Implement HIV progression on ART

[mmcleod89]

EFFECT OF NACTIVE

Major refactoring should simplify / compactify this code substantially.

[mmcleod89]

if t ge 2 then cd4=cd4_tm1+cc_tm1; 

	if vl > 6.5 then vl=6.5;

	if . < cd4  lt 0 then cd4 =0;

* add variability to cd4 for those on art;
	if t ge 2 and nactive_tm1 ge 0 then do; cd4 =(sqrt(cd4 )+ sd_cd4*rand('normal'))**2; end;

	if  t ge 2 and tcur_tm1 ge 0 and cd4  gt cmax then cd4 =cmax+(rand('normal')*50);
	if . < vl lt 0 then vl=0;

	if t ge 2 then do;
		newmut_tm1=newmut_tm1*fold_change_mut_risk;
		* if started_prep_hiv_test_sens and prep_oral=1 then newmut_tm1=newmut_tm1*0.33; * due to test at 1 month from start of prep - jul17; 
		* dependent_on_time_step_length ;	* lapr define which prep? ; 
																					* removed becuase not necessarily assuming a 1 month test ;		
		if newmut_tm1 gt 1 then newmut_tm1=1;
	end;

We mustn't forget about this effect on newmut outside of the main NACTIVE loop