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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
codebook
* 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 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 {
capture confirm string variable `var'
if _rc==0 {
rename `var' a
gen `var' = date(a, "YMD")
drop a
format %td `var'
sum `var',f
sum `var' if covid_therapeutics!="" ,f
sum `var' if covid_therapeutics_hosp!="" ,f
}
}
*the following date variables had no observation*
*hiv_aids_nhsd_icd10
*transplant_all_y_codes_opcs4
*transplant_thymus_opcs4
*transplant_conjunctiva_y_code_op
*transplant_conjunctiva_opcs4
*transplant_stomach_opcs4
*transplant_ileum_1_Y_codes_opcs4
*transplant_ileum_2_Y_codes_opcs4
*transplant_ileum_1_opcs4
*transplant_ileum_2_opcs4
tab covid_therapeutics
tab registered_treated
tab covid_therapeutics_hosp
tab registered_treated_hosp
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!=""
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