Guard growth-rate functions against insufficient data explicitly

Co-authored-by: sbfnk <sebastian.funk@lshtm.ac.uk>

Author: sbfnk

inst/stan/functions/generated_quantities.stan

@@ -92,6 +92,11 @@ vector calculate_growth_infections(vector infections, int seeding_time) {
   int t = num_elements(infections);
   int ot = t - seeding_time;
   int start = 1 + seeding_time;
+  if (ot <= 1) {
+    reject(
+      "seeding_time must be >1 time step shorter than the infections vector."
+    );
+  }
   vector[t] log_inf = log(infections);
   vector[ot - 1] growth = log_inf[(1+start):t] - log_inf[start:(t - 1)];
   return(growth);
@@ -118,21 +123,26 @@ vector calculate_growth_infness(vector infections, int seeding_time,
   int t = num_elements(infections);
   int ot = t - seeding_time;
   int start = 1 + seeding_time;
-  if (ot <= 1) {
-    reject("seeding_time must >1 time step shorter than infections vector.");
-    }
+  // mean generation time, will always be >= 1
+  int gt_length = num_elements(gt_rev_pmf);
+  int mean_gen = to_int(round( // round weighted mean to nearest int
+    dot_product(reverse(linspaced_vector(gt_length, 1, gt_length)), gt_rev_pmf)
+    ));
+  // a shifted growth rate needs more modeled points than the mean generation
+  // time, otherwise the shift below would index out of range
+  if (ot <= mean_gen) {
+    reject(
+      "infections vector must be longer than seeding_time by more than the ",
+      "mean generation time."
+    );
+  }
   // infectiousness
   vector[ot] infness_log = rep_vector(1e-5, ot);
   for (s in 1:ot) {
     infness_log[s] += log(update_infectiousness(
       infections, gt_rev_pmf, seeding_time, s
     ));
   }
-  // mean generation time, will always be >= 1
-  int gt_length = num_elements(gt_rev_pmf);
-  int mean_gen = to_int(round( // round weighted mean to nearest int
-    dot_product(reverse(linspaced_vector(gt_length, 1, gt_length)), gt_rev_pmf)
-    ));
   // growth rate
   vector[ot - 1] growth = infness_log[2:ot] - infness_log[1:(ot - 1)];  
   // shift by mean_gen (most recent growth rates remain undefined)