From 544997e4bda7aaa88664163598d6954bbca8d960 Mon Sep 17 00:00:00 2001
From: Sam <s.e.abbott12@gmail.com>
Date: Wed, 11 Oct 2023 18:58:47 +0100
Subject: [PATCH] correct damping term

---
 README.Rmd                          | 2 +-
 inst/stan/functions/infections.stan | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/README.Rmd b/README.Rmd
index 8028e7c7b..9b1b9e12a 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -144,7 +144,7 @@ estimates <- epinow(
   delays = delay_opts(incubation_period + reporting_delay),
   rt = rt_opts(
     prior = list(mean = 2, sd = 0.2),
-    incidence_feedback = list(mean = 0, sd = 0.0001)
+    incidence_feedback = list(mean = 0.01, sd = 0.01)
   ),
   stan = stan_opts(cores = 4, control = list(adapt_delta = 0.99)),
   verbose = interactive()
diff --git a/inst/stan/functions/infections.stan b/inst/stan/functions/infections.stan
index c6ffbd1ce..474e6a293 100644
--- a/inst/stan/functions/infections.stan
+++ b/inst/stan/functions/infections.stan
@@ -48,7 +48,7 @@ vector generate_infections(vector oR, int uot, vector gt_rev_pmf,
   for (s in 1:ot) {
     infectiousness[s] = update_infectiousness(infections, gt_rev_pmf, uot, s);
     if (if_present) {
-      infections[s + uot] = exp(
+      R[s] = exp(
         log(R[s]) - incidence_feedback[1] .* infectiousness[s]
       );
     }