debug allocation of missing reference effects

epinowcast · seabbs · Sep 20, 2022 · Jul 31, 2022 · Jul 31, 2022 · Jul 31, 2022
commit f172d8a98b65a3795e15e08d28294e80bb3b6aef
diff --git a/R/model-modules.R b/R/model-modules.R
@@ -330,8 +330,8 @@ enw_missing <- function(formula = ~1, data) {
     data_list <- enw_formula_as_data_list(
       prefix = "miss", drop_intercept = FALSE
     )
-    data_list$missing_ref <- numeric(0)
-    data_list$obs_by_rep <- numeric(0)
+    data_list$missing_reference <- numeric(0)
+    data_list$obs_by_report <- numeric(0)
     data_list$model_miss <- 0
     data_list$miss_obs <- 0
   } else {

diff --git a/inst/stan/epinowcast.stan b/inst/stan/epinowcast.stan
@@ -300,7 +300,7 @@ generated quantities {
     // Draw from observation model for observed counts with report and reference
     pp_obs_tmp = obs_rng(log_exp_obs, phi, model_obs);
     } 
-    
+
     // Likelihood by snapshot (rather than by observation)
     profile("generated_loglik") {
     if (ologlik) {

diff --git a/inst/stan/functions/apply_missing_reference_effects.stan b/inst/stan/functions/apply_missing_reference_effects.stan
@@ -5,7 +5,8 @@ vector apply_missing_reference_effects(int start, int end, vector obs,
   vector[n[3]] alloc_obs;
   for (i in start:end) {
     array[3] int l = filt_obs_indexes(i, i, csl, sl);
-    alloc_obs[(l[1] + 1):l[2]] = alloc_obs[(l[1] + 1):l[2]] + miss_ref_lprop[i];
+    alloc_obs[(l[1] + 1):l[2]] =
+      segment(obs, l[1] + 1, l[3]) + miss_ref_lprop[i];
   }
   return(alloc_obs);        
 }