get_outbreak_data

Generate outbreak data from model output

Usage

get_outbreak_data(
  case_data = c(),
  year_data = c(),
  p_rep_severe = 1,
  p_rep_death = 1
)

Arguments

case_data

Vector of cases by time point summed over age

year_data

Vector of year values corresponding to case data

p_rep_severe

probability of a severe infection being reported

p_rep_death

probability of a death being reported '

Details

Takes in case (infection) data output by Full_Model_OD() or case_data_generate(), uses severe and fatal infection rates and reporting probabilities to calculate the number of reported cases, and outputs a list of reported outbreaks. An outbreak is assumed to be reported when one or more cases is reported, and continues until no new cases have been reported for 10 days.