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304_ps_model.do
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304_ps_model.do
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********************************************************************************
*
* Do-file: propensity score cox model
* Project: Sotrovimab-Paxlovid-Molnupiravir
* Date: 24/4/23
* Programmed by: Katie Bechman
* Description: create and run ps model
* Data used: main.dta
* Data created: psoutput
* Other output: logfiles, printed to folder $Logdir
* User installed ado: (place .ado file(s) in analysis folder)
****************************************************************************************************************
**Set filepaths
//global projectdir "C:\Users\k1635179\OneDrive - King's College London\Katie\OpenSafely\Safety mAB and antivirals\Safety-Sotrovimab-Paxlovid-Molnupiravir"
global projectdir `c(pwd)'
di "$projectdir"
capture mkdir "$projectdir/output/data"
capture mkdir "$projectdir/output/figures"
capture mkdir "$projectdir/output/tables"
global logdir "$projectdir/logs"
di "$logdir"
* Open a log file
cap log close
log using "$logdir/ps_model.log", replace
*Set Ado file path
adopath + "$projectdir/analysis/ado"
* SET Index date
global indexdate = "01/03/2020"
use "$projectdir/output/data/main", clear
* Models
global agesex age i.sex
global adj age i.sex i.region_nhs i.imdq5 i.ethnicity 1b.bmi_group ///
paxlovid_contraindicated i.vaccination_status diabetes chronic_cardiac_disease chronic_respiratory_disease hypertension ///
downs_syndrome solid_cancer haem_disease renal_disease liver_disease imid_on_drug immunosuppression hiv_aids organ_transplant rare_neuro
global adj2 age i.sex i.region_nhs i.imdq5 i.ethnicity 1b.bmi_group
global adj3 age i.sex i.region_nhs i.imdq5 i.ethnicity 1b.bmi_group ///
paxlovid_contraindicated i.vaccination_status diabetes chronic_cardiac_disease chronic_respiratory_disease hypertension
global adj4 age i.sex i.region_nhs i.imdq5 White 1b.bmi_group ///
paxlovid_contraindicated i.vaccination_status diabetes chronic_cardiac_disease chronic_respiratory_disease hypertension ///
dementia care_home serious_mental_illness
* Balance
global bal_agesex age sex
global bal_adj age sex region_nhs imdq5 ethnicity bmi_group ///
paxlovid_contraindicated vaccination_status diabetes chronic_cardiac_disease chronic_respiratory_disease hypertension ///
downs_syndrome solid_cancer haem_disease renal_disease liver_disease imid_on_drug immunosuppression hiv_aids organ_transplant rare_neuro
global bal_adj2 age sex region_nhs imdq5 ethnicity bmi_group
global bal_adj3 age sex region_nhs imdq5 ethnicity bmi_group ///
paxlovid_contraindicated vaccination_status diabetes chronic_cardiac_disease chronic_respiratory_disease hypertension
global bal_adj4 age sex region_nhs imdq5 ethnicity bmi_group ///
paxlovid_contraindicated vaccination_status diabetes chronic_cardiac_disease chronic_respiratory_disease hypertension ///
dementia care_home serious_mental_illness
* Outcome
global ae_disease ae_diverticulitis ///
ae_diarrhoea ///
ae_taste ///
ae_rash ///
ae_bronchospasm ///
ae_contactderm ///
ae_dizziness ///
ae_nausea_vomit ///
ae_headache ///
ae_anaphylaxis ///
ae_drugreaction ///
ae_ra ///
ae_sle ///
ae_psorasis ///
ae_psa ///
ae_axspa ///
ae_ibd
global ae_disease_serious ae_diverticulitis_serious ///
ae_diarrhoea_serious ///
ae_taste_serious ///
ae_rash_serious ///
ae_contactderm_serious ///
ae_dizziness_serious ///
ae_nausea_vomit_serious ///
ae_headache_serious ///
ae_anaphylaxis_serious ///
ae_drugreaction_serious ///
ae_ra_serious ///
ae_sle_serious ///
ae_psorasis_serious ///
ae_psa_serious ///
ae_axspa_serious ///
ae_ibd_serious
global ae_combined ae_all ///
ae_all_serious ///
ae_spc_all ///
ae_spc_serious ///
ae_drug_all ///
ae_drug_serious ///
ae_imae_all ///
ae_imae_serious
** Hazard of summary
****************************************************************************************************************
*1. Individual drug V No Drug
// SOTROVIMAB //
tempname coxoutput_propensity_sot
postfile `coxoutput_propensity_sot' str20(model) str20(fail) ///
hr_sot lc_sot uc_sot ///
using "$projectdir/output/tables/cox_propensity_sot", replace
preserve
keep if drug==0 | drug==1
foreach model in agesex adj adj2 adj3 adj4 {
logistic drug $`model'
predict p_drug_`model'
twoway (histogram p_drug_`model' if drug==1, color(green)) (histogram p_drug_`model' if drug==0, fcolor(none) lcolor(black)), ///
legend(order(1 "No Drug" 2 "Sotrovimab")) name(histogram_sot`model', replace) saving("$projectdir/output/figures/histogram_sot_`model'", replace)
gen iptw_`model' = 1/p_drug_`model' if drug==1
replace iptw_`model' = 1/(1-p_drug_`model') if drug==0
foreach fail in $ae_combined {
stset stop_`fail' [pw=iptw_`model'], id(patient_id) origin(time start_date) enter(time start_date) failure(fail_`fail'==1)
stcox i.drug, vce(robust)
matrix b = r(table)
local hr_sot = b[1,2]
local lc_sot = b[5,2]
local uc_sot = b[6,2]
post `coxoutput_propensity_sot' ("`fail'") ("`model'") (`hr_sot') (`lc_sot') (`uc_sot')
}
}
pbalchk drug $bal_agesex
pbalchk drug $bal_agesex, wt(iptw_agesex) graph
graph save "$projectdir/output/figures/sot_match_agesex", replace
pbalchk drug $bal_adj
pbalchk drug $bal_adj, wt(iptw_adj) graph
graph save "$projectdir/output/figures/sot_match_adj", replace
pbalchk drug $bal_adj2
pbalchk drug $bal_adj2, wt(iptw_adj2) graph
graph save "$projectdir/output/figures/sot_match_adj2", replace
pbalchk drug $bal_adj3
pbalchk drug $bal_adj3, wt(iptw_adj3) graph
graph save "$projectdir/output/figures/sot_match_adj3", replace
pbalchk drug $bal_adj4
pbalchk drug $bal_adj4, wt(iptw_adj4) graph
graph save "$projectdir/output/figures/sot_match_adj4", replace
restore
postclose `coxoutput_propensity_sot'
// PAXLOVID //
tempname coxoutput_propensity_pax
postfile `coxoutput_propensity_pax' str20(model) str20(fail) ///
hr_pax lc_pax uc_pax ///
using "$projectdir/output/tables/cox_propensity_pax", replace
preserve
keep if drug==0 | drug==2
replace drug=1 if drug==2
lab define drug 0 "Control" 1 "Paxlovid", replace
label values drug drug
foreach model in agesex adj adj2 adj3 adj4 {
logistic drug $`model'
predict p_drug_`model'
twoway (histogram p_drug_`model' if drug==1, color(green)) (histogram p_drug_`model' if drug==0, fcolor(none) lcolor(black)), ///
legend(order(1 "No Drug" 2 "Paxlovid")) name(histogram_pax_`model', replace) saving("$projectdir/output/figures/histogram_pax_`model'", replace)
graph export "$projectdir/output/figures/histogram_pax_`model'.svg", as(svg) replace
gen iptw_`model' = 1/p_drug_`model' if drug==1
replace iptw_`model' = 1/(1-p_drug_`model') if drug==0
foreach fail in $ae_combined {
stset stop_`fail' [pw=iptw_`model'], id(patient_id) origin(time start_date) enter(time start_date) failure(fail_`fail'==1)
stcox i.drug, vce(robust)
matrix b = r(table)
local hr_pax = b[1,2]
local lc_pax = b[5,2]
local uc_pax = b[6,2]
post `coxoutput_propensity_pax' ("`fail'") ("`model'") (`hr_pax') (`lc_pax') (`uc_pax')
}
}
pbalchk drug $bal_agesex
pbalchk drug $bal_agesex, wt(iptw_agesex) graph
graph save "$projectdir/output/figures/pax_match_agesex", replace
pbalchk drug $bal_adj
pbalchk drug $bal_adj, wt(iptw_adj) graph
graph save "$projectdir/output/figures/pax_match_adj", replace
pbalchk drug $bal_adj2
pbalchk drug $bal_adj2, wt(iptw_adj2) graph
graph save "$projectdir/output/figures/pax_match_adj2", replace
pbalchk drug $bal_adj3
pbalchk drug $bal_adj3, wt(iptw_adj3) graph
graph save "$projectdir/output/figures/pax_match_adj3", replace
pbalchk drug $bal_adj4
pbalchk drug $bal_adj4, wt(iptw_adj4) graph
graph save "$projectdir/output/figures/pax_match_adj4", replace
restore
postclose `coxoutput_propensity_pax'
// MOLNUPAVIR //
tempname coxoutput_propensity_mol
postfile `coxoutput_propensity_mol' str20(model) str20(fail) ///
hr_mol lc_mol uc_mol ///
using "$projectdir/output/tables/cox_propensity_mol", replace
preserve
keep if drug==0 | drug==3
replace drug=1 if drug==3
lab define drug 0 "Control" 1 "Molnupavir", replace
label values drug drug
foreach model in agesex adj adj2 adj3 adj4 {
logistic drug $`model'
predict p_drug_`model'
twoway (histogram p_drug_`model' if drug==1, color(green)) (histogram p_drug_`model' if drug==0, fcolor(none) lcolor(black)), ///
legend(order(1 "No Drug" 2 "Molnupavir")) name(histogram_mol_`model', replace) saving("$projectdir/output/figures/histogram_mol_`model'", replace)
graph export "$projectdir/output/figures/histogram_mol_`model'.svg", as(svg) replace
gen iptw_`model' = 1/p_drug_`model' if drug==1
replace iptw_`model' = 1/(1-p_drug_`model') if drug==0
foreach fail in $ae_combined {
stset stop_`fail' [pw=iptw_`model'], id(patient_id) origin(time start_date) enter(time start_date) failure(fail_`fail'==1)
stcox i.drug, vce(robust)
matrix b = r(table)
local hr_mol = b[1,2]
local lc_mol = b[5,2]
local uc_mol = b[6,2]
post `coxoutput_propensity_mol' ("`fail'") ("`model'") (`hr_mol') (`lc_mol') (`uc_mol')
}
}
pbalchk drug $bal_agesex
pbalchk drug $bal_agesex, wt(iptw_agesex) graph
graph save "$projectdir/output/figures/mol_match_agesex", replace
pbalchk drug $bal_adj
pbalchk drug $bal_adj, wt(iptw_adj) graph
graph save "$projectdir/output/figures/mol_match_adj", replace
pbalchk drug $bal_adj2
pbalchk drug $bal_adj2, wt(iptw_adj2) graph
graph save "$projectdir/output/figures/mol_match_adj2", replace
pbalchk drug $bal_adj3
pbalchk drug $bal_adj3, wt(iptw_adj3) graph
graph save "$projectdir/output/figures/mol_match_adj3", replace
pbalchk drug $bal_adj4
pbalchk drug $bal_adj4, wt(iptw_adj4) graph
graph save "$projectdir/output/figures/mol_match_adj4", replace
restore
postclose `coxoutput_propensity_mol'
** Histogram figures
graph combine "$projectdir/output/figures/histogram_sot_agesex" "$projectdir/output/figures/histogram_pax_agesex" "$projectdir/output/figures/histogram_mol_agesex", ///
title("histogram agesex adjusted model") saving("$projectdir/output/figures/histogram_agesex", replace)
graph export "$projectdir/output/figures/histogram_agesex.svg", as(svg) replace
graph combine "$projectdir/output/figures/histogram_sot_adj" "$projectdir/output/figures/histogram_pax_adj" "$projectdir/output/figures/histogram_mol_adj", ///
title("histogram adjusted model") saving("$projectdir/output/figures/histogram_adj", replace)
graph export "$projectdir/output/figures/histogram_adj.svg", as(svg) replace
graph combine "$projectdir/output/figures/histogram_sot_adj2" "$projectdir/output/figures/histogram_pax_adj2" "$projectdir/output/figures/histogram_mol_adj2", ///
title("histogram adjusted model 2") saving("$projectdir/output/figures/histogram_adj2", replace)
graph export "$projectdir/output/figures/histogram_adj2.svg", as(svg) replace
graph combine "$projectdir/output/figures/histogram_sot_adj3" "$projectdir/output/figures/histogram_pax_adj3" "$projectdir/output/figures/histogram_mol_adj3", ///
title("histogram adjusted model 3") saving("$projectdir/output/figures/histogram_adj3", replace)
graph export "$projectdir/output/figures/histogram_adj3.svg", as(svg) replace
graph combine "$projectdir/output/figures/histogram_sot_adj4" "$projectdir/output/figures/histogram_pax_adj4" "$projectdir/output/figures/histogram_mol_adj4", ///
title("histogram adjusted model 4") saving("$projectdir/output/figures/histogram_adj4", replace)
graph export "$projectdir/output/figures/histogram_adj4.svg", as(svg) replace
** Balancing figures
graph combine "$projectdir/output/figures/sot_match_agesex.gph" "$projectdir/output/figures/pax_match_agesex.gph" "$projectdir/output/figures/mol_match_agesex.gph" ///
, title("PS balancing agesex model") saving("$projectdir/output/figures/balance_agesex", replace)
graph export "$projectdir/output/figures/balance_agesex.svg", as(svg) replace
graph combine "$projectdir/output/figures/sot_match_adj.gph" "$projectdir/output/figures/pax_match_adj.gph" "$projectdir/output/figures/mol_match_adj.gph" ///
, title("PS balancing adjusted model") saving("$projectdir/output/figures/balance_adj", replace)
graph export "$projectdir/output/figures/balance_adj.svg", as(svg) replace
graph combine "$projectdir/output/figures/sot_match_adj2.gph" "$projectdir/output/figures/pax_match_adj2.gph" "$projectdir/output/figures/mol_match_adj2.gph" ///
, title("PS balancing adjusted model 2") saving("$projectdir/output/figures/balance_adj2", replace)
graph export "$projectdir/output/figures/balance_adj2.svg", as(svg) replace
graph combine "$projectdir/output/figures/sot_match_adj3.gph" "$projectdir/output/figures/pax_match_adj3.gph" "$projectdir/output/figures/mol_match_adj3.gph" ///
, title("PS balancing adjusted model 3") saving("$projectdir/output/figures/balance_adj3", replace)
graph export "$projectdir/output/figures/balance_adj3.svg", as(svg) replace
graph combine "$projectdir/output/figures/sot_match_adj4.gph" "$projectdir/output/figures/pax_match_adj4.gph" "$projectdir/output/figures/mol_match_adj4.gph" ///
, title("PS balancing adjusted model 4") saving("$projectdir/output/figures/balance_adj4", replace)
graph export "$projectdir/output/figures/balance_adj4.svg", as(svg) replace
*******************************************************************************
use "$projectdir/output/tables/cox_propensity_sot", clear
merge 1:1 model fail using "$projectdir/output/tables/cox_propensity_pax", nogenerate
merge 1:1 model fail using "$projectdir/output/tables/cox_propensity_mol", nogenerate
foreach var of varlist hr* lc* uc* {
format `var' %3.2f
}
save "$projectdir/output/tables/cox_propensity", replace
export delimited using "$projectdir/output/tables/cox_propensity.csv", replace
** Hazard of disease events
****************************************************************************************************************
use "$projectdir/output/data/main", clear
// SOTROVIMAB //
tempname coxoutput_propensity_sot_dis
postfile `coxoutput_propensity_sot_dis' str20(model) str20(fail) ///
hr_sot lc_sot uc_sot ///
using "$projectdir/output/tables/cox_propensity_sot_dis", replace
preserve
keep if drug==0 | drug==1
foreach model in agesex adj adj2 adj3 adj4 {
logistic drug $`model'
predict p_drug_`model'
gen iptw_`model' = 1/p_drug_`model' if drug==1
replace iptw_`model' = 1/(1-p_drug_`model') if drug==0
foreach fail in $ae_disease $ae_disease_serious {
stset stop_`fail' [pw=iptw_`model'], id(patient_id) origin(time start_date) enter(time start_date) failure(fail_`fail'==1)
stcox i.drug, vce(robust)
matrix b = r(table)
local hr_sot = b[1,2]
local lc_sot = b[5,2]
local uc_sot = b[6,2]
post `coxoutput_propensity_sot_dis' ("`fail'") ("`model'") (`hr_sot') (`lc_sot') (`uc_sot')
}
}
restore
postclose `coxoutput_propensity_sot_dis'
// PAXLOVID //
tempname coxoutput_propensity_pax_dis
postfile `coxoutput_propensity_pax_dis' str20(model) str20(fail) ///
hr_pax lc_pax uc_pax ///
using "$projectdir/output/tables/cox_propensity_pax_dis", replace
preserve
keep if drug==0 | drug==2
replace drug=1 if drug==2
lab define drug 0 "Control" 1 "Paxlovid", replace
label values drug drug
foreach model in agesex adj adj2 adj3 adj4 {
logistic drug $`model'
predict p_drug_`model'
gen iptw_`model' = 1/p_drug_`model' if drug==1
replace iptw_`model' = 1/(1-p_drug_`model') if drug==0
foreach fail in $ae_disease $ae_disease_serious {
stset stop_`fail' [pw=iptw_`model'], id(patient_id) origin(time start_date) enter(time start_date) failure(fail_`fail'==1)
stcox i.drug, vce(robust)
matrix b = r(table)
local hr_pax = b[1,2]
local lc_pax = b[5,2]
local uc_pax = b[6,2]
post `coxoutput_propensity_pax_dis' ("`fail'") ("`model'") (`hr_pax') (`lc_pax') (`uc_pax')
}
}
restore
postclose `coxoutput_propensity_pax_dis'
// MOLNUPAVIR //
tempname coxoutput_propensity_mol_dis
postfile `coxoutput_propensity_mol_dis' str20(model) str20(fail) ///
hr_mol lc_mol uc_mol ///
using "$projectdir/output/tables/cox_propensity_mol_dis", replace
preserve
keep if drug==0 | drug==3
replace drug=1 if drug==3
lab define drug 0 "Control" 1 "Molnupavir", replace
label values drug drug
foreach model in agesex adj adj2 adj3 adj4 {
logistic drug $`model'
predict p_drug_`model'
gen iptw_`model' = 1/p_drug_`model' if drug==1
replace iptw_`model' = 1/(1-p_drug_`model') if drug==0
foreach fail in $ae_disease $ae_disease_serious {
stset stop_`fail' [pw=iptw_`model'], id(patient_id) origin(time start_date) enter(time start_date) failure(fail_`fail'==1)
stcox i.drug, vce(robust)
matrix b = r(table)
local hr_mol = b[1,2]
local lc_mol = b[5,2]
local uc_mol = b[6,2]
post `coxoutput_propensity_mol_dis' ("`fail'") ("`model'") (`hr_mol') (`lc_mol') (`uc_mol')
}
}
restore
postclose `coxoutput_propensity_mol_dis'
*******************************************************************************
use "$projectdir/output/tables/cox_propensity_sot_dis", clear
merge 1:1 model fail using "$projectdir/output/tables/cox_propensity_pax_dis", nogenerate
merge 1:1 model fail using "$projectdir/output/tables/cox_propensity_mol_dis", nogenerate
foreach var of varlist hr* lc* uc* {
format `var' %3.2f
}
save "$projectdir/output/tables/cox_propensity_disease", replace
export delimited using "$projectdir/output/tables/cox_propensity_disease.csv", replace
log close