From 998cadd517dc1454f9de148a7c2cf3bb715d6de1 Mon Sep 17 00:00:00 2001
From: Sebastian Funk <sebastian.funk@lshtm.ac.uk>
Date: Tue, 4 Jul 2023 21:01:03 +0100
Subject: [PATCH] fix rebase errors

---
 R/create.R                        | 2 +-
 inst/stan/data/simulation_rt.stan | 1 -
 inst/stan/simulate_secondary.stan | 8 ++++++--
 3 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/R/create.R b/R/create.R
index 10ef0e7ea..8fa6d90f5 100644
--- a/R/create.R
+++ b/R/create.R
@@ -562,7 +562,7 @@ create_initial_conditions <- function(data) {
       if (data$seeding_time > 1) {
         out$initial_growth <- array(rnorm(1, data$prior_growth, 0.01))
       }
-      out$base_cov <- rnorm(
+      out$base_cov <- array(rnorm(
         n = 1, mean = convert_to_logmean(data$r_mean, data$r_sd),
         sd = convert_to_logsd(data$r_mean, data$r_sd) * 0.1
       ))
diff --git a/inst/stan/data/simulation_rt.stan b/inst/stan/data/simulation_rt.stan
index 53aadcc05..3a882df2c 100644
--- a/inst/stan/data/simulation_rt.stan
+++ b/inst/stan/data/simulation_rt.stan
@@ -1,6 +1,5 @@
   real initial_infections[seeding_time ? n : 0, 1]; // initial logged infections
   real initial_growth[seeding_time > 1 ? n : 0, 1]; //initial growth
-  int gt_dist[1];                    // 0 = lognormal; 1 = gamma
   vector[n] R[t - seeding_time]; // reproduction number
   int pop;                       // susceptible population
 
diff --git a/inst/stan/simulate_secondary.stan b/inst/stan/simulate_secondary.stan
index 2f4c711ee..27e5271cf 100644
--- a/inst/stan/simulate_secondary.stan
+++ b/inst/stan/simulate_secondary.stan
@@ -49,9 +49,13 @@ generated quantities {
       );
     // weekly reporting effect
     if (week_effect > 1) {
-      secondary = day_of_week_effect(secondary, day_of_week, to_vector(day_of_week_simplex[i]));
+      secondary = day_of_week_effect(
+        secondary, day_of_week, to_vector(day_of_week_simplex[i])
+      );
     }
     // simulate secondary reports
-    sim_secondary[i] = report_rng(tail(secondary, all_dates ? t : h), rep_phi[i], obs_dist);
+    sim_secondary[i] = report_rng(
+      tail(secondary, all_dates ? t : h), rep_phi[i], obs_dist
+    );
   }
 }