 1 & has_pbc==1
local event = round(r(N),6)
di "udca events = " `event'
qui su total_follow_up if udca==1 & number==1 & has_pbc==1
local person_mth = round(r(mean),6)/30
local rate = 100000*(`event'/`person_mth')
if `event'>10 & `event'!=. {
file write tablecontent ("`outcome'") _tab ("UDCA") _tab (`event') _tab %10.0f (`person_mth') _tab %3.2f (`rate') _tab
cap estimates use "./output/tempdata/crude_`outcome'"
cap lincom udca, eform
file write tablecontent %4.2f (r(estimate)) _tab ("(") %4.2f (r(lb)) (" - ") %4.2f (r(ub)) (")") _tab %4.2f (r(lb)) _tab %4.2f (r(ub)) _tab
cap estimates clear
cap estimates use "./output/tempdata/p_adj_model_`outcome'"
cap lincom udca, eform
file write tablecontent %4.2f (r(estimate)) _tab ("(") %4.2f (r(lb)) (" - ") %4.2f (r(ub)) (")") _tab %4.2f (r(lb)) _tab %4.2f (r(ub)) _tab
cap estimates clear
cap estimates use "./output/tempdata/adj_model_`outcome'"
cap lincom udca, eform
file write tablecontent %4.2f (r(estimate)) _tab ("(") %4.2f (r(lb)) (" - ") %4.2f (r(ub)) (")") _tab %4.2f (r(lb)) _tab %4.2f (r(ub)) _tab _n
cap estimates clear
}
else {
file write tablecontent ("`outcome'") _tab ("UDCA") _tab ("redact") _n
continue
}
drop total_follow_up
}
else {
file write tablecontent ("`outcome'") _tab ("redact") _n
continue
}
}
file write tablecontent _n ("PSC only sensitivity analysis") _n
file write tablecontent ("Outcome") _tab ("Exposure status") _tab ("events") _tab ("total_person_mths") _tab ("Rate") _tab ("unadj_hr") _tab ///
("unadj_ci") _tab ("unadj_lci") _tab ("unadj_uci") _tab ("p_adj_hr") _tab ("p_adj_ci") _tab ("p_adj_lci") _tab ("p_adj_uci") _tab ("f_adj_hr") _tab ("f_adj_ci") _tab ("f_adj_lci") _tab ("f_adj_uci") _tab _n
* Cox models and Schoenfeld residual plots for each outcome
foreach outcome in died_covid_any hosp_any composite_any {
use ./output/an_dataset_`outcome', clear
drop if stp==""
* Open file to write results
describe
gen index_date = date("01/03/2020", "DMY")
stset stop, fail(`outcome'_flag) id(patient_id) enter(index_date) origin(index_date)
count if `outcome'_flag==1 & has_pbc==0
if r(N) > 10 {
sts graph, by(udca) title("`outcome'") graphregion(fcolor(white)) ylabel(.75(.1)1)
graph export ./output/graphs/km_psc_`outcome'.svg, as(svg) replace
* Cox model - crude
stcox udca if has_pbc==0, strata(stp) vce(robust)
estimates save "./output/tempdata/crude_`outcome'", replace
eststo model10
parmest, label eform format(estimate p lb ub) saving("./output/tempdata/surv_crude_psc_`outcome'", replace) idstr("crude_`outcome'")
estat phtest, detail
* Plot schoenfeld residuals
estat phtest, plot(udca) ///
graphregion(fcolor(white)) ///
ylabel(, nogrid labsize(small)) ///
xlabel(, labsize(small)) ///
xtitle("Time", size(small)) ///
ytitle("Scaled Schoenfeld Residuals", size(small)) ///
msize(small) ///
mcolor(gs6) ///
msymbol(circle_hollow) ///
scheme(s1mono) ///
title ("`outcome'", position(11) size(medsmall)) ///
name(uni_plot_psc_`outcome') ///
note("")
* Cox model - age and sex adjusted
stcox udca age_tv male if has_pbc==0, strata(stp) vce(robust)
estimates save "./output/tempdata/p_adj_model_`outcome'", replace
eststo model11
parmest, label eform format(estimate p lb ub) saving("./output/tempdata/p_surv_adj_psc_`outcome'", replace) idstr("adj_`outcome'")
estat phtest, detail
* Cox model - fully adjusted
stcox udca age_tv male any_high_risk_condition i.eth_bin i.imd ib2.bmi_cat i.smoking severe_disease covid_vacc_first liver_trans if has_pbc==0, strata(stp) vce(robust)
estimates save "./output/tempdata/adj_model_`outcome'", replace
eststo model12
parmest, label eform format(estimate p lb ub) saving("./output/tempdata/surv_adj_psc_`outcome'", replace) idstr("adj_`outcome'")
estat phtest, detail
* Plot Schoenfeld residuals
estat phtest, plot(udca) ///
graphregion(fcolor(white)) ///
ylabel(, nogrid labsize(small)) ///
xlabel(, labsize(small)) ///
xtitle("Time", size(small)) ///
ytitle("Scaled Schoenfeld Residuals", size(small)) ///
msize(small) ///
mcolor(gs6) ///
msymbol(circle_hollow) ///
scheme(s1mono) ///
title ("Adjusted `outcome'", position(11) size(medsmall)) ///
name(adj_plot_psc_`outcome') ///
note("")
graph combine uni_plot_psc_`outcome' adj_plot_psc_`outcome'
graph export ./output/graphs/schoenplot_psc_`outcome'.svg, as(svg) replace
* Cox model - fully adjusted with binary ethnicity variable
stcox udca age_tv male any_high_risk_condition i.ethnicity i.imd ib2.bmi_cat i.smoking severe_disease covid_vacc_first liver_trans if has_pbc==0, strata(stp) vce(robust)
* flag single row for each person
bys patient_id (start): gen number = _n==_N
tab number
* Count number unexposed at any time
bys patient_id : egen unexposed_ever = min(udca)
tab unexposed_ever if number==1 & has_pbc==0
safecount if unexposed_ever==0 & has_pbc==0 & number==1
local denominator = r(N)
safecount if udca == 0 & `outcome'_flag == 1 & has_pbc==0
local event = round(r(N),6)
di "no udca events = " `event'
bysort udca has_pbc: egen total_follow_up = total(_t) if number==1
su total_follow_up if udca==0 & number==1 & has_pbc==0
local person_mth = round(r(mean),6)/30
di `person_mth'
local rate = 100000*(`event'/`person_mth')
di `rate'
if `event'>10 & `event'!=. {
file write tablecontent ("`outcome'") _tab ("No UDCA") _tab (`event') _tab %10.0f (`person_mth') _tab %3.2f (`rate') _tab
file write tablecontent ("1.00") _tab _tab ("1.00") _n
}
else {
file write tablecontent ("`outcome'") _tab ("No UDCA") _tab ("redact") _n
continue
}
* Count number exposed at any time
bys patient_id : egen exposed_ever = max(udca)
tab exposed_ever if number==1 & has_pbc==0
qui safecount if exposed_ever==1 & number==1 & has_pbc==0
local denominator = r(N)
qui safecount if udca == 1 & `outcome'_flag == 1 & has_pbc==0
local event = round(r(N),6)
di "udca events = " `event'
su total_follow_up if udca==1 & number==1 & has_pbc==0
local person_mth = round(r(mean),6)/30
local rate = 100000*(`event'/`person_mth')
if `event'>10 & `event'!=. {
file write tablecontent ("`outcome'") _tab ("UDCA") _tab (`event') _tab %10.0f (`person_mth') _tab %3.2f (`rate') _tab
cap estimates use "./output/tempdata/crude_`outcome'"
cap lincom udca, eform
file write tablecontent %4.2f (r(estimate)) _tab ("(") %4.2f (r(lb)) (" - ") %4.2f (r(ub)) (")") _tab %4.2f (r(lb)) _tab %4.2f (r(ub)) _tab
cap estimates clear
cap estimates use "./output/tempdata/p_adj_model_`outcome'"
cap lincom udca, eform
file write tablecontent %4.2f (r(estimate)) _tab ("(") %4.2f (r(lb)) (" - ") %4.2f (r(ub)) (")") _tab %4.2f (r(lb)) _tab %4.2f (r(ub)) _tab
cap estimates clear
cap estimates use "./output/tempdata/adj_model_`outcome'"
cap lincom udca, eform
file write tablecontent %4.2f (r(estimate)) _tab ("(") %4.2f (r(lb)) (" - ") %4.2f (r(ub)) (")") _tab %4.2f (r(lb)) _tab %4.2f (r(ub)) _tab _n
cap estimates clear
}
else {
file write tablecontent ("`outcome'") _tab ("UDCA") _tab ("redact") _n
continue
}
drop total_follow_up
}
else {
file write tablecontent ("`outcome'") _tab ("redact") _n
continue
}
}
* Take out people prescribed OCA at baseline
file write tablecontent _n ("Remove people prescribed OCA sensitivity analysis") _n
file write tablecontent ("Outcome") _tab ("Exposure status") _tab ("events") _tab ("total_person_mths") _tab ("Rate") _tab ("unadj_hr") _tab ///
("unadj_ci") _tab ("unadj_lci") _tab ("unadj_uci") _tab ("p_adj_hr") _tab ("p_adj_ci") _tab ("p_adj_lci") _tab ("p_adj_uci") _tab ("f_adj_hr") _tab ("f_adj_ci") _tab ("f_adj_lci") _tab ("f_adj_uci") _tab _n
* Cox models and Schoenfeld residual plots for each outcome
foreach outcome in died_covid_any hosp_any composite_any {
use ./output/an_dataset_`outcome', clear
merge m:1 patient_id using ./output/baseline_oca_n
tab _merge
drop _merge
drop if stp==""
* Open file to write results
describe
gen index_date = date("01/03/2020", "DMY")
drop if oca_bl==1 | prescribed_oca_n==1
stset stop, fail(`outcome'_flag) id(patient_id) enter(index_date) origin(index_date)
count if `outcome'_flag==1
if r(N) > 10 {
sts graph, by(udca) title("`outcome'") graphregion(fcolor(white)) ylabel(.75(.1)1)
graph export ./output/graphs/km_oca_`outcome'.svg, as(svg) replace
* Cox model - crude
stcox udca, strata(stp) vce(robust)
estimates save "./output/tempdata/crude_`outcome'", replace
eststo model7
parmest, label eform format(estimate p lb ub) saving("./output/tempdata/surv_crude_oca_`outcome'", replace) idstr("crude_`outcome'")
estat phtest, detail
* Plot schoenfeld residuals
estat phtest, plot(udca) ///
graphregion(fcolor(white)) ///
ylabel(, nogrid labsize(small)) ///
xlabel(, labsize(small)) ///
xtitle("Time", size(small)) ///
ytitle("Scaled Schoenfeld Residuals", size(small)) ///
msize(small) ///
mcolor(gs6) ///
msymbol(circle_hollow) ///
scheme(s1mono) ///
title ("`outcome'", position(11) size(medsmall)) ///
name(uni_plot_oca_`outcome') ///
note("")
* Cox model - age and sex adjusted
stcox udca age_tv male, strata(stp) vce(robust)
estimates save "./output/tempdata/p_adj_model_`outcome'", replace
eststo model8
parmest, label eform format(estimate p lb ub) saving("./output/tempdata/p_surv_adj_oca_`outcome'", replace) idstr("adj_`outcome'")
estat phtest, detail
* Cox model - fully adjusted
stcox udca age_tv male any_high_risk_condition i.eth_bin i.imd ib2.bmi_cat i.smoking severe_disease covid_vacc_first liver_trans, strata(stp) vce(robust)
estimates save "./output/tempdata/adj_model_`outcome'", replace
eststo model9
parmest, label eform format(estimate p lb ub) saving("./output/tempdata/surv_adj_oca_`outcome'", replace) idstr("adj_`outcome'")
estat phtest, detail
* Plot Schoenfeld residuals
estat phtest, plot(udca) ///
graphregion(fcolor(white)) ///
ylabel(, nogrid labsize(small)) ///
xlabel(, labsize(small)) ///
xtitle("Time", size(small)) ///
ytitle("Scaled Schoenfeld Residuals", size(small)) ///
msize(small) ///
mcolor(gs6) ///
msymbol(circle_hollow) ///
scheme(s1mono) ///
title ("Adjusted `outcome'", position(11) size(medsmall)) ///
name(adj_plot_oca_`outcome') ///
note("")
graph combine uni_plot_oca_`outcome' adj_plot_oca_`outcome'
graph export ./output/graphs/schoenplot_oca_`outcome'.svg, as(svg) replace
* Cox model - fully adjusted with binary ethnicity variable
stcox udca age_tv male any_high_risk_condition i.ethnicity i.imd ib2.bmi_cat i.smoking severe_disease covid_vacc_first liver_trans, strata(stp) vce(robust)
* flag single row for each person
bys patient_id (start): gen number = _n==_N
tab number
* Count number unexposed at any time
bys patient_id : egen unexposed_ever = min(udca)
tab unexposed_ever if number==1
safecount if unexposed_ever==0 & number==1
local denominator = r(N)
safecount if udca == 0 & `outcome'_flag == 1
local event = round(r(N),6)
di "no udca events = " `event'
bysort udca: egen total_follow_up = total(_t) if number==1
su total_follow_up if udca==0 & number==1
local person_mth = round(r(mean),6)/30
di `person_mth'
local rate = 100000*(`event'/`person_mth')
di `rate'
if `event'>10 & `event'!=. {
file write tablecontent ("`outcome'") _tab ("No UDCA") _tab (`event') _tab %10.0f (`person_mth') _tab %3.2f (`rate') _tab
file write tablecontent ("1.00") _tab _tab ("1.00") _n
}
else {
file write tablecontent ("`outcome'") _tab ("No UDCA") _tab ("redact") _n
continue
}
* Count number exposed at any time
bys patient_id : egen exposed_ever = max(udca)
tab exposed_ever if number==1
qui safecount if exposed_ever==1 & number==1
local denominator = r(N)
qui safecount if udca == 1 & `outcome'_flag == 1
local event = round(r(N),6)
di "udca events = " `event'
qui su total_follow_up if udca==1 & number==1
local person_mth = round(r(mean),6)/30
local rate = 100000*(`event'/`person_mth')
if `event'>10 & `event'!=. {
file write tablecontent ("`outcome'") _tab ("UDCA") _tab (`event') _tab %10.0f (`person_mth') _tab %3.2f (`rate') _tab
cap estimates use "./output/tempdata/crude_`outcome'"
cap lincom udca, eform
file write tablecontent %4.2f (r(estimate)) _tab ("(") %4.2f (r(lb)) (" - ") %4.2f (r(ub)) (")") _tab %4.2f (r(lb)) _tab %4.2f (r(ub)) _tab
cap estimates clear
cap estimates use "./output/tempdata/p_adj_model_`outcome'"
cap lincom udca, eform
file write tablecontent %4.2f (r(estimate)) _tab ("(") %4.2f (r(lb)) (" - ") %4.2f (r(ub)) (")") _tab %4.2f (r(lb)) _tab %4.2f (r(ub)) _tab
cap estimates clear
cap estimates use "./output/tempdata/adj_model_`outcome'"
cap lincom udca, eform
file write tablecontent %4.2f (r(estimate)) _tab ("(") %4.2f (r(lb)) (" - ") %4.2f (r(ub)) (")") _tab %4.2f (r(lb)) _tab %4.2f (r(ub)) _tab _n
cap estimates clear
}
else {
file write tablecontent ("`outcome'") _tab ("UDCA") _tab ("redact") _n
continue
}
drop total_follow_up
}
else {
file write tablecontent ("`outcome'") _tab ("redact") _n
continue
}
}
* sensitivity analysis - explore vaccinations
file write tablecontent _n ("vaccinations sensitivity analysis") _n
file write tablecontent ("Outcome") _tab ("Exposure status") _tab ("events") _tab ("total_person_wks") _tab ("Rate") _tab ("unadj_hr") _tab ///
("unadj_ci") _tab ("unadj_lci") _tab ("unadj_uci") _tab ("p_adj_hr") _tab ("p_adj_ci") _tab ("p_adj_lci") _tab ("p_adj_uci") _tab ("f_adj_hr") _tab ("f_adj_ci") _tab ("f_adj_lci") _tab ("f_adj_uci") _tab _n
* Cox models and Schoenfeld residual plots for each outcome
foreach outcome in died_covid_any hosp_any composite_any {
use ./output/an_dataset_`outcome'_vacc, clear
* Open file to write results
missings report
drop if stp==""
describe
gen index_date = date("01/03/2021", "DMY")
* Flag records where outcome or end_date prior to 1st March 2021
bys patient_id: egen end_date = max(stop)
stset stop, fail(`outcome'_flag) id(patient_id) enter(index_date) origin(index_date)
count if `outcome'_flag==1
if r(N) > 10 {
sts graph, by(udca) title("`outcome'") graphregion(fcolor(white)) ylabel(.75(.1)1)
graph export ./output/graphs/km_vacc_`outcome'.svg, as(svg) replace
* Cox model - crude
stcox udca, strata(stp) vce(robust)
estimates save "./output/tempdata/crude_`outcome'", replace
eststo model7
parmest, label eform format(estimate p lb ub) saving("./output/tempdata/surv_crude_vacc_`outcome'", replace) idstr("crude_`outcome'")
estat phtest, detail
* Plot schoenfeld residuals
estat phtest, plot(udca) ///
graphregion(fcolor(white)) ///
ylabel(, nogrid labsize(small)) ///
xlabel(, labsize(small)) ///
xtitle("Time", size(small)) ///
ytitle("Scaled Schoenfeld Residuals", size(small)) ///
msize(small) ///
mcolor(gs6) ///
msymbol(circle_hollow) ///
scheme(s1mono) ///
title ("`outcome'", position(11) size(medsmall)) ///
name(uni_plot_vacc_`outcome') ///
note("")
* Cox model - age and sex adjusted
stcox udca age_tv male, strata(stp) vce(robust)
estimates save "./output/tempdata/p_adj_model_`outcome'", replace
eststo model8
parmest, label eform format(estimate p lb ub) saving("./output/tempdata/p_surv_adj_vacc_`outcome'", replace) idstr("adj_`outcome'")
estat phtest, detail
* Cox model - fully adjusted
stcox udca age_tv male any_high_risk_condition i.eth_bin i.imd ib2.bmi_cat i.smoking severe_disease i.vacc_count_tv liver_trans ib5.time_vacc_cat, strata(stp) vce(robust)
estimates save "./output/tempdata/adj_model_`outcome'", replace
eststo model9
parmest, label eform format(estimate p lb ub) saving("./output/tempdata/surv_adj_vacc_`outcome'", replace) idstr("adj_`outcome'")
estat phtest, detail
* Plot Schoenfeld residuals
estat phtest, plot(udca) ///
graphregion(fcolor(white)) ///
ylabel(, nogrid labsize(small)) ///
xlabel(, labsize(small)) ///
xtitle("Time", size(small)) ///
ytitle("Scaled Schoenfeld Residuals", size(small)) ///
msize(small) ///
mcolor(gs6) ///
msymbol(circle_hollow) ///
scheme(s1mono) ///
title ("Adjusted `outcome'", position(11) size(medsmall)) ///
name(adj_plot_vacc_`outcome') ///
note("")
graph combine uni_plot_vacc_`outcome' adj_plot_vacc_`outcome'
graph export ./output/graphs/schoenplot_vacc_`outcome'.svg, as(svg) replace
* Cox model - fully adjusted with categorical ethnicity variable
stcox udca age_tv male any_high_risk_condition i.ethnicity i.imd ib2.bmi_cat i.smoking severe_disease i.vacc_count_tv liver_trans ib5.time_vacc_cat, strata(stp) vce(robust)
* flag single row for each person
bys patient_id (start): gen number = _n==_N
tab number
* Count number unexposed at any time
bys patient_id : egen unexposed_ever = min(udca)
tab unexposed_ever if number==1
safecount if unexposed_ever==0 & number==1
local denominator = r(N)
safecount if udca == 0 & `outcome'_flag == 1
local event = round(r(N),6)
di "no udca events = " `event'
bysort udca: egen total_follow_up = total(_t) if number==1
su total_follow_up if udca==0 & number==1
local person_mth = round(r(mean),6)/30
di `person_mth'
local rate = 100000*(`event'/`person_mth')
di `rate'
if `event'>10 & `event'!=. {
file write tablecontent ("`outcome'") _tab ("No UDCA") _tab (`event') _tab %10.0f (`person_mth') _tab %3.2f (`rate') _tab
file write tablecontent ("1.00") _tab _tab ("1.00") _n
}
else {
file write tablecontent ("`outcome'") _tab ("No UDCA") _tab ("redact") _n
continue
}
* Count number exposed at any time
bys patient_id : egen exposed_ever = max(udca)
tab exposed_ever if number==1
qui safecount if exposed_ever==1 & number==1
local denominator = r(N)
qui safecount if udca == 1 & `outcome'_flag == 1
local event = round(r(N), 5)
di "udca events = " `event'
qui su total_follow_up if udca==1 & number==1
local person_mth = round(r(mean),6)/30
local rate = 100000*(`event'/`person_mth')
if `event'>10 & `event'!=. {
file write tablecontent ("`outcome'") _tab ("UDCA") _tab (`event') _tab %10.0f (`person_mth') _tab %3.2f (`rate') _tab
cap estimates use "./output/tempdata/crude_`outcome'"
cap lincom udca, eform
file write tablecontent %4.2f (r(estimate)) _tab ("(") %4.2f (r(lb)) (" - ") %4.2f (r(ub)) (")") _tab %4.2f (r(lb)) _tab %4.2f (r(ub)) _tab
cap estimates clear
cap estimates use "./output/tempdata/p_adj_model_`outcome'"
cap lincom udca, eform
file write tablecontent %4.2f (r(estimate)) _tab ("(") %4.2f (r(lb)) (" - ") %4.2f (r(ub)) (")") _tab %4.2f (r(lb)) _tab %4.2f (r(ub)) _tab
cap estimates clear
cap estimates use "./output/tempdata/adj_model_`outcome'"
cap lincom udca, eform
file write tablecontent %4.2f (r(estimate)) _tab ("(") %4.2f (r(lb)) (" - ") %4.2f (r(ub)) (")") _tab %4.2f (r(lb)) _tab %4.2f (r(ub)) _tab _n
cap estimates clear
}
else {
file write tablecontent ("`outcome'") _tab ("UDCA") _tab ("redact") _n
continue
}
drop total_follow_up
}
else {
file write tablecontent ("`outcome'") _tab ("redact") _n
continue
}
}
file close tablecontent