R/examples/get_tau_typed_permute.R

In IDSpatialStats: Estimate Global Clustering in Infectious Disease

\donttest{

data(DengueSimulationR02)

r.max<-seq(20,1000,20)
r.min<-seq(0,980,20)
r.mid<-(r.max+r.min)/2

#Lets see if there's a difference in spatial dependence by time case occurs
type <- 2 - (DengueSimR02[,"time"] < 120)
tmp <- cbind(DengueSimR02, type=type)

typed.tau <- get.tau.typed(tmp, typeA=1, typeB=2, r=r.max, r.low=r.min, 
                           comparison.type = "independent")

typed.tau.type.null<-get.tau.typed.permute(tmp, typeA=1, typeB=2, r=r.max, r.low=r.min, 
                                           permutations=100, comparison.type = "independent")

null.ci <- apply(typed.tau.type.null[,-(1:2)], 1, quantile, probs=c(0.025,0.975))

plot(r.mid, typed.tau$tau, ylim=c(0.3,4), log="y", cex.axis=1.25, 
     xlab="Distance (m)", ylab="Tau", cex.main=0.9, lwd=2, type="n")
abline(h=1,lty=1)
lines(r.mid,typed.tau$tau,pch=20,col=1,lwd=3)
lines(r.mid, null.ci[1,] , lty=2)
lines(r.mid, null.ci[2,] , lty=2)

}