Title: Spatial Empirical Dynamic Modeling
Description: Inferring causal associations in cross-sectional earth system data with extensions to convergent cross mapping from Sugihara et al. (2012) <doi:10.1126/science.1227079> and partial cross mapping as described in Ma et al. (2020) <doi:10.1038/s41467-020-16238-0>.
Author: Wenbo Lv [aut, cre, cph]
Maintainer: Wenbo Lv <lyu.geosocial@gmail.com>
Diff between spEDM versions 1.2 dated 2025-01-14 and 1.3 dated 2025-02-01
spEDM-1.2/spEDM/R/ccm_formatoutput.R |only spEDM-1.2/spEDM/R/variable_check.R |only spEDM-1.3/spEDM/DESCRIPTION | 14 spEDM-1.3/spEDM/MD5 | 89 +++-- spEDM-1.3/spEDM/NAMESPACE | 6 spEDM-1.3/spEDM/NEWS.md | 28 + spEDM-1.3/spEDM/R/RcppExports.R | 116 ++++++- spEDM-1.3/spEDM/R/detectThreads.R |only spEDM-1.3/spEDM/R/embedded.R |only spEDM-1.3/spEDM/R/formatoutput_s3.R |only spEDM-1.3/spEDM/R/gccm.R | 67 ++-- spEDM-1.3/spEDM/R/globals.R | 2 spEDM-1.3/spEDM/R/scpcm.R |only spEDM-1.3/spEDM/R/simplex.R |only spEDM-1.3/spEDM/R/smap.R |only spEDM-1.3/spEDM/R/variable_check_prepare.R |only spEDM-1.3/spEDM/R/xmapdf.R | 42 ++ spEDM-1.3/spEDM/inst/doc/GCCM.Rmd | 203 ++++++++---- spEDM-1.3/spEDM/inst/doc/GCCM.html | 306 +++++++++++------- spEDM-1.3/spEDM/man/detectThreads.Rd |only spEDM-1.3/spEDM/man/embedded.Rd |only spEDM-1.3/spEDM/man/figures/gccm/fig1-1.png |binary spEDM-1.3/spEDM/man/figures/gccm/fig3-1.png |binary spEDM-1.3/spEDM/man/gccm.Rd | 35 +- spEDM-1.3/spEDM/man/simplex.Rd |only spEDM-1.3/spEDM/man/smap.Rd |only spEDM-1.3/spEDM/src/CppGridUtils.cpp | 137 ++++++-- spEDM-1.3/spEDM/src/CppGridUtils.h | 26 + spEDM-1.3/spEDM/src/CppLatticeUtils.cpp | 191 +++++++---- spEDM-1.3/spEDM/src/CppLatticeUtils.h | 12 spEDM-1.3/spEDM/src/CppStats.cpp | 459 +++++++++++++++++++++++++--- spEDM-1.3/spEDM/src/CppStats.h | 37 ++ spEDM-1.3/spEDM/src/Forecast4Grid.cpp |only spEDM-1.3/spEDM/src/Forecast4Grid.h |only spEDM-1.3/spEDM/src/Forecast4Lattice.cpp |only spEDM-1.3/spEDM/src/Forecast4Lattice.h |only spEDM-1.3/spEDM/src/GCCM4Grid.cpp | 107 +++++- spEDM-1.3/spEDM/src/GCCM4Grid.h | 12 spEDM-1.3/spEDM/src/GCCM4Lattice.cpp | 75 ++-- spEDM-1.3/spEDM/src/GCCM4Lattice.h | 22 - spEDM-1.3/spEDM/src/GridExp.cpp | 278 ++++++++++++++++ spEDM-1.3/spEDM/src/HelperFuns.cpp |only spEDM-1.3/spEDM/src/HelperFuns.h |only spEDM-1.3/spEDM/src/LatticeExp.cpp | 303 ++++++++++++++++-- spEDM-1.3/spEDM/src/Makevars | 6 spEDM-1.3/spEDM/src/Makevars.win | 6 spEDM-1.3/spEDM/src/RcppExports.cpp | 433 ++++++++++++++++++++++++-- spEDM-1.3/spEDM/src/SCPCM4Grid.cpp |only spEDM-1.3/spEDM/src/SCPCM4Grid.h |only spEDM-1.3/spEDM/src/SCPCM4Lattice.cpp |only spEDM-1.3/spEDM/src/SCPCM4Lattice.h |only spEDM-1.3/spEDM/src/SMap.cpp |only spEDM-1.3/spEDM/src/SMap.h |only spEDM-1.3/spEDM/src/SimplexProjection.cpp | 83 ++++- spEDM-1.3/spEDM/src/SimplexProjection.h | 34 +- spEDM-1.3/spEDM/src/StatsExp.cpp |only spEDM-1.3/spEDM/src/spEDMDataStruct.h |only spEDM-1.3/spEDM/vignettes/GCCM.Rmd | 203 ++++++++---- spEDM-1.3/spEDM/vignettes/GCCM.Rmd.orig | 51 ++- 59 files changed, 2733 insertions(+), 650 deletions(-)
Title: R and C++ Interfaces to 'spdlog' C++ Header Library for Logging
Description: The mature and widely-used C++ logging library 'spdlog' by Gabi Melman provides
many desirable features. This package bundles these header files for easy use by R packages
from both their R and C or C++ code. Explicit use via 'LinkingTo:' is also supported. Also
see the 'spdl' package which enhanced this package with a consistent R and C++ interface.
Author: Dirk Eddelbuettel [aut, cre] ,
Gabi Melman [aut] ,
Victor Zverovic [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppSpdlog versions 0.0.19 dated 2024-11-11 and 0.0.20 dated 2025-02-01
ChangeLog | 11 DESCRIPTION | 8 MD5 | 69 build/partial.rdb |binary inst/NEWS.Rd | 7 inst/examples/exampleFour.cpp |only inst/include/spdlog/cfg/env.h | 4 inst/include/spdlog/common.h | 7 inst/include/spdlog/details/file_helper-inl.h | 3 inst/include/spdlog/details/os-inl.h | 12 inst/include/spdlog/details/os.h | 4 inst/include/spdlog/fmt/bin_to_hex.h | 2 inst/include/spdlog/fmt/bundled/args.h | 48 inst/include/spdlog/fmt/bundled/base.h | 3316 ++++++++++----------- inst/include/spdlog/fmt/bundled/chrono.h | 846 ++--- inst/include/spdlog/fmt/bundled/color.h | 42 inst/include/spdlog/fmt/bundled/compile.h | 70 inst/include/spdlog/fmt/bundled/format-inl.h | 109 inst/include/spdlog/fmt/bundled/format.h | 2373 ++++++--------- inst/include/spdlog/fmt/bundled/os.h | 98 inst/include/spdlog/fmt/bundled/ostream.h | 131 inst/include/spdlog/fmt/bundled/printf.h | 237 - inst/include/spdlog/fmt/bundled/ranges.h | 228 - inst/include/spdlog/fmt/bundled/std.h | 121 inst/include/spdlog/fmt/bundled/xchar.h | 143 inst/include/spdlog/sinks/ansicolor_sink-inl.h | 18 inst/include/spdlog/sinks/ansicolor_sink.h | 7 inst/include/spdlog/sinks/basic_file_sink-inl.h | 6 inst/include/spdlog/sinks/basic_file_sink.h | 1 inst/include/spdlog/sinks/daily_file_sink.h | 1 inst/include/spdlog/sinks/null_sink.h | 2 inst/include/spdlog/sinks/rotating_file_sink-inl.h | 6 inst/include/spdlog/sinks/rotating_file_sink.h | 1 inst/include/spdlog/sinks/stdout_sinks-inl.h | 9 inst/include/spdlog/tweakme.h | 7 inst/include/spdlog/version.h | 2 36 files changed, 3802 insertions(+), 4147 deletions(-)
Title: Superefficient Estimation of Future Conditional Hazards Based on
Marker Information
Description: Provides a nonparametric smoothed kernel estimator for the future conditional hazard rate function when time-dependent covariates are present, a bandwidth selector for the estimator's implementation and pointwise and uniform confidence bands. Methods used in the package refer to Bagkavos, Isakson, Mammen, Nielsen and Proust-Lima (2025) <doi:10.1093/biomet/asaf008>.
Author: Dimitrios Bagkavos [aut, cre],
Alex Isakson [ctb],
Enno Mammen [ctb],
Jens Nielsen [ctb],
Cecile Proust-Lima [ctb]
Maintainer: Dimitrios Bagkavos <dimitrios.bagkavos@gmail.com>
Diff between HQM versions 0.1.4 dated 2024-12-12 and 1.0 dated 2025-02-01
DESCRIPTION | 8 ++++---- MD5 | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-)
Title: Clean and Analyze Continuous Glucose Monitor Data
Description: This code provides several different functions for cleaning and analyzing continuous glucose monitor data. Currently it works with 'Dexcom', 'iPro 2', 'Diasend', 'Libre', or 'Carelink' data. The cleandata() function takes a directory of CGM data files and prepares them for analysis. cgmvariables() iterates through a directory of cleaned CGM data files and produces a single spreadsheet with data for each file in either rows or columns. The column format of this spreadsheet is compatible with REDCap data upload. cgmreport() also iterates through a directory of cleaned data, and produces PDFs of individual and aggregate AGP plots. Please visit <https://github.com/childhealthbiostatscore/R-Packages/> to download the new-user guide.
Author: Tim Vigers [aut, cre]
Maintainer: Tim Vigers <timothy.vigers@cuanschutz.edu>
Diff between cgmanalysis versions 3.0 dated 2025-01-30 and 3.0.1 dated 2025-02-01
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/cgmvariables.R | 17 ++++++++++++++++- 3 files changed, 21 insertions(+), 6 deletions(-)
Title: Wrapper for the 'CVD Prevent' Application Programming Interface
Description: Provides an R wrapper to the 'CVD Prevent' application
programming interface (API). Users can make API requests through
built-in R functions. The Cardiovascular Disease Prevention Audit
(CVDPREVENT) is an England-wide primary care audit that automatically
extracts routinely held GP health data.
<https://bmchealthdocs.atlassian.net/wiki/spaces/CP/pages/317882369/CVDPREVENT+API+Documentation>.
Author: Craig Parylo [aut, cre, cph] ,
Cardiovascular Disease Prevention Audit [ant]
Maintainer: Craig Parylo <craig.parylo2@nhs.net>
Diff between cvdprevent versions 0.2.0 dated 2024-10-16 and 0.2.1 dated 2025-02-01
DESCRIPTION | 7 MD5 | 20 NEWS.md | 2 R/cvd_api_functions.R | 4112 +-- README.md | 128 build/vignette.rds |binary inst/doc/using_cvdprevent.R | 608 inst/doc/using_cvdprevent.Rmd | 1196 - inst/doc/using_cvdprevent.html |33327 ++++++++++++++++---------------- tests/testthat/test-cvd_api_functions.R | 496 vignettes/using_cvdprevent.Rmd | 1196 - 11 files changed, 20665 insertions(+), 20427 deletions(-)
Title: Classes and Methods for Spatial Data
Description: Classes and methods for spatial
data; the classes document where the spatial location information
resides, for 2D or 3D data. Utility functions are provided, e.g. for
plotting data as maps, spatial selection, as well as methods for
retrieving coordinates, for subsetting, print, summary, etc. From this
version, 'rgdal', 'maptools', and 'rgeos' are no longer used at all,
see <https://r-spatial.org/r/2023/05/15/evolution4.html> for details.
Author: Edzer Pebesma [aut, cre],
Roger Bivand [aut],
Barry Rowlingson [ctb],
Virgilio Gomez-Rubio [ctb],
Robert Hijmans [ctb],
Michael Sumner [ctb],
Don MacQueen [ctb],
Jim Lemon [ctb],
Finn Lindgren [ctb],
Josh O'Brien [ctb],
Joseph O'Rourke [ctb],
Patrick [...truncated...]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between sp versions 2.1-4 dated 2024-04-30 and 2.2-0 dated 2025-02-01
sp-2.1-4/sp/demo/webmap.R |only sp-2.1-4/sp/inst/include |only sp-2.2-0/sp/DESCRIPTION | 10 sp-2.2-0/sp/MD5 | 59 ++-- sp-2.2-0/sp/build/vignette.rds |binary sp-2.2-0/sp/demo/00Index | 1 sp-2.2-0/sp/inst/NEWS.Rd | 11 sp-2.2-0/sp/inst/doc/CRS_warnings.html | 204 ++++++++-------- sp-2.2-0/sp/inst/doc/csdacm.R | 31 +- sp-2.2-0/sp/inst/doc/csdacm.Rnw | 5 sp-2.2-0/sp/inst/doc/csdacm.pdf |binary sp-2.2-0/sp/inst/doc/intro_sp.pdf |binary sp-2.2-0/sp/inst/doc/retiring_rgdal_geos_1.html | 295 ++++++++++++++---------- sp-2.2-0/sp/inst/doc/sp_gallery.R |only sp-2.2-0/sp/inst/doc/sp_gallery.Rmd |only sp-2.2-0/sp/inst/doc/sp_gallery.html |only sp-2.2-0/sp/man/GridsDatums.Rd | 4 sp-2.2-0/sp/man/bubble.Rd | 4 sp-2.2-0/sp/man/image.Rd | 2 sp-2.2-0/sp/man/mapasp.Rd | 2 sp-2.2-0/sp/man/spplot.Rd | 12 sp-2.2-0/sp/man/stack.Rd | 2 sp-2.2-0/sp/src/gcdist.c | 2 sp-2.2-0/sp/src/init.c | 2 sp-2.2-0/sp/src/pip.c | 8 sp-2.2-0/sp/src/pip2.c | 22 - sp-2.2-0/sp/src/sp.h | 62 ++--- sp-2.2-0/sp/src/sp_xports.c | 234 +++++++++---------- sp-2.2-0/sp/src/zerodist.c | 10 sp-2.2-0/sp/tests/grid.R | 6 sp-2.2-0/sp/tests/grid.Rout.save | 75 ------ sp-2.2-0/sp/vignettes/csdacm.Rnw | 5 sp-2.2-0/sp/vignettes/sp_gallery.Rmd |only 33 files changed, 549 insertions(+), 519 deletions(-)
Title: Remote Sensing Data Analysis
Description: Toolbox for remote sensing image processing and analysis such as
calculating spectral indexes, principal component transformation, unsupervised
and supervised classification or fractional cover analyses.
Author: Benjamin Leutner [aut] ,
Ned Horning [aut],
Jakob Schwalb-Willmann [aut] ,
Robert J. Hijmans [ctb] ,
Konstantin Mueller [aut, cre]
Maintainer: Konstantin Mueller <konstantinfinn.mueller@gmx.de>
Diff between RStoolbox versions 1.0.0 dated 2024-04-25 and 1.0.1 dated 2025-02-01
DESCRIPTION | 13 MD5 | 235 +- NAMESPACE | 228 +- NEWS.md | 553 ++--- R/RStoolbox-package.R | 274 +- R/RcppExports.R | 110 - R/classifyQA.R | 216 - R/cloudMask.R | 308 +- R/coregisterImages.R | 416 +-- R/encodeQA.R | 196 - R/estimateHaze.R | 268 +- R/fCover.R | 456 ++-- R/fortify-raster.R | 32 R/getMeta.R | 180 - R/getValidation.R | 144 - R/ggR.R | 392 +-- R/ggRGB.R | 470 ++-- R/histMatch.R | 280 +- R/internalFunctions.R | 895 ++++---- R/mesma.R | 355 +-- R/mlc.R | 166 - R/normImage.R | 102 R/oneHotEncode.R | 88 R/panSharpen.R | 188 - R/pifMatch.R | 238 +- R/radCor.R | 576 ++--- R/rasterCVA.R | 210 - R/rasterEntropy.R | 50 R/rasterPCA.R | 174 - R/readEE.R | 108 R/readMeta.R | 694 +++--- R/readSLI.R | 334 +-- R/rescaleImage.R | 212 - R/rsOpts.R | 38 R/sam.R | 126 - R/saveRSTBX.R | 178 - R/spectralIndices.R | 508 ++-- R/stackMeta.R | 204 - R/superClass.R | 1091 +++++----- R/tasseledCap.R | 138 - R/topCor.R | 512 ++-- R/unsuperClass.R | 358 +-- R/utils-pipe.R | 28 R/validateMap.R | 166 - R/zzz.R | 38 README.md | 460 ++-- inst/CITATION |only inst/external/EarthExplorer_LS8.txt | 106 inst/external/vegSpec.sli.hdr | 44 man/RStoolbox.Rd | 1 man/fortifySpatRaster.Rd | 46 man/lsat.Rd | 34 man/mesma.Rd | 4 man/pipe.Rd | 40 man/rlogo.Rd | 32 man/rsOpts.Rd | 6 man/sen2.Rd | 32 man/spectralIndices.Rd | 40 man/srtm.Rd | 32 man/srtm_sen2.Rd | 32 man/superClass.Rd | 1 src/RcppExports.cpp | 7 src/init.c | 4 src/spectralIndices.cpp | 86 src/tinyexpr.c |only src/tinyexpr.h |only tests/testthat.R | 12 tests/testthat/helper-testUtils.R | 34 tests/testthat/test-classifyQA.R | 56 tests/testthat/test-cloudMask.R | 30 tests/testthat/test-coregisterImages.R | 22 tests/testthat/test-encodeQA.R | 202 - tests/testthat/test-entropy.R | 32 tests/testthat/test-estimateHaze.R | 54 tests/testthat/test-fCover.R | 70 tests/testthat/test-gainOffsetRescale.R | 38 tests/testthat/test-getMeta.R | 52 tests/testthat/test-getValidation.R | 46 tests/testthat/test-ggplot.R | 188 - tests/testthat/test-histMatch.R | 24 tests/testthat/test-internalFunctions.R | 28 tests/testthat/test-mesma.R | 146 - tests/testthat/test-mlc.R | 50 tests/testthat/test-multicore.R | 78 tests/testthat/test-normImage.R | 92 tests/testthat/test-oneHotEncode.R | 52 tests/testthat/test-panSharpen.R | 34 tests/testthat/test-pifMatch.R | 38 tests/testthat/test-radCor.R | 146 - tests/testthat/test-rasterCVA.R | 58 tests/testthat/test-rasterPCA.R | 60 tests/testthat/test-readEE.R | 26 tests/testthat/test-readMeta.R | 24 tests/testthat/test-rescaleImage.R | 68 tests/testthat/test-rsOpts.R | 22 tests/testthat/test-sam.R | 70 tests/testthat/test-saveReadRSTBX.R | 34 tests/testthat/test-sli.R | 78 tests/testthat/test-spectralIndices.R | 161 - tests/testthat/test-stackMeta.R | 16 tests/testthat/test-superClass.R | 330 +-- tests/testthat/test-tasseledCap.R | 22 tests/testthat/test-topCor.R | 48 tests/testthat/test-unsuperClass.R | 152 - tests/testthat/test-validateMap.R | 74 tests/testthat/testdata/earthexplorer/EE_LANDSAT_5.txt | 202 - tests/testthat/testdata/earthexplorer/EE_LANDSAT_7.txt | 202 - tests/testthat/testdata/earthexplorer/EE_LANDSAT_8.txt | 168 - tests/testthat/testdata/earthexplorer/EE_LANDSAT_NEWFORMAT.csv | 6 tests/testthat/testdata/metadata/LC08_L1TP_193024_20180824_20200831_02_T1_MTL.txt | 568 ++--- tests/testthat/testdata/metadata/LC80980762015235LGN00.xml | 348 +-- tests/testthat/testdata/metadata/LE07_L1TP_160031_20110416_20161210_01_T1.xml | 452 ++-- tests/testthat/testdata/metadata/LE07_L1TP_160031_20110416_20161210_01_T1_MTL.TXT | 482 ++-- tests/testthat/testdata/metadata/LT05_L1TP_047027_20101006_20160512_01_T1_MTL.txt | 386 +-- tests/testthat/testdata/metadata/LT05_L1TP_218072_20100801_20161015_01_T1_MTL.txt | 388 +-- tests/testthat/testdata/metadata/mss_MTL.txt | 284 +- tests/testthat/testdata/sli/a.sli.hdr | 46 tests/testthat/testdata/sli/b.sli.hdr | 44 tests/testthat/testdata/sli/c.sli.hdr | 42 tests/testthat/testdata/sli/d.sli.hdr | 44 120 files changed, 10067 insertions(+), 9915 deletions(-)