# RELEASE NOTES ## spatstat 1.52-0 ### 10 August 2017 We thank Nicholas Read, Abdollah Jalilian, Suman Rakshit, Dominic Schuhmacher and Rasmus Waagepetersen for contributions. ### OVERVIEW * Important bug fixes. * Now handles disconnected linear networks. * Effect function is now available for all types of fitted model. * A model can be fitted or re-fitted to a sub-region of data. * More support for measures. * 'Pool' operations improved. * Geometric-mean smoothing. * Changed algorithm defaults in ippm. * Version nickname: "Rudimentary Lathe" ### NEW FUNCTIONS * as.data.frame.envelope Extract function data from an envelope object, including the functions for the simulated data ('simfuns') if they were saved. * is.connected, is.connected.default, is.connected.linnet Determines whether a spatial object consists of one topologically connected piece, or several pieces. * is.connected.ppp Determines whether a point pattern is connected after all pairs of points closer than distance R are joined. * hist.funxy Histogram of values of a spatial function. * model.matrix.ippm Method for 'model.matrix' which allows computation of regular and irregular score components. * harmonise.msr Convert several measures (objects of class 'msr') to a common quadrature scheme. ### SIGNIFICANT USER-VISIBLE CHANGES * Smooth.ppp New argument 'geometric' supports geometric-mean smoothing. * Kinhom New argument 'ratio'. * linearKinhom, linearpcfinhom Changed default behaviour when 'lambda' is a fitted model. New arguments 'update' and 'leaveoneout'. * linearK, linearKinhom, linearpcf, linearpcfinhom, compilepcf Ratio calculations are now supported. New argument 'ratio'. * effectfun Now works for 'ppm', 'kppm', 'lppm', 'dppm', 'rppm' and 'profilepl' objects. * ppm, kppm The argument 'subset' can now be a window (class 'owin') specifying the subset of data to which the model should be fitted. * fitted.lppm New argument 'leaveoneout' allows leave-one-out computation of fitted value. * pool.rat New arguments 'relabel' and 'variance'. * density.lpp The return value is a pixel image of class 'linim' in all cases. * plot.linim, plot.linfun A scale bar is now plotted when style="width". New argument 'legend'. * ippm Default values for the parameters of the optimisation algorithm (nlm.args) have changed. * ippm The internal format of the result has been extended slightly. * bind.fv New argument 'clip'. * as.im.distfun New argument 'approx' specifies the choice of algorithm. * "[.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. * predict.rhohat New argument 'what' determines which value should be calculated: the function estimate, the upper/lower confidence limits, or the standard error. * pool.fv New arguments 'relabel' and 'variance' * pool.rat New argument 'weights'. * plot.msr New argument 'massthresh'. * 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. * density.ppp New argument 'verbose'. * bw.pcf New argument 'verbose'. * hist.im New argument 'xname'. * [.leverage.ppm New argument 'update'. * [.layered Additional arguments '...' are now passed to other methods. * 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. * kppm Refuses to fit a log-Gaussian Cox model with anisotropic covariance. * plot.linim, plot.linfun The return value has a different format. Arguments have been renamed and reorganised. * density.lpp New argument 'old'. * ippm Accelerated. * Smooth.ppp Now exits gracefully if any mark values are NA, NaN or Inf. * timeTaken Now exits gracefully if there is no timing information. * nbfires The unit of length for the coordinates is now specified in this dataset. ### BUG FIXES 1. bw.pcf Results were totally incorrect due to a typo. [Spotted by Abdollah Jalilian and Rasmus Waagepetersen.] Fixed. 2. predict.rho2hat Results were incorrect for a rho2hat object computed from a point pattern. Fixed. 3. 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. 4. linearK, linearKinhom, linearpcf, linearpcfinhom, linearKcross, linearKdot, linearpcfcross, linearpcfdot, linearKcross.inhom, linearKdot.inhom, linearpcfcross.inhom, linearpcfdot.inhom Crashed if the network was disconnected. Fixed. 5. crossdist.lpp Crashed if the network was disconnected. Fixed. 6. countends Crashed if the network was disconnected. Fixed. 7. model.images.ppm Crashed for models fitted using 'covfunargs'. Fixed. 8. model.matrix.ppm Crashed for models fitted using 'covfunargs', if argument 'Q' was given. Fixed. 9. polynom Expansion of some polynomials caused an error message about 'invalid model formula'. Fixed. 10. plot.ppp The argument 'type="n"' did not suppress plotting of the legend, for marked point patterns. Fixed. 11. plot.psp Ignored 'show.all' when 'add=TRUE'. Fixed. 12. intensity.ppm Result had incorrect 'names' attribute in some cases. Fixed. 13. marks<-.ppx The assignment marks(X) <- a, where 'a' is a single atomic value, caused an error if 'X' contained zero points. Fixed 14. model.depends Crashed when applied to regression models fitted by 'gam', or point process models fitted by 'ppm' with 'use.gam=TRUE'. Fixed. 15. pool.fv Crashed sometimes, if the arguments did not have the same set of column names. Fixed. 16. pool.rat Crashed with an error message from 'fmt' if there were more than 20 objects to be pooled. Fixed. 17. linearK The 'theo' column was missing if npoints(X) < 2 and correction="Ang". Fixed. 18. model.matrix.ppm Result was malformed if the model was fitted with 'use.gam=TRUE'. Fixed. 19. effectfun Crashed if 'covname' was omitted, if the model was fitted with 'use.gam=TRUE'. Fixed. 20. nncross.lpp Result had incorrect format if Y was empty, in some cases. Fixed. 21. linearKinhom Plot label for y axis was incorrect. [Spotted by Suman Rakshit.] Fixed. 22. plot.solist If the entries were 'linim' objects, they were plotted using image() so arguments like 'style="w"' were ignored. Fixed. 23. as.ppp.data.frame Crashed if X was an object of class 'tbl_df' from the dplyr package. Fixed. 24. plot.lpp Crashed if there were multiple columns of marks. Fixed.