use CHIEDZA_trial_deidentified_minimal.dta, clear

**************
*Table 1: Descriptive characteristics
preserve
keep if has_hivstatus==1

tab b08sex arm, col
tab agecat arm, col
tab educat arm, col
tab p17incomecat arm, col
tab p17incomecat arm, col m
 tab p110employ arm, col
tab p111mat arm, col
tab everhadsex arm, col

restore

***********
*Table 2: Primary outcome
tab supp_vl arm if hiv==1, col
clan supp_vl sex if hiv==1 , arm(arm) clus(cluster) strata(strata) effect(rr)



*************
*Table 2: Secondary outcomes

*HIV diagnosed
tab  has_hiv_diag2 arm if hiv==1, col
clan has_hiv_diag2 sex if hiv==1, arm(arm) clus(cluster) strata(strata) effect(rr)

*On ART
tab on_art2 arm if has_hiv_diag2==1, col 
clan on_art2 sex if hiv==1 & has_hiv_diag2==1, arm(arm) clus(cluster) strata(strata) effect(rr)

*Virally suppressed
tab supp_vl arm if on_art2==1 & has_hiv_diag2==1, col 
clan supp_vl sex  if hiv==1 & has_hiv_diag2==1 & on_art2==1, arm(arm) clus(cluster) strata(strata) effect(rr)


*******************
*Table 3: outcomes by sex and age

*Primary outcome by sex
clan supp_vl if hiv==1 & sex==1, arm(arm) clus(cluster) strata(strata) effect(rr)
clan supp_vl if hiv==1 & sex==2, arm(arm) clus(cluster) strata(strata) effect(rr)

*Primary outcome by age
clan supp_vl sex if hiv==1 & agecat==1, arm(arm) clus(cluster) strata(strata) effect(rr)
clan supp_vl sex if hiv==1 & agecat==2, arm(arm) clus(cluster) strata(strata) effect(rr)

*Secondary outcomes by sex
clan has_hiv_diag2 if hiv==1 & sex==1, arm(arm) clus(cluster) strata(strata) effect(rr)
clan has_hiv_diag2 if hiv==1 & sex==2, arm(arm) clus(cluster) strata(strata) effect(rr)

clan on_art2 if hiv==1 & has_hiv_diag2==1 & sex==1, arm(arm) clus(cluster) strata(strata) effect(rr)
clan on_art2 if hiv==1 & has_hiv_diag2==1 & sex==2, arm(arm) clus(cluster) strata(strata) effect(rr)

clan supp_vl if hiv==1 & has_hiv_diag2==1 & on_art2==1 & sex==1, arm(arm) clus(cluster) strata(strata) effect(rr)
clan supp_vl if hiv==1 & has_hiv_diag2==1 & on_art2==1 & sex==2, arm(arm) clus(cluster) strata(strata) effect(rr)

*Secondary outcomes by age
clan has_hiv_diag2 sex if hiv==1 & agecat==1, arm(arm) clus(cluster) strata(strata) effect(rr)
clan has_hiv_diag2 sex if hiv==1 & agecat==2, arm(arm) clus(cluster) strata(strata) effect(rr)

clan on_art2 sex if hiv==1 & has_hiv_diag2==1 & agecat==1, arm(arm) clus(cluster) strata(strata) effect(rr)
clan on_art2 sex if hiv==1 & has_hiv_diag2==1 & agecat==2, arm(arm) clus(cluster) strata(strata) effect(rr)

clan supp_vl sex if hiv==1 & has_hiv_diag2==1 & on_art2==1 & agecat==1, arm(arm) clus(cluster) strata(strata) effect(rr)
clan supp_vl sex  if hiv==1 & has_hiv_diag2==1 & on_art2==1 & agecat==2, arm(arm) clus(cluster) strata(strata) effect(rr)



*Sensitvity analysis: assume all indeterminate HIV results are HIV positive and virally suppressed
recode hiv .a=1, gen(hiv_sens1)
gen supp_vl_sens1=supp_vl
recode supp_vl_sens1 .=1 if hiv==.a
clan supp_vl_sens1 sex if hiv_sens1==1, arm(arm) clus(cluster) strata(strata) effect(rr)



************************************************
*Post hoc analysis

*Viral suppression among those with HIV diagnosis 
*Virally suppressed
tab supp_vl arm if  has_hiv_diag2==1, col 
clan supp_vl sex  if hiv==1 & has_hiv_diag2==1 , arm(arm) clus(cluster) strata(strata) effect(rr)
//this includes viral suppression among participants where no ART was detected or reported


*Had an HIV test within the past 12 months
recode p62test 1/3=1 4/5=0 .=0, gen(testin12mths)
tab testin12mths arm, col
clan testin12mths sex , arm(arm) clus(cluster) strata(strata) effect(rr)


*Extended data Table 2: Table comparing characteristics of those on ART by arm
use CHIEDZA_trial_deidentified_minimal.dta, clear

preserve
keep if on_art2==1
tab agecat arm , co chi
tab agecat arm, m
tab b08sex arm, co chi
tab b08sex arm, m
tab p71int arm if p71int<2, co chi
tab p71int arm,m 
tab educat arm, co chi
tab educat arm, m
tab p17incomecat arm, co chi
tab p17incomecat arm, m
tab p110employ arm, co chi
tab p110employ arm, m
tab p111mat arm, co chi
tab p111mat arm, m
tab p15res arm, col chi
tab p15res arm, m 

bysort b00p: tab p17incomecat arm, col chi
by b00p: tab p111mat arm, col chi 
restore

*Extended data table 5: primary outcome among YLWH residing less than median distance from community centre, for >2 years
preserve
keep if within_med==1 & inlist(p15res,3,4) & hiv==1
tab supp_vl arm, col
clan supp_vl sex if hiv==1, arm(arm) clus(cluster) strata(strata) effect(rr)
restore