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150_analyses_option1_table5_stratified_hazardratios.do
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150_analyses_option1_table5_stratified_hazardratios.do
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local mypath="`c(pwd)'/analysis/"
do `mypath'/000_filepaths.do
**// Stratified hazard ratios - comparing groups 1,2 and 1,3
**///////////////////////////////////////////////////////////////////
set more off
use $outdir/input_part1_clean.dta, clear
local refgroup2="COVID-19 without diabetes"
local refgroup3="Pneumonia with diabetes"
**// Loop over each outcome
foreach outcome in "stroke_thrombotic" "stroke_haemorrhagic" "stroke_tia" "stroke_pregnancy" "stroke_any" "mi" "dvt_nopregnancy" "dvt_pregnancy" "dvt_pregnancy_cvt" "dvt_any" ///
"pe_nopregnancy" "pe_pregnancy" "pe_any" "hf" "any_cvd" "aki_nopregnancy" "aki_pregnancy" "aki_any" "liver" "anxiety" "depression" "psychosis" "antidepressant" "anxiolytic" ///
"antipsychotic" "mood_stabiliser" "sleep_insomnia" "sleep_hypersomnia" "sleep_apnoea" "fatigue" "death" {
use $outdir/input_part1_clean.dta, clear
gen expos=(group==1)
gen myend=(min(date_`outcome', date_censor)-date_patient_index)/(365.25/12)
gen myselect=(myend>0)
gen delta=(date_`outcome'==min(date_`outcome', date_censor))
stset myend, f(delta) id(patient_id)
local demogindex=0
**// Loop over each demographic/characteristic
foreach demog in "sex" "age" "ethnic" "imd" "diabetes" "hist_cvd" "hist_renal" "critical" "vaccin" "smoking" "alcohol" "bmi" "hba1c" {
local demogindex=`demogindex'+1
summ cat_`demog'
local numcat_`demog'=r(max)
**// Loop over categories of the demographic/characteristic
forvalues catindex=1(1)`numcat_`demog'' {
capture erase $resultsdir/hr_`outcome'_`demog'_`catindex'.dta
**// Estimate hazard ratios and post
preserve
keep if cat_`demog'==`catindex'
tempname hazardratios
postfile `hazardratios' demogindex catindex groupindex str20(demographic) str25(refgroup) ///
`outcome'_hr1 `outcome'_hr1_lo `outcome'_hr1_hi ///
`outcome'_hr2 `outcome'_hr2_lo `outcome'_hr2_hi ///
`outcome'_hr3 `outcome'_hr3_lo `outcome'_hr3_hi ///
using $resultsdir/hr_`outcome'_`demog'_`catindex'.dta, replace
forvalues k=2(1)3 {
count if group==1 & delta==1
local mycounta=r(N)
count if group==`k' & delta==1
local mycountb=r(N)
if `mycounta'>=8 & `mycountb'>=8 {
forvalues m=1(1)3 {
if `m'==1 {
capture stcox expos if (group==1 | group==`k') & myselect==1
}
if `m'==2 {
capture stcox expos i.cat_sex i.cat_age if (group==1 | group==`k') & myselect==1
}
if `m'==3 {
capture stcox expos i.cat_* if (group==1 | group==`k') & myselect==1
}
if _rc==0 {
matrix M1=e(b)
matrix M2=e(V)
local hr`m' =exp(M1[1,1])
local hr`m'_lo=exp(M1[1,1]-1.96*(M2[1,1]^0.5))
local hr`m'_hi=exp(M1[1,1]+1.96*(M2[1,1]^0.5))
}
if _rc!=0 {
local hr`m' =.
local hr`m'_lo=.
local hr`m'_hi=.
}
}
post `hazardratios' (`demogindex') (`catindex') (`k') ("`demog'") ("`refgroup`k''") ///
(`hr1') (`hr1_lo') (`hr1_hi') (`hr2') (`hr2_lo') (`hr2_hi') (`hr3') (`hr3_lo') (`hr3_hi')
}
else {
post `hazardratios' (`demogindex') (`catindex') (`k') ("`demog'") ("`refgroup`k''") (.) (.) (.) (.) (.) (.) (.) (.) (.)
}
}
postclose `hazardratios'
restore
}
}
}
**// Append categories within each demographic for each outcome
foreach outcome in "stroke_thrombotic" "stroke_haemorrhagic" "stroke_tia" "stroke_pregnancy" "stroke_any" "mi" "dvt_nopregnancy" "dvt_pregnancy" "dvt_pregnancy_cvt" "dvt_any" ///
"pe_nopregnancy" "pe_pregnancy" "pe_any" "hf" "any_cvd" "aki_nopregnancy" "aki_pregnancy" "aki_any" "liver" "anxiety" "depression" "psychosis" "antidepressant" "anxiolytic" ///
"antipsychotic" "mood_stabiliser" "sleep_insomnia" "sleep_hypersomnia" "sleep_apnoea" "fatigue" "death" {
foreach demog in "sex" "age" "ethnic" "imd" "diabetes" "hist_cvd" "hist_renal" "critical" "vaccin" "smoking" "alcohol" "bmi" "hba1c" {
clear
set obs 0
forvalues catindex=1(1)`numcat_`demog'' {
append using $resultsdir/hr_`outcome'_`demog'_`catindex'.dta
erase $resultsdir/hr_`outcome'_`demog'_`catindex'.dta
}
tostring catindex, gen(category) force
order category, after(demographic)
do `mypath'/002_catlab.do
save $resultsdir/hr_`outcome'_`demog'.dta, replace
}
}
**// Append demographics within each outcome
foreach outcome in "stroke_thrombotic" "stroke_haemorrhagic" "stroke_tia" "stroke_pregnancy" "stroke_any" "mi" "dvt_nopregnancy" "dvt_pregnancy" "dvt_pregnancy_cvt" "dvt_any" ///
"pe_nopregnancy" "pe_pregnancy" "pe_any" "hf" "any_cvd" "aki_nopregnancy" "aki_pregnancy" "aki_any" "liver" "anxiety" "depression" "psychosis" "antidepressant" "anxiolytic" ///
"antipsychotic" "mood_stabiliser" "sleep_insomnia" "sleep_hypersomnia" "sleep_apnoea" "fatigue" "death" {
clear
set obs 0
foreach demog in "sex" "age" "ethnic" "imd" "diabetes" "hist_cvd" "hist_renal" "critical" "vaccin" "smoking" "alcohol" "bmi" "hba1c" {
append using $resultsdir/hr_`outcome'_`demog'.dta
erase $resultsdir/hr_`outcome'_`demog'.dta
}
sort demogindex catindex groupindex
**// Tidy presentation of hazard ratios
describe `outcome'_hr*, varlist
foreach myvar in `r(varlist)' {
format `myvar' %12.2f
tostring `myvar', replace force usedisplayformat
}
forvalues m=1(1)3 {
gen newvar`m'=`outcome'_hr`m'+" ("+`outcome'_hr`m'_lo+", "+`outcome'_hr`m'_hi+")"
replace newvar`m'="-" if newvar`m'==". (., .)"
drop `outcome'_hr`m'*
rename newvar`m' `outcome'_hr`m'
}
save $resultsdir/hr_`outcome'.dta, replace
}
**// Merge outcomes
use $resultsdir/hr_stroke_thrombotic.dta, clear
foreach outcome in "stroke_haemorrhagic" "stroke_tia" "stroke_pregnancy" "stroke_any" "mi" "dvt_nopregnancy" "dvt_pregnancy" "dvt_pregnancy_cvt" "dvt_any" ///
"pe_nopregnancy" "pe_pregnancy" "pe_any" "hf" "any_cvd" "aki_nopregnancy" "aki_pregnancy" "aki_any" "liver" "anxiety" "depression" "psychosis" "antidepressant" "anxiolytic" ///
"antipsychotic" "mood_stabiliser" "sleep_insomnia" "sleep_hypersomnia" "sleep_apnoea" "fatigue" "death" {
capture merge 1:1 demogindex catindex groupindex using $resultsdir/hr_`outcome'.dta
if _rc==0 {
drop _merge
erase $resultsdir/hr_`outcome'.dta
}
}
erase $resultsdir/hr_stroke_thrombotic.dta
sort demogindex catindex groupindex
**// Labelling
do `mypath'/001_demoglab.do
**// Tidy
gen temp1=1 if demographic==demographic[_n-1]
replace demographic="" if temp1==1
gen temp2=1 if category==category[_n-1]
replace category="" if temp2==1
drop temp1 temp2
describe, varlist
foreach myvar in `r(varlist)' {
capture gen str=strlen(`myvar')
if _rc==0 {
summ str
format `myvar' %-`r(max)'s
drop str
}
}
drop demogindex catindex groupindex
save $resultsdir/option1_table5_stratified_hazardratios.dta, replace