Adjusted to spatstat.random

spatstat · Feb 11, 2022 · f3f17b6 · f3f17b6
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: spatstat.geom
-Version: 2.3-1
-Date: 2021-12-10
+Version: 2.3-1.001
+Date: 2022-02-11
 Title: Geometrical Functionality of the 'spatstat' Family 
 Authors@R: c(person("Adrian", "Baddeley", 
                     role = c("aut", "cre"),
@@ -21,7 +21,8 @@ Authors@R: c(person("Adrian", "Baddeley",
 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.linnet, maptools (>= 0.9-9), spatial, fftwtools (>= 0.9-8), spatstat (>= 2.0-0)
+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
@@ -1,3 +1,12 @@
+        CHANGES IN spatstat.geom VERSION 2.3-1.001
+
+OVERVIEW
+
+    o 'spatstat.geom' now suggests the package 'spatstat.random'.
+
+    o Updated help files.
+
+
         CHANGES IN spatstat.geom VERSION 2.3-1
 
 OVERVIEW

diff --git a/R/applynbd.R b/R/applynbd.R
@@ -1,6 +1,6 @@
 # 	applynbd.R
 #
-#     $Revision: 1.17 $     $Date: 2016/10/23 10:36:58 $
+#     $Revision: 1.18 $     $Date: 2022/01/04 05:30:06 $
 #
 #  applynbd()
 # For each point, identify either

diff --git a/R/centroid.R b/R/centroid.R
@@ -2,7 +2,7 @@
 #	centroid.S	Centroid of a window
 #			and related operations
 #
-#	$Revision: 1.6 $	$Date: 2014/11/10 08:20:59 $
+#	$Revision: 1.7 $	$Date: 2022/01/04 05:30:06 $
 #
 # Function names (followed by "xypolygon" or "owin")
 #	

diff --git a/R/clickpoly.R b/R/clickpoly.R
@@ -2,7 +2,7 @@
 # clickpoly.R
 #
 #
-# $Revision: 1.10 $  $Date: 2015/10/21 09:06:57 $
+# $Revision: 1.11 $  $Date: 2022/01/04 05:30:06 $
 #
 #
 

diff --git a/R/colourtools.R b/R/colourtools.R
@@ -1,7 +1,7 @@
 #
 #  colourtools.R
 #
-#   $Revision: 1.21 $   $Date: 2019/04/05 09:20:59 $
+#   $Revision: 1.22 $   $Date: 2022/01/04 05:30:06 $
 #
 
 

diff --git a/R/cut.ppp.R b/R/cut.ppp.R
@@ -3,7 +3,7 @@
 #
 #  cut method for ppp objects
 #
-#  $Revision: 1.15 $   $Date: 2016/10/26 09:29:57 $
+#  $Revision: 1.16 $   $Date: 2022/01/04 05:30:06 $
 #
 
 cut.ppp <- function(x, z=marks(x), ...) {

diff --git a/R/deltametric.R b/R/deltametric.R
@@ -3,7 +3,7 @@
 #
 #   Delta metric
 #
-#   $Revision: 1.4 $  $Date: 2014/10/24 00:22:30 $
+#   $Revision: 1.5 $  $Date: 2022/01/04 05:30:06 $
 #
 
 deltametric <- function(A, B, p=2, c=Inf, ...) {

diff --git a/R/distances.psp.R b/R/distances.psp.R
@@ -3,7 +3,7 @@
 #
 #  Hausdorff distance and Euclidean separation for psp objects
 #
-#  $Revision: 1.11 $ $Date: 2015/10/21 09:06:57 $
+#  $Revision: 1.12 $ $Date: 2022/01/04 05:30:06 $
 #
 #
 

diff --git a/R/headtail.R b/R/headtail.R
@@ -3,7 +3,7 @@
 #'
 #'   Methods for head() and tail()
 #'
-#'   $Revision: 1.1 $  $Date: 2016/12/20 01:11:29 $
+#'   $Revision: 1.2 $  $Date: 2022/01/04 05:30:06 $
 
 head.tess <- head.psp <- head.ppx <- head.ppp <- function(x, n=6L, ...) {
   stopifnot(length(n) == 1L)

diff --git a/R/layered.R b/R/layered.R
@@ -3,7 +3,7 @@
 #
 # Simple mechanism for layered plotting
 #
-#  $Revision: 1.39 $  $Date: 2017/06/05 10:31:58 $
+#  $Revision: 1.40 $  $Date: 2022/01/04 05:30:06 $
 #
 
 layered <- function(..., plotargs=NULL, LayerList=NULL) {

diff --git a/R/nncross.R b/R/nncross.R
@@ -2,7 +2,7 @@
 #   nncross.R
 #
 #
-#    $Revision: 1.35 $  $Date: 2021/09/05 10:58:54 $
+#    $Revision: 1.36 $  $Date: 2022/01/04 05:30:06 $
 #
 #  Copyright (C) Adrian Baddeley, Jens Oehlschlaegel and Rolf Turner 2000-2012
 #  Licence: GNU Public Licence >= 2

diff --git a/R/plot.anylist.R b/R/plot.anylist.R
@@ -4,7 +4,7 @@
 ##  Plotting functions for 'solist', 'anylist', 'imlist'
 ##       and legacy class 'listof'
 ##
-##  $Revision: 1.30 $ $Date: 2020/11/17 03:47:24 $
+##  $Revision: 1.31 $ $Date: 2022/01/04 05:30:06 $
 ##
 
 plot.anylist <- plot.solist <- plot.listof <-

diff --git a/R/ppp.R b/R/ppp.R
@@ -4,7 +4,7 @@
 #	A class 'ppp' to define point patterns
 #	observed in arbitrary windows in two dimensions.
 #
-#	$Revision: 4.113 $	$Date: 2020/05/03 03:10:05 $
+#	$Revision: 4.114 $	$Date: 2022/01/04 05:30:06 $
 #
 #	A point pattern contains the following entries:	
 #

diff --git a/R/psp.R b/R/psp.R
@@ -1,7 +1,7 @@
 #
 #  psp.R
 #
-#  $Revision: 1.109 $ $Date: 2020/12/19 05:25:06 $
+#  $Revision: 1.110 $ $Date: 2022/01/04 05:30:06 $
 #
 # Class "psp" of planar line segment patterns
 #

diff --git a/R/randomseg.R b/R/randomseg.R
@@ -1,7 +1,7 @@
 #
 # randomseg.R
 #
-# $Revision: 1.16 $ $Date: 2021/09/10 08:10:54 $
+# $Revision: 1.17 $ $Date: 2022/01/04 05:30:06 $
 #
 
 

diff --git a/R/simplepanel.R b/R/simplepanel.R
@@ -4,7 +4,7 @@
 #  A simple, robust point & click interface
 #     used in rmh visual debugger.
 #
-#  $Revision: 1.14 $  $Date: 2016/04/25 02:34:40 $
+#  $Revision: 1.15 $  $Date: 2022/01/04 05:30:06 $
 #
 
 simplepanel <- function(title, B, boxes, clicks, redraws=NULL, exit=NULL, env) {

diff --git a/R/summary.im.R b/R/summary.im.R
@@ -3,7 +3,7 @@
 #
 #    summary() method for class "im"
 #
-#    $Revision: 1.21 $   $Date: 2016/09/01 02:31:52 $
+#    $Revision: 1.22 $   $Date: 2022/01/04 05:30:06 $
 #
 #    summary.im()
 #    print.summary.im()

diff --git a/R/terse.R b/R/terse.R
@@ -2,7 +2,7 @@
 ##
 ##  code to control terseness and layout of printed output
 ##
-##  $Revision: 1.11 $  $Date: 2016/09/23 02:07:24 $
+##  $Revision: 1.12 $  $Date: 2022/01/04 05:30:06 $
 ##
 
 

diff --git a/R/unnormdensity.R b/R/unnormdensity.R
@@ -1,7 +1,7 @@
 #
 #  unnormdensity.R
 #
-#  $Revision: 1.5 $  $Date: 2016/02/11 10:17:12 $
+#  $Revision: 1.6 $  $Date: 2022/01/04 05:30:06 $
 #
 
 unnormdensity <- function(x, ..., weights=NULL) {

diff --git a/inst/doc/packagesizes.txt b/inst/doc/packagesizes.txt
@@ -9,3 +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
diff --git a/man/WindowOnly.Rd → man/Window.quad.Rd b/man/WindowOnly.Rd → man/Window.quad.Rd
@@ -1,4 +1,4 @@
-\name{WindowOnly}
+\name{Window.quad}
 \alias{Window.quad}
 \alias{Window.quadratcount}
 \alias{Window.tess}
@@ -14,6 +14,7 @@
 }
 \usage{
 
+
  \method{Window}{quad}(X, \dots)
 
  \method{Window}{quadratcount}(X, \dots)
@@ -50,8 +51,8 @@
   \code{\link{owin.object}}
 }
 \examples{
-   X <- quadratcount(cells, 4)
-   Window(X)
+   A <- quadratcount(cells, 4)
+   Window(A)
 }
 \author{
   \spatstatAuthors.

diff --git a/man/as.owin.Rd b/man/as.owin.Rd
@@ -49,10 +49,6 @@ in any of several formats, into an object of class \code{"owin"}.
  \method{as.owin}{funxy}(W, \dots, fatal=TRUE)
 
  \method{as.owin}{boxx}(W, \dots, fatal=TRUE)
-
-
-
-
 }
 \arguments{
   \item{W}{
@@ -132,6 +128,27 @@ in any of several formats, into an object of class \code{"owin"}.
     lies outside the window, is transformed into the logical value
     \code{FALSE}, which is the corresponding convention for window masks.
     \item
+    an object of class \code{"ppm"}, \code{"kppm"}, \code{"slrm"}
+    or \code{"dppm"}
+    representing a fitted point process
+    model. In this case, if \code{from="data"} (the default),
+    \code{as.owin} extracts the  original point
+    pattern data to which the model was fitted, and returns the
+    observation window of this point pattern. If
+    \code{from="covariates"} then \code{as.owin} extracts the
+    covariate images to which the model was fitted,
+    and returns a binary mask window that specifies the pixel locations.
+    \item
+    an object of class \code{"lpp"}
+    representing a point pattern on a linear network.
+    In this case, \code{as.owin} extracts the linear network
+    and returns a window containing this network. 
+    \item
+    an object of class \code{"lppm"}
+    representing a fitted point process model on a linear network.
+    In this case, \code{as.owin} extracts the linear network
+    and returns a window containing this network. 
+    \item
     A \code{data.frame} with exactly three columns. Each row of the
     data frame corresponds to one pixel. Each row contains the
     \eqn{x} and \eqn{y} coordinates of a pixel, and a logical value
@@ -146,6 +163,14 @@ in any of several formats, into an object of class \code{"owin"}.
     defined on a spatial domain. The spatial domain of the function will be
     extracted.
     \item
+    an object of class \code{"rmhmodel"} representing a
+    point process model that can be simulated using \code{\link[spatstat.random]{rmh}}.
+    The window (spatial domain) of the model will be extracted.
+    The window may be \code{NULL} in some circumstances (indicating that the
+    simulation window has not yet been determined). This is not treated
+    as an error, because the argument \code{fatal} defaults to
+    \code{FALSE} for this method.
+    \item
     an object of class \code{"layered"} representing a
     list of spatial objects. See \code{\link{layered}}.
     In this case, \code{as.owin} will be applied to each
@@ -169,6 +194,10 @@ in any of several formats, into an object of class \code{"owin"}.
   will be guessed from the data.
 }
 \seealso{
+  \code{\link[spatstat.core]{as.owin.ppm}},
+  \code{\link[spatstat.random]{as.owin.rmhmodel}},
+  \code{\link[spatstat.linnet]{as.owin.lpp}}.
+  
   \code{\link{owin.object}},
   \code{\link{owin}}.
 

diff --git a/man/bufftess.Rd b/man/bufftess.Rd
@@ -99,7 +99,7 @@ bufftess(X, breaks, W = Window(X), \dots, polygonal = TRUE)
   \code{\link{dirichlet}}, \code{\link{delaunay}},
   \code{\link{quantess}}, \code{\link{quadrats}}
   and 
-  \code{\link[spatstat.core]{rpoislinetess}}.
+  \code{\link[spatstat.random]{rpoislinetess}}.
 }
 \examples{
   X <- cells[c(FALSE,FALSE,FALSE,TRUE)] 

diff --git a/man/domain.Rd b/man/domain.Rd
@@ -47,6 +47,8 @@
  \method{domain}{funxy}(X, \dots)
 
 
+
+
 }
 \arguments{
   \item{X}{
@@ -58,7 +60,7 @@
   }
 }
 \details{
-  The function \code{domain} is generic.
+  The function \code{\link[spatstat.geom]{domain}} is generic.
 
   For a spatial object \code{X} in any number of dimensions, 
   \code{domain(X)} extracts the spatial domain in which \code{X} is
@@ -80,12 +82,16 @@
   \spatstatAuthors.
 }
 \seealso{
+  \code{\link[spatstat.core]{domain.ppm}},
+  \code{\link[spatstat.random]{domain.rmhmodel}},
+  \code{\link[spatstat.linnet]{domain.lpp}}.
   \code{\link{Window}},
-  \code{\link{Frame}}
+  \code{\link{Frame}}.
 }
 \examples{
-  domain(cells)
+  domain(redwood)
   domain(bei.extra$elev)
+  domain(osteo$pts[[1]])
 }
 \keyword{spatial}
 \keyword{manip}
diff --git a/man/macros/defns.Rd b/man/macros/defns.Rd
@@ -14,6 +14,6 @@
 \newcommand{\Prokesova}{\ifelse{latex}{\out{Proke\u{s}ov{\'{a}}}}{Prokesova}}
 \newcommand{\Sarkka}{\ifelse{latex}{\out{S\"{a}rkk\"{a}}}{Sarkka}}
 %% List of all Gibbs interactions 
-\newcommand{\GibbsInteractionsList}{\code{\link{AreaInter}}, \code{\link{BadGey}}, \code{\link{Concom}}, \code{\link{DiggleGatesStibbard}}, \code{\link{DiggleGratton}}, \code{\link{Fiksel}}, \code{\link{Geyer}}, \code{\link{Hardcore}}, \code{\link{HierHard}}, \code{\link{HierStrauss}}, \code{\link{HierStraussHard}}, \code{\link{Hybrid}}, \code{\link{LennardJones}}, \code{\link{MultiHard}}, \code{\link{MultiStrauss}}, \code{\link{MultiStraussHard}}, \code{\link{OrdThresh}}, \code{\link{Ord}}, \code{\link{Pairwise}}, \code{\link{PairPiece}}, \code{\link{Penttinen}}, \code{\link{Poisson}}, \code{\link{Saturated}}, \code{\link{SatPiece}}, \code{\link{Softcore}}, \code{\link{Strauss}}, \code{\link{StraussHard}} and \code{\link{Triplets}}}
+\newcommand{\GibbsInteractionsList}{\code{\link[spatstat.core]{AreaInter}}, \code{\link[spatstat.core]{BadGey}}, \code{\link[spatstat.core]{Concom}}, \code{\link[spatstat.core]{DiggleGatesStibbard}}, \code{\link[spatstat.core]{DiggleGratton}}, \code{\link[spatstat.core]{Fiksel}}, \code{\link[spatstat.core]{Geyer}}, \code{\link[spatstat.core]{Hardcore}}, \code{\link[spatstat.core]{HierHard}}, \code{\link[spatstat.core]{HierStrauss}}, \code{\link[spatstat.core]{HierStraussHard}}, \code{\link[spatstat.core]{Hybrid}}, \code{\link[spatstat.core]{LennardJones}}, \code{\link[spatstat.core]{MultiHard}}, \code{\link[spatstat.core]{MultiStrauss}}, \code{\link[spatstat.core]{MultiStraussHard}}, \code{\link[spatstat.core]{OrdThresh}}, \code{\link[spatstat.core]{Ord}}, \code{\link[spatstat.core]{Pairwise}}, \code{\link[spatstat.core]{PairPiece}}, \code{\link[spatstat.core]{Penttinen}}, \code{\link[spatstat.core]{Poisson}}, \code{\link[spatstat.core]{Saturated}}, \code{\link[spatstat.core]{SatPiece}}, \code{\link[spatstat.core]{Softcore}}, \code{\link[spatstat.core]{Strauss}}, \code{\link[spatstat.core]{StraussHard}} and \code{\link[spatstat.core]{Triplets}}}
 %% List of interactions recognised by RMH code
-\newcommand{\rmhInteractionsList}{\code{\link{AreaInter}}, \code{\link{BadGey}}, \code{\link{DiggleGatesStibbard}}, \code{\link{DiggleGratton}}, \code{\link{Fiksel}}, \code{\link{Geyer}}, \code{\link{Hardcore}}, \code{\link{Hybrid}}, \code{\link{LennardJones}}, \code{\link{MultiStrauss}}, \code{\link{MultiStraussHard}}, \code{\link{PairPiece}}, \code{\link{Penttinen}}, \code{\link{Poisson}}, \code{\link{Softcore}}, \code{\link{Strauss}}, \code{\link{StraussHard}} and \code{\link{Triplets}}}
+\newcommand{\rmhInteractionsList}{\code{\link[spatstat.core]{AreaInter}}, \code{\link[spatstat.core]{BadGey}}, \code{\link[spatstat.core]{DiggleGatesStibbard}}, \code{\link[spatstat.core]{DiggleGratton}}, \code{\link[spatstat.core]{Fiksel}}, \code{\link[spatstat.core]{Geyer}}, \code{\link[spatstat.core]{Hardcore}}, \code{\link[spatstat.core]{Hybrid}}, \code{\link[spatstat.core]{LennardJones}}, \code{\link[spatstat.core]{MultiStrauss}}, \code{\link[spatstat.core]{MultiStraussHard}}, \code{\link[spatstat.core]{PairPiece}}, \code{\link[spatstat.core]{Penttinen}}, \code{\link[spatstat.core]{Poisson}}, \code{\link[spatstat.core]{Softcore}}, \code{\link[spatstat.core]{Strauss}}, \code{\link[spatstat.core]{StraussHard}} and \code{\link[spatstat.core]{Triplets}}}
diff --git a/man/metric.object.Rd b/man/metric.object.Rd
@@ -41,7 +41,6 @@
   Euclidean metric, first check whether the standard function for this
   purpose (for example \code{nndist.ppp}) 
   has an argument named \code{metric}. 
-  the low-level function \code{\link{invoke.metric}}.
   If so, use the standard function
   and add the argument \code{metric}; if not, use
   the low-level function \code{\link{invoke.metric}}.

diff --git a/man/pointsOnLines.Rd b/man/pointsOnLines.Rd
@@ -41,7 +41,7 @@ pointsOnLines(X, eps = NULL, np = 1000, shortok=TRUE)
 \seealso{
   \code{\link{psp}},
   \code{\link{ppp}},
-  \code{\link[spatstat.core]{runifpointOnLines}}
+  \code{\link[spatstat.random]{runifpointOnLines}}
 }
 \examples{
   X <- psp(runif(20), runif(20), runif(20), runif(20),  window=owin())

diff --git a/man/polartess.Rd b/man/polartess.Rd
@@ -97,7 +97,7 @@ polartess(W, \dots, nradial = NULL, nangular = NULL,
   \code{\link{dirichlet}}, \code{\link{delaunay}},
   \code{\link{quantess}},
   \code{\link{bufftess}}
-  and \code{\link[spatstat.core]{rpoislinetess}}.
+  and \code{\link[spatstat.random]{rpoislinetess}}.
 
 }
 \examples{

diff --git a/man/ppp.object.Rd b/man/ppp.object.Rd
@@ -69,15 +69,15 @@
   of the data.
 
   Patterns may be generated at random by
-   \code{\link[spatstat.core]{runifpoint}},
-   \code{\link[spatstat.core]{rpoispp}},
-   \code{\link[spatstat.core]{rMaternI}},
-   \code{\link[spatstat.core]{rMaternII}},
-   \code{\link[spatstat.core]{rSSI}},
-   \code{\link[spatstat.core]{rNeymanScott}},
-   \code{\link[spatstat.core]{rMatClust}},
+   \code{\link[spatstat.random]{runifpoint}},
+   \code{\link[spatstat.random]{rpoispp}},
+   \code{\link[spatstat.random]{rMaternI}},
+   \code{\link[spatstat.random]{rMaternII}},
+   \code{\link[spatstat.random]{rSSI}},
+   \code{\link[spatstat.random]{rNeymanScott}},
+   \code{\link[spatstat.random]{rMatClust}},
    and
-   \code{\link[spatstat.core]{rThomas}}.
+   \code{\link[spatstat.random]{rThomas}}.
 
    Most functions which are intended to operate on a window
    (of class \code{\link{owin}})