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(-)
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(-)
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
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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
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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 - 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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 - 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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
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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(-)
Title: Render 'LaTeX' in Plots
Description: High-level functions to render 'LaTeX' fragments in plots,
including as labels and data symbols in 'ggplot2' plots, plus
low-level functions to
author 'LaTeX' fragments (to produce 'LaTeX' documents),
typeset 'LaTeX' documents (to produce 'DVI' files),
read 'DVI' files (to produce "DVI" objects),
and render "DVI" objects.
Author: Paul Murrell [aut, cre]
Maintainer: Paul Murrell <paul@stat.auckland.ac.nz>
Diff between xdvir versions 0.1-3 dated 2025-07-15 and 0.2-0 dated 2026-01-22
DESCRIPTION | 7 ++--- MD5 | 49 +++++++++++++++++++------------------ NAMESPACE | 2 + R/engine.R | 1 R/fontLib.R | 15 +++++++++-- R/fontspec.R | 32 +++++++++++++++++++++--- R/freetype.R | 7 ++++- R/grob.R | 14 +++++++++- R/harfbuzz.R |only R/luatex.R | 12 ++++++--- R/ops.R | 5 ++- R/xetex.R | 4 +-- R/zzz.R | 21 ++++++++++++++-- build/vignette.rds |binary inst/NEWS.Rd | 9 ++++++ inst/doc/xdvir-intro.R | 49 ++++++++++++++++++++++++++++++------- inst/doc/xdvir-intro.Rmd | 53 +++++++++++++++++++++++++++++++++------- inst/doc/xdvir-intro.html | 7 ++--- man/fontspecPackage.Rd | 9 ++++++ man/grid.latex.Rd | 4 ++- src/freetype.c | 60 ++++++++++++++++++++++++++++++++++++++++++---- src/freetype.h | 2 + src/register.c | 1 tests/dpi.R | 7 ++++- vignettes/xdvir-intro.Rmd | 53 +++++++++++++++++++++++++++++++++------- vignettes/xdvir-intro.bib | 2 - 26 files changed, 337 insertions(+), 88 deletions(-)
Title: Pediatric Complex Chronic Conditions
Description: An implementation of the pediatric complex chronic conditions (CCC)
classification system using R and C++.
Author: Peter DeWitt [aut] ,
Tell Bennett [ctb] ,
James Feinstein [aut] ,
Seth Russell [aut, cre]
Maintainer: Seth Russell <seth.russell@cuanschutz.edu>
Diff between pccc versions 1.0.6 dated 2025-05-16 and 1.0.7 dated 2026-01-22
DESCRIPTION | 10 +++--- MD5 | 26 ++++++++--------- NAMESPACE | 4 -- NEWS.md | 4 ++ R/get_codes.R | 12 -------- R/pccc-package.R | 2 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/pccc-example.R | 64 +++++++++++++++++++++---------------------- inst/doc/pccc-example.html | 9 +++--- inst/doc/pccc-icd-codes.html | 9 +++--- inst/doc/pccc-overview.R | 20 ++++++------- inst/doc/pccc-overview.html | 9 +++--- tests/test_get_codes.R | 9 ------ 14 files changed, 79 insertions(+), 99 deletions(-)
Title: Xsimd C++ Header-Only Library Files
Description: This header-only library provides modern, portable C++ wrappers for SIMD
intrinsics and parallelized, optimized math implementations (SSE, AVX, NEON, AVX512).
By placing this library in this package, we offer an efficient distribution system for
Xsimd <https://github.com/xtensor-stack/xsimd> for R packages using CRAN.
Author: Marc A. Suchard [aut, cre],
Andrew J. Holbrook [aut],
Observational Health Data Sciences and Informatics [cph],
Johan Mabille [cph, ctb] ,
Sylvain Corlay [cph, ctb] ,
Alexander J. Lee [cph, ctb]
Maintainer: Marc A. Suchard <msuchard@ucla.edu>
Diff between RcppXsimd versions 7.1.6-1 dated 2025-11-29 and 7.1.6-2 dated 2026-01-22
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- inst/include/xsimd/memory/xsimd_aligned_allocator.hpp | 4 ++-- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: Create Interactive Gantt Charts with Work Breakdown Structure
Description: Create Primavera-style interactive Gantt charts with Work Breakdown
Structure (WBS) hierarchy and activities. Features include color-coded WBS
items, indented labels, scrollable views for large projects, dynamic date
formatting, and the ability to dim past activities. Built on top of 'plotly'
for interactive visualizations.
Author: Ahmed Aredah [aut, cre]
Maintainer: Ahmed Aredah <Ahmed.Aredah@gmail.com>
Diff between ganttify versions 0.1.8 dated 2025-12-19 and 0.2.1 dated 2026-01-22
DESCRIPTION | 6 MD5 | 16 NAMESPACE | 24 NEWS.md | 236 +- R/Ganttify.R | 4144 ++++++++++++++++++++++++++++------------------------ R/data.R | 106 - README.md | 762 +++++---- man/Ganttify.Rd | 574 +++---- man/test_project.Rd | 130 - 9 files changed, 3260 insertions(+), 2738 deletions(-)
Title: Create Tessellated Hexagon Maps
Description: Create a hexagon tile map display from spatial polygons. Each
polygon is represented by a hexagon tile, placed as close to it's original
centroid as possible, with a focus on maintaining spatial relationship to
a focal point. Developed to aid visualisation and analysis of spatial
distributions across Australia, which can be challenging due to the
concentration of the population on the coast and wide open interior.
Author: Dianne Cook [aut, cre, ths] ,
Stephanie Kobakian [aut] ,
Matt Cowgill [ctb]
Maintainer: Dianne Cook <dicook@monash.edu>
Diff between sugarbag versions 0.1.9 dated 2025-12-06 and 0.1.10 dated 2026-01-22
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/global.R | 3 ++- inst/doc/Tasmania.html | 4 ++-- 5 files changed, 15 insertions(+), 10 deletions(-)
Title: Tidy Population Genetics
Description: We provide a tidy grammar of population genetics, facilitating
the manipulation and analysis of data on biallelic single nucleotide
polymorphisms (SNPs). 'tidypopgen' scales to very large genetic datasets
by storing genotypes on disk, and performing operations on them in
chunks, without ever loading all data in memory. The full
functionalities of the package are described in Carter et al. (2025)
<doi:10.1111/2041-210x.70204>.
Author: Evie Carter [aut],
Eirlys Tysall [aut],
Andrea Manica [aut, cre, cph] ,
Chang Christopher [ctb] ),
Shaun Purcell [ctb] ),
Bengtsson Henrik [ctb] )
Maintainer: Andrea Manica <am315@cam.ac.uk>
Diff between tidypopgen versions 0.4.1 dated 2025-12-20 and 0.4.2 dated 2026-01-22
DESCRIPTION | 6 - MD5 | 23 +++--- NEWS.md | 4 + R/annotate_group_info.R | 4 - R/gt_pca_tidiers.R | 2 R/predict_gt_pca.R | 71 +++++++++++--------- inst/doc/a01_overview.html | 92 +++++++++++++------------- inst/doc/a02_qc.html | 26 +++---- inst/doc/a03_example_clustering_and_dapc.html | 3 inst/doc/tidypopgen.html | 6 - man/predict_gt_pca.Rd | 7 + tests/testthat/Rplots.pdf |only tests/testthat/test_gt_pca.R | 67 ++++++++++++++++++ 13 files changed, 200 insertions(+), 111 deletions(-)
Title: Bounded Time Series Regression
Description: Simulate, estimate and forecast a wide range of regression
based dynamic models for bounded time series, covering the most
commonly applied models in the literature. The main calculations are
done in FORTRAN, which translates into very fast algorithms.
Author: Taiane Schaedler Prass [aut, cre, com] ,
Guilherme Pumi [ctb, aut] ,
Fabio Mariano Bayer [ctb] ,
Jack Joseph Dongarra [ctb] ),
Cleve Moler [ctb] ),
Gilbert Wright Stewart [ctb] ),
Ciyou Zhu [ctb] ,
Richard H. Byrd [ctb] ,
Jorge Nocedal [ctb] ,
Jose L [...truncated...]
Maintainer: Taiane Schaedler Prass <taianeprass@gmail.com>
Diff between BTSR versions 1.0.0 dated 2025-06-18 and 1.0.1 dated 2026-01-22
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- R/btsr.R | 1 - R/functions_misc.R | 4 ++-- build/partial.rdb |binary inst/NEWS.md | 6 ++++++ man/fit.control.Rd | 2 +- man/print.btsr.Rd | 52 ++++++++++++++++++++++++++-------------------------- man/summary.Rd | 2 +- src/01_distrib.f90 | 24 +++++++++++++++--------- 10 files changed, 65 insertions(+), 54 deletions(-)
Title: Constructing Hierarchical Voronoi Tessellations and Overlay
Heatmaps for Data Analysis
Description: Facilitates building topology preserving maps for data analysis.
Author: Zubin Dowlaty [aut, cre],
Mu Sigma, Inc. [cph]
Maintainer: Zubin Dowlaty <zubin.dowlaty@mu-sigma.com>
Diff between HVT versions 25.2.8 dated 2025-12-18 and 26.1.1 dated 2026-01-22
HVT-25.2.8/HVT/NEWS.md |only HVT-26.1.1/HVT/DESCRIPTION | 8 HVT-26.1.1/HVT/MD5 | 31 +- HVT-26.1.1/HVT/R/clusterPlot.R | 187 ++++++++++++++-- HVT-26.1.1/HVT/R/global.R | 2 HVT-26.1.1/HVT/R/mcmc_plots.R | 37 ++- HVT-26.1.1/HVT/R/msm.R | 15 + HVT-26.1.1/HVT/R/plotAnimatedFlowmap.R | 5 HVT-26.1.1/HVT/R/plotHVT.R | 374 +++++++++++++++++++++++++-------- HVT-26.1.1/HVT/R/scoreHVT.R | 257 +++++++++++++++++++++- HVT-26.1.1/HVT/README.md | 52 +++- HVT-26.1.1/HVT/inst/doc/HVT.Rmd | 21 + HVT-26.1.1/HVT/inst/doc/HVT.html | 46 +++- HVT-26.1.1/HVT/man/msm.Rd | 4 HVT-26.1.1/HVT/man/plotHVT.Rd | 11 HVT-26.1.1/HVT/man/scoreHVT.Rd | 18 + HVT-26.1.1/HVT/vignettes/HVT.Rmd | 21 + 17 files changed, 889 insertions(+), 200 deletions(-)
Title: Tree Guided Machine Learning for Personalized Predictions and
Precision Diagnostics
Description: Generalization of the classification and regression tree (CART) model that partitions subjects into terminal nodes and tailors machine learning model to each terminal node.
Author: Yunro Chung [aut, cre]
Maintainer: Yunro Chung <yunro.chung@asu.edu>
Diff between tgml versions 0.3.0 dated 2025-12-11 and 0.4.0 dated 2026-01-22
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/05b.combML_mse.R | 36 ++++++++++++++++++------------------ R/05c.combML_bs.R | 36 ++++++++++++++++++------------------ R/tgml.R | 2 ++ man/tgml.Rd | 34 ++++++++++++++++++---------------- 6 files changed, 65 insertions(+), 61 deletions(-)
Title: Simulate from ODE-Based Models
Description: Fast simulation from ordinary differential equation
(ODE) based models typically employed in quantitative pharmacology and
systems biology.
Author: Kyle T Baron [aut, cre] ,
Bill Gillespie [ctb],
Charles Margossian [ctb],
Devin Pastoor [ctb],
Bill Denney [ctb] ,
Dilawar Singh [ctb],
Felicien Le Louedec [ctb] ,
Timothy Waterhouse [ctb] ,
Kyle Meyer [ctb],
Metrum Research Group [cph]
Maintainer: Kyle T Baron <kyleb@metrumrg.com>
Diff between mrgsolve versions 1.6.1 dated 2025-08-22 and 1.7.2 dated 2026-01-22
DESCRIPTION | 8 +- MD5 | 40 +++++++------- NAMESPACE | 1 NEWS.md | 38 ++++++++++++++ R/Aaaa.R | 2 R/class_build.R | 4 - R/handle_spec_block.R | 9 +++ R/modspec.R | 1 R/mread.R | 5 + inst/WORDLIST | 2 inst/base/modelheader.h | 2 inst/base/mrgsolv.h | 8 +- inst/include/dataobject.h | 6 +- inst/include/odeproblem.h | 31 +++++++---- inst/project/housemodel.cpp | 2 src/dataobject.cpp | 18 +++++- src/devtran.cpp | 52 +++++++++++++++---- src/housemodel-mread-header.h | 2 src/housemodel-mread-source.cpp | 3 - src/odeproblem.cpp | 108 ++++++++++++++++++++++++++++------------ tests/testthat/test-mread.R | 15 +++++ 21 files changed, 268 insertions(+), 89 deletions(-)
Title: Generalized Boosted Regression Models
Description: An implementation of extensions to Freund and Schapire's AdaBoost
algorithm and Friedman's gradient boosting machine. Includes regression
methods for least squares, absolute loss, t-distribution loss, quantile
regression, logistic, multinomial logistic, Poisson, Cox proportional hazards
partial likelihood, AdaBoost exponential loss, Huberized hinge loss, and
Learning to Rank measures (LambdaMart). Originally developed by Greg Ridgeway.
Newer version available at github.com/gbm-developers/gbm3.
Author: Greg Ridgeway [aut, cre] ,
Daniel Edwards [ctb],
Brian Kriegler [ctb],
Stefan Schroedl [ctb],
Harry Southworth [ctb],
Brandon Greenwell [ctb] ,
Bradley Boehmke [ctb] ,
Jay Cunningham [ctb],
GBM Developers [aut]
Maintainer: Greg Ridgeway <gridge@upenn.edu>
Diff between gbm versions 2.2.2 dated 2024-06-28 and 2.2.3 dated 2026-01-22
DESCRIPTION | 18 ++++++++++-------- MD5 | 13 +++++++------ R/plot.gbm.R | 2 +- README.md | 2 +- build/vignette.rds |binary inst/doc/gbm.pdf |binary inst/tinytest/desktop.ini |only man/plot.gbm.Rd | 2 +- 8 files changed, 20 insertions(+), 17 deletions(-)
Title: Topological Connectivity Analysis for Numeric Data
Description: Description: Implementation of topological data analysis methods based on
graph-theoretic approaches for discovering topological structures in data.
The core algorithm constructs topological spaces from graphs following
Nada et al. (2018) <doi:10.1002/mma.4726> "New types of topological
structures via graphs".
Author: Jose Mauricio Gomez Julian [aut, cre]
Maintainer: Jose Mauricio Gomez Julian <isadore.nabi@pm.me>
Diff between topologyR versions 0.1.1 dated 2025-10-03 and 0.1.2 dated 2026-01-22
DESCRIPTION | 8 ++++---- MD5 | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-)
Title: Create and Manage Todolist using 'Todoist.com' API
Description: Allows you to interact with the API of the "Todoist"
platform. 'Todoist' <https://www.todoist.com/> provides an online task
manager service for teams.
Author: Cervan Girard [cre, aut] ,
Vincent Guyader [aut] ,
ThinkR [cph, fnd]
Maintainer: Cervan Girard <cervan@thinkr.fr>
Diff between rtodoist versions 0.1.0 dated 2020-05-14 and 0.2.0 dated 2026-01-22
rtodoist-0.1.0/rtodoist/R/form_presta.R |only rtodoist-0.1.0/rtodoist/man/add_task_in_project.Rd |only rtodoist-0.1.0/rtodoist/man/get_all.Rd |only rtodoist-0.1.0/rtodoist/man/get_id_project.Rd |only rtodoist-0.1.0/rtodoist/man/get_projects.Rd |only rtodoist-0.1.0/rtodoist/man/get_user_id.Rd |only rtodoist-0.1.0/rtodoist/man/get_users.Rd |only rtodoist-0.1.0/rtodoist/man/init_project.Rd |only rtodoist-0.2.0/rtodoist/DESCRIPTION | 49 rtodoist-0.2.0/rtodoist/MD5 | 75 - rtodoist-0.2.0/rtodoist/NAMESPACE | 46 rtodoist-0.2.0/rtodoist/R/all_objects.R | 70 - rtodoist-0.2.0/rtodoist/R/clean_tools.R |only rtodoist-0.2.0/rtodoist/R/open_todoist_website.R | 34 rtodoist-0.2.0/rtodoist/R/projects.R | 67 rtodoist-0.2.0/rtodoist/R/section.R |only rtodoist-0.2.0/rtodoist/R/tasks.R | 449 ++++-- rtodoist-0.2.0/rtodoist/R/todoist-package.R | 1 rtodoist-0.2.0/rtodoist/R/users.R | 200 ++ rtodoist-0.2.0/rtodoist/R/utils-pipe.R | 6 rtodoist-0.2.0/rtodoist/R/utils.R | 32 rtodoist-0.2.0/rtodoist/R/zzz.R | 2 rtodoist-0.2.0/rtodoist/README.md | 87 - rtodoist-0.2.0/rtodoist/build/vignette.rds |binary rtodoist-0.2.0/rtodoist/inst/doc/how_it_works.R | 105 - rtodoist-0.2.0/rtodoist/inst/doc/how_it_works.Rmd | 72 - rtodoist-0.2.0/rtodoist/inst/doc/how_it_works.html | 823 ++++++------ rtodoist-0.2.0/rtodoist/man/add_project.Rd | 4 rtodoist-0.2.0/rtodoist/man/add_responsible_to_task.Rd | 18 rtodoist-0.2.0/rtodoist/man/add_section.Rd |only rtodoist-0.2.0/rtodoist/man/add_tasks_in_project.Rd | 50 rtodoist-0.2.0/rtodoist/man/add_tasks_in_project_from_df.Rd |only rtodoist-0.2.0/rtodoist/man/add_user_in_project.Rd | 11 rtodoist-0.2.0/rtodoist/man/add_users_in_project.Rd | 16 rtodoist-0.2.0/rtodoist/man/call_api.Rd | 10 rtodoist-0.2.0/rtodoist/man/call_api_project_data.Rd |only rtodoist-0.2.0/rtodoist/man/get_all_data.Rd |only rtodoist-0.2.0/rtodoist/man/get_all_projects.Rd |only rtodoist-0.2.0/rtodoist/man/get_all_users.Rd |only rtodoist-0.2.0/rtodoist/man/get_project_id.Rd |only rtodoist-0.2.0/rtodoist/man/get_section_id.Rd |only rtodoist-0.2.0/rtodoist/man/get_tasks.Rd | 2 rtodoist-0.2.0/rtodoist/man/get_tasks_of_project.Rd |only rtodoist-0.2.0/rtodoist/man/get_users_id.Rd |only rtodoist-0.2.0/rtodoist/man/get_users_in_project.Rd |only rtodoist-0.2.0/rtodoist/man/open_todoist_website_profile.Rd | 2 rtodoist-0.2.0/rtodoist/man/pipe.Rd | 9 rtodoist-0.2.0/rtodoist/man/rtodoist-package.Rd | 3 rtodoist-0.2.0/rtodoist/vignettes/how_it_works.Rmd | 72 - 49 files changed, 1463 insertions(+), 852 deletions(-)
Title: Download and Tidy IPC and CH Data
Description: Utilities to access Integrated Food Security Phase Classification
(IPC) and Cadre Harmonisé (CH) food security data. Wrapper functions are
available for all of the 'IPC-CH' Public API (<https://docs.api.ipcinfo.org>)
simplified and advanced endpoints to easily download the data in a clean and
tidy format.
Author: Giulia Martini [aut, cre, cph]
Maintainer: Giulia Martini <giulia.martini@un.org>
Diff between ripc versions 0.3.2 dated 2026-01-10 and 1.0.0 dated 2026-01-22
DESCRIPTION | 9 +- MD5 | 17 ++-- NEWS.md | 4 + R/create_areas_df.R | 172 +++++++++++++++++++++---------------------- R/create_base_df.R | 200 +++++++++++++++++++++++++-------------------------- R/create_groups_df.R | 76 +++++++++---------- R/extract_dates.R | 78 +++++++++---------- R/null_converter.R | 50 ++++++------ R/population_utils.R | 3 tests |only 10 files changed, 309 insertions(+), 300 deletions(-)
Title: AI Coding Agent for 'RStudio'
Description: Provides an 'RStudio' extension with a chat interface for an AI coding agent to help
users with R programming tasks.
Author: Juan Cruz Rodriguez [aut, cre]
Maintainer: Juan Cruz Rodriguez <jcrodriguez@unc.edu.ar>
Diff between myownrobs versions 0.1.0 dated 2025-09-30 and 1.0.0 dated 2026-01-22
myownrobs-0.1.0/myownrobs/R/execute_llm_tools.R |only myownrobs-0.1.0/myownrobs/R/llm_commands.R |only myownrobs-0.1.0/myownrobs/R/myownrobs-package.R |only myownrobs-0.1.0/myownrobs/R/parse_agent_response.R |only myownrobs-0.1.0/myownrobs/R/send_prompt.R |only myownrobs-0.1.0/myownrobs/man/execute_llm_tools.Rd |only myownrobs-0.1.0/myownrobs/man/parse_agent_response.Rd |only myownrobs-0.1.0/myownrobs/man/save_api_key.Rd |only myownrobs-0.1.0/myownrobs/man/send_prompt.Rd |only myownrobs-0.1.0/myownrobs/man/send_prompt_async.Rd |only myownrobs-0.1.0/myownrobs/man/validate_command_args.Rd |only myownrobs-0.1.0/myownrobs/tests/testthat/test-execute_llm_tools.R |only myownrobs-0.1.0/myownrobs/tests/testthat/test-llm_commands.R |only myownrobs-0.1.0/myownrobs/tests/testthat/test-parse_agent_response.R |only myownrobs-0.1.0/myownrobs/tests/testthat/test-send_prompt.R |only myownrobs-1.0.0/myownrobs/DESCRIPTION | 10 myownrobs-1.0.0/myownrobs/MD5 | 118 +++-- myownrobs-1.0.0/myownrobs/NAMESPACE | 29 - myownrobs-1.0.0/myownrobs/R/ai_tool_create_new_file.R | 32 - myownrobs-1.0.0/myownrobs/R/ai_tool_edit_existing_file.R | 36 - myownrobs-1.0.0/myownrobs/R/ai_tool_fetch_url_content.R | 26 - myownrobs-1.0.0/myownrobs/R/ai_tool_file_glob_search.R | 25 - myownrobs-1.0.0/myownrobs/R/ai_tool_grep_search.R | 29 - myownrobs-1.0.0/myownrobs/R/ai_tool_ls_tool.R | 24 - myownrobs-1.0.0/myownrobs/R/ai_tool_read_currently_open_file.R | 21 - myownrobs-1.0.0/myownrobs/R/ai_tool_read_file.R | 27 - myownrobs-1.0.0/myownrobs/R/ai_tool_run_r_command.R | 28 - myownrobs-1.0.0/myownrobs/R/ai_tool_search_and_replace_in_file.R | 61 +- myownrobs-1.0.0/myownrobs/R/ai_tool_search_web.R | 26 - myownrobs-1.0.0/myownrobs/R/config.R | 2 myownrobs-1.0.0/myownrobs/R/configure_provider.R |only myownrobs-1.0.0/myownrobs/R/get_api_key.R | 11 myownrobs-1.0.0/myownrobs/R/get_available_models.R |only myownrobs-1.0.0/myownrobs/R/get_chat_instance.R |only myownrobs-1.0.0/myownrobs/R/get_llm_tools.R |only myownrobs-1.0.0/myownrobs/R/myownrobs.R | 206 +++------- myownrobs-1.0.0/myownrobs/R/settings_module.R | 18 myownrobs-1.0.0/myownrobs/R/turns.R |only myownrobs-1.0.0/myownrobs/R/validate_credentials.R | 72 --- myownrobs-1.0.0/myownrobs/R/validate_policy_acceptance.R | 4 myownrobs-1.0.0/myownrobs/README.md | 63 ++- myownrobs-1.0.0/myownrobs/inst/app/style.css | 2 myownrobs-1.0.0/myownrobs/inst/policy.yaml | 8 myownrobs-1.0.0/myownrobs/man/configure_provider.Rd |only myownrobs-1.0.0/myownrobs/man/content_to_ui.Rd |only myownrobs-1.0.0/myownrobs/man/get_api_key.Rd | 2 myownrobs-1.0.0/myownrobs/man/get_available_models.Rd |only myownrobs-1.0.0/myownrobs/man/get_chat_instance.Rd |only myownrobs-1.0.0/myownrobs/man/get_ellmer_models.Rd |only myownrobs-1.0.0/myownrobs/man/get_llm_tools.Rd |only myownrobs-1.0.0/myownrobs/man/load_turns.Rd |only myownrobs-1.0.0/myownrobs/man/models_deepseek.Rd |only myownrobs-1.0.0/myownrobs/man/myownrobs.Rd | 13 myownrobs-1.0.0/myownrobs/man/myownrobs_server.Rd | 7 myownrobs-1.0.0/myownrobs/man/myownrobs_ui.Rd | 5 myownrobs-1.0.0/myownrobs/man/nice_names.Rd |only myownrobs-1.0.0/myownrobs/man/save_turns.Rd |only myownrobs-1.0.0/myownrobs/man/set_config.Rd | 2 myownrobs-1.0.0/myownrobs/man/turns_to_ui.Rd |only myownrobs-1.0.0/myownrobs/man/validate_credentials.Rd | 7 myownrobs-1.0.0/myownrobs/tests/testthat/test-ai_tool_create_new_file.R | 6 myownrobs-1.0.0/myownrobs/tests/testthat/test-ai_tool_edit_existing_file.R | 8 myownrobs-1.0.0/myownrobs/tests/testthat/test-ai_tool_fetch_url_content.R | 16 myownrobs-1.0.0/myownrobs/tests/testthat/test-ai_tool_file_glob_search.R | 6 myownrobs-1.0.0/myownrobs/tests/testthat/test-ai_tool_grep_search.R | 8 myownrobs-1.0.0/myownrobs/tests/testthat/test-ai_tool_ls_tool.R | 6 myownrobs-1.0.0/myownrobs/tests/testthat/test-ai_tool_read_currently_open_file.R | 4 myownrobs-1.0.0/myownrobs/tests/testthat/test-ai_tool_read_file.R | 6 myownrobs-1.0.0/myownrobs/tests/testthat/test-ai_tool_run_r_command.R | 6 myownrobs-1.0.0/myownrobs/tests/testthat/test-ai_tool_search_and_replace_in_file.R | 55 +- myownrobs-1.0.0/myownrobs/tests/testthat/test-ai_tool_search_web.R | 6 myownrobs-1.0.0/myownrobs/tests/testthat/test-configure_provider.R |only myownrobs-1.0.0/myownrobs/tests/testthat/test-get_api_key.R |only myownrobs-1.0.0/myownrobs/tests/testthat/test-get_available_models.R |only myownrobs-1.0.0/myownrobs/tests/testthat/test-get_chat_instance.R |only myownrobs-1.0.0/myownrobs/tests/testthat/test-get_llm_tools.R |only myownrobs-1.0.0/myownrobs/tests/testthat/test-myownrobs.R |only myownrobs-1.0.0/myownrobs/tests/testthat/test-turns.R |only myownrobs-1.0.0/myownrobs/tests/testthat/test-validate_credentials.R | 109 ----- 79 files changed, 478 insertions(+), 672 deletions(-)
Title: Adverse Event Enrichment Tests
Description: We extend existing gene enrichment tests to perform adverse
event enrichment analysis. Unlike the continuous gene expression data,
adverse event data are counts. Therefore, adverse event data has many zeros
and ties. We propose two enrichment tests. One is a modified Fisher's exact
test based on pre-selected significant adverse events, while the other is
based on a modified Kolmogorov-Smirnov statistic. We add Covariate
adjustment to improve the analysis."Adverse event enrichment tests using
VAERS" Shuoran Li, Lili Zhao (2020) <doi:10.48550/arXiv.2007.02266>.
Author: Shuoran Li [aut],
Hongfan Chen [aut],
Lili Zhao [aut],
Michael Kleinsasser [aut, cre]
Maintainer: Michael Kleinsasser <mkleinsa@umich.edu>
Diff between AEenrich versions 1.1.0 dated 2021-11-01 and 1.1.1 dated 2026-01-22
DESCRIPTION | 10 - MD5 | 23 +-- R/count_cases.R | 351 +++++++++++++++++++++++------------------------- R/data.R | 81 +++++------ R/enrich.R | 275 ++++++++++++++++++------------------- R/odds_ratio.R | 8 - build |only man/AEenrich-package.Rd | 43 +---- man/count_cases.Rd | 2 man/covid1.Rd | 17 +- man/covid2.Rd | 19 +- man/enrich.Rd | 6 man/group.Rd | 13 - 13 files changed, 410 insertions(+), 438 deletions(-)
Title: Shape Constrained Additive Models
Description: Generalized additive models under shape
constraints on the component functions of the linear predictor.
Models can include multiple shape-constrained (univariate
and bivariate) and unconstrained terms. Routines of the
package 'mgcv' are used to set up the model matrix, print,
and plot the results. Multiple smoothing parameter
estimation by the Generalized Cross Validation or similar.
See Pya and Wood (2015) <doi:10.1007/s11222-013-9448-7>
for an overview. A broad selection of shape-constrained
smoothers, linear functionals of smooths with shape constraints,
and Gaussian models with AR1 residuals.
Author: Natalya Pya [aut, cre]
Maintainer: Natalya Pya <nat.pya@gmail.com>
Diff between scam versions 1.2-20 dated 2025-10-14 and 1.2-21 dated 2026-01-22
ChangeLog | 34 -- DESCRIPTION | 10 MD5 | 28 +- NAMESPACE | 30 +- R/emmeans-support.r |only R/plot.r | 17 - R/predict.scam.R | 10 R/scam.r | 45 +-- R/summary.scam.R | 571 ++++++++++++++++++++--------------------- R/uni.smooth.const-with-po.r | 93 +++++- R/vis.scam.r | 2 R/zzz.R |only build/partial.rdb |binary man/linear.functional.terms.Rd | 6 man/scam.Rd | 2 man/scam.emmeans.support.Rd |only man/vcov.scam.Rd |only 17 files changed, 445 insertions(+), 403 deletions(-)
Title: Parametric Time Warping
Description: Parametric Time Warping aligns patterns, i.e., it aims to
put corresponding features at the same locations. The algorithm
searches for an optimal polynomial describing the warping. It
is possible to align one sample to a reference, several samples
to the same reference, or several samples to several
references. One can choose between calculating individual
warpings, or one global warping for a set of samples and one
reference. Two optimization criteria are implemented: RMS (Root
Mean Square error) and WCC (Weighted Cross Correlation). Both
warping of peak profiles and of peak lists are supported. A
vignette for the latter is contained in the inst/doc directory
of the source package - the vignette source can be found on
the package github site. See `citation("ptw")` for more details.
Author: Jan Gerretzen [ctb],
Paul Eilers [aut],
Hans Wouters [ctb],
Tom Bloemberg [aut],
Ron Wehrens [aut, cre]
Maintainer: Ron Wehrens <ron.wehrens@gmail.com>
Diff between ptw versions 1.9-16 dated 2022-01-19 and 1.9-17 dated 2026-01-22
ptw-1.9-16/ptw/build |only ptw-1.9-17/ptw/DESCRIPTION | 11 ++--- ptw-1.9-17/ptw/MD5 | 14 +++--- ptw-1.9-17/ptw/R/ptw-package.R |only ptw-1.9-17/ptw/R/summary.ptw.R | 6 +- ptw-1.9-17/ptw/inst/CITATION | 74 ++++++++++++++++------------------ ptw-1.9-17/ptw/man/mzchannel2pktab.Rd | 4 - ptw-1.9-17/ptw/man/ptw-package.Rd | 50 +++++++++------------- ptw-1.9-17/ptw/man/ptw.Rd | 3 - 9 files changed, 76 insertions(+), 86 deletions(-)
Title: Less Code with More Comprehensive Results
Description: Each function replaces multiple standard R functions. For example,
two function calls, Read() and CountAll(), generate summary statistics for
all variables in the data frame, plus histograms and bar charts. Other
functions provide data aggregation via pivot tables; comprehensive
regression, ANOVA, and t-test; visualizations including integrated
Violin/Box/Scatter plot for a numerical variable, bar chart, histogram,
box plot, density curves, calibrated power curve; reading multiple data
formats with the same call; variable labels; time series with aggregation
and forecasting; color themes; and Trellis (facet) graphics. Also includes
a confirmatory factor analysis of multiple-indicator measurement models,
pedagogical routines for data simulation (e.g., Central Limit Theorem),
generation and rendering of regression instructions for interpretative output,
and both interactive construction of visualizations and interactive
visualizations with plotly.
Author: David W. Gerbing [aut, cre]
Maintainer: David W. Gerbing <gerbing@pdx.edu>
Diff between lessR versions 4.5 dated 2025-12-11 and 4.5.1 dated 2026-01-22
DESCRIPTION | 6 MD5 | 53 - NEWS.md | 57 + R/Chart.R | 135 +++ R/X.R | 117 -- R/XY.R | 271 ++++-- R/dn.main.R | 6 R/dn.plotly.R | 40 R/hier.plotly.R | 397 +++++---- R/param.VBS.R | 2 R/plt.main.R | 105 +- R/plt.plotly.R | 167 +++- R/plt.time.R | 145 +++ R/plt.time_truncate_groups.R |only R/plt.txt.R | 2 R/radar.plotly.R | 18 R/style.R | 2 R/zzz.R | 58 - R/zzz_plotly.R | 101 +- R/zzz_ts.R | 15 data/dataStockPrice.rda |binary inst/doc/intro.Rmd | 2 inst/doc/intro.html | 1775 ++++++++++++++++++++----------------------- man/Chart.Rd | 7 man/Flows.Rd | 20 man/X.Rd | 10 man/XY.Rd | 30 vignettes/intro.Rmd | 2 28 files changed, 1998 insertions(+), 1545 deletions(-)
Title: Help to Fit of a Parametric Distribution to Non-Censored or
Censored Data
Description: Extends the fitdistr() function (of the MASS package) with several functions
to help the fit of a parametric distribution to non-censored or censored data.
Censored data may contain left censored, right censored and interval censored values,
with several lower and upper bounds. In addition to maximum likelihood estimation (MLE),
the package provides moment matching (MME), quantile matching (QME), maximum goodness-of-fit
estimation (MGE) and maximum spacing estimation (MSE) methods (available only for
non-censored data). Weighted versions of MLE, MME, QME and MSE are available. See e.g.
Casella & Berger (2002), Statistical inference, Pacific Grove, for a general introduction
to parametric estimation.
Author: Marie-Laure Delignette-Muller [aut] ,
Christophe Dutang [aut] ,
Regis Pouillot [ctb],
Jean-Baptiste Denis [ctb],
Aurelie Siberchicot [aut, cre]
Maintainer: Aurelie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Diff between fitdistrplus versions 1.2-4 dated 2025-07-03 and 1.2-5 dated 2026-01-22
fitdistrplus-1.2-4/fitdistrplus/tests/t-cvg-algo.R |only fitdistrplus-1.2-4/fitdistrplus/tests/t-fitbench.R |only fitdistrplus-1.2-4/fitdistrplus/tests/t-getparam.R |only fitdistrplus-1.2-4/fitdistrplus/tests/t-init-actuar.R |only fitdistrplus-1.2-4/fitdistrplus/tests/t-manageparam.R |only fitdistrplus-1.2-4/fitdistrplus/tests/t-mledist-cvg-NelderMead.R |only fitdistrplus-1.2-4/fitdistrplus/tests/t-prefit.R |only fitdistrplus-1.2-4/fitdistrplus/tests/t-qmedist-cvg-NelderMead.R |only fitdistrplus-1.2-4/fitdistrplus/tests/t-startfixarg-overall.R |only fitdistrplus-1.2-4/fitdistrplus/tests/t-starting-value-scale-rate.R |only fitdistrplus-1.2-4/fitdistrplus/tests/t-startingvalues-fellerpareto-family.R |only fitdistrplus-1.2-4/fitdistrplus/tests/t-startingvalues-inv-family.R |only fitdistrplus-1.2-4/fitdistrplus/tests/t-startingvalues-invBurr-family.R |only fitdistrplus-1.2-4/fitdistrplus/tests/t-startingvalues-invtrgamma-family.R |only fitdistrplus-1.2-4/fitdistrplus/tests/t-startingvalues-othercont-family.R |only fitdistrplus-1.2-4/fitdistrplus/tests/t-startingvalues-trgamma-family.R |only fitdistrplus-1.2-4/fitdistrplus/tests/t-startingvalues-zeromod-family.R |only fitdistrplus-1.2-4/fitdistrplus/tests/t-startingvalues-zerotrunc-family.R |only fitdistrplus-1.2-4/fitdistrplus/tests/t-startingvalues.R |only fitdistrplus-1.2-4/fitdistrplus/tests/t-util-mmedist-vcov.R |only fitdistrplus-1.2-4/fitdistrplus/tests/t-util-npmle.R |only fitdistrplus-1.2-4/fitdistrplus/tests/t-util-npsurv-mainfunction.R |only fitdistrplus-1.2-4/fitdistrplus/tests/t-util-testdensity.R |only fitdistrplus-1.2-5/fitdistrplus/DESCRIPTION | 6 fitdistrplus-1.2-5/fitdistrplus/MD5 | 149 +- fitdistrplus-1.2-5/fitdistrplus/R/fitdist.R | 16 fitdistrplus-1.2-5/fitdistrplus/build/partial.rdb |binary fitdistrplus-1.2-5/fitdistrplus/build/vignette.rds |binary fitdistrplus-1.2-5/fitdistrplus/inst/doc/FAQ.R | 11 fitdistrplus-1.2-5/fitdistrplus/inst/doc/FAQ.Rmd | 11 fitdistrplus-1.2-5/fitdistrplus/inst/doc/FAQ.html | 389 +++--- fitdistrplus-1.2-5/fitdistrplus/inst/doc/Optimalgo.R | 2 fitdistrplus-1.2-5/fitdistrplus/inst/doc/Optimalgo.Rmd | 2 fitdistrplus-1.2-5/fitdistrplus/inst/doc/Optimalgo.html | 580 +++++----- fitdistrplus-1.2-5/fitdistrplus/inst/doc/fitdistrplus_vignette.R | 2 fitdistrplus-1.2-5/fitdistrplus/inst/doc/fitdistrplus_vignette.Rmd | 2 fitdistrplus-1.2-5/fitdistrplus/inst/doc/fitdistrplus_vignette.html | 51 fitdistrplus-1.2-5/fitdistrplus/inst/doc/starting-values.html | 4 fitdistrplus-1.2-5/fitdistrplus/man/CIcdfplot.Rd | 3 fitdistrplus-1.2-5/fitdistrplus/man/bootdist.Rd | 1 fitdistrplus-1.2-5/fitdistrplus/man/bootdistcens.Rd | 2 fitdistrplus-1.2-5/fitdistrplus/man/descdist.Rd | 3 fitdistrplus-1.2-5/fitdistrplus/man/fitdist.Rd | 27 fitdistrplus-1.2-5/fitdistrplus/man/gofstat.Rd | 2 fitdistrplus-1.2-5/fitdistrplus/man/logLik-plot.Rd | 2 fitdistrplus-1.2-5/fitdistrplus/man/logLik-surface.Rd | 2 fitdistrplus-1.2-5/fitdistrplus/man/mgedist.Rd | 4 fitdistrplus-1.2-5/fitdistrplus/man/mledist.Rd | 5 fitdistrplus-1.2-5/fitdistrplus/man/mmedist.Rd | 4 fitdistrplus-1.2-5/fitdistrplus/man/msedist.Rd | 2 fitdistrplus-1.2-5/fitdistrplus/man/plotdist.Rd | 4 fitdistrplus-1.2-5/fitdistrplus/man/prefit.Rd | 1 fitdistrplus-1.2-5/fitdistrplus/man/qmedist.Rd | 4 fitdistrplus-1.2-5/fitdistrplus/tests/t-CIcdfplot.R | 4 fitdistrplus-1.2-5/fitdistrplus/tests/t-bootdist.R | 6 fitdistrplus-1.2-5/fitdistrplus/tests/t-bootdistcens.R | 3 fitdistrplus-1.2-5/fitdistrplus/tests/t-cdfcomp.R | 4 fitdistrplus-1.2-5/fitdistrplus/tests/t-denscomp.R | 2 fitdistrplus-1.2-5/fitdistrplus/tests/t-descdist.R | 3 fitdistrplus-1.2-5/fitdistrplus/tests/t-fitdist-customoptim.R | 4 fitdistrplus-1.2-5/fitdistrplus/tests/t-fitdist-hessianpb.R | 2 fitdistrplus-1.2-5/fitdistrplus/tests/t-fitdist-test-arguments.R | 10 fitdistrplus-1.2-5/fitdistrplus/tests/t-fitdist.R | 9 fitdistrplus-1.2-5/fitdistrplus/tests/t-fitdistcens.R | 5 fitdistrplus-1.2-5/fitdistrplus/tests/t-gen-max-spacing-estim.R | 2 fitdistrplus-1.2-5/fitdistrplus/tests/t-gofstat.R | 5 fitdistrplus-1.2-5/fitdistrplus/tests/t-llplot.R | 2 fitdistrplus-1.2-5/fitdistrplus/tests/t-lnL-surf.R | 2 fitdistrplus-1.2-5/fitdistrplus/tests/t-mgedist.R | 5 fitdistrplus-1.2-5/fitdistrplus/tests/t-mledist-asymptotic-vcov.R | 2 fitdistrplus-1.2-5/fitdistrplus/tests/t-mledist-nocens.R | 15 fitdistrplus-1.2-5/fitdistrplus/tests/t-mledist-paramsupport.R | 2 fitdistrplus-1.2-5/fitdistrplus/tests/t-mmedist-asymptotic-vcov.R | 2 fitdistrplus-1.2-5/fitdistrplus/tests/t-mmedist.R | 6 fitdistrplus-1.2-5/fitdistrplus/tests/t-msedist.R | 3 fitdistrplus-1.2-5/fitdistrplus/tests/t-parallel.R | 2 fitdistrplus-1.2-5/fitdistrplus/tests/t-plotdist.R | 3 fitdistrplus-1.2-5/fitdistrplus/tests/t-ppcomp.R | 2 fitdistrplus-1.2-5/fitdistrplus/tests/t-qme-discrete.R | 2 fitdistrplus-1.2-5/fitdistrplus/tests/t-qmedist.R | 5 fitdistrplus-1.2-5/fitdistrplus/tests/t-qqcomp.R | 2 fitdistrplus-1.2-5/fitdistrplus/tests/t-quantiledist.R | 1 fitdistrplus-1.2-5/fitdistrplus/tests/t-weird-ppcomp-cens.R | 2 fitdistrplus-1.2-5/fitdistrplus/tests/t-weird-qqcomp-cens.R | 2 fitdistrplus-1.2-5/fitdistrplus/vignettes/FAQ.Rmd | 11 fitdistrplus-1.2-5/fitdistrplus/vignettes/Optimalgo.Rmd | 2 fitdistrplus-1.2-5/fitdistrplus/vignettes/fitdistrplus_vignette.Rmd | 2 87 files changed, 688 insertions(+), 737 deletions(-)
Title: Dose-Response Network Meta-Analysis in a Frequentist Way
Description: A set of functions providing the implementation of the network meta-analysis model with dose-response relationships, predicted values of the fitted model and dose-response plots in a frequentist way.
Author: Maria Petropoulou [aut, cre] ,
Guido Schwarzer [aut]
Maintainer: Maria Petropoulou <m.petropoulou.a@gmail.com>
Diff between netdose versions 0.7-3 dated 2026-01-13 and 0.7-4 dated 2026-01-22
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 10 +++++++++- R/netdose.R | 6 +++--- man/netdose.Rd | 6 +++--- 5 files changed, 23 insertions(+), 15 deletions(-)
Title: Analysis of Korean National Forest Inventory Database
Description: Understanding the current status of forest resources is essential for monitoring changes
in forest ecosystems and generating related statistics. In South Korea, the National Forest
Inventory (NFI) surveys over 4,500 sample plots nationwide every five years and records 70 items,
including forest stand, forest resource, and forest vegetation surveys. Many researchers use NFI
as the primary data for research, such as biomass estimation or analyzing the importance value of
each species over time and space, depending on the research purpose. However, the large volume
of accumulated forest survey data from across the country can make it challenging to manage and
utilize such a vast dataset. To address this issue, we developed an R package that efficiently
handles large-scale NFI data across time and space. The package offers a comprehensive
workflow for NFI data analysis. It starts with data processing, where read_nfi() function
reconstructs NFI data according to the researcher's needs while [...truncated...]
Author: Sinyoung Park [aut, cre] ,
Wonhee Cho [aut, ctb] ,
Inyoo Kim [aut, ctb] ,
Wontaek Lim [aut, ctb] ,
Dongwook W. Ko [aut, ths]
Maintainer: Sinyoung Park <youngsin0306@kookmin.ac.kr>
Diff between knfi versions 1.0.1.9 dated 2024-12-03 and 1.0.2 dated 2026-01-22
DESCRIPTION | 18 ++++++++++-------- MD5 | 44 ++++++++++++++++++++++++-------------------- NAMESPACE | 1 - NEWS.md | 4 ++++ R/biomass_nfi.R | 4 +++- R/cwd_biomass_nfi.R | 3 ++- R/diversity_nfi.R | 6 +++++- R/info_nfi.R | 1 - R/iv_nfi.R | 3 ++- R/read_nfi.R | 4 ++-- R/summary_nfi.R | 3 ++- R/sysdata.rda |binary R/tsvis_nfi.R | 9 +++++---- build/vignette.rds |binary inst/doc/Published.R |only inst/doc/Published.Rmd |only inst/doc/Published.html |only man/biomass_nfi.Rd | 2 +- man/cwd_biomass_nfi.Rd | 2 +- man/diversity_nfi.Rd | 2 +- man/iv_nfi.Rd | 2 +- man/read_nfi.Rd | 4 ++-- man/summary_nfi.Rd | 2 +- man/tsvis_nfi.Rd | 4 ++-- vignettes/Published.Rmd |only 25 files changed, 68 insertions(+), 50 deletions(-)
Title: R Client Package for Circle CI
Description: Tools for interacting with the 'Circle CI' API
(<https://circleci.com/docs/api/v2/>). Besides executing common tasks
such as querying build logs and restarting builds, this package also
helps setting up permissions to deploy from builds.
Author: David Munoz Tord [cre, ctb],
Patrick Schratz [aut] ,
Max Joseph [rev] ,
Sharla Gelfand [rev]
Maintainer: David Munoz Tord <david.munoztord@mailbox.org>
Diff between circle versions 0.7.3 dated 2024-07-31 and 0.7.4 dated 2026-01-22
DESCRIPTION | 14 MD5 | 130 - NAMESPACE | 66 NEWS.md | 21 R/auth.R | 212 +- R/builds.R | 352 +-- R/checkout-key.R | 396 +-- R/circle-package.R | 62 R/circle.R | 152 - R/env-var.R | 268 +- R/format-builds-helpers.R | 316 +-- R/general.R | 380 +-- R/helpers-github.R | 108 - R/use-circle-deploy.R | 138 - README.md | 134 - build/vignette.rds |binary inst/doc/advanced.R |only inst/doc/advanced.Rmd |only inst/doc/advanced.html |only inst/doc/circle.R | 28 inst/doc/circle.Rmd | 308 +-- inst/doc/circle.html | 1011 ++++----- inst/doc/tic.R | 13 inst/doc/tic.Rmd | 275 +- inst/doc/tic.html | 975 ++++----- man/browse_circle_token.Rd | 102 man/builds.Rd | 182 - man/checkout_key.Rd | 220 +- man/circle-package.Rd | 114 - man/circle.Rd | 122 - man/edit_circle_config.Rd | 28 man/enable_repo.Rd | 94 man/env_var.Rd | 166 - man/get_build_artifacts.Rd | 96 man/get_circle_user.Rd | 52 man/github_info.Rd | 62 man/list_projects.Rd | 84 man/new_build.Rd | 102 man/use_circle_deploy.Rd | 98 tests/fixtures/create_checkout_key().yml | 80 tests/fixtures/delete_checkout_key().yml | 166 - tests/fixtures/delete_env_var().yml | 78 tests/fixtures/enable_repo().yml | 78 tests/fixtures/get_build_artifacts().yml | 2662 +++++++++++++------------- tests/fixtures/get_circle_user().yml | 82 tests/fixtures/get_env_vars().yml | 82 tests/fixtures/get_jobs().yml | 2582 ++++++++++++------------- tests/fixtures/has_checkout_key().yml | 86 tests/fixtures/list_projects().yml | 82 tests/fixtures/new_build().yml | 150 - tests/fixtures/retry_workflow().yml | 1856 +++++++++--------- tests/fixtures/s3-print-circle_collection.yml | 1782 ++++++++--------- tests/fixtures/s3-print-circle_job.yml | 2662 +++++++++++++------------- tests/fixtures/s3-print-circle_pipeline.yml | 100 tests/fixtures/s3-print-circle_workflow.yml | 1782 ++++++++--------- tests/fixtures/set_env_var().yml | 76 tests/testthat.R | 8 tests/testthat/helper-circle.R | 30 tests/testthat/test-1-builds.R | 106 - tests/testthat/test-2-print.R | 142 - tests/testthat/test-auth.R | 28 tests/testthat/test-checkout-keys.R | 84 tests/testthat/test-env-vars.R | 98 tests/testthat/test-general.R | 134 - tests/testthat/test-helpers-github.R | 46 vignettes/advanced.Rmd |only vignettes/circle.Rmd | 308 +-- vignettes/tic.Rmd | 275 +- 68 files changed, 11293 insertions(+), 11233 deletions(-)
Title: Download Infectious Disease Data from 'SurvStat' (Robert Koch
Institute)
Description: Provides an interface to the 'SurvStat' web service from the
Robert Koch Institute (<https://tools.rki.de/SurvStat/SurvStatWebService.svc>)
allowing downloads of disease time series stratified
by pathogen type and subtype, age, and geography from notifiable disease
reports in Germany.
Author: Robert Challen [aut, cre] ,
Bristol Vaccine Centre [fnd, cph]
Maintainer: Robert Challen <rob.challen@bristol.ac.uk>
Diff between rsurvstat versions 0.1.2 dated 2026-01-17 and 0.1.3 dated 2026-01-22
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 5 +++++ R/sysdata.rda |binary data/CountyKey71Map.rda |binary 5 files changed, 12 insertions(+), 7 deletions(-)
Title: Wrapper for 'SUNDIALS' Solving ODE and Sensitivity Problem
Description: Wrapper for widely used 'SUNDIALS' software (SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers) and more precisely to its 'CVODES' solver. It is aiming to solve ordinary differential equations (ODE) and optionally pending forward sensitivity problem. The wrapper is made 'R' friendly by allowing to pass custom parameters to user's callback functions. Such functions can be both written in 'R' and in 'C++' ('RcppArmadillo' flavor). In case of 'C++', performance is greatly improved so this option is highly advisable when performance matters. If provided, Jacobian matrix can be calculated either in dense or sparse format. In the latter case 'rmumps' package is used to solve corresponding linear systems. Root finding and pending event management are optional and can be specified as 'R' or 'C++' functions too. This makes them a very flexible tool for controlling the ODE system during the time course simulation. 'SUNDIALS' library was published in Hindmarsh et al. (2005) <doi:1 [...truncated...]
Author: Serguei Sokol [cre, aut],
Carol S. Woodward [ctb],
Daniel R. Reynolds [ctb],
Alan C. Hindmarsh [ctb],
David J. Gardner [ctb],
Cody J. Balos [ctb],
Radu Serban [ctb],
Scott D. Cohen [ctb],
Peter N. Brown [ctb],
George Byrne [ctb],
Allan G. Taylor [ctb [...truncated...]
Maintainer: Serguei Sokol <sokol@insa-toulouse.fr>
Diff between r2sundials versions 7.2.1-3 dated 2025-04-10 and 7.2.1-4 dated 2026-01-22
r2sundials-7.2.1-3/r2sundials/NEWS |only r2sundials-7.2.1-3/r2sundials/R/translate.R |only r2sundials-7.2.1-4/r2sundials/DESCRIPTION | 10 +++++----- r2sundials-7.2.1-4/r2sundials/MD5 | 17 ++++++++--------- r2sundials-7.2.1-4/r2sundials/NEWS.md |only r2sundials-7.2.1-4/r2sundials/R/RcppExports.R | 3 --- r2sundials-7.2.1-4/r2sundials/build/partial.rdb |binary r2sundials-7.2.1-4/r2sundials/inst/COPYRIGHTS | 2 +- r2sundials-7.2.1-4/r2sundials/man/r2cvodes.Rd | 5 ----- r2sundials-7.2.1-4/r2sundials/src/lib/readme.txt | 2 +- r2sundials-7.2.1-4/r2sundials/src/r2sundials.cpp | 3 --- 11 files changed, 15 insertions(+), 27 deletions(-)
Title: Supervised and Unsupervised Self-Organising Maps
Description: Functions to train self-organising maps (SOMs). Also interrogation of the maps and prediction using trained maps are supported. The name of the package refers to Teuvo Kohonen, the inventor of the SOM.
Author: Ron Wehrens [aut, cre],
Johannes Kruisselbrink [aut]
Maintainer: Ron Wehrens <ron.wehrens@gmail.com>
Diff between kohonen versions 3.0.12 dated 2023-06-09 and 3.0.13 dated 2026-01-22
kohonen-3.0.12/kohonen/inst/doc/kohonen-manual_2007.pdf |only kohonen-3.0.13/kohonen/DESCRIPTION | 17 ++++++++-- kohonen-3.0.13/kohonen/MD5 | 13 +++----- kohonen-3.0.13/kohonen/NEWS | 13 +++++++- kohonen-3.0.13/kohonen/R/classvec2classmat.R | 5 ++- kohonen-3.0.13/kohonen/R/plot.kohonen.R | 9 ++++- kohonen-3.0.13/kohonen/R/predict.kohonen.R | 25 ++++++++++------ kohonen-3.0.13/kohonen/build/partial.rdb |binary 8 files changed, 58 insertions(+), 24 deletions(-)
Title: Desparsified Lasso Inference for Time Series
Description: Calculates the desparsified lasso as originally introduced in van de Geer et al. (2014) <doi:10.1214/14-AOS1221>, and provides inference suitable for high-dimensional time series, based on the long run covariance estimator in Adamek et al. (2020) <doi:10.48550/arXiv.2007.10952>. Also estimates high-dimensional local projections by the desparsified lasso, as described in Adamek et al. (2022) <doi:10.48550/arXiv.2209.03218>.
Author: Robert Adamek [cre, aut],
Stephan Smeekes [aut],
Ines Wilms [aut]
Maintainer: Robert Adamek <robertadamek94@gmail.com>
Diff between desla versions 0.3.0 dated 2023-06-29 and 0.3.1 dated 2026-01-22
DESCRIPTION | 9 - MD5 | 52 ++++++++- NEWS.md | 6 + README.md | 1 build/partial.rdb |binary inst/unit_test_reference_files |only inst/unit_tests.R |only src/rcpp_functions.cpp | 216 ++++++++++++++++++++--------------------- 8 files changed, 167 insertions(+), 117 deletions(-)
Title: Causal Graph Interface
Description: Create, query, and modify causal graphs. 'caugi' (Causal Graph
Interface) is a causality-first, high performance graph package that
provides a simple interface to build, structure, and examine causal
relationships.
Author: Frederik Fabricius-Bjerre [aut, cre, cph],
Johan Larsson [aut] ,
Michael Sachs [aut]
Maintainer: Frederik Fabricius-Bjerre <frederik@fabriciusbjerre.dk>
Diff between caugi versions 0.3.1 dated 2025-12-04 and 1.0.0 dated 2026-01-22
caugi-0.3.1/caugi/inst/examples |only caugi-0.3.1/caugi/src/rust/src/graph/dag.rs |only caugi-0.3.1/caugi/src/rust/src/graph/pdag.rs |only caugi-0.3.1/caugi/tools/coding-helpers.R |only caugi-1.0.0/caugi/DESCRIPTION | 25 caugi-1.0.0/caugi/MD5 | 280 caugi-1.0.0/caugi/NAMESPACE | 42 caugi-1.0.0/caugi/NEWS.md | 133 caugi-1.0.0/caugi/R/DSL-parser.R | 44 caugi-1.0.0/caugi/R/aaa-env.R | 22 caugi-1.0.0/caugi/R/adjustment.R | 272 caugi-1.0.0/caugi/R/all-classes.R |only caugi-1.0.0/caugi/R/as_caugi.R | 229 caugi-1.0.0/caugi/R/caugi-package.R | 1 caugi-1.0.0/caugi/R/caugi.R | 171 caugi-1.0.0/caugi/R/caugi_to.R | 56 caugi-1.0.0/caugi/R/edge_operators.R | 4 caugi-1.0.0/caugi/R/extendr-wrappers.R | 44 caugi-1.0.0/caugi/R/format-caugi.R |only caugi-1.0.0/caugi/R/format-dot.R |only caugi-1.0.0/caugi/R/format-graphml.R |only caugi-1.0.0/caugi/R/format-mermaid.R |only caugi-1.0.0/caugi/R/methods.R | 28 caugi-1.0.0/caugi/R/metrics.R | 11 caugi-1.0.0/caugi/R/operations.R | 431 caugi-1.0.0/caugi/R/options.R |only caugi-1.0.0/caugi/R/plot.R |only caugi-1.0.0/caugi/R/queries.R | 573 caugi-1.0.0/caugi/R/registry.R | 37 caugi-1.0.0/caugi/R/simulation.R | 176 caugi-1.0.0/caugi/R/verbs.R | 140 caugi-1.0.0/caugi/R/zzz.R | 1 caugi-1.0.0/caugi/README.md | 42 caugi-1.0.0/caugi/build/partial.rdb |only caugi-1.0.0/caugi/build/vignette.rds |binary caugi-1.0.0/caugi/inst/WORDLIST |only caugi-1.0.0/caugi/inst/doc/get_started.html | 8 caugi-1.0.0/caugi/inst/doc/package_use.html | 4 caugi-1.0.0/caugi/inst/doc/serialization.R |only caugi-1.0.0/caugi/inst/doc/serialization.Rmd |only caugi-1.0.0/caugi/inst/doc/serialization.html |only caugi-1.0.0/caugi/inst/doc/visualization.R |only caugi-1.0.0/caugi/inst/doc/visualization.Rmd |only caugi-1.0.0/caugi/inst/doc/visualization.html |only caugi-1.0.0/caugi/man/add-caugi_plot-caugi_plot.Rd |only caugi-1.0.0/caugi/man/adjustment_set.Rd | 2 caugi-1.0.0/caugi/man/all_adjustment_sets_admg.Rd |only 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caugi-1.0.0/caugi/man/children.Rd | 14 caugi-1.0.0/caugi/man/condition_marginalize.Rd |only caugi-1.0.0/caugi/man/d_separated.Rd | 2 caugi-1.0.0/caugi/man/descendants.Rd | 10 caugi-1.0.0/caugi/man/districts.Rd |only caugi-1.0.0/caugi/man/divide-caugi_plot-caugi_plot.Rd |only caugi-1.0.0/caugi/man/dot-cg_state.Rd | 13 caugi-1.0.0/caugi/man/dot-edge_type_from_anteriors.Rd |only caugi-1.0.0/caugi/man/dot-get_edges.Rd | 4 caugi-1.0.0/caugi/man/dot-not_m_separated_for_all_subsets.Rd |only caugi-1.0.0/caugi/man/edge_types.Rd | 10 caugi-1.0.0/caugi/man/edges.Rd | 10 caugi-1.0.0/caugi/man/exogenize.Rd |only caugi-1.0.0/caugi/man/exogenous.Rd | 10 caugi-1.0.0/caugi/man/export-classes.Rd |only caugi-1.0.0/caugi/man/figures/README-unnamed-chunk-5-1.png |only caugi-1.0.0/caugi/man/figures/og.png |only caugi-1.0.0/caugi/man/figures/og.svg |only caugi-1.0.0/caugi/man/format-caugi.Rd |only caugi-1.0.0/caugi/man/format-dot.Rd |only caugi-1.0.0/caugi/man/format-graphml.Rd |only caugi-1.0.0/caugi/man/format-mermaid.Rd |only caugi-1.0.0/caugi/man/generate_graph.Rd | 4 caugi-1.0.0/caugi/man/is_acyclic.Rd | 10 caugi-1.0.0/caugi/man/is_admg.Rd |only caugi-1.0.0/caugi/man/is_ag.Rd |only caugi-1.0.0/caugi/man/is_caugi.Rd | 10 caugi-1.0.0/caugi/man/is_cpdag.Rd | 10 caugi-1.0.0/caugi/man/is_dag.Rd | 10 caugi-1.0.0/caugi/man/is_empty_caugi.Rd | 10 caugi-1.0.0/caugi/man/is_mag.Rd |only caugi-1.0.0/caugi/man/is_pdag.Rd | 10 caugi-1.0.0/caugi/man/is_ug.Rd | 10 caugi-1.0.0/caugi/man/is_valid_adjustment_admg.Rd |only caugi-1.0.0/caugi/man/is_valid_backdoor.Rd | 4 caugi-1.0.0/caugi/man/knit_print.caugi_export.Rd |only caugi-1.0.0/caugi/man/latent_project.Rd |only caugi-1.0.0/caugi/man/m_separated.Rd |only caugi-1.0.0/caugi/man/makeContent.caugi_edge_grob.Rd |only caugi-1.0.0/caugi/man/markov_blanket.Rd | 10 caugi-1.0.0/caugi/man/moralize.Rd | 3 caugi-1.0.0/caugi/man/mutate_caugi.Rd | 3 caugi-1.0.0/caugi/man/neighbors.Rd | 65 caugi-1.0.0/caugi/man/nodes.Rd | 10 caugi-1.0.0/caugi/man/parents.Rd | 16 caugi-1.0.0/caugi/man/plot.Rd |only caugi-1.0.0/caugi/man/read_caugi.Rd |only caugi-1.0.0/caugi/man/read_graphml.Rd |only caugi-1.0.0/caugi/man/registry.Rd | 2 caugi-1.0.0/caugi/man/same_nodes.Rd | 10 caugi-1.0.0/caugi/man/simulate_data.Rd |only caugi-1.0.0/caugi/man/skeleton.Rd | 3 caugi-1.0.0/caugi/man/spouses.Rd |only caugi-1.0.0/caugi/man/subgraph.Rd | 10 caugi-1.0.0/caugi/man/to_dot.Rd |only caugi-1.0.0/caugi/man/to_graphml.Rd |only caugi-1.0.0/caugi/man/to_mermaid.Rd |only caugi-1.0.0/caugi/man/topological_sort.Rd |only caugi-1.0.0/caugi/man/write_caugi.Rd |only caugi-1.0.0/caugi/man/write_dot.Rd |only caugi-1.0.0/caugi/man/write_graphml.Rd |only caugi-1.0.0/caugi/man/write_mermaid.Rd |only caugi-1.0.0/caugi/src/rust/Cargo.lock | 257 caugi-1.0.0/caugi/src/rust/Cargo.toml | 8 caugi-1.0.0/caugi/src/rust/src/edges/mod.rs | 2 caugi-1.0.0/caugi/src/rust/src/graph/admg |only caugi-1.0.0/caugi/src/rust/src/graph/ag |only caugi-1.0.0/caugi/src/rust/src/graph/alg.rs | 89 caugi-1.0.0/caugi/src/rust/src/graph/alg/acyclic.rs |only caugi-1.0.0/caugi/src/rust/src/graph/alg/reachability.rs |only caugi-1.0.0/caugi/src/rust/src/graph/alg/subsets.rs |only caugi-1.0.0/caugi/src/rust/src/graph/alg/topo_sort.rs |only caugi-1.0.0/caugi/src/rust/src/graph/alg/traversal.rs |only caugi-1.0.0/caugi/src/rust/src/graph/builder.rs | 61 caugi-1.0.0/caugi/src/rust/src/graph/dag |only caugi-1.0.0/caugi/src/rust/src/graph/error.rs |only caugi-1.0.0/caugi/src/rust/src/graph/graphml.rs |only caugi-1.0.0/caugi/src/rust/src/graph/layout |only caugi-1.0.0/caugi/src/rust/src/graph/metrics.rs | 397 caugi-1.0.0/caugi/src/rust/src/graph/mod.rs | 7 caugi-1.0.0/caugi/src/rust/src/graph/pdag |only caugi-1.0.0/caugi/src/rust/src/graph/serialization.rs |only caugi-1.0.0/caugi/src/rust/src/graph/ug.rs | 13 caugi-1.0.0/caugi/src/rust/src/graph/view.rs | 1163 + caugi-1.0.0/caugi/src/rust/src/lib.rs | 465 caugi-1.0.0/caugi/src/rust/vendor.tar.xz |binary caugi-1.0.0/caugi/tests/testthat/test-DSL-parser.R | 18 caugi-1.0.0/caugi/tests/testthat/test-aaa-env.R | 4 caugi-1.0.0/caugi/tests/testthat/test-adjustment.R | 82 caugi-1.0.0/caugi/tests/testthat/test-admg.R |only caugi-1.0.0/caugi/tests/testthat/test-ag.R |only caugi-1.0.0/caugi/tests/testthat/test-aid.R | 8197 +++++++++-- caugi-1.0.0/caugi/tests/testthat/test-as_caugi.R | 67 caugi-1.0.0/caugi/tests/testthat/test-bipartite-layout.R |only caugi-1.0.0/caugi/tests/testthat/test-caugi_graph.R | 33 caugi-1.0.0/caugi/tests/testthat/test-caugi_to.R | 23 caugi-1.0.0/caugi/tests/testthat/test-edge_operators.R | 9 caugi-1.0.0/caugi/tests/testthat/test-export.R |only caugi-1.0.0/caugi/tests/testthat/test-format-caugi.R |only caugi-1.0.0/caugi/tests/testthat/test-format-dot.R |only caugi-1.0.0/caugi/tests/testthat/test-format-graphml.R |only caugi-1.0.0/caugi/tests/testthat/test-format-mermaid.R |only caugi-1.0.0/caugi/tests/testthat/test-metrics.R | 65 caugi-1.0.0/caugi/tests/testthat/test-operations.R | 403 caugi-1.0.0/caugi/tests/testthat/test-plot-composition.R |only caugi-1.0.0/caugi/tests/testthat/test-plot.R |only caugi-1.0.0/caugi/tests/testthat/test-queries.R | 442 caugi-1.0.0/caugi/tests/testthat/test-simulation.R | 278 caugi-1.0.0/caugi/tests/testthat/test-tiered-layout.R |only caugi-1.0.0/caugi/tests/testthat/test-topological-sort.R |only caugi-1.0.0/caugi/tests/testthat/test-verbs.R | 165 caugi-1.0.0/caugi/tools/msrv.R | 8 caugi-1.0.0/caugi/vignettes/references.bib |only caugi-1.0.0/caugi/vignettes/serialization.Rmd |only caugi-1.0.0/caugi/vignettes/visualization.Rmd |only 183 files changed, 13483 insertions(+), 1863 deletions(-)
Title: Extra Functions for 'gtsummary' Table Styling
Description: Provides additional convenience functions for 'gtsummary'
(Sjoberg et al. (2021) <doi:10.32614/RJ-2021-053>) & 'gt' tables,
including automatic variable labeling from dictionaries, standardized
missing value display, and consistent formatting helpers for streamlined
table styling workflows.
Author: Kyle Grealis [aut, cre] ,
Raymond Balise [ctb] ,
Daniel Maya [ctb]
Maintainer: Kyle Grealis <kyleGrealis@proton.me>
Diff between sumExtras versions 0.2.0 dated 2026-01-19 and 0.3.0 dated 2026-01-22
DESCRIPTION | 16 MD5 | 18 NEWS.md | 14 R/clean_table.R | 13 R/extras.R | 54 inst/doc/labeling.html | 1652 +++++++++++++-------------- inst/doc/styling.html | 2530 +++++++++++++++++++++--------------------- inst/doc/sumExtras-intro.html | 1210 ++++++++++---------- man/extras.Rd | 22 man/sumExtras-package.Rd | 1 10 files changed, 2808 insertions(+), 2722 deletions(-)
Title: Causal Inference in Spatiotemporal Event Data
Description: Implementation of Matched Wake Analysis (mwa) for studying causal relationships in spatiotemporal event data, introduced by Schutte and Donnay (2014) <doi:10.1016/j.polgeo.2014.03.001>.
Author: Sebastian Schutte [aut],
Karsten Donnay [aut, cre]
Maintainer: Karsten Donnay <kdonnay@gmx.net>
Diff between mwa versions 0.5.0 dated 2025-09-29 and 0.5.1 dated 2026-01-22
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 4 ++++ R/mwa.R | 19 +------------------ 4 files changed, 12 insertions(+), 25 deletions(-)
Title: Simulate Survival Data
Description: Simulate survival times from standard parametric survival
distributions (exponential, Weibull, Gompertz), 2-component mixture
distributions, or a user-defined hazard, log hazard, cumulative hazard,
or log cumulative hazard function. Baseline covariates can be included
under a proportional hazards assumption.
Time dependent effects (i.e. non-proportional hazards) can be included by
interacting covariates with linear time or a user-defined function of time.
Clustered event times are also accommodated.
The 2-component mixture distributions can allow for a variety of flexible
baseline hazard functions reflecting those seen in practice.
If the user wishes to provide a user-defined
hazard or log hazard function then this is possible, and the resulting
cumulative hazard function does not need to have a closed-form solution.
For details see the supporting paper <doi:10.18637/jss.v097.i03>.
Note that this package is modelled on the 'survsim' package available in
the 'Stata' software (see [...truncated...]
Author: Sam Brilleman [cre, aut, cph],
Alessandro Gasparini [ctb]
Maintainer: Sam Brilleman <sam.brilleman@gmail.com>
Diff between simsurv versions 1.0.0 dated 2021-01-13 and 1.0.1 dated 2026-01-22
DESCRIPTION | 12 LICENSE | 1348 ++++++++--------- MD5 | 58 NAMESPACE | 8 NEWS.md | 145 - R/brcancer.R | 52 R/simsurv.R | 2422 +++++++++++++++---------------- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 42 inst/doc/simsurv_technical.R | 6 inst/doc/simsurv_technical.Rmd | 574 +++---- inst/doc/simsurv_technical.html | 981 ++++++------ inst/doc/simsurv_usage.R | 474 +++--- inst/doc/simsurv_usage.Rmd | 798 +++++----- inst/doc/simsurv_usage.html | 1369 ++++++++--------- man/simsurv.Rd | 2 tests/testthat.R | 8 tests/testthat/helpers/check_bias.R | 24 tests/testthat/helpers/is_exponential.R | 6 tests/testthat/helpers/is_gompertz.R | 6 tests/testthat/helpers/is_weibull.R | 6 tests/testthat/helpers/recover_betas.R | 12 tests/testthat/helpers/recover_gammas.R | 18 tests/testthat/helpers/recover_lambdas.R | 26 tests/testthat/helpers/recover_params.R | 32 tests/testthat/helpers/sim_run.R | 66 tests/testthat/test_simsurv.R | 156 - vignettes/simsurv_technical.Rmd | 574 +++---- vignettes/simsurv_usage.Rmd | 798 +++++----- 30 files changed, 5012 insertions(+), 5011 deletions(-)
Title: Automatic Forecasting Procedure
Description: Implements a procedure for forecasting time series data based on
an additive model where non-linear trends are fit with yearly, weekly, and
daily seasonality, plus holiday effects. It works best with time series
that have strong seasonal effects and several seasons of historical data.
Prophet is robust to missing data and shifts in the trend, and typically
handles outliers well.
Author: Cuong Duong [cre, aut],
Sean Taylor [aut],
Ben Letham [aut]
Maintainer: Cuong Duong <cuong.duong242@gmail.com>
Diff between prophet versions 1.0 dated 2021-03-30 and 1.1.7 dated 2026-01-22
prophet-1.0/prophet/data |only prophet-1.1.7/prophet/DESCRIPTION | 24 prophet-1.1.7/prophet/MD5 | 59 prophet-1.1.7/prophet/NAMESPACE | 1 prophet-1.1.7/prophet/R/data.R | 8 prophet-1.1.7/prophet/R/diagnostics.R | 59 prophet-1.1.7/prophet/R/plot.R | 4 prophet-1.1.7/prophet/R/prophet.R | 143 prophet-1.1.7/prophet/R/stan_backends.R |only prophet-1.1.7/prophet/R/stanmodels.R | 2 prophet-1.1.7/prophet/R/sysdata.rda |only prophet-1.1.7/prophet/R/utilities.R | 2 prophet-1.1.7/prophet/build/vignette.rds |binary prophet-1.1.7/prophet/inst/doc/quick_start.R | 4 prophet-1.1.7/prophet/inst/doc/quick_start.html | 630 ++- prophet-1.1.7/prophet/inst/stan/prophet.stan | 17 prophet-1.1.7/prophet/man/check_cmdstanr.Rd |only prophet-1.1.7/prophet/man/dot-fit.Rd |only prophet-1.1.7/prophet/man/dot-load_model.Rd |only prophet-1.1.7/prophet/man/dot-sampling.Rd |only prophet-1.1.7/prophet/man/dot-stan_args.Rd |only prophet-1.1.7/prophet/man/dyplot.prophet.Rd | 2 prophet-1.1.7/prophet/man/flat_growth_init.Rd | 2 prophet-1.1.7/prophet/man/generated_holidays.Rd | 9 prophet-1.1.7/prophet/man/get_stan_backend.Rd |only prophet-1.1.7/prophet/man/make_all_seasonality_features.Rd | 2 prophet-1.1.7/prophet/man/prophet.Rd | 28 prophet-1.1.7/prophet/man/setup_dataframe.Rd | 2 prophet-1.1.7/prophet/src/Makevars | 5 prophet-1.1.7/prophet/src/Makevars.win | 5 prophet-1.1.7/prophet/src/RcppExports.cpp | 5 prophet-1.1.7/prophet/src/stanExports_prophet.cc | 34 prophet-1.1.7/prophet/src/stanExports_prophet.h | 2161 +++++++------ prophet-1.1.7/prophet/tests/testthat/test_diagnostics.R | 2 prophet-1.1.7/prophet/tests/testthat/test_prophet.R | 5 35 files changed, 1929 insertions(+), 1286 deletions(-)
Title: Spatial Lag Model Trees
Description: Model-based linear model trees adjusting for spatial correlation using a
simultaneous autoregressive spatial lag, Wagner and Zeileis (2019)
<doi:10.1111/geer.12146>.
Author: Martin Wagner [aut] ,
Achim Zeileis [aut, cre] ,
Roger Bivand [ctb]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between lagsarlmtree versions 1.0-1 dated 2019-04-08 and 1.0-2 dated 2026-01-22
lagsarlmtree-1.0-1/lagsarlmtree/NEWS |only lagsarlmtree-1.0-2/lagsarlmtree/DESCRIPTION | 18 ++++++++++-------- lagsarlmtree-1.0-2/lagsarlmtree/MD5 | 14 +++++++------- lagsarlmtree-1.0-2/lagsarlmtree/NEWS.md |only lagsarlmtree-1.0-2/lagsarlmtree/build/partial.rdb |binary lagsarlmtree-1.0-2/lagsarlmtree/data/GrowthNUTS2.rda |binary lagsarlmtree-1.0-2/lagsarlmtree/data/WeightsNUTS2.rda |binary lagsarlmtree-1.0-2/lagsarlmtree/man/WeightsNUTS2.Rd | 7 ++++--- lagsarlmtree-1.0-2/lagsarlmtree/man/lagsarlmtree.Rd | 2 +- 9 files changed, 22 insertions(+), 19 deletions(-)
Title: Local Large Language Model Inference Engine
Description: Enables R users to run large language models locally using 'GGUF' model files
and the 'llama.cpp' inference engine. Provides a complete R interface for loading models,
generating text completions, and streaming responses in real-time. Supports local
inference without requiring cloud APIs or internet connectivity, ensuring complete
data privacy and control. Based on the 'llama.cpp' project by Georgi Gerganov (2023) <https://github.com/ggml-org/llama.cpp>.
Author: Pawan Rama Mali [aut, cre, cph],
Georgi Gerganov [aut, cph] ,
The ggml authors [cph] ,
Jeffrey Quesnelle [ctb, cph] ,
Bowen Peng [ctb, cph] ,
pi6am [ctb] ,
Ivan Yurchenko [ctb] ,
Dirk Eddelbuettel [ctb]
Maintainer: Pawan Rama Mali <prm@outlook.in>
This is a re-admission after prior archival of version 0.1.0 dated 2025-09-22
Diff between edgemodelr versions 0.1.0 dated 2025-09-22 and 0.1.4 dated 2026-01-22
edgemodelr-0.1.0/edgemodelr/src/r_output_redirect.h |only edgemodelr-0.1.4/edgemodelr/DESCRIPTION | 37 edgemodelr-0.1.4/edgemodelr/LICENSE | 2 edgemodelr-0.1.4/edgemodelr/MD5 | 80 edgemodelr-0.1.4/edgemodelr/NAMESPACE | 8 edgemodelr-0.1.4/edgemodelr/R/api.R | 1008 +++++++++- edgemodelr-0.1.4/edgemodelr/R/edgemodelr-package.R | 2 edgemodelr-0.1.4/edgemodelr/R/ollama.R |only edgemodelr-0.1.4/edgemodelr/R/zzz.R | 8 edgemodelr-0.1.4/edgemodelr/cleanup |only edgemodelr-0.1.4/edgemodelr/inst/CITATION |only edgemodelr-0.1.4/edgemodelr/inst/COPYRIGHTS |only edgemodelr-0.1.4/edgemodelr/inst/examples/07_modern_bslib_streaming_chat.R |only edgemodelr-0.1.4/edgemodelr/inst/examples/ollama_integration_example.R |only edgemodelr-0.1.4/edgemodelr/inst/examples/small_model_optimization_example.R |only edgemodelr-0.1.4/edgemodelr/inst/include |only edgemodelr-0.1.4/edgemodelr/man/dot-download_with_curl.Rd |only edgemodelr-0.1.4/edgemodelr/man/dot-download_with_r.Rd |only edgemodelr-0.1.4/edgemodelr/man/dot-download_with_wget.Rd |only edgemodelr-0.1.4/edgemodelr/man/dot-is_valid_gguf_file.Rd |only edgemodelr-0.1.4/edgemodelr/man/dot-robust_download.Rd |only edgemodelr-0.1.4/edgemodelr/man/edge_benchmark.Rd |only edgemodelr-0.1.4/edgemodelr/man/edge_clean_cache.Rd | 4 edgemodelr-0.1.4/edgemodelr/man/edge_download_model.Rd | 80 edgemodelr-0.1.4/edgemodelr/man/edge_download_url.Rd |only edgemodelr-0.1.4/edgemodelr/man/edge_find_gguf_models.Rd |only edgemodelr-0.1.4/edgemodelr/man/edge_find_ollama_models.Rd |only edgemodelr-0.1.4/edgemodelr/man/edge_load_ollama_model.Rd |only edgemodelr-0.1.4/edgemodelr/man/edge_small_model_config.Rd |only edgemodelr-0.1.4/edgemodelr/man/edgemodelr-package.Rd | 6 edgemodelr-0.1.4/edgemodelr/man/test_ollama_model_compatibility.Rd |only edgemodelr-0.1.4/edgemodelr/src/Makevars | 31 edgemodelr-0.1.4/edgemodelr/src/Makevars.win | 86 edgemodelr-0.1.4/edgemodelr/src/RcppExports.cpp | 2 edgemodelr-0.1.4/edgemodelr/src/bindings.cpp | 316 ++- edgemodelr-0.1.4/edgemodelr/src/ggml/ggml-backend-reg.cpp | 149 + edgemodelr-0.1.4/edgemodelr/src/ggml/ggml-cpu/ggml-cpu.c | 20 edgemodelr-0.1.4/edgemodelr/src/ggml/ggml-cpu/ops.h | 10 edgemodelr-0.1.4/edgemodelr/src/ggml/ggml-cpu/unary-ops.cpp | 2 edgemodelr-0.1.4/edgemodelr/src/ggml/ggml-opt.cpp | 2 edgemodelr-0.1.4/edgemodelr/src/ggml/ggml-quants.c | 25 edgemodelr-0.1.4/edgemodelr/src/ggml/ggml.c | 20 edgemodelr-0.1.4/edgemodelr/src/ggml/ggml.h | 7 edgemodelr-0.1.4/edgemodelr/src/llama/llama-grammar.cpp | 2 edgemodelr-0.1.4/edgemodelr/src/llama/llama-impl.cpp | 2 edgemodelr-0.1.4/edgemodelr/src/llama/llama-impl.h | 5 edgemodelr-0.1.4/edgemodelr/src/llama/llama-model.cpp | 2 edgemodelr-0.1.4/edgemodelr/src/llama/llama-quant.cpp | 2 edgemodelr-0.1.4/edgemodelr/src/llama/unicode.cpp | 2 edgemodelr-0.1.4/edgemodelr/tests/testthat/test-e2e-integration.R |only edgemodelr-0.1.4/edgemodelr/tests/testthat/test-model-loading.R | 24 edgemodelr-0.1.4/edgemodelr/tests/testthat/test-small-model-config.R |only edgemodelr-0.1.4/edgemodelr/tests/testthat/test-utility-functions.R |only 53 files changed, 1590 insertions(+), 354 deletions(-)
Title: Fitting Multivariate Bidirectional Mendelian Randomization
Networks Using Bayesian Directed Cyclic Graphical Models
Description: Addressing a central challenge encountered in Mendelian randomization (MR) studies, where MR primarily focuses on discerning the effects of individual exposures on specific outcomes and establishes causal links between them. Using a network-based methodology, the intricacy involving interdependent outcomes due to numerous factors has been tackled through this routine. Based on Ni et al. (2018) <doi:10.1214/17-BA1087>, 'MR.RGM' extends to a broader exploration of the causal landscape by leveraging on network structures and involves the construction of causal graphs that capture interactions between response variables and consequently between responses and instrument variables. The resulting Graph visually represents these causal connections, showing directed edges with effect sizes labeled. 'MR.RGM' facilitates the navigation of various data availability scenarios effectively by accommodating three input formats, i.e., individual-level data and two types of summary-level data. The [...truncated...]
Author: Bitan Sarkar [aut, cre],
Yang Ni [aut]
Maintainer: Bitan Sarkar <bitan@tamu.edu>
Diff between MR.RGM versions 0.0.5 dated 2025-09-29 and 0.1.0 dated 2026-01-22
MR.RGM-0.0.5/MR.RGM/src/Generate.cpp |only MR.RGM-0.0.5/MR.RGM/src/code.cpp |only MR.RGM-0.1.0/MR.RGM/DESCRIPTION | 19 MR.RGM-0.1.0/MR.RGM/MD5 | 55 MR.RGM-0.1.0/MR.RGM/NAMESPACE | 1 MR.RGM-0.1.0/MR.RGM/R/Imports.R |only MR.RGM-0.1.0/MR.RGM/R/NetworkMotif.R | 2 MR.RGM-0.1.0/MR.RGM/R/RGM.R | 1371 ++++++++-- MR.RGM-0.1.0/MR.RGM/R/RcppExports.R | 100 MR.RGM-0.1.0/MR.RGM/README.md | 382 +- MR.RGM-0.1.0/MR.RGM/inst |only MR.RGM-0.1.0/MR.RGM/man/NetworkMotif.Rd | 2 MR.RGM-0.1.0/MR.RGM/man/RGM.Rd | 221 - MR.RGM-0.1.0/MR.RGM/man/figures/README-unnamed-chunk-11-1.png |binary MR.RGM-0.1.0/MR.RGM/man/figures/README-unnamed-chunk-11-2.png |binary MR.RGM-0.1.0/MR.RGM/man/figures/README-unnamed-chunk-12-2.png |only MR.RGM-0.1.0/MR.RGM/man/figures/README-unnamed-chunk-14-1.png |only MR.RGM-0.1.0/MR.RGM/man/figures/README-unnamed-chunk-8-1.png |binary MR.RGM-0.1.0/MR.RGM/src/NetworkMotif.cpp |only MR.RGM-0.1.0/MR.RGM/src/RGM_SpikeSlab_Diag.cpp |only MR.RGM-0.1.0/MR.RGM/src/RGM_SpikeSlab_Diag_Covariates.cpp |only MR.RGM-0.1.0/MR.RGM/src/RGM_SpikeSlab_Diag_Star.cpp |only MR.RGM-0.1.0/MR.RGM/src/RGM_SpikeSlab_Diag_Star_Covariates.cpp |only MR.RGM-0.1.0/MR.RGM/src/RGM_SpikeSlab_IW.cpp |only MR.RGM-0.1.0/MR.RGM/src/RGM_SpikeSlab_IW_Covariates.cpp |only MR.RGM-0.1.0/MR.RGM/src/RGM_SpikeSlab_IW_Star.cpp |only MR.RGM-0.1.0/MR.RGM/src/RGM_SpikeSlab_IW_Star_Covariates.cpp |only MR.RGM-0.1.0/MR.RGM/src/RGM_SpikeSlab_SSSL.cpp |only MR.RGM-0.1.0/MR.RGM/src/RGM_SpikeSlab_SSSL_Covariates.cpp |only MR.RGM-0.1.0/MR.RGM/src/RGM_SpikeSlab_SSSL_Star.cpp |only MR.RGM-0.1.0/MR.RGM/src/RGM_SpikeSlab_SSSL_Star_Covariates.cpp |only MR.RGM-0.1.0/MR.RGM/src/RGM_Threshold_Diag.cpp |only MR.RGM-0.1.0/MR.RGM/src/RGM_Threshold_Diag_Covariates.cpp |only MR.RGM-0.1.0/MR.RGM/src/RGM_Threshold_Diag_Star.cpp |only MR.RGM-0.1.0/MR.RGM/src/RGM_Threshold_Diag_Star_Covariates.cpp |only MR.RGM-0.1.0/MR.RGM/src/RGM_Threshold_IW.cpp |only MR.RGM-0.1.0/MR.RGM/src/RGM_Threshold_IW_Covariates.cpp |only MR.RGM-0.1.0/MR.RGM/src/RGM_Threshold_IW_Star.cpp |only MR.RGM-0.1.0/MR.RGM/src/RGM_Threshold_IW_Star_Covariates.cpp |only MR.RGM-0.1.0/MR.RGM/src/RGM_Threshold_SSSL.cpp |only MR.RGM-0.1.0/MR.RGM/src/RGM_Threshold_SSSL_Covariates.cpp |only MR.RGM-0.1.0/MR.RGM/src/RGM_Threshold_SSSL_Star.cpp |only MR.RGM-0.1.0/MR.RGM/src/RGM_Threshold_SSSL_Star_Covariates.cpp |only MR.RGM-0.1.0/MR.RGM/src/RcppExports.cpp | 641 ++-- 44 files changed, 2051 insertions(+), 743 deletions(-)
Title: Wavelet System Prediction
Description: The wavelet-based variance transformation method is used for system modelling and prediction. It refines predictor spectral representation using Wavelet Theory, which leads to improved model specifications and prediction accuracy. Details of methodologies used in the package can be found in Jiang, Z., Sharma, A., & Johnson, F. (2020) <doi:10.1029/2019WR026962>, Jiang, Z., Rashid, M. M., Johnson, F., & Sharma, A. (2020) <doi:10.1016/j.envsoft.2020.104907>, and Jiang, Z., Sharma, A., & Johnson, F. (2021) <doi:10.1016/J.JHYDROL.2021.126816>.
Author: Ze Jiang [aut, cre] ,
Md. Mamunur Rashid [aut] ,
Ashish Sharma [aut] ,
Fiona Johnson [aut]
Maintainer: Ze Jiang <ze.jiang@unsw.edu.au>
Diff between WASP versions 1.4.4 dated 2024-07-20 and 1.4.5 dated 2026-01-22
DESCRIPTION | 21 MD5 | 14 build/vignette.rds |binary data/datalist | 22 inst/doc/WASP.R | 1587 ++++++++--------- inst/doc/WASP.Rmd | 9 inst/doc/WASP.html | 4680 ++++++++++++++++++++++++++--------------------------- vignettes/WASP.Rmd | 9 8 files changed, 3172 insertions(+), 3170 deletions(-)
Title: Exploratory Data Analysis for the 'spatstat' Family
Description: Functionality for exploratory data analysis and nonparametric analysis of
spatial data, mainly spatial point patterns,
in the 'spatstat' family of packages.
(Excludes analysis of spatial data on a linear network,
which is covered by the separate package 'spatstat.linnet'.)
Methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Monte Carlo, Diggle-Cressie-Loosmore-Ford, Dao-Genton, two-stage Monte Carlo) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov, ANOVA) are also supported.
Author: Adrian Baddeley [aut, cre, cph] ,
Rolf Turner [aut, cph] ,
Ege Rubak [aut, cph] ,
Kasper Klitgaard Berthelsen [ctb],
Warick Brown [cph],
Achmad Choiruddin [ctb],
Ya-Mei Chang [ctb],
Jean-Francois Coeurjolly [ctb],
Lucia Cobo Sanchez [ctb, cph],
Ottma [...truncated...]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.explore versions 3.6-0 dated 2025-11-22 and 3.7-0 dated 2026-01-22
DESCRIPTION | 18 +-- MD5 | 178 +++++++++++++++++------------------ NAMESPACE | 2 NEWS | 48 +++++++++ R/FGmultiInhom.R | 20 ++-- R/Fest.R | 6 - R/Gest.R | 7 - R/Gmulti.R | 24 ++-- R/Jest.R | 8 + R/Jinhom.R | 15 +-- R/Jmulti.R | 21 ++-- R/Kinhom.R | 6 - R/Kmulti.R | 27 ++--- R/Kmulti.inhom.R | 16 +-- R/Ksector.R | 6 - R/bw.CvL.R | 2 R/bw.CvL.adaptive.R | 2 R/bw.diggle.R | 2 R/cdftest.R | 2 R/clarkevans.R | 2 R/clusterset.R | 4 R/compileCDF.R | 2 R/exactppm.R | 6 + R/fasp.R | 16 ++- R/hasenvelope.R | 2 R/laslett.R | 2 R/localpcf.R | 2 R/markcorr.R | 194 +++++++++++++++++++++++++-------------- R/metriccontact.R | 6 - R/nncount.R | 2 R/pairs.im.R | 2 R/pcf.R | 6 - R/pcfinhom.R | 6 - R/pcfmulti.R | 14 +- R/pcfmulti.inhom.R | 14 +- R/plot.fasp.R | 145 ++++++++++++++++------------- R/plot.fv.R | 12 +- R/rho2hat.R | 2 R/rhohat.R | 2 R/smoothfun.R | 2 R/spatialcdf.R | 2 R/ssf.R | 2 R/tolcon.R | 2 R/transect.R | 2 inst/doc/packagesizes.txt | 1 inst/info/packagesizes.txt | 1 man/Emark.Rd | 8 + man/Fest.Rd | 6 + man/Finhom.Rd | 6 + man/FmultiInhom.Rd | 8 + man/Gcross.Rd | 7 + man/Gcross.inhom.Rd | 6 + man/Gdot.Rd | 7 + man/Gdot.inhom.Rd | 7 + man/Gest.Rd | 6 + man/Ginhom.Rd | 6 + man/Gmulti.Rd | 6 + man/GmultiInhom.Rd | 8 + man/Jcross.Rd | 6 + man/Jdot.Rd | 6 + man/Jest.Rd | 6 + man/Jinhom.Rd | 6 + man/Jmulti.Rd | 8 + man/Kcross.Rd | 9 + man/Kcross.inhom.Rd | 7 + man/Kdot.Rd | 8 + man/Kdot.inhom.Rd | 7 + man/Kinhom.Rd | 5 - man/Kmark.Rd | 6 + man/Kmulti.inhom.Rd | 6 + man/Ksector.Rd | 6 + man/markconnect.Rd | 6 + man/markcorr.Rd | 56 ++++++++--- man/markcrosscorr.Rd | 15 ++- man/markequal.Rd | 6 + man/markvario.Rd | 6 + man/pcf.ppp.Rd | 6 + man/pcfcross.Rd | 6 + man/pcfcross.inhom.Rd | 6 + man/pcfdot.Rd | 6 + man/pcfdot.inhom.Rd | 6 + man/pcfinhom.Rd | 7 + man/pcfmulti.Rd | 6 + man/plot.fasp.Rd | 7 + man/rectcontact.Rd | 7 + man/spatstat.explore-internal.Rd | 4 man/spatstat.explore-package.Rd | 2 tests/testsEtoF.R | 16 +++ tests/testsGtoJ.R | 2 tests/testsS.R | 45 +++++++++ 90 files changed, 828 insertions(+), 417 deletions(-)
More information about spatstat.explore at CRAN
Permanent link
Title: Radiocarbon Equations
Description: Provides functions for the calibration of radiocarbon dates, as well as options to calculate different radiocarbon-related timescales (cal BP, cal BC/AD, C14 age, F14C, pMC, D14C) and estimating the effects of contamination or local reservoir offsets (Reimer and Reimer 2001 <doi:10.1017/S0033822200038339>). The methods follow long-established recommendations such as Stuiver and Polach (1977) <doi:10.1017/S0033822200003672> and Reimer et al. (2004) <doi:10.1017/S0033822200033154>. This package uses the calibration curves from the data package 'rintcal'.
Author: Maarten Blaauw [aut, cre] ,
Paula Reimer [ctb] ,
Vegard Martinsen [ctb]
Maintainer: Maarten Blaauw <maarten.blaauw@qub.ac.uk>
Diff between rice versions 1.6.0 dated 2026-01-08 and 1.6.2 dated 2026-01-22
DESCRIPTION | 6 +- MD5 | 26 ++++----- NEWS.md | 8 ++ R/calibrate.R | 6 +- R/marine.R | 140 ++++++++++++++------------------------------------- R/rice.R | 1 README.md | 7 -- build/partial.rdb |binary build/vignette.rds |binary data/shells.rda |binary inst/doc/rice.R | 16 ++++- inst/doc/rice.Rmd | 20 +++++-- inst/doc/rice.html | 144 ++++++++++++++++++++++++++--------------------------- vignettes/rice.Rmd | 20 +++++-- 14 files changed, 186 insertions(+), 208 deletions(-)
Title: (Randomized) Quasi-Random Number Generators
Description: Functionality for generating (randomized) quasi-random numbers in
high dimensions.
Author: Marius Hofert [aut, cre],
Christiane Lemieux [aut]
Maintainer: Marius Hofert <mhofert@hku.hk>
Diff between qrng versions 0.0-10 dated 2024-02-29 and 0.0-11 dated 2026-01-22
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/qrng.R | 2 ++ demo/test_functions.R | 5 +++-- 4 files changed, 12 insertions(+), 9 deletions(-)
Title: Easily Create Presentation-Ready Display Tables
Description: Build display tables from tabular data with an easy-to-use
set of functions. With its progressive approach, we can construct
display tables with a cohesive set of table parts. Table values can be
formatted using any of the included formatting functions. Footnotes
and cell styles can be precisely added through a location targeting
system. The way in which 'gt' handles things for you means that you
don't often have to worry about the fine details.
Author: Richard Iannone [aut, cre] ,
Joe Cheng [aut],
Barret Schloerke [aut] ,
Shannon Haughton [aut],
Ellis Hughes [aut] ,
Alexandra Lauer [aut] ,
Romain Francois [aut],
JooYoung Seo [aut] ,
Ken Brevoort [aut] ,
Olivier Roy [aut],
Posit Software, PBC [cph, [...truncated...]
Maintainer: Richard Iannone <rich@posit.co>
Diff between gt versions 1.2.0 dated 2025-12-16 and 1.3.0 dated 2026-01-22
DESCRIPTION | 16 LICENSE | 2 MD5 | 265 ++++----- NAMESPACE | 2 NEWS.md | 28 R/as_data_frame.R | 2 R/build_data.R | 11 R/cols_add.R | 2 R/cols_align.R | 2 R/cols_align_decimal.R | 2 R/cols_hide.R | 2 R/cols_label.R | 2 R/cols_merge.R | 2 R/cols_move.R | 2 R/cols_units.R | 2 R/cols_width.R | 2 R/compile_scss.R | 22 R/data_color.R | 2 R/datasets.R | 2 R/dt__.R | 2 R/dt_body.R | 11 R/dt_boxhead.R | 2 R/dt_cols_merge.R | 2 R/dt_data.R | 2 R/dt_footnotes.R | 2 R/dt_formats.R | 2 R/dt_groups_rows.R | 2 R/dt_has_built.R | 2 R/dt_heading.R | 2 R/dt_locale.R | 2 R/dt_options.R | 3 R/dt_row_groups.R | 2 R/dt_row_order.R |only R/dt_source_notes.R | 2 R/dt_spanners.R | 2 R/dt_stub_df.R | 101 +++ R/dt_stubhead.R | 2 R/dt_styles.R | 2 R/dt_substitutions.R | 2 R/dt_summary.R | 2 R/dt_summary_cols.R | 2 R/dt_transforms.R | 2 R/export.R | 2 R/extract.R | 6 R/fmt.R | 21 R/fmt_date_time.R | 2 R/fmt_number.R | 21 R/format_data.R | 41 - R/format_vec.R | 4 R/gt-package.R | 2 R/gt.R | 3 R/gt_group.R | 2 R/gt_preview.R | 2 R/gt_split.R | 2 R/gtsave.R | 2 R/helpers.R | 12 R/image.R | 2 R/info_tables.R | 613 ++++++++++++++++++++- R/knitr-utils.R | 4 R/location_methods.R | 2 R/modify_rows.R | 177 ++++++ R/nanoplot.R | 2 R/opts.R | 2 R/print.R | 2 R/quarto.R | 2 R/reexports.R | 2 R/render_as_html.R | 2 R/render_as_i_html.R | 2 R/resolver.R | 12 R/rows_add.R | 4 R/shiny.R | 2 R/substitution.R | 2 R/summary_columns.R | 6 R/summary_rows.R | 2 R/tab_create_modify.R | 12 R/tab_footnote.R | 14 R/tab_info.R | 2 R/tab_options.R | 15 R/tab_remove.R | 2 R/tab_style.R | 25 R/tab_style_body.R | 2 R/text_transform.R | 2 R/topics.R | 2 R/utils.R | 21 R/utils_color_contrast.R | 2 R/utils_environments.R | 2 R/utils_examples.R | 2 R/utils_general_str_formatting.R | 2 R/utils_plots.R | 2 R/utils_render_common.R | 24 R/utils_render_grid.R | 7 R/utils_render_html.R | 54 + R/utils_render_latex.R | 490 ++++++++++++++-- R/utils_render_rtf.R | 22 R/utils_render_xml.R | 2 R/utils_units.R | 2 R/z_utils_render_footnotes.R | 2 R/zzz.R | 3 inst/gt_tables/fa_icons_vec.rds |binary inst/gt_tables/info_conversions.rds |binary inst/gt_tables/info_flags.rds |binary inst/gt_tables/info_google_fonts.rds |binary inst/gt_tables/info_icons.rds |binary inst/gt_tables/info_paletteer.rds |binary man/cells_stub.Rd | 14 man/fmt_currency.Rd | 8 man/fmt_integer.Rd | 8 man/fmt_number.Rd | 8 man/fmt_number_si.Rd | 2 man/fmt_tf.Rd | 8 man/grand_summary_rows.Rd | 1 man/info_currencies.Rd | 1 man/info_date_style.Rd | 1 man/info_flags.Rd | 3 man/info_google_fonts.Rd | 1 man/info_icons.Rd | 3 man/info_locales.Rd | 1 man/info_paletteer.Rd | 1 man/info_tf_style.Rd |only man/info_time_style.Rd | 1 man/info_unit_conversions.Rd | 3 man/row_group_order.Rd | 1 man/row_order.Rd |only man/rows_add.Rd | 3 man/summary_columns.Rd | 5 man/summary_rows.Rd | 1 man/tab_options.Rd | 8 man/vec_fmt_number_si.Rd | 2 tests/testthat/Rplots.pdf |binary tests/testthat/helper-gt_object.R | 4 tests/testthat/test-l_cell_text_alignment.R | 198 ++++++ tests/testthat/test-l_cols_align.R | 35 + tests/testthat/test-l_cols_width.R | 137 ++++ tests/testthat/test-multicolumn_stub_latex.R | 78 ++ tests/testthat/test-multicolumn_stub_na_handling.R | 24 135 files changed, 2272 insertions(+), 486 deletions(-)
Title: Functions to Create Publication-Quality Plots
Description: Contains several plotting functions such as barplots, scatterplots, heatmaps, as well as functions to combine plots and assist in the creation of these plots. These functions will give users great ease of use and customization options in broad use for biomedical applications, as well as general purpose plotting. Each of the functions also provides valid default settings to make plotting data more efficient and producing high quality plots with standard colour schemes simpler. All functions within this package are capable of producing plots that are of the quality to be presented in scientific publications and journals. P'ng et al.; BPG: Seamless, automated and interactive visualization of scientific data; BMC Bioinformatics 2019 <doi:10.1186/s12859-019-2610-2>.
Author: Paul Boutros [aut, cre],
Christine P'ng [ctb],
Jeff Green [ctb],
Stephenie Prokopec [ctb],
Ontario Institute for Cancer Research [cph],
The R Core Team [cph],
The R Foundation [cph],
Robert Gentleman [ctb],
Ross Ihaka [ctb],
Caden Bugh [ctb],
Dan Kni [...truncated...]
Maintainer: Paul Boutros <PBoutros@sbpdiscovery.org>
Diff between BoutrosLab.plotting.general versions 7.1.2 dated 2024-10-04 and 7.1.5 dated 2026-01-22
BoutrosLab.plotting.general-7.1.2/BoutrosLab.plotting.general/NEWS |only BoutrosLab.plotting.general-7.1.5/BoutrosLab.plotting.general/DESCRIPTION | 21 BoutrosLab.plotting.general-7.1.5/BoutrosLab.plotting.general/MD5 | 21 BoutrosLab.plotting.general-7.1.5/BoutrosLab.plotting.general/NEWS.md | 26 BoutrosLab.plotting.general-7.1.5/BoutrosLab.plotting.general/R/create.violinplot.R | 527 +++++----- BoutrosLab.plotting.general-7.1.5/BoutrosLab.plotting.general/R/force.colour.scheme.R | 6 BoutrosLab.plotting.general-7.1.5/BoutrosLab.plotting.general/R/legend.grob.R | 4 BoutrosLab.plotting.general-7.1.5/BoutrosLab.plotting.general/build/vignette.rds |binary BoutrosLab.plotting.general-7.1.5/BoutrosLab.plotting.general/inst/doc/PlottingGuide.pdf |binary BoutrosLab.plotting.general-7.1.5/BoutrosLab.plotting.general/man/create.heatmap.Rd | 2 BoutrosLab.plotting.general-7.1.5/BoutrosLab.plotting.general/man/create.violinplot.Rd | 14 BoutrosLab.plotting.general-7.1.5/BoutrosLab.plotting.general/man/legend.grob.Rd | 2 12 files changed, 343 insertions(+), 280 deletions(-)
More information about BoutrosLab.plotting.general at CRAN
Permanent link
Title: Area-to-Area Kriging
Description: Point-scale variogram deconvolution from irregular/regular spatial support according to Goovaerts, P., (2008) <doi: 10.1007/s11004-007-9129-1>; ordinary area-to-area (co)Kriging and area-to-point (co)Kriging.
Author: Maogui Hu [aut, cre],
Yanwei Huang [ctb],
Roger Bivand [ctb]
Maintainer: Maogui Hu <humg@lreis.ac.cn>
Diff between atakrig versions 0.9.8.1 dated 2023-10-09 and 0.9.8.2 dated 2026-01-21
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- man/ataCoKriging.Rd | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Strength Training Manual R-Language Functions
Description: Strength training prescription using percent-based approach requires
numerous computations and assumptions. 'STMr' package allow users to estimate
individual reps-max relationships, implement various progression tables, and
create numerous set and rep schemes. The 'STMr' package is originally created as
a tool to help writing Jovanović M. (2020) Strength Training Manual
<ISBN:979-8604459898>.
Author: Mladen Jovanovic [aut, cre]
Maintainer: Mladen Jovanovic <coach.mladen.jovanovic@gmail.com>
Diff between STMr versions 0.1.6 dated 2023-11-02 and 0.1.7 dated 2026-01-21
DESCRIPTION | 8 LICENSE | 2 MD5 | 151 ++++++++------- NAMESPACE | 2 NEWS.md | 13 + R/adj-perc-1RM.R | 3 R/adj-reps.R | 3 R/create-example.R | 4 R/estimate-functions.R | 40 +--- R/estimate-mixed-functions.R | 42 ++-- R/estimate-quantile-functions.R | 42 ++-- R/estimate-rolling.R | 1 R/generate-progression-table.R | 5 R/get-perc-1RM.R | 1 R/get-reps.R | 1 R/plot-progression-table.R | 17 - R/plot-vertical.R | 2 R/progression-table-DI.R | 2 R/progression-table-RIR.R | 28 +- R/progression-table-perc-MR.R | 39 +++ R/progression-table-perc-drop.R | 27 +- R/progression-table-rel-int.R | 2 R/progression-table-variable-DI.R |only R/progression-table-variable-RIR.R |only R/progression-table.R | 6 R/release-S3.R | 1 R/release.R | 1 R/schemes-S3.R | 7 R/schemes.R | 1 R/utils.R | 61 +++++- R/vertical-planning.R | 3 README.md | 293 +++++++++++++++--------------- inst/CITATION | 4 man/adj_perc_1RM.Rd | 3 man/adj_reps.Rd | 3 man/create_example.Rd | 3 man/figures/README-unnamed-chunk-15-1.png |binary man/figures/README-unnamed-chunk-16-1.png |binary man/figures/README-unnamed-chunk-17-1.png |binary man/figures/README-unnamed-chunk-18-1.png |binary man/figures/README-unnamed-chunk-19-1.png |only man/figures/README-unnamed-chunk-23-1.png |only man/figures/README-unnamed-chunk-25-1.png |binary man/figures/README-unnamed-chunk-26-1.png |binary man/figures/README-unnamed-chunk-27-1.png |binary man/figures/README-unnamed-chunk-28-1.png |binary man/figures/README-unnamed-chunk-29-1.png |binary man/figures/README-unnamed-chunk-30-1.png |only man/figures/README-unnamed-chunk-35-1.png |binary man/figures/README-unnamed-chunk-36-1.png |binary man/figures/README-unnamed-chunk-37-1.png |binary man/figures/README-unnamed-chunk-38-1.png |binary man/figures/README-unnamed-chunk-39-1.png |binary man/figures/README-unnamed-chunk-40-1.png |binary man/figures/README-unnamed-chunk-41-1.png |binary man/figures/README-unnamed-chunk-42-1.png |binary man/figures/README-unnamed-chunk-43-1.png |binary man/figures/README-unnamed-chunk-43-2.png |only man/figures/README-unnamed-chunk-43-3.png |only man/figures/README-unnamed-chunk-44-1.png |binary man/figures/README-unnamed-chunk-45-1.png |binary man/figures/README-unnamed-chunk-46-1.png |binary man/figures/README-unnamed-chunk-47-1.png |only man/figures/README-unnamed-chunk-50-1.png |only man/figures/README-unnamed-chunk-53-1.png |only man/figures/README-unnamed-chunk-55-1.png |only man/figures/README-unnamed-chunk-57-1.png |only man/figures/README-unnamed-chunk-59-1.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/figures/README-unnamed-chunk-60-1.png |only man/figures/README-unnamed-chunk-62-1.png |binary man/figures/README-unnamed-chunk-64-1.png |binary man/figures/README-unnamed-chunk-65-1.png |binary man/figures/README-unnamed-chunk-66-1.png |binary man/figures/README-unnamed-chunk-67-1.png |binary man/figures/README-unnamed-chunk-68-1.png |binary man/figures/README-unnamed-chunk-69-1.png |binary man/figures/README-unnamed-chunk-70-1.png |binary man/figures/README-unnamed-chunk-71-1.png |binary man/figures/README-unnamed-chunk-72-1.png |binary man/figures/README-unnamed-chunk-73-1.png |only man/plot_progression_table.Rd | 4 man/progression_table.Rd | 155 +++++++++++++++ man/sig_pad.Rd |only 84 files changed, 613 insertions(+), 367 deletions(-)
Title: Extensible Data Structures for Multivariate Analysis
Description: Provides a set of basic and extensible data structures and functions for multivariate analysis, including dimensionality reduction techniques, projection methods, and preprocessing functions. The aim of this package is to offer a flexible and user-friendly framework for multivariate analysis that can be easily extended for custom requirements and specific data analysis tasks.
Author: Bradley Buchsbaum [aut, cre]
Maintainer: Bradley Buchsbaum <brad.buchsbaum@gmail.com>
Diff between multivarious versions 0.3.0 dated 2026-01-21 and 0.3.1 dated 2026-01-21
DESCRIPTION | 6 - MD5 | 24 ++--- NEWS.md | 17 +++ inst/doc/Extending.R | 95 ++++++--------------- inst/doc/Extending.Rmd | 115 ++++++++----------------- inst/doc/Extending.html | 175 +++++++++++++++------------------------ inst/doc/Multiblock.html | 2 inst/doc/Nystrom.html | 4 inst/doc/Partial_Projection.html | 2 inst/doc/PreProcessing.html | 2 inst/doc/SVD_PCA.html | 2 man/cPCAplus.Rd | 8 + vignettes/Extending.Rmd | 115 ++++++++----------------- 13 files changed, 220 insertions(+), 347 deletions(-)
Title: Equal-Area Hex Grids on the 'Snyder' 'ISEA' 'Icosahedron'
Description: Provides functions to build and use equal-area hexagonal discrete
global grids using the 'Snyder' 'ISEA' projection ('Snyder' 1992
<doi:10.3138/27H7-8K88-4882-1752>). Implements the 'ISEA' discrete global grid
system ('Sahr', 'White' and 'Kimerling' 2003 <doi:10.1559/152304003100011090>).
Includes a fast 'C++' core for projection and aperture quantization, and
'sf'/'terra'-compatible R wrappers for grid generation and coordinate assignment.
Output is compatible with 'dggridR' for interoperability.
Author: Gilles Colling [aut, cre, cph]
Maintainer: Gilles Colling <gilles.colling051@gmail.com>
Diff between hexify versions 0.3.3 dated 2026-01-20 and 0.3.8 dated 2026-01-21
DESCRIPTION | 6 MD5 | 95 - NEWS.md | 43 R/hexify_map.R | 2 R/plot_methods.R | 24 README.md | 196 ++- inst/doc/quickstart.html | 4 inst/doc/visualization.html | 4 inst/doc/workflows.R | 3 inst/doc/workflows.Rmd | 3 inst/doc/workflows.html | 33 man/figures |only man/plot-HexData-missing-method.Rd | 24 src/coordinate_transforms.cpp | 7 src/projection_forward.cpp | 138 ++ tests/testthat-full |only tests/testthat/Rplots.pdf |binary tests/testthat/fixtures |only tests/testthat/generate_cache.R |only tests/testthat/test-aperture-3.R | 500 ++++---- tests/testthat/test-aperture-4.R | 390 +++--- tests/testthat/test-aperture-7.R | 359 +++-- tests/testthat/test-aperture-mixed.R | 645 +++++----- tests/testthat/test-assign.R | 1 tests/testthat/test-cell-id.R | 541 ++++---- tests/testthat/test-classes.R | 847 ++++++------- tests/testthat/test-coercion.R | 261 ++-- tests/testthat/test-constants.R | 1 tests/testthat/test-constructors.R | 305 ++--- tests/testthat/test-conversions.R | 1585 +++++++++++++------------- tests/testthat/test-core.R |only tests/testthat/test-dggrid-compat-functions.R | 289 ++-- tests/testthat/test-dggrid-compat.R | 668 +++++----- tests/testthat/test-grid-helpers.R | 320 ++--- tests/testthat/test-grid-wrappers.R | 3 tests/testthat/test-grid.R | 1 tests/testthat/test-hexify-function.R | 1 tests/testthat/test-hexify-heatmap.R | 641 +++++----- tests/testthat/test-hierarchical-index.R | 241 +-- tests/testthat/test-icosahedron.R | 301 ++-- tests/testthat/test-index-utils.R | 1 tests/testthat/test-index-z3.R | 22 tests/testthat/test-index-z7.R | 1 tests/testthat/test-index-zorder.R | 44 tests/testthat/test-plot-methods.R | 681 +++++------ tests/testthat/test-polygons.R | 4 tests/testthat/test-projection-forward.R | 402 +++--- tests/testthat/test-projection-inverse.R | 730 ++++++----- tests/testthat/test-stats.R | 1 tests/testthat/test-visualization.R | 1520 ++++++++++++------------ vignettes/workflows.Rmd | 3 51 files changed, 6134 insertions(+), 5757 deletions(-)
Title: Computational Test for Conditional Independence
Description: Tool for performing computational testing for conditional independence between variables in a dataset. 'CCI' implements permutation in combination with Monte Carlo Cross-Validation in generating null distributions and test statistics. For more details see Computational Test for Conditional Independence (2024) <doi:10.3390/a17080323>.
Author: Christian Thorjussen [aut, cre] ,
Kristian Hovde Liland [aut]
Maintainer: Christian Thorjussen <christianbern@gmail.com>
Diff between CCI versions 0.3.4 dated 2025-09-11 and 0.3.6 dated 2026-01-21
DESCRIPTION | 19 MD5 | 55 - NAMESPACE | 8 R/CCI.direction.R | 82 +- R/CCI.test.R | 131 ++- R/QQplot.R | 33 R/perm.test.R | 81 +- R/plot.R | 2 R/reports.R | 4 R/test.gen.R | 157 ++-- R/utils.R | 211 +++++ R/wrappers.R | 560 +++++++++++++-- README.md | 524 +++++++------- build |only inst/doc |only man/CCI.test.Rd | 43 + man/QQplot.Rd | 3 man/add_interaction_terms.Rd | 4 man/is_categorical_Z_any.Rd |only man/make_strata_from_categorical_Z.Rd |only man/perm.test.Rd | 58 - man/permute_within_strata.Rd |only man/plot.CCI.Rd | 2 man/test.gen.Rd | 54 + man/unclean_formula.Rd |only man/wrapper_knn.Rd |only man/wrapper_ranger.Rd | 92 +- man/wrapper_svm.Rd | 5 man/wrapper_xgboost.Rd | 7 tests/testthat/dev.R | 1205 +++++++++++++++++++++++++++++++++- vignettes |only 31 files changed, 2692 insertions(+), 648 deletions(-)
Title: Extracts Environmental Data from 'ERDDAP™' Web Services
Description: Contains three functions that access
environmental data from any 'ERDDAP™' data web service. The rxtracto() function extracts
data along a trajectory for a given "radius" around the point. The
rxtracto_3D() function extracts data in a box. The rxtractogon() function
extracts data in a polygon. All of those three function use the 'rerddap' package
to extract the data, and should work with any 'ERDDAP™' server.
There are also two functions, plotBBox() and plotTrack() that use the 'plotdap'
package to simplify the creation of maps of the data.
Author: Roy Mendelssohn [aut, cre],
Marie Auger-Methe [ctb],
Sunny Bak-Hospital [ctb]
Maintainer: Roy Mendelssohn <roy.mendelssohn@noaa.gov>
Diff between rerddapXtracto versions 1.2.3 dated 2025-04-26 and 1.2.4 dated 2026-01-21
rerddapXtracto-1.2.3/rerddapXtracto/R/getFIleCoords.R |only rerddapXtracto-1.2.4/rerddapXtracto/DESCRIPTION | 12 rerddapXtracto-1.2.4/rerddapXtracto/MD5 | 42 - rerddapXtracto-1.2.4/rerddapXtracto/NEWS.md | 12 rerddapXtracto-1.2.4/rerddapXtracto/R/checkBounds.R | 7 rerddapXtracto-1.2.4/rerddapXtracto/R/checkInput.R | 4 rerddapXtracto-1.2.4/rerddapXtracto/R/getFileCoords.R |only rerddapXtracto-1.2.4/rerddapXtracto/R/interp.R | 24 rerddapXtracto-1.2.4/rerddapXtracto/R/plotBBox.R | 1 rerddapXtracto-1.2.4/rerddapXtracto/R/remapCoords.R | 4 rerddapXtracto-1.2.4/rerddapXtracto/R/rxtracto.R | 407 +++++----- rerddapXtracto-1.2.4/rerddapXtracto/R/rxtracto_3D.R | 7 rerddapXtracto-1.2.4/rerddapXtracto/R/rxtractogon.R | 3 rerddapXtracto-1.2.4/rerddapXtracto/R/utils.R | 3 rerddapXtracto-1.2.4/rerddapXtracto/README.md | 2 rerddapXtracto-1.2.4/rerddapXtracto/build/vignette.rds |binary rerddapXtracto-1.2.4/rerddapXtracto/inst/doc/UsingrerddapXtracto.R | 43 - rerddapXtracto-1.2.4/rerddapXtracto/inst/doc/UsingrerddapXtracto.Rmd | 79 + rerddapXtracto-1.2.4/rerddapXtracto/inst/doc/UsingrerddapXtracto.html | 149 ++- rerddapXtracto-1.2.4/rerddapXtracto/man/rxtracto.Rd | 6 rerddapXtracto-1.2.4/rerddapXtracto/man/rxtracto_3D.Rd | 2 rerddapXtracto-1.2.4/rerddapXtracto/man/rxtractogon.Rd | 2 rerddapXtracto-1.2.4/rerddapXtracto/vignettes/UsingrerddapXtracto.Rmd | 79 + 23 files changed, 563 insertions(+), 325 deletions(-)
More information about rerddapXtracto at CRAN
Permanent link
Title: Calculating Bilateral and Multilateral Price Indexes
Description: Preparing a scanner data set for price dynamics calculations (data selecting, data classification, data matching, data filtering). Computing bilateral and multilateral indexes. For details on these methods see: Diewert and Fox (2020)
<doi:10.1080/07350015.2020.1816176>, Białek (2019) <doi:10.2478/jos-2019-0014> or Białek (2020) <doi:10.2478/jos-2020-0037>.
Author: Jacek Bialek [aut, cre]
Maintainer: Jacek Bialek <jacek.bialek@uni.lodz.pl>
Diff between PriceIndices versions 0.2.6 dated 2025-12-12 and 0.2.7 dated 2026-01-21
DESCRIPTION | 6 +- MD5 | 12 ++--- NEWS.md | 6 ++ R/dataRSM.R | 2 R/f_bilateral_indices.R | 100 +++++++++++++++++++++++++++++++++++------------- data/dataRSM.rda |binary man/dataRSM.Rd | 2 7 files changed, 91 insertions(+), 37 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 0.1.0 dated 2025-11-24 and 0.1.1 dated 2026-01-21
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 4 ++++ R/geom-point-sorted.r | 2 +- R/stat-half-ydensity.R | 1 - build/vignette.rds |binary man/stat_half_ydensity.Rd | 3 --- 7 files changed, 14 insertions(+), 14 deletions(-)
Title: Flexible and Robust Agreement and Reliability Analyses
Description: Reliability and agreement analyses often have limited software support. Therefore, this package was created to make agreement and reliability analyses easier for the average researcher. The functions within this package include simple tests of agreement, agreement analysis for nested and replicate data, and provide robust analyses of reliability. In addition, this package contains a set of functions to help when planning studies looking to assess measurement agreement.
Author: Aaron Caldwell [aut, cre]
Maintainer: Aaron Caldwell <arcaldwell49@gmail.com>
Diff between SimplyAgree versions 0.2.1 dated 2025-02-24 and 0.3.0 dated 2026-01-21
DESCRIPTION | 10 MD5 | 131 +- NAMESPACE | 40 NEWS.md | 13 R/agree_coef.R | 4 R/agree_np.R | 8 R/agreement_limit.R | 8 R/dem_reg.R | 605 +++++++++--- R/deming_power.R |only R/globals.R | 11 R/jmvagree.h.R | 10 R/jmvagreemulti.h.R | 8 R/jmvdeming.b.R | 141 ++ R/jmvdeming.h.R | 6 R/loa_plot_functions.R | 6 R/methods.loa.R | 2 R/methods.loa_mermod.R | 2 R/methods.simple_agree.R | 10 R/methods.simple_eiv.R | 1333 +++++++++++++++++++++++++--- R/methods.simple_reli.R | 2 R/methods.tolerance_delta.R | 4 R/other_functions.R | 40 R/pb_reg.R |only R/power_agree_expected_half.R |only R/power_agreement_assurance.R |only R/power_exact_agreement.R |only R/quantile_funs.R | 4 R/reli_stats.R | 90 + R/simple_plot_functions.R | 178 ++- README.md | 182 ++- build/partial.rdb |binary build/vignette.rds |binary inst/doc/Deming.R | 71 + inst/doc/Deming.Rmd | 209 +++- inst/doc/Deming.html | 480 ++++++++-- inst/doc/agree_tests.R | 44 inst/doc/agree_tests.Rmd | 37 inst/doc/agree_tests.html | 119 -- inst/doc/agreement_analysis.html | 18 inst/doc/power_sample_size_vignette.R |only inst/doc/power_sample_size_vignette.Rmd |only inst/doc/power_sample_size_vignette.html |only inst/doc/reanalysis.html | 9 inst/doc/reliability_analysis.html | 7 man/SimplyAgree-package.Rd | 2 man/agree_assurance.Rd |only man/agree_coef.Rd | 4 man/agree_expected_half.Rd |only man/dem_reg.Rd | 75 + man/deming_power.Rd |only man/deming_sample_size.Rd |only man/figures/logo.png |only man/jmvagree.Rd | 10 man/jmvagreemulti.Rd | 8 man/jmvdeming.Rd | 6 man/joint_test.Rd |only man/loa-methods.Rd | 2 man/loa_mermod-methods.Rd | 2 man/pb_reg.Rd |only man/power_agreement_exact.Rd |only man/simple_agree-methods.Rd | 4 man/simple_eiv-methods.Rd | 117 ++ man/simple_reli-methods.Rd | 2 man/tolerance_delta-methods.Rd | 2 tests/testthat/test-agree_nest.R | 54 - tests/testthat/test-agree_reps.R | 32 tests/testthat/test-dem_reg.R | 400 ++++++++ tests/testthat/test-deming_power.R |only tests/testthat/test-pb_reg.R |only tests/testthat/test-reli_stats.R | 1 tests/testthat/test-simple_eiv_methods.R |only tests/testthat/test_agree_power_functions.R |only tests/testthat/test_agree_test.R | 26 vignettes/Deming.Rmd | 209 +++- vignettes/agree_tests.Rmd | 37 vignettes/power_sample_size_vignette.Rmd |only vignettes/refs.bib | 99 ++ 77 files changed, 3932 insertions(+), 1002 deletions(-)
Title: Estimating Hierarchical Linear Models for Single-Case Designs
Description: Provides a set of tools for estimating hierarchical linear
models and effect sizes based on data from single-case designs.
Functions are provided for calculating standardized mean difference effect sizes that
are directly comparable to standardized mean differences estimated from between-subjects randomized experiments,
as described in Hedges, Pustejovsky, and Shadish (2012) <DOI:10.1002/jrsm.1052>;
Hedges, Pustejovsky, and Shadish (2013) <DOI:10.1002/jrsm.1086>;
Pustejovsky, Hedges, and Shadish (2014) <DOI:10.3102/1076998614547577>;
and Chen, Pustejovsky, Klingbeil, and Van Norman (2023) <DOI:10.1016/j.jsp.2023.02.002>.
Includes an interactive web interface.
Author: James Pustejovsky [aut, cre],
Man Chen [aut],
Bethany Hamilton [aut]
Maintainer: James Pustejovsky <jepusto@gmail.com>
Diff between scdhlm versions 0.7.3 dated 2024-02-25 and 0.7.4 dated 2026-01-21
scdhlm-0.7.3/scdhlm/tests/testthat/Rplots.pdf |only scdhlm-0.7.4/scdhlm/DESCRIPTION | 11 +-- scdhlm-0.7.4/scdhlm/MD5 | 13 +--- scdhlm-0.7.4/scdhlm/NEWS.md | 4 + scdhlm-0.7.4/scdhlm/build/partial.rdb |binary scdhlm-0.7.4/scdhlm/build/vignette.rds |binary scdhlm-0.7.4/scdhlm/inst/doc/Estimating-effect-sizes.R | 2 scdhlm-0.7.4/scdhlm/inst/doc/Estimating-effect-sizes.html | 43 +++++++------- 8 files changed, 39 insertions(+), 34 deletions(-)
Title: 'fxl' Single Case Design Charting Package
Description: The 'fxl' Charting package is used to prepare and design single case design figures that are typically prepared in spreadsheet software. With 'fxl', there is no need to leave the R environment to prepare these works and many of the more unique conventions in single case experimental designs can be performed without the need for physically constructing features of plots (e.g., drawing annotations across plots). Support is provided for various different plotting arrangements (e.g., multiple baseline), annotations (e.g., brackets, arrows), and output formats (e.g., svg, rasters).
Author: Shawn Gilroy [aut, cre, cph]
Maintainer: Shawn Gilroy <sgilroy1@lsu.edu>
Diff between fxl versions 1.7.2 dated 2024-12-20 and 1.7.3 dated 2026-01-21
COPYING | 1352 DESCRIPTION | 12 MD5 | 324 NAMESPACE | 146 R/data.R | 406 R/element-anno-arrows-draw.R | 106 R/element-anno-arrows.R | 122 R/element-anno-brackets-draw.R | 128 R/element-anno-brackets.R | 116 R/element-anno-guide-line-draw.R | 176 R/element-anno-guide-line.R | 86 R/element-anno-rect-draw.R | 82 R/element-anno-rect.R | 72 R/element-axis-x.R | 186 R/element-axis-y.R | 142 R/element-criterion-draw.R | 174 R/element-criterion-line.R | 74 R/element-label-facet-draw.R | 114 R/element-label-facet.R | 110 R/element-label-phase-draw.R | 288 R/element-label-phase.R | 124 R/element-label-title.R | 80 R/element-label-xlabel.R | 98 R/element-label-ylabel.R | 98 R/element-legend-draw.R | 104 R/element-legend.R | 132 R/element-line-cumsum-line-draw.R | 116 R/element-line-cumsum-line.R | 84 R/element-line-draw.R | 140 R/element-line.R | 78 R/element-phasechange-draw.R | 214 R/element-phasechange-multiple.R | 54 R/element-phasechange-single.R | 74 R/element-point-cumsum-point-draw.R | 168 R/element-point-cumsum-point.R | 90 R/element-point-draw.R | 242 R/element-point.R | 112 R/element-support-bar-draw.R | 280 R/element-support-bar.R | 148 R/fxl-debugging.R | 488 R/fxl-map.R | 28 R/fxl-print-semilog.R | 1054 R/fxl-print.R | 1136 R/fxl-save.R | 116 R/fxl-utilities.R | 198 R/fxl.R | 392 README.md | 462 build/vignette.rds |binary demo/00Index | 46 demo/annotatedplot.R | 814 demo/atd_concurrentoperant.R | 320 demo/beezdemandInd.R | 158 demo/challenge_1.R | 602 demo/challenge_2.R | 680 demo/challenge_3.R | 644 demo/challenge_4.R | 1150 demo/changing_criterion.R | 386 demo/cigarettepolicy.R | 388 demo/concurrentplot.R | 498 demo/cumulativeplot.R | 570 demo/faplot.R | 210 demo/faplotintegrity.R | 414 demo/greyed_training.R | 632 demo/multiplebaselineplot.R | 302 demo/reports_academic.R | 386 demo/reports_academic_celeration_classes.R | 564 demo/reports_academic_celeration_classes_local_norms.R | 616 demo/reports_academic_rti.R | 536 demo/run_all_demos.R | 44 demo/run_coverage.R | 56 demo/semilogplot.R | 394 demo/silvermanplot.R | 338 inst/CITATION | 24 inst/doc/fxl.R | 4292 +-- inst/doc/fxl.Rmd | 5092 +-- inst/doc/fxl.html | 4206 +- man/Challenge1Data.Rd | 58 man/Challenge2Data.Rd | 46 man/Challenge4Data.Rd | 58 man/GelinoEtAl2022.Rd | 60 man/Gilroyetal2015.Rd | 54 man/Gilroyetal2019.Rd | 60 man/Gilroyetal2019Tx.Rd | 58 man/Gilroyetal2021.Rd | 56 man/KoffarnusEtAl2011.Rd | 48 man/LozyEtAl2020.Rd | 52 man/SimulatedAcademicFluency.Rd | 50 man/assert_input_type.Rd | 42 man/cnvrt_coords.Rd | 54 man/draw_arrows.Rd | 48 man/draw_bar_support.Rd | 52 man/draw_brackets.Rd | 48 man/draw_cumsum_lines.Rd | 48 man/draw_cumsum_points.Rd | 48 man/draw_guide_line.Rd | 48 man/draw_label_facet.Rd | 48 man/draw_label_phase.Rd | 48 man/draw_legend.Rd | 40 man/draw_lines.Rd | 48 man/draw_points.Rd | 52 man/draw_rect.Rd | 52 man/draw_scr_criterion.Rd | 48 man/draw_scr_plines.Rd | 48 man/figures/dragon-cairo.ps.xml | 8504 ++--- man/figures/like-cairo-mod.ps.xml | 614 man/figures/scorpion-cairo.ps.xml |12826 ++++----- man/figures/skinner-cairo.ps.xml |24178 ++++++++--------- man/figures/star-cairo-mod.ps.xml | 1138 man/isValidAXSCharacter.Rd | 38 man/isValidAestheticMapping.Rd | 38 man/isValidCharacterVector.Rd | 42 man/isValidDataFrame.Rd | 38 man/isValidLogicalVector.Rd | 42 man/isValidNumericVector.Rd | 42 man/print.fxl.Rd | 46 man/print.fxlsemilog.Rd | 46 man/scr_anno_arrows.Rd | 98 man/scr_anno_brackets.Rd | 92 man/scr_anno_guide_line.Rd | 74 man/scr_anno_rect.Rd | 52 man/scr_bar_support.Rd | 104 man/scr_criterion_lines.Rd | 68 man/scr_cumsum_lines.Rd | 56 man/scr_cumsum_points.Rd | 74 man/scr_label_facet.Rd | 86 man/scr_label_phase.Rd | 92 man/scr_legend.Rd | 140 man/scr_lines.Rd | 56 man/scr_plines.Rd | 56 man/scr_plines_mbd.Rd | 48 man/scr_plot.Rd | 140 man/scr_points.Rd | 86 man/scr_save.Rd | 80 man/scr_title.Rd | 60 man/scr_xlabel.Rd | 80 man/scr_xoverride.Rd | 98 man/scr_ylabel.Rd | 80 man/scr_yoverride.Rd | 80 man/var_map.Rd | 34 tests/testthat.R | 10 tests/testthat/Rplots.pdf |binary tests/testthat/test-demo-annotatedplot.R | 742 tests/testthat/test-demo-changingcriterion.R | 626 tests/testthat/test-demo-cigarettepolicy.R | 382 tests/testthat/test-demo-concurrentplot.R | 516 tests/testthat/test-demo-cumulativeplot.R | 536 tests/testthat/test-demo-cumulativeplot_single.R | 192 tests/testthat/test-demo-faplot.R | 156 tests/testthat/test-demo-faplotintegrity.R | 208 tests/testthat/test-demo-faplotintegrity_extra.R | 380 tests/testthat/test-demo-multiplebaseline_greyed.R | 1008 tests/testthat/test-demo-multiplebaselineplot.R | 256 tests/testthat/test-demo-semilogplot.R | 368 tests/testthat/test-demo-semilogplot_multi.R | 528 tests/testthat/test-demo-silvermanplot.R | 302 tests/testthat/test-element-bar.R | 390 tests/testthat/test-element-label-facet.R | 190 tests/testthat/test-element-label-phase.R | 190 tests/testthat/test-element-scr_arrows.R | 462 tests/testthat/test-element-scr_xoverride.R | 1252 tests/testthat/test-element-scr_yoverride.R | 640 tests/testthat/test-fxl.R | 800 vignettes/fxl.Rmd | 5092 +-- 163 files changed, 50463 insertions(+), 50449 deletions(-)
Title: Incorporate Expert Opinion with Parametric Survival Models
Description: Enables users to incorporate expert opinion with parametric survival analysis using a Bayesian or frequentist approach. Expert Opinion can be provided on the survival probabilities at certain time-point(s) or for the difference in mean survival between two treatment arms. Please reference it's use as Cooney, P., White, A. (2023) <doi:10.1177/0272989X221150212>.
Author: Philip Cooney [aut, cre] ,
Arthur White [ths]
Maintainer: Philip Cooney <phcooney@tcd.ie>
Diff between expertsurv versions 1.4.0 dated 2025-02-20 and 1.4.1 dated 2026-01-21
expertsurv-1.4.0/expertsurv/inst/REFERENCES.bib.sav.tmp |only expertsurv-1.4.1/expertsurv/DESCRIPTION | 13 +++++++------ expertsurv-1.4.1/expertsurv/MD5 | 9 ++++----- expertsurv-1.4.1/expertsurv/R/predict.flexsurvreg.R | 2 +- expertsurv-1.4.1/expertsurv/build/partial.rdb |binary expertsurv-1.4.1/expertsurv/inst/NEWS.txt | 11 +++++++++++ 6 files changed, 23 insertions(+), 12 deletions(-)
Title: 'Mangal' Client
Description: An interface to the 'Mangal' database - a collection of ecological networks. This package includes functions to work with the 'Mangal RESTful API' methods (<https://mangal-interactions.github.io/mangal-api/>).
Author: Steve Vissault [aut, ctb] ,
Kevin Cazelles [aut, cre] ,
Gabriel Bergeron [aut, ctb],
Benjamin Mercier [aut, ctb],
Clement Violet [aut, ctb],
Dominique Gravel [aut],
Timothee Poisot [aut],
Thomas Lin Pedersen [rev] ,
Anna Willoughby [rev]
Maintainer: Kevin Cazelles <kevin.cazelles@insileco.io>
This is a re-admission after prior archival of version 2.1.3 dated 2023-03-30
Diff between rmangal versions 2.1.3 dated 2023-03-30 and 2.2.2 dated 2026-01-21
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Title: PWIGLS for Two-Level Multivariate and Multilevel Linear Models
Description: Estimates two-level multilevel linear model and two-level multivariate linear multilevel model with weights following Probability Weighted Iterative Generalised Least Squares approach. For details see Veiga et al.(2014) <doi:10.1111/rssc.12020>.
Author: Alinne Veiga [aut, cre] ,
Joao Messa [aut, trl, com]
Maintainer: Alinne Veiga <alinne.veiga@ibge.gov.br>
Diff between pwlmm versions 1.1.1 dated 2022-06-13 and 1.1.2 dated 2026-01-21
DESCRIPTION | 17 - MD5 | 24 - NAMESPACE | 3 R/RcppExports.R | 24 - R/pwigls2.R | 6 build/vignette.rds |binary demo/Eg_pwigls2.R | 27 -- demo/Eg_wmlmm.R | 37 +- inst/doc/pwlmm.R | 2 inst/doc/pwlmm.Rmd | 19 + inst/doc/pwlmm.html | 682 ++++++++++++++++++++++++++++++++++++++++++---------- tests |only vignettes/pwlmm.Rmd | 19 + 13 files changed, 668 insertions(+), 192 deletions(-)
Title: Estimating Genome-Wide Significance for Whole Genome Sequencing
Studies, Either Single SNP Tests or Region-Based Tests
Description: The correlations and linkage disequilibrium between tests can vary as a function of minor allele frequency thresholds used to filter variants, and also varies with different choices of test statistic for region-based tests. Appropriate genome-wide significance thresholds can be estimated empirically through permutation on only a small proportion of the whole genome.
Author: Changjiang Xu [aut, cre],
Celia M.T. Greenwood [ctb]
Maintainer: Changjiang Xu <changjiang.h.xu@gmail.com>
Diff between GWsignif versions 1.2 dated 2016-09-12 and 1.2.1 dated 2026-01-21
DESCRIPTION | 15 +++++++++------ MD5 | 6 +++--- man/GWsignif-package.Rd | 2 +- man/GWsignif.Rd | 12 ++---------- 4 files changed, 15 insertions(+), 20 deletions(-)
Title: Workflow for Cluster Randomised Trials with Spillover
Description: Design, workflow and statistical analysis of Cluster Randomised Trials of (health) interventions where there may be spillover between the arms (see <https://thomasasmith.github.io/index.html>).
Author: Thomas Smith [aut, cre, cph] ,
Lea Multerer [ctb],
Mariah Silkey [ctb]
Maintainer: Thomas Smith <Thomas-a.Smith@unibas.ch>
Diff between CRTspat versions 1.3.2 dated 2025-01-27 and 1.4.0 dated 2026-01-21
CRTspat-1.3.2/CRTspat/man/figures |only CRTspat-1.3.2/CRTspat/vignettes/example6b.r-2.png |only CRTspat-1.4.0/CRTspat/DESCRIPTION | 15 CRTspat-1.4.0/CRTspat/LICENSE | 4 CRTspat-1.4.0/CRTspat/MD5 | 156 +- CRTspat-1.4.0/CRTspat/NAMESPACE | 118 +- CRTspat-1.4.0/CRTspat/NEWS.md | 53 - CRTspat-1.4.0/CRTspat/R/CRTanalysis_methods.R |only CRTspat-1.4.0/CRTspat/R/CRTsp.R | 682 ++++++------- CRTspat-1.4.0/CRTspat/R/CRTspat-package.R | 40 CRTspat-1.4.0/CRTspat/R/analyseCRT.R | 1095 ++++++--------------- CRTspat-1.4.0/CRTspat/R/designCRT.R | 4 CRTspat-1.4.0/CRTspat/R/plotCRT.R | 71 - CRTspat-1.4.0/CRTspat/R/simulateCRT.R | 7 CRTspat-1.4.0/CRTspat/R/stananalysis.R |only CRTspat-1.4.0/CRTspat/R/surround.R | 13 CRTspat-1.4.0/CRTspat/R/utils.R | 10 CRTspat-1.4.0/CRTspat/README.md | 97 - CRTspat-1.4.0/CRTspat/build/vignette.rds |binary CRTspat-1.4.0/CRTspat/inst/doc/Usecase1.Rmd | 25 CRTspat-1.4.0/CRTspat/inst/doc/Usecase1.html | 30 CRTspat-1.4.0/CRTspat/inst/doc/Usecase10.Rmd |only CRTspat-1.4.0/CRTspat/inst/doc/Usecase10.html |only CRTspat-1.4.0/CRTspat/inst/doc/Usecase2.Rmd | 109 -- CRTspat-1.4.0/CRTspat/inst/doc/Usecase2.html | 88 - CRTspat-1.4.0/CRTspat/inst/doc/Usecase3.Rmd | 4 CRTspat-1.4.0/CRTspat/inst/doc/Usecase3.html | 11 CRTspat-1.4.0/CRTspat/inst/doc/Usecase4.Rmd | 97 - CRTspat-1.4.0/CRTspat/inst/doc/Usecase4.html | 213 +--- CRTspat-1.4.0/CRTspat/inst/doc/Usecase5.Rmd | 262 ++--- CRTspat-1.4.0/CRTspat/inst/doc/Usecase5.html | 309 +++-- CRTspat-1.4.0/CRTspat/inst/doc/Usecase6.Rmd | 64 - CRTspat-1.4.0/CRTspat/inst/doc/Usecase6.html | 60 - CRTspat-1.4.0/CRTspat/inst/doc/Usecase7.Rmd | 3 CRTspat-1.4.0/CRTspat/inst/doc/Usecase7.html | 7 CRTspat-1.4.0/CRTspat/inst/doc/Usecase8.html | 5 CRTspat-1.4.0/CRTspat/man/CRTanalysis.Rd | 308 +++-- CRTspat-1.4.0/CRTspat/man/CRTpower.Rd | 2 CRTspat-1.4.0/CRTspat/man/CRTsp.Rd | 140 +- CRTspat-1.4.0/CRTspat/man/CRTspat-package.Rd | 42 CRTspat-1.4.0/CRTspat/man/aggregateCRT.Rd | 64 - CRTspat-1.4.0/CRTspat/man/coef.CRTanalysis.Rd | 2 CRTspat-1.4.0/CRTspat/man/compute_mesh.Rd | 4 CRTspat-1.4.0/CRTspat/man/fitted.CRTanalysis.Rd | 2 CRTspat-1.4.0/CRTspat/man/latlong_as_xy.Rd | 74 - CRTspat-1.4.0/CRTspat/man/plotCRT.Rd | 264 ++--- CRTspat-1.4.0/CRTspat/man/predict.CRTanalysis.Rd | 2 CRTspat-1.4.0/CRTspat/man/randomizeCRT.Rd | 104 - CRTspat-1.4.0/CRTspat/man/readdata.Rd | 50 CRTspat-1.4.0/CRTspat/man/residuals.CRTanalysis.Rd | 2 CRTspat-1.4.0/CRTspat/man/simulateCRT.Rd | 291 ++--- CRTspat-1.4.0/CRTspat/man/specify_buffer.Rd | 80 - CRTspat-1.4.0/CRTspat/man/specify_clusters.Rd | 140 +- CRTspat-1.4.0/CRTspat/man/summary.CRTanalysis.Rd | 50 CRTspat-1.4.0/CRTspat/tests/testthat.R | 8 CRTspat-1.4.0/CRTspat/tests/testthat/test3.R | 28 CRTspat-1.4.0/CRTspat/tests/testthat/test4_8..R | 98 - CRTspat-1.4.0/CRTspat/tests/testthat/test9.R | 9 CRTspat-1.4.0/CRTspat/tests/testthat/tests1_2.R | 76 - CRTspat-1.4.0/CRTspat/vignettes/Usecase1.Rmd | 25 CRTspat-1.4.0/CRTspat/vignettes/Usecase10.Rmd |only CRTspat-1.4.0/CRTspat/vignettes/Usecase10.Rmd.orig |only CRTspat-1.4.0/CRTspat/vignettes/Usecase11.Rmd.orig | 90 - CRTspat-1.4.0/CRTspat/vignettes/Usecase2.Rmd | 109 -- CRTspat-1.4.0/CRTspat/vignettes/Usecase2.Rmd.orig | 236 ++-- CRTspat-1.4.0/CRTspat/vignettes/Usecase3.Rmd | 4 CRTspat-1.4.0/CRTspat/vignettes/Usecase3.Rmd.orig | 2 CRTspat-1.4.0/CRTspat/vignettes/Usecase4.Rmd | 97 - CRTspat-1.4.0/CRTspat/vignettes/Usecase4.Rmd.orig | 29 CRTspat-1.4.0/CRTspat/vignettes/Usecase5.Rmd | 262 ++--- CRTspat-1.4.0/CRTspat/vignettes/Usecase5.Rmd.orig | 36 CRTspat-1.4.0/CRTspat/vignettes/Usecase6.Rmd | 64 - CRTspat-1.4.0/CRTspat/vignettes/Usecase7.Rmd | 3 CRTspat-1.4.0/CRTspat/vignettes/Usecase7.Rmd.orig | 3 CRTspat-1.4.0/CRTspat/vignettes/Usecase8.Rmd.orig | 326 +++--- CRTspat-1.4.0/CRTspat/vignettes/Usecase9.Rmd.orig | 76 - CRTspat-1.4.0/CRTspat/vignettes/example10e.r-1.png |only CRTspat-1.4.0/CRTspat/vignettes/example10f.r-1.png |only CRTspat-1.4.0/CRTspat/vignettes/example2a.r-2.png |binary CRTspat-1.4.0/CRTspat/vignettes/example3b.r-1.png |binary CRTspat-1.4.0/CRTspat/vignettes/example5b.r-1.png |binary CRTspat-1.4.0/CRTspat/vignettes/example5d.r-1.png |binary CRTspat-1.4.0/CRTspat/vignettes/example6e.r-1.png |binary CRTspat-1.4.0/CRTspat/vignettes/runVignette.R | 2 84 files changed, 3150 insertions(+), 3706 deletions(-)
Title: Stochastic Frontier Analysis
Description: Provides a user-friendly framework for estimating a wide variety of cross-sectional and panel stochastic frontier models. Suitable for a broad range of applications, the implementation offers extensive flexibility in specification and estimation techniques.
Author: David Bernstein [aut, cre] ,
Christopher Parmeter [aut],
Alexander Stead [aut]
Maintainer: David Bernstein <davebernstein1@gmail.com>
This is a re-admission after prior archival of version 1.0-1 dated 2014-01-06
Diff between sfa versions 1.0-1 dated 2014-01-06 and 1.0.4 dated 2026-01-21
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Title: Penalized Linear Mixed Models for Correlated Data
Description: Fits penalized linear mixed models that correct for
unobserved confounding factors. 'plmmr' infers and corrects for the
presence of unobserved confounding effects such as population
stratification and environmental heterogeneity. It then fits a linear
model via penalized maximum likelihood. Originally designed for the
multivariate analysis of single nucleotide polymorphisms (SNPs)
measured in a genome-wide association study (GWAS), 'plmmr' eliminates
the need for subpopulation-specific analyses and post-analysis p-value
adjustments. Functions for the appropriate processing of 'PLINK'
files are also supplied. For examples, see the package homepage.
<https://pbreheny.github.io/plmmr/>.
Author: Tabitha K. Peter [aut] ,
Anna C. Reisetter [aut] ,
Yujing Lu [aut],
Oscar A. Rysavy [aut],
Patrick J. Breheny [aut, cre]
Maintainer: Patrick J. Breheny <patrick-breheny@uiowa.edu>
Diff between plmmr versions 4.2.1 dated 2025-03-03 and 4.2.2 dated 2026-01-21
plmmr-4.2.1/plmmr/R/check_for_file_extension.R |only plmmr-4.2.1/plmmr/man/check_for_file_extension.Rd |only plmmr-4.2.2/plmmr/DESCRIPTION | 30 +-- plmmr-4.2.2/plmmr/MD5 | 155 ++++++++-------- plmmr-4.2.2/plmmr/NEWS.md | 5 plmmr-4.2.2/plmmr/R/add_predictors.R | 25 +- plmmr-4.2.2/plmmr/R/align_ids.R | 22 +- plmmr-4.2.2/plmmr/R/big_cbind.R | 17 - plmmr-4.2.2/plmmr/R/coef-cv-plmm.R | 8 plmmr-4.2.2/plmmr/R/coef-plmm.R | 22 -- plmmr-4.2.2/plmmr/R/construct_variance.R | 27 +- plmmr-4.2.2/plmmr/R/count_constant_features.R | 8 plmmr-4.2.2/plmmr/R/count_cores.R | 6 plmmr-4.2.2/plmmr/R/create_design.R | 18 - plmmr-4.2.2/plmmr/R/create_design_filebacked.R | 114 +++++------- plmmr-4.2.2/plmmr/R/create_design_in_memory.R | 24 +- plmmr-4.2.2/plmmr/R/create_log.R | 5 plmmr-4.2.2/plmmr/R/cv-plmm.R | 203 ++++++++++------------ plmmr-4.2.2/plmmr/R/cvf.R | 109 ++++++----- plmmr-4.2.2/plmmr/R/data.R | 2 plmmr-4.2.2/plmmr/R/eigen_K.R | 21 +- plmmr-4.2.2/plmmr/R/estimate_eta.R | 4 plmmr-4.2.2/plmmr/R/fbm2bm.R | 4 plmmr-4.2.2/plmmr/R/find_example_data.R | 6 plmmr-4.2.2/plmmr/R/get_data.R | 14 - plmmr-4.2.2/plmmr/R/get_hostname.R | 2 plmmr-4.2.2/plmmr/R/impute_snp_data.R | 13 - plmmr-4.2.2/plmmr/R/index_samples.R | 18 - plmmr-4.2.2/plmmr/R/lam_names.R | 4 plmmr-4.2.2/plmmr/R/log_lik.R | 16 - plmmr-4.2.2/plmmr/R/name_and_count_bigsnp.R | 10 - plmmr-4.2.2/plmmr/R/penalties.R | 9 plmmr-4.2.2/plmmr/R/plmm.R | 54 ++--- plmmr-4.2.2/plmmr/R/plmm_checks.R | 75 ++++---- plmmr-4.2.2/plmmr/R/plmm_fit.R | 86 ++++----- plmmr-4.2.2/plmmr/R/plmm_format.R | 4 plmmr-4.2.2/plmmr/R/plmm_prep.R | 44 ++-- plmmr-4.2.2/plmmr/R/plot-cv-plmm.R | 67 +++---- plmmr-4.2.2/plmmr/R/plot-plmm.R | 36 ++- plmmr-4.2.2/plmmr/R/predict-plmm.R | 41 ++-- plmmr-4.2.2/plmmr/R/predict_within_cv.R | 10 - plmmr-4.2.2/plmmr/R/pretty_time.R | 4 plmmr-4.2.2/plmmr/R/print-summary-cv-plmm.R | 17 + plmmr-4.2.2/plmmr/R/print-summary-plmm.R | 16 - plmmr-4.2.2/plmmr/R/process_delim.R | 39 ++-- plmmr-4.2.2/plmmr/R/process_plink.R | 97 +++++----- plmmr-4.2.2/plmmr/R/read_data_files.R | 22 +- plmmr-4.2.2/plmmr/R/read_plink_files.R | 16 - plmmr-4.2.2/plmmr/R/relatedness_mat.R | 31 +-- plmmr-4.2.2/plmmr/R/rotate_filebacked.R | 9 plmmr-4.2.2/plmmr/R/setup_lambda.R | 34 +-- plmmr-4.2.2/plmmr/R/standardize_filebacked.R | 17 + plmmr-4.2.2/plmmr/R/standardize_matrix.R | 46 ++-- plmmr-4.2.2/plmmr/R/subset_bigsnp.R | 6 plmmr-4.2.2/plmmr/R/summary-cv-plmm.R | 18 - plmmr-4.2.2/plmmr/R/summary-plmm.R | 36 +-- plmmr-4.2.2/plmmr/R/untransform.R | 6 plmmr-4.2.2/plmmr/R/untransform_delim.R | 22 -- plmmr-4.2.2/plmmr/R/untransform_in_memory.R | 29 +-- plmmr-4.2.2/plmmr/R/untransform_plink.R | 24 +- plmmr-4.2.2/plmmr/README.md | 20 -- plmmr-4.2.2/plmmr/build/partial.rdb |binary plmmr-4.2.2/plmmr/build/vignette.rds |binary plmmr-4.2.2/plmmr/inst/doc/getting-started.html | 15 - plmmr-4.2.2/plmmr/inst/extdata/penncath_lite.bed |only plmmr-4.2.2/plmmr/man/coef.cv_plmm.Rd | 6 plmmr-4.2.2/plmmr/man/coef.plmm.Rd | 2 plmmr-4.2.2/plmmr/man/create_design_filebacked.Rd | 14 - plmmr-4.2.2/plmmr/man/cv_plmm.Rd | 41 ++-- plmmr-4.2.2/plmmr/man/plmm.Rd | 12 - plmmr-4.2.2/plmmr/man/plmm_fit.Rd | 5 plmmr-4.2.2/plmmr/man/plmmr-package.Rd | 4 plmmr-4.2.2/plmmr/man/predict.plmm.Rd | 2 plmmr-4.2.2/plmmr/man/process_delim.Rd | 2 plmmr-4.2.2/plmmr/man/process_plink.Rd | 16 - plmmr-4.2.2/plmmr/man/rotate_filebacked.Rd | 2 plmmr-4.2.2/plmmr/man/standardize_filebacked.Rd | 3 plmmr-4.2.2/plmmr/man/standardize_in_memory.Rd | 2 plmmr-4.2.2/plmmr/src/big_standardize.cpp | 18 + plmmr-4.2.2/plmmr/src/standardize.cpp | 12 - 80 files changed, 1011 insertions(+), 992 deletions(-)
Title: An Implementation of Z-Curves
Description: An implementation of z-curves - a method for estimating expected discovery
and replicability rates on the bases of test-statistics of published studies. The package
provides functions for fitting the density, EM, and censored EM version (Bartoš & Schimmack, 2022,
<doi:10.15626/MP.2021.2720>; Schimmack & Bartoš, 2023, <doi: 10.1371/journal.pone.0290084>),
as well as the original density z-curve (Brunner & Schimmack, 2020, <doi:10.15626/MP.2018.874>).
Furthermore, the package provides summarizing and plotting functions for the fitted z-curve objects.
See the aforementioned articles for more information about the z-curves, expected discovery
and replicability rates, validation studies, and limitations.
Author: Frantisek Bartos [aut, cre],
Ulrich Schimmack [aut]
Maintainer: Frantisek Bartos <f.bartos96@gmail.com>
Diff between zcurve versions 2.4.5 dated 2025-09-05 and 2.4.6 dated 2026-01-21
DESCRIPTION | 8 - MD5 | 32 ++--- R/RcppExports.R | 16 +- R/main.R | 7 + R/zcurve_EM.R | 10 + R/zcurve_clustered.R | 1 build/partial.rdb |binary man/control_EM.Rd | 3 src/RcppExports.cpp | 36 +++-- src/zcurveEM.cpp | 29 +++- tests/testthat/_snaps/zcurve/z-curve-cens-em-ggplot.svg | 56 ++++---- tests/testthat/_snaps/zcurve/z-curve-clustered-mixed-ggplot-1.svg | 64 +++++----- tests/testthat/_snaps/zcurve/z-curve-clustered-mixed-ggplot-2.svg | 64 +++++----- tests/testthat/_snaps/zcurve/z-curve-em-ggplot.svg | 60 ++++----- tests/testthat/_snaps/zcurve/z-curve-kd2-ggplot.svg | 60 ++++----- tests/testthat/_snaps/zcurve/z-curve-mixed-em-ggplot.svg | 56 ++++---- tests/testthat/test-zcurve.R | 8 - 17 files changed, 274 insertions(+), 236 deletions(-)
Title: Particle Learning of Gaussian Processes
Description: Sequential Monte Carlo (SMC) inference for fully Bayesian
Gaussian process (GP) regression and classification models by
particle learning (PL) following Gramacy & Polson (2011) <doi:10.48550/arXiv.0909.5262>.
The sequential nature of inference
and the active learning (AL) hooks provided facilitate thrifty
sequential design (by entropy) and optimization
(by improvement) for classification and
regression models, respectively.
This package essentially provides a generic
PL interface, and functions (arguments to the interface) which
implement the GP models and AL heuristics. Functions for
a special, linked, regression/classification GP model and
an integrated expected conditional improvement (IECI) statistic
provide for optimization in the presence of unknown constraints.
Separable and isotropic Gaussian, and single-index correlation
functions are supported.
See the examples section of ?plgp and demo(package="plgp")
for an index of demos.
Author: Robert B. Gramacy [aut, cre]
Maintainer: Robert B. Gramacy <rbg@vt.edu>
Diff between plgp versions 1.1-12 dated 2022-10-19 and 1.1-13 dated 2026-01-21
ChangeLog | 9 ++++++++- DESCRIPTION | 18 +++++++++++------- MD5 | 8 ++++---- src/matrix.c | 10 +++++----- src/rhelp.h | 2 +- 5 files changed, 29 insertions(+), 18 deletions(-)
Title: Extensible Data Structures for Multivariate Analysis
Description: Provides a set of basic and extensible data structures and functions for multivariate analysis, including dimensionality reduction techniques, projection methods, and preprocessing functions. The aim of this package is to offer a flexible and user-friendly framework for multivariate analysis that can be easily extended for custom requirements and specific data analysis tasks.
Author: Bradley Buchsbaum [aut, cre]
Maintainer: Bradley Buchsbaum <brad.buchsbaum@gmail.com>
Diff between multivarious versions 0.2.0 dated 2024-03-28 and 0.3.0 dated 2026-01-21
multivarious-0.2.0/multivarious/R/bootstrap_pca.R |only multivarious-0.2.0/multivarious/man/bootstrap.pca.Rd |only multivarious-0.2.0/multivarious/man/classifier.projector.Rd |only multivarious-0.2.0/multivarious/man/compose_projectors.Rd |only multivarious-0.2.0/multivarious/man/convert_domain.Rd |only multivarious-0.2.0/multivarious/man/nystrom_embedding.Rd |only multivarious-0.2.0/multivarious/man/partial_projector.projector.Rd |only multivarious-0.2.0/multivarious/man/print.bi_projector_union.Rd |only multivarious-0.2.0/multivarious/man/print.composed_projector.Rd |only multivarious-0.2.0/multivarious/man/print.projector.Rd |only multivarious-0.2.0/multivarious/tests/testthat/test-biprojector_union.R |only multivarious-0.3.0/multivarious/DESCRIPTION | 22 multivarious-0.3.0/multivarious/MD5 | 272 +- multivarious-0.3.0/multivarious/NAMESPACE | 122 + multivarious-0.3.0/multivarious/NEWS.md |only multivarious-0.3.0/multivarious/R/all_generic.R | 372 ++- 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multivarious-0.3.0/multivarious/R/projector.R | 403 ++- multivarious-0.3.0/multivarious/R/regress.R | 277 ++ multivarious-0.3.0/multivarious/R/svd.R | 112 - multivarious-0.3.0/multivarious/R/twoway_projector.R | 524 ++++ multivarious-0.3.0/multivarious/R/utils.R | 150 + multivarious-0.3.0/multivarious/README.md | 15 multivarious-0.3.0/multivarious/build/partial.rdb |only multivarious-0.3.0/multivarious/build/vignette.rds |binary multivarious-0.3.0/multivarious/inst/doc/CPCAplus.R |only multivarious-0.3.0/multivarious/inst/doc/CPCAplus.Rmd |only multivarious-0.3.0/multivarious/inst/doc/CPCAplus.html |only multivarious-0.3.0/multivarious/inst/doc/Classifier.R |only multivarious-0.3.0/multivarious/inst/doc/Classifier.Rmd |only multivarious-0.3.0/multivarious/inst/doc/Classifier.html |only multivarious-0.3.0/multivarious/inst/doc/Composing_Projectors.R |only multivarious-0.3.0/multivarious/inst/doc/Composing_Projectors.Rmd |only 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multivarious-0.3.0/multivarious/man/projector.Rd | 11 multivarious-0.3.0/multivarious/man/rank_score.Rd |only multivarious-0.3.0/multivarious/man/reconstruct.Rd | 19 multivarious-0.3.0/multivarious/man/reconstruct.composed_projector.Rd |only multivarious-0.3.0/multivarious/man/reconstruct.pca.Rd |only multivarious-0.3.0/multivarious/man/reconstruct.regress.Rd |only multivarious-0.3.0/multivarious/man/reconstruct_new.Rd |only multivarious-0.3.0/multivarious/man/regress.Rd | 20 multivarious-0.3.0/multivarious/man/reprocess.cross_projector.Rd | 4 multivarious-0.3.0/multivarious/man/reprocess.nystrom_approx.Rd |only multivarious-0.3.0/multivarious/man/rf_classifier.projector.Rd | 34 multivarious-0.3.0/multivarious/man/robust_inv_vTv.Rd |only multivarious-0.3.0/multivarious/man/rotate.Rd | 4 multivarious-0.3.0/multivarious/man/rotate.pca.Rd |only multivarious-0.3.0/multivarious/man/scores.plsc.Rd |only multivarious-0.3.0/multivarious/man/screeplot.Rd |only multivarious-0.3.0/multivarious/man/screeplot.pca.Rd |only multivarious-0.3.0/multivarious/man/std_scores.svd.Rd |only multivarious-0.3.0/multivarious/man/subspace_similarity.Rd |only multivarious-0.3.0/multivarious/man/summary.composed_projector.Rd |only multivarious-0.3.0/multivarious/man/svd_wrapper.Rd | 9 multivarious-0.3.0/multivarious/man/topk.Rd |only multivarious-0.3.0/multivarious/man/transfer.Rd |only multivarious-0.3.0/multivarious/man/transfer.cross_projector.Rd |only multivarious-0.3.0/multivarious/man/transform.Rd |only multivarious-0.3.0/multivarious/man/truncate.composed_projector.Rd |only multivarious-0.3.0/multivarious/man/variables_used.Rd |only multivarious-0.3.0/multivarious/man/vars_for_component.Rd |only multivarious-0.3.0/multivarious/tests/testthat/test-geneig-subspace.R |only multivarious-0.3.0/multivarious/tests/testthat/test_biprojector_union.R |only multivarious-0.3.0/multivarious/tests/testthat/test_bootstrap.R |only multivarious-0.3.0/multivarious/tests/testthat/test_classifier.R | 37 multivarious-0.3.0/multivarious/tests/testthat/test_cpca.R |only multivarious-0.3.0/multivarious/tests/testthat/test_cross_projector.R |only multivarious-0.3.0/multivarious/tests/testthat/test_cv.R |only multivarious-0.3.0/multivarious/tests/testthat/test_discriminant_projector.R |only multivarious-0.3.0/multivarious/tests/testthat/test_geneig.R |only multivarious-0.3.0/multivarious/tests/testthat/test_geneig_methods.R |only multivarious-0.3.0/multivarious/tests/testthat/test_nystrom.R | 194 + multivarious-0.3.0/multivarious/tests/testthat/test_pca.R | 76 multivarious-0.3.0/multivarious/tests/testthat/test_plsc.R |only multivarious-0.3.0/multivarious/tests/testthat/test_preprocess.R | 196 + multivarious-0.3.0/multivarious/tests/testthat/test_projector.R | 99 multivarious-0.3.0/multivarious/tests/testthat/test_reconstruct_new_biprojector.R |only multivarious-0.3.0/multivarious/tests/testthat/test_regress.R | 11 multivarious-0.3.0/multivarious/vignettes/CPCAplus.Rmd |only multivarious-0.3.0/multivarious/vignettes/Classifier.Rmd |only multivarious-0.3.0/multivarious/vignettes/Composing_Projectors.Rmd |only multivarious-0.3.0/multivarious/vignettes/CrossValidation.Rmd |only multivarious-0.3.0/multivarious/vignettes/Extending.Rmd |only multivarious-0.3.0/multivarious/vignettes/Introduction.Rmd | 163 - multivarious-0.3.0/multivarious/vignettes/Multiblock.Rmd |only multivarious-0.3.0/multivarious/vignettes/Nystrom.Rmd |only multivarious-0.3.0/multivarious/vignettes/PLSC.Rmd |only multivarious-0.3.0/multivarious/vignettes/Partial_Projection.Rmd |only multivarious-0.3.0/multivarious/vignettes/PermutationTesting.Rmd |only multivarious-0.3.0/multivarious/vignettes/PreProcessing.Rmd |only multivarious-0.3.0/multivarious/vignettes/Regress.Rmd |only multivarious-0.3.0/multivarious/vignettes/SVD_PCA.Rmd |only multivarious-0.3.0/multivarious/vignettes/albers.css |only 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Title: GWR, Mixed GWR with Spatial Autocorrelation and Multiscale GWR
(Top-Down Scale Approaches)
Description: Provides methods for Geographically Weighted Regression with spatial autocorrelation (Geniaux and Martinetti 2017) <doi:10.1016/j.regsciurbeco.2017.04.001>. Implements Multiscale Geographically Weighted Regression with Top-Down Scale approaches (Geniaux 2026) <doi:10.1007/s10109-025-00481-4>.
Author: Ghislain Geniaux [aut, cre],
Davide Martinetti [aut],
Cesar Martinez [aut]
Maintainer: Ghislain Geniaux <ghislain.geniaux@inrae.fr>
Diff between mgwrsar versions 1.1 dated 2025-02-20 and 1.3.1 dated 2026-01-21
mgwrsar-1.1/mgwrsar/R/ApproxiWv.R |only mgwrsar-1.1/mgwrsar/R/SSR.R |only mgwrsar-1.1/mgwrsar/R/bias_gwrsar.R |only mgwrsar-1.1/mgwrsar/R/built_Vseq.R |only mgwrsar-1.1/mgwrsar/R/dh_AICc.R |only mgwrsar-1.1/mgwrsar/R/fill_DGPTAB.R |only mgwrsar-1.1/mgwrsar/R/golden_search_bandwidth_AICc.R |only mgwrsar-1.1/mgwrsar/R/init_DGPTAB.R |only mgwrsar-1.1/mgwrsar/R/init_param_tds.R |only mgwrsar-1.1/mgwrsar/R/mgwr_stage1.R |only mgwrsar-1.1/mgwrsar/R/modc.R |only mgwrsar-1.1/mgwrsar/R/model_conf.R |only mgwrsar-1.1/mgwrsar/R/pastlm.R |only mgwrsar-1.1/mgwrsar/R/row_prod.R |only mgwrsar-1.1/mgwrsar/R/shepard_smooth_16tg.R |only mgwrsar-1.1/mgwrsar/R/simu.R |only mgwrsar-1.1/mgwrsar/R/stage1_tds_mgwr.R |only mgwrsar-1.1/mgwrsar/R/stage1_tds_mgwr_H.R |only mgwrsar-1.1/mgwrsar/R/stage2_atds_mgwr.R |only mgwrsar-1.1/mgwrsar/R/starting_model_atds_gwr.R |only mgwrsar-1.1/mgwrsar/R/starting_model_tds_mgwr.R |only mgwrsar-1.1/mgwrsar/R/summary_mgwrsar.R |only mgwrsar-1.1/mgwrsar/R/tds_mgwr.R |only mgwrsar-1.1/mgwrsar/inst/doc/GWR-and-Mixed-GWR-with-spatial-autocorrelation.html.asis |only mgwrsar-1.1/mgwrsar/inst/doc/GWR-with-Space-Time-Kernels.html.asis |only mgwrsar-1.1/mgwrsar/inst/doc/Intro_french_data.html.asis |only mgwrsar-1.1/mgwrsar/inst/doc/Multiscale-GWR-using-top-down-scale-approach.html.asis |only mgwrsar-1.1/mgwrsar/inst/doc/Speeding_up_GWR_like_models.html.asis |only mgwrsar-1.1/mgwrsar/man/INST_C.Rd |only mgwrsar-1.1/mgwrsar/man/PhWY_C.Rd |only mgwrsar-1.1/mgwrsar/man/Proj_C.Rd |only mgwrsar-1.1/mgwrsar/man/QRcpp2_C.Rd |only mgwrsar-1.1/mgwrsar/man/Sl_C.Rd |only mgwrsar-1.1/mgwrsar/man/modc.Rd |only mgwrsar-1.1/mgwrsar/man/tds_mgwr.Rd |only mgwrsar-1.1/mgwrsar/vignettes/GWR-and-Mixed-GWR-with-spatial-autocorrelation.html.asis |only mgwrsar-1.1/mgwrsar/vignettes/GWR-with-Space-Time-Kernels.html.asis |only mgwrsar-1.1/mgwrsar/vignettes/Intro_french_data.html.asis |only mgwrsar-1.1/mgwrsar/vignettes/Multiscale-GWR-using-top-down-scale-approach.html.asis |only mgwrsar-1.1/mgwrsar/vignettes/Speeding_up_GWR_like_models.html.asis |only mgwrsar-1.3.1/mgwrsar/DESCRIPTION | 29 mgwrsar-1.3.1/mgwrsar/MD5 | 206 mgwrsar-1.3.1/mgwrsar/NAMESPACE | 64 mgwrsar-1.3.1/mgwrsar/NEWS.md | 48 mgwrsar-1.3.1/mgwrsar/R/AICc.R | 1 mgwrsar-1.3.1/mgwrsar/R/ApproxiW.R | 15 mgwrsar-1.3.1/mgwrsar/R/Beta_extropolation.R |only mgwrsar-1.3.1/mgwrsar/R/GWR.R | 117 mgwrsar-1.3.1/mgwrsar/R/INST_C.R | 14 mgwrsar-1.3.1/mgwrsar/R/MGWR.R | 166 mgwrsar-1.3.1/mgwrsar/R/MGWRSAR.R | 80 mgwrsar-1.3.1/mgwrsar/R/PhWY_C.R | 14 mgwrsar-1.3.1/mgwrsar/R/Proj_C.R | 12 mgwrsar-1.3.1/mgwrsar/R/QRcpp2_C.R | 13 mgwrsar-1.3.1/mgwrsar/R/Sl_C.R | 14 mgwrsar-1.3.1/mgwrsar/R/TDS_MGWR.R |only mgwrsar-1.3.1/mgwrsar/R/aicc_f.R | 5 mgwrsar-1.3.1/mgwrsar/R/assign_control.R | 2 mgwrsar-1.3.1/mgwrsar/R/atds_gwr.R | 81 mgwrsar-1.3.1/mgwrsar/R/cell.quadtree.R |only mgwrsar-1.3.1/mgwrsar/R/cell.quadtree.leaf.R |only mgwrsar-1.3.1/mgwrsar/R/compute_Rk.R |only mgwrsar-1.3.1/mgwrsar/R/compute_ts.R |only 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Title: Full Featured Implementation of Hash Tables/Associative
Arrays/Dictionaries
Description: Implements a data structure similar to hashes in Perl and dictionaries in Python but with a purposefully R flavor. For objects of appreciable size, access using hashes outperforms native named lists and vectors.
Author: Christopher Brown [aut],
John Hughes [cre, ctb]
Maintainer: John Hughes <drjphughesjr@gmail.com>
Diff between hash versions 2.2.6.3 dated 2023-08-19 and 2.2.6.4 dated 2026-01-21
DESCRIPTION | 10 +++++----- MD5 | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-)
Title: Grouped Hyper Data Frame
Description: An S3 class 'groupedHyperframe' that inherits from hyper data frame. Batch processes and aggregation of hyper column(s) over a nested grouping structure.
Author: Tingting Zhan [aut, cre] ,
Inna Chervoneva [ctb]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Diff between groupedHyperframe versions 0.3.2 dated 2025-11-25 and 0.3.3 dated 2026-01-21
groupedHyperframe-0.3.2/groupedHyperframe/R/randLabel_test.R |only groupedHyperframe-0.3.2/groupedHyperframe/man/Math.ppp.Rd |only groupedHyperframe-0.3.2/groupedHyperframe/man/foobar.Rd |only groupedHyperframe-0.3.2/groupedHyperframe/man/superimpose.groupedHyperframe.Rd |only groupedHyperframe-0.3.3/groupedHyperframe/DESCRIPTION | 22 groupedHyperframe-0.3.3/groupedHyperframe/MD5 | 93 ++-- groupedHyperframe-0.3.3/groupedHyperframe/NAMESPACE | 83 +++ groupedHyperframe-0.3.3/groupedHyperframe/R/0PACKAGE.R | 3 groupedHyperframe-0.3.3/groupedHyperframe/R/Defunct.R | 77 +-- groupedHyperframe-0.3.3/groupedHyperframe/R/Math.R |only groupedHyperframe-0.3.3/groupedHyperframe/R/Surv.R |only groupedHyperframe-0.3.3/groupedHyperframe/R/aggregate.R | 13 groupedHyperframe-0.3.3/groupedHyperframe/R/aggregate_marks.R | 10 groupedHyperframe-0.3.3/groupedHyperframe/R/append_marks.R | 57 ++ groupedHyperframe-0.3.3/groupedHyperframe/R/as.groupedHyperframe.R | 4 groupedHyperframe-0.3.3/groupedHyperframe/R/attr_.R |only groupedHyperframe-0.3.3/groupedHyperframe/R/data_doc.R | 1 groupedHyperframe-0.3.3/groupedHyperframe/R/fvlist.R | 41 + groupedHyperframe-0.3.3/groupedHyperframe/R/groupedHyperframe.R | 144 +++++- groupedHyperframe-0.3.3/groupedHyperframe/R/kerndens.R | 6 groupedHyperframe-0.3.3/groupedHyperframe/R/lastLegal.R | 1 groupedHyperframe-0.3.3/groupedHyperframe/R/op_hyperframe.R | 12 groupedHyperframe-0.3.3/groupedHyperframe/R/op_ppp.R | 30 - groupedHyperframe-0.3.3/groupedHyperframe/R/op_ppplist.R | 227 +++++----- groupedHyperframe-0.3.3/groupedHyperframe/R/ppp_S3.R | 48 -- groupedHyperframe-0.3.3/groupedHyperframe/R/rlabelRes.R |only groupedHyperframe-0.3.3/groupedHyperframe/R/superimpose.hyperframe.R | 87 --- groupedHyperframe-0.3.3/groupedHyperframe/R/vectorlist.R | 74 ++- groupedHyperframe-0.3.3/groupedHyperframe/R/vignette.R | 87 +++ groupedHyperframe-0.3.3/groupedHyperframe/R/vtrapz.R | 65 +- groupedHyperframe-0.3.3/groupedHyperframe/inst/doc/intro.html | 16 groupedHyperframe-0.3.3/groupedHyperframe/man/append_marks_set.Rd | 6 groupedHyperframe-0.3.3/groupedHyperframe/man/as.list.fvlist.Rd |only groupedHyperframe-0.3.3/groupedHyperframe/man/attr_.Rd |only groupedHyperframe-0.3.3/groupedHyperframe/man/bib.Rd | 2 groupedHyperframe-0.3.3/groupedHyperframe/man/cli_.Rd | 20 groupedHyperframe-0.3.3/groupedHyperframe/man/cumvtrapz.Rd | 4 groupedHyperframe-0.3.3/groupedHyperframe/man/defunct.Rd | 12 groupedHyperframe-0.3.3/groupedHyperframe/man/dot-ns_generic.Rd |only groupedHyperframe-0.3.3/groupedHyperframe/man/global_envelope_test_.Rd |only groupedHyperframe-0.3.3/groupedHyperframe/man/groupGeneric_fvlist.Rd |only groupedHyperframe-0.3.3/groupedHyperframe/man/groupGeneric_ppp.Rd |only groupedHyperframe-0.3.3/groupedHyperframe/man/groupGeneric_ppplist.Rd |only groupedHyperframe-0.3.3/groupedHyperframe/man/groupGeneric_psp.Rd |only groupedHyperframe-0.3.3/groupedHyperframe/man/groupGeneric_tess.Rd |only groupedHyperframe-0.3.3/groupedHyperframe/man/groupedHyperframe-package.Rd | 7 groupedHyperframe-0.3.3/groupedHyperframe/man/is.vectorlist.Rd | 2 groupedHyperframe-0.3.3/groupedHyperframe/man/kerndens.Rd | 4 groupedHyperframe-0.3.3/groupedHyperframe/man/print.cumv.Rd |only groupedHyperframe-0.3.3/groupedHyperframe/man/print.groupedHyperframe.Rd | 3 groupedHyperframe-0.3.3/groupedHyperframe/man/print.summary.groupedHyperframe.Rd |only groupedHyperframe-0.3.3/groupedHyperframe/man/print.vectorlist.Rd |only groupedHyperframe-0.3.3/groupedHyperframe/man/rds2versiondate.Rd |only groupedHyperframe-0.3.3/groupedHyperframe/man/rlabelRes.Rd |only groupedHyperframe-0.3.3/groupedHyperframe/man/sub-.cumv.Rd |only groupedHyperframe-0.3.3/groupedHyperframe/man/summary.Surv.Rd |only groupedHyperframe-0.3.3/groupedHyperframe/man/summary.groupedHyperframe.Rd |only groupedHyperframe-0.3.3/groupedHyperframe/man/superimpose.hyperframe.Rd | 5 groupedHyperframe-0.3.3/groupedHyperframe/man/t.vectorlist.Rd | 2 groupedHyperframe-0.3.3/groupedHyperframe/man/visualize_vtrapz.Rd | 8 60 files changed, 792 insertions(+), 484 deletions(-)
More information about groupedHyperframe at CRAN
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Title: Fitting Finite Mixture of Scale Mixture of Skew-Normal
Distributions
Description: Functions to fit finite mixture of scale mixture of skew-normal (FM-SMSN) distributions, details in Prates, Lachos and Cabral (2013) <doi: 10.18637/jss.v054.i12>, Cabral, Lachos and Prates (2012) <doi:10.1016/j.csda.2011.06.026> and Basso, Lachos, Cabral and Ghosh (2010) <doi:10.1016/j.csda.2009.09.031>.
Author: Marcos Prates [aut, cre, trl] ,
Victor Lachos [aut] ,
Celso Cabral [aut]
Maintainer: Marcos Prates <marcosop@est.ufmg.br>
Diff between mixsmsn versions 1.1-11 dated 2025-04-23 and 1.1-12 dated 2026-01-21
ChangeLog | 4 ++++ DESCRIPTION | 11 ++++++----- MD5 | 6 +++--- R/mix.print.R | 4 ++-- 4 files changed, 15 insertions(+), 10 deletions(-)
Title: Time Series Forecasting Functions
Description: Fundamental time series forecasting models such as autoregressive integrated moving average (ARIMA), exponential smoothing, and simple moving average are included. For ARIMA models, the output follows the traditional parameterisation by Box and Jenkins (1970, ISBN: 0816210942, 9780816210947). Furthermore, there are functions for detailed time series exploration and decomposition, respectively. All data and result visualisations are generated by 'ggplot2' instead of conventional R graphical output. For more details regarding the theoretical background of the models see Hyndman, R.J. and Athanasopoulos, G. (2021) <https://otexts.com/fpp3/>.
Author: Ka Yui Karl Wu [aut, cre]
Maintainer: Ka Yui Karl Wu <karlwuky@suss.edu.sg>
Diff between tsforecast versions 1.2.1 dated 2025-12-19 and 1.3.0 dated 2026-01-21
tsforecast-1.2.1/tsforecast/R/tsforecast_1.2.1.R |only tsforecast-1.3.0/tsforecast/DESCRIPTION | 8 +-- tsforecast-1.3.0/tsforecast/MD5 | 51 +++++++++++----------- tsforecast-1.3.0/tsforecast/NAMESPACE | 11 ++++ tsforecast-1.3.0/tsforecast/R/tsforecast_1.3.0.R |only tsforecast-1.3.0/tsforecast/inst/examples/tsgarch |only tsforecast-1.3.0/tsforecast/inst/examples/tslm |only tsforecast-1.3.0/tsforecast/man/airport.Rd | 2 tsforecast-1.3.0/tsforecast/man/is.outlier.Rd | 2 tsforecast-1.3.0/tsforecast/man/predict.Rd | 8 +++ tsforecast-1.3.0/tsforecast/man/ts-functions.Rd | 2 tsforecast-1.3.0/tsforecast/man/tsacf.Rd | 9 +++ tsforecast-1.3.0/tsforecast/man/tsarima.Rd | 5 +- tsforecast-1.3.0/tsforecast/man/tsboxplot.Rd | 2 tsforecast-1.3.0/tsforecast/man/tsconvert.Rd | 2 tsforecast-1.3.0/tsforecast/man/tsdecomp.Rd | 2 tsforecast-1.3.0/tsforecast/man/tsdiff.Rd | 2 tsforecast-1.3.0/tsforecast/man/tsesm.Rd | 2 tsforecast-1.3.0/tsforecast/man/tsexplore.Rd | 2 tsforecast-1.3.0/tsforecast/man/tsforecast.Rd | 8 +++ tsforecast-1.3.0/tsforecast/man/tshistogram.Rd | 2 tsforecast-1.3.0/tsforecast/man/tslag.Rd | 8 ++- tsforecast-1.3.0/tsforecast/man/tslineplot.Rd | 2 tsforecast-1.3.0/tsforecast/man/tslm.Rd |only tsforecast-1.3.0/tsforecast/man/tsmltest.Rd | 2 tsforecast-1.3.0/tsforecast/man/tsmodeleval.Rd | 2 tsforecast-1.3.0/tsforecast/man/tsmovav.Rd | 2 tsforecast-1.3.0/tsforecast/man/tsqqplot.Rd | 2 tsforecast-1.3.0/tsforecast/man/tsscatterplot.Rd | 2 29 files changed, 88 insertions(+), 52 deletions(-)
Title: Overlap Detection in n-Dimensional Space
Description: Uses support vector machines to identify a perfectly separating hyperplane (linear or curvilinear) between two entities in high-dimensional space. If this plane exists, the entities do not overlap. Applications include overlap detection in morphological, resource or environmental dimensions. More details can be found in: Brown et al. (2020) <doi:10.1111/2041-210X.13363> .
Author: Matilda Brown [aut, cre] ,
Greg Jordan [aut]
Maintainer: Matilda Brown <m.brown2@kew.org>
Diff between hyperoverlap versions 1.1.3 dated 2025-09-23 and 1.1.4 dated 2026-01-21
DESCRIPTION | 8 +- MD5 | 14 ++-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/hyperoverlap-vignette.R | 4 - inst/doc/hyperoverlap-vignette.Rmd | 4 - inst/doc/hyperoverlap-vignette.html | 109 ++++++++++++++++++++++-------------- vignettes/hyperoverlap-vignette.Rmd | 4 - 8 files changed, 84 insertions(+), 59 deletions(-)
Title: Data Management and Analysis of Tests
Description: A system for the management, assessment, and psychometric analysis of data from educational and psychological tests.
Author: Gunter Maris [aut],
Timo Bechger [aut],
Jesse Koops [aut, cre],
Ivailo Partchev [aut]
Maintainer: Jesse Koops <jesse.koops@cito.nl>
Diff between dexter versions 1.7.0 dated 2025-09-26 and 1.7.2 dated 2026-01-21
DESCRIPTION | 8 +-- MD5 | 54 ++++++++++++------------ NEWS.md | 3 + R/misc_anon.R | 1 R/plausible_values.R | 4 - R/plots.R | 6 ++ R/profile_analysis.R | 10 ++-- R/progress.R | 7 ++- R/resp_data.R | 2 R/standards.R | 4 - R/suf_stats.R | 7 ++- R/theta_functions.R | 6 +- R/tia.R | 9 ++-- build/vignette.rds |binary inst/doc/DIF_vignette.html | 10 ++-- inst/doc/Equating.html | 18 ++++---- inst/doc/Plausible_Values.html | 16 +++---- inst/doc/Test_Individual_differences.html | 14 +++--- inst/doc/dexter.html | 66 +++++++++++++++--------------- inst/doc/profile-plots.html | 20 ++++----- man/information.Rd | 6 +- man/plausible_values.Rd | 4 - man/plot.enorm.Rd | 3 - man/profile_plot.Rd | 4 + man/profiles.Rd | 10 ++-- man/standards_3dc.Rd | 2 man/standards_db.Rd | 2 man/tia_tables.Rd | 3 - 28 files changed, 163 insertions(+), 136 deletions(-)
Title: Optimal Pairing and Matching via Linear Assignment
Description: Solves optimal pairing and matching problems using linear assignment
algorithms. Provides implementations of the Hungarian method (Kuhn 1955)
<doi:10.1002/nav.3800020109>, Jonker-Volgenant shortest path algorithm
(Jonker and Volgenant 1987) <doi:10.1007/BF02278710>, Auction algorithm
(Bertsekas 1988) <doi:10.1007/BF02186476>, cost-scaling
(Goldberg and Kennedy 1995) <doi:10.1007/BF01585996>, scaling algorithms
(Gabow and Tarjan 1989) <doi:10.1137/0218069>, push-relabel (Goldberg and
Tarjan 1988) <doi:10.1145/48014.61051>, and Sinkhorn entropy-regularized
transport (Cuturi 2013) <doi:10.48550/arxiv.1306.0895>. Designed for
matching plots, sites, samples, or any pairwise optimization problem.
Supports rectangular matrices, forbidden assignments, data frame inputs,
batch solving, k-best solutions, and pixel-level image morphing for
visualization. Includes automatic preprocessing with variable health
checks, multiple scaling methods (standardized, [...truncated...]
Author: Gilles Colling [aut, cre, cph]
Maintainer: Gilles Colling <gilles.colling051@gmail.com>
Diff between couplr versions 1.0.8 dated 2026-01-21 and 1.0.10 dated 2026-01-21
DESCRIPTION | 6 - MD5 | 48 +++++----- inst/doc/algorithms.R | 24 ++--- inst/doc/algorithms.Rmd | 54 +++++------ inst/doc/algorithms.html | 72 +++++++-------- inst/doc/comparison.R | 2 inst/doc/comparison.Rmd | 30 +++--- inst/doc/comparison.html | 144 +++++++++++++++--------------- inst/doc/getting-started.R | 2 inst/doc/getting-started.Rmd | 2 inst/doc/getting-started.html | 6 - inst/doc/matching-workflows.Rmd | 16 +-- inst/doc/matching-workflows.html | 32 +++--- inst/doc/pixel-morphing.Rmd | 172 ++++++++++++++++++------------------ inst/doc/pixel-morphing.html | 174 ++++++++++++++++++------------------- inst/doc/troubleshooting.Rmd | 2 inst/doc/troubleshooting.html | 8 - src/solvers/solve_auction.cpp | 50 ++++++++-- src/solvers/solve_auction_rcpp.cpp | 27 ++++- vignettes/algorithms.Rmd | 54 +++++------ vignettes/comparison.Rmd | 30 +++--- vignettes/getting-started.Rmd | 2 vignettes/matching-workflows.Rmd | 16 +-- vignettes/pixel-morphing.Rmd | 172 ++++++++++++++++++------------------ vignettes/troubleshooting.Rmd | 2 25 files changed, 595 insertions(+), 552 deletions(-)
Title: OLS, Moderated, Logistic, and Count Regressions Made Simple
Description: Provides SPSS- and SAS-like output for least squares multiple regression,
logistic regression, and count variable regressions. Detailed output is also provided for
OLS moderated regression, interaction plots, and Johnson-Neyman
regions of significance. The output includes standardized
coefficients, partial and semi-partial correlations, collinearity diagnostics,
plots of residuals, and detailed information about simple slopes for interactions.
The output for some functions includes Bayes Factors and, if requested,
regression coefficients from Bayesian Markov Chain Monte Carlo analyses.
There are numerous options for model plots.
The REGIONS_OF_SIGNIFICANCE function also provides
Johnson-Neyman regions of significance and plots of interactions for both lm
and lme models. There is also a function for partial and semipartial
correlations and a function for conducting Cohen's
set correlation analyses.
Author: Brian P. O'Connor [aut, cre]
Maintainer: Brian P. O'Connor <brian.oconnor@ubc.ca>
Diff between SIMPLE.REGRESSION versions 0.2.8 dated 2025-11-19 and 0.3.1 dated 2026-01-21
DESCRIPTION | 8 MD5 | 66 - NAMESPACE | 4 R/COUNT_REGRESSION.R | 477 +++++-------- R/LOGISTIC_REGRESSION.R | 347 +++------ R/MODERATED_REGRESSION.R | 1163 +++++++++++++------------------- R/OLS_REGRESSION.R | 532 +-------------- R/PLOT_MODEL.R | 175 +--- R/REGIONS_OF_SIGNIFICANCE.R | 29 R/utilities_boc.R | 1269 ++++++++++++++++++++++++++++-------- data/data_Halvorson_2022_pois.rda |binary data/data_Kremelburg_2011.rda |binary data/data_Meyers_2013.rda |binary man/COUNT_REGRESSION.Rd | 79 +- man/LOGISTIC_REGRESSION.Rd | 61 + man/MODERATED_REGRESSION.Rd | 70 + man/OLS_REGRESSION.Rd | 84 +- man/PARTIAL_COR.Rd | 9 man/PLOT_MODEL.Rd | 23 man/REGIONS_OF_SIGNIFICANCE.Rd | 8 man/SET_CORRELATION.Rd | 9 man/SIMPLE.REGRESSION-package.Rd | 11 man/data_Bauer_Curran_2005.Rd | 1 man/data_Cohen_Aiken_West_2003_9.Rd | 3 man/data_DeLeo_2013.Rd | 6 man/data_Halvorson_2022_log.Rd | 5 man/data_Halvorson_2022_pois.Rd | 6 man/data_Huitema_2011.Rd | 2 man/data_Kremelburg_2011.Rd | 13 man/data_Meyers_2013.Rd | 1 man/data_OConnor_Dvorak_2001.Rd | 3 man/data_Orme_2009_2.Rd | 4 man/data_Orme_2009_5.Rd | 9 man/data_Pituch_Stevens_2016.Rd | 1 34 files changed, 2260 insertions(+), 2218 deletions(-)
More information about SIMPLE.REGRESSION at CRAN
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Title: Reading, Quality Control and Preprocessing of MBA (Multiplex
Bead Assay) Data
Description: Speeds up the process of loading raw data from MBA (Multiplex Bead Assay) examinations, performs quality control checks, and automatically normalises the data, preparing it for more advanced, downstream tasks. The main objective of the package is to create a simple environment for a user, who does not necessarily have experience with R language. The package is developed within the project 'PvSTATEM', which is an international project aiming for malaria elimination.
Author: Jakub Grzywaczewski [aut, cre],
Tymoteusz Kwiecinski [aut] ,
Mateusz Nizwantowski [aut],
Przemyslaw Biecek [ths] ,
Nuno Sepulveda [ths]
Maintainer: Jakub Grzywaczewski <jakubzgrzywaczewski@gmail.com>
Diff between SerolyzeR versions 1.3.1 dated 2025-10-21 and 1.4.0 dated 2026-01-21
SerolyzeR-1.3.1/SerolyzeR/inst/img/overview.png |only SerolyzeR-1.4.0/SerolyzeR/DESCRIPTION | 9 - SerolyzeR-1.4.0/SerolyzeR/MD5 | 65 ++++--- SerolyzeR-1.4.0/SerolyzeR/NAMESPACE | 1 SerolyzeR-1.4.0/SerolyzeR/R/classes-plate_builder.R | 78 ++++++-- SerolyzeR-1.4.0/SerolyzeR/R/config.R | 4 SerolyzeR-1.4.0/SerolyzeR/R/generate_report.R | 1 SerolyzeR-1.4.0/SerolyzeR/R/helpers.R | 67 +++++++ SerolyzeR-1.4.0/SerolyzeR/R/parser-bioplex.R |only SerolyzeR-1.4.0/SerolyzeR/R/parser.R | 55 +++++- SerolyzeR-1.4.0/SerolyzeR/R/plots-plate.R | 2 SerolyzeR-1.4.0/SerolyzeR/R/plots-standard_curve.R | 32 ++- SerolyzeR-1.4.0/SerolyzeR/R/process-dir.R | 8 SerolyzeR-1.4.0/SerolyzeR/R/process-file.R | 2 SerolyzeR-1.4.0/SerolyzeR/R/process-plate.R | 2 SerolyzeR-1.4.0/SerolyzeR/build/partial.rdb |binary SerolyzeR-1.4.0/SerolyzeR/inst/doc/example_script.Rmd | 2 SerolyzeR-1.4.0/SerolyzeR/inst/doc/example_script.html | 50 ++--- SerolyzeR-1.4.0/SerolyzeR/inst/extdata/synthetic_bioplex.xlsx |only SerolyzeR-1.4.0/SerolyzeR/inst/extdata/synthetic_bioplex_layout.xlsx |only SerolyzeR-1.4.0/SerolyzeR/inst/img/EU.jpg |binary SerolyzeR-1.4.0/SerolyzeR/inst/templates/levey_jennings_report_template.Rmd | 87 +++++++--- SerolyzeR-1.4.0/SerolyzeR/inst/templates/plate_report_template.Rmd | 58 +++--- SerolyzeR-1.4.0/SerolyzeR/man/extract_header_information.Rd |only SerolyzeR-1.4.0/SerolyzeR/man/get_header_end_idx.Rd |only SerolyzeR-1.4.0/SerolyzeR/man/handle_datetime.Rd | 4 SerolyzeR-1.4.0/SerolyzeR/man/move_legend_to_separate_plot.Rd |only SerolyzeR-1.4.0/SerolyzeR/man/plot_standard_curve_stacked.Rd | 8 SerolyzeR-1.4.0/SerolyzeR/man/process_dir.Rd | 4 SerolyzeR-1.4.0/SerolyzeR/man/process_file.Rd | 2 SerolyzeR-1.4.0/SerolyzeR/man/read_bioplex_format.Rd |only SerolyzeR-1.4.0/SerolyzeR/man/read_luminex_data.Rd | 4 SerolyzeR-1.4.0/SerolyzeR/man/save_csv.Rd |only SerolyzeR-1.4.0/SerolyzeR/man/translate_sample_names_to_sample_types.Rd | 4 SerolyzeR-1.4.0/SerolyzeR/tests/testthat/test-integration.R | 12 + SerolyzeR-1.4.0/SerolyzeR/tests/testthat/test-plate_builder.R | 50 +++++ SerolyzeR-1.4.0/SerolyzeR/tests/testthat/test-process-dir.R | 2 SerolyzeR-1.4.0/SerolyzeR/vignettes/example_script.Rmd | 2 38 files changed, 455 insertions(+), 160 deletions(-)
Title: Working with Ethiopian Dates
Description: A robust and efficient solution for working with Ethiopian dates. It can seamlessly convert to and from Gregorian dates.
It is designed to be compatible with the 'tidyverse' data workflow, including plotting with 'ggplot2'.
It ensures lightning-fast computations by integrating high-performance 'C++' code through 'Rcpp' package.
Author: Gutama Girja Urago [aut, cre, cph]
Maintainer: Gutama Girja Urago <girjagutama@gmail.com>
Diff between ethiodate versions 0.3.0 dated 2025-12-19 and 0.3.1 dated 2026-01-21
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ NEWS.md | 4 ++++ R/Ops-date.R | 8 ++++---- README.md | 2 +- inst/doc/parsing.html | 10 +++++----- tests/testthat/test-Ops.R | 2 +- 7 files changed, 26 insertions(+), 22 deletions(-)
Title: Miscellaneous Helper Functions for B. Bischl
Description: Miscellaneous helper functions for and from B. Bischl and
some other guys, mainly for package development.
Author: Bernd Bischl [aut, cre],
Michel Lang [aut],
Jakob Bossek [aut],
Daniel Horn [aut],
Jakob Richter [aut],
Dirk Surmann [aut]
Maintainer: Bernd Bischl <bernd_bischl@gmx.net>
Diff between BBmisc versions 1.13 dated 2022-09-29 and 1.13.1 dated 2026-01-21
DESCRIPTION | 8 MD5 | 353 +++++++++++++++++----------------- NEWS.md |only R/FileCache.R | 3 R/addClasses.R | 5 R/argsAsNamedList.R | 3 R/asMatrix.R | 5 R/asQuoted.R | 3 R/binPack.R | 3 R/btwn.R | 5 R/catf.R | 3 R/checkArg.R | 8 R/checkListElementClass.R | 3 R/chunk.R | 3 R/clipString.R | 5 R/coalesce.R | 2 R/collapse.R | 3 R/collapsef.R | 3 R/computeMode.R | 3 R/convertDataFrameCols.R | 5 R/convertInteger.R | 6 R/convertListOfRowsToDataFrame.R | 2 R/convertMatrixType.R | 3 R/convertRowsToList.R | 3 R/convertToShortString.R | 2 R/dapply.R | 3 R/directory.R | 6 R/do.call2.R | 3 R/dropNamed.R | 5 R/ensureVector.R | 3 R/explode.R | 3 R/extractSubList.R | 5 R/factor.R | 3 R/filterNull.R | 5 R/getAttributeNames.R | 6 R/getClass1.R | 5 R/getFirstLast.R | 5 R/getMaxColIndex.R | 3 R/getMaxIndex.R | 3 R/getOperatingSystem.R | 5 R/getRelativePath.R | 3 R/getUnixTime.R | 3 R/getUsedFactorLevels.R | 3 R/hasAttributes.R | 5 R/insert.R | 3 R/isExpensiveExampleOk.R | 3 R/isFALSE.R | 5 R/isProperlyNamed.R | 3 R/isScalarNA.R | 3 R/isScalarValue.R | 3 R/isSubset.R | 5 R/isSuperset.R | 5 R/isValidName.R | 5 R/is_error.R | 3 R/itostr.R | 3 R/lib.R | 3 R/load2.R | 5 R/lsort.R | 5 R/makeDataFrame.R | 5 R/makeProgressBar.R | 2 R/makeS3Obj.R | 3 R/makeSimpleFileLogger.R | 3 R/mapValues.R | 2 R/messagef.R | 3 R/namedList.R | 2 R/names2.R | 3 R/nin.R | 5 R/normalize.R | 2 R/optimizeSubInts.R | 2 R/printHead.R | 3 R/printStrToChar.R | 5 R/printToChar.R | 5 R/rangeVal.R | 3 R/requirePackages.R | 2 R/rowLapply.R | 3 R/save2.R | 3 R/seq.R | 3 R/setAttribute.R | 5 R/setClasses.R | 5 R/setRowColNames.R | 5 R/setValue.R | 3 R/sortByCol.R | 5 R/splitPath.R | 3 R/splitTime.R | 3 R/stopf.R | 3 R/strrepeat.R | 5 R/suppressAll.R | 5 R/symdiff.R | 5 R/system3.R | 3 R/toRangeStr.R | 5 R/vapply.R | 2 R/warningf.R | 3 R/which.first.R | 5 R/zzz_deprecated.R | 5 man/addClasses.Rd | 4 man/argsAsNamedList.Rd | 2 man/asMatrixCols.Rd | 4 man/asQuoted.Rd | 2 man/binPack.Rd | 2 man/btwn.Rd | 4 man/cFactor.Rd | 2 man/catf.Rd | 2 man/checkArg.Rd | 2 man/checkListElementClass.Rd | 2 man/chunk.Rd | 2 man/clipString.Rd | 4 man/coalesce.Rd | 2 man/collapse.Rd | 2 man/collapsef.Rd | 5 man/computeMode.Rd | 2 man/convertDataFrameCols.Rd | 4 man/convertInteger.Rd | 2 man/convertIntegers.Rd | 2 man/convertListOfRowsToDataFrame.Rd | 2 man/convertMatrixType.Rd | 2 man/convertRowsToList.Rd | 2 man/convertToShortString.Rd | 2 man/dapply.Rd | 2 man/deprecated.Rd | 2 man/do.call2.Rd | 2 man/dropNamed.Rd | 4 man/ensureVector.Rd | 2 man/explode.Rd | 2 man/extractSubList.Rd | 4 man/filterNull.Rd | 2 man/getAttributeNames.Rd | 6 man/getClass1.Rd | 4 man/getFirst.Rd | 4 man/getMaxIndex.Rd | 2 man/getMaxIndexOfRows.Rd | 2 man/getOperatingSystem.Rd | 4 man/getUnixTime.Rd | 2 man/getUsedFactorLevels.Rd | 2 man/hasAttributes.Rd | 4 man/insert.Rd | 2 man/isExpensiveExampleOk.Rd | 2 man/isFALSE.Rd | 4 man/isScalarNA.Rd | 2 man/isSubset.Rd | 4 man/isSuperset.Rd | 4 man/isValidName.Rd | 2 man/lib.Rd | 2 man/load2.Rd | 4 man/lsort.Rd | 4 man/makeDataFrame.Rd | 4 man/makeFileCache.Rd | 2 man/makeProgressBar.Rd | 2 man/makeS3Obj.Rd | 2 man/makeSimpleFileLogger.Rd | 2 man/messagef.Rd | 2 man/namedList.Rd | 2 man/names2.Rd | 2 man/nin.Rd | 4 man/normalize.Rd | 2 man/optimizeSubInts.Rd | 2 man/printHead.Rd | 2 man/printStrToChar.Rd | 4 man/printToChar.Rd | 4 man/rangeVal.Rd | 2 man/requirePackages.Rd | 2 man/rowLapply.Rd | 2 man/save2.Rd | 2 man/seq_row.Rd | 2 man/setAttribute.Rd | 4 man/setClasses.Rd | 4 man/setRowNames.Rd | 4 man/setValue.Rd | 2 man/sortByCol.Rd | 4 man/splitTime.Rd | 2 man/stopf.Rd | 2 man/strrepeat.Rd | 2 man/suppressAll.Rd | 2 man/symdiff.Rd | 4 man/system3.Rd | 2 man/toRangeStr.Rd | 4 man/warningf.Rd | 2 man/which.first.Rd | 4 tests/testthat/test_requirePackages.R | 1 178 files changed, 536 insertions(+), 394 deletions(-)
Title: Log Execution of Scripts
Description: Logging of scripts suitable for clinical trials using
'Quarto' to create nice human readable logs. 'whirl' enables
execution of scripts in batch, while simultaneously creating logs for
the execution of each script, and providing an overview summary log of
the entire batch execution.
Author: Aksel Thomsen [aut, cre],
Lovemore Gakava [aut],
Cervan Girard [aut],
Kristian Troejelsgaard [aut],
Steffen Falgreen Larsen [aut],
Vladimir Obucina [aut],
Michael Svingel [aut],
Skander Mulder [aut],
Oliver Lundsgaard [aut],
Novo Nordisk A/S [cph]
Maintainer: Aksel Thomsen <oath@novonordisk.com>
Diff between whirl versions 0.3.1 dated 2025-08-25 and 0.3.2 dated 2026-01-21
DESCRIPTION | 12 MD5 | 56 NEWS.md | 7 R/log.R | 34 R/mdformats.R | 2 R/renv.R | 2 R/run.R | 9 R/whirl-options.R | 6 R/whirl_r_session.R | 107 - build/vignette.rds |binary inst/documents/dummy.qmd | 19 inst/documents/log.qmd | 39 inst/documents/python.qmd | 5 inst/examples/prg1_log.html |only inst/examples/success_log.html |only man/run.Rd | 5 man/whirl-options-params.Rd | 2 man/whirl-options.Rd | 10 tests/testthat/scripts/error_log.html | 2042 ++++++---------------- tests/testthat/scripts/py_dependencies_log.html | 2206 +++++++----------------- tests/testthat/scripts/py_error_log.html | 2073 ++++++---------------- tests/testthat/scripts/py_success_log.html | 2067 ++++++---------------- tests/testthat/scripts/py_warning_log.html | 2069 ++++++---------------- tests/testthat/scripts/success_log.html | 2037 ++++++---------------- tests/testthat/scripts/warning_log.html | 2051 ++++++---------------- tests/testthat/test-examples.R | 1 tests/testthat/test-mdformats.R | 4 tests/testthat/test-python.R | 13 tests/testthat/test-run.R | 17 tests/testthat/test-whirl_r_session.R | 6 30 files changed, 4473 insertions(+), 10428 deletions(-)
Title: Rocket-Fast Clinical Research Reporting
Description: Description of the tables, both grouped and not grouped, with some associated data management actions,
such as sorting the terms of the variables and deleting terms with zero numbers.
Author: USMR CHU de Bordeaux [aut, cre],
Valentine Renaudeau [aut],
Marion Kret [aut],
Matisse Decilap [aut],
Sahardid Mohamed Houssein [aut],
Thomas Ferte [aut]
Maintainer: USMR CHU de Bordeaux <astreinte.usmr@chu-bordeaux.fr>
Diff between RastaRocket versions 1.0.0 dated 2025-11-20 and 1.0.1 dated 2026-01-21
RastaRocket-1.0.0/RastaRocket/R/ordonner_var_qualitatives_function.R |only RastaRocket-1.0.0/RastaRocket/man/ordonner_variables_qualitatives.Rd |only RastaRocket-1.0.1/RastaRocket/DESCRIPTION | 6 RastaRocket-1.0.1/RastaRocket/MD5 | 30 RastaRocket-1.0.1/RastaRocket/NAMESPACE | 1 RastaRocket-1.0.1/RastaRocket/NEWS.md | 23 RastaRocket-1.0.1/RastaRocket/R/ajouter_label_ndm_function.R | 45 - RastaRocket-1.0.1/RastaRocket/R/desc_var_function.R | 28 RastaRocket-1.0.1/RastaRocket/R/prepare_table.R | 38 RastaRocket-1.0.1/RastaRocket/README.md | 18 RastaRocket-1.0.1/RastaRocket/inst/doc/DescribeAE.html | 446 +++++----- RastaRocket-1.0.1/RastaRocket/inst/doc/RastaRocketVignette.Rmd | 4 RastaRocket-1.0.1/RastaRocket/inst/doc/RastaRocketVignette.html | 7 RastaRocket-1.0.1/RastaRocket/inst/doc/SetupProject.html | 4 RastaRocket-1.0.1/RastaRocket/man/desc_var.Rd | 2 RastaRocket-1.0.1/RastaRocket/man/prepare_table.Rd | 2 RastaRocket-1.0.1/RastaRocket/vignettes/RastaRocketVignette.Rmd | 4 17 files changed, 344 insertions(+), 314 deletions(-)
Title: An Implementation of Rapid Assessment Method for Older People
Description: An implementation of the Rapid Assessment Method for Older People
or RAM-OP <https://www.helpage.org/resource/rapid-assessment-method-for-older-people-ramop-manual/>.
It provides various functions that allow the user to design and plan the
assessment and analyse the collected data. RAM-OP provides accurate and
reliable estimates of the needs of older people.
Author: Mark Myatt [aut, cph] ,
Ernest Guevarra [aut, cre, cph] ,
Pascale Fritsch [aut],
Katja Siling [aut],
HelpAge International [cph],
Elrha [fnd]
Maintainer: Ernest Guevarra <ernest@guevarra.io>
Diff between oldr versions 0.2.3 dated 2025-01-24 and 0.2.4 dated 2026-01-21
DESCRIPTION | 16 MD5 | 44 NAMESPACE | 4 NEWS.md | 9 R/00-oldr.R | 6 R/01-opIndicators.R | 2 R/05-merge_op.R | 11 R/08-report.R | 49 README.md | 82 - build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 4 inst/WORDLIST | 6 inst/doc/oldr.html | 97 + inst/doc/ram_op_workflow.html | 2264 ++++++++++++++++++++++------------------ man/create_op.Rd | 2 man/merge_op.Rd | 6 man/oldr.Rd | 2 man/report_op_docx.Rd | 10 man/report_op_html.Rd | 10 man/report_op_odt.Rd | 10 man/report_op_pdf.Rd | 4 tests/testthat/test-10-report.R | 36 23 files changed, 1545 insertions(+), 1129 deletions(-)
Title: Generalised Linear Mixed Models in R
Description: Specification, analysis, simulation, and fitting of generalised linear mixed models.
Includes Markov Chain Monte Carlo Maximum likelihood model fitting for a range of models,
non-linear fixed effect specifications, a wide range of flexible covariance functions that can be combined arbitrarily,
robust and bias-corrected standard error estimation, power calculation, data simulation, and more.
Author: Sam Watson [aut, cre]
Maintainer: Sam Watson <S.I.Watson@bham.ac.uk>
Diff between glmmrBase versions 1.1.0 dated 2025-09-29 and 1.2.0 dated 2026-01-21
glmmrBase-1.1.0/glmmrBase/inst/include/glmmr/optim/lbfgs |only glmmrBase-1.1.0/glmmrBase/inst/include/glmmr/optim/lbfgs.h |only glmmrBase-1.1.0/glmmrBase/inst/include/glmmr/optim/lbfgsb.h |only glmmrBase-1.2.0/glmmrBase/DESCRIPTION | 16 glmmrBase-1.2.0/glmmrBase/MD5 | 68 glmmrBase-1.2.0/glmmrBase/R/Betadist.R | 13 glmmrBase-1.2.0/glmmrBase/R/R6Model.R | 641 ++--- glmmrBase-1.2.0/glmmrBase/R/R6covariance.R | 34 glmmrBase-1.2.0/glmmrBase/R/RcppExports.R | 128 - glmmrBase-1.2.0/glmmrBase/README.md |only glmmrBase-1.2.0/glmmrBase/build/partial.rdb |binary glmmrBase-1.2.0/glmmrBase/inst/include/glmmr.h | 36 glmmrBase-1.2.0/glmmrBase/inst/include/glmmr/algo.h | 14 glmmrBase-1.2.0/glmmrBase/inst/include/glmmr/ar1covariance.hpp |only glmmrBase-1.2.0/glmmrBase/inst/include/glmmr/covariance.hpp | 824 ++---- glmmrBase-1.2.0/glmmrBase/inst/include/glmmr/family.hpp | 11 glmmrBase-1.2.0/glmmrBase/inst/include/glmmr/general.h | 27 glmmrBase-1.2.0/glmmrBase/inst/include/glmmr/hsgpcovariance.hpp | 185 - glmmrBase-1.2.0/glmmrBase/inst/include/glmmr/interpreter.h | 91 glmmrBase-1.2.0/glmmrBase/inst/include/glmmr/maths.h | 643 +++-- glmmrBase-1.2.0/glmmrBase/inst/include/glmmr/matrixw.hpp | 23 glmmrBase-1.2.0/glmmrBase/inst/include/glmmr/model.hpp | 277 +- glmmrBase-1.2.0/glmmrBase/inst/include/glmmr/modelbits.hpp | 82 glmmrBase-1.2.0/glmmrBase/inst/include/glmmr/modelmatrix.hpp | 801 ++---- glmmrBase-1.2.0/glmmrBase/inst/include/glmmr/modelmcmc.hpp | 239 - glmmrBase-1.2.0/glmmrBase/inst/include/glmmr/modeloptim.hpp | 1278 ++++------ glmmrBase-1.2.0/glmmrBase/inst/include/glmmr/nngpcovariance.hpp | 241 - glmmrBase-1.2.0/glmmrBase/inst/include/glmmr/optim/optim.h | 703 ----- glmmrBase-1.2.0/glmmrBase/inst/include/glmmr/randomeffects.hpp | 101 glmmrBase-1.2.0/glmmrBase/man/Covariance.Rd | 5 glmmrBase-1.2.0/glmmrBase/man/Model.Rd | 294 +- glmmrBase-1.2.0/glmmrBase/man/exponential.Rd |only glmmrBase-1.2.0/glmmrBase/src/RcppExports.cpp | 432 +-- glmmrBase-1.2.0/glmmrBase/src/model_module.cpp | 603 ++-- 34 files changed, 3534 insertions(+), 4276 deletions(-)
Title: 'vcd' Extensions and Additions
Description: Provides additional data sets, methods and documentation to complement the 'vcd' package for Visualizing Categorical Data
and the 'gnm' package for Generalized Nonlinear Models.
In particular, 'vcdExtra' extends mosaic, assoc and sieve plots from 'vcd' to handle 'glm()' and 'gnm()' models and
adds a 3D version in 'mosaic3d'. Additionally, methods are provided for comparing and visualizing lists of
'glm' and 'loglm' objects. This package is now a support package for the book, "Discrete Data Analysis with R" by
Michael Friendly and David Meyer.
Author: Michael Friendly [aut, cre] ,
David Meyer [ctb],
Achim Zeileis [ctb] ,
Duncan Murdoch [ctb],
Heather Turner [ctb] ,
David Firth [ctb],
Daniel Sabanes Bove [ctb],
Matt Kumar [ctb],
Shuguang Sun [ctb]
Maintainer: Michael Friendly <friendly@yorku.ca>
Diff between vcdExtra versions 0.8.7 dated 2025-12-11 and 0.9.0 dated 2026-01-21
DESCRIPTION | 49 ++++++++++++----------- MD5 | 57 ++++++++++++++------------- NAMESPACE | 3 + NEWS.md | 14 ++++++ R/data.R | 4 - R/datasets.R | 86 +++++++++++++++++++++++++---------------- R/loglin-utilities.R | 36 +++-------------- R/woolf_test.R |only build/vignette.rds |binary inst/doc/a1-creating.html | 9 ++-- inst/doc/a2-tests.html | 23 ++++++---- inst/doc/a3-loglinear.html | 9 ++-- inst/doc/a4-mosaics.html | 9 ++-- inst/doc/a5-demo-housing.html | 9 ++-- inst/doc/a6-mobility.html | 9 ++-- inst/doc/a7-continuous.html | 13 +++--- inst/doc/datasets.html | 9 ++-- inst/doc/tidyCats.Rmd | 18 +++++--- inst/doc/tidyCats.html | 35 ++++++++++------ man/CMHtest.Rd | 1 man/Depends.Rd | 2 man/GKgamma.Rd | 1 man/HLtest.Rd | 1 man/WorkerSat.Rd | 2 man/datasets.Rd | 27 +++++++----- man/figures |only man/loglin-utilities.Rd | 36 +++-------------- man/woolf_test.Rd |only man/zero.test.Rd | 3 - vignettes/fig/tidyCat-logo.png |only vignettes/tidyCats.Rmd | 18 +++++--- 31 files changed, 264 insertions(+), 219 deletions(-)
Title: NHDPlus Tools
Description: Tools for traversing and working with National Hydrography Dataset Plus (NHDPlus) data. All methods implemented in 'nhdplusTools' are available in the NHDPlus documentation available from the US Environmental Protection Agency <https://www.epa.gov/waterdata/basic-information>.
Author: David Blodgett [aut, cre] ,
Mike Johnson [aut] ,
Marc Weber [ctb] ,
Josh Erickson [ctb],
Lauren Koenig [ctb]
Maintainer: David Blodgett <dblodgett@usgs.gov>
Diff between nhdplusTools versions 1.4.1 dated 2025-12-05 and 1.4.2 dated 2026-01-21
DESCRIPTION | 6 MD5 | 75 +- NAMESPACE | 1 NEWS.md | 5 R/calc_network.R | 124 ++- R/discover_nhdplus.R | 141 ++-- R/get_nhdplus.R | 5 R/get_nhdplushr.R | 698 +++++++++++----------- R/get_nldi.R | 4 R/get_oaproc.R | 8 R/oafeat_tools.R | 53 + R/plot_nhdplus.R | 3 R/run_plus_attributes.R | 5 R/subset_nhdplus.R | 5 inst/doc/get_3dhp_data.html | 5 inst/doc/get_data_overview.R | 2 inst/doc/get_data_overview.Rmd | 686 ++++++++++----------- inst/doc/get_data_overview.html | 69 -- inst/doc/indexing.html | 16 inst/doc/nhdplusTools.html | 197 ++---- inst/doc/nhdplushr.html | 30 inst/doc/plot_nhdplus.html | 19 inst/extdata/3dhp_yahara_flowlines.R |only man/add_plus_network_attributes.Rd | 2 man/calculate_arbolate_sum.Rd | 2 man/calculate_total_drainage_area.Rd | 2 man/discover_nhdplus_id.Rd | 16 man/get_nhdplus.Rd | 4 man/get_split_catchment.Rd | 8 man/query_usgs_oafeat.Rd | 1 tests/testthat/test_00_plot_integration_nhdplus.R | 1 tests/testthat/test_02_subset.R | 4 tests/testthat/test_02_subset_extras.R | 370 +++++------ tests/testthat/test_calc_network.R | 211 +++--- tests/testthat/test_geoconnex.R | 2 tests/testthat/test_get_codes.R | 258 ++++---- tests/testthat/test_get_path.R | 311 ++++----- tests/testthat/test_run_plus_attributes.R | 8 vignettes/get_data_overview.Rmd | 686 ++++++++++----------- 39 files changed, 2050 insertions(+), 1993 deletions(-)
Title: Wavelet Methods for Analysing Locally Stationary Time Series
Description: Fitting models for, and simulation of, trend locally stationary
wavelet (TLSW) time series models, which take account of time-varying
trend and dependence structure in a univariate time series. The TLSW model,
and its estimation, is described in McGonigle, Killick and Nunes (2022a)
<doi:10.1111/jtsa.12643>, (2022b) <doi:10.1214/22-EJS2044>. Further information regarding the use of the package, along with detailed examples, can be found in McGonigle, Killick and Nunes (2025) <doi:10.18637/jss.v115.i10>. New users will
likely want to start with the TLSW function.
Author: Euan T. McGonigle [aut, cre],
Rebecca Killick [aut],
Matthew Nunes [aut]
Maintainer: Euan T. McGonigle <e.t.mcgonigle@soton.ac.uk>
Diff between TrendLSW versions 1.0.4 dated 2025-11-24 and 1.0.6 dated 2026-01-21
TrendLSW-1.0.4/TrendLSW/data/celegensbio.RData |only TrendLSW-1.0.4/TrendLSW/man/celegensbio.Rd |only TrendLSW-1.0.6/TrendLSW/DESCRIPTION | 8 ++++---- TrendLSW-1.0.6/TrendLSW/MD5 | 17 +++++++++-------- TrendLSW-1.0.6/TrendLSW/NEWS.md | 8 ++++++++ TrendLSW-1.0.6/TrendLSW/R/TLSW.R | 3 +++ TrendLSW-1.0.6/TrendLSW/R/TLSWlacf.R | 4 ++++ TrendLSW-1.0.6/TrendLSW/data/celegansbio.RData |only TrendLSW-1.0.6/TrendLSW/inst |only TrendLSW-1.0.6/TrendLSW/man/TLSW.Rd | 3 +++ TrendLSW-1.0.6/TrendLSW/man/TLSWlacf.Rd | 3 +++ TrendLSW-1.0.6/TrendLSW/man/celegansbio.Rd |only 12 files changed, 34 insertions(+), 12 deletions(-)
Title: Tidy Complex 'JSON'
Description: Turn complex 'JSON' data into tidy data frames.
Author: Jeremy Stanley [aut],
Cole Arendt [aut, cre]
Maintainer: Cole Arendt <cole@benetist.com>
This is a re-admission after prior archival of version 0.3.2 dated 2023-01-06
Diff between tidyjson versions 0.3.2 dated 2023-01-06 and 0.3.3.1 dated 2026-01-21
tidyjson-0.3.2/tidyjson/man/as_tibble.Rd |only tidyjson-0.3.2/tidyjson/man/bind_rows.Rd |only tidyjson-0.3.2/tidyjson/man/filter.Rd |only tidyjson-0.3.2/tidyjson/man/pipe.Rd |only tidyjson-0.3.3.1/tidyjson/DESCRIPTION | 12 tidyjson-0.3.3.1/tidyjson/MD5 | 35 tidyjson-0.3.3.1/tidyjson/NAMESPACE | 3 tidyjson-0.3.3.1/tidyjson/NEWS.md | 7 tidyjson-0.3.3.1/tidyjson/R/json_schema.R | 2 tidyjson-0.3.3.1/tidyjson/R/tbl_json.R | 3 tidyjson-0.3.3.1/tidyjson/R/tidyjson-package.R | 3 tidyjson-0.3.3.1/tidyjson/R/utils.R | 27 tidyjson-0.3.3.1/tidyjson/README.md | 215 +- tidyjson-0.3.3.1/tidyjson/build/vignette.rds |binary tidyjson-0.3.3.1/tidyjson/inst/doc/introduction-to-tidyjson.R | 12 tidyjson-0.3.3.1/tidyjson/inst/doc/introduction-to-tidyjson.html | 392 ++--- tidyjson-0.3.3.1/tidyjson/inst/doc/visualizing-json.R | 10 tidyjson-0.3.3.1/tidyjson/inst/doc/visualizing-json.html | 774 +++++----- tidyjson-0.3.3.1/tidyjson/man/json_schema.Rd | 2 tidyjson-0.3.3.1/tidyjson/man/reexports.Rd |only tidyjson-0.3.3.1/tidyjson/man/tidyjson.Rd | 1 21 files changed, 797 insertions(+), 701 deletions(-)
Title: Single-Source Capture-Recapture Models
Description: Implementation of single-source capture-recapture methods for population size estimation using zero-truncated, zero-one truncated and zero-truncated one-inflated Poisson, Geometric and Negative Binomial regression as well as Zelterman's and Chao's regression. Package includes point and interval estimators for the population size with variances estimated using analytical or bootstrap method. Details can be found in: van der Heijden et all. (2003) <doi:10.1191/1471082X03st057oa>, Böhning and van der Heijden (2019) <doi:10.1214/18-AOAS1232>, Böhning et al. (2020) Capture-Recapture Methods for the Social and Medical Sciences or Böhning and Friedl (2021) <doi:10.1007/s10260-021-00556-8>.
Author: Piotr Chlebicki [aut, ctb] ,
Maciej Beresewicz [aut, cre]
Maintainer: Maciej Beresewicz <maciej.beresewicz@ue.poznan.pl>
Diff between singleRcapture versions 0.2.3 dated 2025-02-13 and 1.0.0 dated 2026-01-21
DESCRIPTION | 14 MD5 | 36 - NEWS.md | 293 +++++----- R/documentationFiles.R | 8 R/oiztgeom.R | 275 +++------ R/oiztnegbin.R | 669 +++++++++++----------- R/oiztpoisson.R | 272 ++++----- R/ztoigeom.R | 275 +++++---- R/ztoinegbin.R | 669 ++++++++++------------ R/ztoipoisson.R | 272 ++++----- README.md | 22 build/singleRcapture.pdf |binary build/stage23.rdb |binary inst/CITATION |only inst/doc/singleRcapture.Rmd | 207 +++---- inst/doc/singleRcapture.html | 1024 +++++++++++++++++------------------ inst/tinytest/test_inflated_hurdle.R | 124 ++-- man/figures/logo.png |only man/singleRmodels.Rd | 8 vignettes/singleRcapture.Rmd | 207 +++---- 20 files changed, 2203 insertions(+), 2172 deletions(-)
More information about singleRcapture at CRAN
Permanent link
Title: Modules for 'ShinyItemAnalysis'
Description: Package including additional modules for interactive
'ShinyItemAnalysis' application for the psychometric analysis of
educational tests, psychological assessments, health-related and other
types of multi-item measurements, or ratings from multiple raters.
Author: Patricia Martinkova [aut, cre] ,
Jan Netik [aut] ,
Adela Hladka [aut]
Maintainer: Patricia Martinkova <martinkova@cs.cas.cz>
Diff between SIAmodules versions 0.1.2 dated 2025-03-28 and 0.1.3 dated 2026-01-21
DESCRIPTION | 29 +- MD5 | 26 +- NAMESPACE | 2 NEWS.md | 13 + R/SIAmodules-package.R | 1 R/read_me.R | 6 R/sm_cat.R | 535 ++++++++++++++++++++++++++++++---------------- R/sm_dif_c.R | 14 - R/sm_irr.R | 28 +- README.md | 4 inst/CITATION |only inst/sc/restr_range.R | 4 man/SIAmodules-package.Rd | 2 man/figures/logo.svg |only man/sm_cat_internal.Rd | 8 15 files changed, 426 insertions(+), 246 deletions(-)
Title: Run the 'Open-WBO' MaxSAT Solver
Description: Provides a wrapper for running the bundled 'Open-WBO' Maximum Satisfiability
(MaxSAT) solver (<https://github.com/sat-group/open-wbo>).
Users can pass command-line arguments to the solver and capture its output
as a character string or file.
Author: Matthias Ollech [aut, cre],
Ruben Martins, Vasco Manquinho, Ines Lynce [cph]
Maintainer: Matthias Ollech <ollech@gmx.com>
Diff between Rwbo versions 0.1.1 dated 2026-01-16 and 0.1.2 dated 2026-01-21
Rwbo-0.1.1/Rwbo/src/open_wbo/Makefile.in |only Rwbo-0.1.1/Rwbo/src/open_wbo/configure |only Rwbo-0.1.2/Rwbo/DESCRIPTION | 6 +- Rwbo-0.1.2/Rwbo/LICENCE.note | 8 +-- Rwbo-0.1.2/Rwbo/MD5 | 23 ++++------ Rwbo-0.1.2/Rwbo/NEWS.md | 6 ++ Rwbo-0.1.2/Rwbo/src/Makevars | 13 +++-- Rwbo-0.1.2/Rwbo/src/Makevars.win | 13 +---- Rwbo-0.1.2/Rwbo/src/open_wbo/Main.cc | 2 Rwbo-0.1.2/Rwbo/src/open_wbo/Makefile |only Rwbo-0.1.2/Rwbo/src/open_wbo/MaxSAT_Partition.h | 8 --- Rwbo-0.1.2/Rwbo/src/open_wbo/solvers/glucose4.1/parallel/Main.cc | 2 Rwbo-0.1.2/Rwbo/src/open_wbo/solvers/glucose4.1/simp/Main.cc | 2 Rwbo-0.1.2/Rwbo/src/open_wbo/solvers/glucose4.1/utils/System.h | 3 - 14 files changed, 40 insertions(+), 46 deletions(-)
Title: 'shiny' Applications for Statistical and Psychometric Analysis
Description: Toolbox with 'shiny' applications for widely used psychometric
methods. Those methods include following analysis: Item analysis, item response theory calibration, principal component analysis,
confirmatory factor analysis - structural equation modeling, generating simulated data.
References:
Chalmers (2012, <doi:10.18637/jss.v048.i06>);
Revelle (2022, <https://CRAN.R-project.org/package=psych Version = 2.2.9.>);
Rosseel (2012, <doi:10.18637/jss.v048.i02>);
Magis & Raiche (2012, <doi:10.18637/jss.v048.i08>);
Magis & Barrada (2017, <doi:10.18637/jss.v076.c01>).
Author: Celal Deha Dogan [aut] ,
Eren Can Aybek [aut, cre] ,
Sumeyra Soysal [ctb]
Maintainer: Eren Can Aybek <erencan@aybek.net>
This is a re-admission after prior archival of version 0.4 dated 2023-09-24
Diff between RSP versions 0.4 dated 2023-09-24 and 0.5 dated 2026-01-21
DESCRIPTION | 17 +++++++------ MD5 | 30 ++++++++++++------------ R/04-cfa.R | 22 +++++++++-------- R/05-dataSim.R | 6 ++-- R/07-internal.R | 2 - build/vignette.rds |binary inst/doc/INTRO_RSP.R | 42 +++++++++++++++++----------------- inst/doc/INTRO_RSP.html | 1 tests/testthat/test-01-itemAnalysis.R | 5 ++-- tests/testthat/test-02-irt.R | 5 ++-- tests/testthat/test-03-pca.R | 5 ++-- tests/testthat/test-04-cfa.R | 5 ++-- tests/testthat/test-05-dataSim.R | 5 ++-- tests/testthat/test-06-fa.R | 5 ++-- tests/testthat/test-07-internal.R | 5 ++-- tests/testthat/test-zzz.R | 11 +++++++- 16 files changed, 92 insertions(+), 74 deletions(-)
Title: Regression Models and Utilities for Repeated Measures and Panel
Data
Description: Provides an object type and associated tools for storing and
wrangling panel data. Implements several methods for creating regression
models that take advantage of the unique aspects of
panel data. Among other capabilities, automates the "within-between"
(also known as "between-within" and "hybrid") panel regression specification
that combines the desirable aspects of both fixed effects and random effects
econometric models and fits them as multilevel models
(Allison, 2009 <doi:10.4135/9781412993869.d33>;
Bell & Jones, 2015 <doi:10.1017/psrm.2014.7>). These models can also be
estimated via generalized estimating equations
(GEE; McNeish, 2019 <doi:10.1080/00273171.2019.1602504>) and Bayesian
estimation is (optionally) supported via 'Stan'.
Supports estimation of asymmetric effects models via first differences
(Allison, 2019 <doi:10.1177/2378023119826441>) as well as a generalized
linear model extension thereof using GEE.
Author: Jacob A. Long [aut, cre]
Maintainer: Jacob A. Long <jacob.long@sc.edu>
This is a re-admission after prior archival of version 0.7.8 dated 2023-08-22
Diff between panelr versions 0.7.8 dated 2023-08-22 and 1.0.0 dated 2026-01-21
DESCRIPTION | 25 MD5 | 101 +- NAMESPACE | 42 NEWS.md | 63 + R/asym_gee.R | 2 R/balance_panel.R |only R/basis_utils.R |only R/model_frame.R | 168 +-- R/panel_data.R | 95 + R/reconstruct.R | 57 - R/reshapers.R | 166 +-- R/utils.R | 464 +++++++-- R/vctrs-panel_data.R |only R/wb_data_prep.R | 216 +++- R/wb_formula.R |only R/wb_gee.R | 10 R/wb_lmer.R | 44 R/wb_stan.R | 39 R/wb_utils.R | 1775 +++++++++++++++++++----------------- R/zzz.R |only README.md | 526 +++++----- build/vignette.rds |binary inst/doc/reshape.html | 136 +- inst/doc/wbm.R | 9 inst/doc/wbm.Rmd | 31 inst/doc/wbm.html | 236 ++-- man/InteractionConfig.Rd |only man/WBFormula.Rd |only man/WBFormula_from_parser.Rd |only man/as_parser_list.Rd |only man/balance_panel.Rd |only man/basis_function_registry.Rd |only man/basis_utils.Rd |only man/bt.Rd |only man/bt_if_needed.Rd |only man/build_panel_data.Rd |only man/detect_matrix_terms.Rd |only man/evaluate_basis_term.Rd |only man/expand_basis_columns.Rd |only man/expand_matrix_terms_in_data.Rd |only man/extract_basis_variable.Rd |only man/extract_fn_name.Rd |only man/extract_ranef_vars.Rd |only man/generate_basis_colnames.Rd |only man/get_interactions.WBFormula.Rd |only man/get_meanvar.Rd |only man/has_gaps.Rd |only man/has_interactions.Rd |only man/is_known_basis_fn.Rd |only man/is_matrix_term.Rd |only man/is_panel_sorted.Rd |only man/is_varying_term.Rd |only man/is_within_model.Rd |only man/make_interaction_config.Rd |only man/nobs.wbm.Rd | 4 man/panel_data-vctrs.Rd |only man/predict.wbgee.Rd | 6 man/predict.wbm.Rd | 33 man/print.WBFormula.Rd |only man/process_matrix_term.Rd |only man/reconstruct_basis_call.Rd |only man/scan_gaps.Rd |only man/should_demean_ints.Rd |only man/un_bt.Rd |only man/update_pf_for_matrix_terms.Rd |only man/use_old_style_ints.Rd |only man/wbm.Rd | 17 tests/testthat/test-balance_panel.R |only tests/testthat/test-utils.R | 16 tests/testthat/test-vctrs.R |only tests/testthat/test_splines.R |only tests/testthat/test_wbgee.R | 25 tests/testthat/test_wbm.R | 116 ++ vignettes/wbm.Rmd | 31 74 files changed, 2725 insertions(+), 1728 deletions(-)
Title: Bayesian Package for Network Changepoint Analysis
Description: Network changepoint analysis for undirected network data. The package implements a hidden Markov network change point model (Park and Sohn (2020)). Functions for break number detection using the approximate marginal likelihood and WAIC are also provided. This version includes performance optimizations with vectorized MCMC operations and modern ggplot2-based visualizations with colorblind-friendly palettes.
Author: Jong Hee Park [aut, cre],
Yunkyu Sohn [aut]
Maintainer: Jong Hee Park <jongheepark@snu.ac.kr>
Diff between NetworkChange versions 0.8 dated 2022-03-04 and 1.0.0 dated 2026-01-21
DESCRIPTION | 37 +++--- MD5 | 73 ++++++------ NAMESPACE | 27 +++- R/NetworkChange-package.r | 9 - R/NetworkChange.r | 20 +-- R/NetworkChangeRobust.r | 2 R/NetworkStatic.R | 2 R/ULUstateSample.r | 223 ++++++++++++++++++------------------- R/Utils.R | 135 +++++++++++++++++++++- R/drawpostanalysis.R | 52 ++++---- R/globals.R |only R/multiplot.R | 43 +++---- R/plotContour.R | 12 + R/plotU.R | 73 +++++------- R/plotV.R | 69 ++++++----- R/plotnetarray.R | 39 +++--- R/updateU.R | 40 ++++-- R/updateUm.R | 44 +++++-- R/updateV.R | 53 ++++++-- R/updateVm.R | 62 ++++++---- man/NetworkChange.Rd | 2 man/NetworkChangeRobust.Rd | 2 man/NetworkStatic.Rd | 2 man/ULUstateSample.Rd | 3 man/ULUstateSample.mpfr.Rd | 3 man/combineVm.Rd |only man/drawPostAnalysis.Rd | 3 man/figures/package-overview.png |only man/multiplot.Rd | 10 - man/plotContour.Rd | 7 - man/plotU.Rd | 3 man/plotV.Rd | 11 + man/plotnetarray.Rd | 4 man/scale_color_networkchange.Rd |only man/scale_color_networkchange_c.Rd |only man/scale_fill_networkchange.Rd |only man/theme_networkchange.Rd |only man/updateU.Rd | 3 man/updateUm.Rd | 3 man/updateV.Rd | 3 man/updateVm.Rd | 3 41 files changed, 669 insertions(+), 408 deletions(-)
Title: Measuring Ecosystem Multi-Functionality and Its Decomposition
Description: Provide simple functions to (i) compute a class of
multi-functionality measures for a single ecosystem for given
function weights, (ii) decompose gamma multi-functionality
for pairs of ecosystems and K ecosystems (K can be greater than 2)
into a within-ecosystem component (alpha multi-functionality)
and an among-ecosystem component (beta multi-functionality).
In each case, the correlation between functions can be corrected for.
Based on biodiversity and ecosystem function data, this software
also facilitates graphics for assessing biodiversity-ecosystem
functioning relationships across scales.
Author: Anne Chao [aut, cre],
Chun-Yu Liu [ctb],
KaiHsiang Hu [ctb]
Maintainer: Anne Chao <chao@stat.nthu.edu.tw>
Diff between MF.beta4 versions 1.1.1 dated 2024-12-08 and 1.1.2 dated 2026-01-21
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS | 4 ++++ R/Mainfun.R | 9 +++++---- build/vignette.rds |binary inst/doc/Introduction.pdf |binary 6 files changed, 17 insertions(+), 12 deletions(-)
Title: Material Management
Description: A set of functions, classes and methods for performing ABC and ABC/XYZ analyses, identifying overperforming, underperforming and constantly performing items, and plotting, analyzing as well as predicting the temporal development of items.
Author: Leon Binder [cre, aut],
Bernhard Bauer [aut],
Michael Scholz [aut]
Maintainer: Leon Binder <leon.binder@th-deg.de>
Diff between matman versions 1.1.3 dated 2021-12-13 and 1.1.4 dated 2026-01-21
DESCRIPTION | 8 - MD5 | 42 ++++---- NAMESPACE | 1 NEWS.md | 3 R/ABCXYZanalysis.R | 2 man/ABCXYZData-class.Rd | 84 ++++++++--------- man/Amount.Rd | 60 ++++++------ man/Forecast-class.Rd | 92 +++++++++---------- man/Stocks.Rd | 52 +++++----- man/computeOverperformer.Rd | 138 ++++++++++++++-------------- man/computeUnderperformer.Rd | 138 ++++++++++++++-------------- man/detectTimeVariations.Rd | 114 +++++++++++------------ man/expandData.Rd | 130 +++++++++++++------------- man/matmanDemo.Rd | 42 ++++---- man/plot-ABCXYZData-ANY-method.Rd | 136 ++++++++++++++-------------- man/plotValueSeries.Rd | 134 +++++++++++++-------------- man/predictValue.Rd | 184 +++++++++++++++++++------------------- man/show-ABCXYZData-method.Rd | 74 +++++++-------- man/show-Forecast-method.Rd | 74 +++++++-------- man/summary-ABCXYZData-method.Rd | 100 ++++++++++---------- man/summary-Forecast-method.Rd | 78 ++++++++-------- man/summary.Rd | 80 ++++++++-------- 22 files changed, 885 insertions(+), 881 deletions(-)
Title: Post-Estimation Utilities for 'lavaan' Fitted Models
Description: Companion toolbox for structural equation models fitted with 'lavaan'. Provides post-estimation diagnostics and graphics that operate directly on a fitted object using its estimates and covariance, and refits auxiliary models when needed. The package relies on 'lavaan' (Rosseel, 2012) <doi:10.18637/jss.v048.i02>.
Author: Giuseppe Corbelli [aut, cre]
Maintainer: Giuseppe Corbelli <giuseppe.corbelli@uninettunouniversity.net>
Diff between lavinteract versions 0.3.4 dated 2025-11-13 and 0.3.5 dated 2026-01-21
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 7 ++++++- inst/CITATION | 4 ++-- 4 files changed, 14 insertions(+), 9 deletions(-)
Title: Create Hexagon Sticker in R
Description: Helper functions for creating reproducible hexagon sticker purely in R.
Author: Guangchuang Yu [aut, cre],
Laurent Gatto [ctb],
Johannes Rainer [ctb],
Sebastian Gibb [ctb],
Robert Corty [ctb],
Thomas Neitmann [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between hexSticker versions 0.5.0 dated 2025-09-18 and 0.5.1 dated 2026-01-21
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 5 +++++ R/sticker.R | 6 +++--- 4 files changed, 14 insertions(+), 9 deletions(-)
Title: Handle Air Quality Data from the European Environment Agency
Data Portal
Description: This software downloads and manages air quality data from the European Environmental Agency (EEA) dataflow (<https://www.eea.europa.eu/data-and-maps/data/aqereporting-9>).
See the web page <https://eeadmz1-downloads-webapp.azurewebsites.net/> for details on the EEA's Air Quality Download Service.
The package allows dynamically mapping the stations, summarising and time aggregating the measurements and building spatial interpolation maps.
See the web page <https://www.eea.europa.eu/en> for further information on EEA activities and history.
Further details, as well as, an extended vignette of the main functions included in the package, are available at the GitHub web page dedicated to the project.
Author: Paolo Maranzano [aut, cre, cph] ,
Riccardo Borgoni [aut, cph] ,
Samir Doghmi [aut, cph],
Agostino Tassan Mazzocco [aut, cph]
Maintainer: Paolo Maranzano <pmaranzano.ricercastatistica@gmail.com>
This is a re-admission after prior archival of version 1.0.1 dated 2025-03-20
Diff between EEAaq versions 1.0.1 dated 2025-03-20 and 1.0.2 dated 2026-01-21
DESCRIPTION | 26 ++-- MD5 | 55 ++++---- R/EEAaq_export.R | 8 - R/EEAaq_get_data.R | 277 ++++++++++++++++---------------------------- R/EEAaq_get_stations.R | 3 R/EEAaq_idw_map.R | 45 +++---- R/EEAaq_import.R | 5 R/EEAaq_map_stations.R | 135 +++++++-------------- R/EEAaq_summary.R | 17 +- R/EEAaq_time_aggregate.R | 14 -- R/data.R | 1 R/get_LAU.R | 2 R/get_NUTS.R | 1 R/get_pollutant.R | 6 R/get_stations.R | 56 ++++---- R/globals.R | 13 +- R/handle_dates.R | 13 +- R/is_EEAaq_df.R | 5 build |only inst |only man/EEAaq_export.Rd | 7 - man/EEAaq_get_data.Rd | 5 man/EEAaq_idw_map.Rd | 29 +--- man/EEAaq_import.Rd | 5 man/EEAaq_map_stations.Rd | 29 ++-- man/EEAaq_summary.Rd | 17 -- man/EEAaq_time_aggregate.Rd | 14 -- man/is_EEAaq_df.Rd | 5 vignettes |only 29 files changed, 340 insertions(+), 453 deletions(-)
Title: Distributional Random Forests
Description: An implementation of distributional random forests as introduced in Cevid & Michel & Naf & Meinshausen & Buhlmann (2022) <doi:10.48550/arXiv.2005.14458>.
Author: Jeffrey Naf [cre],
Loris Michel [aut],
Domagoj Cevid [aut]
Maintainer: Jeffrey Naf <jeffrey.naf@unige.ch>
Diff between drf versions 1.2.0 dated 2025-12-08 and 1.3.0 dated 2026-01-21
DESCRIPTION | 8 MD5 | 24 +- R/RcppExports.R | 4 R/analysis_tools.R | 58 ++++- R/drf.R | 19 + R/predict.R | 176 +++++++++++------- man/drf.Rd | 20 +- man/get_sample_weights.Rd | 31 ++- man/predict.drf.Rd | 105 ++++++++++ src/AnalysisToolsBindings.cpp | 108 ++++++++++- src/RcppExports.cpp | 17 + src/src/prediction/collector/SampleWeightComputer.cpp | 13 + src/src/prediction/collector/SampleWeightComputer.h | 4 13 files changed, 477 insertions(+), 110 deletions(-)
Title: Supplements the 'gtsummary' Package for Pharmaceutical Reporting
Description: Tables summarizing clinical trial results are often complex
and require detailed tailoring prior to submission to a health
authority. The 'crane' package supplements the functionality of the
'gtsummary' package for creating these often highly bespoke tables in
the pharmaceutical industry.
Author: Daniel D. Sjoberg [aut] ,
Emily de la Rua [aut] ,
Davide Garolini [aut] ,
Abinaya Yogasekaram [ctb] ,
Joe Zhu [cre] ,
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Joe Zhu <joe.zhu@roche.com>
Diff between crane versions 0.3.0 dated 2025-12-06 and 0.3.1 dated 2026-01-21
DESCRIPTION | 47 ++++--- MD5 | 40 ++++-- NAMESPACE | 138 +++++++++++++--------- NEWS.md | 12 + R/annotate_gg_km.R |only R/as_ggplot.R |only R/crane-package.R | 49 ++++--- R/forest.R |only R/get_cox_pairwise_df.R |only R/gg_km.R |only R/gg_km_utils.R |only R/tbl_null_report.R | 61 ++++----- R/tbl_roche_subgroups.R |only README.md | 116 +++++++++--------- inst/WORDLIST | 57 +++++---- man/annotate_gg_km.Rd |only man/as_ggplot.Rd |only man/crane-package.Rd | 9 - man/df2gg.Rd |only man/extract_plot_data.Rd |only man/g_forest.Rd |only man/get_cox_pairwise_df.Rd |only man/gg_forest_plot.Rd |only man/gg_km.Rd |only man/h_tbl_median_surv.Rd |only man/h_xticks.Rd |only man/tbl_roche_subgroups.Rd |only tests/testthat/test-add_blank_rows.R | 210 +++++++++++++++++----------------- tests/testthat/test-forestplot.R |only tests/testthat/test-gg_km.R |only tests/testthat/test-tbl_null_report.R | 30 ++-- 31 files changed, 427 insertions(+), 342 deletions(-)
Title: Optimal Pairing and Matching via Linear Assignment
Description: Solves optimal pairing and matching problems using linear assignment
algorithms. Provides implementations of the Hungarian method (Kuhn 1955)
<doi:10.1002/nav.3800020109>, Jonker-Volgenant shortest path algorithm
(Jonker and Volgenant 1987) <doi:10.1007/BF02278710>, Auction algorithm
(Bertsekas 1988) <doi:10.1007/BF02186476>, cost-scaling
(Goldberg and Kennedy 1995) <doi:10.1007/BF01585996>, scaling algorithms
(Gabow and Tarjan 1989) <doi:10.1137/0218069>, push-relabel (Goldberg and
Tarjan 1988) <doi:10.1145/48014.61051>, and Sinkhorn entropy-regularized
transport (Cuturi 2013) <doi:10.48550/arxiv.1306.0895>. Designed for
matching plots, sites, samples, or any pairwise optimization problem.
Supports rectangular matrices, forbidden assignments, data frame inputs,
batch solving, k-best solutions, and pixel-level image morphing for
visualization. Includes automatic preprocessing with variable health
checks, multiple scaling methods (standardized, [...truncated...]
Author: Gilles Colling [aut, cre, cph]
Maintainer: Gilles Colling <gilles.colling051@gmail.com>
Diff between couplr versions 1.0.6 dated 2026-01-20 and 1.0.8 dated 2026-01-21
DESCRIPTION | 6 MD5 | 54 - NEWS.md | 14 R/matching_diagnostics.R | 6 R/matching_parallel.R | 12 R/matching_preprocessing.R | 4 inst/CITATION | 2 inst/doc/algorithms.Rmd | 49 + inst/doc/algorithms.html | 227 ++++---- inst/doc/comparison.R | 4 inst/doc/comparison.Rmd | 55 + inst/doc/comparison.html | 207 ++++--- inst/doc/getting-started.Rmd | 883 ++++++++++++++++---------------- inst/doc/getting-started.html | 44 - inst/doc/matching-workflows.R | 6 inst/doc/matching-workflows.Rmd | 119 ++++ inst/doc/matching-workflows.html | 413 ++++++++------ inst/doc/pixel-morphing.Rmd | 56 ++ inst/doc/pixel-morphing.html | 304 +++++------ inst/doc/troubleshooting.Rmd | 8 inst/doc/troubleshooting.html | 41 - src/gabow_tarjan/utils_gabow_tarjan.cpp | 11 vignettes/algorithms.Rmd | 49 + vignettes/comparison.Rmd | 55 + vignettes/getting-started.Rmd | 883 ++++++++++++++++---------------- vignettes/matching-workflows.Rmd | 119 ++++ vignettes/pixel-morphing.Rmd | 56 ++ vignettes/troubleshooting.Rmd | 8 28 files changed, 2174 insertions(+), 1521 deletions(-)
Title: Functions to Fit Cell Volume Distributions and Thereby Estimate
Cell Growth Rates and Division Times
Description: Implements a methodology for using cell volume
distributions to estimate cell growth rates and division times
that is described in the paper, "Cell Volume Distributions
Reveal Cell Growth Rates and Division Times", by Michael
Halter, John T. Elliott, Joseph B. Hubbard, Alessandro Tona
and Anne L. Plant, which appeared in the Journal of Theoretical
Biology. In order to reproduce the analysis used to obtain
Table 1 in the paper, execute the command
"example(fitVolDist)".
Author: Katharine M. Mullen [aut, cre],
Michael Halter [aut],
John Lu [aut],
Nathan Dodder [aut]
Maintainer: Katharine M. Mullen <katharine.mullen@stat.ucla.edu>
Diff between cellVolumeDist versions 1.4 dated 2022-04-24 and 1.5 dated 2026-01-21
DESCRIPTION | 36 ++++++++++++++++++++++-------- MD5 | 6 ++--- man/A10_vSMC_volume_data.Rd | 52 ++++++++++++++++++++++---------------------- man/NIH3T3_volume_data.Rd | 18 +++++++-------- 4 files changed, 64 insertions(+), 48 deletions(-)
More information about cellVolumeDist at CRAN
Permanent link
Title: Random Generation Functionality for the 'spatstat' Family
Description: Functionality for random generation of spatial data in the 'spatstat' family of packages.
Generates random spatial patterns of points according to many simple rules (complete spatial randomness,
Poisson, binomial, random grid, systematic, cell), randomised alteration of patterns
(thinning, random shift, jittering), simulated realisations of random point processes including
simple sequential inhibition, Matern inhibition models, Neyman-Scott cluster processes
(using direct, Brix-Kendall, or hybrid algorithms),
log-Gaussian Cox processes, product shot noise cluster processes
and Gibbs point processes (using Metropolis-Hastings birth-death-shift algorithm,
alternating Gibbs sampler, or coupling-from-the-past perfect simulation).
Also generates random spatial patterns of line segments,
random tessellations, and random images (random noise, random mosaics).
Excludes random generation on a linear network,
which is covered by the separate package 'spatstat.linnet'.
Author: Adrian Baddeley [aut, cre, cph] ,
Rolf Turner [aut, cph] ,
Ege Rubak [aut, cph] ,
Tilman Davies [aut, cph] ,
Kasper Klitgaard Berthelsen [ctb, cph],
David Bryant [ctb, cph],
Ya-Mei Chang [ctb, cph],
Ute Hahn [ctb],
Abdollah Jalilian [ctb],
Dominic Sc [...truncated...]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.random versions 3.4-3 dated 2025-11-21 and 3.4-4 dated 2026-01-21
spatstat.random-3.4-3/spatstat.random/R/pkgRandomFields.R |only spatstat.random-3.4-4/spatstat.random/DESCRIPTION | 18 +++---- spatstat.random-3.4-4/spatstat.random/MD5 | 24 +++++----- spatstat.random-3.4-4/spatstat.random/NAMESPACE | 3 - spatstat.random-3.4-4/spatstat.random/NEWS | 12 +++++ spatstat.random-3.4-4/spatstat.random/R/kraever.R |only spatstat.random-3.4-4/spatstat.random/R/randomseg.R | 4 + spatstat.random-3.4-4/spatstat.random/inst/doc/packagesizes.txt | 1 spatstat.random-3.4-4/spatstat.random/inst/info/packagesizes.txt | 1 spatstat.random-3.4-4/spatstat.random/man/rMaternI.Rd | 8 ++- spatstat.random-3.4-4/spatstat.random/man/rMaternII.Rd | 9 ++- spatstat.random-3.4-4/spatstat.random/man/rjitter.psp.Rd | 3 - spatstat.random-3.4-4/spatstat.random/man/spatstat.random-internal.Rd | 8 --- spatstat.random-3.4-4/spatstat.random/man/spatstat.random-package.Rd | 8 ++- 14 files changed, 60 insertions(+), 39 deletions(-)
More information about spatstat.random at CRAN
Permanent link
Title: Embed 'SWI'-'Prolog'
Description: Interface to 'SWI'-'Prolog', <https://www.swi-prolog.org/>. This package is normally not loaded directly, please refer to package 'rolog' instead. The purpose of this package is to provide the 'Prolog' runtime on systems that do not have a software installation of 'SWI'-'Prolog'.
Author: Matthias Gondan [aut, com, cre] ,
Jan Wielemaker [ctb, cph] ,
European Commission [fnd]
Maintainer: Matthias Gondan <Matthias.Gondan-Rochon@uibk.ac.at>
Diff between rswipl versions 10.1.1 dated 2026-01-08 and 10.1.1.1 dated 2026-01-21
rswipl-10.1.1.1/rswipl/DESCRIPTION | 8 rswipl-10.1.1.1/rswipl/MD5 | 181 ++--- rswipl-10.1.1.1/rswipl/NEWS.md | 4 rswipl-10.1.1.1/rswipl/src/swipl-devel/boot/tabling.pl | 4 rswipl-10.1.1.1/rswipl/src/swipl-devel/boot/toplevel.pl | 3 rswipl-10.1.1.1/rswipl/src/swipl-devel/library/check_installation.pl | 2 rswipl-10.1.1.1/rswipl/src/swipl-devel/library/prolog_deps.pl | 63 + rswipl-10.1.1.1/rswipl/src/swipl-devel/packages/cpp/test_cpp.cpp | 2 rswipl-10.1.1.1/rswipl/src/swipl-devel/packages/xpce/cmake/XPCESources.cmake | 2 rswipl-10.1.1.1/rswipl/src/swipl-devel/packages/xpce/man/reference/class/graphical.doc |binary rswipl-10.1.1.1/rswipl/src/swipl-devel/packages/xpce/prolog/lib/emacs/emacs.pl | 3 rswipl-10.1.1.1/rswipl/src/swipl-devel/packages/xpce/prolog/lib/emacs/fundamental_mode.pl | 3 rswipl-10.1.1.1/rswipl/src/swipl-devel/packages/xpce/prolog/lib/emacs/markdown_mode.pl |only rswipl-10.1.1.1/rswipl/src/swipl-devel/packages/xpce/prolog/lib/emacs/prolog_mode.pl | 9 rswipl-10.1.1.1/rswipl/src/swipl-devel/packages/xpce/prolog/lib/man/v_manual.pl | 9 rswipl-10.1.1.1/rswipl/src/swipl-devel/packages/xpce/prolog/lib/swi/pce_profile.pl | 8 rswipl-10.1.1.1/rswipl/src/swipl-devel/packages/xpce/src/ker/error.c | 48 - rswipl-10.1.1.1/rswipl/src/swipl-devel/packages/xpce/src/sdl/sdldraw.c | 2 rswipl-10.1.1.1/rswipl/src/swipl-devel/packages/xpce/src/txt/terminal.c | 19 rswipl-10.1.1.1/rswipl/src/swipl-devel/scripts/configure | 3 rswipl-10.1.1.1/rswipl/src/swipl-devel/src/CMakeLists.txt | 32 rswipl-10.1.1.1/rswipl/src/swipl-devel/src/SWI-Prolog.h | 4 rswipl-10.1.1.1/rswipl/src/swipl-devel/src/minizip/unzip.c | 2 rswipl-10.1.1.1/rswipl/src/swipl-devel/src/minizip/unzip.h | 2 rswipl-10.1.1.1/rswipl/src/swipl-devel/src/minizip/zip.c | 16 rswipl-10.1.1.1/rswipl/src/swipl-devel/src/minizip/zip.h | 10 rswipl-10.1.1.1/rswipl/src/swipl-devel/src/mkvmi.c | 2 rswipl-10.1.1.1/rswipl/src/swipl-devel/src/os/dtoa.c | 2 rswipl-10.1.1.1/rswipl/src/swipl-devel/src/os/pl-file.c | 2 rswipl-10.1.1.1/rswipl/src/swipl-devel/src/os/pl-files.c | 2 rswipl-10.1.1.1/rswipl/src/swipl-devel/src/os/pl-fmt.c | 30 rswipl-10.1.1.1/rswipl/src/swipl-devel/src/os/pl-fmt.h | 2 rswipl-10.1.1.1/rswipl/src/swipl-devel/src/os/pl-glob.c | 7 rswipl-10.1.1.1/rswipl/src/swipl-devel/src/os/pl-os.c | 11 rswipl-10.1.1.1/rswipl/src/swipl-devel/src/os/pl-stream.c | 4 rswipl-10.1.1.1/rswipl/src/swipl-devel/src/os/pl-tai.c | 24 rswipl-10.1.1.1/rswipl/src/swipl-devel/src/pl-alloc.c | 2 rswipl-10.1.1.1/rswipl/src/swipl-devel/src/pl-alloc.h | 2 rswipl-10.1.1.1/rswipl/src/swipl-devel/src/pl-arith.c | 4 rswipl-10.1.1.1/rswipl/src/swipl-devel/src/pl-arith.h | 2 rswipl-10.1.1.1/rswipl/src/swipl-devel/src/pl-comp.c | 328 +++++----- rswipl-10.1.1.1/rswipl/src/swipl-devel/src/pl-comp.h | 14 rswipl-10.1.1.1/rswipl/src/swipl-devel/src/pl-cont.c | 6 rswipl-10.1.1.1/rswipl/src/swipl-devel/src/pl-copyterm.c | 36 - rswipl-10.1.1.1/rswipl/src/swipl-devel/src/pl-copyterm.h | 2 rswipl-10.1.1.1/rswipl/src/swipl-devel/src/pl-debug.c | 8 rswipl-10.1.1.1/rswipl/src/swipl-devel/src/pl-debug.h | 1 rswipl-10.1.1.1/rswipl/src/swipl-devel/src/pl-dict.c | 111 +-- rswipl-10.1.1.1/rswipl/src/swipl-devel/src/pl-dict.h | 6 rswipl-10.1.1.1/rswipl/src/swipl-devel/src/pl-error.c | 2 rswipl-10.1.1.1/rswipl/src/swipl-devel/src/pl-error.h | 2 rswipl-10.1.1.1/rswipl/src/swipl-devel/src/pl-event.c | 57 - rswipl-10.1.1.1/rswipl/src/swipl-devel/src/pl-event.h | 17 rswipl-10.1.1.1/rswipl/src/swipl-devel/src/pl-fli.c | 12 rswipl-10.1.1.1/rswipl/src/swipl-devel/src/pl-funct.c | 3 rswipl-10.1.1.1/rswipl/src/swipl-devel/src/pl-gc.c | 62 + rswipl-10.1.1.1/rswipl/src/swipl-devel/src/pl-gc.h | 14 rswipl-10.1.1.1/rswipl/src/swipl-devel/src/pl-global.h | 4 rswipl-10.1.1.1/rswipl/src/swipl-devel/src/pl-gmp.c | 22 rswipl-10.1.1.1/rswipl/src/swipl-devel/src/pl-incl.h | 99 ++- rswipl-10.1.1.1/rswipl/src/swipl-devel/src/pl-index.c | 30 rswipl-10.1.1.1/rswipl/src/swipl-devel/src/pl-init.c | 2 rswipl-10.1.1.1/rswipl/src/swipl-devel/src/pl-prims.c | 244 +++---- rswipl-10.1.1.1/rswipl/src/swipl-devel/src/pl-prims.h | 22 rswipl-10.1.1.1/rswipl/src/swipl-devel/src/pl-pro.c | 2 rswipl-10.1.1.1/rswipl/src/swipl-devel/src/pl-proc.c | 27 rswipl-10.1.1.1/rswipl/src/swipl-devel/src/pl-proc.h | 4 rswipl-10.1.1.1/rswipl/src/swipl-devel/src/pl-prof.c | 44 - rswipl-10.1.1.1/rswipl/src/swipl-devel/src/pl-prof.h | 2 rswipl-10.1.1.1/rswipl/src/swipl-devel/src/pl-qlf.c | 54 - rswipl-10.1.1.1/rswipl/src/swipl-devel/src/pl-read.c | 17 rswipl-10.1.1.1/rswipl/src/swipl-devel/src/pl-rec.c | 30 rswipl-10.1.1.1/rswipl/src/swipl-devel/src/pl-segstack.h | 2 rswipl-10.1.1.1/rswipl/src/swipl-devel/src/pl-setup.c | 2 rswipl-10.1.1.1/rswipl/src/swipl-devel/src/pl-srcfile.c | 22 rswipl-10.1.1.1/rswipl/src/swipl-devel/src/pl-srcfile.h | 8 rswipl-10.1.1.1/rswipl/src/swipl-devel/src/pl-supervisor.c | 6 rswipl-10.1.1.1/rswipl/src/swipl-devel/src/pl-tabling.c | 42 - rswipl-10.1.1.1/rswipl/src/swipl-devel/src/pl-tabling.h | 6 rswipl-10.1.1.1/rswipl/src/swipl-devel/src/pl-termhash.c | 9 rswipl-10.1.1.1/rswipl/src/swipl-devel/src/pl-thread.c | 6 rswipl-10.1.1.1/rswipl/src/swipl-devel/src/pl-trace.c | 38 - rswipl-10.1.1.1/rswipl/src/swipl-devel/src/pl-trie.c | 4 rswipl-10.1.1.1/rswipl/src/swipl-devel/src/pl-variant.c | 30 rswipl-10.1.1.1/rswipl/src/swipl-devel/src/pl-vmi.c | 6 rswipl-10.1.1.1/rswipl/src/swipl-devel/src/pl-wam.c | 45 - rswipl-10.1.1.1/rswipl/src/swipl-devel/src/pl-wam.h | 4 rswipl-10.1.1.1/rswipl/src/swipl-devel/src/pl-write.c | 7 rswipl-10.1.1.1/rswipl/src/swipl-devel/src/pl-zip.c | 2 rswipl-10.1.1.1/rswipl/src/swipl-devel/tests/core/test_format.pl | 26 rswipl-10.1.1/rswipl/inst/swipl |only rswipl-10.1.1/rswipl/src/swipl-devel/packages/clib/process.c.rej |only rswipl-10.1.1/rswipl/src/swipl-devel/packages/cpp/test_cpp.cpp.rej |only rswipl-10.1.1/rswipl/src/swipl-devel/packages/cpp/test_cpp.pl.rej |only 94 files changed, 1115 insertions(+), 969 deletions(-)
Title: Plot Raster Map Tiles from Open Street Map and Other Sources
Description: Download and plot Open Street Map <https://www.openstreetmap.org/>,
Bing Maps <https://www.bing.com/maps> and other tiled map sources. Use to create
basemaps quickly and add hillshade to vector-based maps.
Author: Dewey Dunnington [aut, cre] ,
Timothee Giraud [ctb]
Maintainer: Dewey Dunnington <dewey@fishandwhistle.net>
Diff between rosm versions 0.3.0 dated 2023-08-27 and 0.3.1 dated 2026-01-21
DESCRIPTION | 11 ++++++----- MD5 | 10 +++++----- NEWS.md | 7 +++++++ R/url.R | 2 +- man/osm_url_spec.Rd | 2 +- tests/testthat/test-deprecated.R | 8 +++++++- 6 files changed, 27 insertions(+), 13 deletions(-)
Title: An Interface to the Nexus Class Library
Description: An interface to the Nexus Class Library which allows parsing
of NEXUS, Newick and other phylogenetic tree file formats. It provides
elements of the file that can be used to build phylogenetic objects
such as ape's 'phylo' or phylobase's 'phylo4(d)'. This functionality
is demonstrated with 'read_newick_phylo()' and 'read_nexus_phylo()'.
Author: Francois Michonneau [aut, cre] ,
Ben Bolker [aut] ,
Mark Holder [aut] ,
Paul Lewis [aut] ,
Brian O'Meara [aut]
Maintainer: Francois Michonneau <francois.michonneau@gmail.com>
Diff between rncl versions 0.8.8 dated 2025-12-08 and 0.8.9 dated 2026-01-21
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 4 ++++ README.md | 17 +---------------- build/partial.rdb |binary src/ncl/nxscharactersblock.h | 13 +++++++------ src/nxscharactersblock.cpp | 23 +++++++++++------------ 7 files changed, 32 insertions(+), 43 deletions(-)
Title: Read 'Bibtex' Files and Convert Between Bibliography Formats
Description: Read and write 'Bibtex' files. Convert between bibliography
formats, including 'Bibtex', 'Biblatex', 'PubMed', 'Endnote', and
'Bibentry'. Includes a port of the 'bibutils' utilities by Chris
Putnam <https://sourceforge.net/projects/bibutils/>. Supports all
bibliography formats and character encodings implemented in
'bibutils'.
Author: Georgi N. Boshnakov [aut, cre] ),
Chris Putman [aut] ,
Richard Mathar [ctb] ,
Johannes Wilm [ctb] ,
R Core Team [ctb]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>
Diff between rbibutils versions 2.4 dated 2025-11-07 and 2.4.1 dated 2026-01-21
rbibutils-2.4.1/rbibutils/DESCRIPTION | 19 ++-- rbibutils-2.4.1/rbibutils/MD5 | 47 +++++----- rbibutils-2.4.1/rbibutils/NAMESPACE | 5 - rbibutils-2.4.1/rbibutils/NEWS.md | 17 +++ rbibutils-2.4.1/rbibutils/R/bib.R | 44 ++++----- rbibutils-2.4.1/rbibutils/R/bibentry.R | 47 +++++++++- rbibutils-2.4.1/rbibutils/build/partial.rdb |binary rbibutils-2.4.1/rbibutils/inst/REFERENCES.bib | 8 + rbibutils-2.4.1/rbibutils/inst/doc/rbibutils.Rnw | 2 rbibutils-2.4.1/rbibutils/inst/doc/rbibutils.pdf |binary rbibutils-2.4.1/rbibutils/man/bibstyle_JSSextra.Rd |only rbibutils-2.4.1/rbibutils/src/name.c | 28 +++++ rbibutils-2.4.1/rbibutils/tests/testthat/test-https.R | 6 - rbibutils-2.4.1/rbibutils/tests/testthat/xampl2biblatex.rds |binary rbibutils-2.4.1/rbibutils/tests/testthat/xampl2biblatex.rds_sav4 |only rbibutils-2.4.1/rbibutils/tests/testthat/xampl_1.rds |binary rbibutils-2.4.1/rbibutils/tests/testthat/xampl_1.rds_sav4 |only rbibutils-2.4.1/rbibutils/tests/testthat/xampl_bbl2bib.rds |binary rbibutils-2.4.1/rbibutils/tests/testthat/xampl_bbl2bib.rds_sav4 |only rbibutils-2.4.1/rbibutils/tests/testthat/xampl_bib2ads.rds |binary rbibutils-2.4.1/rbibutils/tests/testthat/xampl_bib2ads.rds_sav4 |only rbibutils-2.4.1/rbibutils/tests/testthat/xampl_bib2end.rds |binary rbibutils-2.4.1/rbibutils/tests/testthat/xampl_bib2end.rds_sav4 |only rbibutils-2.4.1/rbibutils/tests/testthat/xampl_bib2isi.rds |binary rbibutils-2.4.1/rbibutils/tests/testthat/xampl_bib2isi.rds_sav4 |only rbibutils-2.4.1/rbibutils/tests/testthat/xampl_isi2bib.rds |binary rbibutils-2.4.1/rbibutils/tests/testthat/xampl_isi2bib.rds_sav4 |only rbibutils-2.4.1/rbibutils/vignettes/rbibutils.Rnw | 2 rbibutils-2.4/rbibutils/man/register_JSSextra.Rd |only 29 files changed, 162 insertions(+), 63 deletions(-)
Title: Functions to Make Surveys Processing Easier
Description: Set of functions to make the processing and analysis of
surveys easier : interactive shiny apps and addins for data recoding,
contingency tables, dataset metadata handling, and several convenience
functions.
Author: Julien Barnier [aut, cre],
Francois Briatte [aut],
Joseph Larmarange [aut]
Maintainer: Julien Barnier <julien.barnier@cnrs.fr>
Diff between questionr versions 0.8.1 dated 2025-06-10 and 0.8.2 dated 2026-01-21
DESCRIPTION | 6 - MD5 | 10 +-- NEWS.md | 4 + build/vignette.rds |binary inst/doc/recoding_addins.html | 4 - tests/testthat/test_tables.R | 127 +++++++++++++++++++++++++++++++----------- 6 files changed, 110 insertions(+), 41 deletions(-)
Title: Identify Characteristics of Patients in the OMOP Common Data
Model
Description: Identify the characteristics of patients in data mapped to the
Observational Medical Outcomes Partnership (OMOP) common data model.
Author: Marti Catala [aut, cre] ,
Yuchen Guo [aut] ,
Mike Du [aut] ,
Kim Lopez-Guell [aut] ,
Edward Burn [aut] ,
Nuria Mercade-Besora [aut] ,
Xintong Li [ctb] ,
Xihang Chen [ctb]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>
Diff between PatientProfiles versions 1.4.4 dated 2025-10-29 and 1.4.5 dated 2026-01-21
DESCRIPTION | 8 MD5 | 40 +- NEWS.md | 13 R/addDemographics.R | 3 R/addDemographicsQuery.R | 3 R/checks.R | 120 ++++++- R/formats.R | 16 - R/summariseResult.R | 518 +++++++++++++++++----------------- R/sysdata.rda |binary inst/doc/cohort-intersect.html | 90 ++--- inst/doc/concept-intersect.html | 92 +++--- inst/doc/demographics.html | 234 +++++++-------- inst/doc/summarise.html | 244 ++++++++++------ inst/doc/table-intersect.html | 92 +++--- man/addInObservation.Rd | 3 man/addInObservationQuery.Rd | 3 man/summariseResult.Rd | 21 + man/variableTypes.Rd | 8 tests/testthat/test-checks.R | 4 tests/testthat/test-format.R | 29 - tests/testthat/test-summariseResult.R | 329 +++++++++++++++++++-- 21 files changed, 1155 insertions(+), 715 deletions(-)
More information about PatientProfiles at CRAN
Permanent link
Title: Convenient Access to NYC Open Data API Endpoints
Description: Provides a unified set of helper functions to access datasets
from the NYC Open Data platform <https://opendata.cityofnewyork.us/>.
Functions return results as tidy tibbles and support optional filtering,
sorting, and row limits via the Socrata API. The package includes endpoints
for 311 service requests, DOB job applications, juvenile justice metrics,
school safety, environmental data, event permitting, and additional
citywide datasets.
Author: Christian Martinez [aut, cre]
Maintainer: Christian Martinez <c.martinez0@outlook.com>
Diff between nycOpenData versions 0.1.3 dated 2026-01-09 and 0.1.4 dated 2026-01-21
DESCRIPTION | 8 - MD5 | 149 ++++++++++----------- NEWS.md | 13 + R/nyc_311.R | 68 +++++++-- R/nyc_any_dataset.R | 21 +- R/nyc_borough_community_report.R | 25 +-- R/nyc_cause_of_death.R | 25 +-- R/nyc_city_record.R | 25 +-- R/nyc_civil_service_list.R | 25 +-- R/nyc_daily_attendance_2018_2019.R | 26 +-- R/nyc_detention_admissions.R | 25 +-- R/nyc_dhs_daily_report.R | 30 ++-- R/nyc_dob_job_applications.R | 25 +-- R/nyc_dob_permit_issuance.R | 25 +-- R/nyc_domestic_violence_annual_report.R | 26 +-- R/nyc_dop_Juvenile_cases.R | 25 +-- R/nyc_dop_juvenile_rearrest_rate.R | 25 +-- R/nyc_film_permits.R | 29 ++-- R/nyc_for_hire_vehicles.R | 25 +-- R/nyc_homeless_drop_in_centers.R | 25 +-- R/nyc_homeless_population_by_year.R | 25 +-- R/nyc_medallion_drivers_active.R | 32 ++-- R/nyc_medallion_drivers_authorized.R | 28 ++- R/nyc_motor_vehicle_collisions_crashes.R | 25 +-- R/nyc_museum_locations.R | 26 +-- R/nyc_nypd_hate_crimes.R | 25 +-- R/nyc_open_parking_camera_violations.R | 26 +-- R/nyc_period_attendance_reporting.R | 26 +-- R/nyc_permit_events_historic.R | 30 +--- R/nyc_pets_in_shelters.R | 25 +-- R/nyc_restaurant_inspection_results.R | 25 +-- R/nyc_runaway_and_homeless_youth_daily_census.R | 25 +-- R/nyc_school_discharge.R | 25 +-- R/nyc_school_discharge_report_2013_2015.R | 29 ++-- R/nyc_street_hail_livery_active.R | 28 ++- R/nyc_tlc_new_driver_app_status.R | 25 +-- R/nyc_tree_census_2015.R | 25 +-- R/nyc_urban_park_animal_condition.R | 24 +-- R/nyc_violent_disruptive_school_incidents.R | 25 +-- R/utils_request.R |only man/nyc_311.Rd | 19 +- man/nyc_any_dataset.Rd | 18 +- man/nyc_borough_community_report.Rd | 20 +- man/nyc_cause_of_death.Rd | 20 +- man/nyc_city_record.Rd | 20 +- man/nyc_civil_service_list.Rd | 20 +- man/nyc_daily_attendance_2018_2019.Rd | 24 ++- man/nyc_detention_admissions.Rd | 20 +- man/nyc_dhs_daily_report.Rd | 23 ++- man/nyc_dob_job_applications.Rd | 19 +- man/nyc_dob_permit_issuance.Rd | 20 +- man/nyc_domestic_violence_annual_report.Rd | 24 ++- man/nyc_dop_Juvenile_cases.Rd | 20 +- man/nyc_dop_juvenile_rearrest_rate.Rd | 24 ++- man/nyc_film_permits.Rd | 23 ++- man/nyc_for_hire_vehicles.Rd | 20 +- man/nyc_homeless_drop_in_centers.Rd | 20 +- man/nyc_homeless_population_by_year.Rd | 24 ++- man/nyc_medallion_drivers_active.Rd | 26 ++- man/nyc_medallion_drivers_authorized.Rd | 27 ++- man/nyc_motor_vehicle_collisions_crashes.Rd | 24 ++- man/nyc_museum_locations.Rd | 20 +- man/nyc_nypd_hate_crimes.Rd | 20 +- man/nyc_open_parking_camera_violations.Rd | 24 ++- man/nyc_period_attendance_reporting.Rd | 24 ++- man/nyc_permit_events_historic.Rd | 24 +-- man/nyc_pets_in_shelters.Rd | 20 +- man/nyc_restaurant_inspection_results.Rd | 24 ++- man/nyc_runaway_and_homeless_youth_daily_census.Rd | 24 ++- man/nyc_school_discharge.Rd | 20 +- man/nyc_school_discharge_report_2013_2015.Rd | 27 ++- man/nyc_street_hail_livery_active.Rd | 26 ++- man/nyc_tlc_new_driver_app_status.Rd | 24 ++- man/nyc_tree_census_2015.Rd | 20 +- man/nyc_urban_park_animal_condition.Rd | 24 ++- man/nyc_violent_disruptive_school_incidents.Rd | 24 ++- 76 files changed, 1183 insertions(+), 761 deletions(-)
Title: Multivariate (Dynamic) Generalized Additive Models
Description: Fit Bayesian Dynamic Generalized Additive Models to multivariate observations. Users can build nonlinear State-Space models that can incorporate semiparametric effects in observation and process components, using a wide range of observation families. Estimation is performed using Markov Chain Monte Carlo with Hamiltonian Monte Carlo in the software 'Stan'. References: Clark & Wells (2023) <doi:10.1111/2041-210X.13974>.
Author: Nicholas J Clark [aut, cre] ,
KANK Karunarathna [ctb] ,
Sarah Heaps [ctb] ,
Scott Pease [ctb] ,
Matthijs Hollanders [ctb]
Maintainer: Nicholas J Clark <nicholas.j.clark1214@gmail.com>
Diff between mvgam versions 1.1.593 dated 2025-09-05 and 1.1.594 dated 2026-01-21
DESCRIPTION | 8 MD5 | 252 ++-- NEWS.md | 3 R/as.data.frame.mvgam.R | 2 R/backends.R | 2080 ++++++++++++++++++------------------ R/conditional_effects.R | 2 R/dynamic.R | 334 ++--- R/ensemble.R | 464 ++++---- R/evaluate_mvgams.R | 34 R/families.R | 2 R/fevd.mvgam.R | 346 ++--- R/forecast.mvgam.R | 2 R/get_mvgam_priors.R | 2 R/gratia_methods.R | 2 R/hindcast.mvgam.R | 2 R/how_to_cite.R | 2 R/index-mvgam.R | 544 ++++----- R/irf.mvgam.R | 2 R/jsdgam.R | 12 R/lfo_cv.mvgam.R | 894 +++++++-------- R/logLik.mvgam.R | 2 R/loo.mvgam.R | 2 R/lv_correlations.R | 248 ++-- R/mcmc_plot.mvgam.R | 2 R/monotonic.R | 2 R/mvgam.R | 10 R/mvgam_diagnostics.R | 2 R/mvgam_trend_types.R | 10 R/ordinate.jsdgam.R | 666 +++++------ R/pairs.mvgam.R | 2 R/plot.mvgam.R | 696 ++++++------ R/plot_mvgam_factors.R | 316 ++--- R/plot_mvgam_fc.R | 1976 +++++++++++++++++----------------- R/plot_mvgam_resids.R | 504 ++++---- R/plot_mvgam_trend.R | 846 +++++++------- R/posterior_epred.mvgam.R | 8 R/ppc.mvgam.R | 6 R/predict.mvgam.R | 2 R/residual_cor.R | 649 +++++------ R/residuals.mvgam.R | 2 R/score.mvgam_forecast.R | 2 R/stability.R | 596 +++++----- R/stan_utils.R | 2 R/summary.mvgam.R | 8 R/tidier_methods.R | 1053 +++++++++--------- R/update.mvgam.R | 2 README.md | 24 inst/doc/data_in_mvgam.R | 81 - inst/doc/data_in_mvgam.Rmd | 872 +++++++-------- inst/doc/data_in_mvgam.html | 201 +-- inst/doc/forecast_evaluation.R | 59 - inst/doc/forecast_evaluation.html | 446 +++---- inst/doc/mvgam_overview.R | 114 - inst/doc/mvgam_overview.html | 591 +++++----- inst/doc/nmixtures.R | 58 - inst/doc/nmixtures.html | 187 +-- inst/doc/shared_states.R | 51 inst/doc/shared_states.Rmd | 2 inst/doc/shared_states.html | 265 ++-- inst/doc/time_varying_effects.R | 72 - inst/doc/time_varying_effects.Rmd | 2 inst/doc/time_varying_effects.html | 327 ++--- inst/doc/trend_formulas.R | 98 - inst/doc/trend_formulas.Rmd | 2 inst/doc/trend_formulas.html | 426 +++---- man/RW.Rd | 2 man/ZMVN.Rd | 6 man/augment.mvgam.Rd | 2 man/code.Rd | 2 man/conditional_effects.mvgam.Rd | 2 man/dynamic.Rd | 2 man/ensemble.mvgam_forecast.Rd | 2 man/evaluate_mvgams.Rd | 34 man/fevd.mvgam.Rd | 2 man/fitted.mvgam.Rd | 2 man/forecast.mvgam.Rd | 2 man/get_mvgam_priors.Rd | 2 man/gratia_mvgam_enhancements.Rd | 2 man/hindcast.mvgam.Rd | 2 man/how_to_cite.mvgam.Rd | 2 man/index-mvgam.Rd | 2 man/irf.mvgam.Rd | 2 man/jsdgam.Rd | 8 man/lfo_cv.mvgam.Rd | 2 man/logLik.mvgam.Rd | 2 man/loo.mvgam.Rd | 2 man/lv_correlations.Rd | 6 man/mcmc_plot.mvgam.Rd | 2 man/monotonic.Rd | 2 man/mvgam.Rd | 6 man/mvgam_diagnostics.Rd | 2 man/mvgam_draws.Rd | 2 man/mvgam_families.Rd | 2 man/mvgam_use_cases.Rd | 114 - man/ordinate.jsdgam.Rd | 2 man/pairs.mvgam.Rd | 2 man/piecewise_trends.Rd | 2 man/plot.mvgam.Rd | 2 man/plot_mvgam_factors.Rd | 2 man/plot_mvgam_forecasts.Rd | 2 man/plot_mvgam_resids.Rd | 2 man/plot_mvgam_trend.Rd | 2 man/posterior_epred.mvgam.Rd | 2 man/posterior_linpred.mvgam.Rd | 2 man/posterior_predict.mvgam.Rd | 2 man/pp_check.mvgam.Rd | 2 man/ppc.mvgam.Rd | 2 man/predict.mvgam.Rd | 2 man/residual_cor.jsdgam.Rd | 9 man/residuals.mvgam.Rd | 2 man/score.mvgam_forecast.Rd | 2 man/stability.mvgam.Rd | 2 man/summary.mvgam.Rd | 2 man/update.mvgam.Rd | 2 tests/testthat/test-RW.R | 964 ++++++++-------- tests/testthat/test-binomial.R | 10 tests/testthat/test-dynamic.R | 406 +++---- tests/testthat/test-gp.R | 976 ++++++++-------- tests/testthat/test-jsdgam.R | 22 tests/testthat/test-mvgam-methods.R | 2 tests/testthat/test-mvgam.R | 32 tests/testthat/test-mvgam_priors.R | 10 tests/testthat/test-offset.R | 6 vignettes/data_in_mvgam.Rmd | 872 +++++++-------- vignettes/shared_states.Rmd | 2 vignettes/time_varying_effects.Rmd | 2 vignettes/trend_formulas.Rmd | 2 127 files changed, 9979 insertions(+), 10075 deletions(-)
Title: Easily Apply Formats to Data
Description: Contains a set of functions that can be used to apply
formats to data frames or vectors. The package aims to provide
functionality similar to that of SAS® formats. Formats are assigned to
the format attribute on data frame columns. Then when the fdata()
function is called, a new data frame is created with the column data
formatted as specified. The package also contains a value() function
to create a user-defined format, similar to a SAS® user-defined format.
Author: David Bosak [aut, cre],
Chen Ling [aut]
Maintainer: David Bosak <dbosak01@gmail.com>
Diff between fmtr versions 1.7.0 dated 2025-11-26 and 1.7.1 dated 2026-01-21
DESCRIPTION | 9 +- MD5 | 26 +++--- NEWS.md | 5 + R/fapply.R | 169 +++++++++++++++++++++++++++++++++++++++-- R/fmtr.R | 22 +++++ R/timewd.R |only inst/doc/fmtr-convenience.html | 4 inst/doc/fmtr-fapply.html | 4 inst/doc/fmtr-fapply2.html | 4 inst/doc/fmtr-fcat.html | 4 inst/doc/fmtr-fdata.html | 4 inst/doc/fmtr-helpers.html | 4 man/FormattingStrings.Rd | 24 +++++ man/fapply.Rd | 84 ++++++++++++++++++++ tests/testthat/test-timewd.R |only 15 files changed, 329 insertions(+), 34 deletions(-)
Title: High Performance Container Data Types
Description: Provides high performance container data types such
as queues, stacks, deques, dicts and ordered dicts. Benchmarks
<https://randy3k.github.io/collections/articles/benchmark.html> have
shown that these containers are asymptotically more efficient than
those offered by other packages.
Author: Randy Lai [aut, cre],
Andrea Mazzoleni [cph] ,
Yann Collet [cph]
Maintainer: Randy Lai <randy.cs.lai@gmail.com>
Diff between collections versions 0.3.9 dated 2025-08-18 and 0.3.10 dated 2026-01-21
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- src/deque.c | 2 +- src/xxh.c | 36 +++++++++++++++++++++++++++++++++--- 4 files changed, 41 insertions(+), 11 deletions(-)
Title: Efficient Phylogenetics on Large Trees
Description: Efficient phylogenetic analyses on massive phylogenies comprising up to millions of tips. Functions include pruning, rerooting, calculation of most-recent common ancestors, calculating distances from the tree root and calculating pairwise distances. Calculation of phylogenetic signal and mean trait depth (trait conservatism), ancestral state reconstruction and hidden character prediction of discrete characters, simulating and fitting models of trait evolution, fitting and simulating diversification models, dating trees, comparing trees, and reading/writing trees in Newick format. Citation: Louca, Stilianos and Doebeli, Michael (2017) <doi:10.1093/bioinformatics/btx701>.
Author: Stilianos Louca [aut, cre, cph]
Maintainer: Stilianos Louca <louca.research@gmail.com>
Diff between castor versions 1.8.4 dated 2025-08-24 and 1.8.5 dated 2026-01-21
DESCRIPTION | 8 - MD5 | 42 +++--- NAMESPACE | 1 R/RcppExports.R | 8 - R/auxiliary_routines.R | 111 ++++++++++++---- R/expanded_tree_from_jplace.r | 18 ++ R/get_ancestral_nodes.R | 8 - R/get_subtree_with_tips.R | 6 R/hsp_binomial.R | 22 +-- R/hsp_mk_model.R | 29 ++-- R/hsp_naive.R |only R/plot_tree_radial.R | 251 +++++++++++++++++++++++++++++++----- R/read_fastq.R | 25 ++- man/expanded_tree_from_jplace.Rd | 25 +++ man/get_ancestral_nodes.Rd | 18 ++ man/hsp_binomial.Rd | 4 man/hsp_empirical_probabilities.Rd | 12 + man/hsp_max_parsimony.Rd | 2 man/hsp_mk_model.Rd | 3 man/hsp_naive.Rd |only man/plot_tree_radial.Rd | 111 +++++++++++----- src/RcppExports.cpp | 27 ++- src/phylogenetics_cpp_routines.cpp | 253 ++++++++++++++++++++++++++----------- 23 files changed, 729 insertions(+), 255 deletions(-)
Title: Blocked Weighted Bootstrap
Description: The blocked weighted bootstrap (BBW) is an estimation technique
for use with data from two-stage cluster sampled surveys in which either
prior weighting (e.g. population-proportional sampling or PPS as used in
Standardized Monitoring and Assessment of Relief and Transitions or SMART
surveys) or posterior weighting (e.g. as used in rapid assessment method or
RAM and simple spatial sampling method or S3M surveys) is implemented. See
Cameron et al (2008) <doi:10.1162/rest.90.3.414> for application of
bootstrap to cluster samples. See Aaron et al (2016)
<doi:10.1371/journal.pone.0163176> and Aaron et al (2016)
<doi:10.1371/journal.pone.0162462> for application of the blocked weighted
bootstrap to estimate indicators from two-stage cluster sampled surveys.
Author: Mark Myatt [aut, cph] ,
Ernest Guevarra [aut, cre, cph]
Maintainer: Ernest Guevarra <ernestgmd@gmail.com>
Diff between bbw versions 0.3.0 dated 2025-01-16 and 0.3.1 dated 2026-01-21
DESCRIPTION | 18 - MD5 | 26 - NEWS.md | 5 README.md | 88 +++-- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 6 inst/WORDLIST | 4 inst/doc/bbw-estimation.html | 643 +++++++++++++++++++++++++------------------ inst/doc/bbw-parallel.html | 531 +++++++++++++++++------------------ inst/doc/bbw.Rmd | 4 inst/doc/bbw.html | 114 +++++-- man/bbw.Rd | 2 vignettes/bbw.Rmd | 4 14 files changed, 817 insertions(+), 628 deletions(-)
Title: 'Arrow' Database Connectivity ('ADBC') Driver Manager
Description: Provides a developer-facing interface to 'Arrow' Database
Connectivity ('ADBC') for the purposes of driver development, driver
testing, and building high-level database interfaces for users. 'ADBC'
<https://arrow.apache.org/adbc/> is an API standard for database access
libraries that uses 'Arrow' for result sets and query parameters.
Author: Dewey Dunnington [aut, cre] ,
Apache Arrow [aut, cph],
Apache Software Foundation [cph]
Maintainer: Dewey Dunnington <dewey@dunnington.ca>
Diff between adbcdrivermanager versions 0.21.0 dated 2025-11-20 and 0.22.0 dated 2026-01-21
DESCRIPTION | 6 MD5 | 25 +- R/helpers.R | 12 + man/read_adbc.Rd | 8 src/c/driver/postgresql/connection.cc | 35 +++ src/c/driver/postgresql/result_helper.cc | 10 - src/c/driver/sqlite/sqlite.cc | 8 src/c/driver/sqlite/statement_reader.c | 9 src/c/driver_manager/adbc_driver_manager.cc | 234 ++++++++++++++++++------- src/c/driver_manager/entrypoint.c |only src/c/validation/adbc_validation.cc | 11 - src/c/validation/adbc_validation_connection.cc | 2 src/c/validation/adbc_validation_statement.cc | 28 +- src/c/validation/adbc_validation_util.h | 17 + 14 files changed, 298 insertions(+), 107 deletions(-)
More information about adbcdrivermanager at CRAN
Permanent link
Title: Publication-Ready Descriptive, Bivariate, Regression,
Correlation and Diagnostic Accuracy Tools for Medical and
Dental Data
Description: The 'dentomedical' package provides a comprehensive suite of tools for
medical and dental research. It includes automated descriptive statistics,
bivariate analysis with intelligent test selection, logistic regression,
and diagnostic accuracy assessment. All functions generate publication-ready tables using 'flextable', ensuring reproducibility and
clarity suitable for manuscripts, reports, and clinical research workflows.
Author: Umar Hussain [aut, cre],
Nikolaos Pandis [aut]
Maintainer: Umar Hussain <drumarhussain@gmail.com>
Diff between dentomedical versions 0.1.3 dated 2025-12-04 and 0.2.0 dated 2026-01-21
dentomedical-0.1.3/dentomedical/man/norm_sum.Rd |only dentomedical-0.2.0/dentomedical/DESCRIPTION | 26 - dentomedical-0.2.0/dentomedical/LICENSE | 4 dentomedical-0.2.0/dentomedical/MD5 | 41 + dentomedical-0.2.0/dentomedical/NAMESPACE | 44 + dentomedical-0.2.0/dentomedical/R/category.R |only dentomedical-0.2.0/dentomedical/R/correlation.R |only dentomedical-0.2.0/dentomedical/R/global.R |only dentomedical-0.2.0/dentomedical/R/impute_missing.R |only dentomedical-0.2.0/dentomedical/R/linear_regression.R | 230 +++++---- dentomedical-0.2.0/dentomedical/R/logistic_regression.R | 133 +++-- dentomedical-0.2.0/dentomedical/R/normality.R | 6 dentomedical-0.2.0/dentomedical/R/post_hoc.R |only dentomedical-0.2.0/dentomedical/R/recode_function.R |only dentomedical-0.2.0/dentomedical/R/stratified.R |only dentomedical-0.2.0/dentomedical/R/sum_crosstab.R |only dentomedical-0.2.0/dentomedical/R/sum_stat.R | 365 +++++++++------ dentomedical-0.2.0/dentomedical/R/sum_stat_p.R | 102 +--- dentomedical-0.2.0/dentomedical/man/category.Rd |only dentomedical-0.2.0/dentomedical/man/impute_missing.Rd |only dentomedical-0.2.0/dentomedical/man/linreg.Rd | 35 - dentomedical-0.2.0/dentomedical/man/logreg.Rd | 21 dentomedical-0.2.0/dentomedical/man/recode_data.Rd |only dentomedical-0.2.0/dentomedical/man/sum_cor.Rd |only dentomedical-0.2.0/dentomedical/man/sum_crosstab.Rd |only dentomedical-0.2.0/dentomedical/man/sum_norm.Rd |only dentomedical-0.2.0/dentomedical/man/sum_posthoc.Rd |only dentomedical-0.2.0/dentomedical/man/sum_stat.Rd | 46 + dentomedical-0.2.0/dentomedical/man/sum_stat_p.Rd | 67 +- dentomedical-0.2.0/dentomedical/man/sum_stat_p_strata.Rd |only 30 files changed, 681 insertions(+), 439 deletions(-)
Title: 'Arrow' Database Connectivity ('ADBC') 'PostgreSQL' Driver
Description: Provides a developer-facing interface to the 'Arrow' Database
Connectivity ('ADBC') 'PostgreSQL' driver for the purposes of building high-level
database interfaces for users. 'ADBC' <https://arrow.apache.org/adbc/> is
an API standard for database access libraries that uses 'Arrow' for result
sets and query parameters.
Author: Dewey Dunnington [aut, cre] ,
Apache Arrow [aut, cph],
Apache Software Foundation [cph]
Maintainer: Dewey Dunnington <dewey@dunnington.ca>
Diff between adbcpostgresql versions 0.21.0 dated 2025-11-19 and 0.22.0 dated 2026-01-21
DESCRIPTION | 6 MD5 | 36 ++- R/adbcpostgresql-package.R | 3 man/adbcpostgresql.Rd | 3 src/arrow-adbc |only src/c/driver/postgresql/connection.cc | 40 +++- src/c/driver/postgresql/database.cc | 5 src/c/driver/postgresql/postgresql.cc | 5 src/c/driver/postgresql/result_helper.cc | 15 + src/c/driver/postgresql/result_reader.cc | 5 src/c/driver/postgresql/statement.cc | 5 src/c/driver/sqlite/sqlite.cc | 8 src/c/driver/sqlite/statement_reader.c | 9 src/c/driver_manager/adbc_driver_manager.cc | 234 ++++++++++++++++++------- src/c/driver_manager/entrypoint.c |only src/c/validation/adbc_validation.cc | 11 - src/c/validation/adbc_validation_connection.cc | 2 src/c/validation/adbc_validation_statement.cc | 28 +- src/c/validation/adbc_validation_util.h | 17 + tests/testthat/test-adbcpostgres-package.R | 24 ++ 20 files changed, 347 insertions(+), 109 deletions(-)
More information about adbcpostgresql at CRAN
Permanent link
Title: 'Arrow' Database Connectivity ('ADBC') 'SQLite' Driver
Description: Provides a developer-facing interface to the 'Arrow' Database
Connectivity ('ADBC') 'SQLite' driver for the purposes of building high-level
database interfaces for users. 'ADBC' <https://arrow.apache.org/adbc/> is
an API standard for database access libraries that uses 'Arrow' for result
sets and query parameters.
Author: Dewey Dunnington [aut, cre] ,
Apache Arrow [aut, cph],
Apache Software Foundation [cph]
Maintainer: Dewey Dunnington <dewey@dunnington.ca>
Diff between adbcsqlite versions 0.21.0 dated 2025-11-19 and 0.22.0 dated 2026-01-20
DESCRIPTION | 6 MD5 | 31 +-- R/adbcsqlite-package.R | 3 man/adbcsqlite.Rd | 3 src/arrow-adbc |only src/c/driver/postgresql/connection.cc | 35 +++ src/c/driver/postgresql/result_helper.cc | 10 - src/c/driver/sqlite/sqlite.cc | 8 src/c/driver/sqlite/statement_reader.c | 9 src/c/driver_manager/adbc_driver_manager.cc | 234 ++++++++++++++++++------- src/c/driver_manager/entrypoint.c |only src/c/validation/adbc_validation.cc | 11 - src/c/validation/adbc_validation_connection.cc | 2 src/c/validation/adbc_validation_statement.cc | 28 +- src/c/validation/adbc_validation_util.h | 17 + src/common |only tests/testthat/test-adbcsqlite-package.R | 18 + 17 files changed, 310 insertions(+), 105 deletions(-)
Title: Biologically Informed Metabolomic Libraries from 'PubChem'
Description: All 'PubChem' compounds are downloaded to a local computer, but for each compound, only partial records are used. The data are organized into small files referenced by 'PubChem' CID. This package also contains functions to parse the biologically relevant compounds from all 'PubChem' compounds, using biological database sources, pathway presence, and taxonomic relationships. Taxonomy is used to generate a lowest common ancestor taxonomy ID (NCBI) for each biological metabolite, which then enables creation of taxonomically specific metabolome databases for any taxon.
Author: Corey Broeckling [aut, cre]
Maintainer: Corey Broeckling <cbroeckl@colostate.edu>
Diff between pubchem.bio versions 1.0.3 dated 2025-12-12 and 1.0.5 dated 2026-01-20
DESCRIPTION | 9 - MD5 | 30 ++--- NAMESPACE | 2 NEWS.md | 11 +- R/build.pubchem.bio.R | 71 ++++++++++++- R/build.taxon.metabolome.R | 1 R/export.CompoundDb.R | 57 ++++++---- R/get.pubchem.ftp.R | 48 ++++++++ R/globals.R | 2 R/utils-pipe.R |only data/cid.lca.rda |binary inst/doc/pubchem.bio.vignette.R | 3 inst/doc/pubchem.bio.vignette.Rmd | 3 inst/doc/pubchem.bio.vignette.html | 199 ++++++++++++++++++------------------- man/build.pubchem.bio.Rd | 5 man/pipe.Rd |only vignettes/pubchem.bio.vignette.Rmd | 3 17 files changed, 293 insertions(+), 151 deletions(-)
Title: The FPCdpca Criterion on Distributed Principal Component
Analysis
Description: We consider optimal subset selection in the setting that one needs to use only one data subset to represent the whole data set with minimum information loss, and devise a novel intersection-based criterion on selecting optimal subset, called as the FPC criterion, to handle with the optimal sub-estimator in distributed principal component analysis; That is, the FPCdpca. The philosophy of the package is described in Guo G. (2025) <doi:10.1016/j.physa.2024.130308>.
Author: Guangbao Guo [aut, cre] ,
Jiarui Li [aut]
Maintainer: Guangbao Guo <ggb11111111@163.com>
Diff between FPCdpca versions 0.3.0 dated 2025-05-08 and 0.4.0 dated 2026-01-20
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/FPC.R | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Fitting and Tuning Regularized Cause-Specific Cox Models with
Elastic-Net Penalty
Description: Flexible tools to fit, tune and obtain absolute risk predictions from regularized cause-specific cox models with elastic-net penalty.
Author: Shahin Roshani [aut, cre, cph]
Maintainer: Shahin Roshani <s.roshani@nki.nl>
Diff between CSCNet versions 0.1.3 dated 2026-01-08 and 0.1.4 dated 2026-01-20
DESCRIPTION | 10 - MD5 | 18 +- NAMESPACE | 3 NEWS.md | 8 R/tune_penCSC.R | 59 ++++-- inst/doc/CSCNet.R | 120 ++++++------- inst/doc/CSCNet.Rmd | 117 ++++++------- inst/doc/CSCNet.html | 439 +++++++++++++++++++++++++++++---------------------- man/tune_penCSC.Rd | 321 ++++++++++++++++++------------------- vignettes/CSCNet.Rmd | 117 ++++++------- 10 files changed, 631 insertions(+), 581 deletions(-)
Title: Interface to Download Data on Pests and Hosts from 'EPPO'
Description: Set of tools to automatize extraction of data on pests from 'EPPO
Data Services' and 'EPPO Global Database' and to put them into tables with
human readable format. Those function use 'EPPO database API', thus you
first need to register on <https://data.eppo.int> (free of charge).
Additional helpers allow to download, check and connect to
'SQLite EPPO database'.
Author: Michal Jan Czyz [aut, cre]
Maintainer: Michal Jan Czyz <m.czyz.j@gmail.com>
Diff between pestr versions 0.8.2 dated 2021-01-20 and 0.8.4 dated 2026-01-20
pestr-0.8.2/pestr/R/pestr.R |only pestr-0.8.4/pestr/DESCRIPTION | 14 pestr-0.8.4/pestr/LICENSE | 4 pestr-0.8.4/pestr/MD5 | 91 pestr-0.8.4/pestr/NAMESPACE | 38 pestr-0.8.4/pestr/NEWS.md | 439 +- pestr-0.8.4/pestr/R/eppo_api.R | 378 +- pestr-0.8.4/pestr/R/eppo_citation_helpers.R |only pestr-0.8.4/pestr/R/eppo_database_tools.R | 401 +- pestr-0.8.4/pestr/R/eppo_full_table.R | 86 pestr-0.8.4/pestr/R/eppo_tabletools.R | 1045 +++--- pestr-0.8.4/pestr/R/make_eppo_token.R | 155 pestr-0.8.4/pestr/R/message_helpers.R | 149 pestr-0.8.4/pestr/R/pestr-package.R |only pestr-0.8.4/pestr/README.md | 390 +- pestr-0.8.4/pestr/build/vignette.rds |binary pestr-0.8.4/pestr/inst/doc/pestr_example_n_of_taxon.R | 149 pestr-0.8.4/pestr/inst/doc/pestr_example_n_of_taxon.Rmd | 296 - pestr-0.8.4/pestr/inst/doc/pestr_example_n_of_taxon.html | 595 +-- pestr-0.8.4/pestr/inst/doc/pestr_workflow.R | 314 - pestr-0.8.4/pestr/inst/doc/pestr_workflow.Rmd | 577 +-- pestr-0.8.4/pestr/inst/doc/pestr_workflow.html | 2368 +++++++------- pestr-0.8.4/pestr/inst/doc/pra_tables.R |only pestr-0.8.4/pestr/inst/doc/pra_tables.Rmd |only pestr-0.8.4/pestr/inst/doc/pra_tables.html |only pestr-0.8.4/pestr/inst/figures/pestr-hex_center.png |binary pestr-0.8.4/pestr/man/check_eppo_token.Rd | 66 pestr-0.8.4/pestr/man/create_eppo_token.Rd | 64 pestr-0.8.4/pestr/man/eppo_citation.Rd |only pestr-0.8.4/pestr/man/eppo_database.Rd | 121 pestr-0.8.4/pestr/man/eppo_names_tables.Rd | 90 pestr-0.8.4/pestr/man/eppo_table_full.Rd | 60 pestr-0.8.4/pestr/man/eppo_tabletools.Rd | 266 - pestr-0.8.4/pestr/man/pestr.Rd | 38 pestr-0.8.4/pestr/tests/testthat.R | 8 pestr-0.8.4/pestr/tests/testthat/eppocodes.sqlite |binary pestr-0.8.4/pestr/tests/testthat/mocked_taxo.RDS |binary pestr-0.8.4/pestr/tests/testthat/test-citation.R |only pestr-0.8.4/pestr/tests/testthat/test-message_helpers.R | 16 pestr-0.8.4/pestr/tests/testthat/test-null_eppocodes.R | 18 pestr-0.8.4/pestr/tests/testthat/test-raw_eppocode_util.R | 38 pestr-0.8.4/pestr/tests/testthat/test-raw_eppocodes.R | 96 pestr-0.8.4/pestr/tests/testthat/test_api.R | 72 pestr-0.8.4/pestr/tests/testthat/test_database.R | 36 pestr-0.8.4/pestr/tests/testthat/test_dbnameextraction.R | 82 pestr-0.8.4/pestr/tests/testthat/test_tabletools.R | 873 ++--- pestr-0.8.4/pestr/tests/testthat/test_token.R | 34 pestr-0.8.4/pestr/vignettes/alert_style.css | 428 +- pestr-0.8.4/pestr/vignettes/pestr_example_n_of_taxon.Rmd | 296 - pestr-0.8.4/pestr/vignettes/pestr_workflow.Rmd | 577 +-- pestr-0.8.4/pestr/vignettes/pra_tables.Rmd |only 51 files changed, 5642 insertions(+), 5126 deletions(-)
Title: Prediction Explanation with Dependence-Aware Shapley Values
Description: Complex machine learning models are often hard to interpret. However, in
many situations it is crucial to understand and explain why a model made a specific
prediction. Shapley values is the only method for such prediction explanation framework
with a solid theoretical foundation. Previously known methods for estimating the Shapley
values do, however, assume feature independence. This package implements methods which accounts for any feature
dependence, and thereby produces more accurate estimates of the true Shapley values.
An accompanying 'Python' wrapper ('shaprpy') is available through PyPI.
Author: Martin Jullum [cre, aut] ,
Lars Henry Berge Olsen [aut] ,
Annabelle Redelmeier [aut],
Jon Lachmann [aut] ,
Nikolai Sellereite [aut] ,
Anders Loeland [ctb],
Jens Christian Wahl [ctb],
Camilla Lingjaerde [ctb],
Norsk Regnesentral [cph, fnd]
Maintainer: Martin Jullum <Martin.Jullum@nr.no>
Diff between shapr versions 1.0.7 dated 2025-12-22 and 1.0.8 dated 2026-01-20
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Title: Nonparametric Change Point Detection for Multivariate Time
Series
Description: Implements the nonparametric moving sum procedure for detecting
changes in the joint characteristic function (NP-MOJO) for multiple change
point detection in multivariate time series. See McGonigle, E. T., Cho, H.
(2025) <doi:10.1093/biomet/asaf024> for description of the NP-MOJO methodology.
Author: Euan T. McGonigle [aut, cre],
Haeran Cho [aut]
Maintainer: Euan T. McGonigle <e.t.mcgonigle@soton.ac.uk>
Diff between CptNonPar versions 0.3.1 dated 2025-11-25 and 0.3.2 dated 2026-01-20
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ R/multilag.cpts.merge.R | 6 +++--- 4 files changed, 13 insertions(+), 9 deletions(-)
Title: Datasets from "Modelling Survival Data in Medical Research" by
Collett
Description: Datasets for the book entitled "Modelling Survival Data in Medical Research" by Collett (2023) <doi:10.1201/9781003282525>. The datasets provide extensive examples of time-to-event data.
Author: Mark Clements [aut, cre] ,
Enoch Yi-Tung Chen [ctb]
Maintainer: Mark Clements <mark.clements@ki.se>
Diff between collett versions 0.1.0 dated 2025-01-09 and 0.1.2 dated 2026-01-20
DESCRIPTION | 21 +++++++++---- MD5 | 23 +++++++++++---- NAMESPACE | 17 +++++++++++ R/data.R | 75 +++++++++++++++++++++++++++++++++++++++++++++++++ R/utilities.R |only build/partial.rdb |binary data/simdata.rda |only inst/doc |only man/Datasets.Rd | 5 +++ man/collett-package.Rd | 9 ++++- man/simdata.Rd |only man/utilities.Rd |only 12 files changed, 135 insertions(+), 15 deletions(-)
Title: Dynamic Relational Event Analysis and Modeling
Description: A set of tools for relational and event analysis, including two- and one-mode network brokerage and structural measures, and helper functions optimized for relational event analysis with large datasets, including creating relational risk sets, computing network statistics, estimating relational event models, and simulating relational event sequences. For more information on relational event models, see Butts (2008) <doi:10.1111/j.1467-9531.2008.00203.x>, Lerner and Lomi (2020) <doi:10.1017/nws.2019.57>, Bianchi et al. (2024) <doi:10.1146/annurev-statistics-040722-060248>, and Butts et al. (2023) <doi:10.1017/nws.2023.9>. In terms of the structural measures in this package, see Leal (2025) <doi:10.1177/00491241251322517>, Burchard and Cornwell (2018) <doi:10.1016/j.socnet.2018.04.001>, and Fujimoto et al. (2018) <doi:10.1017/nws.2018.11>. This package was developed with support from the National Science Foundation’s (NSF) Human Networks and Data [...truncated...]
Author: Kevin A. Carson [aut, cre] ,
Diego F. Leal [aut]
Maintainer: Kevin A. Carson <kacarson@arizona.edu>
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dream-1.0.0/dream/man/remstats_reciprocity.Rd |only dream-1.0.0/dream/man/remstats_repetition.Rd |only dream-1.0.0/dream/man/remstats_triads.Rd |only dream-1.0.0/dream/man/simulateRESeq.Rd | 6 dream-1.0.0/dream/man/simulate_rem_seq.Rd |only dream-1.0.0/dream/man/southern.women.Rd | 6 dream-1.0.0/dream/src/RcppExports.cpp | 345 +++ dream-1.0.0/dream/src/burteffectiveinC.cpp |only dream-1.0.0/dream/src/burtsconstraintinc.cpp |only dream-1.0.0/dream/src/computeREMweightsv1.cpp |only dream-1.0.0/dream/src/computeREMweightsv2.cpp |only dream-1.0.0/dream/src/computeincomingsharedpartnersrem.cpp |only dream-1.0.0/dream/src/computeincomingtwopathsrem.cpp |only dream-1.0.0/dream/src/computeoutgoingsharedpartrem.cpp |only dream-1.0.0/dream/src/computeouttwopathsrem.cpp |only dream-1.0.0/dream/src/lealrcpp.cpp |only dream-1.0.0/dream/src/nonrankrecency.cpp |only dream-1.0.0/dream/src/persistenceREM.cpp |only dream-1.0.0/dream/src/prefattachincppREM.cpp |only dream-1.0.0/dream/src/prefattachincppwithtimespan.cpp |only dream-1.0.0/dream/src/processonemodeseq.cpp |only dream-1.0.0/dream/src/processtmeventseq.cpp |only dream-1.0.0/dream/src/recencyrankc.cpp |only dream-1.0.0/dream/src/remfourcycles.cpp |only dream-1.0.0/dream/src/tmdegreecentrailty.cpp |only dream-1.0.0/dream/src/twomodeegodisthomocpp.cpp |only 162 files changed, 1601 insertions(+), 3802 deletions(-)
Title: Real-Time Disease Surveillance
Description: Supports modelling real-time case data to facilitate the real-time
surveillance of infectious diseases and other point phenomena. The package provides automated computational grid generation over
an area of interest with methods to map covariates between geographies, model fitting including spatially aggregated case counts,
and predictions and visualisation. Both Bayesian and maximum likelihood methods are provided. Log-Gaussian Cox Processes are described by
Diggle et al. (2013) <doi:10.1214/13-STS441> and we provide both the low-rank approximation for Gaussian processes
described by Solin and Särkkä (2020) <doi:10.1007/s11222-019-09886-w> and Riutort-Mayol et al (2023) <doi:10.1007/s11222-022-10167-2> and the
nearest neighbour Gaussian process described by Datta et al (2016) <doi:10.1080/01621459.2015.1044091>.
Author: Sam Watson [aut, cre]
Maintainer: Sam Watson <s.i.watson@bham.ac.uk>
Diff between rts2 versions 0.9.1 dated 2025-09-11 and 0.10.1 dated 2026-01-20
rts2-0.10.1/rts2/DESCRIPTION | 16 rts2-0.10.1/rts2/MD5 | 110 rts2-0.10.1/rts2/NAMESPACE | 5 rts2-0.10.1/rts2/R/RcppExports.R | 292 -- rts2-0.10.1/rts2/R/disaggregate.R |only rts2-0.10.1/rts2/R/griddata_class.R | 1576 +++++--------- rts2-0.10.1/rts2/R/print_mcmlrts.R | 63 rts2-0.10.1/rts2/R/stanmodels.R | 4 rts2-0.10.1/rts2/README.md |only rts2-0.10.1/rts2/build/partial.rdb |binary rts2-0.10.1/rts2/inst/stan/rtsbayes.stan | 33 rts2-0.10.1/rts2/man/birmingham_crime.Rd | 34 rts2-0.10.1/rts2/man/boundary.Rd | 32 rts2-0.10.1/rts2/man/coef.rtsFit.Rd | 38 rts2-0.10.1/rts2/man/confint.rtsFit.Rd | 38 rts2-0.10.1/rts2/man/covariance.parameters.Rd | 34 rts2-0.10.1/rts2/man/disaggregate_covariate.Rd |only rts2-0.10.1/rts2/man/disaggregate_positive.Rd |only rts2-0.10.1/rts2/man/example_points.Rd | 34 rts2-0.10.1/rts2/man/family.rtsFit.Rd | 38 rts2-0.10.1/rts2/man/fitted.rtsFit.Rd | 40 rts2-0.10.1/rts2/man/fixed.effects.Rd | 34 rts2-0.10.1/rts2/man/flat_disaggregate.Rd |only rts2-0.10.1/rts2/man/formula.grid.Rd | 42 rts2-0.10.1/rts2/man/formula.rtsFit.Rd | 42 rts2-0.10.1/rts2/man/grid.Rd | 324 +- rts2-0.10.1/rts2/man/logLik.rtsFit.Rd | 40 rts2-0.10.1/rts2/man/predict.grid.Rd | 138 - rts2-0.10.1/rts2/man/predict.rtsFit.Rd | 40 rts2-0.10.1/rts2/man/print.rtsFit.Rd | 50 rts2-0.10.1/rts2/man/print.rtsFitSummary.Rd | 44 rts2-0.10.1/rts2/man/random.effects.Rd | 34 rts2-0.10.1/rts2/man/residuals.grid.Rd | 44 rts2-0.10.1/rts2/man/residuals.rtsFit.Rd | 44 rts2-0.10.1/rts2/man/summary.grid.Rd | 38 rts2-0.10.1/rts2/man/summary.rtsFit.Rd | 48 rts2-0.10.1/rts2/man/vcov.grid.Rd | 40 rts2-0.10.1/rts2/man/vcov.rtsFit.Rd | 40 rts2-0.10.1/rts2/src/RcppExports.cpp | 1118 +-------- rts2-0.10.1/rts2/src/region_model.cpp |only rts2-0.10.1/rts2/src/region_model.h |only rts2-0.10.1/rts2/src/stanExports_rtsbayes.cc | 34 rts2-0.10.1/rts2/src/stanExports_rtsbayes.h | 1190 ++++------ rts2-0.10.1/rts2/src/stanExports_rtslgcp_region.cc | 34 rts2-0.9.1/rts2/inst/cmdstan |only rts2-0.9.1/rts2/inst/include |only rts2-0.9.1/rts2/inst/stan/rtsmcml_poisson.stan |only rts2-0.9.1/rts2/inst/stan/rtsmcml_poisson_region.stan |only rts2-0.9.1/rts2/src/model_module.cpp |only rts2-0.9.1/rts2/src/stanExports_rtsmcml_poisson.cc |only rts2-0.9.1/rts2/src/stanExports_rtsmcml_poisson.h |only rts2-0.9.1/rts2/src/stanExports_rtsmcml_poisson_region.cc |only rts2-0.9.1/rts2/src/stanExports_rtsmcml_poisson_region.h |only 53 files changed, 2062 insertions(+), 3743 deletions(-)
Title: User Friendly Data Visualization
Description: A comprehensive visualization toolkit built with coders of all
skill levels and color-vision impaired audiences in mind. It allows creation
of finely-tuned, publication-quality figures from single function calls.
Visualizations include scatter plots, compositional bar plots, violin, box,
and ridge plots, and more. Customization ranges from size and title
adjustments to discrete-group circling and labeling, hidden data overlay
upon cursor hovering via ggplotly() conversion, and many more, all with
simple, discrete inputs. Color blindness friendliness is powered by legend
adjustments (enlarged keys), and by allowing the use of shapes or
letter-overlay in addition to the carefully selected dittoColors().
Author: Daniel Bunis [aut, cre]
Maintainer: Daniel Bunis <daniel.bunis@ucsf.edu>
Diff between dittoViz versions 1.0.5 dated 2025-12-09 and 1.0.6 dated 2026-01-20
DESCRIPTION | 6 +- MD5 | 22 ++++----- NEWS.md | 9 +++ R/scatterHex.R | 99 ++++++++---------------------------------- R/scatterPlot.R | 19 ++++++-- R/utils_plot_mods.R | 25 ++++++++-- R/yPlot.R | 67 +++++++++++++--------------- man/scatterHex.Rd | 99 ++++++++---------------------------------- man/scatterPlot.Rd | 16 ++++-- tests/testthat/test-hover.R | 10 +++- tests/testthat/test-scatter.R | 26 +++++++++++ tests/testthat/test-y.R | 52 +++++++++++++++++++--- 12 files changed, 221 insertions(+), 229 deletions(-)
Title: Imputation of Missing Data in Sequence Analysis
Description: Multiple imputation of missing data in a dataset using MICT or
MICT-timing methods. The core idea of the algorithms is to fill gaps of
missing data, which is the typical form of missing data in a longitudinal
setting, recursively from their edges. Prediction is based on either a
multinomial or random forest regression model. Covariates and
time-dependent covariates can be included in the model.
Author: Kevin Emery [aut, cre],
Anthony Guinchard [aut],
Andre Berchtold [aut],
Kamyar Taher [aut]
Maintainer: Kevin Emery <kevin.emery@unige.ch>
Diff between seqimpute versions 2.2.0 dated 2025-01-15 and 2.2.1 dated 2026-01-20
seqimpute-2.2.0/seqimpute/R/plots.R |only seqimpute-2.2.1/seqimpute/DESCRIPTION | 6 seqimpute-2.2.1/seqimpute/MD5 | 42 +- seqimpute-2.2.1/seqimpute/NEWS.md | 15 seqimpute-2.2.1/seqimpute/R/checks.R | 49 +- seqimpute-2.2.1/seqimpute/R/final.transform.R | 27 - seqimpute-2.2.1/seqimpute/R/methods.seqimp.R | 5 seqimpute-2.2.1/seqimpute/R/mict.internal.R | 100 ++--- seqimpute-2.2.1/seqimpute/R/mict.timing.R | 230 ++++++------ seqimpute-2.2.1/seqimpute/R/seqQuickLook.R | 55 +- seqimpute-2.2.1/seqimpute/R/seqTrans.R | 79 +--- seqimpute-2.2.1/seqimpute/R/seqaddNA.R | 15 seqimpute-2.2.1/seqimpute/R/seqimpute.R | 173 ++++----- seqimpute-2.2.1/seqimpute/R/seqmissIplot.R |only seqimpute-2.2.1/seqimpute/R/seqmissfplot.R |only seqimpute-2.2.1/seqimpute/R/seqmissimplic.R |only seqimpute-2.2.1/seqimpute/build/vignette.rds |binary seqimpute-2.2.1/seqimpute/inst/doc/vignette.pdf |binary seqimpute-2.2.1/seqimpute/man/seqaddNA.Rd | 2 seqimpute-2.2.1/seqimpute/man/seqimpute.Rd | 446 ++++++++++++------------ seqimpute-2.2.1/seqimpute/man/seqmissIplot.Rd | 100 ++--- seqimpute-2.2.1/seqimpute/man/seqmissfplot.Rd | 122 +++--- seqimpute-2.2.1/seqimpute/man/seqmissimplic.Rd | 5 seqimpute-2.2.1/seqimpute/man/summary.seqimp.Rd | 38 +- 24 files changed, 759 insertions(+), 750 deletions(-)
Title: Perform a Relative Weights Analysis
Description: Perform a Relative Weights Analysis (RWA) (a.k.a. Key Drivers Analysis) as per the method described
in Tonidandel & LeBreton (2015) <DOI:10.1007/s10869-014-9351-z>, with its original roots in Johnson (2000) <DOI:10.1207/S15327906MBR3501_1>. In essence, RWA decomposes
the total variance predicted in a regression model into weights that accurately reflect the proportional
contribution of the predictor variables, which addresses the issue of multi-collinearity. In typical scenarios,
RWA returns similar results to Shapley regression, but with a significant advantage on computational performance.
Author: Martin Chan [aut, cre]
Maintainer: Martin Chan <martinchan53@gmail.com>
Diff between rwa versions 0.1.0 dated 2025-07-16 and 0.1.1 dated 2026-01-20
rwa-0.1.0/rwa/man/extract_ci.Rd |only rwa-0.1.0/rwa/man/run_rwa_bootstrap.Rd |only rwa-0.1.1/rwa/DESCRIPTION | 6 rwa-0.1.1/rwa/MD5 | 38 rwa-0.1.1/rwa/NAMESPACE | 1 rwa-0.1.1/rwa/NEWS.md | 18 rwa-0.1.1/rwa/R/bootstrap_rwa.R | 232 +- rwa-0.1.1/rwa/R/rwa.R | 67 rwa-0.1.1/rwa/README.md | 7 rwa-0.1.1/rwa/build/vignette.rds |binary rwa-0.1.1/rwa/inst/WORDLIST | 4 rwa-0.1.1/rwa/inst/doc/bootstrap-confidence-intervals.html | 129 - rwa-0.1.1/rwa/inst/doc/evaluating-rwa-method-reference.Rmd | 122 - rwa-0.1.1/rwa/inst/doc/evaluating-rwa-method-reference.html | 1063 +++++------- rwa-0.1.1/rwa/inst/doc/introduction-to-rwa.Rmd | 74 rwa-0.1.1/rwa/inst/doc/introduction-to-rwa.html | 105 - rwa-0.1.1/rwa/tests/testthat/test-bootstrap.R | 8 rwa-0.1.1/rwa/tests/testthat/test-rwa.R | 331 ++- rwa-0.1.1/rwa/vignettes/README.md | 1 rwa-0.1.1/rwa/vignettes/evaluating-rwa-method-reference.Rmd | 122 - rwa-0.1.1/rwa/vignettes/introduction-to-rwa.Rmd | 74 21 files changed, 1313 insertions(+), 1089 deletions(-)
Title: Regression by Composition
Description: Flexible statistical modelling using a modular framework for
regression, in which groups of transformations are composed together
and act on probability distributions.
Author: Daniel Farewell [aut, cre, cph] ,
Simon Schoenbuchner [ctb]
Maintainer: Daniel Farewell <farewelld@cardiff.ac.uk>
Diff between rbc versions 0.1.0 dated 2024-11-06 and 0.1.1 dated 2026-01-20
rbc-0.1.0/rbc/man/AIC.RegressionByComposition.Rd |only rbc-0.1.1/rbc/DESCRIPTION | 13 ++-- rbc-0.1.1/rbc/MD5 | 26 +++++--- rbc-0.1.1/rbc/NAMESPACE | 4 + rbc-0.1.1/rbc/NEWS.md | 6 ++ rbc-0.1.1/rbc/R/DataFeatures.R | 27 ++++++--- rbc-0.1.1/rbc/R/S3methods.R | 16 +---- rbc-0.1.1/rbc/R/append_flow.R | 2 rbc-0.1.1/rbc/R/flows.R | 68 +++++++++++++++++++++++ rbc-0.1.1/rbc/R/rbc.R | 4 - rbc-0.1.1/rbc/data/starr.rda |binary rbc-0.1.1/rbc/man/BinomialGLM.Rd |only rbc-0.1.1/rbc/man/Cinch.Rd |only rbc-0.1.1/rbc/man/PowerOdds.Rd |only rbc-0.1.1/rbc/man/rbc.Rd | 4 - rbc-0.1.1/rbc/tests/testthat/test-DataFeatures.R |only rbc-0.1.1/rbc/tests/testthat/test-S3methods.R |only 17 files changed, 128 insertions(+), 42 deletions(-)
Title: Beyond the Border - Kernel Density Estimation for Urban
Geography
Description: The kernelSmoothing() function allows you to square and smooth geolocated data. It calculates a classical kernel smoothing (conservative) or a geographically weighted median. There are four major call modes of the function.
The first call mode is kernelSmoothing(obs, epsg, cellsize, bandwidth) for a classical kernel smoothing and automatic grid.
The second call mode is kernelSmoothing(obs, epsg, cellsize, bandwidth, quantiles) for a geographically weighted median and automatic grid.
The third call mode is kernelSmoothing(obs, epsg, cellsize, bandwidth, centroids) for a classical kernel smoothing and user grid.
The fourth call mode is kernelSmoothing(obs, epsg, cellsize, bandwidth, quantiles, centroids) for a geographically weighted median and user grid.
Geographically weighted summary statistics : a framework for localised exploratory data analysis, C.Brunsdon & al., in Computers, Environment and Urban Systems C.Brunsdon & al. (2002) <doi:10.1016/S0198-9715(01)00009-6>,
S [...truncated...]
Author: Arlindo Dos Santos [aut],
Francois Semecurbe [aut],
Julien Pramil [aut],
Solene Colin [cre, ctb],
Kim Antunez [ctb],
Auriane Renaud [ctb],
Farida Marouchi [ctb],
Joachim Timoteo [ctb],
Institut national de la statistique et des etudes economiques [cp [...truncated...]
Maintainer: Solene Colin <solene.colin@insee.fr>
Diff between btb versions 0.2.1 dated 2025-03-17 and 0.2.2 dated 2026-01-20
DESCRIPTION | 8 +++---- MD5 | 16 +++++++-------- NEWS.md | 10 +++++++++ build/vignette.rds |binary inst/doc/btb.html | 20 +++++++++---------- inst/doc/logo.R | 2 - inst/doc/logo.Rmd | 2 - inst/doc/logo.html | 54 +++++++++++++++++++++++++++-------------------------- vignettes/logo.Rmd | 2 - 9 files changed, 63 insertions(+), 51 deletions(-)
Title: Spatial Logistic Gaussian Process for Field Density Estimation
Description: Provides tools for conditional and spatially dependent
density estimation using Spatial Logistic Gaussian Processes (SLGPs).
The approach represents probability densities through finite-rank
Gaussian process priors transformed via a spatial logistic density
transformation, enabling flexible non-parametric modeling of
heterogeneous data. Functionality includes density prediction,
quantile and moment estimation, sampling methods, and preprocessing
routines for basis functions. Applications arise in spatial statistics,
machine learning, and uncertainty quantification.
The methodology builds on the framework of Leonard (1978)
<doi:10.1111/j.2517-6161.1978.tb01655.x>, Lenk (1988) <doi:10.1080/01621459.1988.10478625>,
Tokdar (2007) <doi:10.1198/106186007X210206>, Tokdar (2010) <doi:10.1214/10-BA605>,
and is further aligned with recent developments
in Bayesian non-parametric modelling: see Gautier (2023) <https://boristheses.unibe.ch/4377/>,
and Gautier (2025) &l [...truncated...]
Author: Athenais Gautier [aut, cre]
Maintainer: Athenais Gautier <athenais.gautier@onera.fr>
Diff between SLGP versions 1.0.0 dated 2025-09-05 and 1.0.1 dated 2026-01-20
DESCRIPTION | 6 - MD5 | 40 +++--- R/PredictAndSimulate.R | 151 +++++++++++++++++++++---- R/SLGPclass.R | 2 R/datamanagement.R | 52 +++++++- R/slgp.R | 112 +++++++++++++++---- inst/doc/IntroductionSLGP.html | 73 ++++++------ inst/doc/SLGPdiscrete.html | 2 inst/extdata/composed_model.rds |binary inst/extdata/simple_model.rds |binary inst/stan/likelihoodComposed.stan | 128 +++++++++++---------- inst/stan/likelihoodSimple.stan | 106 +++++++++--------- man/SLGP-class.Rd | 2 man/pre_comput_NN.Rd | 2 man/pre_comput_WNN.Rd | 3 man/pre_comput_nothing.Rd | 2 man/predictSLGP_newNode.Rd | 5 man/retrainSLGP.Rd | 7 - man/slgp.Rd | 7 - src/stanExports_likelihoodComposed.h | 206 ++++++++++++++++++++--------------- src/stanExports_likelihoodSimple.h | 165 +++++++++++++++++----------- 21 files changed, 693 insertions(+), 378 deletions(-)
Title: Draw Samples with the Desired Properties from a Data Set
Description: A tool to sample data with the desired properties.Samples can be
drawn by purposive sampling with determining distributional
conditions, such as deviation from normality (skewness and kurtosis),
and sample size in quantitative research studies.
For purposive sampling, a researcher has something in mind and participants that
fit the purpose of the study are included (Etikan,Musa, & Alkassim, 2015)
<doi:10.11648/j.ajtas.20160501.11>.Purposive sampling can be useful for answering
many research questions (Klar & Leeper, 2019)
<doi:10.1002/9781119083771.ch21>.
Author: Kubra Atalay Kabasakal [aut, cre] ,
Huseyin Yildiz [ctb]
Maintainer: Kubra Atalay Kabasakal <katalay@hacettepe.edu.tr>
Diff between drawsample versions 1.0.1 dated 2022-09-05 and 1.0.2 dated 2026-01-20
DESCRIPTION | 12 ++++++------ MD5 | 8 ++++---- R/globals.R | 3 ++- build/partial.rdb |binary inst/CITATION | 29 +++++++++++++---------------- 5 files changed, 25 insertions(+), 27 deletions(-)
Title: A C++11 Interface for R's C Interface
Description: Provides a header only, C++11 interface to R's C
interface. Compared to other approaches 'cpp11' strives to be safe
against long jumps from the C API as well as C++ exceptions, conform
to normal R function semantics and supports interaction with 'ALTREP'
vectors.
Author: Davis Vaughan [aut, cre] ,
Jim Hester [aut] ,
Romain Francois [aut] ,
Benjamin Kietzman [ctb],
Posit Software, PBC [cph, fnd]
Maintainer: Davis Vaughan <davis@posit.co>
Diff between cpp11 versions 0.5.2-2 dated 2026-01-06 and 0.5.3 dated 2026-01-20
DESCRIPTION | 6 MD5 | 52 - NEWS.md | 12 README.md | 2 build/vignette.rds |binary inst/doc/FAQ.Rmd | 2 inst/doc/FAQ.html | 15 inst/doc/converting.html | 5 inst/doc/cpp11.R | 344 +++++----- inst/doc/cpp11.Rmd | 14 inst/doc/cpp11.html | 108 ++- inst/doc/internals.Rmd | 2 inst/doc/internals.html | 7 inst/doc/motivations.R | 58 - inst/doc/motivations.Rmd | 12 inst/doc/motivations.html | 1193 +++++++++++--------------------------- inst/include/cpp11/data_frame.hpp | 40 - inst/include/cpp11/function.hpp | 3 inst/include/cpp11/list.hpp | 7 inst/include/cpp11/named_arg.hpp | 2 inst/include/cpp11/r_vector.hpp | 10 inst/include/cpp11/sexp.hpp | 5 tests/testthat/_snaps/register.md | 8 vignettes/FAQ.Rmd | 2 vignettes/cpp11.Rmd | 14 vignettes/internals.Rmd | 2 vignettes/motivations.Rmd | 12 27 files changed, 772 insertions(+), 1165 deletions(-)