Fix cross-references to satisfy CRAN

spatstat · Jul 9, 2024 · 1754b09 · 1754b09
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: spatstat.geom
-Version: 3.3-1
-Date: 2024-07-06
+Version: 3.3-2
+Date: 2024-07-09
 Title: Geometrical Functionality of the 'spatstat' Family 
 Authors@R: c(person("Adrian", "Baddeley", 
                     role = c("aut", "cre", "cph"),

diff --git a/NEWS b/NEWS
@@ -1,8 +1,14 @@
+        CHANGES IN spatstat.geom VERSION 3.3-2
+
+OVERVIEW
+
+    o Tweaks to documentation to satisfy the package checker.
+
         CHANGES IN spatstat.geom VERSION 3.3-1
 
 OVERVIEW
 
-    o Tweaks to documentation to  satisfy the package checker.
+    o Tweaks to documentation to satisfy the package checker.
 
         CHANGES IN spatstat.geom VERSION 3.3-0
 

diff --git a/inst/doc/packagesizes.txt b/inst/doc/packagesizes.txt
@@ -27,4 +27,4 @@ date version nhelpfiles nobjects ndatasets Rlines srclines
 "2024-01-26" "3.2-8" 452 1204 0 36234 15822
 "2024-02-28" "3.2-9" 452 1209 0 36325 15824
 "2024-07-05" "3.3-0" 442 1186 0 35638 15596
-"2024-07-06" "3.3-1" 442 1186 0 35638 15596
+"2024-07-09" "3.3-2" 442 1186 0 35638 15596
diff --git a/inst/info/packagesizes.txt b/inst/info/packagesizes.txt
@@ -27,4 +27,4 @@ date version nhelpfiles nobjects ndatasets Rlines srclines
 "2024-01-26" "3.2-8" 452 1204 0 36234 15822
 "2024-02-28" "3.2-9" 452 1209 0 36325 15824
 "2024-07-05" "3.3-0" 442 1186 0 35638 15596
-"2024-07-06" "3.3-1" 442 1186 0 35638 15596
+"2024-07-09" "3.3-2" 442 1186 0 35638 15596
diff --git a/man/Window.tess.Rd b/man/Window.tess.Rd
@@ -33,20 +33,20 @@
   \item{\dots}{Ignored.}
 }
 \value{
-  An object of class \code{"owin"} (see \code{\link{owin.object}})
+  An object of class \code{"owin"} (see \code{\link[spatstat.geom]{owin.object}})
   specifying an observation window.
 }
 \details{
-  These are methods for the generic function \code{\link{Window}}
+  These are methods for the generic function \code{\link[spatstat.geom]{Window}}
   which extract the spatial window in which the object \code{X}
   is defined. 
 }
 \seealso{
-  \code{\link{Window}},
-  \code{\link{Window.ppp}},
-  \code{\link{Window.psp}}.
+  \code{\link[spatstat.geom]{Window}},
+  \code{\link[spatstat.geom]{Window.ppp}},
+  \code{\link[spatstat.geom]{Window.psp}}.
 
-  \code{\link{owin.object}}
+  \code{\link[spatstat.geom]{owin.object}}
 }
 \examples{
    A <- quadratcount(cells, 4)

diff --git a/man/affine.im.Rd b/man/affine.im.Rd
@@ -13,7 +13,7 @@
   \item{mat}{Matrix representing a linear transformation.}
   \item{vec}{Vector of length 2 representing a translation.}
   \item{\dots}{
-    Optional arguments passed to \code{\link{as.mask}}
+    Optional arguments passed to \code{\link[spatstat.geom]{as.mask}}
     controlling the pixel resolution of the transformed image.
   }
 }

diff --git a/man/affine.owin.Rd b/man/affine.owin.Rd
@@ -17,7 +17,7 @@
     will be processed by \code{\link{rescue.rectangle}}.
   }
   \item{\dots}{
-    Optional arguments passed to \code{\link{as.mask}}
+    Optional arguments passed to \code{\link[spatstat.geom]{as.mask}}
     controlling the pixel resolution of the transformed window,
     if \code{X} is a binary pixel mask.
   }

diff --git a/man/as.im.Rd b/man/as.im.Rd
@@ -73,9 +73,9 @@
   \item{\dots}{Additional arguments passed to \code{X} when \code{X}
     is a function.}
   \item{eps,dimyx,xy,rule.eps}{
-    Optional parameters passed to \code{\link{as.mask}}
+    Optional parameters passed to \code{\link[spatstat.geom]{as.mask}}
     which determine the pixel array geometry.
-    See \code{\link{as.mask}}.
+    See \code{\link[spatstat.geom]{as.mask}}.
   }
   \item{na.replace}{Optional value to replace \code{NA} entries in the
     output image.

diff --git a/man/as.matrix.owin.Rd b/man/as.matrix.owin.Rd
@@ -9,15 +9,15 @@
 }
 \arguments{
   \item{x}{A window (object of class \code{"owin"}).}
-  \item{\dots}{Arguments passed to \code{\link{as.mask}} to control the
+  \item{\dots}{Arguments passed to \code{\link[spatstat.geom]{as.mask}} to control the
     pixel resolution.}
 }
 \details{
   The function \code{as.matrix.owin} converts a window to a
   logical matrux.
 
   It first converts the window \code{x} into a binary pixel mask
-  using \code{\link{as.mask}}. It then extracts the pixel entries
+  using \code{\link[spatstat.geom]{as.mask}}. It then extracts the pixel entries
   as a logical matrix.
 
   The resulting matrix has entries that are

diff --git a/man/as.polygonal.Rd b/man/as.polygonal.Rd
@@ -53,7 +53,7 @@ as.polygonal(W, repair=FALSE)
 \seealso{
   \code{\link{owin}},
   \code{\link{as.owin}},
-  \code{\link{as.mask}},
+  \code{\link[spatstat.geom]{as.mask}},
   \code{\link{simplify.owin}}
 }
 \examples{

diff --git a/man/bdist.pixels.Rd b/man/bdist.pixels.Rd
@@ -10,7 +10,7 @@
 \arguments{
   \item{w}{A window (object of class \code{"owin"}).}
   \item{\dots}{
-    Arguments passed to \code{\link{as.mask}} to determine
+    Arguments passed to \code{\link[spatstat.geom]{as.mask}} to determine
     the pixel resolution.}
   \item{style}{
     Character string (partially matched) determining the format of
@@ -53,7 +53,7 @@
 
   If the window is a rectangle or a polygonal region,
   the grid of pixels is determined by the arguments \code{"\dots"} 
-  passed to \code{\link{as.mask}}. The distance from each pixel to the
+  passed to \code{\link[spatstat.geom]{as.mask}}. The distance from each pixel to the
   boundary is calculated exactly, using analytic geometry.
   This is slower but more accurate than in the case of a binary mask.
 

diff --git a/man/boundingcircle.Rd b/man/boundingcircle.Rd
@@ -40,7 +40,7 @@ boundingcircle(x, \dots)
     A window (object of class \code{"owin"}), or another spatial object. 
   }
   \item{\dots}{
-    Arguments passed to \code{\link{as.mask}} to determine the
+    Arguments passed to \code{\link[spatstat.geom]{as.mask}} to determine the
     pixel resolution for the calculation.
   }
 }

diff --git a/man/bufftess.Rd b/man/bufftess.Rd
@@ -25,7 +25,7 @@ bufftess(X, breaks, W = Window(X), \dots, polygonal = TRUE)
     tessellation will be constructed.
   }
   \item{\dots}{
-    Optional arguments passed to \code{\link{as.mask}} controlling the
+    Optional arguments passed to \code{\link[spatstat.geom]{as.mask}} controlling the
     pixel resolution when \code{polygonal=FALSE},
     and optional arguments passed to \code{\link[base]{cut.default}}
     controlling the labelling of the distance bands.
@@ -90,7 +90,7 @@ bufftess(X, breaks, W = Window(X), \dots, polygonal = TRUE)
   Polygonal calculations are performed using \code{\link{dilation}}
   and \code{\link{setminus.owin}}. Pixel calculations are performed
   using \code{\link{distmap}} and \code{\link{cut.im}}. See
-  \code{\link{as.mask}} for details of arguments that control pixel
+  \code{\link[spatstat.geom]{as.mask}} for details of arguments that control pixel
   resolution. 
 
   For other kinds of tessellations, see 

diff --git a/man/closing.Rd b/man/closing.Rd
@@ -24,7 +24,7 @@
     or a point pattern (object of class \code{"ppp"}).
   }
   \item{r}{positive number: the radius of the closing.}
-  \item{\dots}{extra arguments passed to \code{\link{as.mask}}
+  \item{\dots}{extra arguments passed to \code{\link[spatstat.geom]{as.mask}}
     controlling the pixel resolution, if a pixel approximation is used}
   \item{polygonal}{
     Logical flag indicating whether to compute a polygonal

diff --git a/man/commonGrid.Rd b/man/commonGrid.Rd
@@ -13,15 +13,15 @@ commonGrid(\dots)
   \item{\dots}{
     Any number of pixel images (objects of class \code{"im"}),
     binary masks (objects of class \code{"owin"} of type \code{"mask"})
-    or data which can be converted to binary masks by \code{\link{as.mask}}.
+    or data which can be converted to binary masks by \code{\link[spatstat.geom]{as.mask}}.
   } 
 }
 \details{
   This function determines a common spatial resolution and spatial domain
   for several spatial objects. 
 
   The arguments \code{\dots} may be pixel images,
-  binary masks, or other spatial objects acceptable to \code{\link{as.mask}}.
+  binary masks, or other spatial objects acceptable to \code{\link[spatstat.geom]{as.mask}}.
 
   The common pixel grid is determined by inspecting all the pixel images
   and binary masks in the argument list, finding the pixel grid with the
@@ -32,7 +32,7 @@ commonGrid(\dots)
   at the chosen pixel resolution.
   Use \code{\link{as.im}(X, W=M)} to convert a pixel image \code{X} to this new
   pixel resolution.
-  Use \code{\link{as.mask}(W, xy=M)} to convert a window \code{W}
+  Use \code{\link[spatstat.geom]{as.mask}(W, xy=M)} to convert a window \code{W}
   to a binary mask at this new pixel resolution.
   See the Examples.
 }

diff --git a/man/connected.Rd b/man/connected.Rd
@@ -31,7 +31,7 @@ connected(X, \dots)
     or \code{"interpreted"}. See Details.
   }
   \item{\dots}{
-    Arguments passed to \code{\link{as.mask}} to determine the
+    Arguments passed to \code{\link[spatstat.geom]{as.mask}} to determine the
     pixel resolution.
   }
   \item{connect}{

diff --git a/man/connected.tess.Rd b/man/connected.tess.Rd
@@ -16,7 +16,7 @@
     A tessellation (object of class \code{"tess"}).
   }
   \item{\dots}{
-    Arguments passed to \code{\link{as.mask}} to determine the
+    Arguments passed to \code{\link[spatstat.geom]{as.mask}} to determine the
     pixel resolution.
   }
 }

diff --git a/man/covering.Rd b/man/covering.Rd
@@ -14,7 +14,7 @@
   }
   \item{r}{positive number: the radius of the covering discs.}
   \item{\dots}{
-    extra arguments passed to \code{\link{as.mask}}
+    extra arguments passed to \code{\link[spatstat.geom]{as.mask}}
     controlling the pixel resolution for the calculations.
   }
   \item{giveup}{

diff --git a/man/deltametric.Rd b/man/deltametric.Rd
@@ -27,7 +27,7 @@ deltametric(A, B, p = 2, c = Inf, ...)
     Either a positive numeric value, or \code{Inf}.
   }
   \item{\dots}{
-    Arguments passed to \code{\link{as.mask}} to determine the
+    Arguments passed to \code{\link[spatstat.geom]{as.mask}} to determine the
     pixel resolution of the distance maps computed by \code{\link{distmap}}.
   }
 }
@@ -68,7 +68,7 @@ deltametric(A, B, p = 2, c = Inf, ...)
   numerically.
   The accuracy of the computation depends on the pixel resolution
   which is controlled through the extra arguments \code{\dots} passed
-  to \code{\link{as.mask}}.
+  to \code{\link[spatstat.geom]{as.mask}}.
 }
 \value{
   A numeric value.

diff --git a/man/dilation.Rd b/man/dilation.Rd
@@ -21,7 +21,7 @@
     or a point pattern (object of class \code{"ppp"}).
   }
   \item{r}{positive number: the radius of dilation.}
-  \item{\dots}{extra arguments passed to \code{\link{as.mask}}
+  \item{\dots}{extra arguments passed to \code{\link[spatstat.geom]{as.mask}}
     controlling the pixel resolution, if the pixel approximation is
     used; or passed to \code{\link{disc}} if the polygonal approximation
     is used.
@@ -52,7 +52,7 @@
   to the dilation is computed.
   If \code{polygonal=FALSE} then a pixel approximation
   to the dilation is computed from the distance map of \code{w}.
-  The arguments \code{"\dots"} are passed to \code{\link{as.mask}}
+  The arguments \code{"\dots"} are passed to \code{\link[spatstat.geom]{as.mask}}
   to control the pixel resolution.
 
   When \code{w} is a window, the default (when \code{polygonal=NULL})

diff --git a/man/disc.Rd b/man/disc.Rd
@@ -44,7 +44,7 @@ Creates a circular window
 
   If \code{mask=TRUE}, then the disc is approximated by a binary pixel
   mask. The resolution of the mask is controlled by
-  the arguments \code{\dots} which are passed to \code{\link{as.mask}}.
+  the arguments \code{\dots} which are passed to \code{\link[spatstat.geom]{as.mask}}.
 
   The argument \code{radius} must be a single positive number.
   The argument \code{centre} specifies the disc centre: it can be either 
@@ -62,7 +62,7 @@ Creates a circular window
   \code{\link{discs}},
   \code{\link{owin.object}},
   \code{\link{owin}},
-  \code{\link{as.mask}}
+  \code{\link[spatstat.geom]{as.mask}}
 }
 \note{This function can also be used to generate regular polygons,
   by setting \code{npoly} to a small integer value. For example

diff --git a/man/discretise.Rd b/man/discretise.Rd
@@ -33,7 +33,7 @@
   deleted by the discretisation.
   If \code{move.points=TRUE}, the point coordinates are also discretised.
 
-  The window is first discretised using \code{\link{as.mask}}.
+  The window is first discretised using \code{\link[spatstat.geom]{as.mask}}.
   Next,
   \itemize{
     \item If \code{move.points=TRUE}, each point of \code{X}
@@ -50,13 +50,13 @@
 
   The arguments \code{eps}, \code{dimyx}, \code{xy} and \code{rule.eps}
   control the fineness of the pixel array. They are passed to
-  \code{\link{as.mask}}.
+  \code{\link[spatstat.geom]{as.mask}}.
 
   If \code{eps}, \code{dimyx} and \code{xy} are all absent or
   \code{NULL}, and if the window of \code{X} is of type \code{"mask"}
   to start with, then \code{discretise(X)} returns \code{X} unchanged.
 
-  See \code{\link{as.mask}} for further details
+  See \code{\link[spatstat.geom]{as.mask}} for further details
   about the arguments \code{eps}, \code{dimyx},
   \code{xy} and \code{rule.eps}, and the process of converting
   a window to one of type \code{mask}.
@@ -78,7 +78,7 @@
   and \rolf
 }
 \seealso{
-  \code{\link{as.mask}}
+  \code{\link[spatstat.geom]{as.mask}}
 }
 \examples{
   X <- demopat

diff --git a/man/discs.Rd b/man/discs.Rd
@@ -23,7 +23,7 @@
     \emph{diameters}.)
   }
   \item{\dots}{
-    Optional arguments passed to \code{\link{as.mask}} to determine
+    Optional arguments passed to \code{\link[spatstat.geom]{as.mask}} to determine
     the pixel resolution, if \code{mask=TRUE}.
   }
   \item{separate}{

diff --git a/man/distmap.Rd b/man/distmap.Rd
@@ -16,7 +16,7 @@
     a window (object of class \code{"owin"}) or a
     line segment pattern (object of class \code{"psp"}).
   }
-  \item{\dots}{Arguments passed to \code{\link{as.mask}}
+  \item{\dots}{Arguments passed to \code{\link[spatstat.geom]{as.mask}}
     to control pixel resolution.
   }
 }

diff --git a/man/distmap.owin.Rd b/man/distmap.owin.Rd
@@ -14,7 +14,7 @@
     A window (object of class \code{"owin"}).
   }
   \item{\dots}{
-    Arguments passed to \code{\link{as.mask}}
+    Arguments passed to \code{\link[spatstat.geom]{as.mask}}
     to control pixel resolution.
   }
   \item{discretise}{
@@ -70,7 +70,7 @@
   then the window will first be converted to a binary pixel mask
   and the discrete path distances will be computed.
 
-  The arguments \code{\dots} are passed to \code{\link{as.mask}}
+  The arguments \code{\dots} are passed to \code{\link[spatstat.geom]{as.mask}}
   to control the pixel resolution.
   
   This function is a method for the generic \code{\link{distmap}}.

diff --git a/man/distmap.ppp.Rd b/man/distmap.ppp.Rd
@@ -13,7 +13,7 @@
 \arguments{
   \item{X}{A point pattern (object of class \code{"ppp"}).
   }
-  \item{\dots}{Arguments passed to \code{\link{as.mask}}
+  \item{\dots}{Arguments passed to \code{\link[spatstat.geom]{as.mask}}
     to control pixel resolution.
   }
   \item{clip}{

diff --git a/man/distmap.psp.Rd b/man/distmap.psp.Rd
@@ -13,7 +13,7 @@
 \arguments{
   \item{X}{A line segment pattern (object of class \code{"psp"}).
   }
-  \item{\dots}{Arguments passed to \code{\link{as.mask}}
+  \item{\dots}{Arguments passed to \code{\link[spatstat.geom]{as.mask}}
     to control pixel resolution.
   }
   \item{extras}{

diff --git a/man/domain.Rd b/man/domain.Rd
@@ -87,8 +87,8 @@
   \code{\link[spatstat.explore]{domain.quadrattest}},
   \code{\link[spatstat.random]{domain.rmhmodel}},
   \code{\link[spatstat.linnet]{domain.lpp}}.
-  \code{\link{Window}},
-  \code{\link{Frame}}.
+  \code{\link[spatstat.geom]{Window}},
+  \code{\link[spatstat.geom]{Frame}}.
 }
 \examples{
   domain(redwood)