CHANGES IN spatstat.geom VERSION 3.2-9 OVERVIEW o Some geometry code accelerated. NEW FUNCTIONS o summary.symbolmap, print.summary.symbolmap Method for 'summary' for symbol maps. SIGNIFICANT USER-VISIBLE CHANGES o as.rectangle Accelerated in many cases. o diameter.owin Accelerated when the window is a rectangle. o nncross.ppp Slightly accelerated. o owin Accelerated in many cases. CHANGES IN spatstat.geom VERSION 3.2-8 OVERVIEW o Improvements to window geometry code. o Improvements to symbol map displays. SIGNIFICANT USER-VISIBLE CHANGES o is.subset.owin Algorithm slightly modified to give better results when the two polygons share some common edges. o plot.ppp New argument 'minsize' specifies the size of the smallest symbol used to represent the marks, when the marks are numeric. o plot.ppp New argument 'zerosize' specifies the size of the symbol used to represent the mark value 0, when marks are numeric. o plot.symbolmap New argument 'representatives' specifies which data values will be shown in the plot. 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. CHANGES IN spatstat.geom VERSION 2.2-2 OVERVIEW o Bug fix in package information. CHANGES IN spatstat.geom VERSION 2.2-1 OVERVIEW o More options for converting a window to a mask. o Minor improvements and internal upgrades. NEW FUNCTIONS o owin2mask Convert a window to a mask, with various options, affecting the treatment of the boundary. SIGNIFICANT USER-VISIBLE CHANGES o where.max, where.min Argument 'x' may be either a pixel image (class 'im') or data that can be converted to a pixel image by 'as.im'. CHANGES IN spatstat.geom VERSION 2.2-0 OVERVIEW o We thank Warick Brown for contributions. o Buffer tessellation o New options for distmap.psp NEW FUNCTIONS o bufftess Distance buffer tessellation SIGNIFICANT USER-VISIBLE CHANGES o distmap.psp New arguments 'extras' and 'clip' CHANGES IN spatstat.geom VERSION 2.1-0 OVERVIEW o We thank Hank Stevens for contributions. o Extension to 'discretise'. o Bug fix in nncross o Minor improvements and bug fixes SIGNIFICANT USER-VISIBLE CHANGES o discretise New argument 'move.points' determines whether the point coordinates are also discretised. o summary.im Output improved when the image is empty (i.e. when all pixel values are undefined). BUG FIXES o nncross.ppp If the argument 'by' was given, some of the results were incorrect. [Spotted by Hank Stevens.] Fixed. o nncross.ppp, nncross.pp3 If 'iX' and 'iY' were given, some of the results were incorrect. Fixed. CHANGES IN spatstat.geom VERSION 2.0-1 OVERVIEW o Minor bug fix BUG FIXES o pixellate.ppp crashed if 'weights' contained any NA values. Fixed. CHANGES IN spatstat.geom VERSION 2.0-0 OVERVIEW o Reduced package dependence. o Improvement to venn.tess. o Changed default value of 'stringsAsFactors'. SIGNIFICANT USER-VISIBLE CHANGES o spatstat.geom No longer depends on 'spatstat.sparse'. o venn.tess New argument 'labels'. o hyperframe, as.im.function The formal default value of 'stringsAsFactors' has been changed to 'NULL' to conform to changes in R. (The actual default value is TRUE for R < 4.1.0 and FALSE for R >= 4.1.0) o plot.psp The code for 'style="width"' has been completely rewritten, so that it no longer depends on plot.linim, and is more efficient. The formal argument list has been extended. o integral.im Accelerated in the case where 'domain' is a tessellation. o cbind.hyperframe Row names are not altered (previously they were altered using 'make.names') o [.ppx New argument 'clip' BUG FIXES o colourmap If a colour map was applied to numbers lying outside the range of the colour map, the wrong number of NA's was sometimes produced. Fixed. o MinkowskiSum Crashed sometimes with an error message about 'sumconnected'. Fixed. o hyperframe Crashed if the argument 'row.names' was given and the hyperframe had exactly one row. Fixed. CHANGES IN spatstat.geom VERSION 1.65-8 OVERVIEW o Reduced package dependence. SIGNIFICANT USER-VISIBLE CHANGES o spatstat.geom No longer depends on 'spatstat.sparse'. CHANGES IN spatstat.geom VERSION 1.65-7 OVERVIEW o Tweak. CHANGES IN spatstat.geom VERSION 1.65-6 OVERVIEW o We thank Jean-Francois Coeurjolly for contributions. o Bug fix in 'inradius' BUG FIXES o inradius Coded incorrectly for rectangular windows. [Spotted by Jean-Francois Coeurjolly] Fixed. CHANGES IN spatstat.geom VERSION 1.65-5 OVERVIEW o Minor changes to satisfy CRAN. CHANGES IN spatstat.geom VERSION 1.65-4 OVERVIEW o Minor changes to satisfy CRAN. CHANGES IN spatstat.geom VERSION 1.65-3 OVERVIEW o NEWS file initialised. CHANGES IN spatstat.geom VERSION 1.65-2 OVERVIEW o Minor changes to satisfy CRAN. CHANGES IN spatstat.geom VERSION 1.65-1 OVERVIEW o Minor changes to satisfy CRAN. CHANGES IN spatstat.geom VERSION 1.65-0 OVERVIEW o Package initialised at version 1.65-0 from a subset of spatstat. o Increased speed for large datasets. o Bug fix in crossdist.pp3 with periodic distances. o Bug fixes and minor improvements. SIGNIFICANT USER-VISIBLE CHANGES o spatstat.geom The package 'spatstat.geom' has been created from a subset of the code in the original 'spatstat' package version 1.65-0. It contains definitions of geometrical objects (windows, point patterns, pixel images, etc) and operations on them (geometry, superposition, image arithmetic, etc). o Execution The 'spatstat.geom' package is slightly faster than the corresponding code in the 'spatstat' package, because the procedure for calling internal C functions has been streamlined. o dirichletEdges New argument 'clip'. o harmonise.im The result belongs to class 'solist' and 'imlist' so that it can be plotted. BUG FIXES o crossdist.pp3 Results with periodic=TRUE were partially incorrect. Fixed. o affine.owin For mask windows, the pixel resolution of the result was too fine, leading to very large datasets. Fixed. o affine.im If the transformation matrix was not diagonal, the pixel resolution of the result was too fine, leading to very large datasets. Fixed. o plot.ppp For a point pattern in a binary mask window, if both arguments 'col' and 'cols' were given, the points were coloured according to 'col', which was incorrect. Fixed. o dirichletEdges Crashed if any edges crossed the boundary of the window. Fixed. o unitname Spatial datasets with incorrect internal format (or using an out-of-date version of the spatstat format) caused an error if the 'units' package was loaded. Fixed.