R Under development (unstable) (2024-07-03 r86870 ucrt) -- "Unsuffered Consequences"
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> #'
> #'   Header for all (concatenated) test files
> #'
> #'   Require spatstat.geom
> #'   Obtain environment variable controlling tests.
> #'
> #'   $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $
> 
> require(spatstat.geom)
Loading required package: spatstat.geom
Loading required package: spatstat.data
Loading required package: spatstat.univar
spatstat.univar 3.0-0
spatstat.geom 3.3-0
> FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0)
> ALWAYS   <- TRUE
> cat(paste("--------- Executing",
+           if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of",
+           "test code -----------\n"))
--------- Executing **RESTRICTED** subset of test code -----------
> #
> #    tests/nndist.R
> #
> # Check that nndist and nnwhich give
> # results consistent with direct calculation from pairdist
> #
> # Similarly for nncross and distfun
> #
> # Also test whether minnndist(X) == min(nndist(X))
> #
> #   $Revision: 1.39 $  $Date: 2021/05/20 09:31:23 $
> #
> 
> 
> local({
+   eps <- sqrt(.Machine$double.eps)
+   f <- function(mat,k) { apply(mat, 1, function(z,n) { sort(z)[n]  }, n=k+1) }
+   g <- function(mat,k) { apply(mat, 1, function(z,n) { order(z)[n] }, n=k+1) }
+ 
+   ## .......  Two dimensions ................
+   if(ALWAYS) {
+     X <- runifrect(24)
+ 
+     nn <- nndist(X)
+     nnP <- f(pairdist(X), 1)
+     if(any(abs(nn - nnP) > eps))
+       stop("nndist.ppp does not agree with pairdist")
+ 
+     nn5 <- nndist(X, k=5)
+     nn5P <- f(pairdist(X), 5)
+     if(any(abs(nn5 - nn5P) > eps))
+       stop("nndist.ppp(k=5) does not agree with pairdist")
+ 
+     nw <- nnwhich(X)
+     nwP <- g(pairdist(X), 1)
+     if(any(nw != nwP))
+       stop("nnwhich.ppp does not agree with pairdist")
+ 
+     nw5 <- nnwhich(X, k=5)
+     nw5P <- g(pairdist(X), 5)
+     if(any(nw5 != nw5P))
+       stop("nnwhich.ppp(k=5) does not agree with pairdist")
+   }
+ 
+   if(FULLTEST) {
+     a <- nndist(X, method="test")
+     b <- nnwhich(X, method="test")
+     a <- nndist(X, method="test", k=1:2)
+     b <- nnwhich(X, method="test", k=1:2)
+     a2 <- nndist(cells[1:3], k=1:3)
+     b2 <- nnwhich(cells[1:3], k=1:3)
+     a3 <- nndist(cells[1])
+     b3 <- nnwhich(cells[1])
+     m <- factor((1:npoints(X)) %% 2 == 0)
+     a4 <- nndist.default(X, by=m, k=2)
+     b4 <- nnwhich.default(X, by=m, k=2)
+   }
+ 
+   if(ALWAYS) {
+     ## nncross.ppp without options
+     Y <- runifrect(30)
+     Y <- Y[nndist(Y) > 0.02]
+     nc <- nncross(X,Y)
+     ncd <- nc$dist
+     ncw <- nc$which
+     cd <- crossdist(X,Y)
+     cdd <- apply(cd, 1, min)
+     cdw <- apply(cd, 1, which.min)
+     if(any(abs(ncd - cdd) > eps))
+       stop("nncross()$dist does not agree with apply(crossdist(), 1, min)")
+     if(any(ncw != cdw))
+       stop("nncross()$which does not agree with apply(crossdist(), 1, which.min)")
+ 
+     ## nncross with sort on x
+     nc <- nncross(X,Y, sortby="x")
+     ncd <- nc$dist
+     ncw <- nc$which
+     if(any(abs(ncd - cdd) > eps))
+       stop("nncross(sortby=x)$dist does not agree with apply(crossdist(), 1, min)")
+     if(any(ncw != cdw))
+       stop("nncross(sortby=x)$which does not agree with apply(crossdist(), 1, which.min)")
+ 
+     ## nncross with data pre-sorted on x
+     Y <- Y[order(Y$x)]
+     nc <- nncross(X,Y, is.sorted.Y=TRUE, sortby="x")
+     ncd <- nc$dist
+     ncw <- nc$which
+     cd <- crossdist(X,Y)
+     cdd <- apply(cd, 1, min)
+     cdw <- apply(cd, 1, which.min)
+     if(any(abs(ncd - cdd) > eps))
+       stop("For sorted data, nncross()$dist does not agree with apply(crossdist(), 1, min)")
+     if(any(ncw != cdw))
+       stop("For sorted data, nncross()$which does not agree with apply(crossdist(), 1, which.min)")
+ 
+     ## sanity check for nncross with k > 1
+   ndw <- nncross(X, Y, k=1:4, what="which")
+     if(any(is.na(ndw)))
+       stop("NA's returned by nncross.ppp(k > 1, what='which')")
+     nnc4 <- nncross(X, Y, k=1:4)
+     iswhich <- (substr(colnames(nnc4), 1, nchar("which")) == "which")
+     ndw <- nnc4[,iswhich]
+     if(any(is.na(ndw)))
+       stop("NA's returned by nncross.ppp(k > 1)$which")
+   
+     ## test of correctness for nncross with k > 1
+     flipcells <- flipxy(cells)
+     calcwhich <- nncross(cells, flipcells, k=1:4, what="which")
+     truewhich <- t(apply(crossdist(cells,flipcells), 1, order))[,1:4]
+     if(any(calcwhich != truewhich))
+       stop("nncross(k > 1) gives wrong answer")
+   }
+ 
+   if(FULLTEST) {
+     ## example from Hank Stevens
+     A <- data.frame(
+           m= c("K", "K", "A1", "A2", "G", "A2", "A3"),
+           x=c(4.85, 6.76, 10.58, 19.18, 15.74, 19.08, 12.27),
+           y=c(5.60, 12.92, 11.14, 17.22, 5.74, 1.24, 2.20),
+          stringsAsFactors=TRUE
+     )
+     X <- with(A, ppp(x, y, marks=m, window=bounding.box.xy(x, y)))
+     suspect <- nncross(X, X[7], iX=1:7, iY=7L)$dist
+     correct <- c(pairdist(X)[1:6, 7], Inf)
+     maxer <- max(abs(suspect[1:6] - correct[1:6]))
+     if(maxer > 0.001)
+       stop("Error in nncross (Inf values) in Hank Stevens example")
+     if(suspect[7] != Inf)
+       stop("Error in nncross (finite values) in Hank Stevens example")
+     M <- as.matrix(minnndist(X, by=marks(X)))
+     M[is.infinite(M)] <- 0
+     maxer <- max(abs(M - t(M)))
+     if(maxer > 0.001)
+       stop("Error in minnndist(by) in Hank Stevens example")
+   }
+ 
+   if(ALWAYS) {
+     #' cover some C code blocks
+     Z <- runifrect(50)
+     X <- Z[1:30]
+     Y <- Z[20:50]
+     iX <- 1:30
+     iY <- 20:50
+     Ndw <- nncross(X,Y, iX, iY, k=3)
+     Nw  <- nncross(X,Y, iX, iY, k=3, what="which")
+     Nd  <- nncross(X,Y, iX, iY, k=3, what="dist")
+   }
+ 
+   if(FULLTEST) {
+     ## special cases
+     nndist(X[FALSE])
+     nndist(X[1])
+     nndist(X[1:3], k=4)
+     nndist(X[1:3], k=1:4)
+     nnwhich(X[FALSE])
+     nnwhich(X[1])
+     nnwhich(X[1:3], k=4)
+     nnwhich(X[1:3], k=1:4)
+     nncross(X[1:3], Y[FALSE])
+     nncross(X[1:3], Y[1])
+     nncross(X[1:3], Y[1:3], k=4)
+     nncross(X[1:3], Y[1:3], k=1:4)
+   }
+   
+   ## .......  Three dimensions ................
+ 
+   if(ALWAYS) {
+     rthree <- function(n) { pp3(runif(n), runif(n), runif(n), box3(c(0,1))) }
+     XX <- rthree(42)
+     X <- XX[1:20]
+     nn <- nndist(X)
+     nnP <- f(pairdist(X), 1)
+     if(any(abs(nn - nnP) > eps))
+       stop("nndist.pp3 does not agree with pairdist")
+ 
+     nn5 <- nndist(X, k=5)
+     nn5P <- f(pairdist(X), 5)
+     if(any(abs(nn5 - nn5P) > eps))
+       stop("nndist.pp3(k=5) does not agree with pairdist")
+ 
+     nw <- nnwhich(X)
+     nwP <- g(pairdist(X), 1)
+     if(any(nw != nwP))
+       stop("nnwhich.pp3 does not agree with pairdist")
+ 
+     nw5 <- nnwhich(X, k=5)
+     nw5P <- g(pairdist(X), 5)
+     if(any(nw5 != nw5P))
+       stop("nnwhich.pp3(k=5) does not agree with pairdist")
+ 
+     ff <- function(mat,k) { apply(mat, 1, function(z,n) { sort(z)[n]  }, n=k) }
+     gg <- function(mat,k) { apply(mat, 1, function(z,n) { order(z)[n] }, n=k) }
+ 
+     Y <- rthree(20)
+     Y <- Y[nndist(Y) > 0.02]
+     DXY <- crossdist(X,Y)
+     a <- nncross(X,Y)
+     a <- nncross(X,Y, what="dist")
+     a <- nncross(X,Y, what="which")
+     if(any(a != gg(DXY, 1)))
+       stop("incorrect result from nncross.pp3(what='which')")
+     a2 <- nncross(X,Y, k=2)
+     a2 <- nncross(X,Y, what="dist", k=2)
+     a2 <- nncross(X,Y, what="which", k=2)
+     if(any(a2 != gg(DXY, 2)))
+       stop("incorrect result from nncross.pp3(k=2, what='which')")
+   }
+ 
+   if(FULLTEST) {
+     X <- XX
+     iX <- 1:42
+     iZ <- 30:42
+     Z <- X[iZ]
+     b <- nncross(X, Z, iX=iX, iY=iZ)
+     b <- nncross(X, Z, iX=iX, iY=iZ, what="which")
+     b <- nncross(X, Z, iX=iX, iY=iZ, what="dist")
+     b2 <- nncross(X, Z, iX=iX, iY=iZ, k=2)
+     b2 <- nncross(X, Z, iX=iX, iY=iZ, what="which", k=2)
+     b2 <- nncross(X, Z, iX=iX, iY=iZ, what="dist", k=2)
+     e1 <- nncross(X, Y[1:3], k=2:4)
+     c1 <- nncross(X, Y, sortby="var")
+     c2 <- nncross(X, Y, sortby="x")
+     c3 <- nncross(X, Y, sortby="y")
+     c4 <- nncross(X, Y, sortby="z")
+     Xsort <- X[order(coords(X)$x)]
+     c5 <- nncross(Xsort, Y, is.sorted.X=TRUE, sortby="x")
+     Ysort <- Y[order(coords(Y)$x)]
+     c6 <- nncross(Xsort, Ysort, is.sorted.X=TRUE, is.sorted.Y=TRUE, sortby="x")
+   }
+ 
+   if(FULLTEST) {
+     ## special cases
+     nndist(X[FALSE])
+     nndist(X[1])
+     nndist(X[1:3], k=4)
+     nndist(X[1:3], k=1:4)
+     nnwhich(X[FALSE])
+     nnwhich(X[1])
+     nnwhich(X[1:3], k=4)
+     nnwhich(X[1:3], k=1:4)
+     nncross(X[1:3], Y[FALSE])
+     nncross(X[1:3], Y[1])
+     nncross(X[1:3], Y[1:3], k=4)
+     nncross(X[1:3], Y[1:3], k=1:4)
+   }
+   
+   ## .......  m dimensions ................
+ 
+   if(ALWAYS) {
+     rx <- function(n) {
+       B <- boxx(c(0,1),c(0,1),c(0,1),c(0,1))
+       df <- replicate(4, runif(n), simplify=FALSE)
+       names(df) <- letters[23:26]
+       ppx(as.data.frame(df), B)
+     }
+     ## X <- runifpointx(42, B)
+     ## Y <- runifpointx(50, B)
+     X <- rx(42)
+     Y <- rx(50)
+     Y <- Y[nndist(Y) > 0.02]
+     DXY <- crossdist(X,Y)
+   
+     nn <- nndist(X)
+     nnP <- f(pairdist(X), 1)
+     if(any(abs(nn - nnP) > eps))
+       stop("nndist.ppx does not agree with pairdist")
+ 
+     nn5 <- nndist(X, k=5)
+     nn5P <- f(pairdist(X), 5)
+     if(any(abs(nn5 - nn5P) > eps))
+       stop("nndist.ppx(k=5) does not agree with pairdist")
+   
+     nw <- nnwhich(X)
+     nwP <- g(pairdist(X), 1)
+     if(any(nw != nwP))
+       stop("nnwhich.ppx does not agree with pairdist")
+ 
+     nw5 <- nnwhich(X, k=5)
+     nw5P <- g(pairdist(X), 5)
+     if(any(nw5 != nw5P))
+       stop("nnwhich.ppx(k=5) does not agree with pairdist")
+ 
+     a <- nncross(X,Y)
+     ncd <- nncross(X,Y, what="dist")
+     ncw <- nncross(X,Y, what="which")
+     if(any(ncw != gg(DXY, 1)))
+       stop("incorrect result from nncross.ppx(what='which')")
+     a2 <- nncross(X,Y, k=2)
+     ncd <- nncross(X,Y, what="dist", k=2)
+     ncw <- nncross(X,Y, what="which", k=2)
+     if(any(ncw != gg(DXY, 2)))
+       stop("incorrect result from nncross.ppx(k=2, what='which')")
+   }
+ 
+   if(FULLTEST) {
+     ## special cases
+     nndist(X[FALSE])
+     nndist(X[1])
+     nndist(X[1:3], k=4)
+     nndist(X[1:3], k=1:4)
+     nnwhich(X[FALSE])
+     nnwhich(X[1])
+     nnwhich(X[1:3], k=4)
+     nnwhich(X[1:3], k=1:4)
+     nncross(X[1:3], Y[FALSE])
+     nncross(X[1:3], Y[1])
+     nncross(X[1:3], Y[1:3], k=4)
+     nncross(X[1:3], Y[1:3], k=1:4)
+   }
+ 
+   if(ALWAYS) {
+     ## test of agreement between nngrid.h and knngrid.h
+     ##    dimyx=23 (found by trial-and-error) ensures that there are no ties 
+     a <- as.matrix(nnmap(cells, what="which", dimyx=23))
+     b <- as.matrix(nnmap(cells, what="which", dimyx=23, k=1:2)[[1]])
+     if(any(a != b))
+       stop("algorithms in nngrid.h and knngrid.h disagree")
+     
+     ## minnndist correctness
+     X <- redwood3
+     eps <- sqrt(.Machine$double.eps)
+     mfast <- minnndist(X)
+     mslow <- min(nndist(X))
+     if(abs(mfast-mslow) > eps)
+       stop("minnndist(X) disagrees with min(nndist(X))")
+ 
+     ## maxnndist correctness
+     mfast <- maxnndist(X)
+     mslow <- max(nndist(X))
+     if(abs(mfast-mslow) > eps)
+       stop("maxnndist(X) disagrees with max(nndist(X))")
+   }
+ 
+   if(ALWAYS) {
+     ## minnndist, maxnndist code blocks
+     Y <- superimpose(amacrine, amacrine[10:20])
+     a <- maxnndist(Y, positive=TRUE)
+     u <- maxnndist(Y, positive=TRUE, by=marks(Y))
+     b <- minnndist(Y, positive=TRUE)
+     v <- minnndist(Y, positive=TRUE, by=marks(Y))
+ 
+     ## nnmap code blocks
+     A <- nnmap(cells[FALSE])
+     A <- nnmap(cells, sortby="var")
+     A <- nnmap(cells, sortby="x")
+     A <- nnmap(cells, sortby="y")
+     B <- nnmap(cells[1:3], k=4)
+     B <- nnmap(cells[1:3], k=2:4)
+     D <- nnmap(cells, outputarray=TRUE)
+   }
+ 
+   if(ALWAYS) {
+     #' tests for has.close()
+     #' (the default method uses nndist or pairdist, and can be trusted!)
+     a <- has.close(redwood, 0.05)
+     b <- has.close.default(redwood, 0.05)
+     if(any(a != b)) stop("Incorrect result for has.close(X, r)")
+ 
+     a <- has.close(redwood, 0.05, periodic=TRUE)
+     a <- has.close.default(redwood, 0.05, periodic=TRUE)
+     if(any(a != b)) stop("Incorrect result for has.close(X, r, periodic=TRUE)")
+ 
+     Y <- split(amacrine)
+     a <- with(Y, has.close(on, 0.05, off))
+     b <- with(Y, has.close.default(on, 0.05, off))
+     if(any(a != b)) stop("Incorrect result for has.close(X, r, Y)")
+ 
+     a <- with(Y, has.close(on, 0.05, off, periodic=TRUE))
+     b <- with(Y, has.close.default(on, 0.05, off, periodic=TRUE))
+     if(any(a != b)) stop("Incorrect result for has.close(X, r, Y, periodic=TRUE)")
+   }
+ 
+   if(ALWAYS) {
+     b <- bdist.pixels(letterR, style="coords")
+     d <- bdist.pixels(letterR, dimyx=64, method="interpreted")
+   }
+ 
+   if(FULLTEST) {
+       ## nnfun.ppp
+     h <- nnfun(cells)
+     Z <- as.im(h)
+     d <- domain(h)
+     h <- nnfun(amacrine, value="mark")
+     d <- domain(h)
+     Z <- as.im(h)
+     h <- nnfun(longleaf, value="mark")
+     d <- domain(h)
+     Z <- as.im(h)
+   }
+ 
+ })
Warning message:
data contain duplicated points 
> 
> 
> proc.time()
   user  system elapsed 
   1.15    0.14    1.28