sample_cases_history: Draws a possible history (or histories) of cases

In ben18785/incidenceinflation: Estimate R0 Given Case Reporting Delays

Draws a possible history (or histories) of cases

Description

The distribution being drawn from at each onset time t 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_cases_history(
  observation_onset_df,
  max_cases,
  Rt_function,
  serial_parameters,
  reporting_parameters,
  p_gamma_cutoff = 0.99,
  maximise = FALSE,
  kappa = NULL,
  is_negative_binomial = FALSE
)

Arguments

observation_onset_df	a tibble with four columns: time_onset, time_reported, cases_reported, reporting_piece_index
max_cases	maximum possible cases thought to arise on a given day
Rt_function	takes day as an input and outputs an Rt value
serial_parameters	named list of 'mean' and 'sd' of gamma distribution characterising the serial interval distribution
reporting_parameters	a tibble with three columns: reporting_piece_index, mean, sd.
p_gamma_cutoff	a p value (0 <= p <= 1) indicating the threshold above which we deem certainty
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)

Value

a tibble with an extra cases_estimated column

ben18785/incidenceinflation documentation built on Feb. 8, 2024, 2:36 a.m.