R Under development (unstable) (2025-08-21 r88668 ucrt) -- "Unsuffered Consequences"
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> library(lgcp)

 Welcome to 'lgcp': Log-Gaussian Cox Process
 B. M. Taylor & T. M. Davies & B. S. Rowlingson & P. J. Diggle.

Type '?lgcp' for details.

Type 'lgcpvignette()' to view the basic package vignette.

Type 'lgcpbayes()' to view the Bayesian package vignette.

Type 'citation("lgcp")' to view the citation for this package.

Please see the lgcp package NEWS file for latest additions, changes and bug fixes.

Note, RandomFields covariance functions are currently unavailable.
> library(spatstat.explore)
Loading required package: spatstat.data
Loading required package: spatstat.univar
spatstat.univar 3.1-4
Loading required package: spatstat.geom
spatstat.geom 3.5-0
Loading required package: spatstat.random
spatstat.random 3.4-1
Loading required package: nlme
spatstat.explore 3.5-2
> library(sp)
> 
> polylist <- list()
> # a pentagon
> vert1 <- t(sapply((0:4)*(2*pi/5),function(theta){return(5*c(cos(theta),sin(theta)))}))
> vert1 <- rbind(vert1,vert1[1,])
> polylist[[1]] <- Polygons(list(Polygon(vert1)),ID="1")
> 
> # a diamond shape
> vert2 <- matrix(c(-8,-10,-12,-10,0,2,0,-2),4,2)
> vert2 <- rbind(vert2,vert2[1,])
> polylist[[2]] <- Polygons(list(Polygon(vert2)),ID="2")
> 
> # a square with a rectangular hole
> vert3 <- matrix(c(0,0,2,2,-10,-12,-12,-10),4,2)
> vert3 <- rbind(vert3,vert3[1,])
> vert4 <- matrix(c(0.25,0.75,0.75,0.25,-10.5,-10.5,-11.5,-11.5),4,2)
> vert4 <- rbind(vert4,vert4[1,])
> polylist[[3]] <- Polygons(list(Polygon(vert3),Polygon(vert4,hole=TRUE)),ID="3") 
> 
> 
> sP <- SpatialPolygons(polylist)
> 
> df <- data.frame(list(atrisk=c(1,2,3)))
> 
> spdf <- SpatialPolygonsDataFrame(sP,df)
> 
> sar <- spatialAtRisk(spdf)
> sar
$atrisk
[1] 0.002803899 0.041666667 0.125000000

$spdf
class       : SpatialPolygonsDataFrame 
features    : 3 
extent      : -12, 5, -12, 4.755283  (xmin, xmax, ymin, ymax)
crs         : NA 
variables   : 1
names       :              atrisk 
min values  : 0.00280389926463538 
max values  :               0.125 

attr(,"class")
[1] "fromSPDF"      "spatialAtRisk"
attr(,"NC")
[1] 356.6462  48.0000  24.0000
> 
> rotsar <- affine(sar,mat=rotmat(pi/6))
> 
> # Now test simulation code:
> #sim <- lgcpSim(affine(owin(poly=list(x=c(-15,-15,5,5),y=c(5,-15,-15,5))),rotmat(pi/6)),model.parameters=lgcppars(sigma=2,phi=1,theta=3),cellwidth=0.2,spatial.intensity=affine(sar,rotmat(pi/6)),temporal.intensity=function(x){100},plot=TRUE)
> #sim <- lgcpSim(owin(poly=list(x=c(-15,-15,5,5),y=c(5,-15,-15,5))),model.parameters=lgcppars(sigma=2,phi=1,theta=3),cellwidth=0.2,spatial.intensity=sar,temporal.intensity=function(x){100},plot=TRUE)
> 
> 
> proc.time()
   user  system elapsed 
   8.79    0.60    9.40