NEWS

---

spatstat.explore 3.3-2.001

OVERVIEW

• Tweaks to bandwidth selection.

SIGNIFICANT USER-VISIBLE CHANGES

• bw.ppl Argument 'shortcut' now defaults to TRUE.

spatstat.explore 3.3-2 (2024-08-21)

OVERVIEW

• Tweaks to documentation.
• Internal repairs.
• Internal changes to satisfy package checker.

spatstat.explore 3.3-1 (2024-07-15)

OVERVIEW

• Internal changes to satisfy package checker.

spatstat.explore 3.3-0

OVERVIEW

• 'spatstat.explore' now depends on package 'spatstat.univar'.
• Some functions have been moved to 'spatstat.univar'.
• Minor improvements.

PACKAGE DEPENDENCE

• spatstat.explore now depends on the new package 'spatstat.univar'
• Some functions have been moved from 'spatstat.explore' to 'spatstat.univar'.

SIGNIFICANT USER-VISIBLE CHANGES

• cbind.fv, bind.fv Additional arguments may be functions in the R language.

DELETED FUNCTIONS

• bw.abram The generic 'bw.abram' has been moved to the new package 'spatstat.univar'.
• CDF, CDF.density The generic 'CDF' and method 'CDF.density' have been moved to the new package 'spatstat.univar'.
• densityAdaptiveKernel The generic 'densityAdaptiveKernel' has been moved to the new package 'spatstat.univar'.
• dkernel, pkernel, qkernel, rkernel These functions have been moved to the new package 'spatstat.univar'.
• kernel.factor, kernel.moment, kernel.squint These functions have been moved to the new package 'spatstat.univar'.
• kaplan.meier, reduced.sample, km.rs These functions have been moved to the new package 'spatstat.univar'.
• quantile.density This method has been moved to the new package 'spatstat.univar'.
• stieltjes This function has been moved to the new package 'spatstat.univar'.

spatstat.explore 3.2-7 (2024-03-21)

OVERVIEW

• Bug fixes.
• Internal improvements.

BUG FIXES

• SpatialMedian.ppp, SpatialQuantile.ppp Argument ‘sigma’ was ignored in some calculations. Fixed.

spatstat.explore 3.2-6 (2024-02-01)

OVERVIEW

• We thank Mohomed Abraj, Marcelino de la Cruz and Stephanie Hogg for contributions.
• Spatially weighted median and quantile of mark values.
• Adaptive estimation of intensity for split point patterns.
• Anisotropic bandwidth selection
• Boyce index.
• Internal improvements.
• Bug fixes.

NEW FUNCTIONS

• SpatialMedian.ppp, SpatialQuantile.ppp Spatially weighted median and quantile of mark values of a point pattern.
• boyce Boyce index and continuous Boyce index.
• densityAdaptiveKernel.splitppp A method for 'densityAdaptiveKernel' for split point patterns.

SIGNIFICANT USER-VISIBLE CHANGES

• bw.ppl New argument ‘varcov1’ for anisotropic bandwidth selection.
• bw.smoothppp New argument ‘varcov1’ for anisotropic bandwidth selection.

BUG FIXES

• studpermu.test The code required each group to consist of at least 3 point patterns, rather than 2 point patterns (as stated in the documentation). Fixed.
• Jest Ignored pixel resolution argument 'eps'. Fixed.
• scanLRTS Pixel resolution arguments 'dimyx', 'eps', 'xy' were not correctly handled. Fixed.

spatstat.explore 3.2-5 (2023-10-22)

OVERVIEW

• Minor corrections in documentation.

spatstat.explore 3.2-4

OVERVIEW

• Integration of functions.
• Changed defaults for Clark-Evans Test.
• spatstat.explore no longer suggests package 'maptools'.
• Minor improvements and bug fixes.

NEW FUNCTIONS

• integral.fv Compute the integral of a function.

SIGNIFICANT USER-VISIBLE CHANGES

• density.ppp New argument 'sameas'.
• clarkevans.test The asymptotic test is now available for any choice of edge correction.
• clarkevans.test New argument 'method' determines whether to use the asymptotic test or Monte Carlo test. The default has changed to method='asymptotic'.
• clarkevans.test Default edge correction has changed, to avoid bias.

BUG FIXES

• kernel.squint The return value was incorrect if the argument 'bw' was given. Fixed.
• pcf The variance approximation was calculated incorrectly (due to the bug in kernel.squint). Fixed.
• quantile.density Crashed if 'probs' contained NA values and 'names=FALSE'. Fixed.
• bw.smoothppp Crashed if every point in 'X' was duplicated. Fixed.

spatstat.explore 3.2-3 (2023-09-07)

OVERVIEW

• Improvements to envelope methods.
• Suppress warning messages from density.default.
• Minor improvements and bug fixes.

NEW FUNCTIONS

• compileCDF Low level utility for calculating cumulative distribution function of distance variable.

SIGNIFICANT USER-VISIBLE CHANGES

• circdensity Improved output of 'print' method
• envelope All methods for ‘envelope’ now accept a summary function in which the function argument is not named 'r'. This includes functions such as ‘transect.im’ and ‘roc’.
• plot.bermantest Improved layout for plots of Berman's Z2 test.
• plot.fv New argument 'clip.xlim'.
• circdensity Suppress annoying warning messages from density.default.
• compileK, compilepcf Suppress annoying warning messages from density.default.
• rhohat Suppress annoying warning messages from density.default.

BUG FIXES

• envelope methods Results were malformed if the name of the function argument was not "r". Fixed.

spatstat.explore 3.2-1 (2023-05-13)

OVERVIEW

• Internal bug fixes.

spatstat.explore 3.2-0

OVERVIEW

• We thank Jonatan Gonzalez for contributions.
• Changed the calculation of standard errors in density.ppp and relrisk.ppp.
• Inline arithmetic for function tables ('fv') and arrays ('fasp')
• Standard error calculation for Smooth.ppp (experimental)
• multitype pair correlation functions can save numerator and denominator.
• multitype inhomogeneous J functions.
• More support for automatic bandwidth selection.
• Bug fixes in calculation of standard errors.

NEW FUNCTIONS

• Math.fv, Complex.fv, Summary.fv, Ops.fv Methods for arithmetic operations for function tables (class 'fv')
• Math.fasp, Complex.fasp, Summary.fasp, Ops.fasp Methods for arithmetic operations for function arrays (class 'fasp')
• Gcross.inhom, Gdot.inhom Multitype G functions for inhomogeneous point processes.
• Jcross.inhom, Jdot.inhom, Jmulti.inhom Multitype J functions for inhomogeneous point processes.
• summary.bw.optim, print.summary.bw.optim Method for 'summary' of optimised bandwidth objects (class 'bw.optim'). These are the objects produced by the bandwidth selection functions such as bw.diggle, bw.scott, bw.pcf

SIGNIFICANT USER-VISIBLE CHANGES

• density.ppp Standard error calculation is now available with any smoothing kernel.
• density.ppp The interpretation of 'weights' in the calculation of standard error has changed. New argument 'wtype' controls this interpretation.
• relrisk.ppp The interpretation of 'weights' in the calculation of standard error has changed. New argument 'wtype' controls this interpretation.
• relrisk.ppp New argument 'fudge' specifies a constant numeric value that will be added to each estimate of point process intensity before calculation of relative risk.
• Smooth.ppp Standard error calculation is now supported (Experimental).
• pcfcross, pcfdot, pcfmulti New argument 'ratio' makes it possible to save the numerator and denominator of the function estimates, so that estimates can be pooled.
• bw.relrisk.ppp Additional arguments '...' are now passed to 'density.ppp'.
• eval.fasp Automatically-generated labels have been improved.
• relrisk.ppp Issues a warning if numerical underflow is detected.
• rhohat.ppp, rhohat.quad New argument 'rule.eps' passed to 'as.mask'.

BUG FIXES

• density.ppp Calculation of standard error was slightly incorrect if edge=TRUE. Fixed.
• relrisk.ppp Calculation of standard error was incorrect for non-Gaussian kernels. Fixed.

spatstat.explore 3.1-0 (2023-03-14)

OVERVIEW

• Pair correlation functions allow more control over smoothing parameters.
• Improved support for one-dimensional smoothing kernels.
• Bug fixes in plot.fv.
• Internal improvements and bug fixes.

SIGNIFICANT USER-VISIBLE CHANGES

• kernel.moment New arguments 'mean' and 'sd'. Computation accelerated for kernel='cosine' or 'optcosine'. All cases are now computed using analytic expressions, for m <= 2.
• bw.abram This function is now generic, with a method for class 'ppp'.
• pcfinhom, pcfdot.inhom, pcfcross.inhom New arguments 'adjust.sigma' and 'adjust.bw' allow separate adjustment of the one-dimensional smoothing bandwidth 'bw' and the spatial smoothing bandwidth 'sigma'.

BUG FIXES

• plot.fv When the argument 'log' was given, the plotted curves were incorrectly clipped, or were missing altogether. Fixed.
• plot.fv If 'add=TRUE', and if the existing plot was created using logarithmic axes, the logarithmic scale was ignored. Fixed.
• plot.fv Sometimes gave an obscure warning about 'rebound.owin', when 'xlim' or 'ylim' was given. Fixed.

spatstat.explore 3.0-6 (2023-01-26)

OVERVIEW

• Internal improvements and bug fixes.

spatstat.explore 3.0-5 (2022-11-10)

OVERVIEW

• Bug fix in pcf.
• We thank Maximilian Hesselbarth for contributions.

BUG FIXES

• pcf.ppp Estimates were incorrectly scaled (they were incorrectly multiplied by the area of the window.) Spotted by Maximilian Hesselbarth. Bug introduced in spatstat.explore 3.0-0. Fixed.

spatstat.explore 3.0-4

OVERVIEW

• Bug fix in Kest in a very special case.
• We thank 'Marjolein9' for contributions.

BUG FIXES

• Kest Isotropic edge correction weight was computed incorrectly for a data point lying exactly on a corner of a rectangular window. Spotted by GitHub contributor 'Marjolein9'. Fixed.

spatstat.explore 3.0-3 (2022-11-04)

OVERVIEW

• Tweaks to placate package checker.

spatstat.explore 3.0-2

OVERVIEW

• Tweaks to placate package checker.

spatstat.explore 3.0-1

OVERVIEW

• Tweaks to placate package checker.

spatstat.explore 3.0-0

OVERVIEW

• New package
• We thank Marie-Colette van Lieshout and Daniel Manrique-Castano for contributions.
• Periodic edge correction for K function.
• Changed denominator in K function and pair correlation function.
• Bandwidth selection for adaptive kernel estimation of intensity.
• U-shaped curves in 'rhohat'.
• Radial cumulative integral of an image.
• Minor improvements.

NEW FUNCTIONS

• bw.CvL.adaptive Bandwidth selection for adaptive kernel estimation of intensity.
• radcumint Radial cumulative integral of an image.

SIGNIFICANT USER-VISIBLE CHANGES

• 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).
• spatstat.explore The new package 'spatstat.explore' contains the code for exploratory data analysis and nonparametric analysis of spatial data. Examples include 'density.ppp', 'Kest', 'envelope', 'rhohat', 'clarkevans.test'.
• NEWS The NEWS file for the new package 'spatstat.explore' contains older news items from the defunct package 'spatstat.core' (for functions which are now in 'spatstat.explore').
• Kest, Kdot, Kcross, Ldot, Lcross, Kmulti These functions now accept the option 'correction="periodic"' to compute the periodic (toroidal) edge correction estimate.
• Kest, pcf, Ksector, Kdot, Kcross, Kmulti When ratio=TRUE, the denominator is now equal to the number of pairs of points considered. This does not affect the estimate of the summary function, but it changes the calculation of pooled estimates when the estimates were obtained from different sized windows.
• markcorr, markcrosscorr These functions now allow negative mark values when normalise=FALSE.
• marktable This function now works for point patterns in three dimensions (class 'pp3') and point patterns on a network (class 'lpp').
• bw.relrisk This function is now generic, with a method for class 'ppp'
• compileK, compilepcf These functions have a new argument 'samplesize'. If 'ratio=TRUE' the numerator and denominator will be rescaled by a common factor so that the denominator is equal to 'samplesize'.
• adaptive.density Now accepts 'method="nearest"' and passes the data to 'nndensity'.
• rhohat.ppp New options 'smoother="mountain"' and 'smoother="valley"' for estimating a unimodal function (U-shaped curve).
• rhohat.ppp If the covariate is a 'distfun', the name of the unit of length is saved and displayed on the plot.
• rhohat.ppp New arguments 'jitter', 'jitterfactor', 'interpolate' allow greater control over the calculation.
• rhohat.ppp New argument 'do.CI' specifies whether to calculate confidence bands.

spatstat.explore 2.4-4.010

OVERVIEW

• Internal improvements.

spatstat.explore 2.4-4

OVERVIEW

• Bug fixes and minor improvements.

BUG FIXES

• rhohat.ppp The argument 'subset' was not handled correctly in the internal data. The estimated function 'rho' was correct, but if 'predict.rhohat' was applied, predictions were computed only in the 'subset', and were possibly incorrect values. Fixed.
• Gfox, Jfox Warnings were issued about text formatting errors (mentioning 'sprintf' or 'fmt'). Fixed.

spatstat.explore 2.4-3

OVERVIEW

• We thank Art Stock for contributions.
• Bug fixes and minor improvements.

BUG FIXES

• Smooth.ppp Crashed when 'kernel' was a function, 'at="points"' and 'scalekernel=FALSE'. Fixed.
• Finhom, Ginhom, Jinhom Crashed when ratio=TRUE. [Spotted by Art Stock.] Fixed.
• envelope Crashed for some of the summary functions when ratio=TRUE. [Spotted by Art Stock.] Fixed.
• "[.rat" Crashed in some cases. Fixed.
• Kcross The result of Kcross() was 'invisible', i.e. it was not automatically printed. Fixed.

spatstat.explore 2.4-2

OVERVIEW

• Internal bug fixes.

spatstat.explore 2.4-1

OVERVIEW

• We thank Frederic Lavancier, Sebastian Meyer, Suman Rakshit and Sven Wagner for contributions.
• Improved approximation of intensity of Gibbs models.
• Experimental code to represent (theoretical) point process models
• Extract more information about a point process model.
• Internal improvements and bug fixes.

SIGNIFICANT USER-VISIBLE CHANGES

• relrisk.ppp Ratios which are close to 0/0 are handled more effectively, reducing the likelihood of strange-looking plots when 'sigma' is very small.

BUG FIXES

• density.ppp Crashed if the observation window had zero area. Fixed.
• dirichletVoronoi.ppp Crashed randomly, with obscure error messages from 'im' or 'eval.im', when argument 'f' had a small value. [Spotted by Suman Rakshit.] Fixed.
• dirichletVoronoi.ppp Rarely, produced an image containing NA values. [Spotted by Suman Rakshit.] Fixed.
• vcov.ppm Crashed in some cases, with message 'object lamdel not found'. [Spotted by Sven Wagner.] Fixed.

spatstat.explore 2.4-0

OVERVIEW

• We thank Sriram Ramamurthy for contributions.
• spatstat.core now depends on the new package 'spatstat.random'.
• Functions for generating random patterns have been removed.
• Minor improvements and bug fixes

SIGNIFICANT USER-VISIBLE CHANGES

• package structure The code for generating random spatial patterns (including 'rpoispp', 'rMatClust', 'rThomas', 'rNeymanScott', 'rStrauss', 'rmh') has been removed from 'spatstat.core' and placed in a new package 'spatstat.random'. This new package is required by 'spatstat.core'.
• reload.or.compute New argument 'context'

BUG FIXES

• reload.or.compute Scoping error (crashed sometimes if called from a non-global environment). Fixed.

spatstat.explore 2.3-2

OVERVIEW

• Minor improvements and bug fixes.
• We thank Jonas Brehmer for contributions.

SIGNIFICANT USER-VISIBLE CHANGES

• pcf Improved error message

BUG FIXES

• edge.Ripley Results were incorrect for data points lying exactly at the corners of a rectangle. Fixed.

spatstat.explore 2.3-1

OVERVIEW

• Covariates in ppm and mppm may be functions that depend on the marks as well as the spatial coordinates.
• Automatic selection of threshold for defining a binary predictor.
• Random perturbation of line segments.
• Minor extensions, performance improvements, and bug fixes.

NEW FUNCTIONS

• thresholdSelect, thresholdCI Select the optimal threshold for converting a numerical predictor to a binary predictor.
• coef<-.fii Changes the coefficients of a fitted interaction object (a method for the generic "coef<-")

SIGNIFICANT USER-VISIBLE CHANGES

• distcdf Improved regularisation algorithm. Argument 'nr=NULL' is now accepted. New argument 'delta' allows the result to be interpolated onto a finer grid.
• collapse.fv Columns identified by the arguments 'same' and 'different' may now be absent from some of the 'fv' objects that will be collapsed.
• Kest When the argument 'domain' is given, the calculation of estimates of K(r) has changed slightly, to adhere more closely to the description in the help file.
• reload.or.compute Now prints a message indicating whether the data were recomputed or reloaded from file. New argument 'verbose'.
• pool.envelope Now uses the value of 'nrank' which was used in the original envelopes.
• Kmulti New argument 'rmax'.
• Kinhom No longer issues a warning about changed behaviour in the case where 'lambda' is a fitted model.
• pcfinhom No longer issues a warning about changed behaviour in the case where 'lambda' is a fitted model.

BUG FIXES

• segregation.test The test statistic was calculated as the mean, rather than the sum, of discrepancies between probabilities. (The p-value was not affected.) Fixed.
• Kest If 'domain' was specified, 'rmax' was ignored. Fixed.
• edge.Ripley Value was incorrect for a point lying exactly on a corner. Fixed.
• edge.Ripley Crashed when method="interpreted", if a point lay exactly on a corner. Fixed.
• plot.fv, plot.envelope Crashed when trying to display a significance band of width zero around a constant function. Fixed.
• collapse.fv Crashed if 'length(same) > 1'. Fixed.

spatstat.explore 2.3-0

OVERVIEW

• Transect of an image along a curve.
• Image cross-correlation and cross-covariance.
• Minor bug fixes.

NEW FUNCTIONS

• cov.im, cor.im Correlation or covariance between several pixel images.

SIGNIFICANT USER-VISIBLE CHANGES

• transect.im New argument 'curve' allows the user to specify a curved transect.

BUG FIXES

• rhohat The rug plot (produced by plot.rhohat) was incorrect when rhohat was called with method="piecewise". Fixed.
• markcrosscorr Did not recognise the option 'correction="none"'. Fixed.
• roc.ppp The default plot of the result of roc.ppp did not include the diagonal line 'y=x'. Fixed.

spatstat.explore 2.2-0

OVERVIEW

• We thank Abdollah Jalilian, Yongtao Guan and Rasmus Waagepetersen for contributions.
• estimation of the spatial covariance function of a pixel image
• simulation of the product shot noise Cox process.
• extensions to rhohat

NEW FUNCTIONS

• rPSNCP Generate simulated realisations of the product shot noise Cox process. Contributed by Abdollah Jalilian, Yongtao Guan and Rasmus Waagepetersen.
• spatcov Estimate the spatial covariance function of a pixel image.
• pairMean Compute the mean of a specified function of interpoint distance between random points in a window.

SIGNIFICANT USER-VISIBLE CHANGES

• rhohat New option (smoother='piecewise') computes a piecewise-constant estimate of rho(z).
• rhohat The result now includes the 'average' intensity rho.
• distcdf Arguments which are NULL will be treated as missing.
• distcdf New argument 'savedenom'.

spatstat.explore 2.1-2

OVERVIEW

• Reduced CRAN check time.

spatstat.explore 2.1-1

OVERVIEW

• Minor bug fix

spatstat.explore 2.1-0

OVERVIEW

• densityfun.ppp handles query points outside original window
• Minor improvements and bug fixes.

SIGNIFICANT USER-VISIBLE CHANGES

• densityfun.ppp The resulting function can now handle query points which lie outside the window of the original data, and has argument 'drop=TRUE' which specifies how to handle them.
• rpoint New argument 'forcewin' forces the code to use the window 'win' when 'f' is a pixel image.

BUG FIXES

• cdf.test Crashed if the covariate was constant. Fixed.

spatstat.explore 2.0-0

OVERVIEW

• We thank Tilman Davies, Greg McSwiggan and Suman Rakshit for contributions.
• 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.
• Diffusion kernel smoothing.
• More support for spatial logistic regression models.
• predict.mppm now works for multitype point process models.
• Improved handling of 'newdata' in predict.mppm.
• More support for multi-dimensional patterns.

NEW FUNCTIONS

• densityHeat New generic function for diffusion kernel estimation of intensity
• densityHeat.ppp Diffusion kernel estimation of intensity for point pattern in 2 dimensions. This is an alternative to density.ppp.
• intersect.boxx Compute intersection of boxes in multi-dimensional space
• scale.boxx, scale.ppx Methods for 'scale' for boxes and patterns in multi-dimensional space
• shift.boxx, shift.ppx Methods for 'shift' for boxes and patterns in multi-dimensional space
• is.boxx Determine whether an object is a multidimensional box

SIGNIFICANT USER-VISIBLE CHANGES

• rotmean The result now has the same 'unitname' as the input object X. New argument 'adjust' controls the smoothing bandwidth.
• rlabel New argument 'group' specifies that the points are divided into several groups, and that relabelling is applied within each group.
• Kcross, Gcross, Jcross Function labels (shown on the plot legend) have been improved when i = j.
• anova.mppm Issues a warning when applied to random-effects models (models fitted using the argument 'random').

BUG FIXES

• Gest If correction="rs" or correction="km", then both the reduced-sample (border correction) and Kaplan-Meier corrected estimates were calculated. [Spotted by Gopalan Nair.] Fixed.
• simulate.rhohat Crashed when applied to rhohat objects computed from data on a linear network. Fixed.

spatstat.explore 1.65-11

OVERVIEW

• Internal tweaks.

spatstat.explore 1.65-10

OVERVIEW

• Minor corrections to documentation.

spatstat.explore 1.65-9

OVERVIEW

• We thank Ian Buller for a suggestion.
• weights permitted in density calculation for line segments.

SIGNIFICANT USER-VISIBLE CHANGES

• density.psp New argument 'weights'.

spatstat.explore 1.65-8

OVERVIEW

• Minor changes to appease the compiler.

spatstat.explore 1.65-7

OVERVIEW

• We thank Michael Chirico for a contribution.
• Minor changes to appease the compiler.

spatstat.explore 1.65-6

OVERVIEW

• We thank Tilman Davies and Pavel Fibich for contributions.
• Increased speed for large datasets.

SIGNIFICANT USER-VISIBLE CHANGES

• rSSI Accelerated.
• overall speed Changes have been made to the internal code of spatstat which should accelerate computations involving large datasets.
• localpcf, localpcfinhom New argument 'rvalue'.

BUG FIXES

• rLGCP Simulation results for log-Gaussian Cox processes were incorrect unless the pixel dimensions and pixel spacings were identical on the horizontal and vertical axes. (If pixel dimensions were not specified, then the results were incorrect whenever the Frame of the simulation window was not a square.) [Spotted by Tilman Davies.] Fixed.
• Vmark Crashed if normalise=TRUE when there was only one column of marks. (Spotted by Pavel Fibich.) Fixed.
• nnclean Crashed if k >= npoints(X). Fixed.

spatstat.explore 1.65-5

OVERVIEW

• Minor changes required by CRAN.

spatstat.explore 1.65-1

OVERVIEW

• Added NEWS file.

spatstat.explore 1.65-0

OVERVIEW

• Package initialised at version 1.65-0

SIGNIFICANT USER-VISIBLE CHANGES

• spatstat.core The package 'spatstat.core' has been created from a subset of the code in the original 'spatstat' package version 1.65-0. It contains the core functionality for statistical analysis of spatial data. For an overview, see help("spatstat.core-package")
• Execution The 'spatstat.core' package is slightly faster than the corresponding code in the 'spatstat' package, because the procedure for calling internal C functions has been streamlined.