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 BUGS 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. BUGS 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. BUGS 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' BUGS 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' BUGS 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. BUGS 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. BUGS 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. BUGS 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.