EpiNow2 (version 1.1.0)

get_regional_results: Get Combined Regional Results

Description

Get Combined Regional Results

Usage

get_regional_results(regional_output, results_dir, date, 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.

forecast

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

Value

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

Examples

# NOT RUN {

# }
# NOT RUN {
# Construct example distributions
generation_time <- list(mean = EpiNow2::covid_generation_times[1, ]$mean,
                        mean_sd = EpiNow2::covid_generation_times[1, ]$mean_sd,
                        sd = EpiNow2::covid_generation_times[1, ]$sd,
                        sd_sd = EpiNow2::covid_generation_times[1, ]$sd_sd,
                        max = 30)
                          
incubation_period <- list(mean = EpiNow2::covid_incubation_period[1, ]$mean,
                          mean_sd = EpiNow2::covid_incubation_period[1, ]$mean_sd,
                          sd = EpiNow2::covid_incubation_period[1, ]$sd,
                          sd_sd = EpiNow2::covid_incubation_period[1, ]$sd_sd,
                          max = 30)
                   
reporting_delay <- list(mean = log(10),
                        mean_sd = 0.8,
                        sd = log(2),
                        sd_sd = 0.1,
                        max = 30)
                        
# Uses example case vector from EpiSoon
cases <- EpiNow2::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,
                                incubation_period = incubation_period,
                                reporting_delay = reporting_delay,
                                samples = 2000, warmup = 200, cores = ifelse(interactive(), 4, 1),
                                adapt_delta = 0.95, chains = 4, verbose = TRUE,
                                summary = FALSE)
                                
get_regional_results(regional_out$regional, forecast = TRUE)

# }