This tutorial documents how to use EpiModel to solve new deterministic compartmental models (DCMs). New model types incorporate model compartments, parameters, and structures different from the built-in SI/SIR/SIS model types in EpiModel. This extension tutorial assumes a solid familiarity with both R programming and epidemic model parameterization the other tutorials. If you are not familiar with DCMs or running this model class in EpiModel, consult the Basic DCMs with EpiModel tutorial.

The EpiModel DCM Framework

First load the EpiModel package:

library(EpiModel)

To start let’s examine the mathematical syntax for our basic SI model in a closed population (no births or deaths). We first run this model in EpiModel to see the normal syntax that avoids any specific reference to the model function specifying the mathematical structure. As detailed in the basic tutorial, EpiModel automatically chooses the correct model function as a result of the input parameters, initial conditions, and control settings.

param <- param.dcm(inf.prob = 0.5, act.rate = 0.25)
init <- init.dcm(s.num = 500, i.num = 1)
control <- control.dcm(type = "SI", nsteps = 100)
mod <- dcm(param, init, control)
plot(mod)