EpiNow2 (version 1.1.0)

report_cases: Report case counts by date of report

Description

Report case counts by date of report

Usage

report_cases(
  case_estimates,
  case_forecast = NULL,
  delays,
  type = "sample",
  reporting_effect
)

Arguments

case_estimates

A data.table of case estimates with the following variables: date, sample, cases

case_forecast

A data.table of case forecasts with the following variables: date, sample, cases. If not supplied the default is not to incorporate forecasts.

delays

A list of delays (i.e incubation period/reporting delay) between infection and report. Each list entry must also be a list containing the mean, standard deviation of the mean (mean_sd), standard deviation (sd), standard deviation of the standard deviation and the maximum allowed value for the that delay (assuming a lognormal distribution with all parameters excepting the max allowed value on the log scale).

type

Character string indicating the method to use to transform counts. Supports either "sample" which approximates sampling or "median" would shift by the median of the distribution.

reporting_effect

A data.table giving the weekly reporting effect with the following variables: sample (must be the same as in nowcast), effect (numeric scaling factor for each weekday), day (numeric 1 - 7 (1 = Monday and 7 = Sunday)). If not supplied then no weekly reporting effect is assumed.

Value

A list of data.tables. The first entry contains the following variables sample, date and cases with the second being summarised across samples.

Examples

# NOT RUN {
## Define example cases
cases <- EpiNow2::example_confirmed[1:40]

 
## Set up example generation time
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)
## Set                   
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(5),
                        mean_sd = log(2),
                        sd = log(2),
                        sd_sd = log(1.5),
                        max = 30)
                        
## Run model
out <- EpiNow2::estimate_infections(cases, family = "negbin",
                                    generation_time = generation_time,
                                    delays = list(incubation_period, reporting_delay),
                                    samples = 1000, warmup = 200, 
                                    cores = ifelse(interactive(), 4, 1), chains = 4,
                                    estimate_rt =  FALSE, verbose = TRUE)
                            
                     
reported_cases <- report_cases(case_estimates = out$samples[variable == "infections"][, 
                                                            cases := value][, value := NULL],
                               delays = list(incubation_period, reporting_delay),
                               type = "sample")
                               
print(reported_cases)
# }