add examples for analysis results

R/data.R

@@ -21,3 +21,21 @@
 #' An example data frame of observed cases
 #' @format A data frame containing cases reported on each date.
 "example_confirmed"
+
+#' Example estimate_infections output
+#'
+#' @description `r lifecycle::badge("stable")`
+#' An example output of `estimate_infections` containing 200 samples.
+#' See here for details:
+#'  https://github.com/epiforecasts/EpiNow2/blob/main/data-raw/estimate_infections.R # nolint
+#' @format An `estimate_infections` object with the results
+"example_estimate_infections"
+
+#' Example regional_epinow output
+#'
+#' @description `r lifecycle::badge("stable")`
+#' An example output of `regional_epinow` containing 200 samples per region.
+#' See here for details:
+#'  https://github.com/epiforecasts/EpiNow2/blob/main/data-raw/estimate_infections.R # nolint
+#' @format A list with the results
+"example_regional_epinow"

data-raw/estimate-infections.R

@@ -0,0 +1,47 @@
+library("EpiNow2")
+library("here")
+
+# get example case counts
+reported_cases <- example_confirmed[1:60]
+
+# set up example generation time
+generation_time <- get_generation_time(
+  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", fixed = TRUE
+)
+# delays between infection and case report, with uncertainty
+incubation_period_uncertain <- get_incubation_period(
+  disease = "SARS-CoV-2", source = "lauer"
+)
+reporting_delay <- dist_spec(
+  mean = convert_to_logmean(2, 1), mean_sd = 0,
+  sd = convert_to_logsd(2, 1), sd_sd = 0, max = 10
+)
+
+# default settings but assuming that delays are fixed rather than uncertain
+example_estimate_infections <- estimate_infections(reported_cases,
+  generation_time = generation_time_opts(generation_time),
+  delays = delay_opts(incubation_period + reporting_delay),
+  rt = rt_opts(prior = list(mean = 2, sd = 0.1)),
+  stan = stan_opts(samples = 200, control = list(adapt_delta = 0.95))
+)
+
+cases <- example_confirmed[1:60]
+cases <- data.table::rbindlist(list(
+  data.table::copy(cases)[, region := "testland"],
+  cases[, region := "realland"]
+))
+
+example_regional_epinow <- regional_epinow(
+  reported_cases = cases,
+  generation_time = generation_time_opts(generation_time),
+  delays = delay_opts(incubation_period + reporting_delay),
+  rt = rt_opts(prior = list(mean = 2, sd = 0.2)),
+  stan = stan_opts( samples = 200, control = list(adapt_delta = 0.95))
+)
+
+usethis::use_data(example_estimate_infections, overwrite = TRUE)
+usethis::use_data(example_regional_epinow, overwrite = TRUE)