Get Combined Regional Results — get_regional

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

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.

Examples

# \donttest{
# 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 from EpiSoon
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,
  delays = delay_opts(incubation_period, reporting_delay),
  rt = rt_opts(rw = 7), gp = NULL,
  output = c("regions", "latest"),
  target_folder = dir,
  return_output = TRUE
)
#> INFO [2022-03-28 03:35:27] Producing following optional outputs: regions, latest
#> Logging threshold set at INFO for the EpiNow2 logger
#> Writing EpiNow2 logs to the console and: /var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T//RtmpqbXERq/regional-epinow/2020-03-22.log
#> Logging threshold set at INFO for the EpiNow2.epinow logger
#> Writing EpiNow2.epinow logs to: /var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T//RtmpqbXERq/epinow/2020-03-22.log
#> INFO [2022-03-28 03:35:28] Reporting estimates using data up to: 2020-03-22
#> INFO [2022-03-28 03:35:28] Saving estimates to : /var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T//RtmpqbXERq/results
#> INFO [2022-03-28 03:35:28] Producing estimates for: testland, realland
#> INFO [2022-03-28 03:35:28] Regions excluded: none
#> INFO [2022-03-28 03:36:31] Completed estimates for: testland
#> INFO [2022-03-28 03:37:40] Completed estimates for: realland
#> INFO [2022-03-28 03:37:40] Completed regional estimates
#> INFO [2022-03-28 03:37:40] Regions with estimates: 2
#> INFO [2022-03-28 03:37:40] Regions with runtime errors: 0
#> INFO [2022-03-28 03:37:40] Saving timings information to : /var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T//RtmpqbXERq/results
# from output
results <- get_regional_results(regional_out$regional, samples = FALSE)
names(results)
#> [1] "estimates"

# from a folder
folder_results <- get_regional_results(results_dir = dir, samples = FALSE)
names(folder_results)
#> [1] "estimates"
# }