ssir {ATQ}

Stochastic SIR simulation

Description

This function runs a stochastic Susceptible-Infectious-Removed (SIR) epidemic simulation. It can run a single simulation or multiple replications. Also simulates laboratory confirmed cases

Usage

ssir(
  N,
  T = 300,
  alpha,
  avg_start = 45,
  min_start = 20,
  inf_period = 4,
  inf_init = 32,
  report = 0.02,
  lag = 7,
  rep = NULL
)

Arguments

N

Numeric. The total population size.

T

Numeric. The duration of the simulation in time steps. Default is 300.

alpha

Numeric. The transmission rate. Must be a number between 0 and 1.

avg_start

Numeric. The average start day of the epidemic. Default is 45.

min_start

Numeric. The minimum start day of the epidemic. Default is 20.

inf_period

Numeric. The duration of the infectious period in time steps. Default is 4.

inf_init

Numeric. The initial number of infected individuals. Default is 32.

report

Numeric. The proportion of cases that are reported. Default is 0.02.

lag

Numeric. The average delay in reporting cases. Default is 7.

rep

Numeric or NULL. The number of simulation replications to run. If NULL or 1, a single simulation is run.

Value

If rep is NULL or 1, returns an object of class "ssir_epidemic" containing:

new_inf

Vector of new infections at each time step

reported_cases

Vector of reported cases at each time step

S

Vector of susceptible individuals at each time step

I

Vector of infectious individuals at each time step

R

Vector of removed individuals at each time step

parameters

List of input parameters

If rep > 1, returns an object of class "ssir_epidemic_multi" containing multiple simulation results.

Examples

# Run a single simulation
result <- ssir(N = 10000, T = 300, alpha = 0.3, inf_period = 4,
inf_init = 32, report = 0.02, lag = 7)

# Run multiple simulations
multi_result <- ssir(N = 10000, T = 300, alpha = 0.3, inf_period = 4, inf_init = 32,
report = 0.02, lag = 7, rep = 100)