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Merge pull request #299 from UCL/andrew_pr_20
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adding transmission through breastfeeding
@andrew-phillips-1
andrew-phillips-1 authored Oct 2, 2024

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2 parents 349b05a + d29556c commit ba1aca1
Showing 2 changed files with 53 additions and 44 deletions.
92 changes: 50 additions & 42 deletions create_wide_file.sas
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Original file line number Diff line number Diff line change
@@ -17,12 +17,11 @@ set a;
if cald=2023.25; ***Update as required;
s_alive = s_alive_m + s_alive_w ;
sf_2023 = 10000000 / s_alive; ***If calibrating to a specific setting, change 10000000 to desired 15+ population size;
keep run sf_2023;
sf=sf_2023;
keep run sf sf_2023;
proc sort; by run;run;


%let sf=sf_2023;


data y;
merge a sf;
@@ -53,18 +52,27 @@ discount_10py = 1/(1.10**(cald-&year_start_disc));

* ================================================================================= ;

ly = s_ly * &sf; *life years;
dly = s_dly * &sf; *discounted life years;
ly = s_ly * sf; *life years;
dly = s_dly * sf; *discounted life years;

s_ddaly = s_dead_ddaly + s_live_ddaly;

***Scaling up to annual discounted DALYs in the whole population;
ddaly = s_ddaly * &sf * 4;
ddaly = s_ddaly * sf * 4;


***These are additional potential DALYs to include which have not so far been included;

ddaly_mtct = s_ddaly_mtct * &sf * 4; ***Crude estimate of number of DALYs incurred in a child born with HIV;
s_mtct = s_birth_with_inf_child + s_child_infected_breastfeeding ;

ddaly_yll_mtct = s_mtct * sf * 4 * 5 * discount ; * 5 yll dalys per infected child ;

ddaly_mtct = ddaly_yll_mtct + (s_ddaly_mtct * sf * 4); * adding the yll to the live dalys;

* ddalys accounting for mtct;

ddaly_ac_mtct = ddaly + ddaly_mtct;



* ================================================================================= ;
@@ -77,15 +85,15 @@ ddaly_mtct = s_ddaly_mtct * &sf * 4; ***Crude estimate of number of DALYs incur
* ts1m - 12 instead of 4;

***These are scaled up discounted costs;
dzdv_cost = s_dcost_zdv * &sf * 4 / 1000;
dten_cost = s_dcost_ten * &sf * 4 / 1000;
d3tc_cost = s_dcost_3tc * &sf * 4 / 1000;
dnev_cost = s_dcost_nev * &sf * 4 / 1000;
dlpr_cost = s_dcost_lpr * &sf * 4 / 1000;
ddar_cost = s_dcost_dar * &sf * 4 / 1000;
dtaz_cost = s_dcost_taz * &sf * 4 / 1000;
defa_cost = s_dcost_efa * &sf * 4 / 1000;
ddol_cost = s_dcost_dol * &sf * 4 / 1000;
dzdv_cost = s_dcost_zdv * sf * 4 / 1000;
dten_cost = s_dcost_ten * sf * 4 / 1000;
d3tc_cost = s_dcost_3tc * sf * 4 / 1000;
dnev_cost = s_dcost_nev * sf * 4 / 1000;
dlpr_cost = s_dcost_lpr * sf * 4 / 1000;
ddar_cost = s_dcost_dar * sf * 4 / 1000;
dtaz_cost = s_dcost_taz * sf * 4 / 1000;
defa_cost = s_dcost_efa * sf * 4 / 1000;
ddol_cost = s_dcost_dol * sf * 4 / 1000;

if s_dart_cost=. then s_dart_cost=0;
if s_dcost_prep_oral=. then s_dcost_prep_oral=0;
@@ -99,34 +107,34 @@ if s_dcost_condom_dn=. then s_dcost_condom_dn=0;
s_dcost_prep = s_dcost_prep_oral + s_dcost_prep_inj;
s_dcost_prep_visit = s_dcost_prep_visit_oral + s_dcost_prep_visit_inj;

dvis_cost = s_dvis_cost * &sf * 4 / 1000;
dart_cost = s_dart_cost * &sf * 4 / 1000; ***This should be the same as dart_cost_y below (and is not used);
dvl_cost = s_dvl_cost * &sf * 4 / 1000;
dcd4_cost = s_dcd4_cost * &sf * 4 / 1000;
dadc_cost = s_dadc_cost * &sf * 4 / 1000;
dnon_tb_who3_cost = s_dnon_tb_who3_cost * &sf * 4 / 1000;
dtb_cost = s_dtb_cost * &sf * 4 / 1000;
dtest_cost = s_dtest_cost * &sf * 4 / 1000;
dcot_cost = s_dcot_cost * &sf * 4 / 1000;
dres_cost = s_dres_cost * &sf * 4 / 1000;
d_t_adh_int_cost = s_d_t_adh_int_cost * &sf * 4 / 1000;
dcost_prep = s_dcost_prep * &sf * 4 / 1000;
dcost_prep_inj = s_dcost_prep_inj * &sf * 4 / 1000;
dcost_prep_oral = s_dcost_prep_oral * &sf * 4 / 1000;
dcost_prep_visit = s_dcost_prep_visit * &sf * 4 / 1000;
dcost_prep_visit_inj = s_dcost_prep_visit_inj * &sf * 4 / 1000;
dcost_prep_visit_oral = s_dcost_prep_visit_oral * &sf * 4 / 1000;
dcost_prep_ac_adh = s_dcost_prep_ac_adh * &sf * 4 / 1000; ***PrEP cost taking into account adherence to PrEP;
dcost_sw_program = s_dcost_sw_program * &sf * 4 / 1000;

dfullvis_cost = s_dfull_vis_cost * &sf * 4 / 1000;
dcost_circ = s_dcost_circ * &sf * 4 / 1000;
dcost_condom_dn = s_dcost_condom_dn * &sf * 4 / 1000;
dswitchline_cost = s_dcost_switch_line * &sf * 4 / 1000;
dvis_cost = s_dvis_cost * sf * 4 / 1000;
dart_cost = s_dart_cost * sf * 4 / 1000; ***This should be the same as dart_cost_y below (and is not used);
dvl_cost = s_dvl_cost * sf * 4 / 1000;
dcd4_cost = s_dcd4_cost * sf * 4 / 1000;
dadc_cost = s_dadc_cost * sf * 4 / 1000;
dnon_tb_who3_cost = s_dnon_tb_who3_cost * sf * 4 / 1000;
dtb_cost = s_dtb_cost * sf * 4 / 1000;
dtest_cost = s_dtest_cost * sf * 4 / 1000;
dcot_cost = s_dcot_cost * sf * 4 / 1000;
dres_cost = s_dres_cost * sf * 4 / 1000;
d_t_adh_int_cost = s_d_t_adh_int_cost * sf * 4 / 1000;
dcost_prep = s_dcost_prep * sf * 4 / 1000;
dcost_prep_inj = s_dcost_prep_inj * sf * 4 / 1000;
dcost_prep_oral = s_dcost_prep_oral * sf * 4 / 1000;
dcost_prep_visit = s_dcost_prep_visit * sf * 4 / 1000;
dcost_prep_visit_inj = s_dcost_prep_visit_inj * sf * 4 / 1000;
dcost_prep_visit_oral = s_dcost_prep_visit_oral * sf * 4 / 1000;
dcost_prep_ac_adh = s_dcost_prep_ac_adh * sf * 4 / 1000; ***PrEP cost taking into account adherence to PrEP;
dcost_sw_program = s_dcost_sw_program * sf * 4 / 1000;

dfullvis_cost = s_dfull_vis_cost * sf * 4 / 1000;
dcost_circ = s_dcost_circ * sf * 4 / 1000;
dcost_condom_dn = s_dcost_condom_dn * sf * 4 / 1000;
dswitchline_cost = s_dcost_switch_line * sf * 4 / 1000;
if dswitchline_cost=. then dswitchline_cost=0;
if s_dcost_drug_level_test=. then s_dcost_drug_level_test=0;
dcost_drug_level_test = s_dcost_drug_level_test * &sf * 4 / 1000;
dcost_child_hiv = s_dcost_child_hiv * &sf * 4 / 1000;
dcost_drug_level_test = s_dcost_drug_level_test * sf * 4 / 1000;
dcost_child_hiv = s_dcost_child_hiv * sf * 4 / 1000;

dclin_cost = dadc_cost + dnon_tb_who3_cost + dcot_cost + dtb_cost;

5 changes: 3 additions & 2 deletions hiv_synthesis.sas
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Original file line number Diff line number Diff line change
@@ -187,10 +187,11 @@ newp_seed = 7;
%sample(rate_birth_with_infected_child, 0.3 0.4 0.5 0.6, 0.05 0.25 0.6 0.1);
* rate_trans_breastfeeding; %sample_uniform(rate_trans_breastfeeding, 0.05 0.1); * Nduati et al. 2000; * this is rate per 3 months with vl between 4 and 5;
* prob_stop_breastfeeding_yr1; *JAS Apr2023;
prob_stop_breastfeeding_yr1 = 0.02;*73; * 3-monthly probability of stopping breastfeeding in first year after birth;
%sample_uniform(prob_stop_breastfeeding_yr1, 0.01 0.02 0.05);*73; * 3-monthly probability of stopping breastfeeding in first year after birth;
* dependent_on_time_step_length ; *ts1m - switch to 1-month probabilities;
* prob_stop_breastfeeding_yr2; *JAS Apr2023;
prob_stop_breastfeeding_yr2 = 0.132;*5; * 3-monthly probability of stopping breastfeeding in second year after birth;
%sample_uniform(prob_stop_breastfeeding_yr1, 0.07 0.13 0.20);
*5; * 3-monthly probability of stopping breastfeeding in second year after birth;
* see Excel worksheet Breastfeeding probabilities for calculations of probabilities (based on Neves et al 2021 and Zong et al 2021);
* dependent_on_time_step_length ; *ts1m - switch to 1-month probabilities;

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