sirode: Susceptible-infected-recovered (SIR) differential equation...
In reconhub/epicookbook: A cookbook of 'recipes' for epidemiological modeling in R.

Description Usage Details Author(s) See Also Examples

This is a susceptible-infected-recovered (SIR) differential equation model using simecol.

1	example(sirode)

dS(t)/dt = -β S(t) I(t)

dI(t)/dt = β S(t) I(t)- γ I(t)

dR(t)/dt = γ I(t)

The state variables of the model are as follows.

S: The number of susceptible individuals.
I: The number of infected individuals.
R: The number of recovered individuals.

The parameters of the model, and the values used in the example, are as follows.

Symbol	Description	Value
β	Infectivity parameter	0.1
γ	Recovery rate	0.05

Simon Frost (sdwfrost@gmail.com)

sircn.

sir.ode <- function(times,init,parms){
  with(as.list(c(parms,init)), {
  # ODEs
  dS <- -beta*S*I
  dI <- beta*S*I-gamma*I
  dR <- gamma*I
  list(c(dS,dI,dR))
  })
}
parms <- c(beta=0.1,gamma=0.05)
init <- c(S=0.99,I=0.01,R=0) 
times <- seq(0,200,by=0.01)
sir.out <- lsoda(init,times,sir.ode,parms)