R/examples/sim_epidemic.R

In IDSpatialStats: Estimate Global Clustering in Infectious Disease

\donttest{
     
set.seed(1)

dist.func <- alist(n=1, a=1/100, rexp(n, a)) # Exponential transmission kernel with mean = sd = 100

# Simulate epidemic with constant R value
a <- sim.epidemic(R=1.5,
             gen.t.mean=7,
             gen.t.sd=2,
             tot.generations=15,
             min.cases=100,
             trans.kern.func=dist.func)

sim.plot(a)

# Simulate an epidemic with variable R value
r1 <- 2
r2 <- 0.25
tg <- 25
R <- seq(r1, r2, (r2 -r1)/(tg - 1))

b <- sim.epidemic(R=R,
             gen.t.mean=7,
             gen.t.sd=2,
             tot.generations=tg,
             min.cases=100,
             trans.kern.func=dist.func)

sim.plot(b)

}