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an_logit_models.do
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an_logit_models.do
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********************************************************************************
*
* Do-file: an_logit_models.do
*
* Project: SGTF CFR
*
* Programmed by: Daniel Grint
*
* Data used: output/cr_analysis_dataset.dta
*
* Data created:
*
* Other output: an_logit_models.log containing:
* 1-Unadjusted OR and absolute risks for SGTF
* 2-Adjusted OR and absolute risks for SGTF
* 3-Subgroup analyses of OR and absolute risk
*
********************************************************************************
*
* Purpose: This do-file runs logit models, calculating relative (glm) and
* absolute odds (margins)
*
********************************************************************************
* Open a log file
cap log close
log using ./logs/an_logit_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 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 28-DAY RISK POPULATION"
keep if risk_pop==1
tab sgtf risk_28, row
*******************
/* Unadjusted OR */
*******************
glm risk_28 i.sgtf, family(bin) link(logit) eform
* Absolute odds
margins sgtf
*********************************************************************
/* Demographically adjusted OR - 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.home_bin ///
i.region ib1.rural_urban5 ib1.start_week age1 age2 age3 ///
if eth2 != 6 ///
, family(bin) link(logit) eform
*********************************************************************
/* Demographically adjusted OR - 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.home_bin ///
i.region ib1.rural_urban5 ib1.start_week ib2.agegroupA ///
if eth2 != 6 ///
, family(bin) link(logit) eform
***********************************************************
/* Fully adjusted OR - 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 i.home_bin ///
if eth2 != 6 ///
, family(bin) link(logit) eform
**************************************************
/* Fully adjusted OR - 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 i.home_bin ///
if eth2 != 6 ///
, family(bin) link(logit) eform
est store fully
table agegroupA sgtf if e(sample)==1, contents(count patient_id) by(comorb_cat male)
table male comorb_cat if e(sample)==1
* Adjusted absolute risks
margins comorb_cat#male#agegroupA if sgtf==0, post asobserved
* Save risk estimates
matrix est = e(b)
matrix inv_est = est'
svmat inv_est
* Save SE estimates
matrix var = e(V)
matrix diag_var = vecdiag(var)
matrix inv_var = diag_var'
svmat inv_var
gen sq_var = sqrt(inv_var1)
noi disp "CHECK MARGINS ARE CORRECTLY CALCULATED TO MATCH ABOVE"
list inv_est1 sq_var in 1/24
* Re-Calculate CI
gen risk0 = inv_est1*100
gen lb0 = (inv_est1 - invnormal(0.975)*sq_var)*100
gen ub0 = (inv_est1 + invnormal(0.975)*sq_var)*100
order lb ub, after(risk0)
est restore fully
* Adjusted absolute risks
margins comorb_cat#male#agegroupA if sgtf==1, post asobserved
* Save risk estimates
matrix est1 = e(b)
matrix inv_estx = est1'
svmat inv_estx
* Save SE estimates
matrix var1 = e(V)
matrix diag_var1 = vecdiag(var1)
matrix inv_varx = diag_var1'
svmat inv_varx
gen sq_varx = sqrt(inv_varx1)
noi disp "CHECK MARGINS ARE CORRECTLY CALCULATED TO MATCH ABOVE"
list inv_estx1 sq_varx in 1/24
* Re-Calculate CI
gen risk1 = inv_estx1*100
gen lb1 = (inv_estx1 - invnormal(0.975)*sq_varx)*100
gen ub1 = (inv_estx1 + invnormal(0.975)*sq_varx)*100
order lb1 ub1, after(risk1)
* Adjusted risk difference
est restore fully
margins comorb_cat#male#agegroupA, dydx(sgtf) post asobserved
* Save risk estimates
matrix diff = e(b)
matrix diff = diff[1, 25..48]
matrix inv_diff = diff'
svmat inv_diff
* Save SE estimates
matrix dvar = e(V)
matrix diag_dvar = vecdiag(dvar)
matrix inv_dvar = diag_dvar'
matrix inv_dvar = inv_dvar[25..48,1]
svmat inv_dvar
gen sq_dvar = sqrt(inv_dvar1)
noi disp "CHECK MARGINS ARE CORRECTLY CALCULATED TO MATCH ABOVE"
list inv_diff1 sq_dvar in 1/24
* Re-Calculate CI
gen diff1 = inv_diff1*100
gen dlb = (inv_diff1 - invnormal(0.975)*sq_dvar)*100
gen dub = (inv_diff1 + invnormal(0.975)*sq_dvar)*100
order dlb dub, after(diff1)
gen risk_labels = "Female: 0-<65" in 1
replace risk_labels = "65-<75" in 2
replace risk_labels = "75-<85" in 3
replace risk_labels = "85+" in 4
replace risk_labels = "Male: 0-<65" in 5
replace risk_labels = "65-<75" in 6
replace risk_labels = "75-<85" in 7
replace risk_labels = "85+" in 8
replace risk_labels = "Female: 0-<65" in 9
replace risk_labels = "65-<75" in 10
replace risk_labels = "75-<85" in 11
replace risk_labels = "85+" in 12
replace risk_labels = "Male: 0-<65" in 13
replace risk_labels = "65-<75" in 14
replace risk_labels = "75-<85" in 15
replace risk_labels = "85+" in 16
replace risk_labels = "Female: 0-<65" in 17
replace risk_labels = "65-<75" in 18
replace risk_labels = "75-<85" in 19
replace risk_labels = "85+" in 20
replace risk_labels = "Male: 0-<65" in 21
replace risk_labels = "65-<75" in 22
replace risk_labels = "75-<85" in 23
replace risk_labels = "85+" in 24
***********************************
/* Output table of absolute risk */
***********************************
cap file close tablecontent
file open tablecontent using ./output/table3_abs_risk.txt, write text replace
file write tablecontent ("Table 3: Absolute risk of death by 28-days") _n _n
file write tablecontent ("Comorbidities/Sex/Age group") _tab ///
("non-VOC (95% CI)") _tab ///
("VOC (95% CI)") _tab ///
("Diff (95% CI)") _n
forvalues i=1/24 {
preserve
keep if _n == `i'
if inlist(`i',5,13,21) {
file write tablecontent _n
}
if `i'==1 {
file write tablecontent _n ("No Comorbidities") _n
}
if `i'==9 {
file write tablecontent _n ("1 Comorbidity") _n
}
if `i'==17 {
file write tablecontent _n ("2+ Comorbidities") _n
}
file write tablecontent %9s (risk_labels) _tab %4.2f (risk0) (" (") %4.2f (lb0) ("-") %4.2f (ub0) (")") _tab %4.2f (risk1) (" (") %4.2f (lb1) ("-") %4.2f (ub1) (")") _tab %4.2f (diff1) (" (") %4.2f (dlb) ("-") %4.2f (dub) (")") _n
restore
}
file close tablecontent
* Risks as balanced
est restore fully
margins comorb_cat#male#agegroupA, post asbalanced over(sgtf) grand
est restore fully
margins comorb_cat#male#agegroupA, post over(sgtf) grand
***********************
/* Subgroup analyses */
***********************
/* Fully adjusted OR - 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 i.home_bin ///
if eth2 != 6 ///
, family(bin) link(logit) eform
est store e_no_int
* Constant VOC effect over subgroups
lincom 1.sgtf, eform
/* 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 i.home_bin ///
if eth2 != 6 ///
, family(bin) link(logit) eform
est store e_ageX
lrtest e_no_int e_ageX
* Age group VOC vs. non-VOC OR
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+
/* 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 i.home_bin ///
if eth2 != 6 ///
, family(bin) link(logit) eform
est store e_ethX
* Test for interaction
lrtest e_no_int e_ethX
* Ethnicity VOC vs. non-VOC OR
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#6.eth2, eform // Missing
/* 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 i.home_bin ///
if eth2 != 6 ///
, family(bin) link(logit) eform
est store e_comorbX
* Test for interaction
lrtest e_no_int e_comorbX
* Comorbidities VOC vs. non-VOC OR
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
/* 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 i.home_bin ///
if eth2 != 6 ///
, family(bin) link(logit) eform
est store e_imdX
* Test for interaction
lrtest e_no_int e_imdX
* IMD VOC vs. non-VOC OR
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
/* Epi week */
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 ib2.start_weekA i.home_bin ///
if eth2 != 6 ///
, family(bin) link(logit) eform
est store e_week
glm risk_28 i.sgtf##ib2.start_weekA 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 i.home_bin ///
if eth2 != 6 ///
, family(bin) link(logit) eform
est store e_weekX
* Test for interaction
lrtest e_no_int e_weekX
* Epi week VOC vs. non-VOC OR
lincom 1.sgtf + 1.sgtf#2.start_week, eform // week 1/2
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
lincom 1.sgtf + 1.sgtf#8.start_week, eform // week 8
/* 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 i.home_bin ///
if eth2 != 6 ///
, family(bin) link(logit) eform
est store e_regionX
* Test for interaction
lrtest e_no_int e_regionX
* NHS region VOC vs. non-VOC OR
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
*********************************************************************
/* 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 i.home_bin, ///
family(bin) link(logit) eform
* Age grouped
glm risk_28 i.sgtf i.comorb_cat ib1.imd i.smoke_nomiss2 ib2.agegroupA i.home_bin, ///
family(bin) link(logit) eform
* With region
glm risk_28 i.sgtf i.comorb_cat ib1.imd i.smoke_nomiss2 ib2.agegroupA i.home_bin i.region, ///
family(bin) link(logit) eform
log close
insheet using ./output/table3_abs_risk.txt, clear
export excel using ./output/table3_abs_risk.xlsx, replace