tests/EpiILM.network.R

In vineetha-warriyar/EpiILM: Spatial and Network Based Individual Level Models for Epidemics

# Load the EpiILM package
library("EpiILM")
set.seed(101)

# sample size
n <- 500

# Generating an undirected binary contact network:
contact <- matrix(0, n, n)
for(i in 1:(n-1)) {
	contact[i, ((i+1):n)] <- rbinom((n-i), 1, 0.05)
	contact[((i+1):n), i] <- contact[i, ((i+1):n)]
	}
contact

# Generating the susceptibility and transmissibilty covariates:
X1 <- round(rexp(n, 1/100))
X1
X2 <- round(rgamma(n, 50, 0.5))
X2
# Simulate epidemic form SIR network-based ILM

infp <- rep(3, n)
SIR.net <- epidata(type = "SIR", n = 500, tmax = 50,
     sus.par = c(0.003, 0.002), trans.par = c(0.0003, 0.0002),
     contact = contact, infperiod = infp,
     Sformula = ~ -1 + X1 + X2, Tformula = ~ -1 + X1 + X2)
SIR.net

# epimcmc function to estimate the model parameters:
t_end <- max(SIR.net$inftime)
prior_par <- matrix(rep(1, 4), ncol = 2, nrow = 2)

# This took 305.7 seconds on an Apple MacBook Pro with i5-core Intel 2.4 GHz
# processors with 8 GB of RAM.
mcmcout_SIR.net <- epimcmc(SIR.net, tmax = t_end, niter = 100,
        Sformula = ~-1 + X1 + X2, Tformula = ~-1 + X1 + X2,
        sus.par.ini = c(0.003, 0.01), trans.par.ini = c(0.01, 0.01),
        pro.sus.var = c(0.0, 0.1), pro.trans.var = c(0.1, 0.1),
        prior.sus.dist = c("gamma", "gamma"), prior.trans.dist = c("gamma", "gamma"),
        prior.sus.par = prior_par, prior.trans.par = prior_par,
        adapt = TRUE, acc.rate = 0.5)

# Summary of MCMC results
summary(mcmcout_SIR.net)

# Posterior predictive forecasting
# Posterior prediction starting from time point 5
pred.SIR.net.point.5 <- pred.epi(SIR.net, xx = mcmcout_SIR.net, tmin = 5,
         Sformula = ~-1 + X1 + X2, Tformula = ~-1 + X1 + X2,
         criterion = "newly infectious",
         n.samples = 50)
pred.SIR.net.point.5

# Posterior prediction starting from time point 14
pred.SIR.net.point.8 <- pred.epi(SIR.net, xx = mcmcout_SIR.net, tmin = 14,
        Sformula = ~-1 + X1 + X2, Tformula = ~-1 + X1 + X2,
        criterion = "newly infectious",
        n.samples = 50)
pred.SIR.net.point.8