R Under development (unstable) (2023-10-18 r85349 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
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 -----------
> ## badwindowcheck.R
> ## $Revision: 1.3 $  $Date: 2020/04/28 12:58:26 $
> ##
> 
> local({
+   if(ALWAYS) {
+     ## Simple example of self-crossing polygon
+     x <- read.table("selfcross.txt", header=TRUE)
+     ## Auto-repair
+     w <- owin(poly=x)
+ 
+     ## Real data involving various quirks
+     b <- read.table("badwindow.txt", header=TRUE)
+     b <- split(b, factor(b$i))
+     b <- lapply(b, function(z) { as.list(z[,-3]) })
+     ## make owin without checking
+     W <- owin(poly=b, check=FALSE, fix=FALSE)
+     ## Apply stringent checks
+     owinpolycheck(W,verbose=FALSE)
+     ## Auto-repair
+     W2 <- owin(poly=b)
+   }
+ })
> 
> 
> 
> 
> ##  tests/closeshave.R
> ## check 'closepairs/crosspairs' code
> ## validity and memory allocation
> ## $Revision: 1.29 $ $Date: 2022/06/06 10:09:56 $
> 
> ## ------- All this code must be run on every hardware -------
> local({
+   r <- 0.12
+ 
+   close.all <- closepairs(redwood, r)
+   close.ij <- closepairs(redwood, r, what="indices")
+   close.ijd <- closepairs(redwood, r, what="ijd")
+   close.every <- closepairs(redwood, r, what="all", distinct=FALSE)
+ 
+   ## test agreement
+   stopifnot(identical(close.ij, close.all[c("i","j")]))
+   stopifnot(identical(close.ijd, close.all[c("i","j","d")]))
+ 
+   ## validate basic format of result
+   checkformat <- function(object, callstring) {
+     if(length(unique(lengths(object))) > 1)
+       stop(paste("Result of", callstring,
+                  "contains vectors with different lengths"))
+     return(invisible(TRUE))
+   }
+   checkformat(close.all, "closepairs(redwood, r)")  
+   checkformat(close.ij, "closepairs(redwood, r, what='indices')")  
+   checkformat(close.ijd, "closepairs(redwood, r, what='ijd')")  
+   checkformat(close.every,
+               "closepairs(redwood, r, what='all', distinct=FALSE)")  
+ 
+   #' test memory overflow code
+   close.cigar <- closepairs(redwood, r, what="ijd", nsize=2)
+   close.cigar <- closepairs(redwood, r, what="ijd", nsize=2, periodic=TRUE)
+ 
+   #' test special cases
+   onepoint <- redwood[1]
+   checkformat(closepairs(onepoint, r),
+               "closepairs(onepoint, r)")
+   checkformat(closepairs(onepoint, r, what="indices"),
+               "closepairs(onepoint, r, what='indices')")
+   checkformat(closepairs(onepoint, r, what="ijd"),
+               "closepairs(onepoint, r, what='ijd')")
+   checkformat(closepairs(onepoint, r, what="all", distinct=FALSE),
+               "closepairs(onepoint, r, what='all', distinct=FALSE)")
+   
+   #' ..............  crosspairs ..................................
+   Y <- split(amacrine)
+   on <- Y$on
+   off <- Y$off
+   
+   cross.all <- crosspairs(on, off, r)
+   cross.ij <- crosspairs(on, off, r, what="indices")
+   cross.ijd <- crosspairs(on, off, r, what="ijd")
+   cross.every <- crosspairs(on, off, r, what="all", distinct=FALSE)
+   cross.period <- crosspairs(on, off, r, periodic=TRUE)
+   cross.exclude <- crosspairs(cells, cells[1:32], 0.1, iX=1:42, iY=1:32)
+ 
+   ## validate basic format
+   checkformat(cross.all, "crosspairs(on, off, r)")
+   checkformat(cross.ij, "crosspairs(on, off, r, what='indices')")
+   checkformat(cross.ijd, "crosspairs(on, off, r, what='ijd')")
+   checkformat(cross.every, "crosspairs(on, off, r, what='all', distinct=FALSE)")
+   checkformat(cross.period, "crosspairs(on, off, r, periodic=TRUE)")
+   checkformat(cross.exclude, "crosspairs(cells, cells[], r, iX, iY)")
+   
+   ## test agreement
+   stopifnot(identical(cross.ij, cross.all[c("i","j")]))
+   stopifnot(identical(cross.ijd, cross.all[c("i","j","d")]))
+ 
+   # closethresh vs closepairs: EXACT agreement
+   thresh <- 0.08
+   clt <- closethresh(redwood, r, thresh)
+   cl <- with(closepairs(redwood, r),
+              list(i=i, j=j, th = (d <= thresh)))
+   if(!identical(cl, clt))
+     stop("closepairs and closethresh disagree")
+ 
+   reordered <- function(a) {
+     o <- with(a, order(i,j))
+     as.list(as.data.frame(a)[o,,drop=FALSE])
+   }
+   samesame <- function(a, b) {
+     identical(reordered(a), reordered(b))
+   }
+   
+   ## ...............................................
+   #' compare with older, slower code
+   op <- spatstat.options(closepairs.newcode=FALSE,
+                          closepairs.altcode=FALSE,
+                          crosspairs.newcode=FALSE)
+   ## ...............................................
+   old.close.ij <- closepairs(redwood, r, what="indices")
+   old.cross.ij <- crosspairs(on, off, r, what="indices")
+   stopifnot(samesame(close.ij, old.close.ij))
+   stopifnot(samesame(cross.ij, old.cross.ij))
+   # execute only:
+   old.close.every <- closepairs(redwood, r, what="all", distinct=FALSE)
+   old.close.once <- closepairs(redwood, r, what="all", twice=FALSE)
+   #' test memory overflow code
+   old.close.cigar <- closepairs(redwood, r, what="ijd", nsize=2)
+   old.close.cigar <- closepairs(redwood, r, what="ijd", nsize=2, periodic=TRUE)
+   
+   ## ...............................................
+   spatstat.options(op)
+   ## ...............................................
+ 
+   ## ...............................................
+   #' alternative code - execution only
+   op <- spatstat.options(closepairs.newcode=FALSE,
+                          closepairs.altcode=TRUE)
+   alt.close.ij <- closepairs(redwood, r, what="indices")
+   alt.close.ijd <- closepairs(redwood, r, what="ijd")
+   alt.close.all <- closepairs(redwood, r, what="all")
+   #' test memory overflow code
+   alt.close.cigar <- closepairs(redwood, r, what="ijd", nsize=2)
+   alt.close.cigar <- closepairs(redwood, r, what="ijd", nsize=2, periodic=TRUE)
+   spatstat.options(op)
+   ## ...............................................
+   
+   # Rasmus' example
+   R <- 0.04
+   U <- as.ppp(gridcenters(owin(), 50, 50), W=owin())
+   cp <- crosspairs(U, U, R)
+   G <- matrix(0, npoints(U), npoints(U))
+   G[cbind(cp$i, cp$j)] <- 1
+   if(!isSymmetric(G))
+     stop("crosspairs is not symmetric in Rasmus example")
+ 
+   #' periodic distance
+   pclose <- function(X, R, method=c("raw", "C")) {
+     method <- match.arg(method)
+     switch(method,
+            raw = {
+              D <- pairdist(X, periodic=TRUE)
+              diag(D) <- Inf
+              result <- which(D <= R, arr.ind=TRUE)
+            },
+            C = {
+              result <- closepairs(X, R, periodic=TRUE, what="indices")
+            })
+     result <- as.data.frame(result)
+     colnames(result) <- c("i","j")
+     return(result)
+   }
+   #' pick a threshold value which avoids GCC bug 323
+   RR <- 0.193
+   A <- pclose(redwood, RR, "raw")
+   B <- pclose(redwood, RR, "C")
+   if(!samesame(A,B))
+     stop("closepairs.ppp(periodic=TRUE) gives wrong answer")
+ 
+   #' other functions that don't have a help file
+   niets <- crosspairquad(quadscheme(cells), 0.1)
+ 
+   #' other code blocks
+   u <- closepairs(cells, 0.09, periodic=TRUE, what="all")
+   v <- closepairs(cells, 0.07, twice=FALSE, neat=TRUE)
+   #' tight cluster - guess count does not work
+   Xc <- runifrect(100, square(0.01))
+   Window(Xc) <- square(1)
+   z <- closepairs(Xc, 0.02, what="indices", distinct=FALSE)
+   z <- closepairs(Xc, 0.02, what="ijd",     distinct=FALSE)
+   z <- closepairs(Xc, 0.02, what="all",     distinct=FALSE)
+   #' same task, older code
+   aop <- spatstat.options(closepairs.newcode=FALSE)
+   z <- closepairs(Xc, 0.02, what="indices", distinct=FALSE)
+   z <- closepairs(Xc, 0.02, what="ijd",     distinct=FALSE)
+   z <- closepairs(Xc, 0.02, what="all",     distinct=FALSE)
+   spatstat.options(aop)
+ 
+   #' experimental
+   r <- 0.08
+   a <- closepairs(redwood, r)
+   b <- tweak.closepairs(a, r, 26, 0.1, 0.1)
+ })
Using nsize = 2
Using nsize = 2
Using nsize = 2
Using nsize = 2
Using nsize = 2
Using nsize = 2
> 
> local({
+   #' Three-dimensional
+   ##          X <- runifpoint3(100)
+   X <- pp3(runif(100), runif(100), runif(100), box3(c(0,1)))
+   cl <- closepairs(X, 0.2, what="indices")
+   cl <- closepairs(X, 0.2, what="ijd")
+   cl <- closepairs(X, 0.2, distinct=FALSE)
+   cl <- closepairs(X, 0.2, distinct=FALSE, what="indices")
+   cl <- closepairs(X, 0.2, distinct=FALSE, what="ijd")
+   cl <- closepairs(X, 0.2, twice=FALSE, neat=TRUE)
+   #' Test memory overflow code
+   cl <- closepairs(X, 0.2, what="ijd", nsize=2)
+   #' trap obsolete usage
+   cl <- closepairs(X, 0.2, ordered=FALSE)
+   #' crosspairs
+   ##      Y <- runifpoint3(100)
+   Y <- pp3(runif(100), runif(100), runif(100), box3(c(0,1)))
+   cr <- crosspairs(X, Y, 0.2, what="indices")
+   cr <- crosspairs(X, Y, 0.2, what="ijd")
+   #' Test memory overflow code
+   cr <- crosspairs(X, Y, 0.2, what="ijd", nsize=2)
+   #' experimental
+   rr <- 0.2
+   cl <- closepairs(X, rr)
+   ii <- cl$i[[1]]
+   xl <- tweak.closepairs(cl, rr, ii, 0.05, -0.05, 0.05)
+ })
Using nsize = 2
Using nsize = 2
Warning message:
In closepairs.pp3(X, 0.2, ordered = FALSE) :
  Obsolete argument 'ordered' has been replaced by 'twice'
> 
> reset.spatstat.options()
> #'
> #'   tests/cluck.R
> #'
> #'   Tests of "click*" functions
> #'   using queueing feature of spatstatLocator
> #'
> #'   $Revision: 1.8 $ $Date: 2022/10/23 00:45:36 $
> 
> local({
+   #' clickppp
+   if(ALWAYS) {
+     spatstat.utils::queueSpatstatLocator(runif(5), runif(5))
+     XA <- clickppp(hook=square(0.5))
+   }
+   if(FULLTEST) {
+     spatstat.utils::queueSpatstatLocator(runif(6), runif(6))
+     XB <- clickppp(n=3, types=c("a", "b"))
+   }
+   if(ALWAYS) {
+     #' clickbox
+     spatstat.utils::queueSpatstatLocator(runif(2), runif(2))
+     BB <- clickbox()
+     #' clickdist
+     spatstat.utils::queueSpatstatLocator(runif(2), runif(2))
+     dd <- clickdist()
+     #' clickpoly
+     hex <- vertices(disc(radius=0.4, centre=c(0.5, 0.5), npoly=6))
+     spatstat.utils::queueSpatstatLocator(hex)
+     PA <- clickpoly()
+   }
+   if(FULLTEST) {
+     holy <- vertices(disc(radius=0.2, centre=c(0.5, 0.5), npoly=6))
+     holy <- lapply(holy, rev)
+     spatstat.utils::queueSpatstatLocator(concatxy(hex, holy))
+     PB <- clickpoly(np=2, nv=6)
+   }
+   if(ALWAYS) {
+     #' identify.psp
+     E <- edges(letterR)[c(FALSE, TRUE)]
+     Z <- ppp(c(2.86, 3.65, 3.15), c(1.69, 1.98, 2.56), window=Frame(letterR))
+     spatstat.utils::queueSpatstatLocator(Z)
+     identify(E)
+   }
+ })
Ready to click..
Click two corners of a box
to add points: click left mouse button in window
       to exit: press ESC or click middle mouse button
 [The last point should NOT repeat the first point]
[1] 10  3 15
> ## tests/colour.R
> ##
> ##  Colour value manipulation and colour maps
> ##
> ## $Revision: 1.10 $ $Date: 2022/10/23 00:37:44 $
> ##
> 
> local({
+   if(FULLTEST) {
+     f <- function(n) grey(seq(0,1,length=n))
+     z <- to.grey(f)
+ 
+     h <- colourmap(rainbow(9), range=c(0.01, 0.1))
+     plot(h, labelmap=100)
+   }
+ 
+   if(ALWAYS) {
+     a <- colourmap(rainbow(12), range=as.Date(c("2018-01-01", "2018-12-31")))
+     print(a)
+     print(summary(a))
+     a(as.Date("2018-06-15"))
+ 
+     g <- colourmap(rainbow(4),
+                    breaks=as.Date(c("2018-01-01", "2018-04-01",
+                                     "2018-07-01", "2018-10-01", "2018-12-31")))
+     print(g)
+     print(summary(g))
+     g(as.Date("2018-06-15"))
+   }
+ 
+   if(FULLTEST) {
+     b <- colourmap(rainbow(12), inputs=month.name)
+     print(b)
+     print(summary(b))
+     to.grey(b)
+     to.grey(b, transparent=TRUE)
+     plot(b, vertical=FALSE)
+     plot(b, vertical=TRUE)
+     plot(b, vertical=FALSE, gap=0)
+     plot(b, vertical=TRUE, gap=0)
+     plot(b, vertical=FALSE, xlim=c(0, 2))
+     plot(b, vertical=TRUE, xlim=c(0,2))
+     plot(b, vertical=FALSE, ylim=c(0, 2))
+     plot(b, vertical=TRUE, ylim=c(0,2))
+ 
+     argh <- list(a="iets", e="niets", col=b, f=42)
+     arr <- col.args.to.grey(argh)
+     rrgh <- col.args.to.grey(argh, transparent=TRUE)
+   }
+ 
+   if(ALWAYS) {
+     #' constant colour map
+     colourmap("grey", range=c(0.01, 0.1))
+     colourmap("grey", range=as.Date(c("2018-01-01", "2018-12-31")))
+     colourmap("grey",
+               breaks=as.Date(c("2018-01-01", "2018-04-01",
+                                "2018-07-01", "2018-10-01", "2018-12-31")))
+     colourmap("grey", inputs=month.name)
+   }
+ 
+   if(FULLTEST) {
+     #' empty colour map
+     niets <- lut()
+     print(niets)
+     summary(niets)
+     niets <- colourmap()
+     print(niets)
+     summary(niets)
+     plot(niets)
+   }
+ 
+   if(FULLTEST) {
+     #' interpolation - of transparent colours
+     co <- colourmap(inputs=c(0, 0.5, 1),
+                     rgb(red=c(1,0,0), green=c(0,1,0), blue=c(0,0,1),
+                         alpha=c(0.3, 0.6, 0.9)))
+     tco <- interp.colourmap(co)
+   }
+ })
Colour map for the range [2018-01-01, 2018-12-31] 
                   interval  colour
1  [2018-01-01, 2018-01-31) #FF0000
2  [2018-01-31, 2018-03-03) #FF8000
3  [2018-03-03, 2018-04-02) #FFFF00
4  [2018-04-02, 2018-05-02) #80FF00
5  [2018-05-02, 2018-06-02) #00FF00
6  [2018-06-02, 2018-07-02) #00FF80
7  [2018-07-02, 2018-08-01) #00FFFF
8  [2018-08-01, 2018-09-01) #0080FF
9  [2018-09-01, 2018-10-01) #0000FF
10 [2018-10-01, 2018-10-31) #8000FF
11 [2018-10-31, 2018-12-01) #FF00FF
12 [2018-12-01, 2018-12-31] #FF0080
Colour map for the range [2018-01-01, 2018-12-31] 
                   interval  colour
1  [2018-01-01, 2018-01-31) #FF0000
2  [2018-01-31, 2018-03-03) #FF8000
3  [2018-03-03, 2018-04-02) #FFFF00
4  [2018-04-02, 2018-05-02) #80FF00
5  [2018-05-02, 2018-06-02) #00FF00
6  [2018-06-02, 2018-07-02) #00FF80
7  [2018-07-02, 2018-08-01) #00FFFF
8  [2018-08-01, 2018-09-01) #0080FF
9  [2018-09-01, 2018-10-01) #0000FF
10 [2018-10-01, 2018-10-31) #8000FF
11 [2018-10-31, 2018-12-01) #FF00FF
12 [2018-12-01, 2018-12-31] #FF0080
Colour map for the range [2018-01-01, 2018-12-31] 
                  interval  colour
1 [2018-01-01, 2018-04-01) #FF0000
2 [2018-04-01, 2018-07-01) #80FF00
3 [2018-07-01, 2018-10-01) #00FFFF
4 [2018-10-01, 2018-12-31] #8000FF
Colour map for the range [2018-01-01, 2018-12-31] 
                  interval  colour
1 [2018-01-01, 2018-04-01) #FF0000
2 [2018-04-01, 2018-07-01) #80FF00
3 [2018-07-01, 2018-10-01) #00FFFF
4 [2018-10-01, 2018-12-31] #8000FF
> 
> # tests/correctC.R
> # check for agreement between C and interpreted code
> # for interpoint distances etc.
> # $Revision: 1.8 $ $Date: 2020/12/03 03:06:04 $
> 
> if(ALWAYS) { # depends on hardware
+ local({
+   eps <- .Machine$double.eps * 4
+ 
+   checkagree <- function(A, B, blurb) {
+     maxerr <- max(abs(A-B))
+     cat("Discrepancy", maxerr, "for", blurb, fill=TRUE)
+     if(maxerr > eps) 
+       stop(paste("Algorithms for", blurb, "disagree"))
+     return(TRUE)
+   }
+ 
+   ## pairdist.ppp
+   set.seed(190901)
+   ## X <- rpoispp(42)
+   X <- runifrect(max(2, rpois(1, 42)))
+   dC <- pairdist(X, method="C")
+   dR <- pairdist(X, method="interpreted")
+   checkagree(dC, dR, "pairdist()")
+ 
+   dCp <- pairdist(X, periodic=TRUE, method="C")
+   dRp <- pairdist(X, periodic=TRUE, method="interpreted")
+   checkagree(dCp, dRp, "pairdist(periodic=TRUE)")
+ 
+   dCp2 <- pairdist(X, periodic=TRUE, squared=TRUE, method="C")
+   dRp2 <- pairdist(X, periodic=TRUE, squared=TRUE, method="interpreted")
+   checkagree(dCp2, dRp2, "pairdist(periodic=TRUE, squared=TRUE)")
+ 
+   ## crossdist.ppp
+   ## Y <- rpoispp(42)
+   Y <- runifrect(max(2, rpois(1, 42)))
+   dC <- crossdist(X, Y, method="C")
+   dR <- crossdist(X, Y, method="interpreted")
+   checkagree(dC, dR, "crossdist()")
+ 
+   dC <- crossdist(X, Y, periodic=TRUE, method="C")
+   dR <- crossdist(X, Y, periodic=TRUE, method="interpreted")
+   checkagree(dC, dR, "crossdist(periodic=TRUE)")
+ 
+   dC2 <- crossdist(X, Y, periodic=TRUE, squared=TRUE, method="C")
+   dR2 <- crossdist(X, Y, periodic=TRUE, squared=TRUE, method="interpreted")
+   checkagree(dC2, dR2, "crossdist(periodic=TRUE, squared=TRUE)")
+ 
+   # nndist.ppp
+   nnC <- nndist(X, method="C")
+   nnI <- nndist(X, method="interpreted")
+   checkagree(nnC, nnI, "nndist()")
+ 
+   nn3C <- nndist(X, k=3, method="C")
+   nn3I <- nndist(X, k=3, method="interpreted")
+   checkagree(nn3C, nn3I, "nndist(k=3)")
+ 
+   # nnwhich.ppp
+   nwC <- nnwhich(X, method="C")
+   nwI <- nnwhich(X, method="interpreted")
+   checkagree(nwC, nwI, "nnwhich()")
+ 
+   nw3C <- nnwhich(X, k=3, method="C")
+   nw3I <- nnwhich(X, k=3, method="interpreted")
+   checkagree(nw3C, nw3I, "nnwhich(k=3)")
+ 
+   # whist
+   set.seed(98123)
+   x <- runif(1000)
+   w <- sample(1:5, 1000, replace=TRUE)
+   b <- seq(0,1,length=101)
+   op <- spatstat.options(Cwhist=TRUE)
+   aT <- whist(x,b,w)
+   spatstat.options(Cwhist=FALSE)
+   aF <- whist(x,b,w)
+   if(!all(aT == aF))
+     stop("Algorithms for whist disagree")
+   spatstat.options(op)
+ })
+ 
+ reset.spatstat.options()
+ }
Discrepancy 0 for pairdist()
Discrepancy 0 for pairdist(periodic=TRUE)
Discrepancy 0 for pairdist(periodic=TRUE, squared=TRUE)
Discrepancy 0 for crossdist()
Discrepancy 5.551115e-17 for crossdist(periodic=TRUE)
Discrepancy 0 for crossdist(periodic=TRUE, squared=TRUE)
Discrepancy 0 for nndist()
Discrepancy 0 for nndist(k=3)
Discrepancy 0 for nnwhich()
Discrepancy 0 for nnwhich(k=3)
> 
> proc.time()
   user  system elapsed 
   2.85    0.53    3.34