RELEASE NOTES spatstat 1.11-2 12 March 2007 OVERVIEW New dataset. Several new functions and improvements. Changes to the handling of illegal points in a point pattern. NEW DATASET anemones Kooijman's beadlet anemones dataset from Upton and Fingleton (1985) NEW DEMONSTRATION demo(data) Type demo(data) to display all the datasets installed with spatstat. NEW FUNCTIONS ks.test.ppm Kolmogorov-Smirnov test of goodness-of-fit for a Poisson point process model. [<-.im A method for "[<-" for pixel images has been implemented. This makes it possible to change the pixel values in a subset of an image. See help("[<-.im") ewcdf Weighted version of 'ecdf' (empirical cumulative distribution function) clickpoly Interactively draw a polygonal window bounding.box.xy convexhull.xy Convenience functions for finding the smallest rectangle or convex polygon containing a set of points. IMPROVEMENTS/ENHANCEMENTS [.im The subset method for pixel images now accepts a logical-valued pixel image as the subset index 'i' in x[i] Kmeasure Now has argument 'varcov' allowing anisotropic smoothing. quadrat.test This function is now generic, with methods for point patterns (quadrat.test.ppp) and for point process models (quadrat.test.ppm). The argument 'fit' is no longer needed or used. bounding.box Now accepts arguments of class "ppp" and "im" as well as "owin" as.im Now has argument 'dimyx' to control pixel array dimensions. Behaviour improved. ppm quadscheme default.dummy spatstat.options The minimum allowable number of dummy points in a quadrature scheme is now controlled by spatstat.options("ndummy.min"). ripras New argument 'shape' print.ppm Output is slightly neater. CHECKING POINT PATTERNS A ppp object contains (x,y) coordinates of points together with a spatial window. It is essential that the points in a ppp object lie inside the window. In spatstat 1.11-0 and 1.11-1, when a new dataset was created using ppp(), the system checked whether the (x,y) points all lie inside the window. If there were any such `illegal' points a fatal error was generated. For the convenience of users dealing with messy data, in spatstat 1.11-2 we have changed the following functions: ppp If any points are found to lie outside the window, instead of causing a fatal error, the `illegal' points are now removed from the point pattern, and the remaining `legal' points are returned as a ppp object. A warning message reports how many points were illegal. The `illegal' points are still accessible, as an attribute called "rejects" of the ppp object. plot.ppp, print.ppp If a ppp object has an attribute called "rejects" then this object is also plotted/printed. as.ppp as.ppp removes the "rejects" attribute if there is one. all other functions All other functions ignore the "rejects" attribute, and use only the `legal' points. CHANGED DATASETS copper The components of the copper dataset named 'points' and 'lines' have been renamed 'Points' and 'Lines' to avoid name conflicts when the copper dataset is attached. BUGS [1] persp.im Crashed in R 2.4.1 with message "illegal 'z' limits" if the image was constant. Fixed. [2] plot methods Some of the plot functions crashed with the message 'Internal error: function "points" not found" This occurred if a dataset called 'points' existed. Fixed. [3] affine For the case where the window is a rectangle and the transformation matrix is diagonal, (i) code was incorrect; the shift operation was not applied to the window. (ii) an error occurred if there were negative values in the diagonal of the transformation matrix. Fixed.