R: generalized version of 'get.tau'

get.tau {IDSpatialStats}

R Documentation

generalized version of `get.tau`

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

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")

[Package IDSpatialStats version 0.4.0 Index]

generalized version of get.tau