Agent Multigroup

A Multi-group SEIR Model

Parameter values

  # the transmission rate matrix
  beta = matrix(c(0.4, 0.2, 0.2, 0.3), nrow=2)
  # the recovery rate
  gamma = newExpWaitingTime(0.2)
  # the rate leaving the latent stage and becoming infectious
  sigma=0.5
  # the population size
  N = 10000

Create the Simulation and Initialize the agents

The state of an agent is an R list. At most one of the value can be unnamed, others must be named. The names are called domains, and their values can be any R value.

In this example, there are two domains, an unnamed one denoting the infections status, and a named one specifying the group it is in.

  # initialize a simulation with N agents
  sim = Simulation$new(N)
  for (i in 1:n) {
    sim$setState(i, list(if (i <= 20) "I" else "S", group=i %% 2))
  }

Add Loggers

See the details of Counter objects and the Logger class in the SEIR model page.

The following counts the number of agents in the states specified by "from".

  sim$addLogger(newCounter("S1", from=list("S", group=0)))
  sim$addLogger(newCounter("S2", list("S", group=1)))
  sim$addLogger(newCounter("E1", list("E", group=0)))
  sim$addLogger(newCounter("E2", list("E", group=1)))
  sim$addLogger(newCounter("I1", list("I", group=0)))
  sim$addLogger(newCounter("I2", list("I", group=1)))
  sim$addLogger(newCounter("R1", list("R", group=0)))
  sim$addLogger(newCounter("R2", list("R", group=1)))

Mixing Pattern

We create a random mixing object and add it to the simulation

  m = newRandomMixing()
  sim$addContact(m)

Transitions

See details of transitions int he SEIR model.

  sim$addTransition("E"->"I", sigma)
  sim$addTransition("I"->"R", gamma)
  sim$addTransition(list("I", group=0) + list("S", group=0) -> 
                      list("I", group=0) + list("E", group=0) ~ m, beta[1, 1]) 
  sim$addTransition(list("I", group=0) + list("S", group=1) -> 
                      list("I", group=0) + list("E", group=1) ~ m, beta[1, 2]) 
  sim$addTransition(list("I", group=1) + list("S", group=0) -> 
                      list("I", group=1) + list("E", group=0) ~ m, beta[2, 1]) 
  sim$addTransition(list("I", group=1) + list("S", group=1) -> 
                      list("I", group=1) + list("E", group=1) ~ m, beta[2, 2]) 

Run the Simulation

  result = sim$run(0:250)
  print(result)