Log Message:
(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.