Title: Memory Management in R by Delayed Assignments
Description: Allows objects to be stored on disc and automatically
recalled into memory, as required, by delayed assignment.
Author: Bill Venables [aut, cre],
based on original code by David Brahm [aut]
Maintainer: Bill Venables <Bill.Venables@gmail.com>
Diff between SOAR versions 0.99-11 dated 2013-12-11 and 1.0-1 dated 2026-01-23
SOAR-0.99-11/SOAR/inst/NEWS |only SOAR-0.99-11/SOAR/man/NAME.Rd |only SOAR-0.99-11/SOAR/vignettes/Makefile |only SOAR-1.0-1/SOAR/DESCRIPTION | 20 SOAR-1.0-1/SOAR/MD5 | 31 SOAR-1.0-1/SOAR/NAMESPACE | 18 SOAR-1.0-1/SOAR/R/SOAR.R | 640 ++++++------ SOAR-1.0-1/SOAR/build/vignette.rds |binary SOAR-1.0-1/SOAR/inst/doc/SOAR.R | 46 SOAR-1.0-1/SOAR/inst/doc/SOAR.Rnw | 1796 +++++++++++++++++------------------ SOAR-1.0-1/SOAR/inst/doc/SOAR.pdf |binary SOAR-1.0-1/SOAR/man/Attach.Rd | 3 SOAR-1.0-1/SOAR/man/Objects.Rd | 3 SOAR-1.0-1/SOAR/man/Remove.Rd | 3 SOAR-1.0-1/SOAR/man/SOAR-package.Rd | 3 SOAR-1.0-1/SOAR/man/Search.Rd | 108 +- SOAR-1.0-1/SOAR/man/Store.Rd | 3 SOAR-1.0-1/SOAR/vignettes/SOAR.Rnw | 1796 +++++++++++++++++------------------ 18 files changed, 2257 insertions(+), 2213 deletions(-)
Title: Lightweight Reproducible Reporting
Description: Distributed reproducible computing framework, adopting
ideas from git, docker and other software. By defining a
lightweight interface around the inputs and outputs of an
analysis, a lot of the repetitive work for reproducible research
can be automated. We define a simple format for organising and
describing work that facilitates collaborative reproducible
research and acknowledges that all analyses are run multiple times
over their lifespans.
Author: Rich FitzJohn [aut, cre],
Robert Ashton [aut],
Martin Eden [aut],
Alex Hill [aut],
Wes Hinsley [aut],
Mantra Kusumgar [aut],
Paul Lietar [aut],
James Thompson [aut],
Katy Gaythorpe [aut],
Imperial College of Science, Technology and Medicine [cph]
Maintainer: Rich FitzJohn <rich.fitzjohn@gmail.com>
Diff between orderly versions 2.0.0 dated 2025-10-09 and 2.0.3 dated 2026-01-23
DESCRIPTION | 11 MD5 | 30 - R/location_packit.R | 2 build/vignette.rds |binary inst/doc/collaboration.html | 29 - inst/doc/dependencies.html | 61 +-- inst/doc/details.html | 5 inst/doc/introduction.html | 167 +++++----- inst/doc/migrating.html | 7 inst/doc/plugins.R | 212 ------------- inst/doc/plugins.html | 529 ---------------------------------- inst/doc/query.html | 11 inst/doc/troubleshooting.html | 33 +- tests/testthat/test-location-packit.R | 6 tests/testthat/test-location.R | 2 tests/testthat/test-util.R | 2 16 files changed, 187 insertions(+), 920 deletions(-)
Title: R Markdown Templates for Journal of Data Science
Description: Customized R Markdown templates for authoring articles
for Journal of Data Science.
Author: Wenjie Wang [aut, cre] ,
Jun Yan [aut]
Maintainer: Wenjie Wang <wang@wwenjie.org>
Diff between jds.rmd versions 0.3.3 dated 2023-06-20 and 0.3.4 dated 2026-01-23
jds.rmd-0.3.3/jds.rmd/man/jds.rmd-package.Rd |only jds.rmd-0.3.4/jds.rmd/DESCRIPTION | 12 +- jds.rmd-0.3.4/jds.rmd/MD5 | 10 - jds.rmd-0.3.4/jds.rmd/NEWS.md | 7 + jds.rmd-0.3.4/jds.rmd/R/pkg-doc.R | 7 - jds.rmd-0.3.4/jds.rmd/inst/rmarkdown/templates/pdf_article/resources/jdsart.cls | 60 +++++++--- jds.rmd-0.3.4/jds.rmd/man/jds.rmd.Rd |only 7 files changed, 67 insertions(+), 29 deletions(-)
Title: Within Outlying Mean Indexes: Refining the 'OMI' Analysis
Description: Complementary indexes calculation to the Outlying Mean Index analysis to explore niche shift of a community and biological constraint within an Euclidean space, with graphical displays. For details see Karasiewicz 'et al.' (2017) <doi:10.7717/peerj.3364>.
Author: Stephane Karasiewicz [aut, cre]
Maintainer: Stephane Karasiewicz <skaraz.science@gmail.com>
This is a re-admission after prior archival of version 1.5 dated 2022-07-15
Diff between subniche versions 1.5 dated 2022-07-15 and 1.6 dated 2026-01-23
DESCRIPTION | 30 +++++++++++++++------------- MD5 | 54 ++++++++++++++++++++++++++------------------------- NAMESPACE | 2 - R/convexhull.R |only R/eigenbar.R | 1 R/plot.subniche.R | 48 ++++----------------------------------------- R/plot_NR.R | 6 ++--- R/plot_NR_sp.R | 6 ++--- R/plot_dym.R | 6 ++--- R/plot_dym_sp.R | 6 ++--- R/subarea.R | 13 ++++++------ R/subniche.R | 5 ++-- R/subplot.R | 11 +++++----- R/subplot_K.R | 11 +++++----- R/subplot_sp.R | 6 ++--- build/partial.rdb |binary inst/CITATION | 33 +++++++++++++++++-------------- man/convexhull.Rd |only man/eigenbar.Rd | 1 man/plot.subniche.Rd | 3 +- man/plot_NR.Rd | 5 ++-- man/plot_NR_sp.Rd | 5 ++-- man/plot_dym.Rd | 5 ++-- man/plot_dym_sp.Rd | 5 ++-- man/subarea.Rd | 1 man/subniche.Rd | 5 ++-- man/subplot.Rd | 5 ++-- man/subplot_K.Rd | 5 ++-- man/subplot_sp.Rd | 5 ++-- 29 files changed, 134 insertions(+), 149 deletions(-)
More information about OptimalBinningWoE at CRAN
Permanent link
Title: Probabilistic Record Linkage Using Pretrained Text Embeddings
Description: Links datasets through fuzzy string matching using pretrained text embeddings. Produces more accurate record linkage when lexical string distance metrics are a poor guide to match quality (e.g., "Patricia" is more lexically similar to "Patrick" than it is to "Trish"). Capable of performing multilingual record linkage. Methods are described in Ornstein (2025) <doi:10.1017/pan.2025.10016>.
Author: Joe Ornstein [aut, cre, cph]
Maintainer: Joe Ornstein <jornstein@uga.edu>
Diff between fuzzylink versions 0.2.5 dated 2025-08-29 and 0.3.0 dated 2026-01-23
DESCRIPTION | 10 - LICENSE | 4 MD5 | 36 ++-- NEWS.md | 4 R/check_match.R | 120 ++------------- R/dot.R | 26 +-- R/fuzzylink.R | 4 R/get_embeddings.R | 362 +++++++++++++++++++++++----------------------- R/get_similarity_matrix.R | 88 +++++------ R/get_training_set.R | 160 ++++++++++---------- R/hand_label.R | 66 ++++---- R/mistral_api_key.R | 144 +++++++++--------- R/openai_api_key.R | 144 +++++++++--------- R/utils.R | 28 +-- README.md | 27 +-- man/check_match.Rd | 2 man/dot.Rd | 44 ++--- man/fuzzylink.Rd | 4 man/hand_label.Rd | 34 ++-- 19 files changed, 611 insertions(+), 696 deletions(-)
Title: Docorate (Decorate + Output) Displays
Description: A framework for creating production outputs. Users can frame a table, listing, or figure with headers and footers and save to an output file. Stores an intermediate 'docorator' object for reproducibility and rendering to multiple output types.
Author: Becca Krouse [aut, cre],
Shannon Haughton [aut],
Seongbin Hong [aut],
Dragoș Moldovan-Gruenfeld [aut],
GlaxoSmithKline Research & Development Limited [cph, fnd]
Maintainer: Becca Krouse <becca.z.krouse@gsk.com>
Diff between docorator versions 0.5.1 dated 2026-01-08 and 0.5.2 dated 2026-01-23
DESCRIPTION | 6 MD5 | 19 - NAMESPACE | 1 NEWS.md | 6 R/render.R | 4 R/scale_gt.R | 4 R/utils_fancyhdr.R | 2 R/utils_gt.R | 41 ++- inst/doc/display_sizing.html | 440 ++++++++++++++++++++--------------------- man/apply_to_gt_group.Rd |only tests/testthat/test-utils_gt.R | 17 - 11 files changed, 278 insertions(+), 262 deletions(-)
More information about BinaryReplicates at CRAN
Permanent link
Title: Exploring Biological Relevance of Environmental Chemistry
Observations
Description: Data analysis package for estimating potential biological effects from chemical concentrations in environmental samples. Included are a set of functions to analyze, visualize, and organize measured concentration data as it relates to user-selected chemical-biological interaction benchmark data such as water quality criteria. The intent of these analyses is to develop a better understanding of the potential biological relevance of environmental chemistry data. Results can be used to prioritize which chemicals at which sites may be of greatest concern. These methods are meant to be used as a screening technique to predict potential for biological influence from chemicals that ultimately need to be validated with direct biological assays. A description of the analysis can be found in Blackwell (2017) <doi:10.1021/acs.est.7b01613>.
Author: Laura DeCicco [aut, cre] ,
Steven Corsi [aut] ,
Daniel Villeneuve [aut] ,
Brett Blackwell [aut] ,
Gerald Ankley [aut] ,
Alison Appling [rev] ,
Dalma Martinovic [rev]
Maintainer: Laura DeCicco <ldecicco@usgs.gov>
Diff between toxEval versions 1.4.1 dated 2025-09-30 and 1.4.2 dated 2026-01-23
DESCRIPTION | 6 +-- MD5 | 26 ++++++------- NEWS | 4 ++ R/plot_group_boxplots.R | 5 +- R/plot_tox_endpoints.R | 6 +-- README.md | 36 +++++++++++------- inst/doc/Chemical_names.html | 2 - inst/doc/Introduction.html | 8 ++-- inst/doc/PrepareData.html | 62 +++++++++++++++---------------- man/figures/README-unnamed-chunk-7-1.png |binary man/figures/README-unnamed-chunk-7-3.png |binary man/figures/logo.png |binary man/plot_tox_boxplots.Rd | 5 +- man/plot_tox_endpoints.Rd | 6 +-- 14 files changed, 86 insertions(+), 80 deletions(-)
Title: Reference Based Multiple Imputation
Description: Implements standard and reference based multiple imputation methods for continuous
longitudinal endpoints (Gower-Page et al. (2022) <doi:10.21105/joss.04251>). In particular,
this package supports deterministic conditional mean imputation and jackknifing as described
in Wolbers et al. (2022) <doi:10.1002/pst.2234>, Bayesian multiple imputation as described
in Carpenter et al. (2013) <doi:10.1080/10543406.2013.834911>, and bootstrapped maximum
likelihood imputation as described in von Hippel and Bartlett (2021) <doi: 10.1214/20-STS793>.
Author: Lukas A. Widmer [aut, cre],
Craig Gower-Page [aut],
Isaac Gravestock [aut],
Alessandro Noci [aut],
Marcel Wolbers [ctb],
Daniel Sabanes Bove [aut],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Lukas A. Widmer <lukas_andreas.widmer@novartis.com>
This is a re-admission after prior archival of version 1.5.2 dated 2025-10-28
Diff between rbmi versions 1.5.2 dated 2025-10-28 and 1.6.0 dated 2026-01-23
rbmi-1.5.2/rbmi/man/clear_model_cache.Rd |only rbmi-1.5.2/rbmi/man/get_session_hash.Rd |only rbmi-1.5.2/rbmi/tests/scripts/rcmdcheck.sh |only rbmi-1.5.2/rbmi/tests/scripts/testthat-full.sh |only rbmi-1.5.2/rbmi/tests/scripts/testthat.sh |only rbmi-1.6.0/rbmi/DESCRIPTION | 20 - rbmi-1.6.0/rbmi/MD5 | 66 ++--- rbmi-1.6.0/rbmi/NAMESPACE | 3 rbmi-1.6.0/rbmi/NEWS.md | 8 rbmi-1.6.0/rbmi/R/utilities.R | 178 ++++++------- rbmi-1.6.0/rbmi/README.md | 6 rbmi-1.6.0/rbmi/build/partial.rdb |binary rbmi-1.6.0/rbmi/build/vignette.rds |binary rbmi-1.6.0/rbmi/inst/doc/advanced.html | 2 rbmi-1.6.0/rbmi/inst/doc/quickstart.html | 236 +++++++++--------- rbmi-1.6.0/rbmi/man/get_unique_hash.Rd |only rbmi-1.6.0/rbmi/man/rbmi-package.Rd | 9 rbmi-1.6.0/rbmi/man/rbmi-settings.Rd | 9 rbmi-1.6.0/rbmi/tests/scripts/core.sh |only rbmi-1.6.0/rbmi/tests/scripts/cran.sh |only rbmi-1.6.0/rbmi/tests/scripts/documentation.sh |only rbmi-1.6.0/rbmi/tests/scripts/extended.sh |only rbmi-1.6.0/rbmi/tests/scripts/vignettes.sh | 12 rbmi-1.6.0/rbmi/tests/testthat.R | 8 rbmi-1.6.0/rbmi/tests/testthat/_snaps/mmrm.md | 8 rbmi-1.6.0/rbmi/tests/testthat/helper-misc.R | 12 rbmi-1.6.0/rbmi/tests/testthat/setup.R | 18 - rbmi-1.6.0/rbmi/tests/testthat/test-draws.R | 3 rbmi-1.6.0/rbmi/tests/testthat/test-fullusage.R | 32 +- rbmi-1.6.0/rbmi/tests/testthat/test-longData.R | 2 rbmi-1.6.0/rbmi/tests/testthat/test-mcmc.R | 44 +-- rbmi-1.6.0/rbmi/tests/testthat/test-mmrm.R | 20 + rbmi-1.6.0/rbmi/tests/testthat/test-parallel.R | 2 rbmi-1.6.0/rbmi/tests/testthat/test-pool.R | 2 rbmi-1.6.0/rbmi/tests/testthat/test-print.R | 28 +- rbmi-1.6.0/rbmi/tests/testthat/test-reproducibility.R | 6 rbmi-1.6.0/rbmi/tests/testthat/test-utilities.R | 21 - rbmi-1.6.0/rbmi/vignettes/build.R | 2 rbmi-1.6.0/rbmi/vignettes/quickstart.Rmd | 6 39 files changed, 386 insertions(+), 377 deletions(-)
Title: Easy Access to NetCDF Files with CF Metadata Conventions
Description: Network Common Data Form ('netCDF') files are widely used for
scientific data. Library-level access in R is provided through packages
'RNetCDF' and 'ncdf4'. Package 'ncdfCF' is built on top of 'RNetCDF' and
makes the data and its attributes available as a set of R6 classes that are
informed by the Climate and Forecasting Metadata Conventions. Access to the
data uses standard R subsetting operators and common function forms.
Author: Patrick Van Laake [aut, cre, cph]
Maintainer: Patrick Van Laake <patrick@vanlaake.net>
Diff between ncdfCF versions 0.7.0 dated 2025-09-13 and 0.8.0 dated 2026-01-23
ncdfCF-0.7.0/ncdfCF/R/CFResource.R |only ncdfCF-0.7.0/ncdfCF/inst/doc/R-CF.R |only ncdfCF-0.7.0/ncdfCF/inst/doc/R-CF.Rmd |only ncdfCF-0.7.0/ncdfCF/inst/doc/R-CF.html |only ncdfCF-0.7.0/ncdfCF/inst/doc/Using_ncdfCF.R |only ncdfCF-0.7.0/ncdfCF/inst/doc/Using_ncdfCF.Rmd |only ncdfCF-0.7.0/ncdfCF/inst/doc/Using_ncdfCF.html |only ncdfCF-0.7.0/ncdfCF/man/CFResource.Rd |only ncdfCF-0.7.0/ncdfCF/vignettes/R-CF.Rmd |only ncdfCF-0.7.0/ncdfCF/vignettes/Using_ncdfCF.Rmd |only ncdfCF-0.8.0/ncdfCF/DESCRIPTION | 23 ncdfCF-0.8.0/ncdfCF/LICENSE | 2 ncdfCF-0.8.0/ncdfCF/MD5 | 179 +-- ncdfCF-0.8.0/ncdfCF/NAMESPACE | 5 ncdfCF-0.8.0/ncdfCF/NEWS.md | 31 ncdfCF-0.8.0/ncdfCF/R/AOI.R | 38 ncdfCF-0.8.0/ncdfCF/R/AOImethod.R | 2 ncdfCF-0.8.0/ncdfCF/R/CFAuxiliaryLongLat.R | 56 - ncdfCF-0.8.0/ncdfCF/R/CFAxis.R | 166 ++ ncdfCF-0.8.0/ncdfCF/R/CFAxisCharacter.R | 41 ncdfCF-0.8.0/ncdfCF/R/CFAxisDiscrete.R | 22 ncdfCF-0.8.0/ncdfCF/R/CFAxisLatitude.R | 38 ncdfCF-0.8.0/ncdfCF/R/CFAxisLongitude.R | 36 ncdfCF-0.8.0/ncdfCF/R/CFAxisNumeric.R | 46 ncdfCF-0.8.0/ncdfCF/R/CFAxisTime.R | 136 +- ncdfCF-0.8.0/ncdfCF/R/CFAxisVertical.R | 127 +- ncdfCF-0.8.0/ncdfCF/R/CFBounds.R | 77 - ncdfCF-0.8.0/ncdfCF/R/CFData.R |only ncdfCF-0.8.0/ncdfCF/R/CFDataset.R | 209 ++- ncdfCF-0.8.0/ncdfCF/R/CFGridMapping.R | 18 ncdfCF-0.8.0/ncdfCF/R/CFGroup.R |only ncdfCF-0.8.0/ncdfCF/R/CFLabel.R | 141 +- ncdfCF-0.8.0/ncdfCF/R/CFObject.R | 407 ++----- ncdfCF-0.8.0/ncdfCF/R/CFStandardNames.R | 2 ncdfCF-0.8.0/ncdfCF/R/CFVariable.R | 559 +++++----- ncdfCF-0.8.0/ncdfCF/R/CFVariableL3b.R | 43 ncdfCF-0.8.0/ncdfCF/R/CFVerticalParametricTerm.R | 5 ncdfCF-0.8.0/ncdfCF/R/NCDimension.R | 21 ncdfCF-0.8.0/ncdfCF/R/NCGroup.R | 405 ++----- ncdfCF-0.8.0/ncdfCF/R/NCObject.R | 65 - ncdfCF-0.8.0/ncdfCF/R/NCResource.R |only ncdfCF-0.8.0/ncdfCF/R/NCVariable.R | 107 + ncdfCF-0.8.0/ncdfCF/R/makeCFObjects.R | 256 +++- ncdfCF-0.8.0/ncdfCF/R/ncdfCF-package.R | 12 ncdfCF-0.8.0/ncdfCF/R/ops.R | 8 ncdfCF-0.8.0/ncdfCF/R/readCF.R | 431 ++++--- ncdfCF-0.8.0/ncdfCF/R/utils.R | 29 ncdfCF-0.8.0/ncdfCF/README.md | 190 +-- ncdfCF-0.8.0/ncdfCF/TODO | 68 - ncdfCF-0.8.0/ncdfCF/build/vignette.rds |binary ncdfCF-0.8.0/ncdfCF/inst/doc/ncdfCF.R |only ncdfCF-0.8.0/ncdfCF/inst/doc/ncdfCF.Rmd |only ncdfCF-0.8.0/ncdfCF/inst/doc/ncdfCF.html |only ncdfCF-0.8.0/ncdfCF/inst/extdata/ERA5land_Rwanda_20160101.nc |binary ncdfCF-0.8.0/ncdfCF/inst/extdata/pr_day_EC-Earth3-CC_ssp245_r1i1p1f1_gr_20230101-20231231_vncdfCF.nc |binary ncdfCF-0.8.0/ncdfCF/man/CFAuxiliaryLongLat.Rd | 33 ncdfCF-0.8.0/ncdfCF/man/CFAxis.Rd | 77 + ncdfCF-0.8.0/ncdfCF/man/CFAxisCharacter.Rd | 26 ncdfCF-0.8.0/ncdfCF/man/CFAxisDiscrete.Rd | 21 ncdfCF-0.8.0/ncdfCF/man/CFAxisLatitude.Rd | 26 ncdfCF-0.8.0/ncdfCF/man/CFAxisLongitude.Rd | 24 ncdfCF-0.8.0/ncdfCF/man/CFAxisNumeric.Rd | 26 ncdfCF-0.8.0/ncdfCF/man/CFAxisTime.Rd | 57 - ncdfCF-0.8.0/ncdfCF/man/CFAxisVertical.Rd | 62 - ncdfCF-0.8.0/ncdfCF/man/CFBounds.Rd | 50 ncdfCF-0.8.0/ncdfCF/man/CFData.Rd |only ncdfCF-0.8.0/ncdfCF/man/CFDataset.Rd | 197 +++ ncdfCF-0.8.0/ncdfCF/man/CFGridMapping.Rd | 35 ncdfCF-0.8.0/ncdfCF/man/CFGroup.Rd |only ncdfCF-0.8.0/ncdfCF/man/CFLabel.Rd | 117 +- ncdfCF-0.8.0/ncdfCF/man/CFObject.Rd | 171 +-- ncdfCF-0.8.0/ncdfCF/man/CFVariable.Rd | 199 ++- ncdfCF-0.8.0/ncdfCF/man/CFVariableL3b.Rd | 27 ncdfCF-0.8.0/ncdfCF/man/CFVerticalParametricTerm.Rd | 27 ncdfCF-0.8.0/ncdfCF/man/NCDimension.Rd | 10 ncdfCF-0.8.0/ncdfCF/man/NCGroup.Rd | 263 +--- ncdfCF-0.8.0/ncdfCF/man/NCObject.Rd | 16 ncdfCF-0.8.0/ncdfCF/man/NCResource.Rd |only ncdfCF-0.8.0/ncdfCF/man/NCVariable.Rd | 66 + ncdfCF-0.8.0/ncdfCF/man/arrayOps.Rd | 3 ncdfCF-0.8.0/ncdfCF/man/as_CF.Rd | 38 ncdfCF-0.8.0/ncdfCF/man/create_ncdf.Rd |only ncdfCF-0.8.0/ncdfCF/man/dim.CFAxis.Rd | 7 ncdfCF-0.8.0/ncdfCF/man/dimnames.Rd | 6 ncdfCF-0.8.0/ncdfCF/man/figures/README-export-1.png |binary ncdfCF-0.8.0/ncdfCF/man/groups.Rd |only ncdfCF-0.8.0/ncdfCF/man/makeAxis.Rd | 12 ncdfCF-0.8.0/ncdfCF/man/makeCharacterAxis.Rd | 5 ncdfCF-0.8.0/ncdfCF/man/makeDiscreteAxis.Rd | 5 ncdfCF-0.8.0/ncdfCF/man/makeLatitudeAxis.Rd | 11 ncdfCF-0.8.0/ncdfCF/man/makeLongitudeAxis.Rd | 11 ncdfCF-0.8.0/ncdfCF/man/makeTimeAxis.Rd | 5 ncdfCF-0.8.0/ncdfCF/man/makeVerticalAxis.Rd | 11 ncdfCF-0.8.0/ncdfCF/man/ncdfCF-package.Rd | 13 ncdfCF-0.8.0/ncdfCF/man/open_ncdf.Rd | 10 ncdfCF-0.8.0/ncdfCF/man/str.CFAxis.Rd | 1 ncdfCF-0.8.0/ncdfCF/man/str.CFDataset.Rd | 1 ncdfCF-0.8.0/ncdfCF/man/sub-sub-.CFDataset.Rd | 2 ncdfCF-0.8.0/ncdfCF/tests/testthat/test-CFVariableL3b.R |only ncdfCF-0.8.0/ncdfCF/tests/testthat/test-CFobjects.R | 60 - ncdfCF-0.8.0/ncdfCF/tests/testthat/test-all.R | 73 - ncdfCF-0.8.0/ncdfCF/vignettes/ncdfCF.Rmd |only 102 files changed, 3410 insertions(+), 2395 deletions(-)
Title: Preprocessing and Analyzing Web Tracking Data
Description: Data structures and methods to work with web tracking data. The functions cover data preprocessing steps, enriching web tracking data with external information and methods for the analysis of digital behavior as used in several academic papers (e.g., Clemm von Hohenberg et al., 2023 <doi:10.17605/OSF.IO/M3U9P>; Stier et al., 2022 <doi:10.1017/S0003055421001222>).
Author: David Schoch [aut, cre] ,
Bernhard Clemm von Hohenberg [aut] ,
Frank Mangold [aut] ,
Sebastian Stier [aut]
Maintainer: David Schoch <david@schochastics.net>
Diff between webtrackR versions 0.3.1 dated 2024-04-30 and 0.3.2 dated 2026-01-23
DESCRIPTION | 26 +++---- MD5 | 20 ++--- NEWS.md | 5 + R/wt_dt.R | 3 README.md | 102 +++++++++++++-------------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/webtrackR.Rmd | 4 - inst/doc/webtrackR.html | 172 +++++++++++++++++++++++------------------------ man/webtrackR-package.Rd | 5 - vignettes/webtrackR.Rmd | 4 - 11 files changed, 172 insertions(+), 169 deletions(-)
Title: Text Plots
Description: Visualise complex relations in texts. This is done by providing functionalities for displaying
text co-occurrence networks, text correlation networks, dependency relationships as well as text clustering and semantic text 'embeddings'.
Feel free to join the effort of providing interesting text visualisations. Do note that to avoid the risk of CRAN archival that you should put packages as much as possible in Suggests.
Package 'ggalt' is available in the CRAN archive: <https://cran.r-project.org/package=ggalt>.
Author: Jan Wijffels [aut, cre, cph],
BNOSAC [cph],
Sacha Epskamp [ctb, cph] ,
Ingo Feinerer and Kurt Hornik [ctb, cph]
Maintainer: Jan Wijffels <jwijffels@bnosac.be>
Diff between textplot versions 0.2.2 dated 2022-07-17 and 0.2.3 dated 2026-01-23
DESCRIPTION | 11 - MD5 | 40 ++-- NEWS.md | 5 R/textplot_embedding_2d.R | 4 build/vignette.rds |binary inst/doc/textplot-examples.R | 298 ++++++++++++++++---------------- inst/doc/textplot-examples.Rnw | 4 inst/doc/textplot-examples.pdf |binary man/example_btm.Rd | 50 ++--- man/example_embedding.Rd | 26 +- man/example_embedding_clusters.Rd | 30 +-- man/example_udpipe.Rd | 28 +-- man/textplot_bar.Rd | 180 +++++++++---------- man/textplot_bitermclusters.Rd | 174 +++++++++--------- man/textplot_cooccurrence.Rd | 138 +++++++------- man/textplot_correlation_glasso.Rd | 132 +++++++------- man/textplot_correlation_lines.Rd | 230 ++++++++++++------------ man/textplot_correlation_lines_attrs.Rd | 56 +++--- man/textplot_dependencyparser.Rd | 160 ++++++++--------- man/textplot_embedding_2d.Rd | 164 ++++++++--------- vignettes/textplot-examples.Rnw | 4 21 files changed, 870 insertions(+), 864 deletions(-)
Title: Sequential Trial Emulation
Description: Implementation of sequential trial emulation for the analysis of observational databases.
The 'SEQTaRget' software accommodates time-varying treatments and confounders, as well as binary
and failure time outcomes. 'SEQTaRget' allows to compare both static and dynamic strategies,
can be used to estimate observational analogs of intention-to-treat
and per-protocol effects, and can adjust for potential selection bias
induced by losses-to-follow-up. (Paper to come).
Author: Ryan O'Dea [aut, cre] ,
Alejandro Szmulewicz [aut] ,
Tom Palmer [aut] ,
Miguel Hernan [aut] ,
The President and Fellows of Harvard College [cph]
Maintainer: Ryan O'Dea <ryan.odea@psi.ch>
Diff between SEQTaRget versions 1.3.3 dated 2026-01-08 and 1.3.4 dated 2026-01-23
SEQTaRget-1.3.3/SEQTaRget/man/prepare.data.Rd |only SEQTaRget-1.3.4/SEQTaRget/DESCRIPTION | 10 - SEQTaRget-1.3.4/SEQTaRget/MD5 | 36 ++-- SEQTaRget-1.3.4/SEQTaRget/NEWS.md | 8 SEQTaRget-1.3.4/SEQTaRget/R/SEQexpand.R | 3 SEQTaRget-1.3.4/SEQTaRget/R/SEQuential.R | 5 SEQTaRget-1.3.4/SEQTaRget/R/globals.R |only SEQTaRget-1.3.4/SEQTaRget/R/internal_analysis.R | 122 +++++++++++--- SEQTaRget-1.3.4/SEQTaRget/R/internal_fatglmHelpers.R | 163 +++++++++++++++---- SEQTaRget-1.3.4/SEQTaRget/R/internal_hazard.R | 43 +++-- SEQTaRget-1.3.4/SEQTaRget/R/internal_survival.R | 61 ++++--- SEQTaRget-1.3.4/SEQTaRget/R/internal_weights.R | 21 +- SEQTaRget-1.3.4/SEQTaRget/inst/doc/SEQuential.html | 94 +++++----- SEQTaRget-1.3.4/SEQTaRget/inst/doc/seqopts.Rmd | 2 SEQTaRget-1.3.4/SEQTaRget/inst/doc/seqopts.html | 2 SEQTaRget-1.3.4/SEQTaRget/man/init_formula_cache.Rd |only SEQTaRget-1.3.4/SEQTaRget/man/inline.pred.Rd | 11 + SEQTaRget-1.3.4/SEQTaRget/man/internal.hazard.Rd | 2 SEQTaRget-1.3.4/SEQTaRget/man/internal.weights.Rd | 4 SEQTaRget-1.3.4/SEQTaRget/man/prepare.data_cached.Rd |only SEQTaRget-1.3.4/SEQTaRget/vignettes/seqopts.Rmd | 2 21 files changed, 401 insertions(+), 188 deletions(-)
Title: Retrieval-Augmented Generation (RAG) Workflows
Description: Provides tools for implementing Retrieval-Augmented
Generation (RAG) workflows with Large Language Models (LLM). Includes
functions for document processing, text chunking, embedding
generation, storage management, and content retrieval. Supports
various document types and embedding providers ('Ollama', 'OpenAI'),
with 'DuckDB' as the default storage backend. Integrates with the
'ellmer' package to equip chat objects with retrieval capabilities.
Designed to offer both sensible defaults and customization options
with transparent access to intermediate outputs. For a review of
retrieval-augmented generation methods, see Gao et al. (2023)
"Retrieval-Augmented Generation for Large Language Models: A Survey"
<doi:10.48550/arXiv.2312.10997>.
Author: Tomasz Kalinowski [aut, cre],
Daniel Falbel [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Tomasz Kalinowski <tomasz@posit.co>
Diff between ragnar versions 0.2.1 dated 2025-08-19 and 0.3.0 dated 2026-01-23
DESCRIPTION | 19 MD5 | 113 ++- NAMESPACE | 6 NEWS.md | 192 ++++-- R/aaa-utils.R | 41 - R/ellmer.R | 147 ++++ R/embed-azure.R |only R/embed-bedrock.R | 30 R/embed-databricks.R | 1 R/embed-gemini.R | 7 R/embed-snowflake.R |only R/embed-vertex.R | 5 R/embed.R | 76 ++ R/ingest.R | 303 ++++++++-- R/markdown-chunk.R | 6 R/ragnar-package.R | 75 ++ R/read-html.R | 15 R/read-markdown.R | 108 +++ R/retrieve.R | 19 R/store-v1.R | 7 R/store-v2.R | 26 R/store.R | 96 ++- README.md | 142 ++-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/ragnar.Rmd | 12 inst/doc/ragnar.html | 24 inst/python/_ragnartools/__pycache__/__init__.cpython-312.pyc |only inst/python/_ragnartools/__pycache__/__init__.cpython-313.pyc |only inst/python/_ragnartools/__pycache__/atlas.cpython-311.pyc |only inst/python/_ragnartools/__pycache__/markitdown.cpython-311.pyc |binary inst/python/_ragnartools/__pycache__/markitdown.cpython-312.pyc |only inst/python/_ragnartools/__pycache__/markitdown.cpython-313.pyc |only inst/python/_ragnartools/atlas.py |only inst/python/_ragnartools/markitdown.py | 43 + inst/python/unpin-youtube-transcript-api.txt |only inst/store-inspector/modules.R | 269 ++++++-- inst/store-inspector/www/inspector.js |only man/embed_azure_openai.Rd |only man/embed_bedrock.Rd | 4 man/embed_google_vertex.Rd | 9 man/embed_ollama.Rd | 2 man/embed_snowflake.Rd |only man/mcp_serve_store.Rd |only man/ragnar-package.Rd | 2 man/ragnar_find_links.Rd | 6 man/ragnar_read.Rd | 2 man/ragnar_register_tool_retrieve.Rd | 2 man/ragnar_retrieve.Rd | 2 man/ragnar_retrieve_bm25.Rd | 4 man/ragnar_retrieve_vss.Rd | 2 man/ragnar_retrieve_vss_and_bm25.Rd | 2 man/ragnar_store_atlas.Rd |only man/ragnar_store_create.Rd | 2 man/ragnar_store_ingest.Rd |only man/ragnar_store_inspect.Rd | 31 - man/read_as_markdown.Rd | 63 ++ tests/testthat/_snaps/store.md | 2 tests/testthat/test-embed-azure.R |only tests/testthat/test-embed-snowflake.R |only tests/testthat/test-extra-cols.R | 2 tests/testthat/test-ingest.R |only tests/testthat/test-read-markdown-youtube.R |only tests/testthat/test-read-markdown.R | 20 tests/testthat/test-store-v2.R | 65 ++ tools/configure_deps.R | 1 vignettes/ragnar.Rmd | 12 67 files changed, 1580 insertions(+), 437 deletions(-)
Title: Inference on the Overlap Coefficient
Description: Provides functions to construct confidence intervals for the Overlap Coefficient (OVL). OVL measures the similarity between two distributions through the overlapping area of their distribution functions. Given its intuitive description and ease of visual representation by the straightforward depiction of the amount of overlap between the two corresponding histograms based on samples of measurements from each one of the two distributions, the development of accurate methods for confidence interval construction can be useful for applied researchers. Implements methods based on the work of Franco-Pereira, A.M., Nakas, C.T., Reiser, B., and Pardo, M.C. (2021) <doi:10.1177/09622802211046386> as well as extensions for multimodal distributions proposed by Alcaraz-Peñalba, A., Franco-Pereira, A., and Pardo, M.C. (2025) <doi:10.1007/s10182-025-00545-2>.
Author: Alba M. Franco-Pereira [aut, cre, cph],
Christos T. Nakas [aut],
Benjamin Reiser [aut],
M.Carmen Pardo [aut],
Alba Alcaraz-Penalba [aut, cph]
Maintainer: Alba M. Franco-Pereira <albfranc@ucm.es>
Diff between OVL.CI versions 0.1.0 dated 2023-11-13 and 0.1.1 dated 2026-01-23
DESCRIPTION | 23 +- MD5 | 145 ++++++++++-------- NAMESPACE | 20 +- NEWS.md | 8 R/EM.R |only R/FIM_mixture_normals.R |only R/OVL.BCAN.R | 14 - R/OVL.BCPB.R | 14 - R/OVL.BCbias.R | 14 - R/OVL.D.R | 10 - R/OVL.DBC.R | 12 - R/OVL.DBCL.R | 12 - R/OVL.Delta.mix.R |only R/OVL.GPQ.R |only R/OVL.GPQ.mix.R |only R/OVL.K.R | 12 - R/OVL.KPB.R | 12 - R/OVL.LogitBCAN.R | 14 - R/OVL.LogitD.R | 10 - R/OVL.LogitDBC.R | 12 - R/OVL.LogitDBCL.R | 11 - R/OVL.LogitK.R | 12 - R/OVL_derivates_1.R |only R/OVL_derivates_2.R |only R/OVL_mix.R |only R/U.R | 17 -- R/data.R | 10 - R/data_mix.R |only R/dnorm_mixture.R |only R/encontrar_raices.R |only R/kernel.e.R | 12 - R/kernel.e.density.R | 18 -- R/kernel.g.R | 13 - R/kernel.g.density.R | 18 -- R/likbox.R | 18 -- R/ssdd.R | 12 - data/mixnorm_data.rda |only man/EM.Rd |only man/FIM_mixture_normals.Rd |only man/OVL.BCAN.Rd | 14 - man/OVL.BCPB.Rd | 14 - man/OVL.BCbias.Rd | 14 - man/OVL.D.Rd | 10 - man/OVL.DBC.Rd | 12 - man/OVL.DBCL.Rd | 12 - man/OVL.Delta.mix.Rd |only man/OVL.GPQ.Rd |only man/OVL.GPQ.mix.Rd |only man/OVL.K.Rd | 12 - man/OVL.KPB.Rd | 12 - man/OVL.LogitBCAN.Rd | 14 - man/OVL.LogitD.Rd | 10 - man/OVL.LogitDBC.Rd | 12 - man/OVL.LogitDBCL.Rd | 12 - man/OVL.LogitK.Rd | 12 - man/OVL_derivates_1.Rd |only man/OVL_derivates_2.Rd |only man/OVL_mix.Rd |only man/U.Rd | 18 -- man/dnorm_mixture.Rd |only man/encontrar_raices.Rd |only man/kernel.e.Rd | 13 - man/kernel.e.density.Rd | 19 -- man/kernel.g.Rd | 13 - man/kernel.g.density.Rd | 19 -- man/likbox.Rd | 19 -- man/mixnorm_data.Rd |only man/ssdd.Rd | 13 - man/test_data.Rd | 10 - tests/testthat/test_EM.R |only tests/testthat/test_FIM_mixture_normals.R |only tests/testthat/test_LogitBCAN.R | 4 tests/testthat/test_LogitD.R | 4 tests/testthat/test_LogitDBC.R | 4 tests/testthat/test_LogitDBCL.R | 4 tests/testthat/test_LogitK.R | 4 tests/testthat/test_OVL.BCAN.R | 4 tests/testthat/test_OVL.BCPB.R | 4 tests/testthat/test_OVL.BCbias.R | 4 tests/testthat/test_OVL.D.R | 4 tests/testthat/test_OVL.DBCL.R | 4 tests/testthat/test_OVL.Delta.mix.R |only tests/testthat/test_OVL.GPQ.R |only tests/testthat/test_OVL.GPQ.mix.R |only tests/testthat/test_OVL.K.R | 4 tests/testthat/test_OVL.KPB.R | 4 tests/testthat/test_OVL_derivates_1&OVL_derivates_2.R |only tests/testthat/test_dnorm_mixture.R |only tests/testthat/test_encontrar_raices.R |only 89 files changed, 393 insertions(+), 412 deletions(-)
Title: Model-Based Clustering of Network Data
Description: Clustering unilayer and multilayer network data by means of finite mixtures is the main utility of netClust.
Author: Shuchismita Sarkar [aut, cre],
Volodymyr Melnykov [aut]
Maintainer: Shuchismita Sarkar <ssarkar@bgsu.edu>
This is a re-admission after prior archival of version 1.0.1 dated 2020-07-07
Diff between netClust versions 1.0.1 dated 2020-07-07 and 1.0.2 dated 2026-01-23
netClust-1.0.1/netClust/data/netData.RData |only netClust-1.0.1/netClust/data/netDataID.RData |only netClust-1.0.2/netClust/DESCRIPTION | 18 +++--- netClust-1.0.2/netClust/MD5 | 26 ++++----- netClust-1.0.2/netClust/R/RcppExports.R | 16 +++++ netClust-1.0.2/netClust/build/partial.rdb |binary netClust-1.0.2/netClust/data/netData.rda |only netClust-1.0.2/netClust/data/netDataID.rda |only netClust-1.0.2/netClust/man/netClust-package.Rd | 45 +++++++++------ netClust-1.0.2/netClust/man/netData.Rd | 4 - netClust-1.0.2/netClust/man/netDataID.Rd | 2 netClust-1.0.2/netClust/man/rcpparma_hello_world.Rd |only netClust-1.0.2/netClust/src/Makevars | 2 netClust-1.0.2/netClust/src/Makevars.win | 2 netClust-1.0.2/netClust/src/RcppExports.cpp | 52 ++++++++++++++++++ netClust-1.0.2/netClust/src/netClust.cpp | 54 +++++++++---------- netClust-1.0.2/netClust/src/rcpparma_hello_world.cpp |only 17 files changed, 148 insertions(+), 73 deletions(-)
Title: The Time Series Modeling Companion to 'healthyR'
Description: Hospital time series data analysis workflow tools, modeling, and automations.
This library provides many useful tools to review common administrative time
series hospital data. Some of these include average length of stay, and
readmission rates. The aim is to provide a simple and consistent verb
framework that takes the guesswork out of everything.
Author: Steven Sanderson [aut, cre, cph]
Maintainer: Steven Sanderson <spsanderson@gmail.com>
This is a re-admission after prior archival of version 0.3.1 dated 2024-10-11
Diff between healthyR.ts versions 0.3.1 dated 2024-10-11 and 0.3.2 dated 2026-01-23
DESCRIPTION | 16 MD5 | 242 ++--- NAMESPACE | 1 NEWS.md | 775 +++++++++--------- R/00_global_variables.R | 36 R/augment-ts-acceleration.R | 170 +-- R/augment-ts-growth.R | 142 +-- R/augment-ts-velocity.R | 164 +-- R/boilerplate-autoarima-xgboost.R | 546 ++++++------ R/boilerplate-autoarima.R | 550 ++++++------ R/boilerplate-croston.R | 546 ++++++------ R/boilerplate-exp-smoothing.R | 554 ++++++------ R/boilerplate-glmnet.R | 546 ++++++------ R/boilerplate-lm.R | 362 ++++---- R/boilerplate-mars.R | 536 ++++++------ R/boilerplate-misc-functions.R | 76 - R/boilerplate-nnetar.R | 546 ++++++------ R/boilerplate-prophet-reg.R | 548 ++++++------ R/boilerplate-prophet-xgboost.R | 560 ++++++------- R/boilerplate-smooth-es.R | 564 ++++++------- R/boilerplate-svm-poly.R | 552 ++++++------ R/boilerplate-svm-rbf.R | 548 ++++++------ R/boilerplate-theta.R | 352 ++++---- R/boilerplate-xgboost.R | 536 ++++++------ R/brownian-motion-plot.R | 200 ++-- R/calibrate-plot-list.R | 264 +++--- R/diagnostic_plots.R | 630 +++++++------- R/helper-model-extraction.R | 176 ++-- R/internal-event-backward.R | 126 +- R/internal-event-both.R | 128 +- R/internal-event-forward.R | 126 +- R/simulate-ts-arima.R | 2 R/stat-adf-test.R | 226 ++--- R/stats-confidence-intervals.R | 130 +-- R/step-ts-acceleration.R | 368 ++++---- R/step-ts-velocity.R | 366 ++++---- R/tidy-fft.R | 572 ++++++------- R/ts-auto-recipe.R | 370 ++++---- R/ts-brownian-motion-augment.R | 368 ++++---- R/ts-brownian-motion.R | 202 ++-- R/ts-calendar-heatmap-plt.R | 266 +++--- R/ts-compare-data.R | 234 ++--- R/ts-event-analysis-plot.R | 512 +++++------ R/ts-event-analysis-tbl.R | 374 ++++---- R/ts-fcst-sim.R | 554 ++++++------ R/ts-feature-cluster-plt.R | 354 ++++---- R/ts-feature-cluster-tbl.R | 380 ++++---- R/ts-geometric-brownian-motion-augment.R | 432 +++++----- R/ts-geometric-brownian-motion.R | 238 ++--- R/ts-info-tbl.R | 294 +++--- R/ts-lag-correlation.R | 400 ++++----- R/ts-ma-plt.R | 507 ++++------- R/ts-model-compare.R | 500 +++++------ R/ts-model-rank.R | 220 ++--- R/ts-model-tuner.R | 612 +++++++------- R/ts-qq-plot.R | 266 +++--- R/ts-random-walk-plot.R |only R/ts-random-walk.R | 224 ++--- R/ts-skedactiy-plot.R | 268 +++--- R/ts-sma-plot.R | 312 +++---- R/ts-splits-plot.R | 148 +-- R/ts-to-tbl.R | 128 +- R/ts-tune-spec-template.R | 476 +++++------ R/ts-vva-plot.R | 214 ++-- R/utils-auto-stationarize.R | 148 +-- R/utils-difflog-stationary.R | 184 ++-- R/utils-doublediff-stationary.R | 168 +-- R/utils-doubledifflog-stationary.R | 176 ++-- R/utils-get-boilerplate-fit-wflw.R | 150 +-- R/utils-log-trans-stationary.R | 164 +-- R/utils-singlediff-stationary.R | 166 +-- R/utils-tidy-eval.R | 98 +- R/utils-time-helpers.R | 156 +-- R/vec-ts-acceleration.R | 120 +- R/vec-ts-growth-rate.R | 232 ++--- R/vec-ts-velocity.R | 120 +- R/wfs-arima-boost.R | 368 ++++---- R/wfs-arima-reg.R | 220 ++--- R/wfs-ets-reg.R | 390 ++++----- R/wfs-linear-reg.R | 250 ++--- R/wfs-mars-reg.R | 274 +++--- R/wfs-nnetar-reg.R | 270 +++--- R/wfs-prophet-reg.R | 440 +++++----- R/wfs-svm-poly-reg.R | 274 +++--- R/wfs-svm-rbf.R | 260 +++--- R/wfs-xgboost-reg.R | 284 +++--- README.md | 322 +++++-- build/vignette.rds |binary inst/doc/getting-started.html | 31 inst/doc/using-tidy-fft.html | 35 man/auto_stationarize.Rd | 140 +-- man/ci_hi.Rd | 72 - man/ci_lo.Rd | 72 - man/figures/README-ts_random_walk_ggplot_layers-1.png |binary man/figures/README-unnamed-chunk-2-1.png |binary man/figures/README-unnamed-chunk-3-1.png |binary man/figures/README-unnamed-chunk-4-1.png |binary man/figures/README-unnamed-chunk-4-2.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/ts_adf_test.Rd | 98 +- man/ts_arima_simulator.Rd | 2 man/ts_brownian_motion.Rd | 136 +-- man/ts_brownian_motion_augment.Rd | 166 +-- man/ts_brownian_motion_plot.Rd | 111 +- man/ts_event_analysis_plot.Rd | 145 +-- man/ts_extract_auto_fitted_workflow.Rd | 106 +- man/ts_geometric_brownian_motion.Rd | 166 +-- man/ts_geometric_brownian_motion_augment.Rd | 194 ++-- man/ts_get_date_columns.Rd | 108 +- man/ts_growth_rate_augment.Rd | 94 +- man/ts_growth_rate_vec.Rd | 136 +-- man/ts_is_date_class.Rd | 100 +- man/ts_lag_correlation.Rd | 206 ++-- man/ts_ma_plot.Rd | 18 man/ts_qq_plot.Rd | 1 man/ts_random_walk_plot.Rd |only man/ts_scedacity_scatter_plot.Rd | 3 man/ts_wfs_xgboost.Rd | 226 ++--- man/util_difflog_ts.Rd | 150 +-- man/util_doublediff_ts.Rd | 150 +-- man/util_doubledifflog_ts.Rd | 152 +-- man/util_log_ts.Rd | 148 +-- man/util_singlediff_ts.Rd | 148 +-- 123 files changed, 15052 insertions(+), 14931 deletions(-)
Title: Plotting Football Matches Expected Goals (xG) Stats with
'Understat' Data
Description: Scrapes football match shots data from 'Understat' <https://understat.com/> and visualizes it using interactive plots:
- A detailed shot map displaying the location, type, and xG value of shots taken by both teams.
- An xG timeline chart showing the cumulative xG for each team over time, annotated with the details of scored goals.
Author: Aymen Nasri [aut, cre, cph]
Maintainer: Aymen Nasri <aymennasrii@proton.me>
Diff between ggfootball versions 0.2.2 dated 2026-01-23 and 0.3.0 dated 2026-01-23
DESCRIPTION | 11 +--- MD5 | 10 +-- NEWS.md | 14 +++++ R/understat_scraper.R | 137 ++++++++++++++++++++++---------------------------- R/xg_chart.R | 27 +++++++-- R/xg_map.R | 72 +++++++++++++++++++------- 6 files changed, 161 insertions(+), 110 deletions(-)
Title: Geolocalização De Endereços Brasileiros (Geocoding Brazilian
Addresses)
Description: Método simples e eficiente de geolocalizar dados no Brasil. O
pacote é baseado em conjuntos de dados espaciais abertos de endereços
brasileiros, utilizando como fonte principal o Cadastro Nacional de Endereços
para Fins Estatísticos (CNEFE). O CNEFE é publicado pelo Instituto Brasileiro
de Geografia e Estatística (IBGE), órgão oficial de estatísticas e geografia
do Brasil. (A simple and efficient method for geolocating data in Brazil. The
package is based on open spatial datasets of Brazilian addresses, primarily
using the Cadastro Nacional de Endereços para Fins Estatísticos (CNEFE),
published by the Instituto Brasileiro de Geografia e Estatística (IBGE),
Brazil's official statistics and geography agency.)
Author: Rafael H. M. Pereira [aut, cre] ,
Daniel Herszenhut [aut] ,
Gabriel Garcia de Almeida [aut] ,
Arthur Bazolli [ctb],
Pedro Milreu Cunha [ctb],
ITpS - Instituto Todos pela Saude [fnd],
Ipea - Instituto de Pesquisa Economica Aplicada [cph, fnd]
Maintainer: Rafael H. M. Pereira <rafa.pereira.br@gmail.com>
Diff between geocodebr versions 0.5.0 dated 2025-12-09 and 0.6.0 dated 2026-01-23
geocodebr-0.5.0/geocodebr/tests/tests_rafa/benchmark_callr.R |only geocodebr-0.5.0/geocodebr/tests/tests_rafa/utils2_noserialize.R |only geocodebr-0.6.0/geocodebr/DESCRIPTION | 12 geocodebr-0.6.0/geocodebr/MD5 | 78 +- geocodebr-0.6.0/geocodebr/NEWS.md | 22 geocodebr-0.6.0/geocodebr/R/busca_por_cep.R | 53 + geocodebr-0.6.0/geocodebr/R/cache.R | 36 - geocodebr-0.6.0/geocodebr/R/create_geocodebr_db.R | 25 geocodebr-0.6.0/geocodebr/R/definir_campos.R | 19 geocodebr-0.6.0/geocodebr/R/download_cnefe.R | 35 - geocodebr-0.6.0/geocodebr/R/geocode.R | 308 +++++----- geocodebr-0.6.0/geocodebr/R/geocode_orig.R | 169 ++--- geocodebr-0.6.0/geocodebr/R/geocode_reverso.R | 95 +-- geocodebr-0.6.0/geocodebr/R/geocodebr-package.R | 43 + geocodebr-0.6.0/geocodebr/R/match_cases.R | 39 - geocodebr-0.6.0/geocodebr/R/match_cases_probabilistic.R | 76 +- geocodebr-0.6.0/geocodebr/R/match_weighted_cases.R | 53 + geocodebr-0.6.0/geocodebr/R/match_weighted_cases_probabilistic.R | 65 +- geocodebr-0.6.0/geocodebr/R/progress_bar.R | 14 geocodebr-0.6.0/geocodebr/R/register_cnefe_tables.R | 68 -- geocodebr-0.6.0/geocodebr/R/string_dist.R | 18 geocodebr-0.6.0/geocodebr/R/trata_empates_geocode_duckdb.R | 46 - geocodebr-0.6.0/geocodebr/R/utils.R | 299 ++++++--- geocodebr-0.6.0/geocodebr/README.md | 2 geocodebr-0.6.0/geocodebr/inst/doc/geocode.R | 52 - geocodebr-0.6.0/geocodebr/inst/doc/geocode.Rmd | 11 geocodebr-0.6.0/geocodebr/inst/doc/geocode.html | 55 + geocodebr-0.6.0/geocodebr/inst/doc/geocode_reverso.R | 38 - geocodebr-0.6.0/geocodebr/inst/doc/geocode_reverso.html | 55 + geocodebr-0.6.0/geocodebr/inst/doc/geocodebr.R | 116 +-- geocodebr-0.6.0/geocodebr/inst/doc/geocodebr.Rmd | 12 geocodebr-0.6.0/geocodebr/inst/doc/geocodebr.html | 26 geocodebr-0.6.0/geocodebr/man/geocode.Rd | 10 geocodebr-0.6.0/geocodebr/man/geocodebr.Rd | 1 geocodebr-0.6.0/geocodebr/man/roxygen/templates/precision_section.R | 10 geocodebr-0.6.0/geocodebr/tests/tests_rafa/benchmark_20k.R |only geocodebr-0.6.0/geocodebr/tests/tests_rafa/benchmark_LIKE.R | 12 geocodebr-0.6.0/geocodebr/tests/tests_rafa/benchmark_reg_adm.R | 274 ++------ geocodebr-0.6.0/geocodebr/tests/tests_rafa/group_for_parallel.R |only geocodebr-0.6.0/geocodebr/tests/testthat/test-geocode.R | 2 geocodebr-0.6.0/geocodebr/vignettes/geocode.Rmd | 11 geocodebr-0.6.0/geocodebr/vignettes/geocodebr.Rmd | 12 42 files changed, 1231 insertions(+), 1041 deletions(-)
Title: High-Performance 'GeoJSON' and 'JSON' Serialization
Description: Converts R data frames and 'sf' spatial objects into 'JSON' and
'GeoJSON' strings. The core encoders are implemented in 'Rust' using the
'extendr' framework and are designed to efficiently serialize large
tabular and spatial datasets. Returns serialized 'JSON' text, allowing
applications such as 'shiny' or web APIs to transfer data to
client-side 'JavaScript' libraries without additional encoding overhead.
Author: Alex Jorion [aut, cre],
The authors of the dependency Rust crates [ctb]
Maintainer: Alex Jorion <alex.jorion@firstzeroenergy.com>
Diff between fastgeojson versions 0.1.2 dated 2026-01-19 and 0.1.3 dated 2026-01-23
DESCRIPTION | 6 ++--- MD5 | 16 ++++++------- NEWS.md | 4 +++ README.md | 5 ---- configure | 38 ++++++++++++++++++++++++++++++-- src/Makevars.in | 59 +++++++++++++++++++++++++++----------------------- src/Makevars.win | 61 ++++++++++++++++++++++++++-------------------------- src/rust/Cargo.lock | 2 - src/rust/Cargo.toml | 2 - 9 files changed, 116 insertions(+), 77 deletions(-)
Title: Create, Stow, and Read Data Packages
Description: Data frame, tibble, or tbl objects are converted to data package objects using specific metadata labels (name, version, title, homepage, description). A data package object ('dpkg') can be written to disk as a 'parquet' file or released to a 'GitHub' repository. Data package objects can be read into R from online repositories and downloaded files are cached locally across R sessions.
Author: Cole Brokamp [aut, cre, cph]
Maintainer: Cole Brokamp <cole@colebrokamp.com>
Diff between dpkg versions 0.6.1 dated 2025-01-08 and 0.6.2 dated 2026-01-23
DESCRIPTION | 14 ++-- MD5 | 26 ++++---- NEWS.md | 7 ++ R/dpkg_release_gh.R | 95 ++++++++++++++++++++++++++------ R/dpkg_tibble.R | 31 +++++++--- R/read_write_dpkg.R | 34 +++++++++-- R/stow.R | 70 +++++++++++++++-------- man/stow.Rd | 20 +++--- tests/testthat/test-check_name.R | 4 - tests/testthat/test-dpkg.R | 19 ++++-- tests/testthat/test-dpkg_tidy_methods.R | 13 +++- tests/testthat/test-read_dpkg.R | 23 ++++++- tests/testthat/test-stow.R | 17 ++++- tests/testthat/test-write_dpkg.R | 5 + 14 files changed, 269 insertions(+), 109 deletions(-)
Title: Predict Carbon Emissions for UK SMEs
Description: Predict Scope 1, 2 and 3 carbon emissions for UK Small and Medium-sized Enterprises (SMEs), using Standard Industrial Classification (SIC) codes and annual turnover data, as well as Scope 1 carbon emissions for UK farms. The 'carbonpredict' package provides single and batch prediction, plotting, and workflow tools for carbon accounting and reporting. The package utilises pre-trained models, leveraging rich classified transaction data to accurately predict Scope 1, 2 and 3 carbon emissions for UK SMEs as well as identifying emissions hotspots. It also provides Scope 1 carbon emissions predictions for UK farms of types: Cereals ex. rice, Dairy, Mixed farming, Sheep and goats, Cattle & buffaloes, Poultry, Animal production and Support for crop production. The methodology used to produce the estimates in this package is fully detailed in the following peer-reviewed publications: Phillpotts, A., Owen. A., Norman, J., Trendl, A., Gathergood, J., Jobst, Norbert., Leake, D. (2025) <doi [...truncated...]
Author: Hamza Suleman [aut, cre, cph],
Alec Phillpotts [ctb, aut],
Jasmine Wells [ctb, aut],
David Leake [ctb, aut]
Maintainer: Hamza Suleman <Hamza.Suleman@lloydsbanking.com>
Diff between carbonpredict versions 2.0.0 dated 2025-10-29 and 2.0.1 dated 2026-01-23
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- README.md | 6 ++++-- 3 files changed, 10 insertions(+), 8 deletions(-)
Title: Vector Helpers
Description: Defines new notions of prototype and size that are used to
provide tools for consistent and well-founded type-coercion and
size-recycling, and are in turn connected to ideas of type- and
size-stability useful for analysing function interfaces.
Author: Hadley Wickham [aut],
Lionel Henry [aut],
Davis Vaughan [aut, cre],
data.table team [cph] and
their contribution to R's order),
Posit Software, PBC [cph, fnd]
Maintainer: Davis Vaughan <davis@posit.co>
Diff between vctrs versions 0.7.0 dated 2026-01-16 and 0.7.1 dated 2026-01-23
DESCRIPTION | 6 ++--- MD5 | 14 ++++++------ NEWS.md | 4 +++ inst/doc/stability.html | 4 +-- src/rlang/env.h | 5 +++- src/type-data-frame.c | 14 +++++++----- src/type-factor.c | 54 +++++++++++++++++++++++++++--------------------- src/version.c | 2 - 8 files changed, 60 insertions(+), 43 deletions(-)
Title: Standardization-Based Effect Estimation with Optional Prior
Covariance Adjustment
Description: The Prognostic Regression Offsets with Propagation of
ERrors (for Treatment Effect Estimation) package facilitates
direct adjustment for experiments and observational studies that
is compatible with a range of study designs and covariance
adjustment strategies. It uses explicit specification of clusters,
blocks and treatment allocations to furnish probability of
assignment-based weights targeting any of several average
treatment effect parameters, and for standard error calculations
reflecting these design parameters. For covariance adjustment of
its Hajek and (one-way) fixed effects estimates, it enables
offsetting the outcome against predictions from a dedicated
covariance model, with standard error calculations propagating
error as appropriate from the covariance model.
Author: Josh Errickson [cre, aut],
Josh Wasserman [aut],
Mark Fredrickson [ctb],
Adam Sales [ctb],
Xinhe Wang [ctb],
Ben Hansen [aut]
Maintainer: Josh Errickson <jerrick@umich.edu>
Diff between propertee versions 1.0.3 dated 2025-10-28 and 1.0.4 dated 2026-01-23
DESCRIPTION | 6 MD5 | 42 +- NAMESPACE | 1 NEWS.md | 6 R/SandwichLayerVariance.R | 413 ++++++++++++++++++++-------- R/as.lmitt.R | 58 ++- R/summary.teeMod.R | 38 ++ R/teeMod.R | 170 +++++++---- build/partial.rdb |binary build/vignette.rds |binary inst/doc/RDD.html | 9 inst/doc/intro-to-propertee.html | 15 - inst/doc/non-binary-treatment.html | 9 man/as_lmitt.Rd | 10 man/cluster_iss.Rd | 58 ++- man/dot-compute_IK_dof.Rd | 48 ++- man/dot-get_dof.Rd | 70 ++++ man/dot-rcorrect.Rd | 28 + tests/testthat/test.SandwichLayerVariance.R | 229 +++++++++++---- tests/testthat/test.summary.teeMod.R | 15 - tests/testthat/test.teeMod.R | 388 +++++++++++++++++--------- tests/testthat/test.variations_of_lm.R | 24 + 22 files changed, 1167 insertions(+), 470 deletions(-)
Title: Model and Learner Summaries for 'mlr3'
Description: Concise and interpretable summaries for machine learning
models and learners of the 'mlr3' ecosystem. The package takes
inspiration from the summary function for (generalized) linear models
but extends it to non-parametric machine learning models, based on
generalization performance, model complexity, feature importances and
effects, and fairness metrics.
Author: Susanne Dandl [aut, cre] ,
Marc Becker [aut] ,
Bernd Bischl [aut] ,
Giuseppe Casalicchio [aut] ,
Ludwig Bothmann [aut]
Maintainer: Susanne Dandl <dandls.datascience@gmail.com>
Diff between mlr3summary versions 0.1.0 dated 2024-04-24 and 0.1.1 dated 2026-01-23
mlr3summary-0.1.0/mlr3summary/README.md |only mlr3summary-0.1.0/mlr3summary/demo |only mlr3summary-0.1.0/mlr3summary/inst/mlr3summary_playground.Rmd |only mlr3summary-0.1.0/mlr3summary/inst/results.rda |only mlr3summary-0.1.0/mlr3summary/inst/results_runtime.rda |only mlr3summary-0.1.0/mlr3summary/inst/runtime.png |only mlr3summary-0.1.0/mlr3summary/inst/runtime_experiments.R |only mlr3summary-0.1.0/mlr3summary/inst/runtimes.txt |only mlr3summary-0.1.0/mlr3summary/inst/runtimes_lm.rda |only mlr3summary-0.1.0/mlr3summary/inst/runtimes_lm_parallel.rda |only mlr3summary-0.1.0/mlr3summary/inst/runtimes_rf.rda |only mlr3summary-0.1.0/mlr3summary/inst/runtimes_rf_parallel.rda |only mlr3summary-0.1.1/mlr3summary/DESCRIPTION | 46 +++-- mlr3summary-0.1.1/mlr3summary/MD5 | 40 +---- mlr3summary-0.1.1/mlr3summary/NAMESPACE | 1 mlr3summary-0.1.1/mlr3summary/NEWS.md |only mlr3summary-0.1.1/mlr3summary/R/bibentries.R | 34 ++-- mlr3summary-0.1.1/mlr3summary/R/credit_data.R | 5 mlr3summary-0.1.1/mlr3summary/R/get_complexity.R | 53 +++--- mlr3summary-0.1.1/mlr3summary/R/get_effects.R | 73 ++++----- mlr3summary-0.1.1/mlr3summary/R/get_importances.R | 74 ++++----- mlr3summary-0.1.1/mlr3summary/R/summary.R | 77 ++++------ mlr3summary-0.1.1/mlr3summary/R/utils.R | 13 - mlr3summary-0.1.1/mlr3summary/R/zzz.R | 3 mlr3summary-0.1.1/mlr3summary/inst/CITATION |only mlr3summary-0.1.1/mlr3summary/man/summary.Learner.Rd | 5 mlr3summary-0.1.1/mlr3summary/man/summary_control.Rd | 2 27 files changed, 202 insertions(+), 224 deletions(-)
Title: Retrieval Functions for USGS and EPA Hydrology and Water Quality
Data
Description: Collection of functions to help retrieve U.S. Geological Survey
and U.S. Environmental Protection Agency water quality and
hydrology data from web services.
Author: Laura DeCicco [aut, cre] ,
Robert Hirsch [aut] ,
David Lorenz [aut],
Jordan Read [ctb],
Jordan Walker [ctb],
Lindsay Platt [ctb],
David Watkins [aut] ,
David Blodgett [aut] ,
Mike Johnson [aut] ,
Aliesha Krall [ctb] ,
Lee Stanish [ctb] ,
Joeseph Zemm [...truncated...]
Maintainer: Laura DeCicco <ldecicco@usgs.gov>
Diff between dataRetrieval versions 2.7.21 dated 2025-08-20 and 2.7.22 dated 2026-01-23
dataRetrieval-2.7.21/dataRetrieval/man/constructUseURL.Rd |only dataRetrieval-2.7.22/dataRetrieval/DESCRIPTION | 15 dataRetrieval-2.7.22/dataRetrieval/MD5 | 166 +-- dataRetrieval-2.7.22/dataRetrieval/NAMESPACE | 4 dataRetrieval-2.7.22/dataRetrieval/NEWS | 17 dataRetrieval-2.7.22/dataRetrieval/R/AAA.R | 12 dataRetrieval-2.7.22/dataRetrieval/R/constructNWISURL.R | 63 - dataRetrieval-2.7.22/dataRetrieval/R/construct_api_requests.R | 324 +----- dataRetrieval-2.7.22/dataRetrieval/R/dataRetrievals-package.R | 46 dataRetrieval-2.7.22/dataRetrieval/R/deal_with_empty.R |only dataRetrieval-2.7.22/dataRetrieval/R/findNLDI.R | 24 dataRetrieval-2.7.22/dataRetrieval/R/get_ogc_data.R |only dataRetrieval-2.7.22/dataRetrieval/R/get_ogc_documentation.R |only dataRetrieval-2.7.22/dataRetrieval/R/readNWISpCode.R | 1 dataRetrieval-2.7.22/dataRetrieval/R/readNWISunit.R | 126 -- dataRetrieval-2.7.22/dataRetrieval/R/read_waterdata.R | 35 dataRetrieval-2.7.22/dataRetrieval/R/read_waterdata_continuous.R |only dataRetrieval-2.7.22/dataRetrieval/R/read_waterdata_daily.R | 85 - dataRetrieval-2.7.22/dataRetrieval/R/read_waterdata_field_measurements.R | 49 dataRetrieval-2.7.22/dataRetrieval/R/read_waterdata_latest_continuous.R | 46 dataRetrieval-2.7.22/dataRetrieval/R/read_waterdata_latest_daily.R |only dataRetrieval-2.7.22/dataRetrieval/R/read_waterdata_metadata.R | 64 - dataRetrieval-2.7.22/dataRetrieval/R/read_waterdata_monitoring_location.R | 95 - dataRetrieval-2.7.22/dataRetrieval/R/read_waterdata_parameter_codes.R | 59 - dataRetrieval-2.7.22/dataRetrieval/R/read_waterdata_samples.R | 4 dataRetrieval-2.7.22/dataRetrieval/R/read_waterdata_ts_meta.R | 67 - dataRetrieval-2.7.22/dataRetrieval/R/rejigger_cols.R |only dataRetrieval-2.7.22/dataRetrieval/R/setAccess.R | 2 dataRetrieval-2.7.22/dataRetrieval/R/sysdata.rda |binary dataRetrieval-2.7.22/dataRetrieval/R/walk_pages.R | 318 +---- dataRetrieval-2.7.22/dataRetrieval/inst/CITATION | 5 dataRetrieval-2.7.22/dataRetrieval/inst/doc/dataRetrieval.R | 79 - dataRetrieval-2.7.22/dataRetrieval/inst/doc/dataRetrieval.Rmd | 164 --- dataRetrieval-2.7.22/dataRetrieval/inst/doc/dataRetrieval.html | 533 +++------- dataRetrieval-2.7.22/dataRetrieval/inst/extdata/temperatureAndFlow.RData |binary dataRetrieval-2.7.22/dataRetrieval/man/check_OGC_requests.Rd | 4 dataRetrieval-2.7.22/dataRetrieval/man/check_waterdata_sample_params.Rd | 2 dataRetrieval-2.7.22/dataRetrieval/man/constructNWISURL.Rd | 4 dataRetrieval-2.7.22/dataRetrieval/man/construct_api_requests.Rd | 8 dataRetrieval-2.7.22/dataRetrieval/man/construct_waterdata_sample_request.Rd | 2 dataRetrieval-2.7.22/dataRetrieval/man/countyCd.Rd | 9 dataRetrieval-2.7.22/dataRetrieval/man/countyCdLookup.Rd | 2 dataRetrieval-2.7.22/dataRetrieval/man/findNLDI.Rd | 2 dataRetrieval-2.7.22/dataRetrieval/man/getWebServiceData.Rd | 2 dataRetrieval-2.7.22/dataRetrieval/man/get_nldi_sources.Rd | 2 dataRetrieval-2.7.22/dataRetrieval/man/get_ogc_params.Rd |only dataRetrieval-2.7.22/dataRetrieval/man/importNGWMN.Rd | 2 dataRetrieval-2.7.22/dataRetrieval/man/importRDB1.Rd | 2 dataRetrieval-2.7.22/dataRetrieval/man/importWQP.Rd | 2 dataRetrieval-2.7.22/dataRetrieval/man/importWaterML1.Rd | 2 dataRetrieval-2.7.22/dataRetrieval/man/importWaterML2.Rd | 2 dataRetrieval-2.7.22/dataRetrieval/man/parameterCdFile.Rd | 9 dataRetrieval-2.7.22/dataRetrieval/man/parse_WQP.Rd | 2 dataRetrieval-2.7.22/dataRetrieval/man/readNGWMNdata.Rd | 2 dataRetrieval-2.7.22/dataRetrieval/man/readNGWMNlevels.Rd | 2 dataRetrieval-2.7.22/dataRetrieval/man/readNGWMNsites.Rd | 2 dataRetrieval-2.7.22/dataRetrieval/man/readNWISdata.Rd | 2 dataRetrieval-2.7.22/dataRetrieval/man/readNWISgwl.Rd | 16 dataRetrieval-2.7.22/dataRetrieval/man/readNWISmeas.Rd | 9 dataRetrieval-2.7.22/dataRetrieval/man/readNWISpCode.Rd | 1 dataRetrieval-2.7.22/dataRetrieval/man/readNWISpeak.Rd | 7 dataRetrieval-2.7.22/dataRetrieval/man/readNWISrating.Rd | 3 dataRetrieval-2.7.22/dataRetrieval/man/readNWISstat.Rd | 7 dataRetrieval-2.7.22/dataRetrieval/man/readNWISuse.Rd | 30 dataRetrieval-2.7.22/dataRetrieval/man/readNWISuv.Rd | 20 dataRetrieval-2.7.22/dataRetrieval/man/readWQPdata.Rd | 2 dataRetrieval-2.7.22/dataRetrieval/man/readWQPqw.Rd | 2 dataRetrieval-2.7.22/dataRetrieval/man/readWQPsummary.Rd | 2 dataRetrieval-2.7.22/dataRetrieval/man/read_waterdata.Rd | 5 dataRetrieval-2.7.22/dataRetrieval/man/read_waterdata_continuous.Rd |only dataRetrieval-2.7.22/dataRetrieval/man/read_waterdata_daily.Rd | 55 - dataRetrieval-2.7.22/dataRetrieval/man/read_waterdata_field_measurements.Rd | 36 dataRetrieval-2.7.22/dataRetrieval/man/read_waterdata_latest_continuous.Rd | 40 dataRetrieval-2.7.22/dataRetrieval/man/read_waterdata_latest_daily.Rd |only dataRetrieval-2.7.22/dataRetrieval/man/read_waterdata_metadata.Rd | 18 dataRetrieval-2.7.22/dataRetrieval/man/read_waterdata_monitoring_location.Rd | 61 - dataRetrieval-2.7.22/dataRetrieval/man/read_waterdata_parameter_codes.Rd | 13 dataRetrieval-2.7.22/dataRetrieval/man/read_waterdata_samples.Rd | 2 dataRetrieval-2.7.22/dataRetrieval/man/read_waterdata_ts_meta.Rd | 59 - dataRetrieval-2.7.22/dataRetrieval/man/stateCd.Rd | 9 dataRetrieval-2.7.22/dataRetrieval/man/stateCdLookup.Rd | 2 dataRetrieval-2.7.22/dataRetrieval/man/summarize_waterdata_samples.Rd | 2 dataRetrieval-2.7.22/dataRetrieval/man/whatWQPdata.Rd | 2 dataRetrieval-2.7.22/dataRetrieval/man/wqpSpecials.Rd | 2 dataRetrieval-2.7.22/dataRetrieval/man/wqp_check_status.Rd | 2 dataRetrieval-2.7.22/dataRetrieval/tests/testthat/tests_general.R | 70 - dataRetrieval-2.7.22/dataRetrieval/tests/testthat/tests_imports.R | 60 - dataRetrieval-2.7.22/dataRetrieval/tests/testthat/tests_userFriendly_fxns.R | 178 +-- dataRetrieval-2.7.22/dataRetrieval/vignettes/dataRetrieval.Rmd | 164 --- 89 files changed, 1257 insertions(+), 2091 deletions(-)
Title: "Risk Model Regression and Analysis with Complex Non-Linear
Models"
Description: Performs survival analysis using general non-linear models. Risk models can be the sum or product of terms. Each term is the product of exponential/linear functions of covariates. Additionally sub-terms can be defined as a sum of exponential, linear threshold, and step functions. Cox Proportional hazards <https://en.wikipedia.org/wiki/Proportional_hazards_model>, Poisson <https://en.wikipedia.org/wiki/Poisson_regression>, and Fine-Gray competing risks <https://www.publichealth.columbia.edu/research/population-health-methods/competing-risk-analysis> regression are supported. This work was sponsored by NASA Grants 80NSSC19M0161 and 80NSSC23M0129 through a subcontract from the National Council on Radiation Protection and Measurements (NCRP). The computing for this project was performed on the Beocat Research Cluster at Kansas State University, which is funded in part by NSF grants CNS-1006860, EPS-1006860, EPS-0919443, ACI-1440548, CHE-1726332, and NIH P20GM113109.
Author: Eric Giunta [aut, cre] ,
Amir Bahadori [ctb] ,
Dan Andresen [ctb] ,
Linda Walsh [ctb] ,
Benjamin French [ctb] ,
Lawrence Dauer [ctb] ,
John Boice Jr [ctb] ,
Kansas State University [cph],
NASA [fnd],
NCRP [fnd],
NRC [fnd]
Maintainer: Eric Giunta <egiunta@ksu.edu>
Diff between Colossus versions 1.4.6 dated 2025-12-16 and 1.4.9 dated 2026-01-23
DESCRIPTION | 10 MD5 | 235 ++++----- NAMESPACE | 20 NEWS.md | 16 R/BasicRun.R | 486 ++++++++++++++++-- R/CaseControl_Regression.R | 30 - R/Cox_Regression.R | 72 +- R/LogitRegression.R | 10 R/ObjValidate.R | 107 +--- R/PlotTypes.R | 50 + R/Poisson_Regression.R | 238 ++++----- R/RcppExports.R | 253 ++++----- R/SurvTypes.R | 172 ++++-- R/Utility.R | 385 ++++++++------ R/utils-roxygen.R | 17 configure | 2 inst/WORDLIST | 1 inst/doc/Alt_Run_Opt.R | 9 inst/doc/Alt_Run_Opt.Rmd | 29 - inst/doc/Alt_Run_Opt.html | 127 ++-- inst/doc/Control_Options.Rmd | 6 inst/doc/Control_Options.html | 32 + inst/doc/Dose_Formula_Inputs.R | 1 inst/doc/Dose_Formula_Inputs.Rmd | 20 inst/doc/Dose_Formula_Inputs.html | 51 + inst/doc/Equation_Expression.R | 11 inst/doc/Equation_Expression.Rmd | 52 + inst/doc/Equation_Expression.html | 141 +---- inst/doc/Excess_and_Predicted_Cases.R | 1 inst/doc/Excess_and_Predicted_Cases.Rmd | 5 inst/doc/Excess_and_Predicted_Cases.html | 9 inst/doc/Grad_Hess.R | 38 - inst/doc/Grad_Hess.Rmd | 45 - inst/doc/Grad_Hess.html | 146 ++--- inst/doc/Logistic.R | 3 inst/doc/Logistic.Rmd | 3 inst/doc/Logistic.html | 165 +++--- inst/doc/Matched_Case_Control.R | 3 inst/doc/Matched_Case_Control.Rmd | 3 inst/doc/Matched_Case_Control.html | 113 ++-- inst/doc/Multi_Realization.R | 17 inst/doc/Multi_Realization.Rmd | 17 inst/doc/Multi_Realization.html | 21 inst/doc/Plotting_And_Analysis.R | 123 ++-- inst/doc/Plotting_And_Analysis.Rmd | 125 ++-- inst/doc/Plotting_And_Analysis.html | 139 ++--- inst/doc/SMR_Analysis.R | 10 inst/doc/SMR_Analysis.Rmd | 12 inst/doc/SMR_Analysis.html | 90 ++- inst/doc/Script_Comparison_Epicure.R | 9 inst/doc/Script_Comparison_Epicure.Rmd | 9 inst/doc/Script_Comparison_Epicure.html | 15 inst/doc/Starting-Description.R | 32 - inst/doc/Starting-Description.Rmd | 73 -- inst/doc/Starting-Description.html | 231 +++----- inst/doc/Time_Dep_Cov.R | 1 inst/doc/Time_Dep_Cov.Rmd | 5 inst/doc/Time_Dep_Cov.html | 13 inst/doc/Wald_and_Log_Bound.R | 14 inst/doc/Wald_and_Log_Bound.Rmd | 36 - inst/doc/Wald_and_Log_Bound.html | 287 +++++----- inst/doc/count_time_tables.R | 1 inst/doc/count_time_tables.Rmd | 3 inst/doc/count_time_tables.html | 11 man/Event_Time_Gen.Rd | 21 man/Likelihood_Ratio_Test.Rd | 17 man/get_form_joint.Rd | 4 man/plot.coxres.Rd | 7 man/plotMartingale.Rd |only man/plotMartingale.coxres.Rd |only man/plotMartingale.default.Rd |only man/plotRisk.Rd |only man/plotRisk.coxres.Rd |only man/plotRisk.default.Rd |only man/plotSchoenfeld.Rd |only man/plotSchoenfeld.coxres.Rd |only man/plotSchoenfeld.default.Rd |only man/plotSurvival.Rd |only man/plotSurvival.coxres.Rd |only man/plotSurvival.default.Rd |only src/Calc_Repeated.cpp | 809 +++++-------------------------- src/Calc_Repeated.h | 18 src/Grouping.cpp |only src/Grouping.h |only src/Main_Bound.cpp | 176 +++--- src/Main_Bound.h | 6 src/Main_Functions.cpp | 190 +++++-- src/Main_Functions.h | 2 src/Main_Multi.cpp | 156 +++-- src/Main_Multi.h | 4 src/Omnibus_Pieces.cpp | 334 +++++++----- src/Omnibus_Pieces.h | 13 src/Plot_Extensions.cpp | 73 ++ src/Plot_Extensions.h | 4 src/R_Interface.cpp | 138 ----- src/R_Interface.h | 12 src/RcppExports.cpp | 54 +- src/Step_Calc.cpp | 2 src/Subterms_Risk.cpp | 72 -- src/Subterms_Risk.h | 6 tests/testthat/temp.R |only tests/testthat/test-Assigned.R | 26 tests/testthat/test-Cox_Plot.R | 128 +++- tests/testthat/test-Cox_Regression.R | 4 tests/testthat/test-Formula.R | 72 ++ tests/testthat/test-Logit.R | 4 tests/testthat/test-Multidose.R | 6 tests/testthat/test-Omnibus.R | 68 +- tests/testthat/test-Poisson_Regression.R | 29 - tests/testthat/test-Utility.R | 59 +- vignettes/Alt_Run_Opt.Rmd | 29 - vignettes/Control_Options.Rmd | 6 vignettes/Dose_Formula_Inputs.Rmd | 20 vignettes/Equation_Expression.Rmd | 52 + vignettes/Excess_and_Predicted_Cases.Rmd | 5 vignettes/Grad_Hess.Rmd | 45 - vignettes/Logistic.Rmd | 3 vignettes/Matched_Case_Control.Rmd | 3 vignettes/Multi_Realization.Rmd | 17 vignettes/Plotting_And_Analysis.Rmd | 125 ++-- vignettes/SMR_Analysis.Rmd | 12 vignettes/Script_Comparison_Epicure.Rmd | 9 vignettes/Starting-Description.Rmd | 73 -- vignettes/Time_Dep_Cov.Rmd | 5 vignettes/Wald_and_Log_Bound.Rmd | 36 - vignettes/count_time_tables.Rmd | 3 126 files changed, 3886 insertions(+), 3482 deletions(-)
Title: Vaccine Extension Package for ADaM in 'R' Asset Library
Description: Programming vaccine specific Clinical Data Interchange
Standards Consortium (CDISC) compliant Analysis Data Model (ADaM)
datasets in 'R'. Flat model is followed as per Center for Biologics
Evaluation and Research (CBER) guidelines for creating vaccine
specific domains. ADaM datasets are a mandatory part of any New Drug
or Biologics License Application submitted to the United States Food
and Drug Administration (FDA). Analysis derivations are implemented in
accordance with the "Analysis Data Model Implementation Guide" (CDISC
Analysis Data Model Team (2021),
<https://www.cdisc.org/standards/foundational/adam/adamig-v1-3-release-package>).
The package is an extension package of the 'admiral' package.
Author: Arjun Rubalingam [aut, cre],
Sukalpo Saha [aut, ctb],
Ben Straub [aut],
Vikram S [aut],
Dhivya Kanagaraj [aut],
Federico Baratin [aut],
Yamini Purna Bollu [aut],
Ilse Augustyns [aut],
Kalyani Bodicherla [aut],
Hilde Delanghe [aut],
Lee Armishaw [aut] [...truncated...]
Maintainer: Arjun Rubalingam <arjun.rubalingam@pfizer.com>
Diff between admiralvaccine versions 0.5.0 dated 2025-09-18 and 0.6.0 dated 2026-01-23
DESCRIPTION | 18 MD5 | 64 NAMESPACE | 2 NEWS.md | 13 R/admiralvaccine.R | 1 R/derive_diam_to_sev_records.R | 2 R/derive_var_aval_adis.R | 10 R/derive_vars_crit.R | 2 R/derive_vars_event_flag.R | 4 R/derive_vars_max_flag.R | 6 R/derive_vars_merged_vaccine.R | 2 R/derive_vars_vaxdt.R | 2 R/post_process_reacto.R | 2 README.md | 2 build/vignette.rds |binary inst/WORDLIST | 154 inst/doc/adce.R | 344 +- inst/doc/adce.html | 2811 ++++++++-------- inst/doc/adface.R | 710 ++-- inst/doc/adface.html | 4548 +++++++++++++-------------- inst/doc/adis.R | 882 ++--- inst/doc/adis.html | 4277 ++++++++++++------------- inst/doc/admiralvaccine.R | 78 inst/doc/admiralvaccine.Rmd | 8 inst/doc/admiralvaccine.html | 834 ++-- inst/doc/adsl.R | 294 - inst/doc/adsl.html | 1591 ++++----- tests/testthat/test-derive_fever_records.R | 5 tests/testthat/test-derive_var_aval_adis.R | 118 tests/testthat/test-derive_vars_event_flag.R | 2 tests/testthat/test-derive_vars_params.R | 2 tests/testthat/test-derive_vars_vaxdt.R | 13 vignettes/admiralvaccine.Rmd | 8 33 files changed, 8414 insertions(+), 8395 deletions(-)
More information about admiralvaccine at CRAN
Permanent link
Title: Easily Access and Maintain Time-Based Versioned Data
(Slowly-Changing-Dimension)
Description: A collection of functions that enable easy access and updating of a database of data over time.
More specifically, the package facilitates type-2 history for data-warehouses and provides a number
of Quality of life improvements for working on SQL databases with R.
For reference see Ralph Kimball and Margy Ross (2013, ISBN 9781118530801).
Author: Rasmus Skytte Randloev [aut, cre, rev] ,
Marcus Munch Gruenewald [aut] ,
Lasse Engbo Christiansen [rev, ctb] ,
Sofia Myrup Otero [rev],
Kim Daniel Jacobsen [ctb],
Statens Serum Institut [cph, fnd]
Maintainer: Rasmus Skytte Randloev <rske@ssi.dk>
Diff between SCDB versions 0.5.2 dated 2026-01-08 and 0.6.0 dated 2026-01-23
DESCRIPTION | 6 MD5 | 39 + NAMESPACE | 2 NEWS.md | 690 +++++++++++++++++----------------- R/0_miscellaneous.R | 5 R/Logger.R | 43 +- R/delta-loading.R |only R/digest_to_checksum.R | 31 - R/update_snapshot.R | 61 ++- build/vignette.rds |binary inst/WORDLIST | 179 ++++++++ inst/doc/benchmarks.html | 4 inst/doc/delta-loading.R |only inst/doc/delta-loading.Rmd |only inst/doc/delta-loading.html |only inst/extdata/benchmarks.rds |binary man/Logger.Rd | 19 man/LoggerNull.Rd | 1 man/delta_loading.Rd |only man/digest_to_checksum.Rd | 5 tests/testthat/setup.R | 2 tests/testthat/test-delta-loading.R |only tests/testthat/test-update_snapshot.R | 79 +++ vignettes/delta-loading.Rmd |only 24 files changed, 741 insertions(+), 425 deletions(-)
Title: Nonparametric Bootstrap and Permutation Tests
Description: Robust nonparametric bootstrap and permutation tests for goodness of fit, distribution equivalence, location, correlation, and regression problems, as described in Helwig (2019a) <doi:10.1002/wics.1457> and Helwig (2019b) <doi:10.1016/j.neuroimage.2019.116030>. Univariate and multivariate tests are supported. For each problem, exact tests and Monte Carlo approximations are available. Five different nonparametric bootstrap confidence intervals are implemented. Parallel computing is implemented via the 'parallel' package.
Author: Nathaniel E. Helwig [aut, cre]
Maintainer: Nathaniel E. Helwig <helwig@umn.edu>
Diff between nptest versions 1.1 dated 2023-04-14 and 1.2 dated 2026-01-23
nptest-1.1/nptest/man/nptest-package.Rd |only nptest-1.2/nptest/ChangeLog | 30 +++++++++ nptest-1.2/nptest/DESCRIPTION | 15 ++-- nptest-1.2/nptest/MD5 | 48 +++++++++----- nptest-1.2/nptest/NAMESPACE | 13 +++ nptest-1.2/nptest/R/np.aov.test.R |only nptest-1.2/nptest/R/np.boot.R | 20 +++++- nptest-1.2/nptest/R/np.cdf.test.R |only nptest-1.2/nptest/R/np.cor.test.R | 2 nptest-1.2/nptest/R/np.lm.test.R |only nptest-1.2/nptest/R/np.loc.test.R | 4 - nptest-1.2/nptest/R/np.reg.test.R | 2 nptest-1.2/nptest/R/plot.np.aov.test.R |only nptest-1.2/nptest/R/plot.np.cdf.test.R |only nptest-1.2/nptest/R/plot.np.lm.test.R |only nptest-1.2/nptest/R/print.np.aov.test.R |only nptest-1.2/nptest/R/print.np.cdf.test.R |only nptest-1.2/nptest/R/print.np.lm.test.R |only nptest-1.2/nptest/R/rand.test.aov1.R |only nptest-1.2/nptest/R/rand.test.aov2.R |only nptest-1.2/nptest/R/rand.test.cdf1.R |only nptest-1.2/nptest/R/rand.test.cdf2.R |only nptest-1.2/nptest/R/rand.test.lm0.R |only nptest-1.2/nptest/R/rand.test.lm1.R | 8 +- nptest-1.2/nptest/R/rand.test.lm2.R | 6 - nptest-1.2/nptest/build/partial.rdb |binary nptest-1.2/nptest/man/np.aov.test.Rd |only nptest-1.2/nptest/man/np.boot.Rd | 101 +++++++++++++++++++++---------- nptest-1.2/nptest/man/np.cdf.test.Rd |only nptest-1.2/nptest/man/np.lm.test.Rd |only nptest-1.2/nptest/man/np.loc.test.Rd | 1 nptest-1.2/nptest/man/np.reg.test.Rd | 5 + nptest-1.2/nptest/man/nptest-internal.Rd | 26 +++++++ nptest-1.2/nptest/man/plot.Rd | 29 ++++++++ 34 files changed, 237 insertions(+), 73 deletions(-)
Title: Integration to 'Apache' 'Arrow'
Description: 'Apache' 'Arrow' <https://arrow.apache.org/> is a cross-language
development platform for in-memory data. It specifies a standardized
language-independent columnar memory format for flat and hierarchical data,
organized for efficient analytic operations on modern hardware. This
package provides an interface to the 'Arrow C++' library.
Author: Neal Richardson [aut],
Ian Cook [aut],
Nic Crane [aut],
Dewey Dunnington [aut] ,
Romain Francois [aut] ,
Jonathan Keane [aut, cre],
Bryce Mecum [aut],
Dragoș Moldovan-Gruenfeld [aut],
Jeroen Ooms [aut],
Jacob Wujciak-Jens [aut],
Javier Luraschi [ctb], [...truncated...]
Maintainer: Jonathan Keane <jkeane@gmail.com>
Diff between arrow versions 22.0.0.1 dated 2025-12-23 and 23.0.0 dated 2026-01-23
arrow-22.0.0.1/arrow/tools/checksums/r-libarrow-darwin-arm64-openssl-1.1-22.0.0.zip.sha512 |only arrow-22.0.0.1/arrow/tools/checksums/r-libarrow-darwin-arm64-openssl-3.0-22.0.0.zip.sha512 |only arrow-22.0.0.1/arrow/tools/checksums/r-libarrow-darwin-x86_64-openssl-1.1-22.0.0.zip.sha512 |only arrow-22.0.0.1/arrow/tools/checksums/r-libarrow-darwin-x86_64-openssl-3.0-22.0.0.zip.sha512 |only arrow-22.0.0.1/arrow/tools/checksums/r-libarrow-linux-x86_64-openssl-1.0-22.0.0.zip.sha512 |only arrow-22.0.0.1/arrow/tools/checksums/r-libarrow-linux-x86_64-openssl-1.1-22.0.0.zip.sha512 |only arrow-22.0.0.1/arrow/tools/checksums/r-libarrow-linux-x86_64-openssl-3.0-22.0.0.zip.sha512 |only arrow-22.0.0.1/arrow/tools/checksums/r-libarrow-windows-x86_64-22.0.0.zip.sha512 |only arrow-22.0.0.1/arrow/tools/cpp/src/arrow/util/bpacking64_codegen.py |only arrow-22.0.0.1/arrow/tools/cpp/src/arrow/util/bpacking64_default_internal.h |only arrow-22.0.0.1/arrow/tools/cpp/src/arrow/util/bpacking_avx2.cc |only arrow-22.0.0.1/arrow/tools/cpp/src/arrow/util/bpacking_avx2_internal.h |only arrow-22.0.0.1/arrow/tools/cpp/src/arrow/util/bpacking_avx512.cc |only arrow-22.0.0.1/arrow/tools/cpp/src/arrow/util/bpacking_avx512_internal.h |only arrow-22.0.0.1/arrow/tools/cpp/src/arrow/util/bpacking_default_internal.h |only arrow-22.0.0.1/arrow/tools/cpp/src/arrow/util/bpacking_neon.cc |only arrow-22.0.0.1/arrow/tools/cpp/src/arrow/util/bpacking_neon_internal.h |only arrow-22.0.0.1/arrow/tools/cpp/src/arrow/vendored/fast_float/simple_decimal_conversion.h |only arrow-22.0.0.1/arrow/tools/cpp/src/arrow/vendored/portable-snippets/safe-math.h |only arrow-23.0.0/arrow/DESCRIPTION | 8 arrow-23.0.0/arrow/MD5 | 690 arrow-23.0.0/arrow/NEWS.md | 17 arrow-23.0.0/arrow/R/array-data.R | 3 arrow-23.0.0/arrow/R/array.R | 27 arrow-23.0.0/arrow/R/arrow-datum.R | 17 arrow-23.0.0/arrow/R/arrow-info.R | 54 arrow-23.0.0/arrow/R/arrow-object.R | 9 arrow-23.0.0/arrow/R/arrow-package.R | 11 arrow-23.0.0/arrow/R/arrow-tabular.R | 3 arrow-23.0.0/arrow/R/arrowExports.R | 8 arrow-23.0.0/arrow/R/buffer.R | 3 arrow-23.0.0/arrow/R/chunked-array.R | 3 arrow-23.0.0/arrow/R/compression.R | 6 arrow-23.0.0/arrow/R/compute.R | 26 arrow-23.0.0/arrow/R/csv.R | 316 arrow-23.0.0/arrow/R/dataset-factory.R | 43 arrow-23.0.0/arrow/R/dataset-format.R | 47 arrow-23.0.0/arrow/R/dataset-partition.R | 6 arrow-23.0.0/arrow/R/dataset-scan.R | 22 arrow-23.0.0/arrow/R/dataset-write.R | 156 arrow-23.0.0/arrow/R/dataset.R | 158 arrow-23.0.0/arrow/R/dictionary.R | 36 arrow-23.0.0/arrow/R/dplyr-across.R | 22 arrow-23.0.0/arrow/R/dplyr-arrange.R | 4 arrow-23.0.0/arrow/R/dplyr-by.R | 18 arrow-23.0.0/arrow/R/dplyr-collect.R | 11 arrow-23.0.0/arrow/R/dplyr-count.R | 4 arrow-23.0.0/arrow/R/dplyr-datetime-helpers.R | 38 arrow-23.0.0/arrow/R/dplyr-eval.R | 9 arrow-23.0.0/arrow/R/dplyr-filter.R | 2 arrow-23.0.0/arrow/R/dplyr-funcs-conditional.R | 92 arrow-23.0.0/arrow/R/dplyr-funcs-datetime.R | 247 arrow-23.0.0/arrow/R/dplyr-funcs-doc.R | 3 arrow-23.0.0/arrow/R/dplyr-funcs-simple.R | 1 arrow-23.0.0/arrow/R/dplyr-funcs-string.R | 119 arrow-23.0.0/arrow/R/dplyr-funcs-type.R | 123 arrow-23.0.0/arrow/R/dplyr-funcs.R | 5 arrow-23.0.0/arrow/R/dplyr-glimpse.R | 16 arrow-23.0.0/arrow/R/dplyr-group-by.R | 22 arrow-23.0.0/arrow/R/dplyr-join.R | 65 arrow-23.0.0/arrow/R/dplyr-mutate.R | 21 arrow-23.0.0/arrow/R/dplyr-select.R | 1 arrow-23.0.0/arrow/R/dplyr-slice.R | 9 arrow-23.0.0/arrow/R/dplyr-summarize.R | 4 arrow-23.0.0/arrow/R/dplyr.R | 20 arrow-23.0.0/arrow/R/duckdb.R | 32 arrow-23.0.0/arrow/R/enums.R | 102 arrow-23.0.0/arrow/R/expression.R | 19 arrow-23.0.0/arrow/R/extension.R | 27 arrow-23.0.0/arrow/R/feather.R | 37 arrow-23.0.0/arrow/R/field.R | 3 arrow-23.0.0/arrow/R/filesystem.R | 50 arrow-23.0.0/arrow/R/install-arrow.R | 28 arrow-23.0.0/arrow/R/io.R | 25 arrow-23.0.0/arrow/R/json.R | 21 arrow-23.0.0/arrow/R/memory-pool.R | 3 arrow-23.0.0/arrow/R/message.R | 36 arrow-23.0.0/arrow/R/metadata.R | 25 arrow-23.0.0/arrow/R/parquet.R | 145 arrow-23.0.0/arrow/R/query-engine.R | 9 arrow-23.0.0/arrow/R/record-batch-reader.R | 7 arrow-23.0.0/arrow/R/record-batch-writer.R | 28 arrow-23.0.0/arrow/R/record-batch.R | 13 arrow-23.0.0/arrow/R/scalar.R | 6 arrow-23.0.0/arrow/R/schema.R | 8 arrow-23.0.0/arrow/R/table.R | 23 arrow-23.0.0/arrow/R/type.R | 102 arrow-23.0.0/arrow/R/udf.R | 3 arrow-23.0.0/arrow/R/util.R | 21 arrow-23.0.0/arrow/README.md | 15 arrow-23.0.0/arrow/configure | 22 arrow-23.0.0/arrow/configure.win | 10 arrow-23.0.0/arrow/man/DictionaryType.Rd | 35 arrow-23.0.0/arrow/man/FixedWidthType.Rd | 17 arrow-23.0.0/arrow/man/Message.Rd | 19 arrow-23.0.0/arrow/man/MessageReader.Rd | 17 arrow-23.0.0/arrow/man/acero.Rd | 3 arrow-23.0.0/arrow/man/concat_tables.Rd | 7 arrow-23.0.0/arrow/man/gs_bucket.Rd | 2 arrow-23.0.0/arrow/man/s3_bucket.Rd | 4 arrow-23.0.0/arrow/man/write_dataset.Rd | 6 arrow-23.0.0/arrow/src/Makevars.in | 2 arrow-23.0.0/arrow/src/Makevars.ucrt | 2 arrow-23.0.0/arrow/src/altrep.cpp | 67 arrow-23.0.0/arrow/src/array_to_vector.cpp | 1 arrow-23.0.0/arrow/src/arrowExports.cpp | 23 arrow-23.0.0/arrow/src/arrow_cpp11.h | 16 arrow-23.0.0/arrow/src/arrow_types.h | 2 arrow-23.0.0/arrow/src/compute-exec.cpp | 3 arrow-23.0.0/arrow/src/compute.cpp | 9 arrow-23.0.0/arrow/src/datatype.cpp | 6 arrow-23.0.0/arrow/tests/testthat/helper-data.R | 22 arrow-23.0.0/arrow/tests/testthat/helper-expectation.R | 13 arrow-23.0.0/arrow/tests/testthat/helper-skip.R | 4 arrow-23.0.0/arrow/tests/testthat/test-Array.R | 14 arrow-23.0.0/arrow/tests/testthat/test-RecordBatch.R | 7 arrow-23.0.0/arrow/tests/testthat/test-Table.R | 17 arrow-23.0.0/arrow/tests/testthat/test-altrep.R | 9 arrow-23.0.0/arrow/tests/testthat/test-backwards-compatibility.R | 4 arrow-23.0.0/arrow/tests/testthat/test-buffer.R | 3 arrow-23.0.0/arrow/tests/testthat/test-chunked-array.R | 28 arrow-23.0.0/arrow/tests/testthat/test-compute-arith.R | 4 arrow-23.0.0/arrow/tests/testthat/test-compute-no-bindings.R | 1 arrow-23.0.0/arrow/tests/testthat/test-compute-sort.R | 1 arrow-23.0.0/arrow/tests/testthat/test-compute-vector.R | 12 arrow-23.0.0/arrow/tests/testthat/test-config.R | 2 arrow-23.0.0/arrow/tests/testthat/test-csv.R | 15 arrow-23.0.0/arrow/tests/testthat/test-dataset-csv.R | 90 arrow-23.0.0/arrow/tests/testthat/test-dataset-write.R | 11 arrow-23.0.0/arrow/tests/testthat/test-dataset.R | 75 arrow-23.0.0/arrow/tests/testthat/test-dplyr-across.R | 22 arrow-23.0.0/arrow/tests/testthat/test-dplyr-arrange.R | 8 arrow-23.0.0/arrow/tests/testthat/test-dplyr-count.R | 1 arrow-23.0.0/arrow/tests/testthat/test-dplyr-filter.R | 8 arrow-23.0.0/arrow/tests/testthat/test-dplyr-funcs-conditional.R | 55 arrow-23.0.0/arrow/tests/testthat/test-dplyr-funcs-datetime.R | 797 arrow-23.0.0/arrow/tests/testthat/test-dplyr-funcs-math.R | 2 arrow-23.0.0/arrow/tests/testthat/test-dplyr-funcs-string.R | 89 arrow-23.0.0/arrow/tests/testthat/test-dplyr-funcs-type.R | 183 arrow-23.0.0/arrow/tests/testthat/test-dplyr-group-by.R | 32 arrow-23.0.0/arrow/tests/testthat/test-dplyr-join.R | 111 arrow-23.0.0/arrow/tests/testthat/test-dplyr-slice.R | 10 arrow-23.0.0/arrow/tests/testthat/test-duckdb.R | 19 arrow-23.0.0/arrow/tests/testthat/test-expression.R | 1 arrow-23.0.0/arrow/tests/testthat/test-field.R | 1 arrow-23.0.0/arrow/tests/testthat/test-filesystem.R | 14 arrow-23.0.0/arrow/tests/testthat/test-gcs.R | 36 arrow-23.0.0/arrow/tests/testthat/test-json.R | 65 arrow-23.0.0/arrow/tests/testthat/test-message-reader.R | 1 arrow-23.0.0/arrow/tests/testthat/test-message.R | 1 arrow-23.0.0/arrow/tests/testthat/test-metadata.R | 49 arrow-23.0.0/arrow/tests/testthat/test-parquet.R | 5 arrow-23.0.0/arrow/tests/testthat/test-query-engine.R | 7 arrow-23.0.0/arrow/tests/testthat/test-read-record-batch.R | 4 arrow-23.0.0/arrow/tests/testthat/test-read-write.R | 1 arrow-23.0.0/arrow/tests/testthat/test-s3-minio.R | 4 arrow-23.0.0/arrow/tests/testthat/test-s3.R | 10 arrow-23.0.0/arrow/tests/testthat/test-scalar.R | 1 arrow-23.0.0/arrow/tests/testthat/test-schema.R | 2 arrow-23.0.0/arrow/tests/testthat/test-thread-pool.R | 1 arrow-23.0.0/arrow/tests/testthat/test-type.R | 3 arrow-23.0.0/arrow/tests/testthat/test-udf.R | 9 arrow-23.0.0/arrow/tests/testthat/test-utf.R | 1 arrow-23.0.0/arrow/tests/testthat/test-util.R | 13 arrow-23.0.0/arrow/tools/LICENSE.txt | 54 arrow-23.0.0/arrow/tools/check-versions.R | 3 arrow-23.0.0/arrow/tools/checksums/r-libarrow-darwin-arm64-23.0.0.zip.sha512 |only arrow-23.0.0/arrow/tools/checksums/r-libarrow-darwin-x86_64-23.0.0.zip.sha512 |only arrow-23.0.0/arrow/tools/checksums/r-libarrow-linux-x86_64-23.0.0.zip.sha512 |only arrow-23.0.0/arrow/tools/checksums/r-libarrow-windows-x86_64-23.0.0.zip.sha512 |only arrow-23.0.0/arrow/tools/cpp/CMakeLists.txt | 12 arrow-23.0.0/arrow/tools/cpp/CMakePresets.json | 17 arrow-23.0.0/arrow/tools/cpp/README.md | 2 arrow-23.0.0/arrow/tools/cpp/build-support/fuzzing/generate_corpuses.sh | 19 arrow-23.0.0/arrow/tools/cpp/build-support/fuzzing/pack_corpus.py | 3 arrow-23.0.0/arrow/tools/cpp/build-support/run-test.sh | 2 arrow-23.0.0/arrow/tools/cpp/cmake_modules/DefineOptions.cmake | 4 arrow-23.0.0/arrow/tools/cpp/cmake_modules/GandivaAddBitcode.cmake | 2 arrow-23.0.0/arrow/tools/cpp/cmake_modules/SetupCxxFlags.cmake | 99 arrow-23.0.0/arrow/tools/cpp/cmake_modules/ThirdpartyToolchain.cmake | 2178 arrow-23.0.0/arrow/tools/cpp/meson.build | 57 arrow-23.0.0/arrow/tools/cpp/meson.options | 19 arrow-23.0.0/arrow/tools/cpp/src/arrow/CMakeLists.txt | 39 arrow-23.0.0/arrow/tools/cpp/src/arrow/acero/hash_join_node.cc | 20 arrow-23.0.0/arrow/tools/cpp/src/arrow/acero/meson.build | 24 arrow-23.0.0/arrow/tools/cpp/src/arrow/acero/sink_node.cc | 5 arrow-23.0.0/arrow/tools/cpp/src/arrow/acero/swiss_join.cc | 26 arrow-23.0.0/arrow/tools/cpp/src/arrow/acero/swiss_join_internal.h | 2 arrow-23.0.0/arrow/tools/cpp/src/arrow/array/CMakeLists.txt | 1 arrow-23.0.0/arrow/tools/cpp/src/arrow/array/array_nested.cc | 110 arrow-23.0.0/arrow/tools/cpp/src/arrow/array/array_nested.h | 20 arrow-23.0.0/arrow/tools/cpp/src/arrow/array/builder_time.h | 2 arrow-23.0.0/arrow/tools/cpp/src/arrow/array/data.h | 2 arrow-23.0.0/arrow/tools/cpp/src/arrow/array/statistics.h | 10 arrow-23.0.0/arrow/tools/cpp/src/arrow/compare.cc | 7 arrow-23.0.0/arrow/tools/cpp/src/arrow/compute/api_vector.cc | 2 arrow-23.0.0/arrow/tools/cpp/src/arrow/compute/api_vector.h | 11 arrow-23.0.0/arrow/tools/cpp/src/arrow/compute/exec.cc | 2 arrow-23.0.0/arrow/tools/cpp/src/arrow/compute/expression.cc | 6 arrow-23.0.0/arrow/tools/cpp/src/arrow/compute/function_internal.h | 7 arrow-23.0.0/arrow/tools/cpp/src/arrow/compute/kernels/aggregate_basic.inc.cc | 4 arrow-23.0.0/arrow/tools/cpp/src/arrow/compute/kernels/codegen_internal.cc | 11 arrow-23.0.0/arrow/tools/cpp/src/arrow/compute/kernels/hash_aggregate.cc | 82 arrow-23.0.0/arrow/tools/cpp/src/arrow/compute/kernels/hash_aggregate_numeric.cc | 44 arrow-23.0.0/arrow/tools/cpp/src/arrow/compute/kernels/scalar_cast_string.cc | 32 arrow-23.0.0/arrow/tools/cpp/src/arrow/compute/kernels/scalar_if_else.cc | 8 arrow-23.0.0/arrow/tools/cpp/src/arrow/compute/kernels/scalar_string_ascii.cc | 9 arrow-23.0.0/arrow/tools/cpp/src/arrow/compute/kernels/vector_swizzle.cc | 16 arrow-23.0.0/arrow/tools/cpp/src/arrow/csv/CMakeLists.txt | 8 arrow-23.0.0/arrow/tools/cpp/src/arrow/csv/chunker.cc | 10 arrow-23.0.0/arrow/tools/cpp/src/arrow/csv/column_builder.cc | 117 arrow-23.0.0/arrow/tools/cpp/src/arrow/csv/column_builder.h | 10 arrow-23.0.0/arrow/tools/cpp/src/arrow/csv/fuzz.cc |only arrow-23.0.0/arrow/tools/cpp/src/arrow/csv/generate_fuzz_corpus.cc |only arrow-23.0.0/arrow/tools/cpp/src/arrow/csv/reader.cc | 24 arrow-23.0.0/arrow/tools/cpp/src/arrow/dataset/discovery.cc | 4 arrow-23.0.0/arrow/tools/cpp/src/arrow/dataset/file_parquet.cc | 54 arrow-23.0.0/arrow/tools/cpp/src/arrow/dataset/meson.build |only arrow-23.0.0/arrow/tools/cpp/src/arrow/engine/meson.build |only arrow-23.0.0/arrow/tools/cpp/src/arrow/engine/simple_extension_type_internal.h | 2 arrow-23.0.0/arrow/tools/cpp/src/arrow/engine/substrait/meson.build |only arrow-23.0.0/arrow/tools/cpp/src/arrow/engine/substrait/relation_internal.cc | 1 arrow-23.0.0/arrow/tools/cpp/src/arrow/filesystem/CMakeLists.txt | 11 arrow-23.0.0/arrow/tools/cpp/src/arrow/filesystem/azurefs.cc | 4 arrow-23.0.0/arrow/tools/cpp/src/arrow/filesystem/gcsfs.cc | 3 arrow-23.0.0/arrow/tools/cpp/src/arrow/filesystem/gcsfs_internal.cc | 5 arrow-23.0.0/arrow/tools/cpp/src/arrow/filesystem/gcsfs_internal.h | 9 arrow-23.0.0/arrow/tools/cpp/src/arrow/filesystem/path_util.cc | 6 arrow-23.0.0/arrow/tools/cpp/src/arrow/filesystem/s3fs.cc | 27 arrow-23.0.0/arrow/tools/cpp/src/arrow/flight/CMakeLists.txt | 5 arrow-23.0.0/arrow/tools/cpp/src/arrow/flight/meson.build | 18 arrow-23.0.0/arrow/tools/cpp/src/arrow/flight/server.cc | 27 arrow-23.0.0/arrow/tools/cpp/src/arrow/flight/server_tracing_middleware.cc | 1 arrow-23.0.0/arrow/tools/cpp/src/arrow/flight/sql/CMakeLists.txt | 11 arrow-23.0.0/arrow/tools/cpp/src/arrow/flight/sql/column_metadata.cc | 6 arrow-23.0.0/arrow/tools/cpp/src/arrow/flight/transport/grpc/customize_grpc.h | 20 arrow-23.0.0/arrow/tools/cpp/src/arrow/flight/transport/grpc/grpc_client.cc | 34 arrow-23.0.0/arrow/tools/cpp/src/arrow/flight/transport/grpc/grpc_server.cc | 7 arrow-23.0.0/arrow/tools/cpp/src/arrow/flight/transport/grpc/util_internal.cc | 36 arrow-23.0.0/arrow/tools/cpp/src/arrow/flight/types.cc | 2 arrow-23.0.0/arrow/tools/cpp/src/arrow/integration/CMakeLists.txt | 8 arrow-23.0.0/arrow/tools/cpp/src/arrow/integration/c_data_integration_internal.cc | 29 arrow-23.0.0/arrow/tools/cpp/src/arrow/integration/meson.build | 6 arrow-23.0.0/arrow/tools/cpp/src/arrow/ipc/file_fuzz.cc | 3 arrow-23.0.0/arrow/tools/cpp/src/arrow/ipc/metadata_internal.cc | 17 arrow-23.0.0/arrow/tools/cpp/src/arrow/ipc/reader.cc | 13 arrow-23.0.0/arrow/tools/cpp/src/arrow/ipc/stream_fuzz.cc | 3 arrow-23.0.0/arrow/tools/cpp/src/arrow/ipc/test_common.cc | 18 arrow-23.0.0/arrow/tools/cpp/src/arrow/memory_pool.cc | 39 arrow-23.0.0/arrow/tools/cpp/src/arrow/memory_pool.h | 42 arrow-23.0.0/arrow/tools/cpp/src/arrow/meson.build | 107 arrow-23.0.0/arrow/tools/cpp/src/arrow/record_batch.cc | 57 arrow-23.0.0/arrow/tools/cpp/src/arrow/telemetry/logging.h | 2 arrow-23.0.0/arrow/tools/cpp/src/arrow/testing/math.cc | 101 arrow-23.0.0/arrow/tools/cpp/src/arrow/testing/math.h | 5 arrow-23.0.0/arrow/tools/cpp/src/arrow/testing/random.cc | 20 arrow-23.0.0/arrow/tools/cpp/src/arrow/type.cc | 8 arrow-23.0.0/arrow/tools/cpp/src/arrow/util/CMakeLists.txt | 18 arrow-23.0.0/arrow/tools/cpp/src/arrow/util/bit_run_reader.cc | 2 arrow-23.0.0/arrow/tools/cpp/src/arrow/util/bit_run_reader.h | 6 arrow-23.0.0/arrow/tools/cpp/src/arrow/util/bit_stream_utils_internal.h | 168 arrow-23.0.0/arrow/tools/cpp/src/arrow/util/bit_util.h | 21 arrow-23.0.0/arrow/tools/cpp/src/arrow/util/bitmap_ops.cc | 20 arrow-23.0.0/arrow/tools/cpp/src/arrow/util/bitmap_reader.h | 2 arrow-23.0.0/arrow/tools/cpp/src/arrow/util/bpacking.cc | 385 arrow-23.0.0/arrow/tools/cpp/src/arrow/util/bpacking_benchmark.cc | 68 arrow-23.0.0/arrow/tools/cpp/src/arrow/util/bpacking_dispatch_internal.h |only arrow-23.0.0/arrow/tools/cpp/src/arrow/util/bpacking_internal.h | 35 arrow-23.0.0/arrow/tools/cpp/src/arrow/util/bpacking_scalar.cc |only arrow-23.0.0/arrow/tools/cpp/src/arrow/util/bpacking_scalar_codegen.py |only arrow-23.0.0/arrow/tools/cpp/src/arrow/util/bpacking_scalar_generated_internal.h |only arrow-23.0.0/arrow/tools/cpp/src/arrow/util/bpacking_scalar_internal.h |only arrow-23.0.0/arrow/tools/cpp/src/arrow/util/bpacking_simd128_generated_internal.h |26889 +++++++++- arrow-23.0.0/arrow/tools/cpp/src/arrow/util/bpacking_simd256_generated_internal.h |16965 +++++- arrow-23.0.0/arrow/tools/cpp/src/arrow/util/bpacking_simd512_generated_internal.h |12003 ++++ arrow-23.0.0/arrow/tools/cpp/src/arrow/util/bpacking_simd_avx2.cc |only arrow-23.0.0/arrow/tools/cpp/src/arrow/util/bpacking_simd_avx512.cc |only arrow-23.0.0/arrow/tools/cpp/src/arrow/util/bpacking_simd_codegen.py | 344 arrow-23.0.0/arrow/tools/cpp/src/arrow/util/bpacking_simd_default.cc |only arrow-23.0.0/arrow/tools/cpp/src/arrow/util/bpacking_simd_internal.h | 195 arrow-23.0.0/arrow/tools/cpp/src/arrow/util/byte_stream_split_internal.h | 4 arrow-23.0.0/arrow/tools/cpp/src/arrow/util/config.h.cmake | 1 arrow-23.0.0/arrow/tools/cpp/src/arrow/util/config_internal.h.cmake | 2 arrow-23.0.0/arrow/tools/cpp/src/arrow/util/decimal.cc | 3 arrow-23.0.0/arrow/tools/cpp/src/arrow/util/endian.h | 2 arrow-23.0.0/arrow/tools/cpp/src/arrow/util/fuzz_internal.cc |only arrow-23.0.0/arrow/tools/cpp/src/arrow/util/fuzz_internal.h |only arrow-23.0.0/arrow/tools/cpp/src/arrow/util/int_util_overflow.h | 171 arrow-23.0.0/arrow/tools/cpp/src/arrow/util/io_util.cc | 41 arrow-23.0.0/arrow/tools/cpp/src/arrow/util/io_util.h | 18 arrow-23.0.0/arrow/tools/cpp/src/arrow/util/meson.build | 32 arrow-23.0.0/arrow/tools/cpp/src/arrow/util/range.h | 17 arrow-23.0.0/arrow/tools/cpp/src/arrow/util/rle_encoding_internal.h | 139 arrow-23.0.0/arrow/tools/cpp/src/arrow/util/string.h | 12 arrow-23.0.0/arrow/tools/cpp/src/arrow/util/task_group.cc | 7 arrow-23.0.0/arrow/tools/cpp/src/arrow/util/test_common.cc | 5 arrow-23.0.0/arrow/tools/cpp/src/arrow/util/test_common.h | 3 arrow-23.0.0/arrow/tools/cpp/src/arrow/util/time.h | 34 arrow-23.0.0/arrow/tools/cpp/src/arrow/util/ubsan.h | 28 arrow-23.0.0/arrow/tools/cpp/src/arrow/util/value_parsing.h | 44 arrow-23.0.0/arrow/tools/cpp/src/arrow/util/vector.h | 9 arrow-23.0.0/arrow/tools/cpp/src/arrow/vendored/CMakeLists.txt | 1 arrow-23.0.0/arrow/tools/cpp/src/arrow/vendored/fast_float/README.md | 8 arrow-23.0.0/arrow/tools/cpp/src/arrow/vendored/fast_float/ascii_number.h | 532 arrow-23.0.0/arrow/tools/cpp/src/arrow/vendored/fast_float/bigint.h | 226 arrow-23.0.0/arrow/tools/cpp/src/arrow/vendored/fast_float/constexpr_feature_detect.h | 23 arrow-23.0.0/arrow/tools/cpp/src/arrow/vendored/fast_float/decimal_to_binary.h | 135 arrow-23.0.0/arrow/tools/cpp/src/arrow/vendored/fast_float/digit_comparison.h | 205 arrow-23.0.0/arrow/tools/cpp/src/arrow/vendored/fast_float/fast_float.h | 104 arrow-23.0.0/arrow/tools/cpp/src/arrow/vendored/fast_float/fast_table.h | 1326 arrow-23.0.0/arrow/tools/cpp/src/arrow/vendored/fast_float/float_common.h | 1144 arrow-23.0.0/arrow/tools/cpp/src/arrow/vendored/fast_float/parse_number.h | 461 arrow-23.0.0/arrow/tools/cpp/src/arrow/vendored/meson.build | 1 arrow-23.0.0/arrow/tools/cpp/src/arrow/vendored/pcg/README.md | 1 arrow-23.0.0/arrow/tools/cpp/src/arrow/vendored/pcg/pcg_uint128.hpp | 15 arrow-23.0.0/arrow/tools/cpp/src/arrow/vendored/portable-snippets/meson.build | 5 arrow-23.0.0/arrow/tools/cpp/src/arrow/vendored/safeint |only arrow-23.0.0/arrow/tools/cpp/src/parquet/CMakeLists.txt | 1 arrow-23.0.0/arrow/tools/cpp/src/parquet/arrow/fuzz.cc | 7 arrow-23.0.0/arrow/tools/cpp/src/parquet/arrow/fuzz_internal.cc |only arrow-23.0.0/arrow/tools/cpp/src/parquet/arrow/fuzz_internal.h |only arrow-23.0.0/arrow/tools/cpp/src/parquet/arrow/generate_fuzz_corpus.cc | 583 arrow-23.0.0/arrow/tools/cpp/src/parquet/arrow/reader.cc | 79 arrow-23.0.0/arrow/tools/cpp/src/parquet/arrow/reader.h | 19 arrow-23.0.0/arrow/tools/cpp/src/parquet/arrow/reader_internal.cc | 117 arrow-23.0.0/arrow/tools/cpp/src/parquet/arrow/reader_writer_benchmark.cc | 30 arrow-23.0.0/arrow/tools/cpp/src/parquet/arrow/schema.cc | 1 arrow-23.0.0/arrow/tools/cpp/src/parquet/bloom_filter_reader.cc | 7 arrow-23.0.0/arrow/tools/cpp/src/parquet/column_io_benchmark.cc | 26 arrow-23.0.0/arrow/tools/cpp/src/parquet/column_reader.cc | 7 arrow-23.0.0/arrow/tools/cpp/src/parquet/column_writer.cc | 168 arrow-23.0.0/arrow/tools/cpp/src/parquet/column_writer.h | 13 arrow-23.0.0/arrow/tools/cpp/src/parquet/decoder.cc | 97 arrow-23.0.0/arrow/tools/cpp/src/parquet/encoder.cc | 48 arrow-23.0.0/arrow/tools/cpp/src/parquet/encryption/crypto_factory.cc | 2 arrow-23.0.0/arrow/tools/cpp/src/parquet/encryption/encryption.cc | 46 arrow-23.0.0/arrow/tools/cpp/src/parquet/encryption/encryption.h | 36 arrow-23.0.0/arrow/tools/cpp/src/parquet/encryption/file_system_key_material_store.cc | 1 arrow-23.0.0/arrow/tools/cpp/src/parquet/encryption/file_system_key_material_store.h | 4 arrow-23.0.0/arrow/tools/cpp/src/parquet/encryption/internal_file_encryptor.cc | 2 arrow-23.0.0/arrow/tools/cpp/src/parquet/encryption/test_encryption_util.h | 1 arrow-23.0.0/arrow/tools/cpp/src/parquet/exception.h | 19 arrow-23.0.0/arrow/tools/cpp/src/parquet/file_writer.cc | 24 arrow-23.0.0/arrow/tools/cpp/src/parquet/geospatial/util_internal.cc | 2 arrow-23.0.0/arrow/tools/cpp/src/parquet/geospatial/util_json_internal.cc | 4 arrow-23.0.0/arrow/tools/cpp/src/parquet/hasher.h | 2 arrow-23.0.0/arrow/tools/cpp/src/parquet/level_conversion_inc.h | 9 arrow-23.0.0/arrow/tools/cpp/src/parquet/meson.build | 1 arrow-23.0.0/arrow/tools/cpp/src/parquet/metadata.cc | 29 arrow-23.0.0/arrow/tools/cpp/src/parquet/page_index.cc | 28 arrow-23.0.0/arrow/tools/cpp/src/parquet/platform.h | 6 arrow-23.0.0/arrow/tools/cpp/src/parquet/properties.cc | 44 arrow-23.0.0/arrow/tools/cpp/src/parquet/properties.h | 49 arrow-23.0.0/arrow/tools/cpp/src/parquet/test_util.h | 6 arrow-23.0.0/arrow/tools/cpp/src/parquet/thrift_internal.h | 38 arrow-23.0.0/arrow/tools/cpp/src/parquet/types.cc | 5 arrow-23.0.0/arrow/tools/cpp/subprojects/README.md | 2 arrow-23.0.0/arrow/tools/cpp/subprojects/packagefiles/substrait |only arrow-23.0.0/arrow/tools/cpp/subprojects/substrait.wrap |only arrow-23.0.0/arrow/tools/cpp/subprojects/utf8proc.wrap |only arrow-23.0.0/arrow/tools/cpp/thirdparty/versions.txt | 12 arrow-23.0.0/arrow/tools/cpp/vcpkg.json | 2 arrow-23.0.0/arrow/tools/dotenv | 8 arrow-23.0.0/arrow/tools/nixlibs.R | 191 arrow-23.0.0/arrow/tools/test-check-versions.R | 1 arrow-23.0.0/arrow/tools/test-nixlibs.R | 107 366 files changed, 61341 insertions(+), 11820 deletions(-)
Title: Parametric Mixture Models for Uncertainty Estimation of
Fatalities in UCDP Conflict Data
Description: Provides functions for estimating uncertainty in the number of fatalities in the Uppsala Conflict Data Program (UCDP) data. The package implements a parametric reported-value Gumbel mixture distribution that accounts for the uncertainty in the number of fatalities in the UCDP data. The model is based on information from a survey on UCDP coders and how they view the uncertainty of the number of fatalities from UCDP events. The package provides functions for making random draws of fatalities from the mixture distribution, as well as to estimate percentiles, quantiles, means, and other statistics of the distribution. Full details on the survey and estimation procedure can be found in Vesco et al (2024).
Author: David Randahl [cre, aut]
Maintainer: David Randahl <david.randahl@pcr.uu.se>
Diff between uncertainUCDP versions 0.7.0 dated 2026-01-20 and 0.7.6 dated 2026-01-23
DESCRIPTION | 12 ++--- MD5 | 10 ++-- NAMESPACE | 2 R/sysdata.rda |binary R/uncertainUCDP.R | 107 ++++++++++++++++++++++++++++++++++++++-------- man/mean_uncertainUCDP.Rd | 8 +-- 6 files changed, 106 insertions(+), 33 deletions(-)
Title: Spatial Ecology Miscellaneous Methods
Description: Collection of R functions and data sets for the support of spatial ecology analyses with a focus on pre, core and post modelling analyses of species distribution, niche quantification and community assembly. Written by current and former members and collaborators of the ecospat group of Antoine Guisan, Department of Ecology and Evolution (DEE) and Institute of Earth Surface Dynamics (IDYST), University of Lausanne, Switzerland. Read Di Cola et al. (2016) <doi:10.1111/ecog.02671> for details.
Author: Olivier Broennimann [cre, aut, ctb],
Valeria Di Cola [aut, ctb],
Blaise Petitpierre [ctb],
Frank Breiner [ctb],
Daniel Scherrer [ctb],
Manuela D`Amen [ctb],
Christophe Randin [ctb],
Robin Engler [ctb],
Wim Hordijk [ctb],
Heidi Mod [ctb],
Julien Potti [...truncated...]
Maintainer: Olivier Broennimann <olivier.broennimann@unil.ch>
Diff between ecospat versions 4.1.2 dated 2025-01-31 and 4.1.3 dated 2026-01-23
DESCRIPTION | 16 +++++++------- MD5 | 38 +++++++++++++++++----------------- NEWS | 6 +++++ R/ecospat.CCV.R | 4 ++- R/ecospat.ESM.R | 13 +++++++---- R/ecospat.boyce.R | 2 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/vignette_ecospat_package.pdf |binary man/ecospat.CCV.modeling.Rd | 5 ++++ man/ecospat.binary.model.Rd | 4 +-- man/ecospat.grid.clim.dyn.Rd | 2 - man/ecospat.niche.dyn.index.Rd | 3 +- man/ecospat.niche.dynIndexProjGeo.Rd | 8 +++---- man/ecospat.niche.equivalency.test.Rd | 2 - man/ecospat.niche.overlap.Rd | 2 - man/ecospat.niche.similarity.test.Rd | 2 - man/ecospat.niche.zProjGeo.Rd | 6 ++--- man/ecospat.occupied.patch.Rd | 4 +-- man/ecospat.rangesize.Rd | 4 +-- 20 files changed, 69 insertions(+), 52 deletions(-)
Title: Automated and Early Detection of Seasonal Epidemic Onset and
Burden Levels
Description: A powerful tool for automating the early detection of seasonal epidemic
onsets in time series data. It offers the ability to estimate growth rates
across consecutive time intervals, calculate the sum of cases (SoC) within
those intervals, and estimate seasonal onsets within user defined seasons.
With use of a disease-specific threshold it also offers the possibility to
estimate seasonal onset of epidemics.
Additionally it offers the ability to estimate burden levels for seasons
based on historical data. It is aimed towards epidemiologists,
public health professionals, and researchers seeking to identify and respond
to seasonal epidemics in a timely fashion.
Author: Sofia Myrup Otero [aut] ,
Kasper Schou Telkamp [aut] ,
Lasse Engbo Christiansen [aut, cre] ,
Rasmus Skytte Randloev [rev] ,
Statens Serum Institut, SSI [cph, fnd]
Maintainer: Lasse Engbo Christiansen <lsec@ssi.dk>
Diff between aedseo versions 1.0.1 dated 2025-11-20 and 1.1.0 dated 2026-01-23
DESCRIPTION | 12 MD5 | 56 ++-- NEWS.md | 264 +++++++++--------- R/autoplot.R | 47 ++- R/combined_seasonal_output.R | 216 +++++++++------ R/epi_calendar.R | 6 R/estimate_disease_threshold.R | 10 R/fit_growth_rate.R | 4 R/fit_percentiles.R | 6 R/generate_seasonal_data.R | 3 R/predict.R | 22 - R/seasonal_burden_levels.R | 14 - R/seasonal_onset.R | 20 - R/summary.R | 40 ++ R/to_time_series.R | 4 inst/doc/aedseo.R | 15 - inst/doc/aedseo.Rmd | 49 ++- inst/doc/aedseo.html | 349 ++++++++++++++----------- inst/doc/burden_levels.html | 6 inst/doc/generate_seasonal_wave.html | 18 - inst/doc/multiple_waves.R | 1 inst/doc/multiple_waves.Rmd | 34 +- inst/doc/multiple_waves.html | 50 ++- inst/doc/seasonal_onset.html | 33 +- man/autoplot.Rd | 19 - man/combined_seasonal_output.Rd | 24 + tests/testthat/test-combined_seasonal_output.R | 142 +++++++++- vignettes/aedseo.Rmd | 49 ++- vignettes/multiple_waves.Rmd | 34 +- 29 files changed, 962 insertions(+), 585 deletions(-)
Title: Auxiliary Functions for Phenological Data Analysis
Description: Provides some easy-to-use functions for time series
analyses of (plant-) phenological data sets. These functions
mainly deal with the estimation of combined phenological time
series and are usually wrappers for functions that are already
implemented in other R packages adapted to the special
structure of phenological data and the needs of phenologists.
Some date conversion functions to handle Julian dates are also
provided.
Author: Joerg Schaber [aut],
Maximilian Lange [cre]
Maintainer: Maximilian Lange <maximilian.lange@ufz.de>
Diff between pheno versions 1.7-0 dated 2022-05-12 and 1.7-1 dated 2026-01-23
DESCRIPTION | 14 +++++++++----- MD5 | 6 +++--- man/connectedSets.Rd | 10 +++++----- man/maxConnectedSet.Rd | 26 +++++++++++++------------- 4 files changed, 30 insertions(+), 26 deletions(-)
Title: Ordinal Regression for High-Dimensional Data
Description: Provides a function for fitting cumulative link, adjacent category, forward and backward continuation ratio, and stereotype ordinal response models when the number of parameters exceeds the sample size, using the the generalized monotone incremental forward stagewise method.
Author: Kellie J. Archer [aut, cre] ,
Jiayi Hou [aut],
Qing Zhou [aut],
Kyle Ferber [aut],
John G. Layne [com, ctr],
Amanda Gentry [rev]
Maintainer: Kellie J. Archer <archer.43@osu.edu>
Diff between ordinalgmifs versions 1.0.8 dated 2023-05-05 and 1.0.9 dated 2026-01-23
DESCRIPTION | 12 ++++++------ MD5 | 16 ++++++++-------- build/partial.rdb |binary data/eyedisease.rda |binary data/hccframe.rda |binary inst/CITATION | 12 ++++++------ inst/doc/ordinalgmifs.Rnw | 11 +---------- inst/doc/ordinalgmifs.pdf |binary vignettes/ordinalgmifs.bib | 2 +- 9 files changed, 22 insertions(+), 31 deletions(-)
Title: Latent Interaction (and Moderation) Analysis in Structural
Equation Models (SEM)
Description: Estimation of interaction (i.e., moderation) effects between latent variables
in structural equation models (SEM).
The supported methods are:
The constrained approach (Algina & Moulder, 2001).
The unconstrained approach (Marsh et al., 2004).
The residual centering approach (Little et al., 2006).
The double centering approach (Lin et al., 2010).
The latent moderated structural equations (LMS) approach (Klein & Moosbrugger, 2000).
The quasi-maximum likelihood (QML) approach (Klein & Muthén, 2007)
The constrained- unconstrained, residual- and double centering- approaches
are estimated via 'lavaan' (Rosseel, 2012), whilst the LMS- and QML- approaches
are estimated via 'modsem' it self. Alternatively model can be
estimated via 'Mplus' (Muthén & Muthén, 1998-2017).
References:
Algina, J., & Moulder, B. C. (2001).
<doi:10.1207/S15328007SEM0801_3>.
"A note on estimating the Jöreskog-Yang model for latent variable interaction using 'LISREL' 8.3."
Klein, A., & Moosb [...truncated...]
Author: Kjell Solem Slupphaug [aut, cre] ,
Mehmet Mehmetoglu [ctb] ,
Matthias Mittner [ctb]
Maintainer: Kjell Solem Slupphaug <slupphaugkjell@gmail.com>
Diff between modsem versions 1.0.15 dated 2025-12-22 and 1.0.16 dated 2026-01-23
DESCRIPTION | 6 MD5 | 69 ++-- R/bootstrap.R | 2 R/calc_se_da.R | 122 ++++++- R/construct_matrices_da.R | 23 - R/equations_lms.R | 10 R/est_h0.R | 70 +++- R/formatted_objects.R | 75 ++++ R/generics_lavaan.R | 6 R/generics_modsem_da.R | 48 +- R/generics_modsem_mplus.R | 8 R/generics_modsem_pi.R | 22 + R/inspect_da.R | 84 ++-- R/labelled_params_da.R | 8 R/model_da.R | 68 ++- R/modsem.R | 2 R/modsem_da.R | 5 R/modsem_pi.R | 2 R/plot_interaction.R | 20 - R/quadrature.R | 204 +++++++---- R/scale_correction_ordered.R | 11 R/simple_slopes.R | 7 R/standardized_solution.R | 9 R/utils.R | 27 + R/utils_da.R | 67 +++ inst/doc/customize_plot_interactions.html | 2 inst/doc/observed_lms_qml.R | 4 inst/doc/observed_lms_qml.Rmd | 17 inst/doc/observed_lms_qml.html | 512 +++++++++++++++++------------- inst/doc/plot_interactions.html | 4 man/parameter_estimates.Rd | 52 ++- man/standardized_estimates.Rd | 3 tests/testthat/test_adaptive_quad.R | 3 tests/testthat/test_ov_int.R |only tests/testthat/test_ovchecks_da.R | 30 - vignettes/observed_lms_qml.Rmd | 17 36 files changed, 1092 insertions(+), 527 deletions(-)
Title: Working with 'MCSim' Models
Description: Tools that facilitate ordinary differential equation (ODE) modeling in 'R'. This package allows one to perform simulations for ODE models that are encoded in the GNU 'MCSim' model specification language (Bois, 2009) <doi:10.1093/bioinformatics/btp162> using ODE solvers from the 'R' package 'deSolve' (Soetaert et al., 2010) <doi:10.18637/jss.v033.i09>.
Author: Dustin F. Kapraun [aut, cre] ,
Todd J. Zurlinden [aut] ,
Andrew J. Shapiro [aut] ,
Ryan D. Friese [aut] ,
Frederic Y. Bois [ctb] ,
Free Software Foundation, Inc. [cph]
Maintainer: Dustin F. Kapraun <kapraun.dustin@epa.gov>
Diff between MCSimMod versions 1.0 dated 2025-08-19 and 1.2 dated 2026-01-23
DESCRIPTION | 10 +- MD5 | 38 +++++----- R/MCSim_model.R | 70 ++++++++++++++---- R/compileModel.R | 142 +++++++++++++++++++++++++++++++------- R/createModel.R | 5 - R/fileHasChanged.R | 6 - R/fixPath.R | 4 - inst/CITATION | 2 inst/doc/details.html | 4 - inst/doc/events_demo.html | 4 - inst/doc/inputs_demo.html | 4 - inst/doc/intro.html | 4 - inst/doc/model_specification.html | 4 - inst/doc/newt_cool_demo.html | 4 - inst/doc/pbpk_demo.html | 4 - inst/doc/pk1_demo.html | 4 - inst/doc/pred_prey_demo.html | 4 - man/Model-class.Rd | 10 +- man/compileModel.Rd | 16 +++- man/createModel.Rd | 9 ++ 20 files changed, 253 insertions(+), 95 deletions(-)
Title: Basic Functions in Knowledge Space Theory Using Matrix
Representation
Description: Knowledge space theory by Doignon and Falmagne (1999)
<doi:10.1007/978-3-642-58625-5> is a set- and order-theoretical
framework, which proposes mathematical formalisms to operationalize
knowledge structures in a particular domain. The 'kstMatrix' package
provides basic functionalities to generate, handle, and manipulate
knowledge structures and knowledge spaces. Opposed to the 'kst'
package, 'kstMatrix' uses matrix representations for knowledge
structures. Furthermore, 'kstMatrix' contains several knowledge spaces
developed by the research group around Cornelia Dowling through
querying experts.
Author: Cord Hockemeyer [aut, cre],
Peter Steiner [aut],
Wai Wong [aut]
Maintainer: Cord Hockemeyer <cord.hockemeyer@uni-graz.at>
Diff between kstMatrix versions 2.2-0 dated 2025-12-18 and 2.2-1 dated 2026-01-23
Changelog | 4 + DESCRIPTION | 12 ++-- MD5 | 10 +-- R/plot.R | 124 ++++++++++++++++++++++++++++++++---------------- inst/doc/kstMatrix.html | 28 +++++----- man/plot.Rd | 11 +++- 6 files changed, 120 insertions(+), 69 deletions(-)
Title: Mass-Spectra Prediction Using the FIORA Model
Description: Provides a wrapper for the python module 'FIORA' as well as a
'shiny'-App to facilitate data processing and visualization. 'FIORA' allows
to predict Mass-Spectra based on the SMILES code of chemical compounds. It
is described in the Nature Communications article by Nowatzky (2025)
<doi:10.1038/s41467-025-57422-4>.
Author: Jan Lisec [aut, cre]
Maintainer: Jan Lisec <jan.lisec@bam.de>
Diff between fioRa versions 0.3.4 dated 2025-11-11 and 0.3.7 dated 2026-01-23
DESCRIPTION | 13 - MD5 | 43 ++-- NAMESPACE | 1 NEWS.md | 22 ++ R/app_ui.R | 10 R/app_utils.R | 222 +++++++++++++++++--- R/fct_install_fiora.R | 25 +- R/fct_read_fiora.R | 37 ++- R/mod_page_fioRa.R | 38 +++ R/mod_selectInputWithButtons.R | 244 ++++++++++------------- R/run_script.R | 42 +++ README.md | 12 - inst/WORDLIST | 4 man/install_fiora.Rd | 5 man/read_fiora.Rd |only man/run_script.Rd | 24 +- tests/spelling.R | 6 tests/testthat.R | 2 tests/testthat/_snaps |only tests/testthat/setup.R |only tests/testthat/test-app_utils.R |only tests/testthat/test-fct_read_fiora.R | 15 + tests/testthat/test-mod_selectInputWithButtons.R |only tests/testthat/test-run_script.R | 5 24 files changed, 534 insertions(+), 236 deletions(-)
Title: Interface to Download Meteorological (and Hydrological) Datasets
Description: Automatize downloading of meteorological and hydrological data from publicly available repositories:
OGIMET (<http://ogimet.com/index.phtml.en>),
University of Wyoming - atmospheric vertical profiling data (<http://weather.uwyo.edu/upperair/>),
Polish Institute of Meteorology and Water Management - National Research Institute (<https://danepubliczne.imgw.pl>),
and National Oceanic & Atmospheric Administration (NOAA).
This package also allows for searching geographical coordinates for each observation and calculate distances to the nearest stations.
Author: Bartosz Czernecki [aut, cre] ,
Arkadiusz Glogowski [aut] ,
Jakub Nowosad [aut] ,
IMGW-PIB [ctb]
Maintainer: Bartosz Czernecki <nwp@amu.edu.pl>
Diff between climate versions 1.2.5 dated 2025-10-29 and 1.2.7 dated 2026-01-23
DESCRIPTION | 6 MD5 | 41 ++--- NAMESPACE | 1 NEWS.md | 8 + R/hydro_imgw_daily.R | 21 ++ R/match_imgw_wmoid_inds.R |only R/meteo_imgw_daily.R | 296 +++++++++++++++++++++++---------------- R/meteo_imgw_hourly.R | 224 +++++++++++++++++------------ R/meteo_imgw_monthly.R | 242 +++++++++++++++++-------------- R/meteo_noaa_hourly.R | 6 R/nearest_stations_noaa.R | 8 - R/nearest_stations_ogimet.R | 2 R/test_url.R | 51 ++---- README.md | 11 - inst/doc/getstarted.Rmd | 4 inst/doc/getstarted.html | 333 +++++++++++++++++++++++++++++++++++--------- man/meteo_imgw_daily.Rd | 8 - man/meteo_imgw_hourly.Rd | 4 man/meteo_imgw_monthly.Rd | 14 + man/meteo_noaa_hourly.Rd | 4 man/test_url.Rd | 8 - vignettes/getstarted.Rmd | 4 22 files changed, 834 insertions(+), 462 deletions(-)
Title: Pediatrics Extension Package for ADaM in 'R' Asset Library
Description: A toolbox for programming Clinical Data Standards Interchange
Consortium (CDISC) compliant Analysis Data Model (ADaM) datasets in R.
ADaM datasets are a mandatory part of any New Drug or Biologics
License Application submitted to the United States Food and Drug
Administration (FDA). Analysis derivations are implemented in
accordance with the "Analysis Data Model Implementation Guide" (CDISC
Analysis Data Model Team, 2021,
<https://www.cdisc.org/standards/foundational/adam>). The package is
an extension package of the 'admiral' package for pediatric clinical
trials.
Author: Fanny Gautier [aut, cre] ,
Ross Farrugia [aut],
Zelos Zhu [aut],
Sukalpo Saha [aut],
Lina Patil [aut],
Samia Kabi [aut],
Laura Liao [ctb],
Remigiusz Kudlacz [ctb],
Pierre Wallet [ctb],
Amin Sherzad [ctb],
David Freedman [ctb],
Mahmoud Hamza [ctb],
Cy [...truncated...]
Maintainer: Fanny Gautier <fanny.gautier@cytel.com>
Diff between admiralpeds versions 0.2.1 dated 2025-08-20 and 0.3.0 dated 2026-01-23
DESCRIPTION | 10 +- MD5 | 37 +++++------ NAMESPACE | 1 NEWS.md | 40 +++++++++-- R/bin_utils.R | 8 +- R/derive_interp_records.R | 8 ++ R/derive_params_growth_age.R | 52 +++++++++------ R/derive_params_growth_height.R | 35 ++++++---- README.md | 10 +- build/vignette.rds |binary inst/WORDLIST | 5 + inst/templates/ad_advs.R | 8 +- man/derive_interp_records.Rd | 21 +++++- man/derive_params_growth_age.Rd | 84 +++++++++++++++++++------ man/derive_params_growth_height.Rd | 68 ++++++++++++++++---- man/find_closest_bin.Rd | 18 ++++- man/get_bins.Rd | 12 ++- man/roxygen/rdx_meta.R |only tests/testthat/test-derive_interp_records.R | 2 tests/testthat/test-derive_params_growth_age.R | 7 +- 20 files changed, 304 insertions(+), 122 deletions(-)
Title: Official Gridded Data from the German Census 2022
Description: Provides fast and easy access to German census grid data
from the 2011 and 2022 censuses <https://www.zensus2022.de/>, including a
wide range of socio-economic indicators at multiple spatial resolutions
(100m, 1km, 10km). Enables efficient download, processing, and analysis
of large census datasets covering population, households, families,
dwellings, and buildings. Harmonized data structures allow direct
comparison with the 2011 census, supporting temporal and spatial analyses.
Facilitates conversion of data into common formats for spatial analysis and
mapping ('terra', 'sf', 'ggplot2').
Author: Jonas Lieth [cre, aut, cph]
Maintainer: Jonas Lieth <jslth@outlook.com>
Diff between z22 versions 1.1.0 dated 2025-10-29 and 1.1.4 dated 2026-01-23
DESCRIPTION | 10 - MD5 | 42 ++++---- NEWS.md | 7 + R/categories.R | 155 +++++++++++++++++++++++------- R/check.R | 4 R/data.R | 31 ------ R/utils.R | 2 inst/doc/z22.Rmd | 58 +++++------ inst/doc/z22.html | 73 ++++++-------- man/categories.Rd | 81 +++++++++++++-- man/figures/vignette/100m_plot-1.png |binary man/figures/vignette/allcells_plot-1.png |binary man/figures/vignette/multiplot-1.png |binary man/figures/vignette/normalize_plot-1.png |binary man/figures/vignette/patchwork_plot-1.png |binary man/z22-package.Rd | 2 man/z22_data.Rd | 5 man/z22_grid.Rd | 2 tests/testthat/test-pkg.R | 9 + vignettes/precompute.R |only vignettes/z22.Rmd | 58 +++++------ vignettes/z22.Rmd.orig | 14 ++ vignettes/z22.md |only 23 files changed, 343 insertions(+), 210 deletions(-)
Title: Forecasting Models for Tidy Time Series
Description: Provides a collection of commonly used univariate and multivariate
time series forecasting models including automatically selected exponential
smoothing (ETS) and autoregressive integrated moving average (ARIMA) models.
These models work within the 'fable' framework provided by the 'fabletools'
package, which provides the tools to evaluate, visualise, and combine models
in a workflow consistent with the tidyverse.
Author: Mitchell O'Hara-Wild [aut, cre],
Rob Hyndman [aut],
Earo Wang [aut],
Gabriel Caceres [ctb] ,
Christoph Bergmeir [ctb] ,
Tim-Gunnar Hensel [ctb],
Timothy Hyndman [ctb]
Maintainer: Mitchell O'Hara-Wild <mail@mitchelloharawild.com>
Diff between fable versions 0.4.1 dated 2024-11-04 and 0.5.0 dated 2026-01-23
DESCRIPTION | 17 - MD5 | 73 +++--- NAMESPACE | 10 NEWS.md | 23 ++ R/00_specials.R | 6 R/VARIMA.R | 115 ++++++---- R/ar.R | 4 R/arfima.R |only R/arima.R | 172 ++++++++++----- R/checks.R | 8 R/compat-purrr.R | 4 R/croston.R | 14 - R/ets.R | 80 ++++--- R/etsmodel.R | 34 +-- R/lagwalk.R | 24 +- R/lm.R | 2 R/mean.R | 8 R/nnetar.R | 25 +- R/theta.R | 8 R/utils.R | 10 R/var.R | 4 R/vecm.R | 2 README.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST | 16 + inst/doc/fable.R | 8 inst/doc/fable.html | 81 +++---- inst/doc/transformations.html | 3 man/ARFIMA.Rd |only man/ARIMA.Rd | 12 + man/ETS.Rd | 2 man/RW.Rd | 1 man/VARIMA.Rd | 73 ++++-- man/interpolate.ETS.Rd |only src/etsTargetFunction.cpp | 4 src/etsTargetFunction.h | 6 src/etscalc.c | 465 +++++++++++++++++++++--------------------- tests/testthat/test-ets.R | 39 ++- 39 files changed, 804 insertions(+), 551 deletions(-)
Title: A Rainclouds Geom for 'ggplot2'
Description: The 'geom_rain()' function adds different geoms together using 'ggplot2' to create raincloud plots.
Author: Nicholas Judd [aut, cre] ,
Jordy van Langen [aut] ,
Micah Allen [ctb] ,
Rogier Kievit [aut]
Maintainer: Nicholas Judd <nickkjudd@gmail.com>
Diff between ggrain versions 0.1.1 dated 2026-01-21 and 0.1.2 dated 2026-01-23
ggrain-0.1.1/ggrain/inst/book.bib |only ggrain-0.1.1/ggrain/inst/paper.md |only ggrain-0.1.2/ggrain/DESCRIPTION | 6 +++--- ggrain-0.1.2/ggrain/MD5 | 8 +++----- ggrain-0.1.2/ggrain/NEWS.md | 4 ++++ ggrain-0.1.2/ggrain/README.md | 3 +-- 6 files changed, 11 insertions(+), 10 deletions(-)
Title: Visualisation of Sequential Probability Distributions Using Fan
Charts
Description: Visualise sequential distributions using a range of plotting
styles. Sequential distribution data can be input as either simulations or
values corresponding to percentiles over time. Plots are added to
existing graphic devices using the fan function. Users can choose from four
different styles, including fan chart type plots, where a set of coloured
polygon, with shadings corresponding to the percentile values are layered
to represent different uncertainty levels. Full details in R Journal article; Abel (2015) <doi:10.32614/RJ-2015-002>.
Author: Guy J. Abel [aut, cre]
Maintainer: Guy J. Abel <g.j.abel@gmail.com>
Diff between fanplot versions 4.0.0 dated 2021-08-02 and 4.0.1 dated 2026-01-23
DESCRIPTION | 16 ++++++++------ MD5 | 22 ++++++++++---------- NAMESPACE | 8 ------- NEWS.md | 7 ++++++ R/fan.R | 62 ++++++++++++++++++++++++++++----------------------------- R/fan0.R | 2 - R/psplitnorm.R | 4 +-- R/qsplitnorm.R | 4 +-- R/rsplitnorm.R | 2 - demo/sv_fan.R | 2 - inst/CITATION | 15 ++++++------- man/fan.Rd | 4 +-- 12 files changed, 75 insertions(+), 73 deletions(-)
Title: Self-Validated Ensemble Models with Lasso and Relaxed Elastic
Net Regression
Description: Tools for fitting self-validated ensemble models (SVEM; Lemkus et al. (2021) <doi:10.1016/j.chemolab.2021.104439>) in small-sample design-of-experiments and related workflows, using elastic net and relaxed elastic net regression via 'glmnet' (Friedman et al. (2010) <doi:10.18637/jss.v033.i01>). Fractional random-weight bootstraps with anti-correlated validation copies are used to tune penalty paths by validation-weighted AIC/BIC. Supports Gaussian and binomial responses, deterministic expansion helpers for shared factor spaces, prediction with bootstrap uncertainty, and a random-search optimizer that respects mixture constraints and combines multiple responses via desirability functions. Also includes a permutation-based whole-model test for Gaussian SVEM fits (Karl (2024) <doi:10.1016/j.chemolab.2024.105122>). Package code was drafted with assistance from generative AI tools.
Author: Andrew T. Karl [cre, aut]
Maintainer: Andrew T. Karl <akarl@asu.edu>
Diff between SVEMnet versions 3.1.4 dated 2025-11-28 and 3.2.0 dated 2026-01-23
SVEMnet-3.1.4/SVEMnet/tests/testthat/testthat-problems.rds |only SVEMnet-3.2.0/SVEMnet/DESCRIPTION | 11 SVEMnet-3.2.0/SVEMnet/MD5 | 49 - SVEMnet-3.2.0/SVEMnet/NAMESPACE | 4 SVEMnet-3.2.0/SVEMnet/NEWS | 5 SVEMnet-3.2.0/SVEMnet/R/SVEMnet.R | 169 +++- SVEMnet-3.2.0/SVEMnet/R/bigexp.R | 346 ++++++++- SVEMnet-3.2.0/SVEMnet/R/glmnet_with_cv.R | 191 ++++- SVEMnet-3.2.0/SVEMnet/R/lipid_screen.R | 3 SVEMnet-3.2.0/SVEMnet/R/plot.svemtest.R | 14 SVEMnet-3.2.0/SVEMnet/R/select_candidates.R | 61 + SVEMnet-3.2.0/SVEMnet/R/spec_limit_utility.R | 188 +--- SVEMnet-3.2.0/SVEMnet/R/svem_random_table_multi.R | 403 ++++++---- SVEMnet-3.2.0/SVEMnet/R/svem_score_random.R | 416 +++++------ SVEMnet-3.2.0/SVEMnet/R/svem_select_score_from_table.R | 188 ---- SVEMnet-3.2.0/SVEMnet/R/svem_significance_test_parallel.R | 277 +++++-- SVEMnet-3.2.0/SVEMnet/R/svem_wmt_multi.R | 105 +- SVEMnet-3.2.0/SVEMnet/man/SVEMnet-package.Rd | 7 SVEMnet-3.2.0/SVEMnet/man/bigexp_terms.Rd | 94 ++ SVEMnet-3.2.0/SVEMnet/man/lipid_screen.Rd | 3 SVEMnet-3.2.0/SVEMnet/man/svem_random_table_multi.Rd | 144 --- SVEMnet-3.2.0/SVEMnet/man/svem_score_random.Rd | 22 SVEMnet-3.2.0/SVEMnet/man/svem_select_from_score_table.Rd | 152 ---- SVEMnet-3.2.0/SVEMnet/man/svem_significance_test_parallel.Rd | 34 SVEMnet-3.2.0/SVEMnet/tests/testthat/test_extras.R | 5 SVEMnet-3.2.0/SVEMnet/tests/testthat/test_scoring.R | 179 ++++ 26 files changed, 1870 insertions(+), 1200 deletions(-)
Title: Schumaker Shape-Preserving Spline
Description: This is a shape preserving spline <doi:10.1137/0720057>
which is guaranteed to be monotonic and concave or convex if the
data is monotonic and concave or convex. It does not use any
optimisation and is therefore quick and smoothly converges to a
fixed point in economic dynamics problems including value function
iteration. It also automatically gives the first two derivatives
of the spline and options for determining behaviour when evaluated
outside the interpolation domain.
Author: Stuart Baumann [aut, cre],
Margaryta Klymak [aut]
Maintainer: Stuart Baumann <stuart@stuartbaumann.com>
Diff between schumaker versions 1.2.1 dated 2021-09-09 and 1.2.2 dated 2026-01-23
DESCRIPTION | 19 MD5 | 18 NAMESPACE | 1 R/Schumaker.R | 140 ++-- build/vignette.rds |binary inst/doc/schumaker.R | 266 +++------ inst/doc/schumaker.Rmd | 501 +++++++---------- inst/doc/schumaker.html | 1066 +++++++++++++++++++++++--------------- man/impute_gradients.Rd |only tests/testthat/test_schumaker_2.R |only vignettes/schumaker.Rmd | 501 +++++++---------- 11 files changed, 1302 insertions(+), 1210 deletions(-)
Title: qPCR Data Analysis
Description: Tools for qPCR data analysis using Delta Ct and Delta Delta Ct methods, including t-tests, ANOVA, ANCOVA, repeated-measures models, and publication-ready visualizations. The package supports multiple target, and multiple reference genes, and uses a calculation framework adopted from Ganger et al. (2017) <doi:10.1186/s12859-017-1949-5> and Taylor et al. (2019) <doi:10.1016/j.tibtech.2018.12.002>, covering both the Livak and Pfaffl methods.
Author: Ghader Mirzaghaderi [aut, cre, cph]
Maintainer: Ghader Mirzaghaderi <mirzaghaderi@gmail.com>
Diff between rtpcr versions 2.1.1 dated 2026-01-08 and 2.1.2 dated 2026-01-23
rtpcr-2.1.1/rtpcr/R/ANOVA_DCt.r |only rtpcr-2.1.1/rtpcr/R/ANOVA_DDCt.r |only rtpcr-2.1.1/rtpcr/R/Means_DDCt.r |only rtpcr-2.1.1/rtpcr/R/REPEATED_DDCt.r |only rtpcr-2.1.1/rtpcr/R/TTEST_DDCt.r |only rtpcr-2.1.1/rtpcr/R/efficiency.r |only rtpcr-2.1.1/rtpcr/R/globalVariables.r |only rtpcr-2.1.1/rtpcr/R/meanTech.r |only rtpcr-2.1.1/rtpcr/R/multiplot.r |only rtpcr-2.1.1/rtpcr/R/package_data.r |only rtpcr-2.1.1/rtpcr/R/plotFactor.r |only rtpcr-2.1.1/rtpcr/R/qpcrhlpr.r |only rtpcr-2.1.1/rtpcr/data/Lee_etal2020qPCR.rda |only rtpcr-2.1.1/rtpcr/data/data_efficiency.rda |only rtpcr-2.1.1/rtpcr/inst/extdata/Lee_etal2020qPCR.csv |only rtpcr-2.1.1/rtpcr/inst/extdata/data_efficiency.csv |only rtpcr-2.1.1/rtpcr/inst/extdata/farokh_et_al_2025.csv |only rtpcr-2.1.1/rtpcr/man/Lee_etal2020qPCR.Rd |only rtpcr-2.1.1/rtpcr/man/data_efficiency.Rd |only rtpcr-2.1.2/rtpcr/DESCRIPTION | 17 rtpcr-2.1.2/rtpcr/MD5 | 167 ++-- rtpcr-2.1.2/rtpcr/NAMESPACE | 4 rtpcr-2.1.2/rtpcr/NEWS.md | 30 rtpcr-2.1.2/rtpcr/R/ANCOVA_DDCt.R |only rtpcr-2.1.2/rtpcr/R/ANOVA_DCt.R |only rtpcr-2.1.2/rtpcr/R/ANOVA_DDCt.R |only rtpcr-2.1.2/rtpcr/R/Means_DDCt.R |only rtpcr-2.1.2/rtpcr/R/REPEATED_DDCt.R |only rtpcr-2.1.2/rtpcr/R/TTEST_DDCt.R |only rtpcr-2.1.2/rtpcr/R/WILCOX_DDCt.R |only rtpcr-2.1.2/rtpcr/R/compute_wDCt.R |only rtpcr-2.1.2/rtpcr/R/efficiency.R |only rtpcr-2.1.2/rtpcr/R/globalVariables.R |only rtpcr-2.1.2/rtpcr/R/long_to_wide.R |only rtpcr-2.1.2/rtpcr/R/meanTech.R |only rtpcr-2.1.2/rtpcr/R/multiplot.R |only rtpcr-2.1.2/rtpcr/R/package_data.R |only rtpcr-2.1.2/rtpcr/R/plotFactor.R |only rtpcr-2.1.2/rtpcr/R/qpcrhlpr.R |only rtpcr-2.1.2/rtpcr/data/data_1factor.rda |binary rtpcr-2.1.2/rtpcr/data/data_1factor_Two_ref.rda |binary rtpcr-2.1.2/rtpcr/data/data_1factor_one_ref.rda |binary rtpcr-2.1.2/rtpcr/data/data_1factor_one_ref_Eff.rda |binary rtpcr-2.1.2/rtpcr/data/data_2factor.rda |binary rtpcr-2.1.2/rtpcr/data/data_2factor3ref.rda |binary rtpcr-2.1.2/rtpcr/data/data_2factorBlock.rda |binary rtpcr-2.1.2/rtpcr/data/data_2factorBlock3ref.rda |binary rtpcr-2.1.2/rtpcr/data/data_3factor.rda |binary rtpcr-2.1.2/rtpcr/data/data_Heffer2020PlosOne.rda |only rtpcr-2.1.2/rtpcr/data/data_Lee_etal2020qPCR.rda |only rtpcr-2.1.2/rtpcr/data/data_Yuan2006PMCBioinf.rda |only rtpcr-2.1.2/rtpcr/data/data_efficiency1.rda |only rtpcr-2.1.2/rtpcr/data/data_efficiency_Yuan2006PMCBioinf.rda |only rtpcr-2.1.2/rtpcr/data/data_repeated_measure_3bLock.rda |only rtpcr-2.1.2/rtpcr/data/data_ttest18genes.rda |only rtpcr-2.1.2/rtpcr/data/data_withTechRep.rda |binary rtpcr-2.1.2/rtpcr/inst/doc/Manual.R | 78 -- rtpcr-2.1.2/rtpcr/inst/doc/Manual.Rmd | 183 ++--- rtpcr-2.1.2/rtpcr/inst/doc/Manual.html | 366 +++++----- rtpcr-2.1.2/rtpcr/inst/extdata/data_1factor.csv | 2 rtpcr-2.1.2/rtpcr/inst/extdata/data_1factor_Two_ref.csv | 2 rtpcr-2.1.2/rtpcr/inst/extdata/data_1factor_one_ref.csv | 2 rtpcr-2.1.2/rtpcr/inst/extdata/data_1factor_one_ref_Eff.csv | 2 rtpcr-2.1.2/rtpcr/inst/extdata/data_2factor.csv | 2 rtpcr-2.1.2/rtpcr/inst/extdata/data_2factorBlock.csv | 2 rtpcr-2.1.2/rtpcr/inst/extdata/data_2factorBlock3ref.csv | 50 - rtpcr-2.1.2/rtpcr/inst/extdata/data_3factor.csv | 2 rtpcr-2.1.2/rtpcr/inst/extdata/data_Heffer2020PlosOne.csv |only rtpcr-2.1.2/rtpcr/inst/extdata/data_Lee_etal2020qPCR.csv |only rtpcr-2.1.2/rtpcr/inst/extdata/data_Yuan2006PMCBioinf.csv |only rtpcr-2.1.2/rtpcr/inst/extdata/data_efficiency1.csv |only rtpcr-2.1.2/rtpcr/inst/extdata/data_efficiency_Yuan2006PMCBioinf.csv |only rtpcr-2.1.2/rtpcr/inst/extdata/data_repeated_measure_1.csv | 2 rtpcr-2.1.2/rtpcr/inst/extdata/data_repeated_measure_2.csv | 2 rtpcr-2.1.2/rtpcr/inst/extdata/data_repeated_measure_3bLock.csv | 2 rtpcr-2.1.2/rtpcr/inst/extdata/data_ttest18genes.csv |only rtpcr-2.1.2/rtpcr/inst/extdata/data_withTechRep.csv | 38 - rtpcr-2.1.2/rtpcr/man/ANCOVA_DDCt.Rd |only rtpcr-2.1.2/rtpcr/man/ANOVA_DCt.Rd | 37 - rtpcr-2.1.2/rtpcr/man/ANOVA_DDCt.Rd | 104 +- rtpcr-2.1.2/rtpcr/man/Means_DDCt.Rd | 33 rtpcr-2.1.2/rtpcr/man/REPEATED_DDCt.Rd | 118 +-- rtpcr-2.1.2/rtpcr/man/TTEST_DDCt.Rd | 47 - rtpcr-2.1.2/rtpcr/man/WILCOX_DDCt.Rd |only rtpcr-2.1.2/rtpcr/man/compute_wDCt.Rd |only rtpcr-2.1.2/rtpcr/man/data_1factor.Rd | 6 rtpcr-2.1.2/rtpcr/man/data_1factor_Two_ref.Rd | 8 rtpcr-2.1.2/rtpcr/man/data_1factor_one_ref.Rd | 10 rtpcr-2.1.2/rtpcr/man/data_1factor_one_ref_Eff.Rd | 6 rtpcr-2.1.2/rtpcr/man/data_2factor.Rd | 6 rtpcr-2.1.2/rtpcr/man/data_2factor3ref.Rd | 2 rtpcr-2.1.2/rtpcr/man/data_2factorBlock.Rd | 10 rtpcr-2.1.2/rtpcr/man/data_2factorBlock3ref.Rd | 24 rtpcr-2.1.2/rtpcr/man/data_3factor.Rd | 6 rtpcr-2.1.2/rtpcr/man/data_Heffer2020PlosOne.Rd |only rtpcr-2.1.2/rtpcr/man/data_Lee_etal2020qPCR.Rd |only rtpcr-2.1.2/rtpcr/man/data_Yuan2006PMCBioinf.Rd |only rtpcr-2.1.2/rtpcr/man/data_efficiency1.Rd |only rtpcr-2.1.2/rtpcr/man/data_efficiency_Yuan2006PMCBioinf.Rd |only rtpcr-2.1.2/rtpcr/man/data_repeated_measure_1.Rd | 2 rtpcr-2.1.2/rtpcr/man/data_repeated_measure_2.Rd | 2 rtpcr-2.1.2/rtpcr/man/data_repeated_measure_3bLock.Rd |only rtpcr-2.1.2/rtpcr/man/data_ttest18genes.Rd |only rtpcr-2.1.2/rtpcr/man/data_withTechRep.Rd | 10 rtpcr-2.1.2/rtpcr/man/efficiency.Rd | 101 +- rtpcr-2.1.2/rtpcr/man/figures/dataStructure1.png |binary rtpcr-2.1.2/rtpcr/man/figures/logo.png |binary rtpcr-2.1.2/rtpcr/man/figures/techrep.png |binary rtpcr-2.1.2/rtpcr/man/globalVariables.Rd | 2 rtpcr-2.1.2/rtpcr/man/long_to_wide.Rd |only rtpcr-2.1.2/rtpcr/man/meanTech.Rd | 21 rtpcr-2.1.2/rtpcr/man/multiplot.Rd | 36 rtpcr-2.1.2/rtpcr/man/plotFactor.Rd | 52 - rtpcr-2.1.2/rtpcr/vignettes/Manual.Rmd | 183 ++--- 114 files changed, 987 insertions(+), 792 deletions(-)
Title: Mechanistic Simulation of Species Range Dynamics
Description: Integrates population dynamics and dispersal into a
mechanistic virtual species simulator. The package can be used to
study the effects of environmental change on population growth and
range shifts. It allows for simple and straightforward definition of
population dynamics (including positive density dependence), extensive
possibilities for defining dispersal kernels, and the ability to
generate virtual ecologist data. Learn more about the 'rangr' at
<https://docs.ropensci.org/rangr/>. This work was supported by
the National Science Centre, Poland, grant no. 2018/29/B/NZ8/00066 and
the Poznań Supercomputing and Networking Centre (grant no. pl0090-01).
Author: Katarzyna Markowska [aut, cre],
Lechoslaw Kuczynski [aut],
Tad Dallas [rev],
Joanne Potts [rev]
Maintainer: Katarzyna Markowska <katarzyna.markowska@amu.edu.pl>
Diff between rangr versions 1.0.8 dated 2025-12-17 and 1.0.9 dated 2026-01-23
DESCRIPTION | 10 ++++++---- MD5 | 8 ++++---- NEWS.md | 6 ++++++ inst/doc/rangr.html | 2 +- man/rangr-package.Rd | 2 +- 5 files changed, 18 insertions(+), 10 deletions(-)
Title: Probabilistic Forecast Combination Using CRPS Learning
Description: Combine probabilistic forecasts using CRPS learning algorithms proposed in Berrisch, Ziel (2021) <doi:10.48550/arXiv.2102.00968> <doi:10.1016/j.jeconom.2021.11.008>. The package implements multiple online learning algorithms like Bernstein online aggregation; see Wintenberger (2014) <doi:10.48550/arXiv.1404.1356>. Quantile regression is also implemented for comparison purposes. Model parameters can be tuned automatically with respect to the loss of the forecast combination. Methods like predict(), update(), plot() and print() are available for convenience. This package utilizes the optim C++ library for numeric optimization <https://github.com/kthohr/optim>.
Author: Jonathan Berrisch [aut, cre] ,
Florian Ziel [aut]
Maintainer: Jonathan Berrisch <Jonathan@Berrisch.biz>
Diff between profoc versions 1.3.3 dated 2024-09-21 and 1.3.4 dated 2026-01-23
profoc-1.3.3/profoc/vignettes/methods.html |only profoc-1.3.4/profoc/DESCRIPTION | 13 profoc-1.3.4/profoc/MD5 | 21 profoc-1.3.4/profoc/NEWS.md | 10 profoc-1.3.4/profoc/build/partial.rdb |binary profoc-1.3.4/profoc/inst/doc/class.html | 4 profoc-1.3.4/profoc/inst/doc/production.html | 4 profoc-1.3.4/profoc/inst/doc/profoc.html | 4 profoc-1.3.4/profoc/src/batch.cpp | 628 +++++++++----------- profoc-1.3.4/profoc/src/conline.cpp | 137 ++-- profoc-1.3.4/profoc/src/oracle.cpp | 846 +++++++++++++-------------- profoc-1.3.4/profoc/src/splines.cpp | 264 ++++---- 12 files changed, 968 insertions(+), 963 deletions(-)
Title: Extract Remote Sensing Vegetation Phenology
Description: The merits of 'TIMESAT' and 'phenopix' are adopted. Besides, a simple and
growing season dividing method and a practical snow elimination method
based on Whittaker were proposed. 7 curve fitting methods and 4 phenology
extraction methods were provided. Parameters boundary are considered for
every curve fitting methods according to their ecological meaning.
And 'optimx' is used to select best optimization method for different
curve fitting methods.
Reference:
Kong, D., (2020). R package: A state-of-the-art Vegetation Phenology extraction
package, phenofit version 0.3.1, <doi:10.5281/zenodo.5150204>;
Kong, D., Zhang, Y., Wang, D., Chen, J., & Gu, X. (2020). Photoperiod Explains
the Asynchronization Between Vegetation Carbon Phenology and Vegetation Greenness
Phenology. Journal of Geophysical Research: Biogeosciences, 125(8), e2020JG005636.
<doi:10.1029/2020JG005636>;
Kong, D., Zhang, Y., Gu, X., & Wang, D. (2019). A robust method for reconstructing
global MODIS EVI ti [...truncated...]
Author: Dongdong Kong [aut, cre],
Mingzhong Xiao [aut],
Yongqiang Zhang [aut],
Xihui Gu [aut],
Jianjian Cui [aut]
Maintainer: Dongdong Kong <kongdd.sysu@gmail.com>
This is a re-admission after prior archival of version 0.3.10 dated 2025-05-25
Diff between phenofit versions 0.3.10 dated 2025-05-25 and 0.3.11 dated 2026-01-23
DESCRIPTION | 8 MD5 | 12 R/findpeaks.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/phenofit-procedures.html | 493 +++++++++++++++++++------------------- inst/doc/phenofit_CA-NS6.html | 388 ++++++++++++++--------------- 7 files changed, 459 insertions(+), 444 deletions(-)
Title: Data Manipulation Functions Implemented in C
Description: Basic functions, implemented in C, for large data manipulation. Fast vectorised ifelse()/nested if()/switch() functions, psum()/pprod() functions equivalent to pmin()/pmax() plus others which are missing from base R. Most of these functions are callable at C level.
Author: Morgan Jacob [aut, cph],
Sebastian Krantz [ctb, cre]
Maintainer: Sebastian Krantz <sebastian.krantz@graduateinstitute.ch>
Diff between kit versions 0.0.20 dated 2025-04-17 and 0.0.21 dated 2026-01-23
kit-0.0.20/kit/inst/NEWS.Rd |only kit-0.0.20/kit/tests/test_kit.Rout.save |only kit-0.0.21/kit/DESCRIPTION | 23 - kit-0.0.21/kit/MD5 | 42 +- kit-0.0.21/kit/NAMESPACE | 6 kit-0.0.21/kit/NEWS.md |only kit-0.0.21/kit/R/call.R | 7 kit-0.0.21/kit/build |only kit-0.0.21/kit/inst/doc |only kit-0.0.21/kit/man/count.Rd | 6 kit-0.0.21/kit/man/fpos.Rd | 8 kit-0.0.21/kit/man/funique.Rd | 6 kit-0.0.21/kit/man/iif.Rd | 4 kit-0.0.21/kit/man/nif.Rd | 2 kit-0.0.21/kit/man/psort.Rd | 10 kit-0.0.21/kit/man/psum.Rd | 59 ++- kit-0.0.21/kit/man/shareData.Rd | 6 kit-0.0.21/kit/man/topn.Rd | 8 kit-0.0.21/kit/man/vswitch.Rd | 12 kit-0.0.21/kit/src/init.c | 6 kit-0.0.21/kit/src/kit.h | 3 kit-0.0.21/kit/src/psum.c | 504 ++++++++++++++++++++++++++++++++ kit-0.0.21/kit/tests/test_kit.R | 98 +++++- kit-0.0.21/kit/vignettes |only 24 files changed, 716 insertions(+), 94 deletions(-)
Title: Plotting Football Matches Expected Goals (xG) Stats with
'Understat' Data
Description: Scrapes football match shots data from 'Understat' <https://understat.com/> and visualizes it using interactive plots:
- A detailed shot map displaying the location, type, and xG value of shots taken by both teams.
- An xG timeline chart showing the cumulative xG for each team over time, annotated with the details of scored goals.
Author: Aymen Nasri [aut, cre, cph]
Maintainer: Aymen Nasri <aymennasrii@proton.me>
This is a re-admission after prior archival of version 0.2.1 dated 2025-03-22
Diff between ggfootball versions 0.2.1 dated 2025-03-22 and 0.2.2 dated 2026-01-23
ggfootball-0.2.1/ggfootball/R/team_formation.R |only ggfootball-0.2.2/ggfootball/DESCRIPTION | 8 +-- ggfootball-0.2.2/ggfootball/MD5 | 17 +++---- ggfootball-0.2.2/ggfootball/NEWS.md | 4 + ggfootball-0.2.2/ggfootball/R/understat_scraper.R | 49 ++++++++++++++++++++-- ggfootball-0.2.2/ggfootball/R/xg_chart.R | 4 + ggfootball-0.2.2/ggfootball/R/xg_map.R | 4 + ggfootball-0.2.2/ggfootball/README.md | 3 - ggfootball-0.2.2/ggfootball/man/xg_chart.Rd | 2 ggfootball-0.2.2/ggfootball/man/xg_map.Rd | 2 10 files changed, 74 insertions(+), 19 deletions(-)
Title: Population Genetic Data Analysis Using Genepop
Description: Makes the Genepop software available in R. This software implements a mixture of traditional population genetic methods and some more focused developments: it computes exact tests for Hardy-Weinberg equilibrium, for population differentiation and for genotypic disequilibrium among pairs of loci; it computes estimates of F-statistics, null allele frequencies, allele size-based statistics for microsatellites, etc.; and it performs analyses of isolation by distance from pairwise comparisons of individuals or population samples.
Author: Francois Rousset [aut, cre, cph] ,
Jimmy Lopez [ctb],
Alexandre Genin [ctb],
Khalid Belkhir [ctb]
Maintainer: Francois Rousset <francois.rousset@umontpellier.fr>
Diff between genepop versions 1.2.11 dated 2025-08-27 and 1.2.14 dated 2026-01-23
DESCRIPTION | 8 MD5 | 34 inst/NEWS.Rd | 5 inst/doc/GenepopS.Rmd | 9 inst/doc/GenepopS.pdf |binary inst/doc/GenepopS.tex | 15 inst/doc/all-menu-options.html | 10 inst/doc/bibliography.html | 10 inst/doc/code-maintenance-credits-contact-etc..html | 10 inst/doc/copyright.html | 10 inst/doc/evaluating-the-performance-of-inferences-for-isolation-by-distance.html | 10 inst/doc/installing-genepop-and-session-examples.html | 16 inst/doc/introduction.html | 16 inst/doc/methods.html | 10 inst/doc/sec-settings.html | 10 inst/doc/the-input-file.html | 10 src/F_est.cpp | 525 +++++----- src/GenepopS.cpp | 2 18 files changed, 364 insertions(+), 346 deletions(-)
Title: Describe, Package, and Share Biodiversity Data
Description: The Darwin Core data standard is widely used to share
biodiversity information, most notably by the Global Biodiversity Information
Facility and its partner nodes; but converting data to this standard can be
tricky. 'galaxias' is functionally similar to 'devtools', but with a focus on
building Darwin Core Archives rather than R packages, enabling data to be
shared and re-used with relative ease. For details see
Wieczorek and colleagues (2012) <doi:10.1371/journal.pone.0029715>.
Author: Martin Westgate [aut, cre],
Shandiya Balasubramaniam [aut],
Dax Kellie [aut]
Maintainer: Martin Westgate <martin.westgate@csiro.au>
This is a re-admission after prior archival of version 0.1.1 dated 2025-10-22
Diff between galaxias versions 0.1.1 dated 2025-10-22 and 0.1.2 dated 2026-01-23
DESCRIPTION | 8 MD5 | 26 - NEWS.md | 5 build/vignette.rds |binary inst/doc/events-example.R | 4 inst/doc/events-example.html | 54 +-- inst/doc/occurrences-example.R | 17 - inst/doc/occurrences-example.Rmd | 53 ++- inst/doc/occurrences-example.html | 620 +++++++++++++++++++------------------- inst/doc/quick_start_guide.R | 82 ++--- inst/doc/quick_start_guide.Rmd | 6 inst/doc/quick_start_guide.html | 65 ++- vignettes/occurrences-example.Rmd | 53 ++- vignettes/quick_start_guide.Rmd | 6 14 files changed, 534 insertions(+), 465 deletions(-)
Title: Comparison of Bioregionalization Methods
Description: The main purpose of this package is to propose a transparent methodological framework to compare bioregionalization methods based on hierarchical and non-hierarchical clustering algorithms (Kreft & Jetz (2010) <doi:10.1111/j.1365-2699.2010.02375.x>) and network algorithms (Lenormand et al. (2019) <doi:10.1002/ece3.4718> and Leroy et al. (2019) <doi:10.1111/jbi.13674>).
Author: Maxime Lenormand [aut, cre] ,
Boris Leroy [aut] ,
Pierre Denelle [aut]
Maintainer: Maxime Lenormand <maxime.lenormand@inrae.fr>
Diff between bioregion versions 1.2.0 dated 2025-01-31 and 1.3.0 dated 2026-01-23
bioregion-1.2.0/bioregion/NEWS.md |only bioregion-1.2.0/bioregion/README.md |only bioregion-1.2.0/bioregion/man/figures/zscore_scheme.svg |only bioregion-1.3.0/bioregion/DESCRIPTION | 28 bioregion-1.3.0/bioregion/MD5 | 154 - bioregion-1.3.0/bioregion/NAMESPACE | 18 bioregion-1.3.0/bioregion/R/as_bioregion_pairwise.R |only bioregion-1.3.0/bioregion/R/betapart_to_bioregion.R | 12 bioregion-1.3.0/bioregion/R/bind_pairwise.R |only bioregion-1.3.0/bioregion/R/bioregion_colors.R |only bioregion-1.3.0/bioregion/R/bioregion_metrics.R | 2 bioregion-1.3.0/bioregion/R/bioregionalization_metrics.R | 27 bioregion-1.3.0/bioregion/R/compare_bioregionalizations.R | 50 bioregion-1.3.0/bioregion/R/cut_tree.R | 37 bioregion-1.3.0/bioregion/R/dissimilarity.R | 6 bioregion-1.3.0/bioregion/R/exportGDF.R | 340 ++ bioregion-1.3.0/bioregion/R/find_optimal_n.R | 108 bioregion-1.3.0/bioregion/R/generic_functions.R | 1344 +++++++--- bioregion-1.3.0/bioregion/R/hclu_diana.R | 55 bioregion-1.3.0/bioregion/R/hclu_hierarclust.R | 153 - bioregion-1.3.0/bioregion/R/hclu_optics.R | 28 bioregion-1.3.0/bioregion/R/install_binaries.R | 190 - bioregion-1.3.0/bioregion/R/iterative_hierarchical_consensus_tree.R | 5 bioregion-1.3.0/bioregion/R/map_bioregions.R | 219 + bioregion-1.3.0/bioregion/R/net_to_mat.R | 8 bioregion-1.3.0/bioregion/R/netclu_beckett.R | 12 bioregion-1.3.0/bioregion/R/netclu_greedy.R | 29 bioregion-1.3.0/bioregion/R/netclu_infomap.R | 30 bioregion-1.3.0/bioregion/R/netclu_labelprop.R | 29 bioregion-1.3.0/bioregion/R/netclu_leadingeigen.R | 28 bioregion-1.3.0/bioregion/R/netclu_leiden.R | 29 bioregion-1.3.0/bioregion/R/netclu_louvain.R | 28 bioregion-1.3.0/bioregion/R/netclu_oslom.R | 28 bioregion-1.3.0/bioregion/R/netclu_walktrap.R | 29 bioregion-1.3.0/bioregion/R/nhclu_affprop.R | 130 bioregion-1.3.0/bioregion/R/nhclu_clara.R | 27 bioregion-1.3.0/bioregion/R/nhclu_clarans.R | 28 bioregion-1.3.0/bioregion/R/nhclu_dbscan.R | 35 bioregion-1.3.0/bioregion/R/nhclu_kmeans.R | 27 bioregion-1.3.0/bioregion/R/nhclu_pam.R | 27 bioregion-1.3.0/bioregion/R/similarity.R | 12 bioregion-1.3.0/bioregion/R/similarity_dissimilarity_conversion.R | 12 bioregion-1.3.0/bioregion/R/site_species_metrics.R | 1150 +++++--- bioregion-1.3.0/bioregion/R/site_species_subset.R | 59 bioregion-1.3.0/bioregion/R/utils.R | 742 +++++ bioregion-1.3.0/bioregion/build/partial.rdb |binary bioregion-1.3.0/bioregion/build/vignette.rds |binary bioregion-1.3.0/bioregion/inst/CITATION |only bioregion-1.3.0/bioregion/inst/REFERENCES.bib | 58 bioregion-1.3.0/bioregion/inst/doc/a5_2_summary_metrics.R |only bioregion-1.3.0/bioregion/inst/doc/a5_2_summary_metrics.Rmd |only bioregion-1.3.0/bioregion/inst/doc/a5_2_summary_metrics.html |only bioregion-1.3.0/bioregion/inst/doc/a5_3_compare_bioregionalizations.R |only bioregion-1.3.0/bioregion/inst/doc/a5_3_compare_bioregionalizations.Rmd |only bioregion-1.3.0/bioregion/inst/doc/a5_3_compare_bioregionalizations.html |only bioregion-1.3.0/bioregion/inst/doc/bioregion.Rmd | 37 bioregion-1.3.0/bioregion/inst/doc/bioregion.html | 163 - bioregion-1.3.0/bioregion/inst/doc/citations.Rmd |only bioregion-1.3.0/bioregion/inst/doc/citations.html |only bioregion-1.3.0/bioregion/man/as_bioregion_pairwise.Rd |only bioregion-1.3.0/bioregion/man/betapart_to_bioregion.Rd | 8 bioregion-1.3.0/bioregion/man/bind_pairwise.Rd |only bioregion-1.3.0/bioregion/man/bioregion_colors.Rd |only bioregion-1.3.0/bioregion/man/bioregion_metrics.Rd | 2 bioregion-1.3.0/bioregion/man/bioregionalization_metrics.Rd | 2 bioregion-1.3.0/bioregion/man/compare_bioregionalizations.Rd | 8 bioregion-1.3.0/bioregion/man/cut_tree.Rd | 8 bioregion-1.3.0/bioregion/man/dissimilarity.Rd | 6 bioregion-1.3.0/bioregion/man/dissimilarity_to_similarity.Rd | 6 bioregion-1.3.0/bioregion/man/exportGDF.Rd |only bioregion-1.3.0/bioregion/man/figures/05_map_fish_bipartite_infomap.png |only bioregion-1.3.0/bioregion/man/figures/05_network_fish_basic.png |only bioregion-1.3.0/bioregion/man/figures/05_network_fish_bipartite_colored.png |only bioregion-1.3.0/bioregion/man/figures/05_network_fish_unipartite_weighted.png |only bioregion-1.3.0/bioregion/man/figures/comparison_Bray-Curtis.png |only bioregion-1.3.0/bioregion/man/figures/comparison_Jaccard.png |only bioregion-1.3.0/bioregion/man/figures/core_terms.svg |only bioregion-1.3.0/bioregion/man/find_optimal_n.Rd | 6 bioregion-1.3.0/bioregion/man/hclu_diana.Rd | 8 bioregion-1.3.0/bioregion/man/hclu_hierarclust.Rd | 25 bioregion-1.3.0/bioregion/man/install_binaries.Rd | 6 bioregion-1.3.0/bioregion/man/map_bioregions.Rd | 45 bioregion-1.3.0/bioregion/man/nhclu_affprop.Rd | 6 bioregion-1.3.0/bioregion/man/nhclu_dbscan.Rd | 4 bioregion-1.3.0/bioregion/man/similarity.Rd | 8 bioregion-1.3.0/bioregion/man/similarity_to_dissimilarity.Rd | 6 bioregion-1.3.0/bioregion/man/site_species_metrics.Rd | 379 ++ bioregion-1.3.0/bioregion/man/site_species_subset.Rd | 12 bioregion-1.3.0/bioregion/vignettes/a5_2_summary_metrics.Rmd |only bioregion-1.3.0/bioregion/vignettes/a5_3_compare_bioregionalizations.Rmd |only bioregion-1.3.0/bioregion/vignettes/bioregion.Rmd | 37 bioregion-1.3.0/bioregion/vignettes/citations.Rmd |only bioregion-1.3.0/bioregion/vignettes/style_citation.csl |only 93 files changed, 4708 insertions(+), 1407 deletions(-)
Title: Custom Legends with Statistical Comparison Brackets
Description: Add publication-quality custom legends with vertical brackets. Designed for displaying statistical comparisons between groups,
commonly used in scientific publications for showing significance levels.
Features include adaptive positioning, automatic bracket spacing for overlapping
comparisons, font family inheritance, and support for asterisks, p-values,
or custom labels. Compatible with 'ggplot2' graphics.
Author: Yoshiaki Sato [aut, cre]
Maintainer: Yoshiaki Sato <h20gg702@outlook.jp>
Diff between vbracket versions 1.0.2 dated 2026-01-07 and 1.1.0 dated 2026-01-23
DESCRIPTION | 6 +-- MD5 | 6 +-- R/annotation_grob.R | 57 ++++++++++++++++++++------------- R/custom_legend_with_brackets.R | 69 +++++++++++++++++++++++----------------- 4 files changed, 82 insertions(+), 56 deletions(-)
Title: Trust, but Verify
Description: Declarative template-based framework for verifying that objects
meet structural requirements, and auto-composing error messages when they do
not.
Author: Brodie Gaslam [aut, cre],
Paxdiablo [cph] ,
R Core Team [cph] ,
Michael Chirico [ctb]
Maintainer: Brodie Gaslam <brodie.gaslam@yahoo.com>
Diff between vetr versions 0.2.19 dated 2025-11-23 and 0.2.20 dated 2026-01-23
DESCRIPTION | 6 MD5 | 135 ++++++++++----------- NEWS.md | 16 ++ R/abstract.R | 26 ++-- R/alike.R | 2 R/benchmark.R | 2 R/cstringr.R | 2 R/helper.R | 2 R/misc.R | 2 R/settings.R | 2 R/system.R | 2 R/templates.R | 2 R/type.R | 2 R/validate.R | 2 R/validators.R | 2 R/vetr-package.R | 2 inst/doc/alike.html | 12 - inst/doc/vetr.html | 10 - man/abstract.Rd | 19 +-- src/alike.c | 115 ++++++++---------- src/alike.h | 5 src/assumptions.c | 2 src/attr.c | 189 ++++++++++++++---------------- src/backports.c |only src/backports.h | 10 + src/cstringr-ext.c | 2 src/cstringr.c | 2 src/cstringr.h | 2 src/cstringrtest.c | 2 src/envtrack.c | 2 src/eval.c | 2 src/fun.c | 4 src/init.c | 3 src/lang.c | 12 - src/merge.c | 2 src/misc-alike.c | 87 ++++--------- src/misc.c | 2 src/parse.c | 2 src/pfhash.c | 2 src/pfhash.h | 2 src/r-copied.c | 2 src/recurse.c | 2 src/settings.c | 2 src/settings.h | 2 src/strsub.c | 2 src/trackinghash.c | 2 src/trackinghash.h | 2 src/type.c | 18 +- src/validate.c | 2 src/validate.h | 2 src/valname.c | 2 tests/unitizer/abstract.R | 26 +++- tests/unitizer/abstract.unitizer/data.rds |binary tests/unitizer/alike.R | 16 ++ tests/unitizer/alike.unitizer/data.rds |binary tests/unitizer/all-bw.R | 2 tests/unitizer/classes.R | 2 tests/unitizer/cstringr.R | 2 tests/unitizer/eval.R | 2 tests/unitizer/internal.R | 2 tests/unitizer/internal.unitizer/data.rds |binary tests/unitizer/language.R | 2 tests/unitizer/misc.R | 13 +- tests/unitizer/misc.unitizer/data.rds |binary tests/unitizer/parse.R | 2 tests/unitizer/tev.R | 2 tests/unitizer/type.R | 2 tests/unitizer/validate.R | 2 tests/unitizer/validate.args.R | 2 69 files changed, 417 insertions(+), 395 deletions(-)
Title: Tools for Generating and Handling of UUIDs
Description: Tools for generating and handling of UUIDs (Universally Unique Identifiers).
Author: Simon Urbanek [aut, cre, cph] ,
Theodore Ts'o [aut, cph]
Maintainer: Simon Urbanek <Simon.Urbanek@r-project.org>
Diff between uuid versions 1.2-1 dated 2024-07-29 and 1.2-2 dated 2026-01-23
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 7 +++++++ man/UUIDgenerate.Rd | 13 ++++++++++++- src/R.c | 11 +++++++++-- src/Ruuid.c | 7 +++++++ src/randutils.c | 2 +- 7 files changed, 46 insertions(+), 14 deletions(-)
Title: 'tidyverse' Methods and 'ggplot2' Helpers for 'terra' Objects
Description: Extension of the 'tidyverse' for 'SpatRaster' and
'SpatVector' objects of the 'terra' package. It includes also new
'geom_' functions that provide a convenient way of visualizing 'terra'
objects with 'ggplot2'.
Author: Diego Hernangomez [aut, cre, cph] ,
Dewey Dunnington [ctb] ,
ggplot2 authors [cph] ,
Andrea Manica [ctb]
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>
Diff between tidyterra versions 0.7.2 dated 2025-04-14 and 1.0.0 dated 2026-01-23
tidyterra-0.7.2/tidyterra/R/as_coordinates.R |only tidyterra-0.7.2/tidyterra/R/as_sf.R |only tidyterra-0.7.2/tidyterra/R/as_spatraster.R |only tidyterra-0.7.2/tidyterra/R/as_spatvector.R |only tidyterra-0.7.2/tidyterra/R/as_tibble-Spat.R |only tidyterra-0.7.2/tidyterra/R/compare_spatrasters.R |only tidyterra-0.7.2/tidyterra/R/drop_na-Spat.R |only tidyterra-0.7.2/tidyterra/R/geom_spat_contour.R |only tidyterra-0.7.2/tidyterra/R/geom_spat_contour_fill.R |only tidyterra-0.7.2/tidyterra/R/geom_spat_contour_text.R |only tidyterra-0.7.2/tidyterra/R/geom_spatraster.R |only tidyterra-0.7.2/tidyterra/R/geom_spatraster_rgb.R |only tidyterra-0.7.2/tidyterra/R/geom_spatvector.R |only tidyterra-0.7.2/tidyterra/R/is_regular_grid.R |only tidyterra-0.7.2/tidyterra/R/pull_crs.R |only tidyterra-0.7.2/tidyterra/R/replace_na-Spat.R |only tidyterra-0.7.2/tidyterra/R/scales_coltab.R |only tidyterra-0.7.2/tidyterra/R/scales_cross_blended.R |only tidyterra-0.7.2/tidyterra/R/scales_grass.R |only tidyterra-0.7.2/tidyterra/R/scales_hypso.R |only tidyterra-0.7.2/tidyterra/R/scales_princess.R |only tidyterra-0.7.2/tidyterra/R/scales_terrain.R |only tidyterra-0.7.2/tidyterra/R/scales_whitebox.R |only tidyterra-0.7.2/tidyterra/R/scales_wiki.R |only tidyterra-0.7.2/tidyterra/R/stat_spat_coordinates.R |only tidyterra-0.7.2/tidyterra/R/stat_spatraster.R |only tidyterra-0.7.2/tidyterra/tests/testthat/test-as_coordinates.R |only tidyterra-0.7.2/tidyterra/tests/testthat/test-as_sf.R |only tidyterra-0.7.2/tidyterra/tests/testthat/test-as_spatraster.R |only tidyterra-0.7.2/tidyterra/tests/testthat/test-as_spatvector.R |only tidyterra-0.7.2/tidyterra/tests/testthat/test-as_tibble-Spat.R |only tidyterra-0.7.2/tidyterra/tests/testthat/test-compare_spatrasters.R |only tidyterra-0.7.2/tidyterra/tests/testthat/test-drop_na-Spat.R |only tidyterra-0.7.2/tidyterra/tests/testthat/test-geom_spat_contour.R |only tidyterra-0.7.2/tidyterra/tests/testthat/test-geom_spat_contour_fill.R |only tidyterra-0.7.2/tidyterra/tests/testthat/test-geom_spat_contour_text.R |only tidyterra-0.7.2/tidyterra/tests/testthat/test-geom_spatraster_1lyr.R |only tidyterra-0.7.2/tidyterra/tests/testthat/test-geom_spatraster_1lyr_coltab.R |only tidyterra-0.7.2/tidyterra/tests/testthat/test-geom_spatraster_3lyr.R |only tidyterra-0.7.2/tidyterra/tests/testthat/test-geom_spatraster_3lyr_coltab.R |only tidyterra-0.7.2/tidyterra/tests/testthat/test-geom_spatraster_rgb.R |only tidyterra-0.7.2/tidyterra/tests/testthat/test-geom_spatvector.R |only tidyterra-0.7.2/tidyterra/tests/testthat/test-keep_coltab.R |only tidyterra-0.7.2/tidyterra/tests/testthat/test-pull_crs.R |only tidyterra-0.7.2/tidyterra/tests/testthat/test-replace_na-Spat.R |only tidyterra-0.7.2/tidyterra/tests/testthat/test-scales_col_cross_blended.R |only tidyterra-0.7.2/tidyterra/tests/testthat/test-scales_col_hypso.R |only tidyterra-0.7.2/tidyterra/tests/testthat/test-scales_col_terrain.R |only tidyterra-0.7.2/tidyterra/tests/testthat/test-scales_col_whitebox.R |only tidyterra-0.7.2/tidyterra/tests/testthat/test-scales_col_wiki.R |only tidyterra-0.7.2/tidyterra/tests/testthat/test-scales_coltab.R |only tidyterra-0.7.2/tidyterra/tests/testthat/test-scales_fill_cross_blended.R |only tidyterra-0.7.2/tidyterra/tests/testthat/test-scales_fill_hypso.R |only tidyterra-0.7.2/tidyterra/tests/testthat/test-scales_fill_terrain.R |only tidyterra-0.7.2/tidyterra/tests/testthat/test-scales_fill_whitebox.R |only tidyterra-0.7.2/tidyterra/tests/testthat/test-scales_fill_wiki.R |only tidyterra-0.7.2/tidyterra/tests/testthat/test-scales_grass.R |only tidyterra-0.7.2/tidyterra/tests/testthat/test-scales_princess.R |only tidyterra-0.7.2/tidyterra/tests/testthat/test-stat_spatraster.R |only tidyterra-1.0.0/tidyterra/DESCRIPTION | 33 tidyterra-1.0.0/tidyterra/MD5 | 423 +++--- tidyterra-1.0.0/tidyterra/NAMESPACE | 19 tidyterra-1.0.0/tidyterra/NEWS.md | 470 +++--- tidyterra-1.0.0/tidyterra/R/arrange-SpatVector.R | 12 tidyterra-1.0.0/tidyterra/R/as-coordinates.R |only tidyterra-1.0.0/tidyterra/R/as-sf.R |only tidyterra-1.0.0/tidyterra/R/as-spatraster.R |only tidyterra-1.0.0/tidyterra/R/as-spatvector.R |only tidyterra-1.0.0/tidyterra/R/as-tibble-Spat.R |only tidyterra-1.0.0/tidyterra/R/autoplot-Spat.R | 63 tidyterra-1.0.0/tidyterra/R/bind-cols-SpatVector.R | 23 tidyterra-1.0.0/tidyterra/R/bind-rows-SpatVector.R | 17 tidyterra-1.0.0/tidyterra/R/compare-spatrasters.R |only tidyterra-1.0.0/tidyterra/R/count-tally-SpatVector.R | 53 tidyterra-1.0.0/tidyterra/R/data.R | 20 tidyterra-1.0.0/tidyterra/R/distinct-SpatVector.R | 265 +-- tidyterra-1.0.0/tidyterra/R/drop-na-Spat.R |only tidyterra-1.0.0/tidyterra/R/fill-SpatVector.R | 25 tidyterra-1.0.0/tidyterra/R/filter-Spat.R | 33 tidyterra-1.0.0/tidyterra/R/fortify-Spat.R | 316 ++-- tidyterra-1.0.0/tidyterra/R/geom-spat-contour-fill.R |only tidyterra-1.0.0/tidyterra/R/geom-spat-contour-text.R |only tidyterra-1.0.0/tidyterra/R/geom-spat-contour.R |only tidyterra-1.0.0/tidyterra/R/geom-spatraster-rgb.R |only tidyterra-1.0.0/tidyterra/R/geom-spatraster.R |only tidyterra-1.0.0/tidyterra/R/geom-spatvector.R |only tidyterra-1.0.0/tidyterra/R/glance-Spat.R |only tidyterra-1.0.0/tidyterra/R/glimpse-Spat.R | 146 +- tidyterra-1.0.0/tidyterra/R/group-by-SpatVector.R | 37 tidyterra-1.0.0/tidyterra/R/group-data-SpatVector.R | 2 tidyterra-1.0.0/tidyterra/R/grouped-SpatVector.R | 2 tidyterra-1.0.0/tidyterra/R/is-regular-grid.R |only tidyterra-1.0.0/tidyterra/R/join-SpatVector.R | 118 + tidyterra-1.0.0/tidyterra/R/mutate-Spat.R | 25 tidyterra-1.0.0/tidyterra/R/pivot-long-SpatVector.R | 48 tidyterra-1.0.0/tidyterra/R/pivot-wide-SpatVector.R | 87 - tidyterra-1.0.0/tidyterra/R/pull-Spat.R | 20 tidyterra-1.0.0/tidyterra/R/pull-crs.R |only tidyterra-1.0.0/tidyterra/R/relocate-Spat.R | 19 tidyterra-1.0.0/tidyterra/R/rename-Spat.R | 10 tidyterra-1.0.0/tidyterra/R/replace-na-Spat.R |only tidyterra-1.0.0/tidyterra/R/required-pkgs-Spat.R |only tidyterra-1.0.0/tidyterra/R/rowwise-SpatVector.R | 36 tidyterra-1.0.0/tidyterra/R/scales-coltab.R |only tidyterra-1.0.0/tidyterra/R/scales-cross-blended.R |only tidyterra-1.0.0/tidyterra/R/scales-grass.R |only tidyterra-1.0.0/tidyterra/R/scales-hypso.R |only tidyterra-1.0.0/tidyterra/R/scales-princess.R |only tidyterra-1.0.0/tidyterra/R/scales-terrain.R |only tidyterra-1.0.0/tidyterra/R/scales-whitebox.R |only tidyterra-1.0.0/tidyterra/R/scales-wiki.R |only tidyterra-1.0.0/tidyterra/R/select-Spat.R | 15 tidyterra-1.0.0/tidyterra/R/slice-Spat.R | 237 ++- tidyterra-1.0.0/tidyterra/R/stat-spat-coordinates.R |only tidyterra-1.0.0/tidyterra/R/stat-spatraster.R |only tidyterra-1.0.0/tidyterra/R/summarise-SpatVector.R | 250 +-- tidyterra-1.0.0/tidyterra/R/sysdata.rda |binary tidyterra-1.0.0/tidyterra/R/tidy-Spat.R |only tidyterra-1.0.0/tidyterra/R/utils-pipe.R | 28 tidyterra-1.0.0/tidyterra/R/utils.R | 23 tidyterra-1.0.0/tidyterra/README.md | 64 tidyterra-1.0.0/tidyterra/build/partial.rdb |binary tidyterra-1.0.0/tidyterra/build/vignette.rds |binary tidyterra-1.0.0/tidyterra/data/cross_blended_hypsometric_tints_db.rda |binary tidyterra-1.0.0/tidyterra/data/grass_db.rda |binary tidyterra-1.0.0/tidyterra/data/hypsometric_tints_db.rda |binary tidyterra-1.0.0/tidyterra/data/princess_db.rda |binary tidyterra-1.0.0/tidyterra/data/volcano2.rda |binary tidyterra-1.0.0/tidyterra/inst/WORDLIST | 22 tidyterra-1.0.0/tidyterra/inst/doc/tidyterra.Rmd | 33 tidyterra-1.0.0/tidyterra/inst/doc/tidyterra.html | 21 tidyterra-1.0.0/tidyterra/inst/doc/welcome.Rmd | 147 +- tidyterra-1.0.0/tidyterra/inst/doc/welcome.html | 125 - tidyterra-1.0.0/tidyterra/inst/schemaorg.json | 5 tidyterra-1.0.0/tidyterra/man/arrange.SpatVector.Rd | 10 tidyterra-1.0.0/tidyterra/man/as_coordinates.Rd | 9 tidyterra-1.0.0/tidyterra/man/as_sf.Rd | 5 tidyterra-1.0.0/tidyterra/man/as_spatraster.Rd | 9 tidyterra-1.0.0/tidyterra/man/as_spatvector.Rd | 7 tidyterra-1.0.0/tidyterra/man/as_tibble.Spat.Rd | 7 tidyterra-1.0.0/tidyterra/man/autoplot.Spat.Rd | 17 tidyterra-1.0.0/tidyterra/man/bind_rows.SpatVector.Rd | 2 tidyterra-1.0.0/tidyterra/man/chunks/grassdec.Rmd | 12 tidyterra-1.0.0/tidyterra/man/compare_spatrasters.Rd | 2 tidyterra-1.0.0/tidyterra/man/count.SpatVector.Rd | 26 tidyterra-1.0.0/tidyterra/man/cross_blended_hypsometric_tints_db.Rd | 4 tidyterra-1.0.0/tidyterra/man/drop_na.Spat.Rd | 25 tidyterra-1.0.0/tidyterra/man/fill.SpatVector.Rd | 16 tidyterra-1.0.0/tidyterra/man/filter-joins.SpatVector.Rd | 4 tidyterra-1.0.0/tidyterra/man/filter.Spat.Rd | 12 tidyterra-1.0.0/tidyterra/man/fortify.Spat.Rd | 106 - tidyterra-1.0.0/tidyterra/man/geom_spat_contour.Rd | 14 tidyterra-1.0.0/tidyterra/man/geom_spatraster.Rd | 12 tidyterra-1.0.0/tidyterra/man/geom_spatraster_rgb.Rd | 4 tidyterra-1.0.0/tidyterra/man/ggspatvector.Rd | 17 tidyterra-1.0.0/tidyterra/man/glance.Spat.Rd |only tidyterra-1.0.0/tidyterra/man/glimpse.Spat.Rd | 16 tidyterra-1.0.0/tidyterra/man/grass_db.Rd | 4 tidyterra-1.0.0/tidyterra/man/group-by.SpatVector.Rd | 24 tidyterra-1.0.0/tidyterra/man/hypsometric_tints_db.Rd | 6 tidyterra-1.0.0/tidyterra/man/is_regular_grid.Rd | 2 tidyterra-1.0.0/tidyterra/man/mutate-joins.SpatVector.Rd | 8 tidyterra-1.0.0/tidyterra/man/mutate.Spat.Rd | 8 tidyterra-1.0.0/tidyterra/man/pivot_longer.SpatVector.Rd | 2 tidyterra-1.0.0/tidyterra/man/pivot_wider.SpatVector.Rd | 10 tidyterra-1.0.0/tidyterra/man/princess_db.Rd | 6 tidyterra-1.0.0/tidyterra/man/pull.Spat.Rd | 16 tidyterra-1.0.0/tidyterra/man/pull_crs.Rd | 4 tidyterra-1.0.0/tidyterra/man/reexports.Rd | 20 tidyterra-1.0.0/tidyterra/man/relocate.Spat.Rd | 6 tidyterra-1.0.0/tidyterra/man/rename.Spat.Rd | 6 tidyterra-1.0.0/tidyterra/man/replace_na.Spat.Rd | 8 tidyterra-1.0.0/tidyterra/man/required_pkgs.Spat.Rd |only tidyterra-1.0.0/tidyterra/man/rowwise.SpatVector.Rd | 34 tidyterra-1.0.0/tidyterra/man/roxygen/meta.R | 1 tidyterra-1.0.0/tidyterra/man/scale_coltab.Rd | 31 tidyterra-1.0.0/tidyterra/man/scale_cross_blended.Rd | 44 tidyterra-1.0.0/tidyterra/man/scale_grass.Rd | 42 tidyterra-1.0.0/tidyterra/man/scale_hypso.Rd | 44 tidyterra-1.0.0/tidyterra/man/scale_princess.Rd | 38 tidyterra-1.0.0/tidyterra/man/scale_terrain.Rd | 38 tidyterra-1.0.0/tidyterra/man/scale_whitebox.Rd | 38 tidyterra-1.0.0/tidyterra/man/scale_wiki.Rd | 38 tidyterra-1.0.0/tidyterra/man/select.Spat.Rd | 10 tidyterra-1.0.0/tidyterra/man/slice.Spat.Rd | 48 tidyterra-1.0.0/tidyterra/man/stat_spat_coordinates.Rd | 4 tidyterra-1.0.0/tidyterra/man/summarise.SpatVector.Rd | 15 tidyterra-1.0.0/tidyterra/man/tidy.Spat.Rd |only tidyterra-1.0.0/tidyterra/man/tidyterra-package.Rd | 2 tidyterra-1.0.0/tidyterra/tests/testthat/_snaps |only tidyterra-1.0.0/tidyterra/tests/testthat/test-arrange-SpatVector.R | 16 tidyterra-1.0.0/tidyterra/tests/testthat/test-as-coordinates.R |only tidyterra-1.0.0/tidyterra/tests/testthat/test-as-sf.R |only tidyterra-1.0.0/tidyterra/tests/testthat/test-as-spatraster.R |only tidyterra-1.0.0/tidyterra/tests/testthat/test-as-spatvector.R |only tidyterra-1.0.0/tidyterra/tests/testthat/test-as-tibble-Spat.R |only tidyterra-1.0.0/tidyterra/tests/testthat/test-autoplot-Spat.R | 225 +-- tidyterra-1.0.0/tidyterra/tests/testthat/test-bind-cols-SpatVector.R | 31 tidyterra-1.0.0/tidyterra/tests/testthat/test-bind-rows-SpatVector.R | 1 tidyterra-1.0.0/tidyterra/tests/testthat/test-compare-spatrasters.R |only tidyterra-1.0.0/tidyterra/tests/testthat/test-count-tally-SpatVector.R | 27 tidyterra-1.0.0/tidyterra/tests/testthat/test-distinct-SpatVector.R | 25 tidyterra-1.0.0/tidyterra/tests/testthat/test-drop-na-Spat.R |only tidyterra-1.0.0/tidyterra/tests/testthat/test-fill-SpatVector.R | 6 tidyterra-1.0.0/tidyterra/tests/testthat/test-filter-Spat.R | 37 tidyterra-1.0.0/tidyterra/tests/testthat/test-fortify-Spat.R | 80 - tidyterra-1.0.0/tidyterra/tests/testthat/test-geom-spat-contour-fill.R |only tidyterra-1.0.0/tidyterra/tests/testthat/test-geom-spat-contour-text.R |only tidyterra-1.0.0/tidyterra/tests/testthat/test-geom-spat-contour.R |only tidyterra-1.0.0/tidyterra/tests/testthat/test-geom-spatraster-rgb.R |only tidyterra-1.0.0/tidyterra/tests/testthat/test-geom-spatraster.R |only tidyterra-1.0.0/tidyterra/tests/testthat/test-geom-spatvector.R |only tidyterra-1.0.0/tidyterra/tests/testthat/test-glance-Spat.R |only tidyterra-1.0.0/tidyterra/tests/testthat/test-glimpse-Spat.R | 16 tidyterra-1.0.0/tidyterra/tests/testthat/test-group-by-SpatVector-terra.R | 25 tidyterra-1.0.0/tidyterra/tests/testthat/test-group-by-SpatVector.R | 47 tidyterra-1.0.0/tidyterra/tests/testthat/test-group-data-SpatVector.R | 7 tidyterra-1.0.0/tidyterra/tests/testthat/test-join-SpatVector.R | 6 tidyterra-1.0.0/tidyterra/tests/testthat/test-keep-coltab.R |only tidyterra-1.0.0/tidyterra/tests/testthat/test-mutate-Spat.R | 38 tidyterra-1.0.0/tidyterra/tests/testthat/test-pivot-long-SpatVector.R | 105 - tidyterra-1.0.0/tidyterra/tests/testthat/test-pivot-wide-SpatVector.R | 58 tidyterra-1.0.0/tidyterra/tests/testthat/test-pull-Spat.R | 8 tidyterra-1.0.0/tidyterra/tests/testthat/test-pull-crs.R |only tidyterra-1.0.0/tidyterra/tests/testthat/test-relocate-Spat.R | 13 tidyterra-1.0.0/tidyterra/tests/testthat/test-rename-Spat.R | 25 tidyterra-1.0.0/tidyterra/tests/testthat/test-replace-na-Spat.R |only tidyterra-1.0.0/tidyterra/tests/testthat/test-required-pkgs-Spat.R |only tidyterra-1.0.0/tidyterra/tests/testthat/test-rowwise-SpatVector-terra.R | 25 tidyterra-1.0.0/tidyterra/tests/testthat/test-rowwise-SpatVector.R | 8 tidyterra-1.0.0/tidyterra/tests/testthat/test-scales-coltab.R |only tidyterra-1.0.0/tidyterra/tests/testthat/test-scales-cross-blended.R |only tidyterra-1.0.0/tidyterra/tests/testthat/test-scales-grass.R |only tidyterra-1.0.0/tidyterra/tests/testthat/test-scales-hypso.R |only tidyterra-1.0.0/tidyterra/tests/testthat/test-scales-princess.R |only tidyterra-1.0.0/tidyterra/tests/testthat/test-scales-terrain.R |only tidyterra-1.0.0/tidyterra/tests/testthat/test-scales-whitebox.R |only tidyterra-1.0.0/tidyterra/tests/testthat/test-scales-wiki.R |only tidyterra-1.0.0/tidyterra/tests/testthat/test-select-Spat.R | 37 tidyterra-1.0.0/tidyterra/tests/testthat/test-slice-SpatRaster.R | 147 -- tidyterra-1.0.0/tidyterra/tests/testthat/test-slice-SpatVector.R | 80 - tidyterra-1.0.0/tidyterra/tests/testthat/test-stat-spat-coordinates.R |only tidyterra-1.0.0/tidyterra/tests/testthat/test-stat-spatraster.R |only tidyterra-1.0.0/tidyterra/tests/testthat/test-summarise-SpatVector.R | 705 +++++----- tidyterra-1.0.0/tidyterra/tests/testthat/test-tidy-Spat.R |only tidyterra-1.0.0/tidyterra/tests/testthat/test-transmute-Spat.R | 10 tidyterra-1.0.0/tidyterra/tests/testthat/test-utils.R | 1 tidyterra-1.0.0/tidyterra/vignettes/aggregate-1.png |binary tidyterra-1.0.0/tidyterra/vignettes/aggregate-2.png |binary tidyterra-1.0.0/tidyterra/vignettes/lux_ggplot-1.png |binary tidyterra-1.0.0/tidyterra/vignettes/paper.bib | 573 ++++---- tidyterra-1.0.0/tidyterra/vignettes/rgb-1.png |binary tidyterra-1.0.0/tidyterra/vignettes/tidyterra.Rmd | 33 tidyterra-1.0.0/tidyterra/vignettes/welcome.Rmd | 147 +- 254 files changed, 3599 insertions(+), 3148 deletions(-)
Title: Visualizing the Performance of Scoring Classifiers
Description: ROC graphs, sensitivity/specificity curves, lift charts,
and precision/recall plots are popular examples of trade-off
visualizations for specific pairs of performance measures. ROCR is a
flexible tool for creating cutoff-parameterized 2D performance curves
by freely combining two from over 25 performance measures (new
performance measures can be added using a standard interface).
Curves from different cross-validation or bootstrapping runs can be
averaged by different methods, and standard deviations, standard
errors or box plots can be used to visualize the variability across
the runs. The parameterization can be visualized by printing cutoff
values at the corresponding curve positions, or by coloring the
curve according to cutoff. All components of a performance plot can
be quickly adjusted using a flexible parameter dispatching
mechanism. Despite its flexibility, ROCR is easy to use, with only
three commands and reasonable default values for all optional
parameters.
Author: Tobias Sing [aut],
Oliver Sander [aut],
Niko Beerenwinkel [aut],
Thomas Lengauer [aut],
Thomas Unterthiner [ctb],
Felix G.M. Ernst [cre]
Maintainer: Felix G.M. Ernst <felix.gm.ernst@outlook.com>
Diff between ROCR versions 1.0-11 dated 2020-05-02 and 1.0-12 dated 2026-01-23
DESCRIPTION | 14 +++++----- MD5 | 32 +++++++++++------------ R/performance.R | 10 +++---- R/prediction.R | 2 - R/zzz.R | 6 ++-- README.md | 6 ++-- build/vignette.rds |binary inst/CITATION | 22 ++++++++-------- inst/doc/ROCR.R | 28 ++++++++++---------- inst/doc/ROCR.Rmd | 4 +- inst/doc/ROCR.html | 63 ++++++++++++++++++++++++++++++++++------------- man/performance-class.Rd | 2 - man/performance.Rd | 8 ++--- man/plot-methods.Rd | 6 ++-- man/prediction-class.Rd | 2 - man/prediction.Rd | 2 - vignettes/ROCR.Rmd | 4 +- 17 files changed, 121 insertions(+), 90 deletions(-)
Title: Update and Manipulate Rd Documentation Objects
Description: Functions for manipulation of R documentation objects,
including functions reprompt() and ereprompt() for updating 'Rd'
documentation for functions, methods and classes; 'Rd' macros for
citations and import of references from 'bibtex' files for use in
'Rd' files and 'roxygen2' comments; 'Rd' macros for evaluating and
inserting snippets of 'R' code and the results of its evaluation or
creating graphics on the fly; and many functions for manipulation of
references and Rd files.
Author: Georgi N. Boshnakov [aut, cre] ,
Duncan Murdoch [ctb]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>
Diff between Rdpack versions 2.6.4 dated 2025-04-08 and 2.6.5 dated 2026-01-23
Rdpack-2.6.4/Rdpack/man/set_Rdpack_bibstyle.Rd |only Rdpack-2.6.5/Rdpack/DESCRIPTION | 23 Rdpack-2.6.5/Rdpack/MD5 | 56 Rdpack-2.6.5/Rdpack/NAMESPACE | 5 Rdpack-2.6.5/Rdpack/NEWS.md | 24 Rdpack-2.6.5/Rdpack/R/bib.R | 2670 ++++------ Rdpack-2.6.5/Rdpack/build/partial.rdb |binary Rdpack-2.6.5/Rdpack/build/vignette.rds |binary Rdpack-2.6.5/Rdpack/inst/REFERENCES.bib | 15 Rdpack-2.6.5/Rdpack/inst/doc/Inserting_bibtex_references.R | 36 Rdpack-2.6.5/Rdpack/inst/doc/Inserting_bibtex_references.Rnw | 2 Rdpack-2.6.5/Rdpack/inst/doc/Inserting_bibtex_references.pdf |binary Rdpack-2.6.5/Rdpack/inst/doc/Inserting_figures_and_evaluated_examples.R | 18 Rdpack-2.6.5/Rdpack/inst/doc/Inserting_figures_and_evaluated_examples.Rnw | 21 Rdpack-2.6.5/Rdpack/inst/doc/Inserting_figures_and_evaluated_examples.pdf |binary Rdpack-2.6.5/Rdpack/inst/pkgdown.yml |only Rdpack-2.6.5/Rdpack/man/Rdpack-package.Rd | 43 Rdpack-2.6.5/Rdpack/man/Rdpack_bibstyles.Rd | 18 Rdpack-2.6.5/Rdpack/man/insert_ref.Rd | 4 Rdpack-2.6.5/Rdpack/man/macros/refmacros.Rd | 50 Rdpack-2.6.5/Rdpack/man/predefined.Rd | 8 Rdpack-2.6.5/Rdpack/tests/testthat/StructureClasses.Rd | 362 - Rdpack-2.6.5/Rdpack/tests/testthat/as.character.f_usage.Rd | 124 Rdpack-2.6.5/Rdpack/tests/testthat/myshow-methods.Rd | 40 Rdpack-2.6.5/Rdpack/tests/testthat/show.Rd | 162 Rdpack-2.6.5/Rdpack/tests/testthat/test-bib.R | 9 Rdpack-2.6.5/Rdpack/vignettes/Inserting_bibtex_references.Rnw | 2 Rdpack-2.6.5/Rdpack/vignettes/Inserting_bibtex_references.org | 14 Rdpack-2.6.5/Rdpack/vignettes/Inserting_figures_and_evaluated_examples.Rnw | 21 Rdpack-2.6.5/Rdpack/vignettes/Inserting_figures_and_evaluated_examples.org | 2 30 files changed, 1821 insertions(+), 1908 deletions(-)
Title: Partial Dependence Plots
Description: A general framework for constructing partial dependence (i.e.,
marginal effect) plots from various types machine learning models
in R.
Author: Brandon M. Greenwell [aut, cre]
Maintainer: Brandon M. Greenwell <greenwell.brandon@gmail.com>
Diff between pdp versions 0.8.2 dated 2024-10-28 and 0.8.3 dated 2026-01-23
pdp-0.8.2/pdp/inst/tinytest/test_xgboost_pima.R |only pdp-0.8.3/pdp/DESCRIPTION | 17 +++--- pdp-0.8.3/pdp/MD5 | 39 +++++++------- pdp-0.8.3/pdp/NEWS.md | 7 ++ pdp-0.8.3/pdp/R/autoplot.R | 4 - pdp-0.8.3/pdp/R/get_predictions.R | 9 +-- pdp-0.8.3/pdp/R/get_task.R | 14 ++--- pdp-0.8.3/pdp/README.md | 2 pdp-0.8.3/pdp/build/vignette.rds |binary pdp-0.8.3/pdp/inst/doc/pdp-approximate.pdf |binary pdp-0.8.3/pdp/inst/doc/pdp-intro.pdf |binary pdp-0.8.3/pdp/inst/doc/pdp-link-function.pdf |binary pdp-0.8.3/pdp/inst/tinytest/test_get_training_data.R | 5 + pdp-0.8.3/pdp/inst/tinytest/test_pkg_C50.R | 4 + pdp-0.8.3/pdp/inst/tinytest/test_pkg_MASS.R | 4 + pdp-0.8.3/pdp/inst/tinytest/test_pkg_e1071.R | 4 + pdp-0.8.3/pdp/inst/tinytest/test_pkg_party.R | 4 + pdp-0.8.3/pdp/inst/tinytest/test_pkg_ranger.R | 4 + pdp-0.8.3/pdp/inst/tinytest/test_pkg_stats.R | 4 + pdp-0.8.3/pdp/inst/tinytest/test_pkg_xgboost.R | 50 ++++++++----------- pdp-0.8.3/pdp/tests/tinytest.R | 2 21 files changed, 99 insertions(+), 74 deletions(-)
Title: Utilities for Working with NEON Data
Description: NEON data packages can be accessed through the NEON Data Portal <https://www.neonscience.org>
or through the NEON Data API (see <https://data.neonscience.org/data-api> for documentation). Data delivered from
the Data Portal are provided as monthly zip files packaged within a parent zip file, while individual files
can be accessed from the API. This package provides tools that aid in discovering, downloading, and reformatting
data prior to use in analyses. This includes downloading data via the API, merging data tables by type, and
converting formats. For more information, see the readme file at <https://github.com/NEONScience/NEON-utilities>.
Author: Claire Lunch [aut, cre, ctb],
Christine Laney [aut, ctb],
Nathan Mietkiewicz [aut, ctb],
Eric Sokol [aut, ctb],
Kaelin Cawley [aut, ctb],
NEON [aut]
Maintainer: Claire Lunch <clunch@battelleecology.org>
Diff between neonUtilities versions 3.0.2 dated 2025-09-26 and 3.0.3 dated 2026-01-23
DESCRIPTION | 8 +++---- MD5 | 24 ++++++++++----------- NEWS.md | 10 +++++++++ R/getTimeIndex.R | 5 +++- R/getZipUrls.R | 5 ++-- R/schemaFromVar.R | 5 ++++ R/stackByTable.R | 4 +-- R/stackDataFilesArrow.R | 13 +++++++++-- R/stackFrameFiles.R | 42 ++++++++++++++++++++++++++++++++++---- R/sysdata.rda |binary R/zipsByProduct.R | 26 ++++++++++++++++------- README.md | 53 +++++++++++++++++++++++++++++++++++++++++++++--- data/table_types.rda |binary 13 files changed, 156 insertions(+), 39 deletions(-)
Title: Minimal Type Guesser
Description: Port the type guesser from 'readr' (so-called 'readr' first edition parsing engine, now superseded by 'vroom').
Author: Chung-hong Chan [aut, cre] ,
Hadley Wickham [aut] ,
Jim Hester [aut] ,
Romain Francois [ctb] ,
Jennifer Bryan [aut] ,
Shelby Bearrows [ctb] ,
Posit Software, PBC [cph] ,
David Olson [aut]
Maintainer: Chung-hong Chan <chainsawtiney@gmail.com>
Diff between minty versions 0.0.5 dated 2025-01-07 and 0.0.6 dated 2026-01-23
DESCRIPTION | 17 +++++++++-------- MD5 | 4 ++-- README.md | 10 ++++------ 3 files changed, 15 insertions(+), 16 deletions(-)
Title: Tools for Analyzing Mixed Effect Regression Models
Description: Provides methods for extracting results from mixed-effect model
objects fit with the 'lme4' package. Allows construction of prediction intervals
efficiently from large scale linear and generalized linear mixed-effects models.
This method draws from the simulation framework used in the Gelman and Hill (2007) textbook:
Data Analysis Using Regression and Multilevel/Hierarchical Models.
Author: Jared E. Knowles [aut, cre],
Carl Frederick [aut],
Alex Whitworth [ctb]
Maintainer: Jared E. Knowles <jared@civilytics.com>
Diff between merTools versions 0.6.3 dated 2025-09-05 and 0.6.4 dated 2026-01-23
DESCRIPTION | 8 MD5 | 20 NEWS.md | 94 - R/helpers.R | 27 R/merExtract.R | 1 build/vignette.rds |binary inst/doc/Using_predictInterval.html | 1841 +++++++++++++++--------------- inst/doc/imputation.html | 2147 ++++++++++++++++++------------------ inst/doc/marginal_effects.html | 859 +++++++------- inst/doc/merToolsIntro.html | 1557 +++++++++++++------------- tests/testthat/_snaps/predict2.md | 20 11 files changed, 3300 insertions(+), 3274 deletions(-)
Title: Fast K-Mer Counting and Clustering for Biological Sequence
Analysis
Description: Contains tools for rapidly computing distance matrices
and clustering large sequence datasets using fast alignment-free
k-mer counting and recursive k-means partitioning.
See Vinga and Almeida (2003) <doi:10.1093/bioinformatics/btg005>
for a review of k-mer counting methods and applications for
biological sequence analysis.
Author: Shaun Wilkinson [aut, cre]
Maintainer: Shaun Wilkinson <shaunpwilkinson@gmail.com>
Diff between kmer versions 1.1.2 dated 2019-05-20 and 1.1.3 dated 2026-01-23
DESCRIPTION | 13 MD5 | 30 - README.md | 13 build/vignette.rds |binary inst/CITATION | 13 inst/doc/kmer-vignette.R | 12 inst/doc/kmer-vignette.Rmd | 2 inst/doc/kmer-vignette.html | 720 +++++++++++++++++++++++++++++++++----------- man/kcount.Rd | 11 man/kdistance.Rd | 11 man/kmer.Rd | 14 man/mbed.Rd | 3 man/otu.Rd | 11 src/Makevars | 3 src/RcppExports.cpp | 5 vignettes/kmer-vignette.Rmd | 2 16 files changed, 646 insertions(+), 217 deletions(-)
Title: Datasets, Functions and Scripts for Semiparametric Regression
Supporting Harezlak, Ruppert & Wand (2018)
Description: The book "Semiparametric Regression with R" by J. Harezlak, D. Ruppert & M.P. Wand (2018, Springer; ISBN: 978-1-4939-8851-8) makes use of datasets and scripts to explain semiparametric regression concepts. Each of the book's scripts are contained in this package as well as datasets that are not within other R packages. Functions that aid semiparametric regression analysis are also included.
Author: Jaroslaw Harezlak [aut],
David Ruppert [aut],
Matt P. Wand [aut, cre]
Maintainer: Matt P. Wand <matt.wand@uts.edu.au>
Diff between HRW versions 1.0-5 dated 2021-11-23 and 1.0-6 dated 2026-01-23
DESCRIPTION | 13 ++++---- MD5 | 62 +++++++++++++++++++++--------------------- R/createBoundary.r | 6 ++-- data/BCR.rda |binary data/BanglaContrac.rda |binary data/BostonMortgages.rda |binary data/CHD.rda |binary data/SydneyRealEstate.rda |binary data/SydneyRealEstateBdry.rda |binary data/TreasuryRate.rda |binary data/UtahPEF.rda |binary data/WarsawApts.rda |binary data/brainImage.rda |binary data/capm.rda |binary data/carAuction.rda |binary data/coral.rda |binary data/femSBMD.rda |binary data/growthIndiana.rda |binary data/indonRespir.rda |binary data/lidar.rda |binary data/ozoneSub.rda |binary data/plankton.rda |binary data/protein.rda |binary data/ragweed.rda |binary data/scallop.rda |binary data/schoolResults.rda |binary data/yields.rda |binary demo/BCRana.R | 2 - demo/npReg.R | 8 +---- demo/ozoneAna.R | 2 - man/BostonMortgages.Rd | 2 - man/SydneyRealEstate.Rd | 2 - 32 files changed, 47 insertions(+), 50 deletions(-)
Title: Download Map Data from GISCO API - Eurostat
Description: Tools to download data from the GISCO (Geographic Information
System of the Commission) Eurostat database
<https://ec.europa.eu/eurostat/web/gisco>. Global and European map
data available. This package is in no way officially related to or
endorsed by Eurostat.
Author: Diego Hernangomez [aut, cre, cph] ,
Eurostat [cph] ,
EuroGeographics [cph]
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>
Diff between giscoR versions 1.0.0 dated 2025-12-10 and 1.0.1 dated 2026-01-23
giscoR-1.0.0/giscoR/R/zzz.R |only giscoR-1.0.1/giscoR/DESCRIPTION | 6 giscoR-1.0.1/giscoR/MD5 | 143 - giscoR-1.0.1/giscoR/NEWS.md | 14 giscoR-1.0.1/giscoR/R/data.R | 2 giscoR-1.0.1/giscoR/R/gisco-address-api.R | 712 ++++----- giscoR-1.0.1/giscoR/R/gisco-attributions.R | 8 giscoR-1.0.1/giscoR/R/gisco-bulk-download.R | 4 giscoR-1.0.1/giscoR/R/gisco-cache.R | 734 +++++----- giscoR-1.0.1/giscoR/R/gisco-get-cached-db.R | 13 giscoR-1.0.1/giscoR/R/gisco-get-communes.R | 4 giscoR-1.0.1/giscoR/R/gisco-get-countries.R | 2 giscoR-1.0.1/giscoR/R/gisco-get-education.R | 4 giscoR-1.0.1/giscoR/R/gisco-get-grid.R | 6 giscoR-1.0.1/giscoR/R/gisco-get-healthcare.R | 4 giscoR-1.0.1/giscoR/R/gisco-get-lau.R | 4 giscoR-1.0.1/giscoR/R/gisco-get-metadata.R | 4 giscoR-1.0.1/giscoR/R/gisco-get-unit-urban-audit.R | 6 giscoR-1.0.1/giscoR/R/gisco-get-urban-audit.R | 4 giscoR-1.0.1/giscoR/R/gisco-id-api.R | 2 giscoR-1.0.1/giscoR/R/utils-country.R | 11 giscoR-1.0.1/giscoR/R/utils-sf.R | 2 giscoR-1.0.1/giscoR/R/utils-url.R | 10 giscoR-1.0.1/giscoR/R/utils.R | 295 ++-- giscoR-1.0.1/giscoR/README.md | 6 giscoR-1.0.1/giscoR/build/stage23.rdb |binary giscoR-1.0.1/giscoR/data/gisco_db.rda |binary giscoR-1.0.1/giscoR/inst/COPYRIGHTS | 2 giscoR-1.0.1/giscoR/inst/WORDLIST | 4 giscoR-1.0.1/giscoR/inst/doc/giscoR.Rmd | 4 giscoR-1.0.1/giscoR/inst/doc/giscoR.html | 4 giscoR-1.0.1/giscoR/inst/schemaorg.json | 2 giscoR-1.0.1/giscoR/man/chunks/education_meta.Rmd | 2 giscoR-1.0.1/giscoR/man/chunks/healthcare_meta.Rmd | 2 giscoR-1.0.1/giscoR/man/gisco_address_api.Rd | 4 giscoR-1.0.1/giscoR/man/gisco_attributions.Rd | 8 giscoR-1.0.1/giscoR/man/gisco_bulk_download.Rd | 2 giscoR-1.0.1/giscoR/man/gisco_clear_cache.Rd | 2 giscoR-1.0.1/giscoR/man/gisco_db.Rd | 4 giscoR-1.0.1/giscoR/man/gisco_get_airports.Rd | 2 giscoR-1.0.1/giscoR/man/gisco_get_cached_db.Rd | 2 giscoR-1.0.1/giscoR/man/gisco_get_census.Rd | 2 giscoR-1.0.1/giscoR/man/gisco_get_coastal_lines.Rd | 2 giscoR-1.0.1/giscoR/man/gisco_get_communes.Rd | 6 giscoR-1.0.1/giscoR/man/gisco_get_countries.Rd | 2 giscoR-1.0.1/giscoR/man/gisco_get_education.Rd | 8 giscoR-1.0.1/giscoR/man/gisco_get_grid.Rd | 8 giscoR-1.0.1/giscoR/man/gisco_get_healthcare.Rd | 10 giscoR-1.0.1/giscoR/man/gisco_get_lau.Rd | 8 giscoR-1.0.1/giscoR/man/gisco_get_metadata.Rd | 2 giscoR-1.0.1/giscoR/man/gisco_get_nuts.Rd | 2 giscoR-1.0.1/giscoR/man/gisco_get_ports.Rd | 2 giscoR-1.0.1/giscoR/man/gisco_get_postal_codes.Rd | 2 giscoR-1.0.1/giscoR/man/gisco_get_unit.Rd | 8 giscoR-1.0.1/giscoR/man/gisco_get_units.Rd | 2 giscoR-1.0.1/giscoR/man/gisco_get_urban_audit.Rd | 6 giscoR-1.0.1/giscoR/man/gisco_nuts_2024.Rd | 2 giscoR-1.0.1/giscoR/man/gisco_set_cache_dir.Rd | 12 giscoR-1.0.1/giscoR/tests/testthat/_snaps/gisco-bulk-download.md | 60 giscoR-1.0.1/giscoR/tests/testthat/_snaps/gisco-get-metadata.md | 4 giscoR-1.0.1/giscoR/tests/testthat/_snaps/gisco-get-unit-urban-audit.md | 2 giscoR-1.0.1/giscoR/tests/testthat/_snaps/utils-country.md | 4 giscoR-1.0.1/giscoR/tests/testthat/_snaps/utils-url.md | 24 giscoR-1.0.1/giscoR/tests/testthat/test-gisco-cache.R | 315 ++-- giscoR-1.0.1/giscoR/tests/testthat/test-gisco-get-metadata.R | 162 +- giscoR-1.0.1/giscoR/tests/testthat/test-gisco-get-unit-urban-audit.R | 412 ++--- giscoR-1.0.1/giscoR/tests/testthat/test-gisco-get-urban-audit.R | 500 +++--- giscoR-1.0.1/giscoR/tests/testthat/test-gisco-id-api.R | 12 giscoR-1.0.1/giscoR/tests/testthat/test-utils-url.R | 627 ++++---- giscoR-1.0.1/giscoR/tests/testthat/test-utils.R | 313 ++-- giscoR-1.0.1/giscoR/vignettes/africa-1.png |binary giscoR-1.0.1/giscoR/vignettes/country-1.png |binary giscoR-1.0.1/giscoR/vignettes/giscoR.Rmd | 4 73 files changed, 2306 insertions(+), 2261 deletions(-)
Title: Analysis with Profile Hidden Markov Models
Description: Designed for the development and application of
hidden Markov models and profile HMMs for biological sequence analysis.
Contains functions for multiple and pairwise sequence alignment,
model construction and parameter optimization, file import/export,
implementation of the forward, backward and Viterbi algorithms for
conditional sequence probabilities, tree-based sequence weighting,
and sequence simulation.
Features a wide variety of potential applications including
database searching, gene-finding and annotation, phylogenetic
analysis and sequence classification.
Based on the models and algorithms described in Durbin et
al (1998, ISBN: 9780521629713).
Author: Shaun Wilkinson [aut, cre]
Maintainer: Shaun Wilkinson <shaunpwilkinson@gmail.com>
Diff between aphid versions 1.3.5 dated 2022-12-05 and 1.3.6 dated 2026-01-23
DESCRIPTION | 13 +- MD5 | 32 ++--- R/aphid.R | 4 R/derivePHMM.R | 10 - R/utils.R | 2 README.md | 9 + build/vignette.rds |binary inst/CITATION | 10 - inst/doc/aphid-vignette.R | 14 +- inst/doc/aphid-vignette.Rmd | 5 inst/doc/aphid-vignette.html | 270 +++++++++++++++++++++---------------------- man/aphid.Rd | 13 +- man/derivePHMM.Rd | 4 src/Makevars | 3 src/RcppExports.cpp | 5 vignettes/aphid-vignette.Rmd | 5 vignettes/aphid.bib | 10 - 17 files changed, 220 insertions(+), 189 deletions(-)