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501_redacted_table.do
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501_redacted_table.do
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********************************************************************************
*
* Do-file: redacted_table.do
* Project: Sotrovimab-Paxlovid-Molnupiravir
* Date: 25/07/23
* Programmed by: Katie Bechman
* Description: data management, reformat variables, categorise variables, label variables
* Data used: data in memory (from output/input.csv)
* Data created: analysis main.dta (main analysis dataset)
* Other output: logfiles, printed to folder $Logdir
* User installed ado: (place .ado file(s) in analysis folder)
****************************************************************************************************************
**Set filepaths
//global projectdir "C:\Users\k1635179\OneDrive - King's College London\Katie\OpenSafely\Safety mAB and antivirals\Safety-Sotrovimab-Paxlovid-Molnupiravir"
global projectdir `c(pwd)'
di "$projectdir"
capture mkdir "$projectdir/output/data"
capture mkdir "$projectdir/output/figures"
capture mkdir "$projectdir/output/tables"
global logdir "$projectdir/logs"
di "$logdir"
* Open a log file
cap log close
log using "$logdir/redacted_table.log", replace
*Set Ado file path
adopath + "$projectdir/analysis/ado"
*******************************************************************************************************************
** Main analysis
**Baseline table redacted and rounded
clear *
save "$projectdir/output/tables/baseline_table_redact_all.dta", replace emptyok
use "$projectdir/output/data/main", clear
set type double
** labeling
foreach var of varlist downs_syndrome_comb solid_cancer_comb haem_disease_comb liver_disease_comb renal_disease_comb imid_on_drug_comb immunosuppression_comb hiv_aids_comb organ_transplant_comb rare_neuro_comb eligible dementia serious_mental_illness care_home diabetes chronic_cardiac_disease hypertension chronic_respiratory_disease prior_covid paxlovid_contraindicated {
recode `var' . = 0
label define `var' 1 "yes" 0 "no", replace
label values `var' `var'
}
foreach var of varlist pre_drug_test downs_syndrome_comb solid_cancer_comb haem_disease_comb liver_disease_comb renal_disease_comb imid_on_drug_comb immunosuppression_comb hiv_aids_comb organ_transplant_comb rare_neuro_comb eligible dementia serious_mental_illness care_home diabetes chronic_cardiac_disease hypertension chronic_respiratory_disease prior_covid paxlovid_contraindicated prior_covid vaccination_status region_nhs imdq5 bmi_group ethnicity sex age_group{
preserve
contract `var'
gen variable = `"`var'"'
label variable `var' "`var'"
decode `var', gen(categories)
gen count_mid_all = (ceil(_freq/6)*6) - (floor(6/2) * (_freq!=0))
egen total_mid_all = total(count)
egen non_missing=sum(count) if categories!=""
drop if categories==""
gen percent_mid_all = round((count/non_missing)*100, 0.1)
gen missing_mid_all=(total-non_missing)
list variable `var' count percent total missing
keep variable categories count percent total missing
order variable categories count percent total missing
append using "$projectdir/output/tables/baseline_table_redact_all.dta"
save "$projectdir/output/tables/baseline_table_redact_all.dta", replace
restore
}
use "$projectdir/output/tables/baseline_table_redact_all.dta", clear
export excel "$projectdir/output/tables/baseline_table_redact_bydrug.xls", replace sheet("overall") keepcellfmt firstrow(variables)
**Catergorical table by drug subdiagnoses - tagged to above excel
use "$projectdir/output/data/main", clear
decode drug, gen(drug_str)
local index=0
levelsof drug_str, local(levels)
foreach i of local levels {
clear *
save "$projectdir/output/tables/baseline_table_redact_`i'.dta", replace emptyok
di `index'
if `index'==0 {
local col = word("`c(ALPHA)'", `index'+7)
}
else if `index'>0 & `index'<=22 {
local col = word("`c(ALPHA)'", `index'+5)
}
di "`col'"
if `index'==0 {
local `index++'
local `index++'
local `index++'
local `index++'
local `index++'
local `index++'
}
else {
local `index++'
local `index++'
local `index++'
local `index++'
}
di `index'
use "$projectdir/output/data/main", clear
decode drug, gen(drug_str)
foreach var of varlist downs_syndrome_comb solid_cancer_comb haem_disease_comb liver_disease_comb renal_disease_comb imid_on_drug_comb immunosuppression_comb hiv_aids_comb organ_transplant_comb rare_neuro_comb eligible dementia serious_mental_illness care_home diabetes chronic_cardiac_disease hypertension chronic_respiratory_disease prior_covid paxlovid_contraindicated {
recode `var' . = 0
label define `var' 1 "yes" 0 "no", replace
label values `var' `var'
}
foreach var of varlist pre_drug_test downs_syndrome_comb solid_cancer_comb haem_disease_comb liver_disease_comb renal_disease_comb imid_on_drug_comb immunosuppression_comb hiv_aids_comb organ_transplant_comb rare_neuro_comb eligible dementia serious_mental_illness care_home diabetes chronic_cardiac_disease hypertension chronic_respiratory_disease prior_covid paxlovid_contraindicated prior_covid vaccination_status region_nhs imdq5 bmi_group ethnicity sex age_group{
preserve
keep if drug_str=="`i'"
contract `var'
gen variable = `"`var'"'
label variable `var' "`var'"
decode `var', gen(categories)
gen count_mid_`i' = (ceil(_freq/6)*6) - (floor(6/2) * (_freq!=0))
egen total_mid_`i' = total(count)
egen non_missing=sum(count) if categories!=""
drop if categories==""
gen percent_mid_`i' = round((count/non_missing)*100, 0.1)
gen missing_mid_`i'=(total-non_missing)
list `var' count percent total missing
keep count percent total missing
order(count), first
append using "$projectdir/output/tables/baseline_table_redact_`i'.dta"
save "$projectdir/output/tables/baseline_table_redact_`i'.dta", replace
restore
}
display `index'
display "`col'"
use "$projectdir/output/tables/baseline_table_redact_`i'.dta", clear
export excel "$projectdir/output/tables/baseline_table_redact_bydrug.xls", sheet("Overall", modify) cell("`col'1") keepcellfmt firstrow(variables)
}
*Output tables as CSVs
import excel "$projectdir/output/tables/baseline_table_redact_bydrug.xls", clear
export delimited using "$projectdir/output/tables/baseline_table_redact_bydrug.csv" , replace
**2. Continous variables
clear *
save "$projectdir/output/tables/baseline_table_redact_mean.dta", replace emptyok
use "$projectdir/output/data/main", clear
decode drug, gen(drug_str)
foreach var of varlist age bmi {
preserve
collapse (count) "`var'_count"=`var' (mean) mean=`var' (sd) stdev=`var' (median) median=`var' (p25) p25=`var' (p75) p75=`var', by(drug_str)
gen variable = "`var'"
rename *count freq
gen count_mid = (ceil(freq/6)*6) - (floor(6/2) * (freq!=0))
drop freq
order variable drug_str count mean stdev median p25 p75
list variable drug_str count mean stdev median p25 p75
append using "$projectdir/output/tables/baseline_table_redact_mean.dta"
save "$projectdir/output/tables/baseline_table_redact_mean.dta", replace
restore
preserve
collapse (count) "`var'_count"=`var' (mean) mean=`var' (sd) stdev=`var' (median) median=`var' (p25) p25=`var' (p75) p75=`var'
gen variable = "`var'"
rename *count freq
gen count_mid = (ceil(freq/6)*6) - (floor(6/2) * (freq!=0))
drop freq
gen drug_str = "all"
order variable drug_str count mean stdev median p25 p75
list variable drug_str count mean stdev median p25 p75
append using "$projectdir/output/tables/baseline_table_redact_mean.dta"
save "$projectdir/output/tables/baseline_table_redact_mean.dta", replace
restore
}
use "$projectdir/output/tables/baseline_table_redact_mean.dta", clear
save "$projectdir/output/tables/baseline_table_redact_mean.dta", replace
export delimited using "$projectdir/output/tables/baseline_table_redact_mean.csv", replace
*******************************************************************************************************************
** Sensitivity analysis
**Baseline table redacted and rounded
clear *
save "$projectdir/output/tables/baseline_table_redact_all_sens.dta", replace emptyok
use "$projectdir/output/data/sensitivity_analysis", clear
set type double
tab pre_drug_test drug
drop if covid_test_5d!=1 & drug >0
tab pre_drug_test drug
** labeling
foreach var of varlist downs_syndrome_comb solid_cancer_comb haem_disease_comb liver_disease_comb renal_disease_comb imid_on_drug_comb immunosuppression_comb hiv_aids_comb organ_transplant_comb rare_neuro_comb eligible dementia serious_mental_illness care_home diabetes chronic_cardiac_disease hypertension chronic_respiratory_disease prior_covid paxlovid_contraindicated {
recode `var' . = 0
label define `var' 1 "yes" 0 "no", replace
label values `var' `var'
}
foreach var of varlist pre_drug_test downs_syndrome_comb solid_cancer_comb haem_disease_comb liver_disease_comb renal_disease_comb imid_on_drug_comb immunosuppression_comb hiv_aids_comb organ_transplant_comb rare_neuro_comb eligible dementia serious_mental_illness care_home diabetes chronic_cardiac_disease hypertension chronic_respiratory_disease prior_covid paxlovid_contraindicated prior_covid vaccination_status region_nhs imdq5 bmi_group ethnicity sex age_group{
preserve
contract `var'
gen variable = `"`var'"'
label variable `var' "`var'"
decode `var', gen(categories)
gen count_mid_all = (ceil(_freq/6)*6) - (floor(6/2) * (_freq!=0))
egen total_mid_all = total(count)
egen non_missing=sum(count) if categories!=""
drop if categories==""
gen percent_mid_all = round((count/non_missing)*100, 0.1)
gen missing_mid_all=(total-non_missing)
list variable `var' count percent total missing
keep variable categories count percent total missing
order variable categories count percent total missing
append using "$projectdir/output/tables/baseline_table_redact_all_sens.dta"
save "$projectdir/output/tables/baseline_table_redact_all_sens.dta", replace
restore
}
use "$projectdir/output/tables/baseline_table_redact_all_sens.dta", clear
export excel "$projectdir/output/tables/baseline_table_redact_bydrug_sens.xls", replace sheet("overall") keepcellfmt firstrow(variables)
**Catergorical table by drug subdiagnoses - tagged to above excel
use "$projectdir/output/data/sensitivity_analysis", clear
tab pre_drug_test drug
drop if covid_test_5d!=1 & drug >0
tab pre_drug_test drug
decode drug, gen(drug_str)
local index=0
levelsof drug_str, local(levels)
foreach i of local levels {
clear *
save "$projectdir/output/tables/baseline_table_redact_sens_`i'.dta", replace emptyok
di `index'
if `index'==0 {
local col = word("`c(ALPHA)'", `index'+7)
}
else if `index'>0 & `index'<=22 {
local col = word("`c(ALPHA)'", `index'+5)
}
di "`col'"
if `index'==0 {
local `index++'
local `index++'
local `index++'
local `index++'
local `index++'
local `index++'
}
else {
local `index++'
local `index++'
local `index++'
local `index++'
}
di `index'
use "$projectdir/output/data/sensitivity_analysis", clear
tab pre_drug_test drug
drop if covid_test_5d!=1 & drug >0
tab pre_drug_test drug
decode drug, gen(drug_str)
foreach var of varlist downs_syndrome_comb solid_cancer_comb haem_disease_comb liver_disease_comb renal_disease_comb imid_on_drug_comb immunosuppression_comb hiv_aids_comb organ_transplant_comb rare_neuro_comb eligible dementia serious_mental_illness care_home diabetes chronic_cardiac_disease hypertension chronic_respiratory_disease prior_covid paxlovid_contraindicated {
recode `var' . = 0
label define `var' 1 "yes" 0 "no", replace
label values `var' `var'
}
foreach var of varlist pre_drug_test downs_syndrome_comb solid_cancer_comb haem_disease_comb liver_disease_comb renal_disease_comb imid_on_drug_comb immunosuppression_comb hiv_aids_comb organ_transplant_comb rare_neuro_comb eligible dementia serious_mental_illness care_home diabetes chronic_cardiac_disease hypertension chronic_respiratory_disease prior_covid paxlovid_contraindicated prior_covid vaccination_status region_nhs imdq5 bmi_group ethnicity sex age_group{
preserve
keep if drug_str=="`i'"
contract `var'
gen variable = `"`var'"'
label variable `var' "`var'"
decode `var', gen(categories)
gen count_mid_`i' = (ceil(_freq/6)*6) - (floor(6/2) * (_freq!=0))
egen total_mid_`i' = total(count)
egen non_missing=sum(count) if categories!=""
drop if categories==""
gen percent_mid_`i' = round((count/non_missing)*100, 0.1)
gen missing_mid_`i'=(total-non_missing)
list `var' count percent total missing
keep count percent total missing
order(count), first
append using "$projectdir/output/tables/baseline_table_redact_sens_`i'.dta"
save "$projectdir/output/tables/baseline_table_redact_sens_`i'.dta", replace
restore
}
display `index'
display "`col'"
use "$projectdir/output/tables/baseline_table_redact_sens_`i'.dta", clear
export excel "$projectdir/output/tables/baseline_table_redact_bydrug_sens.xls", sheet("Overall", modify) cell("`col'1") keepcellfmt firstrow(variables)
}
*Output tables as CSVs
import excel "$projectdir/output/tables/baseline_table_redact_bydrug_sens.xls", clear
export delimited using "$projectdir/output/tables/baseline_table_redact_bydrug_sens.csv" , replace
**2. Continous variables
clear *
save "$projectdir/output/tables/baseline_table_redact_mean_sens.dta", replace emptyok
use "$projectdir/output/data/sensitivity_analysis", clear
tab pre_drug_test drug
drop if covid_test_5d!=1 & drug >0
tab pre_drug_test drug
decode drug, gen(drug_str)
foreach var of varlist age bmi {
preserve
collapse (count) "`var'_count"=`var' (mean) mean=`var' (sd) stdev=`var' (median) median=`var' (p25) p25=`var' (p75) p75=`var', by(drug_str)
gen variable = "`var'"
rename *count freq
gen count_mid = (ceil(freq/6)*6) - (floor(6/2) * (freq!=0))
drop freq
order variable drug_str count mean stdev median p25 p75
list variable drug_str count mean stdev median p25 p75
append using "$projectdir/output/tables/baseline_table_redact_mean_sens.dta"
save "$projectdir/output/tables/baseline_table_redact_mean_sens.dta", replace
restore
preserve
collapse (count) "`var'_count"=`var' (mean) mean=`var' (sd) stdev=`var' (median) median=`var' (p25) p25=`var' (p75) p75=`var'
gen variable = "`var'"
rename *count freq
gen count_mid = (ceil(freq/6)*6) - (floor(6/2) * (freq!=0))
drop freq
gen drug_str = "all"
order variable drug_str count mean stdev median p25 p75
list variable drug_str count mean stdev median p25 p75
append using "$projectdir/output/tables/baseline_table_redact_mean_sens.dta"
save "$projectdir/output/tables/baseline_table_redact_mean_sens.dta", replace
restore
}
use "$projectdir/output/tables/baseline_table_redact_mean_sens.dta", clear
save "$projectdir/output/tables/baseline_table_redact_mean_sens.dta", replace
export delimited using "$projectdir/output/tables/baseline_table_redact_mean_sens.csv", replace
log close