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Upstream changes: bug fixes
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This micro happened because of a significant bug in the Windows
packaging of qgis, even though the Windows packagingbits in question
are outside the qgis release tarball, to reduce conufsion among
Windows users. On other than Windows, this release is equivalenet to
3.16.12. It's updated in pkgsrc to avoid the perception that it needs
to be updated.
Upstream changes:
- The version number (and associated hash) has changed.
- There are NEWS entries aout what will be in 3.16.14
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upstream changes: bugfixes and minor improvements
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All checksums have been double-checked against existing RMD160 and
SHA512 hashes
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Fix for: Shared object "libprotobuf.so.28" not found
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Upstream lacks NEWS, but obviously this should be a bugfix release
from 2.5.4.
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and whitespace rationalization
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Packaging changes:
Use cmake instead of the now-deleted autotools, introducing a
regression in "make test" where the installed version is tested
instead of the build tree version.
Upstream changes:
Changes in 3.10.0
2021-10-20
- New things:
- CAPI: GEOSDistanceWithin, GEOSPreparedDistanceWithin
(#1124, Sandro Santilli)
- Output WKT using positional precision with the ryu
library (#868, Paul Ramsey)
- geosop CLI for GEOS (Martin Davis)
- Full doxygen of the C-API (Paul Ramsey)
- GeometryFixer class for validity enforcement (Martin Davis, Paul Ramsey)
- CAPI: GEOSDensify (Brendan Ward)
- CAPI: GEOSCoordSeq_copyFromArrays, GEOSCoordSeq_copyFromBuffer,
GEOSCoordSeq_copyToArrays, GEOSCoordSeq_copyToBuffer (Daniel Baston)
- CAPI: GEOSMakeValidWithParams new validity enforcement approach from
https://github.com/locationtech/jts/pull/704, uses GeometryFixer
(Paul Ramsey, Martin Davis)
- CAPI: GEOSWKBWriter_getFlavor, GEOSWKBWriter_setFlavor support
outputting ISO or Extended WKB flavors (#466, Paul Ramsey)
- CAPI: GEOSConstrainedDelaunayTriangulation, builds a constrained
triangulation of an input Polygon or MultiPolygon,
returning a GeometryCollection(Polygon) of the triangles.
- Fixes/Improvements:
- Preserve ordering of lines in overlay results (Martin Davis)
- Check for invalid geometry before fixing polygonal result in Densifier
and DPSimplifier (Martin Davis)
- Fix overlay handling of flat interior lines (JTS-685, Martin Davis)
- Fix IsValidOp to correctly report invalid nested MultiPolygons (#1112, Martin Davis)
- Fix BufferOp to avoid artifacts in certain polygon buffers (#1101, Martin Davis)
- Fix IsValidOp to correctly report certain kinds of invalid LinearRings (Martin Davis)
- Improve STRtree performance through TemplateSTRtree implementation (Daniel Baston)
- Fix DiscreteFrechetDistance to use initial points of input lines (#1128, Martin Davis)
- Changes:
- Autoconf build system is dropped in favour of CMake
See README.md and INSTALL.md for examples of usage
- Libtool is no longer used for in favour of CMake
Therefor libgeos.la is no longer built/installed
- #1094, #1090: Drop inlines.cpp to address duplicate symbols on many platforms
(Regina Obe)
- GH475: Do not return NaN from GEOSProjectNormalized_r (Paul Ramsey)
- GH442: BufferOp now returns unique_ptr<Geometry> result (Paul Ramsey)
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-Updated dependencies
-Cleaned up newer clippy lints
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3.23.1: 2021-09-21
Improve ubx cycle detection.
Add quirks for Jackson Labs nonstandard NMEA
Change STATUS_NO_FIX to STATUS_UNK to avoid confusion with fix mode.
Change STATUS_FIX to STATUS_GPS to avoid confusion with fix mode.
Change STATUS_DGPS_FIX to STATUS_DGPS to avoid confusion with fix mode.
Split SOURCE_ACM from SOURCE_USB. ACM has no speeds.
Add speeds 1 mbps, 1.152 mbps, 1.5 mbps, and higher. When libc supports them.
Improve autobaud.
Add new u-blox M10 messages.
Fix u-blox M6, M7 initialization issues.
Various ubxtool and gpxlogger updates.
Add mtk3301_speed_switcher()
No API, ABI changes.
Fallback to "python3" if "python" not found.
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upstream changes: bug fixes
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# version 0.5-3
* `read_stars()` accepts a function (or list with functions) as first argument,
allowing for saving `stars` objects that read from package directories resolving
platform-dependent paths at run-time
* handle categorical rasters starting at value 0 (by adding 1, and warning); #428
* add `%in%` method; #424
* `read_stars` gains an argument `tolerance` to control tolerance in
dimension value comparisons; #414
* binary Ops (like `+`, `-`, `*` etc.) work for `stars_proxy` objects; #390
* `st_rasterize` rasterizes multiple attributes, and handles factors
(when sf >= 0.9-9)
* `write_stars` deals better with `stars_proxy` objects; #404
* fix regression in reading some `stars_proxy` objects; #379
* add `[<-` (partially) and `is.na` methods for `stars_proxy` objects; #402
* add `replace_na` methods; #402
# version 0.5-2
* read and write factor levels as GDAL category names; write color table; #392
* handle `normalize_path` for choosing to `proxy`; #391
* ignore units when there are different units accross bands of a subdataset
* speed up `st_rgb` using faster `st_apply` approach; #315, #390
* improve handling of crs in Spatial objects (avoid loss of wkt comments)
* correctly write band subsets for smaller proxy objects; #291
* write arbitrarily cropped proxy objects; #291
* speed up `st_apply` when a function is provided that works on chunks
at a time; #390
* warn when breaks = "quantile" results in a single class; #388
* fix `[` bug selecting bands in proxy objects; #388
* for `stars_proxy` objects, `write_stars` writes all objects into a
multi-layer file; #385
* multi-file proxy objects can be `st_warp`ed with `use_gdal = TRUE`; #385
# version 0.5-1
* fix weird GDAL-related bug in stars2 vignette
* `read_ncdf` does not take time as mid-points of regular intervals,
but as starting points; #378
# version 0.5-0
* fix handling of rasters with color tables; #375
* `st_apply` and other methods for `stars_proxy` objects handle ... ; #374
* add `st_bbox`, `st_crs` methods for terra's `SpatVector` objects;
https://github.com/mtennekes/tmap/issues/536
* add `st_bbox`, `st_crs` and `st_as_stars` methods for terra's
`SpatRaster` objects; https://github.com/mtennekes/tmap/issues/536
* allow for multi-resolution attributes in `stars_proxy` objects
(e.g., all gray scale sentinel-2 bands); see vignettes 2 and 7 for
examples.
* `plot` defaults to a categorical color scale when plotting a factor
variable; https://github.com/mtennekes/tmap/issues/526
* `st_extract` extracts space-time points if `time_column` is
specified, and handles time intervals; #352
* add `[[<-.stars` method, which is now called by `$<-.stars`, so that
array names can be set programmatically
* add `transmute` methods
* `plot.stars` calls `droplevels` if a factor array has any `NA` levels; #339
* `read_stars` reads `NaN`s as `NA`; #333
* improve `st_extract` method for both `stars` and `stars_proxy`
objects; interpolation options are reduced to bilinear; #322, #279,
#290
* better handle categorical rasters that do not start at value 1; #329
* plot layout can be controlled with `mfrow = c(nr, nc)` argument
* `stars_proxy` objects have a normalized path; #331
* cropping or selecting with `bbox` treats cells always as small
polygons; #330
* add faster `st_extract` method for `stars` objects; #322
* added vignette: "How `raster` functions map to `stars` functions",
by Sebastien Rochette; #122, #325
* fix bug in dimension `values` field when downsampling; #324
* `write_stars` also writes out band names; #323
* add `rgdal` to Suggests:
* each `call_list` entry of a `stars_proxy` object carries its proper
calling environment; #309
* `st_as_sf.stars` copes with zero attribute (empty) stars objects
* add `st_set_bbox` generic, to set raster extent, motivated by #315
* set up tic, with great help from @pat-s, #313
* get rid of more `proj4string`s for representing coordinate reference
systems; #312
* as(x, "Spatial") correctly handles `from` dimension values different
from one
* `read_stars` now sets the `BANDNAME` GDAL metadata item, or else the
band's GetDescription() as the band's dimension values
* `st_as_stars.data.frame` reads simple tables (non-raster data) if
`dims` has length less than 2
* band descriptions are in the band dimension values
* dimension tables are simpler, and are shown properly in Rstudio
* `st_rgb` gains a `probs` argument, to cut off and stretch based on
quantiles
* `as(x, "Raster")` merges multiple attributes before converting to
raster brick
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(From: NEWS)
--- 17-July-2020, version 3.3-13
overhaul of crs to be ready for PROJ6
several bug fixes (see https://github.com/rspatial/raster/issues?q=is%3Aissue+)
--- 18-April-2020, version 3.1-5
improvements:
new arguments "smin", "smax" and "samplesize" to "stretch"; and bug
fixes. See https://github.com/rspatial/raster/issues/70
layer names in GTiff files are now read from file. Requested by Kyle Taylor
https://github.com/rspatial/raster/issues/88
bug fixes:
parallel version of extract with polygons and "fun" messed up the
order of the values (reported by
Jacory). https://github.com/rspatial/raster/issues/79
raster::predict bug when using factors (reported by
vvirkki). https://github.com/rspatial/raster/issues/73
distanceFromPoints with large files:
https://github.com/rspatial/raster/issues/103
colortable lost when cropping RasterBrick:
https://github.com/rspatial/raster/issues/105
Error in stack() when providing both bands and varname:
https://github.com/rspatial/raster/issues/97
rasterize and multi-polygon containing hole: https://github.com/rspatial/raster/issues/93
Upside down raster: https://github.com/rspatial/raster/issues/95 (a
warning is given, not really fixed yet)
Extract to data.frame bug:
https://stackoverflow.com/questions/61174280/r-rasterextract-fails-to-create-data-frame
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0.1.5.00X
===================
Major changes:
- New function `add_osm_features` to enable OR-combinations of features in
single queries.
0.1.5
===================
Minor changes:
- Bug fix in `getbb()` via #232, thanks to @changwoo-lee
- hard-code WKT string for EPSG:4326, to avoid obsolete proj4strings (#218)
- bug fix in `print` method via #236; thanks to @odeleongt
0.1.4
===================
Major changes:
- New `osm_enclosing()` function; thanks to @barryrowlingson via #199
- `opq()` now has additional `datetime` and `datetime2` parameters which can be
used to extract historical data prior to `datetime`, or differences between
two datetimes by specifying `datetime2`; thanks to @neogeomat for the idea in
issue#179.
- opq() also has additional `nodes_only` parameter to return nodes as points
only, for efficient extraction of strictly point-based OSM data; thanks to
@gdkrmr for the idea in issue#221.
Minor changes:
- New contributor Enrico Spinielli (@espinielli), via #207, #210, #211, #212 - Thanks!
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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.
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# ggspatial 1.1.5
* Added a `NEWS.md` file to track changes to the package.
* Suppressed discarded datum warnings that resulted from loading
of test data.
* Suppressed discarded datum warnings that resulted from
'rosm' package operations.
* Fixed an error that caused RStudio to crash from excessive
memory allocation resulting when trying to plot a single point
with `annotation_map_tile()` (#74).
* Ensured that packages in 'Suggests' are used conditionally in
tests and examples.
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Defines types of spatial data on a linear network and provides
functionality for geometrical operations, data analysis and modelling
of data on a linear network, in the 'spatstat' family of packages.
Contains definitions and support for linear networks, including
creation of networks, geometrical measurements, topological
connectivity, geometrical operations such as inserting and deleting
vertices, intersecting a network with another object, and interactive
editing of networks. Data types defined on a network include point
patterns, pixel images, functions, and tessellations. Exploratory
methods include kernel estimation of intensity on a network,
K-functions and pair correlation functions on a network, simulation
envelopes, nearest neighbour distance and empty space distance,
relative risk estimation with cross-validated bandwidth selection.
Formal hypothesis tests of random pattern (chi-squared,
Kolmogorov-Smirnov, Monte Carlo, Diggle-Cressie-Loosmore-Ford,
Dao-Genton, two-stage Monte Carlo) and tests for covariate effects
(Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov, ANOVA) are also
supported. Parametric models can be fitted to point pattern data using
the function lppm() similar to glm(). Only Poisson models are
implemented so far. Models may involve dependence on covariates and
dependence on marks. Models are fitted by maximum likelihood. Fitted
point process models can be simulated, automatically. Formal
hypothesis tests of a fitted model are supported (likelihood ratio
test, analysis of deviance, Monte Carlo tests) along with basic tools
for model selection (stepwise(), AIC()) and variable selection (sdr).
Tools for validating the fitted model include simulation envelopes,
residuals, residual plots and Q-Q plots, leverage and influence
diagnostics, partial residuals, and added variable plots. Random point
patterns on a network can be generated using a variety of models.
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Functionality for data analysis and modelling of spatial data, mainly
spatial point patterns, in the 'spatstat' family of packages.
(Excludes analysis of spatial data on a linear network, which is
covered by the separate package 'spatstat.linnet'.) Exploratory
methods include quadrat counts, K-functions and their simulation
envelopes, nearest neighbour distance and empty space statistics, Fry
plots, pair correlation function, kernel smoothed intensity, relative
risk estimation with cross-validated bandwidth selection, mark
correlation functions, segregation indices, mark dependence
diagnostics, and kernel estimates of covariate effects. Formal
hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov,
Monte Carlo, Diggle-Cressie-Loosmore-Ford, Dao-Genton, two-stage Monte
Carlo) and tests for covariate effects (Cox-Berman-Waller-Lawson,
Kolmogorov-Smirnov, ANOVA) are also supported. Parametric models can
be fitted to point pattern data using the functions ppm(), kppm(),
slrm(), dppm() similar to glm(). Types of models include Poisson,
Gibbs and Cox point processes, Neyman-Scott cluster processes, and
determinantal point processes. Models may involve dependence on
covariates, inter-point interaction, cluster formation and dependence
on marks. Models are fitted by maximum likelihood, logistic
regression, minimum contrast, and composite likelihood methods. A
model can be fitted to a list of point patterns (replicated point
pattern data) using the function mppm(). The model can include random
effects and fixed effects depending on the experimental design, in
addition to all the features listed above. Fitted point process models
can be simulated, automatically. Formal hypothesis tests of a fitted
model are supported (likelihood ratio test, analysis of deviance,
Monte Carlo tests) along with basic tools for model selection
(stepwise(), AIC()) and variable selection (sdr). Tools for validating
the fitted model include simulation envelopes, residuals, residual
plots and Q-Q plots, leverage and influence diagnostics, partial
residuals, and added variable plots.
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Defines sparse three-dimensional arrays and supports standard
operations on them. The package also includes utility functions for
matrix calculations that are common in statistics, such as quadratic
forms.
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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'.
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# Please note that **rgdal** will be retired by the end of 2023, plan
transition to sf/stars/terra functions using GDAL and PROJ at your
earliest convenience.
# Version 1.5-27 (development, rev. 1149-)
* Correcting logic error in check for MXE UCRT builds (temporary)
# Version 1.5-26 (2021-09-15, rev. 1141-1148)
* Mute use of PROJ CDN for MXE UCRT builds (temporary)
* Run autoupdate on configure.ac to handle obsolete AC_HELP_STRING etc.
# Version 1.5-25 (2021-09-08, rev. 1122-1140)
* Add environment variable access to --with-data-copy by
PROJ_GDAL_DATA_COPY (https://github.com/r-spatial/sf/issues/1605)
* Adaptations for PROJ 8.
* Handle mixed 2D/3D in readOGR():
(https://github.com/r-spatial/sf/issues/1683)
* Add tweak for UCRT builds.
* Thin examples for spTransform().
# Version 1.5-23 (2021-02-03, rev. 1120-1121)
* Further fallout after removing valgrind issues.
# Version 1.5-22 (2021-02-02, rev. 1106-1119)
* Attempt to remove further valgrind leak in proj6.cpp: PROJcopyEPSG()
and in ogr_proj.cpp, both wrongly placed object destructors.
* Modified roundtripping all declared projections in ?project examples
because some listed projections for PROJ >= 5 provoke valgrind
leakages by returning very large out-of-scope values for input
coordinates (0, 0); inversion of these is not attempted; some listed
projections are not projections.
# Version 1.5-21 (2021-01-27, rev. 1093-1105)
* Suggest **rgeos** to write pre-SFS multipolygon objects to avoid
unpleasant workaround.
* Try to eliminate current valgrind leaks, starting from
(https://github.com/r-spatial/gstat/issues/82).
* Try to increase robustness to installation with early PROJ 6
versions, which often lack functionality found necessary later (for
example visualization order); the code had assumed that this
function always was available and behaved as it now does. There are
now graceful failures when not available.
# Version 1.5-19 (2021-01-05, rev. 1083-1092)
* Dan Baston: raster speedups
* PROJ 7.2.1 includes a bug-fix for `+proj=ob_tran` cases that
required changes in detection and handling of target/source CRS
reversal,
https://lists.osgeo.org/pipermail/proj/2020-December/009999.html
# Version 1.5-18 (2020-10-13, rev. 1071-1082)
* condition `tests/test_enforce_xy.R` on PROJ >= 6 and GDAL >= 3
(email BDR, I forgot to re-check with PROJ-5.2.0/GDAL-2.2.4).
* Adaptation to EPSG 10 database format started (from PROJ 7.2);
choose DB columns by name not number in vignette.
# Version 1.5-17 (2020-10-08, rev. 1051-1070)
* `"CRS"` instantiation now prefers PROJ: use
`rgdal::set_prefer_proj(FALSE)` to return to earlier behaviour. It
seems that access from C/C++ code to mechanisms in PROJ offers more
depth than going through GDAL to PROJ. This `"CRS"` instantiation in
**sp** and **raster**; Proj4 and WKT2 strings may differ depending
on whether instantiation is straight from PROJ or goes via
GDAL. Confirmed with multiple reverse dependency checks over almost
900 CRAN packages.
* By default use PROJ function to extract the source CRS from a
`"BOUNDCRS"`. When `+towgs84=` is given, PROJ and GDAL see the
apparent source Proj4 string as implicitly implying a coordinate
operation transforming to target WGS84, leading to the WKT2
representation being a `"BOUNDCRS"`, not a `"PROJCRS"` or
`"GEOGCRS"`, and thus causing misunderstandings later in searching
for the most accurate coordinate operation for a transformation. May
be controlled by setting the `get_source_if_boundcrs=` in
`sp::CRS()` from **sp** 1.4-4 (2020-10-07). Confirmed with multiple
reverse dependency checks over almost 900 CRAN packages.
* Add support for instantiating from `"OGC:CRS84"` to provide a
guaranteed GIS/visualization axis order WGS84 instantiator
(preferred to `"EPSG:4326"`).
* Permit empty string in `SRS_string=` argument to `sp::CRS()` and
functions called by it.
* Use GDAL `ORSIsProjected()` instead of simply looking for
`"+proj=longlat"` in the Proj4 string representation where possible.
# Version 1.5-16 (2020-08-07, rev. 1047-1050)
* Typo in C code; use `try()` around Area-of-Interest calculation for
coordinate operations (email BDR, I forgot to re-check with
PROJ-5.2.0/GDAL-2.2.4).
# Version 1.5-15 (2020-08-04, rev. 1020-1046)
* Add support for instantiating from `"ESRI:"`.
* Add Area-of-Interest to coordinate operation search (reduces the
number of candidates found in many cases), and use in
`rgdal::spTransform()` by default (`use_aoi=FALSE` to suppress);
illustrate in vignette
https://cran.r-project.org/web/packages/rgdal/vignettes/CRS_projections_transformations.html.
* Harden to condition on PROJ functions only available from 6.2.0;
block `"+proj=ob_tran` tests for PROJ 6.0.0-6.1.1.
* Support PROJ CDN https://cdn.proj.org for on-demand download of
transformation grids if requested by user; document in vignette
https://cran.r-project.org/web/packages/rgdal/vignettes/CRS_projections_transformations.html.
# Version 1.5-12 (2020-06-26, rev. 1007-1019)
* Further corrections to `configure.ac` for older PROJ/GDAL versions
# Version 1.5-10 (2020-06-09, rev. 991-1006)
* Corrections to `configure.ac` for older PROJ/GDAL versions
# Version 1.5-8 (2020-05-28, rev. 846-990)
* Released to match **sp** 1.4.0 (2020-02-21) to 1.4-2 (2020-05-20)
following months of development adapting to breaking changes in the
external libraries used here: PROJ and GDAL; see also
https://cran.r-project.org/web/packages/sp/news.html.
* Expose `options("rgdal_show_exportToProj4_warnings"="none")` to mute
Proj4 string degradation warnings.
* Add new vignette
https://cran.r-project.org/web/packages/rgdal/vignettes/CRS_projections_transformations.html.
* CRAN Windows binary uses PROJ >= 6 and GDAL >= 3
* Add PROJ-based CRS comparison: `compare_CRS()`.
* `project()` and `spTransform()` use WKT2 comment if available,
fallback to Proj4 representation if not.
* List coordinate operations (based on pyproj code): `list_coordOps()`.
* Add `enforce_xy=` arguments to try to ensure that only
GIS/visualization axis order is present.
* Add `"CRS"` object comment carrying WKT2 (2019) multiline string
representation on read operations.
* Use `"CRS"` object comment carrying WKT2 (2019) multiline string
representation on write operations.
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CHANGES IN spatstat.utils VERSION 2.2-0
OVERVIEW
o New function to compute breakpoints for a cut operation.
o Internal tweaks to improve efficiency.
NEW FUNCTIONS
o exactCutBreaks
Compute the exact numerical values of the breakpoints
used in cut.default.
CHANGES IN spatstat.utils VERSION 2.1-0
OVERVIEW
o New functions providing NA and zero values, and empty vectors,
of the appropriate type.
NEW FUNCTIONS
o RelevantNA
Return a missing value of the appropriate type.
o RelevantEmpty
Return a zero-length vector of the appropriate type.
o RelevantZero
Return a value equivalent to 0, of the appropriate type.
CHANGES IN spatstat.utils VERSION 2.0-1
OVERVIEW
o Tweaks.
CHANGES IN spatstat.utils VERSION 2.0-0
OVERVIEW
o Updated to new spatstat family.
SIGNIFICANT USER-VISIBLE CHANGES
o package dependence
spatstat.utils now suggests the package spatstat.core
which is part of the new spatstat family.
CHANGES IN spatstat.utils VERSION 1.20-0
OVERVIEW
o Computation is slightly accelerated.
SIGNIFICANT USER-VISIBLE CHANGES
o general
Overall speed of computation is slightly increased.
CHANGES IN spatstat.utils VERSION 1.19-0
OVERVIEW
o Minor improvements.
CHANGES IN spatstat.utils VERSION 1.18-0
OVERVIEW
o Minor improvements.
SIGNIFICANT USER-VISIBLE CHANGES
o do.call.matched, do.call.without
New argument 'envir' determines the environment in which
the call will be evaluated.
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# version 1.0-2
* `st_read()` and `st_write()` using GDAL handle binary attributes
(OFTBinary fields) ; #1721
* a `pivot_longer` method is added for `sf` objects (the `data.frame`
method works, but raises a warning)
* `rbind.sf` preserves primary geometry column; #1717
* `configure` constrains using `--static` to `Darwin` platform; #1702,
#1712, #1713
* old-style `crs` objects created with sf < 0.9-0 generate a message,
and will cause a warning in the future.
* when `st_crs()` is called with a WKT2 as text input, its `input`
field will be replaced with the CRS name (if it has one).
* GEOS (>= 3.9.0) operations use `GEOSGeom_setPrecision_r` to set
precision of geometries; #1535
* `st_read()` with specified `query` ignores argument `layers`, and
warns if it is given; #1444
# version 1.0-1
* fix regression in `st_intersection()`: when using s2 attributes were
assigned wrongly; #1704
* `crs` (sf) to `CRS` (sp) conversion no longer needs validation by
`rgdal`; https://github.com/edzer/sp/issues/107
* retrieve ESRI's WKT version of CRS by `st_crs(id)$WKT1_ESRI`; #1690
# version 1.0-0
* add `s2` to Imports:
* add Dewey Dunnington to contributors
* `sf_use_s2()` prints a message when using s2 has been switched to on or off.
* use `s2` spherical geometry as default when coordinates are ellipsoidal. This can
be switched off (defaulting to planar geometry, using GEOS, as in sf < 1.0-0)
by setting environment variable `_SF_USE_S2` to `false` before package `sf`
is loaded, or by `sf_use_s2(FALSE)`; #1649
* `st_nearest_feature()` with missing `y` returns nearest features in
the remaining set of `x`; https://github.com/r-spatial/s2/issues/111
* `st_write()` gains an argument `config_options` to set GDAL config
options; #1618
* fix regression in `sf_project(..., keep = TRUE)`; #1635
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Provides R bindings for Google's s2 library for geometric calculations
on the sphere. High-performance constructors and exporters provide
high compatibility with existing spatial packages, transformers
construct new geometries from existing geometries, predicates provide
a means to select geometries based on spatial relationships, and
accessors extract information about geometries.
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Provides a minimal R and C++ API for parsing well-known binary and
well-known text representation of geometries to and from R-native
formats. Well-known binary is compact and fast to parse; well-known
text is human-readable and is useful for writing tests. These formats
are only useful in R if the information they contain can be accessed
in R, for which high-performance functions are provided here.
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# Please note that **rgeos** will be retired by the end of 2023, plan
transition to sf functions using GEOS at your earliest convenience.
# Version 0.5-7 (development, rev. 641-675)
* adapt to OverlayNG in GEOS 3.9
* update Windows static library to GEOS 3.9
* add gMinumumRotatedRectangle() and gMaximumInscribedCircle() for GEOS 3.9
* adapt configure.ac for GEOS 3.10
* add support for structured geometry fixer in gMakeValid() from 3.10
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# Version 1.1-2 (development, rev. 392-397)
* Version check for forthcoming GEOS 3.10
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Changes in 1.2.0
======================
* Change max allowed zoom for various maps (Rolf Eike Beer, Philipe Weyland)
* Add copyright notices to maps (Patrick Salecker)
* Add configureable user-agent property for apps to clearly identify themselves (Patrick Salecker)
* Remove dependency on gnome-common (Patrick Salecker, Hubert Kowalski)
* Add user_data support to points (Martijn Goedhart)
* Add breakable and shade_alpha properties to polygons (Samuel Cowen)
* Python example updated to Python3 (Felipe S. S. Schneider)
* Add Glade catalog file for better glade integration (Davide Gessa)
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# countrycode 1.3.0
* destination argument accepts a vector of strings and tries one after
the other
* countryname(warn=TRUE) by default
* better class checks
* countryname defaults to `country.name.en` for missing country names
(nomatch=NULL)
* Vietnam: better regex and support for vdem
* Namibia fixes: eurostat, genc2c, wb_api2c, ecb
* Various regex improvements
* Congo French disambiguation
# countrycode 1.2.0
* New 'countryname' function converts country names from any language
(thanks to @davidsjoberg)
* New `guess_field` function guesses which code a vector uses
* Bug in dict build inserted NA in region variable (Thanks to M. Pascariu)
* Added region23 with the old, more granular regions
* Added unicode.symbol, which converts to emoji flags
* Added ISO 4217 currency name, alpha, and numeric codes
* Added UN region codes and names
* Added IANA ccTLD codes
* Improved various regexes
# countrycode 1.1.3
* Added Demographic and Health Surveys (thanks to @mcooper)
# countrycode 1.1.2
* Updated World Bank regions with manual additions
# countrycode 1.1.1
* Bug: Typo prevented users for using "p4n" as origin code
* Fixed bad icao.region codes (Thanks to @espinielli)
* Added country name "United Arab Republic" and its regex (Thanks to
Gina Reynolds)
* Added SOM to wb code (Thanks to Fabian Besche)
* Added Vietnam to codelist_panel
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upstream changes are bugfixes and minor improvements
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(This should have been part of the very recent gdal commit.)
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Upstream changes are bugfixes.
One bugfix is applied locally and has been fixed differently upstream.
This version mostly passes gdal's tests on NetBSD 9 amd64, if one
rebuilds base sqlite3 with rtree.
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