get_regional_results {EpiNow2}

Get Combined Regional Results

Description

Summarises results across regions either from input or from disk. See the examples for details.

Usage

get_regional_results(
  regional_output,
  results_dir,
  date,
  samples = TRUE,
  forecast = FALSE
)

Arguments

regional_output

A list of output as produced by regional_epinow and stored in the regional list.

results_dir

A character string indicating the folder containing the EpiNow2 results to extract.

date

A Character string (in the format "yyyy-mm-dd") indicating the date to extract data for. Defaults to "latest" which finds the latest results available.

samples

Logical, defaults to TRUE. Should samples be returned.

forecast

Logical, defaults to FALSE. Should forecast results be returned.

Value

A list of estimates, forecasts and estimated cases by date of report.

Author(s)

Sam Abbott

Examples

# construct example distributions
generation_time <- get_generation_time(
 disease = "SARS-CoV-2", source = "ganyani"
)
incubation_period <- get_incubation_period(
 disease = "SARS-CoV-2", source = "lauer"
)
reporting_delay <- estimate_delay(rlnorm(100, log(6), 1), max_value = 10)

# example case vector
cases <- example_confirmed[1:30]
cases <- data.table::rbindlist(list(
  data.table::copy(cases)[, region := "testland"],
  cases[, region := "realland"]
))

# save results to tmp folder
dir <- file.path(tempdir(check = TRUE), "results")
# run multiregion estimates
regional_out <- regional_epinow(
  reported_cases = cases,
  generation_time = generation_time_opts(generation_time),
  delays = delay_opts(incubation_period + reporting_delay),
  rt = rt_opts(rw = 7), gp = NULL,
  output = c("regions", "latest"),
  target_folder = dir,
  return_output = TRUE
)
# from output
results <- get_regional_results(regional_out$regional, samples = FALSE)
names(results)

# from a folder
folder_results <- get_regional_results(results_dir = dir, samples = FALSE)
names(folder_results)