CVS commit: pkgsrc/geography/R-spatstat.geom

["Makoto Fujiwara" <mef%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   mef
Date:           Fri Jun 12 13:51:11 UTC 2026

Modified Files:
        pkgsrc/geography/R-spatstat.geom: Makefile distinfo

Log Message:
geography/R-spatstat.geom) Updated 3.3.5 to 3.8.1

        CHANGES IN spatstat.geom VERSION 3.8-1

OVERVIEW

    o Minor correction.

SIGNIFICANT USER-VISIBLE CHANGES

    o union.owin, intersect.owin, setminus.owin
    Default value of 'rescue' set to 'FALSE'.

        CHANGES IN spatstat.geom VERSION 3.8-0

OVERVIEW

    o Improved handling of boundary pixels when discretising a polygonal window.

    o Improved handling of 'rejected' points.

    o Bug fixes and minor improvements.

SIGNIFICANT USER-VISIBLE CHANGES

    o pixellate.ppp, pixellate.owin, pixellate.psp
    These methods now accept the argument 'rule.pix' passed to 'owin2mask'.
    This makes it possible to ensure that boundary pixels which partially
    intersect the window are included in the resulting pixel image,
    by setting rule.pix="cover".

    o as.im
    Methods for as.im now accept argument 'rule.pix' passed to 'owin2mask'.
    This makes it possible to ensure that boundary pixels which partially
    intersect the window are included in the resulting pixel image,
    by setting rule.pix="cover".

    o "[.im"
    New argument 'rule.pix' controls the handling of boundary pixels
    in computations like x[W] where W is a polygonal window.

    o as.layered.ppp
    Now handles rejected points in attr(x, "rejects")
    and retrieves them as a layer in the resulting layered object.

    o as.ppp.ppp
    No longer checks for duplicated points (unless checkdup=TRUE is specified).
    No longer checks for points lying outside the window (unless check=TRUE
    is specified).

    o plot.ppp
    New argument 'show.rejects' determines whether rejected points are plotted.

    o project2segment
    Accelerated by 20 percent.

    o project2set
    Now supports projection to a polygonal window.
    New argument 'polygonal'.

    o bdist.pixels
    Accelerated for polygonal windows.

    o owin2mask
    Changed formal arguments. First argument is now called 'w'.
    Formal argument 'op' renamed 'rule.pix'.
    All arguments must be given by name except for the first argument.

    o union.owin, intersect.owin, setminus.owin
    New argument 'rescue'.

BUG FIXES

    o plot.im
    Argument 'box=TRUE' was not handled correctly.
    Fixed.

    o plot.im, plot.layered, plot.msr, plot.owin, plot.ppp, plot.psp:
    Display of the main title was mangled if argument 'main' was
    an 'expression' with length > 1.
    Fixed.

        CHANGES IN spatstat.geom VERSION 3.7-3

OVERVIEW

    o We thank Alexey Sergushichev for contributions.

    o Urgent bug fix.

BUG FIXES

    o distmap.ppp
    Argument 'squared' was inverted, so that the result
    contained the squared distances if and only if squared=FALSE.
    [Spotted by Alexey Sergushichev.]
    Fixed.

        CHANGES IN spatstat.geom VERSION 3.7-2

OVERVIEW

    o Minor improvements and bug fixes.

SIGNIFICANT USER-VISIBLE CHANGES

    o erosion.owin
    When shrink.frame=TRUE, the frame of the resulting window
    is always the erosion of the original frame by distance r,
    as promised in the help file.

BUG FIXES

    o erosion.owin, dilation.owin
    The 'unitname' of w was sometimes ignored.
    Fixed.

        CHANGES IN spatstat.geom VERSION 3.7-1

OVERVIEW

    o We thank Ute Hahn for contributions.

    o Support function, Feret diameter, polar body, Voronoi flower.

    o Merge tiles in a tessellation.

    o Return squared nearest neighbour distances.

    o Bug fix in Minkowski sum.

    o Summary method for tessellations.

    o Minor improvements and bug fixes.

NEW FUNCTIONS

    o mergeTiles
    Merge tiles in a tessellation.

    o FeretDiamFun
    Create a function that computes the Feret diameter of a domain at any angle.

    o FeretBox
    Compute the tightest rectangle enclosing a domain at any angle.

    o minFeretDiam, maxFeretDiam
    Minimum or maximum Feret diameter of a domain

    o SupportFun
    Create a function that computes the support function of a domain.

    o polarbody
    Compute the polar body of a domain.

    o voronoiFlower
    Compute the Voronoi flower of a domain.

    o summary.tess, print.summary.tess
    Method for 'summary' for tessellations.

SIGNIFICANT USER-VISIBLE CHANGES

    o distmap.ppp
    New option 'squared=TRUE' returns the squared distances,
    reducing computation time.

    o distmap.ppp
    New option 'extras=FALSE' avoids returning additional attributes,
    reducing computation time.

    o nnmap.ppp
    New option 'squared=TRUE' returns the squared distances,
    reducing computation time.

    o nndist.ppp, nndist.default, nncross.ppp, nncross.default
    New option 'squared=TRUE' returns the squared nearest neighbour distances,
    reducing computation time.

    o print.summary.owin
    Output can now be abbreviated by
    increasing the value of spatstat.options('terse')

    o print.summary.psp
    Output can now be abbreviated by
    increasing the value of spatstat.options('terse')

BUG FIXES

    o MinkowskiSum, operator %(+)%
    Result was often incorrect for non-convex sets
    (and was not symmetric in A and B).
    [Spotted by Ute Hahn]
    Fixed.

    o im.apply
    Did not preserve the name of the unit of length.
    Fixed.

        CHANGES IN spatstat.geom VERSION 3.7-0

OVERVIEW

    o We thank Alexey Sergushichev for contributions.

    o Level sets calculated using analytic geometry, for some functions.

    o More options for perspective plots.

    o Easier control over transparency of image plots.

    o Scramble the colours when plotting a point pattern or segment pattern.

    o Signed distance transform and signed distance function

    o Minor improvements and bug fixes.

NEW FUNCTIONS

    o default.colourmap
    Default colour map for a vector or factor.

    o levelset.im
    The function previously called 'levelset' is now a method for class 'im'.

    o levelset.distfun
    Method for level sets for distance functions.

    o levelset.tessfun
    Method for level sets for functions created by as.function.tess

SIGNIFICANT USER-VISIBLE CHANGES

    o default.symbolmap.ppp
    For a multitype point pattern, 'cols' can be a 'function(n)'

    o default.symbolmap.ppp
    New argument 'scramble.cols'

    o distfun.owin
    New argument 'signed'

    o distmap.owin
    New argument 'signed'

    o levelset
    This function is now generic, with methods for 'im' and 'distfun'.

    o multiplicity
    Methods for 'multiplicity' can now handle objects of larger size.

    o persp.im
    The pixel values of 'colin' can be colour values.
    New argument 'valuesAreColours'.

    o persp.ppp
    Now plots the 'zlab' label alongside the vertical scale bar.

    o persp.ppp
    Argument 'col.base' can be a pixel image, which will be
    rendered as a colour image in perspective view on the horizontal plane.

    o persp.ppp
    New argument 'show.window'.

    o plot.im
    New argument 'opacity' controls semi-transparency of colours.

    o plot.ppp
    New argument 'scramble.cols'.

    o plot.psp
    New argument 'scramble.cols'.

    o tileindex
    New arguments 'close.gaps' and 'all.inside'.

    o plot.colourmap
    New argument 'do.plot'

    o plot.symbolmap
    New argument 'do.plot'

BUG FIXES

    o connected.im
    Crashed if the image consisted of a single pixel.
    [Spotted by Alexey Sergushichev]
    Fixed.

    o contour.funxy
    Returned NULL rather than the result of 'contour.im' as intended.
    Fixed.

    o is.subset.owin
    Crashed if one of the arguments was an empty window.

    o persp.funxy
    Returned NULL rather than the result of 'persp.im' as intended.
    Fixed.

    o plot.funxy
    Returned NULL rather than the result of 'plot.im' as intended.
    Fixed.

    o plot.psp
    Crashed if x had logical-valued marks.
    Fixed.

    o plot.tess
    Crashed when do.col=TRUE, for a tessellation consisting of a single tile.
    Fixed.

    o plot.im
    Partially disobeyed 'do.plot=FALSE' because it started a graphics device
    if no graphics device was open.
    Fixed.

    o plot.layered
    Crashed in some cases with message "plot.new has not been called yet".
    Fixed.

        CHANGES IN spatstat.geom VERSION 3.6-1

OVERVIEW

    o Find centroids of tiles of a tessellation.

    o More options for converting a tessellation to an image.

    o Minor internal improvements and bug fixes.

SIGNIFICANT USER-VISIBLE CHANGES

    o owin2mask
    Arguments '...' that are not recognised by 'as.mask'
    are now silently ignored, rather than causing an error.

    o as.im.tess
    New argument 'rule.tile' specifies how to determine,
    for each pixel, the tile of the tessellation that covers the pixel.

NEW FUNCTIONS

    o tile.centroids
    Find the centroids of the tiles of a tessellation
    and return them as a point pattern.

BUG FIXES

    o incircle
    Gave incorrect results for some irregular windows.
    Fixed.

        CHANGES IN spatstat.geom VERSION 3.6-0

OVERVIEW

    o More facilities for handling NA objects.

    o More facilities for drawing a background behind a plot.

    o 'clickpoly' allows vertices to be snapped (rounded) onto a grid

    o Improvements to perspective views of images.

    o More options for disc windows.

    o Internal improvements.

SIGNIFICANT USER-VISIBLE CHANGES

    o solapply, anylapply
    If an entry of the list is an 'NAobject', the result for that entry
    will be an 'NAobject'.

    o with.hyperframe
    If a column in the hyperframe contains 'NA object' entries,
    and if the name of that column is included in the expression
    being evaluated, then the result of evaluation is an 'NA' or 'NA object'
    in the relevant row.

    o plot.owin, plot.psp
    New argument 'background' specifies an object (or a colour)
    that will be plotted before x is plotted, and will
    therefore appear underneath it.

    o plot.ppp, plot.im
    Argument 'background' can be a single colour value.

    o clickpoly
    Allows user-selected locations of vertices to be snapped (rounded)
    to the nearest grid points. New arguments 'snap.step' and 'snap.origin'.

    o disc
    New argument 'type' allows the user to specify an inscribed polygon
    or a circumscribed polygon.

    o as.ppp, as.owin, as.im, domain, Frame, Window
    These generic functions now have methods for class 'NAobject'
    which return an 'NAobject'.

    o nobjects, npoints
    These generic functions now have methods for class 'NAobject'
    which return an NA integer value.

    o marks, "marks<-"
    These generic functions now have methods for class 'NAobject'
    which return an 'NAobject'.

    o persp.im
    Improved appearance when apron=TRUE and the image domain is not a rectangle.

    o hyperframe
    Removed slight inconsistencies in the internal format
    produced in different cases.

        CHANGES IN spatstat.geom VERSION 3.5-0

OVERVIEW

    o Missing or unavailable (NA) spatial objects.

    o Interactively identify tiles of a tessellation.

    o Remove small holes from a window.

    o New options for defining nearest neighbours.

    o im.apply handles vector-valued functions.

    o Backgrounds for plots of point patterns.

    o Concatenate layered objects.

    o Connected components of polygonal windows.

    o Bug fixes and minor improvements.

NEW FUNCTIONS

    o fillholes.owin
    Remove small holes from a window.

    o identify.tess
    Interactively identify tiles of a tessellation.

    o NAobject
    Create an NA object of a specified class.

    o is.NAobject
    Recognise whether an object is a missing or unavailable (NA) object.

    o is.na.hyperframe
    Returns a logical matrix indicating which entries of the hyperframe
    are NA values or NA objects.

    o c.layered
    Method for the generic 'c' for layered objects.
    Enables two or more layered objects to be concatenated,
    correctly retaining their plot arguments.

SIGNIFICANT USER-VISIBLE CHANGES

    o compatible.im
    Accelerated in the common case where all rasters are identical.

    o connected.owin
    New argument 'polygonal' allows calculation of connected components
    using polygonal geometry instead of pixel-based algorithm.

    o harmonise.im
    Accelerated in the common case where all rasters are identical.

    o identify.psp
    New arguments 'paint' and 'paint.args'.

    o im.apply
    Now handles vector-valued functions.

    o nnmark
    New arguments 'ties' and 'proper'.

    o nndist
    New argument 'proper'.

    o nnwhich
    New argument 'proper'.

    o pixellate.psp
    New option: what='indicator'

    o plot.im
    The position of text next to the colour ribbon can now be
    controlled by 'riblab$side'.

    o plot.im
    Placement of main title improved, in some cases.

    o plot.ppp
    New arguments 'background' and 'clip.background' allow the user to specify
    an object that will be plotted before the point pattern x, and will
    therefore appear underneath it.

    o "[<-.hyperframe"
    In an assignment like x[i,j] <- NA, if column j contains
    spatial objects, the NA value will be coerced to an 'NAobject'
    of the appropriate class.

BUG FIXES

    o delaunay
    Crashed in some cases when X contained exactly 3 points.
    Fixed.

    o plot.im
    riblab$side was ignored.
    Fixed.

    o "[<-.hyperframe"
    Results of x[i,j] <- value were malformed if i and j were
    single numeric values equivalent to integers but not stored as integers,
    i.e. values with is.integer(i) = FALSE.
    Fixed.

        CHANGES IN spatstat.geom VERSION 3.4-1

OVERVIEW

    o Bug fix.

BUG FIXES

    o default.symbolmap.ppp
    Crashed in some cases, for marks of class 'Date'.
    Fixed.

        CHANGES IN spatstat.geom VERSION 3.4-0

OVERVIEW

    o Nonlinear colour maps and symbol maps.

    o Backgrounds for image plots.

    o `im.apply` handles larger datasets.

    o `quadratcount.ppp` supports left-closed, right-open rectangular tiles.

    o Minor improvements and bug fixes.

SIGNIFICANT USER-VISIBLE CHANGES

    o colourmap
    New arguments 'compress', 'decompress' for nonlinear colour maps.

    o default.symbolmap.ppp
    Argument 'marktransform' renamed 'transform' for consistency.

    o im.apply
    Improved algorithm avoids violating memory limits, handles larger datasets.

    o lut
    New arguments 'compress', 'decompress' for nonlinear lookup tables.

    o plot.colourmap
    New argument 'at' determines the position of tick marks on the axis.

    o plot.im
    New arguments 'background' and 'clip.background' allow the user to specify
    an object that will be plotted before the image x, and will therefore appear
    underneath it.

    o plot.im
    Return value has attribute 'at' giving the position of tick marks
    on the axis next to the colour ribbon.

    o plot.yardstick
    New arguments 'zebra.scale' and 'do.txt'.

    o quadratcount.ppp
    New argument 'left.open' controls the treatment of data points
    which lie on the boundary between two rectangular quadrats.

    o symbolmap
    New arguments 'transform', 'compress', 'decompress'
    for nonlinear symbol maps.

BUG FIXES

    o plot.solist, plot.imlist
    When 'equal.scales=TRUE' and 'equal.ribbon=TRUE',
    the argument 'log=TRUE' was ignored.
    Fixed.

    o plot.im
    If log=TRUE, the colour map returned by plot.im
    represented the colours applied to log10(x) rather than x.
    Fixed.

    o flipxy.psp
    The line segments were unchanged.
    Fixed.

        CHANGES IN spatstat.geom VERSION 3.3-6

OVERVIEW

    o We thank Warick Brown, Tilman Davies and Martin Hazelton
    for contributions.

    o Methods for functions which are constant on each tile of a tessellation.

    o Minor improvements.

NEW FUNCTIONS

    o integral.tessfun
    Integral of a function which is constant on each tile of a tessellation

    o print.tessfun, plot.tessfun, as.tess.tessfun
    Methods for the class 'tessfun' of functions which are constant
    on each tile of a tessellation.

SIGNIFICANT USER-VISIBLE CHANGES

    o plot.yardstick
    New argument 'style' allows different styles of plotting a scale bar
    including a zebra pattern (style = "zebra").

    o plot.yardstick
    New arguments 'zebra.step', 'zebra.width', 'zebra.col'.

    o as.mask
    Corrected a warning message.


To generate a diff of this commit:
cvs rdiff -u -r1.6 -r1.7 pkgsrc/geography/R-spatstat.geom/Makefile \
    pkgsrc/geography/R-spatstat.geom/distinfo

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Modified files:

Index: pkgsrc/geography/R-spatstat.geom/Makefile
diff -u pkgsrc/geography/R-spatstat.geom/Makefile:1.6 pkgsrc/geography/R-spatstat.geom/Makefile:1.7
--- pkgsrc/geography/R-spatstat.geom/Makefile:1.6       Wed Feb 12 12:32:31 2025
+++ pkgsrc/geography/R-spatstat.geom/Makefile   Fri Jun 12 13:51:11 2026
@@ -1,7 +1,7 @@
-# $NetBSD: Makefile,v 1.6 2025/02/12 12:32:31 wiz Exp $
+# $NetBSD: Makefile,v 1.7 2026/06/12 13:51:11 mef Exp $
 
 R_PKGNAME=     spatstat.geom
-R_PKGVER=      3.3-5
+R_PKGVER=      3.8-1
 CATEGORIES=    geography
 
 MAINTAINER=    pkgsrc-users%NetBSD.org@localhost
Index: pkgsrc/geography/R-spatstat.geom/distinfo
diff -u pkgsrc/geography/R-spatstat.geom/distinfo:1.6 pkgsrc/geography/R-spatstat.geom/distinfo:1.7
--- pkgsrc/geography/R-spatstat.geom/distinfo:1.6       Wed Feb 12 12:32:31 2025
+++ pkgsrc/geography/R-spatstat.geom/distinfo   Fri Jun 12 13:51:11 2026
@@ -1,5 +1,5 @@
-$NetBSD: distinfo,v 1.6 2025/02/12 12:32:31 wiz Exp $
+$NetBSD: distinfo,v 1.7 2026/06/12 13:51:11 mef Exp $
 
-BLAKE2s (R/spatstat.geom_3.3-5.tar.gz) = 1cb2a893f61ff1e1ca58b5a2cacb42ba26c9154d14dca01fc3d63c6a18d4b66f
-SHA512 (R/spatstat.geom_3.3-5.tar.gz) = 6ce931f9e66d274e9b3a31855e06f32f9c57baacd766f9395009df4e7dd2be1ee930c304129fb42685e29ef7ea2970e1d2a301ee829c309420776e9e208552b6
-Size (R/spatstat.geom_3.3-5.tar.gz) = 775805 bytes
+BLAKE2s (R/spatstat.geom_3.8-1.tar.gz) = a9315c934e0adf5af4fc50da6647e25f6393c00707dd401c8113c34bf448b380
+SHA512 (R/spatstat.geom_3.8-1.tar.gz) = c565ff490ac3055140a9ac0f09df761f6d36cf2090e9b6beda5ef66b4d91896ba8fcb18d98dcbdb03127949413f2d53059673939479074f833d0013f5530e12f
+Size (R/spatstat.geom_3.8-1.tar.gz) = 831127 bytes