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R-spatstat.geom: update to 3.3.5. 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.
(geography/R-spatstat.geom) Updated 3.2.7 to 3.3.4
CHANGES IN spatstat.explore VERSION 3.3-3
OVERVIEW
o relative risk estimation using diffusion.
o smoothing using diffusion.
o Tweaks to bandwidth selection.
NEW FUNCTIONS
o relriskHeat, relriskHeat.ppp
Relative risk estimation using diffusion.
o blurHeat, blurHeat.im
Image smoothing using diffusion.
o SmoothHeat, SmoothHeat.ppp
Smoothing numerical values observed at points, using diffusion.
o bw.relriskHeatppp
Bandwidth selection for relriskHeat.ppp
SIGNIFICANT USER-VISIBLE CHANGES
o bw.ppl
Argument 'shortcut' now defaults to TRUE.
CHANGES IN spatstat.explore VERSION 3.3-2
OVERVIEW
o Tweaks to documentation.
o Internal repairs.
o Internal changes to satisfy package checker.
CHANGES IN spatstat.explore VERSION 3.3-1
OVERVIEW
o Internal changes to satisfy package checker.
CHANGES IN spatstat.explore VERSION 3.3-0
OVERVIEW
o 'spatstat.explore' now depends on package 'spatstat.univar'.
o Some functions have been moved to 'spatstat.univar'.
o Minor improvements.
PACKAGE DEPENDENCE
o spatstat.explore now depends on the new package 'spatstat.univar'
o Some functions have been moved
from 'spatstat.explore' to 'spatstat.univar'.
SIGNIFICANT USER-VISIBLE CHANGES
o cbind.fv, bind.fv
Additional arguments may be functions in the R language.
DELETED FUNCTIONS
o bw.abram
The generic 'bw.abram' has been moved
to the new package 'spatstat.univar'.
o CDF, CDF.density
The generic 'CDF' and method 'CDF.density' have been moved
to the new package 'spatstat.univar'.
o densityAdaptiveKernel
The generic 'densityAdaptiveKernel' has been moved
to the new package 'spatstat.univar'.
o dkernel, pkernel, qkernel, rkernel
These functions have been moved to the new package 'spatstat.univar'.
o kernel.factor, kernel.moment, kernel.squint
These functions have been moved to the new package 'spatstat.univar'.
o kaplan.meier, reduced.sample, km.rs
These functions have been moved to the new package 'spatstat.univar'.
o quantile.density
This method has been moved to the new package 'spatstat.univar'.
o stieltjes
This function has been moved to the new package 'spatstat.univar'.
(geography/R-spatstat.geom) Updated 2.2.2 to 3.2.7
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.
o owin
If argument 'mask' is a logical matrix,
NA entries will be accepted, and converted to FALSE.
CHANGES IN spatstat.geom VERSION 2.3-0
OVERVIEW
o Quantile transformation.
o Distance metric based on a convex set.
o Basic support for calculations using non-Euclidean distance metrics.
o Improvements to 'rjitter'.
NEW CLASSES
o metric
An object of class 'metric' represents a distance metric.
See help(metric.object).
NEW FUNCTIONS
o transformquantiles
Transform the quantiles of a vector, matrix, array or pixel image.
o convexmetric
Distance metric based on a convex set.
o mean.ecdf, mean.ewcdf
Calculate the mean of an empirical cumulative distribution function.
o invoke.metric
Low level function to perform a desired operation using a given metric.
o rjitter.ppp
This function was previously called 'rjitter'. It is now a method
for the new generic function 'rjitter'.
SIGNIFICANT USER-VISIBLE CHANGES
o pairdist.ppp, crossdist.ppp, nndist.ppp, nnwhich.ppp, nncross.ppp
New argument 'metric' specifies a non-Euclidean distance metric
to measure the distances.
o distmap.ppp, distmap.owin, distmap.psp
New argument 'metric' specifies a non-Euclidean distance metric
to measure the distances.
o disc
New argument 'metric' specifies a non-Euclidean distance metric
defining the disc.
o rjitter
The function previously called 'rjitter' is now called 'rjitter.ppp'
and is now a method for the new generic 'rjitter'.
o rjitter.ppp
The argument 'radius' may be a numeric vector, specifying a different
displacement radius for each data point.
BUG FIXES
o as.mask
Crashed if 'Frame(w)' had zero height or zero width.
Fixed.
geography: Replace RMD160 checksums with BLAKE2s checksums All checksums have been double-checked against existing RMD160 and SHA512 hashes
geography: Remove SHA1 hashes for distfiles
(geography/R-spatstat.geom) import R-spatstat.geom-2.2.2 Defines types of spatial data such as point patterns, mainly in two dimensions, but also in higher dimensions. Provides class support, and functions for geometrical operations on spatial data, used in the 'spatstat' family of packages. Excludes spatial data on a linear network, which are covered by the separate package 'spatstat.linnet'.