regional_runtimes | R Documentation |
Used internally by regional_epinow
to summarise region run times.
regional_runtimes(
regional_output = NULL,
target_folder = NULL,
target_date = NULL,
return_output = FALSE
)
regional_output |
A list of output as produced by |
target_folder |
Character string specifying where to save results (will create if not present). |
target_date |
A character string giving the target date for which to extract results (in the format "yyyy-mm-dd"). Defaults to latest available estimates. |
return_output |
Logical, defaults to FALSE. Should output be returned, this automatically updates to TRUE if no directory for saving is specified. |
A data.table of region run times
regional_summary regional_epinow
# example delays
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 = 15)
cases <- example_confirmed[1:30]
cases <- data.table::rbindlist(list(
data.table::copy(cases)[, region := "testland"],
cases[, region := "realland"]
))
# run basic nowcasting pipeline
regional_out <- regional_epinow(
reported_cases = cases,
generation_time = generation_time_opts(generation_time),
delays = delay_opts(incubation_period + reporting_delay),
stan = stan_opts(samples = 100, warmup = 100),
output = c("region", "timing")
)
regional_runtimes(regional_output = regional_out$regional)
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