CHANGES IN spatstat VERSION 1.39-1
OVERVIEW
o Urgent bug fix.
o We thank Suman Rakshit and Brian Ripley for contributions.
BUG FIXES
o bdry.mask, convexhull
In R-devel only, these functions could return an empty window,
causing errors in other packages.
[Spotted by Brian Ripley.]
Fixed.
o project2segment
An error occurred if any line segments had length zero.
[Spotted by Suman Rakshit.]
Fixed.
CHANGES IN spatstat VERSION 1.39-0
OVERVIEW
o We thank Shane Frank, Shaaban Ghalandarayeshi, Ute Hahn,
Mahdieh Khanmohammadi, Nicoletta Nava, Jens Randel Nyengaard,
Sebastian Schutte, Rasmus Waagepetersen and Carl G. Witthoft
for contributions.
o ANOVA extended to Gibbs models.
o Improved algorithm for locally-scaled K-function.
o Leave-one-out calculation of fitted values in ppm objects.
o New dataset: presynaptic vesicles.
o Geometrical operations with windows and images.
o More edge corrections for K-function.
o Improved handling and plotting of 'fv' objects.
o Utilities for perspective views of surfaces.
o New classes 'anylist', 'solist' will ultimately replace 'listof'.
o Bug fixes.
o Version nickname: 'Smoke and Mirrors'
NEW DATASETS
o vesicles
Synaptic vesicles
(includes raw data files for training purposes)
NEW CLASSES
o anylist
List of objects.
(A replacement for 'listof')
o solist
List of two-dimensional spatial objects.
(A replacement for some uses of 'listof')
NEW FUNCTIONS
o perspPoints, perspLines, perspSegments, perspContour
Draw points and lines on a surface, as seen in perspective view.
o hopskel.test
Hopkins-Skellam test of CSR
o project2set
For each data point in a point pattern X, find the nearest
spatial location in a given window W.
o stienen, stienenset
Stienen diagrams
o dirichlet.vertices
Vertices of the Dirichlet tessellation
o discs
Union of discs.
Given a point pattern dataset recording the locations and diameters
of objects, find the region covered by the objects.
o increment.fv
Increments of a summary function: g(x) = f(x+h)-f(x-h).
o rotmean
Rotational average of pixel values in an image
o fardist
Distance from each pixel/data point to farthest part of window boundary
o circumradius.owin
Circumradius of a window
o rmax.Trans, rmax.Ripley
Compute the maximum distance 'r' for which the
translation edge correction and isotropic edge correction
are valid.
o is.grey
Determines whether a colour value is a shade of grey.
o harmonise
Convert several objects of the same class to a common format.
(New generic function with existing methods harmonise.im and harmonise.fv)
o area
New generic function, with methods for 'owin' and 'default'.
o Fhazard
Hazard rate of empty space function
o anylist, as.anylist, [.anylist, [<-.anylist, print.anylist, summary.anylist
Support for new class 'anylist'
o solist, as.solist, [.solist, [<-.solist, print.solist, summary.solist
Support for new class 'solist'
o plot.anylist, plot.solist
Plot methods for the classes 'anylist' and 'solist'
(Currently identical to 'plot.listof')
SIGNIFICANT USER-VISIBLE CHANGES
o anova.ppm
Now applies to Gibbs models as well as Poisson models,
using adjusted composite likelihood ratio test statistic.
o persp.im
If visible=TRUE, the algorithm will also calculate which pixels of x
are visible in the perspective view. This is useful for drawing
points or lines on a perspective surface.
o Kscaled
Improved algorithm [thanks to Ute Hahn.]
New arguments 'renormalise' and 'normpower' allow renormalisation
of intensity, similar to Kinhom.
o Kest
New option: correction="rigid" computes the rigid motion correction.
o pairwise interactions
Fitted parameters and other calculations for pairwise interaction models
DiggleGatesStibbard, DiggleGratton, Fiksel, Geyer, Strauss
may change slightly due to a change in handling numerical rounding effects.
o eval.fv
Functions no longer need to have exactly the same sequence of 'r' values.
They will now be made compatible using 'harmonise.fv'.
o fitted.ppm
New argument 'leaveoneout' allows leave-one-out calculation
of fitted intensity at original data points.
o Kinhom, Linhom
New argument 'leaveoneout' specifies whether the leave-one-out rule
should be applied when calculating the fitted intensities.
o crosspaircounts
Results may change slightly due to a change in handling numerical
rounding effects.
o Fest, Gest
New argument 'domain' supports bootstrap methods.
o plot.fv
New argument 'mathfont' determines the font (e.g. plain, italic, bold)
for mathematical expressions on the axes and in the legend.
Defaults to italic.
o scanpp
Upgraded to handle multiple columns of mark data.
o circumradius
The function 'circumradius' is now generic, with methods
for the classes 'owin' and 'linnet'.
o edge.Trans
New argument 'give.rmax'
o fvnames, plot.fv
The symbol '.a' is now recognised. It stands for 'all function values'.
o as.function.fv
Argument 'extrapolate' can have length 1 or 2.
o varblock
New argument 'confidence' determines the confidence level.
o $<-.fv
This can now be used to add an extra column to an 'fv' object
(previously it refused).
o minnndist, maxnndist
New argument 'positive'. If TRUE, coincident points are ignored:
the nearest-neighbour distance of a point is the distance to the
nearest point that does not coincide with the current point.
o plot.fv
Improved handling of 'shade' argument.
o Kmeasure
Now passes '...' arguments to as.mask()
o Ksector
Now allows start < 0.
New arguments 'units' and 'domain'.
o pairorient
New arguments 'units' and 'domain'.
o eroded.areas
New argument 'subset'
o disc
New argument 'delta'
o plot.plotppm
New argument 'pppargs'
o harmonise.fv, harmonise.im
These are now methods for the new generic 'harmonise'
o Fest, Gest
These functions now also compute the theoretical value of hazard
for a Poisson process, if correction = "km".
o with.fv
Improved mathematical labels.
o Gfox, Jfox
Improved mathematical labels.
o area.owin
This function is now a method for the new generic 'area'
o edges
Default for argument 'check' changed to FALSE.
BUG FIXES
o varblock
Calculations were incorrect if more than one column of
edge corrections was computed.
[Bug introduced in spatstat 1.21-1, november 2010.]
Fixed.
o varblock
Crashed if one of the quadrats contained no data points.
Fixed.
o lohboot
Interval was calculated wrongly when global=TRUE and fun="Lest" or "Linhom".
Fixed.
o nnmark
Crashed when at="points" if there was only a single column of marks.
[Spotted by Shane Frank.]
Fixed.
o plot.msr
Some elements of the plot were omitted or cut off.
Fixed.
o plot.msr
Did not work with 'equal.scales=TRUE'.
Fixed.
o plot.msr, augment.msr
Crashed if every data point was duplicated.
Fixed.
o as.im.owin
Crashed if X was a 1 x 1 pixel array.
Fixed.
o owin
Coordinates of polygon data were altered slightly when fix=TRUE.
[Spotted by Carl Witthoft.]
Fixed.
o objects of class 'fv'
Assigning a new value to names(x) or colnames(x) or dimnames(x)
would cause the internal data format to become corrupted.
Fixed.
o to.grey, complementarycolour
Did not work properly on 'colourmap' objects.
Fixed.
o Kest
Ignored argument 'var.approx' if the window was a rectangle.
Fixed.
o rmh.ppm, rmhmodel.ppm
Ignored the argument 'new.coef'.
[Spotted by Sebastian Schutte]
Fixed.
o as.function.fv
The meanings of 'extrapolate=TRUE' and 'extrapolate=FALSE' were swapped.
Fixed.
o varblock
Handled the case 'fun=Lest' incorrectly.
Fixed.
o [.fv
Sometimes garbled the internal data format, causing plot.fv to crash.
Fixed.
o range.fv
Sometimes returned NA even when na.rm=TRUE.
Fixed.
o Fest
Argument 'eps' was not interpreted correctly.
Fixed.
o plot.fv
Argument 'lwd' was not passed to legend()
o flipxy.owin
Sometimes deleted the name of the unit of length.
Fixed.
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=
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.