Control Settings for Stochastic Individual Contact Models

Sets the controls for stochastic individual contact models simulated with icm.

Usage

control.icm(
  type,
  nsteps,
  nsims = 1,
  initialize.FUN = initialize.icm,
  infection.FUN = NULL,
  recovery.FUN = NULL,
  departures.FUN = NULL,
  arrivals.FUN = NULL,
  prevalence.FUN = NULL,
  verbose = FALSE,
  verbose.int = 0,
  skip.check = FALSE,
  ...
)

Arguments

type: Disease type to be modeled, with the choice of "SI" for Susceptible-Infected diseases, "SIR" for Susceptible-Infected-Recovered diseases, and "SIS" for Susceptible-Infected-Susceptible diseases.
nsteps: Number of time steps to solve the model over. This must be a positive integer.
nsims: Number of simulations to run.
initialize.FUN: Module to initialize the model at the outset, with the default function of initialize.icm.
infection.FUN: Module to simulate disease infection, with the default function of infection.icm.
recovery.FUN: Module to simulate disease recovery, with the default function of recovery.icm.
departures.FUN: Module to simulate departures or exits, with the default function of departures.icm.
arrivals.FUN: Module to simulate arrivals or entries, with the default function of arrivals.icm.
prevalence.FUN: Module to calculate disease prevalence at each time step, with the default function of prevalence.icm.
verbose: If TRUE, print model progress to the console.
verbose.int: Time step interval for printing progress to console, where 0 (the default) prints completion status of entire simulation and positive integer x prints progress after every x time steps.
skip.check: If TRUE, skips the default error checking for the structure and consistency of the parameter values, initial conditions, and control settings before running base epidemic models. Setting this to FALSE is recommended when running models with new modules specified.
...: Additional control settings passed to model.

Value

An EpiModel object of class control.icm.

Details

control.icm sets the required control settings for any stochastic individual contact model solved with the icm function. Controls are required for both base model types and when passing original process modules. For all base models, the type argument is a necessary parameter and it has no default.

New Modules

Base ICM models use a set of module functions that specify how the individual agents in the population are subjected to infection, recovery, demographics, and other processes. Core modules are those listed in the .FUN arguments. For each module, there is a default function used in the simulation. The default infection module, for example, is contained in the infection.icm function.

For original models, one may substitute replacement module functions for any of the default functions. New modules may be added to the workflow at each time step by passing a module function via the ... argument.