sample_true_cases_single_onset: Samples a case count arising on a given onset day
In ben18785/incidenceinflation: Estimate R0 Given Case Reporting Delays

sample_true_cases_single_onset

R Documentation

Samples a case count arising on a given onset day

Description

The distribution being drawn from is given by:

p(cases_true_t|data, Rt, reporting_params, serial_params) \propto p(data|cases_true, reporting_params) p(cases_true_t|cases_true_t_1, cases_true_t_2, ..., Rt, serial_params)

Usage

sample_true_cases_single_onset(
  observation_df,
  cases_history,
  max_cases,
  Rt,
  day_onset,
  serial_parameters,
  reporting_parameters,
  ndraws = 1,
  maximise = FALSE,
  kappa = NULL,
  is_negative_binomial = FALSE
)

Arguments

`observation_df`	a two-column data frame with columns 'time_reported' and 'cases_reported'
`cases_history`	a vector containing history of cases arranged from recent to past
`max_cases`	maximum possible cases thought to arise on a given day
`Rt`	effective reproduction number
`day_onset`	day when case originates
`serial_parameters`	named list of 'mean' and 'sd' of gamma distribution characterising the serial interval distribution
`reporting_parameters`	named list of 'mean' and 'sd' of gamma distribution characterising the reporting delay distribution
`ndraws`	number of draws of cases
`maximise`	rather than sample a case count give the case count with the maximum probability (by default is FALSE)
`kappa`	overdispersion parameter
`is_negative_binomial`	if negative-binomial renewal model specified (defaults to FALSE)