From def59fdeaf7278c18bdb0c3be354c2a1a98d273c Mon Sep 17 00:00:00 2001 From: Jenny Smith Date: Tue, 27 Feb 2024 09:52:16 +0000 Subject: [PATCH 1/3] Update hiv_synthesis.sas --- hiv_synthesis.sas | 197 +++++++++++++++++++++++++++------------------- 1 file changed, 114 insertions(+), 83 deletions(-) diff --git a/hiv_synthesis.sas b/hiv_synthesis.sas index e48d81cb..a7755104 100644 --- a/hiv_synthesis.sas +++ b/hiv_synthesis.sas @@ -2222,18 +2222,18 @@ who may be dead and hence have caldate{t} missing; end; *PrEP interventions; *JAS Apr2023 and Oct23; - *option 15: Oral TDF/FTC PrEP for AGWY; + *option 15: Oral TDF/FTC PrEP for AGYW; *option 16: Oral TDF/FTC PrEP for FSW; - *option 17: Oral TDF/FTC PrEP for sero-discordant couples; - *option 18: Oral TDF/FTC PrEP for pregnant and breastfeeding women; + *option 17: Oral TDF/FTC PrEP for sero-discordant couples (SDC); + *option 18: Oral TDF/FTC PrEP for pregnant and breastfeeding women (PLW); *option 19: Dapivirine ring for AGYW; *option 20: Dapivirine ring for FSW; - *option 21: Dapivirine ring for sero-discordant couples; - *option 22: Dapivirine ring for pregnant and breastfeeding women; + *option 21: Dapivirine ring for sero-discordant couples (SDC); + *option 22: Dapivirine ring for pregnant and breastfeeding women (PLW); *option 23: Injectable PrEP for AGYW; *option 24: Injectable PrEP for FSW; - *option 25: Injectable PrEP for Sero-discordant couples; - *option 26: Injectable PrEP for pregnant and breastfeeding women; + *option 25: Injectable PrEP for Sero-discordant couples (SDC); + *option 26: Injectable PrEP for pregnant and breastfeeding women (PLW); if option in (15 19 23) then prep_any_strategy=3; * All PrEP options for AGYW; if option in (16 20 24) then prep_any_strategy=2; * All PrEP options for FSW; @@ -2245,7 +2245,6 @@ who may be dead and hence have caldate{t} missing; date_prep_oral_intro=&year_interv; if caldate{t}=&year_interv then do; pref_prep_oral_beta_s1=pref_prep_oral_beta_s1*3; * From Vales code, this is to match oral PrEP uptake to Zim target MIHPSA JAS Jul23; - pref_prep_oral=rand('beta',pref_prep_oral_beta_s1,5); end; end; * All vaginal ring PrEP options; @@ -2253,7 +2252,6 @@ who may be dead and hence have caldate{t} missing; date_prep_vr_intro=&year_interv; if caldate{t}=&year_interv then do; pref_prep_vr_beta_s1=pref_prep_oral_beta_s1*3; * MIHPSA: can adjust this to match vr PrEP uptake to oral PrEP target JAS Jul23; - pref_prep_vr=.; if gender=2 then pref_prep_vr=rand('beta',pref_prep_vr_beta_s1,5); * women only; end; end; * All injectable PrEP options; @@ -2261,108 +2259,107 @@ who may be dead and hence have caldate{t} missing; date_prep_inj_intro=&year_interv; if caldate{t}=&year_interv then do; pref_prep_inj_beta_s1=pref_prep_oral_beta_s1*3; * MIHPSA: can adjust this to match inj PrEP uptake to oral PrEP target JAS Jul23; - pref_prep_inj=rand('beta',pref_prep_inj_beta_s1,5); end; end; * Oral PrEP; - *option 15: Oral TDF/FTC PrEP for AGWY; + *option 15: Oral TDF/FTC PrEP for AGYW; if option = 15 then do; *Following values need to change; - eff_rate_test_startprep_any=0.95; - eff_prob_prep_oral_b=0.95; - eff_rate_choose_stop_prep_oral=0.001; - eff_prob_prep_any_restart_choice=0.25; + eff_rate_test_startprep_any=0.4; + eff_prob_prep_oral_b=0.9; + eff_rate_choose_stop_prep_oral=0.01; + eff_prob_prep_any_restart_choice=0.5; end; *option 16: Oral TDF/FTC PrEP for FSW; if option = 16 then do; - eff_rate_test_startprep_any=0.95; - eff_prob_prep_oral_b=0.95; - eff_rate_choose_stop_prep_oral=0.001; - eff_prob_prep_any_restart_choice=0.25; + eff_rate_test_startprep_any=0.4; + eff_prob_prep_oral_b=0.4; + eff_rate_choose_stop_prep_oral=0.01; + eff_prob_prep_any_restart_choice=0.5; end; *option 17: Oral TDF/FTC PrEP for sero-discordant couples (SDC); if option = 17 then do; - eff_rate_test_startprep_any=0.95; - eff_prob_prep_oral_b=0.95; - eff_rate_choose_stop_prep_oral=0.001; - eff_prob_prep_any_restart_choice=0.25; + eff_rate_test_startprep_any=0.4; + eff_prob_prep_oral_b=0.4; + eff_rate_choose_stop_prep_oral=0.01; + eff_prob_prep_any_restart_choice=0.5; end; *option 18: Oral TDF/FTC PrEP for pregnant and breastfeeding women (PLW); if option = 18 then do; - eff_rate_test_startprep_any=0.95; - eff_prob_prep_oral_b=0.95; - eff_rate_choose_stop_prep_oral=0.001; - eff_prob_prep_any_restart_choice=0.25; + eff_rate_test_startprep_any=0.2; + eff_prob_prep_oral_b=0.9; + eff_rate_choose_stop_prep_oral=0.01; + eff_prob_prep_any_restart_choice=0.5; end; * Dapivirine ring; *option 19: Dapivirine ring for AGYW; if option = 19 then do; - eff_rate_test_startprep_any=0.95; - eff_prob_prep_vr_b=0.95; - eff_rate_choose_stop_prep_vr=0.001; - eff_prob_prep_any_restart_choice=0.25; + eff_rate_test_startprep_any=0.4; + eff_prob_prep_vr_b=0.9; + eff_rate_choose_stop_prep_vr=0.01; + eff_prob_prep_any_restart_choice=0.5; end; *option 20: Dapivirine ring for FSW; if option = 20 then do; - eff_rate_test_startprep_any=0.95; - eff_prob_prep_vr_b=0.95; - eff_rate_choose_stop_prep_vr=0.001; - eff_prob_prep_any_restart_choice=0.25; + eff_rate_test_startprep_any=0.6; + eff_prob_prep_vr_b=0.6; + eff_rate_choose_stop_prep_vr=0.01; + eff_prob_prep_any_restart_choice=0.5; end; *option 21: Dapivirine ring for SDC; if option = 21 then do; - eff_rate_test_startprep_any=0.95; - eff_prob_prep_vr_b=0.95; - eff_rate_choose_stop_prep_vr=0.001; - eff_prob_prep_any_restart_choice=0.25; + eff_rate_test_startprep_any=0.6; + eff_prob_prep_vr_b=0.6; + eff_rate_choose_stop_prep_vr=0.01; + eff_prob_prep_any_restart_choice=0.5; end; *option 22: Dapivirine ring for PLW; if option = 22 then do; - eff_rate_test_startprep_any=0.95; - eff_prob_prep_vr_b=0.95; - eff_rate_choose_stop_prep_vr=0.001; - eff_prob_prep_any_restart_choice=0.25; + eff_rate_test_startprep_any=0.2; + eff_prob_prep_vr_b=0.9; + eff_rate_choose_stop_prep_vr=0.01; + eff_prob_prep_any_restart_choice=0.5; end; * Injectable PrEP; *option 23: Injectable PrEP for AGYW; if option = 23 then do; - eff_rate_test_startprep_any=0.95; - eff_prob_prep_inj_b=0.95; - eff_rate_choose_stop_prep_inj=0.001; - eff_prob_prep_any_restart_choice=0.25; + eff_rate_test_startprep_any=0.4; + eff_prob_prep_inj_b=0.9; + eff_rate_choose_stop_prep_inj=0.01; + eff_prob_prep_any_restart_choice=0.5; end; *option 24: Injectable PrEP for FSW; if option = 24 then do; - eff_rate_test_startprep_any=0.95; - eff_prob_prep_inj_b=0.95; - eff_rate_choose_stop_prep_inj=0.001; - eff_prob_prep_any_restart_choice=0.25; + eff_rate_test_startprep_any=0.4; + eff_prob_prep_inj_b=0.4; + eff_rate_choose_stop_prep_inj=0.01; + eff_prob_prep_any_restart_choice=0.5; end; *option 25: Injectable PrEP for SDC; if option = 25 then do; - eff_rate_test_startprep_any=0.95; - eff_prob_prep_inj_b=0.95; - eff_rate_choose_stop_prep_inj=0.001; - eff_prob_prep_any_restart_choice=0.25; + eff_rate_test_startprep_any=0.4; + eff_prob_prep_inj_b=0.4; + eff_rate_choose_stop_prep_inj=0.01; + eff_prob_prep_any_restart_choice=0.5; end; *option 26: Injectable PrEP for PLW; if option = 26 then do; - eff_rate_test_startprep_any=0.95; - eff_prob_prep_inj_b=0.95; - eff_rate_choose_stop_prep_inj=0.001; - eff_prob_prep_any_restart_choice=0.25; + eff_rate_test_startprep_any=0.2; + eff_prob_prep_inj_b=0.9; + eff_rate_choose_stop_prep_inj=0.01; + eff_prob_prep_any_restart_choice=0.5; end; @@ -4693,16 +4690,20 @@ if t ge 2 and (registd ne 1) and caldate{t} >= min(date_prep_oral_intro, date_pr (newp ge 1 or (epdiag=1 and epart ne 1) or (ep=1 and epart ne 1 and (r < 0.05 or (r < 0.5 and epi=1)))) then prep_any_elig=1; end; - if prep_any_strategy=2 then do; *FSW; - r = rand('Uniform'); + if prep_any_strategy=2 then do; *FSW; * Continuous r_prep JAS 5thFeb2024; + r_prep_tm1=r_prep; + if prep_any_elig_tm1=1 then r_prep=r_prep_tm1; + else r_prep = rand('Uniform'); if gender=2 and sw=1 and - (newp ge 1 or (epdiag=1 and epart ne 1) or (ep=1 and epart ne 1 and (r < 0.05 or (r < 0.5 and epi=1)))) then prep_any_elig=1; + (newp ge 1 or (epdiag=1 and epart ne 1) or (ep=1 and epart ne 1 and (r_prep < 0.05 or (r_prep < 0.5 and epi=1)))) then prep_any_elig=1; end; - if prep_any_strategy=3 then do; *AGYW; - r = rand('Uniform'); + if prep_any_strategy=3 then do; *AGYW; * Continuous r_prep JAS 5thFeb2024; + r_prep_tm1=r_prep; + if prep_any_elig_tm1=1 then r_prep=r_prep_tm1; + else r_prep = rand('Uniform'); if gender=2 and 15<=age<25 and - (newp ge 1 or (epdiag=1 and epart ne 1) or (ep=1 and epart ne 1 and (r < 0.05 or (r < 0.5 and epi=1)))) then prep_any_elig=1; + (newp ge 1 or (epdiag=1 and epart ne 1) or (ep=1 and epart ne 1 and (r_prep < 0.05 or (r_prep < 0.5 and epi=1)))) then prep_any_elig=1; end; if prep_any_strategy=4 then do; * used in oral prep ms and cab-la resistance ms; @@ -4784,7 +4785,9 @@ if t ge 2 and (registd ne 1) and caldate{t} >= min(date_prep_oral_intro, date_pr if prep_any_strategy=16 then do; * Pregnant and breastfeeding women (PLW) - new for MIHPSA Zimbabwe; *JAS Apr2023; * Note that there is a component of sexual behaviour in prep eligibility for pregnant and breastfeeding women; - if gender=2 and (pregnant=1 or breastfeeding=1) and ( newp ge 1 or newp_tm1 ge 1 or newp_tm2 ge 1 or ep=1 ) then prep_any_elig=1; + if gender=2 and (pregnant=1 or breastfeeding=1) and + (newp ge 1 or (epdiag=1 and epart ne 1) or (ep=1 and epart ne 1 and (r < 0.05 or (r < 0.5 and epi=1)))) then prep_any_elig=1; + *( newp ge 1 or newp_tm1 ge 1 or newp_tm2 ge 1 or ep=1 ) then prep_any_elig=1; * replaced with code to match AGYW above Jan24; end; if prep_any_elig=1 then date_most_recent_prep_any_elig=caldate{t}; @@ -14285,7 +14288,6 @@ end; *Number of people eligible for PrEP; -*Number of people eligible for any PrEP; elig_prep_any_w_1524 = 0; elig_prep_any_w_2534 = 0; elig_prep_any_w_3544 = 0; elig_prep_any_w_1549 = 0; elig_prep_any_w_1564 = 0; if gender = 2 and 15 <= age < 25 then do; if prep_any_elig=1 then elig_prep_any_w_1524 = 1; end; @@ -14294,6 +14296,8 @@ if gender = 2 and 35 <= age < 45 then do; if prep_any_elig=1 then elig_prep_any_ if gender = 2 and 15 <= age < 50 then do; if prep_any_elig=1 then elig_prep_any_w_1549 = 1; end; if gender = 2 and 15 <= age < 65 then do; if prep_any_elig=1 then elig_prep_any_w_1564 = 1; end; if sw=1 then do; elig_prep_any_sw = 0; if prep_any_elig = 1 then elig_prep_any_sw = 1; end; +if sdc=1 then do; elig_prep_any_sdc = 0; if prep_any_elig = 1 then elig_prep_any_sdc = 1; end; +if plw=1 then do; elig_prep_any_plw = 0; if prep_any_elig = 1 then elig_prep_any_plw = 1; end; prep_any_w_1524 = 0; prep_any_w_2534 = 0; prep_any_w_3544 = 0; prep_any_w_1549 = 0; if gender = 2 and 15 <= age < 25 then do; if prep_any=1 then prep_any_w_1524 = 1; end; @@ -14301,9 +14305,10 @@ if gender = 2 and 25 <= age < 35 then do; if prep_any=1 then prep_any_w_2534 = if gender = 2 and 35 <= age < 45 then do; if prep_any=1 then prep_any_w_3544 = 1; end; if gender = 2 and 15 <= age < 49 then do; if prep_any=1 then prep_any_w_1549 = 1; end; - elig_prep_any_m_1564 = 0; if gender = 1 and 15 <= age < 65 then do; if prep_any_elig=1 then elig_prep_any_m_1564 = 1; end; - +prep_any_m_1549 = 0; prep_any_m_1564 = 0; +if gender = 1 and 15 <= age < 49 then do; if prep_any=1 then prep_any_m_1549 = 1; end; +if gender = 1 and 15 <= age < 64 then do; if prep_any=1 then prep_any_m_1564 = 1; end; * number on prep women age 15-24; prep_oral_w_1524 = 0 ; if prep_oral=1 and gender =2 and 15 <= age < 25 then prep_oral_w_1524 = 1 ; @@ -14624,6 +14629,22 @@ if prep_vr_tm3=1 or prep_vr_tm2=1 or prep_vr_tm1=1 or prep_vr=1 then do; if pregnant=1 or breastfeeding=1 then prep_vr_ly_plw=1; end; +*To calculate number of current users (SDC and PLW only, AGYW and SW are coded above); +prep_any_sdc = 0; prep_oral_sdc = 0; prep_inj_sdc = 0; prep_vr_sdc = 0; +if sdc = 1 then do; + if prep_any = 1 then prep_any_sdc = 1; + if prep_oral = 1 then prep_oral_sdc = 1; + if prep_inj = 1 then prep_inj_sdc = 1; + if prep_vr = 1 then prep_vr_sdc = 1; +end; +prep_any_plw = 0; prep_oral_plw = 0; prep_inj_plw = 0; prep_vr_plw = 0; +if plw = 1 then do; + if prep_any = 1 then prep_any_plw = 1; + if prep_oral = 1 then prep_oral_plw = 1; + if prep_inj = 1 then prep_inj_plw = 1; + if prep_vr = 1 then prep_vr_plw = 1; +end; + * To calculate number ever initiated on oral PrEP; prep_oral_ever_1524w=0;prep_oral_ever_sw=0;prep_oral_ever_sdc=0;prep_oral_ever_plw=0; if prep_oral_ever=1 then do; @@ -16757,6 +16778,8 @@ if 15 <= age and (death = . or caldate&j = death ) then do; s_i_m_1549_np + i_m_1549_np ; s_i_w_1549_np + i_w_1549_np ; + s_sdc + sdc ; + /*resistance*/ s_tam1_ + tam1_ ; s_tam2_ + tam2_ ; s_tam3_ + tam3_ ; s_m184m_ + m184m_ ; s_k103m_ + k103m_ ; s_y181m_ + y181m_ ; s_g190m_ + g190m_ ; @@ -16791,6 +16814,8 @@ if 15 <= age and (death = . or caldate&j = death ) then do; s_prep_oral_w + prep_oral_w; s_prep_inj_w + prep_inj_w; s_prep_oral_m + prep_oral_m; s_prep_vr_w + prep_vr_w; s_prep_inj_m + prep_inj_m; s_prep_any_sw + prep_any_sw ; s_prep_oral_sw + prep_oral_sw ; s_prep_inj_sw + prep_inj_sw ; s_prep_vr_sw + prep_vr_sw ; s_prep_any_w_1524 + prep_any_w_1524 ; s_prep_oral_w_1524 + prep_oral_w_1524 ; s_prep_inj_w_1524 + prep_inj_w_1524 ; s_prep_vr_w_1524 + prep_vr_w_1524 ; + s_prep_any_sdc + prep_any_sdc; s_prep_oral_sdc + prep_oral_sdc; s_prep_inj_sdc + prep_inj_sdc; s_prep_vr_sdc + prep_vr_sdc; + s_prep_any_plw + prep_any_plw; s_prep_oral_plw + prep_oral_plw; s_prep_inj_plw + prep_inj_plw; s_prep_vr_plw + prep_vr_plw; s_elig_prep_any_m_1564 + elig_prep_any_m_1564 ;s_elig_prep_any_w_1564 + elig_prep_any_w_1564 ; s_infected_prep_any + infected_prep_any ; s_infected_prep_oral + infected_prep_oral ; s_infected_prep_inj + infected_prep_inj ; s_infected_prep_vr + infected_prep_vr ; s_prep_any_ever + prep_any_ever ; s_primary_prep + primary_prep ; s_hiv1_prep_oral + hiv1_prep_oral ; s_prim_r_prep + prim_r_prep ; @@ -16824,7 +16849,8 @@ if 15 <= age and (death = . or caldate&j = death ) then do; s_prep_oral_ever_1524w + prep_oral_ever_1524w; s_prep_oral_ever_sw + prep_oral_ever_sw; s_prep_oral_ever_sdc + prep_oral_ever_sdc; s_prep_oral_ever_plw + prep_oral_ever_plw; s_prep_inj_ever_1524w + prep_inj_ever_1524w; s_prep_inj_ever_sw + prep_inj_ever_sw; s_prep_inj_ever_sdc + prep_inj_ever_sdc; s_prep_inj_ever_plw + prep_inj_ever_plw; s_prep_vr_ever_1524w + prep_vr_ever_1524w; s_prep_vr_ever_sw + prep_vr_ever_sw; s_prep_vr_ever_sdc + prep_vr_ever_sdc; s_prep_vr_ever_plw + prep_vr_ever_plw; - s_elig_prep_any_sw + elig_prep_any_sw ; s_elig_prep_any_w_1549 + elig_prep_any_w_1549; s_prep_any_w_1549 + prep_any_w_1549; + s_elig_prep_any_sw + elig_prep_any_sw ; s_elig_prep_any_sdc + elig_prep_any_sdc ; s_elig_prep_any_plw + elig_prep_any_plw ; + s_elig_prep_any_w_1549 + elig_prep_any_w_1549; s_prep_any_w_1549 + prep_any_w_1549; s_elig_prep_any_w_1524 + elig_prep_any_w_1524 ; s_elig_prep_any_w_2534 + elig_prep_any_w_2534 ; s_elig_prep_any_w_3544 + elig_prep_any_w_3544 ; s_prep_any_w_2534 + prep_any_w_2534 ; s_prep_any_w_3544 + prep_any_w_3544 ; s_inf_prep_any_source_prep_r + inf_prep_any_source_prep_r ; s_prepinfect_prep_r + prepinfect_prep_r ; s_prepinfect_prep_r_p + prepinfect_prep_r_p ; s_infected_prep_no_r + infected_prep_no_r ; @@ -17379,7 +17405,7 @@ if 15 <= age and (death = . or caldate&j = death ) then do; s_pregnant_onart_vl_vhigh + pregnant_onart_vl_vhigh ; s_pregnant_onart_vl_vvhigh + pregnant_onart_vl_vvhigh ; s_birth_with_inf_child + birth_with_inf_child ; s_child_with_resistant_hiv + child_with_resistant_hiv ; s_give_birth_with_hiv + give_birth_with_hiv ; s_onart_birth_with_inf_child_res + onart_birth_with_inf_child_res ; s_onart_birth_with_inf_child + onart_birth_with_inf_child ; - s_breastfeeding + breastfeeding ; + s_breastfeeding + breastfeeding ; s_plw + plw; /*circumcision*/ @@ -18561,6 +18587,7 @@ s_i_age1_m_newp s_i_age2_m_newp s_i_age3_m_newp s_i_age4_m_newp s_i_age5_m_newp s_i_age1_w_newp s_i_age2_w_newp s_i_age3_w_newp s_i_age4_w_newp s_i_age5_w_newp s_i_m_1549_np s_i_w_1549_np s_i_w_newp s_i_m_newp +s_sdc /*resistance*/ s_tam1_ s_tam2_ s_tam3_ s_m184m_ s_k103m_ s_y181m_ s_g190m_ s_nnm_ s_q151m_ s_k65m_ @@ -18611,12 +18638,14 @@ s_prep_vr_ly_1524w s_prep_vr_ly_sw s_prep_vr_ly_sdc s_prep_vr_ly_plw s_prep_oral_ever_1524w s_prep_oral_ever_sw s_prep_oral_ever_sdc s_prep_oral_ever_plw s_prep_inj_ever_1524w s_prep_inj_ever_sw s_prep_inj_ever_sdc s_prep_inj_ever_plw s_prep_vr_ever_1524w s_prep_vr_ever_sw s_prep_vr_ever_sdc s_prep_vr_ever_plw -s_elig_prep_any_sw +s_elig_prep_any_sw s_elig_prep_any_sdc s_elig_prep_any_plw s_onprep_inj_m s_onprep_inj_w s_onprep_vr_w s_onprep_oral_m s_onprep_oral_w s_elig_prep_any_w_1549 s_prep_any_w_1549 s_elig_prep_any_w_1524 s_elig_prep_any_w_2534 s_elig_prep_any_w_3544 s_prep_any_w_1524 s_prep_any_w_2534 s_prep_any_w_3544 s_prep_oral_w_1524 s_prep_inj_w_1524 s_prep_vr_w_1524 +s_prep_any_sdc s_prep_oral_sdc s_prep_inj_sdc s_prep_vr_sdc +s_prep_any_plw s_prep_oral_plw s_prep_inj_plw s_prep_vr_plw s_inf_prep_any_source_prep_r s_prepinfect_prep_r s_prepinfect_prep_r_p s_infected_prep_no_r s_infected_prep_r s_started_prep_any_in_primary s_started_prep_oral_in_primary s_started_prep_inj_in_primary s_started_prep_vr_in_primary @@ -18977,7 +19006,7 @@ s_want_no_more_children s_pregnant_ntd s_pregnant_vlg1000 s_pregnant_o_dol s_pregnant_onart_vl_vhigh s_pregnant_onart_vl_vvhigh s_birth_with_inf_child s_child_with_resistant_hiv s_give_birth_with_hiv s_onart_birth_with_inf_child_res s_onart_birth_with_inf_child -s_breastfeeding +s_breastfeeding s_plw /*circumcision*/ s_mcirc s_mcirc_1519m s_mcirc_2024m s_mcirc_2529m s_mcirc_3034m s_mcirc_3539m s_mcirc_4044m s_mcirc_4549m @@ -19510,7 +19539,7 @@ s_i_age1_m_newp s_i_age2_m_newp s_i_age3_m_newp s_i_age4_m_newp s_i_age5_m_newp s_i_age1_w_newp s_i_age2_w_newp s_i_age3_w_newp s_i_age4_w_newp s_i_age5_w_newp s_i_m_1549_np s_i_w_1549_np s_i_w_newp s_i_m_newp - +s_sdc /*resistance*/ s_tam1_ s_tam2_ s_tam3_ s_m184m_ s_k103m_ s_y181m_ s_g190m_ s_nnm_ s_q151m_ s_k65m_ s_p32m_ s_p33m_ s_p46m_ s_p47m_ s_p50vm_ s_p50lm_ s_p54m_ s_p76m_ s_p82m_ s_p84m_ s_p88m_ s_p90m_ s_pim_ @@ -19557,14 +19586,15 @@ s_prep_vr_ly_1524w s_prep_vr_ly_sw s_prep_vr_ly_sdc s_prep_vr_ly_plw s_prep_oral_ever_1524w s_prep_oral_ever_sw s_prep_oral_ever_sdc s_prep_oral_ever_plw s_prep_inj_ever_1524w s_prep_inj_ever_sw s_prep_inj_ever_sdc s_prep_inj_ever_plw s_prep_vr_ever_1524w s_prep_vr_ever_sw s_prep_vr_ever_sdc s_prep_vr_ever_plw -s_elig_prep_any_sw +s_elig_prep_any_sw s_elig_prep_any_sdc s_elig_prep_any_plw s_onprep_inj_m s_onprep_inj_w s_onprep_vr_w s_onprep_oral_m s_onprep_oral_w s_elig_prep_any_w_1549 s_prep_any_w_1549 s_elig_prep_any_w_1524 s_elig_prep_any_w_2534 s_elig_prep_any_w_3544 s_prep_any_w_1524 s_prep_any_w_2534 s_prep_any_w_3544 s_prep_oral_w_1524 s_prep_inj_w_1524 s_prep_vr_w_1524 - +s_prep_any_sdc s_prep_oral_sdc s_prep_inj_sdc s_prep_vr_sdc +s_prep_any_plw s_prep_oral_plw s_prep_inj_plw s_prep_vr_plw s_inf_prep_any_source_prep_r s_prepinfect_prep_r s_prepinfect_prep_r_p s_infected_prep_no_r s_infected_prep_r s_started_prep_any_in_primary s_started_prep_oral_in_primary s_started_prep_inj_in_primary s_started_prep_vr_in_primary s_onprep_3_i_prep_no_r s_onprep_6_i_prep_no_r s_onprep_9_i_prep_no_r @@ -19918,7 +19948,7 @@ s_want_no_more_children s_pregnant_ntd s_pregnant_vlg1000 s_pregnant_o_dol s_pregnant_onart_vl_vhigh s_pregnant_onart_vl_vvhigh s_birth_with_inf_child s_child_with_resistant_hiv s_give_birth_with_hiv s_onart_birth_with_inf_child_res s_onart_birth_with_inf_child -s_breastfeeding +s_breastfeeding s_plw /*circumcision*/ s_mcirc s_mcirc_1519m s_mcirc_2024m s_mcirc_2529m s_mcirc_3034m s_mcirc_3539m s_mcirc_4044m s_mcirc_4549m @@ -20105,7 +20135,7 @@ end; -%update_r1(da1=1,da2=2,e=1,f=2,g=1,h=8,j=1,s=0); * core starts in 1989, Zim starts in 1984 JAS Sep23; +%update_r1(da1=1,da2=2,e=1,f=2,g=1,h=8,j=1,s=0); * core starts in 1989, Zim, SA and Malawi start in 1984 JAS Sep23; %update_r1(da1=2,da2=1,e=2,f=3,g=1,h=8,j=2,s=0); %update_r1(da1=1,da2=2,e=3,f=4,g=1,h=8,j=3,s=0); %update_r1(da1=2,da2=1,e=4,f=5,g=1,h=8,j=4,s=0); @@ -20470,7 +20500,7 @@ data r1 ; set a ; %update_r1(da1=1,da2=2,e=5,f=6,g=349,h=356,j=353,s=0); %update_r1(da1=2,da2=1,e=6,f=7,g=349,h=356,j=354,s=0); %update_r1(da1=1,da2=2,e=7,f=8,g=349,h=356,j=355,s=0); -%update_r1(da1=2,da2=1,e=8,f=9,g=349,h=356,j=356,s=0); * end of 2077 (core), end of 2072 (Zim) JAS Sep23; +%update_r1(da1=2,da2=1,e=8,f=9,g=349,h=356,j=356,s=0); * end of 2077 (core), end of 2072 (Malawi, SA, Zim) JAS Sep23; * end of s=0 JAS Sep2023; @@ -21315,7 +21345,7 @@ s_i_age1_w_newp s_i_age2_w_newp s_i_age3_w_newp s_i_age4_w_newp s_i_age5_w_newp m15r m25r m35r m45r m55r w15r w25r w35r w45r w55r s_i_m_1549_np s_i_w_1549_np s_i_w_newp s_i_m_newp - +s_sdc /*resistance*/ s_tam1_ s_tam2_ s_tam3_ s_m184m_ s_k103m_ s_y181m_ s_g190m_ s_nnm_ s_q151m_ s_k65m_ s_p32m_ s_p33m_ s_p46m_ s_p47m_ s_p50vm_ s_p50lm_ s_p54m_ s_p76m_ s_p82m_ s_p84m_ s_p88m_ s_p90m_ s_pim_ @@ -21362,14 +21392,15 @@ s_prep_vr_ly_1524w s_prep_vr_ly_sw s_prep_vr_ly_sdc s_prep_vr_ly_plw s_prep_oral_ever_1524w s_prep_oral_ever_sw s_prep_oral_ever_sdc s_prep_oral_ever_plw s_prep_inj_ever_1524w s_prep_inj_ever_sw s_prep_inj_ever_sdc s_prep_inj_ever_plw s_prep_vr_ever_1524w s_prep_vr_ever_sw s_prep_vr_ever_sdc s_prep_vr_ever_plw -s_elig_prep_any_sw +s_elig_prep_any_sw s_elig_prep_any_sdc s_elig_prep_any_plw s_onprep_inj_m s_onprep_inj_w s_onprep_vr_w s_onprep_oral_m s_onprep_oral_w s_elig_prep_any_w_1549 s_prep_any_w_1549 s_elig_prep_any_w_1524 s_elig_prep_any_w_2534 s_elig_prep_any_w_3544 s_prep_any_w_1524 s_prep_any_w_2534 s_prep_any_w_3544 s_prep_oral_w_1524 s_prep_inj_w_1524 s_prep_vr_w_1524 - +s_prep_any_sdc s_prep_oral_sdc s_prep_inj_sdc s_prep_vr_sdc +s_prep_any_plw s_prep_oral_plw s_prep_inj_plw s_prep_vr_plw s_inf_prep_any_source_prep_r s_prepinfect_prep_r s_prepinfect_prep_r_p s_infected_prep_no_r s_infected_prep_r s_started_prep_any_in_primary s_started_prep_oral_in_primary s_started_prep_inj_in_primary s_started_prep_vr_in_primary s_onprep_3_i_prep_no_r s_onprep_6_i_prep_no_r s_onprep_9_i_prep_no_r @@ -21721,7 +21752,7 @@ s_want_no_more_children s_pregnant_ntd s_pregnant_vlg1000 s_pregnant_o_dol s_pregnant_onart_vl_vhigh s_pregnant_onart_vl_vvhigh s_birth_with_inf_child s_child_with_resistant_hiv s_give_birth_with_hiv s_onart_birth_with_inf_child_res s_onart_birth_with_inf_child -s_breastfeeding +s_breastfeeding s_plw /*circumcision*/ s_mcirc s_mcirc_1519m s_mcirc_2024m s_mcirc_2529m s_mcirc_3034m s_mcirc_3539m s_mcirc_4044m s_mcirc_4549m From 317d404c3b2f3559f06e656206e6580fe7db8c80 Mon Sep 17 00:00:00 2001 From: Jenny Smith Date: Tue, 27 Feb 2024 09:55:42 +0000 Subject: [PATCH 2/3] Update hiv_synthesis.sas --- hiv_synthesis.sas | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/hiv_synthesis.sas b/hiv_synthesis.sas index a7755104..e1d844b9 100644 --- a/hiv_synthesis.sas +++ b/hiv_synthesis.sas @@ -19540,6 +19540,7 @@ s_i_age1_w_newp s_i_age2_w_newp s_i_age3_w_newp s_i_age4_w_newp s_i_age5_w_newp s_i_m_1549_np s_i_w_1549_np s_i_w_newp s_i_m_newp s_sdc + /*resistance*/ s_tam1_ s_tam2_ s_tam3_ s_m184m_ s_k103m_ s_y181m_ s_g190m_ s_nnm_ s_q151m_ s_k65m_ s_p32m_ s_p33m_ s_p46m_ s_p47m_ s_p50vm_ s_p50lm_ s_p54m_ s_p76m_ s_p82m_ s_p84m_ s_p88m_ s_p90m_ s_pim_ @@ -19595,6 +19596,7 @@ s_prep_any_w_1524 s_prep_any_w_2534 s_prep_any_w_3544 s_prep_oral_w_1524 s_prep_inj_w_1524 s_prep_vr_w_1524 s_prep_any_sdc s_prep_oral_sdc s_prep_inj_sdc s_prep_vr_sdc s_prep_any_plw s_prep_oral_plw s_prep_inj_plw s_prep_vr_plw + s_inf_prep_any_source_prep_r s_prepinfect_prep_r s_prepinfect_prep_r_p s_infected_prep_no_r s_infected_prep_r s_started_prep_any_in_primary s_started_prep_oral_in_primary s_started_prep_inj_in_primary s_started_prep_vr_in_primary s_onprep_3_i_prep_no_r s_onprep_6_i_prep_no_r s_onprep_9_i_prep_no_r @@ -21346,6 +21348,7 @@ m15r m25r m35r m45r m55r w15r w25r w35r w45r w55r s_i_m_1549_np s_i_w_1549_np s_i_w_newp s_i_m_newp s_sdc + /*resistance*/ s_tam1_ s_tam2_ s_tam3_ s_m184m_ s_k103m_ s_y181m_ s_g190m_ s_nnm_ s_q151m_ s_k65m_ s_p32m_ s_p33m_ s_p46m_ s_p47m_ s_p50vm_ s_p50lm_ s_p54m_ s_p76m_ s_p82m_ s_p84m_ s_p88m_ s_p90m_ s_pim_ @@ -21401,6 +21404,7 @@ s_prep_any_w_1524 s_prep_any_w_2534 s_prep_any_w_3544 s_prep_oral_w_1524 s_prep_inj_w_1524 s_prep_vr_w_1524 s_prep_any_sdc s_prep_oral_sdc s_prep_inj_sdc s_prep_vr_sdc s_prep_any_plw s_prep_oral_plw s_prep_inj_plw s_prep_vr_plw + s_inf_prep_any_source_prep_r s_prepinfect_prep_r s_prepinfect_prep_r_p s_infected_prep_no_r s_infected_prep_r s_started_prep_any_in_primary s_started_prep_oral_in_primary s_started_prep_inj_in_primary s_started_prep_vr_in_primary s_onprep_3_i_prep_no_r s_onprep_6_i_prep_no_r s_onprep_9_i_prep_no_r From e597c15c5f1641e21b43aa5630bce724e8a31291 Mon Sep 17 00:00:00 2001 From: Jenny Smith Date: Tue, 27 Feb 2024 11:47:18 +0000 Subject: [PATCH 3/3] Update hiv_synthesis.sas --- hiv_synthesis.sas | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/hiv_synthesis.sas b/hiv_synthesis.sas index e1d844b9..84502130 100644 --- a/hiv_synthesis.sas +++ b/hiv_synthesis.sas @@ -11739,7 +11739,7 @@ so a proportion (15%) are classified as non-who4_; * kombewa kenya dhs 2011-2015 (includes AIDS deaths) 15-49 males: 0.0065 females 0.0044 50-64: males 0.0191 females 0.0104 65+ males: 0.0617 females: 0.0464 -CVD death ~ 10% of deaths in > 50�s 3% in 15-49�s +CVD death ~ 10% of deaths in > 50s 3% in 15-49s * kombewa kenya dhs 2011-2015 (includes AIDS deaths) so reduce all cause mortality by 0.93 / 0.90 since cvd death now separated