Skip to content
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

Jump to bottom

Pop structure and circumcision #264

Merged
merged 4 commits into from
Nov 13, 2023
Merged

Pop structure and circumcision #264

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
c1d5bc6
Pop structure and circumcision
ValentinaCambiano Nov 13, 2023
d3b95a7
Update Zim parameters
ValentinaCambiano Nov 13, 2023
b590145
Update Zim_parameters.sas
ValentinaCambiano Nov 13, 2023
8bb46d3
Update Zim_parameters.sas
ValentinaCambiano Nov 13, 2023
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
110 changes: 52 additions & 58 deletions Zim_parameters.sas
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -8,49 +8,26 @@ caldate1=1984;
caldate_never_dot=1984;
startyr = 1991 + 0.25;

* inc_cat; inc_cat = 1 ;


* SEXUAL BEHAVIOUR;

* ych_risk_beh_newp; %sample(ych_risk_beh_newp, 0.5 0.6 0.7 , 0.4 0.3 0.3);
* ych_risk_beh_ep; %sample_uniform(ych_risk_beh_ep, 0.8 0.9 0.95);
* p_rred_p; %sample_uniform(p_rred_p, 0.4 0.5 0.6);
* p_hsb_p; %sample(p_hsb_p, 0.05 0.08 0.15 0.25, 0.25 0.25 0.25 0.25);
* newp_factor; %sample_uniform(newp_factor, 1 2 3 5 );
* ych2_risk_beh_newp; %sample(ych2_risk_beh_newp,
0.95 0.99 1 ,
0.3 0.3 4 );
* inc_cat; inc_cat = 4 ;


* HIV TESTING;

* date_start_testing; date_start_testing = 2005 ;
* test_targeting; *%sample(test_targeting, 1.1 1.3 1.5, 0.4 0.4 0.2); *Vale - 20211026, not specific to Zim before;
*%sample(test_targeting, 1 1.25 1.5, 0.6 0.3 0.1); *Vale - 20211123;
%sample(test_targeting, 1 1.1 1.3, 0.7 0.2 0.1);*Vale - 20220105;
* an_lin_incr_test; *%sample(an_lin_incr_test,
0.0100 0.015 0.0200 ,
0.50 0.50 0.00 );
*%sample(an_lin_incr_test,
0.0100 0.015 0.0200 ,
0.70 0.30 0.00 );
%sample(an_lin_incr_test,
* test_targeting; %sample(test_targeting, 1 1.1 1.3, 0.7 0.2 0.1);*Vale - 20220105;
* an_lin_incr_test; %sample(an_lin_incr_test,
0.005 0.01 0.015,
0.6 0.3 0.1);*Vale - 20220105;
* date_test_rate_plateau; date_test_rate_plateau = 2019 ;
* fold_rate_decr_test_future;*%sample_uniform(fold_rate_decr_test_future, 0.1 0.2 0.33);
%sample_uniform(fold_rate_decr_test_future, 0.00125 0.00165 0.0025 0.00375);
* fold_rate_decr_test_future;%sample_uniform(fold_rate_decr_test_future, 0.25 0.33 0.5 0.75);

* rate_anc_inc; *%sample_uniform(rate_anc_inc, 0.005 0.01 0.03 0.05 0.10); *Mar2023;
%sample(rate_anc_inc, 0.005 0.01 0.03 0.05 0.10, 0.15 0.15 0.3 0.2 0.2);
* rate_anc_inc; %sample_uniform(rate_anc_inc, 0.025 0.03 0.035);
* prob_test_2ndtrim; %sample_uniform(prob_test_2ndtrim, 0.7 0.75 0.8 0.85 0.0 0.95 1.00);
* prob_test_postdel; prob_test_postdel=0.95;
* prob_test_postdel; %sample_uniform(prob_test_postdel, 0.25 0.5 0.75);

* NATURAL PROGRESSION AND RISK OF HIV RELATED CONDITIONS;
*Vale - 20211026: all the changes in the section "NATURAL PROGRESSION...." are taken from SA;
* fold_change_in_risk_base_rate;
*%sample_uniform(fold_change_in_risk_base_rate, 0.7 0.8 0.9);
%sample_uniform(fold_change_in_risk_base_rate, 0.85 1.0); *Vale - 20211123;
* it is 0.85 rather than 1 in south africa parameter sets, and 1 in Malawi as there is no evidence
that this lower rate holds in malawi ;
Expand All @@ -69,43 +46,60 @@ rate_ch_art_init_str_9 = 0.1 ;
* rate_int_choice; %sample_uniform(rate_int_choice, 0.0020 0.0030 0.0040);*Vale - 20220105;


* SEX WORKERS;
* base_rate_sw; *%sample(base_rate_sw, 0.0015 0.0020 0.0025, 0.2 0.2 0.6);*Vale - 20211026, not specific to Zim before;
*Vale - 20211123, removed;
* base_rate_stop_sexwork; *%sample_uniform(base_rate_stop_sexwork, 0.015 0.030 0.045);*Vale - 20211026, not specific to Zim before;
*Vale - 20211123, removed;
* SEX WORKERS;

* base_rate_sw; %sample(base_rate_sw, 0.0014 0.0018, 0.7 0.3);*20231002;
* base_rate_stop_sexwork; %sample(base_rate_stop_sexwork, 0.010 0.015 0.020, 0.25 0.25 0.5);


* rr_sw_age_3549; rr_sw_age_3549 = 0.25;
* age_effect_stop_sexwork; *No need to specify as it was hard coded and the output was ok;

* sw_trans_matrix; %sample(sw_trans_matrix, 1 2 3, 0.10 0.45 0.45);
* 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;

***Change these parameters as are assuming higher attendance than in core and Zim has Sisters program in place;
* 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_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_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, 0.50 0.75);
* effect_sw_prog_pers_sti; %sample_uniform(effect_sw_prog_pers_sti, 0.50 0.75);

* CIRCUMCISION;

* circ_inc_rate; *circ_inc_rate = 0.001;
*%sample(circ_inc_rate,
0.001 0.003 0.01 0.1,
0.1 0.6 0.2 0.1);*Vale - 20211026;
*%sample(circ_inc_rate, 0.001 0.002 0.003,
0.25 0.5 0.25);*Vale - 20211104;
%sample(circ_inc_rate, 0.0001 0.001 0.002,
* circ_inc_rate; %sample(circ_inc_rate, 0.0001 0.001 0.002,
0.25 0.5 0.25);
* prob_birth_circ; *prob_birth_circ = 0.2 ;
%sample(prob_birth_circ,
* prob_birth_circ; %sample(prob_birth_circ,
0.05 0.1 0.15,
0.25 0.5 0.25); *Vale - 20211026;

* rel_incr_circ_post_2013; *%sample(rel_incr_circ_post_2013,
0.8 1 3 7,
0.10 0.25 0.25 0.40);
*if circ_inc_rate=0.1 then rel_incr_circ_post_2013=min(rel_incr_circ_post_2013, 1);
*%sample(rel_incr_circ_post_2013,
1 3 5,
0.25 0.5 0.25);
%sample(rel_incr_circ_post_2013,
4 5 6,
0.25 0.5 0.25);

***Higher circ post 2015 - adding this here as if we increase the above, we will miss the DHS data point in 2015 on circ prev;
* rel_incr_circ_post_2015; %sample(rel_incr_circ_post_2015,
7 8 9,
0.35 0.5 0.20);
*abs_decr_birth_circ; %sample(abs_decr_birth_circ,
0 0.002 0.004,
0.20 0.20 0.60 );

* rel_incr_circ_post_2013; %sample(rel_incr_circ_post_2013,
2 3 4,
0.25 0.5 0.25); *Vale - 20230823;
* rel_incr_circ_post_2023; %sample(rel_incr_circ_post_2023,
2 3 4,
0.25 0.5 0.25); *Vale - 20231010;


***Too many people on PrEP;
Expand Down
Loading
Loading