Merge fefe19b into 3fd7b08

epiforecasts · Jul 4, 2023 · 8929be0 · 8929be0
2 parents 3fd7b08 + fefe19b
commit 8929be0
Showing 1 changed file with 7 additions and 6 deletions.
diff --git a/inst/stan/functions/infections.stan b/inst/stan/functions/infections.stan
@@ -27,14 +27,15 @@ vector generate_infections(vector oR, int uot, vector gt_rev_pmf,
   int t = ot + uot;
   vector[ot] R = oR;
   real exp_adj_Rt;
-  vector[t] infections = rep_vector(1e-5, t);
-  vector[ot] cum_infections = rep_vector(0, ot);
-  vector[ot] infectiousness = rep_vector(1e-5, ot);
+  vector[t] infections = rep_vector(0, t);
+  vector[ot] cum_infections;
+  vector[ot] infectiousness;
   // Initialise infections using daily growth
   infections[1] = exp(initial_infections[1]);
   if (uot > 1) {
+    real growth = exp(initial_growth[1]);
     for (s in 2:uot) {
-      infections[s] = exp(initial_infections[1] + initial_growth[1] * (s - 1));
+      infections[s] = infections[s - 1] * growth;
     }
   }
   // calculate cumulative infections
@@ -43,13 +44,13 @@ vector generate_infections(vector oR, int uot, vector gt_rev_pmf,
   }
   // iteratively update infections
   for (s in 1:ot) {
-    infectiousness[s] += update_infectiousness(infections, gt_rev_pmf, uot, s);
+    infectiousness[s] = update_infectiousness(infections, gt_rev_pmf, uot, s);
     if (pop && s > nht) {
       exp_adj_Rt = exp(-R[s] * infectiousness[s] / (pop - cum_infections[nht]));
       exp_adj_Rt = exp_adj_Rt > 1 ? 1 : exp_adj_Rt;
       infections[s + uot] = (pop - cum_infections[s]) * (1 - exp_adj_Rt);
     }else{
-      infections[s + uot] += R[s] * infectiousness[s];
+      infections[s + uot] = R[s] * infectiousness[s];
     }
     if (pop && s < ot) {
       cum_infections[s + 1] = cum_infections[s] + infections[s + uot];