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NEWS
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CHANGES IN spatstat.geom VERSION 3.3-6.020
OVERVIEW
o Nonlinear colour maps and symbol maps.
o `im.apply` handles larger datasets.
o `quadratcount.ppp` supports left-closed, right-open rectangular tiles.
o Minor improvements and bug fixes.
SIGNIFICANT USER-VISIBLE CHANGES
o colourmap
New arguments 'compress', 'decompress' for nonlinear colour maps.
o default.symbolmap.pp
Argument 'marktransform' renamed 'transform' for consistency.
o im.apply
Improved algorithm avoids violating memory limits, handles larger datasets.
o lut
New arguments 'compress', 'decompress' for nonlinear lookup tables.
o plot.colourmap
New argument 'at' determines the position of tick marks on the axis.
o plot.im
Return value has attribute 'at' giving the position of tick marks
on the axis next to the colour ribbon.
o quadratcount.ppp
New argument 'left.open' controls the treatment of data points
which lie on the boundary between two rectangular quadrats.
o symbolmap
New arguments 'transform', 'compress', 'decompress'
for nonlinear symbol maps.
BUG FIXES
o plot.solist, plot.imlist
When 'equal.scales=TRUE' and 'equal.ribbon=TRUE',
the argument 'log=TRUE' was ignored.
Fixed.
o plot.im
If log=TRUE, the colour map returned by plot.im
represented the colours applied to log10(x) rather than x.
Fixed.
CHANGES IN spatstat.geom VERSION 3.3-6
OVERVIEW
o We thank Warick Brown, Tilman Davies and Martin Hazelton
for contributions.
o Methods for functions which are constant on each tile of a tessellation.
o Minor improvements.
NEW FUNCTIONS
o integral.tessfun
Integral of a function which is constant on each tile of a tessellation
o print.tessfun, plot.tessfun, as.tess.tessfun
Methods for the class 'tessfun' of functions which are constant
on each tile of a tessellation.
SIGNIFICANT USER-VISIBLE CHANGES
o plot.yardstick
New argument 'style' allows different styles of plotting a scale bar
including a zebra pattern (style = "zebra").
o plot.yardstick
New arguments 'zebra.step', 'zebra.width', 'zebra.col'.
o as.mask
Corrected a warning message.
CHANGES IN spatstat.geom VERSION 3.3-5
OVERVIEW
o We thank Stephanie Hogg and Tingting Zhan for contributions.
o Improvements to plotting of images, and arrays of images.
o More control over plotting of colour maps, symbol maps and texture maps.
o hyperframes handle a 'Surv' object as a single column.
o Bug fixes and minor improvements.
NEW FUNCTIONS
o rev.colourmap
Reverses the sequence of colour values in a colour map.
A method for the generic 'rev'.
SIGNIFICANT USER-VISIBLE CHANGES
o hyperframe
An object of class 'Surv' from the 'survival' package
is now treated as a single column of data
(mimicking the behaviour of 'data.frame')
[Requested by Tingting Zhan]
o plot.im
New argument 'drop.ribbon' determines whether a ribbon will be displayed
in the case where the pixel values are all equal.
Default behaviour has changed.
o plot.im
New argument 'reverse.col' allows the sequence of colours to be reversed.
[Suggested by Stephanie Hogg.]
o plot.imlist, image.imlist, image.listof
If equal.ribbon=TRUE and equal.scales=TRUE, the colour ribbon
is now neatly aligned with the plotted images.
o plot.solist, plot.anylist
Arguments 'adorn.left', 'adorn.right', 'adorn.bottom', 'adorn.top'
may now be objects of class 'colourmap' or 'symbolmap'.
o plot.solist, plot.anylist
New argument 'adorn.args'.
o plot.imlist, image.imlist, image.listof
New argument 'equal.scales'.
o plot.colourmap
New formal argument 'side'.
o plot.symbolmap
New formal argument 'side'.
o plot.texturemap
New formal argument 'side'.
o persp.im
Now recognises argument 'adj.main' controlling the position of main title.
o persp.ppp
Now recognises argument 'adj.main' controlling the position of main title.
BUG FIXES
o rotate.im
Did not preserve the name of the unit of length.
[Spotted by Stephanie Hogg.]
Fixed.
o unstack.ppp
If 'marks(x)' was a data frame with a single column,
the data frame structure was retained, when it should have been dropped.
[Spotted by Tingting Zhan.]
Fixed.
CHANGES IN spatstat.geom VERSION 3.3-4
OVERVIEW
o Tessellations can have any kind of marks.
o More control over default colours.
o Minor improvements.
NEW FUNCTIONS
o default.image.colours, reset.default.image.colours
Control the default colours used for plotting images in spatstat.
SIGNIFICANT USER-VISIBLE CHANGES
o tess, marks<-.tess
A tessellation can now have any kind of marks
(vector, list, data frame or hyperframe).
o intersect.tess
Now handles marks of any kind (vector, list, data frame or hyperframe).
o pixelquad
Now accepts arguments passed to 'as.mask' to control the pixel resolution.
o persp.ppp
Now draws a reference scale bar for the vertical scale, by default.
New arguments 'legend', 'legendpos', 'leg.args', 'leg.col'.
o persp.ppp
Optionally draws a symbol at the top of each spike.
New arguments 'type', 'point.args'.
CHANGES IN spatstat.geom VERSION 3.3-3
OVERVIEW
o Perspective plot of spatial point pattern with numerical marks.
o Improvements to rjitter.ppp
o Tweaks to documentation.
NEW FUNCTIONS
o persp.ppp
For a spatial point pattern with numeric marks,
generate a perspective plot in which each data point is
shown as a vertical spike, with height proportional to the mark value.
SIGNIFICANT USER-VISIBLE CHANGES
o rjitter.ppp
New argument 'adjust' allows the default radius to be adjusted.
o rjitter.ppp
The resulting point pattern now has attribute 'radius'.
o rjitter.ppp
If 'retry=TRUE', the resulting point pattern now has attribute 'tries'
which reports the number of trials that were required.
CHANGES IN spatstat.geom VERSION 3.3-2
OVERVIEW
o Tweaks to documentation to satisfy the package checker.
CHANGES IN spatstat.geom VERSION 3.3-1
OVERVIEW
o Tweaks to documentation to satisfy the package checker.
CHANGES IN spatstat.geom VERSION 3.3-0
OVERVIEW
o 'spatstat.geom' now depends on the new package 'spatstat.univar'.
o Some functions have been moved into the package 'spatstat.univar'.
o Tweaked plot functions.
o More support for diagram objects.
o Stability improvements and bug fixes.
PACKAGE DEPENDENCE
o spatstat.geom
'spatstat.geom' now depends on the new package 'spatstat.univar'.
Several functions that were previously provided in 'spatstat.geom'
have been moved to 'spatstat.univar'.
NEW FUNCTIONS
o default.symbolmap.ppp
The algorithm for determining the graphical symbol map used by plot.ppp.
o default.symbolmap
New generic.
o affine.diagramobj, reflect.diagramobj, rotate.diagramobj
Methods for geometrical transformations of diagram objects.
SIGNIFICANT USER-VISIBLE CHANGES
o identify.ppp
Automatically starts a new plot device and displays `x`
if there is no plot device open.
o identify.psp
Identified segments are highlighted.
Automatically starts a new plot device and displays `x`
if there is no plot device open.
o plot.owin
New argument 'adj.main' controls the justification of the text
in the main title.
o plot.colourmap
New argument 'nticks' controls the number of axis tick marks
when the colourmap is defined on a continuous range of numerical values.
o plot.colourmap
New argument 'box' controls whether a box will be drawn around the colours.
o plot.tess
Changed the default values for do.col and do.labels
o layout.boxes
Argument 'aspect' can be NA or Inf indicating that the aspect ratio
of the boxes is unconstrained.
o simplepanel
Improved stability.
o shift
Improved stability
o as.colourmap.symbolmap
A warning message, occurring when the symbolmap contains more than one
colour map, is suppressed if the colour maps are identical.
o plot.symbolmap
Suppressed warning message (occurring when colour.only=TRUE)
about the symbolmap containing several colour maps,
when the colour maps were identical.
DELETED FUNCTIONS
o ewcdf
This function has been moved to the new package 'spatstat.univar'
along with most of the methods for class 'ewcdf'.
o mean.ewcdf, quantile.ewcdf, quantilefun.ewcdf
These methods have been moved to the new package 'spatstat.univar'.
o hotrod
This function has been moved to the new package 'spatstat.univar'.
o integral
The generic 'integral' and the method 'integral.density'
have been moved to the new package 'spatstat.univar'.
o quantilefun, quantilefun.ewcdf
The generic 'quantilefun' and the method 'quantile.ewcdf'
have been moved to the new package 'spatstat.univar'.
o rounding, rounding.default
The generic 'rounding' and the method 'rounding.default'
have been moved to the new package 'spatstat.univar'.
o transformquantiles
This function has been moved to the new package 'spatstat.univar'.
o weighted.median
This function has been moved to the new package 'spatstat.univar'.
o whist
This function has been moved to the new package 'spatstat.univar'.
o uniquemap, uniquemap.default, uniquemap.data.frame, uniquemap.matrix
The generic 'uniquemap' and these methods have been
moved to the new package 'spatstat.univar'.
o unnormdensity
This function has been moved to the new package 'spatstat.univar'.
BUG FIXES
o plot.ppp, default.symbolmap.ppp
Ignored 'zerosize' in some cases.
Fixed.
o plot.symbolmap
Issued strange warnings in some cases.
Fixed.
o symbolmap
Crashed in some instances when 'inputs' was given
and the graphical parameters included both functions and vectors.
Fixed.
CHANGES IN spatstat.geom VERSION 3.2-9
OVERVIEW
o Some geometry code accelerated.
NEW FUNCTIONS
o summary.symbolmap, print.summary.symbolmap
Method for 'summary' for symbol maps.
SIGNIFICANT USER-VISIBLE CHANGES
o as.rectangle
Accelerated in many cases.
o diameter.owin
Accelerated when the window is a rectangle.
o nncross.ppp
Slightly accelerated.
o owin
Accelerated in many cases.
CHANGES IN spatstat.geom VERSION 3.2-8
OVERVIEW
o Improvements to window geometry code.
o Improvements to symbol map displays.
SIGNIFICANT USER-VISIBLE CHANGES
o is.subset.owin
Algorithm slightly modified to give better results when
the two polygons share some common edges.
o plot.ppp
New argument 'minsize' specifies the size of the smallest symbol
used to represent the marks, when the marks are numeric.
o plot.ppp
New argument 'zerosize' specifies the size of the symbol
used to represent the mark value 0, when marks are numeric.
o plot.symbolmap
New argument 'representatives' specifies which data values
will be shown in the plot.
CHANGES IN spatstat.geom VERSION 3.2-7
OVERVIEW
o Minor corrections to the help files.
CHANGES IN spatstat.geom VERSION 3.2-6
OVERVIEW
o Minor improvements.
o spatstat.geom no longer suggests 'maptools'.
SIGNIFICANT USER-VISIBLE CHANGES
o as.im.tess
New argument 'values'.
CHANGES IN spatstat.geom VERSION 3.2-5
OVERVIEW
o Extension of distance transform algorithm.
o Improvement to progress reports.
o Suppress annoying warnings.
o Further bug fix in quadratcount
SIGNIFICANT USER-VISIBLE CHANGES
o distmap.owin
New argument 'connect'.
o progressreport
The estimated time of completion is also printed, if the remaining time
is longer than 10 minutes.
o unnormdensity
Suppress annoying warning messages from density.default.
This affects many functions in the spatstat family of packages.
BUG FIXES
o quadratcount
Crashed if argument 'tess' was a rectangular grid tessellation.
Fixed.
CHANGES IN spatstat.geom VERSION 3.2-4
OVERVIEW
o Connected component transform can now use a 4-connected grid.
o Bug fixes in quadrat counting code.
SIGNIFICANT USER-VISIBLE CHANGES
o connected.owin, connected.im
New argument 'connect' specifies the connectivity of the raster,
either 4 or 8 neighbours for each pixel.
o round.ppp, round.pp3, round.ppx
Now has ellipsis argument '...' for conformity with generic 'round'
BUG FIXES
o as.mask
If 'w' was a rectangle and 'xy' was specified,
the pixel entries were all TRUE, instead of
only being TRUE within the window 'w'.
Fixed.
o intensity.quadratcount
Results were incorrect if the quadrats were a mixture of
irregular polygons and rectangles.
o quadratcount.ppp
If the window was irregular and some of the tiles did not intersect
the window, the counts were given the wrong tile labels.
Fixed.
o plot.quadratcount
If the window was irregular and some of the tiles did not intersect
the window, the counts were displayed in the wrong tiles.
Fixed.
CHANGES IN spatstat.geom VERSION 3.2-2
OVERVIEW
o Bug fixes and minor improvements.
SIGNIFICANT USER-VISIBLE CHANGES
o as.mask
Improved numerical performance (rounding error).
BUG FIXES
o quantess.owin
The window of the resulting tessellation was sometimes slightly different
from the original window M.
Fixed.
o intensity.quadratcount
Results were incorrect if the quadrats were the intersections of
a rectangular grid with an irregular window and all quadrats were nonempty.
Fixed.
CHANGES IN spatstat.geom VERSION 3.2-1
OVERVIEW
o Fixed errors and omissions in documentation.
o Minor improvements in C code.
CHANGES IN spatstat.geom VERSION 3.2-0
OVERVIEW
o We thank Warick Brown and Tilman Davies for suggestions.
o More options for converting polygons to a binary mask.
o More options for controlling pixel size.
o Improvement to progress reports.
o Minor tweaks to package documentation.
NEW FUNCTIONS
o psp2mask
Function 'as.mask.psp' has been renamed 'psp2mask'.
The old function 'as.mask.psp' still exists, but it will
soon be deprecated, and ultimately removed.
SIGNIFICANT USER-VISIBLE CHANGES
o owin2mask
New options op="majority" and op="minority".
If op="majority", a pixel belongs to the resulting mask if
at least half of the pixel area is covered by the window.
o as.mask
New argument 'rule.eps' specifies what to do when the
desired pixel size is not a divisor of the frame size.
o as.im
Many methods for 'as.im' now have argument 'rule.eps'.
o discretise
New argument 'rule.eps'
o distfun
New argument 'rule.eps'
o nnfun
New argument 'rule.eps'
o progressreport
New argument 'formula' controls the calculation of estimated time remaining.
o progressreport
New argument 'savehistory' specifies whether to save the elapsed times
when the function was called.
CHANGES IN spatstat.geom VERSION 3.1-0
OVERVIEW
o Methods for "[[" and "[[<-" for hyperframes.
o Colour map for pH values.
o Restrict a colour map to a narrower range of values.
o Integral of a one-dimensional density estimate.
o Minor improvements and bug fixes.
NEW FUNCTIONS
o "[[.hyperframe", "[[<-.hyperframe"
Methods for "[[" and "[[<-" for hyperframes.
o pHcolourmap, pHcolour
Colour map for values of pH
o restrict.colourmap
Restrict a colourmap to a narrower range of values.
o integral.density
Compute the integral of a one-dimensional kernel density estimate.
o as.colourmap
Extract colour information from an object.
SIGNIFICANT USER-VISIBLE CHANGES
o plot.symbolmap
New argument colour.only makes it possible to display only the
colour map information in a symbolmap.
o "[.hyperframe", "[<-.hyperframe"
Improved error message when the format of index i or j is not supported.
o unnormdensity
Computation accelerated.
o unnormdensity
Handles datasets containing fewer than 2 values.
BUG FIXES
o unnormdensity
If 'weights' was a single numerical value 'w', the calculation incorrectly
assigned the weight for each observation to be 'w/n' where 'n=length(x)'.
Fixed.
o unnormdensity
A crash could occur if 'x' was a very long vector,
with an error message originating from 'deparse1'.
Fixed.
CHANGES IN spatstat.geom VERSION 3.0-6
OVERVIEW
o Bug fix.
BUG FIXES
o harmoniseLevels
Crashed sometimes, in older versions of R,
with an obscure error message from 'mapply'.
Fixed.
CHANGES IN spatstat.geom VERSION 3.0-5
OVERVIEW
o Convert several factors or factor-valued images to a common set of levels.
o Extension to rjitter
o Alternative to rjitter
o Quantile function as a function
o Improvements to plot code.
NEW FUNCTIONS
o harmoniseLevels
Given several factors or factor-valued pixel images,
convert them all to have the same set of factor levels.
o rexplode
'Explode' a point pattern by randomly displacing each
group of duplicated points to make a circular pattern
around the original location. An alternative to 'rjitter'.
o quantilefun
Return a function that computes any quantiles of a given dataset.
SIGNIFICANT USER-VISIBLE CHANGES
o rjitter.ppp
If 'trim=TRUE', the displacement radius will be constrained
to be less than or equal to the distance from the data point
to the window boundary.
o plot.ppp
For multitype point patterns, a warning is issued if
the plot legend does not represent every possible type of point
due to space restrictions.
o plot.symbolmap
New argument 'warn'.
o plot.symbolmap
Issues a warning if the plot of a discrete symbol map does not
represent every possible input value, due to space restrictions.
o plot.solist
When equal.ribbon=TRUE, the images may now be factor-valued
or character-valued. Character-valued images will be converted
to factor-valued images. The common colour map will combine the
levels of all the factor images.
BUG FIXES
o "[<-.im"
Errors occurred in x[] <- v when x and v were both factor-valued
but with different sets of levels.
o rjitter.ppp
If retry=FALSE, marks were ignored.
Fixed.
CHANGES IN spatstat.geom VERSION 3.0-4
OVERVIEW
o Improvements to perspective plots.
SIGNIFICANT USER-VISIBLE CHANGES
o perspPoints, perspLines, perspSegments, perspContour
New argument 'occluded' specifies whether the surface
should be treated as opaque or transparent.
CHANGES IN spatstat.geom VERSION 3.0-3
OVERVIEW
o Minor internal changes to satisfy package checker.
CHANGES IN spatstat.geom VERSION 3.0-2
OVERVIEW
o Minor internal changes to satisfy package checker.
CHANGES IN spatstat.geom VERSION 3.0-1
OVERVIEW
o Minor internal changes.
CHANGES IN spatstat.geom VERSION 3.0-0
OVERVIEW
o Minor improvements and bug fixes.
o Changes to package dependence.
NEW FUNCTIONS
o is.linnet
Test whether an object is a linear network.
o as.data.frame.ppplist
Method for 'as.data.frame' for lists of point patterns.
SIGNIFICANT USER-VISIBLE CHANGES
o Package dependence
spatstat.geom now suggests the new packages spatstat.explore and
spatstat.model, which have replaced spatstat.core.
o crosspairs.ppp
New argument 'periodic' specifies whether to use
periodic (toroidal) distances.
o crosspairs.ppp
New arguments 'iX', 'iY' make it possible to eliminate pairs
in which the two points are identical.
o bufftess
The result now has attribute 'breaks' which is the vector of
distance breakpoints.
o contour.im
New argument 'log' specifies whether the contour lines
should be equally spaced on a logarithmic scale.
o plot.im, image.im
New argument 'addcontour' specifies that contour lines should be drawn
over the image plot.
o invoke.symbolmap
New argument 'angleref'.
o funxy
The result now has a unitname, inherited from the argument W.
o integral.im
New argument 'weight' specifies a weight function for the integration.
o markstat, applynbd
These functions now work for point patterns in three dimensions
(class 'pp3') and point patterns on a network (class 'lpp').
o plot.psp
New argument 'use.marks', for consistency with other methods.
BUG FIXES
o framedist.pixels
Result was always a matrix, regardless of the value of 'style'.
Fixed.
o plot.im
Ignored ribargs$labels.
Fixed.
o plot.ppp
Crashed with an obscure message when argument 'shape' was given,
unless argument 'size' was also given.
Fixed.
o closepairs
Crashed if npoints(X)^2 exceeded the largest possible integer.
Fixed.
o crosspairs
Crashed if npoints(X) * npoints(Y) exceeded the largest possible integer.
Fixed.
CHANGES IN spatstat.geom VERSION 2.4-0
OVERVIEW
o We thank Fernando Milesi, Suman Rakshit and Mark Walsh for contributions.
o Bug fixes in 'distmap' and 'distfun'.
o Bug fixes in 'closepairs'.
o Bug fixes in 'nncross.ppp'.
o Minor improvements and bug fixes.
NEW FUNCTIONS
o framedist.pixels
Computes distance from each pixel to the enclosing rectangle.
SIGNIFICANT USER-VISIBLE CHANGES
o nncross.ppp
When X is a point pattern and Y is a line segment pattern,
higher order neighbours (k > 1) are now supported.
o intersect.tess
New argument 'keepempty'.
o unnormdensity
Argument 'weights' may have length 1.
New argument 'defaults'.
o distmap.owin
Behaviour has been altered so that, when X is a binary mask, the results of
distmap(X, invert=TRUE) and distmap(complement.owin(X)) are identical.
This affects a few pixels close to the edge of the frame.
[Suggested by Fernando Milesi.]
o distmap.ppp
New argument 'clip'.
BUG FIXES
o distmap.owin
If the window was a binary mask, the distance values were
slightly too large (by a factor 1 + 1/n where n is the pixel grid dimension),
due to a coding error.
[Spotted by Fernando Milesi.]
Fixed.
o distfun.owin
If the window was a binary mask, the distance values were
slightly too small (typically reduced by 1/20 of a pixel width).
[Spotted by Fernando Milesi.]
Fixed.
o distmap.owin
Values were incorrect if X was an empty window (is.empty(X) = TRUE).
Fixed.
o distmap.ppp, distmap.psp
Values were incorrect if X was an empty pattern (npoints(X) = 0).
Fixed.
o distmap.psp
Values were incorrect if X was an empty pattern (nsegments(X) = 0).
Fixed.
o closepairs.ppp
If distinct=FALSE and what="all", the resulting vectors
'yi' and 'yj' contained incorrect values, and had the wrong length.
Fixed.
o nncross.ppp
When k > 1, distance values were incorrectly replaced by 'Inf' in some cases.
Fixed.
o closepairs.ppp
Crashed with a message 'unable to allocate memory'
if the window of X had zero area.
Fixed.
o crosspairs.ppp
Crashed with a message 'unable to allocate memory'
if the window of Y had zero area.
Fixed.
o closepairs.pp3
Crashed with a message 'unable to allocate memory'
if the domain of X had zero volume.
Fixed.
o crosspairs.pp3
Crashed with a message 'unable to allocate memory'
if the domain of Y had zero volume.
Fixed.
o as.im.owin
If 'value' was a categorical (factor) value, the result was not a factor-valued image.
Fixed.
o tile.areas
For a tessellation defined by a pixel image,
the result of tile.areas() was not a numeric vector.
[Spotted by Suman Rakshit.]
Fixed.
o dirichlet
Rarely, the number of tiles in the tessellation
was less than the number of unique data points.
This occurred only when the window was a binary mask.
[Spotted by Suman Rakshit.]
Fixed.
CHANGES IN spatstat.geom VERSION 2.3-2
OVERVIEW
o 'spatstat.geom' now suggests the package 'spatstat.random'.
o Updated help files to refer to 'spatstat.random'.
CHANGES IN spatstat.geom VERSION 2.3-1
OVERVIEW
o New options for weighted.quantile
o Minor improvements.
SIGNIFICANT USER-VISIBLE CHANGES
o weighted.quantile
New argument 'type' allows the user to choose between several rules
for the weighted quantile.
o weighted.median
New argument 'type' allows the user to choose between several rules
for the weighted median. The default rule has changed.
o perspSegments
Improved quality of result when pixels are not square.
o nndist.ppp, nnwhich.ppp
Argument 'by' can be a factor, a logical vector,
a pixel image with factor values, a tessellation, a window,
the string 'marks' (if marks(x) is a factor),
or the name of one of the columns of marks (if marks(x) is a data frame).
o nndist.pp3, nnwhich.pp3
Argument 'by' can be a factor, a logical vector,
the string 'marks' (if marks(x) is a factor), or
the name of one of the columns of marks (if marks(x) is a data frame).
o split.ppp, split.ppx
The argument 'f' may now be the character string "marks",
signifying 'f=marks(X)', provided 'marks(X)' is a factor.