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testsK.R
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#'
#' Header for all (concatenated) test files
#'
#' Require spatstat.explore
#' Obtain environment variable controlling tests.
#'
#' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $
require(spatstat.explore)
FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0)
ALWAYS <- TRUE
cat(paste("--------- Executing",
if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of",
"test code -----------\n"))
#'
#' tests/Kfuns.R
#'
#' Various K and L functions and pcf
#'
#' $Revision: 1.42 $ $Date: 2022/05/23 03:42:49 $
#'
#' Assumes 'EveryStart.R' was run
if(FULLTEST) {
Cells <- cells
Amacrine <- amacrine
Redwood <- redwood
} else {
## reduce numbers of data + dummy points
spatstat.options(npixel=32, ndummy.min=16)
Cells <- cells[c(FALSE, TRUE)]
Amacrine <- amacrine[c(FALSE, TRUE)]
Redwood <- redwood[c(FALSE, TRUE)]
}
myfun <- function(x,y){(x+1) * y } # must be outside
local({
if(FULLTEST) {
#' supporting code
rmax.rule("Kscaled", owin(), 42)
implemented.for.K(c("border", "bord.modif", "translate", "good", "best"),
"polygonal", TRUE)
implemented.for.K(c("border", "bord.modif", "translate", "good", "best"),
"mask", TRUE)
implemented.for.K(c("border", "isotropic"), "mask", TRUE)
implemented.for.K(c("border", "isotropic"), "mask", FALSE)
#' shortcuts
D <- density(Cells)
K <- Kborder.engine(Cells, rmax=0.4, weights=D, ratio=TRUE)
K <- Knone.engine(Cells, rmax=0.4, weights=D, ratio=TRUE)
allcor <- c("none", "border", "bord.modif","isotropic", "translate")
K <- Krect.engine(Cells, rmax=0.4, ratio=TRUE, correction=allcor)
K <- Krect.engine(Cells, rmax=0.4, ratio=TRUE, correction=allcor,
weights=D)
K <- Krect.engine(Cells, rmax=0.4, ratio=TRUE, correction=allcor,
use.integers=FALSE)
#' Kest special code blocks
K <- Kest(Cells, var.approx=TRUE, ratio=FALSE)
Z <- distmap(Cells) + 1
Kb <- Kest(Cells, correction=c("border","bord.modif"),
weights=Z, ratio=TRUE)
Kn <- Kest(Cells, correction="none",
weights=Z, ratio=TRUE)
Knb <- Kest(Cells, correction=c("border","bord.modif","none"),
weights=Z, ratio=TRUE)
}
if(ALWAYS) {
bigint <- 50000 # This is only "big" on a 32-bit system where
# sqrt(.Machine$integer.max) = 46340.9
X <- runifpoint(bigint)
Z <- as.im(1/bigint, owin())
Kb <- Kest(X, correction=c("border","bord.modif"),
rmax=0.02, weights=Z, ratio=TRUE)
}
if(FULLTEST) {
Kn <- Kest(X, correction="none",
rmax=0.02, weights=Z, ratio=TRUE)
Knb <- Kest(X, correction=c("border","bord.modif","none"),
rmax=0.02, weights=Z, ratio=TRUE)
#' pcf.ppp special code blocks
pr <- pcf(Cells, ratio=TRUE, var.approx=TRUE)
pc <- pcf(Cells, domain=square(0.5))
pcr <- pcf(Cells, domain=square(0.5), ratio=TRUE)
pw <- pcf(Redwood, correction="none")
pwr <- pcf(Redwood, correction="none", ratio=TRUE)
pv <- pcf(Redwood, kernel="rectangular")
p1 <- pcf(Redwood[1])
#' pcf.fv
K <- Kest(Redwood)
g <- pcf(K, method="a")
g <- pcf(K, method="c")
g <- pcf(K, method="d")
#' Kinhom code blocks
X <- rpoispp(function(x,y) { 100 * x }, 100, square(1))
lambda <- 100 * X$x
Kin <- Kinhom(X, lambda, correction=c("none", "border"))
lambda2 <- outer(lambda, lambda, "*")
Ki2 <- Kinhom(X, lambda2=lambda2, diagonal=FALSE,
correction=c("translate", "isotropic"))
}
if(ALWAYS) {
#' edge corrections
rr <- rep(0.1, npoints(Cells))
eC <- edge.Ripley(Cells, rr)
eI <- edge.Ripley(Cells, rr, method="interpreted")
if(max(abs(eC-eI)) > 0.1)
stop("Ripley edge correction results do not match")
}
if(FULLTEST) {
a <- rmax.Ripley(square(1))
a <- rmax.Rigid(square(1))
a <- rmax.Ripley(as.polygonal(square(1)))
a <- rmax.Rigid(as.polygonal(square(1)))
a <- rmax.Ripley(letterR)
a <- rmax.Rigid(letterR)
}
if(ALWAYS) {
#' run slow code for edge correction and compare results
op <- spatstat.options(npixel=128)
X <- Redwood[c(TRUE, FALSE, FALSE, FALSE)]
Window(X) <- as.polygonal(Window(X))
Eapprox <- edge.Trans(X)
Eexact <- edge.Trans(X, exact=TRUE)
maxrelerr <- max(abs(1 - range(Eapprox/Eexact)))
if(maxrelerr > 0.1)
stop(paste("Exact and approximate algorithms for edge.Trans disagree by",
paste0(round(100*maxrelerr), "%")),
call.=FALSE)
spatstat.options(op)
}
})
local({
if(FULLTEST) {
#' ---- multitype ------
K <- Kcross(Amacrine, correction=c("none", "bord.modif"))
K <- Kcross(Amacrine, correction=c("none", "bord", "bord.modif"),
ratio=TRUE)
#' inhomogeneous multitype
K2 <- Kcross.inhom(Amacrine, lambdaX=densityfun(Amacrine))
K3 <- Kcross.inhom(Amacrine, lambdaX=density(Amacrine, at="points"))
K5 <- Kcross.inhom(Amacrine, correction="bord.modif")
#' markconnect, markcorr
M <- markconnect(Amacrine, "on", "off", normalise=TRUE)
M <- markcorr(longleaf, normalise=TRUE,
correction=c("isotropic", "translate", "border", "none"))
M <- markcorr(longleaf, normalise=TRUE, fargs=list())
#' Kmark (=markcorrint)
X <- runifpoint(100) %mark% runif(100)
km <- Kmark(X, f=atan2)
km <- Kmark(X, f1=sin)
km <- Kmark(X, f="myfun")
aa <- Kmark(X, normalise=FALSE, returnL=FALSE)
aa <- Kmark(X, normalise=FALSE, returnL=TRUE)
aa <- Kmark(X, normalise=TRUE, returnL=FALSE)
aa <- Kmark(X, normalise=TRUE, returnL=TRUE)
}
})
local({
if(FULLTEST) {
#' various modified K functions
#'
#' directional K functions
#'
a <- Ksector(swedishpines,
-pi/2, pi/2, units="radians",
correction=c("none", "border", "bord.modif",
"Ripley", "translate"),
ratio=TRUE)
plot(a)
#'
#' local K functions
#'
Z <- as.im(intensity(swedishpines), W=Window(swedishpines))
ZX <- Z[swedishpines]
a <- localLinhom(swedishpines, lambda=Z)
a <- localLinhom(swedishpines, lambda=ZX)
a <- localLinhom(swedishpines, lambda=Z, correction="none")
a <- localLinhom(swedishpines, lambda=Z, correction="translate")
a <- localLcross(Amacrine)
a <- localLcross(Amacrine, from="off", to="off")
a <- localKdot(Amacrine)
a <- localLdot(Amacrine)
a <- localKcross.inhom(Amacrine)
a <- localLcross.inhom(Amacrine)
Zed <- solapply(intensity(amacrine), as.im, W=Window(amacrine))
Lum <- evaluateCovariateAtPoints(Zed, Amacrine)
moff <- (marks(Amacrine) == "off")
a <- localLcross.inhom(Amacrine, from="off", to="on", lambdaX=Zed)
a <- localLcross.inhom(Amacrine, from="off", to="on", lambdaX=Lum)
a <- localLcross.inhom(Amacrine, from="off", to="on",
lambdaFrom=Lum[moff], lambdaTo=Lum[!moff])
a <- localLcross.inhom(Amacrine, from="off", to="on", lambdaX=Zed,
correction="none")
a <- localLcross.inhom(Amacrine, from="off", to="on", lambdaX=Zed,
correction="translate")
#'
#' cases of resolve.lambda.cross
#'
h <- resolve.lambda.cross(Amacrine, moff, !moff)
h <- resolve.lambda.cross(Amacrine, moff, !moff, lambdaX=Zed)
h <- resolve.lambda.cross(Amacrine, moff, !moff, lambdaX=Lum)
h <- resolve.lambda.cross(Amacrine, moff, !moff,
lambdaI=Zed[["off"]], lambdaJ=Zed[["on"]])
h <- resolve.lambda.cross(Amacrine, moff, !moff,
lambdaI=Lum[moff], lambdaJ=Lum[!moff])
d <- densityfun(unmark(Amacrine), sigma=0.1)
dm <- lapply(split(Amacrine), densityfun, sigma=0.1)
h <- resolve.lambda.cross(Amacrine, moff, !moff, lambdaX=d)
h <- resolve.lambda.cross(Amacrine, moff, !moff,
lambdaI=dm[["off"]], lambdaJ=dm[["on"]])
h <- resolve.lambda.cross(Amacrine, moff, !moff,
lambdaX=function(x,y,m){ d(x,y) })
#'
#' multitype inhomogeneous pcf
#'
g <- pcfcross.inhom(Amacrine,
lambdaI=dm[["off"]], lambdaJ=dm[["on"]])
#'
#' lohboot code blocks
#'
Ared <- lohboot(Redwood, fun="Kest", block=TRUE,
Vcorrection=TRUE, global=FALSE, correction="none")
Bred <- lohboot(Redwood, block=TRUE, basicboot=TRUE, global=FALSE)
Cred <- lohboot(Redwood, fun=Kest, block=TRUE, global=TRUE,
correction="translate")
Dred <- lohboot(Redwood, Lest)
Kred <- lohboot(Redwood, Kinhom)
Lred <- lohboot(Redwood, Linhom)
gred <- lohboot(Redwood, pcfinhom, sigma=0.1)
#'
X <- runifpoint(100, letterR)
AX <- lohboot(X, block=TRUE, nx=7, ny=10)
#' multitype
b <- lohboot(Amacrine, Kcross)
b <- lohboot(Amacrine, Lcross)
b <- lohboot(Amacrine, Kdot)
b <- lohboot(Amacrine, Ldot)
b <- lohboot(Amacrine, Kcross.inhom)
b <- lohboot(Amacrine, Lcross.inhom)
## Kscaled
A <- Lscaled(japanesepines, renormalise=TRUE, correction="all")
}
})
local({
if(ALWAYS) {
#' From Ege, in response to a stackoverflow question.
#' The following example has two points separated by r = 1 with 1/4 of the
#' circumference outside the 10x10 window (i.e. area 100).
#' Thus the value of K^(r) should jump from 0 to
#' 100/(2\cdot 1)\cdot ((3/4)^{-1} + (3/4)^{-1}) = 100 \cdot 4/3 = 133.333.
x <- c(4.5,5.5)
y <- c(10,10)-sqrt(2)/2
W <- square(10)
X <- ppp(x, y, W)
compere <- function(a, b, where, tol=1e-6) {
descrip <- paste("discrepancy in isotropic edge correction", where)
err <- as.numeric(a) - as.numeric(b)
maxerr <- max(abs(err))
blurb <- paste(descrip, "is", paste0(signif(maxerr, 4), ","),
if(maxerr > tol) "exceeding" else "within",
"tolerance of", tol)
message(blurb)
if(maxerr > tol) {
message(paste("Discrepancies:", paste(err, collapse=", ")))
stop(paste("excessive", descrip), call.=FALSE)
}
invisible(TRUE)
}
## Testing:
eX <- edge.Ripley(X, c(1,1))
compere(eX, c(4/3,4/3), "at interior point of rectangle")
## Corner case:
Y <- X
Y$x <- X$x-4.5+sqrt(2)/2
eY <- edge.Ripley(Y, c(1,1))
compere(eY, c(2,4/3), "near corner of rectangle")
## Invoke polygonal code
Z <- rotate(Y, pi/4)
eZdebug <- edge.Ripley(Z, c(1,1), internal=list(debug=TRUE))
compere(eZdebug, c(2,4/3), "at interior point of polygon (debug on)")
## test validity without debugger,in case of quirks of compiler optimisation
eZ <- edge.Ripley(Z, c(1,1))
compere(eZ, c(2,4/3), "at interior point of polygon (debug off)")
}
})
reset.spatstat.options()