update touchstone

epiforecasts · Oct 22, 2023 · c52c381 · c52c381
1 parent 56473c5
commit c52c381
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Showing 2 changed files with 14 additions and 23 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 = generation_time,
-    delays = delays,
+    generation_time = fixed_generation_time,
+    delays = fixed_delays,
     rt = rt_opts(prior = list(mean = 2, sd = 0.2)),
     stan = stan_opts(
       cores = 2, samples = 500, chains = 2,
@@ -25,8 +25,8 @@ touchstone::benchmark_run(
   expr_before_benchmark = { source("touchstone/setup.R") },
   uncertain = { epinow(
     reported_cases = reported_cases,
-    generation_time = u_generation_time,
-    delays = u_delays,
+    generation_time = example_generation_time,
+    delays = delays,
     rt = rt_opts(prior = list(mean = 2, sd = 0.2)),
     stan = stan_opts(
       cores = 2, samples = 500, chains = 2,
@@ -41,7 +41,7 @@ touchstone::benchmark_run(
   expr_before_benchmark = { source("touchstone/setup.R") },
   no_delays = { epinow(
     reported_cases = reported_cases,
-    generation_time = generation_time,
+    generation_time = 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 = generation_time,
-    delays = delays,
+    generation_time = fixed_generation_time,
+    delays = 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 = generation_time,
-    delays = delays,
+    generation_time = fixed_generation_time,
+    delays = fixed_delays,
     rt = rt_opts(prior = list(mean = 2, sd = 0.2), rw = 7),
     gp = NULL,
     stan = stan_opts(

diff --git a/touchstone/setup.R b/touchstone/setup.R
@@ -2,18 +2,9 @@ library("EpiNow2")
 
 reported_cases <- example_confirmed[1:60]
 
-# get uncertain example delays
-u_generation_time <- example_generation_time
-u_incubation_period <- example_incubation_period
-# set uncertain reporting delay
-u_reporting_delay <- dist_spec(
-  mean = convert_to_logmean(2, 1), mean_sd = 0.1,
-  sd = convert_to_logsd(2, 1), sd_sd = 0.1, max = 15
-)
+fixed_generation_time <- fix_dist(example_generation_time)
+fixed_incubation_period <- fix_dist(example_incubation_period)
+fixed_reporting_delay <- fix_dist(example_reporting_delay)
 
-generation_time <- fix_dist(u_generation_time)
-incubation_period <- fix_dist(u_incubation_period)
-reporting_delay <- fix_dist(u_reporting_delay)
-
-u_delays <- delay_opts(u_incubation_period + u_reporting_delay)
-delays <- delay_opts(incubation_period + reporting_delay)
+delays <- delay_opts(example_incubation_period + example_reporting_delay)
+fixed_delays <- delay_opts(fixed_incubation_period + fixed_reporting_delay)