Description Usage Arguments Value Examples
View source: R/SIR_solve_model.R
A function to calculate the deterministic estimates of the number infected versus time and the average number of descendant infections (ANDI) for a deterministic Susceptible, Infected, Recovered (SIR) model
1 | SIR_solve_model(N, R0, fsusc, delta_t = 0.01)
|
N |
the population size |
R0 |
the reproduction number |
fsusc |
the initial fraction susceptible |
delta_t |
time step to solve model |
list model compartment values vs time and ANDI
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 | ## Not run:
require("ANDI")
require("deSolve")
N = 1000
I0 = 1
S0 = N-I0
gamma = 1
R0 = 1.5
set.seed(78998026)
a = SIR_agent(N,I0,S0,gamma,R0)
b = SIR_solve_model(N,R0,S0/N,0.1)
par(mfrow=c(1,1))
plot(a$time,a$I,xlab="Time",ylab="Prevalence",main=paste("R0=",R0," and N=",N,sep=""))
lines(b$results$time,b$results$I,col=2,lwd=4)
legend("topright",legend=c("ABMC","deterministic"),col=c(1,2),bty="n",lwd=4,cex=0.8)
cat("Est ANDI, ABMC and deterministic: ",round(mean(a$ANDI),1)," ",round(b$ANDI,1),"\n",sep="")
cat("Est final size, ABMC and deterministic: ",a$final_size," ",b$final_size,"\n",sep="")
## End(Not run)
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