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anaphylaxis_untreated.do
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anaphylaxis_untreated.do
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********************************************************************************
*
* Do-file: data preparation and descriptives.do
*
* Project: sotrovimab-and-molnupiravir
*
* 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/anaphylaxis_untreated, replace t
clear
* import dataset
import delimited ./output/input_anaphylaxis_untreated.csv, delimiter(comma) varnames(1) case(preserve)
*codebook
drop if cancer_opensafely_snomed_new==""&immunosuppresant_drugs_nhsd==""&oral_steroid_drugs_nhsd==""&immunosupression_nhsd_new==""&solid_organ_transplant_nhsd_new==""&downs_syndrome_nhsd==""&haematological_disease_nhsd==""&ckd_stage_5_nhsd==""&liver_disease_nhsd==""&hiv_aids_nhsd==""&multiple_sclerosis_nhsd==""&motor_neurone_disease_nhsd==""&myasthenia_gravis_nhsd==""&huntingtons_disease_nhsd==""
* Convert strings to dates *
foreach var of varlist sotrovimab_covid_therapeutics molnupiravir_covid_therapeutics paxlovid_covid_therapeutics remdesivir_covid_therapeutics ///
casirivimab_covid_therapeutics date_treated start_date ///
death_date dereg_date last_vaccination_date ///
cancer_opensafely_snomed_new immunosuppresant_drugs_nhsd ///
oral_steroid_drugs_nhsd immunosupression_nhsd_new solid_organ_transplant_nhsd_new ///
downs_syndrome_nhsd haematological_disease_nhsd ckd_stage_5_nhsd liver_disease_nhsd hiv_aids_nhsd ///
multiple_sclerosis_nhsd motor_neurone_disease_nhsd myasthenia_gravis_nhsd huntingtons_disease_nhsd ///
death_with_anaphylaxis_date death_with_anaph_underly_date death_with_anaphylaxis_date2 ///
death_with_anaph_underly_date2 death_with_anaphylaxis_date3 death_with_anaphylaxis_date_pre death_with_anaph_underly_date_pr hospitalisation_anaph ///
hosp_discharge_anaph hospitalisation_anaph_underly hospitalisation_anaph2 hospitalisation_anaph_underly2 hospitalisation_anaph3 hospitalisation_anaph_pre ///
hosp_anaph_underly_pre AE_anaph AE_anaph2 AE_anaph3 AE_anaph4 AE_anaph_pre AE_anaph2_pre GP_anaph GP_anaph2 GP_anaph_pre GP_anaph2_pre {
capture confirm string variable `var'
if _rc==0 {
rename `var' a
gen `var' = date(a, "YMD")
drop a
format %td `var'
}
}
*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
*describe
*check hosp/death event date range*
codebook hospitalisation_anaph AE_anaph death_date last_vaccination_date
codebook hospitalisation_anaph AE_anaph death_date last_vaccination_date if registered_eligible==0
keep if registered_eligible==1
*describe COVID therapy*
gen treated=(date_treated!=.)
keep if treated==0
*exclusion criteria*
sum age,de
*keep if age>=18 & age<110
tab sex,m
*keep if sex=="F"|sex=="M"
tab has_died,m
*keep if has_died==0
*tab registered_eligible,m
*keep if registered_eligible==1
*tab covid_test_positive covid_positive_previous_30_days,m
*keep if covid_test_positive==1 & covid_positive_previous_30_days==0
*drop if primary_covid_hospital_discharge!=.|primary_covid_hospital_admission!=.
*drop if any_covid_hospital_admission_dat!=.|any_covid_hospital_discharge_dat!=.
keep if start_date>=mdy(12,16,2021)&start_date<=mdy(01,28,2023)
*10 high risk groups: downs_syndrome, solid_cancer, haematological_disease, renal_disease, liver_disease, imid,
*immunosupression, hiv_aids, solid_organ_transplant, rare_neurological_conditions, high_risk_group_combined
replace oral_steroid_drugs_nhsd=. if oral_steroid_drug_nhsd_3m_count < 2 & oral_steroid_drug_nhsd_12m_count < 4
gen imid_nhsd=min(oral_steroid_drugs_nhsd, immunosuppresant_drugs_nhsd)
gen rare_neuro_nhsd = min(multiple_sclerosis_nhsd, motor_neurone_disease_nhsd, myasthenia_gravis_nhsd, huntingtons_disease_nhsd)
*high risk group only based on codelists*
gen downs_syndrome=(downs_syndrome_nhsd<=start_date)
gen solid_cancer_new=(cancer_opensafely_snomed_new<=start_date)
gen haema_disease=( haematological_disease_nhsd <=start_date)
gen renal_disease=( ckd_stage_5_nhsd <=start_date)
gen liver_disease=( liver_disease_nhsd <=start_date)
gen imid=( imid_nhsd <=start_date)
gen immunosupression_new=( immunosupression_nhsd_new <=start_date)
gen hiv_aids=( hiv_aids_nhsd <=start_date)
gen solid_organ_new=( solid_organ_transplant_nhsd_new<=start_date)
gen rare_neuro=( rare_neuro_nhsd <=start_date)
gen high_risk_group_new=(( downs_syndrome + solid_cancer_new + haema_disease + renal_disease + liver_disease + imid + immunosupression_new + hiv_aids + solid_organ_new + rare_neuro )>0)
tab high_risk_group_new,m
keep if high_risk_group_new==1
*anaphylaxis events*
*death *
sum death_with_anaphylaxis_date,f
gen death=(death_with_anaphylaxis_date!=.)
tab death
gen day_death=death_with_anaphylaxis_date-start_date
sum day_death, de
gen death_28d=(death_with_anaphylaxis_date!=.&day_death<=28)
tab death_28d
sum death_with_anaph_underly_date ,f
sum death_with_anaph_underly_date if day_death<=28,f
sum death_with_anaphylaxis_date2 ,f
sum death_with_anaph_underly_date2 ,f
sum death_with_anaphylaxis_date3 ,f
sum death_with_anaphylaxis_date_pre ,f
sum death_with_anaph_underly_date_pr ,f
*hosp*
sum hospitalisation_anaph ,f
gen hosp=(hospitalisation_anaph!=.)
tab hosp
gen day_hosp=hospitalisation_anaph-start_date
sum day_hosp, de
gen hosp_28d=(hospitalisation_anaph!=.&day_hosp<=28)
tab hosp_28d
gen day_discharge=hosp_discharge_anaph-hospitalisation_anaph
sum day_discharge,de
sum hospitalisation_anaph_underly ,f
sum hospitalisation_anaph_underly if day_hosp<=28,f
sum hospitalisation_anaph2 ,f
sum hospitalisation_anaph2 if day_hosp<=28,f
sum hospitalisation_anaph_underly2 ,f
sum hospitalisation_anaph3 ,f
sum hospitalisation_anaph3 if day_hosp<=28,f
sum hospitalisation_anaph_pre ,f
sum hosp_anaph_underly_pre ,f
*A&E*
sum AE_anaph ,f
gen AE=(AE_anaph!=.)
tab AE
gen day_AE=AE_anaph-start_date
sum day_AE, de
gen AE_28d=(AE_anaph!=.&day_AE<=28)
tab AE_28d
sum AE_anaph2 ,f
sum AE_anaph3 ,f
sum AE_anaph4 ,f
gen AE_28d2=(AE_anaph2!=.&day_AE<=28)
tab AE_28d2
sum AE_anaph2 if day_AE<=28,f
sum AE_anaph3 if day_AE<=28,f
sum AE_anaph4 if day_AE<=28,f
sum AE_anaph_pre ,f
sum AE_anaph2_pre ,f
*GP*
sum GP_anaph ,f
gen GP=(GP_anaph!=.)
tab GP
gen day_GP=GP_anaph-start_date
sum day_GP, de
gen GP_28d=(GP_anaph!=.&day_GP<=28)
tab GP_28d
tostring GP_anaph_code,replace
tab GP_anaph_code ,m
tab GP_anaph_code if day_GP<=28,m
sum GP_anaph2 ,f
sum GP_anaph2 if day_GP<=28,f
sum GP_anaph_pre ,f
sum GP_anaph2_pre ,f
*combine 4 data sources*
tab hosp_28d AE_28d,row
tab hosp_28d AE_28d2,row
tab hosp_28d GP_28d,row
tab AE_28d GP_28d,row
tab AE_28d2 GP_28d,row
gen anaph_all=(death_28d+hosp_28d+AE_28d+GP_28d)>0
tab anaph_all
gen anaph_all2=(death_28d+hosp_28d+AE_28d2+GP_28d)>0
tab anaph_all2
*by age*
log close