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AL006c_cox_regression_interactions_imd.do
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AL006c_cox_regression_interactions_imd.do
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********************************************************************************
*
* Do-file: AL006c_cox_regression_interactions_imd.do
*
* Programmed by: Fizz & Krishnan & John
*
* Data used: analysis/
* data_ldanalysis_cohort1.dta
* data_ldanalysis_cohort2.dta
*
* Data created: None
*
* Other output: Log file: logs/AL006a_cox_regression_inter_age_wave`i'_`out'_`exp'.log
* Estimates: output/
* ldcox_inter_age_wave`i'_`out'_`exp'.out
*
* i = Wave (1 or 2)
* out = outcome (coviddeath covidadmission)
* exp = exposure (ldr ldr_cat ldr_carecat ds cp ldr_group
*
********************************************************************************
*
* Purpose: This do-file fits a series of adjusted Cox models for the
* learning disability work and obtains the crude rates,
* exploring interactions with deprivation (IMD).
*
********************************************************************************
**********************
* Input parameters *
**********************
local wave `1'
local outcome `2'
local exposure `3'
local i = `wave'
local out = "`outcome'"
local exp = "`exposure'"
noi di "Wave:" `i'
noi di "Outcome: `out'"
noi di "Exposure: `exp'"
**************************
* Adopath and log file *
**************************
clear all
set more off
* Open a log file
cap log close
log using "logs/AL006c_cox_regression_inter_imd_wave`i'_`out'_`exp'", replace t
* Categories of various exposures
local lo_ldr = 0
local hi_ldr = 1
local lo_ldr_cat = 0
local hi_ldr_cat = 2
local hi_ldr = 1
local lo_ldr_carecat= 0
local hi_ldr_carecat= 2
local lo_ds = 0
local hi_ds = 1
local lo_cp = 0
local hi_cp = 1
local lo_ldr_group = 0
local hi_ldr_group = 5
* Open temporary file to post results
tempfile ldrfile
tempname ldrresults
postfile `ldrresults' wave str15(outcome) str15(exposure) str20(model) ///
expcat imd lnhr sehr using `ldrfile'
* Open dataset (complete case ethnicity)
use "analysis/data_ldanalysis_cohort`i'.dta", clear
drop if ethnicity_5>=.
* Only keep data for adults
keep if child==0
/* Declare data to be survival */
stset stime_`out'`i', fail(`out'`i') scale(365.25)
/* Fit Cox models */
* Confounder only model
stcox i.`exp'##i.imd age1 age2 age3 male i.ethnicity_5, ///
strata(stpcode) cluster(household_id)
forvalues k = `lo_`exp'' (1) `hi_`exp'' {
capture qui di _b[`k'.`exp']
if _rc==0 {
post `ldrresults' (`i') ("`out'") ("`exp'") ///
("Confounders") ///
(`k') (1) (_b[`k'.`exp']) (_se[`k'.`exp'])
}
forvalues l = 2 (1) 5 {
capture qui di _b[`k'.`exp'#`l'.imd]
if _rc==0 {
lincom `k'.`exp' + `k'.`exp'#`l'.imd
post `ldrresults' (`i') ("`out'") ("`exp'") ///
("Confounders") ///
(`k') (`l') (r(estimate)) (r(se))
}
}
}
* All variables
stcox i.`exp'##i.imd age1 age2 age3 male ///
i.ethnicity_5 resid_care_ldr ///
obese40 ///
respiratory asthma_severe ///
cardiac af dvt_pe i.diabcat ///
liver stroke tia dementia ///
i.kidneyfn ///
spleen transplant dialysis ///
immunosuppression i.cancerHaem ///
autoimmune ibd cancerExhaem1yr, ///
strata(stpcode) cluster(household_id)
forvalues k = `lo_`exp'' (1) `hi_`exp'' {
capture qui di _b[`k'.`exp']
if _rc==0 {
post `ldrresults' (`i') ("`out'") ("`exp'") ///
("All") ///
(`k') (1) (_b[`k'.`exp']) (_se[`k'.`exp'])
}
forvalues l = 2 (1) 5 {
capture qui di _b[`k'.`exp'#`l'.imd]
if _rc==0 {
lincom `k'.`exp' + `k'.`exp'#`l'.imd
post `ldrresults' (`i') ("`out'") ("`exp'") ///
("All") ///
(`k') (`l') (r(estimate)) (r(se))
}
}
}
postclose `ldrresults'
use `ldrfile', clear
*************************
* Tidy output for HRs *
*************************
* Outcome
rename outcome out
gen outcome = 1 if out=="coviddeath"
replace outcome = 2 if out=="covidadmission"
replace outcome = 3 if out=="composite"
label define outcome 1 "COVID-19 death" ///
2 "COVID-19 admission" ///
3 "Composite"
label values outcome outcome
drop out
* Exposure
rename exposure exp
gen exposure = 1 if exp=="ldr"
replace exposure = 2 if exp=="ldr_cat"
replace exposure = 3 if exp=="ldr_carecat"
replace exposure = 4 if exp=="ds"
replace exposure = 5 if exp=="cp"
replace exposure = 6 if exp=="ldr_group"
label define exposure 1 "Learning disability register" ///
2 "LDR Severe vs mild" ///
3 "LDR by residential care" ///
4 "Down's syndrome" ///
5 "Cerebral Palsy" ///
6 "Combined grouping"
label values exposure exposure
drop exp
* IMD categories
label define imd 1 "1 least deprived" ///
2 "2" ///
3 "3" ///
4 "4" ///
5 "5 most deprived"
label values imd imd
* Categories of exposure
gen category = "No" if expcat==0
replace category = "Yes" if inlist(exposure, 1, 4, 5) & expcat==1
replace category = "LDR, mild" if inlist(exposure, 2) & expcat==1
replace category = "LDR, profound" if inlist(exposure, 2) & expcat==2
replace category = "LDR, community" if inlist(exposure, 3) & expcat==1
replace category = "LDR, residential care" if inlist(exposure, 3) & expcat==2
replace category = "DS but not LDR" if inlist(exposure, 6) & expcat==1
replace category = "DS and LDR" if inlist(exposure, 6) & expcat==2
replace category = "CP but not LDR" if inlist(exposure, 6) & expcat==3
replace category = "CP and LDR" if inlist(exposure, 6) & expcat==4
replace category = "LDR with no DS or CP" if inlist(exposure, 6) & expcat==5
* Model adjustment
gen adjustment = 1 if model=="Confounders"
replace adjustment = 2 if model=="All"
label define adj 1 "Confounders" 2 "All"
label values adjustment adj
drop model
* Hazard ratio with 95% confidence interval
gen cl = exp(lnhr - invnorm(0.975)*sehr)
gen cu = exp(lnhr + invnorm(0.975)*sehr)
gen hr = exp(lnhr)
gen hr_ci = string(round(hr, 0.01)) + " (" ///
+ string(round(cl, 0.01)) + ", " ///
+ string(round(cu, 0.01)) + ")"
replace hr_ci = "" if expcat==0
drop cl cu hr lnhr sehr
* Put in wide format
reshape wide hr_ci, i(wave outcome exposure expcat imd) j(adjust)
rename hr_ci1 hr_conf
rename hr_ci2 hr_all
order wave outcome exposure imd category hr*
sort wave outcome exposure imd expcat
* Save data
outsheet using "output/ldcox_inter_imd_wave`i'_`out'_`exp'", replace
log close