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data_preparation_and_descriptives_feasibility.do
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data_preparation_and_descriptives_feasibility.do
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********************************************************************************
*
* Do-file: data_preparation_and_descriptives.do
*
* Project: sotrovimab-and-Paxlovid
*
* Programmed by: Bang Zheng
*
* Data used: output/input.csv
*
* Data created: output/main.dta (main analysis dataset)
*
* Other output: logs/data_preparation.log
*
********************************************************************************
*
* Purpose: This do-file creates the variables required for the
* main analysis and saves into Stata dataset, and describes
* variables by drug groups.
*
********************************************************************************
* Open a log file
cap log close
log using ./logs/data_preparation_feasibility, replace t
clear
* import dataset
import delimited ./output/input_feasibility.csv, delimiter(comma) varnames(1) case(preserve)
*describe
keep if covid_test_positive_date!=""
* Convert strings to dates *
foreach var of varlist covid_test_positive_date covid_test_positive_date2 covid_hosp_not_pri_admission covid_hosp_not_pri_admission2 covid_hosp_admission covid_hosp_admission2 ///
sotrovimab_GP paxlovid_GP molnupiravir_GP remdesivir_GP ///
date_treated_GP sotrovimab_covid_therapeutics_o paxlovid_covid_therapeutics_o molnupiravir_covid_therapeutics_ remdesivir_covid_therapeutics_o casirivimab_covid_therapeutics_o ///
date_treated_out death_with_covid_date death_date all_hosp_admission all_hosp_admission2 date_treated date_treated_hosp {
capture confirm string variable `var'
if _rc==0 {
rename `var' a
gen `var' = date(a, "YMD")
drop a
format %td `var'
sum `var',f de
}
}
log close
exit, clear
gen infect_month=month(covid_test_positive_date)
tab infect_month
gen infect_month2=month(covid_test_positive_date2)
tab infect_month2
tab region_nhs,m
tab region_nhs infect_month, row
tab region_nhs infect_month2, row
tab stp,m
tab stp infect_month, row
tab stp infect_month2, row
gen sotro_month_o=month(sotrovimab_covid_therapeutics_o)
gen pax_month_o=month(paxlovid_covid_therapeutics_o)
gen mol_month_o=month(molnupiravir_covid_therapeutics_)
gen rem_month_o=month(remdesivir_covid_therapeutics_o)
gen treated_month_o=month(date_treated_out)
tab sotro_month_o
tab pax_month_o
tab mol_month_o
tab rem_month_o
tab treated_month_o
tab region_nhs sotro_month_o, row
tab region_nhs pax_month_o, row
tab region_nhs mol_month_o, row
tab region_nhs rem_month_o, row
tab region_nhs treated_month_o, row
tab stp treated_month_o,row
gen sotro_month_GP=month(sotrovimab_GP)
gen pax_month_GP=month(paxlovid_GP)
gen mol_month_GP=month(molnupiravir_GP)
gen rem_month_GP=month(remdesivir_GP)
gen treated_month_GP=month(date_treated_GP)
tab sotro_month_GP
tab pax_month_GP
tab mol_month_GP
tab rem_month_GP
tab treated_month_GP
tab region_nhs sotro_month_GP, row
tab region_nhs pax_month_GP, row
tab region_nhs mol_month_GP, row
tab region_nhs rem_month_GP, row
tab region_nhs treated_month_GP, row
tab stp treated_month_GP,row
gen sotro_month=min(sotro_month_o,sotro_month_GP)
gen pax_month=min(pax_month_o,pax_month_GP)
gen mol_month=min(mol_month_o,mol_month_GP)
gen rem_month=min(rem_month_o,rem_month_GP)
gen treated_month=min(treated_month_o,treated_month_GP)
tab sotro_month
tab pax_month
tab mol_month
tab rem_month
tab treated_month
tab region_nhs sotro_month, row
tab region_nhs pax_month, row
tab region_nhs mol_month, row
tab region_nhs rem_month, row
tab region_nhs treated_month, row
tab stp treated_month,row
gen covid_hosp_not_pri_month=month(covid_hosp_not_pri_admission)
tab covid_hosp_not_pri_month
tab region_nhs covid_hosp_not_pri_month,row
tab stp covid_hosp_not_pri_month,row
gen covid_hosp_month=month(covid_hosp_admission)
tab covid_hosp_month
tab region_nhs covid_hosp_month,row
tab stp covid_hosp_month,row
gen all_hosp_admission_month=month(all_hosp_admission)
tab all_hosp_admission_month
tab region_nhs all_hosp_admission_month,row
tab stp all_hosp_admission_month,row
gen all_hosp_admission_month2=month(all_hosp_admission2)
tab all_hosp_admission_month2
tab region_nhs all_hosp_admission_month2,row
tab stp all_hosp_admission_month2,row
gen death_with_covid_month=month(death_with_covid_date)
tab death_with_covid_month
tab region_nhs death_with_covid_month,row
tab stp death_with_covid_month,row
gen death_month=month(death_date)
tab death_month
tab region_nhs death_month,row
tab stp death_month,row
clear
* import dataset
import delimited ./output/input_feasibility.csv, delimiter(comma) varnames(1) case(preserve)
*describe
keep if date_treated_GP!="" | date_treated_out!=""
* Convert strings to dates *
foreach var of varlist covid_test_positive_date covid_test_positive_date2 sotrovimab_GP paxlovid_GP molnupiravir_GP remdesivir_GP ///
date_treated_GP sotrovimab_covid_therapeutics_o paxlovid_covid_therapeutics_o molnupiravir_covid_therapeutics_ remdesivir_covid_therapeutics_o casirivimab_covid_therapeutics_o ///
date_treated_out {
capture confirm string variable `var'
if _rc==0 {
rename `var' a
gen `var' = date(a, "YMD")
drop a
format %td `var'
sum `var',f
}
}
gen infect_month=month(covid_test_positive_date)
tab infect_month
gen infect_month2=month(covid_test_positive_date2)
tab infect_month2
tab region_nhs,m
tab region_nhs infect_month, row
tab region_nhs infect_month2, row
tab stp,m
tab stp infect_month, row
tab stp infect_month2, row
gen sotro_month_o=month(sotrovimab_covid_therapeutics_o)
gen pax_month_o=month(paxlovid_covid_therapeutics_o)
gen mol_month_o=month(molnupiravir_covid_therapeutics_)
gen rem_month_o=month(remdesivir_covid_therapeutics_o)
gen treated_month_o=month(date_treated_out)
tab sotro_month_o
tab pax_month_o
tab mol_month_o
tab rem_month_o
tab treated_month_o
tab region_nhs sotro_month_o, row
tab region_nhs pax_month_o, row
tab region_nhs mol_month_o, row
tab region_nhs rem_month_o, row
tab region_nhs treated_month_o, row
tab stp treated_month_o,row
gen sotro_month_GP=month(sotrovimab_GP)
gen pax_month_GP=month(paxlovid_GP)
gen mol_month_GP=month(molnupiravir_GP)
gen rem_month_GP=month(remdesivir_GP)
gen treated_month_GP=month(date_treated_GP)
tab sotro_month_GP
tab pax_month_GP
tab mol_month_GP
tab rem_month_GP
tab treated_month_GP
tab region_nhs sotro_month_GP, row
tab region_nhs pax_month_GP, row
tab region_nhs mol_month_GP, row
tab region_nhs rem_month_GP, row
tab region_nhs treated_month_GP, row
tab stp treated_month_GP,row
gen sotro_month=min(sotro_month_o,sotro_month_GP)
gen pax_month=min(pax_month_o,pax_month_GP)
gen mol_month=min(mol_month_o,mol_month_GP)
gen rem_month=min(rem_month_o,rem_month_GP)
gen treated_month=min(treated_month_o,treated_month_GP)
tab sotro_month
tab pax_month
tab mol_month
tab rem_month
tab treated_month
tab region_nhs sotro_month, row
tab region_nhs pax_month, row
tab region_nhs mol_month, row
tab region_nhs rem_month, row
tab region_nhs treated_month, row
tab stp treated_month,row
by treated_month, sort: count if infect_month==treated_month|infect_month==(treated_month-1)
clear
* import dataset
import delimited ./output/input_feasibility.csv, delimiter(comma) varnames(1) case(preserve)
*describe
keep if all_hosp_admission!=""
* Convert strings to dates *
foreach var of varlist covid_test_positive_date covid_test_positive_date2 covid_hosp_not_pri_admission covid_hosp_not_pri_admission2 covid_hosp_admission covid_hosp_admission2 ///
all_hosp_admission all_hosp_admission2 {
capture confirm string variable `var'
if _rc==0 {
rename `var' a
gen `var' = date(a, "YMD")
drop a
format %td `var'
sum `var',f
}
}
gen covid_hosp_not_pri_month=month(covid_hosp_not_pri_admission)
tab covid_hosp_not_pri_month
tab region_nhs covid_hosp_not_pri_month,row
tab stp covid_hosp_not_pri_month,row
gen covid_hosp_month=month(covid_hosp_admission)
tab covid_hosp_month
tab region_nhs covid_hosp_month,row
tab stp covid_hosp_month,row
gen all_hosp_admission_month=month(all_hosp_admission)
tab all_hosp_admission_month
tab region_nhs all_hosp_admission_month,row
tab stp all_hosp_admission_month,row
gen all_hosp_admission_month2=month(all_hosp_admission2)
tab all_hosp_admission_month2
tab region_nhs all_hosp_admission_month2,row
tab stp all_hosp_admission_month2,row
gen infect_month=month(covid_test_positive_date)
by covid_hosp_not_pri_month, sort: count if infect_month==covid_hosp_not_pri_month|infect_month==(covid_hosp_not_pri_month-1)
clear
* import dataset
import delimited ./output/input_feasibility.csv, delimiter(comma) varnames(1) case(preserve)
*describe
keep if death_date!=""
* Convert strings to dates *
foreach var of varlist death_with_covid_date death_date {
capture confirm string variable `var'
if _rc==0 {
rename `var' a
gen `var' = date(a, "YMD")
drop a
format %td `var'
sum `var',f
}
}
gen death_with_covid_month=month(death_with_covid_date)
tab death_with_covid_month
tab region_nhs death_with_covid_month,row
tab stp death_with_covid_month,row
gen death_month=month(death_date)
tab death_month
tab region_nhs death_month,row
tab stp death_month,row
log close
exit, clear
*codebook
keep if date_treated!=""|date_treated_hosp!=""|all_hosp_admission!=""
* Convert strings to dates *
foreach var of varlist sotrovimab_covid_therapeutics molnupiravir_covid_therapeutics paxlovid_covid_therapeutics remdesivir_covid_therapeutics ///
casirivimab_covid_therapeutics tocilizumab_covid_therapeutics sarilumab_covid_therapeutics baricitinib_covid_hosp date_treated ///
sotrovimab_covid_hosp paxlovid_covid_hosp molnupiravir_covid_hosp remdesivir_covid_hosp casirivimab_covid_hosp tocilizumab_covid_hosp sarilumab_covid_hosp ///
date_treated_hosp start_date death_with_covid_date death_with_covid_underly_date death_date covid_hosp_not_pri_admission covid_hosp_not_pri_discharge ///
covid_hosp_not_pri_admission2 covid_hosp_not_pri_discharge2 covid_hosp_admission covid_hosp_discharge covid_hosp_admission2 covid_hosp_discharge2 ///
all_hosp_admission all_hosp_discharge all_hosp_admission2 all_hosp_discharge2 all_hosp_admission_onset covid_hosp_admission_onset covid_hosp_not_pri_onset ///
all_hosp_admission_hosp covid_hosp_admission_hosp covid_hosp_not_pri_hosp covid_test_positive_date covid_test_positive_date2 covid_test_positive_onset ///
covid_test_positive_hosp covid_test_positive_all_hosp covid_test_positive_all_hosp2 covid_test_positive_covid_hosp covid_test_positive_covid_hosp2 ///
covid_test_positive_not_pri covid_test_positive_not_pri2 {
capture confirm string variable `var'
if _rc==0 {
rename `var' a
gen `var' = date(a, "YMD")
drop a
format %td `var'
sum `var',f
}
}
tab covid_therapeutics
tab registered_treated
tab covid_therapeutics_hosp
tab registered_treated_hosp
tab covid_therapeutics if date_treated>=mdy(12,16,2021)
tab covid_therapeutics_hosp if date_treated_hosp>=mdy(12,16,2021)
tab high_risk_cohort_covid_therapeut
tab high_risk_cohort_covid_therapeut if covid_therapeutics!=""
tab high_risk_cohort_covid_therapeut if covid_therapeutics_hosp!=""
*check hosp records*
gen treated_onset=(date_treated!=.)
gen treated_hosp=(date_treated_hosp!=.)
count if treated_onset==1&((date_treated>=covid_hosp_not_pri_admission&date_treated<=covid_hosp_not_pri_discharge)|(date_treated>=covid_hosp_not_pri_admission2&date_treated<=covid_hosp_not_pri_discharge2))
count if treated_onset==1&((date_treated>=covid_hosp_admission&date_treated<=covid_hosp_discharge)|(date_treated>=covid_hosp_admission2&date_treated<=covid_hosp_discharge2))
count if treated_onset==1&((date_treated>=all_hosp_admission&date_treated<=all_hosp_discharge)|(date_treated>=all_hosp_admission2&date_treated<=all_hosp_discharge2))
count if treated_onset==1&(((date_treated+1)>=covid_hosp_not_pri_admission&(date_treated-1)<=covid_hosp_not_pri_discharge)|((date_treated+1)>=covid_hosp_not_pri_admission2&(date_treated-1)<=covid_hosp_not_pri_discharge2))
count if treated_onset==1&(((date_treated+3)>=covid_hosp_not_pri_admission&(date_treated-3)<=covid_hosp_not_pri_discharge)|((date_treated+3)>=covid_hosp_not_pri_admission2&(date_treated-3)<=covid_hosp_not_pri_discharge2))
count if treated_onset==1&(((date_treated+1)>=covid_hosp_admission&(date_treated-1)<=covid_hosp_discharge)|((date_treated+1)>=covid_hosp_admission2&(date_treated-1)<=covid_hosp_discharge2))
count if treated_onset==1&(((date_treated+3)>=covid_hosp_admission&(date_treated-3)<=covid_hosp_discharge)|((date_treated+3)>=covid_hosp_admission2&(date_treated-3)<=covid_hosp_discharge2))
count if treated_onset==1&all_hosp_admission_onset!=.
count if treated_onset==1&covid_hosp_admission_onset!=.
count if treated_onset==1&covid_hosp_not_pri_onset!=.
count if treated_hosp==1&((date_treated_hosp>=covid_hosp_not_pri_admission&date_treated_hosp<=covid_hosp_not_pri_discharge)|(date_treated_hosp>=covid_hosp_not_pri_admission2&date_treated_hosp<=covid_hosp_not_pri_discharge2))
count if treated_hosp==1&((date_treated_hosp>=covid_hosp_admission&date_treated_hosp<=covid_hosp_discharge)|(date_treated_hosp>=covid_hosp_admission2&date_treated_hosp<=covid_hosp_discharge2))
count if treated_hosp==1&((date_treated_hosp>=all_hosp_admission&date_treated_hosp<=all_hosp_discharge)|(date_treated_hosp>=all_hosp_admission2&date_treated_hosp<=all_hosp_discharge2))
count if treated_hosp==1&(((date_treated_hosp+1)>=covid_hosp_not_pri_admission&(date_treated_hosp-1)<=covid_hosp_not_pri_discharge)|((date_treated_hosp+1)>=covid_hosp_not_pri_admission2&(date_treated_hosp-1)<=covid_hosp_not_pri_discharge2))
count if treated_hosp==1&(((date_treated_hosp+3)>=covid_hosp_not_pri_admission&(date_treated_hosp-3)<=covid_hosp_not_pri_discharge)|((date_treated_hosp+3)>=covid_hosp_not_pri_admission2&(date_treated_hosp-3)<=covid_hosp_not_pri_discharge2))
count if treated_hosp==1&(((date_treated_hosp+1)>=covid_hosp_admission&(date_treated_hosp-1)<=covid_hosp_discharge)|((date_treated_hosp+1)>=covid_hosp_admission2&(date_treated_hosp-1)<=covid_hosp_discharge2))
count if treated_hosp==1&(((date_treated_hosp+3)>=covid_hosp_admission&(date_treated_hosp-3)<=covid_hosp_discharge)|((date_treated_hosp+3)>=covid_hosp_admission2&(date_treated_hosp-3)<=covid_hosp_discharge2))
count if treated_hosp==1&all_hosp_admission_hosp!=.
count if treated_hosp==1&covid_hosp_admission_hosp!=.
count if treated_hosp==1&covid_hosp_not_pri_hosp!=.
*check covid test*
count if treated_onset==1&covid_test_positive_onset!=.
count if treated_hosp==1&covid_test_positive_hosp!=.
*distinguish onset and hosp*
tab treated_onset if start_date!=.&((start_date>=covid_hosp_not_pri_admission&start_date<=covid_hosp_not_pri_discharge)|(start_date>=covid_hosp_not_pri_admission2&start_date<=covid_hosp_not_pri_discharge2))
tab treated_onset if start_date!=.&((start_date>=covid_hosp_admission&start_date<=covid_hosp_discharge)|(start_date>=covid_hosp_admission2&start_date<=covid_hosp_discharge2))
tab treated_hosp if start_date!=.&((start_date>=covid_hosp_not_pri_admission&start_date<=covid_hosp_not_pri_discharge)|(start_date>=covid_hosp_not_pri_admission2&start_date<=covid_hosp_not_pri_discharge2))
tab treated_hosp if start_date!=.&((start_date>=covid_hosp_admission&start_date<=covid_hosp_discharge)|(start_date>=covid_hosp_admission2&start_date<=covid_hosp_discharge2))
tab treated_onset if start_date!=.&((start_date>=covid_hosp_not_pri_admission&start_date<=covid_hosp_not_pri_discharge&covid_test_positive_not_pri>covid_hosp_not_pri_admission)|(start_date>=covid_hosp_not_pri_admission2&start_date<=covid_hosp_not_pri_discharge2&covid_test_positive_not_pri2>covid_hosp_not_pri_admission2))
tab treated_onset if start_date!=.&((start_date>=covid_hosp_admission&start_date<=covid_hosp_discharge&covid_test_positive_covid_hosp>covid_hosp_admission)|(start_date>=covid_hosp_admission2&start_date<=covid_hosp_discharge2&covid_test_positive_covid_hosp2>covid_hosp_admission2))
tab treated_onset if start_date!=.&((start_date>=all_hosp_admission&start_date<=all_hosp_discharge&covid_test_positive_all_hosp>all_hosp_admission)|(start_date>=all_hosp_admission2&start_date<=all_hosp_discharge2&covid_test_positive_all_hosp2>all_hosp_admission2))
tab treated_onset if start_date!=.&((start_date>=covid_hosp_not_pri_admission&start_date<=covid_hosp_not_pri_discharge&covid_test_positive_not_pri>covid_hosp_not_pri_admission&covid_test_positive_not_pri!=.)|(start_date>=covid_hosp_not_pri_admission2&start_date<=covid_hosp_not_pri_discharge2&covid_test_positive_not_pri2>covid_hosp_not_pri_admission2&covid_test_positive_not_pri2!=.))
tab treated_onset if start_date!=.&((start_date>=covid_hosp_admission&start_date<=covid_hosp_discharge&covid_test_positive_covid_hosp>covid_hosp_admission&covid_test_positive_covid_hosp!=.)|(start_date>=covid_hosp_admission2&start_date<=covid_hosp_discharge2&covid_test_positive_covid_hosp2>covid_hosp_admission2&covid_test_positive_covid_hosp2!=.))
tab treated_onset if start_date!=.&((start_date>=all_hosp_admission&start_date<=all_hosp_discharge&covid_test_positive_all_hosp>all_hosp_admission&covid_test_positive_all_hosp!=.)|(start_date>=all_hosp_admission2&start_date<=all_hosp_discharge2&covid_test_positive_all_hosp2>all_hosp_admission2&covid_test_positive_all_hosp2!=.))
tab treated_hosp if start_date!=.&((start_date>=covid_hosp_not_pri_admission&start_date<=covid_hosp_not_pri_discharge&covid_test_positive_not_pri<=covid_hosp_not_pri_admission)|(start_date>=covid_hosp_not_pri_admission2&start_date<=covid_hosp_not_pri_discharge2&covid_test_positive_not_pri2<=covid_hosp_not_pri_admission2))
tab treated_hosp if start_date!=.&((start_date>=covid_hosp_admission&start_date<=covid_hosp_discharge&covid_test_positive_covid_hosp<=covid_hosp_admission)|(start_date>=covid_hosp_admission2&start_date<=covid_hosp_discharge2&covid_test_positive_covid_hosp2<=covid_hosp_admission2))
tab treated_hosp if start_date!=.&((start_date>=all_hosp_admission&start_date<=all_hosp_discharge&covid_test_positive_all_hosp<=all_hosp_admission)|(start_date>=all_hosp_admission2&start_date<=all_hosp_discharge2&covid_test_positive_all_hosp2<=all_hosp_admission2))
count if tocilizumab_covid_hosp!=.&death_with_covid_date!=.
count if sarilumab_covid_hosp!=.&death_with_covid_date!=.
count if tocilizumab_covid_hosp!=.&death_date!=.
count if sarilumab_covid_hosp!=.&death_date!=.
*check hosp/death event date range*
*codebook covid_hosp_outcome_date2 hospitalisation_outcome_date2 death_date
*exclusion criteria*
log close