avoid conversion

inst/stan/estimate_infections.stan

@@ -156,7 +156,7 @@ model {
 generated quantities {
   array[ot_h] int imputed_reports;
   vector[estimate_r > 0 ? 0: ot_h] gen_R;
-  array[ot_h - 1] real r;
+  vector[ot_h - 1] r;
   real gt_mean;
   real gt_var;
   vector[return_likelihood ? ot : 0] log_lik;

inst/stan/functions/generated_quantities.stan

@@ -30,10 +30,10 @@ vector calculate_Rt(vector infections, int seeding_time,
 }
 
 // Calculate growth rate
-array[] real calculate_growth(vector infections, int seeding_time) {
+vector calculate_growth(vector infections, int seeding_time) {
   int t = num_elements(infections);
   int ot = t - seeding_time;
   vector[t] log_inf = log(infections);
   vector[ot] growth = log_inf[(seeding_time + 1):t] - log_inf[seeding_time:(t - 1)];
-  return(to_array_1d(growth));
+  return(growth);
 }

inst/stan/simulate_infections.stan

@@ -35,7 +35,7 @@ generated quantities {
   matrix[n, t] infections; //latent infections
   matrix[n, t - seeding_time] reports; // observed cases
   array[n, t - seeding_time] int imputed_reports;
-  array[n, t - seeding_time - 1] real r;
+  matrix[n, t - seeding_time - 1] r;
   for (i in 1:n) {
     // generate infections from Rt trace
     vector[delay_type_max[gt_id] + 1] gt_rev_pmf;
@@ -94,6 +94,8 @@ generated quantities {
     imputed_reports[i] = report_rng(
       to_vector(reports[i]), rep_phi[i], model_type
     );
-    r[i] = calculate_growth(to_vector(infections[i]), seeding_time + 1);
+    r[i] = to_row_vector(
+      calculate_growth(to_vector(infections[i]), seeding_time + 1)
+    );
   }
 }