R Under development (unstable) (2023-09-06 r85088 ucrt) -- "Unsuffered Consequences"
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> #'
> #'   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)
Loading required package: spatstat.explore
Loading required package: spatstat.data
Loading required package: spatstat.geom
spatstat.geom 3.2-5
Loading required package: spatstat.random
spatstat.random 3.1-5
Loading required package: nlme
spatstat.explore 3.2-3
> 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/envelopes.R
> #
> #  Test validity of envelope data
> #
> #  $Revision: 1.28 $  $Date: 2022/11/24 01:35:26 $
> #
> 
> local({
+   
+ 
+ 
+ ## check envelope calls from 'alltypes'
+ if(ALWAYS) a <- alltypes(demopat, Kcross, nsim=4, envelope=TRUE)
+ if(FULLTEST) b <- alltypes(demopat, Kcross, nsim=4, envelope=TRUE, global=TRUE)
+ ## check 'transform' idioms
+ if(ALWAYS) A <- envelope(cells, Kest, nsim=4, transform=expression(. - .x))
+ if(FULLTEST) B <- envelope(cells, Kest, nsim=4, transform=expression(sqrt(./pi) - .x))
+ 
+ 
+ # check conditional simulation
+ if(FULLTEST) {
+   e1 <- envelope(cells, Kest, nsim=4, fix.n=TRUE)
+   e2 <- envelope(amacrine, Kest, nsim=4, fix.n=TRUE)
+   e3 <- envelope(amacrine, Kcross, nsim=4, fix.marks=TRUE)
+   e4 <- envelope(finpines, Kest, nsim=4, fix.n=TRUE) # multiple columns of marks
+   e5 <- envelope(finpines, Kest, nsim=4, fix.marks=TRUE)
+ }
+ 
+ 
+ ## check pooling of envelopes in global case
+ E1 <- envelope(cells, Kest, nsim=5, savefuns=TRUE, global=TRUE)
+ E2 <- envelope(cells, Kest, nsim=12, savefuns=TRUE, global=TRUE)
+ p12 <- pool(E1, E2)
+ p12 <- pool(E1, E2, savefuns=TRUE)
+ if(FULLTEST) {
+   F1 <- envelope(cells, Kest, nsim=5,
+                  savefuns=TRUE, savepatterns=TRUE, global=TRUE)
+   F2 <- envelope(cells, Kest, nsim=12,
+                  savefuns=TRUE, savepatterns=TRUE, global=TRUE)
+   p12 <- pool(F1, F2)
+   p12 <- pool(F1, F2, savefuns=TRUE, savepatterns=TRUE)
+   E1r <- envelope(cells, Kest, nsim=5, savefuns=TRUE, global=TRUE,
+                   ginterval=c(0.05, 0.15))
+   E2r <- envelope(cells, Kest, nsim=12, savefuns=TRUE, global=TRUE,
+                   ginterval=c(0.05, 0.15))
+   p12r <- pool(E1r, E2r)
+ }
+ 
+ if(FULLTEST) {
+   #' as.data.frame.envelope
+   Nsim <- 5
+   E <- envelope(cells, nsim=Nsim, savefuns=TRUE)
+   A <- as.data.frame(E)
+   B <- as.data.frame(E, simfuns=TRUE)
+   stopifnot(ncol(B) - ncol(A) == Nsim)
+ }
+ 
+ if(FULLTEST) {
+   #' cases not covered elsewhere
+   A <- envelope(cells, nsim=5, alternative="less",
+                 do.pwrong=TRUE, use.theory=FALSE,
+                 savepatterns=TRUE, savefuns=TRUE)
+   print(A)
+   B <- envelope(A, nsim=5, savefuns=TRUE)
+   D <- envelope(cells, "Lest", nsim=5)
+   
+   UU <- envelope(cells, nsim=5, foreignclass="ppp", clipdata=TRUE)
+   
+   AA <- envelope(cells, nsim=5, jsim=5, alternative="greater", global=TRUE)
+   AA <- envelope(cells, nsim=5, jsim=5, alternative="less", global=TRUE)
+   AA <- envelope(cells, nsim=5, jsim=5, alternative="greater", VARIANCE=TRUE)
+   AA <- envelope(cells, nsim=5, jsim=5, alternative="greater", VARIANCE=TRUE)
+ 
+   #' spotted by Art Stock - bugs in ratfv class support
+   BB <- envelope(redwood, Kinhom, nsim=5, sigma=bw.scott,              ratio=TRUE, correction="border")
+   CC <- envelope(redwood, Kinhom, nsim=5, sigma=bw.scott, global=TRUE, ratio=TRUE, correction="border")
+   DD <- envelope(redwood, Finhom, nsim=5, sigma=bw.scott,              ratio=TRUE, correction="trans")
+   EE <- envelope(redwood, Finhom, nsim=5, sigma=bw.scott, global=TRUE, ratio=TRUE, correction="trans")
+   
+   #'  envelopes based on sample variance
+   E <- envelope(cells, nsim=8, VARIANCE=TRUE)
+   G <- envelope(cells, nsim=8, VARIANCE=TRUE,
+                 use.theory=FALSE, do.pwrong=TRUE)
+   print(G)
+   #' summary method
+   summary(E)
+   summary(envelope(cells, nsim=5, simulate=expression(runifpoint(42))))
+   #' weights argument
+   H1 <- envelope(cells, nsim=4, weights=npoints, savefuns=TRUE)
+   H2 <- envelope(cells, nsim=4, weights=npoints, savefuns=TRUE)
+   J1 <- envelope(cells, nsim=4, weights=npoints, VARIANCE=TRUE)
+   J2 <- envelope(cells, nsim=4, weights=npoints, VARIANCE=TRUE)
+   #' pooling with weights
+   H <- pool(H1, H2)
+   J <- pool(J1, J2)
+   #' pooling envelopes with non-identical attributes
+   H0 <- envelope(cells, nsim=4, savefuns=TRUE)
+   HH <- pool(H0, H1)
+   #' malformed argument 'simulate'
+   A <- replicate(3, list(list(runifpoint(ex=cells))))   # list(list(ppp), list(ppp), list(ppp))
+   E <- envelope(cells, simulate=A, nsim=3)
+   #' undocumented/secret
+   K <- envelope(cells, nsim=4, saveresultof=npoints, collectrubbish=TRUE)
+   #' so secret I've even forgotten how to do it
+   M <- envelope(cells, nsim=4, internal=list(eject="patterns"))
+ }
+ 
+ 
+ if(ALWAYS) {
+   #' Test robustness of envelope() sorting procedure when NA's are present
+   #' Fails with spatstat.utils 1.12-0
+   set.seed(42)
+   EP <- envelope(longleaf, pcf, nsim=10, nrank=2)
+ 
+   #' Test case when the maximum permitted number of failures is exceeded
+   X <- amacrine[1:153] # contains exactly one point with mark='off'
+   #' High probability of generating a pattern with no marks = 'off'
+   E <- envelope(X, Kcross, nsim=39, maxnerr=2, maxerr.action="warn")
+   A <- alltypes(X, Kcross, envelope=TRUE, nsim=39, maxnerr=2)
+ }
+ 
+ if(ALWAYS) {
+   #' Internals: envelope.matrix
+   Y <- matrix(rnorm(200), 10, 20)
+   rr <- 1:10
+   oo <- rnorm(10)
+   zz <- numeric(10)
+   E <- envelope(Y, rvals=rr, observed=oo, nsim=10)
+   E <- envelope(Y, rvals=rr, observed=oo, jsim=1:10)
+   E <- envelope(Y, rvals=rr, observed=oo, theory=zz,
+                 type="global", use.theory=TRUE)
+   E <- envelope(Y, rvals=rr, observed=oo, theory=zz,
+                 type="global", use.theory=TRUE, nsim=10)
+   E <- envelope(Y, rvals=rr, observed=oo, theory=zz,
+                 type="global", use.theory=FALSE, nsim=10)
+   E <- envelope(Y, rvals=rr, observed=oo, type="global",
+                 nsim=10, nsim2=10)
+   E <- envelope(Y, rvals=rr, observed=oo, type="global",
+                 jsim=1:10, jsim.mean=11:20)
+   if(FULLTEST) print(E)
+   E <- envelope(Y, rvals=rr, observed=oo, type="global",
+                 nsim=10, jsim.mean=11:20)
+   E <- envelope(Y, rvals=rr, observed=oo, type="global",
+                 jsim=1:10, nsim2=10)
+ }
+ 
+ if(ALWAYS) {
+   #' quirk with handmade summary functions ('conserve' attribute)
+   Kdif <- function(X, r=NULL) { # note no ellipsis
+     Y <- split(X)
+     K1 <- Kest(Y[[1]], r=r)
+     K2 <- Kest(Y[[2]], r=r)
+     D <- eval.fv(K1-K2)
+     return(D)
+   }
+   envelope(amacrine, Kdif, nsim=3)
+ }
+ 
+ 
+ ## close 'local'
+ })
Generating 4 simulations of CSR  ...
1, 2, 3, 
4.

Done.
Generating 5 simulations of CSR  ...
1, 2, 3, 4, 
5.

Done.
Generating 12 simulations of CSR  ...
1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 
12.

Done.
Generating 10 simulations of CSR  ...
1, 2, 3, 4, 5, 6, 7, 8, 9, 
10.

Done.
Generating 39 simulations of CSR  ...
Error in (function (X, i, j, r = NULL, breaks = NULL, correction = c("border",  : 
  No points have mark i = off
[retrying]
1, 2, 3, 4, Error in (function (X, i, j, r = NULL, breaks = NULL, correction = c("border",  : 
  No points have mark i = off
[retrying]
5, 6, Error in (function (X, i, j, r = NULL, breaks = NULL, correction = c("border",  : 
  No points have mark i = off

Done.
Generating 3 simulations of CSR  ...
1, 2, 
3.

Done.
Pointwise critical envelopes for K1(r)-K2(r)
and observed value for 'amacrine'
Edge correction: "iso"
Obtained from 3 simulations of CSR
Alternative: two.sided
Significance level of pointwise Monte Carlo test: 2/4 = 0.5
................................................................................
     Math.label          
r    r                   
obs  hat((K1-K2))[obs](r)
theo (K1-K2)[theo](r)    
lo   hat((K1-K2))[lo](r) 
hi   hat((K1-K2))[hi](r) 
     Description                                             
r    distance argument r                                     
obs  observed value of K1(r)-K2(r) for data pattern          
theo theoretical value of K1(r)-K2(r) for CSR                
lo   lower pointwise envelope of K1(r)-K2(r) from simulations
hi   upper pointwise envelope of K1(r)-K2(r) from simulations
................................................................................
Default plot formula:  .~r
where "." stands for 'obs', 'theo', 'hi', 'lo'
Columns 'lo' and 'hi' will be plotted as shading (by default)
Recommended range of argument r: [0, 0.25]
Available range of argument r: [0, 0.25]
Unit of length: 662 microns
Warning messages:
1: Exceeded maximum permissible number of  (maxnerr = 2) when evaluating summary function for simulated point patterns 
2: In alltypes(X, Kcross, envelope = TRUE, nsim = 39, maxnerr = 2) :
  3 out of 4 envelopes were not computed, due to errors in evaluating the summary functions for simulated patterns
> #
> #  tests/fastK.R
> #
> # check fast and slow code for Kest
> #       and options not tested elsewhere
> #
> #   $Revision: 1.5 $   $Date: 2020/04/28 12:58:26 $
> #
> if(ALWAYS) {
+ local({
+   ## fast code
+   Kb <- Kest(cells, nlarge=0)
+   Ku <- Kest(cells, correction="none")
+   Kbu <- Kest(cells, correction=c("none", "border"))
+   ## slow code, full set of corrections, sqrt transformation, ratios
+   Ldd <- Lest(unmark(demopat), correction="all", var.approx=TRUE, ratio=TRUE)
+   ## Lotwick-Silverman var approx (rectangular window)
+   Loo <- Lest(cells, correction="all", var.approx=TRUE, ratio=TRUE)
+   ## Code for large dataset
+   nbig <- .Machine$integer.max
+   if(!is.null(nbig)) {
+     nn <- ceiling(sqrt(nbig))
+     if(nn < 1e6) Kbig <- Kest(runifpoint(nn),
+                               correction=c("border", "bord.modif", "none"),
+                               ratio=TRUE)
+   }
+   
+   ## Kinhom
+   lam <- density(cells, at="points", leaveoneout=TRUE)
+   ## fast code
+   Kib <- Kinhom(cells, lam, nlarge=0)
+   Kiu <- Kest(cells, lam, correction="none")
+   Kibu <- Kest(cells, lam, correction=c("none", "border"))
+   ## slow code
+   Lidd <- Linhom(unmark(demopat), sigma=bw.scott)
+ })
+ 
+ }
number of data points exceeds 0 - computing border correction estimate only
number of data points exceeds 0 - computing border correction estimate only
Warning message:
Periodic correction is not defined for non-rectangular windows 
> ## 
> ##    tests/fvproblems.R
> ##
> ##    problems with fv, ratfv and fasp code
> ##
> ##    $Revision: 1.15 $  $Date: 2020/04/28 12:58:26 $
> 
> #' This appears in the workshop notes
> #' Problem detected by Martin Bratschi
> 
> if(FULLTEST) {
+ local({
+   Jdif <- function(X, ..., i) {
+     Jidot <- Jdot(X, ..., i=i)
+     J <- Jest(X, ...)
+     dif <- eval.fv(Jidot - J)
+     return(dif)
+   }
+   Z <- Jdif(amacrine, i="on")
+ })
+ }
> #'
> #'  Test mathlegend code
> #'
> local({
+   K <- Kest(cells)
+   if(FULLTEST) {
+     plot(K)
+     plot(K, . ~ r)
+     plot(K, . - theo ~ r)
+   }
+   if(ALWAYS) {
+     plot(K, sqrt(./pi)  ~ r)
+   }
+   if(FULLTEST) {
+     plot(K, cbind(iso, theo) ~ r)
+     plot(K, cbind(iso, theo) - theo ~ r)
+     plot(K, sqrt(cbind(iso, theo)/pi)  ~ r)
+     plot(K, cbind(iso/2, -theo) ~ r)
+     plot(K, cbind(iso/2, trans/2) - theo ~ r)
+   }
+   if(FULLTEST) {
+     ## test expansion of .x and .y
+     plot(K, . ~ .x)
+     plot(K, . - theo ~ .x)
+     plot(K, .y - theo ~ .x)
+   }
+   if(ALWAYS) {
+     plot(K, sqrt(.y) - sqrt(theo) ~ .x)
+   }
+ 
+   # problems with parsing weird strings in levels(marks(X))
+   # noted by Ulf Mehlig
+   if(ALWAYS) {
+     levels(marks(amacrine)) <- c("Nasticreechia krorluppia", "Homo habilis")
+     plot(Kcross(amacrine))
+     plot(alltypes(amacrine, "K"))
+   }
+   if(FULLTEST) {
+     plot(alltypes(amacrine, "J"))
+     plot(alltypes(amacrine, pcfcross))
+   }
+ })
> 
> #'
> #'  Test quirks related to 'alim' attribute
> 
> if(FULLTEST) {
+ local({
+   K <- Kest(cells)
+   attr(K, "alim") <- NULL
+   plot(K)
+   attr(K, "alim") <- c(0, 0.1)
+   plot(tail(K))
+ })
+ }
> 
> #'
> #' Check that default 'r' vector passes the test for fine spacing
> 
> if(ALWAYS) {
+ local({
+   a <- Fest(cells)
+   A <- Fest(cells, r=a$r)
+   b <- Hest(heather$coarse)
+   B <- Hest(heather$coarse, r=b$r)
+   # from Cenk Icos
+   X <- runifpoint(100, owin(c(0,3), c(0,10)))
+   FX <- Fest(X)
+   FXr <- Fest(X, r=FX$r)
+   JX <- Jest(X)
+ })
+ }
> 
> ##' various functionality in fv.R
> 
> if(ALWAYS) {
+ local({
+   M <- cbind(1:20, matrix(runif(100), 20, 5))
+   A <- as.fv(M)
+   fvlabels(A) <- c("r","%s(r)", "%s[A](r)", "%s[B](r)", "%s[C](r)", "%s[D](r)")
+   A <- rename.fv(A, "M", quote(M(r)))
+   A <- tweak.fv.entry(A, "V1", new.tag="r")
+   A[,3] <- NULL
+   A$hogwash <- runif(nrow(A))
+   fvnames(A, ".") <- NULL
+   #' bind.fv with qualitatively different functions
+   GK <- harmonise(G=Gest(cells), K=Kest(cells))
+   G <- GK$G
+   K <- GK$K
+   ss <- c(rep(TRUE, nrow(K)-10), rep(FALSE, 10))
+   U <- bind.fv(G, K[ss, ], clip=TRUE)
+   #'
+   H <- rebadge.as.crossfun(K, "H", "inhom", 1, 2)
+   H <- rebadge.as.dotfun(K, "H", "inhom", 3)
+   #' text layout
+   op <- options(width=27)
+   print(K)
+   options(width=18)
+   print(K)
+   options(op)
+   #' collapse.fv
+   Kb <- Kest(cells, correction="border")
+   Ki <- Kest(cells, correction="isotropic")
+   collapse.fv(Kb, Ki, same="theo")
+   collapse.fv(anylist(B=Kb, I=Ki), same="theo")
+   collapse.fv(anylist(B=Kb), I=Ki, same="theo")
+   Xlist <- replicate(3, runifpoint(30), simplify=FALSE)
+   Klist <- anylapply(Xlist, Kest) 
+   collapse.fv(Klist, same="theo", different=c("iso", "border"))
+   names(Klist) <- LETTERS[24:26]
+   collapse.fv(Klist, same="theo", different=c("iso", "border"))
+ })
+ }
Function value object 
(class 'fv')
for the function r -> K(r)
...........................
       Math.label      
r      r               
theo   K[pois](r)      
border hat(K)[bord](r) 
trans  hat(K)[trans](r)
iso    hat(K)[iso](r)  
       Description        
r      distance argument r
theo   theoretical [..]   
border  [..]              
trans   [..]              
iso     [..]              
...........................
Default plot formula:  .~r
where "." stands for 
'iso', 'trans', 'border', 
'theo'
Recommended range of 
argument r: [0, 0.25]
Available range of 
argument r: [0, 0.25]
Function value 
object (class 
'fv')
for the function 
r -> K(r)
..................
       Math.label      
r      r               
theo   K[pois](r)      
border hat(K)[bord](r) 
trans  hat(K)[trans](r)
iso    hat(K)[iso](r)  
       Description
r       [..]      
theo    [..]      
border  [..]      
trans   [..]      
iso     [..]      
..................
Default plot 
formula:  .~r
where "." stands 
for 'iso', 
'trans', 
'border', 'theo'
Recommended range 
of argument r: 
[0, 0.25]
Available range 
of argument r: 
[0, 0.25]
Function value object (class 'fv')
for the function r -> K(r)
................................................................
        Math.label        Description                           
r       r                 distance argument r                   
theo    K[pois](r)        theoretical Poisson K(r)              
Xborder X~hat(K)[bord](r) X border-corrected estimate of K(r)   
Xiso    X~hat(K)[iso](r)  X isotropic-corrected estimate of K(r)
Yborder Y~hat(K)[bord](r) Y border-corrected estimate of K(r)   
Yiso    Y~hat(K)[iso](r)  Y isotropic-corrected estimate of K(r)
Zborder Z~hat(K)[bord](r) Z border-corrected estimate of K(r)   
Ziso    Z~hat(K)[iso](r)  Z isotropic-corrected estimate of K(r)
................................................................
Default plot formula:  .~.x
where "." stands for 'theo', 'Xborder', 'Xiso', 'Yborder', 'Yiso', 'Zborder', 
'Ziso'
Recommended range of argument r: [0, 0.25]
Available range of argument r: [0, 0.25]
Warning message:
In bind.fv(G, K[ss, ], clip = TRUE) :
  The column name 'theo' was duplicated. Unique names were generated
> 
> if(FULLTEST) {
+ local({
+   ## rat
+   K <- Kest(cells, ratio=TRUE)
+   G <- Gest(cells, ratio=TRUE)
+   print(K)
+   compatible(K, K)
+   compatible(K, G)
+   H <- rat(K, attr(K, "numerator"), attr(K, "denominator"), check=TRUE)
+ })
+ }
> 
> if(FULLTEST) {
+ local({
+   ## bug in Jmulti.R colliding with breakpts.R
+   B <- owin(c(0,3), c(0,10))
+   Y <- superimpose(A=runifpoint(1212, B), B=runifpoint(496, B))
+   JDX <- Jdot(Y)
+   JCX <- Jcross(Y)
+   Jdif <- function(X, ..., i) {
+     Jidot <- Jdot(X, ..., i=i)
+     J <- Jest(X, ...)
+     dif <- eval.fv(Jidot - J)
+     return(dif)
+   }
+   E <- envelope(Y, Jdif, nsim=19, i="A", simulate=expression(rlabel(Y)))
+ })
+ }
> 
> if(FULLTEST) {
+ local({
+   #' fasp axes, title, dimnames
+   a <- alltypes(amacrine)
+   a$title <- NULL
+   plot(a, samex=TRUE, samey=TRUE)
+   dimnames(a) <- lapply(dimnames(a), toupper)
+ 
+   b <- as.fv(a)
+ })
+ }
> 
> if(FULLTEST) {
+ local({
+   ## plot.anylist (fv)
+   b <- anylist(A=Kcross(amacrine), B=Kest(amacrine))
+   plot(b, equal.scales=TRUE, main=expression(sqrt(pi)))
+   plot(b, arrange=FALSE)
+ })
+ }
> 
> proc.time()
   user  system elapsed 
   5.65    0.48    6.12