Kenv.tor1: Modified envelope of K12hat from random toroidal shifts of...

Kenv.tor1R Documentation

Modified envelope of K12hat from random toroidal shifts of two point patterns

Description

Modification of Kenv.tor() to allow the assignment of a p value to the goodness of fit, following the method outlined in Peter Diggle's 1986 paper (J Neurosci methods 18:115-125) and in his 2002 book.

Usage

Kenv.tor1(pts1, pts2, poly, nsim, s, quiet = FALSE)

Arguments

pts1

First point data set

pts2

Second point data set

poly

Polygon containing the points

nsim

Number of random toroidal shifts to do

s

Vector of distances at which to calculate the envelope

quiet

If FALSE, print a message after every simulation for progress monitoring. If TRUE, print no messages

Value

A list with components: $upper, $lower, real, u, ksim, and rank. The first three components are vectors like s, the next two contain results passed back from the simulations, and the final is a one-element vector with the rank of the observed data set.

Author(s)

Stephen Eglen <stephen@inf.ed.ac.uk>

See Also

Kenv.tor

Examples

data(amacrines)
ama.a <- rbind(amacrines.on, amacrines.off)
ama.bb <- bboxx(bbox(as.points(ama.a)))
ama.t <- seq(from = 0.002, to=.250, by=0.002)
nsim=999
plot(amacrines.on, asp=1, pch=19,
 main="Data set, match figure 1.4 of Diggle(2002)?")
points(amacrines.off, pch=1)
#
k12 <- k12hat(amacrines.on, amacrines.off, ama.bb, ama.t)
#
k11 <- khat(amacrines.on, ama.bb, ama.t)
k22 <- khat(amacrines.off, ama.bb, ama.t)
k00 <- khat(ama.a, ama.bb, ama.t)
theor <- pi * (ama.t^2)
#
plot(ama.t, k12-theor, ylim=c(min( c(k12, k11, k22, k00) - theor),
 max( c(k12, k11, k22, k00) - theor)),
 main="2nd order properties, match figure 4.8 of Diggle (2002)", type="l")
lines(ama.t, -theor)
lines(ama.t, k11-theor, lty=2)
lines(ama.t, k22-theor, lty=3)
lines(ama.t, k00-theor, lty=5)
#
k12.tor <- Kenv.tor(amacrines.on, amacrines.off, ama.bb,
 nsim, ama.t, quiet=TRUE)
plot(ama.t, k12-theor, type="l", main="Output from Kenv.tor")
lines(ama.t, k12.tor$upper-theor, type="l", col="red")
lines(ama.t, k12.tor$lower-theor, type="l", col="red")
#
k12.sims <- Kenv.tor1(amacrines.on, amacrines.off, ama.bb,
 nsim, ama.t, quiet=TRUE)
plot(ama.t, sqrt(k12.sims$real/pi), type="l", asp=1, bty="n",
 main=paste("K12 versus toroidal sims; rank ", k12.sims$rank, "of",
 length(k12.sims$u)))
lines(ama.t, sqrt(k12.sims$upper/pi), col="red")
lines(ama.t, sqrt(k12.sims$lower/pi), col="red")

splancs documentation built on May 29, 2024, 6:22 a.m.

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