get.pi.permute: get the null distribution of the 'get.pi' function

In IDSpatialStats: Estimate Global Clustering in Infectious Disease

Description

Does permutations to calculate the null distribution of get pi if there were no spatial dependence. Randomly reassigns coordinates to each observation permutations times

Usage

get.pi.permute(
  posmat,
  fun,
  r = 1,
  r.low = rep(0, length(r)),
  permutations,
  data.frame = TRUE
)

Arguments

posmat	a matrix with columns type, x and y
fun	the function to evaluate
r	the series of spatial distances we are interested in
r.low	the low end of each range....0 by default
permutations	the number of permute iterations
data.frame	logical indicating whether to return results as a data frame (default = TRUE)

Value

pi values for all the distances we looked at

See Also

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

Examples

#compare normally distributed with uniform points
x<-cbind(1,runif(100,-100,100), runif(100,-100,100))
x<-rbind(x, cbind(2,rnorm(100,0,20), rnorm(100,0,20)))
colnames(x) <- c("type","x","y")

fun<-function(a,b) {
    if(a[1]!=2) return(3)
    if (b[1]==2) return(1)
    return(2)
}

r.max<-seq(10,100,10)
r.min<-seq(0,90,10)
r.mid <- (r.max+r.min)/2

pi<-get.pi(x,fun,r=r.max,r.low=r.min)
pi.null<-get.pi.permute(x,fun,r=r.max,r.low=r.min,permutations=100)

null.ci<-apply(pi.null[,-(1:2)],1,quantile,probs=c(0.25,0.75))

plot(r.mid, pi$pi, type="l")
lines(r.mid, null.ci[1,] , lty=2)
lines(r.mid, null.ci[2,] , lty=2)

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