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an_summary.do
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an_summary.do
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********************************************************************************
*
* Do-file: an_summary.do
*
* Project: SGTF CFR
*
* Programmed by: Daniel Grint
*
* Data used: output/cr_analysis_dataset.dta
*
* Data created:
*
* Other output: an_summary.log
*
*
********************************************************************************
*
* Purpose: This do-file summarises:
* 1-the number of deaths by SGTF status for each covariate
* 2-plots the proportion of SGTF cases over time by NHS region
* 3-plots the number of hospitalisations over time
* 4-plots the number of ICU admissions over time
*
********************************************************************************
* Open a log file
cap log close
log using ./logs/an_summary, replace t
clear
/*
use "C:\Users\EIDEDGRI\Documents\GitHub\SGTF-CFR-research\output\cr_analysis_dataset.dta"
*/
use ./output/cr_analysis_new.dta
* Tabulate number of deaths by SGTF and covariates
foreach var of varlist agegroup agegroupA agegroup6 male imd eth5 eth2 smoke_nomiss smoke_nomiss2 ///
obese4cat hh_total_cat home_bin region rural_urban5 comorb_cat start_week {
noi disp "Table `var'"
table `var' sgtf, contents(count patient_id sum risk_28 mean risk_28 sum cox_death)
}
* DROP IF NO DATA ON SGTF
noi di "DROPPING NO SGTF DATA"
drop if has_sgtf==0
* Tabulate number of deaths by SGTF and covariates
foreach var of varlist agegroup agegroupA agegroup6 male imd eth5 eth2 smoke_nomiss smoke_nomiss2 ///
obese4cat hh_total_cat home_bin region rural_urban5 comorb_cat start_week {
noi disp "Table `var'"
table `var' sgtf, contents(count patient_id sum risk_28 mean risk_28 sum cox_death)
}
* Tabulate number of hosptial admissions by SGTF and covariates
foreach var of varlist agegroup agegroupA agegroup6 male imd eth5 eth2 smoke_nomiss smoke_nomiss2 ///
obese4cat hh_total_cat home_bin region rural_urban5 comorb_cat start_week {
noi disp "Table `var'"
table `var' sgtf, contents(count patient_id sum end_hosp_test mean end_hosp_test)
}
* Tabulate number of ICU admissions by SGTF and covariates
foreach var of varlist agegroup agegroupA agegroup6 male imd eth5 eth2 smoke_nomiss smoke_nomiss2 ///
obese4cat hh_total_cat home_bin region rural_urban5 comorb_cat start_week {
noi disp "Table `var'"
table `var' sgtf, contents(count patient_id sum end_icu_test mean end_icu_test)
}
* Plot SGTF proportion by NHS region
/*
clear
import delimited "C:\Users\EIDEDGRI\Documents\GitHub\SGTF-CFR-research\lookups\VOC_Data_England.csv"
gen week_date = date(week, "DMY")
format week_date %td
drop if week_date < date("16nov2020", "DMY")
gen start_week = 10 if week_date <= date("24jan2021", "DMY")
replace start_week = 9 if week_date <= date("17jan2021", "DMY")
replace start_week = 8 if week_date <= date("10jan2021", "DMY")
replace start_week = 7 if week_date <= date("03jan2021", "DMY")
replace start_week = 6 if week_date <= date("27dec2020", "DMY")
replace start_week = 5 if week_date <= date("20dec2020", "DMY")
replace start_week = 4 if week_date <= date("13dec2020", "DMY")
replace start_week = 3 if week_date <= date("06dec2020", "DMY")
replace start_week = 2 if week_date <= date("29nov2020", "DMY")
replace start_week = 1 if week_date <= date("22nov2020", "DMY")
rename percent_confirmedsgtf phe_sgtf
rename n_total phe_n
rename region region_s
gen region=0 if region_s=="East of England"
replace region=1 if region_s=="East Midlands"
replace region=2 if region_s=="London"
replace region=3 if region_s=="North East"
replace region=4 if region_s=="North West"
replace region=5 if region_s=="South East"
replace region=6 if region_s=="South West"
replace region=7 if region_s=="West Midlands"
replace region=8 if region_s=="Yorkshire and Humber"
keep region start_week week phe_sgtf phe_n
save "C:\Users\EIDEDGRI\Documents\GitHub\SGTF-CFR-research\lookups\VOC_Data_England.dta"
*/
/*
* Drop if unknown SGTF
drop if !inrange(sgtf,0,1)
* Calculate % SGTF by week and region
collapse (mean) sgtf (count) patient_id, by(region start_week)
gen os_sgtf = sgtf*100
rename patient_id os_n
* Merge on PHE data
/*
merge 1:1 region start_week using "C:\Users\EIDEDGRI\Documents\GitHub\SGTF-CFR-research\lookups\VOC_Data_England.dta"
*/
merge 1:1 region start_week using ./lookups/VOC_Data_England.dta
sort region start_week
gen week_date = date(week, "DMY")
format week_date %td
label define epi_week 1 "47" 2 "48" 3 "49" 4 "50" 5 "51" 6 "52" 7 "53" 8 "1" 9 "2" 10 "3"
label values start_week epi_week
line phe_sgtf os_sgtf start_week, by(region) ///
ytitle("% of positive tests with SGTF") ///
xlabel(1(1)10, valuelabel) ///
legend(label(1 "PHE") label(2 "TPP"))
graph export ./output/sgtf_perc_region.svg, as(svg) replace
graph export ./output/sgtf_perc_region.pdf, as(pdf) replace
*/
log close