R/examples/get_tau.R

In IDSpatialStats: Estimate Global Clustering in Infectious Disease

\donttest{

data(DengueSimR01)
data(DengueSimR02)
data(DengueSimRepresentative)

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

sero.type.func<-function(a,b,tlimit=20){
     if(a[5]==b[5]&(abs(a[3]-b[3])<=tlimit)){rc=1}
     else{rc=2}
     return(rc)
}

geno.type.func<-function(a,b,tlimit=20){
     if(a[4]==b[4]&(abs(a[3]-b[3])<=tlimit)){rc=1}
     else{rc=2}
     return(rc)
}

sero.type.rep.func<-function(a,b,tlimit=20){
     if(a[5]==1&b[5]==1&(abs(a[3]-b[3])<=tlimit)){rc=1}
     else{if(a[5]==1&b[5]==-999){rc=2}else{rc=3}}
     return(rc)
}

sero.tau.R01 <- get.tau(DengueSimR01, sero.type.func, r=r.max, r.low=r.min, 
                      comparison.type="independent")
geno.tau.R01 <- get.tau(DengueSimR01, geno.type.func, r=r.max, r.low=r.min, 
                      comparison.type="independent")

sero.tau.R02 <- get.tau(DengueSimR02, sero.type.func, r=r.max, r.low=r.min, 
                      comparison.type="independent")
geno.tau.R02 <- get.tau(DengueSimR02, geno.type.func, r=r.max, r.low=r.min, 
                      comparison.type="independent")

sero.tau.representative <- get.tau(DengueSimRepresentative, sero.type.rep.func, 
                                   r=r.max, r.low=r.min, comparison.type="representative")

## R0 of 1
plot(r.mid,sero.tau.R01$tau,ylim=c(0.3,max(geno.tau.R01$tau)),log="y",
     cex.axis=1.25,col=rgb(t(col2rgb("blue")/255),alpha=0.6),
     xlab="Distance (m)",ylab="Tau",cex.main=0.9,lwd=2,type="l",las=1,cex.axis=0.75)
abline(h=1,lty=2)

abline(v=100,lty=1,lwd=2)
lines(r.mid,geno.tau.R01$tau,pch=20,col=rgb(t(col2rgb("dark green")/255),alpha=0.6),lwd=1)
lines(r.mid,sero.tau.representative$tau,pch=20,col=rgb(t(col2rgb("dark blue")/255),alpha=0.6),lty=2)
legend("topright",
       legend=c("Genotype",
                "Serotype",
                "Serotype (representative population)",
                "Maximum transmission distance"),
       lwd=1,col=c("dark green","blue","blue","black"),
       lty=c(1,1,2,1),bty="n")

## R0 of 2
plot(r.mid,sero.tau.R02$tau,ylim=c(0.3,max(geno.tau.R02)),log="y",
     cex.axis=1.25,col=rgb(t(col2rgb("blue")/255),alpha=0.6),
     xlab="Distance (m)",ylab="Tau",cex.main=0.9,lwd=2,type="l",las=1,cex.axis=0.75)
abline(h=1,lty=2)
abline(v=100,lty=1,lwd=2)
lines(r.mid,geno.tau.R02$tau,pch=20,col=rgb(t(col2rgb("dark green")/255),alpha=0.6),lwd=1)
legend("topright",
       legend=c("Genotype",
                "Serotype",
                "Maximum transmission distance"),
       lwd=1,col=c("dark green","blue","black"),lty=1,bty="n")

}