https://github.com/cran/spatstat
Tip revision: c051fec12a8c32ed44640be5caf8ebff6657624a authored by Adrian Baddeley on 24 July 2011, 14:28:01 UTC
version 1.23-0
version 1.23-0
Tip revision: c051fec
NEWS
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
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.
