From 21e0695ce341207f2a1d81536cc584c68188d480 Mon Sep 17 00:00:00 2001
From: Sebastian Funk <sebastian.funk@lshtm.ac.uk>
Date: Thu, 19 Oct 2023 15:40:01 +0100
Subject: [PATCH] update examples in more places

---
 README.Rmd                      |  4 ++--
 inst/dev/recover-synthetic/rt.R | 33 ++++++++++++++++-----------------
 2 files changed, 18 insertions(+), 19 deletions(-)

diff --git a/README.Rmd b/README.Rmd
index 936560902..dc60382f0 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -193,8 +193,8 @@ Calling `regional_epinow()` runs the `epinow()` on each region in turn (or in pa
 ```{r, message = FALSE, warning = FALSE}
 estimates <- regional_epinow(
   reported_cases = reported_cases,
-  generation_time = generation_time_opts(generation_time),
-  delays = delay_opts(incubation_period + reporting_delay),
+  generation_time = generation_time_opts(example_generation_time),
+  delays = delay_opts(example_incubation_period + reporting_delay),
   rt = rt_opts(prior = list(mean = 2, sd = 0.2), rw = 7),
   gp = NULL,
   stan = stan_opts(cores = 4, warmup = 250, samples = 1000)
diff --git a/inst/dev/recover-synthetic/rt.R b/inst/dev/recover-synthetic/rt.R
index e05d3e6f1..2661d3283 100644
--- a/inst/dev/recover-synthetic/rt.R
+++ b/inst/dev/recover-synthetic/rt.R
@@ -6,11 +6,6 @@ source(here::here("inst", "dev", "recover-synthetic", "plot.R"))
 old_opts <- options()
 options(mc.cores = 4)
 
-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
-)
-
 #' get example delays
 obs <- obs_opts(scale = list(mean = 0.1, sd = 0.025), return_likelihood = TRUE)
 
@@ -18,7 +13,7 @@ obs <- obs_opts(scale = list(mean = 0.1, sd = 0.025), return_likelihood = TRUE)
 # shared simulation settings
 init <- estimate_infections(example_confirmed[1:100],
   generation_time = generation_time_opts(example_generation_time),
-  delays = delay_opts(example_incubation_period + reporting_delay),
+  delays = delay_opts(example_incubation_period + example_reporting_delay),
   rt = rt_opts(prior = list(mean = 2, sd = 0.1), rw = 14),
   gp = NULL, horizon = 0,
   obs = obs
@@ -37,7 +32,9 @@ sim_R <- sims$summarised[variable == "R"]$median
 
 # pull out simulated cases
 posterior_sample <- sims$samples[sample == 1]
-sim_cases <- posterior_sample[variable == "reported_cases", .(date, confirm = value)]
+sim_cases <- posterior_sample[
+  variable == "reported_cases", .(date, confirm = value)
+]
 sim_inf <- posterior_sample[variable == "infections"]$value
 
 save_ggplot(plot(sims), "sims")
@@ -60,8 +57,8 @@ for (method in c("nuts")) {
   # GP
   gp[[method]] <-
     estimate_infections(sim_cases,
-      generation_time = generation_time_opts(generation_time),
-      delays = delay_opts(incubation_period + reporting_delay),
+      generation_time = generation_time_opts(example_generation_time),
+      delays = delay_opts(example_incubation_period + example_reporting_delay),
       rt = rt_opts(prior = list(mean = 2, sd = 0.25)),
       stan = stanopts,
       obs = obs,
@@ -75,8 +72,8 @@ for (method in c("nuts")) {
   # Backcalculation
   backcalc[[method]] <-
     estimate_infections(sim_cases,
-      generation_time = generation_time_opts(generation_time),
-      delays = delay_opts(incubation_period + reporting_delay),
+      generation_time = generation_time_opts(example_generation_time),
+      delays = delay_opts(example_incubation_period + example_reporting_delay),
       rt = NULL,
       stan = stanopts,
       obs = obs,
@@ -90,8 +87,8 @@ for (method in c("nuts")) {
   # RW (weekly)
   weekly_rw[[method]] <-
     estimate_infections(sim_cases,
-      generation_time = generation_time_opts(generation_time),
-      delays = delay_opts(incubation_period + reporting_delay),
+      generation_time = generation_time_opts(example_generation_time),
+      delays = delay_opts(example_incubation_period + example_reporting_delay),
       rt = rt_opts(
         prior = list(mean = 2, sd = 0.25),
         rw = 7
@@ -109,8 +106,8 @@ for (method in c("nuts")) {
   # RW (every month) + stationary Guassian process
   gp_rw[[method]] <-
     estimate_infections(sim_cases,
-      generation_time = generation_time_opts(generation_time),
-      delays = delay_opts(incubation_period + reporting_delay),
+      example_generation_time = generation_time_opts(example_generation_time),
+      delays = delay_opts(example_incubation_period + example_reporting_delay),
       rt = rt_opts(
         prior = list(mean = 2, sd = 0.25), rw = 14, gp_on = "R0"
       ),
@@ -128,8 +125,10 @@ for (method in c("nuts")) {
   if (fit_daily) {
     daily_rw[[method]] <-
       estimate_infections(sim_cases,
-        generation_time = generation_time_opts(generation_time),
-        delays = delay_opts(incubation_period + reporting_delay),
+        example_generation_time = generation_time_opts(example_generation_time),
+        delays = delay_opts(
+          example_incubation_period + example_reporting_delay
+        ),
         rt = rt_opts(
           prior = list(mean = 2, sd = 0.25),
           rw = 1