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#' @export
BOOT.density <- function(pp,hlim=NULL,eta=NULL,type=c("fixed","adaptive"),hp=NULL,
edge=c("uniform","none"),ref.density=NULL,resolution=64,
rmdiag=TRUE,sim.adapt=list(N=50,B=100,dimz=64,objective=FALSE),
parallelise=NA,verbose=TRUE,...){
if(!inherits(pp,"ppp")) stop("'pp' must be of spatstat class \"ppp\"; see ?ppp")
n <- npoints(pp)
W <- Window(pp)
WM <- as.mask(W,dimyx=rep(resolution,2))
# set h-limits if unsupplied
if(is.null(hlim)){
ppu <- pp
marks(ppu) <- NULL
md <- min(nndist(unique(ppu)))
hlim <- c(md,max(md*50,min(diff(W$xrange),diff(W$yrange))/6))
} else {
hlim <- checkran(hlim,"'hlim'")
}
edg <- checkedge(edge,v=0)
if(!is.na(parallelise)){
if(!is.numeric(parallelise)) stop("'parallelise' must be numeric")
if(is.null(parallelise)) parallelise <- NA
parallelise <- round(parallelise[1])
}
typ <- type[1]
if(typ=="fixed"){
if(verbose) cat("Initialising...")
# unleash the grid within
inside <- WM$m
inn <- which(as.vector(inside))
evalyx <- as.matrix(expand.grid(WM$yrow,WM$xcol))
evalyx.redu <- evalyx[inn,]
GN <- length(inn)
edg <- edg=="uniform"
# get reference density and associated diggle edge factors
if(is.null(ref.density)){
if(is.null(eta)){
eta <- OS(pp)
} else {
eta <- checkit(eta,"'eta'")
}
d.eta <- density(pp,eta,edge=edg,positive=TRUE,dimyx=resolution,spill=1)
if(edg){
d.eta$edg[d.eta$edg>1] <- 1
d.etadens <- d.eta$raw/d.eta$edg
d.etaint <- spatstat.univar::integral(d.etadens)
d.etadens <- as.matrix(d.etadens)[inn]/d.etaint
epsilon.eta <- safelookup(d.eta$edg,pp,warn=FALSE)
} else {
d.etadens <- as.matrix(d.eta$raw/spatstat.univar::integral(d.eta$raw))[inn]
epsilon.eta <- rep(1,n)
}
} else {
if(!inherits(ref.density,"bivden")) stop("'ref.density' must be of class \"bivden\"; see ?bivden")
eta <- ref.density$h0
if(!compatible(as.im(WM),ref.density$z)) stop("'ref.density' must be evaluated on identical spatial domain as 'Window(pp)' given 'resolution'")
if(!all(ref.density$h==eta)) stop("'ref.density' must be a fixed-bandwidth density estimate when type = \"fixed\"")
if(edg&&is.null(ref.density$q)) stop("'ref.density' edge-correction must exist if edge = \"uniform\"")
if(is.null(ref.density$q)){
epsilon.eta <- rep(1,n)
} else if(is.vector(ref.density$q)){
epsilon.eta <- ref.density$q
} else {
epsilon.eta <- safelookup(ref.density$q,pp,warn=FALSE)
}
d.etadens <- ref.density$z/spatstat.univar::integral(ref.density$z)
d.etadens <- as.matrix(d.etadens)[inn]
}
if(edg){
# window dressing
use_fftw <- fftw_available()
ifft_scale <- WM$xstep*WM$ystep/(4*resolution^2)
Mpad <- matrix(0,2*resolution,2*resolution)
Mpad[1:resolution,1:resolution] <- inside
fM <- fft2d(Mpad,fftw=use_fftw)
} else {
ifft_scale <- use_fftw <- fM <- NA
}
# fM <- fft2d(Mpad,fftw=use_fftw)
# fK.eta <- kernel2d_fft(eta,WM$xstep,WM$ystep,resolution)
# fK.con <- fft2d(fM*fK.eta,inverse=TRUE,use_fftw)[1:resolution,1:resolution]
# edg.eta <- Mod(fK.con)*ifft_scale
# edg.eta[edg.eta>1] <- 1
# edg.eta <- im(matrix(edge.eta,resolution,resolution),xcol=WM$xcol,yrow=WM$yrow)
# epsilon.eta <- safelookup(edg.eta,pp,warn=FALSE)
# remove expensive constant (just when rmdiag==TRUE) from 'boot.opt.spatial'; supply as argument
if(!rmdiag){
boot3 <- d.etadens^2
} else {
if(n<10000){ ### need more sophisticated solution here
boot3 <- n^(-2)*sum(outer(1:n,1:n,function(i,j) epsilon.eta[i]^(-1)*epsilon.eta[j]^(-1)*kernel2d(pp$x[i]-pp$x[j],pp$y[i]-pp$y[j],sqrt(2*eta^2)))[-seq(1,n^2,n+1)])
} else {
nseq <- 1:n
boot3 <- 0
if(verbose) pb <- txtProgressBar(0,n,char='.')
for(i in nseq){
boot3 <- boot3 + sum(epsilon.eta[i]^(-1)*epsilon.eta[nseq[-i]]^(-1)*kernel2d(pp$x[i]-pp$x[nseq[-i]],pp$y[i]-pp$y[nseq[-i]],sqrt(2*eta^2)))
if(verbose) setTxtProgressBar(pb,i)
}
if(verbose) close(pb)
boot3 <- n^(-2)*boot3
}
}
if(verbose) cat("Done.\nSearching for optimal h in ",prange(hlim),"...\n",sep="")
result <- optimise(boot.opt.spatial.fix,interval=hlim,rmdiag=rmdiag,edg=edg,WM=WM,
resolution=resolution,fM=fM,ifft_scale=ifft_scale,
inn=inn,GN=GN,evalyx.redu=evalyx.redu,pp=pp,
epsilon.eta=epsilon.eta,eta=eta,nn=n,boot3=boot3,
use_fftw=use_fftw,parallelise=parallelise,verb=verbose)$minimum
if(verbose) cat("Done.\n")
} else if(typ=="adaptive"){
if(verbose) cat("Initialising...")
if(is.null(ref.density)){
if(is.null(eta)){
eta <- OS(pp)
} else {
eta <- checkit(eta,"'eta'")
}
if(is.null(hp)){
hp <- eta
} else {
hp <- checkit(hp,"'hp'")
}
d.eta <- density(pp,eta,edge=(edg=="uniform"),positive=TRUE,dimyx=resolution)
} else {
if(!inherits(ref.density,"bivden")) stop("'ref.density' must be of class \"bivden\"; see ?bivden")
if(!compatible(as.im(WM),ref.density$z)) stop("'ref.density' must be evaluated on identical spatial domain as 'Window(pp)' given 'resolution'")
if(is.null(hp)){
hp <- ifelse(is.null(ref.density$hp),ref.density$h0,ref.density$hp)
} else {
hp <- checkit(hp,"'hp'")
}
d.eta <- ref.density$z
}
d.eta <- d.eta/spatstat.univar::integral(d.eta)
if(is.null(sim.adapt)) sim.adapt <- list()
if(is.null(sim.adapt$N)) sim.adapt$N <- 50
if(is.null(sim.adapt$B)) sim.adapt$B <- 100
if(is.null(sim.adapt$dimz)) sim.adapt$dimz <- 64
if(is.null(sim.adapt$objective)) sim.adapt$objective <- FALSE
hhash <- mean(hlim)
h0fac <- hlim/hhash
if(verbose) cat("Done.\nSearching for optimal h0 in ",prange(hlim),":\n",sep="")
resultfull <- boot.opt.spatial.adapt(pp,h0ref=hhash,h0fac=h0fac,hp=hp,
edg=edg,refden=d.eta,N=sim.adapt$N,
B=sim.adapt$B,res=resolution,dimz=sim.adapt$dimz,
verbose=verbose,parallelise=parallelise,...)
result <- resultfull$h
if(sim.adapt$objective) result <- resultfull$mat
} else {
stop("invalid 'type'")
}
return(result)
}
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