control.dcm: Control Settings for Deterministic Compartmental Models

In EpiModel: Mathematical Modeling of Infectious Disease Dynamics

Control Settings for Deterministic Compartmental Models

Description

Sets the controls for deterministic compartmental models simulated with dcm.

Usage

control.dcm(
  type,
  nsteps,
  dt = 1,
  odemethod = "rk4",
  dede = FALSE,
  new.mod = NULL,
  sens.param = TRUE,
  print.mod = FALSE,
  verbose = 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 or vector of times to solve the model over. If the number of time steps, then this must be a positive integer of length 1.
dt	Time unit for model solutions, with the default of 1. Model solutions for fractional time steps may be obtained by setting this to a number between 0 and 1.
odemethod	Ordinary differential equation (ODE) integration method, with the default of the "Runge-Kutta 4" method (see deSolve::ode for other options).
dede	If TRUE, use the delayed differential equation solver, which allows for time-lagged variables.
new.mod	If not running a base model type, a function with a new model to be simulated (see details).
sens.param	If TRUE, evaluate arguments in parameters with length greater than 1 as sensitivity analyses, with one model run per value of the parameter. If FALSE, one model will be run with parameters of arbitrary length (the model may error unless the model function is designed to accomodate parameter vectors).
print.mod	If TRUE, print the model form to the console.
verbose	If TRUE, print model progress to the console.
...	additional control settings passed to model.

Details

control.dcm sets the required control settings for any deterministic compartmental models solved with the dcm function. Controls are required for both base model types and original models. For all base models, the type argument is a necessary parameter and it has no default.

Value

An EpiModel object of class control.dcm.

New Model Functions

The form of the model function for base models may be displayed with the print.mod argument set to TRUE. In this case, the model will not be run. These model forms may be used as templates to write original model functions.

These new models may be input and solved with dcm using the new.mod argument, which requires as input a model function.

See Also

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

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