get.tau: generalized version of 'get.tau'

In IDSpatialStats: Estimate Global Clustering in Infectious Disease

Description

returns the relative probability (or odds) that points at some distance from an index point share some relationship with that point versus the probability (or odds) any point shares that relationship with that point.

Usage

get.tau(
  posmat,
  fun,
  r = 1,
  r.low = rep(0, length(r)),
  comparison.type = "representative",
  data.frame = TRUE
)

Arguments

posmat	a matrix with columns x, y and any other named columns columns needed by fun
fun	a function that takes in two rows of posmat and returns: for pairs included in the numerator (and the denominator for independent data) for pairs that should only be included in the denominator for pairs that should be ignored all together Note that names from posmat are not preserved in calls to fun, so the columns of the matrix should be referenced numerically so this is not available to fun
r	the series of spatial distances (or there maximums) we are interested in
r.low	the low end of each range, 0 by default
comparison.type	what type of points are included in the comparison set. "representative" if comparison set is representative of the underlying population "independent" if comparison set is cases/events coming from an indepedent process
data.frame	logical indicating whether to return results as a data frame (default = TRUE)

Value

The tau value for each distance we look at. If comparison.type is "representative", this is:

tau = get.pi(posmat, fun, r, r.low)/get.pi(posmat,fun,infinity,0)

If comparison.type is "independent", this is:

tau = get.theta(posmat, fun, r, r.low)/get.theta(posmat,fun,infinity,0)

Author(s)

Justin Lessler and Henrik Salje

See Also

Other get.tau: get.tau.bootstrap(), get.tau.ci(), get.tau.permute(), get.tau.typed.bootstrap(), get.tau.typed.permute(), get.tau.typed()

Other spatialtau: get.pi(), get.theta()

Examples

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")

IDSpatialStats documentation built on Aug. 9, 2021, 9:08 a.m.