Skip to content

Changes to testing, PrEP and SW code #318

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
LoveleenB-M merged 5 commits into from
Mar 11, 2026
Merged

Changes to testing, PrEP and SW code #318

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
72db7a1
Update hiv_synthesis.sas
LoveleenB-M Mar 9, 2026
fe04aac
Update hiv_synthesis.sas
LoveleenB-M Mar 9, 2026
0e58921
update
LoveleenB-M Mar 11, 2026
a12c847
Self testing, prep and SW changes
LoveleenB-M Mar 11, 2026
f4d51fb
Update hiv_synthesis.sas
LoveleenB-M Mar 11, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
20 changes: 1 addition & 19 deletions Zim_parameters.sas
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -56,22 +56,8 @@ rate_ch_art_init_str_9 = 0.1 ;

* sw_trans_matrix; %sample(sw_trans_matrix, 1 2 3, 0.10 0.80 0.10);

* sw_art_disadv; %sample(sw_art_disadv, 0 1, 0.10 0.90);
if sw_art_disadv=1 then do;
%sample_uniform(sw_higher_int, 2 5 10 20);
%sample_uniform(rel_sw_lower_adh, 0.8 0.9);
%sample_uniform(sw_higher_prob_loss_at_diag, 2 5 10);
end;

* rate_engage_sw_program; %sample_uniform(rate_engage_sw_program, 0.10 0.20 0.30);
* rate_disengage_sw_program; %sample_uniform(rate_disengage_sw_program, 0.01 0.03);

* date_sw_prog_intro; date_sw_prog_intro=2010;
* sw_program; %sample(sw_program, 0 1, 0.2 0.8);sw_program=1;*Discuss;
if sw_program = 1 then do;
%sample_uniform(rate_engage_sw_program, 0.10 0.20);
%sample_uniform(rate_disengage_sw_program, 0.02 0.05);
end;
* rate_disengage_sw_program;%sample_uniform(rate_disengage_sw_program, 0.01 0.03);

* CIRCUMCISION;

Expand All @@ -95,10 +81,6 @@ rate_ch_art_init_str_9 = 0.1 ;

***Too many people on PrEP;

* rate_test_startprep_any; %sample_uniform(rate_test_startprep_any, 0.10 0.15 0.30);

* prob_prep_oral_b; %sample_uniform(prob_prep_oral_b, 0.05 0.1);

* pref_prep_oral_beta_s1; %sample_uniform(pref_prep_oral_beta_s1, 0.6 0.7 0.8 0.9 1.0 1.1) ;

* rate_choose_stop_prep_oral; %sample_uniform(rate_choose_stop_prep_oral, 0.10 0.20 0.30);
Expand Down
30 changes: 19 additions & 11 deletions hiv_synthesis.sas
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -394,7 +394,7 @@ newp_seed = 7;
self_test_targeting = stt * test_targeting;

* date_self_test_intro; date_self_test_intro = 2018;
* rate_self_test; %sample_uniform(rate_self_test, 0.05 0.1 0.3 0.5 );
* rate_self_test; %sample_uniform(rate_self_test, 0.01 0.03 0.10);

* self_test_sens; self_test_sens = 0.93;

Expand Down Expand Up @@ -656,13 +656,13 @@ newp_seed = 7;
* p_rred_sw_newp; %sample_uniform(p_rred_sw_newp, 0.01 0.03 0.10);
* rate of sex workers moving to one category lower;

* sw_art_disadv; %sample(sw_art_disadv, 0 1, 0.15 0.85);
* sw_art_disadv; %sample(sw_art_disadv, 0 1, 0.10 0.90);
if sw_art_disadv=0 then do; sw_higher_int = 1; rel_sw_lower_adh = 1;sw_higher_prob_loss_at_diag = 1;end;

if sw_art_disadv=1 then do;
%sample_uniform(sw_higher_int, 2 3);
%sample_uniform(sw_higher_int, 2 5 10 20);
%sample_uniform(rel_sw_lower_adh, 0.8 0.9);
%sample_uniform(sw_higher_prob_loss_at_diag, 2 3);
%sample_uniform(sw_higher_prob_loss_at_diag, 2 5 10);
end;

* date_sw_prog_intro; date_sw_prog_intro=2010;
Expand All @@ -676,9 +676,9 @@ newp_seed = 7;
* rate_engage_sw_program; %sample_uniform(rate_engage_sw_program, 0.05 0.10); *previously 0.10;
* rate_disengage_sw_program;%sample_uniform(rate_disengage_sw_program, 0.02 0.04); *previously 0.025;
* effect_sw_prog_newp; %sample_uniform(effect_sw_prog_newp, 0.05 0.10);
* effect_sw_prog_6mtest; %sample_uniform(effect_sw_prog_6mtest, 0.20 0.35 0.50);
* effect_sw_prog_6mtest; %sample_uniform(effect_sw_prog_6mtest, 0.05 0.10 0.15);
* effect_sw_prog_int; %sample_uniform(effect_sw_prog_int, 0.30 0.50 0.70);
* effect_sw_prog_adh; %sample_uniform(effect_sw_prog_adh, 0.10 0.15 0.25);
* effect_sw_prog_adh; %sample_uniform(effect_sw_prog_adh, 0.20 0.35 0.50);
* effect_sw_prog_lossdiag; %sample_uniform(effect_sw_prog_lossdiag, 0.30 0.50 0.70);
* effect_sw_prog_prep_any; %sample_uniform(effect_sw_prog_prep_any, 0.05 0.10);
* effect_sw_prog_pers_sti; %sample_uniform(effect_sw_prog_pers_sti, 0.10 0.20);
Expand Down Expand Up @@ -763,7 +763,7 @@ end;
* prep_dependent_prev_vg1000; %sample(prep_dependent_prev_vg1000, 0 1, 0.80 0.20); * does prep use depend on the prevalence of vl > 1000 in population; * cioa_j ;
* prep_vlg1000_threshold; %sample(prep_vlg1000_threshold, 0.005 0.01, 0.5 0.5); * if prep use depends on prevalence of vl > 1000 in population, what is the threshold ?;

* rate_test_startprep_any; %sample_uniform(rate_test_startprep_any, 0.25 0.5 0.75);
* rate_test_startprep_any; %sample_uniform(rate_test_startprep_any, 0.05 0.10 0.15);
* probability of being tested for hiv with the intent to start prep, if all criteria are fullfilled, including prep_any_willing;
* dependent_on_time_step_length ;
* rate_test_restartprep_any; * removed;
Expand All @@ -786,7 +786,7 @@ and prep_any_willing = 1 and pref_prep_oral > pref_prep_cab / pref_prep_len and

* date_prep_oral_intro; date_prep_oral_intro=2018.25; * Introduction of oral PrEP ;
* dur_prep_oral_scaleup; dur_prep_oral_scaleup=4; * Assume 4 years to scale up oral prep to be consistent with previous analyses;
* prob_prep_oral_b; %sample_uniform(prob_prep_oral_b, 0.05 0.1 0.2 ); * 11dec17; *Probability of starting oral PrEP in people (who are eligible and willing to take oral prep) tested for HIV according to the base rate of testing;
* prob_prep_oral_b; %sample_uniform(prob_prep_oral_b, 0.05 0.1); * 11dec17; *Probability of starting oral PrEP in people (who are eligible and willing to take oral prep) tested for HIV according to the base rate of testing;
* lapr and dpv-vr - define prob_lapr_b and prob_dpv_b which may be different to prob_prep_oral_b - we may need to
redefine prep_any_willing so that it has more than two categories according to which prep forumations the person is willing to take;
* annual_testing_prep_oral; annual_testing_prep_oral=0.25; * frequency of HIV testing for people on oral PrEP (1=annual, 0.5= every 6 months, 0.25=every 3 months);
Expand Down Expand Up @@ -2997,12 +2997,20 @@ if t ge 2 and date_start_testing <= caldate{t} then do; * note that date_start_t
if gender=2 then do; rate_1sttest = rate_1sttest * rr_testing_female ; rate_reptest = rate_reptest * rr_testing_female ; end;
end;


if testing_disrup_covid =1 and covid_disrup_affected = 1 then do; rate_1sttest = 0 ; rate_reptest = 0; end;

***Zim specific; * JAS Feb24;
***Zim specific;
if country = 'Zimbabwe' then do;
if 2020.5 le caldate{t} lt 2021.5 then do; rate_1sttest=rate_1sttest*0.5;rate_reptest=rate_reptest*0.5;end;

if caldate{t} = 2020.5 then do;
rate_1sttest_2020=rate_1sttest*0.1;
rate_reptest_2020=rate_reptest*0.1;
end;

if caldate{t} > 2020.5 then do;
rate_1sttest = max ((rate_1sttest_2020 - ((caldate{t}-2020.5 )*an_lin_incr_test*fold_rate_decr_test_future)), 0.0001);
rate_reptest = max ((rate_reptest_2020 - ((caldate{t}-2020.5 )*an_lin_incr_test*fold_rate_decr_test_future)), 0.0001);
end;
end;

* ts1m;
Expand Down
Loading