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Exact stochastic simulation of the SIRD jump process (Gillespie algorithm)

Source: R/sird_ga_simulate.R
sird_gillespie.Rd

Simulates one exact trajectory of the continuous-time, density-dependent Markov jump process underlying the SIRD-GA model, using the direct Gillespie method, and returns the compartment counts recorded at an equally-spaced observation grid.

Usage

sird_gillespie(
  N,
  S0,
  I0,
  R0,
  lambda,
  gamma,
  alpha,
  Tmax,
  Delta = 1,
  max_events = 50L * N
)

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.

Tmax

Final observation time.

Delta

Spacing of the recorded observation grid (default 1).

max_events

Safety cap on the number of simulated events.

Value

A data frame with columns time, S, I, R, D, recorded on the grid seq(0, Tmax, by = Delta) (state held constant between events, as is standard for jump processes).