R/Fest.R

In spatstat/spatstat.core: Core Functionality of the 'spatstat' Family

#
#	Fest.R
#
#	Computes estimates of the empty space function
#
#	$Revision: 4.47 $	$Date: 2019/11/01 01:32:28 $
#

Fhazard <- function(X, ...) {
  Z <- Fest(X, ...)
  if(!any(names(Z) == "km"))
    stop("Kaplan-Meier estimator 'km' is required for hazard rate")
  conserve <- attr(Z, "conserve")
  ## strip off Poisson F
  Z <- Z[, (colnames(Z) != "theo")]
  ## relabel the fv object
  Z <- rebadge.fv(Z,
                  new.ylab=quote(h(r)),
                  new.fname="h",
                  tags=c("hazard", "theohaz"),
                  new.tags=c("hazard", "theo"),
                  new.labl=c("hat(%s)[km](r)", "%s[pois](r)"),
                  new.desc=c(
                      "Kaplan-Meier estimate of %s",
                      "theoretical Poisson %s"),
                  new.dotnames=c("hazard", "theo"),
                  new.preferred="hazard")
  ## strip off unwanted bits
  Z <- Z[, c("r", "hazard", "theo")]
  attr(Z, "conserve") <- conserve
  return(Z)
}

Fest <- function(X, ..., eps = NULL, r=NULL, breaks=NULL,
                 correction=c("rs", "km", "cs"),
                 domain=NULL) {
  verifyclass(X, "ppp")
  if(!is.null(domain))
    stopifnot(is.subset.owin(domain, Window(X)))

  rorbgiven <- !is.null(r) || !is.null(breaks)
  checkspacing <- !isFALSE(list(...)$checkspacing)
  testme       <- isTRUE(list(...)$testme)
  
  ## Intensity estimate
  W <- Window(X)
  npts <- npoints(X)
  lambda <- npts/area(W)
  
  ## Discretise window
  dwin <- as.mask(W, eps=eps)
  dX <- ppp(X$x, X$y, window=dwin, check=FALSE)
  
  ## Histogram breakpoints
  rmaxdefault <- rmax.rule("F", dwin, lambda)
  breaks <- handle.r.b.args(r, breaks, dwin, eps, rmaxdefault=rmaxdefault)
  rvals <- breaks$r
  rmax  <- breaks$max
  if(testme || (rorbgiven && checkspacing))
      check.finespacing(rvals,
                        if(is.null(eps)) NULL else eps/4,
                        dwin,
                        rmaxdefault=rmaxdefault,
                        action="fatal",
                        rname="r", 
                        context="in Fest(X, r)")
                                
  ## choose correction(s)
  if(is.null(correction)) {
    correction <- c("rs", "km", "cs")
  } else correction <- pickoption("correction", correction,
                           c(none="none",
                             border="rs",
                             rs="rs",
                             KM="km",
                             km="km",
                             Kaplan="km",
                             cs="cs",
                             ChiuStoyan="cs",
                             Hanisch="cs",
                             han="cs",
                             best="km"),
                           multi=TRUE)
  
  ## initialise fv object
  df <- data.frame(r=rvals, theo=1-exp(-lambda * pi * rvals^2))
  Z <- fv(df, "r", substitute(F(r), NULL), "theo", . ~ r,
          c(0,rmax),
          c("r", "%s[pois](r)"), 
          c("distance argument r", "theoretical Poisson %s"),
          fname="F")
  nr <- length(rvals)
  zeroes <- numeric(nr)

  ##  compute distances and censoring distances
  if(X$window$type == "rectangle") {
    ## original data were in a rectangle
    ## output of exactdt() is sufficient
    e <- exactdt(dX)
    dist <- e$d
    bdry <- e$b
    if(!is.null(domain)) {
      ok <- inside.owin(raster.xy(e$w), , domain)
      dist <- dist[ok]
      bdry <- bdry[ok]
    }
  } else {
    ## window is irregular..
    # Distance transform & boundary distance for all pixels
    e <- exactdt(dX)
    b <- bdist.pixels(dX$window, style="matrix")
    ## select only those pixels inside mask
    mm <- dwin$m
    if(!is.null(domain)) {
      ok <- inside.owin(raster.xy(e$w), , domain)
      mm <- as.vector(mm) & ok
    }
    dist <- e$d[mm]
    bdry <- b[mm]
  }
  
  ## censoring indicators
  d <- (dist <= bdry)
  ##  observed distances
  o <- pmin.int(dist, bdry)

  ## start calculating estimates of F
  
  if("none" %in% correction) {
    ##  UNCORRECTED e.d.f. of empty space distances
    if(npts == 0)
      edf <- zeroes
    else {
      hh <- hist(dist[dist <= rmax],breaks=breaks$val,plot=FALSE)$counts
      edf <- cumsum(hh)/length(dist)
    }
    Z <- bind.fv(Z, data.frame(raw=edf), "hat(%s)[raw](r)",
                 "uncorrected estimate of %s", "raw")
  }
  
  if("cs" %in% correction) {
    ## Chiu-Stoyan correction
    if(npts == 0)
      cs <- zeroes
    else {
      ##  uncensored distances
      x <- dist[d]
      ##  weights
      a <- eroded.areas(W, rvals)
      ## calculate Hanisch estimator
      h <- hist(x[x <= rmax], breaks=breaks$val, plot=FALSE)$counts
      H <- cumsum(h/a)
      cs <- H/max(H[is.finite(H)])
    }
    ## add to fv object
    Z <- bind.fv(Z, data.frame(cs=cs),
                 "hat(%s)[cs](r)", 
                 "Chiu-Stoyan estimate of %s",
                 "cs")
  }

  if(any(correction %in% c("rs", "km"))) {
    ## calculate Kaplan-Meier and/or border corrected (Reduced Sample) estimators
    want.rs <- "rs" %in% correction
    want.km <- "km" %in% correction
    selection <- c(want.rs, want.km, want.km, want.km)
    tags <- c("rs", "km", "hazard", "theohaz")[selection]
    labels <- c("hat(%s)[bord](r)", "hat(%s)[km](r)",
                "hat(h)[km](r)", "h[pois](r)")[selection]
    descr <- c("border corrected estimate of %s",
               "Kaplan-Meier estimate of %s",
               "Kaplan-Meier estimate of hazard function h(r)",
               "theoretical Poisson hazard h(r)")[selection]
    if(npts == 0) {
      result <- as.data.frame(matrix(0, nr, length(tags)))
      names(result) <- tags
    } else {
      result <- km.rs.opt(o, bdry, d, breaks, KM=want.km, RS=want.rs)
      result$theohaz <- 2 * pi * lambda * rvals
      result <- as.data.frame(result[tags])
    }
    ## add to fv object
    Z <- bind.fv(Z, result,
                 labels, descr, if(want.km) "km" else "rs")
  }
  
  ## wrap up
  unitname(Z) <- unitname(X)
  
  ## remove 'hazard' from the dotnames
  nama <- names(Z)
  fvnames(Z, ".") <- rev(setdiff(nama, c("r", "hazard", "theohaz")))
  
  ## determine recommended plot range
  attr(Z, "alim") <- with(Z, range(.x[is.finite(.y) & .y <= 0.9]))

  ## arguments to be used in envelope, etc
  attr(Z, "conserve") <- list(checkspacing=FALSE)
  
  return(Z)
}