Nothing
STIKhat <- function(xyt, s.region, t.region, dist, times, lambda, correction = "isotropic", infectious = FALSE){
verifyclass(xyt,"stpp")
if (infectious == TRUE && any(correction!= "isotropic")) stop("For infectious processes, the STIK-function is currently only implemented with the isotropic edge correction method.")
correc=c("none","isotropic","border","modified.border","translate")
id <- match(correction, correc, nomatch = NA)
if (any(nbg <- is.na(id))) {
mess <- paste("unrecognised correction method:", paste(dQuote(correction[nbg]), collapse = ", "))
stop(mess, call. = FALSE)
}
id = unique(id)
correc2 = rep(0,5)
correc2[id] = 1
dup <- any(duplicated(data.frame(xyt[,1], xyt[,2], xyt[,3])))
if (dup == TRUE){
messnbd <- paste("Space-time data contains duplicated points")
warning(messnbd,call. = FALSE)
}
if (missing(s.region)) s.region <- sbox(xyt[,1:2], xfrac=0.01, yfrac=0.01)
if (missing(t.region)){
xr = range(xyt[,3], na.rm = TRUE)
xw = diff(xr)
t.region <- c(xr[1]- 0.01 * xw, xr[2] + 0.01 * xw)
}
bsupt <- max(t.region)
binft <- min(t.region)
xp <- s.region[,1]
yp <- s.region[,2]
nedges <- length(xp)
yp <- yp - min(yp)
nxt <- c(2:nedges, 1)
dx <- xp[nxt] - xp
ym <- (yp + yp[nxt])/2
Areaxy <- -sum(dx * ym)
if (Areaxy > 0){
bdry <- owin(poly = list(x = s.region[,1], y = s.region[,2]))
}else{
bdry <- owin(poly = list(x = s.region[,1][length(s.region[,1]):1], y = s.region[,2][length(s.region[,1]):1]))
}
if (missing(dist)){
rect = as.rectangle(bdry)
maxd = min(diff(rect$xrange), diff(rect$yrange))/4
dist = make.even.breaks(maxd, npos=15)$r
}
if (missing(times)) {
maxt = (bsupt-binft)/4
times = make.even.breaks(maxt, npos=15)$r
}
dist <- sort(dist)
if(dist[1] == 0) dist = dist[-1]
times <- sort(times)
if(times[1] == 0) times = times[-1]
ok <- inside.owin(xyt[,1],xyt[,2],w=bdry)
xyt.ins <- data.frame(x=xyt[,1][ok],y=xyt[,2][ok],t=xyt[,3][ok])
xyt.in <- .intim(xyt.ins,t.region)
pts <- xyt.in[,1:2]
xytimes <- xyt.in[,3]
ptsx <- pts[, 1]
ptsy <- pts[, 2]
ptst <- xytimes
npt <- length(ptsx)
ndist <- length(dist)
ntimes <- length(times)
area <- area(bdry) * (bsupt - binft)
np <- length(s.region[, 1])
polyx <- c(s.region[, 1], s.region[1, 1])
polyy <- c(s.region[, 2], s.region[1, 2])
hkhat <- array(0, dim = c(ndist, ntimes, 5))
if(missing(lambda)){
misl <- 1
lambda <- rep(npt/area, npt)
}
else misl <- 0
if (length(lambda) == 1) lambda <- rep(lambda, npt)
if (infectious==TRUE){infd <- 1} else infd <- 0
storage.mode(hkhat) <- "double"
wbi = array(0, dim = c(npt, ndist, ntimes))
wbimod = array(0, dim = c(npt, ndist, ntimes))
wt = array(0, dim = c(npt, npt))
options(warn = -1)
pppxy = ppp(x = ptsx, y = ptsy, window = bdry)
# correction=="border" and "modified border"
if(any(correction=="border")|any(correction=="modified.border")){
bi=bdist.points(pppxy)
bj=.bdist.times(xytimes,t.region)
for(i in 1:ndist){
for(j in 1:ntimes){
wbi[,i,j] = (bi>dist[i])*(bj>times[j])/sum((bi>dist[i])*(bj>times[j])/lambda)
wbimod[,i,j] = (bi>dist[i])*(bj>times[j])/(eroded.areas(bdry,dist[i])*.eroded.areat(t.region,times[j]))
} }
wbi[is.na(wbi)] <- 0
wbimod[is.na(wbimod)] <- 0
}
# correction=="translate"
if(any(correction=="translate"))
{
wtt = .overlap.tint(xytimes,t.region)
wts = edge.Trans(pppxy)
wt = wtt*wts
wt=1/wt
}
options(warn = 0)
klist <- .Fortran("stikfunction", as.double(ptsx),
as.double(ptsy), as.double(ptst),
as.integer(npt), as.double(polyx),
as.double(polyy), as.integer(np),
as.double(dist), as.integer(ndist),
as.double(times), as.integer(ntimes),
as.double(bsupt), as.double(binft),
as.double(lambda), as.integer(infd),
(hkhat), as.double(wbi), as.double(wbimod),
as.double(wt), as.integer(correc2))
hkhat <- klist[[16]]
hkhat[,,c(1,2,5)]=hkhat[,,c(1,2,5)]/area
Khpp <- matrix(0,ncol=length(times),nrow=length(dist))
for(i in 1:length(dist)) Khpp[i,] <- pi*(dist[i]^2)*times
if (infectious==TRUE){Ktheo <- Khpp}
else Ktheo <- 2*Khpp
if(length(id)==1) Khat=as.array(hkhat[,,id])
else{
Khat=list()
for(i in 1:length(id)) Khat[[i]]=hkhat[,,id[i]]
names(Khat)=correc[id]
}
correction=correc[id]
invisible(return(list(Khat = Khat, Ktheo = Ktheo, dist = dist, times = times, correction = correction, infectious = infectious)))
}
.overlap.tint <- function(times,t.region){
if (missing(t.region)) t.region=range(times)
ntimes=length(times)
a = diff(range(t.region))
wt=matrix(a,ncol=ntimes,nrow=ntimes)
for(i in 1:ntimes){
for(j in 1:ntimes){
if (i!=j){
b = a-abs(times[i]-times[j])
wt[i,j]=a/b
}}}
invisible(return(wt))
}
.bdist.times <- function(times, t.region){
if (missing(t.region)) t.region=range(times)
ntimes=length(times)
a=min(t.region)
b=max(t.region)
bj=NULL
for(j in 1:ntimes){
bj=c(bj,min(c(abs(times[j]-a),abs(times[j]-b))))
}
invisible(return(bj))
}
.eroded.areat <- function(t.region,dist){
a = diff(range(t.region))
b = a-dist
invisible(return(b))
}
.intim <- function(xyt,t.region){
int <- NULL
for(i in 1:length(xyt[,1])){
if (xyt[i,3] > t.region[1] & xyt[i,3] < t.region[2]){
int <- rbind(int,xyt[i,])}
}
int <- as.3dpoints(int)
invisible(return(int))
}
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