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CVS commit: pkgsrc/geography/R-spatstat.geom
Module Name: pkgsrc
Committed By: mef
Date: Sat Jan 13 22:39:42 UTC 2024
Modified Files:
pkgsrc/geography/R-spatstat.geom: Makefile distinfo
Log Message:
(geography/R-spatstat.geom) Updated 2.2.2 to 3.2.7
CHANGES IN spatstat.geom VERSION 3.2-7
OVERVIEW
o Minor corrections to the help files.
CHANGES IN spatstat.geom VERSION 3.2-6
OVERVIEW
o Minor improvements.
o spatstat.geom no longer suggests 'maptools'.
SIGNIFICANT USER-VISIBLE CHANGES
o as.im.tess
New argument 'values'.
CHANGES IN spatstat.geom VERSION 3.2-5
OVERVIEW
o Extension of distance transform algorithm.
o Improvement to progress reports.
o Suppress annoying warnings.
o Further bug fix in quadratcount
SIGNIFICANT USER-VISIBLE CHANGES
o distmap.owin
New argument 'connect'.
o progressreport
The estimated time of completion is also printed, if the remaining time
is longer than 10 minutes.
o unnormdensity
Suppress annoying warning messages from density.default.
This affects many functions in the spatstat family of packages.
BUG FIXES
o quadratcount
Crashed if argument 'tess' was a rectangular grid tessellation.
Fixed.
CHANGES IN spatstat.geom VERSION 3.2-4
OVERVIEW
o Connected component transform can now use a 4-connected grid.
o Bug fixes in quadrat counting code.
SIGNIFICANT USER-VISIBLE CHANGES
o connected.owin, connected.im
New argument 'connect' specifies the connectivity of the raster,
either 4 or 8 neighbours for each pixel.
o round.ppp, round.pp3, round.ppx
Now has ellipsis argument '...' for conformity with generic 'round'
BUG FIXES
o as.mask
If 'w' was a rectangle and 'xy' was specified,
the pixel entries were all TRUE, instead of
only being TRUE within the window 'w'.
Fixed.
o intensity.quadratcount
Results were incorrect if the quadrats were a mixture of
irregular polygons and rectangles.
o quadratcount.ppp
If the window was irregular and some of the tiles did not intersect
the window, the counts were given the wrong tile labels.
Fixed.
o plot.quadratcount
If the window was irregular and some of the tiles did not intersect
the window, the counts were displayed in the wrong tiles.
Fixed.
CHANGES IN spatstat.geom VERSION 3.2-2
OVERVIEW
o Bug fixes and minor improvements.
SIGNIFICANT USER-VISIBLE CHANGES
o as.mask
Improved numerical performance (rounding error).
BUG FIXES
o quantess.owin
The window of the resulting tessellation was sometimes slightly different
from the original window M.
Fixed.
o intensity.quadratcount
Results were incorrect if the quadrats were the intersections of
a rectangular grid with an irregular window and all quadrats were nonempty.
Fixed.
CHANGES IN spatstat.geom VERSION 3.2-1
OVERVIEW
o Fixed errors and omissions in documentation.
o Minor improvements in C code.
CHANGES IN spatstat.geom VERSION 3.2-0
OVERVIEW
o We thank Warick Brown and Tilman Davies for suggestions.
o More options for converting polygons to a binary mask.
o More options for controlling pixel size.
o Improvement to progress reports.
o Minor tweaks to package documentation.
NEW FUNCTIONS
o psp2mask
Function 'as.mask.psp' has been renamed 'psp2mask'.
The old function 'as.mask.psp' still exists, but it will
soon be deprecated, and ultimately removed.
SIGNIFICANT USER-VISIBLE CHANGES
o owin2mask
New options op="majority" and op="minority".
If op="majority", a pixel belongs to the resulting mask if
at least half of the pixel area is covered by the window.
o as.mask
New argument 'rule.eps' specifies what to do when the
desired pixel size is not a divisor of the frame size.
o as.im
Many methods for 'as.im' now have argument 'rule.eps'.
o discretise
New argument 'rule.eps'
o distfun
New argument 'rule.eps'
o nnfun
New argument 'rule.eps'
o progressreport
New argument 'formula' controls the calculation of estimated time remaining.
o progressreport
New argument 'savehistory' specifies whether to save the elapsed times
when the function was called.
CHANGES IN spatstat.geom VERSION 3.1-0
OVERVIEW
o Methods for "[[" and "[[<-" for hyperframes.
o Colour map for pH values.
o Restrict a colour map to a narrower range of values.
o Integral of a one-dimensional density estimate.
o Minor improvements and bug fixes.
NEW FUNCTIONS
o "[[.hyperframe", "[[<-.hyperframe"
Methods for "[[" and "[[<-" for hyperframes.
o pHcolourmap, pHcolour
Colour map for values of pH
o restrict.colourmap
Restrict a colourmap to a narrower range of values.
o integral.density
Compute the integral of a one-dimensional kernel density estimate.
o as.colourmap
Extract colour information from an object.
SIGNIFICANT USER-VISIBLE CHANGES
o plot.symbolmap
New argument colour.only makes it possible to display only the
colour map information in a symbolmap.
o "[.hyperframe", "[<-.hyperframe"
Improved error message when the format of index i or j is not supported.
o unnormdensity
Computation accelerated.
o unnormdensity
Handles datasets containing fewer than 2 values.
BUG FIXES
o unnormdensity
If 'weights' was a single numerical value 'w', the calculation incorrectly
assigned the weight for each observation to be 'w/n' where 'n=length(x)'.
Fixed.
o unnormdensity
A crash could occur if 'x' was a very long vector,
with an error message originating from 'deparse1'.
Fixed.
CHANGES IN spatstat.geom VERSION 3.0-6
OVERVIEW
o Bug fix.
BUG FIXES
o harmoniseLevels
Crashed sometimes, in older versions of R,
with an obscure error message from 'mapply'.
Fixed.
CHANGES IN spatstat.geom VERSION 3.0-5
OVERVIEW
o Convert several factors or factor-valued images to a common set of levels.
o Extension to rjitter
o Alternative to rjitter
o Quantile function as a function
o Improvements to plot code.
NEW FUNCTIONS
o harmoniseLevels
Given several factors or factor-valued pixel images,
convert them all to have the same set of factor levels.
o rexplode
'Explode' a point pattern by randomly displacing each
group of duplicated points to make a circular pattern
around the original location. An alternative to 'rjitter'.
o quantilefun
Return a function that computes any quantiles of a given dataset.
SIGNIFICANT USER-VISIBLE CHANGES
o rjitter.ppp
If 'trim=TRUE', the displacement radius will be constrained
to be less than or equal to the distance from the data point
to the window boundary.
o plot.ppp
For multitype point patterns, a warning is issued if
the plot legend does not represent every possible type of point
due to space restrictions.
o plot.symbolmap
New argument 'warn'.
o plot.symbolmap
Issues a warning if the plot of a discrete symbol map does not
represent every possible input value, due to space restrictions.
o plot.solist
When equal.ribbon=TRUE, the images may now be factor-valued
or character-valued. Character-valued images will be converted
to factor-valued images. The common colour map will combine the
levels of all the factor images.
BUG FIXES
o "[<-.im"
Errors occurred in x[] <- v when x and v were both factor-valued
but with different sets of levels.
o rjitter.ppp
If retry=FALSE, marks were ignored.
Fixed.
CHANGES IN spatstat.geom VERSION 3.0-4
OVERVIEW
o Improvements to perspective plots.
SIGNIFICANT USER-VISIBLE CHANGES
o perspPoints, perspLines, perspSegments, perspContour
New argument 'occluded' specifies whether the surface
should be treated as opaque or transparent.
CHANGES IN spatstat.geom VERSION 3.0-3
OVERVIEW
o Minor internal changes to satisfy package checker.
CHANGES IN spatstat.geom VERSION 3.0-2
OVERVIEW
o Minor internal changes to satisfy package checker.
CHANGES IN spatstat.geom VERSION 3.0-1
OVERVIEW
o Minor internal changes.
CHANGES IN spatstat.geom VERSION 3.0-0
OVERVIEW
o Minor improvements and bug fixes.
o Changes to package dependence.
NEW FUNCTIONS
o is.linnet
Test whether an object is a linear network.
o as.data.frame.ppplist
Method for 'as.data.frame' for lists of point patterns.
SIGNIFICANT USER-VISIBLE CHANGES
o Package dependence
spatstat.geom now suggests the new packages spatstat.explore and
spatstat.model, which have replaced spatstat.core.
o crosspairs.ppp
New argument 'periodic' specifies whether to use
periodic (toroidal) distances.
o crosspairs.ppp
New arguments 'iX', 'iY' make it possible to eliminate pairs
in which the two points are identical.
o bufftess
The result now has attribute 'breaks' which is the vector of
distance breakpoints.
o contour.im
New argument 'log' specifies whether the contour lines
should be equally spaced on a logarithmic scale.
o plot.im, image.im
New argument 'addcontour' specifies that contour lines should be drawn
over the image plot.
o invoke.symbolmap
New argument 'angleref'.
o funxy
The result now has a unitname, inherited from the argument W.
o integral.im
New argument 'weight' specifies a weight function for the integration.
o markstat, applynbd
These functions now work for point patterns in three dimensions
(class 'pp3') and point patterns on a network (class 'lpp').
o plot.psp
New argument 'use.marks', for consistency with other methods.
BUG FIXES
o framedist.pixels
Result was always a matrix, regardless of the value of 'style'.
Fixed.
o plot.im
Ignored ribargs$labels.
Fixed.
o plot.ppp
Crashed with an obscure message when argument 'shape' was given,
unless argument 'size' was also given.
Fixed.
o closepairs
Crashed if npoints(X)^2 exceeded the largest possible integer.
Fixed.
o crosspairs
Crashed if npoints(X) * npoints(Y) exceeded the largest possible integer.
Fixed.
CHANGES IN spatstat.geom VERSION 2.4-0
OVERVIEW
o We thank Fernando Milesi, Suman Rakshit and Mark Walsh for contributions.
o Bug fixes in 'distmap' and 'distfun'.
o Bug fixes in 'closepairs'.
o Bug fixes in 'nncross.ppp'.
o Minor improvements and bug fixes.
NEW FUNCTIONS
o framedist.pixels
Computes distance from each pixel to the enclosing rectangle.
SIGNIFICANT USER-VISIBLE CHANGES
o nncross.ppp
When X is a point pattern and Y is a line segment pattern,
higher order neighbours (k > 1) are now supported.
o intersect.tess
New argument 'keepempty'.
o unnormdensity
Argument 'weights' may have length 1.
New argument 'defaults'.
o distmap.owin
Behaviour has been altered so that, when X is a binary mask, the results of
distmap(X, invert=TRUE) and distmap(complement.owin(X)) are identical.
This affects a few pixels close to the edge of the frame.
[Suggested by Fernando Milesi.]
o distmap.ppp
New argument 'clip'.
BUG FIXES
o distmap.owin
If the window was a binary mask, the distance values were
slightly too large (by a factor 1 + 1/n where n is the pixel grid dimension),
due to a coding error.
[Spotted by Fernando Milesi.]
Fixed.
o distfun.owin
If the window was a binary mask, the distance values were
slightly too small (typically reduced by 1/20 of a pixel width).
[Spotted by Fernando Milesi.]
Fixed.
o distmap.owin
Values were incorrect if X was an empty window (is.empty(X) = TRUE).
Fixed.
o distmap.ppp, distmap.psp
Values were incorrect if X was an empty pattern (npoints(X) = 0).
Fixed.
o distmap.psp
Values were incorrect if X was an empty pattern (nsegments(X) = 0).
Fixed.
o closepairs.ppp
If distinct=FALSE and what="all", the resulting vectors
'yi' and 'yj' contained incorrect values, and had the wrong length.
Fixed.
o nncross.ppp
When k > 1, distance values were incorrectly replaced by 'Inf' in some cases.
Fixed.
o closepairs.ppp
Crashed with a message 'unable to allocate memory'
if the window of X had zero area.
Fixed.
o crosspairs.ppp
Crashed with a message 'unable to allocate memory'
if the window of Y had zero area.
Fixed.
o closepairs.pp3
Crashed with a message 'unable to allocate memory'
if the domain of X had zero volume.
Fixed.
o crosspairs.pp3
Crashed with a message 'unable to allocate memory'
if the domain of Y had zero volume.
Fixed.
o as.im.owin
If 'value' was a categorical (factor) value, the result was not a factor-valued image.
Fixed.
o tile.areas
For a tessellation defined by a pixel image,
the result of tile.areas() was not a numeric vector.
[Spotted by Suman Rakshit.]
Fixed.
o dirichlet
Rarely, the number of tiles in the tessellation
was less than the number of unique data points.
This occurred only when the window was a binary mask.
[Spotted by Suman Rakshit.]
Fixed.
CHANGES IN spatstat.geom VERSION 2.3-2
OVERVIEW
o 'spatstat.geom' now suggests the package 'spatstat.random'.
o Updated help files to refer to 'spatstat.random'.
CHANGES IN spatstat.geom VERSION 2.3-1
OVERVIEW
o New options for weighted.quantile
o Minor improvements.
SIGNIFICANT USER-VISIBLE CHANGES
o weighted.quantile
New argument 'type' allows the user to choose between several rules
for the weighted quantile.
o weighted.median
New argument 'type' allows the user to choose between several rules
for the weighted median. The default rule has changed.
o perspSegments
Improved quality of result when pixels are not square.
o nndist.ppp, nnwhich.ppp
Argument 'by' can be a factor, a logical vector,
a pixel image with factor values, a tessellation, a window,
the string 'marks' (if marks(x) is a factor),
or the name of one of the columns of marks (if marks(x) is a data frame).
o nndist.pp3, nnwhich.pp3
Argument 'by' can be a factor, a logical vector,
the string 'marks' (if marks(x) is a factor), or
the name of one of the columns of marks (if marks(x) is a data frame).
o split.ppp, split.ppx
The argument 'f' may now be the character string "marks",
signifying 'f=marks(X)', provided 'marks(X)' is a factor.
o owin
If argument 'mask' is a logical matrix,
NA entries will be accepted, and converted to FALSE.
CHANGES IN spatstat.geom VERSION 2.3-0
OVERVIEW
o Quantile transformation.
o Distance metric based on a convex set.
o Basic support for calculations using non-Euclidean distance metrics.
o Improvements to 'rjitter'.
NEW CLASSES
o metric
An object of class 'metric' represents a distance metric.
See help(metric.object).
NEW FUNCTIONS
o transformquantiles
Transform the quantiles of a vector, matrix, array or pixel image.
o convexmetric
Distance metric based on a convex set.
o mean.ecdf, mean.ewcdf
Calculate the mean of an empirical cumulative distribution function.
o invoke.metric
Low level function to perform a desired operation using a given metric.
o rjitter.ppp
This function was previously called 'rjitter'. It is now a method
for the new generic function 'rjitter'.
SIGNIFICANT USER-VISIBLE CHANGES
o pairdist.ppp, crossdist.ppp, nndist.ppp, nnwhich.ppp, nncross.ppp
New argument 'metric' specifies a non-Euclidean distance metric
to measure the distances.
o distmap.ppp, distmap.owin, distmap.psp
New argument 'metric' specifies a non-Euclidean distance metric
to measure the distances.
o disc
New argument 'metric' specifies a non-Euclidean distance metric
defining the disc.
o rjitter
The function previously called 'rjitter' is now called 'rjitter.ppp'
and is now a method for the new generic 'rjitter'.
o rjitter.ppp
The argument 'radius' may be a numeric vector, specifying a different
displacement radius for each data point.
BUG FIXES
o as.mask
Crashed if 'Frame(w)' had zero height or zero width.
Fixed.
To generate a diff of this commit:
cvs rdiff -u -r1.1 -r1.2 pkgsrc/geography/R-spatstat.geom/Makefile
cvs rdiff -u -r1.3 -r1.4 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:1.1 pkgsrc/geography/R-spatstat.geom/Makefile:1.2
--- pkgsrc/geography/R-spatstat.geom/Makefile:1.1 Mon Sep 20 08:50:34 2021
+++ pkgsrc/geography/R-spatstat.geom/Makefile Sat Jan 13 22:39:41 2024
@@ -1,7 +1,7 @@
-# $NetBSD: Makefile,v 1.1 2021/09/20 08:50:34 mef Exp $
+# $NetBSD: Makefile,v 1.2 2024/01/13 22:39:41 mef Exp $
R_PKGNAME= spatstat.geom
-R_PKGVER= 2.2-2
+R_PKGVER= 3.2-7
CATEGORIES= geography
MAINTAINER= pkgsrc-users%NetBSD.org@localhost
@@ -9,7 +9,7 @@ COMMENT= Geometrical Functionality of th
LICENSE= gnu-gpl-v2 OR gnu-gpl-v3
DEPENDS+= R-deldir>=0.0.21:../../geography/R-deldir
-DEPENDS+= R-spatstat.data>=2.0:../../geography/R-spatstat.data
+DEPENDS+= R-spatstat.data>=3.0:../../geography/R-spatstat.data
DEPENDS+= R-spatstat.utils>=2.2.0:../../geography/R-spatstat.utils
DEPENDS+= R-polyclip>=1.10.0:../../graphics/R-polyclip
Index: pkgsrc/geography/R-spatstat.geom/distinfo
diff -u pkgsrc/geography/R-spatstat.geom/distinfo:1.3 pkgsrc/geography/R-spatstat.geom/distinfo:1.4
--- pkgsrc/geography/R-spatstat.geom/distinfo:1.3 Tue Oct 26 10:45:07 2021
+++ pkgsrc/geography/R-spatstat.geom/distinfo Sat Jan 13 22:39:41 2024
@@ -1,5 +1,5 @@
-$NetBSD: distinfo,v 1.3 2021/10/26 10:45:07 nia Exp $
+$NetBSD: distinfo,v 1.4 2024/01/13 22:39:41 mef Exp $
-BLAKE2s (R/spatstat.geom_2.2-2.tar.gz) = 9bc211d6c7e3168d84f21110293c106a9d6e9daae18b2acb922fba055331333f
-SHA512 (R/spatstat.geom_2.2-2.tar.gz) = 2e901cb3ef9709e4ae48baa7faaeef15b49a66cb29af1d7e5f1d15dc70ae2c34fe34e3299147cdf72a1f7c437aa7988541e7e30dcff1c9ea74c7b5d030b3d11a
-Size (R/spatstat.geom_2.2-2.tar.gz) = 718756 bytes
+BLAKE2s (R/spatstat.geom_3.2-7.tar.gz) = c54dca2c350df4c3231eac3d66671e54335576c297841151e18534cf5ae4c1ee
+SHA512 (R/spatstat.geom_3.2-7.tar.gz) = d4096a24a1d8a4f073e8e46ed78f585036bd748aab76f567c53b66c236abb53d24ce4ec701b31fb79ea277e4192d758c2daf3116ba702ae8f54ccddc38f6886e
+Size (R/spatstat.geom_3.2-7.tar.gz) = 772736 bytes
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