[Stable] 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"
# }