
        CHANGES IN spatstat.explore VERSION 3.2-5

OVERVIEW

    o Minor corrections in documentation.

        CHANGES IN spatstat.explore VERSION 3.2-4

OVERVIEW

    o Integration of functions.

    o Changed defaults for Clark-Evans Test.

    o spatstat.explore no longer suggests package 'maptools'.
    
    o Minor improvements and bug fixes.

NEW FUNCTIONS

    o integral.fv
    Compute the integral of a function.

SIGNIFICANT USER-VISIBLE CHANGES

    o density.ppp
    New argument 'sameas'.

    o clarkevans.test
    The asymptotic test is now available for any choice of edge correction.

    o clarkevans.test
    New argument 'method' determines whether to use the asymptotic test
    or Monte Carlo test. The default has changed to method='asymptotic'.

    o clarkevans.test
    Default edge correction has changed, to avoid bias.

BUG FIXES

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

    o bw.smoothppp
    Crashed if every point in 'X' was duplicated.
    Fixed.

        CHANGES IN spatstat.explore VERSION 3.2-3

OVERVIEW

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

NEW FUNCTIONS

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

SIGNIFICANT USER-VISIBLE CHANGES

    o circdensity
    Improved output of 'print' method

    o envelope
    All methods for `envelope' now accept a summary function 
    in which the function argument is not named 'r'.
    This includes functions such as `transect.im' and `roc'.
    
    o plot.bermantest
    Improved layout for plots of Berman's Z2 test.

    o plot.fv
    New argument 'clip.xlim'.

    o circdensity
    Suppress annoying warning messages from density.default.
    
    o compileK, compilepcf
    Suppress annoying warning messages from density.default.
    
    o rhohat
    Suppress annoying warning messages from density.default.
    
BUG FIXES

    o envelope methods
    Results were malformed if the name of the function argument was not "r". 
    Fixed.
    
        CHANGES IN spatstat.explore VERSION 3.2-1

OVERVIEW

    o Internal bug fixes.


        CHANGES IN spatstat.explore VERSION 3.2-0

OVERVIEW

    o We thank Jonatan Gonzalez for contributions.
    
    o Changed the calculation of standard errors in density.ppp and relrisk.ppp.

    o Inline arithmetic for function tables ('fv') and arrays ('fasp')

    o Standard error calculation for Smooth.ppp (experimental)
    
    o multitype pair correlation functions can save numerator and denominator.

    o multitype inhomogeneous J functions.

    o More support for automatic bandwidth selection.
    
    o Bug fixes in calculation of standard errors.

NEW FUNCTIONS

    o Math.fv, Complex.fv, Summary.fv, Ops.fv
    Methods for arithmetic operations for function tables (class 'fv')
    
    o Math.fasp, Complex.fasp, Summary.fasp, Ops.fasp
    Methods for arithmetic operations for function arrays (class 'fasp')

    o Gcross.inhom, Gdot.inhom
    Multitype G functions for inhomogeneous point processes.
    
    o Jcross.inhom, Jdot.inhom, Jmulti.inhom
    Multitype J functions for inhomogeneous point processes.

    o summary.bw.optim, print.summary.bw.optim
    Method for 'summary' of optimised bandwidth objects (class 'bw.optim').
    These are the objects produced by the bandwidth selection functions
    such as bw.diggle, bw.scott, bw.pcf
    
SIGNIFICANT USER-VISIBLE CHANGES

    o density.ppp
    Standard error calculation is now available with any smoothing kernel.

    o density.ppp
    The interpretation of 'weights' in the calculation of standard error
    has changed. New argument 'wtype' controls this interpretation.
    
    o relrisk.ppp
    The interpretation of 'weights' in the calculation of standard error
    has changed. New argument 'wtype' controls this interpretation.

    o relrisk.ppp
    New argument 'fudge' specifies a constant numeric value that will be
    added to each estimate of point process intensity before calculation of
    relative risk.
    
    o Smooth.ppp
    Standard error calculation is now supported (Experimental).

    o pcfcross, pcfdot, pcfmulti
    New argument 'ratio' makes it possible to save the numerator and
    denominator of the function estimates, so that estimates can be pooled.
    
    o bw.relrisk.ppp
    Additional arguments '...' are now passed to 'density.ppp'.

    o eval.fasp
    Automatically-generated labels have been improved.

    o relrisk.ppp
    Issues a warning if numerical underflow is detected.

    o rhohat.ppp, rhohat.quad
    New argument 'rule.eps' passed to 'as.mask'.
    
BUG FIXES

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

        CHANGES IN spatstat.explore VERSION 3.1-0

OVERVIEW

    o Pair correlation functions allow more control over smoothing parameters.
    
    o Improved support for one-dimensional smoothing kernels.

    o Bug fixes in plot.fv.

    o Internal improvements and bug fixes.

SIGNIFICANT USER-VISIBLE CHANGES

    o kernel.moment
    New arguments 'mean' and 'sd'.
    Computation accelerated for kernel='cosine' or 'optcosine'.
    All cases are now computed using analytic expressions, for m <= 2.

    o bw.abram
    This function is now generic, with a method for class 'ppp'.

    o pcfinhom, pcfdot.inhom, pcfcross.inhom
    New arguments 'adjust.sigma' and 'adjust.bw' allow
    separate adjustment of the one-dimensional smoothing bandwidth 'bw'
    and the spatial smoothing bandwidth 'sigma'.
    
BUG FIXES

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

        CHANGES IN spatstat.explore VERSION 3.0-6

OVERVIEW

    o Internal improvements and bug fixes.

        CHANGES IN spatstat.explore VERSION 3.0-5

OVERVIEW

    o Bug fix in pcf.

    o We thank Maximilian Hesselbarth for contributions.
    
BUG FIXES

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

        CHANGES IN spatstat.explore VERSION 3.0-4

OVERVIEW

    o Bug fix in Kest in a very special case.

    o We thank 'Marjolein9' for contributions.
    
BUG FIXES

    o Kest
    Isotropic edge correction weight was computed incorrectly
    for a data point lying exactly on a corner of a rectangular window.
    Spotted by GitHub contributor 'Marjolein9'.
    Fixed.
    
        CHANGES IN spatstat.explore VERSION 3.0-3

OVERVIEW

    o Tweaks to placate package checker.


        CHANGES IN spatstat.explore VERSION 3.0-2

OVERVIEW

    o Tweaks to placate package checker.


        CHANGES IN spatstat.explore VERSION 3.0-1

OVERVIEW

    o Tweaks to placate package checker.


        CHANGES IN spatstat.explore VERSION 3.0-0

OVERVIEW

    o New package

    o We thank Marie-Colette van Lieshout and Daniel Manrique-Castano
    for contributions.
    
    o Periodic edge correction for K function.

    o Changed denominator in K function and pair correlation function.
    
    o Bandwidth selection for adaptive kernel estimation of intensity.

    o U-shaped curves in 'rhohat'.

    o Radial cumulative integral of an image.
    
    o Minor improvements.

NEW FUNCTIONS

    o bw.CvL.adaptive
    Bandwidth selection for adaptive kernel estimation of intensity.

    o radcumint
    Radial cumulative integral of an image.
    
SIGNIFICANT USER-VISIBLE CHANGES

    o Package structure
    The package 'spatstat.core' has been split into two packages called
    'spatstat.explore' (for exploratory data analysis)
    and 'spatstat.model' (for modelling and formal inference).

    o spatstat.explore
    The new package 'spatstat.explore' contains the code for
    exploratory data analysis and nonparametric analysis
    of spatial data. Examples include 'density.ppp', 'Kest',
    'envelope', 'rhohat', 'clarkevans.test'.

    o NEWS
    The NEWS file for the new package 'spatstat.explore'
    contains older news items from the defunct package 'spatstat.core'
    (for functions which are now in 'spatstat.explore').

    o Kest, Kdot, Kcross, Ldot, Lcross, Kmulti
    These functions now accept the option 'correction="periodic"'
    to compute the periodic (toroidal) edge correction estimate.

    o Kest, pcf, Ksector, Kdot, Kcross, Kmulti
    When ratio=TRUE, the denominator is now equal to the number of pairs of
    points considered. This does not affect the estimate of the summary
    function, but it changes the calculation of pooled estimates
    when the estimates were obtained from different sized windows.
    
    o markcorr, markcrosscorr
    These functions now allow negative mark values when normalise=FALSE.
    
    o marktable
    This function now works for point patterns in three dimensions (class 'pp3')
    and point patterns on a network (class 'lpp').
    
    o bw.relrisk
    This function is now generic, with a method for class 'ppp'

    o compileK, compilepcf
    These functions have a new argument 'samplesize'.
    If 'ratio=TRUE' the numerator and denominator will be rescaled
    by a common factor so that the denominator is equal to 'samplesize'.

    o adaptive.density
    Now accepts 'method="nearest"' and passes the data to 'nndensity'.

    o rhohat.ppp
    New options 'smoother="mountain"' and 'smoother="valley"'
    for estimating a unimodal function (U-shaped curve).

    o rhohat.ppp
    If the covariate is a 'distfun', the name of the unit of length is saved
    and displayed on the plot.

    o rhohat.ppp
    New arguments 'jitter', 'jitterfactor', 'interpolate' allow greater
    control over the calculation.

    o rhohat.ppp
    New argument 'do.CI' specifies whether to calculate confidence bands.
    
        CHANGES IN spatstat.core VERSION 2.4-4.010

OVERVIEW

    o Internal improvements.


        CHANGES IN spatstat.core VERSION 2.4-4

OVERVIEW

    o Bug fixes and minor improvements.

BUG FIXES

    o rhohat.ppp
    The argument 'subset' was not handled correctly in the internal data.
    The estimated function 'rho' was correct, but if 'predict.rhohat' was applied,
    predictions were computed only in the 'subset', and were possibly incorrect values.
    Fixed.

    o Gfox, Jfox
    Warnings were issued about text formatting errors (mentioning 'sprintf' or 'fmt').
    Fixed.
    
        CHANGES IN spatstat.core VERSION 2.4-3

OVERVIEW

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

BUG FIXES

    o Smooth.ppp
    Crashed when 'kernel' was a function, 'at="points"' and 'scalekernel=FALSE'.
    Fixed.

    o Finhom, Ginhom, Jinhom
    Crashed when ratio=TRUE.
    [Spotted by Art Stock.]
    Fixed.
    
    o envelope
    Crashed for some of the summary functions when ratio=TRUE.
    [Spotted by Art Stock.]
    Fixed.

    o "[.rat"
    Crashed in some cases.
    Fixed.

    o Kcross
    The result of Kcross() was 'invisible',
    i.e. it was not automatically printed.
    Fixed.
    
        CHANGES IN spatstat.core VERSION 2.4-2

OVERVIEW

    o Internal bug fixes.


        CHANGES IN spatstat.core VERSION 2.4-1

OVERVIEW

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

    o Internal improvements and bug fixes.

SIGNIFICANT USER-VISIBLE CHANGES

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

BUG FIXES

    o density.ppp
    Crashed if the observation window had zero area.
    Fixed.

    o dirichletVoronoi.ppp
    Crashed randomly, with obscure error messages from 'im' or 'eval.im',
    when argument 'f' had a small value.
    [Spotted by Suman Rakshit.]
    Fixed.

    o dirichletVoronoi.ppp
    Rarely, produced an image containing NA values.
    [Spotted by Suman Rakshit.]
    Fixed.

    o vcov.ppm
    Crashed in some cases, with message 'object lamdel not found'.
    [Spotted by Sven Wagner.]
    Fixed.
    
        CHANGES IN spatstat.core VERSION 2.4-0

OVERVIEW

    o We thank Sriram Ramamurthy for contributions.

    o spatstat.core now depends on the new package 'spatstat.random'.

    o Functions for generating random patterns have been removed.
    
    o Minor improvements and bug fixes

SIGNIFICANT USER-VISIBLE CHANGES

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

    o reload.or.compute
    New argument 'context' 

BUG FIXES

    o reload.or.compute
    Scoping error (crashed sometimes if called from a non-global environment).
    Fixed.
    
        CHANGES IN spatstat.core VERSION 2.3-2

OVERVIEW

    o Minor improvements and bug fixes.

    o We thank Jonas Brehmer for contributions.

SIGNIFICANT USER-VISIBLE CHANGES

    o pcf
    Improved error message
    
BUG FIXES

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

        CHANGES IN spatstat.core VERSION 2.3-1

OVERVIEW

    o Covariates in ppm and mppm may be functions that depend on the marks
    as well as the spatial coordinates.

    o Automatic selection of threshold for defining a binary predictor.
    
    o Random perturbation of line segments.
    
    o Minor extensions, performance improvements, and bug fixes.

NEW FUNCTIONS

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

SIGNIFICANT USER-VISIBLE CHANGES

    o distcdf
    Improved regularisation algorithm.
    Argument 'nr=NULL' is now accepted.
    New argument 'delta' allows the result to be interpolated
    onto a finer grid.

    o collapse.fv
    Columns identified by the arguments 'same' and 'different'
    may now be absent from some of the 'fv' objects that will be collapsed.

    o Kest
    When the argument 'domain' is given, the calculation of estimates of K(r)
    has changed slightly, to adhere more closely to the description in
    the help file.
    
    o reload.or.compute
    Now prints a message indicating whether the data were recomputed
    or reloaded from file.
    New argument 'verbose'.

    o pool.envelope
    Now uses the value of 'nrank' which was used in the original envelopes.
    
    o Kmulti
    New argument 'rmax'.

    o Kinhom
    No longer issues a warning about changed behaviour in the case where
    'lambda' is a fitted model.
    
    o pcfinhom
    No longer issues a warning about changed behaviour in the case where
    'lambda' is a fitted model.
    
BUG FIXES

    o segregation.test
    The test statistic was calculated as the mean, rather than the sum,
    of discrepancies between probabilities. (The p-value was not affected.)
    Fixed.

    o Kest
    If 'domain' was specified, 'rmax' was ignored.
    Fixed.

    o edge.Ripley
    Value was incorrect for a point lying exactly on a corner.
    Fixed.

    o edge.Ripley
    Crashed when method="interpreted", if a point lay exactly on a corner.
    Fixed.

    o plot.fv, plot.envelope
    Crashed when trying to display a significance band of width zero
    around a constant function.
    Fixed.
    
    o collapse.fv
    Crashed if 'length(same) > 1'.
    Fixed.

        CHANGES IN spatstat.core VERSION 2.3-0

OVERVIEW

    o Transect of an image along a curve.

    o Image cross-correlation and cross-covariance.
    
    o Minor bug fixes.

NEW FUNCTIONS

    o cov.im, cor.im
    Correlation or covariance between several pixel images.
    
SIGNIFICANT USER-VISIBLE CHANGES

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

BUG FIXES

    o rhohat
    The rug plot (produced by plot.rhohat) was incorrect
    when rhohat was called with method="piecewise".
    Fixed.

    o markcrosscorr
    Did not recognise the option 'correction="none"'.
    Fixed.

   o roc.ppp
   The default plot of the result of roc.ppp
   did not include the diagonal line 'y=x'.
   Fixed.
   
        CHANGES IN spatstat.core VERSION 2.2-0

OVERVIEW

    o We thank Abdollah Jalilian, Yongtao Guan and Rasmus Waagepetersen
    for contributions.
    
    o estimation of the spatial covariance function of a pixel image

    o simulation of the product shot noise Cox process.

    o extensions to rhohat
    
NEW FUNCTIONS

    o rPSNCP
    Generate simulated realisations of the product shot noise Cox process.
    Contributed by Abdollah Jalilian, Yongtao Guan and Rasmus Waagepetersen.
    
    o spatcov
    Estimate the spatial covariance function of a pixel image.

    o pairMean
    Compute the mean of a specified function of interpoint distance
    between random points in a window.

SIGNIFICANT USER-VISIBLE CHANGES

    o rhohat
    New option (smoother='piecewise') computes a piecewise-constant
    estimate of rho(z).
    
    o rhohat
    The result now includes the 'average' intensity rho.

    o distcdf
    Arguments which are NULL will be treated as missing.

    o distcdf
    New argument 'savedenom'.
    

        CHANGES IN spatstat.core VERSION 2.1-2

OVERVIEW

    o Reduced CRAN check time.

        CHANGES IN spatstat.core VERSION 2.1-1

OVERVIEW

    o Minor bug fix

        CHANGES IN spatstat.core VERSION 2.1-0

OVERVIEW

    o densityfun.ppp handles query points outside original window

    o Minor improvements and bug fixes.

SIGNIFICANT USER-VISIBLE CHANGES

    o densityfun.ppp
    The resulting function can now handle query points which lie
    outside the window of the original data,
    and has argument 'drop=TRUE' which specifies how to handle them.

    o rpoint
    New argument 'forcewin' forces the code to use the window 'win'
    when 'f' is a pixel image.

BUG FIXES

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

        CHANGES IN spatstat.core VERSION 2.0-0

OVERVIEW

    o We thank Tilman Davies,  Greg McSwiggan and Suman Rakshit
    for contributions.

    o We thank Corey Anderson, Michael Chirico, Andy Craig,
    Marcelino de la Cruz, Tilman Davies, Pavel Fibich,
    Kurt Hornik, Gopalan Nair, Yonatan Rosen and Rasmus Waagepetersen
    for contributions.
    
    o Diffusion kernel smoothing.
    
    o More support for spatial logistic regression models.

    o predict.mppm now works for multitype point process models.

    o Improved handling of 'newdata' in predict.mppm.

    o More support for multi-dimensional patterns.
    
NEW FUNCTIONS

    o densityHeat
    New generic function for diffusion kernel estimation of intensity

    o densityHeat.ppp
    Diffusion kernel estimation of intensity for point pattern in 2 dimensions.
    This is an alternative to density.ppp.

    o intersect.boxx
    Compute intersection of boxes in multi-dimensional space

    o scale.boxx, scale.ppx
    Methods for 'scale' for boxes and patterns in multi-dimensional space

    o shift.boxx, shift.ppx
    Methods for 'shift' for boxes and patterns in multi-dimensional space

    o is.boxx
    Determine whether an object is a multidimensional box

SIGNIFICANT USER-VISIBLE CHANGES

    o rotmean
    The result now has the same 'unitname' as the input object X.
    New argument 'adjust' controls the smoothing bandwidth.
    
    o rlabel
    New argument 'group' specifies that the points are divided into
    several groups, and that relabelling is applied within each group.
    
    o Kcross, Gcross, Jcross
    Function labels (shown on the plot legend) have been
    improved when i = j.

    o anova.mppm
    Issues a warning when applied to random-effects models
    (models fitted using the argument 'random').

BUG FIXES

    o Gest
    If correction="rs" or correction="km", then both the reduced-sample
    (border correction) and Kaplan-Meier corrected estimates were calculated.
    [Spotted by Gopalan Nair.]
    Fixed.

    o simulate.rhohat
    Crashed when applied to rhohat objects computed from data
    on a linear network.
    Fixed.

        CHANGES IN spatstat.core VERSION 1.65-11

OVERVIEW

    o Internal tweaks.
    
        CHANGES IN spatstat.core VERSION 1.65-10

OVERVIEW

    o Minor corrections to documentation.

        CHANGES IN spatstat.core VERSION 1.65-9

OVERVIEW

    o We thank Ian Buller for a suggestion.

    o weights permitted in density calculation for line segments.

SIGNIFICANT USER-VISIBLE CHANGES

    o density.psp
    New argument 'weights'.

        CHANGES IN spatstat.core VERSION 1.65-8

OVERVIEW

    o Minor changes to appease the compiler.

        CHANGES IN spatstat.core VERSION 1.65-7

OVERVIEW

    o We thank Michael Chirico for a contribution.

    o Minor changes to appease the compiler.
    
        CHANGES IN spatstat.core VERSION 1.65-6

OVERVIEW

    o We thank Tilman Davies and Pavel Fibich for contributions.

    o Increased speed for large datasets.

SIGNIFICANT USER-VISIBLE CHANGES

    o rSSI
    Accelerated.
    
    o overall speed
    Changes have been made to the internal code of spatstat 
    which should accelerate computations involving large datasets.

    o localpcf, localpcfinhom
    New argument 'rvalue'.

BUG FIXES

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

    CHANGES IN spatstat.core VERSION 1.65-5

OVERVIEW

    o Minor changes required by CRAN.
    

        CHANGES IN spatstat.core VERSION 1.65-1

OVERVIEW

    o Added NEWS file.


        CHANGES IN spatstat.core VERSION 1.65-0

OVERVIEW

    o Package initialised at version 1.65-0

SIGNIFICANT USER-VISIBLE CHANGES

    o spatstat.core
    The package 'spatstat.core' has been created from a subset
    of the code in the original 'spatstat' package version 1.65-0.
    It contains the core functionality for statistical analysis of
    spatial data. For an overview, see help("spatstat.core-package")

    o Execution
    The 'spatstat.core' package is slightly faster than the corresponding
    code in the 'spatstat' package, because the procedure for calling
    internal C functions has been streamlined.



