Tidied up, submitted to CRAN as 2.3-2

spatstat · Feb 12, 2022 · 0a60b8e · 0a60b8e
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: spatstat.geom
-Version: 2.3-1.001
-Date: 2022-02-11
+Version: 2.3-2
+Date: 2022-02-12
 Title: Geometrical Functionality of the 'spatstat' Family 
 Authors@R: c(person("Adrian", "Baddeley", 
                     role = c("aut", "cre"),
@@ -22,7 +22,6 @@ Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
 Depends: R (>= 3.5.0), spatstat.data (>= 2.0-0), stats, graphics, grDevices, utils, methods
 Imports: spatstat.utils (>= 2.2-0), deldir (>= 1.0-2), polyclip (>= 1.10-0)
 Suggests: spatstat.core, spatstat.random, spatstat.linnet, maptools (>= 0.9-9), spatial, fftwtools (>= 0.9-8), spatstat (>= 2.0-0)
-Additional_repositories: https://spatstat.r-universe.dev
 Description: Defines spatial data types and supports geometrical operations
 	     on them. Data types include point patterns, windows (domains),
 	     pixel images, line segment patterns, tessellations and hyperframes.

diff --git a/NEWS b/NEWS
@@ -1,10 +1,10 @@
-        CHANGES IN spatstat.geom VERSION 2.3-1.001
+        CHANGES IN spatstat.geom VERSION 2.3-2
 
 OVERVIEW
 
     o 'spatstat.geom' now suggests the package 'spatstat.random'.
 
-    o Updated help files.
+    o Updated help files to refer to 'spatstat.random'.
 
 
         CHANGES IN spatstat.geom VERSION 2.3-1

diff --git a/R/as.im.R b/R/as.im.R
@@ -3,7 +3,7 @@
 #
 #    conversion to class "im"
 #
-#    $Revision: 1.59 $   $Date: 2021/06/30 08:23:24 $
+#    $Revision: 1.60 $   $Date: 2022/02/12 06:09:33 $
 #
 #    as.im()
 #
@@ -361,9 +361,13 @@ wrangle2image <- function(values, template) {
   template <- as.im(template)
   tdim <- dim(template)
   nt <- prod(tdim)
-  vdim <- dim(values) # may be NULL
+  if(!is.null(vlev <- levels(values))) {
+    ## flatten and convert to integer
+    if(!is.factor(values)) values <- factor(values, levels=vlev)
+    values <- as.integer(values)
+  } 
   nv <- length(values)
-  vlev <- levels(values)
+  vdim <- dim(values) # may be NULL
   vnames <- NULL
   if(is.null(vdim)) {
     ## vector or factor of values 
@@ -393,17 +397,27 @@ wrangle2image <- function(values, template) {
   }
   ## values is now a matrix or array
   if(is.matrix(values)) {
-    result <- template
-    result[drop=FALSE] <- values
+    if(!is.null(vlev)) values <- factor(values, labels=vlev)
+    result <- im(values,
+                 xcol=template$xcol,
+                 yrow=template$yrow,
+                 xrange=template$xrange,
+                 yrange=template$yrange,
+                 unitname=unitname(template))
     result <- result[W, drop=FALSE]
   } else {
     m <- dim(values)[3L]
     result <- vector(mode="list", length=m)
     for(i in seq_len(m)) {
-      Z <- template
-      Z[drop=FALSE] <- values[,,i]
-      Z <- Z[W, drop=FALSE]
-      result[[i]] <- Z
+      vi <- values[,,i]
+      if(!is.null(vlev)) vi <- factor(vi, labels=vlev)
+      Z <- im(vi,
+              xcol=template$xcol,
+              yrow=template$yrow,
+              xrange=template$xrange,
+              yrange=template$yrange,
+              unitname=unitname(template))
+      result[[i]] <- Z[W, drop=FALSE]
     }
     names(result) <- vnames
     result <- as.solist(result)

diff --git a/R/distancemetrics.R b/R/distancemetrics.R
@@ -3,7 +3,7 @@
 #'
 #'   Metrics on the spatial domain
 #' 
-#'   $Revision: 1.11 $ $Date: 2021/09/05 11:22:57 $
+#'   $Revision: 1.12 $ $Date: 2022/02/12 06:11:18 $
 #'
 #'  An object of class 'metric' is essentially a named list of functions
 #'  where the names specify the tasks. 
@@ -66,7 +66,7 @@ warn.no.metric.support <- function(caller, ..., metric) {
 
 warn.unsupported.args <- function(unsup, ...) {
   given <- list(...)
-  if(any(hit <- names(unsup) %in% names(given))) {
+  if(any(names(unsup) %in% names(given))) {
     values <- resolve.defaults(given, unsup)[names(unsup)]
     changed <- !mapply(identical, x=unsup, y=values)
     if(any(changed)) {

diff --git a/R/nnutils.R b/R/nnutils.R
@@ -3,7 +3,7 @@
 #'
 #'  Utilities for extracting nndist/nncross from distance matrices
 #'
-#'  $Revision: 1.3 $  $Date: 2021/09/26 07:32:16 $
+#'  $Revision: 1.4 $  $Date: 2022/02/12 06:12:14 $
 
 
 PDtoNN <- function(d, what=c("dist", "which"), k=1L, ...) {
@@ -17,7 +17,7 @@ PDtoNN <- function(d, what=c("dist", "which"), k=1L, ...) {
   what   <- match.arg(what, several.ok=TRUE)
   want.dist  <- "dist" %in% what 
   want.which <- "which" %in% what
-  want.both  <- want.dist && want.which
+  ## want.both  <- want.dist && want.which
 
   if(!missing(k)) {
     # k can be a single integer or an integer vector
@@ -87,7 +87,7 @@ XDtoNN <- function(d, what=c("dist", "which"),
   what   <- match.arg(what, several.ok=TRUE)
   want.dist  <- "dist" %in% what 
   want.which <- "which" %in% what
-  want.both  <- want.dist && want.which
+  ## want.both  <- want.dist && want.which
 
   if(!missing(k)) {
     # k can be a single integer or an integer vector

diff --git a/inst/doc/packagesizes.txt b/inst/doc/packagesizes.txt
@@ -9,4 +9,4 @@ date version nhelpfiles nobjects ndatasets Rlines srclines
 "2021-06-15" "2.2-0" 434 1159 0 33744 15115
 "2021-10-09" "2.3-0" 440 1175 0 34553 15173
 "2021-12-10" "2.3-1" 440 1176 0 34643 15173
-"2022-02-11" "2.3-1.001" 440 1176 0 34643 15173
+"2022-02-12" "2.3-2" 440 1176 0 34657 15173
diff --git a/man/matchingdist.Rd b/man/matchingdist.Rd
@@ -62,7 +62,7 @@
 \author{
   Dominic Schuhmacher
   \email{dominic.schuhmacher@stat.unibe.ch}
-  \url{http://dominic.schuhmacher.name/}
+  URL \code{http://dominic.schuhmacher.name/}
 }
 \seealso{
   \code{\link{pppdist}}

diff --git a/man/pppdist.Rd b/man/pppdist.Rd
@@ -178,7 +178,7 @@
 \author{
   Dominic Schuhmacher
   \email{dominic.schuhmacher@mathematik.uni-goettingen.de} \cr
-  \url{http://dominic.schuhmacher.name/}
+  URL \code{http://dominic.schuhmacher.name/}
 }
 \seealso{
   \code{\link{pppmatching.object}}, \code{\link{matchingdist}},

diff --git a/man/pppmatching.Rd b/man/pppmatching.Rd
@@ -46,7 +46,7 @@
 \author{
   Dominic Schuhmacher
   \email{dominic.schuhmacher@stat.unibe.ch}
-  \url{http://dominic.schuhmacher.name/}
+  URL \code{http://dominic.schuhmacher.name/}
 }
 \seealso{
   \code{\link{pppmatching.object}}

diff --git a/man/pppmatching.object.Rd b/man/pppmatching.object.Rd
@@ -56,7 +56,7 @@
 \author{
   Dominic Schuhmacher
   \email{dominic.schuhmacher@stat.unibe.ch}
-  \url{http://dominic.schuhmacher.name/}
+  URL \code{http://dominic.schuhmacher.name/}
 }
 \seealso{
   \code{\link{matchingdist}},