
	CHANGES IN spatstat VERSION 1.38-1

OVERVIEW

   o We thank Ute Hahn and Xavier Raynaud for contributions.

   o Urgent Bug Fixes.

   o Nickname: 'Le Hardi'

NEW FUNCTIONS

   o "[<-.fv", "$<-.fv"
   Subset replacement methods for 'fv' objects.

SIGNIFICANT USER-VISIBLE CHANGES

   o clarkevans.test
   Simulations are now performed with a fixed number of points.

   o plot.owin, plot.ppp, plot.psp, plot.im
   The default size of the outer margin of white space has been
   reduced. 

   o dclf.test
   Improved information in printed output.

BUG FIXES

   o update.ppm
   Results were incorrect in several cases.
   [Spotted by Xavier Raynaud.]
   Bug introduced in spatstat 1.38-0.
   Fixed.

   o Kinhom, Linhom
   Calculations were incorrect if 'lambda' was a fitted point process model.
   [Spotted by Xavier Raynaud.]
   Bug introduced in spatstat 1.38-0.
   Fixed.

   o envelope.envelope
   Ignored the arguments 'global' and 'VARIANCE'.
   Fixed.

   o fv objects
   If 'f' was an object of class 'fv', then an assignment like f$name <- NULL
   mangled the internal format of the object 'f', leading to errors
   in print.fv and plot.fv.
   [Spotted by Ute Hahn.]
   Fixed.

   o split.ppp
   split(X, A) where A is a rectangular tessellation,
   produced errors if the window of 'A' did not include the window of 'X'.
   [Spotted by Ute Hahn.]
   Fixed.

   o names<-.hyperframe
   Mangled the internal format.
   [Spotted by Ute Hahn.]
   Fixed.
   
   o plot.fv
   y axis label was incorrect in some cases when the 'fv' object
   had only a single column of function values.
   [Spotted by Ute Hahn.]
   Fixed.

   
	CHANGES IN spatstat VERSION 1.38-0

OVERVIEW

   o We thank Malissa Baddeley, Colin Beale, Oscar Garcia, Daniel Esser, 
     David Ford, Eric Gilleland, Andrew Hardegen, Philipp Hunziker, 
     Abdollah Jalilian, Tom Lawrence, Lore De Middeleer, Robin Milne, 
     Mike Porter, Suman Rakshit, Pablo Ramon, Jason Rudokas, 
     Christopher Ryan, Dominic Schuhmacher, Medha Uppala 
     and Rasmus Waagepetersen for contributions.

   o spatstat now Requires the package 'goftest' 
     and Suggests the package 'Matrix'.

   o New dataset: 'sporophores'

   o Palm likelihood method for fitting cluster processes and Cox processes.

   o Quasi-likelihood and weighted composite likelihood methods
     for estimating trend in cluster processes and Cox processes.

   o Further extensions to model formulas in ppm and kppm.

   o Faster variance calculations for ppm objects.

   o One-sided tests and one-sided envelopes of summary functions.

   o Cramer-Von Mises and Anderson-Darling tests of spatial distribution.

   o Cressie-Read test statistic in quadrat counting tests.

   o Spatial cumulative distribution functions.

   o Faster algorithm for point pattern matching.

   o Improvements to plots.

   o Increased support for envelopes.

   o New generic functions 'Window', 'Frame' and 'domain'.

   o Directional K-function and directional distribution.

   o Raster calculations accelerated.

   o Summary functions accelerated.

   o Many improvements and bug fixes.

   o Version nickname: 'Wicked Plot'

NEW DATASETS

   o sporophores
   Spatial pattern of three species of mycorrhizal fungi around a tree.
   [Contributed by E. David Ford.]

NEW FUNCTIONS

   o improve.kppm
   Re-estimate the trend in a kppm (cluster or Cox) model
   using quasi-likelihood or weighted first-order composite likelihood.
   [Contributed by Abdollah Jalilian and Rasmus Waagepetersen.]

   o Window, Window<-
   Generic functions to extract and change the window of a spatial object
   in two dimensions. Methods for ppp, psp, im, and many others.

   o Frame, Frame<-
   Generic functions to extract and change the containing rectangle ('frame')
   of a spatial object in two dimensions. 

   o domain
   Generic function to extract the spatial domain of a spatial object
   in any number of dimensions. 

   o Ksector
   Directional version of the K-function.

   o pairorient
   Point pair orientation distribution.

   o spatialcdf
   Compute the spatial cumulative distribution of a spatial covariate,
   optionally using spatially-varying weights.

   o cdf.test 
   [Supersedes 'kstest'.]
   Test of goodness-of-fit of a Poisson point process model.
   The observed and predicted distributions of the values of a 
   spatial covariate are compared using either the
   Kolmogorov-Smirnov, Cramer-Von Mises or Anderson-Darling test.

   o berman.test
   Replaces 'bermantest'.

   o harmonise.fv
   Make several functions compatible.

   o simulate.lppm
   Simulate a fitted point process model on a linear network.

   o subset.ppp, subset.lpp, subset.pp3, subset.ppx
   Methods for 'subset', for point patterns.

   o closepairs.pp3, crosspairs.pp3
   Low-level functions to find all close pairs of points in three dimensions

   o volume.linnet
   Method for the generic 'volume'. Returns the length of the linear network.

   o padimage
   Pad the border of a pixel image.
 
   o as.layered
   Convert spatial data to a layered object.

   o panel.contour, panel.image, panel.histogram
   Panel functions for 'pairs' plots.

   o range.fv, min.fv, max.fv
   Range, minimum and maximum of function values.

SIGNIFICANT USER-VISIBLE CHANGES

   o ppm.formula
   The left hand side of the formula can now be the name of 
   an object in the list 'data', or an expression involving such objects.

   o ppm
   The right hand side of the formula can now include 
   the symbol '.' representing all covariates in the list 'data'.

   o ppm
   New argument 'subset' makes it possible to fit the model
   in a subset of the spatial domain defined by an expression.

   o kppm
   New option: method="palm", will fit the model by maximising Palm likelihood.

   o pppdist
   Substantially accelerated. 
   New argument 'auction' controls choice of algorithm.

   o rhohat
   New arguments 'weights' and 'horvitz' for weighted calculations.

   o persp.im
   Surface heights and colours can now be controlled by different images.
   Option to draw a grey apron around the sides of the perspective plot. 
   Return value has a new attribute 'expand'.

   o plot.listof
   New arguments 'halign' and 'valign' give improved control
   over the alignment of panels.

   o plot.listof
   If all components of the list are objects of class 'fv' 
   representing functions, then if equal.scales=TRUE, these
   functions will all be plotted with the same axes 
   (i.e. the same xlim and the same ylim).

   o envelope
   The argument 'transform' is now processed by 'with.fv'
   giving more options, such as 'transform=expression(. - r)'

   o envelope, dclf.test, mad.test
   One-sided tests and one-sided envelopes can now be produced, 
   by specifying the argument 'alternative'.

   o dclf.test, mad.test
   A pointwise test at fixed distance 'r' can now be performed
   by setting rinterval = c(r,r).

   o envelope
   New arguments 'fix.n' and 'fix.marks' for envelope.ppp and envelope.ppm
   make it easy to generate simulated patterns conditional on the
   total number of points, or on the number of points of each type.

   o quadrat.test
   Can now calculate the Cressie-Read test statistic
   instead of the Pearson X2 statistic.

   o Kres, Gres, Kcom, Gcom, psst, psstA, psstG
   New argument 'model' makes it easier to generate simulation envelopes
   of the residual summary functions.

   o layered, plot.layered
   The layer plot arguments can include the argument '.plot'
   specifying a function to perform the plotting instead of the
   generic 'plot'.

   o deriv.fv
   New arguments make it possible to differentiate a periodic function.

   o ppm
   Argument 'data' or 'covariates' can now include entries
   which are not spatial covariates, provided they do not appear 
   in the model formula.

   o closepairs, crosspairs
   These functions are now generic, with methods for 'ppp' and 'pp3'

   o rLGCP
   Updated to conform to new usage of RandomFields package.
   Argument syntax has changed.
   Now allows control over pixel resolution.

   o bw.diggle
   New arguments 'correction' and 'hmax' for controlling the calculation.

   o predict.lppm
   New argument 'new.coef' for computing predictions with a 
   different vector of model coefficients.

   o predict.ppm
   If 'locations' is a pixel image, its pixels determine the
   spatial locations for prediction.

   o cut.ppp
   Argument 'z' can now be a window.

   o split.ppp
   Argument 'f' can now be a window.

   o print.ppm, summary.ppm, coef.summary.ppm
   The table of parameter estimates, standard errors and confidence intervals
   now also includes the value of the (signed square root) Wald test statistic.

   o plot.im
   Now automatically detects problems in some Windows graphics displays
   and tries to avoid them.

   o plot.im
   The position of axis tick marks alongside the colour ribbon
   can now be controlled using the parameter 'at' in the argument 'ribargs'.

   o plot.ppp
   Can now plot numeric marks using characters chosen by 'pch' or 'chars'
   with size determined by mark value.

   o plot.ppp
   New argument 'meansize' for controlling mark scale.

   o hsvim, rgbim
   New argument 'autoscale' causes automatic scaling of colour channel values.

   o plot.ppp
   If type='n', a legend is now displayed when x is a marked point pattern.

   o whist
   Accelerated by a factor of 5.

   o Fest, Jest
   Accelerated by a factor of 2 to 3.

   o fryplot
   Accelerated.
   Now displays a legend if the point pattern is marked.
   Now handles numerical marks nicely.
   New argument 'axes'.

   o frypoints
   Accelerated.
   New arguments 'to', 'from' and 'dmax'.

   o duplicated.ppp
   New option: rule = 'unmark'

   o rjitter
   Argument 'radius' now has a default.

   o Smooth.msr
   New argument 'drop'

   o LambertW
   Now handles NA and infinite values.

   o update.ppm
   Now handles formulae with a left-hand side.

   o raster.x, raster.y, raster.xy
   These functions can now handle images, as well as masks.

   o Smooth.ppp
   If the mark values are exactly constant, the resulting smoothed values
   are now exactly constant.

   o eval.im, eval.fv, eval.fasp
   Argument 'envir' can now be a list, instead of an environment.

   o plot.ppp
   The printout (of the resulting symbol map object)
   now displays the numerical value of the mark scale.

   o with.fv
   Improved mathematical labels.

   o plot.fv
   Improved mathematical labels on x axis.

   o ppm
   Improved error messages.

   o vcov.ppm
   Computations greatly accelerated for Hybrid interactions
   and for Area-interaction models.

   o vcov.kppm
   Computations greatly accelerated (when fast=TRUE)   

   o interp.im
   Argument 'x' can now be a point pattern.

   o pool.envelope
   Improved handling of text information.

   o miplot
   Improved layout.

   o print.summary.ppp
   Improved layout. 
   Now respects spatstat.options('terse')

   o print.profilepl
   Improved layout. 
   Now respects spatstat.options('terse')

   o anova.ppm
   Now respects spatstat.options('terse')

   o print.fv, print.envelope
   Now respect spatstat.options('terse') and options('width')
   
   o summary.envelope
   Now respects options('width')
   
   o kstest, bermantest
   These functions will soon be Deprecated.
   They are retained only for backward compatibility.

BUG FIXES

   o vcov.ppm
   Sometimes gave wrong answers for Poisson models fitted by method='logi'.
   Fixed.

   o unnormdensity
   If weights were missing, the density was normalised,
   contrary to the documentation.
   Fixed.

   o logLik.ppm, anova.ppm, AIC
   For models fitted by 'ippm', the number of degrees of freedom was incorrect.
   Fixed.

   o im.apply
   Pixels outside the window were not assigned the value NA as they should.
   Fixed.

   o pixellate.owin
   Crashed, unpredictably, if the pixel raster had unequal numbers
   of rows and columns.
   [Spotted by Rasmus Waagepetersen.]
   Fixed.

   o vcov.ppm
   Crashed for pairwise interaction models fitted by method="logi".
   Fixed.

   o predict.ppm
   Crashed for models fitted by method="logi"
   if the model included external covariates.
   Fixed.

   o predict.ppm
   Crashed if the argument 'covariates' or 'data' in the original call to 'ppm'
   included entries that were not spatial covariates. [These entries were
   ignored by ppm but caused predict.ppm to crash.]
   Fixed.

   o simulate.kppm, rNeymanScott, rThomas, rMatClust
   Crashed randomly when simulating an inhomogeneous model.
   [Spotted by Philipp Hunziker.]
   Fixed.
   
   o bw.diggle
   In some extreme cases, generated an error message
   about `NaN values in Foreign function call.'
   [Spotted by Colin Beale.]
   Fixed.

   o textureplot
   Crashed if 'spacing' was too large.
   Fixed.

   o superimpose.psp
   Crashed if the result was empty.
   Fixed.

   o istat
   Crashed with an error message about 'vars'.
   Fixed.

   o dirichlet, delaunay, delaunay.distance
   Crashed in rare cases due to a problem in package 'deldir'. 
   [Spotted by Pierre Legendre.]
   Fixed.

   o rgbim, hsvim
   Crashed if any argument was constant.
   Fixed.

   o scaletointerval
   Crashed if x was constant.
   Fixed.

   o linnet, [.linnet
   Crashed if the result contained only a single vertex.
   [Spotted by Daniel Esser.]
   Fixed.

   o plot.fv
   If some of the function values were NA,
   they were replaced by fictitious values
   (by linearly interpolating).
   Fixed.

   o crossdist.ppp
   Ignored argument 'squared' if periodic=FALSE.
   [Spotted by Mike Porter.]
   Fixed.

   o marks<-.ppp
   Ignored argument 'drop'.
   [Spotted by Oscar Garcia.]
   Fixed.
 
   o update.ppm
   Sometimes did not respect the argument 'use.internal'.
   Fixed.

   o plot.rhohat
   Did not respect the argument 'limitsonly'.
   Fixed.

   o contour.im
   Argument 'axes' defaulted to TRUE, but FALSE was intended.
   Fixed.

   o print.hyperframe, as.data.frame.hyperframe
   Column names were mangled if the hyperframe had a single row.
   Fixed.

   o as.psp.data.frame
   Generated a warning about partially-matched names in a data frame.
   [Spotted by Eric Gilleland.]
   Fixed.

   o plot.leverage.ppm
   Generated a warning from 'contour.default'
   if the leverage function was constant.
   Fixed.

   o plot.diagppm
   Issued warnings about unrecognised graphics parameters.
   Fixed.

   o update.symbolmap
   Discarded information about the range of input values.
   Fixed.

   o plot.fv
   Label for y axis was garbled, if argument 'shade' was given.
   Fixed.

   o plot.ppp
   The legend was sometimes plotted when it should not have been 
   (e.g. when add=TRUE).
   Fixed.

   o plot.listof, plot.im
   In an array of plots, containing both images and other spatial objects,
   the titles of the panels were not correctly aligned.
   Fixed.

   o plot.tess, plot.quadratcount
   Ignored arguments like 'cex.main'.
   Fixed.

   o iplot
   Navigation buttons (Left, Right, Up, Down, Zoom In, Zoom Out)
   did not immediately refresh the plot.
   Fixed.

   o iplot.layered
   Reported an error 'invalid argument type' if all layers were deselected.
   Fixed.

	CHANGES IN spatstat VERSION 1.37-0

OVERVIEW

   o Ege Rubak is now a joint author of spatstat. 

   o We thank Peter Forbes, Tom Lawrence and Mikko Vihtakari for contributions.

   o Spatstat now exceeds 100,000 lines of code.

   o New syntax for point process models (ppm, kppm, lppm)
     equivalent to syntax of lm, glm, ...

   o Covariates in ppm and kppm can now be tessellations.

   o Confidence intervals and prediction intervals for fitted models.

   o Quasirandom point patterns and sequences.

   o Plots using texture fill.

   o Support for mappings from data to graphical symbols and textures.

   o Automatic re-fitting of model in Ginhom, Kinhom, Finhom, Jinhom.

   o Support for Mixed Poisson distribution.

   o Interpretation of mark scale parameters has changed in plot.ppp

   o Syntax of multitype interactions (eg MultiStrauss) has changed.

   o Bug fix in Metropolis-Hastings simulation of 'StraussHard' models

   o Changed default behaviour of perfect simulation algorithms.

   o Improvements to layout of text output.

   o Version nickname: 'Model Prisoner'

NEW CLASSES

   o symbolmap
   An object of class 'symbolmap' represents a mapping
   from data to graphical symbols

   o texturemap
   An object of class 'texturemap' represents a mapping
   from data to graphical textures.

NEW FUNCTIONS

   o split.hyperframe, split<-.hyperframe
   methods for split and split<- for hyperframes.

   o dmixpois, pmixpois, qmixpois, rmixpois
   (log-)normal mixture of Poisson distributions.

   o vdCorput, Halton, Hammersley, rQuasi
   quasirandom sequences and quasirandom point patterns.

   o Smoothfun
   create a function(x,y) equivalent to the result of Smooth.ppp

   o minnndist, maxnndist
   Faster ways to compute min(nndist(X)), max(nndist(X))

   o add.texture
   Draw a simple texture inside a specified region.

   o textureplot
   Display a factor-valued pixel image using texture fill.

   o texturemap
   Create a texture map

   o plot.texturemap
   Plot a texture map in the style of a legend
   
   o symbolmap
   Create a symbol map

   o update.symbolmap
   Modify a symbol map

   o invoke.symbolmap
   Apply symbol map to data values, and plot them

   o plot.symbolmap 
   Plot the symbol map in the style of a legend

   o as.owin.boxx
   Converts a 'boxx' to an 'owin' if possible.

   o ellipse
   Create an elliptical window.

   o clickbox
   Interactively specify a rectangle, by point-and-click on a graphics device.

   o complementarycolour
   Compute the complementary colour value of a given colour value,
   or the complementary colour map of a given colour map.

   o gauss.hermite
   Gauss-Hermite quadrature approximation to the expectation
   of any function of a normally-distributed random variable.	

   o boundingbox
   Generic function, replaces bounding.box

   o edges
   Extract boundary edges of a window. 
   Replaces and extends 'as.psp.owin'

   o pixelcentres
   Extract centres of pixels as a point pattern.

SIGNIFICANT USER-VISIBLE CHANGES

   o ppm, kppm, lppm
   NEW SYNTAX FOR POINT PROCESS MODELS
   The model-fitting functions 'ppm', 'kppm' and 'lppm' now accept
   a syntax similar to 'lm' or 'glm', for example  ppm(X ~ Z), 
   but still accept the older syntax ppm(X, ~Z). 
   To support both kinds of syntax, the functions 'ppm' and 'kppm'
   are now generic, with methods for the classes 'formula', 'ppp' and 'quad'. 
   The 'formula' method handles a syntax like ppm(X ~ Z) while the
   'ppp' method handles the old syntax ppm(X, ~Z).
   Similarly 'lppm' is generic with methods for 'formula' and 'lpp'.

   o ppm, kppm, lppm
   Covariates appearing in the model formula can be objects 
   which exist in the R session, instead of always having to be
   elements of the list `covariates'.
   
   o ppm.formula, kppm.formula, lppm.formula
   Formulae involving polynom() are now expanded, symbolically,
   so that polynom(x, 3) becomes x + I(x^2) + I(x^3) 
   and polynom(x,y,2) becomes x + y + I(x^2) + I(x*y) + I(y^2).
   This neatens the model output, and also makes it possible
   for anova() and step() to add or delete single terms in the polynomial.

   o predict.ppm
   New argument 'interval' allows confidence intervals or prediction intervals
   to be calculated.

   o predict.ppm
   New argument 'total' allows for prediction of the total number of points
   in a specified region.
   
   o plot.ppp, plot.lpp
   For marked point patterns, a legend is automatically added
   to the plot, by default. Arguments have changed: new arguments
   include parameters of the legend, and an optional symbol map.
   Result has changed: it is now an object of class 'symbolmap'.

   o plot.ppp, plot.lpp
   Interpretation of the parameters 'markscale' and 'maxsize' 
   has changed. The size of a circle in the plot is now defined 
   as the circle's diameter instead of its radius. (Size of
   a square is measured, as before, by its side length). 

   o parres
   Now handles the case where the fitted model is not separable
   but its restriction to the given 'subregion' is separable.

   o envelope
   Now issues a warning if the usage of envelope() appears to be `invalid' 
   in the sense that the simulated patterns and the data pattern
   have not been treated equally.

   o Kinhom, Finhom, Ginhom, Jinhom
   New argument 'update'.
   If 'lambda' is a fitted model (class ppm or kppm) and update=TRUE,
   the model is re-fitted to the data pattern, before the intensities
   are computed.

   o rDiggleGratton, rDGS, rHardcore, rStrauss, rStraussHard
   By default the point pattern is now generated on
   a larger window, and trimmed to the original window.
   New argument expand=TRUE.

   o MultiStrauss, MultiHard, MultiStraussHard
   The syntax of these functions has changed.
   The new code should still accept the old syntax.

   o rhohat
   rhohat.ppp and rhohat.quad have new argument 'baseline'

   o ippm
   Algorithm improved. Argument syntax changed.

   o default.dummy, quadscheme
   Dummy points can now be generated by a quasirandom sequence.

   o plot.owin
   The window can now be filled with one of 8 different textures.
   Arguments changed. 

   o ppm, kppm
   Covariates in the model can now be tessellations.

   o [.im
   New argument 'tight' allows the resulting image to be trimmed 
   to the smallest possible rectangle.

   o [.psp, rlinegrid, rpoisline
   These functions now handle binary mask windows.

   o rotate
   The user can specify the centre of rotation.

   o rescale
   rescale() and all its methods now have argument 'unitname'
   which can be used to change the name of the unit of length.

   o anova.ppm
   Output format has been improved. 
   Number of columns of result has changed.

   o print.ppp, print.summary.ppp, print.owin, print.summary.owin,
   print.im, print.summary.im, print.fv, print.msr, print.profilepl
   These functions now avoid over-running the text margin
   (i.e. they respect options('width') where possible).

   o layerplotargs<-
   Now handles any spatial object, converting it to a 'layered' object.

   o effectfun
   Improved display in case se.fit=TRUE.

   o scaletointerval
   New argument 'xrange'

   o contour.im
   New argument 'show.all'.
   Default value of 'axes' changed to FALSE.

   o identify.ppp
   Now handles multivariate marks. 

   o plot.listof
   Improved layout.
   New arguments 'hsep', 'vsep'.
   Argument 'mar.panel' may have length 1, 2 or 4.

   o plot.splitppp
   This function is no longer identical to plot.listof.
   Instead it is a much simpler function which just
   calls plot.listof with equal.scales=TRUE.

   o anova.ppm
   Output is neater.

   o plot.layered
   New argument 'do.plot'

   o plot.psp
   New argument 'do.plot'
   
   o as.psp.owin
   New argument 'window'

   o plot.im, contour.im, textureplot
   New argument 'clipwin'

   o plot.ppp
   New argument 'clipwin'

   o plot.msr
   New argument 'how' allows density to be plotted as image and/or contour

   o diagnose.ppm, plot.diagppm
   More options for 'plot.neg'

   o plot.leverage.ppm, plot.influence.ppm, plot.msr
   Argument 'clipwin' can now be used to restrict the display
   to a subset of the full data.

   o [.hyperframe, [<-.hyperframe, $.hyperframe, $<-.hyperframe
   These functions are now documented.

   o leverage.ppm, influence.ppm, dfbetas.ppm
   Resulting objects are now smaller (in memory size).

   o print.ppm
   Now indicates whether the irregular parameters 'covfunargs'
   were optimised (by profilepl or ippm) or whether they were simply
   provided by the user.

   o plot.ppp
   A point pattern with numerical marks can now be plotted as
   filled dots with colours determined by the marks, 
   by setting pch=21 and bg=<colourmap>

   o colourmap
   Now handles dates and date-time values (of class 'Date' or 'POSIXt').

   o plot.ppp, print.ppp, summary.ppp
   Improved handling of dates and date-time values 
   (of class 'Date' or 'POSIXt') in the marks of a point pattern.

   o cut.im
   Now refuses to handle images whose pixel values are
   factor, logical or character.

   o centroid.owin
   New argument 'as.ppp'

   o superimpose
   Improved default names for columns of marks.

   o Softcore()
   Improved printout.

   o kppm, lgcp.estpcf, lgcp.estK
   Adjusted to new structure of RandomFields package.
   No change in syntax.

   o data(murchison)
   This dataset now belongs to class 'listof' so that it can be
   plotted directly.

   o data(clmfires)
   The format of the covariate data has changed.
   The objects 'clmcov100' and 'clmcov200' are now 
   elements of a list 'clmfires.extra'.

   o bounding.box
   This function is now Deprecated; it has been replaced 
   by the generic boundingbox().

   o as.psp.owin 
   This function is now Deprecated; it has been replaced 
   and extended by the function edges().

   o plot.kstest
   Changed defaults so that the two curves are distinguishable.

   o with.fv
   Improved mathematical labels.

BUG FIXES

   o intensity.quadratcount
   Values were incorrect for a rectangular tessellation
   (the matrix of intensities was transposed).
   Fixed.

   o rmh, simulate.ppm
   Simulation of the Strauss-hard core model (StraussHard) was incorrect
   (intensity of the simulated process was about 15% too low).
   Bug introduced in spatstat 1.31-0 (January 2013).

   o intensity.quadratcount
   Crashed for a rectangular tessellation with only a single row or column.
   Fixed.
   
   o model.images.ppm
   Crashed sometimes if the argument W was given.
   Fixed.

   o eval.im
   Crashed when applied to images with only a single row or column.
   Fixed.

   o ppp, marks<-.ppp
   If the marks were a vector of dates, they were erroneously 
   converted to numbers.
   Fixed.

   o ippm
   Crashed if the model formula included an offset term
   that was not a function.
   Fixed.

   o leverage.ppm
   Crashed sometimes when the model had irregular parameters ('covfunargs').
   Fixed.

   o residuals.ppm
   Crashed sometimes when type='score'.
   Fixed.

   o scaletointerval
   Did not handle dates and date-time values correctly.
   Fixed.

   o rbind.hyperframe, as.list.hyperframe
   Gave incorrect results for hyperframes with 1 row.
   Fixed.

   o Kinhom
   Did not renormalise the result (even when renormalise=TRUE), in some cases.
   Spotted by Peter Forbes.
   Fixed.

   o disc
   If mask=TRUE the disc was erroneously clipped to the square [-1,1] x [-1,1].
   Fixed.

   o plot.fv
   Sometimes shaded the wrong half of the graph 
   when the 'shade' coordinates were infinite.
   Fixed.

   o print.ppm
   Gave an error message if the coefficient vector had length zero.
   Fixed.

   o vcov.ppm
   Gave an error message if the coefficient vector had length zero.
   Fixed.

   o plot.distfun, as.im.distfun
   These functions effectively ignored the argument 'invert' 
   in the original call to distfun.
   Fixed.

   o plot.msr
   Ignored certain additional arguments such as 'pch'.
   Fixed.

   o cut.im
   Crashed if the image had 1 row or 1 column of pixels.
   Fixed.

   o iplot.ppp
   Crashed with message about missing object 'vals'.
   Fixed.

   o effectfun
   Demanded a value for every covariate supplied in the original call to ppm, 
   even for covariates which were not used in the model.
   Fixed.

   o plot.listof, plot.hyperframe
   When plotting 3D point patterns (class pp3), these functions
   issued warnings about 'add' being an unrecognised graphics argument.
   Fixed.

	CHANGES IN spatstat VERSION 1.36-0

OVERVIEW

   o We thank Sebastian Meyer, Kevin Ummer, Jean-Francois Coeurjolly,
   Ege Rubak, Rasmus Waagepetersen, Oscar Garcia and Sourav Das
   for contributions.

   o Important change to package dependencies.

   o Geometrical inconsistencies in polygons are now repaired automatically.

   o Improved quadrature schemes and reduced bias in ppm.

   o New vignette 'Summary of Recent Changes to Spatstat'.

   o Approximation to K function and pcf for Gibbs models.

   o Counterpart of 'apply' for lists of images.

   o Hexagonal grids and tessellations.

   o Extensions to scan test and Allard-Fraley cluster set estimator.

   o Change the parameters of a fitted model before simulating it.

   o Accelerated Kest, Kinhom for rectangular windows.

   o Extensions and improvements to plotting functions.

   o Improvements to labelling of 'fv' objects.

   o New demo of summary functions.

   o More methods for 'intensity'.

   o Version nickname: 'Intense Scrutiny'

NEW FUNCTIONS

   o Kmodel.ppm, pcfmodel.ppm
   Compute approximation to K-function or pair correlation function
   of a Gibbs point process model.

   o im.apply
   Apply a function to corresponding pixel values in several images.

   o hexgrid, hextess
   Create a hexagonal grid of points, or a tessellation of hexagonal tiles

   o shift.tess, rotate.tess, reflect.tess, scalardilate.tess, affine.tess
   Apply a geometrical transformation to a tessellation.

   o quantile.ewcdf
   Extract quantiles from a weighted cumulative distribution function.

   o scanLRTS
   Evaluate the spatially-varying test statistic for the scan test.

   o pcfmulti
   General multitype pair correlation function

   o intensity.splitppp
   Estimate intensity in each component of a split point pattern.

   o intensity.quadratcount
   Use quadrat counts to estimate intensity in each quadrat.

   o as.owin.quadratcount, as.owin.quadrattest
   Extract the spatial window in which quadrat counts were performed.

   o reload.or.compute
   Utility function for R scripts: 
   either reload results from file, or compute them.

   o to.grey
   Convert colour to greyscale.

   o Smooth.im
   Method for Smooth() for pixel images. Currently identical to blur().

   o demo(sumfun)
   Demonstration of nonparametric summary functions in spatstat.

SIGNIFICANT USER-VISIBLE CHANGES

   o Package Dependencies
   spatstat now "Imports" (rather than "Depends" on) 
   the libraries mgcv, deldir, abind, tensor, polyclip.
   This means that these libraries are not accessible to the user
   unless the user explicitly loads them by typing 'library(mgcv)' and so on.

   o owin, as.owin
   Polygon data are no longer subjected to strict checks on 
   geometrical validity (self-crossing points, overlaps etc.)
   Instead, polygon geometry is automatically repaired.
   
   o ppm
   The default quadrature scheme for a point pattern
   has been improved (in the case of a non-rectangular window)
   to remove a possible source of bias.

   o Performance 
   various parts of spatstat now run slightly faster.

   o scan.test 
   Now handles multiple values of circle radius 'r'.

   o plot.scan.test, as.im.scan.test
   These functions can now give the optimal value of circle radius 'r'.

   o pcfcross, pcfdot
   Algorithms have been reimplemented using a single-pass kernel smoother
   and now run much faster. Bandwidth selection rule improved.

   o plot.listof, plot.splitppp
   Default behaviour has changed: panels are now plotted on different scales. 

   o plot.listof, plot.splitppp
   When 'equal.scales=TRUE' the panels are plotted on exactly equal scales
   and are exactly aligned (under certain conditions).

   o ppp, marks.ppp, marks<-.ppp
   New argument 'drop' determines whether a data frame with a single column
   will be converted to a vector.

   o simulate.ppm, rmh.ppm, rmhmodel.ppm
   New argument 'new.coef' allows the user to change the parameters
   of a fitted model, before it is simulated.

   o logLik.ppm
   New argument 'new.coef' allows the user to evaluate the 
   loglikelihood for a different value of the parameter.

   o clusterset
   The argument 'result' has been renamed 'what'.
   It is now possible to give multiple values to 'what'
   so that both types of result can be computed together.

   o residuals.ppm
   Argument 'coefs' has been renamed 'new.coef' for consistency
   with fitted.ppm etc. 

   o residuals.ppm
   If drop=TRUE the window associated with the residuals
   is now taken to be the domain of integration of the composite likelihood.
   
   o intensity.ppp
   Now has argument 'weights'

   o density.ppp, Smooth.ppp, markmean, markvar, intensity.ppp
   Argument 'weights' can now be an 'expression'.

   o pcf
   New argument 'domain' causes the computation to be restricted to 
   a subset of the window.

   o nnclean
   The result now has attributes which give the fitted parameter values,
   information about the fitting procedure, and the histogram bar heights.

   o nnclean
   Extra arguments are now passed to hist.default.

   o plot.tess
   For a tessellation represented by a pixel image, 
   plot.tess no longer treats the pixel labels as palette colours.

   o relrisk
   New argument 'case' allows the user to specify which mark value
   corresponds to the cases in a case-control dataset.

   o Kinhom
   Now accepts correction="good" 

   o spatstat.options
   New option ('monochrome') controls whether plots generated by spatstat
   will be displayed in colour or in greyscale. This will eventually be
   applied to all plot commands in spatstat. 

   o plot.im, persp.im, contour.im, plot.owin, plot.psp, plot.fv, plot.fasp
   These functions now obey spatstat.options('monochrome')

   o plot.ppp, plot.owin, plot.im, plot.psp, plot.tess, plot.layered
   New universal argument 'show.all' determines what happens
   when a plot is added to an existing plot. If show.all = TRUE
   then everything is plotted, including the main title and colour ribbon.

   o plot.ppp
   New argument 'show.window' 

   o plot.im 
   New arguments 'add' and 'do.plot'.
   More arguments recognised by 'ribargs'

   o plot.layered
   New arguments 'add', 'main' 
   Better argument handling.

   o plot.fv
   Improved handling of argument 'shade'

   o layered, layerplotargs, plot.layered
   The plotting argument can now be a list of length 1,
   which will be replicated to the correct length.

   o varblock
   Ugly legends have been repaired.

   o quad.ppm
   New argument 'clip'

   o edge.Trans
   New arguments 'dx', 'dy'

   o disc
   Argument 'centre' can be in various formats.

   o affine, shift
   Argument 'vec' can be in various formats.

   o Geyer, BadGey
   A warning is no longer issued when the parameter 'sat' is fractional.

   o adaptive.density
   Now has argument 'verbose'

   o Smooth.ppp
   'sigma' is now a formal argument of Smooth.ppp

   o plot.quadratcount, plot.quadrattest
   These functions have now been documented.

   o Summary functions and envelopes
   Improved mathematical labels in plots.

   o Kest
   Accelerated, in the case of a rectangular window.

   o Kscaled
   Argument 'lambda' can now be a fitted model (class ppm)

   o print.fv
   Improved layout.

   o plot.bermantest
   Improved graphics.

   o which.max.im
   This function is now deprecated.
   which.max.im(x) is superseded by im.apply(x, which.max)

   o smooth.ppp, smooth.fv, smooth.msr
   These functions are now deprecated, in favour of 'Smooth' with a capital 'S'

BUG FIXES

   o bw.ppl
   Crashed if the point pattern had multiple points at the same location.
   Fixed.

   o quantile
   Crashed when applied to the result of 'ewcdf'.
   Fixed.

   o marks<-.ppp
   Crashed with a message about 'unrecognised format'
   if the current or replacement values of marks
   were date/time values (belonging to class 'Date' or 'POSIXt').
   Fixed.

   o plot.im
   Crashed in case log=TRUE if the window was not a rectangle.
   Fixed.

   o vcov.ppm
   Crashed sometimes for models with a hard core term
   (Hardcore, StraussHard, MultiHard or MultiStrauss interactions).
   Spotted by Rasmus Waagepetersen.
   Fixed.

   o multiplicity.data.frame
   Results were incorrect and included NA's (spotted by Sebastian Meyer).
   Fixed.

   o markvar
   Values were incorrect.
   Fixed.

   o Smooth.ppp
   Ignored argument 'diggle'.
   Fixed.

   o rotate.im, affine.im
   Factor-valued images were not handled correctly.
   Fixed.

   o shift.layered
   If argument 'origin' was used, different layers were shifted by 
   different amounts.
   Fixed.

   o tile.areas
   Sometimes returned a list instead of a numeric vector.
   Fixed.

   o print.ppp
   If the marks were date/time values (belonging to class 'Date' or 'POSIXt'),
   print.ppp reported that they were double precision numbers.
   Fixed.

   o plot.layered
   Graphics were mangled if the argument 'add=FALSE' was given explicitly.
   Fixed.

   o Smooth.ppp
   The argument 'sigma' was only recognised if it was explicitly named.
   For example in 'Smooth(X, 5)' the '5' was ignored.
   Fixed.

   o clusterset
   The bounding frame of the result was smaller than the
   original bounding frame of the point pattern dataset,
   when result="domain" and exact=TRUE.
   Fixed.

   o plot.im
   Ignored argument 'col' if it was a 'function(n)'.
   Fixed.

   o Kinhom
   Ignored argument 'correction' if there were more than 1000 points.
   Fixed.

   o [.fv
   Mangled the plot label for the y axis.
   Fixed.

   o cbind.fv
   Mangled the plot label for the y axis.
   Fixed.

   o plot.envelope
   Main title was always 'x'.
   Fixed.

   o print.ppp
   Ran over the right margin.
   Fixed.

   o union.owin, intersect.owin, setminus.owin
   Sometimes deleted the name of the unit of length.
   Fixed.

	CHANGES IN spatstat VERSION 1.35-0

OVERVIEW

   o We thank Melanie Bell, Leanne Bischof, Ida-Maria Sintorn,
     Ege Rubak, Martin Hazelton, Oscar Garcia, 
     Rasmus Waagepetersen, Abdollah Jalilian
     and Jens Oehlschlaegel for contributions.

   o Support for analysing replicated spatial point patterns.

   o New vignette on analysing replicated spatial point patterns.

   o Objective function surface plots.

   o Estimator of point process intensity using nearest neighbour distances.

   o Improved estimator of pair correlation function.

   o Four new datasets. 

   o Simple point-and-click interface functions for general use.

   o More support for fv objects.

   o More support for ppx objects.

   o Extensions to nearest neighbour functions.

   o Morphological operations accelerated.

   o Bug fix to pair correlation functions.

   o Bug fix to k-th nearest neighbour distances

   o Version nickname: 'Multiple Personality'

NEW CLASSES

  o mppm
  An object of class 'mppm' represents a Gibbs point process model
  fitted to several point pattern datasets. The point patterns may
  be treated as independent replicates of the same point process,
  or as the responses in an experimental design, so that the 
  model may depend on covariates associated with the design.
  Methods for this class include print, plot, predict, anova and so on.

  o objsurf
  An object of class 'objsurf' contains values of the likelihood 
  or objective function in a neighbourhood of the maximum.

  o simplepanel
  An object of class 'simplepanel' represents a spatial arrangement of buttons
  that respond to mouse clicks, supporting a simple, robust graphical interface.
  
NEW FUNCTIONS

  o mppm
  Fit a Gibbs model to several point patterns.
  The point pattern data may be organised as a designed experiment
  and the model may depend on covariates associated with the design.

  o anova.mppm
  Analysis of Deviance for models of class mppm

  o coef.mppm
  Extract fitted coefficients from a model of class mppm

  o fitted.mppm
  Fitted intensity or conditional intensity for a model of class mppm

  o kstest.mppm
  Kolmogorov-Smirnov test of goodness-of-fit for a model of class mppm

  o logLik.mppm
  log likelihood or log pseudolikelihood for a model of class mppm

  o plot.mppm
  Plot the fitted  intensity or conditional intensity of a model of class mppm

  o predict.mppm
  Compute the fitted  intensity or conditional intensity 
  of a model of class mppm

  o quadrat.test
  Quadrat counting test of goodness-of-fit for a model of class mppm

  o residuals.mppm
  Point process residuals for a model of class mppm

  o subfits
  Extract point process models for each individual point pattern dataset,
  from a model of class mppm

  o vcov.mppm
  Variance-covariance matrix for a model of class mppm

  o integral.msr
  Integral of a measure.

  o objsurf
  For a model fitted by optimising an objective function, this command
  computes the objective function in a neighbourhood of the optimal value.

  o contour.objsurf, image.objsurf, persp.objsurf, plot.objsurf
  Plot an 'objsurf' object.

  o fvnames
  Define groups of columns in a function value table, for use in plot.fv, etc

  o multiplicity
  New generic function for which multiplicity.ppp is a method.

  o unique.ppx, duplicated.ppx, multiplicity.ppx
  Methods for unique(), duplicated() and multiplicity() for 'ppx' objects.
  These also work for 'pp3' and 'lpp' objects.

  o closepairs, crosspairs, closepaircounts, crosspaircounts
  Low-level functions for finding all close pairs of points 

  o nndensity 
  Estimate point process intensity using k-th nearest neighbour distances

  o simplepanel, run.simplepanel
  Support for a simple point-and-click interface for general use.

NEW DATASETS

   o pyramidal
   Diggle-Lange-Benes data on pyramidal neurons in cingulate cortex.
   31 point patterns divided into 3 groups.
   
   o waterstriders
   Nummelin-Penttinen waterstriders data.
   Three independent replicates of a point pattern formed by insects.

   o simba
   Simulated data example for mppm.
   Two groups of point patterns with different interpoint interactions.

   o demohyper
   Simulated data example for mppm.
   Point patterns and pixel image covariates, in two groups
   with different regression coefficients.

SIGNIFICANT USER-VISIBLE CHANGES

   o plot.hyperframe
   The argument 'e' now has a different format.
   Instead of plot(h, plot(XYZ)) one must now type plot(h, quote(plot(XYZ)))
   This is necessary in order to avoid problems with 'S4 method dispatch'.
   
   o pcf.ppp, pcfinhom
   New argument 'divisor' enables better performance of the estimator
   of pair correlation function for distances close to zero.
   
   o applynbd
   The arguments N, R and criterion may now be specified together.

   o markstat
   The arguments N and R may now be specified together.

   o ppx
   New argument 'simplify' allows the result to be converted to
   an object of class 'ppp' or 'pp3' if appropriate.

   o as.function.fv
   Now allows multiple columns to be interpolated

   o multiplicity.ppp
   This function is now a method for the generic 'multiplicity'.
   It has also been accelerated.

   o nnfun.ppp, distfun.ppp
   New argument 'k' allows these functions to compute k-th nearest neighbours.

   o rVarGamma, kppm, vargamma.estK, vargamma.estpcf
   New argument 'nu.pcf' provides an alternative way to specify
   the kernel shape in the VarGamma model, instead of the existing
   argument 'nu.ker'. Function calls that use the ambiguous argument
   name 'nu' will no longer be accepted.

   o nnmap
   Image is now clipped to the original window.

   o dilation, erosion, opening, closing
   Polygonal computations greatly accelerated.

   o plot.colourmap
   Improved appearance and increased options, for discrete colourmaps.

   o plot.msr
   Improved appearance

   o plot.ppp, plot.owin
   An `empty' plot can now be generated by setting type="n"

   o nndist.ppp, nnwhich.ppp, nncross.ppp
   Column names of the result are now more informative.

BUG FIXES

   o nncross.ppp
   Results were completely incorrect when k > 1.
   Spotted by Jens Oehschlaegel. 
   Bug was introduced in spatstat 1.34-1. 
   Fixed.

   o rVarGamma
   Simulations were incorrect; they were generated using the wrong value
   of the parameter 'nu.ker'. Spotted by Rasmus Waagepetersen and
   Abdollah Jalilian. Bug was always present.		    
   Fixed.
   
   o pair correlation functions (pcf.ppp, pcfdot, pcfcross, pcfinhom, ...)
   The result had a negative bias at the maximum 'r' value,
   because contributions to the pcf estimate from interpoint distances
   greater than max(r) were mistakenly omitted. 
   Spotted by Rasmus Waagepetersen and Abdollah Jalilian. 
   Bug was always present.
   Fixed.

   o demo(spatstat)
   This demonstration script had some unwanted side-effects, such as
   rescaling the coordinates of standard datasets 'bramblecanes', 
   'amacrine' and 'demopat', which caused the demonstration to crash 
   when it was repeated several times, and caused errors in demo(data).
   Fixed.

   o rmh
   Visual debugger crashed sometimes with message 'XI not found'.
   Fixed.

   o predict.ppm
   Crashed if the model was fitted using 'covfunargs'.
   Fixed.

   o bounding.box
   Crashed if one of the arguments was NULL.
   Fixed.

   o multiplicity.ppp
   Did not handle data frames of marks. 
   Fixed.

	CHANGES IN spatstat VERSION 1.34-1

OVERVIEW

   o We thank Kurt Hornik, Ted Rosenbaum, Ege Rubak and Achim Zeileis
    for contributions.

   o Important bug fix.

SIGNIFICANT USER-VISIBLE CHANGES

   o as.box3
   Now accepts objects of class 'ppx' or 'boxx'.

   o crossdist.ppp, crossdist.pp3, crossdist.default
   New argument 'squared' allows the squared distances to be computed
   (saving computation time in some applications)

BUG FIXES

   o union.owin, is.subset.owin, dilation.owin
   Results were sometimes completely wrong for polygons with holes.
   Spotted by Ted Rosenbaum.
   Fixed.

   o psstA, areaLoss
   Crashed in some cases, with error message
   'Number of items to replace is not a multiple of replacement length'. 
   Spotted by Achim Zeileis.
   Fixed.

	CHANGES IN spatstat VERSION 1.34-0

OVERVIEW

   o We thank Andrew Bevan, Ege Rubak, Aruna Jammalamadaka, 
   Greg McSwiggan, Jeff Marcus, Jose M Blanco Moreno,
   and Brian Ripley for contributions.

   o spatstat and all its dependencies are now Free Open Source.

   o spatstat does not require the package 'gpclib' any more.
   
   o spatstat now depends on the packages 'tensor', 'abind' and 'polyclip'

   o polygon clipping is now enabled always.

   o Substantially more support for point patterns on linear networks.

   o Faster computations for pairwise interaction models.

   o Bug fixes in nearest neighbour calculations.

   o Bug fix in leverage and influence diagnostics.

   o Version nickname: "Window Cleaner"

   o spatstat now requires R version 3.0.2 or later

NEW FUNCTIONS

   o as.lpp
   Convert data to a point pattern on a linear network.

   o distfun.lpp
   Distance function for point pattern on a linear network.

   o eval.linim
   Evaluate expression involving pixel images on a linear network.

   o linearKcross, linearKdot, linearKcross.inhom, linearKdot.inhom
   Multitype K functions for point patterns on a linear network

   o linearmarkconnect, linearmarkequal
   Mark connection function and mark equality function 
   for multitype point patterns on a linear network

   o linearpcfcross, linearpcfdot, linearpcfcross.inhom, linearpcfdot.inhom
   Multitype pair correlation functions for point patterns on a linear network

   o linfun
   New class of functions defined on a linear network

   o nndist.lpp, nnwhich.lpp, nncross.lpp
   Methods for nndist, nnwhich, nncross for point patterns on a linear network

   o nnfun.lpp
   Method for nnfun for point patterns on a linear network

   o vcov.lppm
   Variance-covariance matrix for parameter estimates of a fitted
   point process model on a linear network.

   o bilinearform
   Computes a bilinear form 

   o tilenames, tilenames<-
   Extract or change the names of tiles in a tessellation.

SIGNIFICANT USER-VISIBLE CHANGES

   o package dependencies 
   Previous versions of spatstat used the package 'gpclib' 
   to perform geometrical calculations on polygons.
   Spatstat now uses the package 'polyclip' for polygon calculations instead.

   o free open-source licence
   The restrictive licence conditions of 'gpclib' no longer apply 
   to users of spatstat. Spatstat and all its dependencies are now
   covered by a free open-source licence.

   o polygon clipping
   In previous versions of spatstat, geometrical calculations
   on polygons could be performed 'exactly' using gpclib
   or 'approximately' using pixel discretisation. 
   Polygon calculations are now always performed 'exactly'.
   
   o intersect.owin, union.owin, setminus.owin
   If A and B are polygons, the result is a polygon.

   o erosion, dilation, opening, closing
   If the original set is a polygon, the result is a polygon.

   o intersect.tess, dirichlet
   The tiles of the resulting tessellation are polygons 
   if the input was polygonal.

   o plot.owin
   Polygons with holes can now be plotted with filled colours
   on any device.

   o lppm
   New arguments 'eps' and 'nd' control the quadrature scheme.

   o pairwise interaction Gibbs models
   Many calculations for these models have been accelerated.

BUG FIXES

   o nncross.pp3
   Values were completely incorrect in some cases.
   Usually accompanied by a warning about NA values.
   (Spotted by Andrew Bevan.)
   Fixed.

   o nnmap, nnmark
   A small proportion of pixels had incorrect values.
   [These were the pixels lying on the boundary of a Dirichlet cell.]
   Fixed. 

   o leverage.ppm, influence.ppm, dfbetas.ppm
   Results were incorrect for non-Poisson processes.
   Fixed.

   o distcdf
   Results were incorrect in some cases
   when W was a window and V was a point pattern.
   Fixed.

   o Kcross, Kdot, pcfcross, pcfdot
   Results were incorrect in some rare cases.
   Fixed.

   o as.fv.kppm
   Erroneously returned a NULL value.
   Fixed.

   o vcov.ppm
   For point process models fitted with method = 'logi',
   sometimes crashed with error "object 'fit' not found".
   (Spotted by Ege Rubak).
   Fixed.

   o vcov.ppm
   For multitype point process models, sometimes crashed
   with error "argument 'par' is missing".
   Fixed.

   o plot.im
   Crashed if some of the pixel values were infinite.
   Fixed.

   o owin 
   owin(poly=..) crashed if there were NA's in the polygon coordinates.
   Spotted by Jeff Marcus.
   Fixed.

   o plot.fv
   Crashed, giving an incomprehensible error,
   if the plot formula contained a number with a decimal point.
   Fixed.

   o alltypes
   Crashed if envelopes=TRUE and global=TRUE, 
   with error message 'csr.theo not found'.
   Spotted by Jose M Blanco Moreno.
   Fixed.

   o chop.tess, rMosaicField
   Format of result was garbled in some cases.
   Fixed.

   o vcov.ppm
   Sometimes gave an irrelevant warning "parallel option not available".
   Fixed.

	CHANGES IN spatstat VERSION 1.33-0

OVERVIEW

   o We thank Kurt Hornik and Brian Ripley for advice.

   o The package namespace has been modified.

   o Numerous internal changes.

   o Likelihood cross-validation for smoothing bandwidth.

   o More flexible models of intensity in cluster/Cox processes.

   o New generic function for smoothing.

   o Version nickname: 'Titanic Deckchair'

NEW FUNCTIONS

    o bw.ppl
    Likelihood cross-validation technique 
    for bandwidth selection in kernel smoothing.

    o is.lppm, is.kppm, is.slrm
    Tests whether an object is of class 'lppm', 'kppm' or 'slrm'

    o Smooth
    New generic function for spatial smoothing.

    o Smooth.ppp, Smooth.fv, Smooth.msr
    Methods for Smooth
    (identical to smooth.ppp, smooth.fv, smooth.msr respectively)

    o fitted.kppm
    Method for 'fitted' for cluster/Cox models

SIGNIFICANT USER-VISIBLE CHANGES

    o namespace
    The namespace of the spatstat package has been changed.

    o internal functions
    Some undocumented internal functions are no longer visible,
    as they are no longer exported in the namespace. These functions
    can still be accessed using the form spatstat:::functionname.
    Functions that are not visible are not guaranteed to exist 
    or to remain the same in future. 

    o methods
    For some generic functions defined in the spatstat package,
    it is possible that R may fail to find one of the methods
    for the generic. This is a temporary problem due to a restriction
    on the size of the namespace in R 3.0.1. It will be fixed in 
    future versions of R and spatstat. It only applies to methods
    for a generic which is a spatstat function (such as nndist)
    and does not apply to methods for generics defined elsewhere
    (such as density). In the meantime, if this problem should occur, 
    it can be avoided by calling the method explicitly, in the form
    spatstat:::genericname.classname.

    o speed
    The package should run slightly faster overall, due to the
    improvement of the namespace, and changes to internal code.

    o envelope
    New argument 'envir.simul' determines the environment
    in which to evaluate the expression 'simulate'.

    o kppm
    More flexible models of the intensity, and greater control over the
    intensity fitting procedure, are now possible using the arguments
    'covfunargs', 'use.gam', 'nd', 'eps' passed to ppm.
    Also the argument 'X' may now be a quadrature scheme.

    o distcdf
    Arguments W and V can now be point patterns.

    o Kest
    New option: correction = "good" 
    selects the best edge correction that can be computed in reasonable time.

    o bw.diggle
    Accelerated.

    o predict.ppm
    Calculation of standard error has been accelerated.

    o smooth.ppp, smooth.fv, smooth.msr
    These functions will soon be 'Deprecated' in favour of
    the methods Smooth.ppp, Smooth.fv, Smooth.msr respectively.

    o stratrand, overlap.owin, update.slrm, edge.Trans, edge.Ripley
    These already-existing functions are now documented.

BUG FIXES

    o kppm, matclust.estpcf, pcfmodel
    The pair correlation function of the Matern Cluster Process
    was evaluated incorrectly at distances close to 0.
    This could have affected the fitted parameters 
    in matclust.estpcf() or kppm(clusters="MatClust").
    Fixed.

    o anova.ppm
    Would cause an error in future versions of R
    when 'anova.glm' is removed from the namespace.
    Fixed.

	CHANGES IN spatstat VERSION 1.32-0

OVERVIEW

   o We thank Ege Rubak for major contributions.

   o Thanks also to Patrick Donnelly, Andrew Hardegen,
     Tom Lawrence, Robin Milne, Gopalan Nair and Sean O'Riordan.

   o New 'logistic likelihood' method for fitting Gibbs models.

   o Substantial acceleration of several functions
     including profile maximum pseudolikelihood
     and variance calculations for Gibbs models.

   o Nearest neighbours for point patterns in 3D

   o Nearest-neighbour interpolation in 2D

   o New 'progress plots' 

   o Hard core thresholds can be estimated automatically.

   o More support for colour maps

   o More support for 'fv' objects

   o Spatstat now has version nicknames.
   The current version is "Logistical Nightmare".
 
   o Minor improvements and bug fixes.

NEW FUNCTIONS

   o nncross.pp3
   Method for 'nncross' for point patterns in 3D

   o nnmark
   Mark of nearest neighbour - can be used for interpolation

   o dclf.progress, mad.progress
   Progress plots (envelope representations) for the DCLF and MAD tests.

   o deriv.fv
   Numerical differentiation for 'fv' objects.

   o interp.colourmap
   Smooth interpolation of colour map objects - makes it easy to build
   colour maps with gradual changes in colour

   o tweak.colourmap
   Change individual colour values in a colour map object

   o beachcolourmap
   Colour scheme appropriate for `altitudes' (signed numerical values)

   o as.fv
   Convert various kinds of data to an 'fv' object

   o quadscheme.logi
   Generates quadrature schemes for the logistic method of ppm.

   o beginner
   Introduction for beginners.

SIGNIFICANT USER-VISIBLE CHANGES

   o ppm
   New option: method = "logi" 
   Fits a Gibbs model by the newly developed 'logistic likelihood' method
   which is often faster and more accurate than maximum pseudolikelihood.
   Code contributed by Ege Rubak.
   
   o profilepl
   Greatly accelerated, especially for area-interaction models.

   o vcov.ppm
   Greatly accelerated for higher-order interaction models.

   o smooth.ppp
   Now handles bandwidths equal to zero (by invoking 'nnmark')

   o Hardcore, StraussHard
   The hard core distance 'hc' can now be omitted; 
   it will be estimated from data.

   o plot.ppp
   Now behaves differently if there are multiple columns of marks.
   Each column of marks is plotted, in a series of separate plots
   arranged side-by-side.

   o plot.im
   Argument 'col' can now be a function

   o lohboot
   Now computes confidence intervals for L-functions as well
   (fun="Lest" or fun="Linhom")

   o dclf.test, mad.test
   The argument X can now be an object produced by a previous call
   to dclf.test or mad.

   o plot.fv
   Labelling of plots has been improved in some cases.

   o smooth.fv
   Further options added.

   o density.ppp
   The argument 'weights' can now be a matrix.

   o smooth.ppp
   Accelerated, when there are several columns of marks.

   o density.ppp
   Accelerated slightly.

   o simulate.ppm, simulate.kppm
   The total computation time is also returned.

   o simulate.kppm
   Now catches errors (such as 'insufficient memory').
   
   o latest.news, licence.polygons
   Can now be executed by typing the name of the function without parentheses.

   o latest.news
   The text is now displayed one page at a time.

BUG FIXES

   o Hest, Gfox, Jfox
   The 'raw' estimate was not computed correctly (or at least 
   it was not the raw estimate described in the help files).
   Spotted by Tom Lawrence.
   Fixed.

   o edges2vees
   Format of result was incorrect if there were fewer than 3 edges.
   Fixed.

   o Jfox
   The theoretical value (corresponding to independence between X and Y)
   was erroneously given as 0 instead of 1.
   Spotted by Patrick Donnelly.
   Fixed.

   o ppm, quadscheme, default.dummy 
   If the grid spacing parameter 'eps' was specified,
   the quadrature scheme was sometimes slightly incorrect
   (missing a few dummy points near the window boundary).
   Fixed.

   o print.timed
   Matrices were printed incorrectly.
   Fixed.

	CHANGES IN spatstat VERSION 1.31-3

OVERVIEW

   o spatstat now 'Suggests' the package 'tensor'

   o Code slightly accelerated.

   o More support for pooling of envelopes.

   o Bug fixes.

NEW FUNCTIONS

   o nnmap
   Given a point pattern, finds the k-th nearest point in the pattern
   from each pixel in a raster.

   o coef.fii, coef.summary.fii
   Extract the interaction coefficients of a fitted interpoint interaction

   o edges2vees
   Low-level function for finding triples in a graph.


SIGNIFICANT USER-VISIBLE CHANGES

   o predict.ppm
   New argument 'correction' allows choice of edge correction
   when calculating the conditional intensity.

   o pool.envelope
   New arguments 'savefuns' and 'savepatterns'.

   o pool.envelope
   Envelopes generated with VARIANCE=TRUE can now be pooled.

   o pool.envelope
   The plot settings of the input data are now respected.

   o Numerous functions have been slightly accelerated.

BUG FIXES

   o predict.ppm
   Calculation of the conditional intensity omitted the edge correction
   if correction='translate' or correction='periodic'.
   Fixed.

   o shift.lpp, rotate.lpp, scalardilate.lpp, affine.lpp,
    shift.linnet, rotate.linnet, scalardilate.linnet, affine.linnet
   The enclosing window was not correctly transformed. 
   Fixed.

   o rHardcore, rStraussHard, rDiggleGratton, rDGS
   The return value was invisible.
   Fixed.

   o ppm
   In rare cases the results obtained with forcefit=FALSE and forcefit=TRUE
   were different, due to numerical rounding effects.
   Fixed.

	CHANGES IN spatstat VERSION 1.31-2

OVERVIEW

   o We thank Robin Corria Anslie, Julian Gilbey, Kiran Marchikanti,
   Ege Rubak and Thordis Linda Thorarinsdottir for contributions.

   o spatstat now depends on R 3.0.0

   o More support for linear networks

   o More functionality for nearest neighbours

   o Bug fix in fitting Geyer model

   o Performance improvements and bug fixes

NEW FUNCTIONS

   o affine.lpp, shift.lpp, rotate.lpp, rescale.lpp, scalardilate.lpp
   Geometrical transformations for point patterns on a linear network

   o affine.linnet, shift.linnet, rotate.linnet, 
   rescale.linnet, scalardilate.linnet
   Geometrical transformations for linear networks

   o [.linnet
   Subset operator for linear networks

   o timed
   Records the computation time taken
   
SIGNIFICANT USER-VISIBLE CHANGES

   o nncross
   nncross.ppp can now find the k-th nearest neighbours, for any k.

   o nndist, nnwhich
   New argument 'by' makes it possible to find nearest neighbours
   belonging to specified subsets in a point pattern, for example,
   the nearest neighbour of each type in a multitype point pattern.

   o [.fv
   Now handles the argument 'drop'.

   o with.fv
   Argument 'drop' replaced by new argument 'fun'
   (with different interpretation).

   o [.lpp
   Subset index may now be a window (class 'owin')

   o Kest
   Options correction='border' and correction='none'
   now run about 4 times faster, thanks to Julian Gilbey.

   o density.ppp
   Numerical underflow no longer occurs when sigma is very small
   and 'at="points"'. A warning is no longer issued.
   Thanks to Robin Corria Anslie.

   o crossing.psp
   New argument 'fatal' allows the user to handle empty intersections

   o union.owin
   It is now guaranteed that if A is a subset of B, then union.owin(A,B)=B.

   o plot.colourmap
   Now passes arguments to axis() to control the plot.
   Appearance of plot improved.

   o image.listof
   Now passes arguments to plot.colourmap() if equal.ribbon=TRUE.

   o kppm
   Accelerated (especially for large datasets).

   o plot.envelope
   plot.envelope is now equivalent to plot.fv and is essentially redundant.

   o rThomas, rMatClust, rNeymanScott
   Improved explanations in help files.

   o All functions
   Many functions have been slightly accelerated.

BUG FIXES

   o ppm
   Results were incorrect for the Geyer saturation model
   with a non-integer value of the saturation parameter 'sat'.
   Spotted by Thordis Linda Thorarinsdottir.
   Bug introduced in spatstat 1.20-0, July 2010.
   Fixed.

   o ppm
   Fitting a stationary Poisson process using a nonzero value of 'rbord',
   as in "ppm(X, rbord=R)" with R > 0, gave incorrect results.
   Fixed.

   o predict.slrm
   Crashed with message 
   'longer object length is not a multiple of shorter object length' 
   if the original data window was not a rectangle.
   Fixed.

   o iplot
   Main title was sometimes incorrect.
   Fixed.

   o plot.layered
   Ignored argument 'main' in some cases.
   Fixed.

   o plot.listof, image.listof
   Crashed sometimes with a message 'figure margins too large'
   when equal.ribbon=TRUE.
   Fixed.

   o print.ppx
   Crashed if the object contained local coordinates.
   Fixed.

   o transect.im
   Crashed if the transect lay partially outside the image domain.
   Fixed.

   o rthin
   Crashed if X was empty.
   Fixed.

   o max.im, min.im, range.im
   Ignored additional arguments after the first argument.
   Fixed.

   o update.lppm
   Updated object did not remember the name of the original dataset.
   Fixed.

   o envelope
   Grey shading disappeared from plots of envelope objects 
   when the envelopes were transformed using eval.fv or eval.fasp.
   Fixed.

   
	CHANGES IN spatstat VERSION 1.31-1

OVERVIEW

   o We thank Marcelino de la Cruz, Daniel Esser, Jason Goldstick,
     Abdollah Jalilian, Ege Rubak and Fabrice Vinatier for contributions.

   o Nonparametric estimation and tests for 
     point patterns in a linear network.

   o More support for 'layered' objects.

   o Find clumps in a point pattern.

   o Connected component interaction model.

   o Improvements to interactive plots.

   o Visual debugger for Metropolis-Hastings algorithm.

   o Bug fix in Metropolis-Hastings simulation of Geyer process.

   o Faster Metropolis-Hastings simulation.

   o Faster computation of 'envelope', 'fv' and 'fasp' objects.

   o Improvements and bug fixes.

NEW FUNCTIONS

   o connected.ppp
   Find clumps in a point pattern.

   o kstest.lpp, kstest.lppm
   The spatial Kolmogorov-Smirnov test can now be applied 
   to point patterns on a linear network (class 'lpp') and 
   point processes on a linear network (class 'lppm').

   o bermantest.lpp, bermantest.lppm
   Berman's Z1 and Z2 tests can now be applied to point patterns
   on a linear network (class 'lpp') and point processes on a linear
   network (class 'lppm').

   o rhohat.lpp, rhohat.lppm
   Nonparametric estimation of the dependence of a point pattern
   on a spatial covariate: 'rhohat' now applies to 
   objects of class 'lpp' and 'lppm'.

   o intensity.lpp
   Empirical intensity of a point pattern on a linear network.

   o as.function.rhohat
   Converts a 'rhohat' object to a function,
   with extrapolation beyond the endpoints.

   o [.layered
   Subset operator for layered objects.

   o shift, rotate, affine, rescale, reflect, flipxy, scalardilate
   These geometrical transformations now work for 'layered' objects.

   o iplot.layered
   Interactive plotting for 'layered' objects.

   o as.owin.layered
   Method for as.owin for layered objects.

   o [.owin
   Subset operator for windows, equivalent to intersect.owin.

   o rcellnumber
   Generates random integers for the Baddeley-Silverman counterexample.

   o is.lpp
   Tests whether an object is a point pattern on a linear network.

   o is.stationary.lppm, is.poisson.lppm
   New methods for is.stationary and is.poisson for class 'lppm'

   o sessionLibs
   Print library names and version numbers (for use in Sweave scripts)

SIGNIFICANT USER-VISIBLE CHANGES

   o iplot
   iplot is now generic, with methods for 'ppp', 'layered' and 'default'.
   iplot methods now support zoom and pan navigation.

   o rmh.default
   New argument 'snoop' allows the user to activate a visual debugger
   for the Metropolis-Hastings algorithm.

   o connected
   connected() is now generic, with methods for 'im', 'owin' and 'ppp'.

   o alltypes
   Now works for lpp objects 

   o rlabel
   Now works for lpp, pp3, ppx objects

   o plot.kstest
   Can now perform P-P and Q-Q plots as well.

   o plot.fasp
   New argument 'samey' controls whether all panels 
   have the same y limits.

   o plot.fasp
   Changed default value of 'samex'.

   o Objects of class 'envelope', 'fv' and 'fasp' 
   Reduced computation time and storage required for these objects.
   
   o pcfmodel.kppm
   Improved calculation.

   o plot.fv
   Improved collision-avoidance algorithm
   (for avoiding overlaps between curves and legend)

   o ppm
   Improved error handling

   o envelope
   All methods for 'envelope' now handle fun=NULL   

   o setminus.owin
   Better handling of the case where both arguments are rectangles.

   o rmh
   Simulation has been further accelerated.

   o lppm
   Accelerated.

   o vcov.ppm
   Accelerated.

   o marktable
   Accelerated.

   o Triplets() interaction
   Accelerated.

   o alltypes
   Accelerated when envelope=TRUE.

BUG FIXES

   o rmh
   Simulation of the Geyer saturation process was incorrect.
   [Bug introduced in previous version, spatstat 1.31-0.]
   Fixed.

   o rmh
   Simulation of the Geyer saturation process was 
   incorrectly initialised, so that the results of a short run 
   (i.e. small value of 'nrep') were incorrect, 
   while long runs were correct.
   [Bug introduced in spatstat 1.17-0, october 2009.]
   Fixed.

   o ppm 
   Objects fitted with use.gam=TRUE caused fatal errors in
   various functions including print, summary, vcov and model.frame.
   Spotted by Jason Goldstick.
   Fixed.

   o lpp, runiflpp, rpoislpp
   Empty point patterns caused an error.
   Fixed.

   o rmh.default
   Crashed for hybrid models, with message 
   'Attempt to apply non-function'.
   Spotted by Ege Rubak.
   Fixed.

   o relrisk
   Crashed when 'at="points"' for a multitype pattern
   with more than 2 types.
   Spotted by Marcelino de la Cruz.
   Fixed.

   o erosion.owin, dilation.psp, border
   Ignored the arguments "..." in some cases
   (namely when the window was polygonal and 'gpclib' was disabled).
   Fixed.

   o rsyst, rcell
   Did not correctly handle the argument 'dx'.
   Spotted by Fabrice Vinatier.
   Fixed.

   o correction="trans"
   Various functions such as Kest 
   no longer recognised 'correction = "trans"'.
   Fixed.

   o istat
   Crashed with an error message about envelopes. 
   Fixed.

   o summary.ppm, print.ppm
   p-values which were exactly equal to zero were reported as NA.
   Fixed.

   o [.im
   Crashed if the intersection consisted of
   a single row or column of pixels.
   Fixed.

   o plot.im
   Sometimes incorrectly displayed an image consisting of 
   a single row or column of pixels.
   Fixed.

   o plot.layered
   The plot region was determined by the first layer,
   so that objects in subsequent layers could sometimes 
   fall outside the plot region.
   Fixed.

   o transect.im
   If the arguments 'from' and 'to' were numeric vectors of length 2,
   the result was garbled.
   Fixed.   

   o Inhomogeneous K functions and pair correlation functions
   [Kinhom, pcfinhom, Kcross.inhom, Kdot.inhom, pcfcross.inhom, etc.]
   These functions reported an error 'lambda is not a vector'
   if the intensity argument lambda was computed using density(, at="points").
   Fixed.

   o rlabel
   Did not accept a point pattern with a hyperframe of marks.
   Fixed.

   o alltypes
   Crashed when envelope=TRUE if the summary function 'fun'
   did not have default values for the marks i and j.
   Fixed.

   o Kres, Gres, psst, psstA
   Ignored the unit of length.
   Fixed.

	CHANGES IN spatstat VERSION 1.31-0

OVERVIEW

   o We thank Frederic Lavancier and Ege Rubak for contributions.

   o Major bug fix in simulation of area-interaction process.

   o Metropolis-Hastings simulations accelerated.

   o Rounding of spatial coordinates

   o clmfires dataset corrected.

   o Bug fixes and minor improvements.

NEW FUNCTIONS

   o round.ppp
   Round the spatial coordinates of a point pattern 
   to a specified number of decimal places.

   o rounding
   Determine whether a dataset has been rounded.

SIGNIFICANT USER-VISIBLE CHANGES

   o rmh
   Simulation of the following models has been accelerated:
   areaint, dgs, diggra, fiksel, geyer, hardcore, lennard, multihard,
   strauss, straush, straussm, strausshm.

   o rmh
   The transition history of the simulation (which is saved if 'track=TRUE')
   now also contains the value of the Hastings ratio for each proposal.

   o clmfires
   The clmfires dataset has been modified to remove errors and inconsistencies.

   o plot.linim
   Appearance of the plot has been improved, when style='width'.

   o summary.ppm
   Now reports whether the spatial coordinates have been rounded.

   o dclf.test, mad.test
   The range of distance values ('rinterval') used in the test
   is now printed in the test output, and is saved as an attribute.

BUG FIXES

   o rmh
   Simulation of the Area-Interaction model was completely incorrect.
   Spotted by Frederic Lavancier.
   The bug was introduced in spatstat version 1.23-6 or later.
   Fixed.

   o dclf.test
   The test statistic was incorrectly scaled (by a few percent).
   This did not affect the p-value of the test.
   Fixed.

   o ppx
   If argument 'coord.type' was missing, various errors occurred:
   a crash may have occurred, or the results may have depended
   on the storage type of the data. 
   Spotted by Ege Rubak.
   Fixed. 

   o plot.ppx
   Crashed for 1-dimensional point patterns.
   Spotted by Ege Rubak.
   Fixed.

	CHANGES IN spatstat VERSION 1.30-0


OVERVIEW 

   o We thank Jorge Mateu, Andrew Bevan, Olivier Flores, Marie-Colette van Lieshout, Nicolas Picard and Ege Rubak for contributions.

   o The spatstat manual now exceeds 1000 pages.

   o Hybrids of point process models.

   o Five new datasets

   o Second order composite likelihood method for kppm.

   o Inhomogeneous F, G and J functions.

   o Delaunay graph distance

   o Fixed serious bug in 'lppm' for marked patterns.

   o bug fix in some calculations for Geyer model

   o Improvements to linear networks code

   o Pixel images can now be displayed with a logarithmic colour map.

   o spatstat now formally 'Depends' on the R core package 'grDevices'

   o miscellaneous improvements and bug fixes

NEW DATASETS

   o clmfires
   Forest fires in Castilla-La Mancha

   o gordon
   People sitting on the grass in Gordon Square, London

   o hyytiala 
   Mixed forest in Hyytiala, Finland (marked by species)

   o paracou
   Kimboto trees in Paracou, French Guiana (marked as adult/juvenile)

   o waka
   Trees in Waka national park (marked with diameters)

NEW FUNCTIONS

   o Hybrid
   The hybrid of several point process interactions
   [Joint research with Jorge Mateu and Andrew Bevan]

   o is.hybrid
   Recognise a hybrid interaction or hybrid point process model.

   o Finhom, Ginhom, Jinhom
   Inhomogeneous versions of the F, G and J functions
   [Thanks to Marie-Colette van Lieshout]

   o delaunay.distance
   Graph distance in the Delaunay triangulation.

   o distcdf
   Cumulative distribution function of the distance between
   two independent random points in a given window.

   o bw.frac
   Bandwidth selection based on window geometry

   o shortside.owin, sidelengths.owin
   Side lengths of (enclosing rectangle of) a window

SIGNIFICANT USER-VISIBLE CHANGES

   o ppm
   Can now fit models with 'hybrid' interactions
   [Joint research with Jorge Mateu and Andrew Bevan]

   o kppm
   Now has the option of fitting models using Guan's (2006)
   second order composite likelihood.

   o envelope.lpp
   Now handles multitype point patterns.

   o envelope.envelope
   New argument 'transform' allows the user to apply a transformation
   to previously-computed summary functions.

   o runifpointOnLines, rpoisppOnLines, runiflpp, rpoislpp
   Can now generate multitype point patterns.

   o rmhmodel, rmh, simulate.ppm
   Now handle point process models with 'hybrid' interactions.

   o kppm
   Accelerated, and more reliable, due to better choice of starting values 
   in the optimisation procedure.

   o kppm
   The internal format of kppm objects has changed.

   o minimum contrast estimation
   Error messages from the optimising function 'optim' are now trapped
   and handled.

   o rhohat
   This command is now generic, with methods for ppp, quad, and ppm.

   o raster.x, raster.y, raster.xy
   These functions have a new argument 'drop'

   o summary.ppm
   Improved behaviour when the model covariates are a data frame.

   o progressreport
   Output improved.

   o second order summary functions
   (Kest, Lest, Kinhom, pcf.ppp, Kdot, Kcross, Ldot etc etc)
   These functions now accept correction="translation" as an 
   alternative to correction = "translate", for consistency.

   o plot.im
   New argument 'log' allows colour map to be equally spaced on a log scale.

   o as.owin.ppm, as.owin.kppm
   New argument 'from' allows the user to extract the spatial window
   of the point data (from="points") or the covariate images (from="covariates")

   o dclf.test, mad.test
   The rule for handling tied values of the test statistic has been changed.
   The tied values are now randomly ordered to obtain a randomised integer rank.

   o with.fv
   New argument 'enclos' allows evaluation in other environments

BUG FIXES

   o lppm
   For multitype patterns, the fitted model was completely incorrect
   due to an error in constructing the quadrature scheme.
   Fixed.

   o Geyer
   For point process models with the 'Geyer' interaction, 
   vcov.ppm() and suffstat() sometimes gave incorrect answers.
   [Spotted by Ege Rubak.]
   Fixed.

   o as.im.im
   Did not correctly handle factor-valued images
   if one of the arguments 'dimyx', 'eps', 'xy' was given.
   Fixed.

   o envelope.lppm
   Crashed if the model was multitype.
   Fixed.

   o lpp
   Did not handle empty patterns.
   Fixed.

   o density.ppp
   If 'sigma' was a bandwidth selection function such as bw.scott()
   which returned a numeric vector of length 2, a warning message was issued, 
   and the smoothing bandwidth was erroneously taken to be
   the first element of the vector.
   Fixed.

   o Fest, Jcross, Jdot, Jmulti
   If these functions were computed using correction = 'rs', 
   plotting them would sometimes give an error,      
   with the message "no finite x/y limits".
   Fixed.

   o pcfmodel.kppm
   For models with clusters="VarGamma"
   the value of the pcf at distance r=0 was given as NaN. 
   Fixed.

   o vcov.ppm
   Result was incorrect in rare cases, due to numerical rounding effects.
   Fixed.

   o rLGCP, simulate.kppm
   For models fitted to point patterns in an irregular window, 
   simulation sometimes failed, with a message that the image 'mu' 
   did not cover the simulation window.
   (Spotted by George Limitsios.)
   Fixed.

   o rLGCP, simulate.kppm
   Crashed sometimes with an error about unequal x and y steps
   (from 'GaussRF').
   Fixed.

	CHANGES IN spatstat VERSION 1.29-0

OVERVIEW 

   o We thank Colin Beale, Li Haitao, Frederic Lavancier, Erika Mudrak and Ege Rubak for contributions.

   o random sequential packing
 
   o Allard-Fraley estimator

   o method for pooling several quadrat tests

   o better control over dummy points in ppm

   o more support for data on a linear network

   o nearest neighbour map 

   o changes to subsetting of images

   o improvements and bug fixes 

NEW FUNCTIONS

   o clusterset
   Allard-Fraley estimator of high-density features in a point pattern

   o pool.quadrattest
   Pool several quadrat tests

   o nnfun
   Nearest-neighbour map of a point pattern or a line segment pattern

   o as.ppm
   Converts various kinds of objects to ppm

   o crossdist.lpp
   Shortest-path distances between pairs of points in a linear network

   o nobs.lppm
   Method for 'nobs' for lppm objects.

   o as.linim
   Converts various kinds of objects to 'linim'

   o model.images.slrm
   Method for model.images for slrm objects

   o rotate.im
   Rotate a pixel image

SIGNIFICANT USER-VISIBLE CHANGES

   o "[.im" and "[<-.im"
   New argument 'j' allows any type of matrix indexing to be used.

   o "[.im"
   Default behaviour changed in the case of a rectangular subset.
   New argument 'rescue' can be set to TRUE to reinstate previous behaviour.

   o rSSI
   Performs 'Random Sequential Packing' if n=Inf.

   o ppm
   New argument 'eps' determines the spacing between dummy points.
   (also works for related functions quadscheme, default.dummy, ...)

   o fitted.ppm, predict.ppm
   Argument 'new.coef' specifies a vector of parameter values
   to replace the fitted coefficients of the model.

   o lppm
   Stepwise model selection using step() now works for lppm objects.

   o vcov.slrm
   Can now calculate correlation matrix or Fisher information matrix
   as well as variance-covariance matrix.

   o eval.fv
   Improved behaviour when plotted.

   o "[.fv"
   Improved behaviour when plotted.

   o lohboot
   When the result is plotted, the confidence limits are now shaded.

   o lohboot
   New argument 'global' allows global (simultaneous) confidence bands
   instead of pointwise confidence intervals.

   o vcov.ppm
   Accelerated by 30% in some cases.

   o quadrat.test.splitppp
   The result is now a single object of class 'quadrattest'

   o progressreport
   Improved output (also affects many functions which print progress reports)

   o Full redwood data (redwoodfull)
   Plot function redwoodfull.extra$plotit has been slightly improved.

   o nncross
   This function is now generic, with methods for 'ppp' and 'default'.

   o distfun
   The internal format of objects of class 'distfun' has been changed.

   o duplicated.ppp, unique.ppp   
   New argument 'rule' allows behaviour to be consistent with package 'deldir'

BUG FIXES

   o bdist.tiles
   Values were incorrect in some cases due to numerical error.
   (Spotted by Erika Mudrak.)
   Fixed.

   o vcov.ppm, suffstat
   These functions sometimes gave incorrect values 
   for marked point process models.
   Fixed.

   o simulate.ppm, predict.ppm
   Did not correctly handle the 'window' argument. (Spotted by Li Haitao).
   Fixed.

   o smooth.ppp, markmean
   If sigma was very small, strange values were produced, due to
   numerical underflow. (Spotted by Colin Beale).
   Fixed.

   o MultiHard, MultiStrauss, MultiStraussHard
   Crashed if the data point pattern was empty.
   (Spotted by Ege Rubak).
   Fixed.

   o vcov.ppm
   Crashed sporadically, with multitype interactions.
   (Spotted by Ege Rubak).
   Fixed.

   o rStrauss, rHardcore, rStraussHard, rDiggleGratton, rDGS
   If the simulated pattern was empty, these functions would either
   crash, or return a pattern containing 1 point.
   (Spotted by Frederic Lavancier).
   Fixed.

   o model.matrix.slrm
   Crashed if the model was fitted using split pixels.
   Fixed.

   o residuals.ppm, diagnose.ppm
   Did not always correctly handle models that included offset terms.
   Fixed.

   o project.ppm
   When a model was projected by project.ppm or by ppm(project=TRUE),
   the edge corrections used the projected models were sometimes different
   from the edge corrections in the original model, so that the 
   projected and unprojected models were not comparable.
   Fixed.

   o plot.listof, plot.splitppp
   Crashed sometimes due to a scoping problem.
   Fixed.

   o dclf.test, mad.test
   Crashed if any of the function values were infinite or NaN.
   Fixed.

   o psstA
   Default plot did not show the horizontal line at y=0
   corresponding to a perfect fit.
   Fixed.

   o vcov.ppm
   names attribute was spelt incorrectly in some cases.
   Fixed.


	CHANGES IN spatstat VERSION 1.28-2

OVERVIEW 

   o We thank Thomas Bendtsen, Ya-Mei Chang, Daniel Esser, 
     Robert John-Chandran, Ege Rubak and Yong Song for contributions.

   o New code for Partial Residual Plots and Added Variable Plots.

   o maximum profile pseudolikelihood computations vastly accelerated.

   o New dataset: cells in gastric mucosa

   o now possible to capture every k-th state of Metropolis-Hastings algorithm.

   o size of 'ppm' objects reduced.

   o scope of 'intensity.ppm' extended.

   o quadrat.test can now perform Monte Carlo tests and one/two-sided tests

   o improvements to 'plot.fv'

   o improvement to 'rescale'

   o some datasets reorganised.

   o numerous bug fixes

NEW DATASET

   o mucosa
   Cells in gastric mucosa
   Kindly contributed by Dr Thomas Bendtsen

NEW FUNCTIONS

   o parres
   Partial residual plots for spatial point process models.
   A diagnostic for the form of a covariate effect.

   o addvar
   Added variable plots for spatial point process models.
   A diagnostic for the existence of a covariate effect.

SIGNIFICANT USER-VISIBLE CHANGES

  o profilepl
  Accelerated (typically by a factor of 5).

  o rmh, rmhcontrol
  It is now possible to save every k-th iteration of the Metropolis-Hastings
  algorithm. The arguments 'nsave' and 'nburn' may be given to rmh
  or to rmhcontrol. They specify that the point pattern will be saved
  every 'nsave' iterations, after an initial burn-in of 'nburn' iterations.

  o simulate.ppm
  New argument 'singlerun' determines whether the simulated patterns
  are generated using independent runs of the Metropolis-Hastings algorithm
  or are obtained by performing one long run of the algorithm and saving
  every k-th iteration.

  o exactMPLEstrauss
  New argument 'project' determines whether the parameter gamma
  is constrained to lie in [0,1].

  o intensity.ppm
  Now works for stationary point process models with the interactions
  DiggleGratton, DiggleGatesStibbard, Fiksel, PairPiece and Softcore.

  o plot.fv
  Improved algorithm for avoiding collisions between graphics and legend.

  o plot.fv
  New argument 'log' allows plotting on logarithmic axes.

  o envelope
  Can now calculate an estimate of the true significance level
  of the "wrong" test (which declares the observed summary function
  to be significant if it lies outside the pointwise critical boundary
  anywhere). Controlled by new argument 'do.pwrong'.

  o quadrat.test
  New argument 'alternative' allows choice of alternative hypothesis
  and returns one-sided or two-sided p-values as appropriate.

  o quadrat.test
  Can now perform Monte Carlo test as well 
  (for use in small samples where the chi^2 approximation is inaccurate)

  o Softcore
  Improved numerical stability.
  New argument 'sigma0' for manual control over rescaling.

  o rescale
  If scale argument 's' is missing, then the data are rescaled
  to native units. For example if the current unit is 0.1 metres, 
  coordinates will be re-expressed in metres.

  o psst
  Extra argument 'verbose=TRUE'

  o is.subset.owin
  Accelerated for polygonal windows

  o rmh.default
  'track' is no longer a formal argument of rmh.default; it is now a 
  parameter of rmhcontrol. However there is no change in usage: 
  the argument 'track' can still be given to rmh.default.

  o clf.test
  Has been renamed 'dclf.test' 
  to give proper attribution to Peter Diggle.

  o betacells
  This dataset has been restructured. The vector of cell profile areas,
  formerly given by betacells.extra$area, has now been included
  as a column of marks in the point pattern 'betacells'.

  o ants
  The function ants.extra$plot() has been renamed plotit() 
  for conformity with other datasets.

  o redwoodfull
  The function redwoodfull.extra$plot() has been renamed plotit() 
  for conformity with other datasets.

  o nbfires
  For conformity with other datasets, there is now an object nbfires.extra

BUG FIXES

  o ripras
  Expansion factor was incorrect in the rectangular case.
  Fixed.

  o Triplets
  Crashed sometimes with error "dim(X) must have positive length".
  Fixed.

  o affine.im
  Crashed in the case of a diagonal transformation matrix!
  Spotted by Ege Rubak.
  Fixed.

  o envelope.envelope
  Ignored the argument 'global'.
  Fixed.

  o MultiStraussHard
  The printed output showed the hardcore radii as NULL.
  Spotted by Ege Rubak.
  Fixed.

  o "[.psp"
  Crashed if the data were generated by rpoisline().
  Spotted by Marcelino de la Cruz.
  Fixed.

  o plot.linim
  If style="colour", the main title was always "x".
  Fixed.

  o plot.ppx
  Setting add=TRUE did not prevent the domain being plotted.
  Fixed.

  o rmh
  Crashed if x.start was an empty point pattern.
  Spotted by Ege Rubak.
  Fixed.

  o as.ppp.data.frame
  Crashed if any points lay outside the window.
  Spotted by Ege Rubak.
  Fixed.

  o Ripley isotropic edge correction
  Divide-by-zero error in rare cases.
  Spotted by Daniel Esser.
  Fixed.

  o summary functions
  For many of the summary functions (e.g. Kest, pcf),
  the result of saving the object to disc was an enormous file.
  Spotted by Robert John-Chandran.
  Fixed.

  o pcf.fv
  Default plot was wrongly coloured.
  Fixed.
  
	CHANGES IN spatstat VERSION 1.28-1

OVERVIEW 

   o We thank Ege Rubak, Gopal Nair, Jens Oehlschlaegel and Mike Zamboni
     for contributions.

   o New approximation to the intensity of a fitted Gibbs model.

   o Minor improvements and bug fixes

   o spatstat now 'Suggests' the package 'gsl'

NEW FUNCTIONS

   o intensity, intensity.ppp, intensity.ppm
   Calculate the intensity of a dataset or fitted model.
   Includes new approximation to the intensity of a fitted Gibbs model

   o LambertW
   Lambert's W-function

SIGNIFICANT USER-VISIBLE CHANGES

  o envelope
  Improved plot labels for envelopes that were generated using
  the 'transform' argument.

  o plot.fv
  Improved algorithm for collision detection.

  o plot.im
  Now returns the colour map used.

  o plot.listof, plot.splitppp
  Slight change to handling of plot.begin and plot.end

  o square
  Now accepts vectors of length 2

  o plot.fii
  Increased resolution of the plot obtained from plot(fitin(ppm(...))) 

  o image.listof
  If equal.ribbon=TRUE, the colour ribbon will no longer be 
  displayed repeatedly for each panel, 
  but will now be plotted only once, at the right hand side of the plot array.

BUG FIXES

  o vcov.ppm
  Results were sometimes incorrect for a Gibbs model with non-trivial trend.
  Spotted by Ege Rubak.
  Fixed.

  o nncross
  In rare cases the results could be slightly incorrect.
  Spotted by Jens Oehlschlaegel.
  Fixed.

  o plot.fv
  When add=TRUE, the x limits were sometimes truncated.
  Spotted by Mike Zamboni.
  Fixed.

  o plot.im
  Labels for the tick marks on the colour ribbon
  were sometimes ridiculous, e.g. "2.00000001".
  Fixed.

	CHANGES IN spatstat VERSION 1.28-0

OVERVIEW 

   o We thank Farzaneh Safavimanesh, Andrew Hardegen and Tom Lawrence 
     for contributions.

   o Improvements to 3D summary functions.

   o A multidimensional point pattern (ppx) can now have 'local' coordinates
   as well as spatial and temporal coordinates and marks.

   o Changed format for point patterns on a linear network (lpp).
   Changes are backward compatible. Many computations run faster.

   o More support for fitted cluster models (kppm).

   o split method for multidimensional point patterns (ppx)
   and point patterns on a linear network (lpp).

   o Fixed bug causing errors in plot.im

   o Miscellaneous improvements and bug fixes

NEW FUNCTIONS

   o exactMPLEstrauss
   Fits the stationary Strauss point process model
   using an exact maximum pseudolikelihood technique.
   This is mainly intended for technical investigation of algorithms.

   o split.ppx
   Method for 'split' for multidimensional point patterns (class 'ppx').
   This also works for point patterns on a linear network (class 'lpp').

   o model.images
   This function is now generic, with methods for classes ppm, kppm, lppm

   o model.frame, model.matrix
   These generic functions now have methods for classes kppm, lppm

   o as.owin.kppm, as.owin.lppm
   New methods for 'as.owin' for objects of class kppm, lppm

   o as.linnet.lppm
   Extracts the linear network in which a point process model was fitted.

SIGNIFICANT USER-VISIBLE CHANGES

   o class 'ppx'
   An object of class 'ppx' may now include 'local' coordinates 
   as well as 'spatial' and 'temporal' coordinates, and marks.

   o ppx
   Arguments have changed.
   
   o class 'lpp'
   The internal format of lpp objects has been extended
   (but is backward-compatible). Many computations run faster.
   To convert an object to the new format: X <- lpp(as.ppp(X), as.linnet(X)).

   o F3est
   Calculation of theoretical Poisson curve ('theo') has changed,
   and is now controlled by the argument 'sphere'.

   o rmh, rmhstart
   The initial state ('start') can now be missing or null.

   o im, as.im
   The pixel coordinates in an image object are now generated
   more accurately. This avoids a numerical error in plot.im.

   o eval.fv, eval.fasp
   Evaluation is now applied only to columns that contain
   values of the function itself (rather than values of the
   derivative, hazard rate, etc). This is controlled by the
   new argument 'dotonly'.

   o spatstat.options
   New option 'nvoxel'

   o quad.ppm
   Now accepts kppm objects.

   o str
   This generic function (for inspecting the internal structure of an object)
   now produces sensible output for objects of class 'hyperframe', 'ppx', 'lpp'

   o ppx, coords.ppx, coords<-.ppx
   The arguments to these functions have changed.

   o lgcp.estK, Kmodel
   Computation can be greatly accelerated 
   by setting spatstat.options(fastK.lgcp=TRUE).

   o G3est
   Computation accelerated.

   o envelope
   Computation slightly accelerated.

   o spatstat.options
   New option 'fastK.lgcp' 

BUG FIXES

   o nndist.psp
   Caused an error if length(k) > 1.
   Fixed.

   o plot.im
   Sometimes reported an error 
   "useRaster=TRUE can only be used with a regular grid."
   This was due to numerical rounding effects on the coordinates
   of a pixel image. 
   Fixed.
   
   o plot.fv
   If a formula was used to specify the plot,
   the names of variables in the formula were sometimes
   incorrectly matched to *functions*.
   Spotted by Farzaneh Safavimanesh.
   Fixed.

   o F3est
   Took a very long time if the containing box was very flat,
   due to the default value of 'vside'.
   Fixed.

   o rmh, rmhmodel
   An erroneous warning about 'outdated format of rmhmodel object' 
   sometimes occurred.
   Fixed.

   o marks<-.ppx
   Names of result were incorrect. Fixed.

   o hyperframe class
   Various minor bug fixes.


	CHANGES IN spatstat VERSION 1.27-0

OVERVIEW 

   o Variance estimates are now available for all Gibbs point process models.

   o Cressie-Loosmore-Ford test implemented

   o plot.fv now avoids collisions between the legend and the graphics.

   o Extension to predict.ppm

   o Improvements to envelopes and multitype summary functions. 

   o Line transects of a pixel image.

   o Changes to defaults in Metropolis-Hastings simulations.

   o More geometrical operations

   o Bug fixes.

   o We thank Aruna Jammalamadaka for contributions.

NEW FUNCTIONS

   o clf.test
   Perform the Cressie (1991)/ Loosmore and Ford (2006) test of CSR 
   (or another model)

   o mad.test
   Perform the Maximum Absolute Deviation test of CSR (or another model).

   o convolve.im
   Compute convolution of pixel images.

   o Kmulti.inhom
   Counterpart of 'Kmulti' for spatially-varying intensity.

   o rmhexpand
   Specify a simulation window, or a rule for expanding the
   simulation window, in Metropolis-Hastings simulation (rmh)

   o transect.im
   Extract pixel values along a line transect.

   o affine.im
   Apply an affine transformation to a pixel image.

   o scalardilate
   Perform scalar dilation of a geometrical object 
   relative to a specified origin.

   o reflect
   Reflect a geometrical object through the origin.

   o "[.lpp", "[.ppx"
   Subset operators for the classes "lpp" (point pattern on 
   linear network) and "ppx" (multidimensional space-time
   point pattern).
 
   o is.rectangle, is.polygonal, is.mask
   Determine whether a window w is a rectangle, a domain with polygonal 
   boundaries, or a binary pixel mask.

   o has.offset
   Determines whether a fitted model object (of any kind)
   has an offset.

SIGNIFICANT USER-VISIBLE CHANGES

   o predict.ppm
   This function can now calculate the conditional intensity of a model
   relative to any point pattern X (not just the original data pattern).

   o vcov.ppm
   This function now handles all Gibbs point process models.

   o plot.fv
   Collisions between the legend box and the graphics are now detected
   and avoided. 

   o rmh.ppm, rmh.default, simulate.ppm, qqplot.ppm, envelope.ppm
   These functions now have slightly different default behaviour
   because of changes to the handling of arguments to 'rmhcontrol'.

   o rmhcontrol
   The default value of the parameters 'periodic' and 'expand'
   has changed.

   o rmhcontrol
   The parameter 'expand' can now be in any format 
   acceptable to rmhexpand().

   o rmh.ppm, rmh.default, simulate.ppm
   Any 'rmhcontrol' parameter can now be given directly 
   as an argument to rmh.ppm, rmh.default or simulate.ppm.

   o Kmulti, Gmulti, Jmulti
   The arguments I, J can now be any kind of subset index
   or can be functions that yield a subset index.

   o envelope.envelope
   In envelope(E, fun=NULL) if E does not contain simulated
   summary functions, but does contain simulated point patterns, 
   then 'fun' now defaults to Kest, instead of flagging an error.

   o print.ppp, summary.ppp
   If the point pattern x was generated by Metropolis-Hastings
   simulation using 'rmh', then print(x) and summary(x) show 
   information about the simulation parameters.

   o print.ppm
   Standard errors for the parameter estimates,
   and confidence intervals for the parameters,
   can now be printed for all Gibbs models 
   (but are printed only for Poisson models by default).

   o eval.im
   Images with incompatible dimensions are now resampled 
   to make them compatible (if harmonize=TRUE).

   o spatstat.options
   New option 'print.ppm.SE' controls whether standard errors 
   and confidence intervals are printed for all Gibbs models,
   for Poisson models only, or are never printed.

   o inside.owin
   Now accepts the form list(x,y) for the first argument.

   o image.listof
   New argument 'equal.ribbon' allows several images to be plotted
   with the same colour map.

   o is.subset.owin
   Improved accuracy in marginal cases.

   o expand.owin
   Functionality extended to handle all types of expansion rule.

   o default.rmhcontrol, default.expand
   These functions now work with models of class 'rmhmodel' 
   as well as 'ppm'

   o print.rmhcontrol
   Output improved.

BUG FIXES

   o linearK, linearKinhom
   If any data points were located exactly at a vertex of the 
   linear network, the weights for Ang's correction were incorrect, 
   due to numerical error. This sometimes produced infinite 
   or NA values of the linear K function.
   Fixed.
   
   o predict.ppm
   In some cases, predict.ppm(type="cif") generated a spurious warning 
   that "number of rows of result is not a multiple of vector length."
   Fixed.

   o crossing.psp
   Results were sometimes incorrect due to numerical rounding error
   associated with GCC bug #323.
   Fixed.

   o MultiHard, MultiStrauss, MultiStraussHard
   If the mark values contained non-alphanumeric characters,
   the names of the interaction coefficients in coef(ppm(...)) 
   were sometimes garbled.
   Fixed.

   o profilepl
   For edge corrections other than the border correction,
   an error message about 'rbord' would sometimes occur.
   Fixed.

   o is.marked, is.multitype
   These functions gave the wrong answer for 'lpp' objects.
   Fixed.

   o marks<-.lpp,  marks<-.ppx
   Format of result was garbled if new columns of marks were added.
   Fixed.

   o reach.rmhmodel
   Gave the wrong answer for Geyer and BadGey models.
   Fixed.

   o envelope.envelope
   Ignored the argument 'savefuns'.
   Fixed.

   o BadGey
   Sometimes wrongly asserted that the parameter 'sat' was invalid.
   Occurred only in ppm(project=TRUE).
   Fixed.

	CHANGES IN spatstat VERSION 1.26-1

OVERVIEW 

   o Variance-covariance matrix for Gibbs point process models.

   o Bootstrap confidence bands for pair correlation function and K function.

   o Bug fix in scan test.

   o Area-interaction model accelerated.

   o we thank Jean-Francois Coeurjolly and Ege Rubak for contributions.

NEW FUNCTIONS

  o lohboot
  Computes bootstrap confidence bands for pair correlation function
  and K function using Loh's (2008) mark bootstrap.

SIGNIFICANT USER-VISIBLE CHANGES

  o vcov.ppm
  Now works for all Gibbs point process models, thanks to new code (and theory)
  from Jean-Francois Coeurjolly and Ege Rubak

  o AreaInter
  Computations related to the area-interaction point process 
  (ppm, predict.ppm, residuals.ppm, diagnose.ppm, qqplot.ppm)
  have been accelerated.

BUG FIXES

  o scan.test
  Results were sometimes incorrect due to numerical instability
  (a 'Gibbs phenomenon'). 
  Fixed.
  
	CHANGES IN spatstat VERSION 1.26-0

OVERVIEW 

   o We thank Jens Oehlschlaegel for contributions.

   o Further substantial acceleration of spatstat functions.

   o Workaround for bug in RandomFields package.

   o Numerous modifications to internal code.

NEW FUNCTIONS

   o RandomFieldsSafe
   There is a bug in the package 'RandomFields' (version <= 2.0.54)
   which causes a crash to occur, in the development version of R
   but not in R 2.15.0. To avoid crashing spatstat, we have written
   the temporary, undocumented function RandomFieldsSafe() 
   which returns TRUE if it is safe to use the RandomFields package.
   Examples in the spatstat help files for kppm, lgcp.estK, lgcp.estpcf
   and rLGCP are only executed if RandomFieldsSafe() returns TRUE.

SIGNIFICANT USER-VISIBLE CHANGES

   o Many functions
   Many spatstat functions now run faster, and will handle larger datasets,
   thanks to improvements in the internal code, 
   following suggestions from Jens Oehlschlaegel.

   o Many functions
   The response to an 'Interrupt' signal is slightly slower.

	CHANGES IN spatstat VERSION 1.25-5

OVERVIEW 

   o We thank Ya-Mei Chang, Jens Oehlschlaegel and Yong Song for contributions.

   o Extended functionality of 'rhohat' to local likelihood smoothing
   and bivariate smoothing.

   o Nearest neighbour distance computations accelerated.

   o spatstat now 'Suggests:' the package 'locfit'

NEW FUNCTIONS

   o rho2hat
   Bivariate extension of 'rhohat' for estimating spatial residual risk, 
   or intensity as a function of two covariates.

SIGNIFICANT USER-VISIBLE CHANGES

   o rhohat
   Estimation can now be performed using local likelihood fitting
   with the 'locfit' package, or using kernel smoothing.

   o nncross
   Substantially accelerated.
   New arguments added to control the return value and the sorting of data.

BUG FIXES

   o plot.msr
   Crashed if the argument 'box' was given.
   Fixed.

	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

BUG FIXES
 
    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.

BUG FIXES

    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.

BUG FIXES

    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'

BUG FIXES

    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' 

BUG FIXES

    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.

BUG FIXES

   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.

BUG FIXES

    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.

BUG FIXES

    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.
