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.