Merge pull request #291 from UCL/andrew_pr_15

Updating testing code

hiv_synthesis.sas

@@ -334,6 +334,7 @@ newp_seed = 7;
 
 * date_start_testing;		date_start_testing = 2003.5; 
 * initial_rate_1sttest;		initial_rate_1sttest = 0; 				* dependent_on_time_step_length ;
+* initial_rate_reptest;		initial_rate_reptest = 0;
 * test_rate_who4;			test_rate_who4=0.10;  					* dependent_on_time_step_length ;
 * test_rate_tb;				test_rate_tb  =0.10;  					* dependent_on_time_step_length ;
 * test_rate_non_tb_who3;	test_rate_non_tb_who3=0.05; 			* dependent_on_time_step_length ;
@@ -3076,7 +3077,7 @@ end;
 
 * RATE OF TESTING WHEN HAVE non_tb_who3, WHO4 or TB and for GENERAL POPULATION; 
 
-if date_start_testing lt caldate{t} le 2015  then do; 
+if date_start_testing lt caldate{t} le 2015 then do;
 	test_rate_who4 = min(0.9,test_rate_who4*incr_test_rate_sympt);  
 	test_rate_tb  = min(0.8,test_rate_tb*incr_test_rate_sympt);  
 	test_rate_non_tb_who3 = min(0.7,test_rate_non_tb_who3*incr_test_rate_sympt); * 0.7 mar19;
@@ -3090,18 +3091,21 @@ if date_start_testing lt caldate{t} le 2015  then do;
 			np_lasttest=0; newp_lasttest_tested_this_per=newp_lasttest; newp_lasttest=0;
 		end;
 	end;
-end;	
+end;
 
 
 
 tested_anc=.;
 
-if t ge 2 and date_start_testing <= caldate{t} then do; 
+if t ge 2 and date_start_testing <= caldate{t} then do; * note that date_start_testing is never changed from 2003.5;
 
-		rate_1sttest = initial_rate_1sttest + (min(caldate{t},date_test_rate_plateau)-(date_start_testing+5.5))*an_lin_incr_test;
-		rate_reptest = 0.0000 + (min(caldate{t},date_test_rate_plateau)-(date_start_testing+5.5))*an_lin_incr_test;
-		rate_1sttest_2011 = initial_rate_1sttest + (min(2011,date_test_rate_plateau)-(date_start_testing+5.5))*an_lin_incr_test;
-		rate_reptest_2011 = 0.0000 + (min(2011,date_test_rate_plateau)-(date_start_testing+5.5))*an_lin_incr_test;																					
+		rate_1sttest = initial_rate_1sttest; rate_reptest = initial_rate_reptest;
+		if caldate{t} >= date_start_testing+5.5 then do;
+			rate_1sttest = initial_rate_1sttest + (min(caldate{t},date_test_rate_plateau)-(date_start_testing+5.5))*an_lin_incr_test;
+			rate_reptest = initial_rate_reptest + (min(caldate{t},date_test_rate_plateau)-(date_start_testing+5.5))*an_lin_incr_test;
+			rate_1sttest_2011 = initial_rate_1sttest + (min(2011,date_test_rate_plateau)-(date_start_testing+5.5))*an_lin_incr_test;
+			rate_reptest_2011 = initial_rate_reptest + (min(2011,date_test_rate_plateau)-(date_start_testing+5.5))*an_lin_incr_test;																					
+		end;
 		if gender=2 then do; rate_1sttest = rate_1sttest * rr_testing_female  ; rate_reptest = rate_reptest * rr_testing_female  ;   end;
 
 end;
@@ -3112,7 +3116,7 @@ if caldate{t} >= 2022         then do;
 	***Assuming testing rates are stable after 2022 by multiplying by fold_rate_decr_test_future;
 	if incr_test_year_i = 3 then do; 
 		rate_1sttest = initial_rate_1sttest + (min(caldate{t},date_test_rate_plateau)-(date_start_testing+5.5))*an_lin_incr_test - ((caldate{t}-2022 )*an_lin_incr_test*fold_rate_decr_test_future);
-		rate_reptest = 0.0000 + (min(caldate{t},date_test_rate_plateau)-(date_start_testing+5.5))*an_lin_incr_test - ((caldate{t}-2022)*an_lin_incr_test*fold_rate_decr_test_future);
+		rate_reptest = initial_rate_reptest + (min(caldate{t},date_test_rate_plateau)-(date_start_testing+5.5))*an_lin_incr_test - ((caldate{t}-2022)*an_lin_incr_test*fold_rate_decr_test_future);
 		if gender=2 then do; rate_1sttest = rate_1sttest * rr_testing_female  ; rate_reptest = rate_reptest * rr_testing_female  ;   end;
 		if . lt rate_1sttest lt rate_1sttest_2011 then rate_1sttest = rate_1sttest_2011;
 		if . lt rate_reptest lt rate_reptest_2011 then rate_reptest = rate_reptest_2011;