fix rebase errors

epiforecasts · May 17, 2024 · e543808 · e543808
1 parent a43ccaf
commit e543808
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Showing 3 changed files with 8 additions and 4 deletions.
diff --git a/R/create.R b/R/create.R
@@ -625,7 +625,7 @@ 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
@@ -1,4 +1,4 @@
-  array[n, 1] real initial_infections; // initial logged infections
+  array[n, seeding_time ? 1 : 0] real initial_infections; // initial logged infections
   array[n, seeding_time > 1 ? 1 : 0] real initial_growth; //initial growth
 
   matrix[n, t - seeding_time] R; // reproduction number

diff --git a/inst/stan/simulate_secondary.stan b/inst/stan/simulate_secondary.stan
@@ -62,7 +62,9 @@ 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])
+      );
     }
 
     // truncate near time cases to observed reports
@@ -79,6 +81,8 @@ generated quantities {
     }
 
     // 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
+    );
   }
 }