R/outbreak_setup.R

In covid19risk/impact-sim: Feasibility of controlling 2019-nCoV outbreaks by isolation of cases and contacts

#' Set up initial cases for branching process
#' @author Joel Hellewell
#'
#' @param num.initial.cases Integer number of initial cases
#' @param incfn function that samples from incubation period Weibull distribution; generated using dist_setup
#' @param delayfn function that samples from the onset-to-hospitalisation delay Weibull distribution; generated using dist_setup
#' @param k Numeric skew parameter for sampling the serial interval from the incubation period
#' @param prop.asym Numeric proportion of cases that are sublinical (between 0 and 1)
#'
#' @return data.table of cases in outbreak so far
#' @export
#' @importFrom data.table data.table
#'
#' @examples
#'
#'\dontrun{
#' # incubation period sampling function
#' incfn <- dist_setup(dist_shape = 2.322737,dist_scale = 6.492272)
#' # delay distribution sampling function
#' delayfn <- dist_setup(delay_shape, delay_scale)
#' outbreak_setup(num.initial.cases = 5,incfn,delayfn,k=1.95,prop.asym=0)
#'}
outbreak_setup <- function(num.initial.cases, incfn, delayfn, k, prop.asym, fracApp) {
  # Set up table of initial cases
  inc_samples <- incfn(num.initial.cases)

  case_data <- data.table(exposure = rep(0, num.initial.cases), # Exposure time of 0 for all initial cases
                          asym = purrr::rbernoulli(num.initial.cases, prop.asym),
                          caseid = 1:(num.initial.cases), # set case id
                          infector = 0,
                          missed = TRUE,
                          onset = inc_samples,
                          new_cases = NA,
                          group = sample(c(1,2), size = num.initial.cases, prob = c(fracApp, 1-fracApp), replace = TRUE),
                          infector_group = 2)

  # set isolation time for cluster to minimum time of onset of symptoms + draw from delay distribution
  case_data <- case_data[, isolated_time := onset + delayfn(1)
                         ][, isolated := FALSE]

  case_data$isolated_time[case_data$asym] <- Inf

  # return
  return(case_data)
}