sample_Rt_single_piece: Sample a single Rt value corresponding to a single piecewise-...

In ben18785/incidenceinflation: Estimate R0 Given Case Reporting Delays

Sample a single Rt value corresponding to a single piecewise- constant element of an Rt vector

Description

Sample a single Rt value corresponding to a single piecewise- constant element of an Rt vector

Usage

sample_Rt_single_piece(
  Rt_piece_index,
  cases_history_df,
  Rt_prior_parameters,
  serial_parameters,
  kappa = NULL,
  serial_max = 40,
  ndraws = 1,
  maximise = FALSE,
  is_negative_binomial = FALSE,
  nresamples = 100
)

Arguments

Rt_piece_index	the index of the Rt piece being sampled
cases_history_df	a tibble with three columns: time_onset, cases_true and Rt_index
Rt_prior_parameters	a list with elements 'shape' and 'rate' describing the gamma prior for Rt
serial_parameters	named list of 'mean' and 'sd' of gamma distribution characterising the serial interval distribution
kappa	overdispersion parameter
serial_max	maximum point at which to truncate sum in renewal process
ndraws	number of draws of Rt
maximise	rather than sample a case count give the case count with the maximum probability (by default is FALSE)
is_negative_binomial	if negative-binomial renewal model specified (defaults to FALSE)
nresamples	number of importance resamples of Rt to perform if assuming a negative binomial model

Value

a draw (or draws) for Rt

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