https://github.com/cran/spatstat
Tip revision: 5d0edca8999a842af2ce258da8f917019ba84eb0 authored by Adrian Baddeley on 21 March 2011, 14:59:03 UTC
version 1.21-5.1
version 1.21-5.1
Tip revision: 5d0edca
NEWS
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
BUGS
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.
BUGS
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.
BUGS
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'
BUGS
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'
BUGS
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.
BUGS
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.
BUGS
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.
BUGS
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.
