From abb8d1ceba097faded6064836a009db4190e9f3a Mon Sep 17 00:00:00 2001
From: Sebastian Funk <sebastian.funk@lshtm.ac.uk>
Date: Sat, 23 Nov 2024 12:16:12 +0000
Subject: [PATCH] accumulate after truncation

---
 inst/stan/estimate_secondary.stan | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/inst/stan/estimate_secondary.stan b/inst/stan/estimate_secondary.stan
index 246647ef5..15836243c 100644
--- a/inst/stan/estimate_secondary.stan
+++ b/inst/stan/estimate_secondary.stan
@@ -73,13 +73,6 @@ transformed parameters {
    secondary = day_of_week_effect(secondary, day_of_week, day_of_week_simplex);
  }
 
- // accumulate reports
- if (any_accumulate) {
-   profile("accumulate") {
-     secondary = accumulate_reports(secondary, accumulate);
-   }
- }
-
  // truncate near time cases to observed reports
  if (trunc_id) {
     vector[delay_type_max[trunc_id]] trunc_rev_cmf = get_delay_rev_pmf(
@@ -90,6 +83,13 @@ transformed parameters {
     );
     secondary = truncate_obs(secondary, trunc_rev_cmf, 0);
  }
+
+ // accumulate reports
+ if (any_accumulate) {
+   profile("accumulate") {
+     secondary = accumulate_reports(secondary, accumulate);
+   }
+ }
 }
 
 model {