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[pkgsrc/trunk]: pkgsrc/geography/R-spatstat (geography/R-spatstat) (was) Upda...



details:   https://anonhg.NetBSD.org/pkgsrc/rev/11f88af79bb5
branches:  trunk
changeset: 458842:11f88af79bb5
user:      mef <mef%pkgsrc.org@localhost>
date:      Mon Sep 20 12:25:34 2021 +0000

description:
(geography/R-spatstat) (was) Updated 1.63.2 to 2.2.0. ChangeLog attached, sorry

        CHANGES IN spatstat VERSION 2.2-0

OVERVIEW

    o We thank Warick Brown, Achmad Choiruddin, Jean-Francois Coeurjolly,
    Andrea Gilardi, Yongtao Guan, Abdollah Jalilian, Hank Stevens
    and Rasmus Waagepetersen for contributions.

    o Conditional simulation in kppm.

    o Simulation of the product shot noise Cox process.

    o Information criteria for model selection in kppm

    o Estimation of the spatial covariance function of a pixel image

    o Modified handling of covariates in slrm

    o Buffer tessellation

    o New function for jittering point patterns on a network.

    o Extensions to 'rhohat'

    o densityfun.ppp handles query points outside original window

    o Extension to 'discretise'.

    o Improvement to densityEqualSplit

    o summary method for spatial logistic regression models

    o New options for distmap.psp

    o Improved output in summary.mppm

    o Bug fix in nncross

    o Bug fix in density.lpp

NEW FUNCTIONS

    o bufftess
    Distance buffer tessellation

    o ic
    Information criteria for model selection in ppm and kppm.
    Kindly contributed by Achmad Choiruddin, Jean-Francois Coeurjolly
    and Rasmus Waagepetersen.

    o rPSNCP
    Generate simulated realisations of the product shot noise Cox process.
    Contributed by Abdollah Jalilian, Yongtao Guan and Rasmus Waagepetersen.

    o spatcov
    Estimate the spatial covariance function of a pixel image.

    o summary.slrm, print.summary.slrm
    Summary method for spatial logistic regression models

    o coef.summary.slrm
    Print the fitted coefficients, confidence interval and p-values
    for a spatial logistic regression model.

    o pairMean
    Compute the mean of a specified function of interpoint distance
    between random points in a window.

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


SIGNIFICANT USER-VISIBLE CHANGES

    o simulate.kppm
    Conditional simulation of the model, given a fixed number of points,
    is now supported using the new arguments 'n.cond' and 'w.cond'.

    o densityfun.ppp
    The resulting function can now handle query points which lie
    outside the window of the original data,
    and has argument 'drop=TRUE' which specifies how to handle them.

    o rpoint
    New argument 'forcewin' forces the code to use the window 'win'
    when 'f' is a pixel image.

    o slrm
    In the default case (where dataAtPoints is not given)
    all spatial covariates, including the spatial coordinates x and y,
    are now evaluated at the centre of each pixel. This improves
    consistency with other implementations of spatial logistic regression.

    o slrm
    Silently ignores any arguments '...' that are not recognised by 'as.mask'

    o summary.mppm
    Improved summary of the dependence of the
    interpoint interaction on the covariates.

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

    o pairs.im
    New argument 'drop'.

    o distmap.psp
    New arguments 'extras' and 'clip'

    o discretise
    New argument 'move.points' determines whether the point coordinates
    are also discretised.

    o summary.im
    Output improved when the image is empty (i.e. when all pixel values
    are undefined).

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

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

    o distcdf
    Arguments which are NULL will be treated as missing.

    o distcdf
    New argument 'savedenom'.

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

BUG FIXES

    o nncross.ppp
    If the argument 'by' was given, some of the results were incorrect.
    [Spotted by Hank Stevens.]
    Fixed.

    o nncross.ppp, nncross.pp3
    If 'iX' and 'iY' were given, some of the results were incorrect.
    Fixed.

    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.

    o simulate.kppm
    Conditional simulation crashed on rare occasions,
    with an error about negative probabilities.
    Fixed.

    o model.matrix.mppm
    If the model was fitted using 'gam', the resulting matrix
    did not have an 'assign' attribute.
    Fixed.

    o model.depends
    Crashed for models fitted using 'gam'.
    Fixed.

    o predict.slrm, fitted.slrm
    Crashed if the model was fitted using split pixels (argument 'splitby').
    Fixed.

    o predict.slrm, fitted.slrm
    Crashed in some cases when 'window' was given.
    Fixed.

    o update.slrm
    Failed to find covariates that were provided in 'env'.
    Fixed.

    o cdf.test
    Crashed if the covariate was constant.
    Fixed.

         CHANGES IN spatstat VERSION 2.1-0

OVERVIEW

    o We thank Tilman Davies, Peter Diggle, Greg McSwiggan and Suman Rakshit
    for contributions.

    o diffusion kernel estimate of intensity

    o New dataset 'btb'

    o More support for spatial logistic regression models.

NEW FUNCTIONS

    o densityHeat
    New generic function for diffusion kernel estimation of intensity

    o densityHeat.ppp
    Diffusion kernel estimation of intensity in 2 dimensions

    o densityHeat.lpp
    Diffusion kernel estimation of intensity on a linear network

    o slrm
    'step' can now be applied to models fitted using 'slrm'.

NEW DATASETS

    o btb
    Bovine tuberculosis data, from Prof Peter Diggle.

        CHANGES IN spatstat VERSION 2.0-1

OVERVIEW

    o Minor changes to satisfy CRAN checks.


        CHANGES IN spatstat VERSION 2.0-0

OVERVIEW

    o We thank Corey Anderson, Michael Chirico, Andy Craig,
    Marcelino de la Cruz, Tilman Davies, Pavel Fibich,
    Kurt Hornik, Gopalan Nair, Yonatan Rosen and Rasmus Waagepetersen
    for contributions.

    o spatstat has been divided into 7 sub-packages
    (spatstat.utils, spatstat.data, spatstat.sparse,
    spatstat.geom, spatstat.core, spatstat.linnet and spatstat).

    o Important bug fix in simulation of log-Gaussian Cox processes.

    o Increased speed for large datasets.

    o variance calculations handle larger datasets.

    o predict.mppm now works for multitype point process models.

    o Improved handling of 'newdata' in predict.mppm.

    o More support for multi-dimensional patterns.

    o Changed default value of 'stringsAsFactors'.

    o spatstat now depends on R version 3.5.0 or later.

    o spatstat now requires spatstat.utils version >= 1.18-0

    o spatstat now requires spatstat.data version >= 1.7-0

    o Bug fixes and minor improvements.

    o Version nickname: "Caution: contains small parts"

NEW FUNCTIONS

    o intersect.boxx
    Compute intersection of boxes in multi-dimensional space

    o scale.boxx, scale.ppx
    Methods for 'scale' for boxes and patterns in multi-dimensional space

    o shift.boxx, shift.ppx
    Methods for 'shift' for boxes and patterns in multi-dimensional space

    o is.boxx
    Determine whether an object is a multidimensional box

SIGNIFICANT USER-VISIBLE CHANGES

    o package structure
    The original 'spatstat' package has been divided into 7 sub-packages
    (spatstat.utils, spatstat.data, spatstat.sparse,
    spatstat.geom, spatstat.core, spatstat.linnet and spatstat).
    The remaining 'spatstat' package requires all the other sub-packages.
    Your existing code scripts should still work with minimal changes.

    o overall speed
    Changes have been made to the internal code of spatstat
    which should accelerate computations involving large datasets.

    o vcov.ppm, summary.ppm
    Variance calculations now handle larger datasets
    because they use sparse arrays, by default.

    o dirichletEdges
    New argument 'clip'.

    o rSSI
    Accelerated.

    o localpcf, localpcfinhom
    New argument 'rvalue'.

    o harmonise.im
    The result belongs to class 'solist' and 'imlist'
    so that it can be plotted.

    o hyperframe, as.im.function
    The formal default value of 'stringsAsFactors' has been changed
    to 'NULL' to conform to changes in R. (The actual default value
    is TRUE for R < 4.1.0 and FALSE for R >= 4.1.0)

    o predict.mppm
    Now supports multitype point process models.

    o predict.mppm
    Improved handling of argument 'newdata'

    o densityHeat
    Default behaviour has changed slightly.
    New argument 'finespacing'.

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

    o rotmean
    The result now has the same 'unitname' as the input object X.
    New argument 'adjust' controls the smoothing bandwidth.

    o sessionInfo
    Output now lists packages that are imported but not loaded.

    o rlabel
    New argument 'group' specifies that the points are divided into
    several groups, and that relabelling is applied within each group.

    o plot.psp
    The code for 'style="width"' has been completely rewritten,
    so that it no longer depends on plot.linim, and is more efficient.
    The formal argument list has been extended.

    o mincontrast
    New argument 'action.bad.values' specifies what action is taken
    when the summary function produces NA or NaN or infinite values.

    o sessionLibs
    Package names are now sorted alphabetically.

    o [.linim
    Accelerated.

    o integral.im
    Accelerated in the case where 'domain' is a tessellation.

    o cbind.hyperframe
    Row names are not altered (previously they were altered
    using 'make.names')

    o simulate.ppm
    Now recognises the argument 'window' as an alternative to 'w'.

    o kppm
    Improved numerical robustness.

    o Kcross, Gcross, Jcross
    Function labels (shown on the plot legend) have been
    improved when i = j.

    o anova.mppm
    Issues a warning when applied to random-effects models
    (models fitted using the argument 'random').

    o [.ppx
    New argument 'clip'

BUG FIXES

    o rLGCP, simulate.kppm
    Simulation results for log-Gaussian Cox processes were incorrect
    unless the pixel dimensions and pixel spacings were identical
    on the horizontal and vertical axes. (If pixel dimensions were not
    specified, then the results were incorrect whenever the Frame of the
    simulation window was not a square.)
    [Spotted by Tilman Davies.]
    Fixed.

    o crossdist.pp3
    Results with periodic=TRUE were partially incorrect.
    Fixed.

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

    o colourmap
    If a colour map was applied to numbers lying outside the range of the
    colour map, the wrong number of NA's was sometimes produced.
    Fixed.

    o Gest
    If correction="rs" or correction="km", then both the reduced-sample
    (border correction) and Kaplan-Meier corrected estimates were calculated.
    [Spotted by Gopalan Nair.]
    Fixed.

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

    o rMatClust, rThomas, rCauchy, rVarGamma
    If the fitted model was effectively a Poisson process,
    the result did not have attributes 'Lambda' and 'parents'
    even when the user requested them.
    Fixed.

    o affine.owin
    For mask windows, the pixel resolution of the result
    was too fine, leading to very large datasets.
    Fixed.

    o affine.im
    If the transformation matrix was not diagonal, the pixel resolution
    of the result was too fine, leading to very large datasets.
    Fixed.

    o plot.ppp
    For a point pattern in a binary mask window,
    if both arguments 'col' and 'cols' were given,
    the points were coloured according to 'col', which was incorrect.
    Fixed.

    o dirichletEdges
    Crashed if any edges crossed the boundary of the window.
    Fixed.

    o Vmark
    Crashed if normalise=TRUE when there was only one column of marks.
    (Spotted by Pavel Fibich.)
    Fixed.

    o unitname
    Spatial datasets with incorrect internal format
    (or using an out-of-date version of the spatstat format)
    caused an error if the 'units' package was loaded.
    Fixed.

    o nnclean
    Crashed if k >= npoints(X).
    Fixed.

    o print.ppm
    Crashed sometimes when applied to the result of subfits().
    Fixed.

    o model.matrix.mppm
    Crashed with random-effects models.
    Fixed.

    o anova.mppm
    Crashed with random-effects models.
    Fixed.

    o objsurf.kppm
    Crashed if the model was fitted by Palm likelihood (method="palm")
    or second order composite likelihood (method="clik2").
    Fixed.

    o MinkowskiSum
    Crashed sometimes with an error message about 'sumconnected'.
    Fixed.

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

    o hyperframe
    Crashed if the argument 'row.names' was given
    and the hyperframe had exactly one row.
    Fixed.


        CHANGES IN spatstat VERSION 1.64-1

OVERVIEW

    o Important bug fix in vcov.ppm

    o Relative risk estimation may include case weights.

    o We thank Ian Buller, Brian Ripley, Maximilian Vogtland
    and Maximilian Hesselbarth for contributions.

    o Nickname: 'Help you I can, yes!'

SIGNIFICANT USER-VISIBLE CHANGES

    o rshift.ppp, rshift.splitppp
    New argument 'nsim'.

    o relrisk.ppp
    New argument 'weights'.

    o density.splitppp
    New argument 'weights'.

BUG FIXES

    o vcov.ppm
    Variances were sometimes overestimated for Gibbs models.
    That is, entries of the Fisher information matrix were underestimated,
    because some contributions due to interaction were omitted
    (due to a coding error).
    Fixed.

    o density.ppp
    Crashed when se=TRUE if there were multiple columns of 'weights'.
    Fixed.

    o rbind.hyperframe
    Crashed unless all arguments had the same number of rows.
    (Spotted by Maximilian Vogtland).
    Fixed.

        CHANGES IN spatstat VERSION 1.64-0

OVERVIEW

    o We thank Robert Aue, Tilman Davies, Greg McSwiggan, Tyler Rudolph
    and Rasmus Plenge Waagepetersen for contributions.

    o Interactive graphics functions have been removed to a separate package.

    o spatstat no longer needs the packages 'tcltk' and 'rpanel'.

    o The suggested package 'maptools' should be version 0.9-9 or later.

    o Important bug fix in density.ppp.

    o Add new vertices to a linear network.

    o Relative risk estimation on a network.

    o Leave-one-out density estimation on a network.

    o Improvements and extensions to linear networks code.

    o Improvements to 'nndist' methods.

    o Function lengths.psp has been renamed lengths_psp.

    o Bug fixes related to mppm.

    o Stability improvements.

    o Version nickname: 'Susana Distancia'

NEW FUNCTIONS

    o relrisk.lpp
    Method for 'relrisk' for point patterns on a linear network.

    o bw.relrisklpp
    Bandwidth selection for relative risk on a network.

    o densityfun.lpp
    Method for 'densityfun' for point patterns on a linear network.

    o addVertices
    Add new vertices to a network, at locations outside the existing network.

    o lengths_psp
    This is the new name of the function 'lengths.psp',
    which had to be changed because of a conflict with the generic 'lengths'.

    o densityEqualSplit
    The equal-split algorithm for kernel density estimation on a network
    is now visible as a separate function.

    o densityHeat
    The heat-equation algorithm for kernel density estimation on a network
    is now visible as a separate function. It has also been extended
    to computing leave-one-out density estimates at the data points.

    o hotrod
    Compute the heat kernel kappa(u,v) on a one-dimensional line segment.

    o heatkernelapprox
    Calculate an approximation to the value of the heat kernel
    on a network evaluated at the source point, kappa(u,u).

SIGNIFICANT USER-VISIBLE CHANGES

    o nndist.pp3, nndist.ppx, nndist.lpp
    These functions now recognise the argument 'by'
    allowing computation of the nearest distance to each group of points.

    o pairdist.lpp, crossdist.lpp
    These functions can now handle large networks,
    using the sparse representation.

    o density.lpp, densityQuick.lpp
    Infinite bandwidth (sigma=Inf) is now permitted,
    and results in a density estimate that is constant over all locations.

    o as.linnet.psp
    The resulting network now has an attribute 'camefrom'
    indicating the provenance of each line segment in the network.

    o as.linnet.linnet
    New argument 'maxsize'.

    o repairNetwork
    Increased capability of detecting and repairing inconsistencies.

    o joinVertices
    New argument 'marks'.

    o insertVertices
    Marks attached to the lines of the network are now retained.

    o as.lpp
    Accepts more data formats.

    o iplot, iplot.ppp, iplot.layered, iplot.linnet, iplot.default
    These interactive plotting functions have been removed from spatstat
    into a new package 'spatstat.gui'

    o istat
    This interactive analysis function has been removed from spatstat
    into a new package 'spatstat.gui'

    o crossdist.lpp
    New argument 'check'.

    o lengths.psp
    This function will soon be Deprecated,
    in favour of the new name 'lengths_psp'

    o density.lpp
    Formal arguments changed. No effect on usage.

    o integral.linim
    Now handles complex-valued functions.

    o transect.im
    New argument 'nsample'.

    o bw.lppl
    Accelerated when distance="path".

    o collapse.fv
    Recognises the abbreviations used by fvnames()

BUG FIXES

    o density.ppp
    Edge correction factors were calculated incorrectly when the
    window was not a rectangle, causing a negative bias in the
    estimated intensity. [Spotted by Tilman Davies.]
    Bug introduced in spatstat 1.57-0, october 2018.
    Fixed.

    o mppm
    Internal data were malformed if the interaction was Hardcore()
    or MultiHard() or a hybrid involving these interactions.
    This caused various errors when the fitted model was used.
    Fixed.

    o mppm
    Ignored the arguments 'nd' and 'eps' controlling the quadrature scheme.
    Fixed.

    o "[.linnet", "[.lpp"
    In X[W] where W is a window, if a vertex of the network
    lay exactly on the boundary of W, an edge of length zero was created.
    Fixed.

    o valid.ppm
    Crashed sometimes when applied to the result of subfits().
    Fixed.

    o as.im.densityfun
    Crashed if argument W was missing.
    Fixed.

    o as.linnet.linnet
    This code could crash the R session, when sparse=FALSE, if there was
    insufficient memory available to create the matrix of distances
    between all pairs of network vertices.
    Fixed.

    o Summary.linim
    A spurious warning was generated when the operation any() or all()
    was applied to a logical-valued image on a network.
    Fixed.

    o "[<-.linim"
    Crashed if the assignment would have replaced some existing NA values.
    Fixed.

        CHANGES IN spatstat VERSION 1.63-3

OVERVIEW

    o Minor changes for compatibility with future versions of R

    o Minor improvements

    o Version nickname: "Wet paint"

SIGNIFICANT USER-VISIBLE CHANGES

    o plot.ppp
    The coordinate axes will be plotted if axes=TRUE.
    Axis labels xlab, ylab will be plotted if ann=TRUE.

diffstat:

 geography/R-spatstat/Makefile |  4 +---
 1 files changed, 1 insertions(+), 3 deletions(-)

diffs (18 lines):

diff -r f910f72ca558 -r 11f88af79bb5 geography/R-spatstat/Makefile
--- a/geography/R-spatstat/Makefile     Mon Sep 20 12:20:11 2021 +0000
+++ b/geography/R-spatstat/Makefile     Mon Sep 20 12:25:34 2021 +0000
@@ -1,4 +1,4 @@
-# $NetBSD: Makefile,v 1.2 2021/09/20 12:20:11 mef Exp $
+# $NetBSD: Makefile,v 1.3 2021/09/20 12:25:34 mef Exp $
 
 R_PKGNAME=     spatstat
 R_PKGVER=      2.2-0
@@ -10,8 +10,6 @@
 
 USE_LANGUAGES+=        c c++
 
-# ERROR: dependencies 'spatstat.geom', 'spatstat.core', 'spatstat.linnet' are not available for package 'spatstat'
-
 DEPENDS+=      R-deldir>=0.0.21:../../geography/R-deldir
 DEPENDS+=      R-spatstat.core>=2.1.0:../../geography/R-spatstat.core
 DEPENDS+=      R-spatstat.data>=2.1.0:../../geography/R-spatstat.data



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