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Update country-specific sections #273

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Feb 28, 2024
Merged

Update country-specific sections #273

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c1cca6a
Update MW params
jennifersmith203 Feb 27, 2024
105f4da
Update hiv_synthesis.sas
jennifersmith203 Feb 27, 2024
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24 changes: 14 additions & 10 deletions Malawi_parameters.sas
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Original file line number Diff line number Diff line change
Expand Up @@ -3,21 +3,25 @@
/***************************************************************************/


* country; country='Malawi';
* caldate1; caldate1 = 1984; *core: 1989;
* caldate_never_dot; caldate_never_dot=1984; *core: 1989;

* POPULATION GROWTH AND DEMOGRAPHY;

* inc_cat; inc_cat = 1 ;
* inc_cat; inc_cat = 4 ; * Changed to new inc_cat 4 (specified for Zim) from inc_cat 1 JAS Nov23;

* 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 0.4 );
/** 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 0.4 );*/

* HIV TESTING;

Expand Down
14 changes: 13 additions & 1 deletion SA_parameters.sas
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Original file line number Diff line number Diff line change
@@ -1,3 +1,8 @@
* These parameters are up to date at 17th Oct 2023;
* caldate1, caldate_never_dot and startyr specified here to overwrite core value;
* country added to switch on SA-spcific abort statements;
* Note that rate_anc_inc has been updated from rate_testanc_inc (used in some other SA analyses) to be consistent with the current core program;
* JAS Oct23;

****% on ART of those diag too high***

Expand All @@ -6,6 +11,9 @@
****************** SOUTH AFRICA SPECIFIC PARAMETERS ******************
/***************************************************************************/

* country; country='South Africa';
* caldate1; caldate1 = 1984; *core: 1989;
* caldate_never_dot; caldate_never_dot=1984; *core: 1989;

* POPULATION GROWTH AND DEMOGRAPHY;
* inc_cat; inc_cat = 3;
Expand All @@ -14,7 +22,9 @@

* fold_change_ac_death_rate;fold_change_ac_death_rate_w = 0.65; fold_change_ac_death_rate_m = 0.65;

newp_seed = 10 ;
* INTRODUCTION OF HIV;
* startyr; startyr = 1993;
* newp_seed; newp_seed = 10 ;

* SEXUAL BEHAVIOUR;
* ych_risk_beh_newp; ych_risk_beh_newp = 1;
Expand All @@ -31,6 +41,8 @@ newp_seed = 10 ;
* sex_age_mixing_matrix_w; %sample(sex_age_mixing_matrix_w, 1 2 3 4 5 6 , 0.3 0.3 0.1 0.1 0.1 0.1);




* TRANSMISSION;

* fold_tr; fold_tr = 1;
Expand Down
11 changes: 6 additions & 5 deletions Zim_parameters.sas
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Original file line number Diff line number Diff line change
Expand Up @@ -2,14 +2,15 @@
****************** ZIMBABWE SPECIFIC PARAMETERS ******************
/***************************************************************************/

* country; country='Zimbabwe';
* caldate1; caldate1 = 1984; *core: 1989;
* caldate_never_dot; caldate_never_dot=1984; *core: 1989;

* POPULATION GROWTH AND DEMOGRAPHY;
caldate1=1984;
caldate_never_dot=1984;
startyr = 1991 + 0.25;

* inc_cat; inc_cat = 4 ;
* inc_cat; inc_cat = 4 ;

* INTRODUCTION OF HIV;
* startyr; startyr = 1991 + 0.25;

* HIV TESTING;

Expand Down
52 changes: 38 additions & 14 deletions hiv_synthesis.sas
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Expand Up @@ -128,6 +128,7 @@ run = rand('uniform')*1000000000; run=round(run,1);
dataset_id=trim(left(run));
call symput('dataset_id',dataset_id);

* overwritten in country-specific include statements (SA, Zim, MW) JAS Feb24;
caldate1=1989;
caldate_never_dot=1989;

Expand All @@ -143,7 +144,7 @@ _u57 = rand('uniform'); _u58 = rand('uniform'); _u59 = rand('uniform'); _u60 = r


* start of epidemic;
startyr = 1989 + 0.25;
startyr = 1989 + 0.25; * overwritten in country-specific include statements (SA, Zim) JAS Feb24;
* ts1m;
/*
startyr = 1989 + 1/12;
Expand Down Expand Up @@ -3087,8 +3088,10 @@ if caldate{t} >= &year_interv then do;
end;

if testing_disrup_covid =1 and covid_disrup_affected = 1 then do; rate_1sttest = 0 ; rate_reptest = 0; end;
***Zim specific;
/*if 2020.5 le caldate{t} lt 2021.5 then do; rate_1sttest=rate_1sttest*0.5;rate_reptest=rate_reptest*0.5;end;*/
***Zim specific; * JAS Feb24;
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;
end;


* ts1m;
Expand Down Expand Up @@ -3201,9 +3204,11 @@ if t ge 2 and &year_interv <= caldate{t} and circ_inc_rate_year_i = 4 then do;*o
end;
end;

***Zim specific;
/*if 2020.5 le caldate{t} lt 2021.5 then prob_circ = prob_circ*0.5;*/
/*if vmmc_disrup_covid =1 and covid_disrup_affected = 1 then prob_circ = 0;*/
***Zim specific; *JAS Feb24;
if country = 'Zimbabwe' then do;
if 2020.5 le caldate{t} lt 2021.5 then prob_circ = prob_circ*0.5;
if vmmc_disrup_covid =1 and covid_disrup_affected = 1 then prob_circ = 0;
end;


if prob_circ ne . then prob_circ = min(prob_circ,1);
Expand Down Expand Up @@ -17553,7 +17558,7 @@ hiv_cab = hiv_cab_3m + hiv_cab_6m + hiv_cab_9m + hiv_cab_ge12m ;

/*

proc freq; tables cald hiv ; where death=.; run;
proc freq; tables country cald hiv ; where death=.; run;

*/

Expand Down Expand Up @@ -19172,13 +19177,32 @@ keep_going_1999 keep_going_2004 keep_going_2016 keep_going_2020

;

***Zim specific;
/*
if cald = 1999.5 and (prevalence1549 < 0.08) then do; abort abend; end;
if cald = 2004.5 and (prevalence1549 < 0.07) then do; abort abend; end;
if cald = 2015.5 and (prevalence1549 < 0.12 or prevalence1549 > 0.15 ) then do; abort abend; end;*ZIMPHIA 13.4;
*/
/*if cald = &year_interv and (prevalence1549 > 0.30 or incidence1549 < 0.15 ) then do; abort abend; end;*/
***Malawi specific; *JAS Feb24;
if country = 'Malawi' then do;
if cald = 1998.5 and (prevalence1549 < 0.08 or prevalence1549 > 0.19 ) then do; abort abend; end;
if cald = 1999.5 and (prevalence1549 < 0.08 or prevalence1549 > 0.19 ) then do; abort abend; end;
if cald = 2004.5 and (prevalence1549 < 0.07 or prevalence1549 > 0.20 ) then do; abort abend; end;
if cald = 2016.5 and (prevalence1549 < 0.07 or prevalence1549 > 0.13 ) then do; abort abend; end;
if cald = 2020 and p_vl1000 < 0.75 then do; abort abend; end;
end;

***South Africa specific; *JAS Feb24;
if country = 'South Africa' then do;
if cald = 2017.5 and (prevalence1549 < 0.166 or prevalence1549 > 0.246) then do;
abort abend;
end;
if cald = 2021 and (s_onart < 3333 or s_onart > 6400) then do;
abort abend;
end;
end;

***Zim specific; *JAS Feb24;
if country = 'Zimbabwe' then do;
if cald = 1999.5 and (prevalence1549 < 0.08) then do; abort abend; end;
if cald = 2004.5 and (prevalence1549 < 0.07) then do; abort abend; end;
if cald = 2015.5 and (prevalence1549 < 0.12 or prevalence1549 > 0.15 ) then do; abort abend; end;*ZIMPHIA 13.4;
end;
/*if cald = &year_interv and (prevalence1549 > 0.30 or incidence1549 < 0.15 ) then do; abort abend; end;*/ *QUERY should we be using this line for Zim? JAS Feb24;

* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~;
* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~;
Expand Down
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