control.icm: Control Settings for Stochastic Individual Contact Models

In EpiModel: Mathematical Modeling of Infectious Disease Dynamics

Control Settings for Stochastic Individual Contact Models

Description

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.

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.

Value

An EpiModel object of class control.icm.

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.

See Also

Use param.icm to specify model parameters and init.icm to specify the initial conditions. Run the parameterized model with icm.

EpiModel documentation built on Oct. 12, 2024, 1:06 a.m.