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302_cox_models.do
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302_cox_models.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
cap log close
log using $outdir/cox_models.txt, replace t
tempname measures
postfile `measures' ///
str20(comparator) str20(outcome) str25(analysis) str10(adjustment) ptime_covid num_events_covid rate_covid ///
ptime_comparator num_events_comparator rate_comparator hr lc uc ///
using $tabfigdir/cox_model_summary, replace
foreach an in pneumonia gen_population {
use $outdir/combined_covid_`an'.dta, replace
drop patient_id
gen new_patient_id = _n
global crude i.case
global age_sex i.case i.male age1 age2 age3
global full i.case i.male age1 age2 age3 i.stp i.ethnicity i.imd i.obese4cat_withmiss ///
i.smoke htdiag chronic_respiratory_disease i.asthmacat chronic_cardiac_disease ///
i.diabcat i.cancer_exhaem_cat i.cancer_haem_cat i.reduced_kidney_function_cat2 ///
i.chronic_liver_disease i.dementia i.other_neuro i.organ_transplant i.spleen ///
i.ra_sle_psoriasis i.other_immunosuppression i.hist_dvt i.hist_pe i.hist_stroke i.hist_mi i.hist_aki i.hist_heart_failure
foreach v in stroke dvt pe heart_failure mi aki t2dm {
noi di "Starting analysis for `v' Outcome ..."
forvalues i = 1/3 {
preserve
local skip_1 = 0
local skip_2 = 0
local skip_3 = 0
* Apply exclusion for AKI and diabetes outcomes
if "`v'" == "t1dm" | "`v'" == "t2dm" {
drop if previous_diabetes == 1
local skip_2 = 1
local skip_3 = 1
}
if "`v'" == "aki" {
drop if aki_exclusion_flag == 1
}
if `i' == 1 {
local out `v'
local end_date `v'_end_date
}
if `i' == 2 {
local out `v'_no_gp
local end_date `v'_no_gp_end_date
}
if `i' == 3 {
local out `v'_cens_gp
local end_date `v'_cens_gp_end_date
}
if `skip_`i'' == 0 {
noi di "$group: stset in `a'"
stset `end_date' , id(new_patient_id) failure(`out') enter(indexdate) origin(indexdate)
foreach adjust in crude age_sex full {
if "`adjust'" == "full" & "`v'" == "t2dm" {
* remove diabetes
global full i.case i.male age1 age2 age3 i.stp i.ethnicity i.imd i.obese4cat_withmiss ///
i.smoke htdiag chronic_respiratory_disease i.asthmacat chronic_cardiac_disease ///
i.cancer_exhaem_cat i.cancer_haem_cat i.reduced_kidney_function_cat2 ///
i.chronic_liver_disease i.dementia i.other_neuro i.organ_transplant i.spleen ///
i.ra_sle_psoriasis i.other_immunosuppression i.hist_dvt i.hist_pe i.hist_stroke i.hist_mi i.hist_aki i.hist_heart_failure
}
stcox $`adjust', vce(robust)
matrix b = r(table)
local hr= b[1,2]
local lc = b[5,2]
local uc = b[6,2]
estat phtest, detail
stptime if case == 1
local rate_covid = `r(rate)'
local ptime_covid = `r(ptime)'
local events_covid .
if `r(failures)' == 0 | `r(failures)' > 5 local events_covid `r(failures)'
stptime if case == 0
local rate_comparator = `r(rate)'
local ptime_comparator = `r(ptime)'
local events_comparator .
if `r(failures)' == 0 | `r(failures)' > 5 local events_comparator `r(failures)'
post `measures' ("`an'") ("`v'") ("`out'") ("`adjust'") ///
(`ptime_covid') (`events_covid') (`rate_covid') (`ptime_comparator') (`events_comparator') (`rate_comparator') ///
(`hr') (`lc') (`uc')
}
}
restore
}
}
}
postclose `measures'
* Change postfiles to csv
use $tabfigdir/cox_model_summary, replace
export delimited using $tabfigdir/cox_model_summary.csv, replace
log close