From 32dc551004340dcb71c4bf3a42a81517573947f5 Mon Sep 17 00:00:00 2001
From: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Date: Fri, 6 Sep 2024 15:50:18 +0800
Subject: [PATCH] Change default in bw.ppl

---
 DESCRIPTION                |  4 ++--
 NEWS                       | 11 +++++++++++
 R/bw.ppl.R                 | 11 ++++++++---
 inst/doc/packagesizes.txt  |  2 +-
 inst/info/packagesizes.txt |  2 +-
 man/bw.ppl.Rd              |  8 ++++----
 6 files changed, 27 insertions(+), 11 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 05bdcf8..f1edcc2 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: spatstat.explore
-Version: 3.3-2
-Date: 2024-08-20
+Version: 3.3-2.001
+Date: 2024-09-06
 Title: Exploratory Data Analysis for the 'spatstat' Family
 Authors@R: c(person("Adrian", "Baddeley", 
                     role = c("aut", "cre", "cph"),
diff --git a/NEWS b/NEWS
index 01bf379..a59f1bb 100644
--- a/NEWS
+++ b/NEWS
@@ -1,4 +1,15 @@
 
+        CHANGES IN spatstat.explore VERSION 3.3-2.001
+
+OVERVIEW
+
+    o Tweaks to bandwidth selection.
+
+SIGNIFICANT USER-VISIBLE CHANGES
+
+    o bw.ppl
+    Argument 'shortcut' now defaults to TRUE.
+
         CHANGES IN spatstat.explore VERSION 3.3-2
 
 OVERVIEW
diff --git a/R/bw.ppl.R b/R/bw.ppl.R
index 8a2863e..b4d4ffa 100644
--- a/R/bw.ppl.R
+++ b/R/bw.ppl.R
@@ -3,11 +3,11 @@
 #'
 #'   Likelihood cross-validation for kernel smoother of point pattern
 #'
-#'   $Revision: 1.15 $ $Date: 2024/06/08 23:59:34 $
+#'   $Revision: 1.17 $ $Date: 2024/09/06 07:09:13 $
 #'
 
 bw.ppl <- function(X, ..., srange=NULL, ns=16, sigma=NULL, varcov1=NULL, 
-                   weights=NULL, shortcut=FALSE, warn=TRUE) {
+                   weights=NULL, shortcut=TRUE, warn=TRUE) {
   stopifnot(is.ppp(X))
   if(!is.null(varcov1))
     check.nmatrix(varcov1, 2, things="spatial dimensions", mname="varcov1")
@@ -44,6 +44,7 @@ bw.ppl <- function(X, ..., srange=NULL, ns=16, sigma=NULL, varcov1=NULL,
       cv[i] <- sum(log(lamx))
     }
   } else {
+    IntLam <- numeric(ns)
     for(i in 1:ns) {
       if(is.null(varcov1)) {
         si <- sigma[i]
@@ -57,7 +58,9 @@ bw.ppl <- function(X, ..., srange=NULL, ns=16, sigma=NULL, varcov1=NULL,
                       weights=weights, ...)
       lam <- density(X, sigma=si, varcov=vi,
                      weights=weights, ...)
-      cv[i] <- sum(log(lamx)) - integral.im(lam)
+      mu <- integral.im(lam)
+      cv[i] <- sum(log(lamx)) - mu
+      IntLam[i] <- mu
     }
   }
   result <- bw.optim(cv, sigma, iopt=which.max(cv),
@@ -68,6 +71,8 @@ bw.ppl <- function(X, ..., srange=NULL, ns=16, sigma=NULL, varcov1=NULL,
                      hargnames="srange",
                      unitname=if(is.null(varcov1)) unitname(X) else NULL,
                      template=varcov1, exponent=2)
+  if(!shortcut) 
+    attr(result, "info") <- list(IntegralLambda=IntLam)
   return(result)
 }
 
diff --git a/inst/doc/packagesizes.txt b/inst/doc/packagesizes.txt
index b9f7f30..fdf0e3c 100755
--- a/inst/doc/packagesizes.txt
+++ b/inst/doc/packagesizes.txt
@@ -10,5 +10,5 @@ date version nhelpfiles nobjects ndatasets Rlines srclines
 "2024-01-31" "3.2-6" 241 535 0 32147 6365
 "2024-03-21" "3.2-7" 241 535 0 32149 6365
 "2024-07-09" "3.3-1" 230 517 0 31571 6365
-
 "2024-08-20" "3.3-2" 230 517 0 31571 6364
+"2024-09-06" "3.3-2.001" 230 517 0 31576 6364
diff --git a/inst/info/packagesizes.txt b/inst/info/packagesizes.txt
index b9f7f30..fdf0e3c 100755
--- a/inst/info/packagesizes.txt
+++ b/inst/info/packagesizes.txt
@@ -10,5 +10,5 @@ date version nhelpfiles nobjects ndatasets Rlines srclines
 "2024-01-31" "3.2-6" 241 535 0 32147 6365
 "2024-03-21" "3.2-7" 241 535 0 32149 6365
 "2024-07-09" "3.3-1" 230 517 0 31571 6365
-
 "2024-08-20" "3.3-2" 230 517 0 31571 6364
+"2024-09-06" "3.3-2.001" 230 517 0 31576 6364
diff --git a/man/bw.ppl.Rd b/man/bw.ppl.Rd
index 67f665f..c752258 100644
--- a/man/bw.ppl.Rd
+++ b/man/bw.ppl.Rd
@@ -9,7 +9,7 @@
 }
 \usage{
    bw.ppl(X, \dots, srange=NULL, ns=16, sigma=NULL, varcov1=NULL,
-          weights=NULL, shortcut=FALSE, warn=TRUE)
+          weights=NULL, shortcut=TRUE, warn=TRUE)
 }
 \arguments{
   \item{X}{
@@ -81,9 +81,9 @@
   which can be plotted to show the (rescaled) mean-square error
   as a function of \code{sigma}.
 
-  If \code{shortcut=TRUE}, the computation is accelerated by
+  If \code{shortcut=TRUE} (the default), the computation is accelerated by
   omitting the integral term in the equation above. This is valid
-  because the integral is approximately constant.
+  because the integral is approximately constant. 
 }
 \section{Anisotropic Smoothing}{
   Anisotropic kernel smoothing is available in \code{\link{density.ppp}} using
@@ -118,7 +118,7 @@
   }
   \testonly{
     b1 <- bw.ppl(redwood, srange=c(0.03, 0.07), ns=2)
-    b2 <- bw.ppl(redwood, srange=c(0.03, 0.07), ns=2, shortcut=TRUE)
+    b2 <- bw.ppl(redwood, srange=c(0.03, 0.07), ns=2, shortcut=FALSE)
   }
 }
 \references{