From 0bf9d9c0f8807c5c970828f1e2495d12d3e0d374 Mon Sep 17 00:00:00 2001
From: Sebastian Funk <sebastian.funk@lshtm.ac.uk>
Date: Thu, 9 Feb 2023 17:51:40 +0000
Subject: [PATCH] update touchstone setup

---
 touchstone/.gitignore |  1 +
 touchstone/script.R   | 58 +++++++++++++++++++++----------------------
 touchstone/setup.R    | 18 ++++++++++++++
 3 files changed, 48 insertions(+), 29 deletions(-)
 create mode 100644 touchstone/setup.R

diff --git a/touchstone/.gitignore b/touchstone/.gitignore
index ee8eacf09..8ca6a88d0 100644
--- a/touchstone/.gitignore
+++ b/touchstone/.gitignore
@@ -1,4 +1,5 @@
 *
+!setup.R
 !script.R
 !config.json
 !.gitignore
diff --git a/touchstone/script.R b/touchstone/script.R
index 3c0f72cf3..ea24a4ad8 100644
--- a/touchstone/script.R
+++ b/touchstone/script.R
@@ -9,80 +9,80 @@ touchstone::branch_install()
 
 #  benchmnark README example
 touchstone::benchmark_run(
-  expr_before_benchmark = 'source("touchstone/setup.R")',
-  default = 'epinow(
+  expr_before_benchmark = { source("touchstone/setup.R") },
+  default = { epinow(
     reported_cases = reported_cases,
-    generation_time = generation_time_opts(generation_time),
+    generation_time = generation_time,
     delays = delay_opts(incubation_period, reporting_delay),
     rt = rt_opts(prior = list(mean = 2, sd = 0.2)),
     stan = stan_opts(
       cores = 2, samples = 500, chains = 2,
-      control = list(adapt_delta = 0.95)),
+      control = list(adapt_delta = 0.95), seed = 5339),
     verbose = interactive()
-  )',
-  n = 2
+  ) },
+  n = 1
 )
 
 # benchmark readme example with uncertain delays and gt
 touchstone::benchmark_run(
-  expr_before_benchmark = 'source("touchstone/setup.R")',
-  uncertain = 'epinow(
+  expr_before_benchmark = { source("touchstone/setup.R") },
+  uncertain = { epinow(
     reported_cases = reported_cases,
     generation_time = generation_time_opts(ugeneration_time),
     delays = delay_opts(uincubation_period, reporting_delay),
     rt = rt_opts(prior = list(mean = 2, sd = 0.2)),
     stan = stan_opts(
       cores = 2, samples = 500, chains = 2,
-      control = list(adapt_delta = 0.95)),
+      control = list(adapt_delta = 0.95), seed = 5339),
     verbose = interactive()
-  )',
-  n = 2
+  ) },
+  n = 1
 )
 
 # benchmark readme example without delays
 touchstone::benchmark_run(
-  expr_before_benchmark = 'source("setup.R")',
-  no_delays = 'epinow(
+  expr_before_benchmark = { source("touchstone/setup.R") },
+  no_delays = { epinow(
     reported_cases = reported_cases,
-    generation_time = generation_time_opts(generation_time),
+    generation_time = generation_time,
     rt = rt_opts(prior = list(mean = 2, sd = 0.2)),
     stan = stan_opts(
       cores = 2, samples = 500, chains = 2,
-      control = list(adapt_delta = 0.95)),
+      control = list(adapt_delta = 0.95), seed = 5339),
     verbose = interactive()
-  )',
-  n = 2
+  ) },
+  n = 1
 )
 
 # benchmark readme example with a stationary GP
 touchstone::benchmark_run(
-  expr_before_benchmark = 'source("setup.R")',
-  stationary = 'epinow(
+  expr_before_benchmark = { source("touchstone/setup.R") },
+  stationary = { epinow(
     reported_cases = reported_cases,
-    generation_time = generation_time_opts(generation_time),
+    generation_time = generation_time,
     rt = rt_opts(prior = list(mean = 2, sd = 0.2), gp_on = "R0"),
     stan = stan_opts(
       cores = 2, samples = 500, chains = 2,
-      control = list(adapt_delta = 0.95)),
+      control = list(adapt_delta = 0.95), seed = 5339),
     verbose = interactive()
-  )',
-  n = 2
+  ) },
+  n = 1
 )
 
 # benchmark readme example with a weekly random walk
 touchstone::benchmark_run(
-  expr_before_benchmark = 'source("touchstone/setup.R")',
-  random_walk = 'epinow(
+  expr_before_benchmark = { source("touchstone/setup.R") },
+  random_walk = { epinow(
     reported_cases = reported_cases,
-    generation_time = generation_time_opts(generation_time),
+    generation_time = generation_time,
     rt = rt_opts(prior = list(mean = 2, sd = 0.2), rw = 7),
     gp = NULL,
     stan = stan_opts(
       cores = 2, samples = 500, chains = 2,
-      control = list(adapt_delta = 0.95)),
+      control = list(adapt_delta = 0.95), seed = 5339),
     verbose = interactive()
-  )',
-  n = 2
+  ) },
+  n = 1
 )
 
 # create artifacts used downstream in the GitHub Action
diff --git a/touchstone/setup.R b/touchstone/setup.R
new file mode 100644
index 000000000..3a0d05621
--- /dev/null
+++ b/touchstone/setup.R
@@ -0,0 +1,18 @@
+library("EpiNow2")
+
+reported_cases <- example_confirmed[1:60]
+
+# set up example generation time
+generation_time <- generation_time_opts(
+  disease = "SARS-CoV-2", source = "ganyani", fixed = TRUE
+)
+
+# set delays between infection and case report
+incubation_period <- get_incubation_period(
+  disease = "SARS-CoV-2", source = "lauer"
+)
+
+reporting_delay <- list(
+  mean = convert_to_logmean(2, 1), mean_sd = 0,
+  sd = convert_to_logsd(2, 1), sd_sd = 0, max = 10
+)