SIR_agent: An R function to perform an Agent Based Monte Carlo...

In smtowers/ANDI: An R package with methods to estimate the Average Number of Descendant Infections (ANDI) for a Susceptible, Infected, Recovered disease model

Description

An R function to perform an Agent Based Monte Carlo simulation of a Susceptible, Infected, Recovered (SIR) disease model with homogeneous mixing of the population. The function keeps track of who infected whom, and calculates the average number of descendant infections (ANDI) for the individuals infected in the outbreak

Usage

SIR_agent(N, I_0, S_0, gamma, R0, delta_t = 0)

Arguments

N	The population size
I_0	The initial number infected
S_0	The initial number suscetible
gamma	The recovery rate
R0	The reproduction number
delta_t	time step to solve model (if 0 then dynamically calculated time step used)

Value

list list of model compartment values vs time, and ANDI

Examples

## 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)

smtowers/ANDI documentation built on May 6, 2019, 7:04 p.m.