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an_cox_hosp_icu.do
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an_cox_hosp_icu.do
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********************************************************************************
*
* Do-file: an_cox_hosp_icu.do
*
* Project: SGTF CFR
*
* Programmed by: Daniel Grint
*
* Data used: output/cr_analysis_new.dta
*
* Data created:
*
* Other output: an_cox_hosp.log containing:
* 1-Unadjusted Cox models for SGTF
* 2-Adjusted Cox models for SGTF
*
********************************************************************************
*
* Purpose: This do-file runs Cox PH models, calculating HR for VOC
* vs. non-VOC for death given days spent in ICU
*
********************************************************************************
* Open a log file
cap log close
log using ./logs/an_cox_hosp_icu, replace t
clear
use ./output/cr_analysis_new.dta
* DROP MISSING UTLA
noi di "DROPPING MISSING UTLA DATA"
drop if utla_group==""
* DROP IF NO DATA ON SGTF
noi di "DROPPING NO SGTF DATA"
drop if has_sgtf==0
noi di "SUBSETTING ON COX CENSORED POPULATION"
keep if cox_pop==1
noi di "SUBSETTING ON HOSPITALISED POPULATION"
keep if end_death_hosp != .
noi di "SUBSETTING ON DAYS IN ICU POPULATION"
keep if icu_pop == 1
tab sgtf end_death_hosp, row
*Set up output file
cap file close tablecontent
file open tablecontent using ./output/table2_hr_hosp_icu.txt, write text replace
file write tablecontent ("Table 2: Hazard ratios for VOC vs. non-VOC") _n _n
file write tablecontent ("Estimate") _tab ///
("HR (95% CI)") _tab ///
("P-value") _n
*******************
/* Unadjusted HR */
*******************
stset time_death_hosp, fail(end_death_hosp) scale(1) id(patient_id)
stcox i.sgtf
* Stratified by STP
stcox i.sgtf, strata(stp)
* Stratified by region
stcox i.sgtf, strata(region)
* Stratified by UTLA
stcox i.sgtf, strata(utla_group)
* N (events)
tab sgtf end_death_hosp if e(sample)
* Output unadjusted
lincom 1.sgtf, eform
file write tablecontent _n ("Unadjusted") _tab
file write tablecontent %4.2f (r(estimate)) (" (") %4.2f (r(lb)) ("-") %4.2f (r(ub)) (")") _tab %6.4f (r(p)) _n
* Interaction with time
stcox i.sgtf, tvc(i.sgtf) strata(utla_group)
/*
* Interaction with time excluding November
stcox i.sgtf if study_start >= date("01dec2020", "DMY"), strata(utla_group)
estat phtest, d
stcox i.sgtf if study_start >= date("01dec2020", "DMY"), tvc(i.sgtf) strata(utla_group)
*/
************************
/* Age as spline only */
************************
* Stratified by region
stcox i.sgtf age1 age2 age3 ///
, strata(utla_group)
* N (events)
tab sgtf end_death_hosp if e(sample)
lincom 1.sgtf, eform
file write tablecontent ("Age adj.") _tab
file write tablecontent %4.2f (r(estimate)) (" (") %4.2f (r(lb)) ("-") %4.2f (r(ub)) (")") _tab %6.4f (r(p)) _n
/*
* Age grouped only
stcox i.sgtf ib2.agegroupA ///
, strata(utla_group)
*/
***************************
/* Age and comorbidities */
***************************
* Stratified by region
stcox i.sgtf age1 age2 age3 ib0.comorb_cat ib1.smoke_nomiss2 ib1.obese4cat ///
, strata(utla_group)
* N (events)
tab sgtf end_death_hosp if e(sample)
lincom 1.sgtf, eform
file write tablecontent ("Age + comorb adj.") _tab
file write tablecontent %4.2f (r(estimate)) (" (") %4.2f (r(lb)) ("-") %4.2f (r(ub)) (")") _tab %6.4f (r(p)) _n
*********************************************************************
/* Demographically adjusted HR - age as spline, cat hh size */
/* Not adjusting for comorbidities, obesity, or smoking status */
*********************************************************************
* Stratified by region
stcox i.sgtf i.male ib1.imd ib1.eth2 ib1.hh_total_cat ///
ib1.rural_urban5 ib1.start_week age1 age2 age3 ///
if eth2 != 6 ///
, strata(utla_group)
* N (events)
tab sgtf end_death_hosp if e(sample)
lincom 1.sgtf, eform
file write tablecontent ("Demographically adj.") _tab
file write tablecontent %4.2f (r(estimate)) (" (") %4.2f (r(lb)) ("-") %4.2f (r(ub)) (")") _tab %6.4f (r(p)) _n
*********************************************************************
/* Demographically adjusted HR - age grouped, cat hh size */
/* Not adjusting for comorbidities, obesity, or smoking status */
*********************************************************************
/*
* Stratified by region
stcox i.sgtf i.male ib1.imd ib1.eth2 ib1.hh_total_cat i.home_bin ///
ib1.rural_urban5 ib1.start_week ib2.agegroupA ///
if eth2 != 6 ///
, strata(utla_group)
*/
****************************************************
/* Fully adjusted HR - age as spline, cat hh size */
****************************************************
* Stratified by region
stcox i.sgtf i.male ib1.imd ib1.eth2 ib1.smoke_nomiss2 ib1.obese4cat ib1.hh_total_cat ///
ib1.rural_urban5 ib0.comorb_cat ib1.start_week age1 age2 age3 ///
if eth2 != 6 ///
, strata(utla_group)
est store e_no_int
* N (events)
tab sgtf end_death_hosp if e(sample)
bysort start_weekB: tab sgtf end_death_hosp if e(sample)
bysort comorb_cat: tab sgtf end_death_hosp if e(sample)
bysort eth2: tab sgtf end_death_hosp if e(sample)
bysort imd: tab sgtf end_death_hosp if e(sample)
bysort agegroupB: tab sgtf end_death_hosp if e(sample)
estat phtest, d
lincom 1.sgtf, eform
file write tablecontent ("Fully adj.") _tab
file write tablecontent %4.2f (r(estimate)) (" (") %4.2f (r(lb)) ("-") %4.2f (r(ub)) (")") _tab %6.4f (r(p)) _n
* Plot scaled schoenfeld residuals
estat phtest, plot(1.sgtf)
graph export ./output/cox_shoen_hosp_icu.svg, as(svg) replace
/*
* KM plot
sts graph, surv by(sgtf) ci risktable(, order(1 "non-VOC" 2 "VOC") size(small)) ///
ylabel(0.994(0.001)1, format(%5.3f)) ///
legend(order(2 4) label(2 "non-VOC") label(4 "VOC") rows(1))
graph export ./output/cox_km.svg, as(svg) replace
* Cumulative hazard plot
sts graph, cumhaz by(sgtf) ci ///
ylabel(minmax, format(%5.3f)) ///
legend(order(2 4) label(2 "non-VOC") label(4 "VOC") rows(1))
graph export ./output/cox_cumhaz.svg, as(svg) replace
*/
* Smoothed hazard plot
sts graph, haz by(sgtf) ///
legend(label(1 "non-VOC") label(2 "VOC"))
graph export ./output/cox_haz_hosp_icu.svg, as(svg) replace
/* Subgroup analyses */
* Epi week
stcox i.sgtf i.male ib1.imd ib1.eth2 ib1.smoke_nomiss2 ib1.obese4cat ib1.hh_total_cat ///
ib1.rural_urban5 ib0.comorb_cat ib2.start_weekB age1 age2 age3 ///
if eth2 != 6 ///
, strata(utla_group)
est store e_week
stcox i.sgtf##ib2.start_weekB i.male ib1.imd ib1.eth2 ib1.smoke_nomiss2 ib1.obese4cat ib1.hh_total_cat ///
ib1.rural_urban5 ib0.comorb_cat age1 age2 age3 i.home_bin ///
if eth2 != 6 ///
, strata(utla_group)
est store e_weekX
* Test for interaction
lrtest e_week e_weekX
file write tablecontent _n ("Subgroup analyses") _n
file write tablecontent _n ("Epi. week") _tab _tab %6.4f (r(p)) _n
* Epi week VOC vs. non-VOC HR
lincom 1.sgtf + 1.sgtf#4.start_weekB, eform // week 1/2
file write tablecontent ("16Nov-13Dec") _tab
file write tablecontent %4.2f (r(estimate)) (" (") %4.2f (r(lb)) ("-") %4.2f (r(ub)) (")") _tab %6.4f (r(p)) _n
lincom 1.sgtf + 1.sgtf#5.start_weekB, eform // week 5
file write tablecontent ("14Dec-20Dec") _tab
file write tablecontent %4.2f (r(estimate)) (" (") %4.2f (r(lb)) ("-") %4.2f (r(ub)) (")") _tab %6.4f (r(p)) _n
lincom 1.sgtf + 1.sgtf#6.start_weekB, eform // week 6
file write tablecontent ("21Dec-27Dec") _tab
file write tablecontent %4.2f (r(estimate)) (" (") %4.2f (r(lb)) ("-") %4.2f (r(ub)) (")") _tab %6.4f (r(p)) _n
lincom 1.sgtf + 1.sgtf#7.start_weekB, eform // week 7
file write tablecontent ("28Dec-03Jan") _tab
file write tablecontent %4.2f (r(estimate)) (" (") %4.2f (r(lb)) ("-") %4.2f (r(ub)) (")") _tab %6.4f (r(p)) _n
lincom 1.sgtf + 1.sgtf#8.start_weekB, eform // week 8
file write tablecontent ("04Jan-11Jan") _tab
file write tablecontent %4.2f (r(estimate)) (" (") %4.2f (r(lb)) ("-") %4.2f (r(ub)) (")") _tab %6.4f (r(p)) _n
* Comorbidities
stcox i.sgtf##ib0.comorb_cat i.male ib1.imd ib1.eth2 ib1.smoke_nomiss2 ib1.obese4cat ib1.hh_total_cat ///
ib1.rural_urban5 ib1.start_week age1 age2 age3 i.home_bin ///
if eth2 != 6 ///
, strata(utla_group)
est store e_comorbX
* Test for interaction
lrtest e_no_int e_comorbX
file write tablecontent _n ("Comorbidities") _tab _tab %6.4f (r(p)) _n
* Comorbidities VOC vs. non-VOC HR
lincom 1.sgtf, eform // no comorbs
file write tablecontent ("None") _tab
file write tablecontent %4.2f (r(estimate)) (" (") %4.2f (r(lb)) ("-") %4.2f (r(ub)) (")") _tab %6.4f (r(p)) _n
lincom 1.sgtf + 1.sgtf#1.comorb_cat, eform // 1 comorb
file write tablecontent ("1") _tab
file write tablecontent %4.2f (r(estimate)) (" (") %4.2f (r(lb)) ("-") %4.2f (r(ub)) (")") _tab %6.4f (r(p)) _n
lincom 1.sgtf + 1.sgtf#2.comorb_cat, eform // 2+ comorbs
file write tablecontent ("2+") _tab
file write tablecontent %4.2f (r(estimate)) (" (") %4.2f (r(lb)) ("-") %4.2f (r(ub)) (")") _tab %6.4f (r(p)) _n
* Test for trend
stcox i.sgtf i.male ib1.imd ib1.eth2 ib1.smoke_nomiss2 ib1.obese4cat ib1.hh_total_cat ///
ib1.rural_urban5 c.comorb_cat ib1.start_week age1 age2 age3 i.home_bin ///
if eth2 != 6 ///
, strata(utla_group)
est store e_linco
stcox i.sgtf##c.comorb_cat i.male ib1.imd ib1.eth2 ib1.smoke_nomiss2 ib1.obese4cat ib1.hh_total_cat ///
ib1.rural_urban5 ib1.start_week age1 age2 age3 i.home_bin ///
if eth2 != 6 ///
, strata(utla_group)
est store e_lincoX
lrtest e_linco e_lincoX
local lin_lr_p = r(p)
lincom 1.sgtf#c.comorb_cat, eform
file write tablecontent ("Per unit increase") _tab
file write tablecontent %4.2f (r(estimate)) (" (") %4.2f (r(lb)) ("-") %4.2f (r(ub)) (")") _tab %6.4f (`lin_lr_p') _n
* Ethnicity
stcox i.sgtf##ib1.eth2 i.male ib1.imd ib0.comorb_cat ib1.smoke_nomiss2 ib1.obese4cat ib1.hh_total_cat ///
ib1.rural_urban5 ib1.start_week age1 age2 age3 i.home_bin ///
if eth2 != 6 ///
, strata(utla_group)
est store e_eth2X
* Test for interaction
lrtest e_no_int e_eth2X
file write tablecontent _n ("Ethnicity") _tab _tab %6.4f (r(p)) _n
* Ethnicity VOC vs. non-VOC HR
lincom 1.sgtf, eform // White
file write tablecontent ("White") _tab
file write tablecontent %4.2f (r(estimate)) (" (") %4.2f (r(lb)) ("-") %4.2f (r(ub)) (")") _tab %6.4f (r(p)) _n
*lincom 1.sgtf + 1.sgtf#2.eth5, eform // S Asian
*lincom 1.sgtf + 1.sgtf#3.eth5, eform // Black
*lincom 1.sgtf + 1.sgtf#4.eth5, eform // Mixed
lincom 1.sgtf + 1.sgtf#5.eth2, eform // Other
file write tablecontent ("Not white") _tab
file write tablecontent %4.2f (r(estimate)) (" (") %4.2f (r(lb)) ("-") %4.2f (r(ub)) (")") _tab %6.4f (r(p)) _n
*lincom 1.sgtf + 1.sgtf#6.eth2, eform // Missing
* IMD
stcox i.sgtf##ib1.imd i.male ib1.eth2 ib1.smoke_nomiss2 ib1.obese4cat ib1.hh_total_cat ///
ib1.rural_urban5 ib1.start_week ib0.comorb_cat age1 age2 age3 i.home_bin ///
if eth2 != 6 ///
, strata(utla_group)
est store e_imdX
* Test for interaction
lrtest e_no_int e_imdX
file write tablecontent _n ("IMD") _tab _tab %6.4f (r(p)) _n
* IMD VOC vs. non-VOC HR
lincom 1.sgtf, eform // 1
file write tablecontent ("1 Least deprived") _tab
file write tablecontent %4.2f (r(estimate)) (" (") %4.2f (r(lb)) ("-") %4.2f (r(ub)) (")") _tab %6.4f (r(p)) _n
lincom 1.sgtf + 1.sgtf#2.imd, eform // 2
file write tablecontent ("2") _tab
file write tablecontent %4.2f (r(estimate)) (" (") %4.2f (r(lb)) ("-") %4.2f (r(ub)) (")") _tab %6.4f (r(p)) _n
lincom 1.sgtf + 1.sgtf#3.imd, eform // 3
file write tablecontent ("3") _tab
file write tablecontent %4.2f (r(estimate)) (" (") %4.2f (r(lb)) ("-") %4.2f (r(ub)) (")") _tab %6.4f (r(p)) _n
lincom 1.sgtf + 1.sgtf#4.imd, eform // 4
file write tablecontent ("4") _tab
file write tablecontent %4.2f (r(estimate)) (" (") %4.2f (r(lb)) ("-") %4.2f (r(ub)) (")") _tab %6.4f (r(p)) _n
lincom 1.sgtf + 1.sgtf#5.imd, eform // 5
file write tablecontent ("5 Most deprived") _tab
file write tablecontent %4.2f (r(estimate)) (" (") %4.2f (r(lb)) ("-") %4.2f (r(ub)) (")") _tab %6.4f (r(p)) _n
* Age group
stcox i.sgtf ib2.agegroupB i.male ib1.imd ib1.eth2 ib1.smoke_nomiss2 ib1.obese4cat ib1.hh_total_cat ///
ib1.rural_urban5 ib0.comorb_cat ib1.start_week i.home_bin ///
if eth2 != 6 ///
, strata(utla_group)
est store e_age
stcox i.sgtf##ib2.agegroupB i.male ib1.imd ib1.eth2 ib1.smoke_nomiss2 ib1.obese4cat ib1.hh_total_cat ///
ib1.rural_urban5 ib0.comorb_cat ib1.start_week i.home_bin ///
if eth2 != 6 ///
, strata(utla_group)
est store e_ageX
* Test for interaction
lrtest e_age e_ageX
file write tablecontent _n ("Age group") _tab _tab %6.4f (r(p)) _n
* Age group VOC vs. non-VOC HR
lincom 1.sgtf + 1.sgtf#1.agegroupB, eform // 0-<65
file write tablecontent ("0-<65") _tab
file write tablecontent %4.2f (r(estimate)) (" (") %4.2f (r(lb)) ("-") %4.2f (r(ub)) (")") _tab %6.4f (r(p)) _n
lincom 1.sgtf + 1.sgtf#2.agegroupB, eform // 65-<75
file write tablecontent ("65-<75") _tab
file write tablecontent %4.2f (r(estimate)) (" (") %4.2f (r(lb)) ("-") %4.2f (r(ub)) (")") _tab %6.4f (r(p)) _n
lincom 1.sgtf + 1.sgtf#3.agegroupB, eform // 75+
file write tablecontent ("75+") _tab
file write tablecontent %4.2f (r(estimate)) (" (") %4.2f (r(lb)) ("-") %4.2f (r(ub)) (")") _tab %6.4f (r(p)) _n
* Test for trend
stcox i.sgtf c.agegroupB i.male ib1.imd ib1.eth2 ib1.smoke_nomiss2 ib1.obese4cat ib1.hh_total_cat ///
ib1.rural_urban5 ib0.comorb_cat ib1.start_week i.home_bin ///
if eth2 != 6 ///
, strata(utla_group)
est store e_cage
stcox i.sgtf##c.agegroupB i.male ib1.imd ib1.eth2 ib1.smoke_nomiss2 ib1.obese4cat ib1.hh_total_cat ///
ib1.rural_urban5 ib0.comorb_cat ib1.start_week i.home_bin ///
if eth2 != 6 ///
, strata(utla_group)
est store e_cageX
lrtest e_cage e_cageX
local lin_age_p = r(p)
lincom 1.sgtf#c.agegroupB, eform
file write tablecontent ("Per group increase") _tab
file write tablecontent %4.2f (r(estimate)) (" (") %4.2f (r(lb)) ("-") %4.2f (r(ub)) (")") _tab %6.4f (`lin_age_p') _n
**************************
/* Sensitivity analyses */
**************************
* Include with 28-days follow-up
* Stratified by region
stcox i.sgtf i.male ib1.imd ib1.eth2 ib1.smoke_nomiss2 ib1.obese4cat ib1.hh_total_cat ///
ib1.rural_urban5 ib0.comorb_cat ib1.start_week age1 age2 age3 i.home_bin ///
if eth2 != 6 & risk_pop==1 ///
, strata(utla_group)
* N (events)
tab sgtf end_death_hosp if e(sample)
file write tablecontent _n ("Sensitivity analyses") _n
lincom 1.sgtf, eform
file write tablecontent ("Min. 28-days follow-up") _tab
file write tablecontent %4.2f (r(estimate)) (" (") %4.2f (r(lb)) ("-") %4.2f (r(ub)) (")") _tab %6.4f (r(p)) _n
* Include with 40-days follow-up
* Stratified by region
stcox i.sgtf i.male ib1.imd ib1.eth2 ib1.smoke_nomiss2 ib1.obese4cat ib1.hh_total_cat ///
ib1.rural_urban5 ib0.comorb_cat ib1.start_week age1 age2 age3 i.home_bin ///
if eth2 != 6 & risk_pop_40==1 ///
, strata(utla_group)
* N (events)
tab sgtf end_death_hosp if e(sample)
lincom 1.sgtf, eform
file write tablecontent ("Min. 40-days follow-up") _tab
file write tablecontent %4.2f (r(estimate)) (" (") %4.2f (r(lb)) ("-") %4.2f (r(ub)) (")") _tab %6.4f (r(p)) _n
* NHS England coverage - exclude SE and NE
* Stratified by region
stcox i.sgtf i.male ib1.imd ib1.eth2 ib1.smoke_nomiss2 ib1.obese4cat ib1.hh_total_cat ///
ib1.rural_urban5 ib0.comorb_cat ib1.start_week age1 age2 age3 i.home_bin ///
if eth2 != 6 & !inlist(region,3,5) ///
, strata(utla_group)
* N (events)
tab sgtf end_death_hosp if e(sample)
tab region if e(sample)
lincom 1.sgtf, eform
file write tablecontent ("Exluding NE/SE") _tab
file write tablecontent %4.2f (r(estimate)) (" (") %4.2f (r(lb)) ("-") %4.2f (r(ub)) (")") _tab %6.4f (r(p)) _n
* Discharge as censor
stset time_comp_death, fail(comp_death_hosp) scale(1) id(patient_id)
stcox i.sgtf i.male ib1.imd ib1.eth2 ib1.smoke_nomiss2 ib1.obese4cat ib1.hh_total_cat ///
ib1.rural_urban5 ib0.comorb_cat ib1.start_week age1 age2 age3 i.home_bin ///
if eth2 != 6 ///
, strata(utla_group)
* N (events)
tab sgtf comp_death_hosp if e(sample)
lincom 1.sgtf, eform
file write tablecontent ("Censor at hospital discharge") _tab
file write tablecontent %4.2f (r(estimate)) (" (") %4.2f (r(lb)) ("-") %4.2f (r(ub)) (")") _tab %6.4f (r(p)) _n
**************************************************
/* Fully adjusted HR - age grouped, cat hh size */
**************************************************
/*
* Stratified by region
stcox i.sgtf ib2.agegroupA i.male ib1.imd ib1.eth2 ib1.smoke_nomiss2 ib1.obese4cat ///
ib1.hh_total_cat ib1.rural_urban5 ib0.comorb_cat ib1.start_week i.home_bin ///
if eth2 != 6 ///
, strata(utla_group)
*/
*********************************************************************
/* Causal min adjustment set - age as spline, comorbidities, */
/* deprivation index, and smoking status */
*********************************************************************
stset time_death_hosp, fail(end_death_hosp) scale(1) id(patient_id)
*stcox i.sgtf i.comorb_cat ib1.imd i.smoke_nomiss2 age1 age2 age3 i.home_bin
* Stratified by STP
*stcox i.sgtf i.comorb_cat ib1.imd i.smoke_nomiss2 age1 age2 age3 i.home_bin, strata(stp)
* Stratified by region
stcox i.sgtf i.comorb_cat ib1.imd i.smoke_nomiss2 age1 age2 age3 i.home_bin, strata(utla_group)
* N (events)
tab sgtf end_death_hosp if e(sample)
lincom 1.sgtf, eform
file write tablecontent ("Causal min. adjustment") _tab
file write tablecontent %4.2f (r(estimate)) (" (") %4.2f (r(lb)) ("-") %4.2f (r(ub)) (")") _tab %6.4f (r(p)) _n
* Interaction with time
stcox i.sgtf i.comorb_cat ib1.imd i.smoke_nomiss age1 age2 age3 ///
if eth2 != 6 ///
, strata(utla_group) tvc(i.sgtf)
* Time from positive test
stset time_death_hosp1, fail(end_death_hosp) scale(1) id(patient_id)
stcox i.sgtf i.male ib1.imd ib1.eth2 ib1.smoke_nomiss2 ib1.obese4cat ib1.hh_total_cat ///
ib1.rural_urban5 ib0.comorb_cat ib1.start_week age1 age2 age3 i.home_bin ///
if eth2 != 6 ///
, strata(utla_group)
* Close output table
file write tablecontent _n _n
file close tablecontent
log close
clear
insheet using ./output/table2_hr_hosp_icu.txt, clear
export excel using ./output/table2_hr_hosp_icu.xlsx, replace