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an_risk_models.do
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an_risk_models.do
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********************************************************************************
*
* Do-file: an_risk_models.do
*
* Project: SGTF CFR
*
* Programmed by: Daniel Grint
*
* Data used: output/cr_analysis_dataset.dta
*
* Data created:
*
* Other output: an_risk_models.log containing:
* 1-Unadjusted RR and absolute risks for SGTF
* 2-Adjusted RR and absolute risks for SGTF
* 3-Subgroup analyses of RR and absolute risk
*
********************************************************************************
*
* Purpose: This do-file runs risk models, calculating relative (glm) and
* absolute risk (margins)
*
********************************************************************************
* Open a log file
cap log close
log using ./logs/an_risk_models, replace t
clear
/*
use "C:\Users\EIDEDGRI\Documents\GitHub\SGTF-CFR-research\output\cr_analysis_dataset.dta"
*/
use ./output/cr_analysis_dataset.dta
* DROP IF NO DATA ON SGTF
noi di "DROPPING NO SGTF DATA"
drop if has_sgtf==0
noi di "SUBSETTING ON 28-DAY RISK POPULATION"
keep if risk_pop==1
tab sgtf risk_28, row
*******************
/* Unadjusted RR */
*******************
glm risk_28 i.sgtf, family(bin) link(log) eform
* Absolute risk
margins sgtf
*********************************************************************
/* Demographically adjusted RR - age as spline, continuous hh size */
/* Not adjusting for comorbidities, obesity, or smoking status */
*********************************************************************
glm risk_28 i.sgtf i.male ib1.imd ib1.eth2 household_size ///
i.region ib1.rural_urban5 ib1.start_week age1 age2 age3, ///
family(bin) link(log) eform
* Adjusted absolute risk
margins sgtf
margins sgtf, asbalanced
*********************************************************************
/* Demographically adjusted RR - age grouped, cat hh size */
/* Not adjusting for comorbidities, obesity, or smoking status */
*********************************************************************
glm risk_28 i.sgtf i.male ib1.imd ib1.eth2 ib1.hh_total_cat ///
i.region ib1.rural_urban5 ib1.start_week ib2.agegroupA, ///
family(bin) link(log) eform
* Adjusted absolute risk
margins sgtf
margins sgtf, asbalanced
***********************************************************
/* Fully adjusted RR - age as spline, continuous hh size */
***********************************************************
glm risk_28 i.sgtf i.male ib1.imd ib1.eth2 ib1.smoke_nomiss2 ib1.obese4cat household_size ///
i.region ib1.rural_urban5 ib0.comorb_cat ib1.start_week age1 age2 age3, ///
family(bin) link(log) eform
* Adjusted absolute risk
margins sgtf
margins sgtf, asbalanced
**************************************************
/* Fully adjusted RR - age grouped, cat hh size */
**************************************************
glm risk_28 i.sgtf ib2.agegroupA i.male ib1.imd ib1.eth2 ib1.smoke_nomiss2 ib1.obese4cat ///
ib1.hh_total_cat i.region ib1.rural_urban5 ib0.comorb_cat ib1.start_week, ///
family(bin) link(log) eform
* Adjusted absolute risk
margins sgtf
margins sgtf, asbalanced
***********************
/* Subgroup analyses */
***********************
/* Fully adjusted RR - age grouped, cat hh size */
glm risk_28 i.sgtf ib2.agegroupA i.male ib1.imd ib1.eth2 ib1.smoke_nomiss2 ib1.obese4cat ///
ib1.hh_total_cat i.region ib1.rural_urban5 ib0.comorb_cat ib1.start_week, ///
family(bin) link(log) eform
est store e_no_int
* Constant VOC effect over subgroups
lincom 1.sgtf, eform
margins sgtf
/* Age group */
glm risk_28 i.sgtf##ib2.agegroupA i.male ib1.imd ib1.eth2 ib1.smoke_nomiss2 ib1.obese4cat ///
ib1.hh_total_cat i.region ib1.rural_urban5 ib0.comorb_cat ib1.start_week, ///
family(bin) link(log) eform
est store e_ageX
lrtest e_no_int e_ageX
* Age group VOC vs. non-VOC RR
lincom 1.sgtf, eform // 0-<65
lincom 1.sgtf + 1.sgtf#2.agegroupA, eform // 65-<75
lincom 1.sgtf + 1.sgtf#3.agegroupA, eform // 75-<85
lincom 1.sgtf + 1.sgtf#4.agegroupA, eform // 85+
* Age group marginal risks
margins sgtf, over(agegroupA)
/* Ethnicity */
glm risk_28 i.sgtf##ib1.eth2 ib0.comorb_cat ib2.agegroupA i.male ib1.imd ib1.smoke_nomiss2 ib1.obese4cat ///
ib1.hh_total_cat i.region ib1.rural_urban5 ib1.start_week, ///
family(bin) link(log) eform
est store e_ethX
* Test for interaction
lrtest e_no_int e_ethX
* Ethnicity VOC vs. non-VOC RR
lincom 1.sgtf, eform // White
*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
lincom 1.sgtf + 1.sgtf#9.eth2, eform // Missing
* Ethnicity marginal risks
margins sgtf, over(eth2)
/* Comorbidities */
glm risk_28 i.sgtf##ib0.comorb_cat ib2.agegroupA i.male ib1.imd ib1.eth2 ib1.smoke_nomiss2 ib1.obese4cat ///
ib1.hh_total_cat i.region ib1.rural_urban5 ib1.start_week, ///
family(bin) link(log) eform
est store e_comorbX
* Test for interaction
lrtest e_no_int e_comorbX
* Comorbidities VOC vs. non-VOC RR
lincom 1.sgtf, eform // no comorbs
lincom 1.sgtf + 1.sgtf#1.comorb_cat, eform // 1 comorb
lincom 1.sgtf + 1.sgtf#2.comorb_cat, eform // 2+ comorbs
* Comorbidity marginal risks
margins sgtf, over(comorb_cat)
/* IMD */
glm risk_28 i.sgtf##ib1.imd ib2.agegroupA i.male ib1.eth2 ib1.smoke_nomiss2 ib1.obese4cat ///
ib1.hh_total_cat i.region ib1.rural_urban5 ib0.comorb_cat ib1.start_week, ///
family(bin) link(log) eform
est store e_imdX
* Test for interaction
lrtest e_no_int e_imdX
* IMD VOC vs. non-VOC RR
lincom 1.sgtf, eform // 1 least deprived
lincom 1.sgtf + 1.sgtf#2.imd, eform // 2
lincom 1.sgtf + 1.sgtf#3.imd, eform // 3
lincom 1.sgtf + 1.sgtf#4.imd, eform // 4
lincom 1.sgtf + 1.sgtf#5.imd, eform // 5 most deprived
* IMD marginal risks
margins sgtf, over(imd)
/* Epi week */
glm risk_28 i.sgtf##ib1.start_week ib2.agegroupA i.male ib1.imd ib1.eth2 ib1.smoke_nomiss2 ib1.obese4cat ///
ib1.hh_total_cat i.region ib1.rural_urban5 ib0.comorb_cat, ///
family(bin) link(log) eform
est store e_weekX
* Test for interaction
lrtest e_no_int e_weekX
* Epi week VOC vs. non-VOC RR
lincom 1.sgtf, eform // week 1
lincom 1.sgtf + 1.sgtf#2.start_week, eform // week 2
lincom 1.sgtf + 1.sgtf#3.start_week, eform // week 3
lincom 1.sgtf + 1.sgtf#4.start_week, eform // week 4
lincom 1.sgtf + 1.sgtf#5.start_week, eform // week 5
lincom 1.sgtf + 1.sgtf#6.start_week, eform // week 6
lincom 1.sgtf + 1.sgtf#7.start_week, eform // week 7
* Epi week marginal risks
margins sgtf, over(start_week)
/* NHS region */
/*
glm risk_28 i.sgtf i.agegroupA i.male ib1.imd ib1.eth5 ib1.smoke_nomiss ib1.obese4cat ///
ib1.hh_total_cat ib1.rural_urban5 ib0.comorb_cat ib1.start_week i.region, ///
family(bin) link(log) eform
est store e_region
*/
glm risk_28 i.sgtf##i.region 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, ///
family(bin) link(log) eform
est store e_regionX
* Test for interaction
lrtest e_no_int e_regionX
* NHS region VOC vs. non-VOC RR
lincom 1.sgtf, eform // East
lincom 1.sgtf + 1.sgtf#1.region, eform // East mids
lincom 1.sgtf + 1.sgtf#2.region, eform // London
lincom 1.sgtf + 1.sgtf#3.region, eform // North E
lincom 1.sgtf + 1.sgtf#4.region, eform // North W
lincom 1.sgtf + 1.sgtf#5.region, eform // South E
lincom 1.sgtf + 1.sgtf#6.region, eform // South W
lincom 1.sgtf + 1.sgtf#7.region, eform // West mids
lincom 1.sgtf + 1.sgtf#8.region, eform // Yorks & Hum
* NHS region marginal risks
margins sgtf, over(region)
*********************************************************************
/* Causal min adjustment set - age as spline, comorbidities, */
/* deprivation index, and smoking status */
*********************************************************************
glm risk_28 i.sgtf i.comorb_cat ib1.imd i.smoke_nomiss2 age1 age2 age3, ///
family(bin) link(log) eform
* Adjusted absolute risk
margins sgtf
margins sgtf, asbalanced
* Age grouped
glm risk_28 i.sgtf i.comorb_cat ib1.imd i.smoke_nomiss2 ib2.agegroupA, ///
family(bin) link(log) eform
* Adjusted absolute risk
margins sgtf
margins sgtf, asbalanced
* With region
glm risk_28 i.sgtf i.comorb_cat ib1.imd i.smoke_nomiss2 ib2.agegroupA i.region, ///
family(bin) link(log) eform
* Adjusted absolute risk
margins sgtf
margins sgtf, asbalanced
/*
**********************************
/* Causal min subgroup analyses */
**********************************
/* Causal min adjusted RR */
glm risk_28 i.sgtf i.comorb_cat ib1.imd i.smoke_nomiss age1 age2 age3, ///
family(bin) link(log) eform
est store e_no_int
* Constant VOC effect over subgroups
lincom 1.sgtf, eform
margins sgtf
/* Age group */
replace agegroupA=2 if agegroupA==1
glm risk_28 i.sgtf##i.agegroupA i.comorb_cat ib1.imd i.smoke_nomiss, ///
family(bin) link(log) eform
est store e_ageX
lrtest e_no_int e_ageX
* Age group VOC vs. non-VOC RR
*lincom 1.sgtf, eform // <50
lincom 1.sgtf + 1.sgtf#2.agegroupA, eform // 50-<65
lincom 1.sgtf + 1.sgtf#3.agegroupA, eform // 65-<75
lincom 1.sgtf + 1.sgtf#4.agegroupA, eform // 75-<85
lincom 1.sgtf + 1.sgtf#5.agegroupA, eform // 85+
* Age group marginal risks
margins sgtf, over(agegroupA)
/* Epi week */
glm risk_28 i.sgtf i.start_week i.comorb_cat ib1.imd i.smoke_nomiss age1 age2 age3, ///
family(bin) link(log) eform
est store e_week
glm risk_28 i.sgtf##i.start_week i.comorb_cat ib1.imd i.smoke_nomiss age1 age2 age3, ///
family(bin) link(log) eform
est store e_weekX
* Test for interaction
lrtest e_week e_weekX
* Epi week VOC vs. non-VOC RR
lincom 1.sgtf, eform // week 1
lincom 1.sgtf + 1.sgtf#2.start_week, eform // week 2
lincom 1.sgtf + 1.sgtf#3.start_week, eform // week 3
lincom 1.sgtf + 1.sgtf#4.start_week, eform // week 4
capture lincom 1.sgtf + 1.sgtf#5.start_week, eform // week 5
capture lincom 1.sgtf + 1.sgtf#6.start_week, eform // week 6
capture lincom 1.sgtf + 1.sgtf#7.start_week, eform // week 7
* Epi week marginal risks
margins sgtf, over(start_week)
*/
log close