tweaks

spatstat · Jan 15, 2023 · a8c017f · a8c017f
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: spatstat.explore
-Version: 3.0-5.001
-Date: 2022-11-24
+Version: 3.0-5.002
+Date: 2023-01-15
 Title: Exploratory Data Analysis for the 'spatstat' Family
 Authors@R: c(person("Adrian", "Baddeley", 
                     role = c("aut", "cre", "cph"),
@@ -55,7 +55,7 @@ Authors@R: c(person("Adrian", "Baddeley",
 	     person("Hangsheng", "Wang",
 	            role = "ctb"))
 Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
-Depends: R (>= 3.5.0), spatstat.data (>= 3.0), spatstat.geom (>= 3.0), spatstat.random (>= 3.0), stats, graphics, grDevices, utils, methods, nlme
+Depends: R (>= 3.5.0), spatstat.data (>= 3.0), spatstat.geom (>= 3.0-4.009), spatstat.random (>= 3.0), stats, graphics, grDevices, utils, methods, nlme
 Imports: spatstat.utils (>= 3.0), spatstat.sparse (>= 3.0), goftest (>= 1.2-2), Matrix, abind
 Suggests: sm, maptools (>= 0.9-9), gsl, locfit, spatial, fftwtools (>= 0.9-8), spatstat.linnet (>= 3.0), spatstat.model (>= 3.0), spatstat (>= 3.0)
 Additional_repositories: https://spatstat.r-universe.dev

diff --git a/NEWS b/NEWS
@@ -1,5 +1,5 @@
 
-        CHANGES IN spatstat.explore VERSION 3.0-5.001
+        CHANGES IN spatstat.explore VERSION 3.0-5.002
 
 OVERVIEW
 

diff --git a/R/auc.R b/R/auc.R
@@ -3,7 +3,7 @@
 ##
 ##  Calculate ROC curve or area under it
 ##
-## $Revision: 1.15 $ $Date: 2022/05/22 04:08:02 $
+## $Revision: 1.16 $ $Date: 2023/01/15 02:21:19 $
 
 roc <- function(X, ...) { UseMethod("roc") }
 
@@ -41,11 +41,9 @@ rocModel <- function(lambda, nullmodel, ..., high) {
   p <- seq(0,1,length=1024)
   fobs <- ec(p)
   FZ <- d$values$FZ
+  FZinverse <- quantilefun.ewcdf(FZ)
   lambdavalues <- if(is.im(lambda)) lambda[] else unlist(lapply(lambda, "["))
   F1Z <- ewcdf(lambdavalues, lambdavalues/sum(lambdavalues))    
-  pZ <- get("y", environment(FZ))
-  qZ <- get("x", environment(FZ))
-  FZinverse <- approxfun(pZ, qZ, rule=2)
   ftheo <- 1 - F1Z(FZinverse(1-p))
   df <- data.frame(p=p, fobs=fobs, ftheo=ftheo, fnull=p)
   result <- fv(df,

diff --git a/R/cdftest.R b/R/cdftest.R
@@ -1,7 +1,7 @@
 #
 #  cdftest.R
 #
-#  $Revision: 2.28 $  $Date: 2022/11/03 11:08:33 $
+#  $Revision: 2.33 $  $Date: 2023/01/15 03:23:28 $
 #
 #
 
@@ -199,9 +199,9 @@ spatialCDFframe <- function(model, covariate, ...,
     yyy <- c(yyy, 1)
   }
   if(length(xxx) > 1) {
-    #' non-degenerate cdf
     ## replace by piecewise linear approximation
     FZ <- approxfun(xxx, yyy, rule=2)
+    class(FZ) <- c("interpolatedCDF", class(FZ)) 
   }
   # now apply cdf
   U <- FZ(ZX)
@@ -214,28 +214,13 @@ spatialCDFframe <- function(model, covariate, ...,
     U <- pmax(0, pmin(1, U))
   }
 
-  if(make.quantile.function) {
-    ## right-continuous inverse of FZ
-    pZ <- get("y", environment(FZ))
-    qZ <- get("x", environment(FZ))
-    ok <- !duplicated(pZ)
-    qZ <- qZ[ok]
-    pZ <- pZ[ok]
-    if(length(qZ) > 1) {
-      FZinverse <- approxfun(pZ, qZ, rule=2)
-    } else {
-      ## degenerate
-      FZinverse <- approxfun(c(0,1), rep(qZ, 2), rule=2)
-    }
-  } else FZinverse <- NULL ## to placate package checker
-
   # pack up
   stuff$values$FZ  <- FZ
   stuff$values$FZX <- FZX
   stuff$values$U   <- U
   stuff$values$EN <- sumwts  ## integral of intensity = expected number of pts
   if(make.quantile.function)
-    stuff$values$FZinverse  <- FZinverse
+    stuff$values$FZinverse  <- quantilefun(FZ)    ## right-continuous inverse of FZ
   class(stuff) <- "spatialCDFframe"
   return(stuff)
 }
@@ -288,7 +273,9 @@ plot.cdftest <- function(x, ..., style=c("cdf", "PP", "QQ"),
                     lty=c(lty2char(lty),lty2char(lty0)))
          },
          PP={
-           # plot FZX o (FZ)^{-1}
+           ## plot FZX o (FZ)^{-1}
+           ## y-axis: sample probabilities i/n for i=1, .., n
+           ## x-axis: corresponding reference probabilities P(Z < z_[i])
            pX <- get("y", environment(FZX))
            qX <- get("x", environment(FZX))
            p0 <- FZ(qX)
@@ -305,16 +292,17 @@ plot.cdftest <- function(x, ..., style=c("cdf", "PP", "QQ"),
            abline(0,1, lwd=lwd0, col=col0, lty=lty0)           
          },
          QQ={
-           # plot (FZX)^{-1} o FZ
-           pZ <- get("y", environment(FZ))
-           qZ <- get("x", environment(FZ))
-           FZinverse <- approxfun(pZ, qZ, rule=2)
-           pX <- get("y", environment(FZX))
+           ## plot (FZX)^{-1} o FZ
+           ## x-axis: order statistics z_[i] of values at data points
+           ## y-axis: quantiles of Z on window with probabilities i/n
            qX <- get("x", environment(FZX))
+           pX <- get("y", environment(FZX))
+           FZinverse <- quantilefun(FZ)
            qZX <- FZinverse(pX)
-           Zrange <- range(qZ, qX, qZX)
            xlab <- paste("Theoretical quantile of", covname)
            ylab <- paste("Observed quantile of", covname)
+           qZ <- get("x", environment(FZ))
+           Zrange <- range(qZ, qX, qZX)
            do.call(plot.default,
                    resolve.defaults(
                                     list(x=qZX, y=qX),

diff --git a/inst/doc/packagesizes.txt b/inst/doc/packagesizes.txt
@@ -1,4 +1,4 @@
 date version nhelpfiles nobjects ndatasets Rlines srclines
 "2022-05-25" "3.0-0" 224 500 0 30319 6183
 "2022-11-08" "3.0-4" 226 507 0 30638 6295
-"2022-11-24" "3.0-5.001" 226 507 0 30658 6295
+"2023-01-15" "3.0-5.002" 226 507 0 30644 6295
diff --git a/man/macros/defns.Rd b/man/macros/defns.Rd
@@ -14,6 +14,7 @@
 \newcommand{\ottmar}{Ottmar Cronie \email{ottmar@chalmers.se}}
 \newcommand{\stephenEglen}{Stephen Eglen \email{S.J.Eglen@damtp.cam.ac.uk}}
 \newcommand{\mehdi}{Mehdi Moradi \email{m2.moradi@yahoo.com}}
+\newcommand{\yamei}{Ya-Mei Chang \email{yamei628@gmail.com}}
 % Names with accents
 \newcommand{\Bogsted}{\ifelse{latex}{\out{B\o gsted}}{Bogsted}}
 \newcommand{\Cramer}{\ifelse{latex}{\out{Cram\'er}}{Cramer}}
@@ -37,5 +38,6 @@
 \newcommand{\rmhInteractionsList}{\code{\link[MPKG]{AreaInter}}, \code{\link[MPKG]{BadGey}}, \code{\link[MPKG]{DiggleGatesStibbard}}, \code{\link[MPKG]{DiggleGratton}}, \code{\link[MPKG]{Fiksel}}, \code{\link[MPKG]{Geyer}}, \code{\link[MPKG]{Hardcore}}, \code{\link[MPKG]{Hybrid}}, \code{\link[MPKG]{LennardJones}}, \code{\link[MPKG]{MultiStrauss}}, \code{\link[MPKG]{MultiStraussHard}}, \code{\link[MPKG]{PairPiece}}, \code{\link[MPKG]{Penttinen}}, \code{\link[MPKG]{Poisson}}, \code{\link[MPKG]{Softcore}}, \code{\link[MPKG]{Strauss}}, \code{\link[MPKG]{StraussHard}} and \code{\link[MPKG]{Triplets}}}
 %% Frequent references
 \newcommand{\baddrubaturnbook}{Baddeley, A., Rubak, E. and Turner, R. (2015) \emph{Spatial Point Patterns: Methodology and Applications with R}. Chapman and Hall/CRC Press. }
+\newcommand{\baddchangclustersim}{Baddeley, A. and Chang, Y.-M. (2023) Robust algorithms for simulating cluster point processes. \emph{Journal of Statistical Computation and Simulation}. To appear.}
 
 
diff --git a/man/plot.fv.Rd b/man/plot.fv.Rd
@@ -130,6 +130,12 @@
 \details{
   This is the \code{plot} method for the class \code{"fv"}.
 
+  An object of class \code{"fv"} is a convenient way of storing several different
+  statistical estimates of a summary function; see \code{\link{fv.object}}.
+  The default behaviour, executed by \code{plot(x)}, displays these
+  different estimates as curves with different colours and line styles,
+  and plots a legend explaining them.
+
   The use of the argument \code{fmla} is like \code{plot.formula}, but offers
   some extra functionality.
 
@@ -232,16 +238,15 @@
    plot(K, xlim=xlim, ylim=ylim)
    plot(Kr, xlim=xlim, ylim=ylim)
    par(opa)
+   # For a shortcut, try plot(anylist(K, Kr), equal.scales=TRUE)
 }
 \seealso{
   \code{\link{fv.object}},
   \code{\link[spatstat.explore]{Kest}}
 }
-\author{\adrian
-
-
+\author{
+  \adrian
   and \rolf
-
 }
 \keyword{spatial}
 \keyword{hplot}