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Simulate daily reported cases and deaths from the SIRD jump process

Source: R/sird_ga_incidence.R
sird_ga_simulate_inc.Rd

Runs the exact Gillespie simulator sird_gillespie() and turns the latent daily increments into surveillance counts: reported cases are Binomial(new infections, p) plus N(0, tau2 * new infections) measurement error, reported deaths are Binomial(new deaths, q) plus N(0, tau2_d * new deaths). Counts are rounded and truncated at zero.

Usage

sird_ga_simulate_inc(
  N,
  S0,
  I0,
  R0,
  lambda,
  gamma,
  alpha,
  p,
  tau2,
  q = 1,
  tau2_d = 0,
  Tmax,
  Delta = 1
)

Arguments

N

Population size (integer head count).

S0, I0, R0

Initial compartment counts (integers, S0+I0+R0 <= N).

lambda, gamma, alpha

Transmission, recovery and disease-induced mortality rates.

p, tau2

Case reporting probability and case measurement-error scale.

q, tau2_d

Death reporting probability and death measurement-error scale.

Tmax

Final observation time.

Delta

Spacing of the recorded observation grid (default 1).

Value

A list with latent (the Gillespie output), cases and deaths (numeric vectors of length Tmax / Delta, one count per interval (t_{k-1}, t_k]), new_inf and new_deaths (latent increments).