
        CHANGES IN spatstat.linnet VERSION 3.4-1

OVERVIEW

    o Improved algorithm for integrating a function on a network.

    o Improvements to perspective plot of a function on a network.

    o Identify threads in a network.

    o lppm recognises the local coordinates 'seg' and 'tp'.
    
    o Minor improvements and bug fixes.

NEW FUNCTIONS

    o threads
    Identify threads in a network.
    
SIGNIFICANT USER-VISIBLE CHANGES

    o density.lpp
    Improved message output when verbose=TRUE.
    
    o integral.linfun
    New argument 'exact'. If 'exact=TRUE', a more accurate algorithm is used.

    o lppm
    The model formula may involve the local coordinates 'seg' and 'tp'
    ('seg' is segment number, 'tp' is relative position along the segment)

    o lurking.lppm, lurking.lpp
    Argument 'covariate' can be a function(x,y)
    or one of the strings "x", "y" or "tp".

    o persp.linim
    Improved behaviour close to vertices of the network.
    New argument 'extrapolate'.

    o persp.linim
    Argument 'col.base' can be a pixel image, allowing a colour image
    to be plotted on the horizontal plane at height zero.

    o persp.linim
    New argument 'zadjust' to adjust the vertical scale.

BUG FIXES

    o as.linnet.psp
    Crashed sometimes if the window of X was not convex.
    Fixed.
    
    o lurking.lppm
    Crashed if envelope=TRUE.
    Fixed.

    o plot.linnet
    Disobeyed 'do.plot=FALSE'.
    Fixed.

    o shortestpath
    This function was defined, but was not exported from spatstat.linnet.
    Fixed.

        CHANGES IN spatstat.linnet VERSION 3.4-0

OVERVIEW

    o Diagnostics for a fitted point process model on a linear network.

    o Quadrat counting and quadrat tests on a linear network.

    o More geometrical operations on linear network objects.

    o Pixelwise arithmetic on a linear network.
    
    o Internal improvements.

NEW FUNCTIONS

    o as.lintess
    Convert other kinds of data to a tessellation on a network.

    o diagnose.lppm
    Diagnostic plots for point process model on a linear network.
    
    o eem.lppm
    Stoyan-Grabarnik exponential energy weights diagnostic.

    o harmonise.linim
    Convert several images on a network to a common pixel grid.

    o linim.apply
    Apply a function pixelwise to a list of images on a network.
    
    o lurking.lpp
    Lurking variable plot for point pattern on a linear network.

    o lurking.lppm
    Lurking variable plot for point process model on a linear network.

    o flipxy.linnet
    Swap x and y coordinates of a linear network

    o flipxy.lpp
    Swap x and y coordinates of a point pattern on a linear network

    o parres.lppm
    Partial residual plot for point process model on a linear network.

    o qqplot.lppm
    Residual Q-Q plot for  point process model on a linear network.
    
    o quadratcount.lpp
    Method for quadrat counting on a linear network.

    o quadrat.test.lpp, quadrat.test.lppm
    Methods for quadrat test on a linear network.

    o residuals.lppm
    Residual measure for a point process model on a linear network.

SIGNIFICANT USER-VISIBLE CHANGES

    o as.linnet.psp
    New arguments 'chop' and 'fuse'.

    o bw.voronoi
    New argument 'metric' passed to 'densityVoronoi.lpp'.

    o densityVoronoi.lpp
    New argument 'metric' passed to 'lineardirichlet'.

    o integral.linim, integral.linfun
    Argument 'domain' can be a tessellation on a network (class 'lintess').

    o intersect.lintess
    Improved behaviour when X or Y is a 2D tessellation.

    o lineardirichlet
    New argument 'metric' allows the tessellation to be constructed
    using either the shortest-path distance or Euclidean distance.
    
    o linequad
    Argument 'Y' can be a linear network.
    
    o print.lintess
    Output improved.

BUG FIXES

    o intersect.lintess
    Result was incorrect if X was a tessellation and Y was a linear network.
    Fixed.

        CHANGES IN spatstat.linnet VERSION 3.3-2

OVERVIEW

    o Summary functions handle NA objects.

SIGNIFICANT USER-VISIBLE CHANGES

    o Summary functions
    (linearK, linearKinhom, linearKeuclid,
    linearKcross, linearKdot, linearKcross.inhom, linearKdot.inhom	
    linearpcf, linearpcfinhom, linearpcfEuclid
    linearpcfcross, linearpcfdot, linearpcfcross.inhom, linearpcfdot.inhom	
    linearmarkequal, linearmarkconnect, linearJinhom)
    If X is a missing point pattern, a missing object of class 'fv' is returned.

        CHANGES IN spatstat.linnet VERSION 3.3-1

OVERVIEW

    o Minor changes to documents to satisfy CRAN package checker.


        CHANGES IN spatstat.linnet VERSION 3.3-0

OVERVIEW

    o Extension of ROC curves.

    o Interactively identify segments of a network.

    o Interactively identify tiles of a tessellation on a network.

NEW FUNCTIONS

    o identify.linnet
    Interactively identify segments of a network.
    
    o identify.lintess
    Interactively identify tiles of a tessellation on a network.

    o as.linfun.linnet
    Create a function on a linear network which maps each network segment
    to a specified value.
    
SIGNIFICANT USER-VISIBLE CHANGES

    o roc.lpp
    New argument 'baseline' allows calculation of ROC relative to a baseline.

    o roc.lpp
    New argument 'weights' for numerical weights on the data points.

    o roc.lpp
    New argument 'method' determines the estimation method.
    New options include a kernel smoothing estimate and a monotone estimate.
    
    o roc.lpp
    New arguments 'CI', 'alpha' for calculating confidence intervals.

    o roc.lpp
    New argument 'subset' specifies a sub-region of the spatial domain
    in which the ROC should be calculated.

    o roc.lppm
    New argument 'baseline' allows calculation of ROC relative to a baseline.

    o roc.lppm
    New argument 'method' determines the estimation method.
    New options include a kernel smoothing estimate and a monotone estimate.
    
    o roc.lppm
    New arguments 'CI', 'alpha' for calculating confidence intervals.

    o roc.lppm
    New argument 'subset' specifies a sub-region of the spatial domain
    in which the ROC should be calculated.

    o roc.lppm
    New argument 'leaveoneout' specifies whether to use leave-one-out estimates
    of intensity at the data points.

    o chop.linnet
    Improved labels of tiles in the resulting tessellation.

        CHANGES IN spatstat.linnet VERSION 3.2-6

OVERVIEW

    o Bug fix in "[.lpp"
    
BUG FIXES

    o [.lpp
    Results with snip=TRUE were incorrect in some cases.
    Fixed.

        CHANGES IN spatstat.linnet VERSION 3.2-5

OVERVIEW

    o Minor changes in documentation to satisfy the package checker.


        CHANGES IN spatstat.linnet VERSION 3.2-4

OVERVIEW

    o Bug fix in lppm.

BUG FIXES

    o lppm
    For models involving covariates of class 'lintess', the internal
    structure of the fitted model was corrupted, leading to errors in
    calculating properties of the fitted model, such as predict.lppm.
    [Spotted by Andrea Gilardi.]
    [Bug fix requires spatstat.model 3.3-3.002]
    Fixed.

        CHANGES IN spatstat.linnet VERSION 3.2-3

OVERVIEW

    o Shortest path between two points on a network.

NEW FUNCTIONS

    o shortestpath
    Find the shortest path between two specified points on a network,
    and return it as a line segment pattern.


        CHANGES IN spatstat.linnet VERSION 3.2-2

OVERVIEW

    o Tweaks to documentation.

    o Internal improvements.

        CHANGES IN spatstat.linnet VERSION 3.2-1

OVERVIEW

    o Internal tweaks to satisfy CRAN package checker.


        CHANGES IN spatstat.linnet VERSION 3.2-0

OVERVIEW

    o spatstat.linnet now depends on 'spatstat.univar'.

    o extract the subset of an image that lies on selected segments of network.

    o Minor improvements.

    o Internal improvements.

PACKAGE DEPENDENCE

    o spatstat.linnet
    Now depends on the new package 'spatstat.univar'.

SIGNIFICANT USER-VISIBLE CHANGES

    o identify.lpp
    Automatically starts a new plot device and displays `x`
    if there is no plot device open.
    
    o thinNetwork
    X can be a pixel image on a linear network (object of class 'linim').
    
    o plot.linnet, plot.lpp
    These functions now recognise the argument 'adj.main'.

        CHANGES IN spatstat.linnet VERSION 3.1-5

OVERVIEW

    o Slightly accelerated.

    o Internal stability improvements.

SIGNIFICANT USER-VISIBLE CHANGES

    o spatstat.linnet package
    Some computations slightly accelerated.

        CHANGES IN spatstat.linnet VERSION 3.1-4

OVERVIEW

    o Added a full list of functions to the main help file.

    o Intersection of a 2D tessellation with a network.

    o Internal improvements.

SIGNIFICANT USER-VISIBLE CHANGES

    o intersect.lintess
    Can compute the intersection between a two-dimensional tessellation
    and a linear network (yielding a tessellation on the network).

        CHANGES IN spatstat.linnet VERSION 3.1-3

OVERVIEW

    o Minor corrections to help files.


        CHANGES IN spatstat.linnet VERSION 3.1-2

OVERVIEW

    o Minor improvements to help files.

        CHANGES IN spatstat.linnet VERSION 3.1-1

OVERVIEW

    o Minor improvements

SIGNIFICANT USER-VISIBLE CHANGES

    o rhohat.lpp, rhohat.lppm
    New argument 'rule.eps' passed to 'as.mask'.

    o as.linim.default, as.linim.linfun
    New argument 'rule.eps' passed to 'as.mask'.

        CHANGES IN spatstat.linnet VERSION 3.1-0

OVERVIEW

    o Inhomogeneous K and pcf using automatic estimation of intensity.

    o density.lpp accepts bandwidth selection rules.

    o density.lpp accepts sigma=NULL and has a simple default.

    o Updated package documentation.
    
SIGNIFICANT USER-VISIBLE CHANGES

    o linearKinhom, linearpcfinhom, linearKEuclidInhom, linearpcfEuclidInhom
    Argument 'lambda=NULL' is now interpreted to mean that the intensity
    should be estimated by kernel smoothing. A warning is issued that this
    is different from the previous behaviour.

    o linearKdot.inhom, linearpcfdot.inhom
    Argument 'lambdaI=NULL' or 'lambdadot=NULL' is now interpreted to mean
    that the intensity should be estimated by kernel smoothing.

    o linearKcross.inhom, linearpcfcross.inhom
    Argument 'lambdaI=NULL' or 'lambdaJ=NULL' is now interpreted to mean
    that the intensity should be estimated by kernel smoothing.

    o density.lpp
    Argument 'sigma' can now be a function in the R language,
    assumed to provide a bandwidth selection rule. This function
    will be applied to the point pattern x to compute the bandwidth.

    o density.lpp
    Argument 'sigma=NULL' is now accepted. The default value is one-eighth
    of the length of the shortest side of the bounding box of x.

    o densityQuick.lpp
    Argument 'X' changed to 'x' for consistency.

    o linearpcfinhom
    New arguments 'adjust.sigma', 'bw' and 'adjust.bw'.

    o linearpcfdot.inhom, linearpcfcross.inhom
    New arguments 'adjust.sigma', 'bw' and 'adjust.bw'.

    o linearpcfEuclidInhom
    New arguments 'adjust.sigma', 'bw' and 'adjust.bw'.

        CHANGES IN spatstat.linnet VERSION 3.0-6

OVERVIEW

    o Internal improvements and bug fixes.

        CHANGES IN spatstat.linnet VERSION 3.0-5

OVERVIEW

    o Improvements and bug fixes in 'lppm' class.

    o Minor extension to random generators.
    
SIGNIFICANT USER-VISIBLE CHANGES

    o runiflpp, rpoislpp
    The simulation parameters can be determined from an example
    point pattern, given as the argument 'ex'.
    
    o print.lppm, summary.lppm
    The name of the original point pattern dataset (to which the
    model was fitted) is now printed.

    o print.lppm, summary.lppm
    Improved output.

    o update.lppm
    Internal improvements.
    
        CHANGES IN spatstat.linnet VERSION 3.0-4

OVERVIEW

    o quantile function on a network.
    
    o Minor enhancements and bug fixes.

NEW FUNCTIONS

    o quantilefun.linim
    Quantile function, returned as a function.
    Method for 'quantilefun' for images on a network.

BUG FIXES

    o relrisk.lpp
    Crashed if allow.infinite=FALSE.
    Fixed.
    
        CHANGES IN spatstat.linnet VERSION 3.0-3

OVERVIEW

    o We thank Brian Ripley for contributions.

    o Internal bug fix.

BUG FIXES

    o pairdist.lpp
    Results could have been completely incorrect, due to an internal bug,
    if the linear network data was in the non-sparse representation.
    

        CHANGES IN spatstat.linnet VERSION 3.0-2

OVERVIEW

    o Internal tweaks to satisfy package checker.

        CHANGES IN spatstat.linnet VERSION 3.0-1

OVERVIEW

    o Internal improvements.

        CHANGES IN spatstat.linnet VERSION 3.0-0

OVERVIEW

    o We thank Greg McSwiggan, Fernando Milesi, Mehdi Moradi, Gopalan Nair
    and James Pope for contributions.
    
    o spatstat.linnet now depends on the new packages 'spatstat.explore'
    and 'spatstat.model' rather than the old 'spatstat.core'.

    o Kernel smoothing on a linear network.
    
    o K function and pair correlation function based on Euclidean distance.

    o Inhomogeneous J function on a network.

    o Terminal vertices of a network.
    
    o Points along a network can be drawn as cross-ticks.

    o Marks attached to vertices and segments of a network.
    
    o Important change to K function and pair correlation function
    when 'ratio=TRUE'.

    o U-shaped curves in 'rhohat'.

    o Faster computation of the length of the disc in the shortest path metric.
    
    o Minor improvements and bug fixes.

    o Improvements to internal code.

    o Minor internal changes to package information.

NEW FUNCTIONS

    o lineardisclength
    Compute the length of the disc in the shortest-path metric.
    
    o marks.linnet, marks<-.linnet
    Marks attached to the vertices and segments of a linear network.
    
    o Smooth.lpp
    Kernel smoothing (Nadaraya-Watson) on a linear network.

    o distmap.lpp
    Distance map for a point pattern on a network.
    
    o linearKEuclid, linearpcfEuclid, linearKEuclidInhom, linearpcfEuclidInhom
    K function and pair correlation function based on Euclidean distances.

    o linearJinhom
    Inhomogeneous J function on a linear network.

    o terminalvertices
    Extract the terminal vertices of a linear network.

    o bw.relrisk.lpp
    This function replaces 'bw.relrisklpp'
    and is a method for the generic 'bw.relrisk'.

    o rThomaslpp
    Simulate Thomas cluster process on a network.
    
SIGNIFICANT USER-VISIBLE CHANGES

    o Package dependence
    'spatstat.linnet' now depends on the new packages 'spatstat.explore'
    and 'spatstat.model' rather than the old 'spatstat.core'.
    
    o plot.lpp
    If 'shape="crossticks"', the points will be drawn as
    short line segments perpendicular to the network.

    o linearK, linearpcf, linearKdot, linearKcross, linearpcfcross, linearpcfdot
    When 'ratio=TRUE', the denominator is now equal to the number of
    ordered pairs of data points considered. This does not affect the
    summary function, but it changes the calculation of pooled estimates.
    
    o densityQuick.lpp
    If 'sigma' is a function for selecting a bandwidth,
    additional arguments '...' of densityQuick.lpp will be passed to 'sigma',
    provided they match the name of a formal argument of 'sigma'.

    o bw.relrisklpp
    This function is now deprecated, and is replaced by 'bw.relrisk.lpp',
    a method for the generic 'bw.relrisk'.

    o bw.relrisk.lpp
    When 'method="likelihood"', the cross-validation criterion
    is now defined as the *negative* likelihood. This is consistent with
    'bw.relrisk.ppp', and ensures that the optimum bandwidth is always
    found by minimising the cross-validation criterion.

    o integral.linim, integral.linfun
    New argument 'weight' specifies a weight function for the integration.
    
    o rhohat.lpp, rhohat.lppm
    New options 'smoother="mountain"' and 'smoother="valley"'
    for estimating a unimodal function (U-shaped curve).

    o rhohat.lpp, rhohat.lppm
    If the covariate is a 'distfun' on a network, the unit of length
    will be saved, and will be displayed on the plot.

    o rhohat.lpp, rhohat.lppm
    New arguments 'jitter', 'jitterfactor', 'interpolate' allow greater
    control over the calculation.

    o plot.linnet
    Optionally displays the marks of the segments or marks of the vertices.
    Changed argument list.
    
    o print.linnet, summary.linnet
    These functions print information about marks of the segments or vertices.

    o predict.lppm
    Can now compute standard errors.

    o predict.lppm
    New formal arguments 'covariates' and 'se'.

    o rhohat.lpp, rhohat.lppm
    New argument 'do.CI' specifies whether to calculate confidence bands.
    
BUG FIXES

    o density.lpp
    If 'weights' were given, the results were completely incorrect
    when leaveoneout=TRUE (the default) and at="points".

    o spatstat.model::effectfun
    Results were sometimes incorrect for 'lppm' objects.
    [Spotted by Fernando A. Milesi]
    Fixed.
    
    o predict.lppm
    Ignored argument 'covariates'.
    Fixed.
    
    o rhohat.lpp, rhohat.lppm
    The argument 'subset' was not handled correctly in the internal data.
    The estimated function 'rho' was correct
    but the results of 'predict.rhohat' may have been incorrect
    and were computed only on the 'subset'.
    Fixed.

    o plot.lpp
    Did not display the main title in some cases.
    Fixed.
    
    o "[.lpp", "[.linnet"
    Ignored marks attached to the network segments.
    Fixed.

    o "[.lpp", "[.linnet"
    Crashed if the network vertices had marks, when 'snip=TRUE'.
    Fixed.

    o densityQuick.lpp
    Crashed sometimes with a message about unequal lengths of vectors.
    Fixed.


        CHANGES IN spatstat.linnet VERSION 2.3-2

OVERVIEW

    o 'spatstat.linnet' now depends on 'spatstat.random'.

SIGNIFICANT USER-VISIBLE CHANGES

    o package dependence
    'spatstat.linnet' now depends on the new package 'spatstat.random'.

        CHANGES IN spatstat.linnet VERSION 2.3-1

OVERVIEW

    o More control over resolution of 'linim' objects.
    
    o Improved documentation.

    o Minor improvements and bug fixes.
    
SIGNIFICANT USER-VISIBLE CHANGES

    o as.linim.default, as.linim.linfun
    New argument 'nd'

    o integral.linfun
    New argument 'nd'

    o rjitterlpp, rjitter.lpp
    The function 'rjitterlpp' has been renamed 'rjitter.lpp'
    and is now a method for the generic 'rjitter'.

    o rjitterlpp
    This function still exists, but is now deprecated in favour of 'rjitter.lpp'.

BUG FIXES

    o rjitterlpp
    The argument 'radius' was interpreted as a fraction of segment length
    rather than an absolute distance.
    Fixed.
    

        CHANGES IN spatstat.linnet VERSION 2.3-0

OVERVIEW

    o We thank Suman Rakshit, Greg McSwiggan and Marc Schneble
    for contributions.

    o Sufficient Dimension Reduction on a linear network.
    
    o Perspective-view plots of linfun and linim objects.
    
    o Bug fix to Math.linim

    o Minor additions.

NEW FUNCTIONS

    o sdr.lpp
    Sufficient Dimension Reduction on a linear network.
    [Contributed by Suman Rakshit.]
    
    o persp.linfun, persp.linim
    Perspective-view plots of functions on a linear network (class linim)
    and images on a linear network (class linfun).
    [Written by Adrian Baddeley and Greg McSwiggan.]
    
SIGNIFICANT USER-VISIBLE CHANGES

    o response.lppm
    Method for 'response' for fitted point process models on a network.

BUG FIXES

    o Math.linim
    If 'Z' was a pixel image on a network (class 'linim')
    and 'v' was a single number, then 'Z/v' was a pixel image (class 'im')
    instead of a pixel image on a network (class 'linim').
    [Spotted by Marc Schneble.]
    Fixed.

    o bw.voronoi
    Printed output stated that the cross-validation criterion was minimised
    instead of maximised.


        CHANGES IN spatstat.linnet VERSION 2.2-1

OVERVIEW

    o Minor changes to satisfy CRAN.

        CHANGES IN spatstat.linnet VERSION 2.2-0

OVERVIEW

    o Extensions to rhohat.lpp and rhohat.lppm.
    
    o Internal bug fixes.

SIGNIFICANT USER-VISIBLE CHANGES

    o rhohat.lpp, rhohat.lppm
    New option (smoother='piecewise') computes a piecewise-constant
    estimate of rho(z).

    o rhohat.lpp, rhohat.lppm
    The result now includes the 'average' intensity rho.

        CHANGES IN spatstat.linnet VERSION 2.1-1

OVERVIEW

    o Tweak to satisfy the package checker.


        CHANGES IN spatstat.linnet VERSION 2.1-0

OVERVIEW

    o We thank Andrea Gilardi for contributions.

    o Bug fix in density.lpp

    o Improvement to densityEqualSplit

    o New function for jittering point patterns on a network.

    o Function renamed.

NEW FUNCTIONS

    o rjitterlpp
    Apply random displacements to the points on a linear network.

    o densityHeat.lpp
    Diffusion kernel estimation of intensity on a linear network.
    (formerly known as 'densityHeatlpp' and 'densityHeat', this is
    now a method for the new generic 'densityHeat')

SIGNIFICANT USER-VISIBLE CHANGES

    o densityEqualSplit
    New arguments 'at' and 'leaveoneout' for consistency with other functions.

    o densityHeat
    The function formerly known as 'densityHeat' or 'densityHeatlpp'
    is now renamed 'densityHeat.lpp' and is a method for the generic
    'densityHeat'.

    o density.lpp
    Accelerated when the pattern contains duplicated points.
    
BUG FIXES

    o density.lpp
    The result had the wrong length if 'x' contained duplicated points
    when 'weights' were given and 'at="points"'.
    [Spotted by Andrea Gilardi]
    Fixed.

        CHANGES IN spatstat.linnet VERSION 2.0-0

OVERVIEW

    o We thank Andrea Gilardi for contributions.

    o Function renamed.
    
    o Bug fix in density.lpp

SIGNIFICANT USER-VISIBLE CHANGES

    o densityHeat
    'densityHeat' has been temporarily renamed 'densityHeatlpp',
    to prevent errors in the package checking process.

    o [.linim
    Accelerated.


BUG FIXES

    o deviance.lppm, pseudoR2.lppm
    Results were completely incorrect, due to a coding error.
    Fixed.

    o density.lpp
    Crashed if 'weights' were given and 'x' contained duplicated points.
    [Spotted by Andrea Gilardi]
    Fixed.

    o Lcross.inhom, Kcross.inhom, Kmulti.inhom
    The option 'correction="none"' was accepted but ignored.
    [Spotted by Corey Anderson.]
    Fixed.

    o simulate.rhohat
    Crashed when applied to rhohat objects computed from data
    on a linear network.
    Fixed.
    

        CHANGES IN spatstat.linnet VERSION 1.65-9

OVERVIEW

    o Minor internal changes.

        CHANGES IN spatstat.linnet VERSION 1.65-8

OVERVIEW

    o Function renamed.

SIGNIFICANT USER-VISIBLE CHANGES

    o densityHeat
    'densityHeat' has been renamed 'densityHeat.lpp'.


        CHANGES IN spatstat.linnet VERSION 1.65-7

OVERVIEW

    o Tweaks to satisfy CRAN.


        CHANGES IN spatstat.linnet VERSION 1.65-1

OVERVIEW

    o Added NEWS file.


        CHANGES IN spatstat.linnet VERSION 1.65-0

OVERVIEW

    o Package initialised at version 1.65-0

SIGNIFICANT USER-VISIBLE CHANGES

    o spatstat.linnet
    The package 'spatstat.linnet' has been created from a subset
    of the code in the original 'spatstat' package version 1.65-0.
    It contains the functionality for statistical analysis of
    spatial data on a linear network.
    For an overview, see help("spatstat.linnet-package")

    o Execution
    The 'spatstat.linnet' package is slightly faster than the corresponding
    code in the 'spatstat' package, because the procedure for calling
    internal C functions has been streamlined.



