R Under development (unstable) (2023-10-18 r85349 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> #'
> #'   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
spatstat.geom 3.2-7
> 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/ppp.R
> #'
> #'   $Revision: 1.14 $ $Date: 2022/08/27 04:49:32 $
> #'
> #'  Untested cases in ppp() or associated code
> 
> local({
+   ## X <- runifpoint(10, letterR)
+   ## Y <- runifpoint(10, complement.owin(letterR))
+   Bin  <- owin(c(2.15, 2.45), c(0.85, 3.0))
+   Bout <- owin(c(2.75, 2.92), c(0.85, 1.4))
+   X <- runifrect(10, Bin)[letterR]
+   Y <- runifrect(10, Bout)[complement.owin(letterR)]
+   
+   if(FULLTEST) {
+     #' test handling of points out-of-bounds
+     df <- rbind(as.data.frame(X), as.data.frame(Y))
+     A <- ppp(df$x, df$y, window=letterR, marks=1:20)
+     #' test handling of points with bad coordinates
+     df$x[1:3] <- c(Inf, NA, NaN)
+     df$y[18:20] <- c(Inf, NA, NaN)
+     B <- ppp(df$x, df$y, window=letterR, marks=1:20)
+     D <- ppp(df$x, df$y, window=letterR, marks=data.frame(id=1:20, u=runif(20)))
+   
+     #' test print/summary/plot methods on these bad objects
+     print(A)
+     print(B)
+     print(D)
+     print(summary(A))
+     print(summary(B))
+     print(summary(D))
+     plot(A)
+     plot(B)
+     plot(D)
+     plot(attr(A, "rejects"))
+     plot(attr(B, "rejects"))
+     plot(attr(D, "rejects"))
+   
+     #' subset operator --- cases not covered elsewhere
+     #'   subset index is a logical image
+     Z <- distmap(letterR, invert=TRUE)
+     V <- (Z > 0.2)
+     XV <- X[V]
+     #'   multiple columns of marks
+     fun3 <- finpines[1:3]
+     #'   multiple columns of marks, one of which is a factor
+     U <- finpines
+     marks(U)[,2] <- factor(c(rep("A", 60), rep("B", npoints(U)-60)))
+     UU <- U[1:3, drop=TRUE]
+ 
+     #' cut.ppp
+     CU <- cut(U, "height")
+     CU <- cut(U, breaks=3)
+ 
+     #' cases of [<-.ppp
+     set.seed(999)
+     X <- cells
+     B <- square(0.2)
+     X[B] <- runifrect(3, B)
+     #' checking 'value'
+     Y <- flipxy(X)
+     X[B] <- Y[square(0.3)]
+     ## deprecated use of second argument
+     X[,1:4] <- runifrect(3)  # deprecated
+     X[,B] <- runifrect(3, B) # deprecated 
+     X[1:3, B] <- runifrect(20)
+     A <- superimpose(cells, X, W="convex")
+     A <- superimpose(cells, X, W=ripras)
+     B <- superimpose(concatxy(cells), concatxy(X), W=NULL)
+     ## superimpose.splitppp
+     Y <- superimpose(split(amacrine))
+ 
+     ## catch outdated usage of scanpp
+     d <- system.file("rawdata", "amacrine", package="spatstat.data")
+     if(nzchar(d)) {
+       W <- owin(c(0, 1060/662), c(0, 1))
+       Y <- scanpp("amacrine.txt", dir=d, window=W, multitype=TRUE)
+       print(Y)
+     }
+     ## (bad) usage of cobble.xy
+     xx <- runif(10)
+     yy <- runif(10)
+     W1 <- cobble.xy(xx, yy)
+     W2 <- cobble.xy(xx, yy, boundingbox)
+     Wnope <- cobble.xy(xx, yy, function(x,y) {cbind(x,y)}, fatal=FALSE)
+ 
+     ## as.data.frame.ppplist
+     Z <- runifrect(3, nsim=4)
+     Z[[2]] <- Z[[2]][1]
+     Z[[3]] <- Z[[3]][FALSE]
+     d <- as.data.frame(Z)
+   }
+ })
> 
> #
> # tests/ppx.R
> #
> # Test operations for ppx objects
> #
> #  $Revision: 1.9 $ $Date: 2020/12/04 04:49:40 $
> #
> 
> local({
+   if(ALWAYS) {
+     ## make data
+     df <- data.frame(x=c(1,2,2,1)/4, y=c(1,2,3,1)/4, z=c(2,3,4,3)/5)
+     X <- ppx(data=df, coord.type=rep("s", 3), domain=box3())
+   }
+   if(ALWAYS) {
+     #' methods involving C code
+     unique(X)
+     duplicated(X)
+     anyDuplicated(X)
+     multiplicity(X)
+     uniquemap(X)
+   }
+   if(FULLTEST) {
+     #' general tests
+     print(X)
+     summary(X)
+     plot(X)
+     domain(X)
+     unitname(X) <- c("metre", "metres")
+     unitname(X)
+ 
+     #' subset operator
+     X[integer(0)]
+     Y <- X %mark% data.frame(a=df$x, b=1:4)
+     Y[1:2]
+     Y[FALSE]
+     marks(Y) <- as.data.frame(marks(Y))
+     Y[integer(0)]
+     Y[1:2]
+     Y[FALSE]
+   }
+ 
+   if(FULLTEST) {
+     #' two dimensional
+     A <- ppx(data=df[,1:2], coord.type=rep("s", 2), domain=square(1))
+     plot(A)
+     B <- ppx(data=df[,1:2], coord.type=rep("s", 2), domain=NULL)
+     plot(B)
+     #' one dimensional
+     E <- ppx(data=data.frame(x=runif(10)))
+     plot(E)
+   
+     #' bug
+     stopifnot(identical(unmark(chicago[1]),
+                         unmark(chicago)[1]))
+ 
+     #' ppx with zero points
+     U <- chicago[integer(0)]
+     V <- U %mark% 1
+     V <- U %mark% factor("a")
+ 
+     #' simplify lower-dimensional patterns
+     X3 <- ppx(data=df, coord.type=rep("s", 3), domain=box3(), simplify=TRUE)
+     stopifnot(is.pp3(X3))
+     X2 <- ppx(data=df[,1:2], coord.type=rep("s", 2), domain=square(1), simplify=TRUE)
+     stopifnot(is.ppp(X2))
+ 
+     #' marks<-.ppx
+     M <- as.matrix(X)
+     marks(X) <- df[,1]
+     marks(X) <- df[,integer(0)]
+   }
+ 
+   if(FULLTEST) {
+     ## ............  from Ege ..........................
+     ## Tests for shift:
+     ## Check ppp and ppx shift are the same
+     X <- cells
+     Y <- ppx(coords(cells), domain = boxx(0:1,0:1))
+     Xs <- shift(X, vec = c(1,1))
+     Ys <- shift(Y, vec = c(1,1))
+     stopifnot(all.equal(coords(Xs), coords(Ys),
+                         check.attributes = FALSE))
+     stopifnot(all.equal(domain(Xs), as.owin(domain(Ys)),
+                         check.attributes = FALSE))
+     ## Check a single numeric for vec in shift.ppx
+     stopifnot(identical(Ys, shift(Y, vec = 1)))
+ 
+     ## Tests for scale:
+     dat <- data.frame(x=1:3, y=1:3, m=letters[1:3])
+     xrange <- yrange <- c(0,4)
+     cent <- c(2,2)
+     scal <- c(5,5)
+     X <- as.ppp(dat, W = owin(xrange, yrange))
+     Xscaled <- affine(shift(X, vec = -cent), mat = diag(1/scal))
+     ## Check ppx without domain:
+     Y <- ppx(dat, coord.type = c("spatial", "spatial", "mark"))
+     Yscaled <- scale(Y, center = cent, scale = scal)
+     stopifnot(all.equal(coords(Xscaled),
+                         coords(Yscaled),
+                         check.attributes = FALSE))
+     ## Check ppx with domain:
+     Y$domain <- boxx(xrange, yrange)
+     Yscaled <- scale(Y, center = cent, scale = scal)
+     stopifnot(all.equal(as.boxx(Window(Xscaled)),
+                         domain(Yscaled),
+                         check.attributes = FALSE))
+ 
+     ## Tests for intersect.boxx:
+     ## Should be unit 2D box:
+     A <- intersect.boxx(boxx(c(-1,1),c(0,2)), boxx(c(0,3),c(0,1)))
+     stopifnot(identical(A, boxx(c(0,1),c(0,1))))
+     ## Should be empty (NULL)
+     B <- intersect.boxx(boxx(c(-1,1),c(0,2)),
+                         boxx(c(0,3),c(0,1)),
+                         boxx(c(1,2), c(-1,1)))
+     stopifnot(is.null(B))
+     ## Should be unit 3D box:
+     C <- intersect.boxx(boxx(c(-1,1),c(0,2),c(-1,1)),
+                         boxx(c(0,3),c(0,1),c(0,4)))
+     stopifnot(identical(C, boxx(c(0,1),c(0,1),c(0,1))))
+     ## Should be empty (NULL)
+     D <- intersect.boxx(boxx(c(-1,1),c(0,2),c(-1,1)),
+                         boxx(c(0,3),c(0,1),c(0,4)), NULL)
+     stopifnot(is.null(D))
+ 
+     ## Tests for [.boxx with clip:
+     ## Check ppp and ppx subset with clip are the same
+     X <- cells
+     WX <- shift(domain(X), vec = c(.5,.5))
+     X2 <- X[WX, clip=TRUE]
+     Y <- ppx(coords(X), domain = boxx(c(0,1),c(0,1)))
+     WY <- shift(domain(Y), vec = c(.5,.5))
+     Y2 <- Y[WY, clip=TRUE]
+     stopifnot(all.equal(coords(X2), coords(Y2), check.attributes = FALSE))
+     stopifnot(all.equal(domain(X2), as.owin(domain(Y2))))
+   }
+ 
+ })
> 
> proc.time()
   user  system elapsed 
   1.39    0.20    1.54