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 everyx
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 toFALSE
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 an overview of control settings for base ICM class models,
consult the Basic ICMs tutorial. 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.