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SCCS_first_dose_only_analyses_sens_AZ_vs_PF.do
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SCCS_first_dose_only_analyses_sens_AZ_vs_PF.do
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/*==============================================================================
DO FILE NAME: SCCS_first_dose_only_analyses_sens_AZ_vs_PF.do
PROJECT: Vaccine Safety
DATE: 3rd Sept 2021
AUTHOR: Jemma Walker
DESCRIPTION OF FILE: SCCS analysis of neuro events (GBS, TM and BP) - ratio of ratios AZ vs PF
DATASETS USED: sccs_cutp_data_BP_AZ.dta, sccs_cutp_data_TM_AZ.dta ,sccs_cutp_data_GBS_AZ.dta
sccs_cutp_data_BP_PF.dta, sccs_cutp_data_TM_PF.dta ,sccs_cutp_data_GBS_PF.dta
DATASETS CREATED: none
OTHER OUTPUT: logfile, printed to folder /logs
tables- results_summary_sens_AZ_vs_PF, printed to folder /tables
==============================================================================*/
/* HOUSEKEEPING===============================================================*/
* create folders that do not exist on server
capture mkdir "`c(pwd)'/output/logs"
capture mkdir "`c(pwd)'/output/tables"
capture mkdir "`c(pwd)'/output/temp_data"
* set ado path
adopath + "`c(pwd)'/analysis/extra_ados"
* open a log file
cap log close
log using "`c(pwd)'/output/logs/SCCS_first_dose_only_analyses_sens_AZ_vs_PF.log", replace
/* ANALYSIS===================================================================*/
* Setup file for posting results
tempname results
postfile `results' ///
str4(outcome) str10(brand) str50(analysis) str35(subanalysis) str20(category) str20(vlab) comparison_period irr lc uc ///
using "`c(pwd)'/output/tables/results_summary_sens_AZ_vs_PF", replace
foreach j in BP TM GBS{
use "`c(pwd)'/output/temp_data/sccs_cutp_data_`j'_AZ.dta", clear
append using "`c(pwd)'/output/temp_data/sccs_cutp_data_`j'_PF.dta"
*need numeric variable for interaction term for ratio of ratios- AZ vs PF
gen AZ=1 if first_brand=="AZ"
recode AZ .=0
* local macro var containing nr of events
count if AZ == 1
local eventnum_AZ = r(N)
count if AZ == 0
local eventnum_PF = r(N)
*head to head comparison- AZ vs PF
display "****************"
display "****OUTCOME*****"
display "`j'"
display "****************"
display "AZ VS PF PRIMARY RISK WINDOW AFTER 1ST DOSE"
*vacc1 has 5 levels, non-risk - baseline (0), pre-vacc low 28 days -TM, GBS /14 days BP (1), day 0 (2) days 1-3 (3) and days 4-28 BP, TM / 4-42 GBS (4)
**IF DOSES >1JAN (incl_AZ_PF_compare==1)
*need originals to comapre to limited to >1st Jan as well
di "`j' AZ (RESTRICTED TO DOSES AFTER 1st JAN)"
xtpoisson nevents ib0.vacc1_`j' if first_brand=="AZ" & incl_AZ_PF_compare==1, fe i(patient_id) offset(loginterval) eform
if _rc+(e(converge)==0) == 0 & `eventnum_AZ' > 5 {
mat b = r(table)
forvalues v = 1/4 {
local k = `v' + 1
local vlab: label vacc1_`j'1 `v'
post `results' ("`j'") ("`brand'") ("AZ vs PF primary risk window") ("") ("First = AZ") ("`vlab'") (`v') (b[1,`k']) (b[5,`k']) (b[6,`k'])
}
}
else di "DID NOT CONVERGE - `j' AZ (RESTRICTED TO DOSES AFTER 1st JAN)"
di "`j' PF (RESTRICTED TO DOSES AFTER 1st JAN)"
xtpoisson nevents ib0.vacc1_`j' if first_brand=="PF" & incl_AZ_PF_compare==1, fe i(patient_id) offset(loginterval) eform
if _rc+(e(converge)==0) == 0 & `eventnum_PF' > 5 {
mat b = r(table)
forvalues v = 1/4 {
local k = `v' + 1
local vlab: label vacc1_`j'1 `v'
post `results' ("`j'") ("`brand'") ("AZ vs PF primary risk window") ("") ("First = PF") ("`vlab'") (`v') (b[1,`k']) (b[5,`k']) (b[6,`k'])
}
}
else di "DID NOT CONVERGE - `j' PF (RESTRICTED TO DOSES AFTER 1st JAN)"
di " `j' AZ VS PF"
xtpoisson nevents ib0.vacc1_`j'##AZ if incl_AZ_PF_compare==1, fe i(patient_id) offset(loginterval) eform
if _rc+(e(converge)==0) == 0 & `eventnum_PF' > 5 {
mat b = r(table)
forvalues v = 1/4 {
local k = `v' + 10 + (`v'-1)
local vlab: label vacc1_`j'1 `v'
post `results' ("`j'") ("`brand'") ("AZ vs PF primary risk window") ("") ("AZ vs PF") ("`vlab'") (`v') (b[1,`k']) (b[5,`k']) (b[6,`k'])
}
}
else di "DID NOT CONVERGE - `j' AZ VS PF"
display "ADD IN WEEK PERIOD"
di "`j' AZ (RESTRICTED TO DOSES AFTER 1st JAN) - WEEK ADJ"
xtpoisson nevents ib0.vacc1_`j' ib0.week if first_brand=="AZ" & incl_AZ_PF_compare==1, fe i(patient_id) offset(loginterval) eform
if _rc+(e(converge)==0) == 0 & `eventnum_AZ' > 5 {
mat b = r(table)
forvalues v = 1/4 {
local k = `v' + 1
local vlab: label vacc1_`j'1 `v'
post `results' ("`j'") ("`brand'") ("AZ vs PF primary risk window") ("add in week") ("First = AZ") ("`vlab'") (`v') (b[1,`k']) (b[5,`k']) (b[6,`k'])
}
}
else di "DID NOT CONVERGE - `j' AZ (RESTRICTED TO DOSES AFTER 1st JAN) - WEEK ADJ"
di "`j' PF (RESTRICTED TO DOSES AFTER 1st JAN) - WEEK ADJ"
xtpoisson nevents ib0.vacc1_`j' ib0.week if first_brand=="PF" & incl_AZ_PF_compare==1, fe i(patient_id) offset(loginterval) eform
if _rc+(e(converge)==0) == 0 & `eventnum_PF' > 5 {
mat b = r(table)
forvalues v = 1/4 {
local k = `v' + 1
local vlab: label vacc1_`j'1 `v'
post `results' ("`j'") ("`brand'") ("AZ vs PF primary risk window") ("add in week") ("First = PF") ("`vlab'") (`v') (b[1,`k']) (b[5,`k']) (b[6,`k'])
}
}
else di "DID NOT CONVERGE - `j' PF (RESTRICTED TO DOSES AFTER 1st JAN) - WEEK ADJ"
di "`j' AZ VS PF - WEEK ADJ "
xtpoisson nevents ib0.vacc1_`j'##AZ ib0.week if incl_AZ_PF_compare==1, fe i(patient_id) offset(loginterval) eform
if _rc+(e(converge)==0) == 0 & `eventnum_PF' > 5 {
mat b = r(table)
forvalues v = 1/4 {
local k = `v' + 10 + (`v'-1)
local vlab: label vacc1_`j'1 `v'
post `results' ("`j'") ("`brand'") ("AZ vs PF primary risk window") ("add in week") ("AZ vs PF") ("`vlab'") (`v') (b[1,`k']) (b[5,`k']) (b[6,`k'])
}
}
else di "DID NOT CONVERGE - `j' AZ VS PF - WEEK ADJ "
di "`j' AZ VS PF - WEEK ADJ & INTERACTION"
xtpoisson nevents ib0.vacc1_`j'##AZ ib0.week##AZ if incl_AZ_PF_compare==1, fe i(patient_id) offset(loginterval) eform
if _rc+(e(converge)==0) == 0 & `eventnum_PF' > 5 {
mat b = r(table)
forvalues v = 1/4 {
local k = `v' + 10 + (`v'-1)
local vlab: label vacc1_`j'1 `v'
post `results' ("`j'") ("`brand'") ("AZ vs PF primary risk window") ("add in week interction") ("AZ vs PF") ("`vlab'") (`v') (b[1,`k']) (b[5,`k']) (b[6,`k'])
}
}
else di "DID NOT CONVERGE - `j' AZ VS PF - WEEK ADJ & INTERACTION"
display "ADD IN 2 WEEK PERIOD"
di "`j' AZ (RESTRICTED TO DOSES AFTER 1st JAN) - 2 WEEK ADJ"
xtpoisson nevents ib0.vacc1_`j' ib0.two_week if first_brand=="AZ" & incl_AZ_PF_compare==1, fe i(patient_id) offset(loginterval) eform
if _rc+(e(converge)==0) == 0 & `eventnum_AZ' > 5 {
mat b = r(table)
forvalues v = 1/4 {
local k = `v' + 1
local vlab: label vacc1_`j'1 `v'
post `results' ("`j'") ("`brand'") ("AZ vs PF primary risk window") ("add in 2 week") ("First = AZ") ("`vlab'") (`v') (b[1,`k']) (b[5,`k']) (b[6,`k'])
}
}
else di "DID NOT CONVERGE - `j' AZ (RESTRICTED TO DOSES AFTER 1st JAN) - 2 WEEK ADJ"
di "`j' PF (RESTRICTED TO DOSES AFTER 1st JAN) -2 WEEK ADJ"
xtpoisson nevents ib0.vacc1_`j' ib0.two_week if first_brand=="PF" & incl_AZ_PF_compare==1, fe i(patient_id) offset(loginterval) eform
if _rc+(e(converge)==0) == 0 & `eventnum_PF' > 5 {
mat b = r(table)
forvalues v = 1/4 {
local k = `v' + 1
local vlab: label vacc1_`j'1 `v'
post `results' ("`j'") ("`brand'") ("AZ vs PF primary risk window") ("add in 2 week") ("First = PF") ("`vlab'") (`v') (b[1,`k']) (b[5,`k']) (b[6,`k'])
}
}
else di "DID NOT CONVERGE - `j' PF (RESTRICTED TO DOSES AFTER 1st JAN) -2 WEEK ADJ"
di "`j' AZ VS PF - 2 WEEK ADJ "
xtpoisson nevents ib0.vacc1_`j'##AZ ib0.two_week if incl_AZ_PF_compare==1, fe i(patient_id) offset(loginterval) eform
if _rc+(e(converge)==0) == 0 & `eventnum_PF' > 5 {
mat b = r(table)
forvalues v = 1/4 {
local k = `v' + 10 + (`v'-1)
local vlab: label vacc1_`j'1 `v'
post `results' ("`j'") ("`brand'") ("AZ vs PF primary risk window") ("add in 2 week") ("AZ vs PF") ("`vlab'") (`v') (b[1,`k']) (b[5,`k']) (b[6,`k'])
}
}
else di "DID NOT CONVERGE - `j' AZ VS PF - 2 WEEK ADJ "
di "`j' AZ VS PF - 2 WEEK ADJ & INTERACTION"
xtpoisson nevents ib0.vacc1_`j'##AZ ib0.two_week##AZ if incl_AZ_PF_compare==1, fe i(patient_id) offset(loginterval) eform
if _rc+(e(converge)==0) == 0 & `eventnum_PF' > 5 {
mat b = r(table)
forvalues v = 1/4 {
local k = `v' + 10 + (`v'-1)
local vlab: label vacc1_`j'1 `v'
post `results' ("`j'") ("`brand'") ("AZ vs PF primary risk window") ("add in 2 week interction") ("AZ vs PF") ("`vlab'") (`v') (b[1,`k']) (b[5,`k']) (b[6,`k'])
}
}
else di "DID NOT CONVERGE - `j' AZ VS PF - 2 WEEK ADJ & INTERACTION"
}
* Close post-file
postclose `results'
use "`c(pwd)'/output/tables/results_summary_sens_AZ_vs_PF", clear
export delimited using "`c(pwd)'/output/tables/results_summary_sens_AZ_vs_PF.csv", replace
log close