demo/sirforced.R

In reconhub/epicookbook: A cookbook of 'recipes' for epidemiological modeling in R.

sirforcedode <- new("odeModel",
  main = function(time, init, parms, ...){
    with(as.list(c(init,parms)),{
      # ODEs
      N <- S+I+R
      dS <- mu*N-beta(beta0,beta1,omega,time)*S*I/N-mu*S
      dI <- beta(beta0,beta1,omega,time)*S*I/N-gamma*I-mu*I
      dR <- gamma*I-mu*R
      list(c(dS,dI,dR))
    })},
  equations = list(
    beta = function(beta0,beta1,omega,time){beta0*(1+beta1*sin(omega*time))}
  ),
  parms = c(beta0=10./7,beta1=0.05,omega=2*pi/365,gamma=1./7,mu=1./(70*365)),
  times = c(from=0,to=100*365,by=1),
  init = c(S=99999,I=1,R=0),
  solver = "lsoda"
)
# Simulate until equilibrium
sirforcedode <- sim(sirforcedode)
# Reset initial values
init(sirforcedode) <- unlist(out(sirforcedode)[100*365,2:4])
# Look at 10 years
times(sirforcedode) <- c(from=0,to=10*365,by=1)
# Simulate
sirforcedode <- sim(sirforcedode)