fix rebase errors

epiforecasts · Jul 4, 2023 · 998cadd · 998cadd
1 parent 01de920
commit 998cadd
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Showing 3 changed files with 7 additions and 4 deletions.
diff --git 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
@@ -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
@@ -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
+    );
   }
 }