generate_snapshots: Generates case data with snapshots of reported cases at each...

In ben18785/incidenceinflation: Estimate R0 Given Case Reporting Delays

Generates case data with snapshots of reported cases at each onset day

Description

Generates case data with snapshots of reported cases at each onset day

Usage

generate_snapshots(
  days_total,
  Rt_function,
  serial_parameters,
  reporting_parameters,
  thinned = FALSE,
  kappa = 1000,
  days_max_follow_up = 30,
  initial_parameters = list(mean = 30, length = 20),
  serial_max = 40
)

Arguments

days_total	number of days to simulate process for (post-initial period)
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	either a named list of 'mean' and 'sd' of gamma distribution indicating a single reporting delay distribution for the whole period or a tibble with columns: 'time_onset', 'mean', 'sd' indicating the reporting delay distribution for each time period
thinned	a Boolean indicating whether to thin cases to only informative time points
kappa	over-dispersion parameter of negative binomial
days_max_follow_up	max days at which to simulate reporting case trajectory
initial_parameters	a named list of 'mean' and 'length' which is used to generate seed cases by sampling from a negative binomial distribution
serial_max	maximum point at which to truncate sum in renewal process

Value

a tibble with observed case trajectories for each time of onset

Examples

library(incidenceinflation)
# generate case series for 100 days with time-varying Rt
days_total <- 100

# make Rt interpolation function
v_Rt <- c(rep(1.3, 25), rep(1, 25), rep(2, 50))
Rt_function <- stats::approxfun(1:days_total, v_Rt)

# serial interval parameters
s_params <- list(mean=5, sd=1)

# renewal over-dispersion parameter
kappa <- 2

# reporting delays
r_params <- list(mean=10, sd=5)
reported_cases <- generate_snapshots(
    days_total, Rt_function,
    s_params, r_params)

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