Merge pull request #129 from UCL/Loveleen

Update hiv_synthesis.sas

Author: LoveleenB-M

hiv_synthesis.sas

@@ -419,7 +419,6 @@ prob_prep_restart=1.00; * set to 1 given we have rate_test_restartprep; *Probabi
 prob_prep_visit_counsel=0; *Probability of PrEP adherence counselling happening at drug pick-up;
 prob_prep_restart_choice=0.10; * probability of restarting PrEP after discontinuation even when newp>1;
 * dependent_on_time_step_length ; 
-prepuptake_sw=0.50; *Probability of PrEP uptake if eligible for female sex workers;
 prepuptake_pop=0.20; **Probability of PrEP uptake if eligible for general population;
 pop_wide_tld_prob_egfr=0.5; * probability per 3 months of getting egfr test when pop_wide_tld_prep=1 when indicated (annually);
 * dependent_on_time_step_length ;
@@ -725,8 +724,8 @@ p_neph_stops_after_ten = 0.1;
 										  if e >= 0.66 then effect_sw_prog_adh=1;
 * effect_sw_prog_lossdiag;	e=uniform(0); if e < 0.33 then effect_sw_prog_lossdiag=0.80; if 0.33 <= e < 0.66 then effect_sw_prog_lossdiag=0.60;
 										  if e >= 0.66 then effect_sw_prog_lossdiag=0.40;
-* effect_sw_prog_prep;		e=uniform(0); if e < 0.33 then effect_sw_prog_prep=0.60; if 0.33 <= e < 0.66 then effect_sw_prog_prep=0.75;
-										  if e >= 0.66 then effect_sw_prog_prep=0.90;
+* effect_sw_prog_prep;       e=uniform(0);if e < 0.50 then effect_sw_prog_prep=0.95; if e >= 0.50 then effect_sw_prog_prep=0.80;
+
 
 * tb_base_prob_diag_l;		e=uniform(0); if e < 0.333 then tb_base_prob_diag_l=0.25; if 0.333 <= e < 0.666 then tb_base_prob_diag_l=0.50;
 										  if e >= 0.666 then tb_base_prob_diag_l=0.75;
@@ -765,9 +764,9 @@ p_neph_stops_after_ten = 0.1;
 * prob_prep_restart_choice;  r=uniform(0); if r < 0.33 then prob_prep_restart_choice=0.05; if 0.33 <= r < 0.67 then prob_prep_restart_choice=0.10;
 							if 0.67 <= r then prob_prep_restart_choice=0.20;
 * dependent_on_time_step_length ;
-
-* prepuptake_sw;			r=uniform(0); prepuptake_sw=0.5;  if r > 0.8 then prepuptake_sw =0.10; if r < 0.2 then prepuptake_sw = 0.80;
+							
 * prepuptake_pop;			r=uniform(0); prepuptake_pop=0.2;  if r > 0.8 then prepuptake_pop =0.10; if r < 0.2 then prepuptake_pop = 0.5 ;
+* add_prepuptake_sw;		add_prepuptake_sw=0; ***this may be sampled at a later date;
 
 * note there are three parameters that affect use of prep besides the prep_strategy - prob_prep_b is prob of starting if prep_elig=1 and tested=1
 and prep_willing = 1 - a person cannot be prep_elig=1 if hard_reach=1 - a person prep_elig=1 will only actually have a chance of starting prep
@@ -1612,7 +1611,6 @@ eff_sw_higher_int = sw_higher_int;
 eff_prob_sw_lower_adh = prob_sw_lower_adh;
 eff_sw_higher_prob_loss_at_diag = sw_higher_prob_loss_at_diag;
 sw_program_visit=0;
-eff_prepuptake_sw=prepuptake_sw;
 
 * na defines a "non-adherent person" - not sure if this is reasonable structure for non adherence;
 
@@ -1806,11 +1804,7 @@ if adh_pattern_prep=4 then adhav_pr = adhav*0.50;
 
 
 * willingness to take prep if offered;
-r1=uniform(0); prep_willing_pop = 0; if r1 < prepuptake_pop then prep_willing_pop =1;
-if gender=2 then do;
-r2=uniform(0); prep_willing_sw = prep_willing_pop; 
-if prep_willing_pop=0 and r2 < (prepuptake_sw-prepuptake_pop)/(1-prepuptake_pop) then prep_willing_sw =1;
-end;
+r1=uniform(0); prep_willing = 0; if r1 < prepuptake_pop then prep_willing =1;
 
 hiv=0;
 nip=0;
@@ -2037,8 +2031,7 @@ if sw_program_visit=0 then do; e=uniform(0);
 		eff_sw_higher_int = sw_higher_int * effect_sw_prog_int;
 		eff_prob_sw_lower_adh = prob_sw_lower_adh / effect_sw_prog_adh ;
 		eff_sw_higher_prob_loss_at_diag = sw_higher_prob_loss_at_diag * effect_sw_prog_lossdiag;
-		eff_prepuptake_sw=effect_sw_prog_prep;
-		s= uniform(0); if s < eff_prepuptake_sw and prep_willing_sw = 0 then prep_willing_sw = 1;
+		s= uniform(0); if s < effect_sw_prog_prep and prep_willing = 0 then prep_willing = 1;
 		end;
 	end;
 end; 
@@ -2051,7 +2044,6 @@ else if sw_program_visit=1 then do; e=uniform(0);
 		eff_sw_higher_int = sw_higher_int;
 		eff_prob_sw_lower_adh = prob_sw_lower_adh; 
 		eff_sw_higher_prob_loss_at_diag = sw_higher_prob_loss_at_diag ; 
-		eff_prepuptake_sw=prepuptake_sw;
 end; 
 
 end;
@@ -2157,17 +2149,13 @@ if	higher_future_prep_cov=1 then do;
 							eff_prob_prep_restart_choice = round(eff_prob_prep_restart_choice, 0.01);
 						end;		
 
-* incr_prepuptake_sw_2020;
-						incr_prepuptake_sw_2020 = 0;  
-						if _u34 < 0.95 then do; incr_prepuptake_sw_2020 = 1; 
-							r= uniform(0); if r < 0.95 and prep_willing_sw = 0 then prep_willing_sw = 1;
-						end;		
+	
 
 * incr_prepuptake_pop_2020;
 						incr_prepuptake_pop_2020 = 0;  
 						if _u36 < 0.95 then do; 
 							incr_prepuptake_pop_2020 = 1; 
-							r= uniform(0); if r < 0.8 and prep_willing_pop = 0 then prep_willing_pop = 1;
+							r= uniform(0); if r < 0.8 and prep_willing = 0 then prep_willing = 1;
 						end;	
 
 * prep_strategy;
@@ -3313,6 +3301,10 @@ if gender = 2 and sw_tm1  = 0 then do;
 	if 20 <= age < 25 and life_sex_risk = 3 and e < base_rate_sw*rr_sw_life_sex_risk_3*sqrt(rred_rc) then sw=1;
 	if 25 <= age < 35 and life_sex_risk = 3 and e < base_rate_sw*rr_sw_age_2534*rr_sw_life_sex_risk_3*sqrt(rred_rc) then sw=1;
 	if 35 <= age < 50 and life_sex_risk = 3 and e < base_rate_sw*rr_sw_age_3549*rr_sw_life_sex_risk_3*sqrt(rred_rc) then sw=1;
+
+	if sw=1 then do; r=uniform(0);if prep_willing=0 and r < add_prepuptake_sw then prep_willing=1;end;
+	***currently SW are no more likely to be willing to take prep than gen pop;
+
 	end;
 
 	if ever_sw = 1 then do; * dependent_on_time_step_length ;
@@ -3331,6 +3323,7 @@ end;
 end;
 
 
+
 *initial distribution of newp for sw (need to define tm1 here in order to define number of current partners below);
 if t ge 2 and  sw_tm1 ne 1 and sw=1 then do; 
 	e=uniform(0);
@@ -4069,7 +4062,7 @@ and ((testing_disrup_covid ne 1 or covid_disrup_affected ne 1 )) then do;
 		available with roll-out and interest of PrEP
 		 do not differentiate the probabilty of testing whether they have a short-term or long-term partner;
 
-		if  prep_ever ne 1 and tested ne 1 and prep_elig=1 and (prep_willing_pop=1 or  (sw=1 and prep_willing_sw=1 ))  then do;
+		if  prep_ever ne 1 and tested ne 1 and prep_elig=1 and prep_willing=1  then do;
 			a=uniform(0); if a < eff_rate_test_startprep then do;	
 				tested=1;ever_tested=1;testfor_prep=1;dt_last_test=caldate{t};np_lasttest=0;
 			end; 
@@ -4133,18 +4126,12 @@ if t ge 4 and caldate{t} ge date_prep_intro and registd ne 1 and prep_elig=1 the
 	*it was tested_tm1=1 and hiv_tm1=0. Now changed to tested=1 and commented out hiv_tm1=0 because
 	we want people who are false negative to also start PrEP, this is the reason why hiv=0 is now commented out;
 	if prep_ever ne 1 and tested=1 and (hiv=0 or (hiv=1 and unisensprep > sens_vct)) then do;
-		if sw = 1 then do;
-			if prep_willing_sw=1 then do; 
-				if 		testfor_prep = 1  then do; prep   =1; prep_ever=1; continuous_prep_use=0.25; dt_prep_s=caldate{t}; dt_prep_e=caldate{t};end; 
-				else if testfor_prep ne 1 then do;r=uniform(0); if r < prob_prep_b then do; prep   =1; prep_ever=1; dt_prep_s=caldate{t}; dt_prep_e=caldate{t};end; end;
-			end;
-		end;
-		else if sw ne 1 then do; 
-			if prep_willing_pop=1 then do; 
+	 
+			if prep_willing=1 then do; 
 				if 		testfor_prep = 1  then do;prep   =1; prep_ever=1; continuous_prep_use=0.25; dt_prep_s=caldate{t}; dt_prep_e=caldate{t};end; 
 				else if testfor_prep ne 1 then do;r=uniform(0); if r < prob_prep_b then do; prep   =1; prep_ever=1; dt_prep_s=caldate{t}; dt_prep_e=caldate{t};end; end;
 			end;
-		end;
+
 	started_prep_hiv_test_sens=0;if prep   =1 and (hiv=1 and unisensprep > sens_vct) then do; started_prep_hiv_test_sens=1;started_prep_hiv_test_sens_e=1;end;
 	end;
 	* continuing PrEP;
@@ -4202,10 +4189,10 @@ if pop_wide_tld=1 and prep=1 then pop_wide_tld_prep=1;
 if pop_wide_tld = 1 and registd ne 1 and ( prep_elig = 1 or ( ever_newp = 1 and ever_tested ne 1 ) ) then do;  
 
 	if prep_ever ne 1 then do;   * dependent_on_time_step_length; 
-			r=uniform(0); if (prep_willing_pop=1 or  (sw=1 and prep_willing_sw=1 )) and r < prob_prep_pop_wide_tld then do ;
+			r=uniform(0); if prep_willing=1 and r < prob_prep_pop_wide_tld then do ;
 
 * ts1m ; * replace line above with this:
-*			r=uniform(0); * if (prep_willing_pop=1 or  (sw=1 and prep_willing_sw=1 )) and r < ( 1 - (1 - prob_prep_pop_wide_tld)**(1/3) ) then do ;
+*			r=uniform(0); * if prep_willing=1 and r < ( 1 - (1 - prob_prep_pop_wide_tld)**(1/3) ) then do ;
 
 			prep   =1; pop_wide_tld_prep=1;  prep_ever=1; dt_prep_s=caldate{t}; dt_prep_e=caldate{t};
 			end;
@@ -14295,7 +14282,7 @@ if 15 <= age < 65 and (death = . or caldate&j = death ) then do;
     s_onprep_12_i_prep_no_r + onprep_12_i_prep_no_r ;  s_onprep_18_i_prep_no_r + onprep_18_i_prep_no_r ; s_prepinfect_rm_p + prepinfect_rm_p ;     
 	s_prepinfect_m184m_p + prepinfect_m184m_p ; s_prepinfect_k65m_p + prepinfect_k65m_p ; s_prepinfect_tam_p + prepinfect_tam_p ; 
  	s_prepinfect_rtm + prepinfect_rtm ; s_prepinfect_k65m + prepinfect_k65m ; s_prepinfect_m184m + prepinfect_m184m ; s_prepinfect_tam + prepinfect_tam ;
- 	s_prep_willing_pop + prep_willing_pop ; s_prep_willing_sw + prep_willing_sw ; s_stop_prep_choice + stop_prep_choice ; 
+ 	s_prep_willing + prep_willing ; s_stop_prep_choice + stop_prep_choice ; 
 	s_started_prep_hiv_test_sens + started_prep_hiv_test_sens ; s_cur_res_prep_drug + cur_res_prep_drug ; 
 	s_started_prep_hiv_test_sens_e + started_prep_hiv_test_sens_e ; s_started_prep_in_primary_e +  started_prep_in_primary_e ; 
  	s_cur_res_ten + cur_res_ten ; s_cur_res_3tc + cur_res_3tc ; s_i_65m + i_65m ; s_cur_res_efa + cur_res_efa ;  		   	   		   	     
@@ -14326,7 +14313,7 @@ if 15 <= age < 65 and (death = . or caldate&j = death ) then do;
 	s_tested_4p_m4049_ + tested_4p_m4049_ ; s_tested_4p_m5064_ + tested_4p_m5064_ ; s_tested_4p_w1549_ + tested_4p_w1549_ ; 
 	s_tested_4p_w1519_ + tested_4p_w1519_ ; s_tested_4p_w2024_ + tested_4p_w2024_ ; s_tested_4p_w2529_ + tested_4p_w2529_ ;
 	s_tested_4p_w3039_ + tested_4p_w3039_ ; s_tested_4p_w4049_ + tested_4p_w4049_ ; s_tested_4p_w5064_ + tested_4p_w5064_ ;
- 	s_tested_4p_sw + tested_4p_sw ; s_tested_sw + tested_sw
+ 	s_tested_4p_sw + tested_4p_sw ; s_tested_sw + tested_sw;
 	s_ever_tested_m1549_ + ever_tested_m1549_ ; s_ever_tested_m1519_ + ever_tested_m1519_ ;
     s_ever_tested_m2024_ + ever_tested_m2024_ ; s_ever_tested_m2529_ + ever_tested_m2529_ ; s_ever_tested_m3034_ + ever_tested_m3034_ ;
    	s_ever_tested_m3539_ + ever_tested_m3539_ ; s_ever_tested_m4044_ + ever_tested_m4044_ ; s_ever_tested_m4549_ + ever_tested_m4549_ ;
@@ -15582,7 +15569,7 @@ s_infected_prep_source_prep_r  s_prepinfect_prep_r     s_prepinfect_prep_r_p   s
 s_started_prep_in_primary	   s_tot_yrs_prep  		   s_onprep_3_i_prep_no_r  s_onprep_6_i_prep_no_r  s_onprep_9_i_prep_no_r 
 s_onprep_12_i_prep_no_r 	   s_onprep_18_i_prep_no_r s_prepinfect_rm_p      s_prepinfect_m184m_p    s_prepinfect_k65m_p 
 s_prepinfect_tam_p 			   s_prepinfect_rtm  	   s_prepinfect_k65m	   s_prepinfect_m184m  	   s_prepinfect_tam  
-s_prep_willing_pop  		   s_prep_willing_sw  	   s_stop_prep_choice      s_started_prep_hiv_test_sens  
+s_prep_willing  		    s_stop_prep_choice      s_started_prep_hiv_test_sens  
 s_cur_res_prep_drug 		   s_started_prep_hiv_test_sens_e  				   s_started_prep_in_primary_e
 s_cur_res_ten				   s_cur_res_3tc  		   s_i_65m 				   s_cur_res_efa 			
 s_cur_res_ten_vlg1000 		   s_cur_res_3tc_vlg1000 						   s_cur_res_efa_vlg1000	s_ever_hiv1_prep 
@@ -16399,7 +16386,7 @@ s_infected_prep_source_prep_r  s_prepinfect_prep_r     s_prepinfect_prep_r_p   s
 s_started_prep_in_primary	   s_tot_yrs_prep  		   s_onprep_3_i_prep_no_r  s_onprep_6_i_prep_no_r  s_onprep_9_i_prep_no_r 
 s_onprep_12_i_prep_no_r 	   s_onprep_18_i_prep_no_r s_prepinfect_rm_p      s_prepinfect_m184m_p    s_prepinfect_k65m_p 
 s_prepinfect_tam_p 			   s_prepinfect_rtm  	   s_prepinfect_k65m	   s_prepinfect_m184m  	   s_prepinfect_tam  
-s_prep_willing_pop  		   s_prep_willing_sw  	   s_stop_prep_choice      s_started_prep_hiv_test_sens  
+s_prep_willing  		    	   s_stop_prep_choice      s_started_prep_hiv_test_sens  
 s_cur_res_prep_drug 		   s_started_prep_hiv_test_sens_e  				   s_started_prep_in_primary_e
 s_cur_res_ten				   s_cur_res_3tc  		   s_i_65m 				   s_cur_res_efa 			
 s_cur_res_ten_vlg1000 		   s_cur_res_3tc_vlg1000 						   s_cur_res_efa_vlg1000	s_ever_hiv1_prep 
@@ -17016,7 +17003,7 @@ end;
 
 data x; set cum_l1;
 
-file "/home/rmjxxx/Scratch/_output_base_19_02_21_&dataset_id";  
+file "/home/rmjxxx/Scratch/_output_base_22_02_21_&dataset_id";  
 
 put   
 
@@ -17226,7 +17213,7 @@ s_infected_prep_source_prep_r  s_prepinfect_prep_r     s_prepinfect_prep_r_p   s
 s_started_prep_in_primary	   s_tot_yrs_prep  		   s_onprep_3_i_prep_no_r  s_onprep_6_i_prep_no_r  s_onprep_9_i_prep_no_r 
 s_onprep_12_i_prep_no_r 	   s_onprep_18_i_prep_no_r s_prepinfect_rm_p      s_prepinfect_m184m_p    s_prepinfect_k65m_p 
 s_prepinfect_tam_p 			   s_prepinfect_rtm  	   s_prepinfect_k65m	   s_prepinfect_m184m  	   s_prepinfect_tam  
-s_prep_willing_pop  		   s_prep_willing_sw  	   s_stop_prep_choice      s_started_prep_hiv_test_sens  
+s_prep_willing  		    	   s_stop_prep_choice      s_started_prep_hiv_test_sens  
 s_cur_res_prep_drug 		   s_started_prep_hiv_test_sens_e  				   s_started_prep_in_primary_e
 s_cur_res_ten				   s_cur_res_3tc  		   s_i_65m 				   s_cur_res_efa 			
 s_cur_res_ten_vlg1000 		   s_cur_res_3tc_vlg1000 						   s_cur_res_efa_vlg1000	s_ever_hiv1_prep