update touchstone arguments

epiforecasts · Nov 22, 2023 · 693277c · 693277c
1 parent e3eaaf3
commit 693277c
Showing 1 changed file with 9 additions and 9 deletions.
diff --git a/touchstone/script.R b/touchstone/script.R
@@ -9,8 +9,8 @@ touchstone::benchmark_run(
   expr_before_benchmark = { source("touchstone/setup.R") },
   default = { epinow(
     reported_cases = reported_cases,
-    generation_time = fixed_generation_time,
-    delays = fixed_delays,
+    generation_time = generation_time_opts(fixed_generation_time),
+    delays = delay_opts(fixed_delays),
     rt = rt_opts(prior = list(mean = 2, sd = 0.2)),
     stan = stan_opts(
       cores = 2, samples = 500, chains = 2,
@@ -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(
@@ -39,9 +39,9 @@ touchstone::benchmark_run(
 # benchmark readme example without delays
 touchstone::benchmark_run(
   expr_before_benchmark = { source("touchstone/setup.R") },
-  no_delays = { epinow(
+  delay_opts(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,
@@ -56,8 +56,8 @@ touchstone::benchmark_run(
   expr_before_benchmark = { source("touchstone/setup.R") },
   stationary = { epinow(
     reported_cases = reported_cases,
-    generation_time = fixed_generation_time,
-    delays = fixed_delays,
+    generation_time = generation_time_opts(fixed_generation_time),
+    delays = delay_opts(fixed_delays),
     rt = rt_opts(prior = list(mean = 2, sd = 0.2), gp_on = "R0"),
     stan = stan_opts(
       cores = 2, samples = 500, chains = 2,
@@ -72,8 +72,8 @@ touchstone::benchmark_run(
   expr_before_benchmark = { source("touchstone/setup.R") },
   random_walk = { epinow(
     reported_cases = reported_cases,
-    generation_time = fixed_generation_time,
-    delays = fixed_delays,
+    generation_time = generation_time_opts(fixed_generation_time),
+    delays = delay_opts(fixed_delays),
     rt = rt_opts(prior = list(mean = 2, sd = 0.2), rw = 7),
     gp = NULL,
     stan = stan_opts(