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400_redacted_tables.do
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400_redacted_tables.do
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version 16
/*==============================================================================
DO FILE NAME: redacted output tables
PROJECT: EIA OpenSAFELY project
DATE: 07/03/2022
AUTHOR: J Galloway / M Russell
adapted from C Rentsch
DESCRIPTION OF FILE: redacted output table
DATASETS USED: main data file
DATASETS CREATED: redacted output table
OTHER OUTPUT: logfiles, printed to folder $Logdir
USER-INSTALLED ADO:
(place .ado file(s) in analysis folder)
==============================================================================*/
**Set filepaths
*global projectdir "C:\Users\Mark\OneDrive\PhD Project\OpenSAFELY\Github Practice"
*global projectdir "C:\Users\k1754142\OneDrive\PhD Project\OpenSAFELY\Github Practice"
global projectdir `c(pwd)'
di "$projectdir"
capture mkdir "$projectdir/output/data"
capture mkdir "$projectdir/output/tables"
capture mkdir "$projectdir/output/figures"
global logdir "$projectdir/logs"
di "$logdir"
**Open a log file
cap log close
log using "$logdir/redacted_tables.log", replace
**Set Ado file path
adopath + "$projectdir/analysis/extra_ados"
set scheme plotplainblind
**Set index dates ===========================================================*/
global year_preceding = "01/04/2018"
global start_date = "01/04/2019"
global end_date = "01/10/2023"
*Descriptive statistics======================================================================*/
**Baseline table for all EIA patients
clear *
save "$projectdir/output/data/table_1_rounded_all.dta", replace emptyok
use "$projectdir/output/data/file_eia_all_ehrQL.dta", clear
foreach var of varlist has_12m_post_appt has_6m_post_appt last_gp_prerheum_to21 last_gp_prerheum_to6m rheum_appt_to21 rheum_appt_to6m rheum_appt ckd chronic_liver_disease chronic_resp_disease cancer stroke chronic_cardiac_disease diabcatm hypertension smoke bmicat imd ethnicity male agegroup {
preserve
contract `var'
local v : variable label `var'
gen variable = `"`v'"'
decode `var', gen(categories)
gen count = round(_freq, 5)
egen total = total(count)
egen non_missing=sum(count) if categories!="Not known"
drop if categories=="Not known"
gen percent = round((count/non_missing)*100, 0.1)
gen missing=(total-non_missing)
order total, after(percent)
order missing, after(total)
gen countstr = string(count)
replace countstr = "<8" if count<=7
order countstr, after(count)
drop count
rename countstr count_all
tostring percent, gen(percentstr) force format(%9.1f)
replace percentstr = "-" if count =="<8"
order percentstr, after(percent)
drop percent
rename percentstr percent_all
gen totalstr = string(total)
replace totalstr = "-" if count =="<8"
order totalstr, after(total)
drop total
rename totalstr total_all
gen missingstr = string(missing)
replace missingstr = "-" if count =="<8"
order missingstr, after(missing)
drop missing
rename missingstr missing
list variable categories count percent total missing
keep variable categories count percent total missing
append using "$projectdir/output/data/table_1_rounded_all.dta"
save "$projectdir/output/data/table_1_rounded_all.dta", replace
restore
}
use "$projectdir/output/data/table_1_rounded_all.dta", clear
export excel "$projectdir/output/tables/table_1_rounded_bydiag.xls", replace sheet("Overall") keepcellfmt firstrow(variables)
**Baseline table for EIA subdiagnoses - tagged to above excel
use "$projectdir/output/data/file_eia_all_ehrQL.dta", clear
local index=0
levelsof eia_diag, local(levels)
foreach i of local levels {
clear *
save "$projectdir/output/data/table_1_rounded_`i'.dta", replace emptyok
di `index'
if `index'==0 {
local col = word("`c(ALPHA)'", `index'+6)
}
else if `index'>0 & `index'<=22 {
local col = word("`c(ALPHA)'", `index'+4)
}
di "`col'"
if `index'==0 {
local `index++'
local `index++'
local `index++'
local `index++'
local `index++'
local `index++'
}
else {
local `index++'
local `index++'
local `index++'
local `index++'
}
di `index'
use "$projectdir/output/data/file_eia_all_ehrQL.dta", clear
foreach var of varlist has_12m_post_appt has_6m_post_appt last_gp_prerheum_to21 last_gp_prerheum_to6m rheum_appt_to21 rheum_appt_to6m rheum_appt ckd chronic_liver_disease chronic_resp_disease cancer stroke chronic_cardiac_disease diabcatm hypertension smoke bmicat imd ethnicity male agegroup {
preserve
keep if eia_diag=="`i'"
contract `var'
local v : variable label `var'
gen variable = `"`v'"'
decode `var', gen(categories)
gen count = round(_freq, 5)
egen total = total(count)
egen non_missing=sum(count) if categories!="Not known"
drop if categories=="Not known"
gen percent = round((count/non_missing)*100, 0.1)
gen missing=(total-non_missing)
order total, after(percent)
order missing, after(total)
gen countstr = string(count)
replace countstr = "<8" if count<=7
order countstr, after(count)
drop count
rename countstr count_`i'
tostring percent, gen(percentstr) force format(%9.1f)
replace percentstr = "-" if count =="<8"
order percentstr, after(percent)
drop percent
rename percentstr percent_`i'
gen totalstr = string(total)
replace totalstr = "-" if count =="<8"
order totalstr, after(total)
drop total
rename totalstr total_`i'
gen missingstr = string(missing)
replace missingstr = "-" if count =="<8"
order missingstr, after(missing)
drop missing
rename missingstr missing_`i'
list count percent total missing
keep count percent total missing
append using "$projectdir/output/data/table_1_rounded_`i'.dta"
save "$projectdir/output/data/table_1_rounded_`i'.dta", replace
restore
}
display `index'
display "`col'"
use "$projectdir/output/data/table_1_rounded_`i'.dta", clear
export excel "$projectdir/output/tables/table_1_rounded_bydiag.xls", sheet("Overall", modify) cell("`col'1") keepcellfmt firstrow(variables)
}
**Table of mean outputs - full study period
clear *
save "$projectdir/output/data/table_mean_bydiag_rounded.dta", replace emptyok
use "$projectdir/output/data/file_eia_all_ehrQL.dta", clear
foreach var of varlist rheum_appt_count age {
preserve
collapse (count) "`var'_count"=`var' (mean) mean=`var' (sd) stdev=`var', by(eia_diagnosis)
gen varn = "`var'_count"
gen variable = substr(varn, 1, strpos(varn, "_count") - 1)
drop varn
rename *count freq
gen count = round(freq, 5)
decode eia_diagnosis, gen(diagnosis)
gen countstr = string(count)
replace countstr = "<8" if count<=7
order countstr, after(count)
drop count
rename countstr count
tostring mean, gen(meanstr) force format(%9.1f)
replace meanstr = "-" if count =="<8"
order meanstr, after(mean)
drop mean
rename meanstr mean
tostring stdev, gen(stdevstr) force format(%9.1f)
replace stdevstr = "-" if count =="<8"
order stdevstr, after(stdev)
drop stdev
rename stdevstr stdev
order count, first
order diagnosis, first
order variable, first
list variable diagnosis count mean stdev
keep variable diagnosis count mean stdev
append using "$projectdir/output/data/table_mean_bydiag_rounded.dta"
save "$projectdir/output/data/table_mean_bydiag_rounded.dta", replace
restore
preserve
collapse (count) "`var'_count"=`var' (mean) mean=`var' (sd) stdev=`var'
gen varn = "`var'_count"
gen variable = substr(varn, 1, strpos(varn, "_count") - 1)
drop varn
rename *count freq
gen count = round(freq, 5)
gen countstr = string(count)
replace countstr = "<8" if count<=7
order countstr, after(count)
drop count
rename countstr count
tostring mean, gen(meanstr) force format(%9.1f)
replace meanstr = "-" if count =="<8"
order meanstr, after(mean)
drop mean
rename meanstr mean
tostring stdev, gen(stdevstr) force format(%9.1f)
replace stdevstr = "-" if count =="<8"
order stdevstr, after(stdev)
drop stdev
rename stdevstr stdev
gen diagnosis = "Total"
order count, first
order diagnosis, first
order variable, first
list variable diagnosis count mean stdev
keep variable diagnosis count mean stdev
append using "$projectdir/output/data/table_mean_bydiag_rounded.dta"
save "$projectdir/output/data/table_mean_bydiag_rounded.dta", replace
restore
}
use "$projectdir/output/data/table_mean_bydiag_rounded.dta", clear
export excel "$projectdir/output/tables/table_mean_bydiag_rounded.xls", replace keepcellfmt firstrow(variables)
**Table of median/IQR outputs - full study period
clear *
save "$projectdir/output/data/table_median_bydiag_rounded.dta", replace emptyok
use "$projectdir/output/data/file_eia_all_ehrQL.dta", clear
foreach var of varlist time_gp_rheum_appt time_rheum_eia_code {
preserve
collapse (count) "`var'_count"=`var' (p50) p50_un=`var' (p25) p25_un=`var' (p75) p75_un=`var', by(eia_diagnosis)
gen varn = "`var'_count"
gen variable = substr(varn, 1, strpos(varn, "_count") - 1)
drop varn
rename *count freq
gen count = round(freq, 5)
gen p50 = round(p50_un, 1)
gen p25 = round(p25_un, 1)
gen p75 = round(p75_un, 1)
decode eia_diagnosis, gen(diagnosis)
order count, first
order diagnosis, first
order variable, first
list variable diagnosis count p50 p25 p75
keep variable diagnosis count p50 p25 p75
append using "$projectdir/output/data/table_median_bydiag_rounded.dta"
save "$projectdir/output/data/table_median_bydiag_rounded.dta", replace
restore
preserve
collapse (count) "`var'_count"=`var' (p50) p50_un=`var' (p25) p25_un=`var' (p75) p75_un=`var'
gen varn = "`var'_count"
gen variable = substr(varn, 1, strpos(varn, "_count") - 1)
drop varn
rename *count freq
gen count = round(freq, 5)
gen p50 = round(p50_un, 1)
gen p25 = round(p25_un, 1)
gen p75 = round(p75_un, 1)
gen diagnosis = "Total"
order count, first
order diagnosis, first
order variable, first
list variable diagnosis count p50 p25 p75
keep variable diagnosis count p50 p25 p75
append using "$projectdir/output/data/table_median_bydiag_rounded.dta"
save "$projectdir/output/data/table_median_bydiag_rounded.dta", replace
restore
}
use "$projectdir/output/data/table_median_bydiag_rounded.dta", clear
export excel "$projectdir/output/tables/table_median_bydiag_rounded.xls", replace keepcellfmt firstrow(variables)
**All below analyses are for those with rheum appt + GP appt + 6m+ of follow-up (changed from 12m requirement, for purposes of OpenSAFELY report)
**Table of median/IQR outputs - limited to those with 6m follow-up and rheum/GP appt
clear *
save "$projectdir/output/data/table_median_bydiag_rounded_to21.dta", replace emptyok
use "$projectdir/output/data/file_eia_all_ehrQL.dta", clear
keep if has_6m_post_appt==1
drop if appt_3m>16 | appt_3m==. //up to March 2023
foreach var of varlist time_to_csdmard time_gp_rheum_appt time_rheum_eia_code {
preserve
collapse (count) "`var'_count"=`var' (p50) p50_un=`var' (p25) p25_un=`var' (p75) p75_un=`var', by(eia_diagnosis)
gen varn = "`var'_count"
gen variable = substr(varn, 1, strpos(varn, "_count") - 1)
drop varn
rename *count freq
gen count = round(freq, 5)
gen p50 = round(p50_un, 1)
gen p25 = round(p25_un, 1)
gen p75 = round(p75_un, 1)
decode eia_diagnosis, gen(diagnosis)
order count, first
order diagnosis, first
order variable, first
list variable diagnosis count p50 p25 p75
keep variable diagnosis count p50 p25 p75
append using "$projectdir/output/data/table_median_bydiag_rounded_to21.dta"
save "$projectdir/output/data/table_median_bydiag_rounded_to21.dta", replace
restore
preserve
collapse (count) "`var'_count"=`var' (p50) p50_un=`var' (p25) p25_un=`var' (p75) p75_un=`var'
gen varn = "`var'_count"
gen variable = substr(varn, 1, strpos(varn, "_count") - 1)
drop varn
rename *count freq
gen count = round(freq, 5)
gen p50 = round(p50_un, 1)
gen p25 = round(p25_un, 1)
gen p75 = round(p75_un, 1)
gen diagnosis = "Total"
order count, first
order diagnosis, first
order variable, first
list variable diagnosis count p50 p25 p75
keep variable diagnosis count p50 p25 p75
append using "$projectdir/output/data/table_median_bydiag_rounded_to21.dta"
save "$projectdir/output/data/table_median_bydiag_rounded_to21.dta", replace
restore
}
use "$projectdir/output/data/table_median_bydiag_rounded_to21.dta", clear
export excel "$projectdir/output/tables/table_median_bydiag_rounded_to21.xls", replace sheet("Overall") keepcellfmt firstrow(variables)
**Table of median/IQR outputs by appt year - limited to those with 6m follow-up and rheum/GP appt - tagged to above excel
use "$projectdir/output/data/file_eia_all_ehrQL.dta", clear
keep if has_6m_post_appt==1
drop if appt_3m>16 | appt_3m==. //up to March 2023
recode appt_year 1=2019
recode appt_year 2=2020
recode appt_year 3=2021
recode appt_year 4=2022
recode appt_year 5=2023
local index=0
levelsof appt_year, local(levels)
foreach i of local levels {
clear *
save "$projectdir/output/data/table_median_bydiag_rounded_to21_`i'.dta", replace emptyok
di `index'
if `index'==0 {
local col = word("`c(ALPHA)'", `index'+7)
}
else if `index'>0 & `index'<=21 {
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 "$projectdir/output/data/file_eia_all_ehrQL.dta", clear
keep if has_6m_post_appt==1
drop if appt_3m>16 | appt_3m==. //up to March 2023
recode appt_year 1=2019
recode appt_year 2=2020
recode appt_year 3=2021
recode appt_year 4=2022
recode appt_year 5=2023
keep if appt_year==`i'
foreach var of varlist time_to_csdmard time_gp_rheum_appt time_rheum_eia_code {
preserve
collapse (count) freq=`var' (p50) p50_un=`var' (p25) p25_un=`var' (p75) p75_un=`var', by(eia_diagnosis)
gen count = round(freq, 5)
gen p50 = round(p50_un, 1)
gen p25 = round(p25_un, 1)
gen p75 = round(p75_un, 1)
drop p50_un p25_un p75_un
rename count count_`i'
rename p50 p50_`i'
rename p25 p25_`i'
rename p75 p75_`i'
order count, first
list count p50 p25 p75
keep count p50 p25 p75
append using "$projectdir/output/data/table_median_bydiag_rounded_to21_`i'.dta"
save "$projectdir/output/data/table_median_bydiag_rounded_to21_`i'.dta", replace
restore
preserve
collapse (count) freq=`var' (p50) p50_un=`var' (p25) p25_un=`var' (p75) p75_un=`var'
gen count = round(freq, 5)
gen p50 = round(p50_un, 1)
gen p25 = round(p25_un, 1)
gen p75 = round(p75_un, 1)
drop p50_un p25_un p75_un
rename count count_`i'
rename p50 p50_`i'
rename p25 p25_`i'
rename p75 p75_`i'
order count, first
list count p50 p25 p75
keep count p50 p25 p75
append using "$projectdir/output/data/table_median_bydiag_rounded_to21_`i'.dta"
save "$projectdir/output/data/table_median_bydiag_rounded_to21_`i'.dta", replace
restore
}
display `index'
display "`col'"
use "$projectdir/output/data/table_median_bydiag_rounded_to21_`i'.dta", clear
export excel "$projectdir/output/tables/table_median_bydiag_rounded_to21.xls", sheet("Overall", modify) cell("`col'1") keepcellfmt firstrow(variables)
}
**Table of median/IQR outputs - for OpenSAFELY Report (3 monthly periods) - limited to those with 6m follow-up and rheum/GP appt
clear *
save "$projectdir/output/data/table_median_bydiag_rounded_to21_report.dta", replace emptyok
use "$projectdir/output/data/file_eia_all_ehrQL.dta", clear
keep if has_6m_post_appt==1
drop if appt_3m>16 | appt_3m==. //up to March 2023
foreach var of varlist time_gp_rheum_appt {
preserve
collapse (count) "`var'_count"=`var' (p50) p50_un=`var', by(eia_diagnosis)
gen varn = "`var'_count"
gen variable = substr(varn, 1, strpos(varn, "_count") - 1)
drop varn
rename *count freq
gen count_all = round(freq, 5)
gen p50_all = round(p50_un, 1)
decode eia_diagnosis, gen(diagnosis)
order count, first
order diagnosis, first
order variable, first
list variable diagnosis count_all p50_all
keep variable diagnosis count_all p50_all
append using "$projectdir/output/data/table_median_bydiag_rounded_to21_report.dta"
save "$projectdir/output/data/table_median_bydiag_rounded_to21_report.dta", replace
restore
preserve
collapse (count) "`var'_count"=`var' (p50) p50_un=`var'
gen varn = "`var'_count"
gen variable = substr(varn, 1, strpos(varn, "_count") - 1)
drop varn
rename *count freq
gen count_all = round(freq, 5)
gen p50_all = round(p50_un, 1)
gen diagnosis = "Total"
order count, first
order diagnosis, first
order variable, first
list variable diagnosis count_all p50_all
keep variable diagnosis count_all p50_all
append using "$projectdir/output/data/table_median_bydiag_rounded_to21_report.dta"
save "$projectdir/output/data/table_median_bydiag_rounded_to21_report.dta", replace
restore
}
use "$projectdir/output/data/table_median_bydiag_rounded_to21_report.dta", clear
export excel "$projectdir/output/tables/table_median_bydiag_rounded_to21_report.xls", replace sheet("Overall") keepcellfmt firstrow(variables)
**Table of median/IQR outputs by appt year - for OpenSAFELY Report - limited to those with 6m follow-up and rheum/GP appt - tagged to above excel
use "$projectdir/output/data/file_eia_all_ehrQL.dta", clear
keep if has_6m_post_appt==1
drop if appt_3m>16 | appt_3m==. //up to March 2023
local index=0
levelsof appt_3m, local(levels)
foreach i of local levels {
clear *
save "$projectdir/output/data/table_median_bydiag_rounded_to21_report_`i'.dta", replace emptyok
di `index'
if `index'==0 {
local col = word("`c(ALPHA)'", `index'+5)
}
else if `index'>0 & `index'<=21 {
local col = word("`c(ALPHA)'", `index'+3)
}
else if `index'==22 {
local col = "Y"
}
else if `index'==24 {
local col = "AA"
}
else if `index'==26 {
local col = "AC"
}
else if `index'==28 {
local col = "AE"
}
else if `index'==30 {
local col = "AG"
}
else if `index'==32 {
local col = "AI"
}
di "`col'"
if `index'==0 {
local `index++'
local `index++'
local `index++'
local `index++'
}
else {
local `index++'
local `index++'
}
di `index'
use "$projectdir/output/data/file_eia_all_ehrQL.dta", clear
keep if has_6m_post_appt==1
drop if appt_3m>16 | appt_3m==. //up to March 2023
keep if appt_3m==`i'
foreach var of varlist time_gp_rheum_appt {
preserve
collapse (count) freq=`var' (p50) p50_un=`var', by(eia_diagnosis)
gen count = round(freq, 5)
gen p50 = round(p50_un, 1)
drop p50_un
rename count count_period`i'
rename p50 p50_period`i'
order count, first
list count p50
keep count p50
append using "$projectdir/output/data/table_median_bydiag_rounded_to21_report_`i'.dta"
save "$projectdir/output/data/table_median_bydiag_rounded_to21_report_`i'.dta", replace
restore
preserve
collapse (count) freq=`var' (p50) p50_un=`var'
gen count = round(freq, 5)
gen p50 = round(p50_un, 1)
drop p50_un
rename count count_period`i'
rename p50 p50_period`i'
order count, first
list count p50
keep count p50
append using "$projectdir/output/data/table_median_bydiag_rounded_to21_report_`i'.dta"
save "$projectdir/output/data/table_median_bydiag_rounded_to21_report_`i'.dta", replace
restore
}
display `index'
display "`col'"
use "$projectdir/output/data/table_median_bydiag_rounded_to21_report_`i'.dta", clear
export excel "$projectdir/output/tables/table_median_bydiag_rounded_to21_report.xls", sheet("Overall", modify) cell("`col'1") keepcellfmt firstrow(variables)
}
**ITSA outputs for appt delays - 6m+ only
clear *
save "$projectdir/output/data/ITSA_tables_rounded.dta", replace emptyok
use "$projectdir/output/data/file_eia_all_ehrQL.dta", clear
keep if has_6m_post_appt==1
drop if appt_3m>16 | appt_3m==. //up to March 2023
recode gp_appt_3w 2=0
lab var gp_appt_3w "Rheum appt within 3 weeks"
lab def gp_appt_3w 0 "No" 1 "Yes", modify
lab val gp_appt_3w gp_appt_3w
foreach var of varlist gp_appt_3w {
preserve
collapse (count) "`var'_count"=`var' (mean) mean=`var', by(mo_year_appt_s)
gen varn = "`var'_count"
gen variable = substr(varn, 1, strpos(varn, "_count") - 1)
drop varn
rename *count freq
gen count = round(freq, 5)
gen countstr = string(count)
replace countstr = "<8" if count<=7
order countstr, after(count)
drop count
rename countstr count
tostring mean, gen(meanstr) force format(%9.3f)
replace meanstr = "-" if count =="<8"
order meanstr, after(mean)
drop mean
rename meanstr mean_proportion
order count, first
order mo_year_appt_s, first
order variable, first
list variable mo_year_appt_s count mean_proportion
keep variable mo_year_appt_s count mean_proportion
append using "$projectdir/output/data/ITSA_tables_rounded.dta"
save "$projectdir/output/data/ITSA_tables_rounded.dta", replace
restore
preserve
collapse (count) "`var'_count"=`var' (mean) mean=`var'
gen varn = "`var'_count"
gen variable = substr(varn, 1, strpos(varn, "_count") - 1)
drop varn
rename *count freq
gen count = round(freq, 5)
gen countstr = string(count)
replace countstr = "<8" if count<=7
order countstr, after(count)
drop count
rename countstr count
tostring mean, gen(meanstr) force format(%9.3f)
replace meanstr = "-" if count =="<8"
order meanstr, after(mean)
drop mean
rename meanstr mean_proportion
gen mo_year_appt_s = "Overall"
order count, first
order mo_year_appt_s, first
order variable, first
list variable mo_year_appt_s count mean_proportion
keep variable mo_year_appt_s count mean_proportion
append using "$projectdir/output/data/ITSA_tables_rounded.dta"
save "$projectdir/output/data/ITSA_tables_rounded.dta", replace
restore
}
use "$projectdir/output/data/ITSA_tables_rounded.dta", clear
export excel "$projectdir/output/tables/ITSA_tables_appt_delay_rounded.xls", replace sheet ("GP to Appt") keepcellfmt firstrow(variables)
**ITSA outputs for csDMARDs - 6m+ only
clear *
save "$projectdir/output/data/ITSA_tables_rounded.dta", replace emptyok
use "$projectdir/output/data/file_eia_all_ehrQL.dta", clear
keep if has_6m_post_appt==1
drop if appt_3m>16 | appt_3m==. //up to March 2023
keep if ra_code==1 | psa_code==1 | undiff_code==1
foreach var of varlist csdmard_6m {
preserve
collapse (count) "`var'_count"=`var' (mean) mean=`var', by(mo_year_appt_s)
gen varn = "`var'_count"
gen variable = substr(varn, 1, strpos(varn, "_count") - 1)
drop varn
rename *count freq
gen count = round(freq, 5)
gen countstr = string(count)
replace countstr = "<8" if count<=7
order countstr, after(count)
drop count
rename countstr count
tostring mean, gen(meanstr) force format(%9.3f)
replace meanstr = "-" if count =="<8"
order meanstr, after(mean)
drop mean
rename meanstr mean_proportion
order count, first
order mo_year_appt_s, first
order variable, first
list variable mo_year_appt_s count mean_proportion
keep variable mo_year_appt_s count mean_proportion
append using "$projectdir/output/data/ITSA_tables_rounded.dta"
save "$projectdir/output/data/ITSA_tables_rounded.dta", replace
restore
preserve
collapse (count) "`var'_count"=`var' (mean) mean=`var'
gen varn = "`var'_count"
gen variable = substr(varn, 1, strpos(varn, "_count") - 1)
drop varn
rename *count freq
gen count = round(freq, 5)
gen countstr = string(count)
replace countstr = "<8" if count<=7
order countstr, after(count)
drop count
rename countstr count
tostring mean, gen(meanstr) force format(%9.3f)
replace meanstr = "-" if count =="<8"
order meanstr, after(mean)
drop mean
rename meanstr mean_proportion
gen mo_year_appt_s = "Overall"
order count, first
order mo_year_appt_s, first
order variable, first
list variable mo_year_appt_s count mean_proportion
keep variable mo_year_appt_s count mean_proportion
append using "$projectdir/output/data/ITSA_tables_rounded.dta"
save "$projectdir/output/data/ITSA_tables_rounded.dta", replace
restore
}
use "$projectdir/output/data/ITSA_tables_rounded.dta", clear
export excel "$projectdir/output/tables/ITSA_tables_csdmard_delay_rounded.xls", replace sheet("csDMARD delays") keepcellfmt firstrow(variables)
**csDMARD table for all EIA patients
clear *
save "$projectdir/output/data/drug_byyearanddisease_all.dta", replace emptyok
use "$projectdir/output/data/file_eia_all_ehrQL.dta", clear
keep if has_6m_post_appt==1
drop if appt_3m>16 | appt_3m==. //up to March 2023
keep if ra_code==1 | psa_code==1 | undiff_code==1
foreach var of varlist csdmard_time_22 csdmard_time_21 csdmard_time_20 csdmard_time_19 hcq_time ssz_time mtx_time csdmard_time {
preserve
contract `var'
local v : variable label `var'
gen variable = `"`v'"'
decode `var', gen(categories)
gen count = round(_freq, 5)
egen total = total(count)
gen percent = round((count/total)*100, 0.1)
order total, after(percent)
gen countstr = string(count)
replace countstr = "<8" if count<=7
order countstr, after(count)
drop count
rename countstr count_all
tostring percent, gen(percentstr) force format(%9.1f)
replace percentstr = "-" if count =="<8"
order percentstr, after(percent)
drop percent
rename percentstr percent_all
gen totalstr = string(total)
replace totalstr = "-" if count =="<8"
order totalstr, after(total)
drop total
rename totalstr total_all
list variable categories count percent total
keep variable categories count percent total
append using "$projectdir/output/data/drug_byyearanddisease_all.dta"
save "$projectdir/output/data/drug_byyearanddisease_all.dta", replace
restore
}
use "$projectdir/output/data/drug_byyearanddisease_all.dta", clear
export excel "$projectdir/output/tables/drug_byyearanddisease_rounded.xls", replace sheet("Overall") keepcellfmt firstrow(variables)
**Baseline table for EIA subdiagnoses - tagged to above excel
use "$projectdir/output/data/file_eia_all_ehrQL.dta", clear
keep if has_6m_post_appt==1
drop if appt_3m>16 | appt_3m==. //up to March 2023
keep if ra_code==1 | psa_code==1 | undiff_code==1
local index=0
levelsof eia_diag, local(levels)
foreach i of local levels {
clear *
save "$projectdir/output/data/drug_byyearanddisease_`i'.dta", replace emptyok
di `index'
if `index'==0 {
local col = word("`c(ALPHA)'", `index'+6)
}
else if `index'>0 & `index'<=21 {
local col = word("`c(ALPHA)'", `index'+4)
}
di "`col'"
if `index'==0 {
local `index++'
local `index++'
local `index++'
local `index++'
local `index++'
}
else {
local `index++'
local `index++'
local `index++'
}
di `index'
use "$projectdir/output/data/file_eia_all_ehrQL.dta", clear
keep if has_6m_post_appt==1
drop if appt_3m>16 | appt_3m==. //up to March 2023
keep if ra_code==1 | psa_code==1 | undiff_code==1
foreach var of varlist csdmard_time_22 csdmard_time_21 csdmard_time_20 csdmard_time_19 hcq_time ssz_time mtx_time csdmard_time {
preserve
keep if eia_diag=="`i'"
contract `var'
local v : variable label `var'
gen variable = `"`v'"'
decode `var', gen(categories)
gen count = round(_freq, 5)
egen total = total(count)
gen percent = round((count/total)*100, 0.1)
order total, after(percent)
gen countstr = string(count)
replace countstr = "<8" if count<=7
order countstr, after(count)
drop count
rename countstr count_`i'
tostring percent, gen(percentstr) force format(%9.1f)
replace percentstr = "-" if count =="<8"
order percentstr, after(percent)
drop percent
rename percentstr percent_`i'
gen totalstr = string(total)
replace totalstr = "-" if count =="<8"
order totalstr, after(total)
drop total
rename totalstr total_`i'
list count percent total
keep count percent total
append using "$projectdir/output/data/drug_byyearanddisease_`i'.dta"
save "$projectdir/output/data/drug_byyearanddisease_`i'.dta", replace
restore
}
use "$projectdir/output/data/drug_byyearanddisease_`i'.dta", clear
export excel "$projectdir/output/tables/drug_byyearanddisease_rounded.xls", sheet("Overall", modify) cell("`col'1") keepcellfmt firstrow(variables)
}
**First csDMARD table for all EIA patients (removed leflunomide for OpenSAFELY report due to small counts with more granular time periods)
clear *
save "$projectdir/output/data/first_csdmard.dta", replace emptyok
use "$projectdir/output/data/file_eia_all_ehrQL.dta", clear
keep if has_6m_post_appt==1
drop if appt_3m>16 | appt_3m==. //up to March 2023
drop if first_csDMARD==""
keep if ra_code==1 | psa_code==1 | undiff_code==1
foreach var of varlist first_csDMARD {
preserve
contract `var'
gen count = round(_freq, 5)
egen total = total(count)
gen percent = round((count/total)*100, 0.1)
order total, after(percent)
gen countstr = string(count)
replace countstr = "<8" if count<=7
order countstr, after(count)
drop count
rename countstr count_all
tostring percent, gen(percentstr) force format(%9.1f)
replace percentstr = "-" if count =="<8"
order percentstr, after(percent)
drop percent
rename percentstr percent_all
gen totalstr = string(total)
replace totalstr = "-" if count =="<8"
order totalstr, after(total)
drop total
rename totalstr total_all
list first_csDMARD count percent total
keep first_csDMARD count percent total
append using "$projectdir/output/data/first_csdmard.dta"
save "$projectdir/output/data/first_csdmard.dta", replace
restore
}
use "$projectdir/output/data/first_csdmard.dta", clear
export excel "$projectdir/output/tables/first_csdmard_rounded.xls", replace sheet("Overall") keepcellfmt firstrow(variables)
**First csDMARD table for EIA subdiagnoses - tagged to above excel
use "$projectdir/output/data/file_eia_all_ehrQL.dta", clear
keep if has_6m_post_appt==1
drop if appt_3m>16 | appt_3m==. //up to March 2023
drop if first_csDMARD==""
keep if ra_code==1 | psa_code==1 | undiff_code==1
recode appt_year 1=2019
recode appt_year 2=2020
recode appt_year 3=2021
recode appt_year 4=2022
recode appt_year 5=2023
local index=0
levelsof appt_year, local(levels)
foreach i of local levels {
clear *
save "$projectdir/output/data/first_csdmard_`i'.dta", replace emptyok
di `index'
if `index'==0 {
local col = word("`c(ALPHA)'", `index'+5)
}
else if `index'>0 & `index'<=21 {
local col = word("`c(ALPHA)'", `index'+4)
}
di "`col'"
if `index'==0 {
local `index++'
local `index++'
local `index++'
local `index++'
}
else {
local `index++'
local `index++'
local `index++'
}
di `index'
use "$projectdir/output/data/file_eia_all_ehrQL.dta", clear
keep if has_6m_post_appt==1
drop if appt_3m>16 | appt_3m==. //up to March 2023
drop if first_csDMARD==""
keep if ra_code==1 | psa_code==1 | undiff_code==1
recode appt_year 1=2019
recode appt_year 2=2020
recode appt_year 3=2021
recode appt_year 4=2022
recode appt_year 5=2023
foreach var of varlist first_csDMARD {
preserve
keep if appt_year==`i'
contract `var'
gen count = round(_freq, 5)
egen total = total(count)
gen percent = round((count/total)*100, 0.1)
order total, after(percent)
gen countstr = string(count)
replace countstr = "<8" if count<=7
order countstr, after(count)
drop count
rename countstr count_`i'
tostring percent, gen(percentstr) force format(%9.1f)
replace percentstr = "-" if count =="<8"
order percentstr, after(percent)
drop percent
rename percentstr percent_`i'
gen totalstr = string(total)
replace totalstr = "-" if count =="<8"
order totalstr, after(total)
drop total
rename totalstr total_`i'
list count percent total
keep count percent total
append using "$projectdir/output/data/first_csdmard_`i'.dta"
save "$projectdir/output/data/first_csdmard_`i'.dta", replace
restore
}
display `index'
display "`col'"
use "$projectdir/output/data/first_csdmard_`i'.dta", clear
export excel "$projectdir/output/tables/first_csdmard_rounded.xls", sheet("Overall", modify) cell("`col'1") keepcellfmt firstrow(variables)
}
**First csDMARD table for all EIA patients - version used for report (removed leflunomide due to small counts with more granular time periods)
clear *
save "$projectdir/output/data/first_csdmard_report.dta", replace emptyok
use "$projectdir/output/data/file_eia_all_ehrQL.dta", clear
keep if has_6m_post_appt==1
drop if appt_3m>16 | appt_3m==. //up to March 2023
drop if first_csDMARD==""
keep if ra_code==1 | psa_code==1 | undiff_code==1
foreach var of varlist first_csDMARD {
preserve
contract `var'
gen count = round(_freq, 5)
egen total = total(count)
gen percent = round((count/total)*100, 0.1)
order total, after(percent)
gen countstr = string(count)
replace countstr = "<8" if count<=7
order countstr, after(count)
drop count
rename countstr count_all
tostring percent, gen(percentstr) force format(%9.1f)
replace percentstr = "-" if count =="<8"
order percentstr, after(percent)
drop percent
rename percentstr percent_all
gen totalstr = string(total)