#' #' 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/kernelstuff.R #' #' $Revision: 1.2 $ $Date: 2023/11/05 01:49:45 $ local({ if(FULLTEST) { #' test all cases in kernels.R kernames <- c("gaussian", "rectangular", "triangular", "epanechnikov", "biweight", "cosine", "optcosine") X <- rnorm(20) U <- runif(20) for(ker in kernames) { dX <- dkernel(X, ker) fX <- pkernel(X, ker) qU <- qkernel(U, ker) m0 <- kernel.moment(0, 0, ker) m1 <- kernel.moment(1, 0, ker) m2 <- kernel.moment(2, 0, ker) m3 <- kernel.moment(3, 0, ker) } } }) #' #' tests/Kfuns.R #' #' Various K and L functions and pcf #' #' $Revision: 1.43 $ $Date: 2022/06/17 01:47:08 $ #' #' 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.lambdacross #' h <- resolve.lambdacross(Amacrine, moff, !moff) h <- resolve.lambdacross(Amacrine, moff, !moff, lambdaX=Zed) h <- resolve.lambdacross(Amacrine, moff, !moff, lambdaX=Lum) h <- resolve.lambdacross(Amacrine, moff, !moff, lambdaI=Zed[["off"]], lambdaJ=Zed[["on"]]) h <- resolve.lambdacross(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.lambdacross(Amacrine, moff, !moff, lambdaX=d) h <- resolve.lambdacross(Amacrine, moff, !moff, lambdaI=dm[["off"]], lambdaJ=dm[["on"]]) h <- resolve.lambdacross(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()