## Forced SIR model using R and simecol¶

In [1]:
library(deSolve)
library(simecol)
library(reshape2)

In [2]:
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"
)

In [3]:
# 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)

In [4]:
sirforced_out <- out(sirforcedode)
sirforced_out_long <- melt(sirforced_out,"time")


### Visualisation¶

In [5]:
library(ggplot2)

In [6]:
ggplot(sirforced_out_long[sirforced_out_long\$variable=="I",],aes(x=time,y=value,colour=variable,group=variable))+