CHANGES IN spatstat VERSION 3.3-0 OVERVIEW o Updated version dependencies for spatstat package family. o Updated documentation. CHANGES IN spatstat VERSION 3.2-1 OVERVIEW o List the history of all changes made to a function in spatstat. NEW FUNCTIONS o latest.changes Lists the recent changes that have been made to a particular function in the spatstat family of packages. CHANGES IN spatstat VERSION 3.2-0 OVERVIEW o Tweaks to documentation. CHANGES IN spatstat VERSION 3.1-1 OVERVIEW o Internal changes to satisfy CRAN. CHANGES IN spatstat VERSION 3.1-0 OVERVIEW o New package 'spatstat.univar' o Minor internal improvements. PACKAGE DEPENDENCE o spatstat.univar The new package 'spatstat.univar' has joined the spatstat family. It supports estimation and manipulation of probability distributions of one-dimensional random variables. Some functions have been moved from 'spatstat.geom', 'spatstat.random' and 'spatstat.explore' into the new package 'spatstat.univar'. SIGNIFICANT USER-VISIBLE CHANGES o spatstat.family The list of sub-packages now includes 'spatstat.univar'. CHANGES IN spatstat VERSION 3.0-8 OVERVIEW o Updated package dependencies and documentation. o Vignette on shapefiles updated and reinstated. SIGNIFICANT USER-VISIBLE CHANGES o Vignette 'shapefiles' This vignette has been updated. The new version uses package 'sf' instead of the defunct package 'maptools'. CHANGES IN spatstat VERSION 3.0-7 OVERVIEW o New vignette on function objects (class 'fv' and 'envelope') o Vignette on shapefiles temporarily removed. o Updated cross-references to sub-packages. o Minor changes to package information. SIGNIFICANT USER-VISIBLE CHANGES o Vignette 'fv' New vignette which explains how to manipulate and plot objects of class 'fv' and 'envelope'. o Vignette 'shapefiles' This vignette has been temporarily removed because of its dependence on the defunct packages 'sp' and 'maptools'. It will be rewritten and reinstated soon. CHANGES IN spatstat VERSION 3.0-6 OVERVIEW o Updated cross-references to sub-packages. o Package documentation corrected and updated. CHANGES IN spatstat VERSION 3.0-5 OVERVIEW o Package documentation repaired (latex package issues). CHANGES IN spatstat VERSION 3.0-4 OVERVIEW o Package version information updated. o Minor omissions corrected in vignettes. o Package documentation corrected and updated. CHANGES IN spatstat VERSION 3.0-3 OVERVIEW o Package version information updated. o Minor errors corrected in vignettes. CHANGES IN spatstat VERSION 3.0-2 OVERVIEW o Internal tweaks. CHANGES IN spatstat VERSION 3.0-1 OVERVIEW o Package nicknames are temporarily suppressed. CHANGES IN spatstat VERSION 3.0-0 OVERVIEW o Further split of the spatstat family of packages. o All package versions have been updated to 3.0-x. SIGNIFICANT USER-VISIBLE CHANGES o Package structure The package 'spatstat.core' has been split into two packages called 'spatstat.explore' (for exploratory data analysis) and 'spatstat.model' (for modelling and formal inference). o Package dependence 'spatstat' now depends on the new packages 'spatstat.explore' and 'spatstat.model' which have replaced the old package 'spatstat.core'. o spatstat.family Packages 'spatstat.explore' and 'spatstat.model' have been added and 'spatstat.core' has been deleted from the list of packages. o bugfixes, latest.news Updated to cover the new sub-packages 'spatstat.explore' and 'spatstat.model'. CHANGES IN spatstat VERSION 2.3-4 OVERVIEW o Minor bug fixes and improvements. BUG FIXES o latest.news Did not include news from the new package 'spatstat.random'. Fixed. o spatstat.family Omitted the new package 'spatstat.random'. Fixed. CHANGES IN spatstat VERSION 2.3-3 OVERVIEW o Minor internal changes. CHANGES IN spatstat VERSION 2.3-1 OVERVIEW o spatstat depends on the package 'spatstat.random' SIGNIFICANT USER-VISIBLE CHANGES o package dependence spatstat now depends on the new package 'spatstat.random'. CHANGES IN spatstat VERSION 2.3-0 OVERVIEW o Minor tweaks to package information and documentation o The NEWS file for package='spatstat' now contains only the news for the sub-package 'spatstat'. Other changes in the spatstat family of packages are reported in the NEWS file for the relevant sub-package. o 'latest.news' now collects news from all packages in the spatstat family o 'bugfixes' now collects bug fixes from all packages in the spatstat family o New function 'spatstat.family' NEW FUNCTIONS o spatstat.family Return the names of all packages in the spatstat family. SIGNIFICANT USER-VISIBLE CHANGES o latest.news Now gives the latest news for all packages in the spatstat family. o bugfixes Now lists bugs reported for all packages in the spatstat family. CHANGES IN spatstat VERSION 2.2-0 OVERVIEW o Minor tweaks to package information CHANGES IN spatstat VERSION 2.1-0 OVERVIEW o Minor changes to package structure. CHANGES IN spatstat VERSION 2.0-1 OVERVIEW o Minor changes to satisfy CRAN checks. CHANGES IN spatstat VERSION 2.0-0 OVERVIEW o We thank Corey Anderson, Michael Chirico, Andy Craig, Marcelino de la Cruz, Tilman Davies, Pavel Fibich, Kurt Hornik, Gopalan Nair, Yonatan Rosen and Rasmus Waagepetersen for contributions. o spatstat has been divided into 7 sub-packages (spatstat.utils, spatstat.data, spatstat.sparse, spatstat.geom, spatstat.core, spatstat.linnet and spatstat). o spatstat now depends on R version 3.5.0 or later. o Version nickname: "Caution: contains small parts" SIGNIFICANT USER-VISIBLE CHANGES o package structure The original 'spatstat' package has been divided into 7 sub-packages (spatstat.utils, spatstat.data, spatstat.sparse, spatstat.geom, spatstat.core, spatstat.linnet and spatstat). The remaining 'spatstat' package requires all the other sub-packages. Your existing code scripts should still work with minimal changes. o sessionInfo Output now lists packages that are imported but not loaded. o sessionLibs Package names are now sorted alphabetically. CHANGES IN spatstat VERSION 1.64-1 OVERVIEW o Important bug fix in vcov.ppm o Relative risk estimation may include case weights. o We thank Ian Buller, Brian Ripley, Maximilian Vogtland and Maximilian Hesselbarth for contributions. o Nickname: 'Help you I can, yes!' SIGNIFICANT USER-VISIBLE CHANGES o rshift.ppp, rshift.splitppp New argument 'nsim'. o relrisk.ppp New argument 'weights'. o density.splitppp New argument 'weights'. BUG FIXES o vcov.ppm Variances were sometimes overestimated for Gibbs models. That is, entries of the Fisher information matrix were underestimated, because some contributions due to interaction were omitted (due to a coding error). Fixed. o density.ppp Crashed when se=TRUE if there were multiple columns of 'weights'. Fixed. o rbind.hyperframe Crashed unless all arguments had the same number of rows. (Spotted by Maximilian Vogtland). Fixed. CHANGES IN spatstat VERSION 1.64-0 OVERVIEW o We thank Robert Aue, Tilman Davies, Greg McSwiggan, Tyler Rudolph and Rasmus Plenge Waagepetersen for contributions. o Interactive graphics functions have been removed to a separate package. o spatstat no longer needs the packages 'tcltk' and 'rpanel'. o The suggested package 'maptools' should be version 0.9-9 or later. o Important bug fix in density.ppp. o Add new vertices to a linear network. o Relative risk estimation on a network. o Leave-one-out density estimation on a network. o Improvements and extensions to linear networks code. o Improvements to 'nndist' methods. o Function lengths.psp has been renamed lengths_psp. o Bug fixes related to mppm. o Stability improvements. o Version nickname: 'Susana Distancia' NEW FUNCTIONS o relrisk.lpp Method for 'relrisk' for point patterns on a linear network. o bw.relrisklpp Bandwidth selection for relative risk on a network. o densityfun.lpp Method for 'densityfun' for point patterns on a linear network. o addVertices Add new vertices to a network, at locations outside the existing network. o lengths_psp This is the new name of the function 'lengths.psp', which had to be changed because of a conflict with the generic 'lengths'. o densityEqualSplit The equal-split algorithm for kernel density estimation on a network is now visible as a separate function. o densityHeat The heat-equation algorithm for kernel density estimation on a network is now visible as a separate function. It has also been extended to computing leave-one-out density estimates at the data points. o hotrod Compute the heat kernel kappa(u,v) on a one-dimensional line segment. o heatkernelapprox Calculate an approximation to the value of the heat kernel on a network evaluated at the source point, kappa(u,u). SIGNIFICANT USER-VISIBLE CHANGES o nndist.pp3, nndist.ppx, nndist.lpp These functions now recognise the argument 'by' allowing computation of the nearest distance to each group of points. o pairdist.lpp, crossdist.lpp These functions can now handle large networks, using the sparse representation. o density.lpp, densityQuick.lpp Infinite bandwidth (sigma=Inf) is now permitted, and results in a density estimate that is constant over all locations. o as.linnet.psp The resulting network now has an attribute 'camefrom' indicating the provenance of each line segment in the network. o as.linnet.linnet New argument 'maxsize'. o repairNetwork Increased capability of detecting and repairing inconsistencies. o joinVertices New argument 'marks'. o insertVertices Marks attached to the lines of the network are now retained. o as.lpp Accepts more data formats. o iplot, iplot.ppp, iplot.layered, iplot.linnet, iplot.default These interactive plotting functions have been removed from spatstat into a new package 'spatstat.gui' o istat This interactive analysis function has been removed from spatstat into a new package 'spatstat.gui' o crossdist.lpp New argument 'check'. o lengths.psp This function will soon be Deprecated, in favour of the new name 'lengths_psp' o density.lpp Formal arguments changed. No effect on usage. o integral.linim Now handles complex-valued functions. o transect.im New argument 'nsample'. o bw.lppl Accelerated when distance="path". o collapse.fv Recognises the abbreviations used by fvnames() BUG FIXES o density.ppp Edge correction factors were calculated incorrectly when the window was not a rectangle, causing a negative bias in the estimated intensity. [Spotted by Tilman Davies.] Bug introduced in spatstat 1.57-0, october 2018. Fixed. o mppm Internal data were malformed if the interaction was Hardcore() or MultiHard() or a hybrid involving these interactions. This caused various errors when the fitted model was used. Fixed. o mppm Ignored the arguments 'nd' and 'eps' controlling the quadrature scheme. Fixed. o "[.linnet", "[.lpp" In X[W] where W is a window, if a vertex of the network lay exactly on the boundary of W, an edge of length zero was created. Fixed. o valid.ppm Crashed sometimes when applied to the result of subfits(). Fixed. o as.im.densityfun Crashed if argument W was missing. Fixed. o as.linnet.linnet This code could crash the R session, when sparse=FALSE, if there was insufficient memory available to create the matrix of distances between all pairs of network vertices. Fixed. o Summary.linim A spurious warning was generated when the operation any() or all() was applied to a logical-valued image on a network. Fixed. o "[<-.linim" Crashed if the assignment would have replaced some existing NA values. Fixed. CHANGES IN spatstat VERSION 1.63-3 OVERVIEW o Minor changes for compatibility with future versions of R o Minor improvements o Version nickname: "Wet paint" SIGNIFICANT USER-VISIBLE CHANGES o plot.ppp The coordinate axes will be plotted if axes=TRUE. Axis labels xlab, ylab will be plotted if ann=TRUE. CHANGES IN spatstat VERSION 1.63-2 OVERVIEW o Minor changes to satisfy the package checker. o Version nickname: "I'm sorry Dave, I'm afraid I can't do that" CHANGES IN spatstat VERSION 1.63-1 OVERVIEW o Enhancement to plot.linim o Fill missing pixel values by taking the nearest defined pixel value. o Minor improvements and bug fixes. o spatstat now requires spatstat.utils version 1.17-0. o Version nickname: 'Made from recycled electrons' NEW FUNCTIONS o is.linim Tests whether an object belongs to class 'linim'. o nearestValue Given a pixel image on a subset of a rectangle, extend the image to the entire rectangle, using the nearest well-defined pixel value. SIGNIFICANT USER-VISIBLE CHANGES o markconnect Runs faster and handles much larger datasets. o markvario Runs faster and handles much larger datasets. o markcorr, markconnect, markvario The 'weights' can now be an expression to be evaluated, or a function, or a pixel image, as well as a numeric vector. o Smooth.ppp The 'weights' can now be an expression to be evaluated, or a function, or a pixel image, as well as a numeric vector. o rpoislpp If 'lambda' is a list of 'linim' or 'linfun' objects, then the argument L can be omitted. o plot.linim New argument 'fatten' improves visual appearance when style="colour". o plot.im, plot.owin The coordinate axes will be plotted if axes=TRUE. Axis labels xlab, ylab will be plotted if ann=TRUE. o bugfixes If sincedate="all" or sinceversion="all", then all bugs will be listed. o Jfox New argument 'warn.trim' makes it possible to suppress repeated warnings. o requireversion New argument 'fatal' BUG FIXES o predict.rhohat, simulate.rhohat When applied to a 'rhohat' object computed from linear network data (lpp or lppm), there was a warning about the lengths of vectors, and the results were incorrect. Fixed. o predict.rhohat, simulate.rhohat Crashed when applied to a 'rhohat' object computed from *multitype* linear network data (multitype lpp or lppm). Fixed. o Jfox envelope() commands using the summary function 'Jfox' crashed sometimes with a message about illegal spacing of 'r' values. Fixed. o leverage, influence, dfbetas Crashed when applied to an 'ippm' object in which the irregular components of the score, but not the Hessian, were provided by symbolic differentiation. Fixed. o parres Crashed in rare circumstances, when the data did not contain enough useable values to perform smoothing. Fixed. CHANGES IN spatstat VERSION 1.63-0 OVERVIEW o Compute minimum or maximum nearest-neighbour distance between each pair of types in a multitype point pattern. o Important bug fix in simulations of the multitype hard core process. o Numerous improvements and bug fixes. o Deprecated functions have been removed. o Version nickname: "Trees in space" SIGNIFICANT USER-VISIBLE CHANGES o minnndist, maxnndist New argument 'by' makes it possible to find the minimum or maximum nearest neighbour distance between each pair of possible types in a multitype pattern. o beachcolours If 'sealevel' lies outside 'srange', then 'srange' will be extended to include it (without a warning). o split<-.ppp The default for argument 'un' in 'split<-.ppp' now agrees with the default for the same argument in 'split.ppp'. o lineardisc New argument 'add'. Default plotting behaviour has changed. o rmh, rmh.default The printed output of the debugger (invoked by snoop=TRUE) has been improved. o plot.owin New argument 'use.polypath' controls how to plot a filled polygon when it has holes. o plot.profilepl This function has now been documented, and the graphics improved. o erode.owin, dilate.owin These deprecated functions have now been deleted (replaced by erosion.owin and dilation.owin) o delaunay.distance, delaunay.network These deprecated functions have now been deleted (replaced by delaunayDistance, delaunayNetwork) o dirichlet.edges, dirichlet.network, dirichlet.vertices, dirichlet.weights These deprecated functions have now been deleted (replaced by dirichletEdges, dirichletNetwork, dirichletVertices, dirichletWeights) BUG FIXES o rmh, simulate.ppm, MultiHard Simulated realisations of the multitype hard core model were completely incorrect (the interaction was effectively removed, changing the model into a Poisson process). Fixed. o kppm, AIC For kppm models fitted with method='clik2', the resulting value of logLik() was equal to 1/2 of the correct value. This would have affected model comparison using AIC, and model selection using step(). Fixed. o hyperframe Did not correctly handle date-time values (columns of class 'Date', etc). Fixed o rlpp The resulting pattern was unmarked even when it should have been multitype. Fixed. o idw Estimates were zero if 'se=TRUE' and 'power != 2' and 'at="pixels"'. Fixed. o model.matrix.mppm Sometimes returned a matrix with the wrong number of rows. Fixed. o nncross.ppp Format of output was incorrect if X was an empty pattern. Fixed. o rmh, rmh.default For a marked point process, the debugger did not display the marks. (The rmh debugger is invoked by calling rmh with snoop=TRUE). Fixed. o pairs.im, pairs.linim The argument 'labels' was sometimes ignored. Fixed. o as.im.data.frame Results were incorrect for factor-valued data. Fixed. o relrisk.ppp Crashed if there were more than 2 types of points and method = "leastsquares" or "weightedleastsquares". Fixed. o as.im.nnfun Crashed when applied to a function generated by nnfun.psp. Fixed. o diagnose.ppm Crashed for some models with an error message from 'beachcolours'. Fixed. o predict.rho2hat Crashed if one of the original covariates was a function rather than an image. Fixed. o lineardisc Crashed in some graphics environments. Fixed. o lineardisc Crashed if the network segments had marks. Fixed. o rmh Crashed for multitype models if 'nsave' was specified. Fixed. o vcov.mppm, simulate.mppm Crashed for multitype models with a hardcore interaction component. Fixed. o effectfun Crashed if 'covname' was not the name of a covariate appearing in the model and was not one of the reserved names 'x', 'y', 'marks'. Fixed. CHANGES IN spatstat VERSION 1.62-2 OVERVIEW o Urgent bug fixes and workarounds. o Version nickname: "Shape-shifting lizard" SIGNIFICANT USER-VISIBLE CHANGES o colourmap Argument 'col' is now permitted to have length 1, representing a colour map in which all values are mapped to the same colour. o lut Argument 'outputs' is now permitted to have length 1, representing a lookup table in which all inputs are mapped to the same output value. BUG FIXES o envelope Crashed sometimes, with a message about unrecognised arguments, when applied to a summary function created by the user. Fixed. CHANGES IN spatstat VERSION 1.62-1 OVERVIEW o We thank Mohammad Ghorbani, Ute Hahn, Abdollah Jalilian, Nestor Luambua, Greg McSwiggan, Annie Mollie and Jakob Gulddahl Rasmussen for contributions. o spatstat now requires spatstat.utils version 1.15-0 and goftest version 1.2-2. o Nearest Neighbour Index function can now return mark values. o Important fix in Ripley isotropic correction. o Index of repulsion strength for determinantal point process models. o Nearest neighbours between two point patterns in any number of dimensions. o More options for handling bad simulation outcomes in envelope(). o Bandwidth selectors warn about extreme values of bandwidth. o Tessellations on a linear network can now have marks. o New functions for simulating point processes on a linear network. o More functions for manipulating tessellations on a linear network. o mppm accepts case weights. o Bug fixes and minor improvements. o Nickname: 'An update which will live in infamy' NEW FUNCTIONS o repul Repulsiveness index for a determinantal point process model. o reach.kppm Reach (interaction distance) for a Cox or cluster point process model. o summary.dppm, print.summary.dppm Summary method for determinantal point process models. o nncross.ppx Nearest neighbours between two point patterns in any number of dimensions. o uniquemap.matrix Method for uniquemap for matrices. o repairNetwork Detect and repair inconsistencies in internal data in a linnet or lpp object. o marks<-.lintess, unmark.lintess Assign marks to the tiles of a tessellation on a linear network. o marks.lintess Extract the marks of the tiles of a tessellation on a linear network. o tilenames.lintess Extract the names of the tiles in a tessellation on a linear network o tilenames<-.lintess Change the names of the tiles in a tessellation on a linear network o nobjects.lintess Count the number of tiles in a tessellation on a linear network o as.data.frame.lintess Convert a tessellation on a linear network into a data frame. o rcelllpp Simulate the cell point process on a linear network o rSwitzerlpp Simulate the Switzer-type point process on a linear network o intersect.lintess Form the intersection of two tessellations on a linear network o chop.linnet Divide a linear network into tiles using infinite lines SIGNIFICANT USER-VISIBLE CHANGES o lintess New argument 'marks' Tessellations can now have marks. o tilenames, tilenames<- These functions are now generic, with methods for 'tess' and 'lintess' o mppm New argument 'weights' specifies case weights for each row of data. o unstack.lintess Now handles marks. o plot.lintess Modified to display the marks attached to the tiles. Changed options: style=c("colour", "width", "image"). o as.linfun.lintess The default function values are the marks. o print.lintess, summary.lintess, print.summary.lintess Output now includes information about marks. o nnfun.ppp, nnfun.psp, nnfun.lpp New argument 'value' specifies whether to return the index of the nearest neighbour or the mark value of the nearest neighbour. o envelope.ppp, envelope.ppm, envelope.kppm, envelope.pp3 New arguments 'rejectNA' and 'silent'. o envelope.lpp, envelope.lppm New arguments 'maxnerr', 'rejectNA' and 'silent'. o plot.psp New argument 'col' gives control over the colour map representing the values of marks attached to the segments. o plot.im Some warnings are suppressed when do.plot=FALSE. o plot.linim New explicit argument 'box' determines whether to plot a bounding box. Default is now FALSE in all cases. o Kest, Kinhom, pcf, pcfinhom, edge.Ripley Calculation of isotropic edge correction for polygonal windows has changed slightly. Results are believed to be more accurate. Computation has been accelerated by about 20 percent in typical cases. o bw.diggle, bw.ppl, bw.lppl, bw.pcf, bw.CvL, bw.voronoi A warning is issued if the optimal value of the cross-validation criterion occurs at an endpoint of the search interval. New argument 'warn'. o mad.test, dclf.test, dg.test, bits.test Function values which are infinite, NA or NaN are now ignored in the calculation (with a warning) instead of causing an error. Warning messages are more detailed. o rmhcontrol, rmh The parameter 'nsave' can now be a vector of integers. o diagnose.ppm Accelerated, when type="inverse", for models without a hard core. o uniquemap.data.frame Accelerated for some cases. o vcov.ppm, vcov.mppm New argument 'nacoef.action' specifies what to do if some of the fitted coefficients are NA, NaN or Inf. o Lest, Linhom, Ldot, Lcross, Ldot.inhom, Lcross.inhom These summary functions now have an explicit argument 'correction'. Behaviour is unchanged. o bugfixes Arguments sinceversion="book" or sincedate="book" are interpreted to give all bugs reported after publication of the spatstat book. o cbind.hyperframe, rbind.hyperframe The result now retains the row.names of the original arguments. o print.summary.owin More information is printed. o append.psp Arguments may be NULL. o as.psp Now permits a data frame of marks to have only one column, instead of coercing it to a vector. BUG FIXES o as.linnet.psp Sometimes produced a network with duplicated segments. [Such objects can be repaired using 'repairNetwork'.] Fixed. o edge.Ripley, Kest, Kinhom Isotropic correction weights for polygonal windows were sometimes incorrect for small radius 'r' if the polygon contained many small segments [spotted by Annie Mollie] or if the polygon was very long and thin [spotted by Nestor Luambua]. Problem arose in spatstat 1.60-0. Fixed. o lppm Did not correctly handle the case where the left-hand side of the formula is the name of an entry in the 'data' argument. Fixed. o plot.lpp Did not correctly handle the argument 'which.marks'. Fixed. o plot.im Did not correctly handle the argument 'ribargs$at'. Fixed. o density.lpp Sometimes requested a larger value of 'iterMax' but ignored it. Fixed. o [.linnet, [.lpp Crashed if x contained inconsistent internal data (when index 'j' was a window, and snip=TRUE). Fixed. o plot.linim Crashed if the pixel values were complex numbers. Fixed. o plot.linfun Crashed if the function values were complex numbers. Fixed. o integral.linim, mean.linim Crashed if the image had logical values. Fixed. o Re, Im, Arg, Mod, Conj For pixel images on a linear network (class 'linim') these operations crashed if the pixel values were complex numbers. o studpermu.test Crashed if the hyperframe was very large. Fixed. o studpermu.test Crashed in some cases when the simulated functions were incompatible with each other, due to the use of different edge corrections. Fixed. o vcov.ppm, print.ppm, summary.ppm Crashed in some cases if the fitted coefficients were NA. Fixed. o quantess.owin, quantess.ppp, quantess.im Crashed in some cases because the tile labels were not unique. Fixed. o plot.pp3 Did not correctly handle graphical arguments ('col', 'pch', 'cex') if they were vectors [Spotted by Abdollah Jalilian]. Fixed. o shift.linnet Generated a spurious warning. Fixed. o density.lpp, lixellate Crashed in some cases when a data point was exactly at a vertex. [Spotted by Jakob Gulddahl Rasmussen.] Fixed. o plot.linim Crashed (when style="width") if any pixel values were NaN. Fixed. o Fest, Jest, Jdot, Jcross, Hest, Iest, rectcontact envelope() commands using one of these summary functions crashed sometimes with a message about illegal spacing of 'r' values. Fixed. o plot.linnet, plot.psp Ignored argument 'col' when style="width". Fixed. o rshift.psp Crashed if X had a data frame of marks. [Spotted by Ute Hahn.] Fixed. o Kscaled Crashed if Ripley's isotropic edge correction was selected but the translation edge correction was not. Fixed. CHANGES IN spatstat VERSION 1.61-0 OVERVIEW o We thank Jordan Brown, Tilman Davies and Greg McSwiggan for contributions. o Fast kernel estimation on a linear network using 2D kernels. o Nonparametric maximum likelihood estimation of 'rho'. o Extension of Scott's rule for bandwidth selection. o Cross-validated bandwidth selection on a linear network. o More support for character-valued images. o Random thinning of clumps. o Bug fixes and minor improvements. o Nickname: 'Puppy zoomies' NEW FUNCTIONS o densityQuick.lpp Fast kernel estimator of point process intensity on a network using 2D smoothing kernel. o bw.scott.iso Isotropic version of Scott's rule (for point patterns in any dimension). o data.lppm Extract the original data point pattern from a fitted model of class 'lppm'. o rthinclumps Divide a spatial region into clumps and randomly delete some of them. o dimnames.hyperframe, dimnames<-.hyperframe Methods for extracting and changing the 'dimnames' of a hyperframe. SIGNIFICANT USER-VISIBLE CHANGES o rhohat Estimation by nonparametric maximum likelihood is now supported, assuming the intensity is a monotone function of the covariate. New options: smoother="increasing" and smoother="decreasing". o density.lpp New argument 'distance' offers a choice of different kernel methods. o bw.scott Now handles point patterns of any dimension. New arguments 'isotropic' and 'd'. o bw.ppl New argument 'shortcut' allows faster computation. Additional arguments '...' are now passed to density.ppp. o [<-.im New argument 'drop' controls behaviour when indices are missing as in 'x[] <- value' o mppm Now supports 'self-starting' interactions. o as.im New argument 'stringsAsFactors' is recognised by many methods. It enables the creation of character-string-valued images. o plot.im Axes are now prevented from extending outside the image rectangle. o plot.im New argument 'zap'. o blur New argument 'kernel'. o Smooth.im New argument 'kernel'. o quadrat.test New argument 'df.est'. o edge.Ripley Numerical stability has been improved on some platforms. Results may have changed in marginal cases (e.g. where the circle of radius r centred at X is tangent to an edge of the polygonal window). o rownames, rownames<-, colnames, colnames<- These operations now work for hyperframes. o quadrat.test Improved labelling of test when argument 'CR' is given. o plot.pppmatching This existing function now has a help file. New argument 'adjust'. o solist, is.sob, lintess Objects of class 'lintess' are now recognised as 2D spatial objects for the purposes of solist() and is.sob(). o as.linfun.lintess Functions created by as.linfun.lintess() now generate better output when the function is printed. BUG FIXES o densityVoronoi.lpp Did not correctly handle patterns containing duplicated points. Fixed. o quadrat.test Argument 'CR' was ignored when method="MonteCarlo". Fixed. o localKcross.inhom, localLcross.inhom Argument lambdaX was ignored. Fixed. o "[.linim" Factor values were erroneously converted to integers, in some cases. Fixed. o "[<-.hyperframe" Did not handle some classes of objects correctly. Fixed. o effectfun In a multitype point process model, effectfun() ignored any user-specified value of 'marks'. Fixed. o as.linim.linfun Additional arguments (other than spatial coordinates) were ignored. Fixed. o plot.solist Display output was mangled if one entry in the list was an object that would normally generate multiple panels of graphics, such as an 'lpp' or 'tess' object with multiple columns of marks, or a marked 'msr', 'leverage.ppm' or 'influence.ppm' object. Fixed. o plot.lpp Return value was mangled when x had multiple columns of marks. Fixed. o colourtable Crashed in some cases when 'breaks' was given. Fixed. o rLGCP Crashed if 'win' was not a rectangle and 'mu' was not a constant. Fixed. o intersect.tess Crashed if 'Y' was a window object and 'keepmarks=TRUE'. Fixed. o envelope.lppm Crashed if argument 'simulate' was given. Fixed. o unstack.solist Did not correctly handle objects of class 'lintess'. o unstack.solist Did not correctly handle objects of class 'tess' if they had multiple columns of marks. o plot.pppmatching Issued spurious warnings about unrecognised plot arguments. Fixed. o plot.lintess Issued spurious warnings about unrecognised plot arguments. Fixed. o shift.lpp, rotate.lpp Issued spurious warnings if argument 'origin' was given. Fixed. CHANGES IN spatstat VERSION 1.60-1 OVERVIEW o Version number incremented for administrative reasons. CHANGES IN spatstat VERSION 1.60-0 OVERVIEW o We thank Ottmar Cronie, Tilman Davies, Andrew Hardegen, Tom Lawrence, Robin Milne, Mehdi Moradi, Gopalan Nair, Tim Pollington and Suman Rakshit for contributions. o Random thinning and random labelling of spatial patterns extended to different types of pattern. o Confidence intervals for multitype K functions. o Envelopes for balanced two-stage test o Accelerated some code. o Minor bug fixes and improvements. o Package built under R 3.6.0. o Version nickname: 'Swinging Sixties' NEW FUNCTIONS o bits.envelope Global simulation envelope corresponding to bits.test, the balanced independent two-stage Monte Carlo test. o extrapolate.psp Extrapolate line segments to obtain infinite lines. o uniquemap Map duplicate points to unique representatives. Generic with methods for ppp, lpp, ppx o uniquemap.data.frame Map duplicate rows to unique representatives o localKcross, localLcross, localKdot, localLdot, localKcross.inhom, localLcross.inhom Multitype local K functions. SIGNIFICANT USER-VISIBLE CHANGES o lohboot Now works for multitype K functions Kcross, Kdot, Lcross, Ldot, Kcross.inhom, Lcross.inhom. o Kinhom, pcfinhom Leave-one-out calculation is implemented when 'lambda' is a fitted model of class 'dppm'. o Kcross.inhom, Kdot.inhom, Lcross.inhom, Ldot.inhom Leave-one-out calculation is implemented when 'lambdaX' is a fitted model of class 'dppm'. o rthin, rlabel These functions now work on point patterns of all classes (ppp, lpp, pp3, ppx) and line segment patterns (psp). o bw.abram New argument 'smoother' determines how the pilot estimate is computed. Formal arguments rearranged. o plot.im New argument 'riblab'. o rlabel New arguments 'nsim' and 'drop'. o localK, localKinhom New argument 'rmax'. o rLGCP Accelerated. o anyDuplicated.ppp Accelerated. o duplicated.ppp Accelerated, in most cases. o simulate.kppm Accelerated, for LGCP models. o predict.ppm Accelerated, for models fitted with method="VBlogi" o print.rmhmodel Output improved. BUG FIXES o plot.linim, plot.linfun Not all the entries of 'leg.args' were passed to text.default. Fixed. o densityVoronoi.ppp Did not correctly handle patterns containing duplicated points. Fixed. o markcorr The argument 'correction="none"' did not generate any results. [Spotted by Tim Pollington.] Fixed. o names<-.fv Did not adjust the plotting formula, so that a subsequent call to plot.fv would complain about missing variables. Fixed. o im.apply Crashed if 'FUN' returned factor values. Fixed. o stienenSet Crashed if the data contained duplicated points. Fixed. o predict.ppm, effectfun Crashed in some cases, with the message 'ncol(x)=nrow(v) is not TRUE'. Fixed. o parres Crashed in some cases, with the message 'logical subscript too long'. Fixed. o dclf.test, mad.test, dg.test, bits.test Crashed in some cases if the summary function values were infinite or NA. Fixed. CHANGES IN spatstat VERSION 1.59-0 OVERVIEW o We thank Lucia Cobo Sanchez, Tilman Davies, Maximilian Hesselbarth, Kassel Hingee, Mehdi Moradi, Suman Rakshit, Jan Sulavik and Luke Yates for contributions. o Extensions to adaptive intensity estimators. o 'Dartboard' tessellation using polar coordinates. o Performance improvements. o Minor improvements and bug fixes. o Version nickname: "J'ai omis les oeufs de caille" NEW FUNCTIONS o polartess Tessellation using polar coordinates. o bw.abram Variable bandwidths for adaptive smoothing, using Abramson's Rule. o densityAdaptiveKernel Calculates adaptive estimate of point process intensity using variable-bandwidth kernel estimation. o densityVoronoi, densityVoronoi.ppp Calculates adaptive estimate of point process intensity using tessellation methods. This is an extension of the old function adaptive.density. o densityVoronoi.lpp Voronoi or smoothed Voronoi estimator of intensity for point pattern on a linear network. o coords.quad New method for 'coords', to extract the coordinates of the points in a quadrature scheme. o lineartileindex Low-level function to classify points on a linear network according to which tile of a tessellation they fall inside. SIGNIFICANT USER-VISIBLE CHANGES o latest.news Now prints news documentation for the current major version, by default. New argument 'major'. o quantess The covariate Z can now be "rad" or "ang" representing polar coordinates. New argument 'origin' specifies the origin of polar coordinates. New argument 'eps' controls accuracy of calculation. o envelope The argument 'simulate' can now be a function (such as 'rlabel'). The function will be applied repeatedly to the original data Y, and should yield point patterns of the same kind. o adaptive.density This function can now perform adaptive estimation by two methods: either tessellation-based methods or variable-bandwidth kernel estimation. The calculations are performed by either 'densityVoronoi' or 'densityAdaptiveKernel'. o densityVoronoi This performs the calculations of the old function 'adaptive.density'. New argument 'fixed' specifies the subsampling. New argument 'method' allows a choice between the original algorithm and the recently described 'smoothed Voronoi' estimator. Default value of 'f' changed to 'f=1'. o pcf.ppp Now accepts correction="none". o pairorient Default edge corrections now include 'bord.modif'. o funxy Functions of class 'funxy' can now be applied to quadrature schemes. o lohboot Computation accelerated when the window is a rectangle. o nncorr, nnmean, nnvario New argument 'na.action'. o pp3 New argument 'marks'. o clusterfit New argument 'verbose'. o beachcolours, beachcolourmap Improved positioning of the yellow colour band. o linearK, linearpcf, linearKdot, linearKcross, linearpcfcross, linearpcfdot Computation accelerated for networks which are not connected. o as.linnet.psp Computation accelerated. o as.linfun.lintess Computation accelerated. o selfcut.psp Computation accelerated. The result now has an attribute "camefrom" indicating the provenance of each segment in the result. o bw.stoyan The rule has been modified so that, if the pattern is empty, it is now treated as if it contained 1 point, so that a finite bandwidth value is returned. o rebound.owin Now preserves unitnames of the objects. o rescale.owin, rescale.ppp, rescale.psp The geometrical type of the window is now preserved in all cases (previously if the window was polygonal but was equivalent to a rectangle, the rescaled window was a rectangle). o shift.im, shift.owin, shift.ppp, shift.psp More options for the argument 'origin'. o nnwhich.ppp, nnwhich.default Accelerated, in the case k > 1. o is.subset.owin Improved robustness against numerical error. o plot.im Improved behaviour when the pixel values are almost constant. o Finhom, Ginhom, Jinhom A warning is issued if bias is likely to occur because of undersmoothing. New arguments 'warn.bias' and 'savelambda'. o plot.colourmap Now handles a colourmap defined on an interval of length zero. o ewcdf Computation accelerated. New arguments 'normalise' and 'adjust'. The result does not inherit class 'ecdf' if normalise=FALSE. o spatialcdf Computation accelerated. The result does not inherit class 'ecdf' if normalise=FALSE. o effectfun New argument 'nvalues'. o parres The argument 'covariate' may be omitted if the model involves only one covariate. o alltypes If 'envelope=TRUE' and the envelope computation reaches the maximum permitted number of errors (maxnerr) in evaluating the summary function for the simulated patterns, then instead of triggering a fatal error, the envelope limits will be set to NA. o simulate.kppm Additional arguments '...' are now passed to the function that performs the simulation. BUG FIXES o spatialcdf The argument 'weights' was ignored in some cases. Fixed. o ppp Points inside the window were erroneously rejected as lying outside the window, if the window was a polygon equivalent to a rectangle with sides longer than 10^6 units. Fixed. o inside.owin All results were FALSE if the window was a polygon equivalent to a rectangle with sides longer than 10^6 units. Fixed. o sumouter Result was incorrect (all entries were zero) if 'w' was missing and 'y' was given. Fixed. o extractbranch.lpp Point pattern coordinates were sometimes erroneously set to NA. Fixed. o beachcolours, beachcolourmap The number of colours was not always equal to 'ncolours'. [Spotted by Tilman Davies.] Fixed. o is.subset.owin Sometimes gave the wrong answer for polygonal windows due to numerical rounding error. Fixed. o update.kppm Crashed if the updating information was a point pattern and the original model call did not include a formula. Spotted by Luke Yates. Fixed. o incircle, inpoint Crashed if the window was extremely thin. Fixed. o effectfun Crashed in some obscure cases. Fixed. o closepairs.pp3 Crashed if distinct=FALSE and what="all". Fixed. o update.ippm Crashed if the model was fitted using method="logi". Fixed. o plot.msr Crashed sometimes if x was multitype and multiplot=FALSE. Fixed. o anova.mppm Crashed if applied to a single model, unless the current environment was the global environment. Fixed. o lurking.mppm If 'covariate' was a list of images, the code crashed sometimes with message 'Fisher information is singular'. Fixed. o im Crashed if 'mat' was a 1-dimensional table (class 'table'). Fixed. o dirichlet Crashed if the pattern was empty or contained only 1 point. Fixed. o rjitter Crashed if the pattern contained 0 or 1 points and the argument 'radius' was not specified. Fixed. o quantess.owin Crashed if Z was a function(x,y). Fixed. o quadrat.test The p-value was NA if one of the observed counts was zero, for the Cressie-Read tests with CR not equal to 1 or -1. Fixed. o quadratcount.ppp Sometimes issued an incorrect warning that data points were outside the tessellation, when 'tess' was a tessellation represented by a pixel image. Fixed. o as.linim.linfun Factor-valued functions were converted to integer-valued images. Spotted by Suman Rakshit. Fixed. o plot.linfun Did not display factor-valued functions correctly. Spotted by Suman Rakshit. Fixed. o dclf.test, mad.test Crashed, in rare cases, when applied to an 'envelope' object. Spotted by Jan Sulavik. Fixed. o plot.spatialcdf, plot.ewcdf A horizontal line was plotted at height 1, even if the CDF was unnormalised. Fixed. o plot.tess The names of the tiles were sometimes re-ordered in the legend. Fixed. o rThomas, rMatClust, rCauchy, rVarGamma If the simulation window was not a rectangle, the attribute 'Lambda' was a numeric vector, rather than a pixel image. Fixed. CHANGES IN spatstat VERSION 1.58-2 OVERVIEW o Venn diagram tessellation o Internal bug fixes. NEW FUNCTIONS o venn.tess Venn diagram tessellation. CHANGES IN spatstat VERSION 1.58-1 OVERVIEW o Bug fixes. o Version nickname: "Compliment Sandwich" BUG FIXES o lpp Did not correctly detect some situations where the input data are invalid. Fixed. o lurking.ppp, lurking.ppm Did not correctly detect some situations where the input data are invalid. Fixed. CHANGES IN spatstat VERSION 1.58-0 OVERVIEW o We thank Andrew Bevan, Hamidreza Heydarian and Andrew P Webster for contributions. o Mark-mark scatter plot. o Standard error calculation for inverse-distance weighting o Minor improvements and extensions. o Version nickname: 'Drop Bear' NEW FUNCTIONS o markmarkscatter Mark-mark scatterplot SIGNIFICANT USER-VISIBLE CHANGES o idw Standard errors can now be calculated by setting 'se=TRUE'. o im.apply Computation accelerated, especially when NA's are absent. New arguments 'fun.handles.na' and 'check'. o kppm, dppm, clusterfit Changed precedence rule for handling the algorithm parameters in the minimum contrast algorithm. Individually-named arguments 'q,p,rmax,rmin' now take precedence over entries with the same names in the list 'ctrl'. o rotmean Improved algorithm stability o summary.kppm Prints more information about algorithm convergence. o closepairs.pp3, crosspairs.pp3 Argument 'what' can take the value "ijd" o plot.onearrow Graphical parameters, specified when the object was created, are now taken as the defaults for graphical parameters to the plot. BUG FIXES o rotmean When result="im" the resulting image did not have the same dimensions as the input. [Spotted by Hamidreza Heydarian.] Fixed. o rotmean If argument 'origin' was given, and if result="im" was specified, the resulting image was wrongly displaced. Fixed. o runifpointx Result was mangled when n=0 or n=1. Fixed. CHANGES IN spatstat VERSION 1.57-1 OVERVIEW o Bug fixes. o Version nickname: 'Cartoon Physics' BUG FIXES o multiplicity.default Some entries of the result were incorrectly set to 1. Fixed. o anova.ppm Crashed if adjust=TRUE and the models were fitted with use.gam=TRUE. Fixed. CHANGES IN spatstat VERSION 1.57-0 OVERVIEW o We thank Corey Anderson, Ryan Arellano, Hadrien Commenges, Ottmar Cronie, Tilman Davies, Maximilian Hesselbarth, Kassel Hingee, Tomas Lazauskas, Marie-Colette van Lieshout, Rasmus Waagepetersen and 'daitakahashi' for contributions. o Cronie-van Lieshout bandwidth selection. o Smoothing functions handle non-Gaussian kernels. o Infinite smoothing bandwidths permitted. o Positive confidence limits for rhohat. o Improved bivariate interpolation. o subset() method for line segment patterns. o Important bug fixes in rthin and density.ppp o Minor bug fixes and improvements. o Version nickname: 'Zombie apocalypse' NEW FUNCTIONS o bw.CvL Cronie-Van Lieshout bandwidth selection for density estimation. [Contributed by Ottmar Cronie and Marie-Colette van Lieshout.] o subset.psp Method for 'subset' for line segment patterns. SIGNIFICANT USER-VISIBLE CHANGES o densityfun.ppp, Smoothfun.ppp, Smooth.ppp These commands now handle non-Gaussian kernels. o density.ppp, relrisk.ppp, Smooth.ppp, densityfun.ppp, Smoothfun.ppp Argument 'sigma' can be infinite. o interp.im New argument 'bilinear' specifies the choice of interpolation rule. o rhohat Methods for rhohat have a new argument 'positiveCI' specifying whether confidence limits should be positive. o plot.colourmap New argument 'increasing' specifies whether the colours are displayed in order left-to-right/bottom-to-top. Changed default behaviour for discrete colour maps when vertical=FALSE. o split.ppx Argument 'f' can be a logical vector. o relrisk.ppp If se=TRUE and at="pixels", the result belongs to class 'solist'. o imcov, setcov, convolve.im The name of the unit of length is preserved. o density.ppp Slightly accelerated for non-Gaussian kernels. o bw.scott The two bandwidth values in the result now have names ('sigma.x' and 'sigma.y'). o pairdist.default Now checks whether the data are valid 2-dimensional coordinates. o pixellate.ppp New argument 'savemap' o rtemper New argument 'track'. Code runs slightly faster. o eval.im, eval.linim New argument 'warn'. o Kres, Kcom, Gcom, psstG If any of the calculated weights for the summary function are infinite or NA, they are reset to zero, with a warning, instead of a fatal error. BUG FIXES o rthin If P was close to 1, the result was sometimes an empty point pattern when it should have been identical to X. [Spotted by Maximilian Hesselbarth.] Fixed. o density.ppp Standard error calculations were incorrect when sigma was a single numeric value. The output was equal to 'sqrt(sigma)' times the correct answer. Fixed. o density.ppp Result was incorrect for non-Gaussian kernels when at="points" and leaveoneout=FALSE. Fixed. o density.ppp Did not pass additional arguments "..." to a user-supplied kernel function, in some cases. Fixed. o as.im.function, as.im.funxy If the function values were factor values and the window was not a rectangle, the result was an image with all pixel values NA. [Spotted by Corey Anderson.] Fixed. o plot.funxy If the function values were factor values and the window was not a rectangle, the plot was empty. [Spotted by Corey Anderson.] Fixed. o nnorient Crashed if the border correction did not retain any data points. [Spotted by Tomas Lazauskas.] Fixed. o linim Crashed in some cases with a message about unitnames. Fixed. o density.lpp Default value of 'dx' was sometimes incorrect. Fixed. o rMatClust, rThomas, rCauchy, rVarGamma Issued a spurious warning about bandwidth selection when saveLambda=TRUE. Fixed. o density.ppp Issued a spurious warning about bandwidth selection when 'kernel' was a user-supplied function. Fixed. o clusterfield.function Issued a spurious warning about bandwidth selection. Fixed. o relrisk.ppp Issued a spurious warning if the argument 'case' or 'control' was given, for a bivariate point pattern. Fixed. o superimpose.ppp If 'W' was a character string or function, the behaviour was not exactly as described in the help file. Fixed. o plot.psp If the marks were factor values, the colour map was displayed upside down. Fixed. o eval.fv If one of the 'fv' objects included ratio information (class 'rat') then this was erroneously retained, in some cases. Fixed. o linearKcross Crashed (with a message about a missing value of 'correction') if there were no pairs of points to count. Fixed. o envelope.lpp Crashed (randomly) when fix.n=TRUE and fix.marks=TRUE. Fixed. CHANGES IN spatstat VERSION 1.56-1 OVERVIEW o We thank Agustin Lobo for contributions. o Improvements to infrastructure. o Bug fixes. o Version nickname: "Invisible Friend" NEW FUNCTIONS o as.im.expression New method for 'as.im' for expressions. o flipxy.tess Method for 'flipxy' for tessellations. SIGNIFICANT USER-VISIBLE CHANGES o sdr This is now a generic function, with a method for class 'ppp'. o pointsOnLines The result now has an attribute named "map" which maps each point to its parent line segment. o summary.lpp Improved output. o intersect.owin Argument 'fatal' now defaults to FALSE. o quadrature schemes (class "quad" and "logiquad") Improved print and summary methods. BUG FIXES o cut.lpp Crashed if the marks were a data frame or hyperframe. Fixed. o summary.lpp, print.summary.lpp Output was garbled if the marks were a data frame or hyperframe. Fixed. o integral.linim Crashed if the function had NA values. Fixed. o Tstat Crashed if ratio=TRUE. Fixed. o intersect.owin Ignored argument 'fatal' in some cases. [Spotted by Agustin Lobo.] Fixed. o plot.tess Crashed if do.col=TRUE and 'values' was a factor. Fixed. o pcf.ppp Crashed if 'domain' was given and ratio=TRUE. Fixed. o "[<-.sparse3Darray" Crashed if 'value' was one-dimensional and the indices i, j, k specified a two-dimensional subset of x. Fixed. o plot.quad Crashed if tiles=TRUE for a quadrature scheme created by quadscheme(method="dirichlet", exact=TRUE). Fixed. o bugtable Crashed if there were no bugs! Fixed. o sparse array code An array bounds violation (segmentation fault) could occur. Fixed. o internal code Numerous internal bugs have been fixed. CHANGES IN spatstat VERSION 1.56-0 OVERVIEW o We thank Sebastian Meyer and Suman Rakshit for contributions. o Kernel estimate of intensity as a function(x,y) o Extract discrete and continuous components of a measure. o Improvements and extensions to leverage and influence code. o Plot a line segment pattern using line widths. o Find connected components of each tile in a tessellation. o Geometrical operations on 'distfun' objects. o Join vertices in a linear network. o Distance map and contact distribution for rectangular structuring element. o An infinite number of infinitesimal bugs has been detected and fixed. o Version nickname: "Bondi Tram" NEW FUNCTIONS o densityfun, densityfun.ppp Compute a kernel estimate of intensity of a point pattern and return it as a function of spatial location. o as.im.densityfun Convert function(x,y) to a pixel image. o measureDiscrete, measureContinuous Extract the discrete and continuous components of a measure. o connected.tess Find connected components of each tile in a tessellation and make a new tessellation composed of these pieces. o dffit.ppm Effect change diagnostic DFFIT for spatial point process models. o shift.distfun, rotate.distfun, reflect.distfun, flipxy.distfun, affine.distfun, scalardilate.distfun Methods for geometrical operations on 'distfun' objects. o rescale.distfun Change the unit of length in a 'distfun' object. o plot.indicfun Plot method for indicator functions created by as.function.owin. o Smooth.leverage.ppm, Smooth.influence.ppm Smooth a leverage function or an influence measure. o integral.leverage.ppm, integral.influence.ppm Compute the integral of a leverage function or an influence measure. o mean.leverage.ppm Compute the mean value of a leverage function. o rectdistmap Distance map using rectangular metric. o rectcontact Contact distribution function using rectangular structuring element. o joinVertices Join specified vertices in a linear network. SIGNIFICANT USER-VISIBLE CHANGES o plot.psp Segments can be plotted with widths proportional to their mark values. New argument 'style'. o msr Infinite and NA values are now detected (if check=TRUE) and are reset to zero, with a warning. o leverage.ppm, influence.ppm, dfbetas.ppm Faster computation in some cases. o as.im.nnfun, as.im.smoothfun New argument 'approx' chooses between a fast, approximate algorithm and a slow, exact algorithm. o cdf.test More jittering is applied when jitter=TRUE. Warnings about tied values should not occur any more. o plot.im Improved behaviour when all pixel values are NA. o plot.tess Now generates a separate plot panel for each column of marks, if do.col=TRUE. New argument 'multiplot'. o pcfinhom Now handles correction='good' o solist New argument '.NameBase' o runifpointOnLines, rpoisppOnLines New argument 'drop' o plot.studpermutest This existing function now has a help file. o bdist.points Accelerated, for polygonal windows (thanks to Sebastian Meyer). o linnet When argument 'edges' is specified, the code now checks whether any edges are duplicated. BUG FIXES o kernel.moment Result was incorrect for kernel="cosine" and kernel="optcosine". Fixed. o "[.msr" Format was mangled if the subset contained exactly one quadrature point. Fixed. o tess If a list of tiles was given, and the tiles were pixel images or masks, their pixel resolutions were ignored, and reset to the default 128x128. Fixed. o plot.linim Ignored argument 'legend' when style="colour". [Spotted by Suman Rakshit.] Fixed. o leverage.ppm, influence.ppm, dfbetas.ppm Crashed sometimes if the model was fitted by method="logi". Fixed. o Smooth.ppp Crashed with some combinations of the arguments varcov and weights when X had several columns of marks. Fixed. o plot.tess Crashed sometimes when do.col=TRUE and values=NULL. Fixed. o dilation.ppp Crashed if polygonal=FALSE. o plot.tess Ignored the marks of a tessellation defined by a pixel image. Fixed. o predict.ppm Crashed when computing a confidence interval or prediction interval if 'window' was a tessellation. Fixed. o tiles names(tiles(x)) was not always identical to tilenames(x). Fixed. o model.images.lppm Crashed in many cases. Fixed. o model.images.lppm Names or dimnames were missing in some cases. Fixed. o nncross.ppp Result had the wrong format if npoints(X) = 0 and length(what) = 1. (Spotted by Sebastian Meyer). Fixed. o plot.colourmap Crashed if the colourmap was defined on an interval of dates or times. Fixed. o StraussHard, leverage.ppm, influence.ppm, dfbetas.ppm Leverage and influence calculations generated an error when applied to models fitted with the StraussHard interaction. Fixed. o "[.ppp" Crashed if there were several columns of marks, some of which were factors, and drop=TRUE. Fixed. CHANGES IN spatstat VERSION 1.55-1 OVERVIEW o We thank Jens Astrom, Ines Moncada, Mehdi Moradi and Nicholas Read for contributions. o More support for tessellations. o Improved support for linear networks. o Fixed longstanding bug in leverage and influence diagnostics. o Minor improvements and bug fixes. o Version nickname: "Gamble Responsibly" NEW FUNCTIONS o summary.ssf Summary method for a spatially sampled function (class 'ssf'). o unstack.tess Given a tessellation with multiple columns of marks, take the columns one at a time, and return a list of tessellations, each carrying only one of the original columns of marks. SIGNIFICANT USER-VISIBLE CHANGES o plot.tess This plot method can now fill each tile with a different colour. New arguments 'do.col', 'values', 'col' and 'ribargs'. Old argument 'col' has been renamed 'border' for consistency. o integral.linim, integral.linfun Argument 'domain' can now be a tessellation. o integral.ssf Argument 'domain' can now be a tessellation. o as.owin.default Now accepts a structure with entries named 'xmin,ymin,xmax,ymax' in any order. This handles objects of class 'bbox' in the 'sf' package. o as.owin.default Now detects objects of class "SpatialPolygons" and issues a more helpful error message. o pseudoR2.ppm, pseudoR2.lppm The null model now includes any offset terms, by default. [Suggested by Jens Astrom.] New argument 'keepoffset'. o closepairs.ppp New argument 'periodic' o fitted.ppm New argument 'ignore.hardcore'. o predict.ppm New argument 'ignore.hardcore'. o leverage.ppm, influence.ppm, dfbetas.ppm Computation has been vastly accelerated for models with Geyer interaction fitted using isotropic or translation edge corrections. o leverage.ppm, influence.ppm, dfbetas.ppm Virtually all models and edge corrections are now supported, using a "brute force" algorithm. This can be slow in some cases. o cdf.test Monte Carlo test runs faster. o summary.distfun, summary.funxy Pixel resolution can now be controlled. o persp.funxy Improved z-axis label. o plot.ppp Improved placement of symbol legend when argument 'symap' is given. o plot.msr Changed the default rule for bandwidth for smoothing the density. BUG FIXES o nnmark, as.im.ssf if marks(X) was a matrix rather than a data frame, the results were completely incorrect (and had completely wrong format). Fixed. o predict.mppm If the model included random effects, and if the library 'MASS' was not loaded, the predictions were on the log scale (i.e. they were logarithms of the correct values). [Spotted by Nicholas Read.] Fixed. o leverage.ppm, influence.ppm, dfbetas.ppm Calculations were slightly incorrect for models with a hard core. Fixed. o leverage.ppm The mean leverage value (shown as a contour line in plot.leverage.ppm) was slightly incorrect for Gibbs models. Fixed. o Ops.msr If the input data contained an auxiliary pixel image of the density component of the measure (attribute "smoothdensity") this image was not updated; it was copied to the output unchanged. Plots of the resulting measure were incorrect, but calculations with the measure were correct. Fixed. o integral.msr If the result was a matrix, it was the transpose of the correct answer. Fixed. o "[.linim" The result sometimes had the wrong class. Fixed. o "[.linnet" In calculating L[W] where W is a window, the code ignored segments of L that crossed W without having a vertex in W. Fixed. o nnmap Crashed if W = NULL. Fixed. o density.lpp, nncross.lpp Crashed sometimes with an obscure message about "z$which". [Spotted by Ines Moncada.] Fixed. o as.im.distfun Crashed, for the distfun of a point pattern, if approx=FALSE. Fixed. o as.solist Crashed when x was a 'layered' object. Fixed. o linnet Crashed in some trivial cases where there were no points or lines. Fixed. CHANGES IN spatstat VERSION 1.55-0 OVERVIEW o We thank 'AdriMaz' and Nicholas Read for contributions. o Lurking variable plot for models fitted to several point patterns. o Improvements to code for class 'mppm'. o Improvements to leverage and influence diagnostics. o Improved summary information for funxy and distfun objects. o Bug fixes and improvements. o Removed old warnings and deprecated functions. o Nickname: "Stunned Mullet" NEW FUNCTIONS o contour.leverage.ppm Method for 'contour' for leverage functions of class 'leverage.ppm' o lurking New generic function for lurking variable plots. o lurking.ppp, lurking.ppm These are equivalent to the original function 'lurking'. They are now methods for the new generic 'lurking'. o lurking.mppm New method for class 'mppm' Lurking variable plot for models fitted to several point patterns. o print.lurk Prints information about the object returned by the function 'lurking' representing a lurking variable plot. o model.matrix.mppm Method for 'model.matrix' for models of class 'mppm'. o test.crossing.psp, test.selfcrossing.psp Previously undocumented functions for testing whether segments cross. SIGNIFICANT USER-VISIBLE CHANGES o predict.ppm Now recognises the arguments 'dimyx' and 'eps' for specifying the resolution of the grid of prediction points. o leverage.ppm, dfbetas.ppm Increased the default resolution of the pixel images. Spatial resolution can now be controlled by the arguments 'dimyx', 'eps'. o ppmInfluence The result now belongs to class 'ppmInfluence', for which there are methods for 'leverage', 'influence', 'dfbetas' which extract the desired component. o plot.leverage.ppm New argument 'what'. o persp.leverage.ppm New arguments 'zlab' and 'what'. o as.im.leverage.ppm New argument 'what'. o summary.funxy, summary.distfun Printed information now includes a summary of the function values. o lurking.ppm Accelerated. o "[.psp" Accelerated. o clf.test, conspire, bounding.box, ksmooth.ppp, mpl, superimposePSP, eval.hyper, smooth.fv, smooth.ppp, smooth.msr, rtoro, plot.kstest These deprecated functions have now been removed. o bermantest This deprecated function has now been removed. Use berman.test instead. o kstest This deprecated function has now been removed. Use cdf.test instead. o plot.ppp A very old warning, about the interpretation of the mark scale as the circle diameter, is no longer printed. BUG FIXES o nnmap, nnmark Values were incorrect if the resulting pixel image had unequal numbers of rows and columns. Fixed. o vcov.mppm Format was incorrect (rows/columns were omitted) in some cases. Fixed. o model.matrix.ppm, model.frame.ppm Values were sometimes incorrect when applied to the result of subfits(). To be precise, if 'fit' was an mppm object fitted to a hyperframe that included 'design covariates' (covariates that take a constant value in each row of the hyperframe), and if 'futs <- subfits(fit)', then model.matrix(futs[[i]]) gave incorrect values in the columns corresponding to the design covariates. Fixed. o model.matrix.ppm The attribute 'assign' was omitted, in some cases. Fixed. o simulate.dppm, simulate.detpointprocfamily In dimensions higher than 2, the result was shifted so that it was centred at the origin. Fixed. o Smooth.ppp Crashed if geometric=TRUE and there were several columns of marks. Fixed. o simulate.dppm, simulate.detpointprocfamily Crashed if nsim > 1 and the spatial dimension was not equal to 2. Fixed. o plot.leverage.ppm Contour line was annotated, which was not intended. Fixed. o leverage.ppm The leverage function was oversmoothed, when the model was fitted with method="logi". Fixed. CHANGES IN spatstat VERSION 1.54-0 OVERVIEW o We thank Rochelle Constantine, Lily Kozmian-Ledward, Ian Renner and Leigh Torres for contributions. o New dataset 'cetaceans'. o Gamma correction for colour maps and image plots. o Class 'units' has been renamed 'unitname' to avoid package collision. o Bug fix in leverage code o Tighter bounding box for psp, lpp, linnet objects. o Improved layout in plot.solist o Tools to increase colour saturation. o Connected components of a 3D point pattern. o Accelerated computations on linear networks. o Accelerated simulation of determinantal point processes. o Improved printing of 3D point patterns. o Minor corrections to handling of unitnames. o Nickname: 'Vacuous Mission Statement' NEW DATASETS o cetaceans Nine replicates of a marine survey in New Zealand, consisting of recorded sightings of dolphins, whales and other species. Generously contributed by Lily Kozmian-Ledward, Rochelle Constantine and Leigh Torres. NEW FUNCTIONS o to.saturated Convert a colour value to the corresponding fully-saturated colour. o intensity.psp Compute the average total length of segments per unit area. o boundingbox.psp Bounding box for line segment patterns. This produces a tighter bounding box than the previous default behaviour. o boundingbox.lpp Bounding box for point patterns on a linear network. This produces a tighter bounding box than the previous default behaviour. o boundingbox.linnet Bounding box for a linear network. This produces a tighter bounding box than the previous default behaviour. o "Frame<-.default" New default method for assigning bounding frame to a spatial object. o connected.pp3 Connected components of a 3D point pattern. o colouroutputs, "colouroutputs<-" Extract or assign colour values in a colour map. (Documented a previously-existing function) SIGNIFICANT USER-VISIBLE CHANGES o plot.im New argument 'gamma' supports gamma correction of colour maps. New argument 'ncolours' specifies the default number of colours. o colourmap, lut New argument 'gamma' supports gamma correction of colour maps. o plot.solist, plot.anylist New argument 'panel.vpad' controls vertical space for panel title when equal.scales=FALSE. o class 'units' The class 'units' has been renamed 'unitname' to avoid a clash with other packages. o unitname The generic function 'unitname' now returns an object of class 'unitname'. o print.units, summary.units, print.summary.units, as.character.units, compatible.units These methods are now called print.unitname, summary.unitname, print.summary.unitname, as.character.unitname and compatible.unitname. o as.units This function has been renamed 'as.unitname' and now returns an object of class 'unitname'. o rescale.units This method has been renamed 'rescale.unitname' and now returns an object of class 'unitname'. o profilepl New argument 'fast' controls the use of shorcuts. o reload.or.compute New argument 'force'. o pixellate.ppp, pixellate.owin, pixellate.psp New argument 'DivideByPixelArea'. o density.psp New argument 'at' determines locations where the density is evaluated. o as.solist as.solist(x) always returns an object of class 'solist', removing any additional classes. o lineardirichlet Accelerated. o integral.linim Accelerated. o "[.ppp", "[.lpp", "[.psp" In the expression X[W] where W is a window, if X has a unitname but W does not, the result now inherits the unitname of X. o distfun.ppp New argument 'undef'. o print.pp3 More informative output when x is marked. BUG FIXES o leverage.ppm, influence.ppm, dfbetas.ppm Calculations were slightly incorrect for models fitted using the border correction. Fixed. o integral.linim Gave incorrect value in some extreme cases (where many network segments were shorter than one pixel width). Fixed. o update.kppm Did not function correctly when several additional arguments were given. Fixed. o plot.solist Panel titles were cut off, when equal.scales=FALSE (the default). Fixed. o intersection.owin, union.owin, setminus.owin The result sometimes did not inherit the correct 'unitname'. Fixed. CHANGES IN spatstat VERSION 1.53-2 OVERVIEW o We thank Christophe Biscio and Rasmus Waagepetersen for contributions. o Correction to 'lohboot' o Improvements to ppm and update.ppm o Bug fixes and minor improvements. o Nickname: "Quantum Entanglement" NEW FUNCTIONS o fitin.profilepl Extract the fitted interaction from a model fitted by profile likelihood. SIGNIFICANT USER-VISIBLE CHANGES o lohboot Algorithm has been corrected and extended thanks to Christophe Biscio and Rasmus Waagepetersen. New arguments 'block', 'basicboot', 'Vcorrection'. o ppm.ppp, ppm.quad New argument 'clipwin' o update.ppm For the case 'update(model, X)' where X is a point pattern, if the window of X is different from the original window, then the model is re-fitted from scratch (i.e. use.internal=FALSE). o plot.leverage.ppm A contour line showing the average value of leverage is now drawn on the colour ribbon, as well as on the main image. New argument 'args.contour'. BUG FIXES o lohboot Implementation was completely incorrect. [Spotted and fixed by Christophe Biscio and Rasmus Waagepetersen.] Fixed. o update.ppm Did not always work correctly with formulae that included 'polynom()' terms. Fixed. CHANGES IN spatstat VERSION 1.53-1 OVERVIEW o We thank Suman Rakshit for contributions. o Bug fix in plot.linim o Nickname: "Drongo" BUG FIXES o plot.linim Colour map was mangled if log=TRUE. Fixed. CHANGES IN spatstat VERSION 1.53-0 OVERVIEW o We thank Tilman Davies and Mehdi Moradi for contributions. o Numerous bug fixes for linear networks code. o spatstat now requires the sub-package 'spatstat.data' which contains the datasets. o Minor enhancements and bug fixes. o Nickname: "Tinfoil Hat" NEW FUNCTIONS o "[<-.linim" Subset assignment method for pixel images on a linear network. o nnfromvertex Given a point pattern on a linear network, find the nearest data point from each vertex of the network. o tile.lengths Calculate the length of each tile in a tessellation on a network. o text.ppp, text.lpp, text.psp Methods for 'text' for spatial patterns. SIGNIFICANT USER-VISIBLE CHANGES o datasets All datasets installed in 'spatstat' have now been moved into the sub-package 'spatstat.data'. This should not have any effect on normal use. The 'spatstat.data' package is automatically loaded when spatstat is loaded, and the datasets are lazy-loaded so that they are available in the usual way. To list all datasets you now need to type 'data(package="spatstat.data")' o nbfires This dataset now includes information about the different land and sea borders of New Brunswick. o rhohat New argument 'subset' allows computation for a subset of the data. o predict.lppm Argument 'locations' can now be an 'lpp' object. o ewcdf Argument 'weights' can now be NULL. o plot.msr New arguments 'equal.markscale' and 'equal.ribbon'. o plot.im The number of tick marks in the colour ribbon can now be controlled using the argument 'nint' in 'ribargs'. o plot.symbolmap New argument 'nsymbols' controls the number of symbols plotted. o square Handles a common error in the format of the arguments. o [.linim More robust against artefacts. o [.linnet More robust against artefacts when the subset index is a pixel mask. o linim The image Z is now automatically restricted to the network. New argument 'restrict'. o plot.linim When style="width", negative values are plotted in red (by default). New argument 'negative.args' controls this. o plot.linim New argument 'zlim' specifies the range of values to be mapped. o Summary.linim Recognises the argument 'finite' so that range(x, finite=TRUE) works for a linim object x. o identify.psp Improved placement of labels. Arguments can be passed to text.default to control the plotting of labels. o as.polygonal Accelerated when w is a pixel mask. o density.lpp Accelerated in the default case. o Kinhom Stops gracefully if 'lambda' contains any zero values. o print.linim Prints more information. BUG FIXES o with.msr The value of 'atommass' was incorrect, due to a coding error. Fixed. o [.linim Internal data was sometimes corrupted. Fixed. o as.linim The result had incorrect internal format when Window(X) was a mask and one of the arguments 'eps', 'dimyx', 'xy' was present. Fixed. o as.im.im If W was a rectangle or polygonal window, the pixel resolution of the result was determined by the spatstat defaults, rather than being determined by the image argument X. This was contrary to the rule advertised in help(as.im). Fixed. o density.lpp In the 'slow' case (kernel not Gaussian, or continuous=FALSE), occasionally a pixel could incorrectly be assigned the value 1. [Spotted by Mehdi Moradi.] Fixed. o "[.solist" Ignored the "..." arguments in some cases. Fixed. o density.lpp Ignored the resolution arguments 'eps', 'dimyx' in the default case. Fixed. o plot.msr Plotted the panel titles on top of each other, if how="contour". Fixed. o contour.im Plotted the title text at the wrong place when add=TRUE and show.all=TRUE. Fixed. o predict.lppm Crashed if 'locations' was an 'lpp' object. Fixed. o plot.ppp Crashed if the window had height 0 and width 0 and the pattern had several columns of marks. Fixed. o plot.solist Crashed if all panels had windows of height 0 and width 0. Fixed. o linearK, linearKinhom, linearpcf, linearpcfinhom Crashed if the linear network was disconnected and one component of the network contained fewer than 2 points. Fixed. o integral.linim Crashed in some cases. Fixed. o "[.linim" Crashed in some cases. Fixed. CHANGES IN spatstat VERSION 1.52-1 OVERVIEW o Bug fix to satisfy the development version of R. o Nickname: "Apophenia" SIGNIFICANT USER-VISIBLE CHANGES o Ops.imlist Improved the 'names' of the result. BUG FIXES o bw.smoothppp Crashes in R-devel. Fixed. CHANGES IN spatstat VERSION 1.52-0 OVERVIEW o We thank Nicholas Read, Abdollah Jalilian, Suman Rakshit, Dominic Schuhmacher and Rasmus Waagepetersen for contributions. o Important bug fixes. o Now handles disconnected linear networks. o Effect function is now available for all types of fitted model. o A model can be fitted or re-fitted to a sub-region of data. o More support for measures. o 'Pool' operations improved. o Geometric-mean smoothing. o Changed algorithm defaults in ippm. o Version nickname: "Rudimentary Lathe" NEW FUNCTIONS o as.data.frame.envelope Extract function data from an envelope object, including the functions for the simulated data ('simfuns') if they were saved. o is.connected, is.connected.default, is.connected.linnet Determines whether a spatial object consists of one topologically connected piece, or several pieces. o is.connected.ppp Determines whether a point pattern is connected after all pairs of points closer than distance R are joined. o hist.funxy Histogram of values of a spatial function. o model.matrix.ippm Method for 'model.matrix' which allows computation of regular and irregular score components. o harmonise.msr Convert several measures (objects of class 'msr') to a common quadrature scheme. SIGNIFICANT USER-VISIBLE CHANGES o Smooth.ppp New argument 'geometric' supports geometric-mean smoothing. o Kinhom New argument 'ratio'. o linearKinhom, linearpcfinhom Changed default behaviour when 'lambda' is a fitted model. New arguments 'update' and 'leaveoneout'. o linearK, linearKinhom, linearpcf, linearpcfinhom, compilepcf Ratio calculations are now supported. New argument 'ratio'. o effectfun Now works for 'ppm', 'kppm', 'lppm', 'dppm', 'rppm' and 'profilepl' objects. o ppm, kppm The argument 'subset' can now be a window (class 'owin') specifying the subset of data to which the model should be fitted. o fitted.lppm New argument 'leaveoneout' allows leave-one-out computation of fitted value. o pool.rat New arguments 'relabel' and 'variance'. o density.lpp The return value is a pixel image of class 'linim' in all cases. o plot.linim, plot.linfun A scale bar is now plotted when style="width". New argument 'legend'. o ippm Default values for the parameters of the optimisation algorithm (nlm.args) have changed. o ippm The internal format of the result has been extended slightly. o bind.fv New argument 'clip'. o as.im.distfun New argument 'approx' specifies the choice of algorithm. o "[.psp" New argument 'fragments' specifies whether to keep fragments of line segments that are cut by the new window, or only to retain segments that lie entirely inside the window. o predict.rhohat New argument 'what' determines which value should be calculated: the function estimate, the upper/lower confidence limits, or the standard error. o pool.fv New arguments 'relabel' and 'variance' o pool.rat New argument 'weights'. o plot.msr New argument 'massthresh'. o Ops.msr Calculations like A+B can now be performed even when the measures A and B are not defined on the same quadrature scheme. o density.ppp New argument 'verbose'. o bw.pcf New argument 'verbose'. o hist.im New argument 'xname'. o [.leverage.ppm New argument 'update'. o [.layered Additional arguments '...' are now passed to other methods. o logLik.ppm The warning about pseudolikelihood ('log likelihood not available') is given only once, and is not repeated in subsequent calls, within a spatstat session. o kppm Refuses to fit a log-Gaussian Cox model with anisotropic covariance. o plot.linim, plot.linfun The return value has a different format. Arguments have been renamed and reorganised. o density.lpp New argument 'old'. o ippm Accelerated. o Smooth.ppp Now exits gracefully if any mark values are NA, NaN or Inf. o timeTaken Now exits gracefully if there is no timing information. o nbfires The unit of length for the coordinates is now specified in this dataset. BUG FIXES o bw.pcf Results were totally incorrect due to a typo. [Spotted by Abdollah Jalilian and Rasmus Waagepetersen.] Fixed. o predict.rho2hat Results were incorrect for a rho2hat object computed from a point pattern. Fixed. o density.ppp If the smoothing bandwidth was very small (e.g.\ smaller than pixel width), results were inaccurate if the default resolution was used, and completely wrong if another resolution was specified. [Spotted by Dominic Schuhmacher.] Fixed. o linearK, linearKinhom, linearpcf, linearpcfinhom, linearKcross, linearKdot, linearpcfcross, linearpcfdot, linearKcross.inhom, linearKdot.inhom, linearpcfcross.inhom, linearpcfdot.inhom Crashed if the network was disconnected. Fixed. o crossdist.lpp Crashed if the network was disconnected. Fixed. o countends Crashed if the network was disconnected. Fixed. o model.images.ppm Crashed for models fitted using 'covfunargs'. Fixed. o model.matrix.ppm Crashed for models fitted using 'covfunargs', if argument 'Q' was given. Fixed. o polynom Expansion of some polynomials caused an error message about 'invalid model formula'. Fixed. o plot.ppp The argument 'type="n"' did not suppress plotting of the legend, for marked point patterns. Fixed. o plot.psp Ignored 'show.all' when 'add=TRUE'. Fixed. o intensity.ppm Result had incorrect 'names' attribute in some cases. Fixed. o marks<-.ppx The assignment marks(X) <- a, where 'a' is a single atomic value, caused an error if 'X' contained zero points. Fixed o model.depends Crashed when applied to regression models fitted by 'gam', or point process models fitted by 'ppm' with 'use.gam=TRUE'. Fixed. o pool.fv Crashed sometimes, if the arguments did not have the same set of column names. Fixed. o pool.rat Crashed with an error message from 'fmt' if there were more than 20 objects to be pooled. Fixed. o linearK The 'theo' column was missing if npoints(X) < 2 and correction="Ang". Fixed. o model.matrix.ppm Result was malformed if the model was fitted with 'use.gam=TRUE'. Fixed. o effectfun Crashed if 'covname' was omitted, if the model was fitted with 'use.gam=TRUE'. Fixed. o nncross.lpp Result had incorrect format if Y was empty, in some cases. Fixed. o linearKinhom Plot label for y axis was incorrect. [Spotted by Suman Rakshit.] Fixed. o plot.solist If the entries were 'linim' objects, they were plotted using image() so arguments like 'style="w"' were ignored. Fixed. o as.ppp.data.frame Crashed if X was an object of class 'tbl_df' from the dplyr package. Fixed. o plot.lpp Crashed if there were multiple columns of marks. Fixed. CHANGES IN spatstat VERSION 1.51-0 OVERVIEW o We thank Greg McSwiggan, Mehdi Moradi and Tammy L Silva for contributions. o New fast algorithm for kernel smoothing on a linear network. o Leverage and influence diagnostics extended to Poisson/Gibbs models fitted by logistic composite likelihood. o Two-stage Monte Carlo test. o Dirichlet/Voronoi tessellation on a linear network. o Thinning of point patterns on a linear network. o More support for functions and tessellations on a linear network. o Improvements and bug fixes. o Version nickname: 'Poetic Licence' NEW FUNCTIONS o bits.test: Balanced Independent Two-Stage Monte Carlo test, an improvement on the Dao-Genton test. o lineardirichlet Computes the Dirichlet-Voronoi tessellation associated with a point pattern on a linear network. o domain.lintess, domain.linfun Extract the linear network from a 'lintess' or 'linfun' object. o summary.lintess Summary of a tessellation on a linear network. o clicklpp Interactively add points on a linear network. o envelopeArray Generate an array of envelopes using a function that returns 'fasp' objects. SIGNIFICANT USER-VISIBLE CHANGES o density.lpp New fast algorithm (up to 1000 times faster) for the default case where kernel="gaussian" and continuous=TRUE. Generously contributed by Greg McSwiggan. o leverage.ppm, influence.ppm, dfbetas.ppm These methods now work for models that were fitted by logistic composite likelihood (method='logi'). o rthin Argument X can now be a point pattern on a linear network (class 'lpp'). o fitted.ppm New option: type = "link" o update.kppm New argument 'evaluate'. o integral.linfun New argument 'delta' controls step length of approximation to integral. o as.linim.default New argument 'delta' controls spacing of sample points in internal data. o as.linfun.lintess New argument 'values' specifies the function value for each tile. New argument 'navalue'. BUG FIXES o leverage.ppm, influence.ppm, dfbetas.ppm Results for Gibbs models were incorrect due to a mathematical error. (Results for Poisson models were correct). Fixed. o leverage.ppm, influence.ppm, dfbetas.ppm, ppmInfluence Calculations were incorrect for a Geyer model fitted using an edge correction other than "border" or "none". Fixed. o step, kppm, update.kppm 'step' did not work for kppm objects in some cases due to a scoping problem in update.kppm. Fixed. o improve.kppm Crashed if the window was not a rectangle. Fixed. o pcf.ppp, pcfinhom Crashed if kernel="epa" rather than "epanechnikov". Fixed. o alltypes Crashed if envelope=TRUE and reuse=FALSE. Fixed. o pairdist.lpp, nndist.lpp, nnwhich.lpp, nncross.lpp Crashed if the network was disconnected. Fixed. o as.im.linim, as.linim.linim Additional arguments such as 'eps' and 'dimyx' were ignored. Fixed. o as.im.default Arguments 'eps and 'xy' were ignored if X was a single numeric value. Fixed. o 'timed' class Printing of these objects did not work in some locales. Fixed. o runifpoint Ignored 'drop' argument if the window was a rectangle. Fixed. CHANGES IN spatstat VERSION 1.50-0 OVERVIEW o We thank Richard Cotton, Adrian Heyner, Abdollah Jalilian, Dominic Schuhmacher and Rasmus Waagepetersen for contributions. o spatstat now 'Imports' the package 'spatstat.utils'. o Bandwidth selection for pair correlation function. o Improvements and bug fixes. o Version nickname: 'Bunyip Aristocracy' NEW PACKAGE STRUCTURE o spatstat is being split into several sub-packages, to satisfy the requirements of CRAN. This should not affect the user: existing code will continue to work in the same way. Currently there are two sub-packages, called 'spatstat.utils' and 'spatstat'. Typing 'library(spatstat)' will load the familiar 'spatstat' package which can be used as before, and will silently import the 'spatstat.utils' package. The 'spatstat.utils' package contains utility functions that were originally written for 'spatstat': they were undocumented internal functions in 'spatstat', but are now documented and accessible in a separate package because they may be useful for other purposes. To access these functions, you need to type 'library(spatstat.utils)'. NEW FUNCTIONS o bw.pcf Bandwidth selection for pair correlation function. Original code contributed by Abdollah Jalilian and Rasmus Waagepetersen. o grow.box3 Expand a three-dimensional box. SIGNIFICANT USER-VISIBLE CHANGES o as.owin Now refuses to convert a 'box3' to a two-dimensional window. o pixellate.ppp If the pattern is empty, the result is an integer-valued image (by default) for consistency with the results for non-empty patterns. o ppp If the coordinate vectors x and y contain NA, NaN or infinite values, these points are deleted with a warning, instead of causing a fatal error. o ppm Argument 'interaction' can now be a function that makes an interaction, such as Poisson, Hardcore, MultiHard. o pcf, pcfinhom New argument 'close' for advanced use. o runifpointx, rpoisppx New argument 'drop'. o shapley, ponderosa In these installed datasets, the functions shapley.extra$plotit and ponderosa.extra$plotit have changed slightly (to accommodate the dependence on the package spatstat.utils). o kppm Improved printed output. BUG FIXES o rMaternI, rMaternII If 'win' was a three-dimensional box of class 'box3', the result was a two-dimensional point pattern. [Spotted by Adrian Heyner.] Fixed. o rmhmodel.ppm, simulate.ppm Crashed when applied to a fitted Lennard-Jones model. [Spotted by Dominic Schuhmacher.] Fixed. o leverage.ppm, influence.ppm, dfbetas.ppm Crashed when applied to some hard-core models. Fixed. o "[.ppx" The format of the result was slightly malformed if exactly one point was selected. Fixed. o unmark.lpp, marks<-.lpp The result had class c("lpp", "lpp", "ppx") instead of c("lpp", "ppx"). Fixed. CHANGES IN spatstat VERSION 1.49-0 OVERVIEW o We thank Tilman Davies, Kassel Hingee, Abdollah Jalilian, Brian Ripley and Dominic Schuhmacher for contributions. o spatstat now 'Suggests' the package 'fftwtools'. o Operations on signed measures. o Operations on lists of pixel images. o Improved pixellation of point patterns. o Stieltjes integral extended. o Subset operators extended. o Greatly accelerated 'rmh' when using 'nsave' o Some computations accelerated. o Size of namespace reduced, for efficiency. o Bug fixes. o Version nickname: 'So-Called Software' NEW DEPENDENCIES o fftwtools spatstat now 'Suggests' the package 'fftwtools'. This package provides a very fast implementation of the Fast Fourier Transform, leading to much faster computation in the spatstat functions 'density.ppp', 'relrisk.ppp', 'convolve.im', 'blur', 'scan.test' and many other functions. The 'fftwtools' package requires the external software library 'fftw'. We strongly recommend installing this library if possible. NEW FUNCTIONS o hexagon, regularpolygon Create regular polygons. o Ops.msr Arithmetic operations for measures. o Math.imlist, Ops.imlist, Summary.imlist, Complex.imlist Arithmetic operations for lists of pixel images. o measurePositive, measureNegative, measureVariation, totalVariation Positive and negative parts of a measure, and variation of a measure. o as.function.owin Convert a spatial window to a function (x,y), the indicator function. o as.function.ssf Convert an object of class 'ssf' to a function(x,y) o as.function.leverage.ppm Convert an object of class 'leverage.ppm' to a function(x,y) SIGNIFICANT USER-VISIBLE CHANGES o stieltjes Argument 'M' can be a stepfun object (such as an empirical CDF). o quantile.ewcdf The function is now normalised to the range [0,1] before the quantiles are computed. This can be suppressed by setting normalise=FALSE. o pixellate.ppp New arguments 'fractional' and 'preserve' for more accurate discretisation. o "[.layered" Subset index i can now be an 'owin' object. o "[.solist" Subset index i can now be an 'owin' object. o plot.solist, plot.imlist, plot.anylist Result is now an (invisible) list containing the result from executing the plot of each panel. o ppp New argument 'checkdup'. o Summary.im Argument 'na.rm' is no longer ignored. o cdf.test The methods for classes ppp, ppm, lpp, lppm, slrm have a new argument 'interpolate'. o as.solist The argument x can now be a spatial object; as.solist(cells) is the same as solist(cells). o bw.diggle, bw.ppl, bw.relrisk, bw.smoothppp These functions now extract and store the name of the unit of length from the point pattern dataset. When the bandwidth selection criterion is plotted, the name of the unit of length is shown on the x-axis. o polynom This function now has a help file. o rmhcontrol New parameter 'pstage' determines when to generate random proposal points. o rmh Accelerated, in the case where multiple patterns are saved using 'nsave'. o bdist.pixels Accelerated for polygonal windows. New argument 'method'. o spatstat namespace The namespace of the spatstat package has been shortened (by internally registering the native routines) which should make the package run faster. o sum.im, range.im, max.im, min.im These functions have been removed, as they are now subsumed in Summary.im. BUG FIXES o plot.msr If one of 'nrows' or 'ncols' was specified, but not both, an obscure error occurred. Fixed. o plot.solist, plot.imlist, plot.anylist Crashed if 'nrows' and 'ncols' were given values implying that some rows or columns would not contain any plots. Fixed. o as.ppp.lpp Crashed if there was more than one column of marks. Fixed. o has.close.pp3 Results were incorrect, or a crash occurred, when argument 'Y' was given. Fixed. o rmpoispp If 'lambda' was a list of images, 'names(lambda)' was ignored, rather than serving as the default value of 'types'. Fixed. o bugfixes Output was garbled, in rare cases. Fixed. o kppm Result was malformed when clusters="VarGamma" and method="clik2". Spotted by Abdollah Jalilian. Fixed. o QQversion Plotting labels were malformed. Fixed. CHANGES IN spatstat VERSION 1.48-0 OVERVIEW o We thank Kim Colyvas, Yongtao Guan, Gopalan Nair, Nader Najari, Suman Rakshit, Ian Renner and Hangsheng Wang for contributions. o Sufficient Dimension Reduction for point processes. o Alternating Gibbs Sampler for point process simulation. o Intensity approximation for area-interaction and Geyer models. o New class of spatially sampled functions. o ROC and AUC extended to other types of point patterns and models. o More support for linear networks. o More support for infinite straight lines. o Simulation of 'rhohat' objects. o Kernel smoothing accelerated. o Methods for 'head' and 'tail' for spatial patterns. o More low-level functionality. o Improvements and bug fixes. o spatstat now has more than 1000 help files. o Nickname: 'Model Prisoner' NEW CLASSES o ssf Class of spatially sampled functions. NEW FUNCTIONS o sdr, dimhat Sufficient Dimension Reduction for point processes. Matlab code contributed by Yongtao Guan, translated by Suman Rakshit. o rags, ragsAreaInter, ragsMultiHard Alternating Gibbs Sampler for point processes. o psib Sibling probability (index of clustering strength in a cluster process). o bugfixes List all bug fixes in recent versions of a package. o roc.kppm, roc.lppm, roc.lpp Methods for 'roc' (receiver operating characteristic curve) for fitted models of class 'kppm' and 'lppm' and point patterns of class 'lpp' o auc.kppm, auc.lppm, auc.lpp Methods for 'auc' (area under the ROC curve) for fitted models of class 'kppm' and 'lppm' and point patterns of class 'lpp' o rlpp Random points on a linear network with a specified probability density. o cut.lpp Method for 'cut' for point patterns on a linear network. o crossing.linnet Find crossing points between a linear network and another set of lines. o ssf Create a spatially sampled function o print.ssf, plot.ssf, contour.ssf, image.ssf Display a spatially sampled function o as.im.ssf, as.ppp.ssf, marks.ssf, marks<-.ssf, unmark.ssf, [.ssf, with.ssf Manipulate data in a spatially sampled function o Smooth.ssf Smooth a spatially sampled function o integral.ssf Approximate integral of spatially sampled function o simulate.rhohat Generate a Poisson random point pattern with intensity that is a function of a covariate, given by a 'rhohat' object. o head.ppp, head.ppx, head.psp, head.tess, tail.ppp, tail.ppx, tail.psp, tail.tess Methods for 'head' and 'tail' for spatial patterns. o as.data.frame.tess Convert a tessellation to a data frame. o timeTaken Extract the timing data from a 'timed' object or objects. o rotate.infline, shift.infline, reflect.infline, flipxy.infline Geometrical transformations for infinite straight lines. o whichhalfplane Determine which side of an infinite line a point lies on. o points.lpp Method for 'points' for point patterns on a linear network. o pairs.linim Pairs plot for images on a linear network. o has.close Faster way to check whether a point has a close neighbour. o closetriples Low-level function to find all close triples of points. o matrixpower, matrixsqrt, matrixinvsqrt Raise a matrix to any power. SIGNIFICANT USER-VISIBLE CHANGES o intensity.ppm Intensity approximation is now available for the Geyer saturation process and the area-interaction process (results of research with Gopalan Nair). o envelope.lpp, envelope.lppm New arguments 'fix.n' and 'fix.marks' allow envelopes to be computed using simulations conditional on the observed number of points. o "[.im" The subset index "i" can now be a linear network (object of class 'linnet'). The result of "x[i, drop=FALSE]" is then a pixel image of class 'linim'. o cut.ppp Argument z can be "x" or "y" indicating one of the spatial coordinates. o rThomas, rMatClust, rCauchy, rVarGamma, rPoissonCluster, rNeymanScott New argument 'saveparents'. o lintess Argument 'df' can be missing or NULL, resulting in a tesellation with only one tile. o lpp X can be missing or NULL, resulting in an empty point pattern. o plot.lintess Improved plot method, with more options. o rpoisline Also returns information about the original infinite random lines. o density.ppp, Smooth.ppp Accelerated. o density.psp New argument 'method' controls the method of computation. New faster option 'method="FFT"' o nndist.lpp Accelerated. BUG FIXES o F3est Estimates of F(r) for the largest value of r were wildly incorrect. Fixed. o clip.infline Results were incorrect unless the midpoint of the window was the coordinate origin. Fixed. o integral.linim Results were inaccurate if many of the segment lengths were shorter than the width of a pixel. Fixed. o predict.lppm Bizarre error messages about 'class too long' or 'names too long' occurred if the model was multitype. Fixed. o superimpose Point patterns containing 0 points were ignored when determining the list of possible marks. Fixed. o chop.tess Vertical lines were not handled correctly with pixellated tessellations. Fixed. o timed Argument 'timetaken' was ignored. Fixed. o ppm Crashed if method="logi" and the 'covariates' were a data frame. [Spotted by Kim Colyvas and Ian Renner.] Fixed. o rpoislpp, runiflpp Crashed if nsim > 1. Fixed. o rpoisline Crashed if zero lines were generated. Fixed. o model.frame.ppm Crashed if the original model was fitted to a data frame of covariates and there were NA's amongst the covariate values. [Spotted by Kim Colyvas.] Fixed. o any, all When applied to pixel images (objects of class 'im') the result was sometimes NA when a finite value should have been returned. Fixed. o predict.rhohat When the original data were on a linear network, the result of predict.rhohat did not belong to the correct class 'linim'. Fixed. CHANGES IN spatstat VERSION 1.47-0 OVERVIEW o We thank Marcel Austenfeld, Guy Bayegnak, Tilman Davies, Cenk Icos, Jorge Mateu, Frederico Mestre, Mehdi Moradi, Virginia Morera Pujol, Suman Rakshit and Sven Wagner for contributions. o Non-Gaussian smoothing kernels. o Important bug fix in linearK, linearpcf o Changed internal format of linnet and lpp objects. o Faster computation in linear networks. o Bias correction techniques. o Bounding circle of a spatial object. o Minkowski sum also applicable to point patterns and line segment patterns. o Option to plot marked points as arrows. o Kernel smoothing accelerated. o Workaround for bug in some graphics drivers affecting image orientation. o Bug fixes and improvements. o Version nickname: 'Responsible Gambler' NEW FUNCTIONS o anyNA.im Method for 'anyNA' for pixel images. o bc Bias correction (Newton-Raphson) for fitted model parameters. See also 'rex'. o boundingcircle, boundingcentre Find the smallest circle enclosing a window or point pattern. o "[.linim" Subset operator for pixel images on a linear network. o mean.linim, median.linim, quantile.linim The mean, median, or quantiles of pixel values in a pixel image on a linear network. o rex Richardson extrapolation for numerical integrals and statistical model parameter estimates. o weighted.median, weighted.quantile Median or quantile of numerical data with associated weights. SIGNIFICANT USER-VISIBLE CHANGES o linear networks The internal format of a 'linnet' (linear network) object has been changed. Existing datasets of class 'linnet' and 'lpp' are still supported. However, computation will be faster if they are converted to the new format. To convert a linnet object L to the new format, use L <- as.linnet(L). To convert an lpp object X to the new format, use X <- as.lpp(X). o density.ppp, Smooth.ppp New argument 'kernel' allows the user to specify the smoothing kernel. o density.ppp, Smooth.ppp Argument 'weights' can now be a pixel image. o MinkowskiSum, %(+)% Now accepts arguments which are point patterns or line segment patterns as well as windows. o plot.im New argument 'workaround' to avoid a bug in some device drivers that causes the image to be displayed in the wrong spatial orientation. [Thanks to Marcel Austenfeld for drawing attention to this.] o sumouter New argument 'y' allows computation of asymmetric outer products. o linearKinhom, linearpcfinhom New argument 'normpower'. o rmh.default, rmh.ppm New arguments 'nsim', 'saveinfo'. o symbolmap, plot.ppp, plot.lpp New option: shape="arrows" o rcellnumber New argument 'mu'. o lengths.psp New argument 'squared'. o plot.linfun Now passes arguments to the function being plotted. o as.linnet.psp If the line segment pattern has marks, then the resulting linear network also carries these marks in the $lines component. o summary.owin, summary.im The fraction of frame area that is occupied by the window/image is now reported. o density.ppp, Smooth.ppp Computation accelerated by about 15% in the case where at='points' and kernel='gaussian'. o linearK, linearpcf Accelerated by about 40%. o pixellate.ppp Accelerated in the case where weights are given o density.ppp Accelerated in the cases where weights are given or 'diggle=TRUE' o dilation.ppp Improved geometrical accuracy. Now accepts arguments to control resolution of polygonal approximation. o discs New argument 'npoly'. Accelerated in some cases. o plot.pp3 New arguments 'box.front', 'box.back' control plotting of the box. o grow.rectangle New argument 'fraction'. o nnfun.lpp New argument 'k'. o bw.ppl New argument 'sigma'. o lppm New argument 'random' controls placement of dummy points. o rhohat.lpp New argument 'random' controls placement of dummy points. o quadrat.test.ppm Accelerated in the case where the original window is a rectangle. o kppm, mincontrast, cauchy.estpcf, lgcp.estpcf, matclust.estpcf, thomas.estpcf, vargamma.estpcf A warning about infinite values of the summary function no longer occurs when the default settings are used. o circumradius This function is now deprecated, in favour of 'boundingradius' o print.quad More information is printed. BUG FIXES o linearK, linearpcf, and relatives: These functions were sometimes greatly underestimated when the network had segments shorter than 10 coordinate units. [Bug introduced in spatstat 1.44-0, december 2015.] Fixed. o integral.linim, integral.linfun Results were slightly inaccurate because of a bias in the distribution of sample points. [Bug introduced in spatstat 1.41-0, february 2015.] Fixed. o intensity.ppm Result was incorrect for Gibbs models if the model was *exactly* equivalent to a Poisson process (i.e. if all interaction coefficients were exactly zero). [Bug introduced in spatstat 1.28-1, june 2012.] Fixed. o rSSI Sometimes terminated prematurely. [Spotted by Frederico Mestre.] Fixed. o perspPoints Crashed if the image Z contained NA (i.e. if Z was only defined on a subset of the bounding frame). Spotted by Guy Bayegnak. Fixed. o plot.ppp, plot.lpp Crashed if the argument 'shape' was given. Fixed. o plot.kppm Crashed if the model was not fitted by minimum contrast. Fixed. o superimpose Crashed if the argument was a 'solist' containing line segment patterns. Fixed. o Jest Crashed sometimes, depending on the shape of the observation window. [Spotted by Cenk Icos.] Fixed. o plot.studpermutest Crashed when the summary statistic was a multitype pair correlation function or multitype K function. [Spotted by Sven Wagner.] Fixed. o pool.anylist Crashed with a message about buffer size, if the list was longer than about 100 items. Fixed. o diagnose.ppm, plot.diagppm Crashed in some cases when cumulative=FALSE. Fixed. o leverage.ppm, influence.ppm, dfbetas.ppm Crashed sometimes with a message about wrong replacement length. [Spotted by Virginia Morera Pujol.] Fixed. o as.linnet.psp Crashed with marked segment patterns, if any segments were very short. [Spotted by Suman Rakshit.] Fixed. o stieltjes Returned NA if some values of f were not finite. Fixed. o plot.symbolmap If a new plot window was initialised, it was sometimes too small to contain the geometric figures (circles, squares etc) in the symbol map. Fixed. o plot.ppp, plot.im Ignored xlim, ylim. Fixed. o rhohat.lpp Ignored nd, eps. Fixed. o nnfun.lpp Print method gave incorrect information about the point pattern. Fixed. o "[.fv" The default plot formula was not updated. Fixed. o fitted.ppm The result was sometimes a 1-dimensional array rather than a numeric vector. Fixed. CHANGES IN spatstat VERSION 1.46-1 OVERVIEW o Important bug fix. o Version nickname: 'Spoiler Alert' BUG FIXES o density.ppp, Smooth.ppp The results of density(X, at="points") and Smooth(X, at="points") were incorrect in some cases. The contribution from the left-most data point (the point with the smallest x coordinate) was omitted. [Bug introduced in spatstat 1.26-0, April 2012.] Fixed. CHANGES IN spatstat VERSION 1.46-0 OVERVIEW o We thank Corey Anderson and Sebastian Meyer for contributions. o spatstat now depends on R 3.3.0 or later. o Improvements to inhomogeneous multitype K and L functions. o Variance approximation for pair correlation function. o Leverage and influence for multitype point process models. o Functions for extracting components of vector-valued objects. o Important bug fix in Smooth.ppp o Minor improvements and bug fixes. o Version nickname: 'Multidimensional Toothbrush' NEW FUNCTIONS o split.msr Decompose a measure into parts. o unstack.msr Decompose a vector-valued measure into its component measures. o unstack.ppp, unstack.psp, unstack.lpp Given a spatial pattern with several columns of marks, separate the columns and return a list of spatial patterns, each having only one column of marks. o kernel.squint Integral of squared kernel, for the kernels used in density estimation. SIGNIFICANT USER-VISIBLE CHANGES o Kcross.inhom, Kdot.inhom, Kmulti.inhom, Ldot.inhom, Lcross.inhom These functions now allow intensity values to be given by a fitted point process model. New arguments 'update', 'leaveoneout', 'lambdaX'. o diagnose.ppm Infinite values of 'rbord' are now ignored and treated as zero. This ensures that diagnose.ppm has a sensible default when the fitted model has infinite reach. o pcf.ppp Now calculates an analytic approximation to the variance of the estimate of the pair correlation function (when var.approx=TRUE). Now returns the smoothing bandwidth used, as an attribute of the result. o plot.ppp When 'clipwin' is given, any parts of the boundary of the window of x that lie inside 'clipwin' will also be plotted. o plot.msr Now handles multitype measures. New argument 'multiplot'. o plot.anylist If a list entry x[[i]] belongs to class 'anylist', it will be expanded so that each entry x[[i]][[j]] will be plotted as a separate panel. o influence.ppm, leverage.ppm These can now be applied to multitype point process models and the results can be plotted. o plot.influence.ppm, plot.leverage.ppm New argument 'multiplot'. o plot.anylist, plot.solist, plot.listof New arguments panel.begin.args, panel.end.args o influence.ppm, leverage.ppm, dfbetas.ppm For Gibbs models, memory usage has been dramatically reduced, so the code can handle larger datasets and finer quadrature schemes. BUG FIXES o Smooth.ppp Results were incorrect when at='points' and leaveoneout=FALSE. [Bug introduced in spatstat 1.20-5, October 2010.] Fixed. o funxy Did not correctly handle one-line functions: the resulting objects evaluated the wrong function in some cases. [Spotted by Sebastian Meyer. Bug introduced in spatstat 1.45-0] Fixed. o mppm Did not recognise the variable 'marks' in a formula. Fixed. o Smooth.ppp, bw.smoothppp Crashed if X had two columns of marks and one column was constant. [Bug introduced in spatstat 1.38-0, October 2014] Fixed. o Smooth.ppp Results for 'at="points"' were garbled, for some values of 'sigma', if X had more than one column of marks. [Bug introduced in spatstat 1.38-0, October 2014] Fixed. o plot.layered Crashed if one layer was a point pattern with several columns of marks. Fixed. o plot.ppm Sometimes gave a spurious warning about a singular matrix. Fixed. o setminus.owin Gave wrong or strange answer if the correct answer was empty. Fixed. o parameters.dppm Crashed, due to a typo. Fixed. o progressreport Crashed if n = 1. Fixed. CHANGES IN spatstat VERSION 1.45-2 OVERVIEW o We thank Ottmar Cronie, Virginia Morera Pujol, Sven Wagner and Marie-Colette van Lieshout for contributions. o Recursive-partition point process models. o Minkowski sum, morphological dilation and erosion with any shape. o Important bug fix in spatial CDF tests. o More bug fixes for replicated patterns. o Simulate a model fitted to replicated point patterns. o Inhomogeneous multitype F and G functions. o Summary functions recognise correction="all" o Leverage and influence code handles bigger datasets. o More support for pixel images. o Improved progress reports. o New dataset 'redwood3' o spatstat now Depends on the package 'rpart' o Version nickname: 'Caretaker Mode' NEW DATASETS o redwood3 A more accurate version of the 'redwood' data. NEW FUNCTIONS o as.im.data.frame Build a pixel image from a data frame of coordinates and pixel values. o covering Cover a window using discs of a given radius. o dilationAny, erosionAny, %(-)% Morphological dilation and erosion by any shape. o FmultiInhom, GmultiInhom Inhomogeneous multitype/marked versions of the summary functions Fest, Gest. o kernel.moment Moment or incomplete moment of smoothing kernel. o MinkowskiSum, %(+)% Minkowski sum of two windows: A %(+)% B, or MinkowskiSum(A,B) o nobjects New generic function for counting the number of 'things' in a dataset. There are methods for ppp, ppx, psp, tess. o parameters.interact, parameters.fii Extract parameters from interpoint interactions. [These existing functions are now documented.] o ppmInfluence Calculate leverage.ppm, influence.ppm and dfbetas.ppm efficiently. o rppm, plot.rppm, predict.rppm, prune.rppm Recursive-partition point process models o simulate.mppm Simulate a point process model fitted to replicated point patterns. o update.interact Update the parameters of an interpoint interaction. [This existing function is now documented.] o where.max, where.min Find the spatial location(s) where a pixel image achieves its maximum or minimum value. SIGNIFICANT USER-VISIBLE CHANGES o cdf.test.mppm Now handles Gibbs models. Now recognises covariate="x" or "y". o leverage.ppm, influence.ppm, dfbetas.ppm For Gibbs models, memory usage has been dramatically reduced, so the code can handle larger datasets and finer quadrature schemes. o plot.im Now handles complex-valued images. o connected.im Now handles a logical-valued image properly. o qqplot.ppm Argument 'expr' can now be a list of point patterns, or an envelope object containing a list of point patterns. o as.layered Default method now handles a (vanilla) list of spatial objects. o summary functions The argument 'correction="all"' is now recognised: it selects all the available options. This applies to Fest, F3est, Gest, Gcross, Gdot, Gmulti, G3est, Gfox, Gcom, Gres, Hest, Jest, Jmulti, Jcross, Jdot, Jfox, Kest, Kinhom, Kmulti, Kcross, Kdot, Kcom, Kres, Kmulti.inhom, Kcross.inhom, Kdot.inhom, Kscaled, Ksector, Kmark, K3est, Lscaled, markcorr, markcrosscorr, nnorient, pairorient, pcfinhom, pcfcross.inhom, pcfcross, pcf, Tstat. o clarkevans The argument 'correction="all"' is now recognised: it selects all the available options. [This is also the default.] o predict.mppm The argument 'type="all"' is now recognised: it selects all the available options. [This is also the default.] o plot.kppm The argument 'what="all"' is now recognised: it selects all the available options. [This is also the default.] o connected.im, connected.owin Arguments '...' now determine pixel resolution. o anova.mppm New argument 'fine' o as.owin.data.frame New argument 'step' o discs Now accepts a single numeric value for 'radii'. o plot.ppp, plot.profilepl, plot.quadratcount, plot.quadrattest, plot.tess Now recognise graphics parameters for text, such as 'family' and 'srt' o as.function.tess New argument 'values' specifies the function values. o cdf.test Calculations are more robust against numerical rounding effects. o progressreport Behaviour improved. New arguments 'tick', 'showtime'. o simulate.ppm New argument 'verbose' o compileK, compilepcf These internal functions are now documented. BUG FIXES o cdf.test.ppm Calculation of p-values was incorrect for Gibbs models: 1-p was computed instead of p. [Spotted by Sven Wagner.] Fixed. o subfits The interaction coefficients of the submodels were incorrect for Gibbs models with a multitype interaction (MultiStrauss, etc). [Spotted by Sven Wagner.] Fixed. o subfits Crashed when a Gibbs model included factor-valued spatial covariates and not all levels of the factor were present in each row of the data. [Spotted by Sven Wagner.] Fixed. o subfits For Gibbs models with a multitype interaction (MultiStrauss, etc), computation of the conditional intensity caused an error. [Spotted by Sven Wagner.] Fixed. o diagnose.ppm Crashed if what="smooth", when the original window was a rectangle. [Spotted by Virginia Morera Pujol.] Fixed. o mppm The x and y coordinates were not permitted in the random-effects formula 'random'. [Spotted by Sven Wagner.] Fixed. o vcov.ppm The result had no 'dimnames', if the model was fitted using method="ho". Fixed. CHANGES IN spatstat VERSION 1.45-1 OVERVIEW o This version was never released. CHANGES IN spatstat VERSION 1.45-0 OVERVIEW o We thank Monsuru Adepeju, Mario D'Antuono, Markus Herrmann, Paul Hewson, Kassel Hingee, Greg McSwiggan, Suman Rakshit and Sven Wagner for contributions. o Important bug fix in leverage/influence diagnostics for Gibbs models. o Numerous bug fixes in code for replicated point patterns. o Surgery on linear networks. o Tessellations on a linear network. o Laslett's Transform. o Colour maps for point patterns with continuous marks are easier to define. o Pair correlation function estimates can be pooled. o Stipulate a particular version of a package. o Fixed namespace problems arising when spatstat is not loaded. o Bug fixes and performance improvements. o spatstat now contains 100,000 lines of R code. o Version nickname: 'One Lakh' NEW FUNCTIONS o laslett Laslett's Transform. [Thanks to Kassel Hingee] o lintess Tessellation on a linear network. o divide.linnet Divide a linear network into pieces demarcated by a point pattern. o insertVertices Insert new vertices in a linear network. o thinNetwork Remove vertices and/or segments from a linear network etc o connected.linnet Find connected components of a linear network. o nvertices, nvertices.linnet, nvertices.owin Count the number of vertices in a linear network or vertices of the boundary of a window. o as.data.frame.linim, as.data.frame.linfun Extract a data frame of spatial locations and function values from an object of class 'linim' or 'linfun'. o as.linfun, as.linfun.linim, as.linfun.lintess Convert other kinds of data to a 'linfun' object. o requireversion Require a particular version of a package (for use in stand-alone R scripts). SIGNIFICANT USER-VISIBLE CHANGES o [.linnet, [.lpp New argument 'snip' determines what to do with segments of the network that cross the boundary of the window. Default behaviour has changed. o pcfinhom Default behaviour is changed when 'lambda' is a fitted model. The default is now to re-fit the model to the data before computing pcf. New arguments 'update' and 'leaveoneout' control this. o envelope methods New argument 'funYargs' contains arguments to the summary function when applied to the data pattern only. o plot.ppp, plot.lpp For a point pattern with continuous marks ('real numbers') the colour arguments 'cols', 'fg', 'bg' can now be vectors of colour values, and will be used to determine the default colour map for the marks. o symbolmap Now accepts a vector of colour values for the arguments 'col', 'cols', 'fg', 'bg' if argument 'range' is given. o closepairs.ppp, closepairs.pp3 New arguments 'distinct' and 'neat' allow more options. o closepairs.ppp, closepairs.pp3 Argument 'ordered' has been replaced by 'twice' (but 'ordered' is still accepted, with a warning). o closepairs.ppp, closepairs.pp3 Performance improved (computation time and memory requirements reduced.) This should improve the performance of many functions in spatstat. o Geyer The saturation parameter 'sat' can now be less than 1. o lpp, as.lpp These functions now handle the case where 'seg' and 'tp' are given but 'x' and 'y' are missing. o linnet If the argument 'edges' is given, then this argument now determines the ordering of the sequence of line segments. For example, the i-th row of 'edges' specifies the i-th line segment in as.psp(L). o funxy, distfun The functions created by funxy and distfun have arguments (x,y). The user may now give a ppp or lpp object for the argument 'x', instead of giving two coordinate vectors 'x' and 'y'. o crossing.psp New argument 'details' gives more information about the intersections between the segments. o subset.ppp, subset.lpp, subset.pp3, subset.ppx The argument 'subset' can now be any argument acceptable to the "[" method. o density.lpp New argument 'weights'. o pcf.ppp New argument 'ratio' allows several estimates of pcf to be pooled. o summary.ppm New argument 'fine' selects the algorithm for variance estimation. o texturemap Argument 'textures' can be missing or NULL. o plot.lpp New argument 'show.network' o linnet New argument 'warn' o mppm Performs more checks for consistency of the input data. o mppm New arguments 'gcontrol' and 'reltol.pql' control the fitting algorithm. o edge.Trans New argument 'gW' for efficiency. o pool.fv The default plot of the pooled function no longer includes the variance curves. o clickpoly The polygon is now drawn progressively as the user clicks new vertices. o Kest Accelerated computation (for translation and rigid corrections) when window is an irregular shape. o vcov.ppm, leverage.ppm, influence.ppm, dfbetas.ppm Performance slightly improved, for Gibbs models. o Internal code Performance slightly improved. o Fest, Hest Additional checks for errors in input data. BUGS o leverage.ppm, influence.ppm, parres.ppm, addvar.ppm Calculations were completely incorrect for Gibbs models, due to a coding error. Fixed. o update.kppm If the call to 'update' did not include a formula argument or a point pattern argument, then all arguments were ignored. Example: update(fit, improve.type="quasi") was identical to 'fit'. Fixed. o diagnose.ppm When applied to a model obtained from subfits(), in the default case (oldstyle=FALSE) the variance calculations were incorrect. Consequently the dotted lines representing significance bands were incorrect. An error or warning about negative variances occurred sometimes. However, calculations with oldstyle=TRUE were correct. The default has now been changed to oldstyle=TRUE for such models. o [.lpp The local coordinate 'seg' was completely incorrect, when 'i' was a window. Fixed. o leverage.ppm, influence.ppm, parres.ppm, addvar.ppm Crashed for Gibbs models in which the coefficient vector had length 1, such as the stationary Hardcore model. Fixed. o subfits Crashed if the model included factor-valued spatial covariates. [Spotted by Sven Wagner] Fixed. o subfits If the model included factor-valued spatial covariates, and if not all levels of the factor were present in each row of the data, the resulting objects were malformed and caused errors in other code. [Spotted by Sven Wagner] Fixed. o subfits Crashed with some random-effects formulas. [Spotted by Sven Wagner] Fixed. o improve.kppm An error message about a missing object 'gminus1' occurred when vcov=TRUE, fast.vcov=FALSE and type="clik1" or "wclik1". Fixed. o plot.profilepl Failed with a message about a missing object 'finite'. Fixed. o selfcut.psp Gave an error if marks(A) was a vector rather than a data frame. [Spotted by Paul Hewson.] Fixed. o suffstat Gave an error for point process models with Geyer interaction. Fixed. o nncross.lpp, distfun.lpp Crashed with obscure errors if Y consisted of a single point. Fixed. o scan.test, scanmeasure Crashed sometimes with an error message from 'grow.mask'. Fixed. o dppm Crashed sometimes with a message that the point pattern could not be found. [Scoping bug.] Fixed. o mppm, profilepl Crashed, with a message about 'SpatstatVersion', if the 'spatstat' package was neither loaded nor attached. [Spotted by Markus Herrmann.] Fixed. o qqplot.ppm Crashed sometimes when applied to a model obtained from subfits(). Fixed. o anova.mppm Crashed sometimes with a message about mismatched coefficients. [Spotted by Sven Wagner.] Fixed. o anova.mppm Crashed sometimes with a message about unrecognised option 'type="score"'. [Spotted by Sven Wagner.] Fixed. o split.ppx Crashed if 'f' was not a factor. Fixed. o idw The result was a pixel image defined in the rectangle Frame(X) instead of Window(X). Fixed. o ppm Parameter estimates were slightly inaccurate when the model included the Geyer() interaction and the "isotropic" edge correction was used. Fixed. o [.ppx Crashed if the number of points selected was less than 2. Fixed. o linnet Crashed if there were no line segments at all. Fixed. o kppm, improve.kppm Crashed if the model was stationary and improve.type != "none". Fixed. o as.linim.default Did not correctly handle factor-valued data. Fixed. o texturemap Crashed if no graphical arguments were specified. Fixed. o vcov.mppm Ignored "..." arguments. Fixed. o Kest If ratio=TRUE and correction=c('border', 'none') the result did not contain ratio information. Fixed. o plot.ppp, plot.lpp Arguments 'chars' and 'cols' were ignored in some cases. Fixed. o ppm Ignored argument 'emend'. Fixed. o plot.dppm Gave warnings about unrecognised argument 'objectname'. Fixed. o overlap.owin Sometimes returned a very small negative value, when the correct answer was 0. Fixed. CHANGES IN spatstat VERSION 1.44-1 OVERVIEW o We thank Brian Ripley for contributions. o Urgent bug fix. o More support for replicated point patterns. o More support for tessellations. o Version nickname: 'Gift Horse' NEW FUNCTIONS o as.function.tess Convert a tessellation to a function(x,y). The function value indicates which tile of the tessellation contains the point (x,y). o tileindex Determine which tile of a tessellation contains a given point (x,y). o persp.leverage.ppm Method for persp plots for objects of class leverage.ppm o AIC.mppm, extractAIC.mppm AIC for point process models fitted to replicated point patterns. o nobs.mppm, terms.mppm, getCall.mppm Methods for point process models fitted to replicated point patterns. SIGNIFICANT USER-VISIBLE CHANGES o anova.mppm Now handles Gibbs models, and performs the adjusted composite likelihood ratio test. o update, step These functions now work for models of class 'mppm'. o textureplot Argument x can now be something acceptable to as.im o logLik.mppm New argument 'warn'. BUGS o nncross.lpp, nnwhich.lpp, distfun.lpp Caused a segmentation fault. [Spotted by Brian Ripley.] Fixed. o anova.ppm If a single 'object' was given, and the object was a Gibbs model, then 'adjust' was effectively set to FALSE. Fixed. CHANGES IN spatstat VERSION 1.44-0 OVERVIEW o We thank Jonas Geldmann, Andrew Hardegen, Kassel Hingee, Tom Lawrence, Robin Milne, Gopalan Nair, Suman Rakshit, Peijian Shi and Rasmus Waagepetersen for contributions. o More support for multidimensional point patterns and point processes. o More options for envelopes and related Monte Carlo tests. o More support for model comparison. o k-th nearest neighbours on a linear network. o Penttinen process can be simulated (by Metropolis-Hastings or CFTP). o Calculate the predicted variance of number of points. o Convexifying operation for sets. o Subdivide a linear network. o Accelerated algorithms for linear networks. o Quadrat counting accelerated, in some cases. o Version nickname: 'The Sound of One Hand Typing' NEW FUNCTIONS o rPenttinen Simulate the Penttinen process using perfect simulation. o varcount Given a point process model, compute the predicted variance of the number of points falling in a window. o inside.boxx Test whether multidimensional points lie inside a specified multidimensional box. o lixellate Divide each segment of a linear network into smaller segments. o nsegments.linnet, nsegments.lpp Count the number of line segments in a linear network. o grow.boxx Expand a multidimensional box. o deviance.ppm, deviance.lppm Deviance for a fitted point process model. o pseudoR2 Pseudo-R-squared for a fitted point process model. o tiles.empty Checks whether each tile of a tessellation is empty or nonempty. o summary.linim Summary for a pixel image on a linear network. SIGNIFICANT USER-VISIBLE CHANGES o rMaternI, rMaternII These functions can now generate random patterns in three dimensions and higher dimensions, when the argument 'win' is of class 'box3' or 'boxx'. o "[.ppx" The subset index 'i' may now be a spatial domain of class 'boxx' or 'box3'. o rmh.ppm, rmhmodel.ppm, simulate.ppm A model fitted using the 'Penttinen' interaction can now be simulated. o rmh.default, rmhmodel.default These functions now recognise cif='penttinen' for the Penttinen interaction. o envelope New argument 'clamp' gives greater control over one-sided envelopes. o dclf.test, mad.test, dclf.progress, mad.progress, dclf.sigtrace, mad.sigtrace New argument 'clamp' determines the test statistic for one-sided tests. o dclf.progress, mad.progress, dclf.sigtrace, mad.sigtrace, mctest.progress, mctest.sigtrace, dg.progress, dg.sigtrace New argument 'rmin' determines the left endpoint of the test interval. o dclf.test, mad.test, dg.test, dg.progress, dg.sigtrace, dg.envelope (also accepted by dclf.progress, mad.progress, dclf.sigtrace, mad.sigtrace) New argument 'leaveout' specifies how to calculate the deviation between the observed summary function and nominal reference value. o envelope New argument 'funargs' o Hest Argument X can now be a pixel image with logical values. New argument 'W'. [Based on code by Kassel Hingee.] o nncross.lpp, distfun.lpp New argument 'k' allows calculation of k-th nearest neighbour. Computation accelerated. o logLik.ppm New argument 'absolute'. o plot.kppm New arguments 'pause' and 'xname'. o tess Argument 'window' is ignored when xgrid, ygrid are given. o as.polygonal Can now repair errors in polygon data, if repair=TRUE. o rStrauss, rHardcore, rStraussHard, rDiggleGratton, rDGS, rPenttinen New argument 'drop'. o Kest.fft Now has '...' arguments allowing control of spatial resolution. o lppm Computation accelerated. o quadratcount.ppp Computation accelerated in some cases. o dg.test Computation accelerated. BUGS o runifpointx, rpoisppx Crashed if nsim > 1. Fixed. o triangulate.owin Results were incorrect in some special cases. Fixed. o quadrat.test, clarkevans.test In rare cases, the computed Monte Carlo p-value could have been greater than 1. This could have occurred only when nsim was an even number and when the correct p-value was equal to 1. Fixed. o linearmarkequal Result was a data frame instead of an 'fv' object. Fixed. o point-in-polygon test The function inside.owin could take a very long time to check whether points are inside a polygonal window, if the coordinates were very large numbers. This was due to numerical overflow. (Fixed??) o as.fv.kppm Crashed if the model was not fitted by minimum contrast. Fixed. o plot.fv Crashed in some obscure cases. Fixed. o collapse.fv Did not allow 'same=NULL'. Fixed. o dclf.progress, mad.progress, dg.progress, dclf.sigtrace, mad.sigtrace, dg.sigtrace The results could not be re-plotted using a plot formula, because the internal data were slightly corrupted. Fixed. o Kest.fft Result was incorrectly normalised. Fixed. o crosspairs If X and Y were identical point patterns, the result was not necessarily symmetric (on some machines) due to numerical artifacts. Fixed. o plot.fv Lines were not correctly clipped to the plot region when 'ylim' was given. Fixed. o pool.envelope The 'scale' argument was not handled correctly. Fixed. CHANGES IN spatstat VERSION 1.43-0 OVERVIEW o We thank Leanne Bischof, Christophe Biscio, Belarmain Fandohan, Andrew Hardegen, Frederic Lavancier, Tom Lawrence, Martin Maechler, Greg McSwiggan, Robin Milne, Gopalan Nair, Tuomas Rajala, Suman Rakshit, Ben Ramage, Francois Semecurbe and Ida-Maria Sintorn for contributions. o spatstat now depends on the package 'nlme'. o spatstat now depends on R 3.2.2 or later. o Simulation algorithms have been accelerated; simulation outcomes are *not* identical to those obtained from previous versions of spatstat. o Determinantal point process models. o Random-effects and mixed-effects models for replicated patterns. o Dao-Genton test, and corresponding simulation envelopes. o Simulated annealing and simulated tempering. o spatstat colour tools now handle transparent colours. o Improvements to "[" and subset() methods o Extensions to kernel smoothing on a linear network. o Support for one-dimensional smoothing kernels. o Bug fix in Metropolis-Hastings simulation. o Mark correlation function may include weights. o Cross-correlation version of the mark correlation function. o Variance calculations for replicated patterns. o Penttinen pairwise interaction model. o Contour plots with colours determined by a colour map. o New dataset: Australian states and territories. o More support for multi-dimensional point patterns. o Minor improvements and bug fixes. o Version nickname: "Mixed Effects" NEW DATASET o austates The states and large mainland territories of Australia represented as polygonal regions forming a tessellation. NEW FUNCTIONS o dppm Fit a determinantal point process model to point pattern data. o fitted.dppm, predict.dppm, intensity.dppm Predict a fitted dppm object. o logLik.dppm, AIC.dppm, extractAIC.dppm, nobs.dppm Likelihood and AIC for determinantal point process models (enabling the use of 'step') o coef.dppm, formula.dppm, print.dppm, terms.dppm, labels.dppm, model.frame.dppm, model.matrix.dppm, model.images.dppm, is.stationary.dppm, reach.dppm, unitname.dppm, unitname<-.dppm, Window.dppm Various methods for dppm objects. o parameters.dppm Extract meaningful list of model parameters o objsurf.dppm Objective function surface of a dppm object o residuals.dppm Residual measure for a dppm object. o dppBessel, dppCauchy, dppGauss, dppMatern, dppPowerExp Determinantal Point Process models. o update.dppmodel Set parameter values in a dpp model. o is.stationary.dppmodel, print.dppmodel, reach.dppmodel, valid.dppmodel Basic information about a dpp model o rdpp, simulate.dppmodel Simulation of a dpp model. o intensity.dppmodel, Kmodel.dppmodel, pcfmodel.dppmodel Moments of a dpp model o dim.dppmodel, dppapproxkernel, dppapproxpcf, dppeigen, dppfamily, dppkernel, dppparbounds, dppspecdenrange, dppspecden Helper functions for dpp models. o dclf.sigtrace, mad.sigtrace, mctest.sigtrace Significance trace of Monte Carlo test o dg.test Dao-Genton adjusted Monte Carlo goodness-of-fit test. o dg.envelope Simulation envelopes corresponding to Dao-Genton test. o dg.sigtrace Significance trace for Dao-Genton test o dg.progress Progress plot for Dao-Genton test o markcrosscorr Mark cross-correlation function for point patterns with several columns of marks o fixef.mppm, ranef.mppm Extract fixed effects and random effects from a point process model fitted to replicated point patterns. o rtemper Simulated annealing or simulated tempering. o to.opaque, to.transparent Change transparency value in colours o rgb2hsva Convert RGB to HSV data, like rgb2hsv, but preserving transparency. o superimpose.ppplist, superimpose.splitppp New methods for 'superimpose' for lists of point patterns. o dkernel, pkernel, qkernel, rkernel Probability density, cumulative probability, quantiles and random generation from distributions used in basic one-dimensional kernel smoothing. o kernel.factor Auxiliary calculations for one-dimensional kernel smoothing. o PPversion, QQversion Transformation of a summary function to its P-P or Q-Q counterpart. o spatdim Spatial dimension of any object in the spatstat package. o as.boxx Convert data to a multi-dimensional box. o intensity.ppx Method for 'intensity' for multi-dimensional space-time point patterns. o fourierbasis Evaluate Fourier basis functions in any number of dimensions. o valid New generic function, with methods valid.ppm, valid.lppm, valid.dppmodel o emend, emend.ppm, emend.lppm New generic function with methods for ppm and lppm. emend.ppm is equivalent to project.ppm o Penttinen New pairwise interaction model. o quantile.density Calculates quantiles from kernel density estimates. o CDF.density Calculates cumulative distribution function from kernel density estimates. SIGNIFICANT USER-VISIBLE CHANGES o simulation Several basic simulation algorithms have been accelerated. Consequently, simulation outcomes are not identical to those obtained with previous versions of spatstat, even when the same random seed is used. To ensure compatibility with previous versions of spatstat, revert to the slower code by setting spatstat.options(fastthin=FALSE, fastpois=FALSE). o mppm Now handles models with a random effect component. New argument 'random' is a formula specifying the random effect. o vcov.mppm Now handles models with Gibbs interactions. o [.ppp New argument 'clip' determines whether the window is clipped. o [.ppp The previously-unused argument 'drop' now determines whether to remove unused levels of a factor. o [.pp3, [.lpp, [.ppx, subset.ppp, subset.pp3, subset.lpp, subset.ppx These methods now have an argument 'drop' which determines whether to remove unused levels of a factor. o density.lpp Now supports both the 'equal-split continuous' and 'equal-split discontinuous' smoothers. New argument 'continuous' determines the choice of smoother. o envelope New argument 'scale' allows global envelopes to have width proportional to a specified function of r, rather than constant width. o dclf.test, mad.test, dclf.progress, mad.progress, mctest.progress New argument 'scale' allows summary function values to be rescaled before the comparison is performed. o dclf.test, mad.test New argument 'interpolate' supports interpolation of p-value. o dclf.progress, mad.progress, mctest.progress New argument 'interpolate' supports interpolation of critical value of test. o simulate.ppm New argument 'w' controls the window of the simulated patterns. o default.rmhcontrol, default.rmhexpand New argument 'w'. o markcorr New argument 'weights' allows computation of the weighted version of the mark correlation function. o density.lpp New argument 'kernel' specifies the smoothing kernel. Any of the standard one-dimensional smoothing kernels can be used. o contour.im New argument 'col' specifies the colour of the contour lines. If 'col' is a colour map, then the contours are drawn in different colours. o plot.ppp The default colour for the points is now a transparent grey, if this is supported by the plot device. o rgbim, hsvim New argument 'A' controls the alpha (transparency) channel. o rgb2hex, col2hex, paletteindex, is.colour, samecolour, complementarycolour, is.grey, to.grey These colour tools now handle transparent colours. o rgb2hex New argument 'maxColorValue' o to.grey New argument 'transparent'. o progressreport New argument 'state' New option: style="tk" o rLGCP This function no longer requires the package 'RandomFields' to be loaded explicitly. o kppm Fitting a model with clusters="LGCP" no longer requires the package 'RandomFields' to be loaded explicitly. o rpoispp Accelerated, when 'lambda' is a pixel image. o rthin Accelerated, when 'P' is a single number. o spatstat.options New options 'fastthin' and 'fastpois' enable fast simulation algorithms. Set these options to FALSE to reproduce results obtained with previous versions of spatstat. o split.ppp The splitting variable 'f' can now be a logical vector. o collapse.fv This is now treated as a method for the 'nlme' generic 'collapse'. Its syntax has been adjusted slightly. o diagnose.ppm, plot.diagppm New arguments col.neg, col.smooth control the colour maps. o valid.ppm This is now a method for the generic function 'valid'. o ppm.ppp, ppm.quad New argument 'emend', equivalent to 'project'. o "[<-.im" Accepts an array for 'value'. o as.im.function New argument 'strict'. o bw.ppl New argument 'weights'. o plot.mppm New argument 'se'. o dclf.test, mad.test Formal arguments 'use.theo' and 'internal' have been removed. o predict.kppm, residuals.kppm Now issues a warning when the calculation ignores the cluster/Cox component and treats the model as if it were Poisson. (This currently happens in predict.kppm when se=TRUE or interval != "none", and in residuals.kppm when type != "raw"). BUG FIXES o lpp Crashed if X was a 4-column matrix. Fixed. o plot.fv Crashed with some graphics devices, if legend=TRUE. Fixed. o effectfun Crashed if 'covname' was missing. Fixed. o rVarGamma, rMatClust, rThomas, rCauchy, rNeymanScott Crashed if 'kappa' was a function or image instead of a single number. [Spotted by Ben Ramage.] Fixed. o plot.mppm Crashed with a message about "figure margins too large" unless the argument se=FALSE was given explicitly. Fixed. o opening.owin, closing.owin Crashed sometimes, with a message about a rectangle not containing a window. Fixed. o persp.im Crashed if all pixel values were equal to zero (unless zlim was given). Fixed. o predict.ppm Crashed sometimes if the model was fitted with use.gam=TRUE. o as.linim.linfun Generated an error ('L must be a linear network') if extra arguments were given. o as.function.fv Generated an error when executed in the 'covr' package. Fixed. o rmh, simulate.ppm Results were incorrect for inhomogeneous multitype models simulated with fixall=TRUE (i.e. prescribing a fixed number of points of each type) if the model was segregated (i.e. if different types of points had different first order trend). Fixed. o dclf.progress, mad.progress Ignored the argument 'alternative'. Fixed. o $<-.hyperframe, [<-.hyperframe Result was garbled if 'value' was a hyperframe with one column. o rmh.ppm Argument 'w' was ignored in some cases. Fixed. o Hest There was an artefact at r=0 when conditional=TRUE. Fixed. o [.msr The result of M[W] where W is a window was a measure with window W, instead of intersect.owin(W, Window(M)). Fixed. o pool.envelope Did not always respect the value of 'use.theory'. Fixed. o envelope, pool.envelope If 'ginterval' was given, the results were in a slightly incorrect format. Fixed. o pool.envelope Did not check for compatible values of 'ginterval'. Fixed. CHANGES IN spatstat VERSION 1.42-2 OVERVIEW o We thank Bob Klaver and Harold-Jeffrey Ship for contributions. o Improvements to simulation of Neyman-Scott processes. o Improvements to fitting of Neyman-Scott models. o Extended functionality for pixel images. o Fitted intensity on linear network o Triangulation of windows. o Corrected an edge correction. o Bug fixes and performance improvements. o Nickname: 'Barking at Balloons' NEW FUNCTIONS o triangulate.owin Decompose a spatial window into triangles. o fitted.lppm Fitted intensity values for a point process on a linear network. SIGNIFICANT USER-VISIBLE CHANGES o rThomas, rMatClust, rCauchy, rVarGamma When the model is approximately Poisson, it is simulated using rpoispp. This avoids computations which would require huge amounts of memory. New argument 'poisthresh' controls this behaviour. o update.kppm Now handles additional arguments in any order, with or without names. Changed arguments. Improved behaviour. o kppm, clusterfit New argument 'algorithm' specifies the choice of optimisation algorithm. o kppm Left hand side of formula can now involve entries in the list 'data'. o rotmean New argument 'padzero'. Default behaviour has changed. o rose.default New argument 'weights'. o rose New arguments 'start' and 'clockwise' specify the convention for measuring and plotting angles. o padimage New argument 'W' allows an image to be padded out to fill any window. o union.owin Improved behaviour when there are more than 2 windows. o clusterset Improved behaviour. o affine.owin Allows transformation matrix to be singular, if the window is polygonal. BUG FIXES o spatstat spatstat could not be installed on some 64-bit VM systems because of an apparent bug in R. Fixed. o rThomas, rMatClust, rCauchy, rVarGamma Large values of the scale parameter could cause the algorithm to freeze or require huge amounts of memory. Fixed. o pcf, pcfinhom Crashed if the point pattern was empty. Fixed. o plot.fv Gave an error message if all 'y' values were equal, when legend=TRUE. Fixed. o rose.default Display was incorrect when unit="radian". Fixed. o Kest Ohser-Stoyan rigid motion correction (correction='rigid') was calculated incorrectly at large distances. Fixed. o summary.im Issued a warning about numerical overflow in some cases. [Spotted by Bob Klaver.] Fixed. o plot.im Sometimes warned that 'box' is not a graphical parameter. Fixed. CHANGES IN spatstat VERSION 1.42-1 OVERVIEW o We thank Andrew Hardegen, Tom Lawrence, Robin Milne, Suman Rakshit, and Brian Ripley for contributions. o Urgent bug fix. o More robust simulation of cluster processes. o Slightly accelerated. o Version nickname: 'Vogon Poetry' NEW FUNCTIONS o boundingbox.solist Method for boundingbox for lists of spatial objects. SIGNIFICANT USER-VISIBLE CHANGES o rThomas, rMatClust, rCauchy, rVarGamma, rNeymanScott New faster algorithm which is more robust against extreme values of the parameters. o rNeymanScott New argument 'nonempty' controls choice of algorithm. o solist, as.solist Accelerated. o as.list.hyperframe Accelerated. BUG FIXES o residuals.mppm Brought some computers to a grinding halt, due to the bug in solist(). Fixed. o solist, as.solist In rare cases, the format was corrupted, or the algorithm never terminated. Fixed. CHANGES IN spatstat VERSION 1.42-0 OVERVIEW o We thank Anders Bilgrau, Ute Hahn, Jack Hywood, Tuomas Rajala, Cody Schank, Olivia Semboli and Ben Taylor for contributions. o Version nickname: 'Life, The Universe and Everything' o Permutation test for difference between groups of point patterns. o Variational Bayes estimation for point process models. o Score test in anova.ppm o ROC curve, and discrimination index AUC, for fitted models. o Interactive text editor for spatial datasets. o Tools for analysing data on a tree. o Kernel density/intensity estimation on a linear network. o Random pixel noise. o Improved behaviour of polygon geometry operations. o Improved support for cluster and Cox models. o Improved basic support for owin objects. o Improved support for tessellations. o More hierarchical Gibbs interactions. o Modifications to Kest. o summary method for Cox and cluster models. o class 'listof' is almost completely replaced by 'anylist' and 'solist'. o Improvements and bug fixes. o spatstat now depends on R version 3.2.0 or later. NEW FUNCTIONS o studpermu.test Studentised permutation test for difference between groups of point patterns. Generously contributed by Ute Hahn. o AIC.kppm, extractAIC.kppm, logLik.kppm, nobs.kppm Methods for computing AIC for fitted Cox and cluster models. o transmat Convert pixel arrays between different display conventions. o roc Receiver Operating Characteristic curve. o auc Discrimination index AUC (area under the ROC curve) o edit.ppp, edit.psp, edit.im Interactive text editor works for spatial datasets. o edit.hyperframe Interactive text editor works for hyperframes. o parameters Extract all parameters from a fitted model. o density.lpp Kernel estimation of point process intensity on a linear network. o extractbranch, deletebranch, treeprune, treebranchlabels, begins Tools for analysing data on a tree. o rnoise Random pixel noise. o as.data.frame.owin Convert a window to a data frame. o harmonise.owin Convert several binary mask windows to a common pixel grid. o copyExampleFiles Copy the raw data files from an installed dataset to a chosen folder, for use in a practice exercise. o density.ppplist Method for 'density' for lists of point patterns. o inradius Radius of largest circle inside a window. o mergeLevels Merge different levels of a factor. o relevel.im, relevel.ppp, relevel.ppx Change the reference level of a factor. o simulate.profilepl simulation method for models fitted by profile maximum pseudolikelihood. o predict.rho2hat Prediction method for class rho2hat o with.msr Evaluate (an expression involving) components of a measure. o summary.kppm, print.summary.kppm, coef.summary.kppm Methods for 'summary' and 'coef(summary(..))' for Cox and cluster models. o as.im.funxy Method for as.im for class funxy. o shift.linim, scalardilate.linim, affine.linim Geometrical transformations for 'linim' objects. o Smooth.solist Smooth method for a list of spatial objects. o unitname.tess, unitname<-.tess Tessellations now keep track of the name of the unit of length. o dirichletAreas Faster algorithm for tile.areas(dirichlet(X)). o identify.lpp Method for 'identify' for point patterns on a linear network. o HierStraussHard, HierHard Hierarchical interactions for Gibbs models. o delaunayDistance, delaunayNetwork, dirichletEdges, dirichletNetwork, dirichletVertices, dirichletWeights These functions will replace delaunay.distance, delaunay.network, dirichlet.edges, dirichlet.network, dirichlet.vertices and dirichlet.weights respectively. The latter are now 'deprecated'. SIGNIFICANT USER-VISIBLE CHANGES o ppm Now supports Variational Bayes fitting method. o kppm 'AIC' and 'step' now work for kppm objects fitted using maximum Palm likelihood. o kppm The default for the weight function 'weightfun' has been changed, for better performance. o envelope envelope methods now have argument 'use.theory' specifying whether to use the 'theoretical' value of the summary function when constructing simultaneous envelopes. o anova.ppm Now performs the Score Test, for Poisson models only, if argument test="Rao" or test="score". o Kest New argument 'rmax' controls maximum value of argument 'r' o diagnose.ppm Now computes and prints the null standard deviation of the smoothed Pearson residual field, when appropriate. o nncorr, nnmean, nnvario New argument 'k' specifies k-th nearest neighbour. o quadrat.test.ppp, quadrat.test.quadratcount New argument 'lambda' supports a test of the Poisson process with given intensity 'lambda'. o clickpoly, clickbox These functions now handle graphical arguments to polygon() when drawing the resulting polygon or rectangle. o owin, as.owin, as.mask owin(mask=D) or as.owin(D) or as.mask(D) will produce a binary mask window if D is a data frame with two columns of (x,y) coordinates or a data frame with three columns containing (x,y,logical). o as.owin.data.frame W can now be a data frame with only two columns, giving the spatial coordinates of the pixels that are inside the window. o rose Tick marks now have labels showing the angle (in degrees or radians). o distcdf New argument 'regularise' determines whether values at short distances will be smoothed to avoid discretisation artefacts. o rpoislinetess Return value now has an attribute 'lines' giving the realisation of the Poisson line process. o intersect.owin, union.owin, setminus.owin New argument 'p' controls resolution of polygon clipping algorithm. o intersect.owin, union.owin Arguments may be lists of windows, of class 'solist'. Formal arguments A and B have been removed. o superimpose Now handles lists of point patterns (objects of class 'ppplist' or 'splitppp') o density.ppp New argument 'positive' allows the user to stipulate that density values must be positive (avoiding numerical errors which occasionally produce small negative values). o adaptive.density Now accepts f = 0 (uniform intensity estimate) and f = 1 (Voronoi intensity estimate) as well as 0 < f < 1. Algorithm accelerated. o rSSI Can now generate inhomogeneous patterns. o effectfun Now works for 'kppm' and 'lppm' objects as well. o integral.im, integral.msr Argument 'domain' can now be a tessellation; the integral over each tile of the tessellation is returned. o allstats, compareFit, markcorr, split.ppx, by.ppp Result is now of class 'anylist'. o by.im, density.splitppp, idw, model.images, nnmark, pixellate.ppp, predict.lppm, predict.ppm, quadratcount.splitppp, quadratresample, relrisk, Smooth.msr, split.im, tiles Result is now of class 'solist'. o split.ppp New argument 'reduce'. Result now inherits class 'ppplist' and 'solist', as well as 'splitppp' o rLGCP New argument 'nsim' allows multiple patterns to be generated. o alltypes New argument 'reuse' determines whether all simulation envelopes are based on the same set of simulated patterns, or on independent sets. o rpoispp, runifpoint New argument 'ex' makes it possible to generate a random pattern similar to an example point pattern. o effectfun Argument 'covname' is not needed if the model has only one covariate. o quadratcount Argument 'tess' can now be anything acceptable to as.tess. o tess New argument 'unitname' specifies the name of the unit of length. If it is missing, unitname information will be extracted from the other data. o intersect.tess, chop.tess, quadrats Results of these functions now have the same 'unitname' as their input. o persp.im, nnclean, plot.qqppm, plot.bw.optim These plotting functions now obey spatstat.options('monochrome') o lurking Now returns an object of class 'lurk' which has a plot method. Two-standard-deviation limits are now plotted using grey shading. o marktable New argument 'N' for studying the N nearest neighbours. New argument 'collapse' for manipulating the contingency table. o harmonise.fv Now discards columns with names which do not match. o eval.fv New argument 'equiv' can be used to declare that two columns with different names in different objects are equivalent. o quantile.ewcdf New argument 'type' controls the type of quantile. o plot.imlist New argument 'plotcommand' specifies how to plot each image. o persp.im The lower extent of the apron can now be controlled by 'zlim'. o quadscheme Argument 'method' is partially matched. o Kdot, Ldot New argument 'from' is an alternative to 'i'. o Kcross, Lcross New arguments 'from' and 'to' are alternatives to 'i' and 'j' respectively. o varblock Changed the ordering (and therefore default colours/styles) of curves in the plot, to match other functions like lohboot. o bw.diggle New argument 'nr' controls accuracy. o textureplot Now accepts a pixel image, a tessellation, or anything acceptable to as.tess. o textureplot Line spacing in legend now matches line spacing in main display. o [.tess Subset index can now be a window. o plot.tess Can now plot a text label in each tile. o plot.tess New argument 'do.plot'. o MultiHard, MultiStrauss, MultiStraussHard, HierStrauss Printed output of fitted model now respects spatstat.options('terse'). o print.ppm Reduced redundancy in output in some cases. o print.msr Responds better to spatstat.options('terse'). o print.ppm, print.fii, print.interact Irregular parameters are now printed to the number of significant figures specified by options("digits"). o square New argument 'unitname'. o plot.fv Return value is now invisible. o delaunay.distance, delaunay.network, dirichlet.edges, dirichlet.network, dirichlet.vertices These functions are now 'deprecated', and will be replaced by delaunayDistance, delaunayNetwork, dirichletEdges, dirichletNetwork and dirichletVertices respectively. o data(residualspaper) In the real datasets (Fig1 and Fig11), the name of the unit of length has now been recorded. o rLGCP This function now requires the package 'RandomFields' to be loaded explicitly by library(RandomFields) or require(RandomFields), unless model="exp". o iplot, istat These functions now require the package 'rpanel' to be loaded explicitly by library(rpanel) or require(rpanel). o ppm, quadscheme Improved calculation of Dirichlet weights. o countends New argument 'toler' controls numerical errors o diagnose.ppm Improved handling of additional graphics arguments. o pcf3est Mathematical labels changed. o plot.hyperframe Default margin spacing has been increased. BUG FIXES o Kinhom, Linhom The value of 'theo' was erroneously rescaled by a small amount, when renormalise=TRUE (the default). Fixed. o Kmark Values were erroneously rescaled. Fixed. o union.owin Strange results were sometimes obtained when taking the union of more than two windows. Fixed. o rpoispp3 Implementation was incorrect for nsim > 1. (Results may have been incorrect.) Spotted by Jack Hywood. Fixed. o as.owin.data.frame Crashed if the window was not connected. Fixed. o Frame<- Crashed when applied to a binary mask. Fixed. o rho2hat Crashed if cov1="x" and cov2="y". Fixed. o as.mask Crashed sometimes when only the argument 'xy' was given. Fixed. o ppm Crashed (rarely) when method='ho' if the simulated pattern was empty. Fixed. o istat, iplot Crashed in recent versions of rpanel. Fixed. o convexhull Crashed if applied to a 'psp' object. Fixed. o plot.ppm Crashed with message about 'variable lengths differ'. Fixed. o plot.solist Crashed when applied to a list of point patterns if some patterns had more than one column of marks. Fixed. o Smooth.ppp Crashed if applied to a point pattern with several columns of marks if some of the columns were factors. Fixed. o runifpoint3, rpoispp3 Crashed if nsim > 1. Spotted by Jack Hywood. Fixed. o hist.im Crashed if argument 'freq' was given. Fixed. o MultiStraussHard Generated misleading error messages (e.g. 'model is invalid') when arguments 'iradii' and 'hradii' did not have the same pattern of NA's. Fixed. o plot.solist Figures were sometimes aligned incorrectly when the argument 'panel.args' was given. Fixed. o scaletointerval Results sometimes fell slightly outside the desired interval due to numerical error. Fixed. o plot.solist Behaved incorrectly when plotcommand='persp'. Fixed. o "[.hyperframe" Sometimes returned an 'anylist' when it should have returned a 'solist'. Fixed. o plot.im Did not plot surrounding frame box when ribbon=FALSE. Fixed. o envelope The functions stored when savefuns=TRUE did not inherit the correct name for the unit of length. Fixed. o print.ppm, print.fii, print.interact Layout was misaligned. Fixed. o plot.plotppm Paused for input when it was not appropriate. Fixed. o plot.fv On png devices, the legend box was drawn with a white background, obscuring the main plot. Fixed. o plot.owin, plot.ppp, plot.im There was unnecessary extra space above the main title. Fixed. o plot.rho2hat Colour map ribbon was drawn but not annotated. Fixed. o density.splitppp, density.ppplist Format was out of order if se=TRUE. Fixed. o MultiStraussHard project.ppm sometimes yielded a model that was still invalid. Fixed. CHANGES IN spatstat VERSION 1.41-1 OVERVIEW o This is identical to the major release 1.41-0 except for minor bug fixes. The change log for 1.41-0 is repeated here with minor modifications. o Version nickname: 'Ides of March' o We thank Ahmed El-Gabbas, Ute Hahn, Aruna Jammalamadaka, Ian Renner, Brian Ripley, Torben Tvedebrink and Sasha Voss for contributions. o Fixed a bug causing a segmentation fault. o Standard errors for kernel estimates of intensity. o Test for segregation. o Tessellations may now have marks. o Nested splitting. o More support for cluster models. Reorganised parametrisation. o Sparse data representation of linear networks. o More support for data on a linear network. o New datasets: 'spiders' and 'dendrite'. o Improvements and bug fixes. o spatstat no longer uses Fortran. o spatstat no longer depends on the package 'scatterplot3d'. o spatstat now imports (rather than 'suggests') the Matrix package. NEW DATASETS o dendrite Dendritic spines on the dendrite network of a neuron. A point pattern on a linear network. Generously contributed by Aruna Jammalamadaka. o spiders Spider webs on the mortar lines of a brick wall. A point pattern on a linear network. Generously contributed by Sasha Voss. NEW FUNCTIONS o segregation.test Test of spatial segregation of types in a multitype point pattern. o clusterfield, clusterkernel Compute the cluster kernel (offspring density) of a cluster process model, or compute the cluster field generated by superimposing copies of the cluster kernel at specified locations. o clusterradius Compute the radius of the support of the offspring density of a cluster process model. o as.linnet.psp Convert a line segment pattern to a linear network by guessing the connectivity using a distance threshold. o iplot.linnet, iplot.lpp Methods for interactive plotting 'iplot' for objects of class lpp and linnet. o Mathematical operations are now supported for pixel images on a linear network. See help(Math.linim) o dirichlet.network, delaunay.network The linear networks formed by the Dirichlet tessellation and Delaunay triangulation. o dirichlet.edges The edges of the Dirichlet tessellation. o selfcut.psp Cut line segments where they cross each other. o vertices.linnet Extract the vertices (nodes) of the linear network. o vertexdegree Compute the degree of each vertex in a linear network. o pixellate.linnet Pixellate a linear network. o subset.hyperframe 'subset' method for class 'hyperframe'. o head.hyperframe, tail.hyperframe 'head' and 'tail' methods for hyperframes. o clickdist Measures the distance between two spatial locations clicked by the user. o solapply, anylapply wrappers for 'lapply' which return a list of class 'solist' or 'anylist'. o Kmark Weighted K-function. Identical to 'markcorrint' and will eventually replace it. o marks.tess, marks<-.tess, unmark.tess: Extract or change the marks associated with the tiles of a tessellation. o quantess Quantile tessellation: divide space into pieces which contain equal amounts of 'stuff'. o nestsplit Nested split o integral New generic function for integrating functions, with methods for 'im', 'msr', 'linim' and 'linfun'. o selfcut.psp Cut line segments where they cross each other o as.function.im Convert a pixel image to a function(x,y). o as.linnet.linim Extract the linear network from a 'linim' object. o pool.fv, pool.anylist New methods for 'pool' o Window.linnet Extract the two-dimensional window containing a linear network. SIGNIFICANT USER-VISIBLE CHANGES o linnet, lpp A linear network can now be built in 'sparse matrix' form which requires much less memory. o chicago The Chicago street crimes data are now stored in 'sparse matrix' form. To convert them to non-sparse form, use as.lpp(chicago, sparse=FALSE) o kppm The parametrisation of cluster models has been reorganised. The scale parameter is now always called 'scale'. Results should be backward-compatible. o cauchy.estK, cauchy.estpcf, matclust.estK, matclust.estpcf, thomas.estK, thomas.estpcf, vargamma.estK, vargamma.estpcf The parametrisation of cluster models has been reorganised. The scale parameter is now always called 'scale'. o plot.kppm Also plots the cluster kernel. o density.ppp New argument 'se' allows calculation of standard errors as well. o plot.pp3 Now produces a genuine perspective view. New arguments control the eye position for the perspective view. o Emark, Vmark These functions can now work with multiple columns of marks. o pixellate.psp Can now count the number of segments that intersect each pixel, instead of the total length of intersection. o linfun If g = linfun(f, L), the function f will always be called as f(x,y,seg,tp, ...) It is no longer expected to handle the case where 'seg' and 'tp' are absent. The resulting function g can now be called as g(X) where X is an lpp object, or as g(x,y) or g(x,y,seg,tp) where x,y,seg,tp are coordinates. o tess New argument 'marks' allows marks to be associated with tiles. o anova.lppm Outdated argument 'override' has been removed. o split<-.ppp Preserves the original ordering of the data, if possible. o MultiHard, MultiStrauss, MultiStraussHard, HierStrauss Zero values in the interaction radii are now treated as NA. Improved handling of missing arguments. Printed output now respects options('width') o linearKinhom, linearKcross.inhom, linearKdot.inhom, linearpcfinhom, linearpcfcross.inhom, linearpcfdot.inhom If the intensity argument lambda, lambdaI, lambdaJ, lambdadot is a fitted point process model, the model is first updated by re-fitting it to the data, before computing the fitted intensity. o solutionset The expression will be evaluated using pixel arithmetic (Math.im) if it cannot be evaluated using eval.im. o to.grey Now uses better weights for the R, G, B channels. o rVarGamma Accelerated. o summary.mppm, print.mppm These functions now respect options('width') and spatstat.options('terse'). o print.quadrattest Now respects options('width') and spatstat.options('terse'). o print.pp3 Now respects options('width') o print.lpp Now respects options('width') and options('digits'). o print.owin, print.im, print.summary.owin, print.summary.im Now respect options('width'). o nnmean Now yields a vector, instead of a 1-column matrix, when there is only a single column of marks. o pairdist.psp, crossdist.psp, nndist.psp The option 'method="Fortran"' is no longer supported. The default is 'method="C"'. o [.hyperframe: When a row of data is extracted with drop=TRUE, the result belongs to class 'anylist'. o installation of spatstat A Fortran compiler is no longer needed to compile spatstat from source. o hyperframe class The internal structure of hyperframes has changed slightly: columns of objects are now stored and returned as lists of class 'anylist' or 'solist'. There should be no change in behaviour. o datasets Internal format of the datasets bdspots, bei, clmfires, demohyper, flu, gorillas, heather, Kovesi, murchison, osteo, pyramidal, waterstriders has changed slightly to use the classes 'anylist' and 'solist'. There should be no change in behaviour. o K3est New argument 'ratio'. o spatstat.options New option 'par.points3d' sets default arguments for plot.pp3. o diagnose.ppm New arguments 'xlab', 'ylab', 'rlab' determine the labels in the 4-panel plot, and new argument 'outer' controls their position. The confusing default value for 'compute.sd' has been changed. o iplot.layered New argument 'visible' controls which layers are initially visible. o plot.lpp New argument 'show.window' controls whether to plot the containing window. o textstring Any number of spatial locations (x,y) can be specified, with a corresponding vector of text strings. o plot.hyperframe New argument 'mar' o plot.linnet New argument 'do.plot' o summary.hyperframe Improved output. o eval.linim Improved scoping rules. o pixellate.owin Accelerated. o summary.linnet Now prints more information, and respects options('digits'). o rmpoispp, rmpoint The vector of possible types of points will default to the 'names' vector of the argument 'lambda', 'n', or 'f' where appropriate. o rpoislpp Argument 'L' can be omitted when lambda is a 'linim' or 'linfun' o simulate.ppm, simulate.kppm, simulate.lppm, simulate.slrm New argument 'drop': if nsim = 1 and drop=TRUE, the result is a point pattern rather than a list containing one point pattern. o runifdisc, runifpoint, rpoint, rpoispp, rmpoint, rmpoispp, rMaternI, rMaternII, rSSI, rPoissonCluster, rGaussPoisson, rstrat, rsyst, rcell, rthin, rNeymanScott, rMatClust, rThomas, rCauchy, rVarGamma, rpoispp3, runifpoint3 New argument 'drop': if nsim = 1 and drop=TRUE, the result is a point pattern rather than a list containing one point pattern. o spatstat.options New option 'units.paren' controls the type of parenthesis enclosing the explanatory text about the unit of length, in print.ppm, plot.fv, etc. o closepairs, crosspairs New option: what="ijd" returns only the indices i, j and the distance d o rCauchy, rMatClust, rNeymanScott, rPoissonCluster, rThomas, rVarGamma Argument names have changed. BUG FIXES o sumouter A segmentation fault could occur if any data were NA. Fixed. o simulate.kppm Simulation failed for log-Gaussian Cox processes (in simulate.kppm only) with an error message from the RandomFields package. Fixed. o ppm, predict.ppm, profilepl Crashed sometimes with message "interaction evaluator did not return a matrix". Fixed. o lppm step() did not work correctly on 'lppm' objects. Fixed. o quadscheme If quadscheme() was called explicitly, with the stipulated number of tiles exceeding the number of dummy points given, then the quadrature weights were sometimes vastly inflated - total quadrature weight was much larger than window area. Spotted by Ian Renner. Fixed. o predict.rhohat Result was incorrect for data on a non-rectangular window (and a warning was issued about incorrect vector length). Fixed. o Math.im Unary operators did not work (e.g."-x") Fixed. o density.ppp Crashed when at="points" if the dataset had exactly 1 point. Fixed. o rSSI Crashed if nsim > 1. Fixed. o influence.ppm, leverage.ppm, dfbetas.ppm Crashed or issued a warning if any quadrature points had conditional intensity zero under the model (negative infinite values of the sufficient statistic). Fixed. o clickppp, clickpoly Did not work correctly in the RStudio display device. Fixed. o Iest Ignored the arguments 'r' and 'eps'. Fixed. o markvario Result was garbled, when X had more than one column of marks. Fixed. o rMatClust, rVarGamma, rCauchy, rNeymanScott Result was a list, but not a 'solist', when nsim > 1. Fixed. o print.mppm, summary.mppm, subfits Crashed if a Poisson interaction was implied but not given explicitly. Fixed. o Kest Crashed if ratio=TRUE and the window was a rectangle. Fixed. o anova.ppm Crashed sometimes with message 'models were not all fitted to the same size of dataset'. (This occurred if there were quadrature points with conditional intensity equal to zero in some models but not in all models.) Fixed. o vcov.kppm Occasionally ran out of memory. Fixed. o as.linim.linfun Erroneously converted the pixel values to numeric values. Fixed. o as.owin.layered Ignored layers with zero area. Fixed. o plot.ppm Paused the plot between frames even when there was only one frame. Fixed. o plot.layered Did not allocate space for legends of 'lpp' objects. Fixed. o plot.lpp Ignored symbolmap arguments like 'cex' and confused the arguments 'col' and 'cols'. Fixed. o plot.diagppm Ignored add=TRUE in some cases. Fixed. o iplot.layered Did not handle 'diagramobj' objects correctly. Fixed. o plot.yardstick Changed arguments. CHANGES IN spatstat VERSION 1.41-0 OVERVIEW o We thank Ahmed El-Gabbas, Ute Hahn, Aruna Jammalamadaka, Ian Renner, Brian Ripley, Torben Tvedebrink and Sasha Voss for contributions. o Fixed a bug causing a segmentation fault. o Standard errors for kernel estimates of intensity. o Test for segregation. o Tessellations may now have marks. o Nested splitting. o More support for cluster models. Reorganised parametrisation. o Sparse data representation of linear networks. o More support for data on a linear network. o New datasets: 'spiders' and 'dendrite'. o Improvements and bug fixes. o spatstat no longer uses Fortran. o spatstat no longer depends on the package 'scatterplot3d'. o spatstat now imports (rather than 'suggests') the Matrix package. o Nickname: 'Team Australia' NEW DATASETS o dendrite Dendritic spines on the dendrite network of a neuron. A point pattern on a linear network. Generously contributed by Aruna Jammalamadaka. o spiders Spider webs on the mortar lines of a brick wall. A point pattern on a linear network. Generously contributed by Sasha Voss. NEW FUNCTIONS o segregation.test Test of spatial segregation of types in a multitype point pattern. o clusterfield, clusterkernel Compute the cluster kernel (offspring density) of a cluster process model, or compute the cluster field generated by superimposing copies of the cluster kernel at specified locations. o clusterradius Compute the radius of the support of the offspring density of a cluster process model. o as.linnet.psp Convert a line segment pattern to a linear network by guessing the connectivity using a distance threshold. o iplot.linnet, iplot.lpp Methods for interactive plotting 'iplot' for objects of class lpp and linnet. o Mathematical operations are now supported for pixel images on a linear network. See help(Math.linim) o dirichlet.network, delaunay.network The linear networks formed by the Dirichlet tessellation and Delaunay triangulation. o dirichlet.edges The edges of the Dirichlet tessellation. o selfcut.psp Cut line segments where they cross each other. o vertices.linnet Extract the vertices (nodes) of the linear network. o vertexdegree Compute the degree of each vertex in a linear network. o pixellate.linnet Pixellate a linear network. o subset.hyperframe 'subset' method for class 'hyperframe'. o head.hyperframe, tail.hyperframe 'head' and 'tail' methods for hyperframes. o clickdist Measures the distance between two spatial locations clicked by the user. o solapply, anylapply wrappers for 'lapply' which return a list of class 'solist' or 'anylist'. o Kmark Weighted K-function. Identical to 'markcorrint' and will eventually replace it. o marks.tess, marks<-.tess, unmark.tess: Extract or change the marks associated with the tiles of a tessellation. o quantess Quantile tessellation: divide space into pieces which contain equal amounts of 'stuff'. o nestsplit Nested split o integral New generic function for integrating functions, with methods for 'im', 'msr', 'linim' and 'linfun'. o selfcut.psp Cut line segments where they cross each other o as.function.im Convert a pixel image to a function(x,y). o as.linnet.linim Extract the linear network from a 'linim' object. o pool.fv, pool.anylist New methods for 'pool' o Window.linnet Extract the two-dimensional window containing a linear network. SIGNIFICANT USER-VISIBLE CHANGES o linnet, lpp A linear network can now be built in 'sparse matrix' form which requires much less memory. o chicago The Chicago street crimes data are now stored in 'sparse matrix' form. To convert them to non-sparse form, use as.lpp(chicago, sparse=FALSE) o kppm The parametrisation of cluster models has been reorganised. The scale parameter is now always called 'scale'. Results should be backward-compatible. o cauchy.estK, cauchy.estpcf, matclust.estK, matclust.estpcf, thomas.estK, thomas.estpcf, vargamma.estK, vargamma.estpcf The parametrisation of cluster models has been reorganised. The scale parameter is now always called 'scale'. o plot.kppm Also plots the cluster kernel. o density.ppp New argument 'se' allows calculation of standard errors as well. o plot.pp3 Now produces a genuine perspective view. New arguments control the eye position for the perspective view. o Emark, Vmark These functions can now work with multiple columns of marks. o pixellate.psp Can now count the number of segments that intersect each pixel, instead of the total length of intersection. o linfun If g = linfun(f, L), the function f will always be called as f(x,y,seg,tp, ...) It is no longer expected to handle the case where 'seg' and 'tp' are absent. The resulting function g can now be called as g(X) where X is an lpp object, or as g(x,y) or g(x,y,seg,tp) where x,y,seg,tp are coordinates. o tess New argument 'marks' allows marks to be associated with tiles. o anova.lppm Outdated argument 'override' has been removed. o split<-.ppp Preserves the original ordering of the data, if possible. o MultiHard, MultiStrauss, MultiStraussHard, HierStrauss Zero values in the interaction radii are now treated as NA. Improved handling of missing arguments. Printed output now respects options('width') o linearKinhom, linearKcross.inhom, linearKdot.inhom, linearpcfinhom, linearpcfcross.inhom, linearpcfdot.inhom If the intensity argument lambda, lambdaI, lambdaJ, lambdadot is a fitted point process model, the model is first updated by re-fitting it to the data, before computing the fitted intensity. o solutionset The expression will be evaluated using pixel arithmetic (Math.im) if it cannot be evaluated using eval.im. o to.grey Now uses better weights for the R, G, B channels. o rVarGamma Accelerated. o summary.mppm, print.mppm These functions now respect options('width') and spatstat.options('terse'). o print.quadrattest Now respects options('width') and spatstat.options('terse'). o print.pp3 Now respects options('width') o print.lpp Now respects options('width') and options('digits'). o print.owin, print.im, print.summary.owin, print.summary.im Now respect options('width'). o nnmean Now yields a vector, instead of a 1-column matrix, when there is only a single column of marks. o pairdist.psp, crossdist.psp, nndist.psp The option 'method="Fortran"' is no longer supported. The default is 'method="C"'. o [.hyperframe: When a row of data is extracted with drop=TRUE, the result belongs to class 'anylist'. o installation of spatstat A Fortran compiler is no longer needed to compile spatstat from source. o hyperframe class The internal structure of hyperframes has changed slightly: columns of objects are now stored and returned as lists of class 'anylist' or 'solist'. There should be no change in behaviour. o datasets Internal format of the datasets bdspots, bei, clmfires, demohyper, flu, gorillas, heather, Kovesi, murchison, osteo, pyramidal, waterstriders has changed slightly to use the classes 'anylist' and 'solist'. There should be no change in behaviour. o K3est New argument 'ratio'. o spatstat.options New option 'par.points3d' sets default arguments for plot.pp3. o diagnose.ppm New arguments 'xlab', 'ylab', 'rlab' determine the labels in the 4-panel plot, and new argument 'outer' controls their position. The confusing default value for 'compute.sd' has been changed. o iplot.layered New argument 'visible' controls which layers are initially visible. o plot.lpp New argument 'show.window' controls whether to plot the containing window. o textstring Any number of spatial locations (x,y) can be specified, with a corresponding vector of text strings. o plot.hyperframe New argument 'mar' o plot.linnet New argument 'do.plot' o summary.hyperframe Improved output. o eval.linim Improved scoping rules. o pixellate.owin Accelerated. o summary.linnet Now prints more information, and respects options('digits'). o rmpoispp, rmpoint The vector of possible types of points will default to the 'names' vector of the argument 'lambda', 'n', or 'f' where appropriate. o rpoislpp Argument 'L' can be omitted when lambda is a 'linim' or 'linfun' o simulate.ppm, simulate.kppm, simulate.lppm, simulate.slrm New argument 'drop': if nsim = 1 and drop=TRUE, the result is a point pattern rather than a list containing one point pattern. o runifdisc, runifpoint, rpoint, rpoispp, rmpoint, rmpoispp, rMaternI, rMaternII, rSSI, rPoissonCluster, rGaussPoisson, rstrat, rsyst, rcell, rthin, rNeymanScott, rMatClust, rThomas, rCauchy, rVarGamma New argument 'drop' o spatstat.options New option 'units.paren' controls the type of parenthesis enclosing the explanatory text about the unit of length, in print.ppm, plot.fv, etc. o closepairs, crosspairs New option: what="ijd" returns only the indices i, j and the distance d o rCauchy, rMatClust, rNeymanScott, rPoissonCluster, rThomas, rVarGamma Argument names have changed. BUG FIXES o sumouter A segmentation fault could occur if any data were NA. Fixed. o simulate.kppm Simulation failed for log-Gaussian Cox processes (in simulate.kppm only) with an error message from the RandomFields package. Fixed. o ppm, predict.ppm, profilepl Crashed sometimes with message "interaction evaluator did not return a matrix". Fixed. o lppm step() did not work correctly on 'lppm' objects. Fixed. o quadscheme If quadscheme() was called explicitly, with the stipulated number of tiles exceeding the number of dummy points given, then the quadrature weights were sometimes vastly inflated - total quadrature weight was much larger than window area. Spotted by Ian Renner. Fixed. o predict.rhohat Result was incorrect for data on a non-rectangular window (and a warning was issued about incorrect vector length). Fixed. o Math.im Unary operators did not work (e.g."-x") Fixed. o density.ppp Crashed when at="points" if the dataset had exactly 1 point. Fixed. o rSSI Crashed if nsim > 1. Fixed. o influence.ppm, leverage.ppm, dfbetas.ppm Crashed or issued a warning if any quadrature points had conditional intensity zero under the model (negative infinite values of the sufficient statistic). Fixed. o clickppp, clickpoly Did not work correctly in the RStudio display device. Fixed. o Iest Ignored the arguments 'r' and 'eps'. Fixed. o markvario Result was garbled, when X had more than one column of marks. Fixed. o rMatClust, rVarGamma, rCauchy, rNeymanScott Result was a list, but not a 'solist', when nsim > 1. Fixed. o print.mppm, summary.mppm, subfits Crashed if a Poisson interaction was implied but not given explicitly. Fixed. o Kest Crashed if ratio=TRUE and the window was a rectangle. Fixed. o anova.ppm Crashed sometimes with message 'models were not all fitted to the same size of dataset'. (This occurred if there were quadrature points with conditional intensity equal to zero in some models but not in all models.) Fixed. o vcov.kppm Occasionally ran out of memory. Fixed. o as.linim.linfun Erroneously converted the pixel values to numeric values. Fixed. o as.owin.layered Ignored layers with zero area. Fixed. o plot.ppm Paused the plot between frames even when there was only one frame. Fixed. o plot.layered Did not allocate space for legends of 'lpp' objects. Fixed. o plot.lpp Ignored symbolmap arguments like 'cex' and confused the arguments 'col' and 'cols'. Fixed. o plot.diagppm Ignored add=TRUE in some cases. Fixed. o iplot.layered Did not handle 'diagramobj' objects correctly. Fixed. o plot.yardstick Changed arguments. CHANGES IN spatstat VERSION 1.40-0 OVERVIEW o We thank Markus Herrmann, Peter Kovesi, Andrew Lister, Enrique Miranda, Tuomas Rajala, Brian Ripley, Dominic Schuhmacher and Maxime Woringer for contributions. o Important bug fixes. o Mathematical operators now apply to images. o Parametric estimates of relative risk from fitted point process models. o Standard errors for relative risk (parametric and non-parametric). o Kernel smoothing and rose diagrams for angular data. o Perceptually uniform colour maps. o Hierarchical interactions for multitype patterns. o Hard core parameters in all interactions no longer need to be specified and will be estimated from data. o Improvements to analysis of deviance and model selection. o New datasets. o New vignette, summarising all datasets installed with spatstat. o Tests and diagnostics now include a Monte Carlo option. o Faster checking of large datasets. o Faster simulations. o Code for drawing diagrams (arrows, scale bars). o Version nickname: 'Do The Maths' NEW DATASETS o bdspots Breakdown spots on microelectronic capacitor electrodes. Generously contributed by Prof Enrique Miranda. o Kovesi Colour maps with perceptually uniform contrast. Generously contributed by Peter Kovesi. NEW FUNCTIONS o Mathematical operations are now supported for images. For example: alpha <- atan(bei.extra$grad) * 180/pi See help(Math.im) o relrisk.ppm Spatially-varying probabilities of different types of points predicted by a fitted point process model. o circdensity Kernel density estimate for angular data o rose Rose diagram (rose of directions) for angular data o nnorient Nearest neighbour orientation distribution. o AIC.ppm Calculate AIC of a Gibbs model using Takeuchi's rule. o interp.colours Interpolate a sequence of colour values. o anyDuplicated.ppp, anyDuplicated.ppx Fast replacements for any(duplicated(x)) for point patterns. o textstring, onearrow, yardstick Objects representing a text string, an arrow, or a scale bar, for use in drawing spatial diagrams. o plot.imlist, image.imlist, contour.imlist Methods for the new class 'imlist' o [<-.layered, [[<-.layered More support for class 'layered' SIGNIFICANT USER-VISIBLE CHANGES o (vignettes) New vignette 'datasets' summarises all the datasets installed with the spatstat package. o relrisk The function relrisk is now generic, with methods for ppp and ppm. New argument 'relative' specifies whether to calculate the relative risk or the absolute probability of each type of point. New argument 'se' specifies whether to calculate standard errors. o plot.im The default colour map for plotting images, specified by spatstat.options('image.colfun'), has been changed to a perceptually uniform map. o DiggleGratton, Fiksel, MultiHard, MultiStraussHard The hard core distance parameters in these models can now be omitted by the user, and will be estimated automatically from data (by the 'self-starting' feature of interactions). This was already true of Hardcore and StraussHard. o Hybrid Hybrid models now apply the 'self-starting' feature to each component model. o anova.ppm Can now reconcile models fitted using different dummy points, different values of 'rbord', different values of 'use.gam', etc. o profilepl New argument 'aic' makes it possible to optimise the parameters by minimising AIC. o profilepl No longer requires values for parameters which are 'optional' (such as the hard core distance). o rmh, simulate.ppm, rmh.ppm, rmh.default The Metropolis-Hastings algorithm now starts by deleting any points in the initial state that are 'illegal' (i.e. whose conditional intensity is equal to zero). This ensures that the result of rmh never contains illegal points. o runifpoint, rpoispp, rStrauss, rHardcore, rStraussHard, rDiggleGratton, rDGS, runifdisc, rpoint, rMaternI, rMaternII, rSSI, rPoissonCluster, rGaussPoisson, rstrat, rsyst, rcell, rthin, rjitter, rNeymanScott, rMatClust, rThomas, rCauchy, rVarGamma, rmpoint, rmpoispp, runifpointOnLines, rpoisppOnLines, runiflpp, rpoislpp, runifpointx, rpoisppx, runifpoint3, rpoispp3 These random point pattern generators now have an argument 'nsim' specifying the number of simulated realisations to be generated. o pairorient New argument 'cumulative'. New algorithm to compute kernel estimate of probability density. Default behaviour changed. Argument 'units' has been renamed 'unit' for consistency. Labels and descriptions of columns have been corrected. o predict.ppm New syntax (backward-compatible). New argument 'se' replaces option 'type="se"'. Old argument 'total' is deprecated: use 'window' and set 'type="count"'. o cdf.test The methods for class 'ppm' and 'lppm' now handle Gibbs models and perform a Monte Carlo test in this case. o lurking, diagnose.ppm Lurking variable plot can now include simulation envelopes. o rmh.ppm New argument 'w' determines the window in which the simulated pattern is generated. o ppp Accelerated. o Gcom, Gres When conditional=TRUE and restrict=TRUE, the Hanisch estimate was not calculated exactly as described in Appendix E.1 of Baddeley, Rubak and Moller (2011). The intensity was estimated on the full window rather than the eroded window. Fixed. o step, drop1, add1, extractAIC The AIC of a Gibbs model is now calculated using Takeuchi's rule for the degrees of freedom. o model.matrix.ppm, model.matrix.kppm New argument 'Q' allows prediction at any desired locations. o vcov.ppm New argument 'fine' gives more control over computation. o predict.ppm For multitype models, when the result is a list of images, the names of list entries are now identical to the mark levels (e.g. "hickory" instead of "markhickory") o print.slrm Output now respects options('width') o image.listof New argument 'ribmar' controls margin space around the ribbon when equal.ribbon=TRUE. o integral.im New argument 'domain' specifies the domain of integration. o plot.fasp New argument 'transpose' allows rows and columns to be exchanged. o plot.im The list 'ribargs' can now include the parameter 'labels'. o rmh, rpoint, rpoispp, rmpoint, rmpoispp Accelerated, for inhomogeneous processes. o stienen Now recognises the parameter 'lwd'. o suffstat Accelerated (also affects ppm with method='ho'). o Poisson, AreaInter, BadGey, Concom, DiggleGatesStibbard, DiggleGratton, Fiksel, Geyer, Hardcore, Hybrid, LennardJones, MultiHard, MultiStrauss, MultiStraussHard, OrdThresh, Ord, PairPiece, Pairwise, SatPiece, Saturated, Softcore, Strauss, StraussHard, Triplets These functions can now be printed (by typing the function name) to give a sensible description of the required syntax. o fitin A plot of the fitted interpoint interaction of a point process model e.g. plot(fitin(ppm(swedishpines ~ 1, Strauss(9)))) now shows the unit of length on the x-axis. o fitin Plots of the fitted interpoint interaction are now possible for some higher-order interactions such as Geyer and AreaInter. o anova.ppm New argument 'warn' to suppress warnings. o rmhmodel.ppm Argument 'win' renamed 'w' for consistency with other functions. o print.ppm Printed output for the fitted regular parameters now respects options('digits'). o print.ppm, print.summary.ppm Output now respects options('width') and spatstat.options('terse') o print.ppm By default, standard errors are not printed for a model fitted with method="logi" (due to computational load) o plot.profilepl Now recognises 'lty', 'lwd', 'col' etc o vesicles, gorillas Some of the raw data files for these datasets are also installed in spatstat for demonstration and training purposes. BUG FIXES o rmh, rmh.ppm, rmh.default, simulate.ppm The result of simulating a model with a hard core did not necessarily respect the hard core constraint, and simulation of a model with strong inhibition did not necessarily converge. This only happened if the first order trend was large, the starting state (n.start or x.start) was not given, and the number of iterations (nrep) was not very large. It occurred because of a poor choice for the default starting state. Bug was present since about 2010. Fixed. o markcorrint Results were completely incorrect. Bug introduced in spatstat 1.39-0, october 2014. Fixed. o Kinhom Ignored argument 'reciplambda2' in some cases. Bug introduced in spatstat 1.39-0, october 2014. Fixed. o relrisk When at="pixels", a small fraction of pixel values were sometimes wildly inaccurate, due to numerical errors. This affected the range of values in the result, and therefore the appearance of plots. Fixed. o model.images Crashed if the model was multitype. Fixed. o profilepl Crashed in some cases when the interaction was multitype. [Spotted by Andrew Lister.] Fixed. o profilepl Crashed if the model involved covariates that were not given in a 'data' argument. Fixed. o envelope.ppm Crashed if global=TRUE and savefuns=TRUE. Fixed. o setminus.owin Crashed if the result was empty and the input was polygonal. Fixed. o predict.ppm Crashed sometimes when type="cif" and ngrid was very large. Fixed. o pixelquad If X was a multitype point pattern, the result was mangled. Fixed. o relrisk Did not accept a character string value for the argument 'case'. Fixed. o intensity.ppm Format of result was incorrect for ppm(Y ~ 1) where Y is multitype. Fixed. o $<-.hyperframe Columns containing character values were converted to factors. Fixed. o clickppp Sometimes filled the window in solid black colour.. Fixed. o plot.psp Ignored 'show.all' in some cases. Fixed. o plot.ppp Warned about NA values amongst the marks, even if there were no NA's in the column(s) of marks selected by the argument 'which.marks'. Fixed. o stienen Did not suppress the border circles when border=FALSE. Fixed. CHANGES IN spatstat VERSION 1.39-1 OVERVIEW o Urgent bug fix. o We thank Suman Rakshit and Brian Ripley for contributions. BUG FIXES o bdry.mask, convexhull In R-devel only, these functions could return an empty window, causing errors in other packages. [Spotted by Brian Ripley.] Fixed. o project2segment An error occurred if any line segments had length zero. [Spotted by Suman Rakshit.] Fixed. CHANGES IN spatstat VERSION 1.39-0 OVERVIEW o We thank Shane Frank, Shaaban Ghalandarayeshi, Ute Hahn, Mahdieh Khanmohammadi, Nicoletta Nava, Jens Randel Nyengaard, Sebastian Schutte, Rasmus Waagepetersen and Carl G. Witthoft for contributions. o ANOVA extended to Gibbs models. o Improved algorithm for locally-scaled K-function. o Leave-one-out calculation of fitted values in ppm objects. o New dataset: presynaptic vesicles. o Geometrical operations with windows and images. o More edge corrections for K-function. o Improved handling and plotting of 'fv' objects. o Utilities for perspective views of surfaces. o New classes 'anylist', 'solist' will ultimately replace 'listof'. o Bug fixes. o Version nickname: 'Smoke and Mirrors' NEW DATASETS o vesicles Synaptic vesicles (includes raw data files for training purposes) NEW CLASSES o anylist List of objects. (A replacement for 'listof') o solist List of two-dimensional spatial objects. (A replacement for some uses of 'listof') NEW FUNCTIONS o perspPoints, perspLines, perspSegments, perspContour Draw points and lines on a surface, as seen in perspective view. o hopskel.test Hopkins-Skellam test of CSR o project2set For each data point in a point pattern X, find the nearest spatial location in a given window W. o stienen, stienenset Stienen diagrams o dirichlet.vertices Vertices of the Dirichlet tessellation o discs Union of discs. Given a point pattern dataset recording the locations and diameters of objects, find the region covered by the objects. o increment.fv Increments of a summary function: g(x) = f(x+h)-f(x-h). o rotmean Rotational average of pixel values in an image o fardist Distance from each pixel/data point to farthest part of window boundary o circumradius.owin Circumradius of a window o rmax.Trans, rmax.Ripley Compute the maximum distance 'r' for which the translation edge correction and isotropic edge correction are valid. o is.grey Determines whether a colour value is a shade of grey. o harmonise Convert several objects of the same class to a common format. (New generic function with existing methods harmonise.im and harmonise.fv) o area New generic function, with methods for 'owin' and 'default'. o Fhazard Hazard rate of empty space function o anylist, as.anylist, [.anylist, [<-.anylist, print.anylist, summary.anylist Support for new class 'anylist' o solist, as.solist, [.solist, [<-.solist, print.solist, summary.solist Support for new class 'solist' o plot.anylist, plot.solist Plot methods for the classes 'anylist' and 'solist' (Currently identical to 'plot.listof') SIGNIFICANT USER-VISIBLE CHANGES o anova.ppm Now applies to Gibbs models as well as Poisson models, using adjusted composite likelihood ratio test statistic. o persp.im If visible=TRUE, the algorithm will also calculate which pixels of x are visible in the perspective view. This is useful for drawing points or lines on a perspective surface. o Kscaled Improved algorithm [thanks to Ute Hahn.] New arguments 'renormalise' and 'normpower' allow renormalisation of intensity, similar to Kinhom. o Kest New option: correction="rigid" computes the rigid motion correction. o pairwise interactions Fitted parameters and other calculations for pairwise interaction models DiggleGatesStibbard, DiggleGratton, Fiksel, Geyer, Strauss may change slightly due to a change in handling numerical rounding effects. o eval.fv Functions no longer need to have exactly the same sequence of 'r' values. They will now be made compatible using 'harmonise.fv'. o fitted.ppm New argument 'leaveoneout' allows leave-one-out calculation of fitted intensity at original data points. o Kinhom, Linhom New argument 'leaveoneout' specifies whether the leave-one-out rule should be applied when calculating the fitted intensities. o crosspaircounts Results may change slightly due to a change in handling numerical rounding effects. o Fest, Gest New argument 'domain' supports bootstrap methods. o plot.fv New argument 'mathfont' determines the font (e.g. plain, italic, bold) for mathematical expressions on the axes and in the legend. Defaults to italic. o scanpp Upgraded to handle multiple columns of mark data. o circumradius The function 'circumradius' is now generic, with methods for the classes 'owin' and 'linnet'. o edge.Trans New argument 'give.rmax' o fvnames, plot.fv The symbol '.a' is now recognised. It stands for 'all function values'. o as.function.fv Argument 'extrapolate' can have length 1 or 2. o varblock New argument 'confidence' determines the confidence level. o $<-.fv This can now be used to add an extra column to an 'fv' object (previously it refused). o minnndist, maxnndist New argument 'positive'. If TRUE, coincident points are ignored: the nearest-neighbour distance of a point is the distance to the nearest point that does not coincide with the current point. o plot.fv Improved handling of 'shade' argument. o Kmeasure Now passes '...' arguments to as.mask() o Ksector Now allows start < 0. New arguments 'units' and 'domain'. o pairorient New arguments 'units' and 'domain'. o eroded.areas New argument 'subset' o disc New argument 'delta' o plot.plotppm New argument 'pppargs' o harmonise.fv, harmonise.im These are now methods for the new generic 'harmonise' o Fest, Gest These functions now also compute the theoretical value of hazard for a Poisson process, if correction = "km". o with.fv Improved mathematical labels. o Gfox, Jfox Improved mathematical labels. o area.owin This function is now a method for the new generic 'area' o edges Default for argument 'check' changed to FALSE. BUG FIXES o varblock Calculations were incorrect if more than one column of edge corrections was computed. [Bug introduced in spatstat 1.21-1, november 2010.] Fixed. o varblock Crashed if one of the quadrats contained no data points. Fixed. o lohboot Interval was calculated wrongly when global=TRUE and fun="Lest" or "Linhom". Fixed. o nnmark Crashed when at="points" if there was only a single column of marks. [Spotted by Shane Frank.] Fixed. o plot.msr Some elements of the plot were omitted or cut off. Fixed. o plot.msr Did not work with 'equal.scales=TRUE'. Fixed. o plot.msr, augment.msr Crashed if every data point was duplicated. Fixed. o as.im.owin Crashed if X was a 1 x 1 pixel array. Fixed. o owin Coordinates of polygon data were altered slightly when fix=TRUE. [Spotted by Carl Witthoft.] Fixed. o objects of class 'fv' Assigning a new value to names(x) or colnames(x) or dimnames(x) would cause the internal data format to become corrupted. Fixed. o to.grey, complementarycolour Did not work properly on 'colourmap' objects. Fixed. o Kest Ignored argument 'var.approx' if the window was a rectangle. Fixed. o rmh.ppm, rmhmodel.ppm Ignored the argument 'new.coef'. [Spotted by Sebastian Schutte] Fixed. o as.function.fv The meanings of 'extrapolate=TRUE' and 'extrapolate=FALSE' were swapped. Fixed. o varblock Handled the case 'fun=Lest' incorrectly. Fixed. o [.fv Sometimes garbled the internal data format, causing plot.fv to crash. Fixed. o range.fv Sometimes returned NA even when na.rm=TRUE. Fixed. o Fest Argument 'eps' was not interpreted correctly. Fixed. o plot.fv Argument 'lwd' was not passed to legend() o flipxy.owin Sometimes deleted the name of the unit of length. Fixed. CHANGES IN spatstat VERSION 1.38-1 OVERVIEW o We thank Ute Hahn and Xavier Raynaud for contributions. o Urgent Bug Fixes. o Nickname: 'Le Hardi' NEW FUNCTIONS o "[<-.fv", "$<-.fv" Subset replacement methods for 'fv' objects. SIGNIFICANT USER-VISIBLE CHANGES o clarkevans.test Simulations are now performed with a fixed number of points. o plot.owin, plot.ppp, plot.psp, plot.im The default size of the outer margin of white space has been reduced. o dclf.test Improved information in printed output. BUG FIXES o update.ppm Results were incorrect in several cases. [Spotted by Xavier Raynaud.] Bug introduced in spatstat 1.38-0. Fixed. o Kinhom, Linhom Calculations were incorrect if 'lambda' was a fitted point process model. [Spotted by Xavier Raynaud.] Bug introduced in spatstat 1.38-0. Fixed. o envelope.envelope Ignored the arguments 'global' and 'VARIANCE'. Fixed. o fv objects If 'f' was an object of class 'fv', then an assignment like f$name <- NULL mangled the internal format of the object 'f', leading to errors in print.fv and plot.fv. [Spotted by Ute Hahn.] Fixed. o split.ppp split(X, A) where A is a rectangular tessellation, produced errors if the window of 'A' did not include the window of 'X'. [Spotted by Ute Hahn.] Fixed. o names<-.hyperframe Mangled the internal format. [Spotted by Ute Hahn.] Fixed. o plot.fv y axis label was incorrect in some cases when the 'fv' object had only a single column of function values. [Spotted by Ute Hahn.] Fixed. CHANGES IN spatstat VERSION 1.38-0 OVERVIEW o We thank Malissa Baddeley, Colin Beale, Oscar Garcia, Daniel Esser, David Ford, Eric Gilleland, Andrew Hardegen, Philipp Hunziker, Abdollah Jalilian, Tom Lawrence, Lore De Middeleer, Robin Milne, Mike Porter, Suman Rakshit, Pablo Ramon, Jason Rudokas, Christopher Ryan, Dominic Schuhmacher, Medha Uppala and Rasmus Waagepetersen for contributions. o spatstat now Requires the package 'goftest' and Suggests the package 'Matrix'. o New dataset: 'sporophores' o Palm likelihood method for fitting cluster processes and Cox processes. o Quasi-likelihood and weighted composite likelihood methods for estimating trend in cluster processes and Cox processes. o Further extensions to model formulas in ppm and kppm. o Faster variance calculations for ppm objects. o One-sided tests and one-sided envelopes of summary functions. o Cramer-Von Mises and Anderson-Darling tests of spatial distribution. o Cressie-Read test statistic in quadrat counting tests. o Spatial cumulative distribution functions. o Faster algorithm for point pattern matching. o Improvements to plots. o Increased support for envelopes. o New generic functions 'Window', 'Frame' and 'domain'. o Directional K-function and directional distribution. o Raster calculations accelerated. o Summary functions accelerated. o Many improvements and bug fixes. o Version nickname: 'Wicked Plot' NEW DATASETS o sporophores Spatial pattern of three species of mycorrhizal fungi around a tree. [Contributed by E. David Ford.] NEW FUNCTIONS o improve.kppm Re-estimate the trend in a kppm (cluster or Cox) model using quasi-likelihood or weighted first-order composite likelihood. [Contributed by Abdollah Jalilian and Rasmus Waagepetersen.] o Window, Window<- Generic functions to extract and change the window of a spatial object in two dimensions. Methods for ppp, psp, im, and many others. o Frame, Frame<- Generic functions to extract and change the containing rectangle ('frame') of a spatial object in two dimensions. o domain Generic function to extract the spatial domain of a spatial object in any number of dimensions. o Ksector Directional version of the K-function. o pairorient Point pair orientation distribution. o spatialcdf Compute the spatial cumulative distribution of a spatial covariate, optionally using spatially-varying weights. o cdf.test [Supersedes 'kstest'.] Test of goodness-of-fit of a Poisson point process model. The observed and predicted distributions of the values of a spatial covariate are compared using either the Kolmogorov-Smirnov, Cramer-Von Mises or Anderson-Darling test. o berman.test Replaces 'bermantest'. o harmonise.fv Make several functions compatible. o simulate.lppm Simulate a fitted point process model on a linear network. o subset.ppp, subset.lpp, subset.pp3, subset.ppx Methods for 'subset', for point patterns. o closepairs.pp3, crosspairs.pp3 Low-level functions to find all close pairs of points in three dimensions o volume.linnet Method for the generic 'volume'. Returns the length of the linear network. o padimage Pad the border of a pixel image. o as.layered Convert spatial data to a layered object. o panel.contour, panel.image, panel.histogram Panel functions for 'pairs' plots. o range.fv, min.fv, max.fv Range, minimum and maximum of function values. SIGNIFICANT USER-VISIBLE CHANGES o ppm.formula The left hand side of the formula can now be the name of an object in the list 'data', or an expression involving such objects. o ppm The right hand side of the formula can now include the symbol '.' representing all covariates in the list 'data'. o ppm New argument 'subset' makes it possible to fit the model in a subset of the spatial domain defined by an expression. o kppm New option: method="palm", will fit the model by maximising Palm likelihood. o pppdist Substantially accelerated. New argument 'auction' controls choice of algorithm. o rhohat New arguments 'weights' and 'horvitz' for weighted calculations. o persp.im Surface heights and colours can now be controlled by different images. Option to draw a grey apron around the sides of the perspective plot. Return value has a new attribute 'expand'. o plot.listof New arguments 'halign' and 'valign' give improved control over the alignment of panels. o plot.listof If all components of the list are objects of class 'fv' representing functions, then if equal.scales=TRUE, these functions will all be plotted with the same axes (i.e. the same xlim and the same ylim). o envelope The argument 'transform' is now processed by 'with.fv' giving more options, such as 'transform=expression(. - r)' o envelope, dclf.test, mad.test One-sided tests and one-sided envelopes can now be produced, by specifying the argument 'alternative'. o dclf.test, mad.test A pointwise test at fixed distance 'r' can now be performed by setting rinterval = c(r,r). o envelope New arguments 'fix.n' and 'fix.marks' for envelope.ppp and envelope.ppm make it easy to generate simulated patterns conditional on the total number of points, or on the number of points of each type. o quadrat.test Can now calculate the Cressie-Read test statistic instead of the Pearson X2 statistic. o Kres, Gres, Kcom, Gcom, psst, psstA, psstG New argument 'model' makes it easier to generate simulation envelopes of the residual summary functions. o layered, plot.layered The layer plot arguments can include the argument '.plot' specifying a function to perform the plotting instead of the generic 'plot'. o deriv.fv New arguments make it possible to differentiate a periodic function. o ppm Argument 'data' or 'covariates' can now include entries which are not spatial covariates, provided they do not appear in the model formula. o closepairs, crosspairs These functions are now generic, with methods for 'ppp' and 'pp3' o rLGCP Updated to conform to new usage of RandomFields package. Argument syntax has changed. Now allows control over pixel resolution. o bw.diggle New arguments 'correction' and 'hmax' for controlling the calculation. o predict.lppm New argument 'new.coef' for computing predictions with a different vector of model coefficients. o predict.ppm If 'locations' is a pixel image, its pixels determine the spatial locations for prediction. o cut.ppp Argument 'z' can now be a window. o split.ppp Argument 'f' can now be a window. o print.ppm, summary.ppm, coef.summary.ppm The table of parameter estimates, standard errors and confidence intervals now also includes the value of the (signed square root) Wald test statistic. o plot.im Now automatically detects problems in some Windows graphics displays and tries to avoid them. o plot.im The position of axis tick marks alongside the colour ribbon can now be controlled using the parameter 'at' in the argument 'ribargs'. o plot.ppp Can now plot numeric marks using characters chosen by 'pch' or 'chars' with size determined by mark value. o plot.ppp New argument 'meansize' for controlling mark scale. o hsvim, rgbim New argument 'autoscale' causes automatic scaling of colour channel values. o plot.ppp If type='n', a legend is now displayed when x is a marked point pattern. o whist Accelerated by a factor of 5. o Fest, Jest Accelerated by a factor of 2 to 3. o fryplot Accelerated. Now displays a legend if the point pattern is marked. Now handles numerical marks nicely. New argument 'axes'. o frypoints Accelerated. New arguments 'to', 'from' and 'dmax'. o duplicated.ppp New option: rule = 'unmark' o rjitter Argument 'radius' now has a default. o Smooth.msr New argument 'drop' o LambertW Now handles NA and infinite values. o update.ppm Now handles formulae with a left-hand side. o raster.x, raster.y, raster.xy These functions can now handle images, as well as masks. o Smooth.ppp If the mark values are exactly constant, the resulting smoothed values are now exactly constant. o eval.im, eval.fv, eval.fasp Argument 'envir' can now be a list, instead of an environment. o plot.ppp The printout (of the resulting symbol map object) now displays the numerical value of the mark scale. o with.fv Improved mathematical labels. o plot.fv Improved mathematical labels on x axis. o ppm Improved error messages. o vcov.ppm Computations greatly accelerated for Hybrid interactions and for Area-interaction models. o vcov.kppm Computations greatly accelerated (when fast=TRUE) o interp.im Argument 'x' can now be a point pattern. o pool.envelope Improved handling of text information. o miplot Improved layout. o print.summary.ppp Improved layout. Now respects spatstat.options('terse') o print.profilepl Improved layout. Now respects spatstat.options('terse') o anova.ppm Now respects spatstat.options('terse') o print.fv, print.envelope Now respect spatstat.options('terse') and options('width') o summary.envelope Now respects options('width') o kstest, bermantest These functions will soon be Deprecated. They are retained only for backward compatibility. BUG FIXES o vcov.ppm Sometimes gave wrong answers for Poisson models fitted by method='logi'. Fixed. o unnormdensity If weights were missing, the density was normalised, contrary to the documentation. Fixed. o logLik.ppm, anova.ppm, AIC For models fitted by 'ippm', the number of degrees of freedom was incorrect. Fixed. o im.apply Pixels outside the window were not assigned the value NA as they should. Fixed. o pixellate.owin Crashed, unpredictably, if the pixel raster had unequal numbers of rows and columns. [Spotted by Rasmus Waagepetersen.] Fixed. o vcov.ppm Crashed for pairwise interaction models fitted by method="logi". Fixed. o predict.ppm Crashed for models fitted by method="logi" if the model included external covariates. Fixed. o predict.ppm Crashed if the argument 'covariates' or 'data' in the original call to 'ppm' included entries that were not spatial covariates. [These entries were ignored by ppm but caused predict.ppm to crash.] Fixed. o simulate.kppm, rNeymanScott, rThomas, rMatClust Crashed randomly when simulating an inhomogeneous model. [Spotted by Philipp Hunziker.] Fixed. o bw.diggle In some extreme cases, generated an error message about `NaN values in Foreign function call.' [Spotted by Colin Beale.] Fixed. o textureplot Crashed if 'spacing' was too large. Fixed. o superimpose.psp Crashed if the result was empty. Fixed. o istat Crashed with an error message about 'vars'. Fixed. o dirichlet, delaunay, delaunay.distance Crashed in rare cases due to a problem in package 'deldir'. [Spotted by Pierre Legendre.] Fixed. o rgbim, hsvim Crashed if any argument was constant. Fixed. o scaletointerval Crashed if x was constant. Fixed. o linnet, [.linnet Crashed if the result contained only a single vertex. [Spotted by Daniel Esser.] Fixed. o plot.fv If some of the function values were NA, they were replaced by fictitious values (by linearly interpolating). Fixed. o crossdist.ppp Ignored argument 'squared' if periodic=FALSE. [Spotted by Mike Porter.] Fixed. o marks<-.ppp Ignored argument 'drop'. [Spotted by Oscar Garcia.] Fixed. o update.ppm Sometimes did not respect the argument 'use.internal'. Fixed. o plot.rhohat Did not respect the argument 'limitsonly'. Fixed. o contour.im Argument 'axes' defaulted to TRUE, but FALSE was intended. Fixed. o print.hyperframe, as.data.frame.hyperframe Column names were mangled if the hyperframe had a single row. Fixed. o as.psp.data.frame Generated a warning about partially-matched names in a data frame. [Spotted by Eric Gilleland.] Fixed. o plot.leverage.ppm Generated a warning from 'contour.default' if the leverage function was constant. Fixed. o plot.diagppm Issued warnings about unrecognised graphics parameters. Fixed. o update.symbolmap Discarded information about the range of input values. Fixed. o plot.fv Label for y axis was garbled, if argument 'shade' was given. Fixed. o plot.ppp The legend was sometimes plotted when it should not have been (e.g. when add=TRUE). Fixed. o plot.listof, plot.im In an array of plots, containing both images and other spatial objects, the titles of the panels were not correctly aligned. Fixed. o plot.tess, plot.quadratcount Ignored arguments like 'cex.main'. Fixed. o iplot Navigation buttons (Left, Right, Up, Down, Zoom In, Zoom Out) did not immediately refresh the plot. Fixed. o iplot.layered Reported an error 'invalid argument type' if all layers were deselected. Fixed. CHANGES IN spatstat VERSION 1.37-0 OVERVIEW o Ege Rubak is now a joint author of spatstat. o We thank Peter Forbes, Tom Lawrence and Mikko Vihtakari for contributions. o Spatstat now exceeds 100,000 lines of code. o New syntax for point process models (ppm, kppm, lppm) equivalent to syntax of lm, glm, ... o Covariates in ppm and kppm can now be tessellations. o Confidence intervals and prediction intervals for fitted models. o Quasirandom point patterns and sequences. o Plots using texture fill. o Support for mappings from data to graphical symbols and textures. o Automatic re-fitting of model in Ginhom, Kinhom, Finhom, Jinhom. o Support for Mixed Poisson distribution. o Interpretation of mark scale parameters has changed in plot.ppp o Syntax of multitype interactions (eg MultiStrauss) has changed. o Bug fix in Metropolis-Hastings simulation of 'StraussHard' models o Changed default behaviour of perfect simulation algorithms. o Improvements to layout of text output. o Version nickname: 'Model Prisoner' NEW CLASSES o symbolmap An object of class 'symbolmap' represents a mapping from data to graphical symbols o texturemap An object of class 'texturemap' represents a mapping from data to graphical textures. NEW FUNCTIONS o split.hyperframe, split<-.hyperframe methods for split and split<- for hyperframes. o dmixpois, pmixpois, qmixpois, rmixpois (log-)normal mixture of Poisson distributions. o vdCorput, Halton, Hammersley, rQuasi quasirandom sequences and quasirandom point patterns. o Smoothfun create a function(x,y) equivalent to the result of Smooth.ppp o minnndist, maxnndist Faster ways to compute min(nndist(X)), max(nndist(X)) o add.texture Draw a simple texture inside a specified region. o textureplot Display a factor-valued pixel image using texture fill. o texturemap Create a texture map o plot.texturemap Plot a texture map in the style of a legend o symbolmap Create a symbol map o update.symbolmap Modify a symbol map o invoke.symbolmap Apply symbol map to data values, and plot them o plot.symbolmap Plot the symbol map in the style of a legend o as.owin.boxx Converts a 'boxx' to an 'owin' if possible. o ellipse Create an elliptical window. o clickbox Interactively specify a rectangle, by point-and-click on a graphics device. o complementarycolour Compute the complementary colour value of a given colour value, or the complementary colour map of a given colour map. o gauss.hermite Gauss-Hermite quadrature approximation to the expectation of any function of a normally-distributed random variable. o boundingbox Generic function, replaces bounding.box o edges Extract boundary edges of a window. Replaces and extends 'as.psp.owin' o pixelcentres Extract centres of pixels as a point pattern. SIGNIFICANT USER-VISIBLE CHANGES o ppm, kppm, lppm NEW SYNTAX FOR POINT PROCESS MODELS The model-fitting functions 'ppm', 'kppm' and 'lppm' now accept a syntax similar to 'lm' or 'glm', for example ppm(X ~ Z), but still accept the older syntax ppm(X, ~Z). To support both kinds of syntax, the functions 'ppm' and 'kppm' are now generic, with methods for the classes 'formula', 'ppp' and 'quad'. The 'formula' method handles a syntax like ppm(X ~ Z) while the 'ppp' method handles the old syntax ppm(X, ~Z). Similarly 'lppm' is generic with methods for 'formula' and 'lpp'. o ppm, kppm, lppm Covariates appearing in the model formula can be objects which exist in the R session, instead of always having to be elements of the list `covariates'. o ppm.formula, kppm.formula, lppm.formula Formulae involving polynom() are now expanded, symbolically, so that polynom(x, 3) becomes x + I(x^2) + I(x^3) and polynom(x,y,2) becomes x + y + I(x^2) + I(x*y) + I(y^2). This neatens the model output, and also makes it possible for anova() and step() to add or delete single terms in the polynomial. o predict.ppm New argument 'interval' allows confidence intervals or prediction intervals to be calculated. o predict.ppm New argument 'total' allows for prediction of the total number of points in a specified region. o plot.ppp, plot.lpp For marked point patterns, a legend is automatically added to the plot, by default. Arguments have changed: new arguments include parameters of the legend, and an optional symbol map. Result has changed: it is now an object of class 'symbolmap'. o plot.ppp, plot.lpp Interpretation of the parameters 'markscale' and 'maxsize' has changed. The size of a circle in the plot is now defined as the circle's diameter instead of its radius. (Size of a square is measured, as before, by its side length). o parres Now handles the case where the fitted model is not separable but its restriction to the given 'subregion' is separable. o envelope Now issues a warning if the usage of envelope() appears to be `invalid' in the sense that the simulated patterns and the data pattern have not been treated equally. o Kinhom, Finhom, Ginhom, Jinhom New argument 'update'. If 'lambda' is a fitted model (class ppm or kppm) and update=TRUE, the model is re-fitted to the data pattern, before the intensities are computed. o rDiggleGratton, rDGS, rHardcore, rStrauss, rStraussHard By default the point pattern is now generated on a larger window, and trimmed to the original window. New argument expand=TRUE. o MultiStrauss, MultiHard, MultiStraussHard The syntax of these functions has changed. The new code should still accept the old syntax. o rhohat rhohat.ppp and rhohat.quad have new argument 'baseline' o ippm Algorithm improved. Argument syntax changed. o default.dummy, quadscheme Dummy points can now be generated by a quasirandom sequence. o plot.owin The window can now be filled with one of 8 different textures. Arguments changed. o ppm, kppm Covariates in the model can now be tessellations. o [.im New argument 'tight' allows the resulting image to be trimmed to the smallest possible rectangle. o [.psp, rlinegrid, rpoisline These functions now handle binary mask windows. o rotate The user can specify the centre of rotation. o rescale rescale() and all its methods now have argument 'unitname' which can be used to change the name of the unit of length. o anova.ppm Output format has been improved. Number of columns of result has changed. o print.ppp, print.summary.ppp, print.owin, print.summary.owin, print.im, print.summary.im, print.fv, print.msr, print.profilepl These functions now avoid over-running the text margin (i.e. they respect options('width') where possible). o layerplotargs<- Now handles any spatial object, converting it to a 'layered' object. o effectfun Improved display in case se.fit=TRUE. o scaletointerval New argument 'xrange' o contour.im New argument 'show.all'. Default value of 'axes' changed to FALSE. o identify.ppp Now handles multivariate marks. o plot.listof Improved layout. New arguments 'hsep', 'vsep'. Argument 'mar.panel' may have length 1, 2 or 4. o plot.splitppp This function is no longer identical to plot.listof. Instead it is a much simpler function which just calls plot.listof with equal.scales=TRUE. o anova.ppm Output is neater. o plot.layered New argument 'do.plot' o plot.psp New argument 'do.plot' o as.psp.owin New argument 'window' o plot.im, contour.im, textureplot New argument 'clipwin' o plot.ppp New argument 'clipwin' o plot.msr New argument 'how' allows density to be plotted as image and/or contour o diagnose.ppm, plot.diagppm More options for 'plot.neg' o plot.leverage.ppm, plot.influence.ppm, plot.msr Argument 'clipwin' can now be used to restrict the display to a subset of the full data. o [.hyperframe, [<-.hyperframe, $.hyperframe, $<-.hyperframe These functions are now documented. o leverage.ppm, influence.ppm, dfbetas.ppm Resulting objects are now smaller (in memory size). o print.ppm Now indicates whether the irregular parameters 'covfunargs' were optimised (by profilepl or ippm) or whether they were simply provided by the user. o plot.ppp A point pattern with numerical marks can now be plotted as filled dots with colours determined by the marks, by setting pch=21 and bg= o colourmap Now handles dates and date-time values (of class 'Date' or 'POSIXt'). o plot.ppp, print.ppp, summary.ppp Improved handling of dates and date-time values (of class 'Date' or 'POSIXt') in the marks of a point pattern. o cut.im Now refuses to handle images whose pixel values are factor, logical or character. o centroid.owin New argument 'as.ppp' o superimpose Improved default names for columns of marks. o Softcore() Improved printout. o kppm, lgcp.estpcf, lgcp.estK Adjusted to new structure of RandomFields package. No change in syntax. o data(murchison) This dataset now belongs to class 'listof' so that it can be plotted directly. o data(clmfires) The format of the covariate data has changed. The objects 'clmcov100' and 'clmcov200' are now elements of a list 'clmfires.extra'. o bounding.box This function is now Deprecated; it has been replaced by the generic boundingbox(). o as.psp.owin This function is now Deprecated; it has been replaced and extended by the function edges(). o plot.kstest Changed defaults so that the two curves are distinguishable. o with.fv Improved mathematical labels. BUG FIXES o intensity.quadratcount Values were incorrect for a rectangular tessellation (the matrix of intensities was transposed). Fixed. o rmh, simulate.ppm Simulation of the Strauss-hard core model (StraussHard) was incorrect (intensity of the simulated process was about 15% too low). Bug introduced in spatstat 1.31-0 (January 2013). o intensity.quadratcount Crashed for a rectangular tessellation with only a single row or column. Fixed. o model.images.ppm Crashed sometimes if the argument W was given. Fixed. o eval.im Crashed when applied to images with only a single row or column. Fixed. o ppp, marks<-.ppp If the marks were a vector of dates, they were erroneously converted to numbers. Fixed. o ippm Crashed if the model formula included an offset term that was not a function. Fixed. o leverage.ppm Crashed sometimes when the model had irregular parameters ('covfunargs'). Fixed. o residuals.ppm Crashed sometimes when type='score'. Fixed. o scaletointerval Did not handle dates and date-time values correctly. Fixed. o rbind.hyperframe, as.list.hyperframe Gave incorrect results for hyperframes with 1 row. Fixed. o Kinhom Did not renormalise the result (even when renormalise=TRUE), in some cases. Spotted by Peter Forbes. Fixed. o disc If mask=TRUE the disc was erroneously clipped to the square [-1,1] x [-1,1]. Fixed. o plot.fv Sometimes shaded the wrong half of the graph when the 'shade' coordinates were infinite. Fixed. o print.ppm Gave an error message if the coefficient vector had length zero. Fixed. o vcov.ppm Gave an error message if the coefficient vector had length zero. Fixed. o plot.distfun, as.im.distfun These functions effectively ignored the argument 'invert' in the original call to distfun. Fixed. o plot.msr Ignored certain additional arguments such as 'pch'. Fixed. o cut.im Crashed if the image had 1 row or 1 column of pixels. Fixed. o iplot.ppp Crashed with message about missing object 'vals'. Fixed. o effectfun Demanded a value for every covariate supplied in the original call to ppm, even for covariates which were not used in the model. Fixed. o plot.listof, plot.hyperframe When plotting 3D point patterns (class pp3), these functions issued warnings about 'add' being an unrecognised graphics argument. Fixed. CHANGES IN spatstat VERSION 1.36-0 OVERVIEW o We thank Sebastian Meyer, Kevin Ummer, Jean-Francois Coeurjolly, Ege Rubak, Rasmus Waagepetersen, Oscar Garcia and Sourav Das for contributions. o Important change to package dependencies. o Geometrical inconsistencies in polygons are now repaired automatically. o Improved quadrature schemes and reduced bias in ppm. o New vignette 'Summary of Recent Changes to Spatstat'. o Approximation to K function and pcf for Gibbs models. o Counterpart of 'apply' for lists of images. o Hexagonal grids and tessellations. o Extensions to scan test and Allard-Fraley cluster set estimator. o Change the parameters of a fitted model before simulating it. o Accelerated Kest, Kinhom for rectangular windows. o Extensions and improvements to plotting functions. o Improvements to labelling of 'fv' objects. o New demo of summary functions. o More methods for 'intensity'. o Version nickname: 'Intense Scrutiny' NEW FUNCTIONS o Kmodel.ppm, pcfmodel.ppm Compute approximation to K-function or pair correlation function of a Gibbs point process model. o im.apply Apply a function to corresponding pixel values in several images. o hexgrid, hextess Create a hexagonal grid of points, or a tessellation of hexagonal tiles o shift.tess, rotate.tess, reflect.tess, scalardilate.tess, affine.tess Apply a geometrical transformation to a tessellation. o quantile.ewcdf Extract quantiles from a weighted cumulative distribution function. o scanLRTS Evaluate the spatially-varying test statistic for the scan test. o pcfmulti General multitype pair correlation function o intensity.splitppp Estimate intensity in each component of a split point pattern. o intensity.quadratcount Use quadrat counts to estimate intensity in each quadrat. o as.owin.quadratcount, as.owin.quadrattest Extract the spatial window in which quadrat counts were performed. o reload.or.compute Utility function for R scripts: either reload results from file, or compute them. o to.grey Convert colour to greyscale. o Smooth.im Method for Smooth() for pixel images. Currently identical to blur(). o demo(sumfun) Demonstration of nonparametric summary functions in spatstat. SIGNIFICANT USER-VISIBLE CHANGES o Package Dependencies spatstat now "Imports" (rather than "Depends" on) the libraries mgcv, deldir, abind, tensor, polyclip. This means that these libraries are not accessible to the user unless the user explicitly loads them by typing 'library(mgcv)' and so on. o owin, as.owin Polygon data are no longer subjected to strict checks on geometrical validity (self-crossing points, overlaps etc.) Instead, polygon geometry is automatically repaired. o ppm The default quadrature scheme for a point pattern has been improved (in the case of a non-rectangular window) to remove a possible source of bias. o Performance various parts of spatstat now run slightly faster. o scan.test Now handles multiple values of circle radius 'r'. o plot.scan.test, as.im.scan.test These functions can now give the optimal value of circle radius 'r'. o pcfcross, pcfdot Algorithms have been reimplemented using a single-pass kernel smoother and now run much faster. Bandwidth selection rule improved. o plot.listof, plot.splitppp Default behaviour has changed: panels are now plotted on different scales. o plot.listof, plot.splitppp When 'equal.scales=TRUE' the panels are plotted on exactly equal scales and are exactly aligned (under certain conditions). o ppp, marks.ppp, marks<-.ppp New argument 'drop' determines whether a data frame with a single column will be converted to a vector. o simulate.ppm, rmh.ppm, rmhmodel.ppm New argument 'new.coef' allows the user to change the parameters of a fitted model, before it is simulated. o logLik.ppm New argument 'new.coef' allows the user to evaluate the loglikelihood for a different value of the parameter. o clusterset The argument 'result' has been renamed 'what'. It is now possible to give multiple values to 'what' so that both types of result can be computed together. o residuals.ppm Argument 'coefs' has been renamed 'new.coef' for consistency with fitted.ppm etc. o residuals.ppm If drop=TRUE the window associated with the residuals is now taken to be the domain of integration of the composite likelihood. o intensity.ppp Now has argument 'weights' o density.ppp, Smooth.ppp, markmean, markvar, intensity.ppp Argument 'weights' can now be an 'expression'. o pcf New argument 'domain' causes the computation to be restricted to a subset of the window. o nnclean The result now has attributes which give the fitted parameter values, information about the fitting procedure, and the histogram bar heights. o nnclean Extra arguments are now passed to hist.default. o plot.tess For a tessellation represented by a pixel image, plot.tess no longer treats the pixel labels as palette colours. o relrisk New argument 'case' allows the user to specify which mark value corresponds to the cases in a case-control dataset. o Kinhom Now accepts correction="good" o spatstat.options New option ('monochrome') controls whether plots generated by spatstat will be displayed in colour or in greyscale. This will eventually be applied to all plot commands in spatstat. o plot.im, persp.im, contour.im, plot.owin, plot.psp, plot.fv, plot.fasp These functions now obey spatstat.options('monochrome') o plot.ppp, plot.owin, plot.im, plot.psp, plot.tess, plot.layered New universal argument 'show.all' determines what happens when a plot is added to an existing plot. If show.all = TRUE then everything is plotted, including the main title and colour ribbon. o plot.ppp New argument 'show.window' o plot.im New arguments 'add' and 'do.plot'. More arguments recognised by 'ribargs' o plot.layered New arguments 'add', 'main' Better argument handling. o plot.fv Improved handling of argument 'shade' o layered, layerplotargs, plot.layered The plotting argument can now be a list of length 1, which will be replicated to the correct length. o varblock Ugly legends have been repaired. o quad.ppm New argument 'clip' o edge.Trans New arguments 'dx', 'dy' o disc Argument 'centre' can be in various formats. o affine, shift Argument 'vec' can be in various formats. o Geyer, BadGey A warning is no longer issued when the parameter 'sat' is fractional. o adaptive.density Now has argument 'verbose' o Smooth.ppp 'sigma' is now a formal argument of Smooth.ppp o plot.quadratcount, plot.quadrattest These functions have now been documented. o Summary functions and envelopes Improved mathematical labels in plots. o Kest Accelerated, in the case of a rectangular window. o Kscaled Argument 'lambda' can now be a fitted model (class ppm) o print.fv Improved layout. o plot.bermantest Improved graphics. o which.max.im This function is now deprecated. which.max.im(x) is superseded by im.apply(x, which.max) o smooth.ppp, smooth.fv, smooth.msr These functions are now deprecated, in favour of 'Smooth' with a capital 'S' BUG FIXES o bw.ppl Crashed if the point pattern had multiple points at the same location. Fixed. o quantile Crashed when applied to the result of 'ewcdf'. Fixed. o marks<-.ppp Crashed with a message about 'unrecognised format' if the current or replacement values of marks were date/time values (belonging to class 'Date' or 'POSIXt'). Fixed. o plot.im Crashed in case log=TRUE if the window was not a rectangle. Fixed. o vcov.ppm Crashed sometimes for models with a hard core term (Hardcore, StraussHard, MultiHard or MultiStrauss interactions). Spotted by Rasmus Waagepetersen. Fixed. o multiplicity.data.frame Results were incorrect and included NA's (spotted by Sebastian Meyer). Fixed. o markvar Values were incorrect. Fixed. o Smooth.ppp Ignored argument 'diggle'. Fixed. o rotate.im, affine.im Factor-valued images were not handled correctly. Fixed. o shift.layered If argument 'origin' was used, different layers were shifted by different amounts. Fixed. o tile.areas Sometimes returned a list instead of a numeric vector. Fixed. o print.ppp If the marks were date/time values (belonging to class 'Date' or 'POSIXt'), print.ppp reported that they were double precision numbers. Fixed. o plot.layered Graphics were mangled if the argument 'add=FALSE' was given explicitly. Fixed. o Smooth.ppp The argument 'sigma' was only recognised if it was explicitly named. For example in 'Smooth(X, 5)' the '5' was ignored. Fixed. o clusterset The bounding frame of the result was smaller than the original bounding frame of the point pattern dataset, when result="domain" and exact=TRUE. Fixed. o plot.im Ignored argument 'col' if it was a 'function(n)'. Fixed. o Kinhom Ignored argument 'correction' if there were more than 1000 points. Fixed. o [.fv Mangled the plot label for the y axis. Fixed. o cbind.fv Mangled the plot label for the y axis. Fixed. o plot.envelope Main title was always 'x'. Fixed. o print.ppp Ran over the right margin. Fixed. o union.owin, intersect.owin, setminus.owin Sometimes deleted the name of the unit of length. Fixed. CHANGES IN spatstat VERSION 1.35-0 OVERVIEW o We thank Melanie Bell, Leanne Bischof, Ida-Maria Sintorn, Ege Rubak, Martin Hazelton, Oscar Garcia, Rasmus Waagepetersen, Abdollah Jalilian and Jens Oehlschlaegel for contributions. o Support for analysing replicated spatial point patterns. o New vignette on analysing replicated spatial point patterns. o Objective function surface plots. o Estimator of point process intensity using nearest neighbour distances. o Improved estimator of pair correlation function. o Four new datasets. o Simple point-and-click interface functions for general use. o More support for fv objects. o More support for ppx objects. o Extensions to nearest neighbour functions. o Morphological operations accelerated. o Bug fix to pair correlation functions. o Bug fix to k-th nearest neighbour distances o Version nickname: 'Multiple Personality' NEW CLASSES o mppm An object of class 'mppm' represents a Gibbs point process model fitted to several point pattern datasets. The point patterns may be treated as independent replicates of the same point process, or as the responses in an experimental design, so that the model may depend on covariates associated with the design. Methods for this class include print, plot, predict, anova and so on. o objsurf An object of class 'objsurf' contains values of the likelihood or objective function in a neighbourhood of the maximum. o simplepanel An object of class 'simplepanel' represents a spatial arrangement of buttons that respond to mouse clicks, supporting a simple, robust graphical interface. NEW FUNCTIONS o mppm Fit a Gibbs model to several point patterns. The point pattern data may be organised as a designed experiment and the model may depend on covariates associated with the design. o anova.mppm Analysis of Deviance for models of class mppm o coef.mppm Extract fitted coefficients from a model of class mppm o fitted.mppm Fitted intensity or conditional intensity for a model of class mppm o kstest.mppm Kolmogorov-Smirnov test of goodness-of-fit for a model of class mppm o logLik.mppm log likelihood or log pseudolikelihood for a model of class mppm o plot.mppm Plot the fitted intensity or conditional intensity of a model of class mppm o predict.mppm Compute the fitted intensity or conditional intensity of a model of class mppm o quadrat.test Quadrat counting test of goodness-of-fit for a model of class mppm o residuals.mppm Point process residuals for a model of class mppm o subfits Extract point process models for each individual point pattern dataset, from a model of class mppm o vcov.mppm Variance-covariance matrix for a model of class mppm o integral.msr Integral of a measure. o objsurf For a model fitted by optimising an objective function, this command computes the objective function in a neighbourhood of the optimal value. o contour.objsurf, image.objsurf, persp.objsurf, plot.objsurf Plot an 'objsurf' object. o fvnames Define groups of columns in a function value table, for use in plot.fv, etc o multiplicity New generic function for which multiplicity.ppp is a method. o unique.ppx, duplicated.ppx, multiplicity.ppx Methods for unique(), duplicated() and multiplicity() for 'ppx' objects. These also work for 'pp3' and 'lpp' objects. o closepairs, crosspairs, closepaircounts, crosspaircounts Low-level functions for finding all close pairs of points o nndensity Estimate point process intensity using k-th nearest neighbour distances o simplepanel, run.simplepanel Support for a simple point-and-click interface for general use. NEW DATASETS o pyramidal Diggle-Lange-Benes data on pyramidal neurons in cingulate cortex. 31 point patterns divided into 3 groups. o waterstriders Nummelin-Penttinen waterstriders data. Three independent replicates of a point pattern formed by insects. o simba Simulated data example for mppm. Two groups of point patterns with different interpoint interactions. o demohyper Simulated data example for mppm. Point patterns and pixel image covariates, in two groups with different regression coefficients. SIGNIFICANT USER-VISIBLE CHANGES o plot.hyperframe The argument 'e' now has a different format. Instead of plot(h, plot(XYZ)) one must now type plot(h, quote(plot(XYZ))) This is necessary in order to avoid problems with 'S4 method dispatch'. o pcf.ppp, pcfinhom New argument 'divisor' enables better performance of the estimator of pair correlation function for distances close to zero. o applynbd The arguments N, R and criterion may now be specified together. o markstat The arguments N and R may now be specified together. o ppx New argument 'simplify' allows the result to be converted to an object of class 'ppp' or 'pp3' if appropriate. o as.function.fv Now allows multiple columns to be interpolated o multiplicity.ppp This function is now a method for the generic 'multiplicity'. It has also been accelerated. o nnfun.ppp, distfun.ppp New argument 'k' allows these functions to compute k-th nearest neighbours. o rVarGamma, kppm, vargamma.estK, vargamma.estpcf New argument 'nu.pcf' provides an alternative way to specify the kernel shape in the VarGamma model, instead of the existing argument 'nu.ker'. Function calls that use the ambiguous argument name 'nu' will no longer be accepted. o nnmap Image is now clipped to the original window. o dilation, erosion, opening, closing Polygonal computations greatly accelerated. o plot.colourmap Improved appearance and increased options, for discrete colourmaps. o plot.msr Improved appearance o plot.ppp, plot.owin An `empty' plot can now be generated by setting type="n" o nndist.ppp, nnwhich.ppp, nncross.ppp Column names of the result are now more informative. BUG FIXES o nncross.ppp Results were completely incorrect when k > 1. Spotted by Jens Oehschlaegel. Bug was introduced in spatstat 1.34-1. Fixed. o rVarGamma Simulations were incorrect; they were generated using the wrong value of the parameter 'nu.ker'. Spotted by Rasmus Waagepetersen and Abdollah Jalilian. Bug was always present. Fixed. o pair correlation functions (pcf.ppp, pcfdot, pcfcross, pcfinhom, ...) The result had a negative bias at the maximum 'r' value, because contributions to the pcf estimate from interpoint distances greater than max(r) were mistakenly omitted. Spotted by Rasmus Waagepetersen and Abdollah Jalilian. Bug was always present. Fixed. o demo(spatstat) This demonstration script had some unwanted side-effects, such as rescaling the coordinates of standard datasets 'bramblecanes', 'amacrine' and 'demopat', which caused the demonstration to crash when it was repeated several times, and caused errors in demo(data). Fixed. o rmh Visual debugger crashed sometimes with message 'XI not found'. Fixed. o predict.ppm Crashed if the model was fitted using 'covfunargs'. Fixed. o bounding.box Crashed if one of the arguments was NULL. Fixed. o multiplicity.ppp Did not handle data frames of marks. Fixed. CHANGES IN spatstat VERSION 1.34-1 OVERVIEW o We thank Kurt Hornik, Ted Rosenbaum, Ege Rubak and Achim Zeileis for contributions. o Important bug fix. SIGNIFICANT USER-VISIBLE CHANGES o as.box3 Now accepts objects of class 'ppx' or 'boxx'. o crossdist.ppp, crossdist.pp3, crossdist.default New argument 'squared' allows the squared distances to be computed (saving computation time in some applications) BUG FIXES o union.owin, is.subset.owin, dilation.owin Results were sometimes completely wrong for polygons with holes. Spotted by Ted Rosenbaum. Fixed. o psstA, areaLoss Crashed in some cases, with error message 'Number of items to replace is not a multiple of replacement length'. Spotted by Achim Zeileis. Fixed. CHANGES IN spatstat VERSION 1.34-0 OVERVIEW o We thank Andrew Bevan, Ege Rubak, Aruna Jammalamadaka, Greg McSwiggan, Jeff Marcus, Jose M Blanco Moreno, and Brian Ripley for contributions. o spatstat and all its dependencies are now Free Open Source. o spatstat does not require the package 'gpclib' any more. o spatstat now depends on the packages 'tensor', 'abind' and 'polyclip' o polygon clipping is now enabled always. o Substantially more support for point patterns on linear networks. o Faster computations for pairwise interaction models. o Bug fixes in nearest neighbour calculations. o Bug fix in leverage and influence diagnostics. o Version nickname: "Window Cleaner" o spatstat now requires R version 3.0.2 or later NEW FUNCTIONS o as.lpp Convert data to a point pattern on a linear network. o distfun.lpp Distance function for point pattern on a linear network. o eval.linim Evaluate expression involving pixel images on a linear network. o linearKcross, linearKdot, linearKcross.inhom, linearKdot.inhom Multitype K functions for point patterns on a linear network o linearmarkconnect, linearmarkequal Mark connection function and mark equality function for multitype point patterns on a linear network o linearpcfcross, linearpcfdot, linearpcfcross.inhom, linearpcfdot.inhom Multitype pair correlation functions for point patterns on a linear network o linfun New class of functions defined on a linear network o nndist.lpp, nnwhich.lpp, nncross.lpp Methods for nndist, nnwhich, nncross for point patterns on a linear network o nnfun.lpp Method for nnfun for point patterns on a linear network o vcov.lppm Variance-covariance matrix for parameter estimates of a fitted point process model on a linear network. o bilinearform Computes a bilinear form o tilenames, tilenames<- Extract or change the names of tiles in a tessellation. SIGNIFICANT USER-VISIBLE CHANGES o package dependencies Previous versions of spatstat used the package 'gpclib' to perform geometrical calculations on polygons. Spatstat now uses the package 'polyclip' for polygon calculations instead. o free open-source licence The restrictive licence conditions of 'gpclib' no longer apply to users of spatstat. Spatstat and all its dependencies are now covered by a free open-source licence. o polygon clipping In previous versions of spatstat, geometrical calculations on polygons could be performed 'exactly' using gpclib or 'approximately' using pixel discretisation. Polygon calculations are now always performed 'exactly'. o intersect.owin, union.owin, setminus.owin If A and B are polygons, the result is a polygon. o erosion, dilation, opening, closing If the original set is a polygon, the result is a polygon. o intersect.tess, dirichlet The tiles of the resulting tessellation are polygons if the input was polygonal. o plot.owin Polygons with holes can now be plotted with filled colours on any device. o lppm New arguments 'eps' and 'nd' control the quadrature scheme. o pairwise interaction Gibbs models Many calculations for these models have been accelerated. BUG FIXES o nncross.pp3 Values were completely incorrect in some cases. Usually accompanied by a warning about NA values. (Spotted by Andrew Bevan.) Fixed. o nnmap, nnmark A small proportion of pixels had incorrect values. [These were the pixels lying on the boundary of a Dirichlet cell.] Fixed. o leverage.ppm, influence.ppm, dfbetas.ppm Results were incorrect for non-Poisson processes. Fixed. o distcdf Results were incorrect in some cases when W was a window and V was a point pattern. Fixed. o Kcross, Kdot, pcfcross, pcfdot Results were incorrect in some rare cases. Fixed. o as.fv.kppm Erroneously returned a NULL value. Fixed. o vcov.ppm For point process models fitted with method = 'logi', sometimes crashed with error "object 'fit' not found". (Spotted by Ege Rubak). Fixed. o vcov.ppm For multitype point process models, sometimes crashed with error "argument 'par' is missing". Fixed. o plot.im Crashed if some of the pixel values were infinite. Fixed. o owin owin(poly=..) crashed if there were NA's in the polygon coordinates. Spotted by Jeff Marcus. Fixed. o plot.fv Crashed, giving an incomprehensible error, if the plot formula contained a number with a decimal point. Fixed. o alltypes Crashed if envelopes=TRUE and global=TRUE, with error message 'csr.theo not found'. Spotted by Jose M Blanco Moreno. Fixed. o chop.tess, rMosaicField Format of result was garbled in some cases. Fixed. o vcov.ppm Sometimes gave an irrelevant warning "parallel option not available". Fixed. CHANGES IN spatstat VERSION 1.33-0 OVERVIEW o We thank Kurt Hornik and Brian Ripley for advice. o The package namespace has been modified. o Numerous internal changes. o Likelihood cross-validation for smoothing bandwidth. o More flexible models of intensity in cluster/Cox processes. o New generic function for smoothing. o Version nickname: 'Titanic Deckchair' NEW FUNCTIONS o bw.ppl Likelihood cross-validation technique for bandwidth selection in kernel smoothing. o is.lppm, is.kppm, is.slrm Tests whether an object is of class 'lppm', 'kppm' or 'slrm' o Smooth New generic function for spatial smoothing. o Smooth.ppp, Smooth.fv, Smooth.msr Methods for Smooth (identical to smooth.ppp, smooth.fv, smooth.msr respectively) o fitted.kppm Method for 'fitted' for cluster/Cox models SIGNIFICANT USER-VISIBLE CHANGES o namespace The namespace of the spatstat package has been changed. o internal functions Some undocumented internal functions are no longer visible, as they are no longer exported in the namespace. These functions can still be accessed using the form spatstat:::functionname. Functions that are not visible are not guaranteed to exist or to remain the same in future. o methods For some generic functions defined in the spatstat package, it is possible that R may fail to find one of the methods for the generic. This is a temporary problem due to a restriction on the size of the namespace in R 3.0.1. It will be fixed in future versions of R and spatstat. It only applies to methods for a generic which is a spatstat function (such as nndist) and does not apply to methods for generics defined elsewhere (such as density). In the meantime, if this problem should occur, it can be avoided by calling the method explicitly, in the form spatstat:::genericname.classname. o speed The package should run slightly faster overall, due to the improvement of the namespace, and changes to internal code. o envelope New argument 'envir.simul' determines the environment in which to evaluate the expression 'simulate'. o kppm More flexible models of the intensity, and greater control over the intensity fitting procedure, are now possible using the arguments 'covfunargs', 'use.gam', 'nd', 'eps' passed to ppm. Also the argument 'X' may now be a quadrature scheme. o distcdf Arguments W and V can now be point patterns. o Kest New option: correction = "good" selects the best edge correction that can be computed in reasonable time. o bw.diggle Accelerated. o predict.ppm Calculation of standard error has been accelerated. o smooth.ppp, smooth.fv, smooth.msr These functions will soon be 'Deprecated' in favour of the methods Smooth.ppp, Smooth.fv, Smooth.msr respectively. o stratrand, overlap.owin, update.slrm, edge.Trans, edge.Ripley These already-existing functions are now documented. BUG FIXES o kppm, matclust.estpcf, pcfmodel The pair correlation function of the Matern Cluster Process was evaluated incorrectly at distances close to 0. This could have affected the fitted parameters in matclust.estpcf() or kppm(clusters="MatClust"). Fixed. o anova.ppm Would cause an error in future versions of R when 'anova.glm' is removed from the namespace. Fixed. CHANGES IN spatstat VERSION 1.32-0 OVERVIEW o We thank Ege Rubak for major contributions. o Thanks also to Patrick Donnelly, Andrew Hardegen, Tom Lawrence, Robin Milne, Gopalan Nair and Sean O'Riordan. o New 'logistic likelihood' method for fitting Gibbs models. o Substantial acceleration of several functions including profile maximum pseudolikelihood and variance calculations for Gibbs models. o Nearest neighbours for point patterns in 3D o Nearest-neighbour interpolation in 2D o New 'progress plots' o Hard core thresholds can be estimated automatically. o More support for colour maps o More support for 'fv' objects o Spatstat now has version nicknames. The current version is "Logistical Nightmare". o Minor improvements and bug fixes. NEW FUNCTIONS o nncross.pp3 Method for 'nncross' for point patterns in 3D o nnmark Mark of nearest neighbour - can be used for interpolation o dclf.progress, mad.progress Progress plots (envelope representations) for the DCLF and MAD tests. o deriv.fv Numerical differentiation for 'fv' objects. o interp.colourmap Smooth interpolation of colour map objects - makes it easy to build colour maps with gradual changes in colour o tweak.colourmap Change individual colour values in a colour map object o beachcolourmap Colour scheme appropriate for `altitudes' (signed numerical values) o as.fv Convert various kinds of data to an 'fv' object o quadscheme.logi Generates quadrature schemes for the logistic method of ppm. o beginner Introduction for beginners. SIGNIFICANT USER-VISIBLE CHANGES o ppm New option: method = "logi" Fits a Gibbs model by the newly developed 'logistic likelihood' method which is often faster and more accurate than maximum pseudolikelihood. Code contributed by Ege Rubak. o profilepl Greatly accelerated, especially for area-interaction models. o vcov.ppm Greatly accelerated for higher-order interaction models. o smooth.ppp Now handles bandwidths equal to zero (by invoking 'nnmark') o Hardcore, StraussHard The hard core distance 'hc' can now be omitted; it will be estimated from data. o plot.ppp Now behaves differently if there are multiple columns of marks. Each column of marks is plotted, in a series of separate plots arranged side-by-side. o plot.im Argument 'col' can now be a function o lohboot Now computes confidence intervals for L-functions as well (fun="Lest" or fun="Linhom") o dclf.test, mad.test The argument X can now be an object produced by a previous call to dclf.test or mad. o plot.fv Labelling of plots has been improved in some cases. o smooth.fv Further options added. o density.ppp The argument 'weights' can now be a matrix. o smooth.ppp Accelerated, when there are several columns of marks. o density.ppp Accelerated slightly. o simulate.ppm, simulate.kppm The total computation time is also returned. o simulate.kppm Now catches errors (such as 'insufficient memory'). o latest.news, licence.polygons Can now be executed by typing the name of the function without parentheses. o latest.news The text is now displayed one page at a time. BUG FIXES o Hest, Gfox, Jfox The 'raw' estimate was not computed correctly (or at least it was not the raw estimate described in the help files). Spotted by Tom Lawrence. Fixed. o edges2vees Format of result was incorrect if there were fewer than 3 edges. Fixed. o Jfox The theoretical value (corresponding to independence between X and Y) was erroneously given as 0 instead of 1. Spotted by Patrick Donnelly. Fixed. o ppm, quadscheme, default.dummy If the grid spacing parameter 'eps' was specified, the quadrature scheme was sometimes slightly incorrect (missing a few dummy points near the window boundary). Fixed. o print.timed Matrices were printed incorrectly. Fixed. CHANGES IN spatstat VERSION 1.31-3 OVERVIEW o spatstat now 'Suggests' the package 'tensor' o Code slightly accelerated. o More support for pooling of envelopes. o Bug fixes. NEW FUNCTIONS o nnmap Given a point pattern, finds the k-th nearest point in the pattern from each pixel in a raster. o coef.fii, coef.summary.fii Extract the interaction coefficients of a fitted interpoint interaction o edges2vees Low-level function for finding triples in a graph. SIGNIFICANT USER-VISIBLE CHANGES o predict.ppm New argument 'correction' allows choice of edge correction when calculating the conditional intensity. o pool.envelope New arguments 'savefuns' and 'savepatterns'. o pool.envelope Envelopes generated with VARIANCE=TRUE can now be pooled. o pool.envelope The plot settings of the input data are now respected. o Numerous functions have been slightly accelerated. BUG FIXES o predict.ppm Calculation of the conditional intensity omitted the edge correction if correction='translate' or correction='periodic'. Fixed. o shift.lpp, rotate.lpp, scalardilate.lpp, affine.lpp, shift.linnet, rotate.linnet, scalardilate.linnet, affine.linnet The enclosing window was not correctly transformed. Fixed. o rHardcore, rStraussHard, rDiggleGratton, rDGS The return value was invisible. Fixed. o ppm In rare cases the results obtained with forcefit=FALSE and forcefit=TRUE were different, due to numerical rounding effects. Fixed. CHANGES IN spatstat VERSION 1.31-2 OVERVIEW o We thank Robin Corria Anslie, Julian Gilbey, Kiran Marchikanti, Ege Rubak and Thordis Linda Thorarinsdottir for contributions. o spatstat now depends on R 3.0.0 o More support for linear networks o More functionality for nearest neighbours o Bug fix in fitting Geyer model o Performance improvements and bug fixes NEW FUNCTIONS o affine.lpp, shift.lpp, rotate.lpp, rescale.lpp, scalardilate.lpp Geometrical transformations for point patterns on a linear network o affine.linnet, shift.linnet, rotate.linnet, rescale.linnet, scalardilate.linnet Geometrical transformations for linear networks o [.linnet Subset operator for linear networks o timed Records the computation time taken SIGNIFICANT USER-VISIBLE CHANGES o nncross nncross.ppp can now find the k-th nearest neighbours, for any k. o nndist, nnwhich New argument 'by' makes it possible to find nearest neighbours belonging to specified subsets in a point pattern, for example, the nearest neighbour of each type in a multitype point pattern. o [.fv Now handles the argument 'drop'. o with.fv Argument 'drop' replaced by new argument 'fun' (with different interpretation). o [.lpp Subset index may now be a window (class 'owin') o Kest Options correction='border' and correction='none' now run about 4 times faster, thanks to Julian Gilbey. o density.ppp Numerical underflow no longer occurs when sigma is very small and 'at="points"'. A warning is no longer issued. Thanks to Robin Corria Anslie. o crossing.psp New argument 'fatal' allows the user to handle empty intersections o union.owin It is now guaranteed that if A is a subset of B, then union.owin(A,B)=B. o plot.colourmap Now passes arguments to axis() to control the plot. Appearance of plot improved. o image.listof Now passes arguments to plot.colourmap() if equal.ribbon=TRUE. o kppm Accelerated (especially for large datasets). o plot.envelope plot.envelope is now equivalent to plot.fv and is essentially redundant. o rThomas, rMatClust, rNeymanScott Improved explanations in help files. o All functions Many functions have been slightly accelerated. BUG FIXES o ppm Results were incorrect for the Geyer saturation model with a non-integer value of the saturation parameter 'sat'. Spotted by Thordis Linda Thorarinsdottir. Bug introduced in spatstat 1.20-0, July 2010. Fixed. o ppm Fitting a stationary Poisson process using a nonzero value of 'rbord', as in "ppm(X, rbord=R)" with R > 0, gave incorrect results. Fixed. o predict.slrm Crashed with message 'longer object length is not a multiple of shorter object length' if the original data window was not a rectangle. Fixed. o iplot Main title was sometimes incorrect. Fixed. o plot.layered Ignored argument 'main' in some cases. Fixed. o plot.listof, image.listof Crashed sometimes with a message 'figure margins too large' when equal.ribbon=TRUE. Fixed. o print.ppx Crashed if the object contained local coordinates. Fixed. o transect.im Crashed if the transect lay partially outside the image domain. Fixed. o rthin Crashed if X was empty. Fixed. o max.im, min.im, range.im Ignored additional arguments after the first argument. Fixed. o update.lppm Updated object did not remember the name of the original dataset. Fixed. o envelope Grey shading disappeared from plots of envelope objects when the envelopes were transformed using eval.fv or eval.fasp. Fixed. CHANGES IN spatstat VERSION 1.31-1 OVERVIEW o We thank Marcelino de la Cruz, Daniel Esser, Jason Goldstick, Abdollah Jalilian, Ege Rubak and Fabrice Vinatier for contributions. o Nonparametric estimation and tests for point patterns in a linear network. o More support for 'layered' objects. o Find clumps in a point pattern. o Connected component interaction model. o Improvements to interactive plots. o Visual debugger for Metropolis-Hastings algorithm. o Bug fix in Metropolis-Hastings simulation of Geyer process. o Faster Metropolis-Hastings simulation. o Faster computation of 'envelope', 'fv' and 'fasp' objects. o Improvements and bug fixes. NEW FUNCTIONS o connected.ppp Find clumps in a point pattern. o kstest.lpp, kstest.lppm The spatial Kolmogorov-Smirnov test can now be applied to point patterns on a linear network (class 'lpp') and point processes on a linear network (class 'lppm'). o bermantest.lpp, bermantest.lppm Berman's Z1 and Z2 tests can now be applied to point patterns on a linear network (class 'lpp') and point processes on a linear network (class 'lppm'). o rhohat.lpp, rhohat.lppm Nonparametric estimation of the dependence of a point pattern on a spatial covariate: 'rhohat' now applies to objects of class 'lpp' and 'lppm'. o intensity.lpp Empirical intensity of a point pattern on a linear network. o as.function.rhohat Converts a 'rhohat' object to a function, with extrapolation beyond the endpoints. o [.layered Subset operator for layered objects. o shift, rotate, affine, rescale, reflect, flipxy, scalardilate These geometrical transformations now work for 'layered' objects. o iplot.layered Interactive plotting for 'layered' objects. o as.owin.layered Method for as.owin for layered objects. o [.owin Subset operator for windows, equivalent to intersect.owin. o rcellnumber Generates random integers for the Baddeley-Silverman counterexample. o is.lpp Tests whether an object is a point pattern on a linear network. o is.stationary.lppm, is.poisson.lppm New methods for is.stationary and is.poisson for class 'lppm' o sessionLibs Print library names and version numbers (for use in Sweave scripts) SIGNIFICANT USER-VISIBLE CHANGES o iplot iplot is now generic, with methods for 'ppp', 'layered' and 'default'. iplot methods now support zoom and pan navigation. o rmh.default New argument 'snoop' allows the user to activate a visual debugger for the Metropolis-Hastings algorithm. o connected connected() is now generic, with methods for 'im', 'owin' and 'ppp'. o alltypes Now works for lpp objects o rlabel Now works for lpp, pp3, ppx objects o plot.kstest Can now perform P-P and Q-Q plots as well. o plot.fasp New argument 'samey' controls whether all panels have the same y limits. o plot.fasp Changed default value of 'samex'. o Objects of class 'envelope', 'fv' and 'fasp' Reduced computation time and storage required for these objects. o pcfmodel.kppm Improved calculation. o plot.fv Improved collision-avoidance algorithm (for avoiding overlaps between curves and legend) o ppm Improved error handling o envelope All methods for 'envelope' now handle fun=NULL o setminus.owin Better handling of the case where both arguments are rectangles. o rmh Simulation has been further accelerated. o lppm Accelerated. o vcov.ppm Accelerated. o marktable Accelerated. o Triplets() interaction Accelerated. o alltypes Accelerated when envelope=TRUE. BUG FIXES o rmh Simulation of the Geyer saturation process was incorrect. [Bug introduced in previous version, spatstat 1.31-0.] Fixed. o rmh Simulation of the Geyer saturation process was incorrectly initialised, so that the results of a short run (i.e. small value of 'nrep') were incorrect, while long runs were correct. [Bug introduced in spatstat 1.17-0, october 2009.] Fixed. o ppm Objects fitted with use.gam=TRUE caused fatal errors in various functions including print, summary, vcov and model.frame. Spotted by Jason Goldstick. Fixed. o lpp, runiflpp, rpoislpp Empty point patterns caused an error. Fixed. o rmh.default Crashed for hybrid models, with message 'Attempt to apply non-function'. Spotted by Ege Rubak. Fixed. o relrisk Crashed when 'at="points"' for a multitype pattern with more than 2 types. Spotted by Marcelino de la Cruz. Fixed. o erosion.owin, dilation.psp, border Ignored the arguments "..." in some cases (namely when the window was polygonal and 'gpclib' was disabled). Fixed. o rsyst, rcell Did not correctly handle the argument 'dx'. Spotted by Fabrice Vinatier. Fixed. o correction="trans" Various functions such as Kest no longer recognised 'correction = "trans"'. Fixed. o istat Crashed with an error message about envelopes. Fixed. o summary.ppm, print.ppm p-values which were exactly equal to zero were reported as NA. Fixed. o [.im Crashed if the intersection consisted of a single row or column of pixels. Fixed. o plot.im Sometimes incorrectly displayed an image consisting of a single row or column of pixels. Fixed. o plot.layered The plot region was determined by the first layer, so that objects in subsequent layers could sometimes fall outside the plot region. Fixed. o transect.im If the arguments 'from' and 'to' were numeric vectors of length 2, the result was garbled. Fixed. o Inhomogeneous K functions and pair correlation functions [Kinhom, pcfinhom, Kcross.inhom, Kdot.inhom, pcfcross.inhom, etc.] These functions reported an error 'lambda is not a vector' if the intensity argument lambda was computed using density(, at="points"). Fixed. o rlabel Did not accept a point pattern with a hyperframe of marks. Fixed. o alltypes Crashed when envelope=TRUE if the summary function 'fun' did not have default values for the marks i and j. Fixed. o Kres, Gres, psst, psstA Ignored the unit of length. Fixed. CHANGES IN spatstat VERSION 1.31-0 OVERVIEW o We thank Frederic Lavancier and Ege Rubak for contributions. o Major bug fix in simulation of area-interaction process. o Metropolis-Hastings simulations accelerated. o Rounding of spatial coordinates o clmfires dataset corrected. o Bug fixes and minor improvements. NEW FUNCTIONS o round.ppp Round the spatial coordinates of a point pattern to a specified number of decimal places. o rounding Determine whether a dataset has been rounded. SIGNIFICANT USER-VISIBLE CHANGES o rmh Simulation of the following models has been accelerated: areaint, dgs, diggra, fiksel, geyer, hardcore, lennard, multihard, strauss, straush, straussm, strausshm. o rmh The transition history of the simulation (which is saved if 'track=TRUE') now also contains the value of the Hastings ratio for each proposal. o clmfires The clmfires dataset has been modified to remove errors and inconsistencies. o plot.linim Appearance of the plot has been improved, when style='width'. o summary.ppm Now reports whether the spatial coordinates have been rounded. o dclf.test, mad.test The range of distance values ('rinterval') used in the test is now printed in the test output, and is saved as an attribute. BUG FIXES o rmh Simulation of the Area-Interaction model was completely incorrect. Spotted by Frederic Lavancier. The bug was introduced in spatstat version 1.23-6 or later. Fixed. o dclf.test The test statistic was incorrectly scaled (by a few percent). This did not affect the p-value of the test. Fixed. o ppx If argument 'coord.type' was missing, various errors occurred: a crash may have occurred, or the results may have depended on the storage type of the data. Spotted by Ege Rubak. Fixed. o plot.ppx Crashed for 1-dimensional point patterns. Spotted by Ege Rubak. Fixed. CHANGES IN spatstat VERSION 1.30-0 OVERVIEW o We thank Jorge Mateu, Andrew Bevan, Olivier Flores, Marie-Colette van Lieshout, Nicolas Picard and Ege Rubak for contributions. o The spatstat manual now exceeds 1000 pages. o Hybrids of point process models. o Five new datasets o Second order composite likelihood method for kppm. o Inhomogeneous F, G and J functions. o Delaunay graph distance o Fixed serious bug in 'lppm' for marked patterns. o bug fix in some calculations for Geyer model o Improvements to linear networks code o Pixel images can now be displayed with a logarithmic colour map. o spatstat now formally 'Depends' on the R core package 'grDevices' o miscellaneous improvements and bug fixes NEW DATASETS o clmfires Forest fires in Castilla-La Mancha o gordon People sitting on the grass in Gordon Square, London o hyytiala Mixed forest in Hyytiala, Finland (marked by species) o paracou Kimboto trees in Paracou, French Guiana (marked as adult/juvenile) o waka Trees in Waka national park (marked with diameters) NEW FUNCTIONS o Hybrid The hybrid of several point process interactions [Joint research with Jorge Mateu and Andrew Bevan] o is.hybrid Recognise a hybrid interaction or hybrid point process model. o Finhom, Ginhom, Jinhom Inhomogeneous versions of the F, G and J functions [Thanks to Marie-Colette van Lieshout] o delaunay.distance Graph distance in the Delaunay triangulation. o distcdf Cumulative distribution function of the distance between two independent random points in a given window. o bw.frac Bandwidth selection based on window geometry o shortside.owin, sidelengths.owin Side lengths of (enclosing rectangle of) a window SIGNIFICANT USER-VISIBLE CHANGES o ppm Can now fit models with 'hybrid' interactions [Joint research with Jorge Mateu and Andrew Bevan] o kppm Now has the option of fitting models using Guan's (2006) second order composite likelihood. o envelope.lpp Now handles multitype point patterns. o envelope.envelope New argument 'transform' allows the user to apply a transformation to previously-computed summary functions. o runifpointOnLines, rpoisppOnLines, runiflpp, rpoislpp Can now generate multitype point patterns. o rmhmodel, rmh, simulate.ppm Now handle point process models with 'hybrid' interactions. o kppm Accelerated, and more reliable, due to better choice of starting values in the optimisation procedure. o kppm The internal format of kppm objects has changed. o minimum contrast estimation Error messages from the optimising function 'optim' are now trapped and handled. o rhohat This command is now generic, with methods for ppp, quad, and ppm. o raster.x, raster.y, raster.xy These functions have a new argument 'drop' o summary.ppm Improved behaviour when the model covariates are a data frame. o progressreport Output improved. o second order summary functions (Kest, Lest, Kinhom, pcf.ppp, Kdot, Kcross, Ldot etc etc) These functions now accept correction="translation" as an alternative to correction = "translate", for consistency. o plot.im New argument 'log' allows colour map to be equally spaced on a log scale. o as.owin.ppm, as.owin.kppm New argument 'from' allows the user to extract the spatial window of the point data (from="points") or the covariate images (from="covariates") o dclf.test, mad.test The rule for handling tied values of the test statistic has been changed. The tied values are now randomly ordered to obtain a randomised integer rank. o with.fv New argument 'enclos' allows evaluation in other environments BUG FIXES o lppm For multitype patterns, the fitted model was completely incorrect due to an error in constructing the quadrature scheme. Fixed. o Geyer For point process models with the 'Geyer' interaction, vcov.ppm() and suffstat() sometimes gave incorrect answers. [Spotted by Ege Rubak.] Fixed. o as.im.im Did not correctly handle factor-valued images if one of the arguments 'dimyx', 'eps', 'xy' was given. Fixed. o envelope.lppm Crashed if the model was multitype. Fixed. o lpp Did not handle empty patterns. Fixed. o density.ppp If 'sigma' was a bandwidth selection function such as bw.scott() which returned a numeric vector of length 2, a warning message was issued, and the smoothing bandwidth was erroneously taken to be the first element of the vector. Fixed. o Fest, Jcross, Jdot, Jmulti If these functions were computed using correction = 'rs', plotting them would sometimes give an error, with the message "no finite x/y limits". Fixed. o pcfmodel.kppm For models with clusters="VarGamma" the value of the pcf at distance r=0 was given as NaN. Fixed. o vcov.ppm Result was incorrect in rare cases, due to numerical rounding effects. Fixed. o rLGCP, simulate.kppm For models fitted to point patterns in an irregular window, simulation sometimes failed, with a message that the image 'mu' did not cover the simulation window. (Spotted by George Limitsios.) Fixed. o rLGCP, simulate.kppm Crashed sometimes with an error about unequal x and y steps (from 'GaussRF'). Fixed. CHANGES IN spatstat VERSION 1.29-0 OVERVIEW o We thank Colin Beale, Li Haitao, Frederic Lavancier, Erika Mudrak and Ege Rubak for contributions. o random sequential packing o Allard-Fraley estimator o method for pooling several quadrat tests o better control over dummy points in ppm o more support for data on a linear network o nearest neighbour map o changes to subsetting of images o improvements and bug fixes NEW FUNCTIONS o clusterset Allard-Fraley estimator of high-density features in a point pattern o pool.quadrattest Pool several quadrat tests o nnfun Nearest-neighbour map of a point pattern or a line segment pattern o as.ppm Converts various kinds of objects to ppm o crossdist.lpp Shortest-path distances between pairs of points in a linear network o nobs.lppm Method for 'nobs' for lppm objects. o as.linim Converts various kinds of objects to 'linim' o model.images.slrm Method for model.images for slrm objects o rotate.im Rotate a pixel image SIGNIFICANT USER-VISIBLE CHANGES o "[.im" and "[<-.im" New argument 'j' allows any type of matrix indexing to be used. o "[.im" Default behaviour changed in the case of a rectangular subset. New argument 'rescue' can be set to TRUE to reinstate previous behaviour. o rSSI Performs 'Random Sequential Packing' if n=Inf. o ppm New argument 'eps' determines the spacing between dummy points. (also works for related functions quadscheme, default.dummy, ...) o fitted.ppm, predict.ppm Argument 'new.coef' specifies a vector of parameter values to replace the fitted coefficients of the model. o lppm Stepwise model selection using step() now works for lppm objects. o vcov.slrm Can now calculate correlation matrix or Fisher information matrix as well as variance-covariance matrix. o eval.fv Improved behaviour when plotted. o "[.fv" Improved behaviour when plotted. o lohboot When the result is plotted, the confidence limits are now shaded. o lohboot New argument 'global' allows global (simultaneous) confidence bands instead of pointwise confidence intervals. o vcov.ppm Accelerated by 30% in some cases. o quadrat.test.splitppp The result is now a single object of class 'quadrattest' o progressreport Improved output (also affects many functions which print progress reports) o Full redwood data (redwoodfull) Plot function redwoodfull.extra$plotit has been slightly improved. o nncross This function is now generic, with methods for 'ppp' and 'default'. o distfun The internal format of objects of class 'distfun' has been changed. o duplicated.ppp, unique.ppp New argument 'rule' allows behaviour to be consistent with package 'deldir' BUG FIXES o bdist.tiles Values were incorrect in some cases due to numerical error. (Spotted by Erika Mudrak.) Fixed. o vcov.ppm, suffstat These functions sometimes gave incorrect values for marked point process models. Fixed. o simulate.ppm, predict.ppm Did not correctly handle the 'window' argument. (Spotted by Li Haitao). Fixed. o smooth.ppp, markmean If sigma was very small, strange values were produced, due to numerical underflow. (Spotted by Colin Beale). Fixed. o MultiHard, MultiStrauss, MultiStraussHard Crashed if the data point pattern was empty. (Spotted by Ege Rubak). Fixed. o vcov.ppm Crashed sporadically, with multitype interactions. (Spotted by Ege Rubak). Fixed. o rStrauss, rHardcore, rStraussHard, rDiggleGratton, rDGS If the simulated pattern was empty, these functions would either crash, or return a pattern containing 1 point. (Spotted by Frederic Lavancier). Fixed. o model.matrix.slrm Crashed if the model was fitted using split pixels. Fixed. o residuals.ppm, diagnose.ppm Did not always correctly handle models that included offset terms. Fixed. o project.ppm When a model was projected by project.ppm or by ppm(project=TRUE), the edge corrections used the projected models were sometimes different from the edge corrections in the original model, so that the projected and unprojected models were not comparable. Fixed. o plot.listof, plot.splitppp Crashed sometimes due to a scoping problem. Fixed. o dclf.test, mad.test Crashed if any of the function values were infinite or NaN. Fixed. o psstA Default plot did not show the horizontal line at y=0 corresponding to a perfect fit. Fixed. o vcov.ppm names attribute was spelt incorrectly in some cases. Fixed. CHANGES IN spatstat VERSION 1.28-2 OVERVIEW o We thank Thomas Bendtsen, Ya-Mei Chang, Daniel Esser, Robert John-Chandran, Ege Rubak and Yong Song for contributions. o New code for Partial Residual Plots and Added Variable Plots. o maximum profile pseudolikelihood computations vastly accelerated. o New dataset: cells in gastric mucosa o now possible to capture every k-th state of Metropolis-Hastings algorithm. o size of 'ppm' objects reduced. o scope of 'intensity.ppm' extended. o quadrat.test can now perform Monte Carlo tests and one/two-sided tests o improvements to 'plot.fv' o improvement to 'rescale' o some datasets reorganised. o numerous bug fixes NEW DATASET o mucosa Cells in gastric mucosa Kindly contributed by Dr Thomas Bendtsen NEW FUNCTIONS o parres Partial residual plots for spatial point process models. A diagnostic for the form of a covariate effect. o addvar Added variable plots for spatial point process models. A diagnostic for the existence of a covariate effect. SIGNIFICANT USER-VISIBLE CHANGES o profilepl Accelerated (typically by a factor of 5). o rmh, rmhcontrol It is now possible to save every k-th iteration of the Metropolis-Hastings algorithm. The arguments 'nsave' and 'nburn' may be given to rmh or to rmhcontrol. They specify that the point pattern will be saved every 'nsave' iterations, after an initial burn-in of 'nburn' iterations. o simulate.ppm New argument 'singlerun' determines whether the simulated patterns are generated using independent runs of the Metropolis-Hastings algorithm or are obtained by performing one long run of the algorithm and saving every k-th iteration. o exactMPLEstrauss New argument 'project' determines whether the parameter gamma is constrained to lie in [0,1]. o intensity.ppm Now works for stationary point process models with the interactions DiggleGratton, DiggleGatesStibbard, Fiksel, PairPiece and Softcore. o plot.fv Improved algorithm for avoiding collisions between graphics and legend. o plot.fv New argument 'log' allows plotting on logarithmic axes. o envelope Can now calculate an estimate of the true significance level of the "wrong" test (which declares the observed summary function to be significant if it lies outside the pointwise critical boundary anywhere). Controlled by new argument 'do.pwrong'. o quadrat.test New argument 'alternative' allows choice of alternative hypothesis and returns one-sided or two-sided p-values as appropriate. o quadrat.test Can now perform Monte Carlo test as well (for use in small samples where the chi^2 approximation is inaccurate) o Softcore Improved numerical stability. New argument 'sigma0' for manual control over rescaling. o rescale If scale argument 's' is missing, then the data are rescaled to native units. For example if the current unit is 0.1 metres, coordinates will be re-expressed in metres. o psst Extra argument 'verbose=TRUE' o is.subset.owin Accelerated for polygonal windows o rmh.default 'track' is no longer a formal argument of rmh.default; it is now a parameter of rmhcontrol. However there is no change in usage: the argument 'track' can still be given to rmh.default. o clf.test Has been renamed 'dclf.test' to give proper attribution to Peter Diggle. o betacells This dataset has been restructured. The vector of cell profile areas, formerly given by betacells.extra$area, has now been included as a column of marks in the point pattern 'betacells'. o ants The function ants.extra$plot() has been renamed plotit() for conformity with other datasets. o redwoodfull The function redwoodfull.extra$plot() has been renamed plotit() for conformity with other datasets. o nbfires For conformity with other datasets, there is now an object nbfires.extra BUG FIXES o ripras Expansion factor was incorrect in the rectangular case. Fixed. o Triplets Crashed sometimes with error "dim(X) must have positive length". Fixed. o affine.im Crashed in the case of a diagonal transformation matrix! Spotted by Ege Rubak. Fixed. o envelope.envelope Ignored the argument 'global'. Fixed. o MultiStraussHard The printed output showed the hardcore radii as NULL. Spotted by Ege Rubak. Fixed. o "[.psp" Crashed if the data were generated by rpoisline(). Spotted by Marcelino de la Cruz. Fixed. o plot.linim If style="colour", the main title was always "x". Fixed. o plot.ppx Setting add=TRUE did not prevent the domain being plotted. Fixed. o rmh Crashed if x.start was an empty point pattern. Spotted by Ege Rubak. Fixed. o as.ppp.data.frame Crashed if any points lay outside the window. Spotted by Ege Rubak. Fixed. o Ripley isotropic edge correction Divide-by-zero error in rare cases. Spotted by Daniel Esser. Fixed. o summary functions For many of the summary functions (e.g. Kest, pcf), the result of saving the object to disc was an enormous file. Spotted by Robert John-Chandran. Fixed. o pcf.fv Default plot was wrongly coloured. Fixed. CHANGES IN spatstat VERSION 1.28-1 OVERVIEW o We thank Ege Rubak, Gopal Nair, Jens Oehlschlaegel and Mike Zamboni for contributions. o New approximation to the intensity of a fitted Gibbs model. o Minor improvements and bug fixes o spatstat now 'Suggests' the package 'gsl' NEW FUNCTIONS o intensity, intensity.ppp, intensity.ppm Calculate the intensity of a dataset or fitted model. Includes new approximation to the intensity of a fitted Gibbs model o LambertW Lambert's W-function SIGNIFICANT USER-VISIBLE CHANGES o envelope Improved plot labels for envelopes that were generated using the 'transform' argument. o plot.fv Improved algorithm for collision detection. o plot.im Now returns the colour map used. o plot.listof, plot.splitppp Slight change to handling of plot.begin and plot.end o square Now accepts vectors of length 2 o plot.fii Increased resolution of the plot obtained from plot(fitin(ppm(...))) o image.listof If equal.ribbon=TRUE, the colour ribbon will no longer be displayed repeatedly for each panel, but will now be plotted only once, at the right hand side of the plot array. BUG FIXES o vcov.ppm Results were sometimes incorrect for a Gibbs model with non-trivial trend. Spotted by Ege Rubak. Fixed. o nncross In rare cases the results could be slightly incorrect. Spotted by Jens Oehlschlaegel. Fixed. o plot.fv When add=TRUE, the x limits were sometimes truncated. Spotted by Mike Zamboni. Fixed. o plot.im Labels for the tick marks on the colour ribbon were sometimes ridiculous, e.g. "2.00000001". Fixed. CHANGES IN spatstat VERSION 1.28-0 OVERVIEW o We thank Farzaneh Safavimanesh, Andrew Hardegen and Tom Lawrence for contributions. o Improvements to 3D summary functions. o A multidimensional point pattern (ppx) can now have 'local' coordinates as well as spatial and temporal coordinates and marks. o Changed format for point patterns on a linear network (lpp). Changes are backward compatible. Many computations run faster. o More support for fitted cluster models (kppm). o split method for multidimensional point patterns (ppx) and point patterns on a linear network (lpp). o Fixed bug causing errors in plot.im o Miscellaneous improvements and bug fixes NEW FUNCTIONS o exactMPLEstrauss Fits the stationary Strauss point process model using an exact maximum pseudolikelihood technique. This is mainly intended for technical investigation of algorithms. o split.ppx Method for 'split' for multidimensional point patterns (class 'ppx'). This also works for point patterns on a linear network (class 'lpp'). o model.images This function is now generic, with methods for classes ppm, kppm, lppm o model.frame, model.matrix These generic functions now have methods for classes kppm, lppm o as.owin.kppm, as.owin.lppm New methods for 'as.owin' for objects of class kppm, lppm o as.linnet.lppm Extracts the linear network in which a point process model was fitted. SIGNIFICANT USER-VISIBLE CHANGES o class 'ppx' An object of class 'ppx' may now include 'local' coordinates as well as 'spatial' and 'temporal' coordinates, and marks. o ppx Arguments have changed. o class 'lpp' The internal format of lpp objects has been extended (but is backward-compatible). Many computations run faster. To convert an object to the new format: X <- lpp(as.ppp(X), as.linnet(X)). o F3est Calculation of theoretical Poisson curve ('theo') has changed, and is now controlled by the argument 'sphere'. o rmh, rmhstart The initial state ('start') can now be missing or null. o im, as.im The pixel coordinates in an image object are now generated more accurately. This avoids a numerical error in plot.im. o eval.fv, eval.fasp Evaluation is now applied only to columns that contain values of the function itself (rather than values of the derivative, hazard rate, etc). This is controlled by the new argument 'dotonly'. o spatstat.options New option 'nvoxel' o quad.ppm Now accepts kppm objects. o str This generic function (for inspecting the internal structure of an object) now produces sensible output for objects of class 'hyperframe', 'ppx', 'lpp' o ppx, coords.ppx, coords<-.ppx The arguments to these functions have changed. o lgcp.estK, Kmodel Computation can be greatly accelerated by setting spatstat.options(fastK.lgcp=TRUE). o G3est Computation accelerated. o envelope Computation slightly accelerated. o spatstat.options New option 'fastK.lgcp' BUG FIXES o nndist.psp Caused an error if length(k) > 1. Fixed. o plot.im Sometimes reported an error "useRaster=TRUE can only be used with a regular grid." This was due to numerical rounding effects on the coordinates of a pixel image. Fixed. o plot.fv If a formula was used to specify the plot, the names of variables in the formula were sometimes incorrectly matched to *functions*. Spotted by Farzaneh Safavimanesh. Fixed. o F3est Took a very long time if the containing box was very flat, due to the default value of 'vside'. Fixed. o rmh, rmhmodel An erroneous warning about 'outdated format of rmhmodel object' sometimes occurred. Fixed. o marks<-.ppx Names of result were incorrect. Fixed. o hyperframe class Various minor bug fixes. CHANGES IN spatstat VERSION 1.27-0 OVERVIEW o Variance estimates are now available for all Gibbs point process models. o Cressie-Loosmore-Ford test implemented o plot.fv now avoids collisions between the legend and the graphics. o Extension to predict.ppm o Improvements to envelopes and multitype summary functions. o Line transects of a pixel image. o Changes to defaults in Metropolis-Hastings simulations. o More geometrical operations o Bug fixes. o We thank Aruna Jammalamadaka for contributions. NEW FUNCTIONS o clf.test Perform the Cressie (1991)/ Loosmore and Ford (2006) test of CSR (or another model) o mad.test Perform the Maximum Absolute Deviation test of CSR (or another model). o convolve.im Compute convolution of pixel images. o Kmulti.inhom Counterpart of 'Kmulti' for spatially-varying intensity. o rmhexpand Specify a simulation window, or a rule for expanding the simulation window, in Metropolis-Hastings simulation (rmh) o transect.im Extract pixel values along a line transect. o affine.im Apply an affine transformation to a pixel image. o scalardilate Perform scalar dilation of a geometrical object relative to a specified origin. o reflect Reflect a geometrical object through the origin. o "[.lpp", "[.ppx" Subset operators for the classes "lpp" (point pattern on linear network) and "ppx" (multidimensional space-time point pattern). o is.rectangle, is.polygonal, is.mask Determine whether a window w is a rectangle, a domain with polygonal boundaries, or a binary pixel mask. o has.offset Determines whether a fitted model object (of any kind) has an offset. SIGNIFICANT USER-VISIBLE CHANGES o predict.ppm This function can now calculate the conditional intensity of a model relative to any point pattern X (not just the original data pattern). o vcov.ppm This function now handles all Gibbs point process models. o plot.fv Collisions between the legend box and the graphics are now detected and avoided. o rmh.ppm, rmh.default, simulate.ppm, qqplot.ppm, envelope.ppm These functions now have slightly different default behaviour because of changes to the handling of arguments to 'rmhcontrol'. o rmhcontrol The default value of the parameters 'periodic' and 'expand' has changed. o rmhcontrol The parameter 'expand' can now be in any format acceptable to rmhexpand(). o rmh.ppm, rmh.default, simulate.ppm Any 'rmhcontrol' parameter can now be given directly as an argument to rmh.ppm, rmh.default or simulate.ppm. o Kmulti, Gmulti, Jmulti The arguments I, J can now be any kind of subset index or can be functions that yield a subset index. o envelope.envelope In envelope(E, fun=NULL) if E does not contain simulated summary functions, but does contain simulated point patterns, then 'fun' now defaults to Kest, instead of flagging an error. o print.ppp, summary.ppp If the point pattern x was generated by Metropolis-Hastings simulation using 'rmh', then print(x) and summary(x) show information about the simulation parameters. o print.ppm Standard errors for the parameter estimates, and confidence intervals for the parameters, can now be printed for all Gibbs models (but are printed only for Poisson models by default). o eval.im Images with incompatible dimensions are now resampled to make them compatible (if harmonize=TRUE). o spatstat.options New option 'print.ppm.SE' controls whether standard errors and confidence intervals are printed for all Gibbs models, for Poisson models only, or are never printed. o inside.owin Now accepts the form list(x,y) for the first argument. o image.listof New argument 'equal.ribbon' allows several images to be plotted with the same colour map. o is.subset.owin Improved accuracy in marginal cases. o expand.owin Functionality extended to handle all types of expansion rule. o default.rmhcontrol, default.expand These functions now work with models of class 'rmhmodel' as well as 'ppm' o print.rmhcontrol Output improved. BUG FIXES o linearK, linearKinhom If any data points were located exactly at a vertex of the linear network, the weights for Ang's correction were incorrect, due to numerical error. This sometimes produced infinite or NA values of the linear K function. Fixed. o predict.ppm In some cases, predict.ppm(type="cif") generated a spurious warning that "number of rows of result is not a multiple of vector length." Fixed. o crossing.psp Results were sometimes incorrect due to numerical rounding error associated with GCC bug #323. Fixed. o MultiHard, MultiStrauss, MultiStraussHard If the mark values contained non-alphanumeric characters, the names of the interaction coefficients in coef(ppm(...)) were sometimes garbled. Fixed. o profilepl For edge corrections other than the border correction, an error message about 'rbord' would sometimes occur. Fixed. o is.marked, is.multitype These functions gave the wrong answer for 'lpp' objects. Fixed. o marks<-.lpp, marks<-.ppx Format of result was garbled if new columns of marks were added. Fixed. o reach.rmhmodel Gave the wrong answer for Geyer and BadGey models. Fixed. o envelope.envelope Ignored the argument 'savefuns'. Fixed. o BadGey Sometimes wrongly asserted that the parameter 'sat' was invalid. Occurred only in ppm(project=TRUE). Fixed. CHANGES IN spatstat VERSION 1.26-1 OVERVIEW o Variance-covariance matrix for Gibbs point process models. o Bootstrap confidence bands for pair correlation function and K function. o Bug fix in scan test. o Area-interaction model accelerated. o we thank Jean-Francois Coeurjolly and Ege Rubak for contributions. NEW FUNCTIONS o lohboot Computes bootstrap confidence bands for pair correlation function and K function using Loh's (2008) mark bootstrap. SIGNIFICANT USER-VISIBLE CHANGES o vcov.ppm Now works for all Gibbs point process models, thanks to new code (and theory) from Jean-Francois Coeurjolly and Ege Rubak o AreaInter Computations related to the area-interaction point process (ppm, predict.ppm, residuals.ppm, diagnose.ppm, qqplot.ppm) have been accelerated. BUG FIXES o scan.test Results were sometimes incorrect due to numerical instability (a 'Gibbs phenomenon'). Fixed. CHANGES IN spatstat VERSION 1.26-0 OVERVIEW o We thank Jens Oehlschlaegel for contributions. o Further substantial acceleration of spatstat functions. o Workaround for bug in RandomFields package. o Numerous modifications to internal code. NEW FUNCTIONS o RandomFieldsSafe There is a bug in the package 'RandomFields' (version <= 2.0.54) which causes a crash to occur, in the development version of R but not in R 2.15.0. To avoid crashing spatstat, we have written the temporary, undocumented function RandomFieldsSafe() which returns TRUE if it is safe to use the RandomFields package. Examples in the spatstat help files for kppm, lgcp.estK, lgcp.estpcf and rLGCP are only executed if RandomFieldsSafe() returns TRUE. SIGNIFICANT USER-VISIBLE CHANGES o Many functions Many spatstat functions now run faster, and will handle larger datasets, thanks to improvements in the internal code, following suggestions from Jens Oehlschlaegel. o Many functions The response to an 'Interrupt' signal is slightly slower. CHANGES IN spatstat VERSION 1.25-5 OVERVIEW o We thank Ya-Mei Chang, Jens Oehlschlaegel and Yong Song for contributions. o Extended functionality of 'rhohat' to local likelihood smoothing and bivariate smoothing. o Nearest neighbour distance computations accelerated. o spatstat now 'Suggests:' the package 'locfit' NEW FUNCTIONS o rho2hat Bivariate extension of 'rhohat' for estimating spatial residual risk, or intensity as a function of two covariates. SIGNIFICANT USER-VISIBLE CHANGES o rhohat Estimation can now be performed using local likelihood fitting with the 'locfit' package, or using kernel smoothing. o nncross Substantially accelerated. New arguments added to control the return value and the sorting of data. BUG FIXES o plot.msr Crashed if the argument 'box' was given. Fixed. CHANGES IN spatstat VERSION 1.25-4 OVERVIEW o We thank Jonathan Lee and Sergiy Protsiv for contributions. o Improvements and bug fixes to K function for very large datasets NEW FUNCTIONS o rStraussHard Perfect simulation for Strauss-hardcore process (with gamma <= 1) SIGNIFICANT USER-VISIBLE CHANGES o plot.im The colour ribbon can now be placed left, right, top or bottom using new argument 'ribside' o profilepl Does not generate warnings when some of the candidate models have zero likelihood - for example when fitting model with a hard core. o Kest Now includes fast algorithm for 'correction="none"' which will handle patterns containing millions of points. BUG FIXES o Kest, Lest Gave incorrect values in very large datasets, due to numerical overflow. `Very large' typically means about 1 million points in a random pattern, or 100,000 points in a tightly clustered pattern. [Overflow cannot occur unless there are at least 46,341 points.] [Spotted by Sergiy Protsiv.] Fixed. o Kest, Lest Ignored 'ratio=TRUE' if the argument 'domain' was given. [Spotted by Jonathan Lee.] Fixed. o rjitter Output was sometimes incorrect. [Spotted by Sergiy Protsiv.] Fixed. CHANGES IN spatstat VERSION 1.25-3 OVERVIEW o We thank Daniel Esser for contributions. o Improved support for fitted point process models. o Bug fixes. NEW FUNCTIONS o simulate.slrm Method for 'simulate' for spatial logistic regression models. o labels.ppm, labels.kppm, labels.slrm Methods for 'labels' for fitted point process models. o commonGrid Determine a common spatial domain and pixel resolution for several pixel images and/or binary masks SIGNIFICANT USER-VISIBLE CHANGES o effectfun Now has argument 'se.fit' allowing calculation of standard errors and confidence intervals. o [.msr Now handles character-valued indices. o print.summary.ppm Output gives a more precise description of the fitting method. o ppm, kppm, slrm Confidence intervals for the fitted trend parameters can now be obtained using 'confint' o predict.slrm New argument 'window' o union.owin Now handles a single argument: union.owin(A) returns A. BUG FIXES o selfcrossing.psp y coordinate values were incorrect. [Spotted by Daniel Esser.] Fixed. o as.im.owin Did not handle a binary mask with a 1 x 1 pixel array. Fixed. o predict.slrm Results of predict(object, newdata) were incorrect if the spatial domain of 'newdata' was larger than the original domain. Fixed. o ppm If the model was the uniform Poisson process, the argument 'rbord' was ignored. Fixed. o image subset assignment "[<-.im" Generated an error if the indexing argument 'i' was a point pattern containing zero points. Fixed. o hyperframe subset assignment "[<-.hyperframe" Did not correctly handle the case where a single column of the hyperframe was to be changed. Fixed. o help(bw.relrisk), help(rmh.ppm), help(plot.plotppm) These help files had the side-effect of changing some options in spatstat.options. Fixed. CHANGES IN spatstat VERSION 1.25-2 OVERVIEW o We thank Abdollah Jalilian and Thierry Onkelinx for contributions. o Very Important Bug fixes. o Improved mechanism for handling 'invalid' point processes NEW FUNCTIONS o as.matrix.owin Converts a window to a logical matrix. SIGNIFICANT USER-VISIBLE CHANGES o project.ppm Improved algorithm. Now handles terms in the trend formula as well as the interaction. The projected point process is now obtained by re-fitting the model, and is guaranteed to be the maximum pseudolikelihood fit. o plot.im Now handles many arguments recognised by plot.default such as 'cex.main'. Also handles argument 'box'. New argument 'ribargs' contains parameters controlling the ribbon plot only. o spatstat.options New option 'project.fast' allows a faster shortcut for project.ppm o spatstat.options New options 'rmh.p', 'rmh.q', 'rmh.nrep' determine the default values of the parameters p, q and nrep of the Metropolis-Hastings algorithm. See rmhcontrol o ppm Slightly accelerated. BUG FIXES o nncross, distfun, AreaInter Results of nncross were possibly incorrect when X and Y did not have the same window. This bug affected values of 'distfun' and may also have affected ppm objects with interaction 'AreaInter'. [Spotted by Thierry Onkelinx] Bug introduced in spatstat 1.9-4 (June 2006). Fixed. o rCauchy Simulations were incorrect in the sense that the value of 'omega' was inadvertently doubled (i.e. omega was incorrectly replaced by 2 * omega). Bug introduced in spatstat 1.25-0. Fixed. o plot.im White lines were present in the image display, on some graphics devices, due to changes in R 2.14. Fixed. o update.ppm The result of 'update(object, formula)' sometimes contained errors in the internal format. Bug introduced in spatstat 1.25-0. Fixed. o example(AreaInter), example(bw.smoothppp), example(Kest.fft), example(plot.owin), example(predict.ppm), example(simulate.ppm) Executing these examples had the side-effect of changing some of the parameters in spatstat.options. Fixed. CHANGES IN spatstat VERSION 1.25-1 OVERVIEW o We thank Neba Funwi-Gabga and Jorge Mateu for contributions. o New dataset of gorilla nest sites o New functions for perfect simulation o Bug fix for rare crashes in rStrauss o Code for ensuring a fitted point process model is a valid point process NEW DATASET o gorillas Gorilla nest sites in a National Park in Cameroon. Generously contributed by Neba Funwi-Gabga NEW FUNCTIONS o rDiggleGratton, rDGS, rHardcore Perfect simulation for the Diggle-Gratton process, Diggle-Gates-Stibbard process, and Hardcore process. o bw.scott Scott's rule of thumb for bandwidth selection in multidimensional smoothing o valid.ppm Checks whether a fitted point process model is a valid point process o project.ppm Forces a fitted point process model to be a valid point process SIGNIFICANT USER-VISIBLE CHANGES o ppm New argument 'project' determines whether the fitted model is forced to be a valid point process o linnet Substantially accelerated. o rStrauss Slightly accelerated. o summary.lpp Now prints the units of length. BUG FIXES o rStrauss Crashed rarely (once every 10 000 realisations) with a memory segmentation fault. Fixed. CHANGES IN spatstat VERSION 1.25-0 OVERVIEW o Leverage and influence for point process models o New cluster models (support for model-fitting and simulation). o Fit irregular parameters in trend of point process model o Third order summary statistic. o Improvements to speed and robustness of code. o spatstat now depends on R 2.14 o We thank Abdollah Jalilian and Rasmus Waagepetersen for contributions. NEW FUNCTIONS o leverage.ppm, influence.ppm, dfbetas.ppm Leverage and influence for point process models o ippm Experimental extension to 'ppm' which fits irregular parameters in trend by Fisher scoring algorithm. o Tstat Third order summary statistic for point patterns based on counting triangles. o rCauchy, rVarGamma simulation of a Neyman-Scott process with Cauchy clusters or Variance Gamma (Bessel) clusters. Contributed by Abdollah Jalilian. o rPoissonCluster simulation of a general Poisson cluster process o model.covariates Identify the covariates involved in a model (lm, glm, ppm etc) o as.im.distfun Converts a 'distfun' to a pixel image. o cauchy.estK, cauchy.estpcf, vargamma.estK, vargamma.estpcf Low-level model-fitting functions for the Neyman-Scott process with Cauchy or Variance-Gamma cluster kernel. Contributed by Abdollah Jalilian. SIGNIFICANT USER-VISIBLE CHANGES o kppm Now accepts clusters="Cauchy" or clusters="VarGamma" for the Neyman-Scott process with Cauchy or Variance-Gamma cluster kernel. Code contributed by Abdollah Jalilian. o rNeymanScott Argument 'rcluster' may now take a different format. o psst Argument 'funcorrection' changed to 'funargs' allowing greater flexibility. o plot.fv, plot.envelope New argument 'limitsonly' allows calculation of a common x,y scale for several plots. o overall speed spatstat is now byte-compiled and runs slightly faster. o user interrupt Long calculations in spatstat now respond to the Interrupt/Stop signal. o update.ppm Now runs faster and uses much less memory, when the update only affects the model formula (trend formula). o rNeymanScott, rThomas, rMatClust Accelerated thanks to Rasmus Waagepetersen. o multitype data and models Second order multitype statistics (such as Kcross, pcfcross) and multitype interaction models (such as MultiStrauss) now run faster, by a further 5%. BUG FIXES o distfun Some manipulations involving 'distfun' objects failed if the original data X in distfun(X) did not have a rectangular window. Fixed. CHANGES IN spatstat VERSION 1.24-2 OVERVIEW o Geyer's triplet interaction o more functionality for replicated point patterns o changed default for simulation window in point process simulation o changed default for edge correction in Kcom, Gcom o data in spatstat is now lazy-loaded o bug fixes NEW FUNCTIONS o Triplets Geyer's triplet interaction, for point process models o coef.summary.ppm New method coef.summary.ppm You can now type 'coef(summary(fit))' to extract a table of the fitted coefficients of the point process model 'fit' SIGNIFICANT USER-VISIBLE CHANGES o data in spatstat are now lazy-loaded so you don't have to type data(amacrine), etc. o rmh.default, rmh.ppm, simulate.ppm These now handle the 'triplets' interaction o fryplot Now has arguments 'to' and 'from', allowing selection of a subset of points. o fryplot, frypoints These functions now handle marked point patterns properly. o Kcross, Kdot, Kmulti New argument 'ratio' determines whether the numerator and denominator of the estimate of the multitype K-function will be stored. This enables analysis of replicated point patterns, using 'pool.rat()' to pool the K function estimates. o rmh.ppm, simulate.ppm, default.expand For point process models which have a trend depending only on x and y, the simulation window is now taken to be the same as the original window containing the data (by default). That is, `expansion' does not take place, by default. (In previous versions of spatstat the simulation window was larger than the original data window.) o rmh.ppm, simulate.ppm The argument sequence for these functions has changed. New argument 'expand' allows more explicit control over simulation domain. o Kcom, Gcom New argument 'conditional' gives more explicit control over choice of edge correction in compensator. Simplified defaults for edge correction. o Kinhom Improved plot labels. o profilepl Printed output improved. BUG FIXES o Lest The variance approximations (Lotwick-Silverman and Ripley) obtained with var.approx=TRUE, were incorrect for Lest (although they were correct for Kest) due to a coding error. Fixed. o simulate.ppm Ignored the argument 'control' in some cases. Fixed. o pcf and its relatives (pcfinhom, pcfcross.inhom, pcfdot.inhom) Sometimes gave a warning about 'extra arguments ignored'. Fixed. CHANGES IN spatstat VERSION 1.24-1 OVERVIEW o Spatial Scan Test o Functionality for replicated point patterns o Bug fixes NEW FUNCTIONS o scan.test Spatial scan test of clustering o rat New class of 'ratio objects' o pool.rat New method for 'pool'. Combines K function estimates for replicated point patterns (etc) by computing ratio-of-sums o unnormdensity Weighted kernel density with weights that do not sum to 1 and may be negative. o compatible New generic function with methods for 'fv', 'im', 'fasp' and 'units' SIGNIFICANT USER-VISIBLE CHANGES o Kest New argument 'ratio' determines whether the numerator and denominator of the estimate of the K-function will be stored. This enables analysis of replicated point patterns, using 'pool.rat()' to pool the K function estimates. o Lest Now handles theoretical variance estimates (using delta method) if var.approx=TRUE o as.mask Argument 'eps' can now be a 2-vector, specifying x and y resolutions. o default.expand Behaviour changed slightly. o plot.listof, plot.splitppp, contour.listof, image.listof The arguments 'panel.begin' and 'panel.end' can now be objects such as windows. BUG FIXES o rgbim, hsvim Did not work on images with non-rectangular domains. Fixed. o scaletointerval Did not handle NA's. Fixed. CHANGES IN spatstat VERSION 1.24-0 OVERVIEW o This version was not released publicly. CHANGES IN spatstat VERSION 1.23-6 OVERVIEW o Spatial covariance functions of windows and pixel images. o Area-interaction models can now be fitted in non-rectangular windows o Bug fix for envelope of inhomogeneous Poisson process o Bug fix for raster conversion o New vignette on 'Getting Started with Spatstat' o Code accelerated. NEW FUNCTIONS o imcov Spatial covariance function of pixel image or spatial cross-covariance function of two pixel images o harmonise.im Make several pixel images compatible by converting them to the same pixel grid o contour.listof, image.listof Methods for contour() and image() for lists of objects o dummify Convert data to numeric values by constructing dummy variables. SIGNIFICANT USER-VISIBLE CHANGES o setcov Can now compute the `cross-covariance' between two regions o AreaInter Point process models with the AreaInter() interaction can now be fitted to point pattern data X in any window. o areaGain, areaLoss These now handle arbitrary windows W. They are now more accurate when r is very small. o Kcom Computation vastly accelerated, for non-rectangular windows. o vignettes New vignette 'Getting Started with the Spatstat Package' o nncorr, nnmean, nnvario These functions now handle data frames of marks. BUG FIXES o envelope.ppm If the model was an inhomogeneous Poisson process, the resulting envelope object was incorrect (the simulations were correct, but the envelopes were calculated assuming the model was CSR). Bug was introduced in spatstat 1.23-5. Fixed. o envelope.ppm If the model was an inhomogeneous Poisson process with intensity a function of x and y only, overflow errors sometimes occurred ('insufficient storage' or 'attempting to generate a large number of random points'). Fixed. o as.im.im The result of as.im(X, W) was incorrect if 'W' did not cover 'X'. Fixed. o as.mask The result of as.mask(w, xy) was incorrect if 'xy' did not cover 'w'. Fixed. o plot.fv Legend was incorrectly labelled if 'shade' variables were not included in the plot formula. Fixed. o areaGain, areaLoss Crashed if the radius r was close to zero. Fixed. CHANGES IN spatstat VERSION 1.23-5 OVERVIEW o Bug fix to bandwidth selection. o Functions to pool data from several objects of the same class. o Improvements and bug fixes. o We thank Michael Sumner for contributions. NEW FUNCTIONS o pool Pool data from several objects of the same class o pool.envelope Pool simulated data from several envelope objects and create a new envelope o pool.fasp Pool simulated data from several function arrays and create a new array o envelope.envelope Recalculate an envelope from simulated data using different parameters SIGNIFICANT USER-VISIBLE CHANGES o bw.diggle, bw.relrisk, bw.smoothppp, bw.optim Plot method modified. o model.depends Now also recognises 'offset' terms. BUG FIXES o bw.diggle Bandwidth was too large by a factor of 2. Fixed. o plot.psp Crashed if any marks were NA. Fixed. o pointsOnLines Crashed if any segments had zero length. Ignored argument 'np' in some cases. Fixed. o stieltjes Crashed if M had only a single column of function values. Fixed. CHANGES IN spatstat VERSION 1.23-4 OVERVIEW o Bandwidth selection for density.ppp and smooth.ppp o Layered plots. o Model-handling facilities. o Improvements and bug fixes. NEW FUNCTIONS o bw.diggle Bandwidth selection for density.ppp by mean square error cross-validation. o bw.smoothppp Bandwidth selection for smooth.ppp by least-squares cross-validation. o layered, plot.layered A simple mechanism for controlling plots that consist of several successive layers of data. o model.depends Given a fitted model (of any kind), identify which of the covariates is involved in each term of the model. o model.is.additive Determine whether a fitted model (of any kind) is additive, in the sense that each term in the model involves at most one covariate. SIGNIFICANT USER-VISIBLE CHANGES o smooth.ppp Bandwidth 'sigma' is now selected by least-squares cross-validation o bw.relrisk Computation in large datasets accelerated. New arguments 'hmin', 'hmax' control the range of trial values of bandwidth. o Hest, Gfox, Jfox Improved algebraic labels for plot o spatstat.options New parameter 'n.bandwidth' o density.ppp, smooth.ppp Slightly accelerated. o point-in-polygon test Accelerated. BUG FIXES o with.fv Mathematical labels were incorrect in some cases. Fixed. o bw.relrisk Implementation of method="weightedleastsquares" was incorrect and was equivalent to method="leastsquares". Fixed. o smooth.ppp NaN values occurred if the bandwidth was very small. Fixed. CHANGES IN spatstat VERSION 1.23-3 OVERVIEW o Urgent bug fix. BUG FIXES o crossing.psp Crashed occasionally with a message about NA or NaN values. Fixed. o affine.ppp Crashed if the point pattern was empty. Fixed. CHANGES IN spatstat VERSION 1.23-2 OVERVIEW o Bug fixes. o Several functions have been accelerated. o We thank Marcelino de la Cruz and Ben Madin for contributions. NEW FUNCTIONS o sumouter, quadform Evaluate certain quadratic forms. o flipxy Exchange x and y coordinates. SIGNIFICANT USER-VISIBLE CHANGES o vcov.ppm Accelerated. o owin, as.owin Checking the validity of polygons has been accelerated. o crossing.psp, selfcrossing.psp Accelerated. BUG FIXES o split.ppp If drop=TRUE then some of the point patterns had the wrong windows. Spotted by Marcelino de la Cruz. Fixed. o split.ppp Crashed if the tessellation did not cover the point pattern. Fixed. o predict.ppm Crashed when type="se" if NA's were present. Spotted by Ben Madin. Fixed. o plot.ppp Incorrectly handled the case where both 'col' and 'cols' were present. Fixed. o polygon geometry The point-in-polygon test gave the wrong answer in some boundary cases. Fixed. CHANGES IN spatstat VERSION 1.23-1 OVERVIEW o Important bug fix to 'localpcf'. o Inverse-distance weighted smoothing. o Inhomogeneous versions of neighbourhood density functions. o Internal repairs and bug fixes. o We thank Mike Kuhn and Ben Madin for contributions. NEW FUNCTIONS o idw Inverse-distance weighted smoothing. o localKinhom, localLinhom, localpcfinhom Inhomogeneous versions of localK, localL, localpcf BUG FIXES o localpcf The columns of the result were in the wrong order. [i.e. pair correlation functions were associated with the wrong points.] Fixed. o delaunay If the union of several Delaunay triangles formed a triangle, this was erroneously included in the result of delaunay(). Fixed. o predict.ppm, plot.ppm Sometimes crashed with a warning about 'subscript out of bounds'. Fixed. o point-in-polygon test Vertices of a polygon were sometimes incorrectly classified as lying outside the polygon. Fixed. o Internal code Numerous tweaks and repairs to satisfy the package checker for the future R version 2.14. CHANGES IN spatstat VERSION 1.23-0 OVERVIEW o point patterns on a linear network: new tools including geometrically-corrected linear K function, pair correlation function, point process models, envelopes o changes to renormalisation of estimates in Kinhom and pcfinhom o new dataset: Chicago street crime o spatstat now 'Suggests:' the package RandomFields o spatstat now has a Namespace o we thank Mike Kuhn, Monia Mahling, Brian Ripley for contributions. NEW DATASET o chicago Street crimes in the University district of Chicago. A point pattern on a linear network. NEW FUNCTIONS o envelope.lpp Simulation envelopes for point patterns on a linear network o lineardisc Compute the 'disc' of radius r in a linear network o linearpcf Pair correlation for point pattern on a linear network o linearKinhom, linearpcfinhom Inhomogeneous versions of the K function and pair correlation function for point patterns on a linear network o lppm Fit point process models on a linear network. o anova.lppm Analysis of deviance for point process models on a linear network. o predict.lppm Prediction for point process models on a linear network. o envelope.lppm Simulation envelopes for point process models on a linear network. o linim Pixel image on a linear network o plot.linim Plot a pixel image on a linear network SIGNIFICANT USER-VISIBLE CHANGES o linearK New argument 'correction'. Geometrically-corrected estimation is performed by default (based on forthcoming paper by Ang, Baddeley and Nair) o Kinhom New argument 'normpower' allows different types of renormalisation. o pcfinhom Now performs renormalisation of estimate. Default behaviour changed - estimates are now renormalised by default. BUG FIXES o density.ppp Crashed if argument 'varcov' was given. Fixed. CHANGES IN spatstat VERSION 1.22-4 OVERVIEW o new diagnostics based on score residuals o new dataset o improvements to plotting summary functions o We thank Ege Rubak, Jesper Moller, George Leser, Robert Lamb and Ulf Mehlig for contributions. NEW FUNCTIONS o Gcom, Gres, Kcom, Kres New diagnostics for fitted Gibbs or Poisson point process models based on score residuals. Gcom is the compensator of the G function Gres is the residual of the G function Kcom is the compensator of the K function Kres is the residual of the K function o psst, psstA, psstG New diagnostics for fitted Gibbs or Poisson point process models based on pseudoscore residuals. psst is the pseudoscore diagnostic for a general alternative psstA is the pseudoscore diagnostic for an Area-interaction alternative psstG is the pseudoscore diagnostic for a Geyer saturation alternative o compareFit Computes and compares several point process models fitted to the same dataset, using a chosen diagnostic. o as.interact Extracts the interpoint interaction structure (without parameters) from a fitted point process model or similar object. NEW DATASET o flu Spatial point patterns giving the locations of influenza virus proteins on cell membranes. Kindly released by Dr George Leser and Dr Robert Lamb. SIGNIFICANT USER-VISIBLE CHANGES o pixel images and grids The default size of a pixel grid, given by spatstat.options("npixel"), has been changed from 100 to 128. A power of 2 gives faster and more accurate results in many cases. o residuals.ppm New arguments 'coefs' and 'quad' for advanced use (make it possible to compute residuals from a modified version of the fitted model.) o relrisk New argument 'casecontrol' determines whether a bivariate point pattern should be treated as case-control data. o plot.fv Further improvements in mathematical labels. o plot.fv The formula can now include the symbols .x and .y as abbreviation for the function argument and the recommended function value, respectively. o plot.fv New argument 'add' BUG FIXES o multitype summary functions (Kcross, Kdot, Gcross, Gdot, .....) Plotting these functions generated an error if the name of one of the types of points contained spaces, e.g. "Escherichia coli". Fixed. CHANGES IN spatstat VERSION 1.22-3 OVERVIEW o Important bug fix to simulation code o Miscellaneous improvements o spatstat now depends on R 2.13.0 or later o We thank Ege Rubak, Kaspar Stucki, Vadim Shcherbakov, Jesper Moller and Ben Taylor for contributions. NEW FUNCTIONS o is.stationary, is.poisson New generic functions for testing whether a point process model is stationary and/or Poisson. Methods for ppm, kppm, slrm etc o raster.xy raster coordinates of a pixel mask o zapsmall.im 'zapsmall' for pixel images SIGNIFICANT USER-VISIBLE CHANGES o density.ppp New argument 'diggle' allows choice of edge correction o rotate.owin, affine.owin These functions now handle binary pixel masks. New argument 'rescue' determines whether rectangles will be preserved BUG FIXES o rmh, simulate.ppm Serious bug - simulation was completely incorrect in the case of a multitype point process with an interaction that does not depend on the marks, such as ppm(betacells, ~marks, Strauss(60)) The calling parameters were garbled. Fixed. o effectfun Crashed if the covariate was a function(x,y). Fixed. o lurking Gave erroneous error messages about 'damaged' models. Fixed. o envelope.ppm Did not recognise when the fitted model was equivalent to CSR. Fixed. o plot.ppx Crashed in some cases. Fixed. CHANGES IN spatstat VERSION 1.22-2 OVERVIEW o Fitting and simulation of log-Gaussian Cox processes with any covariance function o More support for 'kppm' and 'rhohat' objects o K-function for point patterns on a linear network o Metropolis-Hastings algorithm now saves its transition history o Easier control of dummy points in ppm o Convert an 'fv' object to an R function o spatstat now depends on the package 'RandomFields' o We thank Abdollah Jalilian, Shen Guochun, Rasmus Waagepetersen, Ege Rubak and Ang Qi Wei for contributions. NEW FUNCTIONS o linearK Computes the Okabe-Yamada network K-function for a point pattern on a linear network. o pairdist.lpp Shortest-path distances between each pair of points on a linear network. o vcov.kppm Asymptotic variance-covariance matrix for regression parameters in kppm object. [Contributed by Abdollah Jalilian and Rasmus Waagepetersen] o rLGCP Simulation of log-Gaussian Cox processes [Contributed by Abdollah Jalilian and Rasmus Waagepetersen] o predict.rhohat Method for 'predict' for objects of class 'rhohat' Computes a pixel image of the predicted intensity. o Kmodel, pcfmodel Generic functions that compute the K-function or pair correlation function of a point process *model*. So far the only methods are for the class 'kppm'. o as.function.fv Converts a function value table (class 'fv') to a function in R o coef.kppm Method for 'coef' for objects of class 'kppm' o unitname, unitname<- These generic functions now have methods for fitted model objects (classes ppm, slrm, kppm, minconfit) and quadrature schemes (quad). o nobs.ppm Method for 'nobs' for class 'ppm'. Returns the number of points in the original data. SIGNIFICANT USER-VISIBLE CHANGES o kppm Can now fit a log-Gaussian Cox process o simulate.kppm Can now simulate a fitted log-Gaussian Cox process o lgcp.estK, lgcp.estpcf These functions previously fitted a log-Gaussian Cox process with exponential covariance. They can now fit a log-Gaussian Cox process with any covariance function implemented by the RandomFields package. o rmh If track=TRUE, the history of transitions of the Metropolis-Hastings algorithm is saved and returned. o ppm New argument 'nd' controls the number of dummy points. o as.fv Now handles objects of class kppm or minconfit. o rhohat If covariate = "x" or "y", the resulting object has the same 'unitname' as the original point pattern data. o rhohat Now has arguments 'eps, 'dimyx' to control pixel resolution. o MultiStrauss, MultiHard, MultiStraussHard Default value of 'types' has been changed to NULL. o data(ants) The auxiliary data 'ants.extra' now includes a function called 'side' determining whether a given location is in the scrub or field region. Can be used as a covariate in ppm, kppm, slrm. o print.ppm Now has argument 'what' to allow only selected information to be printed. BUG FIXES o profilepl Crashed in some cases involving multitype interactions. Fixed. o plot.splitppp Behaved incorrectly if 'main' was an expression. Fixed. o effectfun Crashed in trivial cases. Fixed. o kppm, thomas.estpcf, matclust.estpcf, lgcp.estpcf Gave a spurious warning message. Fixed. o step When applied to ppm objects this gave a spurious warning. Fixed. CHANGES IN spatstat VERSION 1.22-1 OVERVIEW o marked line segment patterns can now be plotted o multitype point process models are now 'self-starting' o new functions to manipulate colour images NEW FUNCTIONS o rgbim, hsvim Specify three colour channels. These functions convert three pixel images with numeric values into a single image whose pixel values are strings representing colours. o scaletointerval Generic utility function to rescale data (including spatial data) to a specified interval SIGNIFICANT USER-VISIBLE CHANGES o plot.im Can now plot images whose pixel values are strings representing colours. New argument 'valuesAreColours' o plot.psp Now handles marked line segment patterns and plots the marks as colours. o MultiHard, MultiStrauss, MultiStraussHard The argument 'types' can now be omitted; it will be inferred from the point pattern data. o rhohat Improved mathematical labels (when the result of rhohat is plotted) o plot.fv Minor improvements in graphics BUG FIXES o several minor bug fixes and improvements to satisfy R-devel CHANGES IN spatstat VERSION 1.22-0 OVERVIEW o support for point patterns on a linear network o 'superimpose' is now generic o improved mathematical labels when plotting functions NEW CLASSES o linnet An object of class 'linnet' represents a linear network, i.e. a connected network of line segments, such as a road network. Methods for this class include plot, print, summary etc. o lpp An object of class 'lpp' represents a point pattern on a linear network, such as a record of the locations of road accidents on a road network. Methods for this class include plot, print, summary etc. NEW FUNCTIONS o runiflpp Uniformly distributed random points on a linear network o rpoislpp Poisson point process on a linear network o clickjoin Interactive graphics to create a linear network o superimpose The function 'superimpose' is now generic, with methods for ppp, psp and a default method. o as.ppp.psp New method for as.ppp extracts the endpoints and marks from a line segment pattern NEW DATASETS o simplenet Simple example of a linear network SIGNIFICANT USER-VISIBLE CHANGES o superimposePSP This function is now deprecated in favour of 'superimpose' o superimpose Now handles data frames of marks. o plot.fv Argument 'legendmath' now defaults to TRUE. New argument 'legendargs' gives more control over appearance of legend. Increased default spacing between lines in legend. o eval.fv, with.fv Functions computed using eval.fv or with.fv now have better labels when plotted. o summary functions (Kest, Kest.fft, Kcross, Kdot, Kmulti, Kinhom, Kcross.inhom, Kdot.inhom, Kmulti.inhom, Lest, Lcross, Ldot, pcf, pcfcross, pcfdot, pcfinhom, pcfcross.inhom, pcfdot.inhom, Fest, Gest, Gcross, Gdot, Gmulti, Jest, Jcross, Jdot, Jmulti, Iest, localL, localK, markcorr, markvario, markconnect, Emark, Vmark, allstats, alltypes) Improved plot labels. BUG FIXES o superimpose If the marks components of patterns consisted of character vectors (rather than factors or non-factor numeric vectors) an error was triggered. Fixed. o plot.fv The y axis limits did not always cover the range of values if the argument 'shade' was used. Fixed. o plot.rhohat The y axis label was sometimes incorrect. Fixed. o plot.rhohat If argument 'xlim' was used, a warning was generated from 'rug'. Fixed. CHANGES IN spatstat VERSION 1.21-6 OVERVIEW o A line segment pattern can now have a data frame of marks. o Various minor extensions and alterations in behaviour NEW FUNCTIONS o nsegments Number of segments in a line segment pattern SIGNIFICANT USER-VISIBLE CHANGES o psp class A line segment pattern (object of class 'psp') can now have a data frame of marks. o density.ppp New argument 'adjust' makes it easy to adjust the smoothing bandwidth o plot.envelope If the upper envelope is NA but the lower envelope is finite, the upper limit is now treated as +Infinity o msr Argument 'continuous' renamed 'density' BUG FIXES o [.psp In X[W] if X is a line segment pattern and W is a polygonal window, marks were sometimes discarded, leading to an error. Fixed. o [.psp In X[W] if X is a line segment pattern and W is a rectangular window, if the marks of X were factor values, they were converted to integers. Fixed. o superimposePSP If the marks were a factor, they were mistakenly converted to integers. Fixed. o is.marked.ppp Did not generate a fatal error when na.action="fatal" as described in the help file. Fixed. CHANGES IN spatstat VERSION 1.21-5 OVERVIEW o Increased numerical stability. o New 'self-starting' feature of interpoint interactions. SIGNIFICANT USER-VISIBLE CHANGES o ppm Interaction objects may now be 'self-starting' i.e. initial parameter estimates can be computed from the point pattern dataset. So far, only the LennardJones() interaction has a self-starting feature. o LennardJones Increased numerical stability. New (optional) scaling argument 'sigma0'. Interpoint distances are automatically rescaled using 'self-starting' feature. o vcov.ppm New argument 'matrix.action' controls what happens when the matrix is ill-conditioned. Changed name of argument 'gamaction' to 'gam.action' o rmhmodel.ppm Default resolution of trend image has been increased. o is.poisson.ppm Accelerated. o ppm, kppm, qqplot.ppm Improved robustness to numerical error CHANGES IN spatstat VERSION 1.21-4 OVERVIEW o Urgent bug fix BUG FIXES o print.summary.ppm exited with an error message, if the model had external covariates. Fixed. CHANGES IN spatstat VERSION 1.21-3 OVERVIEW o Point process model covariates may now depend on additional parameters. o New class of signed measures, for residual analysis. o Miscellaneous improvements and bug fixes. NEW FUNCTIONS o clarkevans.test Classical Clark-Evans test of randomness o msr New class 'msr' of signed measures and vector-valued measures supporting residual analysis. o quadrat.test.quadratcount Method for 'quadrat.test' for objects of class 'quadratcount' (allows a chi-squared test to be performed on quadrat counts rather than recomputing from the original data) o tile.areas Computes areas of tiles in a tessellation (efficiently) SIGNIFICANT USER-VISIBLE CHANGES o ppm The spatial trend can now depend on additional parameters. This is done by allowing spatial covariate functions to have additional parameters: function(x, y, ...) where ... is controlled by the new argument 'covfunargs' to ppm o profilepl Can now maximise over trend parameters as well as interaction parameters o residuals.ppm The value returned by residuals.ppm is now an object of class 'msr'. It can be plotted directly. o eval.im When the argument 'envir' is used, eval.im() now recognises functions as well as variables in 'envir' o colourmap The argument 'col' can now be any kind of colour data o persp.im The 'colmap' argument can now be a 'colourmap' object o ppm The print and summary methods for 'ppm' objects now show standard errors for parameter estimates if the model is Poisson. o quadrat.test The print method for 'quadrattest' objects now displays information about the quadrats o lurking Improved format of x axis label o distmap.ppp Internal code is more robust. BUG FIXES o im Did not correctly handle 1 x 1 arrays. Fixed. o as.mask, pixellate.ppp Weird things happened if the argument 'eps' was set to a value greater than the size of the window. Fixed. CHANGES IN spatstat VERSION 1.21-2 OVERVIEW o New multitype hardcore interaction. o Nonparametric estimation of covariate effects on point patterns. o Output of 'Kmeasure' has been rescaled. o Numerous improvements and bug fixes. NEW FUNCTIONS o MultiHard multitype hard core interaction for use in ppm() o coords<- Assign new coordinates to the points in a point pattern o rhohat Kernel estimate for the effect of a spatial covariate on point process intensity SIGNIFICANT USER-VISIBLE CHANGES o as.ppp.matrix, as.ppp.data.frame These methods for 'as.ppp' now accept a matrix or data frame with any number of columns (>= 2) and interpret the additional columns as marks. o Kmeasure The interpretation of the output has changed: the pixel values are now density estimates. o rmh.ppm, rmhmodel.ppm These functions now accept a point process model fitted with the 'MultiHard' interaction o rmh.default, rmhmodel.default These functions now accept the option: cif='multihard' defining a multitype hard core interaction. o markcorr Now handles a data frame of marks o varblock Improved estimate in the case of the K function o colourmap, lut New argument 'range' makes it easier to specify a colour map or lookup table o [<-.hyperframe Now handles multiple columns o plot.fv Improved y axis labels o spatstat.options New option 'par.fv' controls default parameters for line plotting o rmhmodel More safety checks on parameter values. o quadratresample New argument 'verbose' o smooth.fv Default value of 'which' has been changed. BUG FIXES o Kest If the argument 'domain' was used, the resulting estimate was not correctly normalised. Fixed. o Kest The Lotwick-Silverman variance approximation was incorrectly calculated. (Spotted by Ian Dryden and Igor Chernayavsky). Fixed. o plot.owin, plot.ppp Display of binary masks was garbled if the window was empty or if it was equivalent to a rectangle. Fixed. o plot.bermantest One of the vertical lines for the Z1 test was in the wrong place. Fixed. o marks<-.ppx Crashed in some cases. Fixed. o is.convex An irrelevant warning was issued (for non-convex polygons). Fixed. CHANGES IN spatstat VERSION 1.21-1 OVERVIEW o Confidence intervals for K-function and other statistics o Bug fixes for smoothing and relative risk estimation NEW FUNCTIONS o varblock Variance estimation (and confidence intervals) for summary statistics such as Kest, using subdivision technique o bw.stoyan Bandwidth selection by Stoyan's rule of thumb. o which.max.im Applied to a list of images, this determines which image has the largest value at each pixel. o as.array.im Convert image to array SIGNIFICANT USER-VISIBLE CHANGES o smooth.ppp, markmean, sharpen.ppp, relrisk, bw.relrisk Further acceleration achieved. o Kest Argument 'correction' now explicitly overrides automatic defaults o plot.fv More robust handling of 'shade' BUG FIXES o relrisk Format of relrisk(at="points") was incorrect. Fixed. o bw.relrisk Result was incorrect in the default case method="likelihood" because of previous bug. Fixed. o Jdot, Jcross, Jmulti Return value did not include the hazard function, when correction="km" Fixed. o Jdot, Jcross, Jmulti Format of output was incompatible with format of Jest. Fixed. CHANGES IN spatstat VERSION 1.21-0 OVERVIEW o Implemented Spatial Logistic Regression o Implemented nonparametric estimation of relative risk with bandwidth selection by cross-validation. o Smoothing functions can handle a data frame of marks. o New options in Kinhom; default behaviour has changed. NEW FUNCTIONS o slrm Fit a spatial logistic regression model o anova.slrm, coef.slrm, fitted.slrm, logLik.slrm, plot.slrm, predict.slrm Methods for spatial logistic regression models o relrisk Nonparametric estimation of relative risk o bw.relrisk Automatic bandwidth selection by cross-validation o default.rmhcontrol Sets default values of Metropolis-Hastings parameters SIGNIFICANT USER-VISIBLE CHANGES o smooth.ppp, markmean These functions now accept a data frame of marks. o Kinhom Default behaviour has changed. New argument 'renormalise=TRUE' determines scaling of estimator and affects bias and variance in small samples. o residuals.ppm Now also computes the score residuals. o plot.im New argument 'ribscale' o plot.listof, plot.splitppp New arguments panel.begin, panel.end and panel.args o ppp Now checks for NA/NaN/Inf values in the coordinates o envelope.ppm Changed default value of 'control' New argument 'nrep' o qqplot.ppm Changed default value of 'control' BUG FIXES o marks<-.ppp, setmarks, %mark% A matrix of marks was accepted by ppp() but not by these assignment functions. Fixed. o density.ppp, smooth.ppp, sharpen.ppp, markmean Crashed if the bandwidth was extremely small. Fixed. CHANGES IN spatstat VERSION 1.20-5 OVERVIEW o Accelerated computations of kernel smoothing. o Implemented Choi-Hall data sharpening. NEW FUNCTIONS o sharpen.ppp Performs Choi-Hall data sharpening of a point pattern SIGNIFICANT USER-VISIBLE CHANGES o density.ppp, smooth.ppp Computation has been vastly accelerated for density(X, at="points") and smooth.ppp(X, at="points") o Kinhom Accelerated in case where lambda=NULL o Vignette 'shapefiles' updated CHANGES IN spatstat VERSION 1.20-4 OVERVIEW o New functions for inhomogeneous point patterns and local analysis. o Pair correlation function for 3D point patterns o Minor improvements and bug fixes to simulation code and image functions NEW FUNCTIONS o pcf3est Pair correlation function for 3D point patterns. o Kscaled, Lscaled Estimator of the template K function (and L-function) for a locally-scaled point process. o localpcf Local version of pair correlation function o identify.psp Method for 'identify' for line segment patterns. o as.im.matrix Converts a matrix to a pixel image SIGNIFICANT USER-VISIBLE CHANGES o rMaternI, rMaternII New argument 'stationary=TRUE' controls whether the simulated process is stationary (inside the simulation window). Default simulation behaviour has changed. o im New arguments 'xrange', 'yrange' o envelope Improvements to robustness of code. BUG FIXES o quadratcount If V was a tessellation created using a factor-valued image, quadratcount(X, tess=V) crashed with the error "Tessellation does not contain all the points of X". Fixed. o [.im If Z was a factor valued image and X was a point pattern then Z[X] was not a factor. Fixed. CHANGES IN spatstat VERSION 1.20-3 OVERVIEW o minor improvements (mostly internal). NEW FUNCTIONS o unmark.ppx Method for 'unmark' for general space-time point patterns SIGNIFICANT USER-VISIBLE CHANGES o plot.ppx Now handles marked patterns, in two-dimensional case o as.psp.psp Default value of argument 'check' set to FALSE CHANGES IN spatstat VERSION 1.20-2 OVERVIEW o Extensions to minimum contrast estimation. o Bug fix in simulation of Lennard-Jones model. o More support for distance functions. o Changes to point process simulations. NEW FUNCTIONS o thomas.estpcf Fit Thomas process model by minimum contrast using the pair correlation function (instead of the K-function). o matclust.estpcf Fit Matern Cluster model by minimum contrast using the pair correlation function (instead of the K-function). o lgcp.estpcf Fit log-Gaussian Cox process model by minimum contrast using the pair correlation function (instead of the K-function). o contour.distfun, persp.distfun Methods for 'contour' and 'persp' for distance functions o default.expand Computes default window for simulation of a fitted point process model. SIGNIFICANT USER-VISIBLE CHANGES o kppm Models can now be fitted using either the K-function or the pair correlation function. o ppm The list of covariates can now include windows (objects of class 'owin'). A window will be treated as a logical covariate that equals TRUE inside the window and FALSE outside it. o plot.distfun Pixel resolution can now be controlled. o envelope.ppm, qqplot.ppm The default value of 'control' has changed; simulation results may be slightly different. o rmh Slightly accelerated. BUG FIXES o rmh Simulation of the Lennard-Jones model (cif = 'lennard') was incorrect due to an obscure bug, introduced in spatstat 1.20-1. Fixed. o thomas.estK, matclust.estK, lgcp.estK The value of 'lambda' (if given) was ignored if X was a point pattern. Fixed. CHANGES IN spatstat VERSION 1.20-1 OVERVIEW o Further increases in speed and efficiency of ppm and rmh o New pairwise interaction model NEW FUNCTIONS o DiggleGatesStibbard Diggle-Gates-Stibbard pairwise interaction for use in ppm() SIGNIFICANT USER-VISIBLE CHANGES o ppm has been accelerated by a factor of 10 for the BadGey interaction. o rmh simulation of the Lennard-Jones model (cif='lennard') has been greatly accelerated. o rmh, rmhmodel.ppm Point process models fitted by ppm() using the DiggleGatesStibbard interaction can be simulated automatically using rmh. BUG FIXES o fitin The plot of a fitted Hardcore interaction was incorrect. Fixed. CHANGES IN spatstat VERSION 1.20-0 OVERVIEW o spatstat now contains over 1000 functions. o Substantial increase in speed and efficiency of model-fitting code. o Changes to factor-valued images. SIGNIFICANT USER-VISIBLE CHANGES o ppm has been accelerated by a factor of 10, and can handle datasets with 20,000 points, for the following interactions: DiggleGratton, Fiksel, Geyer, Hardcore, Strauss, StraussHard o predict.ppm accelerated by a factor of 3 (when type = "cif") with vastly reduced memory requirements for the following interactions: DiggleGratton, Fiksel, Geyer, Hardcore, Strauss, StraussHard o pixel images (class "im") The internal representation of factor-valued images has changed. Existing objects in the old format should still work. o im The syntax for creating a factor-valued image has changed. Argument 'lev' has been deleted. o ppm Some warnings have been reworded for greater clarity. BUG FIXES o [.im Mishandled some factor-valued images. Fixed. o hist.im Produced slightly erroneous output for some factor-valued images. Fixed. o plot.owin Filled polygons appeared to contain criss-cross lines on some graphics drivers. Fixed. o deltametric Did not handle windows with different enclosing frames (error message: 'dA and dB are incompatible') Fixed. o quadratcount Crashed if the pattern was empty and the window was a rectangle. (Noticed by Sandro Azaele) Fixed. o rNeymanScott Crashed if the parent process realisation was empty. (Noticed by Sandro Azaele) Fixed. CHANGES IN spatstat VERSION 1.19-3 ACKNOWLEDGEMENTS o We thank David Dereudre for contributions. OVERVIEW o Urgent bug fix to Metropolis-Hastings for Lennard-Jones model. o Miscellaneous additions to plotting and colour management. NEW FUNCTIONS o col2hex, rgb2hex, paletteindex, samecolour Functions for converting and comparing colours. o plot.envelope New method for plotting envelopes. By default the area between the upper and lower envelopes is shaded in grey. SIGNIFICANT USER-VISIBLE CHANGES o plot.fasp If the entries in the array are envelopes, they are plotted using plot.envelope (hence the envelope region is shaded grey). o plot.fv Now displays mathematical notation for each curve, if legendmath=TRUE. o print.fv Now prints the available range of 'r' values as well as the recommended range of 'r' values. BUG FIXES o rmh Simulation of Lennard-Jones model was incorrect; the simulations were effectively Poisson patterns. (Spotted by David Dereudre.) Fixed. o plot.fv Did not correctly handle formulas that included I( ) Fixed. CHANGES IN spatstat VERSION 1.19-2 ACKNOWLEDGEMENTS o We thank Jorge Mateu, Michael Sumner and Sebastian Luque for contributions. OVERVIEW o More support for fitted point process models and pixel images. o Improved plotting of pixel images and envelopes. o Simulation algorithm for Lennard-Jones process. o Improvements and bug fixes to envelopes. o Bug fixes to Metropolis-Hastings simulation. NEW FUNCTIONS o pairs.im Creates a scatterplot matrix for several pixel images. o model.frame.ppm Method for 'model.frame' for point process models. o sort.im Method for 'sort' for pixel images. SIGNIFICANT USER-VISIBLE CHANGES o plot.fv, plot.fasp New argument 'shade' enables confidence intervals or significance bands to be displayed as filled grey shading. o LennardJones The parametrisation of this interaction function has been changed. o rmh, rmhmodel These functions will now simulate a point process model that was fitted using the LennardJones() interaction. o rmh.default, rmhmodel.default These functions will now simulate a point process model with the Lennard-Jones interaction (cif='lennard'). o ecdf This function now works for pixel images. o dim, row, col These functions now work for pixel images. o order This function now works for pixel images. o [.im and [<-.im The subset index can now be any valid subset index for a matrix. o density.ppp, smooth.ppp The return value now has attributes 'sigma' and 'varcov' reporting the smoothing bandwidth. o plot.im The argument 'col' can now be a 'colourmap' object. This makes it possible to specify a fixed mapping between numbers and colours (e.g. so that it is consistent between plots of several different images). o rmh, spatstat.options spatstat.options now recognises the parameter 'expand' which determines the default window expansion factor in rmh. o rmh Improved handling of ppm objects with covariates. o kstest The 'covariate' can now be one of the characters "x" or "y" indicating the Cartesian coordinates. BUG FIXES o model.matrix.ppm For a fitted model that used a large number of quadrature points, model.matrix.ppm sometimes reported an internal error about mismatch between the model matrix and the quadrature scheme. Fixed. o plot.ppx Minor bugs fixed. o rmh In rare cases, the simulated point pattern included multiple points at the origin (0,0). (Bug introduced in spatstat 1.17-0.) Fixed. o rmh, rmhmodel.ppm Crashed when applied to a fitted multitype point process model if the model involved more than one covariate image. (Spotted by Jorge Mateu) Fixed. o density.psp If any segment had zero length, the result contained NaN values. (Spotted by Michael Sumner and Sebastian Luque.) Fixed. o envelope Crashed with fun=Lest or fun=Linhom if the number of points in a simulated pattern exceeded 3000. Fixed. o plot.kstest Main title was corrupted if the covariate was a function. Fixed. CHANGES IN spatstat VERSION 1.19-1 OVERVIEW o New dataset: replicated 3D point patterns. o Improvements to Metropolis-Hastings simulation code. o More support for hyperframes. o Bug fixes. NEW DATASETS o osteo: Osteocyte Lacunae data: replicated 3D point patterns NEW FUNCTIONS o rbind.hyperframe: Method for rbind for hyperframes. o as.data.frame.hyperframe: Converts a hyperframe to a data frame. SIGNIFICANT USER-VISIBLE CHANGES o Fiksel: Fitted point process models (class ppm) with the Fiksel() double exponential interaction can now be simulated by rmh. o rmh.default: Point processes with the Fiksel interaction can now be simulated by specifying parameters in rmh.default. o logLik.ppm: New argument 'warn' controls warnings. o profilepl: No longer issues spurious warnings. BUG FIXES o Hardcore, rmh: Simulation of the 'Hardcore' process was incorrect. The hard core radius was erroneously set to zero so that the simulated patterns were Poisson. Fixed. o fitin: A plot of the pairwise interaction function of a fitted model, generated by plot(fitin(model)) where model <- ppm(...), was sometimes incorrect when the model included a hard core. Fixed. CHANGES IN spatstat VERSION 1.19-0 OVERVIEW o Numerous bugs fixed in the implementation of the Huang-Ogata approximate maximum likelihood method. o New interpoint interaction model. NEW FUNCTIONS o Fiksel: new interpoint interaction: Fiksel's double exponential model. SIGNIFICANT USER-VISIBLE CHANGES o runifpoint, rpoispp, envelope These functions now issue a warning if the number of random points to be generated is very large. This traps a common error in simulation experiments. BUG FIXES o predict.ppm, fitted.ppm: Predictions and fitted values were incorrect for objects fitted using ppm(..., method="ho"). Fixed. o logLik, AIC: Values of logLik() and AIC() were incorrect for objects fitted using ppm(..., method="ho"). Fixed. o profilepl: Results were incorrect if the argument 'method="ho"' was used. Fixed. o fitin The result of fitin() was incorrect for objects fitted using ppm(..., method="ho"). Fixed. o rmhcontrol: rmhcontrol(NULL) generated an error. Fixed. CHANGES IN spatstat VERSION 1.18-4 ACKNOWLEDGEMENTS o We thank Michael Sumner for contributions. BUG FIXES o pixellate.psp: segments shorter than one pixel width were measured incorrectly if the 'weights' argument was present. Fixed. NEW FUNCTIONS o pairdist.ppx, crossdist.ppx, nndist.ppx, nnwhich.ppx: Methods for pairdist, crossdist, nndist, nnwhich for multidimensional point patterns (class 'ppx') o runifpointx, rpoisppx: Random point patterns in any number of dimensions o boxx: Multidimensional box in any number of dimensions o diameter.boxx, volume.boxx, shortside.boxx, eroded.volumes.boxx: Geometrical computations for multidimensional boxes o sum.im, max.im, min.im: Methods for sum(), min(), max() for pixel images. o as.matrix.ppx: Convert a multidimensional point pattern to a matrix SIGNIFICANT USER-VISIBLE CHANGES o plot.ppp: New argument 'zap' o diameter: This function is now generic, with methods for "owin", "box3" and "boxx" o eroded.volumes: This function is now generic, with methods for "box3" and "boxx" CHANGES IN spatstat VERSION 1.18-3 ACKNOWLEDGEMENTS o We thank Michael Sumner for contributions. BUG FIXES o pixellate.psp: segments shorter than one pixel width were measured incorrectly. Fixed. o fv: 'alim' not handled correctly. Fixed. NEW FUNCTIONS o smooth.fv: Applies spline smoothing to the columns of an fv object. CHANGES IN spatstat VERSION 1.18-2 ACKNOWLEDGEMENTS o We thank Michael Sumner for contributions. NEW FUNCTIONS o Gfox, Jfox: Foxall's G and J functions o as.owin.distfun: New method for as.owin extracts the domain of a distfun object. SIGNIFICANT USER-VISIBLE CHANGES o distfun: objects of class 'distfun', when called as functions, will now accept either two vectors (x,y) or a point pattern x. o Hest: this function can now compute the Hanisch estimator. It now has arguments 'r', 'breaks' and 'correction', like other summary functions. o Hest: new argument 'conditional'. BUG FIXES o pixellate.psp: Values were sometimes incorrect due to coding error. (Spotted by Michael Sumner) Fixed. o kstest: Crashed if the covariate contained NA's. Fixed. o kstest: Crashed if X was a multitype point pattern in which some mark values were unrepresented. Fixed. o lurking: Minor bug in handling of NA values. Fixed. o Hest: labels of columns were incorrect. Fixed. CHANGES IN spatstat VERSION 1.18-1 ACKNOWLEDGEMENTS o we thank Andrew Bevan and Ege Rubak for suggestions. NEW FUNCTIONS o Hardcore: Hard core interaction (for use in ppm) o envelope.pp3: simulation envelopes for 3D point patterns o npoints: number of points in a point pattern of any kind SIGNIFICANT USER-VISIBLE CHANGES o rmh.ppm, rmhmodel.ppm: It is now possible to simulate Gibbs point process models that are fitted to multitype point patterns using a non-multitype interaction, e.g. data(amacrine) fit <- ppm(amacrine, ~marks, Strauss(0.1)) rmh(fit, ...) o rmh.ppm, rmhmodel.ppm, rmh.default, rmhmodel.default: Hard core models can be simulated. o rmh.default, rmhmodel.default: The argument 'par' is now required to be a list, in all cases (previously it was sometimes a list and sometimes a vector). o Fest: Calculation has been accelerated in some cases. o summary.pp3 now returns an object of class 'summary.pp3' containing useful summary information. It is plotted by 'plot.summary.pp3'. o F3est, G3est, K3est: these functions now accept 'correction="best"' o union.owin, intersect.owin: these functions now handle any number of windows. o envelope.ppp, envelope.ppm, envelope.kppm: argument lists have changed slightly BUG FIXES o Fest: The result of Fest(X, correction="rs") had a slightly corrupted format, so that envelope(X, Fest, correction="rs") in fact computed the envelopes based on the "km" correction. (Spotted by Ege Rubak). Fixed. o rmh (rmh.ppm, rmhmodel.ppm): rmh sometimes failed for non-stationary point process models, with a message about "missing value where TRUE/FALSE needed". (Spotted by Andrew Bevan). Fixed. o diagnose.ppm, lurking: Calculations were not always correct if the model had conditional intensity equal to zero at some locations. Fixed. o ppm, profilepl: If data points are illegal under the model (i.e. if any data points have conditional intensity equal to zero) the log pseudolikelihood should be -Inf but was sometimes returned as a finite value. Thus profilepl did not always work correctly for models with a hard core. Fixed. o F3est, G3est: Debug messages were printed unnecessarily. Fixed. CHANGES IN spatstat VERSION 1.18-0 ACKNOWLEDGEMENTS o we thank Ege Rubak and Tyler Dean Rudolph for suggestions. HEADLINES o A point pattern is now allowed to have a data frame of marks (previously the marks had to be a vector). o Extended capabilities for 'envelope' and 'kstest'. NEW FUNCTIONS o pixellate.psp, as.mask.psp Convert a line segment pattern to a pixel image or binary mask o as.data.frame.im Convert a pixel image to a data frame SIGNIFICANT USER-VISIBLE CHANGES o A point pattern is now allowed to have a data frame of marks (previously the marks had to be a vector). o Many functions in spatstat now handle point patterns with a data frame of marks. These include print.ppp, summary.ppp, plot.ppp, split.ppp. o finpines, nbfires, shapley: The format of these datasets has changed. They are now point patterns with a data frame of marks. o envelope() is now generic, with methods for "ppp", "ppm" and "kppm". o kstest() now handles multitype point patterns and multitype point process models. o nnclean() now returns a point pattern with a data frame of marks. o plot.ppp() has new argument 'which.marks' to select one column from a data frame of marks to be plotted. o plot.ppp() now handles marks that are POSIX times. o complement.owin now handles any object acceptable to as.owin. BUG FIXES o erosion(w) and opening(w) crashed if w was not a window. Fixed. o diameter() and eroded.areas() refused to work if w was not a window. Fixed. CHANGES IN spatstat VERSION 1.17-6 ACKNOWLEDGEMENTS o We thank Simon Byers and Adrian Raftery for generous contributions. OVERVIEW o Nearest neighbour clutter removal algorithm o New documentation for the 'fv' class. o Minor improvements and bug fixes. NEW FUNCTIONS o nnclean: Nearest neighbour clutter removal for recognising features in spatial point patterns. Technique of Byers and Raftery (1998) [From original code by Simon Byers and Adrian Raftery, adapted for spatstat.] o marks.ppx, marks<-.ppx: Methods for extracting and changing marks in a multidimensional point pattern o latest.news: print news about the current version of the package SIGNIFICANT USER-VISIBLE CHANGES o news: spatstat now has a NEWS file which can be printed by typing news(package="spatstat"). o areaGain, areaLoss: New algorithms in case exact=TRUE. Syntax slightly modified. o with.hyperframe: - The result now inherits 'names' from the row names of the hyperframe. - New argument 'enclos' controls the environment in which the expression is evaluated. - The algorithm is now smarter at simplifying the result when simplify=TRUE. o update.ppm: Tweaked to improve the ability of ppm objects to be re-fitted in different contexts. ADVANCED USERS ONLY o Documentation for the class 'fv' of function value tables - fv: Creates an object of class 'fv' - cbind.fv, collapse.fv: Combine objects of class 'fv' - bind.fv: Add additional columns of data to an 'fv' object BUG FIXES o "$<-.hyperframe" destroyed the row names of the hyperframe. Fixed. o model.matrix.ppm had minor inconsistencies. Fixed. o ppm: The fitted coefficient vector had incorrect format in the default case of a uniform Poisson process. Fixed. o plot.ppx: Crashed if the argument 'main' was given. Fixed. o envelope.ppp: Crashed if the object returned by 'fun' did not include a column called "theo". Fixed.