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04d_eth_an_multivariable_eth5_carehomes.do
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04d_eth_an_multivariable_eth5_carehomes.do
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/*==============================================================================
DO FILE NAME: 04d_eth_an_multivariable_eth5_carehomes
PROJECT: Ethnicity and COVID
AUTHOR: R Mathur (modified from A wong and A Schultze)
DATE: 15 July 2020
DESCRIPTION OF FILE: program 06
univariable regression
multivariable regression
DATASETS USED: data in memory ($tempdir/analysis_dataset_STSET_outcome)
DATASETS CREATED: none
OTHER OUTPUT: logfiles, printed to folder analysis/$logdir
table2, printed to $Tabfigdir
complete case analysis
==============================================================================*/
* Open a log file
global outcomes "tested positivetest hes onscoviddeath ons_noncoviddeath onsdeath"
sysdir set PLUS ./analysis/adofiles
adopath + ./analysis/adofiles
sysdir
* Open a log file
cap log close
macro drop hr
log using ./logs/04d_eth_an_multivariable_eth5, replace t
cap file close tablecontent
file open tablecontent using ./output/table2_eth5.txt, write text replace
file write tablecontent ("Table 2: Association between ethnicity in 5 categories and COVID-19 outcomes - No care homes") _n
file write tablecontent _tab ("Denominator") _tab ("Event") _tab ("Total person-weeks") _tab ("Rate per 1,000") _tab ("Crude") _tab _tab ("Age/Sex Adjusted") _tab _tab ("Age/Sex/IMD Adjusted") _tab _tab ("plus co-morbidities") _tab _tab ("plus hh size") _tab _tab _n
file write tablecontent _tab _tab _tab _tab _tab ("HR") _tab ("95% CI") _tab ("HR") _tab ("95% CI") _tab ("HR") _tab ("95% CI") _tab ("HR") _tab ("95% CI") _tab ("HR") _tab ("95% CI") _tab _tab _n
foreach i of global outcomes {
use ./output/analysis_dataset_STSET_`i'.dta, clear
keep if carehome==1
safetab eth5 `i', missing row
} //end outcomes
foreach i of global outcomes {
di "`i'"
* Open Stata dataset
use ./output/analysis_dataset_STSET_`i'.dta, clear
keep if carehome==1
/* Main Model=================================================================*/
/* Univariable model */
stcox i.eth5, strata(stp) nolog
estimates save ./output/model/crude_`i'_eth5, replace
eststo model1
parmest, label eform format(estimate p lb ub) saving(./output/model/crude_`i'_eth5, replace) idstr(crude_`i'_eth5)
local hr "`hr' ./output/model/crude_`i'_eth5 "
/* Multivariable models */
*Age and gender
stcox i.eth5 i.male age1 age2 age3, strata(stp) nolog
estimates save ./output/model/model0_`i'_eth5, replace
eststo model2
parmest, label eform format(estimate p lb ub) saving(./output/model/model0_`i'_eth5, replace) idstr(model0_`i'_eth5)
local hr "`hr' ./output/model/model0_`i'_eth5 "
* Age, Gender, IMD
stcox i.eth5 i.male age1 age2 age3 i.imd, strata(stp) nolog
if _rc==0{
estimates
estimates save ./output/model/model1_`i'_eth5, replace
eststo model3
parmest, label eform format(estimate p lb ub) saving(./output/model/model1_`i'_eth5, replace) idstr(model1_`i'_eth5)
local hr "`hr' ./output/model/model1_`i'_eth5 "
}
else di "WARNING MODEL1 DID NOT FIT (OUTCOME `i')"
* Age, Gender, IMD and Comorbidities
stcox i.eth5 i.male age1 age2 age3 i.imd ///
i.bmicat_sa i.hba1ccat ///
gp_consult_count ///
i.smoke_nomiss ///
i.hypertension i.bp_cat ///
i.asthma ///
i.chronic_respiratory_disease ///
i.chronic_cardiac_disease ///
i.dm_type ///
i.cancer ///
i.chronic_liver_disease ///
i.stroke ///
i.dementia ///
i.other_neuro ///
i.egfr60 ///
i.esrf ///
i.immunosuppressed ///
i.ra_sle_psoriasis, strata(stp) nolog
if _rc==0{
estimates
estimates save ./output/model/model2_`i'_eth5, replace
eststo model4
parmest, label eform format(estimate p lb ub) saving(./output/model/model2_`i'_eth5, replace) idstr(model2_`i'_eth5)
local hr "`hr' ./output/model/model2_`i'_eth5 "
}
else di "WARNING MODEL2 DID NOT FIT (OUTCOME `i')"
* Age, Gender, IMD and Comorbidities and household size
stcox i.eth5 i.male age1 age2 age3 i.imd ///
i.bmicat_sa i.hba1ccat ///
gp_consult_count ///
i.smoke_nomiss ///
i.hypertension i.bp_cat ///
i.asthma ///
i.chronic_respiratory_disease ///
i.chronic_cardiac_disease ///
i.dm_type ///
i.cancer ///
i.chronic_liver_disease ///
i.stroke ///
i.dementia ///
i.other_neuro ///
i.egfr60 ///
i.esrf ///
i.immunosuppressed ///
i.ra_sle_psoriasis ///
i.hh_total_cat, strata(stp) nolog
estimates save ./output/model/model3_`i'_eth5, replace
eststo model5
parmest, label eform format(estimate p lb ub) saving(./output/model/model3_`i'_eth5, replace) idstr(model3_`i'_eth5)
local hr "`hr' ./output/model/model3_`i'_eth5 "
/* Estout================================================================*/
esttab model1 model2 model3 model4 model5 using ./output/estout_table2_eth5_carehomes.txt, b(a2) ci(2) label wide compress eform ///
title ("`i'") ///
varlabels(`e(labels)') ///
stats(N_sub) ///
append
eststo clear
/* Print table================================================================*/
* Print the results for the main model
* Column headings
file write tablecontent ("`i'") _n
* eth5 labelled columns
local lab1: label eth5 1
local lab2: label eth5 2
local lab3: label eth5 3
local lab4: label eth5 4
local lab5: label eth5 5
local lab6: label eth5 6
/* counts */
* First row, eth5 = 1 (White British) reference cat
qui safecount if eth5==1
local denominator = r(N)
qui safecount if eth5 == 1 & `i' == 1
local event = r(N)
bysort eth5: egen total_follow_up = total(_t)
qui su total_follow_up if eth5 == 1
local person_week = r(mean)/7
local rate = 1000*(`event'/`person_week')
file write tablecontent ("`lab1'") _tab (`denominator') _tab (`event') _tab %10.0f (`person_week') _tab %3.2f (`rate') _tab
file write tablecontent ("1.00") _tab _tab ("1.00") _tab _tab ("1.00") _tab _tab ("1.00") _tab _tab ("1.00") _n
* Subsequent ethnic groups
forvalues eth=2/6 {
qui safecount if eth5==`eth'
local denominator = r(N)
qui safecount if eth5 == `eth' & `i' == 1
local event = r(N)
qui su total_follow_up if eth5 == `eth'
local person_week = r(mean)/7
local rate = 1000*(`event'/`person_week')
file write tablecontent ("`lab`eth''") _tab (`denominator') _tab (`event') _tab %10.0f (`person_week') _tab %3.2f (`rate ') _tab
cap estimates use ./output/model/crude_`i'_eth5
cap lincom `eth'.eth5, eform
file write tablecontent %4.2f (r(estimate)) _tab ("(") %4.2f (r(lb)) (" - ") %4.2f (r(ub)) (")") _tab
cap estimates clear
cap estimates use ./output/model/model0_`i'_eth5
cap lincom `eth'.eth5, eform
file write tablecontent %4.2f (r(estimate)) _tab ("(") %4.2f (r(lb)) (" - ") %4.2f (r(ub)) (")") _tab
cap estimates clear
cap estimates use ./output/model/model1_`i'_eth5
cap lincom `eth'.eth5, eform
file write tablecontent %4.2f (r(estimate)) _tab ("(") %4.2f (r(lb)) (" - ") %4.2f (r(ub)) (")") _tab
cap estimates clear
cap estimates use ./output/model/model2_`i'_eth5
cap lincom `eth'.eth5, eform
file write tablecontent %4.2f (r(estimate)) _tab ("(") %4.2f (r(lb)) (" - ") %4.2f (r(ub)) (")") _tab
cap estimates clear
cap estimates use ./output/model/model3_`i'_eth5
cap lincom `eth'.eth5, eform
file write tablecontent %4.2f (r(estimate)) _tab ("(") %4.2f (r(lb)) (" - ") %4.2f (r(ub)) (")") _n
} //end ethnic group
} //end outcomes
file close tablecontent
************************************************create forestplot dataset
dsconcat `hr'
duplicates drop
split idstr, p(_)
ren idstr1 model
ren idstr2 outcome
drop idstr idstr3
tab model
*save dataset for later
outsheet using ./output/FP_multivariable_eth5_carehomes.txt, replace
* Close log file
log close