R Under development (unstable) (2024-03-21 r86166 ucrt) -- "Unsuffered Consequences"
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> #'
> #'   Header for all (concatenated) test files
> #'
> #'   Require spatstat.model
> #'   Obtain environment variable controlling tests.
> #'
> #'   $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $
> 
> require(spatstat.model)
Loading required package: spatstat.model
Loading required package: spatstat.data
Loading required package: spatstat.geom
spatstat.geom 3.2-9
Loading required package: spatstat.random
spatstat.random 3.2-3
Loading required package: spatstat.explore
Loading required package: nlme
spatstat.explore 3.2-7
Loading required package: rpart
spatstat.model 3.2-11
> 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/testaddvar.R
> #
> # test addvar options
> #
> #   $Revision: 1.3 $  $Date: 2020/05/02 01:32:58 $
> 
> if(FULLTEST) {
+ local({
+   X <-  rpoispp(function(x,y){exp(3+3*x)})
+   model <- ppm(X ~y)
+   addvar(model, "x", crosscheck=TRUE)
+   addvar(model, "x", bw.input="quad")
+   w <- square(0.5)
+   addvar(model, "x", subregion=w)
+   addvar(model, "x", subregion=w, bw.input="points")
+   Z <- as.im(function(x,y) { x }, Window(X))
+   addvar(model, Z)
+ })
+ }
> #
> #   tests/testparres.R
> #
> # additional test of parres
> #
> #  $Revision: 1.8 $  $Date: 2022/05/20 06:59:59 $
> #
> 
> if(FULLTEST) {
+ local({
+ X <-  rpoispp(function(x,y){exp(3+x+2*x^2)})
+ model <- ppm(X ~x+y)
+ 
+ # options in parres (and code blocks in print.parres)
+ parres(model, "x")
+ parres(model, "x", smooth.effect=TRUE)
+ parres(model, "x", bw.input="quad")
+ w <- square(0.5)
+ parres(model, "x", subregion=w)
+ parres(model, "x", subregion=w, bw.input="quad")
+ f <- function(x,y) { x + y }
+ parres(model, f)
+ 
+ # check whether 'update.ppm' has messed up internals
+ mod2 <- update(model, ~x)
+ parres(mod2, "x")
+ 
+ #' other kinds of covariates
+ mod3 <- ppm(X ~ x + offset(y))
+ parres(mod3, "offset(y)")
+ Z <- distmap(runifpoint(3))
+ parres(mod3, Z)
+ mod4 <- ppm(X ~ sin(x), data=solist(B=Z))
+ parres(mod4, "sin(x)")
+ parres(mod4, "B")
+ 
+ #' models with interaction
+ mod5 <- ppm(cells ~ x, AreaInter(0.06))
+ parres(mod5, "x")
+ dlin <- distfun(copper$SouthLines)
+ copfit <- ppm(copper$SouthPoints ~ dlin, Geyer(1,1))
+ parres(copfit, "dlin")
+ 
+ #' covariate need not be specified if there is only one.
+ parres(mod5)
+ parres(copfit)
+ 
+ #' infrastructure
+ ltuae <- evaluateCovariate(42, cells)
+ LTUAE <- evaluateCovariate(ltuae, cells)
+ 
+ fit <- ppm(amacrine ~ x * marks, nd=16)
+ dmat <- model.depends(fit)
+ check.separable(dmat, "x", c(x=FALSE, marks=FALSE), FALSE)
+ check.separable(dmat, "x", c(FALSE, FALSE), FALSE)
+ check.separable(dmat, "x", c(x=FALSE, marks=TRUE), FALSE)
+ })
+ }
> #'
> #'     tests/threedee.R
> #'
> #'     Tests of 3D code 
> #'
> #'      $Revision: 1.8 $ $Date: 2020/05/02 01:32:58 $
> #'
> 
> local({
+   X <- runifpoint3(30)
+   Y <- runifpoint3(20)
+   if(FULLTEST) {
+     A <- runifpoint3(10, nsim=2)
+     Z <- ppsubset(X, 2:4)
+   }
+   ##
+   if(ALWAYS) { # includes C code
+     d <- pairdist(X, periodic=TRUE, squared=TRUE)
+     d <- crossdist(X, Y, squared=TRUE)
+     d <- crossdist(X, Y, squared=TRUE, periodic=TRUE)
+     #' 
+     h <- has.close(X, 0.2)
+     h <- has.close(X, 0.2, periodic=TRUE)
+     h <- has.close(X, 0.2, Y=Y)
+     h <- has.close(X, 0.2, Y=Y, periodic=TRUE)
+     #' code blocks not otherwise reached
+     rmax <- 0.6 * max(nndist(X))
+     g <- G3est(X, rmax=rmax, correction="rs")
+     g <- G3est(X, rmax=rmax, correction="km")
+     g <- G3est(X, rmax=rmax, correction="Hanisch")
+     g <- G3est(X, rmax=rmax, sphere="ideal")
+     g <- G3est(X, rmax=rmax, sphere="digital")
+     v <- sphere.volume()
+     v <- digital.volume()
+     #' older code
+     co <- coords(X)
+     xx <- co$x
+     yy <- co$y
+     zz <- co$z
+     gg1 <- g3engine(xx, yy, zz, correction="Hanisch G3")
+     gg2 <- g3engine(xx, yy, zz, correction="minus sampling")
+     ff1 <- f3engine(xx, yy, zz, correction="no")
+     ff2 <- f3engine(xx, yy, zz, correction="minus sampling")
+   }
+   ##
+   if(ALWAYS) {
+     #'class support
+     X <- runifpoint3(10)
+     print(X)
+     print(X %mark% runif(10))
+     print(X %mark% factor(letters[c(1:5,5:1)]))
+     print(X %mark% data.frame(a=1:10, b=runif(10)))
+     da <- as.Date(paste0("2020-01-0", c(1:5,5:1)))
+     print(X %mark% da)
+     print(X %mark% data.frame(a=1:10, b=da))
+   }
+ })
Three-dimensional point pattern: 10 points
Box: [0, 1] x [0, 1] x [0, 1] units
Marked three-dimensional point pattern: 10 points
marks are numeric, of storage type  'double'
Box: [0, 1] x [0, 1] x [0, 1] units
Marked three-dimensional point pattern: 10 points
Multitype, with levels = a, b, c, d, e 
Box: [0, 1] x [0, 1] x [0, 1] units
Marked three-dimensional point pattern: 10 points
Mark variables: a, b 
Box: [0, 1] x [0, 1] x [0, 1] units
Marked three-dimensional point pattern: 10 points
marks are dates, of class 'Date'
Box: [0, 1] x [0, 1] x [0, 1] units
Marked three-dimensional point pattern: 10 points
Mark variables: a, b 
Box: [0, 1] x [0, 1] x [0, 1] units
Warning messages:
1: In G3est: unrecognised argument 'sphere' was ignored 
2: In G3est: unrecognised argument 'sphere' was ignored 
> #
> # tests/triplets.R
> #
> # test code for triplet interaction 
> #
> # $Revision: 1.9 $ $Date: 2022/05/22 08:45:38 $
> #
> if(ALWAYS) { # C code, platform dependence
+ local({
+   #' valid model
+   fit <- ppm(cells ~1, Triplets(0.1))
+   fit
+   suffstat(fit)
+   #' invalid model 
+   fitR <- ppm(redwood ~1, Triplets(0.1))
+   fitR
+   suffstat(fitR)
+   #' hard core (zero triangles, coefficient is NA)
+   fit0 <- ppm(cells ~1, Triplets(0.05))
+   fit0
+   suffstat(fit0)
+   #' bug case (1 triangle in data)
+   fit1 <- ppm(cells ~1, Triplets(0.15))
+   fit1
+   suffstat(fit1)
+   #' simulation
+   X <- simulate(fit)
+   mod <- list(cif="triplets",par=list(beta=50,gamma=0.2,r=0.07), w=square(1))
+   Xm <- rmh(model=mod,start=list(n.start=5), control=list(nrep=1e5))
+   #' hard core
+   mod$par$gamma <- 0
+   XmHard <- rmh(model=mod,start=list(n.start=5), control=list(nrep=1e5))
+ })
+ }
Checking arguments..determining simulation windows...Starting simulation.
Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings.
Checking arguments..determining simulation windows...Starting simulation.
Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings.
> 
> proc.time()
   user  system elapsed 
   2.51    0.29    2.76