RELEASE NOTES spatstat 1.11-0 12 January 2007 OVERVIEW Internals of the package are being reorganised, in preparation for a major upgrade. Format of ppm objects changed. More stringent checking of function arguments. Improved handling of pixellation effects. Extensions to variance-covariance calculations for fitted models. 4 bug fixes. COMPATIBILITY The internal representation of "ppm" objects has changed. Point process models that were fitted using ppm() in older versions of spatstat are in a format that is now out-of-date. These old objects are still handled correctly by spatstat 1.11-0, as far as we are able. We recommend that these old objects be updated to the current version of spatstat, using `update.ppm', or of course by re-running your original code. The internal representation of "interact" objects has also changed. These objects are created by the functions Poisson(), Strauss(), DiggleGratton(), Geyer(), LennardJones(), MultiStrauss(), MultiStraussHard(), Ord(), OrdThresh(), PairPiece(), Pairwise(), Saturated(), StraussHard() and Softcore(). Similar comments apply. The best advice is to ** save only R scripts ** that generate fitted models, rather than saving the fitted models themselves. NEW FUNCTIONS [.splitppp [<-.splitppp summary.splitppp Methods for the class "splitppp". [.listof [<-.listof summary.listof Methods for the class "listof" as.owin.ppm Method for "as.owin" IMPROVEMENTS/ENHANCEMENTS Kinhom Improved handling of NA's and pixellation effects. If 'lambda' is a pixel image which does not completely cover the observation window of the point pattern X, then X will first be trimmed to a smaller region where the values of lambda are defined. A warning is issued. intersect.owin union.owin Better handling of pixel rasters. (a) If one of the windows is already a binary mask, the default pixel raster is taken from this window. (b) These functions now have a "..." argument which gives complete control over the pixel raster dimensions. ppp as.ppp These functions now check that the (x,y) coordinate points all lie inside the window specified. Checking may be switched off by setting check=FALSE. ppm Now applies more stringent checks on the validity of its arguments `trend' and `interaction'. ppm summary.ppm These now handle the case where covariates = list() or `covariates' is a data frame with zero columns. qqplot.ppm Errors that occur during simulation are now trapped instead of causing a crash. New argument 'maxerr' controls maximum number of such errors that will be tolerated. New default value for 'periodic'. plot.listof plot.splitppp These functions have additional arguments 'nrows' and 'ncols' to control the plot layout. rpoispp rNeymanScott rMatClust rThomas rSSI These functions now check their arguments more stringently. Kest New option: correction="none" computes an estimate of the K function without edge correction. This is a heavily biased estimate and should not be used for data analysis. It is useful for demonstration/instruction purposes. vcov.ppm Now computes Monte Carlo estimate of Fisher information and variance-covariance matrix for any model fitted by Huang-Ogata method (by calling ppm with method="ho"). vcov.ppm New argument 'gamaction' to control handling of models that were fitted using gam(). `INVISIBLE' CHANGES This release contains numerous changes to the internal code for point process models (ppm objects). These changes are in preparation for a future upgrade to spatstat. Most of the changes are not currently visible. BUGS [1] bounding.box The bounding box was incorrect for a pixel image and for a window of type 'mask'. The bounding box was half a pixel too small on each side. Fixed. [2] dilate.owin Due to discretisation errors, dilate(w, r) did not always contain w, for r >= 0, This has now been modified so that dilate(w, r) always contains w, and dilate(w, 0) returns w. [3] lurking, diagnose.ppm Calculation of variance failed (with a message about `non-conformable arrays') when the fitted model had more than one covariate. Fixed. [4] vcov.ppm, lurking These functions crashed when applied to a point process model that was fitted using gam (i.e. by calling ppm with use.gam=TRUE). Fixed.