Hotfix: generation_time_opts use in touchstone benchmarking

epiforecasts · Dec 21, 2023 · b4a0f5f · b4a0f5f
1 parent b8a2b0c
commit b4a0f5f
Showing 1 changed file with 5 additions and 5 deletions.
diff --git a/touchstone/script.R b/touchstone/script.R
@@ -9,7 +9,7 @@ touchstone::benchmark_run(
   expr_before_benchmark = { source("touchstone/setup.R") },
   default = { epinow(
     reported_cases = reported_cases,
-    generation_time = fixed_generation_time,
+    generation_time = generation_time_opts(fixed_generation_time),
     delays = fixed_delays,
     rt = rt_opts(prior = list(mean = 2, sd = 0.2)),
     stan = stan_opts(
@@ -25,7 +25,7 @@ touchstone::benchmark_run(
   expr_before_benchmark = { source("touchstone/setup.R") },
   uncertain = { epinow(
     reported_cases = reported_cases,
-    generation_time = example_generation_time,
+    generation_time = generation_time_opts(example_generation_time),
     delays = delays,
     rt = rt_opts(prior = list(mean = 2, sd = 0.2)),
     stan = stan_opts(
@@ -41,7 +41,7 @@ touchstone::benchmark_run(
   expr_before_benchmark = { source("touchstone/setup.R") },
   no_delays = { epinow(
     reported_cases = reported_cases,
-    generation_time = fixed_generation_time,
+    generation_time = generation_time_opts(fixed_generation_time),
     rt = rt_opts(prior = list(mean = 2, sd = 0.2)),
     stan = stan_opts(
       cores = 2, samples = 500, chains = 2,
@@ -56,7 +56,7 @@ touchstone::benchmark_run(
   expr_before_benchmark = { source("touchstone/setup.R") },
   stationary = { epinow(
     reported_cases = reported_cases,
-    generation_time = fixed_generation_time,
+    generation_time = generation_time_opts(fixed_generation_time),
     delays = fixed_delays,
     rt = rt_opts(prior = list(mean = 2, sd = 0.2), gp_on = "R0"),
     stan = stan_opts(
@@ -72,7 +72,7 @@ touchstone::benchmark_run(
   expr_before_benchmark = { source("touchstone/setup.R") },
   random_walk = { epinow(
     reported_cases = reported_cases,
-    generation_time = fixed_generation_time,
+    generation_time = generation_time_opts(fixed_generation_time),
     delays = fixed_delays,
     rt = rt_opts(prior = list(mean = 2, sd = 0.2), rw = 7),
     gp = NULL,