get_regional_results {EpiNow2} | R Documentation |
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 |
results_dir |
A character string indicating the folder containing the
|
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 |
forecast |
Logical, defaults to |
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)
[Package EpiNow2 version 1.4.0 Index]