Title: Cox Models by Likelihood Based Boosting for a Single Survival
Endpoint or Competing Risks
Description: Provides routines for fitting Cox models by likelihood based
boosting for single event survival data with right censoring or in the
presence of competing risks. The methodology is described in Binder
and Schumacher (2008) <doi:10.1186/1471-2105-9-14> and Binder et al.
(2009) <doi:10.1093/bioinformatics/btp088>.
Author: John Zobolas [cre, aut] ,
Harald Binder [aut]
Maintainer: John Zobolas <bblodfon@gmail.com>
This is a re-admission after prior archival of version 1.4 dated 2013-05-10
Diff between CoxBoost versions 1.4 dated 2013-05-10 and 1.5.1 dated 2025-12-11
CoxBoost-1.4/CoxBoost/R/optimStepSizeFactor.R |only CoxBoost-1.4/CoxBoost/changeLog |only CoxBoost-1.4/CoxBoost/man/optimStepSizeFactor.Rd |only CoxBoost-1.5.1/CoxBoost/DESCRIPTION | 39 CoxBoost-1.5.1/CoxBoost/LICENSE |only CoxBoost-1.5.1/CoxBoost/MD5 | 50 CoxBoost-1.5.1/CoxBoost/NAMESPACE | 39 CoxBoost-1.5.1/CoxBoost/NEWS.md |only CoxBoost-1.5.1/CoxBoost/R/CoxBoost.R | 2144 +++++++++++++++----- CoxBoost-1.5.1/CoxBoost/R/estimPVal.R | 105 CoxBoost-1.5.1/CoxBoost/R/iCoxBoost.R | 379 +++ CoxBoost-1.5.1/CoxBoost/R/resample.CoxBoost.R |only CoxBoost-1.5.1/CoxBoost/R/zzz.R |only CoxBoost-1.5.1/CoxBoost/README.md |only CoxBoost-1.5.1/CoxBoost/build |only CoxBoost-1.5.1/CoxBoost/inst |only CoxBoost-1.5.1/CoxBoost/man/CoxBoost-package.Rd |only CoxBoost-1.5.1/CoxBoost/man/CoxBoost.Rd | 285 ++ CoxBoost-1.5.1/CoxBoost/man/coef.CoxBoost.Rd | 26 CoxBoost-1.5.1/CoxBoost/man/cv.CoxBoost.Rd | 150 + CoxBoost-1.5.1/CoxBoost/man/cvcb.control.Rd | 70 CoxBoost-1.5.1/CoxBoost/man/estimPVal.Rd | 101 CoxBoost-1.5.1/CoxBoost/man/figures |only CoxBoost-1.5.1/CoxBoost/man/iCoxBoost.Rd | 233 +- CoxBoost-1.5.1/CoxBoost/man/optimCoxBoostPenalty.Rd | 102 CoxBoost-1.5.1/CoxBoost/man/plot.CoxBoost.Rd | 32 CoxBoost-1.5.1/CoxBoost/man/predict.CoxBoost.Rd | 86 CoxBoost-1.5.1/CoxBoost/man/predict.iCoxBoost.Rd | 67 CoxBoost-1.5.1/CoxBoost/man/print.CoxBoost.Rd |only CoxBoost-1.5.1/CoxBoost/man/resample.CoxBoost.Rd |only CoxBoost-1.5.1/CoxBoost/man/stabtrajec.Rd |only CoxBoost-1.5.1/CoxBoost/man/summary.CoxBoost.Rd |only CoxBoost-1.5.1/CoxBoost/src/find_best.c | 229 -- CoxBoost-1.5.1/CoxBoost/src/init.c |only 34 files changed, 3137 insertions(+), 1000 deletions(-)
Title: Download and Process Oklahoma Mesonet Data
Description: A collection of functions to download and process weather data from
the Oklahoma Mesonet <https://mesonet.org>. Functions are available for downloading station metadata,
downloading Mesonet time series (MTS) files, importing MTS files into R, and
converting soil temperature change measurements into soil matric potential and
volumetric soil moisture.
Author: Phillip D. Alderman [aut, cre]
Maintainer: Phillip D. Alderman <phillip.alderman@okstate.edu>
Diff between mesonet versions 0.0.1 dated 2025-07-28 and 0.0.2 dated 2025-12-11
DESCRIPTION | 8 ++-- MD5 | 32 ++++++++-------- NEWS.md | 8 ++++ R/mnet_concatenate.R | 3 + R/mnet_download_mts.R | 12 +++++- R/mnet_requisition_list.R | 4 +- R/mnet_retrieve.R | 4 +- R/mnet_site_info.R | 7 ++- R/mnet_summarize.R | 11 ++++- R/mnet_test_cache.R | 56 ++++++++++++++-------------- inst/tinytest/test_01_mnet_site_info.R | 2 - inst/tinytest/test_05_mnet_concatenate.R | 61 +++++++++++++++---------------- man/mnet_concatenate.Rd | 3 + man/mnet_download_mts.Rd | 6 ++- man/mnet_requisition_list.Rd | 2 - man/mnet_retrieve.Rd | 4 +- man/mnet_summarize.Rd | 4 +- 17 files changed, 133 insertions(+), 94 deletions(-)
Title: Custom Visualizations & Functions for Streamlined Analyses of
Single Cell Sequencing
Description: Collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using 'R'. 'scCustomize' aims to provide 1) Customized visualizations for aid in ease of use and to create more aesthetic and functional visuals. 2) Improve speed/reproducibility of common tasks/pieces of code in scRNA-seq analysis with a single or group of functions. For citation please use: Marsh SE (2021) "Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing" <doi:10.5281/zenodo.5706430> RRID:SCR_024675.
Author: Samuel Marsh [aut, cre] ,
Ming Tang [ctb],
Velina Kozareva [ctb],
Lucas Graybuck [ctb],
Zoe Clarke [ctb]
Maintainer: Samuel Marsh <sccustomize@gmail.com>
Diff between scCustomize versions 3.2.3 dated 2025-12-09 and 3.2.4 dated 2025-12-11
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 2 +- R/Utilities.R | 15 ++++++++------- 4 files changed, 16 insertions(+), 15 deletions(-)
Title: Fit and Compare Species-Area Relationship Models Using
Multimodel Inference
Description: Implements the basic elements of the multi-model
inference paradigm for up to twenty species-area relationship models (SAR), using simple
R list-objects and functions, as in Triantis et al. 2012 <DOI:10.1111/j.1365-2699.2011.02652.x>.
The package is scalable and users can easily create their own model and data objects. Additional
SAR related functions are provided.
Author: Thomas J. Matthews [aut, cre] ,
Francois Guilhaumon [aut] ,
Kevin Cazelles [rev]
Maintainer: Thomas J. Matthews <txm676@gmail.com>
Diff between sars versions 2.0.0 dated 2025-03-03 and 2.1.0 dated 2025-12-11
sars-2.0.0/sars/inst/_pkgdown.yml |only sars-2.0.0/sars/tests/testthat/Rplots.pdf |only sars-2.1.0/sars/DESCRIPTION | 22 sars-2.1.0/sars/MD5 | 97 +-- sars-2.1.0/sars/NEWS.md | 7 sars-2.1.0/sars/R/class_plot.R | 233 +++++++-- sars-2.1.0/sars/R/coleman.R | 2 sars-2.1.0/sars/R/gdm.R | 2 sars-2.1.0/sars/R/mod_linear_power.R | 2 sars-2.1.0/sars/R/sar_asymp.R | 2 sars-2.1.0/sars/R/sar_average.R | 13 sars-2.1.0/sars/R/sar_betap.R | 2 sars-2.1.0/sars/R/sar_chapman.R | 2 sars-2.1.0/sars/R/sar_countryside.R | 7 sars-2.1.0/sars/R/sar_epm1.R | 2 sars-2.1.0/sars/R/sar_epm2.R | 2 sars-2.1.0/sars/R/sar_gompertz.R | 2 sars-2.1.0/sars/R/sar_habitat.R | 4 sars-2.1.0/sars/R/sar_heleg.R | 2 sars-2.1.0/sars/R/sar_koba.R | 2 sars-2.1.0/sars/R/sar_loga.R | 2 sars-2.1.0/sars/R/sar_logistic.R | 2 sars-2.1.0/sars/R/sar_mmf.R | 2 sars-2.1.0/sars/R/sar_monod.R | 2 sars-2.1.0/sars/R/sar_negexpo.R | 2 sars-2.1.0/sars/R/sar_p1.R | 2 sars-2.1.0/sars/R/sar_p2.R | 2 sars-2.1.0/sars/R/sar_power.R | 2 sars-2.1.0/sars/R/sar_powerR.R | 2 sars-2.1.0/sars/R/sar_ratio.R | 2 sars-2.1.0/sars/R/sar_threshold.R | 2 sars-2.1.0/sars/R/sar_weibull3.R | 2 sars-2.1.0/sars/R/sar_weibull4.R | 2 sars-2.1.0/sars/README.md | 58 +- sars-2.1.0/sars/inst/REFERENCES.bib | 36 + sars-2.1.0/sars/inst/doc/sars-r-package.R | 68 ++ sars-2.1.0/sars/inst/doc/sars-r-package.Rmd | 127 ++++ sars-2.1.0/sars/inst/doc/sars-r-package.html | 385 +++++++++++++-- sars-2.1.0/sars/inst/model_factory.R | 5 sars-2.1.0/sars/man/countryside_extrap.Rd | 2 sars-2.1.0/sars/man/figures/README-unnamed-chunk-5-1.png |binary sars-2.1.0/sars/man/figures/README-unnamed-chunk-7-1.png |only sars-2.1.0/sars/man/figures/README-unnamed-chunk-7-2.png |only sars-2.1.0/sars/man/figures/README-unnamed-chunk-7-3.png |only sars-2.1.0/sars/man/plot.habitat.Rd | 73 ++ sars-2.1.0/sars/man/sar_countryside.Rd | 3 sars-2.1.0/sars/man/sar_habitat.Rd | 2 sars-2.1.0/sars/tests/testthat/test_countryside.R | 29 + sars-2.1.0/sars/tests/testthat/test_multi.R | 7 sars-2.1.0/sars/tests/testthat/test_power.R | 3 sars-2.1.0/sars/vignettes/REFERENCES.bib | 47 + sars-2.1.0/sars/vignettes/sars-r-package.Rmd | 127 ++++ 52 files changed, 1194 insertions(+), 209 deletions(-)
Title: High-Level Plotting Built Upon 'ggplot2' and Other Plotting
Packages
Description: Provides high-level API and a wide range of options to create stunning, publication-quality plots effortlessly.
It is built upon 'ggplot2' and other plotting packages, and is designed to be easy to use and to work seamlessly with 'ggplot2' objects.
It is particularly useful for creating complex plots with multiple layers, facets, and annotations.
It also provides a set of functions to create plots for specific types of data, such as Venn diagrams, alluvial diagrams, and phylogenetic trees.
The package is designed to be flexible and customizable, and to work well with the 'ggplot2' ecosystem.
The API can be found at <https://pwwang.github.io/plotthis/reference/index.html>.
Author: Panwen Wang [aut, cre]
Maintainer: Panwen Wang <pwwang@pwwang.com>
Diff between plotthis versions 0.8.2 dated 2025-11-10 and 0.9.0 dated 2025-12-11
DESCRIPTION | 6 +++--- MD5 | 26 +++++++++++++------------- R/boxviolinplot.R | 12 +++++++++--- R/densityplot.R | 2 +- R/dimplot.R | 18 +++++++++--------- R/heatmap.R | 8 +++++++- R/network.R | 5 +++-- R/roccurve.R | 3 ++- R/theming.R | 9 +++++---- R/velocityplot.R | 4 ++-- man/Heatmap.Rd | 3 ++- man/HeatmapAtomic.Rd | 3 ++- man/ROCCurve.Rd | 3 ++- man/theme_this.Rd | 3 ++- 14 files changed, 62 insertions(+), 43 deletions(-)
Title: Extract Event Statistics in Hydrologic Time Series
Description: Events from individual hydrologic time series are extracted, and events
are matched across multiple time series. The package has been applied in studies
such as Wasko and Guo (2022) <doi:10.1002/hyp.14563> and Mohammadpour Khoie,
Guo and Wasko (2025) <doi:10.1016/j.envsoft.2025.106521>.
Author: Conrad Wasko [aut, cre],
Danlu Guo [aut],
Mohammad Masoud Mohammadpour Khoie [ctb]
Maintainer: Conrad Wasko <conrad.wasko@gmail.com>
Diff between hydroEvents versions 0.12.0 dated 2025-02-12 and 0.13.0 dated 2025-12-11
DESCRIPTION | 24 +- MD5 | 26 +- NAMESPACE | 39 +-- NEWS.md | 16 - R/calcREIC.R |only R/eventRVEIM.R |only R/plotEvents.R | 13 - R/postCorrection.R |only README.md | 534 ++++++++++++++++++++++++++++---------------------- data/hourlyQ.rda |only man/calcREIC.Rd |only man/eventBaseflow.Rd | 95 ++++---- man/eventMaxima.Rd | 121 +++++------ man/eventMinima.Rd | 121 +++++------ man/eventPOT.Rd | 109 +++++----- man/eventRVEIM.Rd |only man/hourlyQ.Rd |only man/postCorrection.Rd |only 18 files changed, 595 insertions(+), 503 deletions(-)
Title: Calculate Model-Based Metrics of Proportionality on Count-Based
Compositional Data
Description: Calculates metrics of proportionality using the logit-normal multinomial model. It can also provide empirical and plugin estimates of these metrics.
Author: Kevin McGregor [aut, cre, cph],
Nneka Okaeme [aut]
Maintainer: Kevin McGregor <kevin.mcgregor@umanitoba.ca>
Diff between countprop versions 1.0.1 dated 2023-08-18 and 1.1.1 dated 2025-12-11
DESCRIPTION | 12 +-- MD5 | 33 ++++----- NAMESPACE | 2 NEWS.md | 17 ++++ R/mle.R | 79 ++++++++++++++++------ R/proportionality.R | 155 ++++++++++++++++++++++++++------------------ README.md | 12 +++ build/vignette.rds |binary inst/doc/countprop.R | 2 inst/doc/countprop.pdf |binary man/convertSigma.Rd |only man/ebicPlot.Rd | 2 man/logLik.Rd | 6 + man/logitNormalVariation.Rd | 9 +- man/mleLR.Rd | 6 + man/mlePath.Rd | 5 + man/naiveVariation.Rd | 6 + man/pluginVariation.Rd | 2 18 files changed, 232 insertions(+), 116 deletions(-)
Title: Read the Swiss Register of Plant Protection Products
Description: Generate data objects from XML versions of the Swiss
Register of Plant Protection Products. An online version of the
register can be accessed at <https://www.psm.admin.ch/de/produkte>. There is no
guarantee of correspondence of the data read in using this package with that
online version, or with the original registration documents. Also, the
Federal Food Safety and Veterinary Office, coordinating the authorisation of
plant protection products in Switzerland, does not answer requests regarding
this package.
Author: Daniel Baumgartner [ctb] ,
Marcel Mathis [rev, ctb],
Romualdus Kasteel [rev] ,
Elisabeth Lutz [ctb],
Johannes Ranke [aut, cre] ,
Agroscope [cph]
Maintainer: Johannes Ranke <johannes.ranke@agroscope.admin.ch>
Diff between srppp versions 1.1.0 dated 2025-07-17 and 2.0.0 dated 2025-12-11
DESCRIPTION | 12 MD5 | 37 NAMESPACE | 1 NEWS.md | 9 R/resolve_cultures.R | 8 R/srppp-package.R | 1 R/srppp-xml.R | 129 README.md | 3 build/vignette.rds |binary inst/doc/srppp.html | 3314 +++++----- inst/doc/srppp_products_with_MO.html | 755 +- inst/testdata/Daten_Pflanzenschutzmittelverzeichnis_2024-12-16.zip |binary inst/testdata/PublicationData_2025_12_01.xml.xz |only man/resolve_cultures.Rd | 2 man/srppp_xml_get.Rd | 2 tests/testthat/setup.R | 13 tests/testthat/test-alternative_products.R | 23 tests/testthat/test-resolve_cultures.R | 74 tests/testthat/test-srppp_xml.R | 33 tests/testthat/test-use_rates.R | 56 20 files changed, 2354 insertions(+), 2118 deletions(-)
Title: Visualization Tool for Numerical Data on Human/Mouse Organs and
Organelles
Description: A tool for visualizing numerical data (e.g., gene expression, protein abundance) on predefined anatomical maps of human/mouse organs and subcellular organelles. It supports customization of color schemes, filtering by organ systems (for organisms) or organelle types, and generation of optional bar charts for quantitative comparison. The package integrates coordinate data for organs and organelles to plot anatomical/subcellular contours, mapping data values to specific structures for intuitive visualization of biological data distribution.The underlying method was described in the preprint by Zhou et al. (2022) <doi:10.1101/2022.09.07.506938>.
Author: Qirui Shen [aut, cre]
Maintainer: Qirui Shen <shenqr@i.smu.edu.cn>
Diff between OrgHeatmap versions 0.3.1 dated 2025-11-26 and 0.3.2 dated 2025-12-11
DESCRIPTION | 14 ++--- MD5 | 14 ++--- NAMESPACE | 106 ++++++++++++++++++++++----------------------- NEWS.md | 7 +- R/OrgHeatmap.R | 6 +- README.md | 2 data/mouse_organ_coord.rda |binary man/OrgHeatmap.Rd | 4 - 8 files changed, 78 insertions(+), 75 deletions(-)
Title: Curated Datasets and Tools for Epidemiological Data Analysis
Description: Curated datasets and intuitive data management functions to streamline epidemiological data workflows. It is designed to support researchers in quickly accessing clean, structured data and applying essential cleaning, summarizing, visualization, and export operations with minimal effort. Whether you're preparing a cohort for analysis or creating reports, 'DIVINE' makes the process more efficient, transparent, and reproducible.
Author: Natalia Pallares [aut, cre],
Joao Carmezim [aut],
Pau Satorra [aut],
Lucia Blanc [aut],
Cristian Tebe [aut]
Maintainer: Natalia Pallares <npallares@igtp.cat>
Diff between DIVINE versions 0.1.0 dated 2025-11-11 and 0.1.1 dated 2025-12-11
DESCRIPTION | 6 MD5 | 56 +- NEWS.md | 6 R/end_followup.R | 4 R/export_data.R | 8 R/icu.R | 4 R/multi_plot.R | 773 ++++++++++++++++++++------------------- build/vignette.rds |binary data/analytics.rda |binary data/comorbidities.rda |binary data/complications.rda |binary data/concomitant_medication.rda |binary data/demographic.rda |binary data/end_followup.rda |binary data/icu.rda |binary data/inhosp_antibiotics.rda |binary data/inhosp_antivirals.rda |binary data/inhosp_other_treatments.rda |binary data/scores.rda |binary data/symptoms.rda |binary data/vaccine.rda |binary data/vital_signs.rda |binary inst/doc/DIVINE.R | 16 inst/doc/DIVINE.Rmd | 668 ++++++++++++++++----------------- inst/doc/DIVINE.html | 30 - man/end_followup.Rd | 4 man/icu.Rd | 4 man/multi_plot.Rd | 63 +-- vignettes/DIVINE.Rmd | 668 ++++++++++++++++----------------- 29 files changed, 1166 insertions(+), 1144 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] ,
Heather Turner [ctb],
David Meyer [ctb],
Achim Zeileis [ctb] ,
Duncan Murdoch [ctb],
David Firth [ctb],
Matt Kumar [ctb],
Shuguang Sun [ctb],
Daniel Sabanes Bove [ctb]
Maintainer: Michael Friendly <friendly@yorku.ca>
Diff between vcdExtra versions 0.8-6 dated 2025-07-24 and 0.8.7 dated 2025-12-11
vcdExtra-0.8-6/vcdExtra/R/vcdExtra-deprecated.R |only vcdExtra-0.8-6/vcdExtra/build/partial.rdb |only vcdExtra-0.8-6/vcdExtra/man/figures |only vcdExtra-0.8-6/vcdExtra/man/vcdExtra-deprecated.Rd |only vcdExtra-0.8.7/vcdExtra/DESCRIPTION | 27 vcdExtra-0.8.7/vcdExtra/MD5 | 241 +++--- vcdExtra-0.8.7/vcdExtra/NAMESPACE | 246 ++---- vcdExtra-0.8.7/vcdExtra/NEWS.md | 13 vcdExtra-0.8.7/vcdExtra/R/CMHtest.R | 708 ++++++++++++------ vcdExtra-0.8.7/vcdExtra/R/CrabSatellites.R |only vcdExtra-0.8.7/vcdExtra/R/Crossings.R | 76 + vcdExtra-0.8.7/vcdExtra/R/GKgamma.R | 80 +- vcdExtra-0.8.7/vcdExtra/R/HLtest.R | 90 ++ vcdExtra-0.8.7/vcdExtra/R/Kway.R | 93 ++ vcdExtra-0.8.7/vcdExtra/R/LRstats.R | 88 +- vcdExtra-0.8.7/vcdExtra/R/Summarise.R | 89 +- vcdExtra-0.8.7/vcdExtra/R/blogits.R | 54 + vcdExtra-0.8.7/vcdExtra/R/collapse.table.R | 94 ++ vcdExtra-0.8.7/vcdExtra/R/cutfac.R | 73 + vcdExtra-0.8.7/vcdExtra/R/data.R |only vcdExtra-0.8.7/vcdExtra/R/datasets.R | 48 + vcdExtra-0.8.7/vcdExtra/R/expand.dft.R | 48 + vcdExtra-0.8.7/vcdExtra/R/glmlist.R | 98 ++ vcdExtra-0.8.7/vcdExtra/R/logLik.loglm.R | 63 + vcdExtra-0.8.7/vcdExtra/R/loglin-utilities.R | 102 ++ vcdExtra-0.8.7/vcdExtra/R/logseries.R | 185 +++- vcdExtra-0.8.7/vcdExtra/R/mcaplot.R | 96 +- vcdExtra-0.8.7/vcdExtra/R/modFit.R | 41 + vcdExtra-0.8.7/vcdExtra/R/mosaic.glm.R | 219 +++++ vcdExtra-0.8.7/vcdExtra/R/mosaic.glmlist.R | 149 +++ vcdExtra-0.8.7/vcdExtra/R/mosaic3d.R | 184 +++- vcdExtra-0.8.7/vcdExtra/R/print.Kappa.R | 36 vcdExtra-0.8.7/vcdExtra/R/seq_loglm.R | 88 +- vcdExtra-0.8.7/vcdExtra/R/seq_mosaic.R | 80 +- vcdExtra-0.8.7/vcdExtra/R/split3d.R | 78 + vcdExtra-0.8.7/vcdExtra/R/update.xtabs.R | 39 vcdExtra-0.8.7/vcdExtra/R/vcdExtra-package.R |only vcdExtra-0.8.7/vcdExtra/R/zero.test.R | 64 + vcdExtra-0.8.7/vcdExtra/data/CrabSatellites.rda |only vcdExtra-0.8.7/vcdExtra/inst/doc/a1-creating.html | 4 vcdExtra-0.8.7/vcdExtra/inst/doc/a2-tests.html | 10 vcdExtra-0.8.7/vcdExtra/inst/doc/a3-loglinear.html | 4 vcdExtra-0.8.7/vcdExtra/inst/doc/a4-mosaics.html | 4 vcdExtra-0.8.7/vcdExtra/inst/doc/a5-demo-housing.html | 4 vcdExtra-0.8.7/vcdExtra/inst/doc/a6-mobility.html | 4 vcdExtra-0.8.7/vcdExtra/inst/doc/a7-continuous.Rmd | 1 vcdExtra-0.8.7/vcdExtra/inst/doc/a7-continuous.html | 4 vcdExtra-0.8.7/vcdExtra/inst/doc/datasets.html | 6 vcdExtra-0.8.7/vcdExtra/inst/doc/tidyCats.html | 4 vcdExtra-0.8.7/vcdExtra/man/Abortion.Rd | 78 - vcdExtra-0.8.7/vcdExtra/man/Accident.Rd | 99 +- vcdExtra-0.8.7/vcdExtra/man/AirCrash.Rd | 52 - vcdExtra-0.8.7/vcdExtra/man/Alligator.Rd | 61 - vcdExtra-0.8.7/vcdExtra/man/Asbestos.Rd | 79 -- vcdExtra-0.8.7/vcdExtra/man/Bartlett.Rd | 69 - vcdExtra-0.8.7/vcdExtra/man/Burt.Rd | 69 - vcdExtra-0.8.7/vcdExtra/man/CMHtest.Rd | 309 +++---- vcdExtra-0.8.7/vcdExtra/man/Caesar.Rd | 82 -- vcdExtra-0.8.7/vcdExtra/man/Cancer.Rd | 58 - vcdExtra-0.8.7/vcdExtra/man/Cormorants.Rd | 91 +- vcdExtra-0.8.7/vcdExtra/man/CrabSatellites.Rd |only vcdExtra-0.8.7/vcdExtra/man/Crossings.Rd | 79 -- vcdExtra-0.8.7/vcdExtra/man/CyclingDeaths.Rd | 54 - vcdExtra-0.8.7/vcdExtra/man/DaytonSurvey.Rd | 97 +- vcdExtra-0.8.7/vcdExtra/man/Depends.Rd | 44 - vcdExtra-0.8.7/vcdExtra/man/Detergent.Rd | 68 - vcdExtra-0.8.7/vcdExtra/man/Donner.Rd | 146 +-- vcdExtra-0.8.7/vcdExtra/man/Draft1970.Rd | 83 +- vcdExtra-0.8.7/vcdExtra/man/Draft1970table.Rd | 81 -- vcdExtra-0.8.7/vcdExtra/man/Dyke.Rd | 76 - vcdExtra-0.8.7/vcdExtra/man/Fungicide.Rd | 71 - vcdExtra-0.8.7/vcdExtra/man/GKgamma.Rd | 100 +- vcdExtra-0.8.7/vcdExtra/man/GSS.Rd | 46 - vcdExtra-0.8.7/vcdExtra/man/Geissler.Rd | 85 +- vcdExtra-0.8.7/vcdExtra/man/Gilby.Rd | 70 - vcdExtra-0.8.7/vcdExtra/man/Glass.Rd | 95 +- vcdExtra-0.8.7/vcdExtra/man/HLtest.Rd | 123 +-- vcdExtra-0.8.7/vcdExtra/man/HairEyePlace.Rd | 65 - vcdExtra-0.8.7/vcdExtra/man/Hauser79.Rd | 117 +- vcdExtra-0.8.7/vcdExtra/man/Heart.Rd | 43 - vcdExtra-0.8.7/vcdExtra/man/Heckman.Rd | 90 +- vcdExtra-0.8.7/vcdExtra/man/HospVisits.Rd | 62 - vcdExtra-0.8.7/vcdExtra/man/HouseTasks.Rd | 52 - vcdExtra-0.8.7/vcdExtra/man/Hoyt.Rd | 104 +- vcdExtra-0.8.7/vcdExtra/man/ICU.Rd | 127 +-- vcdExtra-0.8.7/vcdExtra/man/JobSat.Rd | 44 - vcdExtra-0.8.7/vcdExtra/man/Kway.Rd | 148 +-- vcdExtra-0.8.7/vcdExtra/man/LRstats.Rd | 114 +- vcdExtra-0.8.7/vcdExtra/man/Mammograms.Rd | 43 - vcdExtra-0.8.7/vcdExtra/man/Mental.Rd | 59 - vcdExtra-0.8.7/vcdExtra/man/Mice.Rd | 62 - vcdExtra-0.8.7/vcdExtra/man/Mobility.Rd | 59 - vcdExtra-0.8.7/vcdExtra/man/PhdPubs.Rd | 69 - vcdExtra-0.8.7/vcdExtra/man/ShakeWords.Rd | 68 - vcdExtra-0.8.7/vcdExtra/man/Summarise.Rd | 105 +- vcdExtra-0.8.7/vcdExtra/man/TV.Rd | 88 +- vcdExtra-0.8.7/vcdExtra/man/Titanicp.Rd | 76 - vcdExtra-0.8.7/vcdExtra/man/Toxaemia.Rd | 76 - vcdExtra-0.8.7/vcdExtra/man/Vietnam.Rd | 70 - vcdExtra-0.8.7/vcdExtra/man/Vote1980.Rd | 75 - vcdExtra-0.8.7/vcdExtra/man/WorkerSat.Rd | 45 - vcdExtra-0.8.7/vcdExtra/man/Yamaguchi87.Rd | 125 +-- vcdExtra-0.8.7/vcdExtra/man/blogits.Rd | 102 +- vcdExtra-0.8.7/vcdExtra/man/collapse.table.Rd | 64 - vcdExtra-0.8.7/vcdExtra/man/cutfac.Rd | 120 +-- vcdExtra-0.8.7/vcdExtra/man/datasets.Rd | 100 +- vcdExtra-0.8.7/vcdExtra/man/expand.dft.Rd | 82 +- vcdExtra-0.8.7/vcdExtra/man/glmlist.Rd | 113 +- vcdExtra-0.8.7/vcdExtra/man/logLik.loglm.Rd | 96 +- vcdExtra-0.8.7/vcdExtra/man/loglin-utilities.Rd | 296 ++----- vcdExtra-0.8.7/vcdExtra/man/logseries.Rd | 127 +-- vcdExtra-0.8.7/vcdExtra/man/mcaplot.Rd | 125 +-- vcdExtra-0.8.7/vcdExtra/man/modFit.Rd | 64 - vcdExtra-0.8.7/vcdExtra/man/mosaic.glm.Rd | 276 +++---- vcdExtra-0.8.7/vcdExtra/man/mosaic.glmlist.Rd | 214 ++--- vcdExtra-0.8.7/vcdExtra/man/mosaic3d.Rd | 281 +++---- vcdExtra-0.8.7/vcdExtra/man/print.Kappa.Rd | 65 - vcdExtra-0.8.7/vcdExtra/man/seq_loglm.Rd | 156 +-- vcdExtra-0.8.7/vcdExtra/man/seq_mosaic.Rd | 122 +-- vcdExtra-0.8.7/vcdExtra/man/split3d.Rd | 115 +- vcdExtra-0.8.7/vcdExtra/man/update.xtabs.Rd | 66 - vcdExtra-0.8.7/vcdExtra/man/vcdExtra-package.Rd | 189 ++-- vcdExtra-0.8.7/vcdExtra/man/zero.test.Rd | 98 +- vcdExtra-0.8.7/vcdExtra/tests |only vcdExtra-0.8.7/vcdExtra/vignettes/a7-continuous.Rmd | 1 125 files changed, 6175 insertions(+), 4683 deletions(-)
Title: Powerful Classes for HTTP Requests and Responses
Description: In order to facilitate parsing of http requests and creating
appropriate responses this package provides two classes to handle a lot of
the housekeeping involved in working with http exchanges. The infrastructure
builds upon the 'rook' specification and is thus well suited to be combined
with 'httpuv' based web servers.
Author: Thomas Lin Pedersen [cre, aut]
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>
Diff between reqres versions 1.1.0 dated 2025-11-06 and 1.2.0 dated 2025-12-11
DESCRIPTION | 12 ++- MD5 | 19 +++-- NAMESPACE | 5 + NEWS.md | 6 + R/aaa.R | 7 + R/mock_request.R |only R/request.R | 105 ++++++++++++++++++----------- R/response.R | 51 +++++++------- man/maybe_request.Rd |only man/mock_request.Rd |only man/random_key.Rd | 2 tests/testthat/_snaps/request_unclassed.md |only tests/testthat/test-request_unclassed.R |only 13 files changed, 133 insertions(+), 74 deletions(-)
Title: Efficient Implementation of Kendall's Correlation Coefficient
Computation
Description: The computational complexity of the implemented algorithm for
Kendall's correlation is O(n log(n)), which is faster than the base R
implementation with a computational complexity of O(n^2). For small vectors
(i.e., less than 100 observations), the time difference is negligible.
However, for larger vectors, the speed difference can be substantial and the
numerical difference is minimal. The references are
Knight (1966) <doi:10.2307/2282833>,
Abrevaya (1999) <doi:10.1016/S0165-1765(98)00255-9>,
Christensen (2005) <doi:10.1007/BF02736122> and
Emara (2024) <https://learningcpp.org/>.
This implementation is described in
Vargas Sepulveda (2025) <doi:10.1371/journal.pone.0326090>.
Author: Mauricio Vargas Sepulveda [aut, cre] ,
Loader Catherine [ctb] ),
Ross Ihaka [ctb] )
Maintainer: Mauricio Vargas Sepulveda <m.vargas.sepulveda@gmail.com>
Diff between kendallknight versions 1.0.0 dated 2025-08-31 and 1.0.1 dated 2025-12-11
kendallknight-1.0.0/kendallknight/R/cpp11.R |only kendallknight-1.0.0/kendallknight/build/vignette.rds |only kendallknight-1.0.0/kendallknight/data |only kendallknight-1.0.0/kendallknight/inst/doc |only kendallknight-1.0.0/kendallknight/man/arcade.Rd |only kendallknight-1.0.0/kendallknight/src/cpp11.cpp |only kendallknight-1.0.0/kendallknight/vignettes |only kendallknight-1.0.1/kendallknight/DESCRIPTION | 12 - kendallknight-1.0.1/kendallknight/MD5 | 30 +-- kendallknight-1.0.1/kendallknight/NEWS.md | 4 kendallknight-1.0.1/kendallknight/R/cpp4r.R |only kendallknight-1.0.1/kendallknight/R/kendallknight-package.R | 20 -- kendallknight-1.0.1/kendallknight/README.md | 30 ++- kendallknight-1.0.1/kendallknight/build/partial.rdb |binary kendallknight-1.0.1/kendallknight/inst/CITATION |only kendallknight-1.0.1/kendallknight/inst/WORDLIST | 2 kendallknight-1.0.1/kendallknight/man/figures/logo.svg | 81 ++-------- kendallknight-1.0.1/kendallknight/man/kendallknight-package.Rd | 2 kendallknight-1.0.1/kendallknight/src/cpp4r.cpp |only kendallknight-1.0.1/kendallknight/src/kendall_correlation.cpp | 8 20 files changed, 70 insertions(+), 119 deletions(-)
Title: Datastore for 'fiery' Web Servers
Description: Provides a persistent datastore for 'fiery' apps. The datastore is
build on top of the 'storr' package and can thus be based on a variety of
backends. The datastore contains both a global and session-scoped section.
Author: Thomas Lin Pedersen [aut, cre] ,
Posit Software, PBC [cph, fnd]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@posit.co>
Diff between firesale versions 0.1.0 dated 2025-08-27 and 0.1.1 dated 2025-12-11
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/FireSale.R | 4 ++++ man/FireSale.Rd | 4 +++- man/firesale-package.Rd | 2 +- 6 files changed, 21 insertions(+), 11 deletions(-)
Title: Simplifies Exploratory Data Analysis
Description: Interactive data exploration with one line of code, automated
reporting or use an easy to remember set of tidy functions for low
code exploratory data analysis.
Author: Roland Krasser [aut, cre]
Maintainer: Roland Krasser <roland.krasser@gmail.com>
Diff between explore versions 1.3.6 dated 2025-10-02 and 1.4.0 dated 2025-12-11
DESCRIPTION | 8 +- MD5 | 82 ++++++++++++------------- NEWS.md | 6 + R/explain-xgboost.R | 130 ++++++++++++++++++++++++++++++++--------- R/explain.R | 25 ++++++- build/vignette.rds |binary inst/doc/abtest.html | 24 +++---- inst/doc/clean-drop.html | 6 - inst/doc/data.html | 6 - inst/doc/describe.html | 6 - inst/doc/explain.html | 52 ++++++++-------- inst/doc/explore-mtcars.html | 34 +++++----- inst/doc/explore-penguins.html | 14 ++-- inst/doc/explore-titanic.html | 24 +++---- inst/doc/explore.html | 58 +++++++++--------- inst/doc/predict.html | 10 +-- inst/doc/report-target.html | 12 +-- inst/doc/report-targetpct.html | 12 +-- inst/doc/report.html | 10 +-- inst/doc/tips-tricks.html | 16 ++--- man/check_vec_low_variance.Rd | 50 +++++++-------- man/create_data_abtest.Rd | 90 ++++++++++++++-------------- man/create_data_esoteric.Rd | 72 +++++++++++----------- man/create_notebook_explore.Rd | 2 man/cut_vec_num_avg.Rd | 38 +++++------ man/drop_obs_if.Rd | 46 +++++++------- man/drop_obs_with_na.Rd | 44 ++++++------- man/drop_var_by_names.Rd | 46 +++++++------- man/drop_var_low_variance.Rd | 46 +++++++------- man/drop_var_no_variance.Rd | 42 ++++++------- man/drop_var_not_numeric.Rd | 42 ++++++------- man/drop_var_with_na.Rd | 42 ++++++------- man/explain_forest.Rd | 2 man/explain_logreg.Rd | 2 man/explain_tree.Rd | 4 - man/explore_col.Rd | 106 ++++++++++++++++----------------- man/get_color.Rd | 72 +++++++++++----------- man/interact.Rd | 54 ++++++++--------- man/log_info_if.Rd | 38 +++++------ man/predict_target.Rd | 2 man/show_color.Rd | 42 ++++++------- man/use_data_wordle.Rd | 42 ++++++------- 42 files changed, 778 insertions(+), 681 deletions(-)
Title: Read bigWig and bigBed Files
Description: Read bigWig and bigBed files using "libBigWig"
<https://github.com/dpryan79/libBigWig>. Provides lightweight access
to the binary bigWig and bigBed formats developed by the UCSC Genome
Browser group.
Author: Jay Hesselberth [aut, cre],
RNA Bioscience Initiative [fnd, cph],
Devon Ryan [cph]
Maintainer: Jay Hesselberth <jay.hesselberth@gmail.com>
Diff between cpp11bigwig versions 0.1.2 dated 2025-08-18 and 0.1.3 dated 2025-12-11
DESCRIPTION | 6 MD5 | 14 - NEWS.md | 4 R/read.r | 49 +----- README.md | 8 - man/read_bigbed.Rd | 10 - src/cpp11bigwig.cpp | 333 ++++++++++++++++++++++++++++++--------------- tests/testthat/test-read.R | 33 ++++ 8 files changed, 293 insertions(+), 164 deletions(-)
Title: Statistical Methods for Phenology Analysis in Temperate Fruit
Trees
Description: The phenology of plants (i.e. the timing of their annual life
phases) depends on climatic cues. For temperate trees and many other plants,
spring phases, such as leaf emergence and flowering, have been found to result
from the effects of both cool (chilling) conditions and heat. Fruit tree
scientists (pomologists) have developed some metrics to quantify chilling
and heat (e.g. see Luedeling (2012) <doi:10.1016/j.scienta.2012.07.011>).
'chillR' contains functions for processing temperature records into
chilling (Chilling Hours, Utah Chill Units and Chill Portions) and heat units
(Growing Degree Hours). Regarding chilling metrics, Chill Portions are often
considered the most promising, but they are difficult to calculate. This package
makes it easy. 'chillR' also contains procedures for conducting a PLS analysis
relating phenological dates (e.g. bloom dates) to either mean temperatures or
mean chill and heat accumulation rates, based on long-term weather and phenology
records (Lued [...truncated...]
Author: Eike Luedeling [aut, cre] ,
Lars Caspersen [aut] ,
Eduardo Fernandez [aut]
Maintainer: Eike Luedeling <eike@eikeluedeling.com>
Diff between chillR versions 0.76 dated 2024-11-14 and 0.77 dated 2025-12-11
DESCRIPTION | 28 +- MD5 | 40 ++- NAMESPACE | 4 R/Kendall.R |only R/chillR-package.R | 10 R/download_baseline_cmip6_ecmwfr.R | 101 +++++++-- R/download_cmip6_ecmwfr.R | 150 +++++++------- R/extract_cmip6_data.R | 69 ++++-- R/plot_phenology_trends.R | 8 R/plot_scenarios.R | 8 R/print.Kendall.R |only R/summary.Kendall.R |only build/partial.rdb |only build/vignette.rds |binary inst/doc/PhenoFlex.html | 208 +++++++++---------- inst/doc/hourly_temperatures.html | 9 man/chillR-package.Rd | 32 ++- man/download_baseline_cmip6_ecmwfr.Rd | 214 ++++++++++---------- man/download_cmip6_ecmwfr.Rd | 360 +++++++++++++++++----------------- man/plot_phenology_trends.Rd | 8 man/plot_scenarios.Rd | 8 src/Kendall.f |only src/RcppExports.cpp | 10 src/init.c |only 24 files changed, 684 insertions(+), 583 deletions(-)
Title: Bioinformatics Modeling with Recursion and Autoencoder-Based
Ensemble
Description: Tools for bioinformatics modeling using recursive transformer-inspired
architectures, autoencoders, random forests, XGBoost, and stacked ensemble models.
Includes utilities for cross-validation, calibration, benchmarking, and threshold
optimization in predictive modeling workflows. The methodology builds on ensemble
learning (Breiman 2001 <doi:10.1023/A:1010933404324>), gradient boosting (Chen and
Guestrin 2016 <doi:10.1145/2939672.2939785>), autoencoders (Hinton and Salakhutdinov
2006 <doi:10.1126/science.1127647>), and recursive transformer efficiency approaches
such as Mixture-of-Recursions (Bae et al. 2025 <doi:10.48550/arXiv.2507.10524>).
Author: MD. Arshad [aut, cre]
Maintainer: MD. Arshad <arshad10867c@gmail.com>
Diff between BioMoR versions 0.1.0 dated 2025-10-03 and 0.1.1 dated 2025-12-10
DESCRIPTION | 10 MD5 | 37 +- R/autoencoder.R | 4 R/train_biomor.R | 4 build/vignette.rds |binary inst/doc/biomor-autoencoder.R | 11 inst/doc/biomor-autoencoder.Rmd | 30 + inst/doc/biomor-autoencoder.html | 608 ++++++++++++++++------------------- inst/doc/biomor-benchmarking.R | 15 inst/doc/biomor-benchmarking.Rmd | 35 +- inst/doc/biomor-benchmarking.html | 654 +++++++++++++++++++------------------- inst/doc/biomor-intro.R | 14 inst/doc/biomor-intro.Rmd | 53 +-- inst/doc/biomor-intro.html | 59 +-- tests/testthat/test_benchmark.R | 4 tests/testthat/test_models.R | 11 tests/testthat/test_utils.R |only vignettes/biomor-autoencoder.Rmd | 30 + vignettes/biomor-benchmarking.Rmd | 35 +- vignettes/biomor-intro.Rmd | 53 +-- 20 files changed, 849 insertions(+), 818 deletions(-)
Title: Analysis of Moderation, Statistical Power, and Optimal Design
for Studies Detecting Difference and Equivalence
Description: Analysis of moderation (ANOMO) method conceptualizes
the difference and equivalence tests as a moderation problem to
test the difference and equivalence of
two estimates (e.g., two means or two effects).
Author: Zuchao Shen [aut, cre]
Maintainer: Zuchao Shen <zuchao.shen@gmail.com>
Diff between anomo versions 1.0.0 dated 2025-02-23 and 1.2.2 dated 2025-12-10
anomo-1.0.0/anomo/R/od.eq.2group.R |only anomo-1.0.0/anomo/R/power.eq.2group.R |only anomo-1.0.0/anomo/man/od.eq.2group.Rd |only anomo-1.0.0/anomo/man/power.eq.2group.Rd |only anomo-1.2.2/anomo/DESCRIPTION | 16 - anomo-1.2.2/anomo/MD5 | 32 +-- anomo-1.2.2/anomo/NAMESPACE | 5 anomo-1.2.2/anomo/R/mcci.R | 294 +++++++++++++++++++------------ anomo-1.2.2/anomo/R/od.1.eq.R |only anomo-1.2.2/anomo/R/plot.power.eq.R |only anomo-1.2.2/anomo/R/power.1.eq.R |only anomo-1.2.2/anomo/R/re.R | 8 anomo-1.2.2/anomo/build/vignette.rds |binary anomo-1.2.2/anomo/inst/doc/anomo.R | 46 +--- anomo-1.2.2/anomo/inst/doc/anomo.Rmd | 100 ++++------ anomo-1.2.2/anomo/inst/doc/anomo.html | 167 ++++++++--------- anomo-1.2.2/anomo/man/mcci.Rd | 80 +++++--- anomo-1.2.2/anomo/man/od.1.eq.Rd |only anomo-1.2.2/anomo/man/plot.power.eq.Rd |only anomo-1.2.2/anomo/man/power.1.eq.Rd |only anomo-1.2.2/anomo/man/re.Rd | 8 anomo-1.2.2/anomo/vignettes/anomo.Rmd | 100 ++++------ 22 files changed, 462 insertions(+), 394 deletions(-)
Title: Pull Spatial Layers from 'WDNR ArcGIS REST API'
Description: Functions for finding and pulling data from the
'Wisconsin Department of Natural Resources ArcGIS REST APIs'
<https://dnrmaps.wi.gov/arcgis/rest/services> and
<https://dnrmaps.wi.gov/arcgis2/rest/services>.
Author: Paul Frater [aut, cre] ,
Zac Driscoll [aut]
Maintainer: Paul Frater <paul.frater@wisconsin.gov>
Diff between wdnr.gis versions 0.1.6 dated 2025-10-13 and 0.1.7 dated 2025-12-10
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/wdnr.gis-package.R | 2 +- man/wdnr.gis-package.Rd | 2 +- 4 files changed, 8 insertions(+), 8 deletions(-)
Title: Machine Coded Genetic Algorithms for Real-Valued Optimization
Problems
Description: Machine coded genetic algorithm (MCGA) is a fast tool for
real-valued optimization problems. It uses the byte
representation of variables rather than real-values. It
performs the classical crossover operations (uniform) on these
byte representations. Mutation operator is also similar to
classical mutation operator, which is to say, it changes a
randomly selected byte value of a chromosome by +1 or -1 with
probability 1/2. In MCGAs there is no need for
encoding-decoding process and the classical operators are
directly applicable on real-values. It is fast and can handle a
wide range of a search space with high precision. Using a
256-unary alphabet is the main disadvantage of this algorithm
but a moderate size population is convenient for many problems.
Package also includes multi_mcga function for multi objective
optimization problems. This function sorts the chromosomes
using their ranks calculated from the non-dominated sorting
algorithm.
Author: Mehmet Hakan Satman [aut, cre]
Maintainer: Mehmet Hakan Satman <mhsatman@istanbul.edu.tr>
Diff between mcga versions 3.0.7 dated 2023-11-27 and 3.0.9 dated 2025-12-10
DESCRIPTION | 14 +++++++++----- MD5 | 6 +++--- src/mcga.h | 2 +- src/multi_mcga.h | 2 +- 4 files changed, 14 insertions(+), 10 deletions(-)
Title: Parse Farm Credit Administration Call Report Data into Tidy Data
Frames
Description: Parses financial condition and performance data (Call Reports) for
institutions in the United States Farm Credit System. Contains functions for
downloading files from the Farm Credit Administration (FCA) Call Report
archive website and reading the files into tidy data frame format.
The archive website can be found at
<https://www.fca.gov/bank-oversight/call-report-data-for-download>.
Author: Michael Thomas [aut, cre],
Ivan Millanes [aut],
Ketchbrook Analytics [cph, fnd]
Maintainer: Michael Thomas <mthomas@ketchbrookanalytics.com>
Diff between fcall versions 0.1.5 dated 2025-11-19 and 0.1.6 dated 2025-12-10
DESCRIPTION | 6 +- MD5 | 10 +-- NEWS.md | 8 ++ R/download_data.R | 15 +++-- README.md | 152 ++++++++++++++++++++++++++------------------------- man/download_data.Rd | 7 +- 6 files changed, 111 insertions(+), 87 deletions(-)
Title: Network Scale-Up Models for Aggregated Relational Data
Description: Provides a variety of Network Scale-up Models for researchers to
analyze Aggregated Relational Data, through the use of Stan and 'glmmTMB'.
Also provides tools for model checking
In this version, the package implements models from
Laga, I., Bao, L., and Niu, X (2023) <doi:10.1080/01621459.2023.2165929>,
Zheng, T., Salganik, M. J., and Gelman, A. (2006) <doi:10.1198/016214505000001168>,
Killworth, P. D., Johnsen, E. C., McCarty, C., Shelley, G. A.,
and Bernard, H. R. (1998) <doi:10.1016/S0378-8733(96)00305-X>, and
Killworth, P. D., McCarty, C., Bernard, H. R., Shelley, G. A., and
Johnsen, E. C. (1998) <doi:10.1177/0193841X9802200205>.
Author: Ian Laga [aut, cre] ,
Owen G. Ward [aut],
Anna L. Smith [aut],
Benjamin Vogel [aut],
Jieyun Wang [aut],
Le Bao [aut],
Xiaoyue Niu [aut]
Maintainer: Ian Laga <ilaga25@gmail.com>
Diff between networkscaleup versions 0.1-2 dated 2024-02-25 and 0.2-1 dated 2025-12-10
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networkscaleup-0.2-1/networkscaleup/src/stanExports_Correlated_x_zglobal.h | 42 networkscaleup-0.2-1/networkscaleup/src/stanExports_Correlated_x_zsubpop.cc | 34 networkscaleup-0.2-1/networkscaleup/src/stanExports_Correlated_x_zsubpop.h | 42 networkscaleup-0.2-1/networkscaleup/src/stanExports_Correlated_x_zsubpop_zglobal.cc | 34 networkscaleup-0.2-1/networkscaleup/src/stanExports_Correlated_x_zsubpop_zglobal.h | 44 networkscaleup-0.2-1/networkscaleup/src/stanExports_Correlated_zglobal.cc | 34 networkscaleup-0.2-1/networkscaleup/src/stanExports_Correlated_zglobal.h | 40 networkscaleup-0.2-1/networkscaleup/src/stanExports_Correlated_zsubpop.cc | 34 networkscaleup-0.2-1/networkscaleup/src/stanExports_Correlated_zsubpop.h | 40 networkscaleup-0.2-1/networkscaleup/src/stanExports_Correlated_zsubpop_zglobal.cc | 34 networkscaleup-0.2-1/networkscaleup/src/stanExports_Correlated_zsubpop_zglobal.h | 42 networkscaleup-0.2-1/networkscaleup/src/stanExports_Overdispersed_Stan.cc | 34 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More information about networkscaleup at CRAN
Permanent link
Title: Likelihood Based Inference for ARIMA Modeling
Description: Estimating and analyzing auto regressive integrated moving average
(ARIMA) models. The primary function in this package is arima(), which fits
an ARIMA model to univariate time series data using a random restart
algorithm. This approach frequently leads to models that have model
likelihood greater than or equal to that of the likelihood obtained by
fitting the same model using the arima() function from the 'stats' package.
This package enables proper optimization of model likelihoods, which is a
necessary condition for performing likelihood ratio tests. This package
relies heavily on the source code of the arima() function of the 'stats'
package. For more information, please see Jesse Wheeler and Edward L.
Ionides (2025) <doi:10.1371/journal.pone.0333993>.
Author: Jesse Wheeler [aut, cre, cph],
Noel McAllister [aut],
Dhajanae Sylvertooth [aut],
Edward Ionides [ctb],
Brian Ripley [ctb] ,
R Core Team [cph]
Maintainer: Jesse Wheeler <jessewheeler@isu.edu>
Diff between arima2 versions 3.4.2 dated 2025-10-31 and 3.4.3 dated 2025-12-10
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NEWS.md | 5 +++++ README.md | 4 ++-- man/figures/README-PlotARMAresults-1.png |binary man/figures/README-PlotARMAresults-2.png |binary 6 files changed, 17 insertions(+), 12 deletions(-)
Title: Data Validation Infrastructure
Description: Declare data validation rules and data quality indicators;
confront data with them and analyze or visualize the results.
The package supports rules that are per-field, in-record,
cross-record or cross-dataset. Rules can be automatically
analyzed for rule type and connectivity. Supports checks implied
by an SDMX DSD file as well. See also Van der Loo
and De Jonge (2018) <doi:10.1002/9781118897126>, Chapter 6
and the JSS paper (2021) <doi:10.18637/jss.v097.i10>.
Author: Mark van der Loo [cre, aut] ,
Edwin de Jonge [aut] ,
Paul Hsieh [ctb]
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between validate versions 1.1.6 dated 2025-11-14 and 1.1.7 dated 2025-12-10
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- NEWS | 7 +++++++ R/compare.R | 4 ++-- inst/doc/JSS_3483.pdf |binary inst/doc/cookbook.Rmd | 4 +--- inst/doc/cookbook.html | 38 ++++++++++++++++++-------------------- inst/tinytest/test_validator.R | 6 +++--- man/cells.Rd | 2 +- man/compare.Rd | 2 +- vignettes/cookbook.Rmd | 4 +--- 11 files changed, 47 insertions(+), 46 deletions(-)
Title: Methods and Classes for the OMOP Common Data Model
Description: Provides definitions of core classes and methods used by analytic
pipelines that query the OMOP (Observational Medical Outcomes Partnership)
common data model.
Author: Marti Catala [aut, cre] ,
Edward Burn [aut] ,
Mike Du [ctb] ,
Yuchen Guo [ctb] ,
Adam Black [ctb] ,
Marta Alcalde-Herraiz [ctb]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>
Diff between omopgenerics versions 1.3.4 dated 2025-12-01 and 1.3.5 dated 2025-12-10
DESCRIPTION | 6 MD5 | 24 NEWS.md | 6 R/classCdmTable.R | 14 R/classCodelist.R | 83 ++- R/classCodelistWithDetails.R | 39 - R/classConceptSetExpression.R | 42 - R/compute.R | 114 ---- R/logger.R | 124 +++++ inst/doc/logging.html | 44 - inst/doc/summarised_result.html | 886 ++++++++++++++++++------------------ tests/testthat/test-classCodelist.R | 3 tests/testthat/test-logger.R | 3 13 files changed, 729 insertions(+), 659 deletions(-)
Title: Double Machine Learning for Static Panel Models with Fixed
Effects
Description: The 'xtdml' package implements partially linear panel regression (PLPR) models with high-dimensional confounding variables and an exogenous treatment variable within the double machine learning framework. The package is used to estimate the structural parameter (treatment effect) in static panel data models with fixed effects using the approaches established in Clarke and Polselli (2025) <doi:10.1093/ectj/utaf011>. 'xtdml' is built on the object-oriented package 'DoubleML' (Bach et al., 2024) <doi:10.18637/jss.v108.i03> using the 'mlr3' ecosystem.
Author: Annalivia Polselli [aut, cre]
Maintainer: Annalivia Polselli <apolselli.econ@gmail.com>
Diff between xtdml versions 0.1.9 dated 2025-11-12 and 0.1.10 dated 2025-12-10
DESCRIPTION | 10 +- MD5 | 26 ++--- NAMESPACE | 3 R/dataset.R | 5 - R/helper.R | 2 R/xtdml_data.R | 36 ++++--- R/xtdml_main.R | 183 +++++++++++++++++++++----------------- R/xtdml_plr.R | 20 +--- R/zzz.R | 39 ++++---- man/make_plpr_data.Rd | 4 man/xtdml.Rd | 82 ++++++++--------- man/xtdml_data.Rd | 32 ++++-- man/xtdml_data_from_data_frame.Rd | 8 - man/xtdml_plr.Rd | 21 ++-- 14 files changed, 249 insertions(+), 222 deletions(-)
Title: Integrative Analysis of Several Related Data Matrices
Description: A generalization of principal component analysis for integrative
analysis. The method finds principal components that describe single matrices
or that are common to several matrices. The solutions are sparse. Rank of
solutions is automatically selected using cross validation. The method is
described in Kallus et al. (2019) <doi:10.48550/arXiv.1911.04927>.
Author: Jonatan Kallus [aut],
Felix Held [ctb, cre]
Maintainer: Felix Held <felix.held@gmail.com>
Diff between mmpca versions 2.0.3 dated 2022-11-15 and 2.0.4 dated 2025-12-10
DESCRIPTION | 17 ++++++++--------- MD5 | 15 ++++++++------- NEWS.md | 6 +++++- README.md | 2 +- src/Makevars.in | 2 -- src/compile_commands.json |only src/fdf.cpp | 6 +++--- src/fdf.h | 8 ++++++++ src/optim.cpp | 1 + 9 files changed, 34 insertions(+), 23 deletions(-)
Title: Multilevel Latent Time Series Models with 'R' and 'Stan'
Description: Fit multilevel manifest or latent time-series models, including popular Dynamic Structural Equation Models (DSEM).
The models can be set up and modified with user-friendly functions and are fit to the data using 'Stan' for Bayesian inference.
Path models and formulas for user-defined models can be easily created with functions using 'knitr'.
Asparouhov, Hamaker, & Muthen (2018) <doi:10.1080/10705511.2017.1406803>.
Author: Kenneth Koslowski [aut, cre, cph] ,
Fabian Muench [aut] ,
Tobias Koch [aut] ,
Jana Holtmann [aut]
Maintainer: Kenneth Koslowski <kenneth.koslowski@uni-leipzig.de>
Diff between mlts versions 2.0.0 dated 2025-12-08 and 2.0.1 dated 2025-12-10
DESCRIPTION | 6 MD5 | 12 NEWS.md | 7 R/mlts_paths.R | 1630 +++++++++++++++++++++++----------------------- R/mlts_sim.R | 978 +++++++++++++-------------- R/mlts_standardized_btw.R | 685 +++++++++---------- R/prepare_data.R | 466 ++++++------- 7 files changed, 1911 insertions(+), 1873 deletions(-)
Title: Easily Convert GDP Data
Description: Convert GDP time series data from one unit to
another. All common GDP units are included, i.e. current and constant
local currency units, US$ via market exchange rates and international
dollars via purchasing power parities.
Author: Johannes Koch [aut, cre]
Maintainer: Johannes Koch <jokoch@pik-potsdam.de>
Diff between GDPuc versions 1.6.0 dated 2025-11-19 and 1.6.1 dated 2025-12-10
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 4 ++++ R/transform_user_input.R | 2 +- 4 files changed, 12 insertions(+), 8 deletions(-)
Title: Vectors Representing Random Variables
Description: Random vectors, called rvecs. An rvec holds
multiple draws, but tries to behave like a standard
R vector, including working well in data frames.
Rvecs are useful for analysing
output from a simulation or a Bayesian analysis.
Author: John Bryant [aut, cre],
Bayesian Demography Limited [cph]
Maintainer: John Bryant <john@bayesiandemography.com>
Diff between rvec versions 0.0.8 dated 2025-07-12 and 1.0.0 dated 2025-12-10
rvec-0.0.8/rvec/man/new_rvec.Rd |only rvec-0.0.8/rvec/tests/testthat/_snaps/plot |only rvec-1.0.0/rvec/DESCRIPTION | 15 rvec-1.0.0/rvec/MD5 | 142 +++--- rvec-1.0.0/rvec/NAMESPACE | 19 rvec-1.0.0/rvec/NEWS.md | 25 + rvec-1.0.0/rvec/R/aaa-rvec-classes.R |only rvec-1.0.0/rvec/R/as_list_col.R | 25 - rvec-1.0.0/rvec/R/atomic_to_rvec.R | 26 - rvec-1.0.0/rvec/R/check-functions.R | 75 +++ rvec-1.0.0/rvec/R/collapse_to_rvec.R | 25 - rvec-1.0.0/rvec/R/compare.R | 2 rvec-1.0.0/rvec/R/constructors.R | 145 +++++- rvec-1.0.0/rvec/R/distributions.R | 312 ++++--------- rvec-1.0.0/rvec/R/draws.R | 419 +++++++++++------ rvec-1.0.0/rvec/R/format.R | 48 +- rvec-1.0.0/rvec/R/if_else_rvec.R | 4 rvec-1.0.0/rvec/R/map_rvec.R | 4 rvec-1.0.0/rvec/R/matrixOps.R | 109 +--- rvec-1.0.0/rvec/R/missing.R | 30 - rvec-1.0.0/rvec/R/pool_draws.R |only rvec-1.0.0/rvec/R/rvec-package.R | 34 - rvec-1.0.0/rvec/R/rvec_to_rvec.R | 20 rvec-1.0.0/rvec/R/util.R | 8 rvec-1.0.0/rvec/R/vec_math.R | 6 rvec-1.0.0/rvec/README.md | 11 rvec-1.0.0/rvec/build/vignette.rds |binary rvec-1.0.0/rvec/inst/doc/vig1_overview.R | 21 rvec-1.0.0/rvec/inst/doc/vig1_overview.Rmd | 78 ++- rvec-1.0.0/rvec/inst/doc/vig1_overview.html | 104 ++-- rvec-1.0.0/rvec/man/as_list_col.Rd | 13 rvec-1.0.0/rvec/man/collapse_to_rvec.Rd | 25 - rvec-1.0.0/rvec/man/dbeta_rvec.Rd | 14 rvec-1.0.0/rvec/man/dbinom_rvec.Rd | 26 - rvec-1.0.0/rvec/man/dcauchy_rvec.Rd | 17 rvec-1.0.0/rvec/man/dchisq_rvec.Rd | 14 rvec-1.0.0/rvec/man/dexp_rvec.Rd | 14 rvec-1.0.0/rvec/man/df_rvec.Rd | 11 rvec-1.0.0/rvec/man/dgamma_rvec.Rd | 16 rvec-1.0.0/rvec/man/dgeom_rvec.Rd | 23 rvec-1.0.0/rvec/man/dhyper_rvec.Rd | 22 rvec-1.0.0/rvec/man/dlnorm_rvec.Rd | 16 rvec-1.0.0/rvec/man/dmultinom_rvec.Rd | 23 rvec-1.0.0/rvec/man/dnbinom_rvec.Rd | 28 - rvec-1.0.0/rvec/man/dnorm_rvec.Rd | 16 rvec-1.0.0/rvec/man/dpois_rvec.Rd | 24 - rvec-1.0.0/rvec/man/draws_all.Rd | 9 rvec-1.0.0/rvec/man/draws_ci.Rd | 11 rvec-1.0.0/rvec/man/draws_fun.Rd | 7 rvec-1.0.0/rvec/man/draws_median.Rd | 14 rvec-1.0.0/rvec/man/draws_min.Rd | 9 rvec-1.0.0/rvec/man/draws_quantile.Rd | 13 rvec-1.0.0/rvec/man/draws_sd.Rd |only rvec-1.0.0/rvec/man/dt_rvec.Rd | 14 rvec-1.0.0/rvec/man/dunif_rvec.Rd | 14 rvec-1.0.0/rvec/man/dweibull_rvec.Rd | 14 rvec-1.0.0/rvec/man/figures |only rvec-1.0.0/rvec/man/if_else_rvec.Rd | 4 rvec-1.0.0/rvec/man/map_rvec.Rd | 4 rvec-1.0.0/rvec/man/missing.Rd | 30 - rvec-1.0.0/rvec/man/new_rvec_blank.Rd |only rvec-1.0.0/rvec/man/new_rvec_deprecated.Rd |only rvec-1.0.0/rvec/man/pool_draws.Rd |only rvec-1.0.0/rvec/man/rvec-matrix-mult.Rd |only rvec-1.0.0/rvec/man/rvec-package.Rd | 25 - rvec-1.0.0/rvec/tests/testthat/test-check-functions.R | 48 ++ rvec-1.0.0/rvec/tests/testthat/test-constructors.R | 423 ++++++++++-------- rvec-1.0.0/rvec/tests/testthat/test-draws.R | 145 ++++++ rvec-1.0.0/rvec/tests/testthat/test-format.R | 2 rvec-1.0.0/rvec/tests/testthat/test-matrixOps.R | 130 +++++ rvec-1.0.0/rvec/tests/testthat/test-pool_draws.R |only rvec-1.0.0/rvec/tests/testthat/test-util.R | 8 rvec-1.0.0/rvec/vignettes/vig1_overview.Rmd | 78 ++- 73 files changed, 1824 insertions(+), 1187 deletions(-)
Title: J&J Innovative Medicine ADaM Test Data
Description: A set of Analysis Data Model (ADaM) datasets constructed by
modifying the ADaM datasets in the 'pharmaverseadam' package to meet J&J Innovative Medicine's
standard data structure for Clinical and Statistical Programming.
Author: David Munoz Tord [aut, cre],
Nicholas Masel [aut],
Joe Kovach [aut],
Mahesh Divakaran [ctb],
J&J Innovative Medicine [cph, fnd]
Maintainer: David Munoz Tord <david.munoztord@mailbox.org>
Diff between pharmaverseadamjnj versions 0.0.1 dated 2025-07-15 and 0.0.2 dated 2025-12-10
pharmaverseadamjnj-0.0.1/pharmaverseadamjnj/R/adaefmq.R |only pharmaverseadamjnj-0.0.1/pharmaverseadamjnj/data/adaefmq.rda |only pharmaverseadamjnj-0.0.1/pharmaverseadamjnj/man/adaefmq.Rd |only pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/DESCRIPTION | 10 - pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/MD5 | 73 +++++----- pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/NEWS.md | 31 +--- pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/R/adae.R | 19 +- pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/R/adaeocmq.R |only pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/R/adagocmq.R |only pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/R/adcm.R | 7 pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/R/adeg.R | 7 pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/R/adex.R | 16 +- pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/R/adexsum.R | 4 pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/R/adlb.R | 19 +- pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/R/adpc.R |only pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/R/adsl.R | 18 +- pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/R/adttesaf.R | 4 pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/R/advs.R | 4 pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/README.md | 28 +++ pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/data/adae.rda |binary pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/data/adaeocmq.rda |only pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/data/adagocmq.rda |only pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/data/adcm.rda |binary pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/data/adeg.rda |binary pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/data/adex.rda |binary pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/data/adexsum.rda |binary pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/data/adlb.rda |binary pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/data/adpc.rda |only pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/data/adsl.rda |binary pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/data/adttesaf.rda |binary pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/data/advs.rda |binary pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/inst |only pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/man/adae.Rd | 17 +- pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/man/adaeocmq.Rd |only pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/man/adagocmq.Rd |only pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/man/adcm.Rd | 5 pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/man/adeg.Rd | 5 pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/man/adex.Rd | 14 - pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/man/adexsum.Rd | 2 pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/man/adlb.Rd | 17 +- pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/man/adpc.Rd |only pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/man/adsl.Rd | 16 +- pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/man/adttesaf.Rd | 2 pharmaverseadamjnj-0.0.2/pharmaverseadamjnj/man/advs.Rd | 2 44 files changed, 179 insertions(+), 141 deletions(-)
More information about pharmaverseadamjnj at CRAN
Permanent link
Title: Download Radar Data for Biological Research
Description: Load polar volume and vertical profile data for
aeroecological research directly into R. With 'getRad' you can access
data from several sources in Europe and the US and standardize it to
facilitate further exploration in tools such as 'bioRad'.
Author: Bart Kranstauber [aut, cre] ,
Pieter Huybrechts [aut] ),
Peter Desmet [aut] ),
Cecilia Nilsson [ctb] ,
Alexander Tedeschi [ctb] ,
Hidde Leijnse [ctb] ,
Bart Hoekstra [ctb] ,
University of Amsterdam [cph] ,
Biodiversa+ [fnd]
Maintainer: Bart Kranstauber <b.kranstauber@uva.nl>
Diff between getRad versions 0.2.3 dated 2025-10-14 and 0.2.4 dated 2025-12-10
DESCRIPTION | 6 +- MD5 | 70 +++++++++++++++--------------- NEWS.md | 8 +++ R/get_pvol.R | 21 ++++----- R/get_pvol_de.R | 9 ++- R/get_pvol_dk.R | 3 - R/get_pvol_ee.R | 8 +-- R/get_pvol_nl.R | 71 +++++++++++++++++++++---------- R/get_pvol_se.R | 7 +-- R/get_pvol_us.R | 8 +-- R/get_vpts.R | 32 +++++-------- R/get_vpts_aloft.R | 11 ++-- R/get_vpts_coverage.R | 2 R/get_vpts_coverage_rmi.R | 8 +-- R/get_weather_radars.R | 33 ++++++++------ R/secrets.R | 16 ++---- R/utils.R | 43 +++++++++++------- R/utils_pvol.R | 2 README.md | 1 inst/doc/supported_sources.R | 2 inst/doc/supported_sources.Rmd | 2 inst/doc/supported_sources.html | 4 - man/figures/README-example-1.png |binary man/figures/README-example-2.png |binary man/figures/README-example-3.png |binary man/figures/README-example-4.png |binary man/figures/README-vpts-1.png |binary man/get_weather_radars.Rd | 4 - tests/testthat/test-get_pvol.R | 6 +- tests/testthat/test-get_pvol_dk.R | 5 -- tests/testthat/test-get_pvol_nl.R | 57 +++++++++++++++++++----- tests/testthat/test-get_pvol_ro.R | 7 +-- tests/testthat/test-get_vpts_aloft.R | 29 +++++------- tests/testthat/test-get_weather_radars.R | 4 - tests/testthat/test-secrets.R | 8 +-- vignettes/supported_sources.Rmd | 2 36 files changed, 276 insertions(+), 213 deletions(-)
Title: Fit Multivariate Diversity-Interactions Models with Repeated
Measures
Description: An add-on package to 'DImodels' for the fitting of biodiversity and ecosystem function relationship study data with multiple ecosystem function responses and/or time points. This package uses the multivariate and repeated measures Diversity-Interactions (DI) methods developed by Kirwan et al. (2009) <doi:10.1890/08-1684.1>, Finn et al. (2013) <doi:10.1111/1365-2664.12041>, and Dooley et al. (2015) <doi:10.1111/ele.12504>.
Author: Laura Byrne [aut, cre] ,
Rishabh Vishwakarma [aut],
Rafael de Andrade Moral [aut],
Caroline Brophy [aut]
Maintainer: Laura Byrne <Laura.Byrne.Work@outlook.com>
Diff between DImodelsMulti versions 1.2.0 dated 2025-08-21 and 1.2.1 dated 2025-12-10
DESCRIPTION | 15 +- MD5 | 39 +++-- NAMESPACE | 1 R/DImodelsMulti_HelpFile.R | 6 R/DImulti_fit.R | 20 ++ R/DImulti_predict.R | 28 +++- R/DImulti_runApp.R |only README.md | 52 +++---- build/vignette.rds |binary inst/doc/DImulti_commonErrors.html | 5 inst/doc/DImulti_onTheta.html | 5 inst/doc/DImulti_prediction.html | 5 inst/doc/DImulti_workflow.Rmd | 3 inst/doc/DImulti_workflow.html | 12 + inst/shiny |only man/Belgium.Rd | 164 ++++++++++++------------ man/Belgium_MV.Rd | 252 ++++++++++++++++++------------------- man/Belgium_RM.Rd | 232 +++++++++++++++++----------------- man/DImodelsMulti.Rd | 6 man/DImulti.Rd | 6 man/DImultiApp.Rd |only vignettes/DImulti_workflow.Rmd | 3 22 files changed, 454 insertions(+), 400 deletions(-)
Title: Covariate-Based Covariance Functions for Nonstationary Spatial
Modeling
Description: Estimation, prediction, and simulation of nonstationary Gaussian process with modular covariate-based covariance functions.
Sources of nonstationarity, such as spatial mean, variance, geometric anisotropy, smoothness, and nugget, can be considered based on spatial characteristics.
An induced compact-supported nonstationary covariance function is provided, enabling fast and memory-efficient computations when handling densely sampled domains.
Author: Federico Blasi [aut, cre] ,
Reinhard Furrer [ctb]
Maintainer: Federico Blasi <federicoblasi@gmail.com>
Diff between cocons versions 0.1.4 dated 2024-12-12 and 0.1.5 dated 2025-12-10
DESCRIPTION | 15 - MD5 | 45 ++--- NEWS.md | 7 R/RcppExports.R | 10 + R/checkFunctions.R | 143 ++++++++++++++++- R/cocons.R | 21 ++ R/getFunctions.R | 103 ++++++++++-- R/methods.R | 62 +++++++ R/neg2loglikelihood.R | 10 - R/optim.R | 262 +++++++++++++++++++++++++++++--- R/profile.R | 5 inst/doc/cocons.pdf |binary man/GetNeg2loglikelihood.Rd | 2 man/GetNeg2loglikelihoodProfile.Rd | 2 man/GetNeg2loglikelihoodREML.Rd | 2 man/GetNeg2loglikelihoodTaper.Rd | 2 man/GetNeg2loglikelihoodTaperProfile.Rd | 2 man/coco.Rd | 5 man/cocoOptim.Rd | 15 - man/getBoundariesV4.Rd |only man/show-methods.Rd |only man/sumsmoothlone.Rd |only src/RcppExports.cpp | 14 + src/cocons_full.cpp | 96 +++++++++-- src/cocons_taper.cpp | 34 +++- 25 files changed, 743 insertions(+), 114 deletions(-)
Title: Text Mining Package
Description: A framework for text mining applications within R.
Author: Ingo Feinerer [aut] ,
Kurt Hornik [aut, cre] ,
Artifex Software, Inc. [ctb, cph]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between tm versions 0.7-16 dated 2025-02-19 and 0.7-17 dated 2025-12-10
DESCRIPTION | 12 +++++------ MD5 | 50 +++++++++++++++++++++++------------------------ build/partial.rdb |binary build/vignette.rds |binary data/acq.rda |binary data/crude.rda |binary inst/doc/extensions.pdf |binary inst/doc/tm.pdf |binary man/Corpus.Rd | 2 - man/PCorpus.Rd | 4 +-- man/PlainTextDocument.Rd | 4 +-- man/SimpleCorpus.Rd | 2 - man/TextDocument.Rd | 2 - man/XMLSource.Rd | 2 - man/XMLTextDocument.Rd | 4 +-- man/foreign.Rd | 2 - man/matrix.Rd | 6 ++--- man/meta.Rd | 2 - man/plot.Rd | 3 +- man/readDOC.Rd | 2 - man/readPDF.Rd | 4 +-- man/readXML.Rd | 2 - man/removeWords.Rd | 2 - man/stemDocument.Rd | 1 man/termFreq.Rd | 2 - man/tokenizer.Rd | 8 +++---- 26 files changed, 59 insertions(+), 57 deletions(-)
Title: Store and Retrieve Data.frames in a Git Repository
Description: The git2rdata package is an R package for writing and reading
dataframes as plain text files. A metadata file stores important
information. 1) Storing metadata allows to maintain the classes of
variables. By default, git2rdata optimizes the data for file storage.
The optimization is most effective on data containing factors. The
optimization makes the data less human readable. The user can turn
this off when they prefer a human readable format over smaller files.
Details on the implementation are available in vignette("plain_text",
package = "git2rdata"). 2) Storing metadata also allows smaller row
based diffs between two consecutive commits. This is a useful feature
when storing data as plain text files under version control. Details
on this part of the implementation are available in
vignette("version_control", package = "git2rdata"). Although we
envisioned git2rdata with a git workflow in mind, you can use it in
combination with other version control systems like subversion [...truncated...]
Author: Thierry Onkelinx [aut, cre] ),
Floris Vanderhaeghe [ctb] ),
Peter Desmet [ctb] ),
Els Lommelen [ctb] ),
Research Institute for Nature and Forest [cph, fnd]
Maintainer: Thierry Onkelinx <thierry.onkelinx@inbo.be>
Diff between git2rdata versions 0.5.0 dated 2025-01-24 and 0.5.1 dated 2025-12-10
DESCRIPTION | 32 - MD5 | 133 +++---- NAMESPACE | 5 NEWS.md | 7 R/clean_data_path.R | 3 R/data_package.R | 47 +- R/datahash.R | 54 ++ R/is_git2rdata.R | 52 ++ R/is_git2rmeta.R | 57 ++- R/list_data.R | 46 +- R/meta.R | 350 ++++++++++++------ R/prune.R | 141 +++++-- R/read_vc.R | 146 +++---- R/recent_commit.R | 60 +-- R/reinstate.R |only R/relabel.R | 17 R/rename_variable.R | 24 - R/update_metadata.R | 54 ++ R/upgrade_data.R | 77 +++- R/verify_vc.R | 5 R/write_vc.R | 188 +++++++--- README.md | 62 ++- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 6 inst/Dockerfile |only inst/Rprofile.site |only inst/doc/efficiency.R | 25 - inst/doc/efficiency.Rmd | 25 - inst/doc/efficiency.html | 83 ++-- inst/doc/metadata.R | 9 inst/doc/metadata.Rmd | 9 inst/doc/metadata.html | 59 +-- inst/doc/plain_text.html | 75 ++-- inst/doc/split_by.html | 9 inst/doc/version_control.html | 85 ++-- inst/doc/workflow.R | 36 - inst/doc/workflow.Rmd | 42 +- inst/doc/workflow.html | 186 +++++---- man/git2rdata-package.Rd | 2 man/is_git2rdata.Rd | 4 man/is_git2rmeta.Rd | 4 man/list_data.Rd | 9 man/prune_meta.Rd | 9 man/read_vc.Rd | 13 man/recent_commit.Rd | 14 man/rm_data.Rd | 9 man/write_vc.Rd | 13 tests/testthat/setup_test_data.R | 27 + tests/testthat/test_a_basics.R | 372 +++++++++++++++++-- tests/testthat/test_b_is_git2rmeta.R | 157 +++++--- tests/testthat/test_b_prune.R | 56 ++ tests/testthat/test_b_special.R | 66 ++- tests/testthat/test_b_update.R | 18 tests/testthat/test_b_verify_vc.R | 9 tests/testthat/test_c_git.R | 561 +++++++++++++++++------------- tests/testthat/test_d_description.R | 52 +- tests/testthat/test_d_recent_commit.R | 167 ++++---- tests/testthat/test_d_relabel.R | 48 +- tests/testthat/test_e_data_package.R | 56 ++ tests/testthat/test_e_empty_label.R | 5 tests/testthat/test_e_non_ascii.R | 21 - tests/testthat/test_e_upgrade.R | 21 - tests/testthat/test_e_validate_metadata.R | 30 + tests/testthat/test_f_split_by.R | 55 ++ tests/testthat/test_g_rename_variable.R | 52 ++ vignettes/efficiency.Rmd | 25 - vignettes/metadata.Rmd | 9 vignettes/workflow.Rmd | 42 +- 69 files changed, 2673 insertions(+), 1462 deletions(-)
Title: Parse 'Tableau' Workbooks into Functional Data
Description: High-performance parsing of 'Tableau' workbook files into
tidy data frames and dependency graphs for other visualization tools
like R 'Shiny' or 'Power BI' replication.
Author: George Arthur [aut, cre]
Maintainer: George Arthur <prigasgenthian48@gmail.com>
Diff between twbparser versions 0.2.3 dated 2025-09-30 and 0.3.1 dated 2025-12-10
twbparser-0.2.3/twbparser/inst/extdata/test-for_zip.twbx |only twbparser-0.3.1/twbparser/DESCRIPTION | 6 twbparser-0.3.1/twbparser/MD5 | 52 - twbparser-0.3.1/twbparser/NAMESPACE | 14 twbparser-0.3.1/twbparser/NEWS.md | 70 - twbparser-0.3.1/twbparser/R/active-bindings.R |only twbparser-0.3.1/twbparser/R/calculated_fields.R | 35 twbparser-0.3.1/twbparser/R/datasources.R | 76 - twbparser-0.3.1/twbparser/R/insights.R |only twbparser-0.3.1/twbparser/R/published.R | 68 - twbparser-0.3.1/twbparser/R/twb_parser.R | 493 +++++----- twbparser-0.3.1/twbparser/R/utils.R | 20 twbparser-0.3.1/twbparser/README.md | 107 +- twbparser-0.3.1/twbparser/inst/doc/twbparser-intro.R | 87 - twbparser-0.3.1/twbparser/inst/doc/twbparser-intro.Rmd | 111 +- twbparser-0.3.1/twbparser/inst/doc/twbparser-intro.html | 222 ++-- twbparser-0.3.1/twbparser/inst/extdata/test_for_zip.twbx |only twbparser-0.3.1/twbparser/man/TwbParser.Rd | 2 twbparser-0.3.1/twbparser/man/extract_calculated_fields.Rd | 15 twbparser-0.3.1/twbparser/man/extract_datasource_details.Rd | 29 twbparser-0.3.1/twbparser/man/extract_named_connections.Rd | 14 twbparser-0.3.1/twbparser/man/twb_charts.Rd |only twbparser-0.3.1/twbparser/man/twb_colors.Rd |only twbparser-0.3.1/twbparser/man/twb_dashboard_filters.Rd |only twbparser-0.3.1/twbparser/man/twb_dashboard_summary.Rd |only twbparser-0.3.1/twbparser/man/twb_dashboards.Rd |only twbparser-0.3.1/twbparser/man/twb_page_composition.Rd |only twbparser-0.3.1/twbparser/man/twb_pages.Rd |only twbparser-0.3.1/twbparser/man/twb_pages_summary.Rd |only twbparser-0.3.1/twbparser/tests/testthat/test-active-bindings.R |only twbparser-0.3.1/twbparser/tests/testthat/test-calculated-fields.R |only twbparser-0.3.1/twbparser/tests/testthat/test-insights.R |only twbparser-0.3.1/twbparser/tests/testthat/test-overview.R |only twbparser-0.3.1/twbparser/tests/testthat/test-utils-extract_named_connections.R | 12 twbparser-0.3.1/twbparser/vignettes/twbparser-intro.Rmd | 111 +- 35 files changed, 863 insertions(+), 681 deletions(-)
Title: Tropical Cyclone (Hurricane, Typhoon) Spatial Hazard Modelling
Description: Methods for generating modelled parametric Tropical Cyclone (TC) spatial hazard fields and time series output at point locations from TC tracks. R's compatibility to simply use fast 'cpp' code via the 'Rcpp' package and the wide range spatial analysis tools via the 'terra' package makes it an attractive open source environment to study 'TCs'. This package estimates TC vortex wind and pressure fields using parametric equations originally coded up in 'python' by 'TCRM' <https://github.com/GeoscienceAustralia/tcrm> and then coded up in 'Cuda' 'cpp' by 'TCwindgen' <https://github.com/CyprienBosserelle/TCwindgen>.
Author: Julian O'Grady [aut, cre]
Maintainer: Julian O'Grady <julian.ogrady@csiro.au>
Diff between TCHazaRds versions 1.1.4 dated 2025-08-24 and 1.1.5 dated 2025-12-10
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- R/WindHazaRds.R | 32 ++++++++++++++++++++++++++------ README.md | 10 ++++++---- inst/doc/Introduction_to_TCHazaRds.R | 3 ++- inst/doc/Introduction_to_TCHazaRds.Rmd | 5 +++-- inst/doc/Introduction_to_TCHazaRds.html | 32 +++++++++++++++++++------------- man/update_Track.Rd | 3 ++- src/TCHazaRds.cpp | 16 ++++++++-------- vignettes/Introduction_to_TCHazaRds.Rmd | 5 +++-- 10 files changed, 82 insertions(+), 50 deletions(-)
Title: Posetic Data Analysis
Description: Build and manipulate partially ordered sets (posets), to perform some data analysis
on them and to implement multi-criteria decision making procedures. Several efficient ways for generating linear extensions are implemented, together with functions for building mutual ranking probabilities, incomparability, dominance and separation scores (Fattore, M., De Capitani, L., Avellone, A., Suardi, A. (2024). A fuzzy posetic toolbox for multi-criteria evaluation on ordinal data systems. ANNALS OF OPERATIONS RESEARCH <doi:10.1007/s10479-024-06352-3>).
Author: Alessandro Avellone [aut, cre],
Lucio De Capitani [aut],
Marco Fattore [aut]
Maintainer: Alessandro Avellone <alessandro.avellone@unimib.it>
Diff between poseticDataAnalysis versions 0.1.1 dated 2025-10-29 and 1.0.0 dated 2025-12-10
DESCRIPTION | 6 MD5 | 8 - src/lexicographicProductPOSet.cpp | 175 ++++++++++++++-------------- src/posetWrapper.cpp | 41 +++--- src/rwrapper.cpp | 234 +++++++++++++++++++------------------- 5 files changed, 232 insertions(+), 232 deletions(-)
More information about poseticDataAnalysis at CRAN
Permanent link
Title: Toolkit for Analysis of Genomic Data
Description: A toolkit for analysis of genomic data. The 'misha' package
implements an efficient data structure for storing genomic data, and
provides a set of functions for data extraction, manipulation and
analysis. Some of the 2D genome algorithms were described in Yaffe and Tanay
(2011) <doi:10.1038/ng.947>.
Author: Misha Hoichman [aut],
Aviezer Lifshitz [aut, cre],
Eitan Yaffe [aut],
Amos Tanay [aut],
Weizmann Institute of Science [cph]
Maintainer: Aviezer Lifshitz <aviezer.lifshitz@weizmann.ac.il>
Diff between misha versions 4.3.12 dated 2025-08-31 and 5.3.1 dated 2025-12-10
misha-4.3.12/misha/R/compute.R |only misha-4.3.12/misha/R/db.R |only misha-4.3.12/misha/R/intervals.R |only misha-4.3.12/misha/R/track.R |only misha-4.3.12/misha/tests/testthat/test-gextract.R |only misha-4.3.12/misha/tests/testthat/test-gintervals.R |only misha-4.3.12/misha/tests/testthat/test-gtrack.import.R |only misha-5.3.1/misha/DESCRIPTION | 13 misha-5.3.1/misha/MD5 | 559 ++- misha-5.3.1/misha/NAMESPACE | 25 misha-5.3.1/misha/NEWS.md | 111 misha-5.3.1/misha/R/compute-analysis.R |only misha-5.3.1/misha/R/compute-bins.R |only misha-5.3.1/misha/R/compute-core.R |only misha-5.3.1/misha/R/compute-distribution.R |only misha-5.3.1/misha/R/compute-partition.R |only misha-5.3.1/misha/R/compute-sequence.R |only misha-5.3.1/misha/R/compute-utils.R |only misha-5.3.1/misha/R/db-attrs.R |only misha-5.3.1/misha/R/db-cache.R |only misha-5.3.1/misha/R/db-core.R |only misha-5.3.1/misha/R/db-create.R |only misha-5.3.1/misha/R/db-dir.R |only misha-5.3.1/misha/R/db-index.R |only misha-5.3.1/misha/R/db-management.R |only misha-5.3.1/misha/R/db-root.R |only misha-5.3.1/misha/R/intervals-annotation.R |only misha-5.3.1/misha/R/intervals-bigset.R |only misha-5.3.1/misha/R/intervals-core.R |only misha-5.3.1/misha/R/intervals-iterator.R |only misha-5.3.1/misha/R/intervals-liftover.R |only misha-5.3.1/misha/R/intervals-load-save.R |only misha-5.3.1/misha/R/intervals-management.R |only misha-5.3.1/misha/R/intervals-operations.R |only misha-5.3.1/misha/R/intervals-tracks.R |only misha-5.3.1/misha/R/intervals-utils.R |only misha-5.3.1/misha/R/misha-package.R | 34 misha-5.3.1/misha/R/neighbors.R |only misha-5.3.1/misha/R/pssm_utils.R |only misha-5.3.1/misha/R/sequence.R | 486 +++ misha-5.3.1/misha/R/track-2d.R | 20 misha-5.3.1/misha/R/track-array.R | 17 misha-5.3.1/misha/R/track-attr.R | 5 misha-5.3.1/misha/R/track-convert.R |only misha-5.3.1/misha/R/track-core.R |only misha-5.3.1/misha/R/track-create.R |only misha-5.3.1/misha/R/track-import.R |only 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misha-5.3.1/misha/tests/testthat/test-gintervals.coverage.R |only misha-5.3.1/misha/tests/testthat/test-gintervals.intersect.R | 11 misha-5.3.1/misha/tests/testthat/test-gintervals.liftover-agg.R |only misha-5.3.1/misha/tests/testthat/test-gintervals.liftover-bin.R |only misha-5.3.1/misha/tests/testthat/test-gintervals.liftover-canonic.R |only misha-5.3.1/misha/tests/testthat/test-gintervals.mapply.R | 20 misha-5.3.1/misha/tests/testthat/test-gintervals.neighbors.R | 510 +++ misha-5.3.1/misha/tests/testthat/test-gintervals.normalize.R | 11 misha-5.3.1/misha/tests/testthat/test-gintervals.quantiles.R | 20 misha-5.3.1/misha/tests/testthat/test-gintervals.summary.R | 20 misha-5.3.1/misha/tests/testthat/test-gintervals1.R |only misha-5.3.1/misha/tests/testthat/test-gintervals2.R |only misha-5.3.1/misha/tests/testthat/test-giterator.cartesian_grid.R | 2 misha-5.3.1/misha/tests/testthat/test-giterator.intervals.R | 2 misha-5.3.1/misha/tests/testthat/test-glookup.R | 2 misha-5.3.1/misha/tests/testthat/test-gpartition.R | 20 misha-5.3.1/misha/tests/testthat/test-gquantiles.R | 2 misha-5.3.1/misha/tests/testthat/test-gsample.R | 2 misha-5.3.1/misha/tests/testthat/test-gscreen.R | 2 misha-5.3.1/misha/tests/testthat/test-gsegment.R | 11 misha-5.3.1/misha/tests/testthat/test-gseq.extract.R | 2 misha-5.3.1/misha/tests/testthat/test-gseq_pwm-parallel.R |only misha-5.3.1/misha/tests/testthat/test-gsummary.R | 2 misha-5.3.1/misha/tests/testthat/test-gtrack-format-conversion.R |only misha-5.3.1/misha/tests/testthat/test-gtrack-multicontig.R |only misha-5.3.1/misha/tests/testthat/test-gtrack.array.R | 11 misha-5.3.1/misha/tests/testthat/test-gtrack.create.R | 89 misha-5.3.1/misha/tests/testthat/test-gtrack.create_dense.R | 53 misha-5.3.1/misha/tests/testthat/test-gtrack.import1.R |only misha-5.3.1/misha/tests/testthat/test-gtrack.import2.R |only misha-5.3.1/misha/tests/testthat/test-gtrack.import3.R |only misha-5.3.1/misha/tests/testthat/test-gtrack.import4.R |only misha-5.3.1/misha/tests/testthat/test-gtrack.import5.R |only misha-5.3.1/misha/tests/testthat/test-gtrack.info.R | 29 misha-5.3.1/misha/tests/testthat/test-gtrack.liftover-agg.R |only misha-5.3.1/misha/tests/testthat/test-gtrack.liftover-bin.R |only misha-5.3.1/misha/tests/testthat/test-gtrack.liftover.R |only misha-5.3.1/misha/tests/testthat/test-gtrack.lookup.R | 29 misha-5.3.1/misha/tests/testthat/test-gtrack.smooth.R | 41 misha-5.3.1/misha/tests/testthat/test-gtrack.var.R | 34 misha-5.3.1/misha/tests/testthat/test-gvtrack.filter.R |only misha-5.3.1/misha/tests/testthat/test-gwilcox.R | 11 misha-5.3.1/misha/tests/testthat/test-indexed-integration.R |only misha-5.3.1/misha/tests/testthat/test-kmer.R | 2 misha-5.3.1/misha/tests/testthat/test-liftover-autoscore-kent.R |only misha-5.3.1/misha/tests/testthat/test-liftover-best_source_cluster.R |only misha-5.3.1/misha/tests/testthat/test-liftover-hg19-hg38.R |only misha-5.3.1/misha/tests/testthat/test-liftover.R |only misha-5.3.1/misha/tests/testthat/test-masked.R |only misha-5.3.1/misha/tests/testthat/test-motifs.R | 11 misha-5.3.1/misha/tests/testthat/test-multicontig-edge-cases-errors.R |only misha-5.3.1/misha/tests/testthat/test-multifasta-import.R |only misha-5.3.1/misha/tests/testthat/test-path-functions.R |only misha-5.3.1/misha/tests/testthat/test-pwm-count-spatial-bidirect.R |only misha-5.3.1/misha/tests/testthat/test-pwm-count.R |only misha-5.3.1/misha/tests/testthat/test-pwm-indexed-gtrack-create.R |only misha-5.3.1/misha/tests/testthat/test-pwm-prego-regression.R |only misha-5.3.1/misha/tests/testthat/test-pwm-sliding-window.R |only misha-5.3.1/misha/tests/testthat/test-pwm-spatial.R |only misha-5.3.1/misha/tests/testthat/test-pwm.R | 277 + misha-5.3.1/misha/tests/testthat/test-random-genome.R |only misha-5.3.1/misha/tests/testthat/test-sequence.R | 1427 +++++++++ misha-5.3.1/misha/tests/testthat/test-track.attrs.R | 275 + misha-5.3.1/misha/tests/testthat/test-vtrack-coverage.R | 2 misha-5.3.1/misha/tests/testthat/test-vtrack-distance-edge.R |only misha-5.3.1/misha/tests/testthat/test-vtrack-max-pos.R |only misha-5.3.1/misha/tests/testthat/test-vtrack-neighbor-count.R |only misha-5.3.1/misha/tests/testthat/test-vtrack-new-funcs.R |only misha-5.3.1/misha/tests/testthat/test-vtrack-values-equivalence.R |only misha-5.3.1/misha/tests/testthat/test-vtrack-values.R |only misha-5.3.1/misha/tests/testthat/test-vtrack.R | 81 misha-5.3.1/misha/vignettes/Database-Formats.Rmd |only misha-5.3.1/misha/vignettes/Manual.Rmd | 245 + 365 files changed, 13370 insertions(+), 2986 deletions(-)
Title: Tools for Quantitative Risk Management
Description: Functions and data sets for reproducing selected results from
the book "Quantitative Risk Management: Concepts, Techniques and Tools".
Furthermore, new developments and auxiliary functions for Quantitative
Risk Management practice.
Author: Marius Hofert [aut, cre],
Kurt Hornik [aut],
Alexander J. McNeil [aut]
Maintainer: Marius Hofert <mhofert@hku.hk>
Diff between qrmtools versions 0.0-18 dated 2025-09-10 and 0.0-19 dated 2025-12-10
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- NAMESPACE | 2 +- R/get_data.R | 23 +++++++++++++---------- inst/NEWS.Rd | 9 +++++++++ inst/doc/ARMA_GARCH_VaR.html | 4 ++-- inst/doc/VaR_bounds.html | 6 +++--- inst/doc/geometric_risk_measures.html | 4 ++-- man/get_data.Rd | 7 +++---- 9 files changed, 46 insertions(+), 35 deletions(-)
Title: Miscellaneous Statistical Functions Used in 'guide-R'
Description: Companion package for the manual
'guide-R : Guide pour l’analyse de données d’enquêtes avec R' available at
<https://larmarange.github.io/guide-R/>. 'guideR' implements miscellaneous
functions introduced in 'guide-R' to facilitate statistical analysis and
manipulation of survey data.
Author: Joseph Larmarange [aut, cre]
Maintainer: Joseph Larmarange <joseph@larmarange.net>
Diff between guideR versions 0.7.0 dated 2025-11-26 and 0.8.0 dated 2025-12-10
DESCRIPTION | 12 MD5 | 59 +- NAMESPACE | 17 NEWS.md | 34 + R/gtsummary_tests.R | 41 ++ R/gtsummary_themes.R | 58 ++ R/mean_sd.R |only R/median_iqr.R |only R/plot_categorical.R |only R/plot_continuous.R |only R/plot_means.R |only R/plot_multiple_answers.R | 9 R/plot_proportions.R | 522 +++++++++++++++++--------- R/proportion.R | 29 - R/safe_pal.R |only R/svyoneway.R |only R/vdiffr-helper.R |only inst/WORDLIST | 6 man/gtsummary_test.Rd | 17 man/gtsummary_themes.Rd | 27 + man/mean_sd.Rd |only man/median_iqr.Rd |only man/plot_categorical.Rd |only man/plot_continuous.Rd |only man/plot_means.Rd |only man/plot_multiple_answers.Rd | 5 man/plot_proportions.Rd | 26 - man/safe_pal.Rd |only man/svyoneway.Rd |only tests/testthat/test-gtsummary-themes.R | 18 tests/testthat/test-mean_sd.R |only tests/testthat/test-median_iqr.R |only tests/testthat/test-observed_vs_theoretical.R | 6 tests/testthat/test-plot_categorical.R |only tests/testthat/test-plot_continuous.R |only tests/testthat/test-plot_inertia_from_tree.R | 5 tests/testthat/test-plot_means.R |only tests/testthat/test-plot_multiple_answers.R | 66 ++- tests/testthat/test-plot_proportions.R | 66 ++- tests/testthat/test-plot_trajectories.R | 29 + tests/testthat/test-svyoneway.R |only 41 files changed, 783 insertions(+), 269 deletions(-)
Title: Functions to Estimate Tree Volume and Phytomass in the Italian
Forest Inventory 2005
Description: Tabacchi et al. (2011) published a very detailed study producing a uniform system of functions to estimate tree volume and
phytomass components (stem, branches, stool). The estimates of the 2005 Italian forest inventory (<https://www.inventarioforestale.org/it/>)
are based on these functions. The study documents the domain of applicability of each function and the equations to quantify estimates
accuracies for individual estimates as well as for aggregated estimates. This package makes the functions available in the R environment.
Version 2 exposes two distinct functions for individual and summary estimates. To facilitate access to the functions, tree species
identification is now based on EPPO species codes (<https://data.eppo.int/>).
Author: Nicola Puletti [aut, cre] ,
Mirko Grotti [aut],
Roberto Scotti [aut]
Maintainer: Nicola Puletti <nicola.puletti@gmail.com>
Diff between ForIT versions 2.5.1 dated 2025-09-22 and 2.5.2 dated 2025-12-10
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- NEWS.md | 8 +++++++- R/ForIT_DataBase.R | 2 +- R/INFCtabulate.R | 2 +- R/INFCvpe.R | 5 ++--- R/INFCvpeSUM.R | 2 +- R/examples/INFCvpeSUM_e.R | 2 +- man/ForIT_DataBase.Rd | 2 +- man/INFCvpe.Rd | 2 +- man/INFCvpeSUM.Rd | 4 ++-- 11 files changed, 30 insertions(+), 25 deletions(-)
Title: Serialize Model Objects with a Consistent Interface
Description: Typically, models in 'R' exist in memory and can be saved via
regular 'R' serialization. However, some models store information in
locations that cannot be saved using 'R' serialization alone. The goal
of 'bundle' is to provide a common interface to capture this
information, situate it within a portable object, and restore it for
use in new settings.
Author: Julia Silge [aut, cre] ,
Simon Couch [aut],
Qiushi Yan [aut],
Max Kuhn [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Julia Silge <julia.silge@posit.co>
Diff between bundle versions 0.1.2 dated 2024-11-12 and 0.1.3 dated 2025-12-10
bundle-0.1.2/bundle/R/package.R |only bundle-0.1.2/bundle/man/bundle_description.Rd |only bundle-0.1.3/bundle/DESCRIPTION | 30 ++-- bundle-0.1.3/bundle/LICENSE | 2 bundle-0.1.3/bundle/MD5 | 86 ++++++----- bundle-0.1.3/bundle/NAMESPACE | 2 bundle-0.1.3/bundle/NEWS.md | 4 bundle-0.1.3/bundle/R/bundle-package.R |only bundle-0.1.3/bundle/R/bundle_bart.R | 6 bundle-0.1.3/bundle/R/bundle_embed.R | 6 bundle-0.1.3/bundle/R/bundle_keras.R | 19 +- bundle-0.1.3/bundle/R/bundle_parsnip.R | 6 bundle-0.1.3/bundle/R/bundle_stacks.R | 8 - bundle-0.1.3/bundle/R/bundle_torch.R | 19 +- bundle-0.1.3/bundle/R/bundle_workflows.R | 12 - bundle-0.1.3/bundle/R/bundle_xgboost.R | 38 +++-- bundle-0.1.3/bundle/R/utils.R | 12 - bundle-0.1.3/bundle/README.md | 64 +++----- bundle-0.1.3/bundle/build/vignette.rds |binary bundle-0.1.3/bundle/inst/doc/bundle.R | 48 +++--- bundle-0.1.3/bundle/inst/doc/bundle.Rmd | 94 +++++++++---- bundle-0.1.3/bundle/inst/doc/bundle.html | 83 ++++++----- bundle-0.1.3/bundle/man/bundle-package.Rd |only bundle-0.1.3/bundle/man/bundle_bart.Rd | 6 bundle-0.1.3/bundle/man/bundle_caret.Rd | 6 bundle-0.1.3/bundle/man/bundle_embed.Rd | 12 - bundle-0.1.3/bundle/man/bundle_h2o.Rd | 2 bundle-0.1.3/bundle/man/bundle_keras.Rd | 16 +- bundle-0.1.3/bundle/man/bundle_parsnip.Rd | 12 - bundle-0.1.3/bundle/man/bundle_stacks.Rd | 10 - bundle-0.1.3/bundle/man/bundle_torch.Rd | 12 - bundle-0.1.3/bundle/man/bundle_workflows.Rd | 18 +- bundle-0.1.3/bundle/man/bundle_xgboost.Rd | 20 +- bundle-0.1.3/bundle/man/figures/lifecycle-deprecated.svg |only bundle-0.1.3/bundle/man/figures/lifecycle-experimental.svg |only bundle-0.1.3/bundle/man/figures/lifecycle-stable.svg |only bundle-0.1.3/bundle/man/figures/lifecycle-superseded.svg |only bundle-0.1.3/bundle/tests/testthat.R | 4 bundle-0.1.3/bundle/tests/testthat/test_bundle_embed.R | 9 - bundle-0.1.3/bundle/tests/testthat/test_bundle_h2o.R | 25 ++- bundle-0.1.3/bundle/tests/testthat/test_bundle_keras.R | 24 ++- bundle-0.1.3/bundle/tests/testthat/test_bundle_parsnip.R | 6 bundle-0.1.3/bundle/tests/testthat/test_bundle_stacks.R | 8 - bundle-0.1.3/bundle/tests/testthat/test_bundle_torch.R | 24 +-- bundle-0.1.3/bundle/tests/testthat/test_bundle_workflows.R | 24 +-- bundle-0.1.3/bundle/tests/testthat/test_bundle_xgboost.R | 29 +++- bundle-0.1.3/bundle/tests/testthat/test_utils.R | 11 - bundle-0.1.3/bundle/vignettes/bundle.Rmd | 94 +++++++++---- 48 files changed, 536 insertions(+), 375 deletions(-)
Title: D-Vine Quantile Regression
Description: Implements D-vine quantile regression models with
parametric or nonparametric pair-copulas. See
Kraus and Czado (2017) <doi:10.1016/j.csda.2016.12.009> and
Schallhorn et al. (2017) <doi:10.48550/arXiv.1705.08310>.
Author: Thomas Nagler [aut, cre],
Dani Kraus [ctb]
Maintainer: Thomas Nagler <mail@tnagler.com>
Diff between vinereg versions 0.11.0 dated 2025-01-11 and 0.12.1 dated 2025-12-10
DESCRIPTION | 10 +++--- MD5 | 22 ++++++------- NEWS.md | 6 +++ R/RcppExports.R | 4 +- R/vinereg.R | 10 +++--- README.md | 30 +++++++++--------- build/vignette.rds |binary inst/doc/abalone-example.html | 33 ++++++++++---------- inst/doc/bike-rental.html | 49 +++++++++++++++---------------- man/figures/README-unnamed-chunk-1-1.png |binary src/RcppExports.cpp | 11 +++--- src/vinereg.cpp | 27 ++++------------- 12 files changed, 99 insertions(+), 103 deletions(-)
Title: Visualise OMOP Results using 'shiny' Applications
Description: Visualise results obtained from analysing data mapped to the
Observational Medical Outcomes Partnership (OMOP) common data model using
'shiny' applications.
Author: Marti Catala [aut, cre] ,
Yuchen Guo [aut] ,
Edward Burn [ctb] ,
Nuria Mercade-Besora [ctb] ,
Elin Rowlands [ctb] ,
Cecilia Campanile [ctb]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>
Diff between OmopViewer versions 0.5.0 dated 2025-11-16 and 0.6.0 dated 2025-12-10
DESCRIPTION | 23 +++++----- MD5 | 38 ++++++++-------- NEWS.md | 12 +++++ R/appStatic.R | 52 ++++++++++++++--------- R/createServer.R | 8 ++- R/data.R | 4 - R/defaultPanels.R | 5 +- R/functions.R | 19 ++++++++ R/report.R |only R/sysdata.rda |binary data/omopViewerPanels.rda |binary data/omopViewerResults.rda |binary inst/brand/complement/darwin.yml | 2 inst/doc/edit_static_content.html | 2 inst/doc/export_static_app.html | 85 +++++++++++++++++++++++++++----------- inst/functions.R | 18 ++++++-- man/exportStaticApp.Rd | 7 +++ man/omopViewerPanels.Rd | 2 man/omopViewerResults.Rd | 2 tests/testthat/_snaps |only tests/testthat/test-choices.R | 2 21 files changed, 194 insertions(+), 87 deletions(-)
Title: Latent Binary Bayesian Neural Networks Using 'torch'
Description: Latent binary Bayesian neural networks (LBBNNs) are implemented using
'torch', an R interface to the LibTorch backend. Supports mean-field variational
inference as well as flexible variational posteriors using normalizing flows.
The standard LBBNN implementation follows Hubin and Storvik (2024) <doi:10.3390/math12060788>,
using the local reparametrization trick as in Skaaret-Lund et al. (2024)
<https://openreview.net/pdf?id=d6kqUKzG3V>. Input-skip connections are also supported,
as described in Høyheim et al. (2025) <doi:10.48550/arXiv.2503.10496>.
Author: Lars Skaaret-Lund [aut, cre],
Aliaksandr Hubin [aut],
Eirik Hoeyheim [aut]
Maintainer: Lars Skaaret-Lund <lars.skaaret-lund@nmbu.no>
Diff between LBBNN versions 0.1.1 dated 2025-12-01 and 0.1.2 dated 2025-12-10
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- NEWS.md | 11 +++++++---- R/LBBNN_Model.R | 3 ++- R/Layers.R | 12 +++++++++++- R/local_explanations.R | 4 +++- R/overwrite_functions.R | 7 +++---- R/plotting_graphs.R | 4 ++-- README.md | 3 +-- man/LBBNN_Linear.Rd | 5 ++++- man/figures/README-unnamed-chunk-6-1.png |binary man/predict.LBBNN_Net.Rd | 14 +++++++++++--- 12 files changed, 59 insertions(+), 34 deletions(-)
Title: Generalized Additive Models
Description: Functions for fitting and working with generalized additive models, as described in chapter 7 of "Statistical Models in S" (Chambers and Hastie (eds), 1991), and "Generalized Additive Models" (Hastie and Tibshirani, 1990).
Author: Trevor Hastie [aut, cre],
Balasubramanian Narasimhan [ctb]
Maintainer: Trevor Hastie <hastie@stanford.edu>
Diff between gam versions 1.22-6 dated 2025-08-22 and 1.22-7 dated 2025-12-10
ChangeLog | 2 ++ DESCRIPTION | 10 +++++----- MD5 | 11 ++++++----- R/gam-package.R | 2 +- cleanup |only man/predict.gam.Rd | 2 +- src/sbart.c | 2 +- 7 files changed, 16 insertions(+), 13 deletions(-)
Title: Test Theory Analysis and Biclustering
Description: Implements comprehensive test data engineering methods as described in
Shojima (2022, ISBN:978-9811699856). Provides statistical techniques for
engineering and processing test data: Classical Test Theory (CTT) with
reliability coefficients for continuous ability assessment; Item Response
Theory (IRT) including Rasch, 2PL, and 3PL models with item/test information
functions; Latent Class Analysis (LCA) for nominal clustering; Latent Rank
Analysis (LRA) for ordinal clustering with automatic determination of cluster
numbers; Biclustering methods including infinite relational models for
simultaneous clustering of examinees and items without predefined cluster
numbers; and Bayesian Network Models (BNM) for visualizing inter-item
dependencies. Features local dependence analysis through LRA and biclustering,
parameter estimation, dimensionality assessment, and network structure
visualization for educational, psychological, and social science research.
Author: Koji Kosugi [aut, cre]
Maintainer: Koji Kosugi <kosugitti@gmail.com>
Diff between exametrika versions 1.7.0 dated 2025-11-22 and 1.8.0 dated 2025-12-10
DESCRIPTION | 6 +-- MD5 | 34 ++++++++++----------- NEWS.md | 71 ++++++++++++++++++++++++++++++++++++++++++++ R/00_EMclus.R | 28 ++++++++--------- R/00_GridSearch.R | 22 +++++++++---- R/00_exametrikaPlot.R | 6 ++- R/05_LCA.R | 11 ++++-- R/06_LRA.R | 13 ++++---- R/07_Biclustering.R | 30 ++++++++++-------- R/07_IRM.R | 36 +++++++++++++--------- R/10_LDB.R | 4 +- R/12_LRA_ordinal.R | 29 ++++++++--------- R/13_LRA_rated.R | 29 ++++++++--------- R/15_Biclustering_nominal.R | 22 +++++++------ R/16_Biclustering_ordinal.R | 24 ++++++++------ man/Biclustering_IRM.Rd | 8 +++- man/GridSearch.Rd | 3 + man/LRA.Rd | 4 +- 18 files changed, 242 insertions(+), 138 deletions(-)
Title: R Interface to the 'DataONE' REST API
Description: Provides read and write access to data and metadata from
the 'DataONE' network <https://www.dataone.org> of data repositories.
Each 'DataONE' repository implements a consistent repository application
programming interface. Users call methods in R to access these remote
repository functions, such as methods to query the metadata catalog, get
access to metadata for particular data packages, and read the data objects
from the data repository. Users can also insert and update data objects on
repositories that support these methods.
Author: Matthew B. Jones [aut, cre] ,
Peter Slaughter [aut] ,
Rob Nahf [aut],
Carl Boettiger [aut] ,
Chris Jones [aut] ,
Bryce Mecum [aut] ,
Jeanette Clark [aut] ,
Jordan Read [ctb] ,
Lauren Walker [aut] ,
Edmund Hart [ctb] ,
Scott Chamberlain [ctb] ,
Regent [...truncated...]
Maintainer: Matthew B. Jones <jones@nceas.ucsb.edu>
This is a re-admission after prior archival of version 2.2.2 dated 2022-06-10
Diff between dataone versions 2.2.2 dated 2022-06-10 and 2.3.0 dated 2025-12-10
DESCRIPTION | 41 +-- MD5 | 248 +++++++++---------- NEWS | 8 R/AbstractTableDescriber.R | 6 R/AuthenticationManager.R | 74 ++--- R/CNode.R | 87 +++--- R/CertificateManager.R | 41 +-- R/D1Client.R | 166 ++++++------ R/D1Node.R | 119 ++++----- R/D1Object.R | 28 +- R/MNode.R | 89 +++--- R/auth_request.R | 37 ++ R/dataone-defunct.R | 76 ++--- R/dataone-deprecated.R | 23 - R/dataone-package.R | 25 + README.md | 44 ++- build/vignette.rds |binary inst/WORDLIST | 158 +++++------- inst/doc/v01-dataone-overview.R | 64 ++-- inst/doc/v01-dataone-overview.Rmd | 2 inst/doc/v01-dataone-overview.html | 187 +++++++------- inst/doc/v02-dataone-federation.R | 22 - inst/doc/v02-dataone-federation.Rmd | 9 inst/doc/v02-dataone-federation.html | 158 ++++++------ inst/doc/v03-searching-dataone.R | 96 +++---- inst/doc/v03-searching-dataone.Rmd | 7 inst/doc/v03-searching-dataone.html | 210 ++++++++-------- inst/doc/v04-download-data.R | 106 ++++---- inst/doc/v04-download-data.Rmd | 2 inst/doc/v04-download-data.html | 209 ++++++++-------- inst/doc/v05-upload-data.R | 124 ++++----- inst/doc/v05-upload-data.html | 363 ++++++++++++++-------------- inst/doc/v06-update-package.R | 106 ++++---- inst/doc/v06-update-package.html | 201 ++++++++------- inst/doc/v07-known-issues.R | 40 +-- inst/doc/v07-known-issues.html | 165 ++++++------ man/AbstractTableDescriber-class.Rd | 20 - man/AuthenticationManager-class.Rd | 60 ++-- man/AuthenticationManager.Rd | 2 man/CNode-class.Rd | 32 +- man/CNode.Rd | 6 man/CertificateManager-class.Rd | 50 +-- man/CertificateManager.Rd | 8 man/D1Client-class.Rd | 32 +- man/D1Client-initialize.Rd | 2 man/D1Client.Rd | 6 man/D1Node-class.Rd | 28 +- man/D1Object-class.Rd | 16 - man/D1Object-initialize.Rd | 2 man/D1Object.Rd | 2 man/MNode-class.Rd | 29 +- man/MNode.Rd | 4 man/addData.Rd | 2 man/archive.Rd | 11 man/auth_delete.Rd | 2 man/auth_get.Rd | 2 man/auth_head.Rd | 10 man/auth_post.Rd | 2 man/auth_put.Rd | 2 man/auth_put_post_delete.Rd | 2 man/canRead.Rd | 2 man/convert.csv.Rd | 2 man/createDataPackage.Rd | 2 man/createObject.Rd | 7 man/d1IdentifierSearch.Rd | 2 man/d1SolrQuery.Rd | 2 man/data.tableAttributeNames.Rd | 10 man/data.tableAttributeOrientation.Rd | 10 man/data.tableAttributeStorageTypes.Rd | 10 man/data.tableAttributeTypes.Rd | 10 man/data.tableMissingValueCodes.Rd | 10 man/data.tableSkipLinesHeader.Rd | 8 man/dataone-defunct.Rd | 82 +++--- man/dataone-deprecated.Rd | 20 - man/dataone.Rd | 24 + man/downloadCert.Rd | 8 man/downloadObject.Rd | 8 man/echoCredentials.Rd | 2 man/encodeUrlPath.Rd | 2 man/encodeUrlQuery.Rd | 2 man/generateIdentifier.Rd | 11 man/getAuthMethod.Rd | 2 man/getAuthSubject.Rd | 2 man/getCN.Rd | 2 man/getCertExpires.Rd | 2 man/getCertLocation.Rd | 4 man/getChecksum.Rd | 2 man/getD1Object.Rd | 2 man/getDataObject.Rd | 12 man/getDataPackage.Rd | 6 man/getEndpoint.Rd | 2 man/getErrorDescription.Rd | 12 man/getFormat.Rd | 2 man/getMN.Rd | 4 man/getMNode.Rd | 6 man/getMNodeId.Rd | 2 man/getObject.Rd | 2 man/getPackage.Rd | 6 man/getSystemMetadata.Rd | 2 man/hasReservation.Rd | 4 man/isAuthValid.Rd | 8 man/isAuthorized.Rd | 4 man/isCertExpired.Rd | 2 man/is_windows.Rd |only man/listFormats.Rd | 4 man/listMemberNodes.Rd | 2 man/listNodes.Rd | 2 man/obscureCert.Rd | 6 man/query.Rd | 10 man/reserveIdentifier.Rd | 2 man/restoreCert.Rd | 6 man/setMNodeId.Rd | 2 man/setObsoletedBy.Rd | 6 man/setPublicAccess.Rd | 6 man/updateObject.Rd | 9 man/updateSystemMetadata.Rd | 9 man/uploadDataObject.Rd | 2 man/uploadDataPackage.Rd | 14 - tests/testthat/helper-base.R | 10 tests/testthat/test.AuthenticationManager.R | 14 - tests/testthat/test.CNode.R | 3 tests/testthat/test.ssl.R |only vignettes/v01-dataone-overview.Rmd | 2 vignettes/v02-dataone-federation.Rmd | 9 vignettes/v03-searching-dataone.Rmd | 7 vignettes/v04-download-data.Rmd | 2 126 files changed, 2106 insertions(+), 2018 deletions(-)
Title: Clustering of Weighted Data
Description: Clusters state sequences and weighted data. It provides an optimized weighted PAM algorithm as well as functions for aggregating replicated cases, computing cluster quality measures for a range of clustering solutions, sequence analysis typology validation using parametric bootstraps and plotting (fuzzy) clusters of state sequences. It further provides a fuzzy and crisp CLARA algorithm to cluster large database with sequence analysis, and a methodological framework for Robustness Assessment of Regressions using Cluster Analysis Typologies (RARCAT).
Author: Matthias Studer [aut, cre],
Leonard Roth [ctb]
Maintainer: Matthias Studer <matthias.studer@unige.ch>
Diff between WeightedCluster versions 1.8-1 dated 2024-12-10 and 2.0 dated 2025-12-10
DESCRIPTION | 19 ++- MD5 | 53 ++++++---- NAMESPACE | 14 +- NEWS | 10 ++ R/amemat.R |only R/bootclustrange.R | 3 R/clara_clustrange.R | 43 ++++++-- R/clustrangefamily.R | 2 R/rarcat.R |only R/wfcmdd.r | 169 +++++++++++++++++++---------------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/BigDataSA.html | 39 ++++---- inst/doc/ClusterExternalValidSA.Rmd | 2 inst/doc/ClusterExternalValidSA.html | 37 ++++--- inst/doc/ClusterValidSA.html | 59 ++++++------ inst/doc/FuzzySA.Rmd | 2 inst/doc/FuzzySA.html | 60 ++++++------ inst/doc/RARCAT.R |only inst/doc/RARCAT.Rmd |only inst/doc/RARCAT.html |only inst/doc/WeightedCluster.pdf |binary inst/doc/WeightedClusterFR.Rnw | 6 - inst/doc/WeightedClusterFR.pdf |binary inst/doc/WeightedClusterPreview.pdf |binary man/rarcat.Rd |only vignettes/ClusterExternalValidSA.Rmd | 2 vignettes/FuzzySA.Rmd | 2 vignettes/RARCAT.Rmd |only vignettes/WeightedClusterFR.Rnw | 6 - vignettes/manual.bib | 3 31 files changed, 298 insertions(+), 233 deletions(-)
More information about WeightedCluster at CRAN
Permanent link
Title: R Interface to W3C Markup Validation Services
Description: R interface to a W3C Markup Validation service.
See <https://validator.w3.org/> for more information.
Author: Kurt Hornik [aut, cre]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between W3CMarkupValidator versions 0.2-1 dated 2025-08-23 and 0.2-2 dated 2025-12-10
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/w3c.R | 31 ++++++++++++++++++++----------- man/w3c_markup_validate.Rd | 19 +++++++++++++++++-- 4 files changed, 43 insertions(+), 19 deletions(-)
More information about W3CMarkupValidator at CRAN
Permanent link
Title: Genome Interval Arithmetic
Description: Read and manipulate genome intervals and signals. Provides
functionality similar to command-line tool suites within R, enabling
interactive analysis and visualization of genome-scale data. Riemondy
et al. (2017) <doi:10.12688/f1000research.11997.1>.
Author: Jay Hesselberth [aut, cre] ,
Kent Riemondy [aut] ,
RNA Bioscience Initiative [fnd, cph]
Maintainer: Jay Hesselberth <jay.hesselberth@cuanschutz.edu>
Diff between valr versions 0.8.4 dated 2025-06-22 and 0.9.0 dated 2025-12-10
valr-0.8.4/valr/R/RcppExports.R |only valr-0.8.4/valr/R/globals.r |only valr-0.8.4/valr/inst/include/DataFrameBuilder.h |only valr-0.8.4/valr/inst/include/IntervalTree.h |only valr-0.8.4/valr/inst/include/IntervalTree_ext.h |only valr-0.8.4/valr/inst/include/genome.h |only valr-0.8.4/valr/inst/include/group_apply.h |only valr-0.8.4/valr/inst/include/grouped_dataframe.h |only valr-0.8.4/valr/inst/include/intervals.h |only valr-0.8.4/valr/inst/include/random.h |only valr-0.8.4/valr/inst/include/utils.h |only valr-0.8.4/valr/man/read_bigwig.Rd |only valr-0.8.4/valr/src/RcppExports.cpp |only valr-0.8.4/valr/src/init.c |only valr-0.8.4/valr/src/valr_utils.cpp |only valr-0.9.0/valr/DESCRIPTION | 24 valr-0.9.0/valr/MD5 | 217 ++-- valr-0.9.0/valr/NAMESPACE | 12 valr-0.9.0/valr/NEWS.md | 32 valr-0.9.0/valr/R/bed12_to_exons.r | 1 valr-0.9.0/valr/R/bed_absdist.r | 14 valr-0.9.0/valr/R/bed_closest.r | 8 valr-0.9.0/valr/R/bed_cluster.r | 5 valr-0.9.0/valr/R/bed_complement.r | 13 valr-0.9.0/valr/R/bed_coverage.R | 25 valr-0.9.0/valr/R/bed_fisher.r | 5 valr-0.9.0/valr/R/bed_flank.r | 5 valr-0.9.0/valr/R/bed_genomecov.R | 15 valr-0.9.0/valr/R/bed_glyph.r | 24 valr-0.9.0/valr/R/bed_intersect.r | 38 valr-0.9.0/valr/R/bed_jaccard.r | 24 valr-0.9.0/valr/R/bed_makewindows.r | 1 valr-0.9.0/valr/R/bed_map.r | 24 valr-0.9.0/valr/R/bed_merge.r | 13 valr-0.9.0/valr/R/bed_partition.r | 5 valr-0.9.0/valr/R/bed_projection.r | 68 - 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valr-0.9.0/valr/man/bed_subtract.Rd | 7 valr-0.9.0/valr/man/bed_window.Rd | 11 valr-0.9.0/valr/man/reexports.Rd |only valr-0.9.0/valr/src/bed12toexons.cpp | 147 +- valr-0.9.0/valr/src/closest.cpp | 327 +++--- valr-0.9.0/valr/src/complement.cpp | 134 +- valr-0.9.0/valr/src/coverage.cpp | 218 ++-- valr-0.9.0/valr/src/cpp11.cpp |only valr-0.9.0/valr/src/dist.cpp | 182 +-- valr-0.9.0/valr/src/flank.cpp | 183 +-- valr-0.9.0/valr/src/gcoverage.cpp | 167 ++- valr-0.9.0/valr/src/intersect.cpp | 210 ++-- valr-0.9.0/valr/src/makewindows.cpp | 145 +- valr-0.9.0/valr/src/merge.cpp | 207 ++- valr-0.9.0/valr/src/partition.cpp | 172 +-- valr-0.9.0/valr/src/random.cpp | 110 +- valr-0.9.0/valr/src/shuffle.cpp | 372 +++---- valr-0.9.0/valr/src/subtract.cpp | 184 ++- valr-0.9.0/valr/tests/testthat/_snaps/glyph/intersect-glyph-is-ok.svg | 78 - valr-0.9.0/valr/tests/testthat/_snaps/glyph/merge-glyph-is-ok.svg | 60 - valr-0.9.0/valr/tests/testthat/test-db.r | 8 valr-0.9.0/valr/tests/testthat/test_absdist.r | 89 - 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Title: Interactively Gate Points
Description: Interactively gate points on a scatter plot. Interactively drawn gates are
recorded and can be applied programmatically to reproduce results exactly. Programmatic gating is
based on the package gatepoints by Wajid Jawaid.
Author: Stefano Mangiola [aut],
Wajid Jawaid [ctb],
William Hutchison [cre, aut]
Maintainer: William Hutchison <hutchison.w@wehi.edu.au>
Diff between tidygate versions 1.0.14 dated 2024-09-17 and 1.0.19 dated 2025-12-10
DESCRIPTION | 25 ++-- MD5 | 20 +-- NAMESPACE | 7 + R/gate_app.R | 7 - R/methods.R | 80 ++++++++++++++- build/stage23.rdb |binary build/vignette.rds |binary inst/doc/introdution.R | 34 +++--- inst/doc/introdution.html | 236 ++++++++++++++++++++-------------------------- man/gate.Rd | 5 man/gate_interactive.Rd | 6 - 11 files changed, 234 insertions(+), 186 deletions(-)
Title: Develop and Use Modular Health Economic Models
Description: A template model module, tools to help find model modules
derived from this template and a programming syntax to use these
modules in health economic analyses. These elements are the
foundation for a prototype software framework for developing living
and transferable models and using those models in reproducible health
economic analyses. The software framework is extended by other R
libraries. For detailed documentation about the framework and how to
use it visit <https://www.ready4-dev.com/>. For a background to the
methodological issues that the framework is attempting to help solve,
see Hamilton et al. (2024) <doi:10.1007/s40273-024-01378-8>.
Author: Matthew Hamilton [aut, cre, cph] ,
Orygen [cph, fnd],
Australian Government Research Training Program [fnd],
VicHealth [fnd],
Victoria University [fnd]
Maintainer: Matthew Hamilton <matthew.hamilton1@monash.edu>
Diff between ready4 versions 0.1.18 dated 2024-09-30 and 0.1.19 dated 2025-12-10
DESCRIPTION | 35 +- MD5 | 422 +++++++++++++++--------------- NAMESPACE | 2 NEWS.md | 4 R/C4_Ready4Project.R |only R/fn_get.R | 72 +++-- R/fn_make.R | 8 R/fn_write.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 38 +- inst/MD_RMDs/index.Rmd | 54 +-- inst/MD_RMDs/index_Body.Rmd | 36 +- inst/MD_Rmarkdown/index.en.Rmarkdown | 56 +-- inst/doc/V_01.R | 2 inst/doc/V_01.Rmd | 162 +++++------ inst/doc/V_01.html | 2 inst/doc/V_02.R | 4 inst/doc/V_02.Rmd | 134 ++++----- inst/doc/V_02.html | 23 - inst/doc/V_03.Rmd | 98 +++--- inst/doc/V_03.html | 2 inst/doc/V_04.R | 4 inst/doc/V_04.Rmd | 8 inst/doc/V_04.html | 55 +-- inst/doc/V_05.R | 8 inst/doc/V_05.Rmd | 122 ++++---- inst/doc/V_05.html | 12 inst/doc/V_06.Rmd | 84 ++--- inst/doc/V_06.html | 2 inst/doc/V_07.Rmd | 78 ++--- inst/doc/V_07.html | 2 inst/doc/ready4.html | 2 man/Ready4Module-class.Rd | 32 +- man/Ready4Private-class.Rd | 32 +- man/Ready4Project-class.Rd |only man/Ready4Public-class.Rd | 32 +- man/add_lups.Rd | 64 ++-- man/add_references.Rd | 58 ++-- man/add_rows_from_fn_args.Rd | 50 +-- man/add_scroll_box.Rd | 58 ++-- man/add_vignette_links.Rd | 70 ++-- man/author-methods.Rd | 38 +- man/authorClasses-methods.Rd | 38 +- man/authorData-methods.Rd | 38 +- man/authorFunctions-methods.Rd | 38 +- man/authorReport-methods.Rd | 38 +- man/authorSlot-methods.Rd | 58 ++-- man/bind_tables_from_loc_files.Rd | 58 ++-- man/characterize-methods.Rd | 38 +- man/characterizeSlot-methods.Rd | 58 ++-- man/depict-methods.Rd | 38 +- man/depictSlot-methods.Rd | 58 ++-- man/deprecated.Rd | 30 +- man/dotdata.Rd | 30 +- man/enhance-methods.Rd | 38 +- man/enhanceSlot-methods.Rd | 58 ++-- man/examples/get_datasets_tb.R | 2 man/examples/get_from_lup_obj.R | 14 man/examples/get_gracefully.R | 78 ++--- man/examples/get_libraries_tb.R | 2 man/examples/get_methods.R | 2 man/examples/get_methods_tb.R | 2 man/examples/get_modules_tb.R | 2 man/examples/make_code_releases_tbl.R | 26 - man/examples/make_datasets_tb.R | 22 - man/examples/make_ds_releases_tbl.R | 2 man/examples/make_methods_tb.R | 8 man/examples/make_modules_tb.R | 8 man/examples/make_programs_tbl.R | 18 - man/examples/print_data.R | 10 man/examples/print_methods.R | 10 man/examples/print_modules.R | 10 man/examples/print_packages.R | 42 +- man/examples/procureSlot_Ready4Module.R | 4 man/examples/renewSlot_Ready4Module.R | 4 man/examples/write_to_copy_rmds.R | 12 man/examples/write_to_render_post.R | 56 +-- man/examples/write_ws.R | 6 man/exhibit-methods.Rd | 38 +- man/exhibitSlot-methods.Rd | 58 ++-- man/figures/lifecycle-archived.svg | 42 +- man/figures/lifecycle-defunct.svg | 42 +- man/figures/lifecycle-maturing.svg | 42 +- man/figures/lifecycle-questioning.svg | 42 +- man/figures/lifecycle-soft-deprecated.svg | 42 +- man/get_badge_urls.Rd | 52 +-- man/get_badges_lup.Rd | 52 +-- man/get_cls_extensions.Rd | 64 ++-- man/get_datasets_tb.Rd | 58 ++-- man/get_digits_from_text.Rd | 36 +- man/get_dv_fls_urls.Rd | 64 ++-- man/get_examples.Rd | 40 +- man/get_excluded_repos.Rd | 46 +-- man/get_fl_extension.Rd | 36 +- man/get_fl_id_from_dv_ls.Rd | 44 +-- man/get_fl_nm_from_path.Rd | 36 +- man/get_from_lup_obj.Rd | 80 ++--- man/get_functions_tb.Rd | 52 +-- man/get_generics.Rd | 58 ++-- man/get_gh_repos.Rd | 36 +- man/get_gracefully.Rd | 6 man/get_libraries_ls.Rd | 46 +-- man/get_libraries_tb.Rd | 50 +-- man/get_manual_urls.Rd | 46 +-- man/get_methods.Rd | 44 +-- man/get_methods_tb.Rd | 50 +-- man/get_modules_tb.Rd | 50 +-- man/get_mthd_titles.Rd | 52 +-- man/get_r4_obj_slots.Rd | 40 +- man/get_rds_from_dv.Rd | 3 man/get_source_code_urls.Rd | 46 +-- man/get_subroutine_repos.Rd | 46 +-- man/get_table_from_loc_file.Rd | 68 ++-- man/ingest-methods.Rd | 38 +- man/ingestSlot-methods.Rd | 58 ++-- man/investigate-methods.Rd | 38 +- man/investigateSlot-methods.Rd | 58 ++-- man/make_additions_tb.Rd | 58 ++-- man/make_code_releases_tbl.Rd | 162 +++++------ man/make_datasets_tb.Rd | 106 +++---- man/make_ds_releases_tbl.Rd | 74 ++--- man/make_dss_tb.Rd | 58 ++-- man/make_files_tb.Rd | 44 +-- man/make_fn_defaults_ls.Rd | 36 +- man/make_framework_pkgs_chr.Rd | 46 +-- man/make_libraries_ls.Rd | 52 +-- man/make_libraries_tb.Rd | 88 +++--- man/make_list_phrase.Rd | 36 +- man/make_local_path_to_dv_data.Rd | 44 +-- man/make_methods_tb.Rd | 98 +++--- man/make_modules_pkgs_chr.Rd | 58 ++-- man/make_modules_tb.Rd | 98 +++--- man/make_programs_tbl.Rd | 120 ++++---- man/make_prompt.Rd | 44 +-- man/manufacture-methods.Rd | 38 +- man/manufactureSlot-methods.Rd | 58 ++-- man/metamorphose-methods.Rd | 38 +- man/metamorphoseSlot-methods.Rd | 58 ++-- man/nseequals.Rd | 30 +- man/pipe.Rd | 30 +- man/print_data.Rd | 100 +++---- man/print_dss.Rd | 76 ++--- man/print_dvs.Rd | 82 ++--- man/print_methods.Rd | 124 ++++---- man/print_modules.Rd | 76 ++--- man/print_packages.Rd | 174 ++++++------ man/print_vignettes.Rd | 118 ++++---- man/procureSlot-methods.Rd | 70 ++-- man/prognosticate-methods.Rd | 38 +- man/prognosticateSlot-methods.Rd | 58 ++-- man/ratify-methods.Rd | 38 +- man/ratifySlot-methods.Rd | 58 ++-- man/ready4-package.Rd | 90 +++--- man/reckon-methods.Rd | 38 +- man/reckonSlot-methods.Rd | 58 ++-- man/remove_lbls_from_df.Rd | 36 +- man/renew-methods.Rd | 38 +- man/rowbind_all_tbs_in_r4_obj.Rd | 44 +-- man/rowbind_tbs_in_r4_obj.Rd | 48 +-- man/share-methods.Rd | 38 +- man/shareSlot-methods.Rd | 58 ++-- man/transform_chr_to_num.Rd | 36 +- man/transform_cls_type_ls.Rd | 36 +- man/update_libraries_ls.Rd | 52 +-- man/update_libraries_tb.Rd | 94 +++--- man/update_pt_fn_args_ls.Rd | 36 +- man/update_tb_r3.Rd | 94 +++--- man/write_all_tbs_in_tbs_r4_to_csvs.Rd | 76 ++--- man/write_blog_entries.Rd | 70 ++-- man/write_citation_cff.Rd | 70 ++-- man/write_conditional_tags.Rd | 76 ++--- man/write_dv_fl_to_loc.Rd | 106 +++---- man/write_env_objs_to_dv.Rd | 112 +++---- man/write_examples.Rd | 70 ++-- man/write_extra_pkgs_to_actions.Rd | 58 ++-- man/write_fls_from_dv.Rd | 88 +++--- man/write_fls_to_dv.Rd | 88 +++--- man/write_fls_to_repo.Rd | 112 +++---- man/write_from_tmp.Rd | 76 ++--- man/write_ingested_dv_fl.Rd | 106 +++---- man/write_library_metadata.Rd | 148 +++++----- man/write_new_credentials.Rd | 70 ++-- man/write_new_dirs.Rd | 58 ++-- man/write_new_files.Rd | 88 +++--- man/write_obj_with_prompt.Rd | 76 ++--- man/write_prj_outp_dirs.Rd | 70 ++-- man/write_tb_to_csv.Rd | 82 ++--- man/write_to_copy_rmds.Rd | 90 +++--- man/write_to_delete_dirs.Rd | 58 ++-- man/write_to_delete_fls.Rd | 64 ++-- man/write_to_dv_from_tbl.Rd | 82 ++--- man/write_to_dv_with_wait.Rd | 118 ++++---- man/write_to_edit_workflow.Rd | 64 ++-- man/write_to_force_links_in.Rd | 64 ++-- man/write_to_publish_dv_ds.Rd | 64 ++-- man/write_to_render_post.Rd | 134 ++++----- man/write_to_trim_html.Rd | 58 ++-- man/write_with_consent.Rd | 106 +++---- man/write_words.Rd | 70 ++-- man/write_ws.Rd | 66 ++-- tests/testthat.R | 24 - tests/testthat/setup.R | 10 tests/testthat/test-fn_get.R | 78 ++--- tests/testthat/test-fn_make.R | 136 ++++----- tests/testthat/test-fn_write.R | 120 ++++---- vignettes/V_01.Rmd | 162 +++++------ vignettes/V_02.Rmd | 134 ++++----- vignettes/V_03.Rmd | 98 +++--- vignettes/V_04.Rmd | 8 vignettes/V_05.Rmd | 122 ++++---- vignettes/V_06.Rmd | 84 ++--- vignettes/V_07.Rmd | 78 ++--- 213 files changed, 5910 insertions(+), 5886 deletions(-)
Title: Multivariate Imputation by Chained Equations
Description: Multiple imputation using Fully Conditional Specification (FCS)
implemented by the MICE algorithm as described in Van Buuren and
Groothuis-Oudshoorn (2011) <doi:10.18637/jss.v045.i03>. Each variable has
its own imputation model. Built-in imputation models are provided for
continuous data (predictive mean matching, normal), binary data (logistic
regression), unordered categorical data (polytomous logistic regression)
and ordered categorical data (proportional odds). MICE can also impute
continuous two-level data (normal model, pan, second-level variables).
Passive imputation can be used to maintain consistency between variables.
Various diagnostic plots are available to inspect the quality of the
imputations.
Author: Stef van Buuren [aut, cre],
Karin Groothuis-Oudshoorn [aut],
Gerko Vink [ctb],
Rianne Schouten [ctb],
Alexander Robitzsch [ctb],
Patrick Rockenschaub [ctb],
Lisa Doove [ctb],
Shahab Jolani [ctb],
Margarita Moreno-Betancur [ctb],
Ian White [ctb],
Phil [...truncated...]
Maintainer: Stef van Buuren <stef.vanbuuren@tno.nl>
Diff between mice versions 3.18.0 dated 2025-05-27 and 3.19.0 dated 2025-12-10
DESCRIPTION | 20 ++++++--- MD5 | 26 +++++++----- NAMESPACE | 4 + NEWS.md | 33 +++++++++++++++ R/barnard.rubin.R | 11 +++-- R/predict_mi.R |only R/summary.R | 65 ++++++++++++++++++++++++------- R/tbc.R | 2 README.md | 2 build/partial.rdb |binary man/mice.Rd | 2 man/predict_mi.Rd |only man/tbc.Rd | 2 tests/testthat/test-banard.rubin.R |only tests/testthat/test-mice.impute.2l.bin.R | 2 tests/testthat/test-predict_mi.R |only 16 files changed, 130 insertions(+), 39 deletions(-)
Title: Hashmaps and Memoization (in-Memory Caching of Repeated
Computations)
Description: A simple in-memory, LRU cache that can be wrapped
around any function to memoize it. The cache is keyed on a hash
of the input data (using 'digest') or on pointer equivalence.
Also includes a generic hashmap object that can key on any object type.
Author: Peter Meilstrup [aut, cre]
Maintainer: Peter Meilstrup <peter.meilstrup@gmail.com>
Diff between memo versions 1.1.1 dated 2023-12-11 and 1.1.2 dated 2025-12-10
memo-1.1.1/memo/vignettes/README-woven.md |only memo-1.1.2/memo/DESCRIPTION | 24 +- memo-1.1.2/memo/MD5 | 38 +-- memo-1.1.2/memo/NAMESPACE | 1 memo-1.1.2/memo/NEWS | 6 memo-1.1.2/memo/R/cache.R | 16 - memo-1.1.2/memo/R/getPointer.R | 1 memo-1.1.2/memo/R/lru.R | 46 ++-- memo-1.1.2/memo/R/map.R | 7 memo-1.1.2/memo/build/vignette.rds |binary memo-1.1.2/memo/inst/doc/README.R | 2 memo-1.1.2/memo/inst/doc/README.html | 248 +++++++++++++++----------- memo-1.1.2/memo/man/lru_cache.Rd | 8 memo-1.1.2/memo/man/memo-package.Rd | 1 memo-1.1.2/memo/src/getPointer.c | 34 +++ memo-1.1.2/memo/src/vadr.c | 9 memo-1.1.2/memo/src/vadr.h | 7 memo-1.1.2/memo/tests/testthat/last.dump.rda |only memo-1.1.2/memo/tests/testthat/test-cache.R | 35 +++ memo-1.1.2/memo/tests/testthat/test-hashmap.R | 1 memo-1.1.2/memo/tests/testthat/test-lru.R | 8 21 files changed, 301 insertions(+), 191 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 0.6.1 dated 2025-01-27 and 1.0.0 dated 2025-12-10
giscoR-0.6.1/giscoR/R/gisco_addressapi.R |only giscoR-0.6.1/giscoR/R/gisco_attributions.R |only giscoR-0.6.1/giscoR/R/gisco_bulk_download.R |only giscoR-0.6.1/giscoR/R/gisco_cache.R |only giscoR-0.6.1/giscoR/R/gisco_check_access.R |only giscoR-0.6.1/giscoR/R/gisco_clear_cache.R |only giscoR-0.6.1/giscoR/R/gisco_get_airports.R |only giscoR-0.6.1/giscoR/R/gisco_get_coastallines.R |only giscoR-0.6.1/giscoR/R/gisco_get_countries.R |only giscoR-0.6.1/giscoR/R/gisco_get_education.R |only giscoR-0.6.1/giscoR/R/gisco_get_grid.R |only giscoR-0.6.1/giscoR/R/gisco_get_healthcare.R |only giscoR-0.6.1/giscoR/R/gisco_get_lau.R |only giscoR-0.6.1/giscoR/R/gisco_get_nuts.R |only giscoR-0.6.1/giscoR/R/gisco_get_postalcodes.R |only giscoR-0.6.1/giscoR/R/gisco_get_units.R |only giscoR-0.6.1/giscoR/R/gisco_get_urban_audit.R |only giscoR-0.6.1/giscoR/R/utils_downloads.R |only giscoR-0.6.1/giscoR/R/utils_names.R |only giscoR-0.6.1/giscoR/data/gisco_coastallines.rda |only giscoR-0.6.1/giscoR/data/gisco_countries.rda |only giscoR-0.6.1/giscoR/data/gisco_nuts.rda |only giscoR-0.6.1/giscoR/man/chunks/addressapi.Rmd |only giscoR-0.6.1/giscoR/man/gisco_addressapi.Rd |only giscoR-0.6.1/giscoR/man/gisco_coastallines.Rd |only giscoR-0.6.1/giscoR/man/gisco_countries.Rd |only giscoR-0.6.1/giscoR/man/gisco_get.Rd |only giscoR-0.6.1/giscoR/man/gisco_get_coastallines.Rd |only giscoR-0.6.1/giscoR/man/gisco_get_postalcodes.Rd |only giscoR-0.6.1/giscoR/man/gisco_nuts.Rd |only giscoR-0.6.1/giscoR/tests/testthat/_snaps/gisco_attributions.md |only giscoR-0.6.1/giscoR/tests/testthat/test-gisco_addressapi.R |only giscoR-0.6.1/giscoR/tests/testthat/test-gisco_attributions.R |only giscoR-0.6.1/giscoR/tests/testthat/test-gisco_bulk_download.R |only giscoR-0.6.1/giscoR/tests/testthat/test-gisco_cache.R |only giscoR-0.6.1/giscoR/tests/testthat/test-gisco_get_airports.R |only giscoR-0.6.1/giscoR/tests/testthat/test-gisco_get_coastallines.R |only giscoR-0.6.1/giscoR/tests/testthat/test-gisco_get_communes.R |only giscoR-0.6.1/giscoR/tests/testthat/test-gisco_get_countries.R |only giscoR-0.6.1/giscoR/tests/testthat/test-gisco_get_education.R |only giscoR-0.6.1/giscoR/tests/testthat/test-gisco_get_grid.R |only giscoR-0.6.1/giscoR/tests/testthat/test-gisco_get_healthcare.R |only giscoR-0.6.1/giscoR/tests/testthat/test-gisco_get_lau.R |only giscoR-0.6.1/giscoR/tests/testthat/test-gisco_get_nuts.R |only giscoR-0.6.1/giscoR/tests/testthat/test-gisco_get_postalcodes.R |only giscoR-0.6.1/giscoR/tests/testthat/test-gisco_get_units.R |only giscoR-0.6.1/giscoR/tests/testthat/test-gisco_get_urban_audit.R |only giscoR-1.0.0/giscoR/DESCRIPTION | 29 giscoR-1.0.0/giscoR/MD5 | 230 +++- giscoR-1.0.0/giscoR/NAMESPACE | 34 giscoR-1.0.0/giscoR/NEWS.md | 274 ++++- giscoR-1.0.0/giscoR/R/data.R | 483 +++++----- giscoR-1.0.0/giscoR/R/docs.R |only giscoR-1.0.0/giscoR/R/gisco-address-api.R |only giscoR-1.0.0/giscoR/R/gisco-attributions.R |only giscoR-1.0.0/giscoR/R/gisco-bulk-download.R |only giscoR-1.0.0/giscoR/R/gisco-cache.R |only giscoR-1.0.0/giscoR/R/gisco-check-access.R |only giscoR-1.0.0/giscoR/R/gisco-get-airports.R |only giscoR-1.0.0/giscoR/R/gisco-get-cached-db.R |only giscoR-1.0.0/giscoR/R/gisco-get-census.R |only giscoR-1.0.0/giscoR/R/gisco-get-coastal-lines.R |only giscoR-1.0.0/giscoR/R/gisco-get-communes.R |only giscoR-1.0.0/giscoR/R/gisco-get-countries.R |only giscoR-1.0.0/giscoR/R/gisco-get-education.R |only giscoR-1.0.0/giscoR/R/gisco-get-grid.R |only giscoR-1.0.0/giscoR/R/gisco-get-healthcare.R |only giscoR-1.0.0/giscoR/R/gisco-get-lau.R |only giscoR-1.0.0/giscoR/R/gisco-get-metadata.R |only giscoR-1.0.0/giscoR/R/gisco-get-nuts.R |only giscoR-1.0.0/giscoR/R/gisco-get-ports.R |only giscoR-1.0.0/giscoR/R/gisco-get-postal-codes.R |only giscoR-1.0.0/giscoR/R/gisco-get-unit-country.R |only giscoR-1.0.0/giscoR/R/gisco-get-unit-nuts.R |only giscoR-1.0.0/giscoR/R/gisco-get-unit-urban-audit.R |only giscoR-1.0.0/giscoR/R/gisco-get-units.R |only giscoR-1.0.0/giscoR/R/gisco-get-urban-audit.R |only giscoR-1.0.0/giscoR/R/gisco-id-api.R |only giscoR-1.0.0/giscoR/R/giscoR-package.R | 9 giscoR-1.0.0/giscoR/R/utils-country.R |only giscoR-1.0.0/giscoR/R/utils-sf.R |only giscoR-1.0.0/giscoR/R/utils-url.R |only giscoR-1.0.0/giscoR/R/utils.R |only giscoR-1.0.0/giscoR/R/zzz.R |only giscoR-1.0.0/giscoR/README.md | 294 ++---- giscoR-1.0.0/giscoR/build/stage23.rdb |only giscoR-1.0.0/giscoR/build/vignette.rds |binary giscoR-1.0.0/giscoR/data/gisco_coastal_lines.rda |only giscoR-1.0.0/giscoR/data/gisco_countries_2024.rda |only giscoR-1.0.0/giscoR/data/gisco_countrycode.rda |binary giscoR-1.0.0/giscoR/data/gisco_db.rda |binary giscoR-1.0.0/giscoR/data/gisco_nuts_2024.rda |only giscoR-1.0.0/giscoR/inst/COPYRIGHTS | 186 ++- giscoR-1.0.0/giscoR/inst/WORDLIST | 65 - 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giscoR-1.0.0/giscoR/man/gisco_db.Rd | 37 giscoR-1.0.0/giscoR/man/gisco_get_airports.Rd | 133 -- giscoR-1.0.0/giscoR/man/gisco_get_cached_db.Rd |only giscoR-1.0.0/giscoR/man/gisco_get_census.Rd |only giscoR-1.0.0/giscoR/man/gisco_get_coastal_lines.Rd |only giscoR-1.0.0/giscoR/man/gisco_get_communes.Rd |only giscoR-1.0.0/giscoR/man/gisco_get_countries.Rd |only giscoR-1.0.0/giscoR/man/gisco_get_education.Rd | 131 +- giscoR-1.0.0/giscoR/man/gisco_get_grid.Rd | 63 - giscoR-1.0.0/giscoR/man/gisco_get_healthcare.Rd | 141 +- giscoR-1.0.0/giscoR/man/gisco_get_lau.Rd | 174 +-- giscoR-1.0.0/giscoR/man/gisco_get_metadata.Rd |only giscoR-1.0.0/giscoR/man/gisco_get_nuts.Rd | 175 ++- giscoR-1.0.0/giscoR/man/gisco_get_ports.Rd |only giscoR-1.0.0/giscoR/man/gisco_get_postal_codes.Rd |only giscoR-1.0.0/giscoR/man/gisco_get_unit.Rd |only giscoR-1.0.0/giscoR/man/gisco_get_units.Rd | 172 +-- giscoR-1.0.0/giscoR/man/gisco_get_urban_audit.Rd | 140 +- giscoR-1.0.0/giscoR/man/gisco_id_api.Rd |only giscoR-1.0.0/giscoR/man/gisco_nuts_2024.Rd |only giscoR-1.0.0/giscoR/man/gisco_set_cache_dir.Rd | 78 + giscoR-1.0.0/giscoR/man/roxygen |only giscoR-1.0.0/giscoR/tests/testthat/_snaps/docs.md |only giscoR-1.0.0/giscoR/tests/testthat/_snaps/gisco-address-api.md |only giscoR-1.0.0/giscoR/tests/testthat/_snaps/gisco-attributions.md |only giscoR-1.0.0/giscoR/tests/testthat/_snaps/gisco-bulk-download.md |only giscoR-1.0.0/giscoR/tests/testthat/_snaps/gisco-cache.md |only giscoR-1.0.0/giscoR/tests/testthat/_snaps/gisco-get-cached-db.md |only giscoR-1.0.0/giscoR/tests/testthat/_snaps/gisco-get-coastal-lines.md |only giscoR-1.0.0/giscoR/tests/testthat/_snaps/gisco-get-communes.md |only giscoR-1.0.0/giscoR/tests/testthat/_snaps/gisco-get-countries.md |only giscoR-1.0.0/giscoR/tests/testthat/_snaps/gisco-get-lau.md |only giscoR-1.0.0/giscoR/tests/testthat/_snaps/gisco-get-metadata.md |only giscoR-1.0.0/giscoR/tests/testthat/_snaps/gisco-get-nuts.md |only giscoR-1.0.0/giscoR/tests/testthat/_snaps/gisco-get-postal-codes.md |only giscoR-1.0.0/giscoR/tests/testthat/_snaps/gisco-get-unit-country.md |only giscoR-1.0.0/giscoR/tests/testthat/_snaps/gisco-get-unit-nuts.md |only giscoR-1.0.0/giscoR/tests/testthat/_snaps/gisco-get-unit-urban-audit.md |only giscoR-1.0.0/giscoR/tests/testthat/_snaps/gisco-get-units.md |only giscoR-1.0.0/giscoR/tests/testthat/_snaps/gisco-get-urban-audit.md |only giscoR-1.0.0/giscoR/tests/testthat/_snaps/gisco-id-api.md |only giscoR-1.0.0/giscoR/tests/testthat/_snaps/utils-country.md |only giscoR-1.0.0/giscoR/tests/testthat/_snaps/utils-url.md |only giscoR-1.0.0/giscoR/tests/testthat/_snaps/utils.md |only giscoR-1.0.0/giscoR/tests/testthat/test-docs.R |only giscoR-1.0.0/giscoR/tests/testthat/test-gisco-address-api.R |only giscoR-1.0.0/giscoR/tests/testthat/test-gisco-attributions.R |only giscoR-1.0.0/giscoR/tests/testthat/test-gisco-bulk-download.R |only giscoR-1.0.0/giscoR/tests/testthat/test-gisco-cache.R |only giscoR-1.0.0/giscoR/tests/testthat/test-gisco-check-access.R |only giscoR-1.0.0/giscoR/tests/testthat/test-gisco-get-airports.R |only giscoR-1.0.0/giscoR/tests/testthat/test-gisco-get-cached-db.R |only giscoR-1.0.0/giscoR/tests/testthat/test-gisco-get-census.R |only giscoR-1.0.0/giscoR/tests/testthat/test-gisco-get-coastal-lines.R |only giscoR-1.0.0/giscoR/tests/testthat/test-gisco-get-communes.R |only giscoR-1.0.0/giscoR/tests/testthat/test-gisco-get-countries.R |only giscoR-1.0.0/giscoR/tests/testthat/test-gisco-get-education.R |only giscoR-1.0.0/giscoR/tests/testthat/test-gisco-get-grid.R |only giscoR-1.0.0/giscoR/tests/testthat/test-gisco-get-healthcare.R |only giscoR-1.0.0/giscoR/tests/testthat/test-gisco-get-lau.R |only giscoR-1.0.0/giscoR/tests/testthat/test-gisco-get-metadata.R |only giscoR-1.0.0/giscoR/tests/testthat/test-gisco-get-nuts.R |only giscoR-1.0.0/giscoR/tests/testthat/test-gisco-get-ports.R |only giscoR-1.0.0/giscoR/tests/testthat/test-gisco-get-postal-codes.R |only giscoR-1.0.0/giscoR/tests/testthat/test-gisco-get-unit-country.R |only giscoR-1.0.0/giscoR/tests/testthat/test-gisco-get-unit-nuts.R |only giscoR-1.0.0/giscoR/tests/testthat/test-gisco-get-unit-urban-audit.R |only giscoR-1.0.0/giscoR/tests/testthat/test-gisco-get-units.R |only giscoR-1.0.0/giscoR/tests/testthat/test-gisco-get-urban-audit.R |only giscoR-1.0.0/giscoR/tests/testthat/test-gisco-id-api.R |only giscoR-1.0.0/giscoR/tests/testthat/test-issues.R |only giscoR-1.0.0/giscoR/tests/testthat/test-utils-country.R |only giscoR-1.0.0/giscoR/tests/testthat/test-utils-sf.R |only giscoR-1.0.0/giscoR/tests/testthat/test-utils-url.R |only giscoR-1.0.0/giscoR/tests/testthat/test-utils.R | 229 +++- giscoR-1.0.0/giscoR/vignettes/africa-1.png |binary giscoR-1.0.0/giscoR/vignettes/country-1.png |binary giscoR-1.0.0/giscoR/vignettes/giscoR-1.png |binary giscoR-1.0.0/giscoR/vignettes/giscoR.Rmd | 222 ++-- 195 files changed, 2356 insertions(+), 1941 deletions(-)
Title: Methods to Convert R Data to YAML and Back
Description: Implements the 'libyaml' 'YAML' 1.1 parser and emitter
(<https://pyyaml.org/wiki/LibYAML>) for R.
Author: Hadley Wickham [cre] ,
Shawn Garbett [ctb] ,
Jeremy Stephens [aut, ctb],
Kirill Simonov [aut],
Yihui Xie [ctb] ,
Zhuoer Dong [ctb],
Jeffrey Horner [ctb],
reikoch [ctb],
Will Beasley [ctb] ,
Brendan O'Connor [ctb],
Michael Quinn [ctb],
Charlie Gao [ct [...truncated...]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between yaml versions 2.3.11 dated 2025-11-28 and 2.3.12 dated 2025-12-10
yaml-2.3.11/yaml/inst/CHANGELOG |only yaml-2.3.11/yaml/inst/implicit.re |only yaml-2.3.11/yaml/inst/tests |only yaml-2.3.11/yaml/tests/RUnit.R |only yaml-2.3.12/yaml/DESCRIPTION | 72 +++++------ yaml-2.3.12/yaml/MD5 | 61 +++++---- yaml-2.3.12/yaml/NAMESPACE | 9 + yaml-2.3.12/yaml/NEWS.md |only yaml-2.3.12/yaml/R/as.yaml.R | 146 +++++++++++++++++++++- yaml-2.3.12/yaml/R/read_yaml.R | 85 +++++++++++-- yaml-2.3.12/yaml/R/verbatim_logical.R | 21 +++ yaml-2.3.12/yaml/R/write_yaml.R | 42 +++++- yaml-2.3.12/yaml/R/yaml-package.R |only yaml-2.3.12/yaml/R/yaml.load.R | 154 ++++++++++++++++++++++- yaml-2.3.12/yaml/R/yaml.load_file.R | 22 ++- yaml-2.3.12/yaml/README.md |only yaml-2.3.12/yaml/build |only yaml-2.3.12/yaml/inst/doc |only yaml-2.3.12/yaml/man/as.yaml.Rd | 155 ++++++++++++++---------- yaml-2.3.12/yaml/man/read_yaml.Rd | 97 +++++++++------ yaml-2.3.12/yaml/man/verbatim_logical.Rd | 49 +++---- yaml-2.3.12/yaml/man/write_yaml.Rd | 44 ++++-- yaml-2.3.12/yaml/man/yaml-package.Rd |only yaml-2.3.12/yaml/man/yaml.load.Rd | 200 +++++++++++++++++-------------- yaml-2.3.12/yaml/src/r_emit.c | 10 - yaml-2.3.12/yaml/src/r_ext.c | 8 - yaml-2.3.12/yaml/src/r_ext.h | 4 yaml-2.3.12/yaml/src/r_parse.c | 12 - yaml-2.3.12/yaml/tests/testthat |only yaml-2.3.12/yaml/tests/testthat.R |only yaml-2.3.12/yaml/vignettes |only 31 files changed, 842 insertions(+), 349 deletions(-)
Title: Variable Importance Plots
Description: A general framework for constructing variable importance plots from
various types of machine learning models in R. Aside from some standard model-
specific variable importance measures, this package also provides model-
agnostic approaches that can be applied to any supervised learning algorithm.
These include 1) an efficient permutation-based variable importance measure,
2) variable importance based on Shapley values (Strumbelj and Kononenko,
2014) <doi:10.1007/s10115-013-0679-x>, and 3) the variance-based
approach described in Greenwell et al. (2018) <doi:10.48550/arXiv.1805.04755>. A
variance-based method for quantifying the relative strength of interaction
effects is also included (see the previous reference for details).
Author: Brandon M. Greenwell [aut, cre] ,
Brad Boehmke [aut]
Maintainer: Brandon M. Greenwell <greenwell.brandon@gmail.com>
Diff between vip versions 0.4.2 dated 2025-12-02 and 0.4.3 dated 2025-12-10
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 4 +++- inst/tinytest/test_pkg_lightgbm.R | 3 +++ inst/tinytest/test_vi_firm.R | 3 +++ inst/tinytest/test_vi_permute.R | 3 +++ 6 files changed, 20 insertions(+), 9 deletions(-)
Title: Targeted Inference
Description: Various methods for targeted and semiparametric inference including
augmented inverse probability weighted (AIPW) estimators for missing data and
causal inference (Bang and Robins (2005) <doi:10.1111/j.1541-0420.2005.00377.x>),
variable importance and conditional average treatment effects (CATE)
(van der Laan (2006) <doi:10.2202/1557-4679.1008>),
estimators for risk differences and relative risks (Richardson et al. (2017)
<doi:10.1080/01621459.2016.1192546>), assumption lean inference for generalized
linear model parameters (Vansteelandt et al. (2022) <doi:10.1111/rssb.12504>).
Author: Klaus K. Holst [aut, cre],
Benedikt Sommer [aut],
Andreas Nordland [aut],
Christian B. Pipper [ctb]
Maintainer: Klaus K. Holst <klaus@holst.it>
Diff between targeted versions 0.6 dated 2025-10-30 and 0.7 dated 2025-12-10
targeted-0.6/targeted/inst/doc/predictionclass.Rmd |only targeted-0.6/targeted/inst/doc/riskregression.Rmd |only targeted-0.6/targeted/inst/tinytest/test_test_sw.R |only targeted-0.6/targeted/vignettes/predictionclass.Rmd |only targeted-0.6/targeted/vignettes/riskregression.Rmd |only targeted-0.7/targeted/DESCRIPTION | 35 targeted-0.7/targeted/MD5 | 98 targeted-0.7/targeted/NAMESPACE | 6 targeted-0.7/targeted/NEWS.md | 54 targeted-0.7/targeted/R/RcppExports.R | 4 targeted-0.7/targeted/R/calibration.R | 10 targeted-0.7/targeted/R/cate.R | 6 targeted-0.7/targeted/R/cumhaz.R | 30 targeted-0.7/targeted/R/design.R | 134 - targeted-0.7/targeted/R/intsurv.R | 2 targeted-0.7/targeted/R/learner.R | 3 targeted-0.7/targeted/R/learner_sl.R | 2 targeted-0.7/targeted/R/learner_stratify.R | 2 targeted-0.7/targeted/R/learner_xgboost.R | 34 targeted-0.7/targeted/R/naivebayes.R | 51 targeted-0.7/targeted/R/riskreg.R | 2 targeted-0.7/targeted/R/targeted-package.R | 2 targeted-0.7/targeted/R/test_intersection_sw.R | 208 + targeted-0.7/targeted/R/truncatedscore.R | 7 targeted-0.7/targeted/build/partial.rdb |binary targeted-0.7/targeted/build/vignette.rds |binary targeted-0.7/targeted/inst/doc/predictionclass.R | 36 targeted-0.7/targeted/inst/doc/predictionclass.html | 1196 +++++----- targeted-0.7/targeted/inst/doc/predictionclass.qmd |only targeted-0.7/targeted/inst/doc/riskregression.R | 35 targeted-0.7/targeted/inst/doc/riskregression.html | 964 +++++--- targeted-0.7/targeted/inst/doc/riskregression.qmd |only targeted-0.7/targeted/inst/include/targeted_RcppExports.h | 8 targeted-0.7/targeted/inst/slowtest/test_sl.R | 50 targeted-0.7/targeted/inst/tinytest/test_cumhaz.R | 14 targeted-0.7/targeted/inst/tinytest/test_design.R | 198 + targeted-0.7/targeted/inst/tinytest/test_intersection_sw.R | 40 targeted-0.7/targeted/inst/tinytest/test_learner.R | 8 targeted-0.7/targeted/inst/tinytest/test_learner_glm.R | 2 targeted-0.7/targeted/inst/tinytest/test_learner_naivebayes.R | 6 targeted-0.7/targeted/inst/tinytest/test_learner_xgboost.R | 10 targeted-0.7/targeted/man/calibration.Rd | 2 targeted-0.7/targeted/man/design.Rd | 6 targeted-0.7/targeted/man/learner_xgboost.Rd | 25 targeted-0.7/targeted/man/naivebayes.Rd | 1 targeted-0.7/targeted/man/targeted-package.Rd | 5 targeted-0.7/targeted/man/test_intersection_sw.Rd | 42 targeted-0.7/targeted/man/test_zmax_onesided.Rd |only targeted-0.7/targeted/src/RcppExports.cpp | 17 targeted-0.7/targeted/src/target/include/target/dykstra.hpp | 9 targeted-0.7/targeted/src/target/src/dykstra.cpp | 17 targeted-0.7/targeted/src/utils_interface.cpp | 10 targeted-0.7/targeted/tests/tinytest.R | 4 targeted-0.7/targeted/vignettes/predictionclass.qmd |only targeted-0.7/targeted/vignettes/riskregression.qmd |only 55 files changed, 2170 insertions(+), 1225 deletions(-)
Title: RDF Library Bindings in R
Description: Provides methods to parse, query and serialize information
stored in the Resource Description Framework (RDF). RDF is described at <https://www.w3.org/TR/rdf-primer/>.
This package supports RDF by implementing an R interface to the Redland RDF C library,
described at <https://librdf.org/docs/api/index.html>. In brief, RDF provides a structured graph
consisting of Statements composed of Subject, Predicate, and Object Nodes.
Author: Matthew B. Jones [aut, cre] ,
Peter Slaughter [aut] ,
Jeroen Ooms [aut] ,
Carl Boettiger [aut] ,
Scott Chamberlain [ctb] ,
David Beckett [cph],
University of Bristol [cph],
Regents of the University of California [cph]
Maintainer: Matthew B. Jones <jones@nceas.ucsb.edu>
Diff between redland versions 1.0.17-18 dated 2024-02-23 and 1.0.17-19 dated 2025-12-10
DESCRIPTION | 22 ++++++++++++---------- MD5 | 21 +++++++++++++++------ NEWS | 7 +++++++ R/redland-package.R | 20 +++++++++++++------- build/vignette.rds |binary inst/Makefile |only inst/config.log |only inst/config.status |only inst/doc/redland_overview.html | 5 +++-- src/redland.c | 6 +++--- tools/Makefile |only tools/NEWS |only tools/README |only tools/aclocal.m4 |only tools/config.log |only tools/config.status |only 16 files changed, 53 insertions(+), 28 deletions(-)
Title: Selection of Linear Estimators
Description: Estimate the mean of a Gaussian vector, by choosing among a large collection of estimators,
following the method developed by Y. Baraud, C. Giraud and S. Huet (2014) <doi:10.1214/13-AIHP539>.
In particular it solves the problem of variable selection by choosing the best predictor among predictors emanating from different methods as lasso,
elastic-net, adaptive lasso, pls, randomForest. Moreover, it can be applied for choosing the tuning parameter in a Gauss-lasso procedure.
Author: Yannick Baraud [aut],
Christophe Giraud [aut],
Sylvie Huet [aut],
Benjamin Auder [cre]
Maintainer: Benjamin Auder <benjamin.auder@universite-paris-saclay.fr>
Diff between LINselect versions 1.1.5 dated 2023-12-07 and 1.1.6 dated 2025-12-10
DESCRIPTION | 19 +++++++++++++------ MD5 | 4 ++-- man/VARselect.Rd | 2 +- 3 files changed, 16 insertions(+), 9 deletions(-)
Title: DBI Package for the DuckDB Database Management System
Description: The DuckDB project is an embedded analytical data management
system with support for the Structured Query Language (SQL). This
package includes all of DuckDB and an R Database Interface (DBI)
connector.
Author: Hannes Muehleisen [aut] ,
Mark Raasveldt [aut] ,
Kirill Mueller [cre] ,
Stichting DuckDB Foundation [cph],
Apache Software Foundation [cph],
PostgreSQL Global Development Group [cph],
The Regents of the University of California [cph],
Cameron Desrocher [...truncated...]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between duckdb versions 1.4.2 dated 2025-11-17 and 1.4.3 dated 2025-12-10
DESCRIPTION | 6 MD5 | 48 - NEWS.md | 21 R/backend-dbplyr__duckdb_connection.R | 18 R/duckdb.R | 6 R/version.R | 2 src/altrepdataframe_relation.dd | 665 ------------- src/connection.dd | 666 ------------- src/convert.dd | 661 ------------- src/database.dd | 668 -------------- src/duckdb.tar.xz |binary src/include/rapi.hpp | 2 src/register.dd | 700 -------------- src/relational.dd | 709 -------------- src/reltoaltrep.dd | 761 --------------- src/rfuns.dd | 654 ------------- src/scan.dd | 664 ------------- src/statement.dd | 762 ---------------- src/transform.dd | 663 ------------- src/types.dd | 663 ------------- src/utils.cpp | 17 src/utils.dd | 671 -------------- tests/testthat/_snaps/error-handling.md | 2 tests/testthat/_snaps/sql.md | 7 tests/testthat/test-backend-dbplyr__duckdb_connection.R | 31 25 files changed, 107 insertions(+), 8960 deletions(-)
Title: Access EPA 'ATTAINS' Data
Description: An R interface to United States Environmental Protection Agency (EPA)
Assessment, Total Maximum Daily Load (TMDL) Tracking and Implementation System
('ATTAINS') data. 'ATTAINS' is the EPA database used to track information
provided by states about water quality assessments conducted under federal
Clean Water Act requirements. ATTAINS information and API information is available at <https://www.epa.gov/waterdata/attains>.
Author: Michael Schramm [aut, cre, cph]
Maintainer: Michael Schramm <mpschramm@gmail.com>
Diff between rATTAINS versions 1.0.1 dated 2025-05-19 and 1.1.0 dated 2025-12-09
rATTAINS-1.0.1/rATTAINS/tests/fixtures/state_summary.yml |only rATTAINS-1.1.0/rATTAINS/DESCRIPTION | 10 rATTAINS-1.1.0/rATTAINS/LICENSE | 4 rATTAINS-1.1.0/rATTAINS/MD5 | 129 - rATTAINS-1.1.0/rATTAINS/NAMESPACE | 62 rATTAINS-1.1.0/rATTAINS/NEWS.md | 145 - rATTAINS-1.1.0/rATTAINS/R/actions.R | 674 +---- rATTAINS-1.1.0/rATTAINS/R/assessment_units.R | 411 +-- rATTAINS-1.1.0/rATTAINS/R/assessments.R | 686 +---- rATTAINS-1.1.0/rATTAINS/R/domain_values.R | 203 - rATTAINS-1.1.0/rATTAINS/R/huc12_summary.R | 373 -- rATTAINS-1.1.0/rATTAINS/R/internal.R | 169 - rATTAINS-1.1.0/rATTAINS/R/plans.R | 454 +-- rATTAINS-1.1.0/rATTAINS/R/rATTAINS-package.R | 32 rATTAINS-1.1.0/rATTAINS/R/state_summary.R | 306 +- rATTAINS-1.1.0/rATTAINS/R/survey.R | 298 -- rATTAINS-1.1.0/rATTAINS/README.md | 441 +-- rATTAINS-1.1.0/rATTAINS/build/vignette.rds |binary rATTAINS-1.1.0/rATTAINS/inst/CITATION | 36 rATTAINS-1.1.0/rATTAINS/inst/doc/Introduction.R | 93 rATTAINS-1.1.0/rATTAINS/inst/doc/Introduction.Rmd | 243 - rATTAINS-1.1.0/rATTAINS/inst/doc/Introduction.html | 1277 +++++----- rATTAINS-1.1.0/rATTAINS/man/actions.Rd | 270 +- rATTAINS-1.1.0/rATTAINS/man/assessment_units.Rd | 202 - rATTAINS-1.1.0/rATTAINS/man/assessments.Rd | 276 +- rATTAINS-1.1.0/rATTAINS/man/domain_values.Rd | 96 rATTAINS-1.1.0/rATTAINS/man/huc12_summary.Rd | 90 rATTAINS-1.1.0/rATTAINS/man/plans.Rd | 140 - rATTAINS-1.1.0/rATTAINS/man/rATTAINS-package.Rd | 48 rATTAINS-1.1.0/rATTAINS/man/state_summary.Rd | 114 rATTAINS-1.1.0/rATTAINS/man/surveys.Rd | 112 rATTAINS-1.1.0/rATTAINS/tests/fixtures/actions_chr_works.yml | 106 rATTAINS-1.1.0/rATTAINS/tests/fixtures/actions_unnest_works.yml | 106 rATTAINS-1.1.0/rATTAINS/tests/fixtures/actions_works.yml | 106 rATTAINS-1.1.0/rATTAINS/tests/fixtures/assessment_units_chr_works.yml | 84 rATTAINS-1.1.0/rATTAINS/tests/fixtures/assessment_units_unnest_works.yml | 84 rATTAINS-1.1.0/rATTAINS/tests/fixtures/assessment_units_works.yml | 84 rATTAINS-1.1.0/rATTAINS/tests/fixtures/assessments_chr_works.yml | 74 rATTAINS-1.1.0/rATTAINS/tests/fixtures/assessments_unnest_works.yml | 74 rATTAINS-1.1.0/rATTAINS/tests/fixtures/assessments_works.yml | 74 rATTAINS-1.1.0/rATTAINS/tests/fixtures/domains_works.yml | 106 rATTAINS-1.1.0/rATTAINS/tests/fixtures/huc12_chr_works.yml | 148 - rATTAINS-1.1.0/rATTAINS/tests/fixtures/huc12_unnest_works.yml | 122 rATTAINS-1.1.0/rATTAINS/tests/fixtures/huc12_works.yml | 122 rATTAINS-1.1.0/rATTAINS/tests/fixtures/plans_chr_works.yml | 388 +-- rATTAINS-1.1.0/rATTAINS/tests/fixtures/plans_summary_works.yml | 200 - rATTAINS-1.1.0/rATTAINS/tests/fixtures/plans_unnest_works.yml | 884 +++--- rATTAINS-1.1.0/rATTAINS/tests/fixtures/plans_works.yml | 388 +-- rATTAINS-1.1.0/rATTAINS/tests/fixtures/single_domain.yml | 60 rATTAINS-1.1.0/rATTAINS/tests/fixtures/state_summary_chr_works.yml | 208 - rATTAINS-1.1.0/rATTAINS/tests/fixtures/state_summary_unnest_works.yml | 208 - rATTAINS-1.1.0/rATTAINS/tests/fixtures/state_summary_works.yml | 208 - rATTAINS-1.1.0/rATTAINS/tests/fixtures/survey_chr_works.yml | 476 +-- rATTAINS-1.1.0/rATTAINS/tests/fixtures/survey_unnest_works.yml | 476 +-- rATTAINS-1.1.0/rATTAINS/tests/fixtures/survey_works.yml | 476 +-- rATTAINS-1.1.0/rATTAINS/tests/testthat.R | 8 rATTAINS-1.1.0/rATTAINS/tests/testthat/setup-rATTAINS.R | 24 rATTAINS-1.1.0/rATTAINS/tests/testthat/test-actions.R | 60 rATTAINS-1.1.0/rATTAINS/tests/testthat/test-assessment_units.R | 59 rATTAINS-1.1.0/rATTAINS/tests/testthat/test-assessments.R | 67 rATTAINS-1.1.0/rATTAINS/tests/testthat/test-domain_values.R | 50 rATTAINS-1.1.0/rATTAINS/tests/testthat/test-huc12_summary.R | 69 rATTAINS-1.1.0/rATTAINS/tests/testthat/test-plans.R | 81 rATTAINS-1.1.0/rATTAINS/tests/testthat/test-state_summary.R | 74 rATTAINS-1.1.0/rATTAINS/tests/testthat/test-survey.R | 58 rATTAINS-1.1.0/rATTAINS/vignettes/Introduction.Rmd | 243 - 66 files changed, 6220 insertions(+), 7229 deletions(-)
Title: Custom Visualizations & Functions for Streamlined Analyses of
Single Cell Sequencing
Description: Collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using 'R'. 'scCustomize' aims to provide 1) Customized visualizations for aid in ease of use and to create more aesthetic and functional visuals. 2) Improve speed/reproducibility of common tasks/pieces of code in scRNA-seq analysis with a single or group of functions. For citation please use: Marsh SE (2021) "Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing" <doi:10.5281/zenodo.5706430> RRID:SCR_024675.
Author: Samuel Marsh [aut, cre] ,
Ming Tang [ctb],
Velina Kozareva [ctb],
Lucas Graybuck [ctb],
Zoe Clarke [ctb]
Maintainer: Samuel Marsh <sccustomize@gmail.com>
Diff between scCustomize versions 3.2.2 dated 2025-11-12 and 3.2.3 dated 2025-12-09
scCustomize-3.2.2/scCustomize/R/Object_Utilities.R |only scCustomize-3.2.3/scCustomize/DESCRIPTION | 14 scCustomize-3.2.3/scCustomize/MD5 | 85 scCustomize-3.2.3/scCustomize/NAMESPACE | 1 scCustomize-3.2.3/scCustomize/NEWS.md | 27 scCustomize-3.2.3/scCustomize/R/Internal_QC_Utilities.R |only scCustomize-3.2.3/scCustomize/R/Internal_Utilities.R | 2868 ---------- scCustomize-3.2.3/scCustomize/R/LIGER_Internal_Utilities.R | 8 scCustomize-3.2.3/scCustomize/R/LIGER_Plotting.R | 13 scCustomize-3.2.3/scCustomize/R/LIGER_Utilities.R | 1 scCustomize-3.2.3/scCustomize/R/Plotting_Seurat.R | 24 scCustomize-3.2.3/scCustomize/R/Plotting_Seurat_Iterative.R | 8 scCustomize-3.2.3/scCustomize/R/Plotting_Statistics.R | 66 scCustomize-3.2.3/scCustomize/R/Read_Write_Data.R | 100 scCustomize-3.2.3/scCustomize/R/Statistics.R | 47 scCustomize-3.2.3/scCustomize/R/Utilities.R | 84 scCustomize-3.2.3/scCustomize/R/Utilities_Objects.R |only scCustomize-3.2.3/scCustomize/man/Add_Alt_Feature_ID.Rd | 2 scCustomize-3.2.3/scCustomize/man/Add_Sample_Meta.Rd | 2 scCustomize-3.2.3/scCustomize/man/Cluster_Stats_All_Samples.Rd | 3 scCustomize-3.2.3/scCustomize/man/Create_CellBender_Merged_Seurat.Rd | 6 scCustomize-3.2.3/scCustomize/man/DimPlot_LIGER.Rd | 6 scCustomize-3.2.3/scCustomize/man/Extract_Sample_Meta.Rd | 2 scCustomize-3.2.3/scCustomize/man/Fetch_Meta.Rd | 2 scCustomize-3.2.3/scCustomize/man/Iterate_PC_Loading_Plots.Rd | 2 scCustomize-3.2.3/scCustomize/man/MAD_Stats.Rd | 3 scCustomize-3.2.3/scCustomize/man/Map_New_Meta.Rd | 2 scCustomize-3.2.3/scCustomize/man/Median_Stats.Rd | 3 scCustomize-3.2.3/scCustomize/man/Merge_Seurat_List.Rd | 2 scCustomize-3.2.3/scCustomize/man/Meta_Remove_Seurat.Rd | 2 scCustomize-3.2.3/scCustomize/man/Percent_Expressing.Rd | 6 scCustomize-3.2.3/scCustomize/man/Plot_Cells_per_Sample.Rd | 3 scCustomize-3.2.3/scCustomize/man/Plot_Median_Genes.Rd | 3 scCustomize-3.2.3/scCustomize/man/Plot_Median_Mito.Rd | 3 scCustomize-3.2.3/scCustomize/man/Plot_Median_Other.Rd | 3 scCustomize-3.2.3/scCustomize/man/Plot_Median_UMIs.Rd | 3 scCustomize-3.2.3/scCustomize/man/Proportion_Plot.Rd | 3 scCustomize-3.2.3/scCustomize/man/Random_Cells_Downsample.Rd | 2 scCustomize-3.2.3/scCustomize/man/ReFilter_SeuratObject.Rd | 2 scCustomize-3.2.3/scCustomize/man/Read10X_GEO.Rd | 2 scCustomize-3.2.3/scCustomize/man/Rename_Clusters.Rd | 3 scCustomize-3.2.3/scCustomize/man/Store_Misc_Info_Seurat.Rd | 2 scCustomize-3.2.3/scCustomize/man/Store_Palette_Seurat.Rd | 2 scCustomize-3.2.3/scCustomize/man/Updated_HGNC_Symbols.Rd | 7 scCustomize-3.2.3/scCustomize/man/Updated_MGI_Symbols.Rd | 7 45 files changed, 193 insertions(+), 3241 deletions(-)
Title: Risk Assessment Plot and Reclassification Metrics
Description: Assessing the comparative performance of two logistic regression models or results of such models or classification models. Discrimination metrics include Integrated Discrimination Improvement (IDI), Net Reclassification Improvement (NRI), and difference in Area Under the Curves (AUCs), Brier scores and Brier skill. Plots include Risk Assessment Plots, Decision curves and Calibration plots. Methods are described in Pickering and Endre (2012) <doi:10.1373/clinchem.2011.167965> and Pencina et al. (2008) <doi:10.1002/sim.2929>.
Author: John W Pickering [aut],
Dimitrios Doudesis [aut],
Daniel Perez Vicencio [cre]
Maintainer: Daniel Perez Vicencio <dvicencio947@gmail.com>
Diff between raptools versions 1.22.0 dated 2025-11-24 and 1.23.0 dated 2025-12-09
DESCRIPTION | 6 MD5 | 29 ++-- NEWS.md | 19 ++ R/raptools.R | 95 ++++++++++---- README.md | 170 +++++++++++++------------- man/figures/README-ggcalibrate-1.png |binary man/figures/README-ggcalibrate_original-1.png |binary man/figures/README-ggcontribute-1.png |binary man/figures/README-ggdecision-1.png |binary man/figures/README-ggrap-1.png |binary man/figures/README-ggrerec-1.png |binary man/figures/README-ggroc-1.png |binary man/figures/logo.png |only man/ggcalibrate.Rd | 14 +- man/ggdecision.Rd | 28 +++- man/ggprerec.Rd | 18 ++ 16 files changed, 245 insertions(+), 134 deletions(-)
Title: A Collection of Large Language Model Assistants
Description: Provides a collection of ergonomic large language model assistants
designed to help you complete repetitive, hard-to-automate tasks quickly.
After selecting some code, press the keyboard shortcut you've chosen to
trigger the package app, select an assistant, and watch your chore be
carried out. While the package ships with a number of chore helpers for R
package development, users can create custom helpers just by writing some
instructions in a markdown file.
Author: Simon Couch [aut, cre] ,
Posit Software, PBC [cph, fnd]
Maintainer: Simon Couch <simon.couch@posit.co>
Diff between chores versions 0.2.0 dated 2025-04-30 and 0.3.0 dated 2025-12-09
DESCRIPTION | 14 MD5 | 70 - NEWS.md | 14 R/directory.R | 14 R/doc-helper-cli.R | 8 R/helper-class.R | 15 R/init-helper.R | 16 R/options.R | 14 R/prompt.R | 5 R/utils.R | 5 README.md | 20 build/vignette.rds |binary inst/doc/chores.Rmd | 23 inst/doc/chores.html | 66 - inst/doc/custom.Rmd | 2 inst/doc/custom.html | 9 inst/doc/gallery.R | 104 - inst/doc/gallery.html | 1616 +++++++++++++++++++++++++++++ inst/prompts/cli-replace.md | 248 ---- man/chores-package.Rd | 2 man/cli_helper.Rd | 8 man/directory.Rd | 6 man/dot-init_helper.Rd | 16 man/helper_options.Rd | 14 tests/testthat/_snaps/helper-add-remove.md | 2 tests/testthat/_snaps/helper-class.md | 6 tests/testthat/_snaps/helper-init.md | 4 tests/testthat/_snaps/utils.md | 4 tests/testthat/test-directory.R | 22 tests/testthat/test-helper-add-remove.R | 4 tests/testthat/test-helper-class.R | 28 tests/testthat/test-helper-init.R | 8 tests/testthat/test-prompt.R | 12 tests/testthat/test-utils.R | 4 vignettes/chores.Rmd | 23 vignettes/custom.Rmd | 2 36 files changed, 1971 insertions(+), 457 deletions(-)
Title: Source a Script and Cache
Description: Provides a function that behaves nearly as base::source() but
implements a caching mechanism on disk, project based. It allows to
quasi source() R scripts that gather data but can fail or consume to
much time to respond even if nothing new is expected. It comes with
tools to check and execute on demand or when cache is invalid the
script.
Author: Xavier Timbeau [aut, cre, cph]
Maintainer: Xavier Timbeau <xavier.timbeau@sciencespo.fr>
Diff between sourcoise versions 0.6.2 dated 2025-05-27 and 1.0.0 dated 2025-12-09
DESCRIPTION | 42 +- LICENSE | 4 MD5 | 95 +++--- NAMESPACE | 23 - NEWS.md | 207 +++++++------- R/cache_tools.R | 372 +++++++++++++------------ R/exec_tools.R | 180 ++++++++---- R/metadata_tools.R | 552 ++++++++++++++++++++++++++++++-------- R/other_tools.R | 116 +++---- R/path_tools.R | 174 ++++++----- R/setroot.R | 58 ++- R/setup_tools.R | 371 ++++++++++++++----------- R/sourcoise.R | 492 ++++++++++++++++++--------------- R/sourcoise_clear.R | 182 +++++++----- R/sourcoise_meta.R | 154 +++++----- R/sourcoise_refresh.R | 387 +++++++++++++++----------- R/sourcoise_status.R | 213 +++++--------- R/zzz.R | 64 ++-- README.md | 274 +++++++++--------- build/vignette.rds |binary inst/doc/advanced.html | 367 +++++++++++++++++-------- inst/doc/advanced.qmd | 136 ++++----- inst/doc/compared.html | 379 +++++++++++++++++--------- inst/doc/compared.qmd | 152 +++++----- inst/doc/sourcoise.html | 459 ++++++++++++++++++++----------- inst/doc/sourcoise.qmd | 264 +++++++++--------- inst/ipch/ipch.qmd | 34 +- inst/ipch/prix_insee.R | 102 +++++-- inst/ipch/slow.R | 10 inst/pkgdown.yml | 18 - inst/some_data.R | 6 inst/synthetic.R | 10 inst/test.qmd | 12 man/set_sourcoise_root.Rd | 66 ++-- man/sourcoise.Rd | 274 +++++++++--------- man/sourcoise_clear.Rd | 88 ++---- man/sourcoise_clear_all.Rd |only man/sourcoise_meta.Rd | 102 +++---- man/sourcoise_refresh.Rd | 163 +++++------ man/sourcoise_reset.Rd | 75 ++--- man/sourcoise_status.Rd | 153 +++++----- tests/testthat.R | 24 - tests/testthat/test-source_args.R | 68 ++-- tests/testthat/test-sourcoise.R | 292 ++++++++++---------- tests/testthat/test-utils.R | 112 +++---- vignettes/_quarto.yaml | 6 vignettes/advanced.qmd | 136 ++++----- vignettes/compared.qmd | 152 +++++----- vignettes/sourcoise.qmd | 264 +++++++++--------- 49 files changed, 4489 insertions(+), 3395 deletions(-)
Title: Mapas de las Divisiones Politicas y Administrativas de Chile
(Maps of the Political and Administrative Divisions of Chile)
Description: Mapas terrestres con topologias simplificadas. Estos mapas no
tienen precision geodesica, por lo que aplica el DFL-83 de 1979 de la Republica
de Chile y se consideran referenciales sin validez legal.
No se incluyen los territorios antarticos y bajo ningun evento estos mapas
significan que exista una cesion u ocupacion de territorios soberanos en
contra del Derecho Internacional por parte de Chile. Esta paquete esta
documentado intencionalmente en castellano asciificado para que funcione sin
problema en diferentes plataformas.
(Terrestrial maps with simplified toplogies. These maps lack geodesic
precision, therefore DFL-83 1979 of the Republic of Chile applies and are
considered to have no legal validity.
Antartic territories are excluded and under no event these maps mean
there is a cession or occupation of sovereign territories against International
Laws from Chile. This package was intentionally documented in asciified
spanish to make it work without problem on different platforms.)
Author: Mauricio Vargas [aut, cre],
Roberto Salas [ctb],
Joshua Kunst [ctb],
Juan Correa [dtc],
Ricardo Aravena [ths],
Pontificia Universidad Catolica de Chile [cph],
Instituto Nacional de Estadisticas [dtc],
Subsecretaria de Desarrollo Regional [dtc],
Bib [...truncated...]
Maintainer: Mauricio Vargas <mavargas11@uc.cl>
Diff between chilemapas versions 0.3.0 dated 2022-07-14 and 0.4.0 dated 2025-12-09
DESCRIPTION | 10 - MD5 | 16 +- NAMESPACE | 5 NEWS.md | 5 R/administrative-maps.R | 28 ++- R/political-maps.R | 16 +- build/vignette.rds |binary inst/doc/chilemapas.R | 8 - inst/doc/chilemapas.html | 335 +++++++++++++++++++++++------------------------ 9 files changed, 223 insertions(+), 200 deletions(-)
Title: Fitting Semi-Parametric Generalized log-Gamma Regression Models
Description: Set of tools to fit a linear multiple or semi-parametric regression
models with the possibility of non-informative random right or left censoring.
Under this setup, the localization parameter of the response variable distribution is modeled by using linear multiple regression
or semi-parametric functions, whose non-parametric components may be approximated
by natural cubic spline or P-splines. The supported distribution for the model error is a generalized log-gamma distribution which includes
the generalized extreme value and standard normal distributions as important special cases. Inference is based on likelihood, penalized likelihood and bootstrap methods.
Lastly, some numerical and graphical devices for diagnostic of the fitted models are offered.
Author: Carlos Alberto Cardozo Delgado [aut, cre, cph] ,
Gilberto Paula [aut],
Luis Vanegas [aut]
Maintainer: Carlos Alberto Cardozo Delgado <cardozorpackages@gmail.com>
Diff between sglg versions 0.2.3 dated 2025-11-27 and 0.2.4 dated 2025-12-09
DESCRIPTION | 10 ++-- MD5 | 24 +++++----- R/aux_fs.R | 20 +++----- R/dglg.R | 5 +- R/glg.R | 29 ++++++------ R/quantile_residuals.R | 6 +- R/sglg.R | 116 ++++++++++++++++++++++++++----------------------- R/survglg.R | 2 man/dglg.Rd | 5 +- man/glg.Rd | 23 +++++---- man/quantile_sglg.Rd | 2 man/sglg.Rd | 40 ++++++++-------- man/survglg.Rd | 2 13 files changed, 150 insertions(+), 134 deletions(-)
Title: Fast Pixel-by-Pixel Image Comparison Using 'odiff'
Description: R bindings to 'odiff', a blazing-fast pixel-by-pixel image
comparison tool <https://github.com/dmtrKovalenko/odiff>. Supports PNG,
JPEG, WEBP, and TIFF with configurable thresholds, antialiasing detection,
and region ignoring. Requires system installation of 'odiff'. Ideal for
visual regression testing in automated workflows.
Author: Ben Wolstenholme [aut, cre]
Maintainer: Ben Wolstenholme <odiffr@benwolst.dev>
Diff between odiffr versions 0.1.0 dated 2025-12-01 and 0.5.1 dated 2025-12-09
DESCRIPTION | 8 MD5 | 95 ++++- NAMESPACE | 11 NEWS.md | 86 ++++ R/binary.R | 6 R/compare_images.R | 282 +++++++++++++++ R/expect.R |only R/report.R |only R/summary.R |only R/update.R | 8 README.md | 104 +++++ inst/doc/getting-started.R | 131 ++++++- inst/doc/getting-started.Rmd | 229 ++++++++++++ inst/doc/getting-started.html | 387 +++++++++++++++++---- man/batch_report.Rd |only man/compare_dirs_report.Rd |only man/compare_image_dirs.Rd |only man/compare_images_batch.Rd | 19 - man/expect_images.Rd |only man/failed_pairs.Rd |only man/passed_pairs.Rd |only man/summary.odiffr_batch.Rd |only tests/testthat/_odiffr |only tests/testthat/helper-images.R | 20 - tests/testthat/test-binary.R | 230 ++++++++++++ tests/testthat/test-compare_images.R | 627 ++++++++++++++++++++++++++++++++++- tests/testthat/test-expect.R |only tests/testthat/test-magick-support.R | 13 tests/testthat/test-report.R |only tests/testthat/test-summary.R |only tests/testthat/test-update.R | 322 +++++++++++++++-- tests/testthat/test-utils.R |only tests/testthat/test-zzz.R |only vignettes/getting-started.Rmd | 229 ++++++++++++ 34 files changed, 2595 insertions(+), 212 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] ,
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 0.4.0 dated 2025-11-18 and 0.5.0 dated 2025-12-09
geocodebr-0.4.0/geocodebr/tests/tests_rafa/empate_duck.R |only geocodebr-0.4.0/geocodebr/tests/tests_rafa/erro_rais.R |only geocodebr-0.4.0/geocodebr/tests/tests_rafa/fts_extension.R |only geocodebr-0.4.0/geocodebr/tests/tests_rafa/release_v2_v3.R |only geocodebr-0.5.0/geocodebr/DESCRIPTION | 16 geocodebr-0.5.0/geocodebr/MD5 | 103 - geocodebr-0.5.0/geocodebr/NAMESPACE | 1 geocodebr-0.5.0/geocodebr/NEWS.md | 38 geocodebr-0.5.0/geocodebr/R/busca_por_cep.R | 34 geocodebr-0.5.0/geocodebr/R/cache.R | 5 geocodebr-0.5.0/geocodebr/R/create_geocodebr_db.R | 12 geocodebr-0.5.0/geocodebr/R/download_cnefe.R | 4 geocodebr-0.5.0/geocodebr/R/error.R | 12 geocodebr-0.5.0/geocodebr/R/geocode.R | 162 + geocodebr-0.5.0/geocodebr/R/geocode_orig.R |only geocodebr-0.5.0/geocodebr/R/geocode_reverso.R | 109 - geocodebr-0.5.0/geocodebr/R/geocodebr-package.R | 2 geocodebr-0.5.0/geocodebr/R/match_cases.R | 29 geocodebr-0.5.0/geocodebr/R/match_cases_probabilistic.R | 111 - geocodebr-0.5.0/geocodebr/R/match_weighted_cases.R | 26 geocodebr-0.5.0/geocodebr/R/match_weighted_cases_probabilistic.R | 121 - geocodebr-0.5.0/geocodebr/R/message.R | 4 geocodebr-0.5.0/geocodebr/R/progress_bar.R | 4 geocodebr-0.5.0/geocodebr/R/register_cnefe_tables.R |only geocodebr-0.5.0/geocodebr/R/string_dist.R |only geocodebr-0.5.0/geocodebr/R/utils.R | 70 geocodebr-0.5.0/geocodebr/README.md | 51 geocodebr-0.5.0/geocodebr/build/vignette.rds |binary geocodebr-0.5.0/geocodebr/inst/doc/geocode.R | 52 geocodebr-0.5.0/geocodebr/inst/doc/geocode.html | 46 geocodebr-0.5.0/geocodebr/inst/doc/geocode_reverso.R | 38 geocodebr-0.5.0/geocodebr/inst/doc/geocode_reverso.html | 56 geocodebr-0.5.0/geocodebr/inst/doc/geocodebr.R | 116 - geocodebr-0.5.0/geocodebr/inst/doc/geocodebr.html | 23 geocodebr-0.5.0/geocodebr/man/apaga_data_release_antigo.Rd | 34 geocodebr-0.5.0/geocodebr/man/busca_por_cep.Rd | 2 geocodebr-0.5.0/geocodebr/man/create_index.Rd | 24 geocodebr-0.5.0/geocodebr/man/figures/logo.svg | 412 ++-- geocodebr-0.5.0/geocodebr/man/geocode.Rd | 31 geocodebr-0.5.0/geocodebr/man/geocode_reverso.Rd | 8 geocodebr-0.5.0/geocodebr/man/geocodebr.Rd | 2 geocodebr-0.5.0/geocodebr/man/roxygen/templates/empates_section.R | 4 geocodebr-0.5.0/geocodebr/man/roxygen/templates/n_cores.R | 3 geocodebr-0.5.0/geocodebr/man/update_input_db.Rd | 44 geocodebr-0.5.0/geocodebr/tests/tests_rafa/benchmark_LIKE.R | 127 + geocodebr-0.5.0/geocodebr/tests/tests_rafa/benchmark_callr.R |only geocodebr-0.5.0/geocodebr/tests/tests_rafa/benchmark_reg_adm.R | 234 -- geocodebr-0.5.0/geocodebr/tests/tests_rafa/cache_string_dist.R |only geocodebr-0.5.0/geocodebr/tests/tests_rafa/cad_unico_subway.R |only geocodebr-0.5.0/geocodebr/tests/tests_rafa/reverse_geocode_alternatives.R | 989 +--------- geocodebr-0.5.0/geocodebr/tests/tests_rafa/test_rafa.R | 5 geocodebr-0.5.0/geocodebr/tests/tests_rafa/utils2_noserialize.R |only geocodebr-0.5.0/geocodebr/tests/testthat/_snaps/download_cnefe.md | 18 geocodebr-0.5.0/geocodebr/tests/testthat/_snaps/error.md | 18 geocodebr-0.5.0/geocodebr/tests/testthat/test-cache.R | 5 geocodebr-0.5.0/geocodebr/tests/testthat/test-download_cnefe.R | 34 geocodebr-0.5.0/geocodebr/tests/testthat/test-geocode.R | 77 geocodebr-0.5.0/geocodebr/tests/testthat/test-geocode_reverso.R | 4 58 files changed, 1265 insertions(+), 2055 deletions(-)
Title: Providing Fast and Flexible Functions for Distance Correlation
Analysis
Description: Provides methods for distance covariance and distance correlation (Szekely, et al. (2007) <doi:10.1214/009053607000000505>), generalized version thereof (Sejdinovic, et al. (2013) <doi:10.1214/13-AOS1140>) and corresponding tests (Berschneider, Bottcher (2018) <doi:10.48550/arXiv.1808.07280>. Distance standard deviation methods (Edelmann, et al. (2020) <doi:10.1214/19-AOS1935>) and distance correlation methods for survival endpoints (Edelmann, et al. (2021) <doi:10.1111/biom.13470>) are also included.
Author: Dominic Edelmann [aut, cre],
Jochen Fiedler [aut]
Maintainer: Dominic Edelmann <dominic.edelmann@dkfz-heidelberg.de>
Diff between dcortools versions 0.1.6 dated 2022-12-09 and 0.1.7 dated 2025-12-09
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 9 +++++++++ R/distcovsurv.R | 32 ++++++++++++++++++++------------ build/partial.rdb |binary inst/REFERENCES.bib | 14 ++++++++------ src/Makevars | 2 +- src/Makevars.win | 2 +- 8 files changed, 50 insertions(+), 31 deletions(-)
Title: Mining NB-Frequent Itemsets and NB-Precise Rules
Description: NBMiner is an implementation of the model-based mining algorithm for mining NB-frequent itemsets and NB-precise rules. Michael Hahsler (2006) <doi:10.1007/s10618-005-0026-2>.
Author: Michael Hahsler [aut, cre, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between arulesNBMiner versions 0.1-8 dated 2021-09-07 and 0.1.9 dated 2025-12-09
arulesNBMiner-0.1-8/arulesNBMiner/R/parameter.R |only arulesNBMiner-0.1.9/arulesNBMiner/DESCRIPTION | 20 arulesNBMiner-0.1.9/arulesNBMiner/MD5 | 26 arulesNBMiner-0.1.9/arulesNBMiner/NEWS.md |only arulesNBMiner-0.1.9/arulesNBMiner/R/AAAonLoad.R | 15 arulesNBMiner-0.1.9/arulesNBMiner/R/Agrawal_data.R |only arulesNBMiner-0.1.9/arulesNBMiner/R/AllClasses.R | 35 arulesNBMiner-0.1.9/arulesNBMiner/R/NBMiner.R | 182 +++- arulesNBMiner-0.1.9/arulesNBMiner/R/NBMinerParameters.R | 520 +++++++------ arulesNBMiner-0.1.9/arulesNBMiner/R/parameters_helper.R |only arulesNBMiner-0.1.9/arulesNBMiner/README.md | 146 +-- arulesNBMiner-0.1.9/arulesNBMiner/build/partial.rdb |binary arulesNBMiner-0.1.9/arulesNBMiner/inst/README_files |only arulesNBMiner-0.1.9/arulesNBMiner/man/Agrawal.Rd | 46 - arulesNBMiner-0.1.9/arulesNBMiner/man/NBMiner.Rd | 83 +- arulesNBMiner-0.1.9/arulesNBMiner/man/NBMinerParameters.Rd | 89 +- arulesNBMiner-0.1.9/arulesNBMiner/man/figures |only 17 files changed, 686 insertions(+), 476 deletions(-)
Title: 'Opal' Data Repository Client and 'DataSHIELD' Utils
Description: Data integration Web application for biobanks by 'OBiBa'. 'Opal' is
the core database application for biobanks. Participant data, once
collected from any data source, must be integrated and stored in a central
data repository under a uniform model. 'Opal' is such a central repository.
It can import, process, validate, query, analyze, report, and export data.
'Opal' is typically used in a research center to analyze the data acquired at
assessment centres. Its ultimate purpose is to achieve seamless
data-sharing among biobanks. This 'Opal' client allows to interact with 'Opal'
web services and to perform operations on the R server side. 'DataSHIELD'
administration tools are also provided.
Author: Yannick Marcon [aut, cre] ,
Amadou Gaye [ctb] ,
OBiBa group [cph]
Maintainer: Yannick Marcon <yannick.marcon@obiba.org>
Diff between opalr versions 3.5.1 dated 2025-11-16 and 3.5.2 dated 2025-12-09
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- R/opal.file.R | 8 +++++--- R/opal.sql.R | 1 + build/vignette.rds |binary inst/doc/datashield-admin.html | 4 ++-- inst/doc/opal-files.html | 4 ++-- inst/doc/opal-projects.html | 4 ++-- inst/doc/opal-rsession.html | 4 ++-- 9 files changed, 25 insertions(+), 22 deletions(-)
Title: Meta-Analytic Effect Size Calculation for Pre-Post Designs with
Correlation Imputation
Description: Tools for the calculation of effect sizes (standardised mean difference) and mean difference in pre-post controlled studies, including robust imputation of missing variances (standard deviation of changes) and correlations (Pearson correlation coefficient). The main function 'metacor_dual()' implements several methods for imputing missing standard deviation of changes or Pearson correlation coefficient, and generates transparent imputation reports. Designed for meta-analyses with incomplete summary statistics. For details on the methods, see Higgins et al. (2023) and Fu et al. (2013).
Author: Iker J. Bautista [aut, cre],
Saul M. Rodriguez [ctb]
Maintainer: Iker J. Bautista <ikerugr@gmail.com>
Diff between metacor versions 1.2.0 dated 2025-09-26 and 1.2.1 dated 2025-12-09
DESCRIPTION | 6 +++--- MD5 | 8 +++++--- NAMESPACE | 1 + R/check_metacor_consistency.R |only inst/doc/introduccion.html | 16 ++++++++-------- man/check_metacor_consistency.Rd |only 6 files changed, 17 insertions(+), 14 deletions(-)
Title: Orchestration of Data Pipelines
Description: Framework for creating and orchestrating data pipelines. Organize, orchestrate, and monitor multiple pipelines in a single project. Use tags to decorate functions with scheduling parameters and configuration.
Author: Will Hipson [cre, aut, cph] ,
Ryan Garnett [aut, ctb, cph]
Maintainer: Will Hipson <will.e.hipson@gmail.com>
Diff between maestro versions 0.7.0 dated 2025-10-31 and 0.7.1 dated 2025-12-09
DESCRIPTION | 8 +-- MD5 | 22 ++++---- NEWS.md | 6 ++ R/MaestroPipeline.R | 27 ++++++---- R/MaestroPipelineList.R | 41 ++++++++++++++++ build/vignette.rds |binary inst/doc/maestro-1-quick-start.html | 8 +-- inst/doc/maestro-3-advanced-scheduling.html | 12 ++-- inst/doc/maestro-4-directed-acyclic-graphs.html | 20 ++++---- inst/doc/maestro-5-logging.html | 60 ++++++++++++------------ inst/doc/maestro-8-conditionals.html | 42 ++++++++-------- man/MaestroPipelineList.Rd | 21 ++++++++ 12 files changed, 171 insertions(+), 96 deletions(-)
Title: 'ggplot2' Based Plots with Statistical Details
Description: Extension of 'ggplot2', 'ggstatsplot' creates graphics with
details from statistical tests included in the plots themselves. It
provides an easier syntax to generate information-rich plots for
statistical analysis of continuous (violin plots, scatterplots,
histograms, dot plots, dot-and-whisker plots) or categorical (pie and
bar charts) data. Currently, it supports the most common types of
statistical approaches and tests: parametric, nonparametric, robust,
and Bayesian versions of t-test/ANOVA, correlation analyses,
contingency table analysis, meta-analysis, and regression analyses.
References: Patil (2021) <doi:10.21105/joss.03236>.
Author: Indrajeet Patil [cre, aut, cph]
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>
Diff between ggstatsplot versions 0.13.3 dated 2025-10-05 and 0.13.4 dated 2025-12-09
DESCRIPTION | 47 +++++++++++++-------------------- MD5 | 34 +++++++++++------------ NEWS.md | 14 +++++++-- R/ggbarstats.R | 11 ++++--- R/ggbetweenstats.R | 3 +- R/ggcoefstats.R | 18 +++++++----- R/ggdotplotstats.R | 11 ++++--- R/ggpiestats.R | 7 ++++ R/ggwithinstats.R | 3 +- README.md | 2 - man/ggstatsplot-package.Rd | 5 --- man/grouped_ggbarstats.Rd | 11 ++++--- man/grouped_ggbetweenstats.Rd | 3 +- man/grouped_ggdotplotstats.Rd | 11 ++++--- man/grouped_ggpiestats.Rd | 7 ++++ man/grouped_ggwithinstats.Rd | 3 +- tests/testthat/_snaps/extract-stats.md | 11 +++++++ tests/testthat/test-extract-stats.R | 1 18 files changed, 115 insertions(+), 87 deletions(-)
Title: Metrics of R Packages
Description: Static code analyses for R packages using the external code-tagging
libraries 'ctags' and 'gtags'. Static analyses enable packages to be
analysed very quickly, generally a couple of seconds at most. The package
also provides access to a database generating by applying the main function
to the full 'CRAN' archive, enabling the statistical properties of any package
to be compared with all other 'CRAN' packages.
Author: Mark Padgham [aut, cre] ,
Michael Sumner [ctb] ,
Jeffrey Hollister [ctb] ,
Egor Kotov [ctb]
Maintainer: Mark Padgham <mark.padgham@email.com>
This is a re-admission after prior archival of version 0.1.1 dated 2022-06-21
Diff between pkgstats versions 0.1.1 dated 2022-06-21 and 0.2.1 dated 2025-12-09
pkgstats-0.1.1/pkgstats/R/archive-trawl.R |only pkgstats-0.1.1/pkgstats/R/extract_tarball.R |only pkgstats-0.1.1/pkgstats/R/pkgstats.R |only pkgstats-0.1.1/pkgstats/configure |only pkgstats-0.1.1/pkgstats/inst/CITATION |only pkgstats-0.1.1/pkgstats/src/Makevars.win |only pkgstats-0.1.1/pkgstats/tools |only pkgstats-0.1.1/pkgstats/vignettes/installation.md |only pkgstats-0.1.1/pkgstats/vignettes/pkgstats.md |only pkgstats-0.2.1/pkgstats/DESCRIPTION | 41 +- pkgstats-0.2.1/pkgstats/MD5 | 125 ++++---- pkgstats-0.2.1/pkgstats/NAMESPACE | 4 pkgstats-0.2.1/pkgstats/NEWS.md |only pkgstats-0.2.1/pkgstats/R/cran-data-archive.R |only pkgstats-0.2.1/pkgstats/R/cran-data-current.R |only pkgstats-0.2.1/pkgstats/R/cran-data-fn-names.R |only pkgstats-0.2.1/pkgstats/R/cran-data-update.R |only pkgstats-0.2.1/pkgstats/R/ctags-install.R | 104 +++++-- pkgstats-0.2.1/pkgstats/R/ctags-test.R | 73 +++-- pkgstats-0.2.1/pkgstats/R/desc-stats.R | 22 + pkgstats-0.2.1/pkgstats/R/external-calls.R | 44 +-- pkgstats-0.2.1/pkgstats/R/extra-stats.R | 51 +-- pkgstats-0.2.1/pkgstats/R/extract-tarball.R |only pkgstats-0.2.1/pkgstats/R/function-names.R | 68 ++-- pkgstats-0.2.1/pkgstats/R/gtags-install.R | 13 pkgstats-0.2.1/pkgstats/R/loc.R | 14 pkgstats-0.2.1/pkgstats/R/onload.R | 18 - pkgstats-0.2.1/pkgstats/R/pkgstats-data-download.R | 6 pkgstats-0.2.1/pkgstats/R/pkgstats-function.R |only pkgstats-0.2.1/pkgstats/R/pkgstats-package.R | 1 pkgstats-0.2.1/pkgstats/R/pkgstats-summary.R | 34 +- pkgstats-0.2.1/pkgstats/R/plot.R | 32 -- pkgstats-0.2.1/pkgstats/R/rd-stats.R | 42 ++ pkgstats-0.2.1/pkgstats/R/roxygen-blocks.R |only pkgstats-0.2.1/pkgstats/R/tag-data-call-graph.R | 9 pkgstats-0.2.1/pkgstats/R/tag-data-ctags.R | 43 +-- pkgstats-0.2.1/pkgstats/R/tag-data-gtags.R | 38 +- pkgstats-0.2.1/pkgstats/R/tag-data.R | 61 ++-- pkgstats-0.2.1/pkgstats/R/utils.R | 62 +++- pkgstats-0.2.1/pkgstats/R/zzz.R |only pkgstats-0.2.1/pkgstats/README.md |only pkgstats-0.2.1/pkgstats/build/vignette.rds |binary pkgstats-0.2.1/pkgstats/inst/doc/installation.R | 20 - pkgstats-0.2.1/pkgstats/inst/doc/installation.Rmd | 18 - pkgstats-0.2.1/pkgstats/inst/doc/installation.html | 143 +++++----- pkgstats-0.2.1/pkgstats/inst/doc/pkgstats.R | 10 pkgstats-0.2.1/pkgstats/inst/doc/pkgstats.Rmd | 6 pkgstats-0.2.1/pkgstats/inst/doc/pkgstats.html | 131 ++++----- pkgstats-0.2.1/pkgstats/man/ctags_install.Rd | 6 pkgstats-0.2.1/pkgstats/man/ctags_test.Rd | 15 - pkgstats-0.2.1/pkgstats/man/desc_stats.Rd | 2 pkgstats-0.2.1/pkgstats/man/dl_pkgstats_data.Rd | 5 pkgstats-0.2.1/pkgstats/man/extract_tarball.Rd | 2 pkgstats-0.2.1/pkgstats/man/loc_stats.Rd | 2 pkgstats-0.2.1/pkgstats/man/pkgstats-package.Rd | 10 pkgstats-0.2.1/pkgstats/man/pkgstats.Rd | 32 +- pkgstats-0.2.1/pkgstats/man/pkgstats_cran_current_from_full.Rd |only pkgstats-0.2.1/pkgstats/man/pkgstats_fns_from_archive.Rd | 16 - pkgstats-0.2.1/pkgstats/man/pkgstats_fns_update.Rd |only pkgstats-0.2.1/pkgstats/man/pkgstats_from_archive.Rd | 23 - pkgstats-0.2.1/pkgstats/man/pkgstats_summary.Rd | 4 pkgstats-0.2.1/pkgstats/man/pkgstats_update.Rd |only pkgstats-0.2.1/pkgstats/man/plot_network.Rd | 2 pkgstats-0.2.1/pkgstats/man/rd_stats.Rd | 4 pkgstats-0.2.1/pkgstats/man/tags_data.Rd | 4 pkgstats-0.2.1/pkgstats/tests/testthat/helper-archive-trawl.R |only pkgstats-0.2.1/pkgstats/tests/testthat/test-archive-trawl.R | 104 +++++-- pkgstats-0.2.1/pkgstats/tests/testthat/test-cran-update.R |only pkgstats-0.2.1/pkgstats/tests/testthat/test-ctags.R | 5 pkgstats-0.2.1/pkgstats/tests/testthat/test-desc-stats.R | 7 pkgstats-0.2.1/pkgstats/tests/testthat/test-fn-names.R |only pkgstats-0.2.1/pkgstats/tests/testthat/test-pkgstats.R | 40 ++ pkgstats-0.2.1/pkgstats/tests/testthat/test-plot-network.R | 9 pkgstats-0.2.1/pkgstats/tests/testthat/test-summary.R | 7 pkgstats-0.2.1/pkgstats/vignettes/installation.Rmd | 18 - pkgstats-0.2.1/pkgstats/vignettes/pkgstats.Rmd | 6 76 files changed, 948 insertions(+), 608 deletions(-)
Title: Mixed Models for Repeated Measures
Description: Mixed models for repeated measures (MMRM) are a popular
choice for analyzing longitudinal continuous outcomes in randomized
clinical trials and beyond; see Cnaan, Laird and Slasor (1997)
<doi:10.1002/(SICI)1097-0258(19971030)16:20%3C2349::AID-SIM667%3E3.0.CO;2-E>
for a tutorial and Mallinckrodt, Lane, Schnell, Peng and Mancuso
(2008) <doi:10.1177/009286150804200402> for a review. This package
implements MMRM based on the marginal linear model without random
effects using Template Model Builder ('TMB') which enables fast and
robust model fitting. Users can specify a variety of covariance
matrices, weight observations, fit models with restricted or standard
maximum likelihood inference, perform hypothesis testing with
Satterthwaite or Kenward-Roger adjustment, and extract least square
means estimates by using 'emmeans'.
Author: Daniel Sabanes Bove [aut, cre] ,
Liming Li [aut] ,
Julia Dedic [aut],
Doug Kelkhoff [aut],
Kevin Kunzmann [aut],
Brian Matthew Lang [aut],
Christian Stock [aut],
Ya Wang [aut],
Craig Gower-Page [ctb],
Dan James [aut],
Jonathan Sidi [aut],
Daniel Leib [...truncated...]
Maintainer: Daniel Sabanes Bove <daniel.sabanes_bove@rconis.com>
Diff between mmrm versions 0.3.15 dated 2025-06-10 and 0.3.16 dated 2025-12-09
mmrm-0.3.15/mmrm/man/h_first_contain_categorical.Rd |only mmrm-0.3.15/mmrm/man/h_get_contrast.Rd |only mmrm-0.3.15/mmrm/tests/testthat/_snaps/car.md |only mmrm-0.3.15/mmrm/tests/testthat/test-car.R |only mmrm-0.3.16/mmrm/DESCRIPTION | 24 mmrm-0.3.16/mmrm/MD5 | 160 - mmrm-0.3.16/mmrm/NAMESPACE | 1 mmrm-0.3.16/mmrm/NEWS.md | 21 mmrm-0.3.16/mmrm/R/between-within.R | 12 mmrm-0.3.16/mmrm/R/component.R | 115 - mmrm-0.3.16/mmrm/R/cov_struct.R | 24 mmrm-0.3.16/mmrm/R/fit.R | 84 mmrm-0.3.16/mmrm/R/interop-car.R | 345 ++- mmrm-0.3.16/mmrm/R/interop-emmeans.R | 42 mmrm-0.3.16/mmrm/R/kenwardroger.R | 48 mmrm-0.3.16/mmrm/R/mmrm-methods.R | 335 ++- mmrm-0.3.16/mmrm/R/residual.R | 7 mmrm-0.3.16/mmrm/R/satterthwaite.R | 3 mmrm-0.3.16/mmrm/R/testing.R | 118 - mmrm-0.3.16/mmrm/R/tidiers.R | 45 mmrm-0.3.16/mmrm/R/tmb-methods.R | 333 ++- mmrm-0.3.16/mmrm/R/tmb.R | 299 +- mmrm-0.3.16/mmrm/R/utils-formula.R | 10 mmrm-0.3.16/mmrm/R/utils-nse.R | 9 mmrm-0.3.16/mmrm/R/utils.R | 692 ++++++ mmrm-0.3.16/mmrm/R/zzz.R | 40 mmrm-0.3.16/mmrm/build/partial.rdb |binary mmrm-0.3.16/mmrm/build/vignette.rds |binary mmrm-0.3.16/mmrm/inst/WORDLIST | 13 mmrm-0.3.16/mmrm/inst/doc/covariance.Rmd | 20 mmrm-0.3.16/mmrm/inst/doc/covariance.html | 23 mmrm-0.3.16/mmrm/inst/doc/hypothesis_testing.Rmd | 94 mmrm-0.3.16/mmrm/inst/doc/hypothesis_testing.html | 166 - mmrm-0.3.16/mmrm/inst/doc/introduction.R | 2 mmrm-0.3.16/mmrm/inst/doc/introduction.html | 200 + mmrm-0.3.16/mmrm/inst/doc/mmrm_review_methods.html | 74 mmrm-0.3.16/mmrm/man/Anova.mmrm.Rd | 22 mmrm-0.3.16/mmrm/man/component.Rd | 5 mmrm-0.3.16/mmrm/man/df_md.Rd | 2 mmrm-0.3.16/mmrm/man/emp_start.Rd | 21 mmrm-0.3.16/mmrm/man/h_anova_single_mmrm_model.Rd |only mmrm-0.3.16/mmrm/man/h_assert_lrt_suitability.Rd |only mmrm-0.3.16/mmrm/man/h_assert_nested_models.Rd |only mmrm-0.3.16/mmrm/man/h_check_columns_nested.Rd |only mmrm-0.3.16/mmrm/man/h_check_cov_struct_nesting.Rd |only mmrm-0.3.16/mmrm/man/h_check_covar_nesting.Rd |only mmrm-0.3.16/mmrm/man/h_check_fits_all_data_same.Rd |only mmrm-0.3.16/mmrm/man/h_construct_model_frame_inputs.Rd | 13 mmrm-0.3.16/mmrm/man/h_contr_sum_type3_contrasts.Rd |only mmrm-0.3.16/mmrm/man/h_dataset_sort_all.Rd |only mmrm-0.3.16/mmrm/man/h_first_term_containing_categ.Rd |only mmrm-0.3.16/mmrm/man/h_fits_common_data.Rd |only mmrm-0.3.16/mmrm/man/h_generate_new_name.Rd |only mmrm-0.3.16/mmrm/man/h_get_minimal_fit_data.Rd |only mmrm-0.3.16/mmrm/man/h_mmrm_tmb_fit.Rd | 12 mmrm-0.3.16/mmrm/man/h_mmrm_tmb_formula_parts.Rd | 1 mmrm-0.3.16/mmrm/man/h_refit_mmrm.Rd |only mmrm-0.3.16/mmrm/man/h_test_md.Rd | 21 mmrm-0.3.16/mmrm/man/h_type2_contrast.Rd |only mmrm-0.3.16/mmrm/man/h_type3_contrasts.Rd |only mmrm-0.3.16/mmrm/man/mmrm_control.Rd | 14 mmrm-0.3.16/mmrm/man/mmrm_tmb_methods.Rd | 41 mmrm-0.3.16/mmrm/man/stats_anova.Rd |only mmrm-0.3.16/mmrm/src/covariance.h | 11 mmrm-0.3.16/mmrm/src/test-covariance.cpp | 68 mmrm-0.3.16/mmrm/src/utils.h | 7 mmrm-0.3.16/mmrm/tests/additional.R |only mmrm-0.3.16/mmrm/tests/testthat/_snaps/interop-car.md |only mmrm-0.3.16/mmrm/tests/testthat/_snaps/kenwardroger.md | 416 +-- mmrm-0.3.16/mmrm/tests/testthat/_snaps/testing.md | 4 mmrm-0.3.16/mmrm/tests/testthat/_snaps/tmb-methods.md | 838 +++---- mmrm-0.3.16/mmrm/tests/testthat/helper-examples.R | 148 + mmrm-0.3.16/mmrm/tests/testthat/test-between-within.R | 31 mmrm-0.3.16/mmrm/tests/testthat/test-component.R | 100 mmrm-0.3.16/mmrm/tests/testthat/test-cov-struct.R | 4 mmrm-0.3.16/mmrm/tests/testthat/test-cpp-covariance.R | 206 + mmrm-0.3.16/mmrm/tests/testthat/test-cpp-utils.R | 92 mmrm-0.3.16/mmrm/tests/testthat/test-emmeans.R | 149 + mmrm-0.3.16/mmrm/tests/testthat/test-empirical.R | 250 +- mmrm-0.3.16/mmrm/tests/testthat/test-fit.R | 108 - mmrm-0.3.16/mmrm/tests/testthat/test-interop-car.R |only mmrm-0.3.16/mmrm/tests/testthat/test-interop-parsnip.R | 25 mmrm-0.3.16/mmrm/tests/testthat/test-interop.R | 16 mmrm-0.3.16/mmrm/tests/testthat/test-kenwardroger.R | 241 +- mmrm-0.3.16/mmrm/tests/testthat/test-mmrm-methods.R | 427 +++ mmrm-0.3.16/mmrm/tests/testthat/test-testing.R | 20 mmrm-0.3.16/mmrm/tests/testthat/test-tidiers.R | 27 mmrm-0.3.16/mmrm/tests/testthat/test-tmb-methods.R | 616 ++++- mmrm-0.3.16/mmrm/tests/testthat/test-tmb.R | 1073 ++++++++-- mmrm-0.3.16/mmrm/tests/testthat/test-utils.R | 58 mmrm-0.3.16/mmrm/vignettes/covariance.Rmd | 20 mmrm-0.3.16/mmrm/vignettes/hypothesis_testing.Rmd | 94 mmrm-0.3.16/mmrm/vignettes/subsections/_intro-hypothesis_testing.Rmd | 33 93 files changed, 6452 insertions(+), 2141 deletions(-)
Title: Robust Methods for High-Dimensional Data
Description: Robust methods for high-dimensional data, in particular linear
model selection techniques based on least angle regression and sparse
regression. Specifically, the package implements robust least angle
regression (Khan, Van Aelst & Zamar, 2007; <doi:10.1198/016214507000000950>),
(robust) groupwise least angle regression (Alfons, Croux & Gelper, 2016;
<doi:10.1016/j.csda.2015.02.007>), and sparse least trimmed squares
regression (Alfons, Croux & Gelper, 2013; <doi:10.1214/12-AOAS575>).
Author: Andreas Alfons [aut, cre] ,
Dirk Eddelbuettel [ctb]
Maintainer: Andreas Alfons <alfons@ese.eur.nl>
Diff between robustHD versions 0.8.2 dated 2025-10-02 and 0.8.3 dated 2025-12-09
DESCRIPTION | 11 MD5 | 56 +- NAMESPACE | 1 NEWS | 488 ++++++++++---------- R/TopGear.R | 160 +++--- R/coef.R | 254 +++++----- R/corHuber.R | 280 +++++------ R/fitted.R | 204 ++++---- R/grouplars.R | 652 +++++++++++++-------------- R/grplars.R | 752 +++++++++++++++---------------- R/lambda0.R | 228 ++++----- R/plot.R | 32 - R/predict.R | 470 +++++++++---------- R/residuals.R | 262 +++++----- R/rlars.R | 704 ++++++++++++++--------------- R/rstandard.R | 334 ++++++------- R/setupCritPlot.R | 5 R/setupDiagnosticPlot.R | 952 +++++++++++++++++++-------------------- R/sparseLTS.R | 1106 +++++++++++++++++++++++----------------------- R/tslars.R | 644 +++++++++++++------------- R/tslarsP.R | 610 ++++++++++++------------- R/winsorize.R | 386 ++++++++-------- build/partial.rdb |binary data/datalist | 4 inst/CITATION | 22 man/TopGear.Rd | 158 +++--- man/rstandard.seqModel.Rd | 226 ++++----- src/corHuber.cpp | 1 src/fastRlars.cpp | 1 29 files changed, 4508 insertions(+), 4495 deletions(-)
Title: Comparing and Visualizing Differences Between Surveys
Description: Easily analyze and visualize differences between samples (e.g., benchmark comparisons, nonresponse comparisons in surveys) on three levels. The comparisons can be univariate, bivariate or multivariate. On univariate level the variables of interest of a survey and a comparison survey (i.e. benchmark) are compared, by calculating one of several difference measures (e.g., relative difference in mean), and an average difference between the surveys. On bivariate level a function can calculate significant differences in correlations for the surveys. And on multivariate levels a function can calculate significant differences in model coefficients between the surveys of comparison. All of those differences can be easily plotted and outputted as a table. For more detailed information on the methods and example use see Rohr, B., Silber, H., & Felderer, B. (2024). Comparing the Accuracy of Univariate, Bivariate, and Multivariate Estimates across Probability and Nonprobability Surveys with Po [...truncated...]
Author: Bjoern Rohr [aut, cre, cph],
Barbara Felderer [aut]
Maintainer: Bjoern Rohr <bjoern.rohr@gesis.org>
Diff between sampcompR versions 0.3.1.2 dated 2025-07-04 and 0.3.2 dated 2025-12-09
sampcompR-0.3.1.2/sampcompR/data/card.RData |only sampcompR-0.3.2/sampcompR/DESCRIPTION | 6 sampcompR-0.3.2/sampcompR/MD5 | 44 +-- sampcompR-0.3.2/sampcompR/NAMESPACE | 1 sampcompR-0.3.2/sampcompR/NEWS.md | 4 sampcompR-0.3.2/sampcompR/R/Bivdiff.R | 7 sampcompR-0.3.2/sampcompR/R/Bivdiff_Plot.R | 4 sampcompR-0.3.2/sampcompR/R/Output_Tables.R | 35 +- sampcompR-0.3.2/sampcompR/R/Unidiff_Plot.R | 129 +++++++++- sampcompR-0.3.2/sampcompR/R/card.R | 12 sampcompR-0.3.2/sampcompR/data/card.rda |only sampcompR-0.3.2/sampcompR/man/R_indicator.Rd | 15 + sampcompR-0.3.2/sampcompR/man/biv_bias_per_variable.Rd | 3 sampcompR-0.3.2/sampcompR/man/biv_compare.Rd | 3 sampcompR-0.3.2/sampcompR/man/biv_compare_table.Rd | 3 sampcompR-0.3.2/sampcompR/man/biv_per_variable.Rd | 3 sampcompR-0.3.2/sampcompR/man/card.Rd | 2 sampcompR-0.3.2/sampcompR/man/heatmap_biv_compare.Rd | 2 sampcompR-0.3.2/sampcompR/man/plot_biv_compare.Rd | 2 sampcompR-0.3.2/sampcompR/man/plot_uni_compare.Rd | 5 sampcompR-0.3.2/sampcompR/tests/testthat/helper_biv_compare.R | 55 ++-- sampcompR-0.3.2/sampcompR/tests/testthat/helper_uni_compare.R | 46 +-- sampcompR-0.3.2/sampcompR/tests/testthat/test-biv_compare_table.R | 28 +- sampcompR-0.3.2/sampcompR/tests/testthat/test-uni_compare_table.R | 14 - 24 files changed, 289 insertions(+), 134 deletions(-)
Title: Temporal Trends in Ecological Niche Models
Description: Computes temporal trends in environmental suitability obtained from ecological niche models, based on a set of species presence point coordinates and predictor variables.
Author: A. Marcia Barbosa [aut, cre],
Joao Alirio [aut],
Nuno Garcia [aut],
Joao Campos [aut],
Ana Claudia Teodoro [aut],
Lia Barbara Duarte [aut],
Isabel Pocas [aut],
Salvador Arenas-Castro [aut],
Neftali Sillero [aut]
Maintainer: A. Marcia Barbosa <ana.marcia.barbosa@gmail.com>
Diff between ecotrends versions 1.1 dated 2025-07-07 and 1.2 dated 2025-12-09
ecotrends |only 1 file changed
Title: Estimate the Four Parameters of Stable Laws using Different
Methods
Description: Estimate the four parameters of stable laws using maximum
likelihood method, generalised method of moments with
finite and continuum number of points, iterative
Koutrouvelis regression and Kogon-McCulloch method. The
asymptotic properties of the estimators (covariance
matrix, confidence intervals) are also provided.
Author: Tarak Kharrat [aut] ,
Georgi N. Boshnakov [aut, cre]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>
Diff between StableEstim versions 2.3 dated 2024-10-24 and 2.4 dated 2025-12-09
DESCRIPTION | 26 MD5 | 28 NAMESPACE | 12 NEWS.md | 16 R/GMMParamsEstim.R | 40 R/InitialGuess.R | 2 R/OutputFileManip.R | 12 R/ToolsFct.R | 15 R/WeightingMatrix.R | 2 README.md | 3 build/partial.rdb |binary inst/REFERENCES.bib | 2114 ++++++++++++++++++++-------------------- man/GMMParametersEstim.Rd | 11 man/McCullochParametersEstim.Rd | 5 man/expect_almost_equal.Rd | 3 15 files changed, 1159 insertions(+), 1130 deletions(-)
Title: Facilities for Simulating from ODE-Based Models
Description: Facilities for running simulations from ordinary
differential equation ('ODE') models, such as pharmacometrics and other
compartmental models. A compilation manager translates the ODE model
into C, compiles it, and dynamically loads the object code into R for
improved computational efficiency. An event table object facilitates
the specification of complex dosing regimens (optional) and sampling
schedules. NB: The use of this package requires both C and
Fortran compilers, for details on their use with R please see
Section 6.3, Appendix A, and Appendix D in the "R Administration and
Installation" manual. Also the code is mostly released under GPL. The
'VODE' and 'LSODA' are in the public domain. The information is available
in the inst/COPYRIGHTS.
Author: Matthew L. Fidler [aut, cre] ,
Wenping Wang [aut],
Alan Hindmarsh [ctb],
Arun Srinivasan [ctb],
Awad H. Al-Mohy [ctb],
Bill Denney [ctb] ,
Cleve Moler [ctb],
David Cooley [ctb],
Drew Schmidt [ctb],
Ernst Hairer [ctb],
Gabriel Staples [ctb],
Gerhard W [...truncated...]
Maintainer: Matthew L. Fidler <matthew.fidler@gmail.com>
Diff between rxode2 versions 5.0.0 dated 2025-11-28 and 5.0.1 dated 2025-12-09
DESCRIPTION | 6 MD5 | 101 +++-- NAMESPACE | 4 NEWS.md | 18 + R/RcppExports.R | 16 R/dfIni.R | 6 R/rxRaw.R |only R/rxode-options.R | 4 R/rxode2.R | 12 R/rxode2_md5.R | 2 R/rxrandom.R | 24 + R/utils.R | 2 data/rxReservedKeywords.rda |binary data/rxResidualError.rda |binary data/rxSyntaxFunctions.rda |binary inst/doc/rxode2-syntax.html | 26 - inst/include/rxode2.h | 4 inst/include/rxode2_model_shared.c | 50 +- inst/include/rxode2_model_shared.h | 92 ++--- inst/include/rxode2parseVer.h | 4 man/rxDeserialize.Rd |only man/rxGetSerialType_.Rd |only man/rxNumLoaded.Rd |only man/rxRawToC.Rd |only man/rxSerialize.Rd |only man/rxUnloadAll.Rd | 2 man/rxbeta.Rd | 2 man/rxbinom.Rd | 1 man/rxcauchy.Rd | 1 man/rxchisq.Rd | 2 man/rxexp.Rd | 2 man/rxf.Rd | 1 man/rxgamma.Rd | 2 man/rxgeom.Rd | 2 man/rxnbinom.Rd | 4 man/rxpois.Rd | 2 man/rxt.Rd | 1 man/rxunif.Rd | 2 man/rxweibull.Rd | 2 src/RcppExports.cpp | 19 - src/approx.cpp | 2 src/codegen.c | 27 - src/codegen.h | 38 -- src/codegen2.h | 30 - src/dlsoda.f | 7 src/init.c | 9 src/par_solve.cpp | 9 src/parseFunsRandom.h | 75 ++-- src/qs.cpp | 83 ++++ src/rxData.cpp | 7 src/rxthreefry.cpp | 660 +++++++++++++++++++++---------------- src/rxthreefry.h | 69 +-- tests/testthat.R | 8 tests/testthat/test-random.R | 28 + tests/testthat/test-raw.R |only 55 files changed, 884 insertions(+), 584 deletions(-)
Title: Version-Control for CRAN, GitHub, and GitLab Packages
Description: Make R scripts reproducible, by ensuring that
every time a given script is run, the same version of the used packages are
loaded (instead of whichever version the user running the script happens to
have installed). This is achieved by using the command
groundhog.library() instead of the base command library(), and including a
date in the call. The date is used to call on the same version of the
package every time (the most recent version available at that date).
Load packages from CRAN, GitHub, or Gitlab.
Author: Uri Simonsohn [aut, cre] ,
Hugo Gruson [ctb, aut]
Maintainer: Uri Simonsohn <urisohn@gmail.com>
Diff between groundhog versions 3.2.3 dated 2025-05-12 and 3.3.0 dated 2025-12-09
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/get.dependencies.R | 2 -- R/get.snowball.R | 12 +++++++++++- R/groundhog.library.R | 26 ++++++++++++++++++++++++++ R/update_cran.toc_if.needed.R | 29 +++++++++++++++++++++++++++-- R/zzz.R | 2 +- 7 files changed, 75 insertions(+), 16 deletions(-)
Title: Building and Managing Local Databases from 'Google Earth Engine'
Description: Simplifies the creation, management, and updating of local databases using data extracted from 'Google Earth Engine' ('GEE'). It integrates with 'GEE' to store, aggregate, and process spatio-temporal data, leveraging 'SQLite' for efficient, serverless storage. The 'geeLite' package provides utilities for data transformation and supports real-time monitoring and analysis of geospatial features, making it suitable for researchers and practitioners in geospatial science. For details, see Kurbucz and Andrée (2025) "Building and Managing Local Databases from Google Earth Engine with the geeLite R Package" <https://hdl.handle.net/10986/43165>.
Author: Marcell T. Kurbucz [aut, cre],
Bo Pieter Johannes Andree [aut]
Maintainer: Marcell T. Kurbucz <m.kurbucz@ucl.ac.uk>
Diff between geeLite versions 1.0.4 dated 2025-12-01 and 1.0.5 dated 2025-12-09
DESCRIPTION | 12 MD5 | 35 NAMESPACE | 3 R/access_db.R | 1540 +++++++++++++++++++++--------------------- R/gee_install.R | 16 R/run_geelite.R | 416 +++++++---- R/set_config.R | 192 ++--- R/utils.R | 51 - README.md | 352 ++++----- man/check_rgee_ready.Rd | 21 man/drive_auth_ready.Rd |only man/ensure_sessioninfo.Rd |only man/gee_install.Rd | 6 man/read_db.Rd | 7 man/set_config.Rd | 4 man/set_depend.Rd | 12 man/update_grid_stats.Rd | 2 tests/testthat.R | 35 tests/testthat/setup.R |only tests/testthat/test-geelite.R | 264 +++---- 20 files changed, 1563 insertions(+), 1405 deletions(-)
Title: Analysis of Basketball Data
Description: Collection of tools to work with European basketball data. Functions available are related to friendly
web scraping, data management and visualization. Data were obtained from <https://www.euroleaguebasketball.net/euroleague/>,
<https://www.euroleaguebasketball.net/eurocup/> and <https://www.acb.com/>, following the instructions
of their respectives robots.txt files, when available. Box score data are available for the three leagues.
Play-by-play and spatial shooting data are also available for the Spanish league. Methods for analysis include a
population pyramid, 2D plots, circular plots of players' percentiles, plots of players' monthly/yearly stats,
team heatmaps, team shooting plots, team four factors plots, cross-tables with the results of regular season games,
maps of nationalities, combinations of lineups, possessions-related variables, timeouts,
performance by periods, personal fouls, offensive rebounds and different types of shooting charts.
Please see Vinue [...truncated...]
Author: Guillermo Vinue [aut, cre]
Maintainer: Guillermo Vinue <guillermo.vinue@uv.es>
Diff between BAwiR versions 1.4.2 dated 2025-11-20 and 1.4.3 dated 2025-12-09
BAwiR-1.4.2/BAwiR/R/get_barplot_monthly_stats.R |only BAwiR-1.4.2/BAwiR/man/get_barplot_monthly_stats.Rd |only BAwiR-1.4.3/BAwiR/DESCRIPTION | 8 - BAwiR-1.4.3/BAwiR/MD5 | 34 ++--- BAwiR-1.4.3/BAwiR/NAMESPACE | 2 BAwiR-1.4.3/BAwiR/NEWS | 7 + BAwiR-1.4.3/BAwiR/R/do_possession.R | 107 ++++++++++++++++- BAwiR-1.4.3/BAwiR/R/do_usage.R | 132 +++++++++++---------- BAwiR-1.4.3/BAwiR/R/get_donut_usage_action.R | 7 - BAwiR-1.4.3/BAwiR/R/get_plot_monthly_stats.R |only BAwiR-1.4.3/BAwiR/R/get_sticker.R | 101 +++++++++------- BAwiR-1.4.3/BAwiR/inst/doc/BAwiR.R | 3 BAwiR-1.4.3/BAwiR/inst/doc/BAwiR.Rmd | 3 BAwiR-1.4.3/BAwiR/inst/doc/BAwiR.html | 9 - BAwiR-1.4.3/BAwiR/inst/doc/BAwiR_pbp.html | 4 BAwiR-1.4.3/BAwiR/inst/doc/BAwiR_sc.html | 4 BAwiR-1.4.3/BAwiR/man/get_donut_usage_action.Rd | 4 BAwiR-1.4.3/BAwiR/man/get_plot_monthly_stats.Rd |only BAwiR-1.4.3/BAwiR/man/get_sticker.Rd | 39 +++--- BAwiR-1.4.3/BAwiR/vignettes/BAwiR.Rmd | 3 20 files changed, 312 insertions(+), 155 deletions(-)
Title: A Bootstrap-Based Power Estimation Tool for Spatial
Transcriptomics
Description: Power estimation and sample size calculation for 10X Visium Spatial Transcriptomics data to detect differential expressed genes between two conditions based on bootstrap resampling. See Shui et al. (2025) <doi:10.1371/journal.pcbi.1013293> for method details.
Author: Lan Shui [aut, cre]
Maintainer: Lan Shui <Lan.Shui@uth.tmc.edu>
Diff between PoweREST versions 0.1.1 dated 2025-08-24 and 0.1.2 dated 2025-12-09
DESCRIPTION | 18 ++++++------ MD5 | 31 ++++++++++----------- NAMESPACE | 2 - R/PoweREST.R | 55 +++++++++++++------------------------ R/PoweREST_gene.R | 72 +++++++++++++++++++------------------------------ R/PoweREST_subset.R | 57 ++++++++++++-------------------------- R/fit_XGBoost.R | 25 ++++++++--------- R/plotly_powerest.R | 14 +++++++-- R/pred_XGBoost.R | 10 +++--- R/utils.R |only R/vis_XGBoost.R | 15 ++++++++-- inst/doc/PoweREST.R | 4 +- inst/doc/PoweREST.Rmd | 4 +- inst/doc/PoweREST.html | 4 +- man/fit_XGBoost.Rd | 8 ++--- man/plotly_powerest.Rd | 1 vignettes/PoweREST.Rmd | 4 +- 17 files changed, 146 insertions(+), 178 deletions(-)
Title: Automated Classification of Mass Spectra
Description: Functions to classify mass spectra in known categories and to determine discriminant mass-to-charge values (m/z). Includes easy-to-use preprocessing pipelines for Matrix Assisted Laser Desorption Ionisation - Time Of Flight Mass Spectrometry (MALDI-TOF) mass spectra, methods to select discriminant m/z from labelled libraries, and tools to predict categories (species, phenotypes, etc.) from selected features. Also provides utilities to build design matrices from peak intensities and labels. While this package was developed with the aim of identifying very similar species or phenotypes of bacteria from MALDI-TOF MS, the functions of this package can also be used to classify other categories associated to mass spectra; or from mass spectra obtained with other mass spectrometry techniques. Parallelized processing and optional C++-accelerated functions are available (notably to deal with large datasets) from version 0.5.0. If you use this package in your research, please cite the associat [...truncated...]
Author: Alexandre Godmer [aut, cre],
Quentin Giai Gianetto [aut],
Karen Druart [aut]
Maintainer: Alexandre Godmer <alexandre.godmer@aphp.fr>
Diff between MSclassifR versions 0.4.0 dated 2025-07-02 and 0.5.0 dated 2025-12-09
DESCRIPTION | 32 + MD5 | 67 ++- NAMESPACE | 64 +-- R/LogReg.R | 607 +++++++++++++++++----------------- R/LogReg_rf_fast.R |only R/PeakDetection.R | 224 ++++++++++-- R/PlotSpectra.R | 220 ++++++++---- R/PredictFastClass.R | 350 +++++++++---------- R/PredictLogReg.R | 530 +++++++++++++++++++---------- R/RcppExports.R |only R/SelectionVar.R | 728 +++++++++++++++++------------------------ R/SelectionVarStat.R | 317 ++++++++++++++--- R/SignalProcessing.R | 130 ++----- R/SignalProcessingUltra.R |only R/alignSpectra_landmark_cpp.R |only R/build_XY_from_peaks.R |only R/build_X_from_peaks_fast.R |only R/cpp-helpers.R |only R/fast_cvpvi.R |only R/fast_mda.R |only R/internal-docs.R |only R/smote_classif.R | 322 +++++++----------- R/utils-core.R |only R/utils-parallel.R |only build/partial.rdb |binary man/LogReg.Rd | 367 ++++++-------------- man/LogReg_rf_fast.Rd |only man/MSclassifR-cpp-helpers.Rd |only man/PeakDetection.Rd | 238 ++++++++----- man/PlotSpectra.Rd | 129 ++++--- man/PredictFastClass.Rd | 228 +++++++----- man/PredictLogReg.Rd | 379 +++++++++------------ man/SelectionVar.Rd | 4 man/SelectionVarStat.Rd | 176 +++++---- man/SignalProcessing.Rd | 190 +++------- man/SignalProcessingUltra.Rd |only man/build_XY_from_peaks.Rd |only man/build_X_from_peaks_fast.Rd |only man/dot-safe_n_workers.Rd |only man/fast_cvpvi.Rd |only man/fast_mda.Rd |only man/msclassifr-internal.Rd |only man/smote_classif.Rd | 141 +++---- src |only 44 files changed, 2879 insertions(+), 2564 deletions(-)
Title: Generalized Synthetic Control Method
Description: Conducts causal inference with interactive fixed-effect models. It imputes counterfactuals for each treated unit using control group information based on a linear interactive fixed effects model that incorporates unit-specific intercepts interacted with time-varying coefficients. This method generalizes the synthetic control method to the case of multiple treated units and variable treatment periods, and improves efficiency and interpretability.
Author: Yiqing Xu [aut, cre] ,
Licheng Liu [aut],
Ziyi Liu [aut],
Shiyun Hu [aut]
Maintainer: Yiqing Xu <yiqingxu@stanford.edu>
Diff between gsynth versions 1.2.1 dated 2021-08-06 and 1.3.1 dated 2025-12-09
gsynth-1.2.1/gsynth/R/RcppExports.R |only gsynth-1.2.1/gsynth/R/core.R |only gsynth-1.2.1/gsynth/R/cumu.R |only gsynth-1.2.1/gsynth/R/interFE.R |only gsynth-1.2.1/gsynth/README.md |only gsynth-1.2.1/gsynth/man/cumuEff.rd |only gsynth-1.2.1/gsynth/man/interFE.Rd |only gsynth-1.2.1/gsynth/man/print.interFE.Rd |only gsynth-1.2.1/gsynth/src |only gsynth-1.3.1/gsynth/DESCRIPTION | 34 gsynth-1.3.1/gsynth/MD5 | 39 gsynth-1.3.1/gsynth/NAMESPACE | 38 gsynth-1.3.1/gsynth/NEWS.md |only gsynth-1.3.1/gsynth/R/default.R | 909 ----------------- gsynth-1.3.1/gsynth/R/effect.R |only gsynth-1.3.1/gsynth/R/plot.R | 1494 +---------------------------- gsynth-1.3.1/gsynth/R/zzz.r | 2 gsynth-1.3.1/gsynth/man/effect.Rd |only gsynth-1.3.1/gsynth/man/gsynth-internal.Rd | 10 gsynth-1.3.1/gsynth/man/gsynth-package.Rd | 7 gsynth-1.3.1/gsynth/man/gsynth.Rd | 91 - gsynth-1.3.1/gsynth/man/plot.gsynth.Rd | 24 gsynth-1.3.1/gsynth/man/print.gsynth.Rd | 10 gsynth-1.3.1/gsynth/man/simdata.Rd | 6 gsynth-1.3.1/gsynth/man/turnout.Rd | 8 25 files changed, 218 insertions(+), 2454 deletions(-)
Title: Graph Visualisation Engine Widget for R and 'shiny' Apps
Description: Create stunning network experiences powered by the 'G6' graph visualisation engine
'JavaScript' library <https://g6.antv.antgroup.com/en>. In 'shiny' mode, modify your
graph directly from the server function to dynamically interact with nodes and edges.
Select your favorite layout among 20 choices. 15 behaviors are available such as
interactive edge creation, collapse-expand and brush select.
17 plugins designed to improve the user experience such as a mini-map,
toolbars and grid lines. Customise the look and feel of your graph with comprehensive
options for nodes, edges and more.
Author: David Granjon [aut, cre],
David Schoch [aut],
cynkra GmbH [fnd],
Bristol Myers Squibb [fnd]
Maintainer: David Granjon <dgranjon@ymail.com>
Diff between g6R versions 0.1.0 dated 2025-07-10 and 0.5.0 dated 2025-12-09
g6R-0.1.0/g6R/man/g6_focus_elements.Rd |only g6R-0.5.0/g6R/DESCRIPTION | 8 g6R-0.5.0/g6R/MD5 | 116 ++-- g6R-0.5.0/g6R/NAMESPACE | 58 ++ g6R-0.5.0/g6R/NEWS.md | 50 + g6R-0.5.0/g6R/R/behaviors.R | 218 +++++++- g6R-0.5.0/g6R/R/elements.R |only g6R-0.5.0/g6R/R/g6.R | 58 +- g6R-0.5.0/g6R/R/igraph.R | 26 - g6R-0.5.0/g6R/R/options.R | 14 g6R-0.5.0/g6R/R/plugins.R | 63 ++ g6R-0.5.0/g6R/R/proxy.R | 597 +++++++++++++++++++++-- g6R-0.5.0/g6R/R/utils.R | 19 g6R-0.5.0/g6R/R/zzz.R |only g6R-0.5.0/g6R/README.md | 7 g6R-0.5.0/g6R/data/lesmis.rda |binary g6R-0.5.0/g6R/data/tree.rda |binary g6R-0.5.0/g6R/inst/doc/g6R.R | 32 + g6R-0.5.0/g6R/inst/doc/g6R.html | 375 ++++++++++---- g6R-0.5.0/g6R/inst/doc/g6R.qmd | 45 + g6R-0.5.0/g6R/inst/examples/dataframe/app.R | 20 g6R-0.5.0/g6R/inst/examples/demo/app.R | 8 g6R-0.5.0/g6R/inst/examples/html/app.R | 1 g6R-0.5.0/g6R/inst/examples/list/app.R | 41 + g6R-0.5.0/g6R/inst/examples/update-plugin/app.R | 9 g6R-0.5.0/g6R/inst/htmlwidgets/g6.js | 2 g6R-0.5.0/g6R/man/as_g6_element.Rd |only g6R-0.5.0/g6R/man/as_g6_elements.Rd |only g6R-0.5.0/g6R/man/brush_select.Rd | 9 g6R-0.5.0/g6R/man/bubble_sets.Rd | 4 g6R-0.5.0/g6R/man/click_select.Rd | 44 + g6R-0.5.0/g6R/man/context_menu.Rd | 32 + g6R-0.5.0/g6R/man/create_edge.Rd | 89 +++ g6R-0.5.0/g6R/man/figures/g6-layers.png |binary g6R-0.5.0/g6R/man/g6-add.Rd | 48 + g6R-0.5.0/g6R/man/g6-element-toggle.Rd | 18 g6R-0.5.0/g6R/man/g6-focus.Rd |only g6R-0.5.0/g6R/man/g6-get.Rd | 2 g6R-0.5.0/g6R/man/g6-remove.Rd | 38 + g6R-0.5.0/g6R/man/g6-set.Rd | 80 +++ g6R-0.5.0/g6R/man/g6-update.Rd | 47 + g6R-0.5.0/g6R/man/g6_data.Rd |only g6R-0.5.0/g6R/man/g6_element.Rd |only g6R-0.5.0/g6R/man/g6_elements.Rd |only g6R-0.5.0/g6R/man/g6_options.Rd | 3 g6R-0.5.0/g6R/man/g6_set_theme.Rd | 152 +++++ g6R-0.5.0/g6R/man/g6_update_behavior.Rd | 37 + g6R-0.5.0/g6R/man/g6_update_layout.Rd |only g6R-0.5.0/g6R/man/g6_update_plugin.Rd | 57 ++ g6R-0.5.0/g6R/man/hull.Rd | 2 g6R-0.5.0/g6R/man/is_g6_data.Rd |only g6R-0.5.0/g6R/man/is_g6_element.Rd |only g6R-0.5.0/g6R/man/is_g6_elements.Rd |only g6R-0.5.0/g6R/man/lasso_select.Rd | 7 g6R-0.5.0/g6R/tests/testthat/_snaps/behaviors.md | 197 ++++--- g6R-0.5.0/g6R/tests/testthat/_snaps/elements.md |only g6R-0.5.0/g6R/tests/testthat/_snaps/layouts.md | 130 +++-- g6R-0.5.0/g6R/tests/testthat/_snaps/plugins.md | 184 ++++--- g6R-0.5.0/g6R/tests/testthat/_snaps/proxy.md | 6 g6R-0.5.0/g6R/tests/testthat/test-elements.R |only g6R-0.5.0/g6R/tests/testthat/test-g6.R | 7 g6R-0.5.0/g6R/tests/testthat/test-igraph.R | 10 g6R-0.5.0/g6R/tests/testthat/test-layouts.R | 347 +++++++++++++ g6R-0.5.0/g6R/tests/testthat/test-plugins.R | 3 g6R-0.5.0/g6R/tests/testthat/test-proxy.R | 157 ++---- g6R-0.5.0/g6R/tests/testthat/test-zzz.R |only g6R-0.5.0/g6R/vignettes/g6R.qmd | 45 + 67 files changed, 2925 insertions(+), 597 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 1.0.4 dated 2025-07-22 and 1.0.5 dated 2025-12-09
DESCRIPTION | 8 +++---- MD5 | 34 ++++++++++++++--------------- NEWS.md | 7 ++++++ R/dittoColors.R | 2 - R/scatterPlot.R | 16 +++++++------- R/utils.R | 16 ++++++++++++++ R/utils_data_gather.R | 4 +-- R/utils_plot_mods.R | 4 +-- R/yPlot.R | 4 +-- man/barPlot.Rd | 4 +-- man/dittoColors.Rd | 2 - man/freqPlot.Rd | 4 +-- man/scatterHex.Rd | 15 ++++++------- man/scatterPlot.Rd | 15 ++++++------- man/yPlot.Rd | 4 +-- tests/testthat/test-hover.R | 11 +++++++++ tests/testthat/test-scatter.R | 16 ++++++++++++++ tests/testthat/test-utils.R | 48 ++++++++++++++++++++++++++++++++++++++++++ 18 files changed, 155 insertions(+), 59 deletions(-)
Title: Calibration Performance
Description: Plots calibration curves and computes statistics for assessing calibration performance. See Lasai et al. (2025) <doi:10.48550/arXiv.2503.08389>, De Cock Campo (2023) <doi:10.48550/arXiv.2309.08559> and Van Calster et al. (2016) <doi:10.1016/j.jclinepi.2015.12.005>.
Author: De Cock Bavo [aut, cre],
Barrenada Lasai [aut],
Nieboer Daan [aut],
Van Calster Ben [aut],
Steyerberg Ewout [aut],
Vergouwe Yvonne [aut]
Maintainer: De Cock Bavo <bavo.decock@kuleuven.be>
Diff between CalibrationCurves versions 2.0.7 dated 2025-07-07 and 3.0.0 dated 2025-12-09
DESCRIPTION | 17 MD5 | 53 +- NAMESPACE | 17 R/CGC.R |only R/MAC2.R |only R/MIXC.R |only R/globals.R |only R/helperFunctions.R | 85 ++++ R/printFunction.R | 30 + R/rcspline.plot.noprint.R | 2 R/val.prob.ci.2.R | 33 + R/valProbCluster.R |only R/valProbSurvival.R | 3 R/valProbggplot.R | 23 - README.md | 12 build/vignette.rds |binary data/clustertestdata.rda |only data/clustertraindata.rda |only inst/CITATION | 17 inst/doc/CalibrationCurves.R | 51 ++ inst/doc/CalibrationCurves.Rmd | 333 +++++++++++++++++ inst/doc/CalibrationCurves.html | 409 ++++++++++++++++++-- man/CGC.Rd |only man/CalibrationCurves.Rd | 5 man/MAC2.Rd |only man/MIXC.Rd |only man/clustertraindata.Rd |only man/print.ClusteredCalibrationCurve.Rd |only man/val.prob.ci.2.Rd | 2 man/valProbCluster.Rd |only man/valProbSurvival.Rd | 3 man/valProbggplot.Rd | 646 ++++++++++++++++----------------- vignettes/CalibrationCurves.Rmd | 333 +++++++++++++++++ vignettes/references.bib | 8 34 files changed, 1665 insertions(+), 417 deletions(-)
More information about CalibrationCurves at CRAN
Permanent link
Title: 'SciViews::R' - Standard Dialog Boxes for Windows, MacOS and
Linuxes
Description: Quickly construct standard dialog boxes for your GUI, including
message boxes, input boxes, list, file or directory selection, ... In case R
cannot display GUI dialog boxes, a simpler command line version of these
interactive elements is also provided as fallback solution.
Author: Philippe Grosjean [aut, cre] ,
Paul Hibbins [ctb]
Maintainer: Philippe Grosjean <phgrosjean@sciviews.org>
Diff between svDialogs versions 1.1.1 dated 2025-08-26 and 1.1.2 dated 2025-12-09
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- NEWS.md | 4 ++++ R/dlg_dir.R | 13 ++++++++++--- R/dlg_input.R | 10 ++++++++-- R/dlg_open.R | 13 ++++++++++--- R/dlg_save.R | 12 ++++++++++-- R/svDialogs-internal.R | 6 ++++++ inst/CITATION | 4 ++-- inst/doc/svDialogs.html | 4 ++-- 10 files changed, 64 insertions(+), 26 deletions(-)
Title: Easily Downloads a Gene Expression Dataset from a GEO Code and
Retrieves the Gene Symbols of Its Probesets
Description: A function that reads in the GEO code of a gene expression dataset, retrieves its data from GEO, (optionally) retrieves the gene symbols of the dataset, and returns a simple dataframe table containing all the data. Platforms available: GPL11532, GPL23126, GPL6244, GPL8300, GPL80, GPL96, GPL570, GPL571, GPL20115, GPL1293, GPL6102, GPL6104, GPL6883, GPL6884, GPL13497, GPL14550, GPL17077, GPL6480. GEO: Gene Expression Omnibus. ID: identifier code. The GEO datasets are downloaded from the URL <https://ftp.ncbi.nlm.nih.gov/geo/series/>. More information can be found in the following manuscript: Davide Chicco, "geneExpressionFromGEO: an R package to facilitate data reading from Gene Expression Omnibus (GEO)". Microarray Data Analysis, Methods in Molecular Biology, volume 2401, chapter 12, pages 187-194, Springer Protocols, 2021, <doi:10.1007/978-1-0716-1839-4_12>.
Author: Davide Chicco [aut, cre]
Maintainer: Davide Chicco <davidechicco@davidechicco.it>
Diff between geneExpressionFromGEO versions 1.2 dated 2025-04-11 and 1.3 dated 2025-12-09
DESCRIPTION | 11 ++--- MD5 | 9 ++-- NAMESPACE | 2 R/geneExpressionFromGEO.r | 77 ++++++++++++++++++++++++++++++++--- man/getDatasetFeaturesFromGEOcode.Rd |only man/getGeneExpressionFromGEO.Rd | 3 - 6 files changed, 86 insertions(+), 16 deletions(-)
More information about geneExpressionFromGEO at CRAN
Permanent link
Title: High Dimensional Categorical Data Visualization
Description: Easy visualization for datasets with more than two categorical variables and additional continuous variables. The package is particularly useful for exploring complex categorical data in the context of pathway analysis across multiple conditions. This package is now in maintenance-only mode and kept for legacy compatibility; for new projects and active development, please use the successor package 'ggdiceplot' (see <https://github.com/maflot/ggdiceplot> and <https://dice-and-domino-plot.readthedocs.io/en/latest/>).
Author: Matthias Flotho [aut, cre]
Maintainer: Matthias Flotho <matthias.flotho@ccb.uni-saarland.de>
Diff between diceplot versions 0.2.1 dated 2025-08-18 and 0.2.2 dated 2025-12-09
DESCRIPTION | 10 +++++----- MD5 | 3 ++- R/zzz.R |only 3 files changed, 7 insertions(+), 6 deletions(-)
Title: Linters for 'box' Modules
Description: Static code analysis of 'box' modules.
The package enhances code quality by providing linters that check for common issues,
enforce best practices, and ensure consistent coding standards.
Author: Ricardo Rodrigo Basa [aut, cre],
Jakub Nowicki [aut],
Mateusz Kolomanski [ctb],
Guilherme Vituri [ctb],
Appsilon Sp. z o.o. [cph]
Maintainer: Ricardo Rodrigo Basa <opensource+rodrigo@appsilon.com>
Diff between box.linters versions 0.10.6 dated 2025-06-26 and 0.10.7 dated 2025-12-09
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS.md | 6 ++++++ R/box_func_import_count_linter.R | 2 +- R/get_box_module_exports.R | 6 +++++- R/zzz.R | 6 ++++-- inst/WORDLIST | 2 +- man/box_default_linters.Rd | 2 +- man/rhino_default_linters.Rd | 2 +- 9 files changed, 30 insertions(+), 18 deletions(-)
Title: Word and Document Vector Models
Description: Create dense vector representation of words and documents using 'quanteda'. Currently implements Word2vec (Mikolov et al., 2013) <doi:10.48550/arXiv.1310.4546> and Latent Semantic Analysis (Deerwester et al., 1990) <doi:10.1002/(SICI)1097-4571(199009)41:6%3C391::AID-ASI1%3E3.0.CO;2-9>.
Author: Kohei Watanabe [aut, cre, cph] ,
Jan Wijffels [aut] ,
BNOSAC [cph] ,
Max Fomichev [ctb, cph]
Maintainer: Kohei Watanabe <watanabe.kohei@gmail.com>
Diff between wordvector versions 0.5.1 dated 2025-06-20 and 0.6.0 dated 2025-12-09
wordvector-0.5.1/wordvector/man/as.matrix.textmodel_wordvector.Rd |only wordvector-0.5.1/wordvector/man/print.textmodel_docvector.Rd |only wordvector-0.5.1/wordvector/man/print.textmodel_wordvector.Rd |only wordvector-0.6.0/wordvector/DESCRIPTION | 8 wordvector-0.6.0/wordvector/MD5 | 69 +- wordvector-0.6.0/wordvector/NAMESPACE | 8 wordvector-0.6.0/wordvector/NEWS.md | 7 wordvector-0.6.0/wordvector/R/RcppExports.R | 4 wordvector-0.6.0/wordvector/R/as.doc2vec.R |only wordvector-0.6.0/wordvector/R/doc2vec.R | 128 +--- wordvector-0.6.0/wordvector/R/lsa.R | 21 wordvector-0.6.0/wordvector/R/utils.R | 189 ++++-- wordvector-0.6.0/wordvector/R/word2vec.R | 169 +++-- wordvector-0.6.0/wordvector/inst/WORDLIST | 4 wordvector-0.6.0/wordvector/man/as.matrix.Rd |only wordvector-0.6.0/wordvector/man/as.textmodel_doc2vec.Rd |only wordvector-0.6.0/wordvector/man/perplexity.Rd |only wordvector-0.6.0/wordvector/man/print.textmodel_doc2vec.Rd |only wordvector-0.6.0/wordvector/man/print.textmodel_word2vec.Rd |only wordvector-0.6.0/wordvector/man/probability.Rd | 19 wordvector-0.6.0/wordvector/man/similarity.Rd | 20 wordvector-0.6.0/wordvector/man/textmodel_doc2vec.Rd | 72 +- wordvector-0.6.0/wordvector/man/textmodel_word2vec.Rd | 27 wordvector-0.6.0/wordvector/src/RcppExports.cpp | 13 wordvector-0.6.0/wordvector/src/dev.h |only wordvector-0.6.0/wordvector/src/word2vec/trainThread.cpp | 155 ++++- wordvector-0.6.0/wordvector/src/word2vec/trainThread.hpp | 31 - wordvector-0.6.0/wordvector/src/word2vec/word2vec.cpp | 19 wordvector-0.6.0/wordvector/src/word2vec/word2vec.hpp | 41 - wordvector-0.6.0/wordvector/src/wordvector.cpp | 157 +++-- wordvector-0.6.0/wordvector/tests/data |only wordvector-0.6.0/wordvector/tests/misc/compare_doc2vec.R |only wordvector-0.6.0/wordvector/tests/misc/probability.R |only wordvector-0.6.0/wordvector/tests/misc/test_large.R | 30 wordvector-0.6.0/wordvector/tests/misc/test_small.R | 80 ++ wordvector-0.6.0/wordvector/tests/testthat/test-as.doc2vec.R |only wordvector-0.6.0/wordvector/tests/testthat/test-doc2vec.R | 197 ++++-- wordvector-0.6.0/wordvector/tests/testthat/test-lsa.R | 46 - wordvector-0.6.0/wordvector/tests/testthat/test-model.R | 96 ++- wordvector-0.6.0/wordvector/tests/testthat/test-pre06.R |only wordvector-0.6.0/wordvector/tests/testthat/test-utils.R | 302 ++++++++-- wordvector-0.6.0/wordvector/tests/testthat/test-word2vec.R | 268 +++++++- 42 files changed, 1610 insertions(+), 570 deletions(-)
Title: Variable Length Markov Chains ('VLMC') Models
Description: Functions, Classes & Methods for estimation, prediction, and
simulation (bootstrap) of Variable Length Markov Chain ('VLMC') Models.
Author: Martin Maechler [aut, cre]
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between VLMC versions 1.4-4 dated 2024-08-19 and 1.4-5 dated 2025-12-09
ChangeLog | 10 ++++++++++ DESCRIPTION | 13 +++++++------ MD5 | 10 +++++----- man/predict.vlmc.Rd | 6 +++--- man/residuals.vlmc.Rd | 4 ++-- src/vlmc.h | 4 ++-- 6 files changed, 29 insertions(+), 18 deletions(-)
Title: Web Application Framework for R
Description: Makes it incredibly easy to build interactive web
applications with R. Automatic "reactive" binding between inputs and
outputs and extensive prebuilt widgets make it possible to build
beautiful, responsive, and powerful applications with minimal effort.
Author: Winston Chang [aut] ,
Joe Cheng [aut],
JJ Allaire [aut],
Carson Sievert [aut, cre] ,
Barret Schloerke [aut] ,
Garrick Aden-Buie [aut] ,
Yihui Xie [aut],
Jeff Allen [aut],
Jonathan McPherson [aut],
Alan Dipert [aut],
Barbara Borges [aut],
Posit Softwa [...truncated...]
Maintainer: Carson Sievert <carson@posit.co>
Diff between shiny versions 1.12.0 dated 2025-12-03 and 1.12.1 dated 2025-12-09
DESCRIPTION | 12 MD5 | 55 +-- NAMESPACE | 2 NEWS.md | 24 + R/bind-cache.R | 2 R/bind-event.R | 4 R/extended-task.R | 31 +- R/otel-attr-srcref.R | 16 - R/otel-collect.R | 7 R/otel-with.R |only R/reactives.R | 18 - R/shiny-options.R | 22 + R/shinywrappers.R | 4 inst/www/shared/busy-indicators/busy-indicators.css | 2 inst/www/shared/shiny-autoreload.js | 2 inst/www/shared/shiny-showcase.css | 2 inst/www/shared/shiny-showcase.js | 2 inst/www/shared/shiny-testmode.js | 2 inst/www/shared/shiny.js | 4 inst/www/shared/shiny.min.js | 4 man/ExtendedTask.Rd | 23 + man/shinyOptions.Rd | 21 - man/withOtelCollect.Rd |only tests/testthat/helper-otel.R |only tests/testthat/test-otel-attr-srcref.R | 306 +++++++++++++------- tests/testthat/test-otel-extended-task.R |only tests/testthat/test-otel-label.R | 21 - tests/testthat/test-otel-mock.R | 95 ++++-- tests/testthat/test-otel-shiny.R | 32 -- tests/testthat/test-otel-with.R |only tests/testthat/test-timer.R | 14 31 files changed, 480 insertions(+), 247 deletions(-)
Title: Reliability Growth Analysis
Description: Modeling and plotting functions for Reliability Growth Analysis (RGA). Models include the Duane (1962) <doi:10.1109/TA.1964.4319640>, Non-Homogeneous Poisson Process (NHPP) by Crow (1975) (No. AMSAATR138), Piecewise Weibull NHPP by Guo et al. (2010) <doi:10.1109/RAMS.2010.5448029>, and Piecewise Weibull NHPP with Change Point Detection based on the 'segmented' package by Muggeo (2024) <https://cran.r-project.org/package=segmented>.
Author: Paul Govan [aut, cre, cph]
Maintainer: Paul Govan <paul.govan2@gmail.com>
This is a re-admission after prior archival of version 0.3.1 dated 2025-11-21
Diff between ReliaGrowR versions 0.3.1 dated 2025-11-21 and 0.3.2 dated 2025-12-09
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ R/duane.R | 6 +++--- R/rga.R | 8 ++++---- inst/doc/RGA.Rmd | 8 ++++---- inst/doc/RGA.html | 8 ++++---- man/ReliaGrowR-package.Rd | 2 +- man/duane.Rd | 6 +++--- man/rga.Rd | 8 ++++---- tests/testthat/Rplots.pdf |binary tests/testthat/test-srr-duane.R | 9 +++++++++ tests/testthat/test-srr-rga.R | 24 +++++++++++++++++++++--- vignettes/RGA.Rmd | 8 ++++---- 13 files changed, 73 insertions(+), 46 deletions(-)
Title: Interface to 'REDCap'
Description: Access data stored in 'REDCap' databases using the Application
Programming Interface (API). 'REDCap' (Research Electronic Data CAPture;
<https://projectredcap.org>, Harris, et al. (2009) <doi:10.1016/j.jbi.2008.08.010>,
Harris, et al. (2019) <doi:10.1016/j.jbi.2019.103208>) is
a web application for building and managing online surveys and databases
developed at Vanderbilt University. The API allows users to access data
and project meta data (such as the data dictionary) from the web
programmatically. The 'redcapAPI' package facilitates the process of
accessing data with options to prepare an analysis-ready data set
consistent with the definitions in a database's data dictionary.
Author: Benjamin Nutter [ctb, aut],
Shawn Garbett [cre, ctb] ,
Savannah Obregon [ctb],
Thomas Obadia [ctb],
Marcus Lehr [ctb],
Brian High [ctb],
Stephen Lane [ctb],
Will Beasley [ctb],
Will Gray [ctb],
Nick Kennedy [ctb],
Tan Hsi-Nien [ctb],
Jeffrey Horner [ [...truncated...]
Maintainer: Shawn Garbett <shawn.garbett@vumc.org>
Diff between redcapAPI versions 2.11.4 dated 2025-10-29 and 2.11.5 dated 2025-12-09
DESCRIPTION | 6 MD5 | 52 - NEWS.md | 10 R/docsUserMethods.R | 6 R/exportRecordsTyped.R | 22 R/exportUsers.R | 167 ++--- R/importUsers.R | 66 +- R/makeApiCall.R | 42 - R/prepUserImportData.R | 310 ++++------ R/redcapDataStructure.R | 3 R/unlockREDCap.R | 1 build/vignette.rds |binary inst/doc/redcapAPI-best-practices.pdf |binary inst/doc/redcapAPI-casting-data.pdf |binary inst/doc/redcapAPI-data-validation.pdf |binary inst/doc/redcapAPI-faq.pdf |binary inst/doc/redcapAPI-getting-started-connecting.pdf |binary inst/doc/redcapAPI-missing-data-detection.pdf |binary inst/doc/redcapAPI-offline-connection.pdf |binary man/makeApiCall.Rd | 5 man/prepUserImportData.Rd | 28 man/recordsTypedMethods.Rd | 2 man/userMethods.Rd | 6 tests/testthat/test-020-redcapConnection-ArgumentValidation.R | 8 tests/testthat/test-101-userMethods-Functionality.R | 21 tests/testthat/test-103-userRoleAssignmentMethods-Functionality.R | 7 tests/testthat/test-361-userStructureVersion.R | 54 + 27 files changed, 458 insertions(+), 358 deletions(-)
Title: Analysis of Diffusion and Contagion Processes on Networks
Description: Empirical statistical analysis, visualization and simulation of
diffusion and contagion processes on networks. The package implements algorithms
for calculating network diffusion statistics such as transmission rate, hazard
rates, exposure models, network threshold levels, infectiousness (contagion),
and susceptibility. The package is inspired by work published in Valente,
et al., (2015) <DOI:10.1016/j.socscimed.2015.10.001>; Valente (1995) <ISBN:
9781881303213>, Myers (2000) <DOI:10.1086/303110>, Iyengar and others (2011)
<DOI:10.1287/mksc.1100.0566>, Burt (1987) <DOI:10.1086/228667>; among others.
Author: George Vega Yon [aut, cre] ,
Thomas Valente [aut, cph] ,
Anibal Olivera Morales [aut, ctb] ,
Stephanie Dyal [ctb] ,
Timothy Hayes [ctb]
Maintainer: George Vega Yon <g.vegayon@gmail.com>
This is a re-admission after prior archival of version 1.23.0 dated 2025-06-12
Diff between netdiffuseR versions 1.23.0 dated 2025-06-12 and 1.24.0 dated 2025-12-09
DESCRIPTION | 25 - MD5 | 55 ++- NAMESPACE | 2 NEWS.md | 8 R/degree_adoption_diagnostic.R |only README.md | 346 ++++++++++------------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/analyzing-medical-innovation-data.html | 20 - inst/doc/introduction-to-netdiffuser.html | 4 man/bass.Rd | 1 man/classify_adopters.Rd | 1 man/cumulative_adopt_count.Rd | 1 man/degree_adoption_diagnostic.Rd |only man/dgr.Rd | 1 man/ego_variance.Rd | 1 man/exposure.Rd | 1 man/figures/README-Adopters-1.png |only man/figures/README-BoringThreshold-1.png |only man/figures/README-Hazard-1.png |only man/figures/README-NiceThreshold-1.png |only man/figures/README-mosaic-1.png |only man/figures/README-plot_diffnet-1.png |only man/figures/README-plot_diffnet2-1.png |only man/figures/README-plot_diffnet2-withmap-1.png |only man/figures/README-plot_infectsuscept-1.png |only man/figures/README-plot_infectsuscept-2.png |only man/hazard_rate.Rd | 1 man/infection.Rd | 1 man/moran.Rd | 1 man/struct_equiv.Rd | 1 man/threshold.Rd | 1 man/vertex_covariate_dist.Rd | 1 src/infection.cpp | 5 tests/testthat/test-degree-adoption-diagnostic.R |only 35 files changed, 241 insertions(+), 236 deletions(-)
Title: Use Foreach to Parallelize via the Future Framework
Description: The 'future' package provides a unifying parallelization framework for R that supports many parallel and distributed backends <doi:10.32614/RJ-2021-048>. The 'foreach' package provides a powerful API for iterating over an R expression in parallel. The 'doFuture' package brings the best of the two together. There are two alternative ways to use this package. The recommended approach is to use 'y <- foreach(...) %dofuture% { ... }', which does not require using 'registerDoFuture()' and has many advantages over '%dopar%'. The alternative is the traditional 'foreach' approach by registering the 'foreach' adapter 'registerDoFuture()' and so that 'y <- foreach(...) %dopar% { ... }' runs in parallelizes with the 'future' framework.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between doFuture versions 1.1.2 dated 2025-07-14 and 1.1.3 dated 2025-12-09
DESCRIPTION | 8 +-- MD5 | 66 +++++++++++++------------- NEWS.md | 8 +++ R/doFuture2.R | 7 -- R/options.R | 26 +++++----- build/vignette.rds |binary inst/doc/doFuture-1-overview.html | 4 - inst/doc/doFuture-2-dopar.html | 4 - inst/doc/doFuture-3-dofuture.html | 4 - inst/testme/deploy.R | 2 inst/testme/test-foreach_dofuture,globals.R | 50 ++++++++++++++++++- man/doFuture.options.Rd | 16 +++--- tests/test-foreach_dofuture,errors.R | 1 tests/test-foreach_dofuture,globals.R | 1 tests/test-foreach_dofuture,nested_colon.R | 1 tests/test-foreach_dofuture,nested_dofuture.R | 1 tests/test-foreach_dofuture,rng.R | 1 tests/test-foreach_dofuture.R | 1 tests/test-foreach_dopar,doRNG,dopar.R | 1 tests/test-foreach_dopar,doRNG,dorng.R | 1 tests/test-foreach_dopar,errors.R | 1 tests/test-foreach_dopar,flavor_dofuture.R | 1 tests/test-foreach_dopar,globals.R | 1 tests/test-foreach_dopar,nested_colon.R | 1 tests/test-foreach_dopar,nested_dopar.R | 1 tests/test-foreach_dopar,options-for-export.R | 1 tests/test-foreach_dopar.R | 1 tests/test-makeChunks.R | 1 tests/test-options,nested.R | 1 tests/test-registerDoFuture.R | 1 tests/test-times.R | 1 tests/test-utils.R | 1 tests/test-with.DoPar.R | 1 tests/test-withDoRNG.R | 1 34 files changed, 144 insertions(+), 73 deletions(-)
Title: Estimate Graph Dimension using Cross-Validated Eigenvalues
Description: Cross-validated eigenvalues are estimated by
splitting a graph into two parts, the training and the test graph.
The training graph is used to estimate eigenvectors, and
the test graph is used to evaluate the correlation between the training
eigenvectors and the eigenvectors of the test graph.
The correlations follow a simple central limit theorem that can
be used to estimate graph dimension via hypothesis testing, see
Chen et al. (2021) <doi:10.48550/arXiv.2108.03336> for details.
Author: Fan Chen [aut] ,
Alex Hayes [cre, aut, cph] ,
Karl Rohe [aut]
Maintainer: Alex Hayes <alexpghayes@gmail.com>
Diff between gdim versions 0.1.0 dated 2023-09-05 and 0.1.1 dated 2025-12-09
gdim-0.1.0/gdim/man/pipe.Rd |only gdim-0.1.1/gdim/DESCRIPTION | 20 +-- gdim-0.1.1/gdim/MD5 | 28 ++-- gdim-0.1.1/gdim/NAMESPACE | 2 gdim-0.1.1/gdim/NEWS.md | 4 gdim-0.1.1/gdim/R/eigcv.R | 89 +++++++++------ gdim-0.1.1/gdim/R/utils.R | 15 -- gdim-0.1.1/gdim/README.md | 21 +-- gdim-0.1.1/gdim/build |only gdim-0.1.1/gdim/man/eigcv.Rd | 7 - gdim-0.1.1/gdim/man/figures/README-unnamed-chunk-3-1.png |binary gdim-0.1.1/gdim/man/gdim-package.Rd | 2 gdim-0.1.1/gdim/man/plot.eigcv.Rd | 7 - gdim-0.1.1/gdim/man/print.eigcv.Rd | 7 - gdim-0.1.1/gdim/tests/testthat/test-eigcv.R | 11 - gdim-0.1.1/gdim/tests/testthat/test-split_graph.R | 1 16 files changed, 107 insertions(+), 107 deletions(-)
Title: Location and Visualization of Clustered Somatic Mutations
Description: Identification and visualization of groups of closely spaced mutations in the DNA sequence of cancer genome. The extremely mutated zones are searched in the symmetric dissimilarity matrix using the anti-Robinson matrix properties. Different data sets are obtained to describe and plot the clustered mutations information.
Author: David Lora [aut, cre]
Maintainer: David Lora <dalora@ucm.es>
This is a re-admission after prior archival of version 1.0.1 dated 2016-04-29
Diff between ClusteredMutations versions 1.0.1 dated 2016-04-29 and 1.0.2 dated 2025-12-09
DESCRIPTION | 21 +- MD5 | 23 +- NAMESPACE | 3 build/partial.rdb |only build/vignette.rds |binary inst/doc/vignetteClustered.R | 218 ++++++++++++------------- inst/doc/vignetteClustered.Rnw | 345 ++++++++++++++++++++-------------------- inst/doc/vignetteClustered.pdf |binary man/PD4107a.Rd | 24 +- man/dissmutmatrix.Rd | 160 +++++++++--------- man/imd.Rd | 161 +++++++++--------- man/showers.Rd | 12 - vignettes/vignetteClustered.Rnw | 345 ++++++++++++++++++++-------------------- 13 files changed, 664 insertions(+), 648 deletions(-)
More information about ClusteredMutations at CRAN
Permanent link
Title: Broadly Useful Convenient and Efficient R Functions
Description: Broadly useful convenient and efficient R functions
that bring users concise and elegant R data analyses.
This package includes easy-to-use functions for
(1) basic R programming
(e.g., set working directory to the path of currently opened file;
import/export data from/to files in any format;
print tables to Microsoft Word);
(2) multivariate computation
(e.g., compute scale sums/means/... with reverse scoring);
(3) reliability analyses and factor analyses;
(4) descriptive statistics and correlation analyses;
(5) t-test, multi-factor analysis of variance (ANOVA),
simple-effect analysis, and post-hoc multiple comparison;
(6) tidy report of statistical models
(to R Console and Microsoft Word);
(7) mediation and moderation analyses (PROCESS);
and (8) additional toolbox for statistics and graphics.
Author: Han Wu Shuang Bao [aut, cre]
Maintainer: Han Wu Shuang Bao <baohws@foxmail.com>
Diff between bruceR versions 2025.8 dated 2025-08-20 and 2025.11 dated 2025-12-09
DESCRIPTION | 10 ++--- MD5 | 30 +++++++-------- NEWS.md | 8 +++- R/bruceR-stats_1_basic.R | 14 +++---- R/bruceR-stats_5_advance.R | 4 +- R/bruceR-stats_6_plot.R | 84 ++++++++++++++++++++++---------------------- R/bruceR.R | 12 +++--- R/bruceR_utils.R | 24 ++++++------ man/PROCESS.Rd | 2 - man/bruceR-package.Rd | 12 +++--- man/grapes-allin-grapes.Rd | 6 +-- man/grapes-anyin-grapes.Rd | 6 +-- man/grapes-nonein-grapes.Rd | 6 +-- man/grapes-partin-grapes.Rd | 6 +-- man/med_summary.Rd | 2 - man/theme_bruce.Rd | 4 +- 16 files changed, 117 insertions(+), 113 deletions(-)
Title: Apply Function to Elements in Parallel using Futures
Description: Implementations of apply(), by(), eapply(), lapply(), Map(), .mapply(), mapply(), replicate(), sapply(), tapply(), and vapply() that can be resolved using any future-supported backend, e.g. parallel on the local machine or distributed on a compute cluster. These future_*apply() functions come with the same pros and cons as the corresponding base-R *apply() functions but with the additional feature of being able to be processed via the future framework <doi:10.32614/RJ-2021-048>.
Author: Henrik Bengtsson [aut, cre, cph] ,
R Core Team [cph, ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between future.apply versions 1.20.0 dated 2025-06-06 and 1.20.1 dated 2025-12-09
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS.md | 9 +++++++++ R/future_apply.R | 2 ++ R/future_lapply.R | 24 +++++++++++++++++++++++- R/future_xapply.R | 2 +- build/vignette.rds |binary inst/doc/future.apply-1-overview.html | 4 ++-- man/future_lapply.Rd | 27 +++++++++++++++++++++++++-- 9 files changed, 74 insertions(+), 18 deletions(-)
Title: Inline Asynchronous Generator Results into Documents
Description: Given a 'coro' asynchronous generator instance that produces text,
write that text into a document selection in 'RStudio' and 'Positron'. This
is particularly helpful for streaming large language model responses into
the user's editor.
Author: Simon Couch [aut, cre],
Posit Software, PBC [cph, fnd]
Maintainer: Simon Couch <simon.couch@posit.co>
Diff between streamy versions 0.2.0 dated 2025-05-21 and 0.2.1 dated 2025-12-09
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/stream.R | 2 +- R/utils.R | 4 ++++ tests/testthat/test-stream.R | 2 ++ 6 files changed, 19 insertions(+), 9 deletions(-)
Title: Sparse Vectors for Use in Data Frames
Description: Provides sparse vectors powered by ALTREP (Alternative
Representations for R Objects) that behave like regular vectors, and
can thus be used in data frames. Also provides tools to convert
between sparse matrices and data frames with sparse columns and
functions to interact with sparse vectors.
Author: Emil Hvitfeldt [aut, cre] ,
Davis Vaughan [ctb],
Posit Software, PBC [cph, fnd]
Maintainer: Emil Hvitfeldt <emil.hvitfeldt@posit.co>
Diff between sparsevctrs versions 0.3.4 dated 2025-05-25 and 0.3.5 dated 2025-12-09
DESCRIPTION | 8 ++-- MD5 | 52 +++++++++++++++--------------- NEWS.md | 4 ++ R/sparse_character.R | 4 ++ R/sparse_double.R | 4 ++ R/sparse_integer.R | 4 ++ R/sparse_logical.R | 4 ++ build/vignette.rds |binary man/coerce_to_sparse_data_frame.Rd | 2 - man/coerce_to_sparse_matrix.Rd | 2 - man/coerce_to_sparse_tibble.Rd | 2 - man/has_sparse_elements.Rd | 2 - man/sparsevctrs-package.Rd | 2 - src/altrep-sparse-double.c | 14 ++++++-- src/altrep-sparse-integer.c | 14 ++++++-- src/altrep-sparse-logical.c | 14 ++++++-- src/altrep-sparse-string.c | 17 ++++++++- src/init.c | 16 +++++++++ src/sparse-utils.h | 6 ++- tests/testthat/_snaps/sparse_character.md | 14 ++++---- tests/testthat/_snaps/sparse_double.md | 14 ++++---- tests/testthat/_snaps/sparse_integer.md | 14 ++++---- tests/testthat/_snaps/sparse_logical.md | 14 ++++---- tests/testthat/test-sparse_character.R | 10 ++--- tests/testthat/test-sparse_double.R | 10 ++--- tests/testthat/test-sparse_integer.R | 10 ++--- tests/testthat/test-sparse_logical.R | 10 ++--- 27 files changed, 174 insertions(+), 93 deletions(-)
Title: (Robust) Mediation Analysis
Description: Perform mediation analysis via the fast-and-robust bootstrap test ROBMED (Alfons, Ates & Groenen, 2022a; <doi:10.1177/1094428121999096>), as well as various other methods. Details on the implementation and code examples can be found in Alfons, Ates, and Groenen (2022b) <doi:10.18637/jss.v103.i13>. Further discussion on robust mediation analysis can be found in Alfons & Schley (2025) <doi:10.1002/wics.70051>.
Author: Andreas Alfons [aut, cre] ,
Nufer Y. Ates [dtc]
Maintainer: Andreas Alfons <alfons@ese.eur.nl>
Diff between robmed versions 1.2.2 dated 2025-09-08 and 1.3.0 dated 2025-12-09
DESCRIPTION | 10 +-- MD5 | 48 +++++++-------- NEWS | 7 ++ R/BSG2014.R | 127 +++++++++++++++++++++++------------------- R/fit_mediation.R | 23 ++----- R/robmed-package.R | 6 - R/setup_weight_plot.R | 6 - R/summary.R | 24 ++----- R/test_mediation.R | 24 ++----- R/weight_plot.R | 6 - build/partial.rdb |binary data/BSG2014.RData |binary inst/CITATION | 9 +- inst/doc/robmed-intro.R | 18 ++--- inst/doc/robmed-intro.Rnw | 23 +++---- inst/doc/robmed-intro.pdf |binary man/BSG2014.Rd | 127 +++++++++++++++++++++++------------------- man/fit_mediation.Rd | 23 ++----- man/robmed-package.Rd | 6 - man/setup_weight_plot.Rd | 6 - man/summary.test_mediation.Rd | 24 ++----- man/test_mediation.Rd | 24 ++----- man/weight_plot.Rd | 6 - vignettes/robmed-intro.Rnw | 23 +++---- vignettes/robmed.bib | 4 - 25 files changed, 277 insertions(+), 297 deletions(-)
Title: Map Pages of Memory
Description: R interface to POSIX mmap and Window's MapViewOfFile.
Author: Jeffrey A. Ryan [aut, cre]
Maintainer: Jeffrey A. Ryan <jeff.a.ryan@gmail.com>
Diff between mmap versions 0.6-22 dated 2023-12-08 and 0.6-23 dated 2025-12-09
DESCRIPTION | 15 ++++++++++----- MD5 | 6 +++--- inst/doc/mmap.pdf |binary src/mmap.c | 10 ++-------- 4 files changed, 15 insertions(+), 16 deletions(-)
Title: A Modular, Integrated Approach to Maximum Entropy Distribution
Modeling
Description: Tools for training, selecting, and evaluating maximum entropy
(and standard logistic regression) distribution models. This package
provides tools for user-controlled transformation of explanatory variables,
selection of variables by nested model comparison, and flexible model
evaluation and projection. It follows principles based on the maximum-
likelihood interpretation of maximum entropy modeling, and uses infinitely-
weighted logistic regression for model fitting. The package is described in
Vollering et al. (2019; <doi:10.1002/ece3.5654>).
Author: Julien Vollering [aut, cre],
Sabrina Mazzoni [aut],
Rune Halvorsen [aut],
Steven Phillips [cph],
Michael Bedward [ctb]
Maintainer: Julien Vollering <julienvollering@gmail.com>
Diff between MIAmaxent versions 1.4.0 dated 2025-10-18 and 1.4.1 dated 2025-12-09
DESCRIPTION | 6 LICENSE | 2 MD5 | 148 - NAMESPACE | 32 NEWS.md | 168 - R/MIAmaxent-package.R | 96 - R/calculateRVA.R | 108 - R/chooseModel.R | 160 - R/compare.R | 176 - R/data.R | 146 - R/deriveVars.R | 300 +-- R/dvsfromev.R | 266 +- R/modelFromLambdas.R | 144 - R/parsdvs.R | 116 - R/parsevs.R | 360 +-- R/plotFOP.R | 328 +-- R/plotResp.R | 216 +- R/plotResp2.R | 162 - R/projectModel.R | 346 +-- R/readData.R | 310 +-- R/runIWLR.R | 162 - R/runLR.R | 68 R/selectDVforEV.R | 276 +- R/selectEV.R | 286 +-- R/splselect.R | 58 R/testAUC.R | 226 +- R/transfclosures.R | 218 +- R/utils.R | 590 +++--- README.md | 172 - build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 22 inst/doc/NCEAS.R | 108 - inst/doc/NCEAS.Rmd | 1168 ++++++------ inst/doc/NCEAS.html | 2 inst/doc/a-modeling-example.Rmd | 964 +++++----- inst/doc/a-modeling-example.html | 12 inst/extdata/EV_categorical/geoberg.asc | 414 ++-- inst/extdata/EV_categorical/geolmja1.asc | 414 ++-- inst/extdata/EV_categorical/lcucor1.asc | 414 ++-- inst/extdata/EV_categorical/lcutilt4.asc | 414 ++-- inst/extdata/EV_categorical/terslpps15.asc | 414 ++-- inst/extdata/EV_continuous/pca1.asc | 414 ++-- inst/extdata/EV_continuous/prbygall.asc | 414 ++-- inst/extdata/EV_continuous/prtilany.asc | 414 ++-- inst/extdata/EV_continuous/teraspif.asc | 414 ++-- inst/extdata/EV_continuous/terdem.asc | 414 ++-- inst/extdata/EV_continuous/terslpdg.asc | 414 ++-- inst/extdata/EV_continuous/tersolrade.asc | 414 ++-- inst/extdata/EV_continuous/tertpi09.asc | 414 ++-- inst/extdata/occurrence_PA.csv | 246 +- inst/extdata/occurrence_PO.csv | 2120 +++++++++++------------ inst/extdata/sommerfeltia/1.lambdas | 22 inst/extdata/sommerfeltia/EV_continuous/EV11.asc | 26 inst/extdata/sommerfeltia/EV_continuous/EV12.asc | 26 inst/extdata/sommerfeltia/EV_continuous/EV13.asc | 26 inst/extdata/sommerfeltia/EV_continuous/EV14.asc | 26 inst/extdata/sommerfeltia/Sp1.csv | 22 man/MIAmaxent-package.Rd | 2 man/chooseModel.Rd | 92 man/deriveVars.Rd | 252 +- man/modelFromLambdas.Rd | 68 man/plotFOP.Rd | 212 +- man/plotResp.Rd | 116 - man/projectModel.Rd | 212 +- man/readData.Rd | 222 +- man/selectDVforEV.Rd | 212 +- man/selectEV.Rd | 248 +- man/testAUC.Rd | 114 - man/toydata_dvs.Rd | 60 man/toydata_seldvs.Rd | 62 man/toydata_selevs.Rd | 64 man/toydata_sp1po.Rd | 58 vignettes/NCEAS.Rmd | 1168 ++++++------ vignettes/a-modeling-example.Rmd | 964 +++++----- 75 files changed, 9975 insertions(+), 9969 deletions(-)
Title: Tools for Easier Analysis of Meteorological Fields
Description: Many useful functions and extensions for dealing with
meteorological data in the tidy data framework. Extends 'ggplot2' for
better plotting of scalar and vector fields and provides commonly used
analysis methods in the atmospheric sciences.
Author: Elio Campitelli [cre, aut]
Maintainer: Elio Campitelli <eliocampitelli@gmail.com>
Diff between metR versions 0.18.2 dated 2025-09-05 and 0.18.3 dated 2025-12-09
DESCRIPTION | 8 - MD5 | 54 ++++---- NEWS.md | 6 R/ReadNetCDF.R | 9 - README.md | 4 build/partial.rdb |binary build/vignette.rds |binary inst/doc/Visualization-tools.html | 236 ++++++++++++++++---------------------- inst/doc/Working-with-data.html | 225 +++++++++++++++--------------------- man/MakeBreaks.Rd | 2 man/MaskLand.Rd | 2 man/ReadNetCDF.Rd | 2 man/Smooth2D.Rd | 2 man/discretised_scale.Rd | 17 +- man/geom_arrow.Rd | 8 - man/geom_contour2.Rd | 10 - man/geom_contour_fill.Rd | 10 - man/geom_contour_tanaka.Rd | 10 - man/geom_relief.Rd | 8 - man/geom_streamline.Rd | 8 - man/geom_text_contour.Rd | 19 +-- man/guide_colourstrip.Rd | 8 - man/label_scales.Rd | 10 - man/scale_divergent.Rd | 15 +- man/scale_longitude.Rd | 4 man/stat_na.Rd | 8 - man/stat_subset.Rd | 8 - tests/testthat/test-ReadNetCDF.R | 9 + 28 files changed, 345 insertions(+), 357 deletions(-)
Title: High-Throughput Toxicokinetics
Description: Pre-made models that can be rapidly tailored to various chemicals
and species using chemical-specific in vitro data and physiological
information. These tools allow incorporation of chemical
toxicokinetics ("TK") and in vitro-in vivo extrapolation ("IVIVE")
into bioinformatics, as described by Pearce et al. (2017)
(<doi:10.18637/jss.v079.i04>). Chemical-specific
in vitro data characterizing toxicokinetics have been obtained
from relatively high-throughput experiments. The
chemical-independent ("generic") physiologically-based ("PBTK") and empirical
(for example, one compartment) "TK" models included here can be
parameterized with in vitro data or in silico predictions which are
provided for thousands of chemicals, multiple exposure routes,
and various species. High throughput toxicokinetics ("HTTK") is the
combination of in vitro data and generic models. We establish the
expected accuracy of HTTK for chemicals without in vivo data
through statistical evaluation of HTTK predicti [...truncated...]
Author: John Wambaugh [aut, cre] ,
Sarah Davidson-Fritz [aut] ,
Robert Pearce [aut] ,
Caroline Ring [aut] ,
Greg Honda [aut] ,
Mark Sfeir [aut],
Matt Linakis [aut] ,
Dustin Kapraun [aut] ,
Kimberly Truong [aut] ,
Colin Thomson [aut] ,
Meredith Scherer [aut] [...truncated...]
Maintainer: John Wambaugh <wambaugh.research@gmail.com>
Diff between httk versions 2.7.3 dated 2025-09-12 and 2.7.4 dated 2025-12-09
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Title: Hierarchical Optimal Matching and Machine Learning Toolbox
Description: Various functions and algorithms are provided here for solving optimal matching
tasks in the context of preclinical cancer studies. Further, various helper and plotting
functions are provided for unsupervised and supervised machine learning as well as longitudinal
mixed-effects modeling of tumor growth response patterns.
Author: Teemu Daniel Laajala [aut, cre]
Maintainer: Teemu Daniel Laajala <teelaa@utu.fi>
Diff between hamlet versions 0.9.6 dated 2018-05-26 and 0.9.8 dated 2025-12-09
DESCRIPTION | 19 +++++++++++++------ MD5 | 32 ++++++++++++++++---------------- NEWS | 1 + R/matchtools.R | 18 +++++++++--------- R/memtools.R | 16 ++++++++-------- R/plottools.R | 26 ++++++++++++++++---------- build/vignette.rds |binary inst/doc/introduction.R | 2 +- inst/doc/introduction.Rnw | 2 +- inst/doc/introduction.pdf |binary man/hamlet-package.Rd | 10 ---------- man/hmap.Rd | 13 +++++++------ man/hmap.key.Rd | 5 ++++- man/match.ga.Rd | 16 ++++++++-------- man/mix.binary.Rd | 2 +- man/mixplot.Rd | 7 ++++--- vignettes/introduction.Rnw | 2 +- 17 files changed, 90 insertions(+), 81 deletions(-)
Title: Model Butcher
Description: Provides a set of S3 generics to axe components of fitted
model objects and help reduce the size of model objects saved to disk.
Author: Joyce Cahoon [aut] ,
Davis Vaughan [aut],
Max Kuhn [cre, aut] ,
Alex Hayes [aut],
Julia Silge [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Max Kuhn <max@posit.co>
Diff between butcher versions 0.3.6 dated 2025-08-18 and 0.4.0 dated 2025-12-09
DESCRIPTION | 41 ++--- MD5 | 240 +++++++++++++++++--------------- NAMESPACE | 16 ++ NEWS.md | 13 + R/axe-generics.R | 97 ++++++++++++- R/butcher-package.R | 13 + R/c5.R | 8 - R/docs.R | 26 +-- R/earth.R | 4 R/elnet.R | 5 R/flexsurvreg.R | 8 - R/function.R | 1 R/glmnet.R | 5 R/kknn.R | 4 R/ksvm.R | 5 R/lm.R | 5 R/locate.R | 18 -- R/mass.R | 14 + R/model_fit.R | 16 -- R/multnet.R | 4 R/new.R | 63 +++++--- R/nnet.R | 5 R/randomForest.R | 4 R/ranger.R | 4 R/recipe.R | 12 - R/rpart.R | 22 -- R/rsample-data.R |only R/rsample-indicators.R |only R/spark.R | 2 R/survreg.R | 4 R/survreg.penal.R | 4 R/tabnet_fit.R |only R/train.recipe.R | 8 - R/ui.R | 8 - R/utilities.R | 15 +- R/weigh.R | 28 +++ R/xgb.R | 51 ++++-- R/xrf.R | 4 README.md | 2 build/stage23.rdb |binary build/vignette.rds |binary inst/doc/available-axe-methods.R | 12 - inst/doc/available-axe-methods.Rmd | 12 - inst/doc/available-axe-methods.html | 46 ++++-- inst/doc/butcher.R | 8 - inst/doc/butcher.Rmd | 8 - inst/doc/butcher.html | 10 - inst/extdata |only man/axe-C5.0.Rd | 10 - man/axe-KMeansCluster.Rd | 2 man/axe-NaiveBayes.Rd | 2 man/axe-bart.Rd | 2 man/axe-coxph.Rd | 2 man/axe-earth.Rd | 6 man/axe-elnet.Rd | 6 man/axe-flexsurvreg.Rd | 8 - man/axe-function.Rd | 2 man/axe-gam.Rd | 2 man/axe-gausspr.Rd | 2 man/axe-glmnet.Rd | 6 man/axe-ipred.Rd | 2 man/axe-kknn.Rd | 6 man/axe-kproto.Rd | 2 man/axe-ksvm.Rd | 6 man/axe-lm.Rd | 6 man/axe-mass.Rd | 15 +- man/axe-mda.Rd | 2 man/axe-model_fit.Rd | 14 - man/axe-multnet.Rd | 6 man/axe-nnet.Rd | 6 man/axe-pls.Rd | 2 man/axe-randomForest.Rd | 6 man/axe-ranger.Rd | 6 man/axe-rda.Rd | 2 man/axe-recipe.Rd | 14 - man/axe-rpart.Rd | 22 -- man/axe-rsample-data.Rd |only man/axe-rsample-indicators.Rd |only man/axe-sclass.Rd | 2 man/axe-spark.Rd | 4 man/axe-survreg.Rd | 6 man/axe-survreg.penal.Rd | 6 man/axe-tabnet_fit.Rd |only man/axe-terms.Rd | 2 man/axe-train.Rd | 2 man/axe-train.recipe.Rd | 10 - man/axe-xgb.Booster.Rd | 33 ++-- man/axe-xrf.Rd | 2 man/butcher-package.Rd | 6 man/new_model_butcher.Rd | 11 + tests/testthat/_snaps/new.md |only tests/testthat/_snaps/rsample.md |only tests/testthat/helper-objects.R | 6 tests/testthat/test-bart.R | 18 +- tests/testthat/test-earth.R | 12 - tests/testthat/test-elnet.R | 7 tests/testthat/test-flexsurvreg.R | 29 ++- tests/testthat/test-gam.R | 6 tests/testthat/test-gausspr.R | 17 -- tests/testthat/test-glmnet.R | 4 tests/testthat/test-ipred.R | 100 ++++++++++--- tests/testthat/test-klaR.R | 8 - tests/testthat/test-kproto.R | 3 tests/testthat/test-ksvm.R | 8 - tests/testthat/test-lm.R | 9 - tests/testthat/test-mass.R | 40 ++++- tests/testthat/test-mda.R | 32 ++-- tests/testthat/test-mixOmics.R | 27 ++- tests/testthat/test-multnet.R | 17 +- tests/testthat/test-new.R |only tests/testthat/test-nnet.R | 6 tests/testthat/test-randomForest.R | 30 ++-- tests/testthat/test-ranger.R | 40 +++-- tests/testthat/test-recipe.R | 266 ++++++++++++++++++++---------------- tests/testthat/test-rpart.R | 19 +- tests/testthat/test-rsample.R |only tests/testthat/test-sclass.R | 5 tests/testthat/test-spark.R | 74 +++++----- tests/testthat/test-survreg.R | 15 +- tests/testthat/test-tabnet_fit.R |only tests/testthat/test-train.R | 48 +++--- tests/testthat/test-train.recipe.R | 24 ++- tests/testthat/test-ui.R | 13 - tests/testthat/test-xgb.R | 104 +++++++++----- tests/testthat/test-xrf.R | 41 ++++- vignettes/available-axe-methods.Rmd | 12 - vignettes/butcher.Rmd | 8 - 127 files changed, 1340 insertions(+), 834 deletions(-)
Title: Semi-Supervised Algorithm for Document Scaling
Description: A word embeddings-based semi-supervised model for document scaling Watanabe (2020) <doi:10.1080/19312458.2020.1832976>.
LSS allows users to analyze large and complex corpora on arbitrary dimensions with seed words exploiting efficiency of word embeddings (SVD, Glove).
It can generate word vectors on a users-provided corpus or incorporate a pre-trained word vectors.
Author: Kohei Watanabe [aut, cre, cph]
Maintainer: Kohei Watanabe <watanabe.kohei@gmail.com>
Diff between LSX versions 1.5.0 dated 2025-09-12 and 1.5.1 dated 2025-12-08
DESCRIPTION | 12 ++++----- MD5 | 20 +++++++-------- NAMESPACE | 1 NEWS.md | 4 +++ R/as.textmodel.R | 18 +++++++++---- R/textmodel_lss.R | 3 +- build/partial.rdb |binary tests/testthat/Rplots.pdf |binary tests/testthat/test-as.textmodel.R | 4 ++- tests/testthat/test-textplot.R | 48 ++++++++++++++++++------------------- tests/testthat/test-utils.R | 1 11 files changed, 63 insertions(+), 48 deletions(-)
Title: Manage Branding and Accessibility of R Projects
Description: A tool for building projects that are visually consistent,
accessible, and easy to maintain. It provides functions for managing
branding assets, applying organization-wide themes using 'brand.yml',
and setting up new projects with accessibility features and correct
branding. It supports 'quarto', 'shiny', and 'rmarkdown' projects, and
integrates with 'ggplot2'. The accessibility features are based
on the Web Content Accessibility Guidelines
<https://www.w3.org/WAI/WCAG22/quickref/?versions=2.1>
and Accessible Rich Internet Applications (ARIA) specifications
<https://www.w3.org/WAI/ARIA/apg/>. The branding framework implements
the 'brand.yml' specification <https://posit-dev.github.io/brand-yml/>.
Author: Willy Ray [aut, cre],
Andrew Pulsipher [aut, ctb] ,
Centers for Disease Control and Prevention's Center for Forecasting and
Outbreak Analytics [fnd]
Maintainer: Willy Ray <william.ray@hsc.utah.edu>
Diff between rbranding versions 0.1.0 dated 2025-11-21 and 0.1.1 dated 2025-12-08
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- inst/doc/ggplot2-integration.html | 8 ++++---- inst/doc/rbranding.html | 2 +- inst/tinytest/test_ggplot2.R | 18 ++++++++---------- 5 files changed, 20 insertions(+), 22 deletions(-)
Title: Simple TD API Client
Description: Upload R data.frame to Arm Treasure Data, see <https://www.treasuredata.com/>.
You can execute database or table handling for resources on Arm Treasure Data.
Author: Aki Ariga [aut, cre, cph]
Maintainer: Aki Ariga <ariga@treasure-data.com>
Diff between RTD versions 0.4.1 dated 2020-07-26 and 0.4.2 dated 2025-12-08
DESCRIPTION | 11 +--- MD5 | 8 +-- NEWS.md | 4 + README.md | 10 +++ tests/testthat/test-td.R | 118 +++++++++++++++++++++++++++++++++++------------ 5 files changed, 110 insertions(+), 41 deletions(-)
Title: 'Praat Picture' Style Plots of Acoustic Data
Description: Quickly and easily generate plots of acoustic data aligned with transcriptions similar to those made in 'Praat' using either derived signals generated directly in R with 'wrassp' or imported derived signals from 'Praat'. Provides easy and fast out-of-the-box solutions but also a high extent of flexibility. Also provides options for embedding audio in figures and animating figures.
Author: Rasmus Puggaard-Rode [aut, cre, cph]
Maintainer: Rasmus Puggaard-Rode <rasmus.puggaard-rode@ling-phil.ox.ac.uk>
Diff between praatpicture versions 1.6.2 dated 2025-08-25 and 1.7.0 dated 2025-12-08
DESCRIPTION | 12 - MD5 | 22 +- NEWS.md | 16 + R/draw_spectralslice.R | 504 ++++++++++++++++++++++++---------------------- R/formantplot.R | 111 +++++++--- R/praatpicture.R | 58 ++++- R/specplot.R | 200 ++++++++++++------ R/waveplot.R | 51 ++-- man/draw_spectralslice.Rd | 14 - man/praatpicture.Rd | 28 ++ man/specplot.Rd | 20 + man/waveplot.Rd | 8 12 files changed, 651 insertions(+), 393 deletions(-)
Title: Hysteretic and Gatekeeping Depressions Model
Description: Implementation of the Hysteretic and Gatekeeping Depressions Model (HGDM) which calculates variable connected/contributing areas and resulting discharge volumes in prairie basins dominated by depressions ("slough" or "potholes"). The small depressions are combined into a single "meta" depression which explicitly models the hysteresis between the storage of water and the connected/contributing areas of the depressions. The largest (greater than 5% of the total depressional area) depression (if it exists) is represented separately to model its gatekeeping, i.e. the blocking of upstream flows until it is filled. The methodolgy is described in detail in Shook and Pomeroy (2025, <doi:10.1016/j.jhydrol.2025.132821>).
Author: Kevin Shook [cre, aut]
Maintainer: Kevin Shook <kshook@kshook.ca>
Diff between HGDMr versions 1.0.0 dated 2025-02-21 and 1.0.1 dated 2025-12-08
DESCRIPTION | 12 ++++++------ MD5 | 6 +++--- inst/doc/HGDMr_examples.html | 9 +++++---- man/HGDMr-package.Rd | 2 +- 4 files changed, 15 insertions(+), 14 deletions(-)
Title: Distributional Random Forests
Description: An implementation of distributional random forests as introduced in Cevid & Michel & Meinshausen & Buhlmann (2020) <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 1.1.0 dated 2021-03-29 and 1.2.0 dated 2025-12-08
DESCRIPTION | 20 MD5 | 143 +- NAMESPACE | 1 R/analysis_tools.R | 8 R/drf.R | 612 ++-------- R/input_utilities.R | 202 +-- R/mmdVariableImportance.R | 4 R/predict.R |only man/drf.Rd | 136 +- man/predict.drf.Rd | 153 +- src/Makevars | 3 src/RcppExports.cpp | 5 src/src/analysis/SplitFrequencyComputer.cpp | 30 src/src/analysis/SplitFrequencyComputer.h | 30 src/src/commons/Data.cpp | 30 src/src/commons/Data.h | 30 src/src/commons/DefaultData.cpp | 30 src/src/commons/DefaultData.h | 30 src/src/commons/SparseData.cpp | 30 src/src/commons/SparseData.h | 30 src/src/commons/globals.h | 19 src/src/commons/utility.cpp | 30 src/src/commons/utility.h | 30 src/src/forest/Forest.cpp | 30 src/src/forest/Forest.h | 30 src/src/forest/ForestOptions.cpp | 30 src/src/forest/ForestOptions.h | 30 src/src/forest/ForestPredictor.cpp | 30 src/src/forest/ForestPredictor.h | 30 src/src/forest/ForestPredictors.cpp | 30 src/src/forest/ForestPredictors.h | 30 src/src/forest/ForestTrainer.cpp | 30 src/src/forest/ForestTrainer.h | 30 src/src/forest/ForestTrainers.cpp | 30 src/src/forest/ForestTrainers.h | 30 src/src/prediction/DefaultPredictionStrategy.h | 30 src/src/prediction/OptimizedPredictionStrategy.h | 30 src/src/prediction/Prediction.cpp | 30 src/src/prediction/Prediction.h | 30 src/src/prediction/PredictionValues.cpp | 30 src/src/prediction/PredictionValues.h | 30 src/src/prediction/RegressionPredictionStrategy.cpp | 30 src/src/prediction/RegressionPredictionStrategy.h | 30 src/src/prediction/collector/OptimizedPredictionCollector.cpp | 30 src/src/prediction/collector/OptimizedPredictionCollector.h | 30 src/src/prediction/collector/PredictionCollector.h | 30 src/src/prediction/collector/SampleWeightComputer.cpp | 30 src/src/prediction/collector/SampleWeightComputer.h | 30 src/src/prediction/collector/TreeTraverser.cpp | 30 src/src/prediction/collector/TreeTraverser.h | 30 src/src/relabeling/NoopRelabelingStrategy.cpp | 30 src/src/relabeling/NoopRelabelingStrategy.h | 30 src/src/relabeling/RelabelingStrategy.h | 30 src/src/sampling/RandomSampler.cpp | 27 src/src/sampling/RandomSampler.h | 30 src/src/sampling/SamplingOptions.cpp | 30 src/src/sampling/SamplingOptions.h | 30 src/src/splitting/FourierSplittingRule.cpp | 30 src/src/splitting/FourierSplittingRule.h | 30 src/src/splitting/RegressionSplittingRule.cpp | 30 src/src/splitting/RegressionSplittingRule.h | 30 src/src/splitting/SplittingRule.h | 30 src/src/splitting/factory/FourierSplittingRuleFactory.cpp | 30 src/src/splitting/factory/FourierSplittingRuleFactory.h | 30 src/src/splitting/factory/RegressionSplittingRuleFactory.cpp | 30 src/src/splitting/factory/RegressionSplittingRuleFactory.h | 30 src/src/splitting/factory/SplittingRuleFactory.h | 30 src/src/tree/Tree.cpp | 8 src/src/tree/Tree.h | 8 src/src/tree/TreeOptions.cpp | 30 src/src/tree/TreeOptions.h | 30 src/src/tree/TreeTrainer.cpp | 30 src/src/tree/TreeTrainer.h | 30 73 files changed, 1372 insertions(+), 1687 deletions(-)
Title: Fast and Beautiful Interactive Visualization for 'Markdown' and
'Shiny'
Description: Apache licensed alternative to 'Highcharter' which provides
functions for both fast and beautiful interactive visualization for 'Markdown'
and 'Shiny'.
Author: Mauricio Vargas Sepulveda [aut, cre, cph] ,
John Coene [aut],
Ariel Alvarado [ctb],
Sylvain Lesage [ctb],
Curran Kelleher [ctb],
Fernando Becerra [ctb],
Natural Earth [dtc],
R Consortium [fnd]
Maintainer: Mauricio Vargas Sepulveda <m.vargas.sepulveda@gmail.com>
This is a re-admission after prior archival of version 1.0.2 dated 2025-11-25
Diff between d3po versions 1.0.2 dated 2025-11-25 and 1.0.3 dated 2025-12-08
DESCRIPTION | 8 MD5 | 32 +-- R/api.R | 52 ++++-- inst/doc/examples.R | 376 ++++++++++++++++++++++++------------------- inst/doc/examples.Rmd | 98 ++++++++--- inst/doc/examples.html | 422 +++++++++++++++++++++++++------------------------ man/po_area.Rd | 5 man/po_bar.Rd | 5 man/po_box.Rd | 5 man/po_donut.Rd | 5 man/po_geomap.Rd | 5 man/po_line.Rd | 5 man/po_network.Rd | 5 man/po_pie.Rd | 5 man/po_scatter.Rd | 5 man/po_treemap.Rd | 5 vignettes/examples.Rmd | 98 ++++++++--- 17 files changed, 689 insertions(+), 447 deletions(-)
Title: Interface to the arXiv API
Description: An interface to the API for 'arXiv',
a repository of electronic preprints for
computer science, mathematics, physics, quantitative biology,
quantitative finance, and statistics.
Author: Karthik Ram [aut] ,
Karl Broman [aut, cre]
Maintainer: Karl Broman <broman@wisc.edu>
Diff between aRxiv versions 0.14 dated 2025-11-14 and 0.16 dated 2025-12-08
DESCRIPTION | 8 ++--- MD5 | 18 ++++++------ NEWS.md | 14 ++++++++++ R/arxiv_open.R | 7 ++++- R/can_arxiv_connect.R | 3 ++ R/clean.R | 7 ++--- R/parse.R | 8 ++++- inst/doc/aRxiv.html | 30 ++++++++++----------- tests/testthat/test-clean.R | 61 ++++++++++++++++++++++++-------------------- tests/testthat/test-sort.R | 6 +--- 10 files changed, 96 insertions(+), 66 deletions(-)
Title: Seamless R and C++ Integration
Description: The 'Rcpp' package provides R functions as well as C++ classes which
offer a seamless integration of R and C++. Many R data types and objects can be
mapped back and forth to C++ equivalents which facilitates both writing of new
code as well as easier integration of third-party libraries. Documentation
about 'Rcpp' is provided by several vignettes included in this package, via the
'Rcpp Gallery' site at <https://gallery.rcpp.org>, the paper by Eddelbuettel and
Francois (2011, <doi:10.18637/jss.v040.i08>), the book by Eddelbuettel (2013,
<doi:10.1007/978-1-4614-6868-4>) and the paper by Eddelbuettel and Balamuta (2018,
<doi:10.1080/00031305.2017.1375990>); see 'citation("Rcpp")' for details.
Author: Dirk Eddelbuettel [aut, cre] ,
Romain Francois [aut] ,
JJ Allaire [aut] ,
Kevin Ushey [aut] ,
Qiang Kou [aut] ,
Nathan Russell [aut],
Inaki Ucar [aut] ,
Doug Bates [aut] ,
John Chambers [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between Rcpp versions 1.1.0.8 dated 2025-12-07 and 1.1.0.8.1 dated 2025-12-08
ChangeLog | 1 + DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- inst/NEWS.Rd | 2 ++ inst/doc/Rcpp-introduction.pdf |binary tests/tinytest.R | 2 +- 6 files changed, 13 insertions(+), 10 deletions(-)
Title: 'knitr' Bootstrap Framework
Description: A framework to create Bootstrap <https://getbootstrap.com/> HTML reports from 'knitr'
'rmarkdown'.
Author: Jim Hester [aut, cre]
Maintainer: Jim Hester <james.f.hester@gmail.com>
Diff between knitrBootstrap versions 1.0.3 dated 2024-02-06 and 1.0.4 dated 2025-12-08
knitrBootstrap-1.0.3/knitrBootstrap/man/knitrBootstrap.Rd |only knitrBootstrap-1.0.4/knitrBootstrap/DESCRIPTION | 20 +++-- knitrBootstrap-1.0.4/knitrBootstrap/MD5 | 38 +++++----- knitrBootstrap-1.0.4/knitrBootstrap/NEWS.md | 3 knitrBootstrap-1.0.4/knitrBootstrap/R/knit_bootstrap.R | 11 +- knitrBootstrap-1.0.4/knitrBootstrap/README.md | 16 ++-- knitrBootstrap-1.0.4/knitrBootstrap/build/vignette.rds |binary knitrBootstrap-1.0.4/knitrBootstrap/inst/doc/cars.Rmd | 2 knitrBootstrap-1.0.4/knitrBootstrap/inst/doc/cars.html | 10 +- knitrBootstrap-1.0.4/knitrBootstrap/inst/doc/illusions.Rmd | 4 - knitrBootstrap-1.0.4/knitrBootstrap/inst/doc/illusions.html | 4 - knitrBootstrap-1.0.4/knitrBootstrap/inst/doc/maps.html | 8 +- knitrBootstrap-1.0.4/knitrBootstrap/inst/doc/two-D.R | 2 knitrBootstrap-1.0.4/knitrBootstrap/inst/doc/two-D.Rmd | 2 knitrBootstrap-1.0.4/knitrBootstrap/inst/doc/two-D.html | 32 +++++--- knitrBootstrap-1.0.4/knitrBootstrap/man/bootstrap_document.Rd | 14 ++- knitrBootstrap-1.0.4/knitrBootstrap/man/knit_bootstrap_md.Rd | 2 knitrBootstrap-1.0.4/knitrBootstrap/man/knitrBootstrap-package.Rd |only knitrBootstrap-1.0.4/knitrBootstrap/vignettes/cars.Rmd | 2 knitrBootstrap-1.0.4/knitrBootstrap/vignettes/illusions.Rmd | 4 - knitrBootstrap-1.0.4/knitrBootstrap/vignettes/two-D.Rmd | 2 21 files changed, 97 insertions(+), 79 deletions(-)
More information about knitrBootstrap at CRAN
Permanent link
Title: Tools for Analyzing QTL Experiments
Description: Analysis of experimental crosses to identify genes
(called quantitative trait loci, QTLs) contributing to variation in
quantitative traits.
Broman et al. (2003) <doi:10.1093/bioinformatics/btg112>.
Author: Karl W Broman [aut, cre] ,
Hao Wu [aut],
Gary Churchill [ctb] ,
Saunak Sen [ctb] ,
Danny Arends [ctb] ,
Robert Corty [ctb],
Timothee Flutre [ctb],
Ritsert Jansen [ctb],
Pjotr Prins [ctb] ,
Lars Ronnegard [ctb],
Rohan Shah [ctb],
Laura Shannon [ctb],
[...truncated...]
Maintainer: Karl W Broman <broman@wisc.edu>
Diff between qtl versions 1.72 dated 2025-11-19 and 1.74 dated 2025-12-08
DESCRIPTION | 8 +-- MD5 | 110 +++++++++++++++++++++--------------------- NEWS.md | 5 + inst/doc/bcsft.pdf |binary inst/doc/rqtltour.pdf |binary inst/doc/rqtltour2.pdf |binary src/countXO.c | 1 src/discan.c | 1 src/discan_covar.c | 1 src/effectscan.c | 1 src/findDupMarkers_notexact.c | 1 src/fitqtl_hk.c | 1 src/fitqtl_hk_binary.c | 1 src/fitqtl_imp.c | 1 src/fitqtl_imp_binary.c | 1 src/hmm_4way.c | 1 src/hmm_bc.c | 1 src/hmm_bci.c | 1 src/hmm_bcsft.c | 1 src/hmm_bgmagic16.c | 1 src/hmm_f2.c | 1 src/hmm_f2i.c | 1 src/hmm_main.c | 1 src/hmm_ri4self.c | 1 src/hmm_ri4sib.c | 1 src/hmm_ri8self.c | 1 src/hmm_ri8selfIRIP1.c | 1 src/hmm_ri8sib.c | 1 src/hmm_util.c | 1 src/inferFounderHap.c | 1 src/info.c | 1 src/lapackutil.c | 1 src/markerlrt.c | 1 src/pickMarkerSubset.c | 1 src/ril48_reorg.c | 2 src/ripple.c | 1 src/scanone_ehk.c | 1 src/scanone_em.c | 1 src/scanone_em_covar.c | 1 src/scanone_hk.c | 1 src/scanone_hk_binary.c | 1 src/scanone_imp.c | 1 src/scanone_mr.c | 1 src/scanone_np.c | 1 src/scantwo_binary_em.c | 1 src/scantwo_binary_hk.c | 1 src/scantwo_em.c | 1 src/scantwo_hk.c | 1 src/scantwo_imp.c | 1 src/scantwo_mr.c | 1 src/scantwopermhk.c | 1 src/simulate.c | 1 src/simulate_ril.c | 1 src/stahl_mf.c | 1 src/summary_scantwo.c | 1 src/test_bcsft.c | 1 56 files changed, 64 insertions(+), 110 deletions(-)
Title: Detecting Changes in Autocorrelated and Fluctuating Signals
Description: Detect abrupt changes in time series with local fluctuations as a random walk process and autocorrelated noise as an AR(1) process. See Romano, G., Rigaill, G., Runge, V., Fearnhead, P. (2021) <doi:10.1080/01621459.2021.1909598>.
Author: Gaetano Romano [aut, cre],
Guillem Rigaill [aut],
Vincent Runge [aut],
Paul Fearnhead [aut]
Maintainer: Gaetano Romano <g.romano@lancaster.ac.uk>
Diff between DeCAFS versions 3.3.3 dated 2023-01-06 and 3.3.5 dated 2025-12-08
DeCAFS-3.3.3/DeCAFS/src/Makevars |only DeCAFS-3.3.5/DeCAFS/DESCRIPTION | 12 ++++++------ DeCAFS-3.3.5/DeCAFS/MD5 | 7 +++---- DeCAFS-3.3.5/DeCAFS/NEWS.md | 14 ++++++++++++++ DeCAFS-3.3.5/DeCAFS/build/partial.rdb |binary 5 files changed, 23 insertions(+), 10 deletions(-)
Title: Multilevel Latent Time Series Models with 'R' and 'Stan'
Description: Fit multilevel manifest or latent time-series models, including popular Dynamic Structural Equation Models (DSEM).
The models can be set up and modified with user-friendly functions and are fit to the data using 'Stan' for Bayesian inference.
Path models and formulas for user-defined models can be easily created with functions using 'knitr'.
Asparouhov, Hamaker, & Muthen (2018) <doi:10.1080/10705511.2017.1406803>.
Author: Kenneth Koslowski [aut, cre, cph] ,
Fabian Muench [aut] ,
Tobias Koch [aut] ,
Jana Holtmann [aut]
Maintainer: Kenneth Koslowski <kenneth.koslowski@uni-leipzig.de>
Diff between mlts versions 1.0.0 dated 2024-06-27 and 2.0.0 dated 2025-12-08
DESCRIPTION | 19 MD5 | 156 NAMESPACE | 39 NEWS.md | 27 R/VARprepare.R | 701 +- R/ar1_data.R | 26 R/create_missings.R | 309 - R/mlts-package.R | 26 R/mlts_fit.R | 998 ++- R/mlts_model.R | 880 ++- R/mlts_model_betw.R | 362 - R/mlts_model_check.R | 52 R/mlts_model_constraint.R | 325 - R/mlts_model_eval.R | 938 +-- R/mlts_model_formula.R | 1761 +++--- R/mlts_model_measurement.R | 529 +- R/mlts_model_paths.R | 2449 ++++----- R/mlts_param_labels.R | 332 - R/mlts_paths.R |only R/mlts_plot.R | 692 +- R/mlts_posterior_sample.R |only R/mlts_pp_check.R |only R/mlts_sim.R | 965 +-- R/mlts_standardized.R | 4 R/mlts_standardized_btw.R | 616 +- R/mlts_standardized_within.R | 414 - R/model_helper_functions.R | 653 ++ R/prepare_data.R | 417 - R/sim_helper_functions.R |only R/stanmodels.R | 56 R/summary.R | 671 +- R/ts_data.R | 28 README.md | 634 +- build/partial.rdb |binary build/vignette.rds |binary configure.win | 10 inst/CITATION | 36 inst/doc/betw_predictors.R | 170 inst/doc/betw_predictors.html | 1466 ++--- inst/doc/manifest_ar.R | 91 inst/doc/manifest_ar.Rmd | 290 - inst/doc/manifest_ar.html | 1201 ++-- inst/doc/manifest_var.R | 18 inst/doc/manifest_var.Rmd | 44 inst/doc/manifest_var.html | 723 +- inst/rmarkdown/templates/formula/skeleton/skeleton.Rmd | 32 inst/rmarkdown/templates/formula/template.yaml | 8 inst/rmarkdown/templates/pathmodel/skeleton/skeleton.Rmd | 48 inst/rmarkdown/templates/pathmodel/template.yaml | 8 inst/stan/VAR_latent.stan | 782 +-- inst/stan/VAR_latentCovsFix.stan | 731 +- inst/stan/VAR_manifest.stan | 565 +- inst/stan/VAR_manifestCovsFix.stan | 530 +- inst/stan/include/license.stan | 28 man/ar1_data.Rd | 54 man/create_missings.Rd | 90 man/figures/README-ar1_plot-1.png |binary man/figures/README-unnamed-chunk-5-1.png |only man/mlts-package.Rd | 60 man/mlts_fit.Rd | 339 - man/mlts_model.Rd | 400 - man/mlts_model_formula.Rd | 104 man/mlts_model_paths.Rd | 110 man/mlts_paths.Rd |only man/mlts_plot.Rd | 228 man/mlts_posterior_sample.Rd |only man/mlts_pp_check.Rd |only man/mlts_sim.Rd | 177 man/mlts_standardized.Rd | 113 man/summary.mltsfit.Rd | 124 man/ts_data.Rd | 56 tests/local/test-mlts_model_formula.R | 174 tests/local/test-mlts_model_paths.R | 172 tests/testthat.R | 24 tests/testthat/test-create_missings.R | 104 tests/testthat/test-mlts_model.R | 56 tests/testthat/test-prepare_data.R | 36 vignettes/apa.csl | 3828 +++++++-------- vignettes/ar1_fit.rds |binary vignettes/betw_preds_fit1.txt | 90 vignettes/betw_preds_fit2.txt | 110 vignettes/manifest_ar.Rmd | 290 - vignettes/manifest_var.Rmd | 44 83 files changed, 15085 insertions(+), 13558 deletions(-)
Title: Estimation of Model-Based Predictions, Contrasts and Means
Description: Implements a general interface for model-based estimations
for a wide variety of models, used in the computation of
marginal means, contrast analysis and predictions. For a list of supported models,
see 'insight::supported_models()'.
Author: Dominique Makowski [aut, cre] ,
Daniel Luedecke [aut] ,
Mattan S. Ben-Shachar [aut] ,
Indrajeet Patil [aut] ,
Remi Theriault [aut]
Maintainer: Dominique Makowski <officialeasystats@gmail.com>
Diff between modelbased versions 0.13.0 dated 2025-08-30 and 0.13.1 dated 2025-12-08
DESCRIPTION | 24 - MD5 | 107 ++++---- NAMESPACE | 4 NEWS.md | 21 + R/as.data.frame.R |only R/estimate_contrasts.R | 24 + R/estimate_contrasts_effectsize.R | 41 ++- R/estimate_grouplevel.R | 206 +++++++++++----- R/estimate_means.R | 83 ++++-- R/estimate_slopes.R | 1 R/format.R | 54 +++- R/get_inequalitycontrasts.R | 2 R/get_marginalcontrasts.R | 35 +- R/get_marginaleffects_type.R | 36 +- R/get_marginalmeans.R | 108 +++++--- R/get_marginaltrends.R | 3 R/options.R | 10 R/residualize_over_grid.R | 2 R/standardize_methods.R | 12 R/summary.R | 2 R/table_footer.R | 28 ++ R/tinyplot.R | 95 ++++++- R/visualisation_recipe.R | 6 R/visualisation_recipe_internal.R | 2 README.md | 20 + build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST | 100 ++----- inst/doc/overview_of_vignettes.Rmd | 1 inst/doc/overview_of_vignettes.html | 2 man/as.data.frame.estimate_contrasts.Rd |only man/describe_nonlinear.Rd | 2 man/estimate_contrasts.Rd | 8 man/estimate_expectation.Rd | 2 man/estimate_grouplevel.Rd | 35 +- man/estimate_means.Rd | 48 +++ man/estimate_slopes.Rd | 4 man/figures/unnamed-chunk-3-1.png |binary man/get_emmeans.Rd | 10 man/modelbased-options.Rd | 9 man/pool_contrasts.Rd | 2 man/pool_predictions.Rd | 2 man/print.estimate_contrasts.Rd | 13 - man/puppy_love.Rd | 64 ++-- man/residualize_over_grid.Rd | 2 man/visualisation_recipe.estimate_predicted.Rd | 51 ++- tests/testthat/test-as.data.frame.R |only tests/testthat/test-attributes_estimatefun.R | 38 ++ tests/testthat/test-equivalence.R |only tests/testthat/test-estimate_contrasts_counterfactual.R |only tests/testthat/test-estimate_contrasts_effectsize.R | 106 ++++++-- tests/testthat/test-estimate_filter.R | 19 + tests/testthat/test-estimate_grouplevel.R | 145 +++++++++++ tests/testthat/test-keep_iterations.R | 47 ++- tests/testthat/test-ordinal.R | 1 tests/testthat/test-plot-grouplevel.R | 2 vignettes/overview_of_vignettes.Rmd | 1 57 files changed, 1180 insertions(+), 460 deletions(-)
Title: Most Likely Transformations: Documentation and Regression Tests
Description: Additional documentation, a package vignette and
regression tests for package mlt.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mlt.docreg versions 1.1-11 dated 2025-10-08 and 1.1-12 dated 2025-12-08
DESCRIPTION | 8 ++++---- MD5 | 16 +++++++++++----- build/vignette.rds |binary inst/NEWS.Rd | 8 ++++++++ inst/doc/mlt.pdf |binary tests/AFT-Ex.Rout.save |only tests/KM-Ex.Rout.save |only tests/faithful.Rout.save |only tests/orm-Ex.Rout.save |only tests/timedep_covar.Rout.save |only tests/truncreg-Ex.Rout.save |only vignettes/defs.tex | 2 +- 12 files changed, 24 insertions(+), 10 deletions(-)
Title: Dice Plot Visualization for 'ggplot2'
Description: Provides 'ggplot2' extensions for creating dice-based visualizations
where each dot position represents a specific categorical variable. The package
includes geom_dice() for displaying presence/absence of categorical variables
using traditional dice patterns. Each dice position (1-6) represents a different
category, with dots shown only when that category is present. This allows
intuitive visualization of up to 6 categorical variables simultaneously.
Author: Matthias Flotho [aut, cre]
Maintainer: Matthias Flotho <matthias.flotho@ccb.uni-saarland.de>
Diff between ggdiceplot versions 0.1.1 dated 2025-10-14 and 1.0.1 dated 2025-12-08
ggdiceplot-0.1.1/ggdiceplot/R/geom-dice-ggproto.R |only ggdiceplot-0.1.1/ggdiceplot/inst |only ggdiceplot-1.0.1/ggdiceplot/DESCRIPTION | 16 +- ggdiceplot-1.0.1/ggdiceplot/MD5 | 19 +- ggdiceplot-1.0.1/ggdiceplot/R/geom-dice-ggprotto.R | 17 +- ggdiceplot-1.0.1/ggdiceplot/R/sample_datasets.R |only ggdiceplot-1.0.1/ggdiceplot/README.md | 123 +++++++++-------- ggdiceplot-1.0.1/ggdiceplot/data/sample_dice_miRNA.rda |only ggdiceplot-1.0.1/ggdiceplot/man/geom_dice.Rd | 2 ggdiceplot-1.0.1/ggdiceplot/man/sample_dice_data1.Rd | 51 ++----- ggdiceplot-1.0.1/ggdiceplot/man/sample_dice_data2.Rd | 45 +----- ggdiceplot-1.0.1/ggdiceplot/man/sample_dice_large.Rd | 48 +----- ggdiceplot-1.0.1/ggdiceplot/man/sample_dice_miRNA.Rd |only 13 files changed, 137 insertions(+), 184 deletions(-)
Title: Adaptive Lasso Quantile Regression with Fixed Effects
Description: Quantile regression with fixed effects solves longitudinal data, considering the individual intercepts as fixed effects. The parametric set of this type of problem used to be huge. Thus penalized methods such as Lasso are currently applied. Adaptive Lasso presents oracle proprieties, which include Gaussianity and correct model selection. Bayesian information criteria (BIC) estimates the optimal tuning parameter lambda. Plot tools are also available.
Author: Ian Meneghel Danilevicz [aut, cre] ,
Pascal Bondon [aut],
Valderio A. Reisen [aut]
Maintainer: Ian Meneghel Danilevicz <iandanilevicz@gmail.com>
Diff between alqrfe versions 1.2 dated 2025-07-03 and 1.3 dated 2025-12-08
alqrfe-1.2/alqrfe/R/LQRFE_main_v3.R |only alqrfe-1.3/alqrfe/DESCRIPTION | 10 +++-- alqrfe-1.3/alqrfe/MD5 | 21 ++++++----- alqrfe-1.3/alqrfe/R/LQRFE_main.R |only alqrfe-1.3/alqrfe/R/RcppExports.R | 17 ++++++--- alqrfe-1.3/alqrfe/man/clean_data.Rd | 2 - alqrfe-1.3/alqrfe/man/mqr.Rd | 2 - alqrfe-1.3/alqrfe/man/mqr_alpha.Rd | 2 - alqrfe-1.3/alqrfe/man/plot_alpha.Rd | 2 - alqrfe-1.3/alqrfe/man/plot_taus.Rd | 2 - alqrfe-1.3/alqrfe/man/qr.Rd | 19 +++++++++- alqrfe-1.3/alqrfe/src/LQRFE_arma.cpp | 62 +++++++++++++++++------------------ alqrfe-1.3/alqrfe/tests |only 13 files changed, 80 insertions(+), 59 deletions(-)
Title: Simulation of Legal Exemption System for European Cartel Law
Description: Monte Carlo simulations of a game-theoretic model for the
legal exemption system of the European cartel law are implemented
in order to estimate the (mean) deterrent effect of this system.
The input and output parameters of the simulated cartel
opportunities can be visualized by three-dimensional projections.
A description of the model is given in Moritz et al. (2018)
<doi:10.1515/bejeap-2017-0235>.
Author: Martin Becker [aut, cre]
Maintainer: Martin Becker <martin.becker@mx.uni-saarland.de>
Diff between SimEUCartelLaw versions 1.0.3 dated 2022-06-13 and 1.0.4 dated 2025-12-08
DESCRIPTION | 11 ++++++----- MD5 | 4 ++-- src/SimEUCartelLaw.c | 1 - 3 files changed, 8 insertions(+), 8 deletions(-)
More information about SimEUCartelLaw at CRAN
Permanent link
Title: Multivariate Synthetic Control Method Using Time Series
Description: Three generalizations of the synthetic control method (which has
already an implementation in package 'Synth') are implemented: first,
'MSCMT' allows for using multiple outcome variables, second, time series
can be supplied as economic predictors, and third, a well-defined
cross-validation approach can be used.
Much effort has been taken to make the implementation as stable as possible
(including edge cases) without losing computational efficiency.
A detailed description of the main algorithms is given in
Becker and Klößner (2018) <doi:10.1016/j.ecosta.2017.08.002>.
Author: Martin Becker [aut, cre] ,
Stefan Kloessner [aut],
Karline Soetaert [com],
Jack Dongarra [cph],
R.J. Hanson [cph],
K.H. Haskell [cph],
Cleve Moler [cph],
LAPACK authors [cph]
Maintainer: Martin Becker <martin.becker@mx.uni-saarland.de>
Diff between MSCMT versions 1.4.0 dated 2024-03-19 and 1.4.1 dated 2025-12-08
DESCRIPTION | 11 ++++++----- MD5 | 20 ++++++++++---------- NEWS | 7 +++++++ build/partial.rdb |binary build/vignette.rds |binary inst/doc/CheckingSynth.R | 2 +- inst/doc/CheckingSynth.html | 6 +++--- inst/doc/UsingTimeSeries.R | 2 +- inst/doc/WorkingWithMSCMT.R | 2 +- inst/doc/WorkingWithMSCMT.html | 32 ++++++++++++++++---------------- src/MSCMT.c | 2 +- 11 files changed, 46 insertions(+), 38 deletions(-)
Title: Extracts the Backbone from Networks
Description: An implementation of methods for extracting a sparse unweighted network (i.e. a backbone)
from an unweighted network (e.g., Hamann et al., 2016 <doi:10.1007/s13278-016-0332-2>), a weighted network
(e.g., Serrano et al., 2009 <doi:10.1073/pnas.0808904106>), or a weighted projection (e.g., Neal et al., 2021
<doi:10.1038/s41598-021-03238-3>).
Author: Zachary Neal [aut, cre] ,
Rachel Domagalski [ctb],
Bruce Sagan [ctb],
Karl Godard [ctb]
Maintainer: Zachary Neal <zpneal@msu.edu>
Diff between backbone versions 3.0.2 dated 2025-10-06 and 3.0.3 dated 2025-12-08
backbone-3.0.2/backbone/R/utils.R |only backbone-3.0.3/backbone/DESCRIPTION | 8 backbone-3.0.3/backbone/MD5 | 37 +- backbone-3.0.3/backbone/NAMESPACE | 3 backbone-3.0.3/backbone/NEWS.md | 5 backbone-3.0.3/backbone/R/backbone.R | 9 backbone-3.0.3/backbone/R/backbone_from_projection.R | 4 backbone-3.0.3/backbone/R/backbone_from_unweighted.R | 26 +- backbone-3.0.3/backbone/R/backbone_from_weighted.R | 8 backbone-3.0.3/backbone/R/functions_s3.R |only backbone-3.0.3/backbone/R/functions_unweighted.R | 3 backbone-3.0.3/backbone/R/functions_util.R |only backbone-3.0.3/backbone/R/functions_weighted.R | 6 backbone-3.0.3/backbone/inst/doc/backbone.R | 24 + backbone-3.0.3/backbone/inst/doc/backbone.Rmd | 37 ++ backbone-3.0.3/backbone/inst/doc/backbone.html | 241 +++++++++---------- backbone-3.0.3/backbone/inst/doc/senate.html | 25 + backbone-3.0.3/backbone/man/backbone.Rd | 4 backbone-3.0.3/backbone/man/bicm.Rd | 2 backbone-3.0.3/backbone/man/fastball.Rd | 2 backbone-3.0.3/backbone/vignettes/backbone.Rmd | 37 ++ 21 files changed, 270 insertions(+), 211 deletions(-)
Title: Penalized Quantile Regression with Fixed Effects
Description: Quantile regression with fixed effects is a general model for longitudinal data. Here we proposed to solve it by several methods. The estimation methods include three loss functions as check, asymmetric least square and asymmetric Huber functions; and three structures as simple regression, fixed effects and fixed effects with penalized intercepts by LASSO.
Author: Ian Meneghel Danilevicz [aut, cre] ,
Valderio A Reisen [aut],
Pascal Bondon [aut]
Maintainer: Ian Meneghel Danilevicz <iandanilevicz@gmail.com>
Diff between pqrfe versions 1.2 dated 2025-11-14 and 1.3 dated 2025-12-08
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Title: Machine-Readable Data Analysis Results with Function Wrappers
Description: You can use the set of wrappers for analytical schemata
to reduce the effort in writing machine-readable data. The set of all-in-one
wrappers will cover widely used functions from data analysis packages.
Author: Olga Lezhnina [aut] ,
Manuel Prinz [aut] ,
Markus Stocker [aut, cre] ,
Open Research Knowledge Graph Project and Contributors [cph]
Maintainer: Markus Stocker <markus.stocker@tib.eu>
Diff between mrap versions 1.0.0 dated 2025-11-25 and 1.0.1 dated 2025-12-08
DESCRIPTION | 18 +++++++++--------- MD5 | 6 +++--- NEWS.md | 4 ++++ man/mrap-package.Rd | 4 ++-- 4 files changed, 18 insertions(+), 14 deletions(-)
Title: Estimate Inverse Probability Weights
Description: Functions to estimate the probability to receive the observed treatment, based on
individual characteristics. The inverse of these probabilities can be used as weights when
estimating causal effects from observational data via marginal structural models. Both point
treatment situations and longitudinal studies can be analysed. The same functions can be used to
correct for informative censoring.
Author: Hung Thai Tran [aut, cre],
Willem M. van der Wal [aut],
Ronald B. Geskus [aut]
Maintainer: Hung Thai Tran <hungtt@oucru.org>
Diff between ipw versions 1.2.1.1 dated 2025-07-28 and 1.2.2 dated 2025-12-08
DESCRIPTION | 23 +++++++++++++++-------- MD5 | 8 ++++---- R/ipwpoint.R | 43 +++++++++++++++++++++++++++++++++++++++++++ build/partial.rdb |binary man/ipwpoint.Rd | 12 +++++++----- 5 files changed, 69 insertions(+), 17 deletions(-)
Title: Automated Multicollinearity Management
Description: Provides a comprehensive and automated workflow for managing multicollinearity in data frames with numeric and/or categorical variables. The package integrates five robust methods into a single function: (1) target encoding of categorical variables based on response values (Micci-Barreca, 2001 (Micci-Barreca, D. 2001 <doi:10.1145/507533.507538>); (2) automated feature prioritization to preserve key predictors during filtering; (3 and 4) pairwise correlation and VIF filtering across all variable types (numeric–numeric, numeric–categorical, and categorical–categorical); (5) adaptive correlation and VIF thresholds. Together, these methods enable a reliable multicollinearity management in most use cases while maintaining model integrity. The package also supports parallel processing and progress tracking via the packages 'future' and 'progressr', and provides seamless integration with the 'tidymodels' ecosystem through a dedicated recipe step.
Author: Blas M. Benito [aut, cre, cph]
Maintainer: Blas M. Benito <blasbenito@gmail.com>
Diff between collinear versions 2.0.0 dated 2024-11-08 and 3.0.0 dated 2025-12-08
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Title: Karl Broman's R Code
Description: Miscellaneous R functions, including functions related to
graphics (mostly for base graphics), permutation tests, running
mean/median, and general utilities.
Author: Karl W Broman [aut, cre] ,
Aimee Teo Broman [ctb]
Maintainer: Karl W Broman <broman@wisc.edu>
Diff between broman versions 0.90 dated 2025-10-10 and 0.92 dated 2025-12-08
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 5 +++++ data/numbers-cap.RData |binary data/numbers.RData |binary src/normalize.c | 1 - src/runningmean.c | 1 - src/runningratio2.c | 1 - 8 files changed, 16 insertions(+), 14 deletions(-)
Title: Tools for Analyzing Crossover Interference
Description: Analysis of crossover interference in experimental crosses,
particularly regarding the gamma model. See, for example,
Broman and Weber (2000) <doi:10.1086/302923>.
Author: Karl W Broman [aut, cre] ,
Il-Youp Kwak [ctb]
Maintainer: Karl W Broman <broman@wisc.edu>
Diff between xoi versions 0.72 dated 2023-03-22 and 0.74 dated 2025-12-08
DESCRIPTION | 15 ++++++++------- MD5 | 18 +++++++++--------- NEWS.md | 5 +++++ data/bssbsb.RData |binary src/GammaS.h | 1 - src/kfunc.c | 1 - src/kwak_coincidence.c | 1 - src/kwak_get_n_xo.c | 1 - src/kwak_identify.c | 1 - src/kwak_intensity.c | 1 - 10 files changed, 22 insertions(+), 22 deletions(-)
Title: Clinical Trial Style Data Readout Listings
Description: Listings are often part of the submission of clinical trial
data in regulatory settings. We provide a framework for the specific
formatting features often used when displaying large datasets in that
context.
Author: Gabriel Becker [aut] ,
Adrian Waddell [aut],
Joe Zhu [aut, cre] ,
Davide Garolini [aut] ,
Emily de la Rua [aut] ,
Abinaya Yogasekaram [ctb] ,
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Joe Zhu <joe.zhu@roche.com>
Diff between rlistings versions 0.2.12 dated 2025-06-15 and 0.2.13 dated 2025-12-08
DESCRIPTION | 19 ++-- MD5 | 44 +++++------ NAMESPACE | 2 NEWS.md | 5 + R/rlistings.R | 50 +++++++----- R/rlistings_methods.R | 45 +++++++++-- inst/WORDLIST | 2 inst/doc/col_formatting.html | 91 +++++++++++------------ inst/doc/large_list.R | 20 +++-- inst/doc/large_list.Rmd | 21 +++-- inst/doc/large_list.html | 79 +++++++++++--------- inst/doc/pagination.html | 7 + inst/doc/ref_footnotes.html | 7 + inst/doc/rlistings.html | 33 ++++---- man/listing_methods.Rd | 16 ++-- man/listings.Rd | 7 + man/make_row_df-listing_df-method.Rd | 13 ++- man/matrix_form-listing_df-method.Rd | 13 ++- man/vec_nlines.Rd | 15 +++ tests/testthat/test-listings.R | 129 ++++++++++++++++++++++++++++++--- tests/testthat/test-paginate_listing.R | 37 +++++++++ tests/testthat/test-print.R | 44 ++++++----- vignettes/large_list.Rmd | 21 +++-- 23 files changed, 496 insertions(+), 224 deletions(-)
Title: Estimating the Number of Essential Genes in a Genome
Description: Estimating the number of essential genes in a genome on
the basis of data from a random transposon mutagenesis experiment,
through the use of a Gibbs sampler.
Lamichhane et al. (2003) <doi:10.1073/pnas.1231432100>.
Author: Karl W Broman [aut, cre]
Maintainer: Karl W Broman <broman@wisc.edu>
Diff between negenes versions 1.2 dated 2025-05-11 and 1.4 dated 2025-12-08
DESCRIPTION | 10 ++--- MD5 | 10 ++--- NEWS.md | 5 ++ build/partial.rdb |binary data/Mtb80.RData |binary src/negenes.c | 94 +++++++++++++++++++++++++----------------------------- 6 files changed, 60 insertions(+), 59 deletions(-)
Title: m-Out-of-n Bootstrap Functions
Description: Functions and examples based on the m-out-of-n bootstrap suggested by
Politis, D.N. and Romano, J.P. (1994) <doi:10.1214/aos/1176325770>.
Additionally there are functions to estimate the scaling factor tau
and the subsampling size m. For a detailed description and a full list
of references, see Dalitz, C. and Lögler, F. (2025)
<doi:10.32614/RJ-2025-031>.
Author: Christoph Dalitz [aut, cre],
Felix Loegler [aut]
Maintainer: Christoph Dalitz <christoph.dalitz@hs-niederrhein.de>
Diff between moonboot versions 1.0.1 dated 2025-02-21 and 2.0.1 dated 2025-12-08
Changelog | 19 ++++++++++++ DESCRIPTION | 12 ++++---- MD5 | 26 ++++++++--------- R/distpower.R | 2 - R/moonboot.R | 78 ++++++++++++++++++++++++++++++---------------------- R/sherman.R | 6 ++-- README.md | 6 ++-- build/partial.rdb |binary inst/CITATION | 16 ++++++---- man/distPower.Rd | 2 - man/estimate.m.Rd | 11 ++++--- man/estimate.tau.Rd | 17 ++++++----- man/mboot.Rd | 4 +- man/mboot.ci.Rd | 20 +++++++++---- 14 files changed, 133 insertions(+), 86 deletions(-)
Title: An Accurate kNN Implementation with Multiple Distance Measures
Description: Similarly to the 'FNN' package, this package allows calculation of the k nearest neighbors (kNN) of a data matrix.
The implementation is based on cover trees introduced by
Alina Beygelzimer, Sham Kakade, and John Langford (2006) <doi:10.1145/1143844.1143857>.
Author: Philipp Angerer [cre, aut] ,
David Crane [cph, aut]
Maintainer: Philipp Angerer <philipp.angerer@helmholtz-muenchen.de>
Diff between knn.covertree versions 1.0 dated 2019-10-28 and 1.1 dated 2025-12-08
DESCRIPTION | 14 +++++++------- MD5 | 13 +++++++------ R/knn.covertree-package.r | 3 +-- README.md | 10 ++++++---- build |only man/knn.Rd | 10 ++++++++-- man/knn.covertree-package.Rd | 21 +++++++++++++++++++-- src/RcppExports.cpp | 5 +++++ 8 files changed, 53 insertions(+), 23 deletions(-)
Title: Fair Gated Algorithm for Targeted Equity
Description: Tools for training and analysing fairness-aware gated neural
networks for subgroup-aware prediction and interpretation in clinical datasets.
Methods draw on prior work in mixture-of-experts neural networks by
Jordan and Jacobs (1994) <doi:10.1007/978-1-4471-2097-1_113>,
fairness-aware learning by Hardt, Price, and Srebro (2016) <doi:10.48550/arXiv.1610.02413>,
and personalised treatment prediction for depression by Iniesta, Stahl, and McGuffin (2016)
<doi:10.1016/j.jpsychires.2016.03.016>.
Author: Rhys Holland [aut, cre],
Raquel Iniesta [aut]
Maintainer: Rhys Holland <rhys.holland@icloud.com>
Diff between fairGATE versions 0.1.0 dated 2025-11-19 and 0.1.1 dated 2025-12-08
DESCRIPTION | 17 +++++++++----- MD5 | 4 +-- inst/doc/introduction-to-fairGATE.html | 40 ++++++++++++++++----------------- 3 files changed, 34 insertions(+), 27 deletions(-)
Title: Ecological Inference in 2x2 Tables
Description: Implements the Bayesian and likelihood methods proposed in Imai, Lu, and Strauss (2008 <doi:10.1093/pan/mpm017>) and (2011 <doi:10.18637/jss.v042.i05>) for ecological inference in 2 by 2 tables as well as the method of bounds introduced by Duncan and Davis (1953). The package fits both parametric and nonparametric models using either the Expectation-Maximization algorithms (for likelihood models) or the Markov chain Monte Carlo algorithms (for Bayesian models). For all models, the individual-level data can be directly incorporated into the estimation whenever such data are available. Along with in-sample and out-of-sample predictions, the package also provides a functionality which allows one to quantify the effect of data aggregation on parameter estimation and hypothesis testing under the parametric likelihood models.
Author: Kosuke Imai [aut, cre],
Ying Lu [aut],
Aaron Strauss [aut],
Hubert Jin [ctb]
Maintainer: Kosuke Imai <imai@Harvard.Edu>
Diff between eco versions 4.0-5 dated 2025-10-23 and 4.0-6 dated 2025-12-08
ChangeLog | 1 + DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ src/fintegrate.c | 2 +- src/gibbsEM.c | 2 +- src/rand.c | 2 +- src/vector.c | 2 +- 7 files changed, 15 insertions(+), 14 deletions(-)
Title: Extracting and Visualizing Bayesian Graphical Models
Description: Fit and visualize the results of a Bayesian analysis of networks commonly found in psychology.
The package supports fitting cross-sectional network models fitted using the packages 'BDgraph', 'bgms' and 'BGGM',
as well as network comparison fitted using the 'bgms' and 'BBGM'.
The package provides the parameter estimates, posterior inclusion probabilities, inclusion Bayes factor, and the
posterior density of the parameters. In addition, for 'BDgraph' and 'bgms' it allows to assess the posterior
structure space. Furthermore, the package comes with an extensive suite for visualizing results.
Author: Karoline Huth [aut, cre] ,
Sara Keetelaar [ctb],
Nikola Sekulovski [ctb],
Gali Geller [ctb]
Maintainer: Karoline Huth <k.huth@uva.nl>
Diff between easybgm versions 0.2.1 dated 2024-10-17 and 0.3.1 dated 2025-12-08
easybgm-0.2.1/easybgm/R/sparse_dense.R |only easybgm-0.2.1/easybgm/man/sparse_or_dense.Rd |only easybgm-0.2.1/easybgm/tests/testthat/_snaps |only easybgm-0.3.1/easybgm/DESCRIPTION | 29 - easybgm-0.3.1/easybgm/MD5 | 58 +- easybgm-0.3.1/easybgm/NAMESPACE | 20 easybgm-0.3.1/easybgm/R/AuxiliaryFunctions.R | 319 +++++++------- easybgm-0.3.1/easybgm/R/bgm_plot_class.R | 118 ++--- easybgm-0.3.1/easybgm/R/easybgm.R | 92 ++-- easybgm-0.3.1/easybgm/R/easybgm_compare.R |only easybgm-0.3.1/easybgm/R/functions.bdgraph.R | 43 + easybgm-0.3.1/easybgm/R/functions.bggm.R | 9 easybgm-0.3.1/easybgm/R/functions.bggmcompare.R |only easybgm-0.3.1/easybgm/R/functions.bgms.R | 278 ++++++++---- easybgm-0.3.1/easybgm/R/functions.bgmscompare.R |only easybgm-0.3.1/easybgm/R/plottingfunctions.bgmCompare.R |only easybgm-0.3.1/easybgm/R/plottingfunctions.bgms.R | 99 +++- easybgm-0.3.1/easybgm/R/plottingfunctions.easybgm.R | 249 +++++++++- easybgm-0.3.1/easybgm/R/summary.easybgm.R | 255 ++++++++--- easybgm-0.3.1/easybgm/R/summary.easybgm_compare.R |only easybgm-0.3.1/easybgm/man/HDI.Rd | 4 easybgm-0.3.1/easybgm/man/centrality.Rd | 12 easybgm-0.3.1/easybgm/man/clusterBayesfactor.Rd |only easybgm-0.3.1/easybgm/man/complexity_probs.Rd | 2 easybgm-0.3.1/easybgm/man/easybgm.Rd | 48 +- easybgm-0.3.1/easybgm/man/easybgm_compare.Rd |only easybgm-0.3.1/easybgm/man/edgeevidence.Rd | 11 easybgm-0.3.1/easybgm/man/network.Rd | 2 easybgm-0.3.1/easybgm/man/print.easybgm_compare.Rd |only easybgm-0.3.1/easybgm/man/prior_sensitivity.Rd | 8 easybgm-0.3.1/easybgm/man/structure.Rd | 2 easybgm-0.3.1/easybgm/man/structure_probs.Rd | 2 easybgm-0.3.1/easybgm/man/summary.easybgm.Rd | 6 easybgm-0.3.1/easybgm/man/summary.easybgm_compare.Rd |only easybgm-0.3.1/easybgm/tests/testthat/Rplots.pdf |binary easybgm-0.3.1/easybgm/tests/testthat/test-easybgm.R | 385 +++++++++++------ 36 files changed, 1410 insertions(+), 641 deletions(-)
Title: Create Scale Linkage Scores
Description: Perform a 'probabilistic' linkage of two data files using a scaling procedure using the methods described in Goldstein, H., Harron, K. and Cortina-Borja, M. (2017) <doi:10.1002/sim.7287>.
Author: Chris Charlton [aut, cre],
Harvey Goldstein [aut]
Maintainer: Chris Charlton <c.charlton@bristol.ac.uk>
Diff between Scalelink versions 1.0 dated 2019-02-20 and 1.0-2 dated 2025-12-08
DESCRIPTION | 12 ++++++------ MD5 | 18 +++++++++--------- NEWS | 8 ++++++++ R/pkgname.R | 5 ++--- man/Scalelink.Rd | 6 ++---- man/calcScores.Rd | 10 ++++++++-- src/Makevars | 1 - src/Makevars.win | 1 - src/RcppExports.cpp | 5 +++++ src/rcpp_build_astar.cpp | 5 ++--- 10 files changed, 42 insertions(+), 29 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 0.8.7 dated 2023-01-08 and 0.8.8 dated 2025-12-08
DESCRIPTION | 20 +++++++++--------- MD5 | 18 ++++++++-------- NAMESPACE | 1 NEWS.md | 4 +++ R/collapse_singles.R | 1 R/rncl-package.R | 3 -- R/rncl.R | 36 ++++++++++++++------------------- README.md | 7 +++--- build/partial.rdb |binary man/rncl.Rd | 55 ++++++++++++++++++++++++++++++++------------------- 10 files changed, 79 insertions(+), 66 deletions(-)
Title: Tools for Highfrequency Data Analysis
Description: Provide functionality to manage, clean and match highfrequency
trades and quotes data, calculate various liquidity measures, estimate and
forecast volatility, detect price jumps and investigate microstructure noise and intraday
periodicity. A detailed vignette can be found in the open-access paper
"Analyzing Intraday Financial Data in R: The highfrequency Package"
by Boudt, Kleen, and Sjoerup (2022, <doi:10.18637/jss.v104.i08>).
Author: Kris Boudt [aut, cre] ,
Jonathan Cornelissen [aut],
Scott Payseur [aut],
Giang Nguyen [ctb],
Onno Kleen [aut] ,
Emil Sjoerup [aut]
Maintainer: Kris Boudt <kris.boudt@ugent.be>
Diff between highfrequency versions 1.0.1 dated 2023-10-04 and 1.0.2 dated 2025-12-08
highfrequency-1.0.1/highfrequency/man/MDtest.Rd |only highfrequency-1.0.1/highfrequency/man/RBPCov_bi.Rd |only highfrequency-1.0.1/highfrequency/man/cholCovrMRCov.Rd |only highfrequency-1.0.2/highfrequency/DESCRIPTION | 14 - highfrequency-1.0.2/highfrequency/MD5 | 75 +++--- highfrequency-1.0.2/highfrequency/NEWS.md | 6 highfrequency-1.0.2/highfrequency/R/HARmodel.R | 4 highfrequency-1.0.2/highfrequency/R/HEAVYmodel.R | 2 highfrequency-1.0.2/highfrequency/R/dataHandling.R | 15 - highfrequency-1.0.2/highfrequency/R/driftBursts.R | 4 highfrequency-1.0.2/highfrequency/R/internalRealizedMeasures.R | 51 +--- highfrequency-1.0.2/highfrequency/R/internalSpotVolAndDrift.R | 24 -- highfrequency-1.0.2/highfrequency/R/liquidityMeasures.R | 2 highfrequency-1.0.2/highfrequency/R/realizedMeasures.R | 13 - highfrequency-1.0.2/highfrequency/R/spotVolAndDrift.R | 114 +++++----- highfrequency-1.0.2/highfrequency/man/AJjumpTest.Rd | 2 highfrequency-1.0.2/highfrequency/man/HARmodel.Rd | 2 highfrequency-1.0.2/highfrequency/man/HEAVYmodel.Rd | 2 highfrequency-1.0.2/highfrequency/man/ReMeDI.Rd | 2 highfrequency-1.0.2/highfrequency/man/ReMeDIAsymptoticVariance.Rd | 2 highfrequency-1.0.2/highfrequency/man/aggregatePrice.Rd | 2 highfrequency-1.0.2/highfrequency/man/businessTimeAggregation.Rd | 2 highfrequency-1.0.2/highfrequency/man/driftBursts.Rd | 2 highfrequency-1.0.2/highfrequency/man/getLiquidityMeasures.Rd | 2 highfrequency-1.0.2/highfrequency/man/getTradeDirection.Rd | 2 highfrequency-1.0.2/highfrequency/man/plot.DBH.Rd | 4 highfrequency-1.0.2/highfrequency/man/plot.HARmodel.Rd | 2 highfrequency-1.0.2/highfrequency/man/plot.HEAVYmodel.Rd | 2 highfrequency-1.0.2/highfrequency/man/predict.HARmodel.Rd | 2 highfrequency-1.0.2/highfrequency/man/print.DBH.Rd | 4 highfrequency-1.0.2/highfrequency/man/quotesCleanup.Rd | 2 highfrequency-1.0.2/highfrequency/man/rQPVar.Rd | 2 highfrequency-1.0.2/highfrequency/man/rSemiCov.Rd | 2 highfrequency-1.0.2/highfrequency/man/rTSCov.Rd | 2 highfrequency-1.0.2/highfrequency/man/rThresholdCov.Rd | 9 highfrequency-1.0.2/highfrequency/man/spotDrift.Rd | 18 - highfrequency-1.0.2/highfrequency/man/spotVol.Rd | 75 +++--- highfrequency-1.0.2/highfrequency/tests/testthat/Rplots.pdf |binary highfrequency-1.0.2/highfrequency/tests/testthat/tests_models.R | 8 highfrequency-1.0.2/highfrequency/tests/testthat/tests_spotvol_and_drift.R | 2 40 files changed, 241 insertions(+), 237 deletions(-)
Title: Circular Visualization
Description: Circular layout is an efficient way for the visualization of huge
amounts of information. Here this package provides an implementation
of circular layout generation in R as well as an enhancement of available
software. The flexibility of the package is based on the usage of low-level
graphics functions such that self-defined high-level graphics can be easily
implemented by users for specific purposes. Together with the seamless
connection between the powerful computational and visual environment in R,
it gives users more convenience and freedom to design figures for
better understanding complex patterns behind multiple dimensional data.
The package is described in Gu et al. 2014 <doi:10.1093/bioinformatics/btu393>.
Author: Zuguang Gu [aut, cre]
Maintainer: Zuguang Gu <z.gu@dkfz.de>
Diff between circlize versions 0.4.16 dated 2024-02-20 and 0.4.17 dated 2025-12-08
DESCRIPTION | 14 - LICENSE | 2 MD5 | 48 +++--- NAMESPACE | 7 NEWS | 20 ++ R/chordDiagram.R | 9 - R/circos.heatmap.R | 36 ++++ R/genomic.R | 15 + R/global.R | 1 R/link.R | 42 ++--- R/low_level.R | 271 ++++++++++++++++++++++++++++++----- R/plot.R | 9 - R/utils.R | 198 +++++++++++++++++++++++++ build/vignette.rds |binary inst/CITATION | 24 +-- inst/doc/circlize.Rmd | 10 - inst/doc/circlize.html | 221 ++++++++++++++++++++++++++-- man/chordDiagram.Rd | 183 +++++++++++++++-------- man/circos.dendrogram.Rd | 3 man/circos.heatmap.get.x.Rd |only man/circos.initializeWithIdeogram.Rd | 2 man/circos.raster.Rd | 3 man/circos.rect.Rd | 3 man/circos.stackedText.Rd |only man/circos.trackPlotRegion.Rd | 2 vignettes/circlize.Rmd | 10 - 26 files changed, 929 insertions(+), 204 deletions(-)
Title: Perform HTTP Requests and Process the Responses
Description: Tools for creating and modifying HTTP requests, then
performing them and processing the results. 'httr2' is a modern
re-imagining of 'httr' that uses a pipe-based interface and solves
more of the problems that API wrapping packages face.
Author: Hadley Wickham [aut, cre],
Posit Software, PBC [cph, fnd],
Maximilian Girlich [ctb]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between httr2 versions 1.2.1 dated 2025-07-22 and 1.2.2 dated 2025-12-08
DESCRIPTION | 14 +-- MD5 | 73 ++++++++--------- NAMESPACE | 1 NEWS.md | 10 ++ R/iterate-responses.R | 15 ++- R/oauth-flow-auth-code.R | 4 R/otel.R |only R/pooled-request.R | 14 +++ R/req-cache.R | 2 R/req-dry-run.R | 2 R/req-error.R | 7 + R/req-perform-connection.R | 36 ++++++-- R/req-perform.R | 53 +++++++++--- R/req-promise.R | 7 - R/req-throttle.R | 22 ++++- R/req-url.R | 8 - R/url.R | 13 +-- R/zzz.R | 1 README.md | 16 +-- inst/doc/httr2.Rmd | 2 inst/doc/httr2.html | 41 +++++---- man/StreamingBody.Rd | 3 man/req_auth_aws_v4.Rd | 2 man/req_cache.Rd | 2 man/req_oauth_auth_code.Rd | 2 man/resps_successes.Rd | 16 ++- tests/testthat/_snaps/req-perform-connection.md | 10 ++ tests/testthat/test-req-body.R | 2 tests/testthat/test-req-dry-run.R | 2 tests/testthat/test-req-perform-connection.R | 99 ++++++++++++++++++++++++ tests/testthat/test-req-perform-parallel.R | 63 +++++++++++++++ tests/testthat/test-req-perform.R | 92 ++++++++++++++++++++++ tests/testthat/test-req-promise.R | 65 +++++++++++++++ tests/testthat/test-req-throttle.R | 53 ++++++++++++ tests/testthat/test-resp-url.R | 2 tests/testthat/test-resp.R | 1 tests/testthat/test-url.R | 18 ++++ vignettes/httr2.Rmd | 2 38 files changed, 627 insertions(+), 148 deletions(-)
Title: ASCII Formatting for Values and Tables
Description: We provide a framework for rendering complex tables to ASCII,
and a set of formatters for transforming values or sets of values into
ASCII-ready display strings.
Author: Gabriel Becker [aut] ,
Adrian Waddell [aut],
Davide Garolini [aut] ,
Emily de la Rua [aut] ,
Abinaya Yogasekaram [ctb] ,
Joe Zhu [aut, cre] ,
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Joe Zhu <joe.zhu@roche.com>
Diff between formatters versions 0.5.11 dated 2025-04-09 and 0.5.12 dated 2025-12-08
DESCRIPTION | 28 ++++++------ MD5 | 61 +++++++++++++-------------- NAMESPACE | 5 ++ NEWS.md | 8 +++ R/format_value.R | 61 +++++++++++++++++++++++---- R/generics.R | 71 ++++++++++++++++++++++++++++++- R/matrix_form.R | 87 +++++++++++++++++++++++++-------------- R/mpf_exporters.R | 13 +++-- R/pagination.R | 76 +++++++++++++++++++++------------- R/tostring.R | 12 ++--- build/vignette.rds |binary inst/WORDLIST | 3 - inst/doc/formatters.html | 9 ++-- man/MatrixPrintForm.Rd | 7 ++- man/export_as_pdf.Rd | 13 ++++- man/export_as_rtf.Rd | 10 ++++ man/export_as_txt.Rd | 13 ++++- man/format_value.Rd | 13 ++++- man/list_formats.Rd | 7 +++ man/make_row_df.Rd | 15 ++++-- man/matrix_form.Rd | 15 ++++-- man/mpf_to_rtf.Rd | 8 +-- man/obj_round_type.Rd |only man/paginate_indices.Rd | 17 ++++--- man/propose_column_widths.Rd | 13 ++++- man/round_fmt.Rd | 26 +++++++++-- man/test_matrix_form.Rd | 12 ++++- man/tostring.Rd | 8 +-- man/vert_pag_indices.Rd | 17 ++++--- tests/testthat/test-formatters.R | 87 ++++++++++++++++++++++++++++++++++++++- tests/testthat/test-listings.R | 2 tests/testthat/test-pagination.R | 53 +++++++++++++++++++++++ 32 files changed, 582 insertions(+), 188 deletions(-)
Title: Tidy and Geospatial Kernel Smoothing
Description: Extensions of the kernel smoothing functions from the 'ks' package for compatibility with the tidyverse and geospatial ecosystems <doi:10.1007/s00180-024-01543-9>.
Author: Tarn Duong [aut, cre]
Maintainer: Tarn Duong <tarn.duong@gmail.com>
Diff between eks versions 1.1.1 dated 2025-07-08 and 1.1.2 dated 2025-12-08
CHANGELOG | 4 ++++ DESCRIPTION | 12 ++++++------ MD5 | 18 +++++++++--------- NAMESPACE | 2 +- R/prelim.R | 14 +++++++++----- R/sf-ks-prelim.R | 11 ++++++----- build/vignette.rds |binary inst/doc/tidysf_kde.html | 22 ++++++++++++---------- man/contour.Rd | 9 +++++++-- man/tidyst_as_kde.Rd | 1 + 10 files changed, 55 insertions(+), 38 deletions(-)
Title: Fast Best Subset Selection
Description: Extremely efficient toolkit for solving the best subset selection problem <https://www.jmlr.org/papers/v23/21-1060.html>. This package is its R interface. The package implements and generalizes algorithms designed in <doi:10.1073/pnas.2014241117> that exploits a novel sequencing-and-splicing technique to guarantee exact support recovery and globally optimal solution in polynomial times for linear model. It also supports best subset selection for logistic regression, Poisson regression, Cox proportional hazard model, Gamma regression, multiple-response regression, multinomial logistic regression, ordinal regression, Ising model reconstruction <doi:10.1080/01621459.2025.2571245>, (sequential) principal component analysis, and robust principal component analysis. The other valuable features such as the best subset of group selection <doi:10.1287/ijoc.2022.1241> and sure independence screening <doi:10.1111/j.1467-9868.2008.00674.x> are also provided.
Author: Jin Zhu [aut, cre] ,
Zezhi Wang [aut],
Liyuan Hu [aut],
Junhao Huang [aut],
Kangkang Jiang [aut],
Yanhang Zhang [aut],
Borui Tang [aut],
Shiyun Lin [aut],
Junxian Zhu [aut],
Canhong Wen [aut],
Heping Zhang [aut] ,
Xueqin Wang [aut] ,
spectra contribu [...truncated...]
Maintainer: Jin Zhu <zhuj1jqx@gmail.com>
Diff between abess versions 0.4.10 dated 2025-04-05 and 0.4.11 dated 2025-12-08
DESCRIPTION | 24 ++++++++++++------------ MD5 | 20 ++++++++++++-------- NAMESPACE | 2 ++ NEWS.md | 4 ++++ R/abess.R | 2 +- R/abessgraph.R |only R/generate.graph.R |only man/abess-package.Rd | 1 - man/abess.Rd | 2 +- man/generate.bmn.data.Rd |only man/slide.Rd |only src/AlgorithmGLM.h | 4 ++-- src/api.cpp | 27 +++++++++++++++++++-------- 13 files changed, 53 insertions(+), 33 deletions(-)
Title: Odds Ratio Tools for Logistic Regression
Description: Produces odds ratio analyses with comprehensive reporting tools. Generates
plots, summary tables, and diagnostic checks for logistic regression models
fitted with 'glm()' using binomial family. Provides visualisation methods,
formatted reporting tables via 'gt', and tools to assess logistic regression
model assumptions.
Author: Craig Parylo [aut, cre, cph]
Maintainer: Craig Parylo <craig.parylo2@nhs.net>
Diff between plotor versions 0.7.0 dated 2025-07-01 and 0.8.0 dated 2025-12-08
plotor-0.7.0/plotor/tests/testthat/test_data/df_correlated.Rds |only plotor-0.7.0/plotor/tests/testthat/test_data/df_diabetes.Rds |only plotor-0.7.0/plotor/tests/testthat/test_data/df_infert.Rds |only plotor-0.7.0/plotor/tests/testthat/test_data/df_separated.Rds |only plotor-0.7.0/plotor/tests/testthat/test_data/df_streptb.Rds |only plotor-0.7.0/plotor/tests/testthat/test_data/df_titanic.Rds |only plotor-0.7.0/plotor/tests/testthat/test_data/df_triple_outcome.Rds |only plotor-0.7.0/plotor/tests/testthat/test_data/lr_correlated_four.Rds |only plotor-0.7.0/plotor/tests/testthat/test_data/lr_correlated_two.Rds |only plotor-0.7.0/plotor/tests/testthat/test_data/lr_diabetes.Rds |only plotor-0.7.0/plotor/tests/testthat/test_data/lr_infert.Rds |only plotor-0.7.0/plotor/tests/testthat/test_data/lr_separated.Rds |only plotor-0.7.0/plotor/tests/testthat/test_data/lr_streptb.Rds |only plotor-0.7.0/plotor/tests/testthat/test_data/lr_titanic.Rds |only plotor-0.7.0/plotor/tests/testthat/test_data/lr_triple_outcome.Rds |only plotor-0.7.0/plotor/tests/testthat/test_data/nonlr_streptb.Rds |only plotor-0.8.0/plotor/DESCRIPTION | 29 plotor-0.8.0/plotor/LICENSE | 4 plotor-0.8.0/plotor/MD5 | 61 plotor-0.8.0/plotor/NAMESPACE | 14 plotor-0.8.0/plotor/NEWS.md | 299 plotor-0.8.0/plotor/R/gt_extras.R | 806 - plotor-0.8.0/plotor/R/plot_or.R | 4550 ++++++---- plotor-0.8.0/plotor/R/plotor-package.R | 16 plotor-0.8.0/plotor/README.md | 481 - plotor-0.8.0/plotor/build/vignette.rds |binary plotor-0.8.0/plotor/inst/doc/using_plotor.R | 334 plotor-0.8.0/plotor/inst/doc/using_plotor.Rmd | 762 - plotor-0.8.0/plotor/inst/doc/using_plotor.html | 3163 +++--- plotor-0.8.0/plotor/man/check_or.Rd | 84 plotor-0.8.0/plotor/man/figures/README-unnamed-chunk-4-1.png |binary plotor-0.8.0/plotor/man/figures/README-unnamed-chunk-4-1.svg | 2370 ++--- plotor-0.8.0/plotor/man/plot_or.Rd | 123 plotor-0.8.0/plotor/man/plotor-package.Rd | 52 plotor-0.8.0/plotor/man/table_or.Rd | 181 plotor-0.8.0/plotor/tests/testthat.R | 24 plotor-0.8.0/plotor/tests/testthat/helper_generate_data.R |only plotor-0.8.0/plotor/tests/testthat/test-plot_or.R | 536 - plotor-0.8.0/plotor/tests/testthat/test_data/make_test_data.R | 1288 +- plotor-0.8.0/plotor/vignettes/using_plotor.Rmd | 762 - 40 files changed, 8824 insertions(+), 7115 deletions(-)
Title: Population and Evolutionary Genetics Analysis System
Description: Functions for reading, writing, plotting, analysing, and manipulating allelic and haplotypic data, including from VCF files, and for the analysis of population nucleotide sequences and micro-satellites including coalescent analyses, linkage disequilibrium, population structure (Fst, Amova) and equilibrium (HWE), haplotype networks, minimum spanning tree and network, and median-joining networks.
Author: Emmanuel Paradis [aut, cre, cph] ,
Thibaut Jombart [aut, cph] ,
Zhian N. Kamvar [aut, cph] ,
Brian Knaus [aut, cph] ,
Klaus Schliep [aut, cph] ,
Alastair Potts [aut, cph] ,
David Winter [aut, cph]
Maintainer: Emmanuel Paradis <Emmanuel.Paradis@ird.fr>
Diff between pegas versions 1.3 dated 2023-12-13 and 1.4 dated 2025-12-08
DESCRIPTION | 29 ++++++----- MD5 | 48 +++++++++---------- NEWS | 38 +++++++++++++++ R/dist.asd.R | 6 +- R/haplotype.R | 111 ++++++++++++++++++++++++++++++++++++++------- R/mjn.R | 52 ++++++++++++--------- R/zzz.R | 5 +- build/partial.rdb |binary build/vignette.rds |binary inst/doc/PlotHaploNet.R | 46 +++++++++--------- inst/doc/PlotHaploNet.Rnw | 3 - inst/doc/PlotHaploNet.pdf |binary inst/doc/ReadingFiles.pdf |binary man/Fst.Rd | 2 man/alleles2loci.Rd | 2 man/amova.Rd | 3 - man/conversion.Rd | 13 ++--- man/hap.div.Rd | 4 + man/haplotype.Rd | 8 ++- man/hw.test.Rd | 4 - man/jaguar.Rd | 2 man/mst.Rd | 45 ++++++++++++------ man/read.gtx.Rd | 3 - man/utilities.Rd | 2 vignettes/PlotHaploNet.Rnw | 3 - 25 files changed, 295 insertions(+), 134 deletions(-)
Title: Tools for Bayesian Analyses
Description: Provides tools for conducting Bayesian analyses and Bayesian model averaging
(Kass and Raftery, 1995, <doi:10.1080/01621459.1995.10476572>,
Hoeting et al., 1999, <doi:10.1214/ss/1009212519>). The package contains
functions for creating a wide range of prior distribution objects, mixing posterior
samples from 'JAGS' and 'Stan' models, plotting posterior distributions, and etc...
The tools for working with prior distribution span from visualization, generating 'JAGS'
and 'bridgesampling' syntax to basic functions such as rng, quantile, and distribution functions.
Author: Frantisek Bartos [aut, cre]
Maintainer: Frantisek Bartos <f.bartos96@gmail.com>
Diff between BayesTools versions 0.2.22 dated 2025-09-14 and 0.2.23 dated 2025-12-08
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 4 ++++ R/JAGS-diagnostics.R | 7 ++++++- R/model-averaging-plots.R | 8 ++++---- build/partial.rdb |binary inst/doc/ComparisonR.html | 6 +++--- inst/doc/SpikeAndSlab.html | 4 ++-- 8 files changed, 29 insertions(+), 20 deletions(-)
Title: Propensity Score Matching of Non-Binary Treatments
Description: Propensity score matching for non-binary treatments.
Author: Jason Bryer [aut, cre]
Maintainer: Jason Bryer <jason@bryer.org>
Diff between TriMatch versions 1.0.0 dated 2025-04-03 and 1.0.1 dated 2025-12-08
DESCRIPTION | 18 +++++++++--------- MD5 | 27 +++++++++++++++------------ NAMESPACE | 5 ++++- NEWS.md | 5 +++++ R/TriMatch-package.R | 1 - R/ezANOVA.R |only R/ezANOVA_main.R |only R/plot.balance.R | 2 +- R/summary.triangle.matches.R | 2 +- build/vignette.rds |binary inst/doc/TriMatch.R | 16 +++++++--------- inst/doc/TriMatch.Rmd | 10 ++++------ inst/doc/TriMatch.pdf |binary man/ezANOVA.Rd |only man/summary.triangle.matches.Rd | 2 +- vignettes/TriMatch.Rmd | 10 ++++------ 16 files changed, 51 insertions(+), 47 deletions(-)
Title: The Plate Plot for Network Meta-Analysis Results
Description: A graphical display of results from network meta-analysis (NMA).
It is suitable for outcomes like odds ratio (OR), risk ratio (RR),
risk difference (RD) and standardized mean difference (SMD).
It also has an option to visually display and compare
the surface under the cumulative ranking (SUCRA) of different treatments.
Author: Zhenxun Wang [aut, cre],
Lifeng Lin [ctb],
Shanshan Zhao [ctb],
Haitao Chu [ctb]
Maintainer: Zhenxun Wang <wang6795@alumni.umn.edu>
Diff between nmaplateplot versions 1.0.2 dated 2024-04-07 and 1.0.3 dated 2025-12-08
DESCRIPTION | 10 MD5 | 22 NEWS.md | 6 R/nmaplateplot.R | 97 R/pe_text_conversion.R | 87 build/vignette.rds |binary inst/doc/nmaplateplot-intro.R | 118 inst/doc/nmaplateplot-intro.Rmd | 135 inst/doc/nmaplateplot-intro.html |20037 +++++++++++++++++++++++++++++++++++++-- man/nmaplateplot-package.Rd | 2 man/plateplot.Rd | 45 vignettes/nmaplateplot-intro.Rmd | 135 12 files changed, 19573 insertions(+), 1121 deletions(-)
Title: Generalized Gamma Probability Distribution
Description: Density, distribution function, quantile function and random generation for the Generalized Gamma proposed in Stacy, E. W. (1962) <doi:10.1214/aoms/1177704481>.
Author: Matheus H. J. Saldanha [aut, cre],
Adriano K. Suzuki [aut]
Maintainer: Matheus H. J. Saldanha <mhjsaldanha@gmail.com>
Diff between ggamma versions 1.0.1 dated 2019-12-15 and 1.0.2 dated 2025-12-08
ggamma-1.0.1/ggamma/man/ggamma.Rd |only ggamma-1.0.2/ggamma/DESCRIPTION | 11 +++++------ ggamma-1.0.2/ggamma/MD5 | 7 ++++--- ggamma-1.0.2/ggamma/NEWS.md |only ggamma-1.0.2/ggamma/R/ggamma-package.R | 5 +---- ggamma-1.0.2/ggamma/man/ggamma-package.Rd |only 6 files changed, 10 insertions(+), 13 deletions(-)
Title: Construct Reproducible Analytic Data Sets as R Packages
Description: A framework to help construct R data packages in a
reproducible manner. Potentially time consuming processing of raw data
sets into analysis ready data sets is done in a reproducible manner
and decoupled from the usual 'R CMD build' process so that data sets
can be processed into R objects in the data package and the data
package can then be shared, built, and installed by others without the
need to repeat computationally costly data processing. The package
maintains data provenance by turning the data processing scripts into
package vignettes, as well as enforcing documentation and version
checking of included data objects. Data packages can be version
controlled on 'GitHub', and used to share data for manuscripts,
collaboration and reproducible research.
Author: Greg Finak [aut, cph] ,
Paul Obrecht [ctb],
Ellis Hughes [ctb] ,
Jimmy Fulp [ctb],
Marie Vendettuoli [ctb] ,
Dave Slager [ctb, cre] ,
Jason Taylor [ctb],
Kara Woo [rev] ,
William Landau [rev]
Maintainer: Dave Slager <dslager@fredhutch.org>
Diff between DataPackageR versions 0.16.1 dated 2024-09-17 and 0.16.2 dated 2025-12-08
DataPackageR-0.16.1/DataPackageR/R/logger.R |only DataPackageR-0.16.1/DataPackageR/tests/testthat/test-logger.R |only DataPackageR-0.16.2/DataPackageR/DESCRIPTION | 19 +- DataPackageR-0.16.2/DataPackageR/MD5 | 48 ++--- DataPackageR-0.16.2/DataPackageR/NAMESPACE | 14 - DataPackageR-0.16.2/DataPackageR/NEWS.md | 17 + DataPackageR-0.16.2/DataPackageR/R/build.R | 44 +---- DataPackageR-0.16.2/DataPackageR/R/digests.R | 21 -- DataPackageR-0.16.2/DataPackageR/R/load_save.R | 1 DataPackageR-0.16.2/DataPackageR/R/processData.R | 87 +--------- DataPackageR-0.16.2/DataPackageR/R/prompt.R | 1 DataPackageR-0.16.2/DataPackageR/R/skeleton.R | 15 - DataPackageR-0.16.2/DataPackageR/R/use.R | 6 DataPackageR-0.16.2/DataPackageR/R/yamlR.R | 17 - DataPackageR-0.16.2/DataPackageR/README.md | 50 ++--- DataPackageR-0.16.2/DataPackageR/build/vignette.rds |binary DataPackageR-0.16.2/DataPackageR/inst/WORDLIST | 2 DataPackageR-0.16.2/DataPackageR/inst/doc/Using_DataPackageR.Rmd | 6 DataPackageR-0.16.2/DataPackageR/inst/doc/Using_DataPackageR.html | 60 +++--- DataPackageR-0.16.2/DataPackageR/inst/doc/YAML_Configuration_Details.R | 12 - DataPackageR-0.16.2/DataPackageR/inst/doc/YAML_Configuration_Details.html | 21 +- DataPackageR-0.16.2/DataPackageR/man/package_build.Rd | 3 DataPackageR-0.16.2/DataPackageR/tests/testthat/test-data-name-change.R | 5 DataPackageR-0.16.2/DataPackageR/tests/testthat/test-edge-cases.R | 2 DataPackageR-0.16.2/DataPackageR/tests/testthat/test-project-path.R | 2 DataPackageR-0.16.2/DataPackageR/vignettes/Using_DataPackageR.Rmd | 6 26 files changed, 166 insertions(+), 293 deletions(-)
Title: Solutions for Common Problems in Base R
Description: Contains functions for solving commonly encountered problems while
programming in R. This package is intended to provide a lightweight
supplement to Base R, and will be useful for almost any R user.
Author: David Bosak [aut, cre],
Duong Tran [ctb]
Maintainer: David Bosak <dbosak01@gmail.com>
Diff between common versions 1.1.3 dated 2024-04-05 and 1.1.4 dated 2025-12-08
DESCRIPTION | 8 MD5 | 35 +- NAMESPACE | 5 NEWS.md | 6 R/common.R | 2 R/operators.R | 541 +++++++++++++++++++++++++++++++++++++++- README.md | 23 + build/vignette.rds |binary inst/doc/common.R | 2 inst/doc/common.Rmd | 33 +- inst/doc/common.html | 47 ++- man/common.Rd | 2 man/grapes-eq-grapes.Rd | 11 man/grapes-ge-grapes.Rd |only man/grapes-gt-grapes.Rd |only man/grapes-le-grapes.Rd |only man/grapes-lt-grapes.Rd |only man/grapes-ne-grapes.Rd |only man/grapes-p-grapes.Rd | 10 tests/testthat/test-operators.R | 224 ++++++++++++++++ vignettes/common.Rmd | 33 +- 21 files changed, 915 insertions(+), 67 deletions(-)
Title: Aster Models
Description: Aster models (Geyer, Wagenius, and Shaw, 2007,
<doi:10.1093/biomet/asm030>; Shaw, Geyer, Wagenius, Hangelbroek, and
Etterson, 2008, <doi:10.1086/588063>; Geyer, Ridley, Latta, Etterson,
and Shaw, 2013, <doi:10.1214/13-AOAS653>) are exponential family
regression models for life
history analysis. They are like generalized linear models except that
elements of the response vector can have different families (e. g.,
some Bernoulli, some Poisson, some zero-truncated Poisson, some normal)
and can be dependent, the dependence indicated by a graphical structure.
Discrete time survival analysis, life table analysis,
zero-inflated Poisson regression, and
generalized linear models that are exponential family (e. g., logistic
regression and Poisson regression with log link) are special cases.
Main use is for data in which there is survival over discrete time periods
and there is additional data about what happens conditional on survival
(e. g., number of offspring). Uses the ex [...truncated...]
Author: Charles J. Geyer [aut, cre]
Maintainer: Charles J. Geyer <geyer@umn.edu>
Diff between aster versions 1.3-6 dated 2025-10-20 and 1.3-7 dated 2025-12-08
CHANGES | 2 ++ DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- R/reaster.R | 2 +- build/partial.rdb |binary build/vignette.rds |binary inst/doc/delta.pdf |binary inst/doc/linkingTo.pdf |binary inst/doc/re.pdf |binary inst/doc/trunc.pdf |binary inst/doc/tutor.pdf |binary 11 files changed, 17 insertions(+), 15 deletions(-)
Title: R Commander Plug-in for the EZR (Easy R) Package
Description: EZR (Easy R) adds a variety of statistical functions, including survival analyses, ROC analyses, metaanalyses, sample size calculation, and so on, to the R commander. EZR enables point-and-click easy access to statistical functions, especially for medical statistics. EZR is platform-independent and runs on Windows, Mac OS X, and UNIX. Its complete manual is available only in Japanese (Chugai Igakusha, ISBN: 978-4-498-10918-6, Nankodo, ISBN: 978-4-524-21861-5, Ohmsha, ISBN: 978-4-274-22632-8), but an report that introduced the investigation of EZR was published in Bone Marrow Transplantation (Nature Publishing Group) as an Open article. This report can be used as a simple manual. It can be freely downloaded from the journal website as shown below. This report has been cited in more than 14,000 scientific articles.
Author: Yoshinobu Kanda [aut, cre]
Maintainer: Yoshinobu Kanda <ycanda-tky@umin.ac.jp>
Diff between RcmdrPlugin.EZR versions 1.68 dated 2024-06-25 and 1.70 dated 2025-12-07
RcmdrPlugin.EZR-1.68/RcmdrPlugin.EZR/inst/etc/menus.txt.262 |only RcmdrPlugin.EZR-1.68/RcmdrPlugin.EZR/inst/etc/menus_old.txt |only RcmdrPlugin.EZR-1.70/RcmdrPlugin.EZR/DESCRIPTION | 15 RcmdrPlugin.EZR-1.70/RcmdrPlugin.EZR/MD5 | 25 RcmdrPlugin.EZR-1.70/RcmdrPlugin.EZR/NEWS | 6 RcmdrPlugin.EZR-1.70/RcmdrPlugin.EZR/R/EZR.R | 171 ++++- RcmdrPlugin.EZR-1.70/RcmdrPlugin.EZR/inst/CHANGES | 6 RcmdrPlugin.EZR-1.70/RcmdrPlugin.EZR/inst/doc/EZR.htm | 315 ++++------ RcmdrPlugin.EZR-1.70/RcmdrPlugin.EZR/inst/doc/EZR.pdf |binary RcmdrPlugin.EZR-1.70/RcmdrPlugin.EZR/inst/etc/menus.txt | 1 RcmdrPlugin.EZR-1.70/RcmdrPlugin.EZR/inst/po/ja/LC_MESSAGES/R-RcmdrPlugin.EZR.mo |binary RcmdrPlugin.EZR-1.70/RcmdrPlugin.EZR/man/EZR.Rd | 9 RcmdrPlugin.EZR-1.70/RcmdrPlugin.EZR/man/EZR.dialogs.Rd | 1 RcmdrPlugin.EZR-1.70/RcmdrPlugin.EZR/po/R-RcmdrPlugin.EZR.mo |only RcmdrPlugin.EZR-1.70/RcmdrPlugin.EZR/po/R-RcmdrPlugin.EZR.po | 11 15 files changed, 358 insertions(+), 202 deletions(-)
More information about RcmdrPlugin.EZR at CRAN
Permanent link
Title: Retrieve and Analyze Clinical Trials Data from Public Registers
Description: A system for querying, retrieving and analyzing
protocol- and results-related information on clinical trials from
four public registers, the 'European Union Clinical Trials Register'
('EUCTR', <https://www.clinicaltrialsregister.eu/>),
'ClinicalTrials.gov' (<https://clinicaltrials.gov/> and also
translating queries the retired classic interface), the
'ISRCTN' (<http://www.isrctn.com/>) and the
'European Union Clinical Trials Information System'
('CTIS', <https://euclinicaltrials.eu/>).
Trial information is downloaded, converted and stored in a database
('PostgreSQL', 'SQLite', 'DuckDB' or 'MongoDB'; via package 'nodbi').
Protocols, statistical analysis plans, informed consent sheets and other
documents in registers associated with trials can also be downloaded.
Other functions implement trial concepts canonically across registers,
identify deduplicated records, easily find and extract variables
(fields) of interest even from complex nested data as used by the
re [...truncated...]
Author: Ralf Herold [aut, cre] ,
Marek Kubica [cph] ,
Ivan Bozhanov [cph]
Maintainer: Ralf Herold <ralf.herold@mailbox.org>
Diff between ctrdata versions 1.25.0 dated 2025-08-26 and 1.25.1 dated 2025-12-07
DESCRIPTION | 16 ++- MD5 | 55 ++++++------- NAMESPACE | 4 NEWS.md | 12 ++ R/ctrLoadQueryIntoDbCtgov2.R | 26 ++++-- R/ctrLoadQueryIntoDbCtis.R | 40 ++++++++- R/ctrLoadQueryIntoDbIsrctn.R | 8 - R/ctrdata-registers.R | 38 ++++----- R/ctrdata-trial-concepts.R | 2 R/dbFindIdsUniqueTrials.R | 3 R/dfTrials2Long.R | 4 R/f_isUniqueTrial.R | 1 R/util_functions.R | 4 README.md | 76 ++++++++++-------- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION |only inst/WORDLIST | 4 inst/doc/ctrdata_install.R | 3 inst/doc/ctrdata_install.Rmd | 16 +++ inst/doc/ctrdata_install.html | 32 +++++-- inst/js/euctr2ndjson.js | 5 - inst/tinytest/ctrdata_ctgov2.R | 10 ++ inst/tinytest/test_ctrdata_function_activesubstance.R | 2 man/ctrdata-package.Rd | 2 man/ctrdata-registers.Rd | 35 ++++---- man/ctrdata-trial-concepts.Rd | 2 man/f.isUniqueTrial.Rd | 1 vignettes/ctrdata_install.Rmd | 16 +++ 29 files changed, 270 insertions(+), 147 deletions(-)
Title: Bayesian Penalized Quantile Regression
Description: Bayesian regularized quantile regression utilizing two major classes of shrinkage priors
(the spike-and-slab priors and the horseshoe family of priors) leads to efficient Bayesian
shrinkage estimation, variable selection and valid statistical inference. In this package,
we have implemented robust Bayesian variable selection with spike-and-slab priors under
high-dimensional linear regression models (Fan et al. (2024) <doi:10.3390/e26090794> and
Ren et al. (2023) <doi:10.1111/biom.13670>), and regularized quantile varying
coefficient models (Zhou et al.(2023) <doi:10.1016/j.csda.2023.107808>). In particular,
valid robust Bayesian inferences under both models in the presence of heavy-tailed errors
can be validated on finite samples. Additional models with spike-and-slab priors include
robust Bayesian group LASSO and robust binary Bayesian LASSO (Fan and Wu (2025)
<doi:10.1002/sta4.70078>). Besides, robust sparse Bayesian regression with the horseshoe
family of (hor [...truncated...]
Author: Kun Fan [aut],
Cen Wu [aut, cre],
Jie Ren [aut],
Xiaoxi Li [aut],
Fei Zhou [aut]
Maintainer: Cen Wu <wucen@ksu.edu>
Diff between pqrBayes versions 1.1.4 dated 2025-07-25 and 1.2.0 dated 2025-12-07
pqrBayes-1.1.4/pqrBayes/R/NonRobust.R |only pqrBayes-1.2.0/pqrBayes/DESCRIPTION | 27 - pqrBayes-1.2.0/pqrBayes/MD5 | 77 +-- pqrBayes-1.2.0/pqrBayes/NEWS.md | 8 pqrBayes-1.2.0/pqrBayes/R/NonRobust_vc.R | 11 pqrBayes-1.2.0/pqrBayes/R/RcppExports.R | 24 + pqrBayes-1.2.0/pqrBayes/R/Robust_vc.R | 11 pqrBayes-1.2.0/pqrBayes/R/coverage.R | 10 pqrBayes-1.2.0/pqrBayes/R/estimation.R | 10 pqrBayes-1.2.0/pqrBayes/R/nonrobust_bin.R | 10 pqrBayes-1.2.0/pqrBayes/R/nonrobust_g.R | 11 pqrBayes-1.2.0/pqrBayes/R/nonrobust_lin.R | 29 + pqrBayes-1.2.0/pqrBayes/R/pqrBayes-package.R | 21 - pqrBayes-1.2.0/pqrBayes/R/pqrBayes.R | 90 +--- pqrBayes-1.2.0/pqrBayes/R/pqrBayes_bin.R | 6 pqrBayes-1.2.0/pqrBayes/R/pqrBayes_g.R | 6 pqrBayes-1.2.0/pqrBayes/R/pqrBayes_lin.R | 6 pqrBayes-1.2.0/pqrBayes/R/pqrBayes_vc.R | 10 pqrBayes-1.2.0/pqrBayes/R/predict.pqrBayes.R | 14 pqrBayes-1.2.0/pqrBayes/R/robust_bin.R | 11 pqrBayes-1.2.0/pqrBayes/R/robust_g.R | 11 pqrBayes-1.2.0/pqrBayes/R/robust_lin.R | 30 + pqrBayes-1.2.0/pqrBayes/R/select.pqrBayes.R | 40 - pqrBayes-1.2.0/pqrBayes/R/select_lin.R | 10 pqrBayes-1.2.0/pqrBayes/R/select_vc.R | 12 pqrBayes-1.2.0/pqrBayes/README.md | 297 +++++++++++--- pqrBayes-1.2.0/pqrBayes/man/coverage.Rd | 74 +-- pqrBayes-1.2.0/pqrBayes/man/data.Rd | 154 +++---- pqrBayes-1.2.0/pqrBayes/man/estimation.pqrBayes.Rd | 80 +-- pqrBayes-1.2.0/pqrBayes/man/pqrBayes-package.Rd | 133 +++--- pqrBayes-1.2.0/pqrBayes/man/pqrBayes.Rd | 394 +++++++++---------- pqrBayes-1.2.0/pqrBayes/man/predict_pqrBayes.Rd | 100 ++-- pqrBayes-1.2.0/pqrBayes/man/print.pqrBayes.Rd | 48 +- pqrBayes-1.2.0/pqrBayes/man/print.pqrBayes.pred.Rd | 48 +- pqrBayes-1.2.0/pqrBayes/man/print.pqrBayes.select.Rd | 48 +- pqrBayes-1.2.0/pqrBayes/man/select.pqrBayes.Rd | 148 +++---- pqrBayes-1.2.0/pqrBayes/src/RcppExports.cpp | 175 ++++++++ pqrBayes-1.2.0/pqrBayes/src/Rhorseshoe+.cpp |only pqrBayes-1.2.0/pqrBayes/src/Rhorseshoe.cpp |only pqrBayes-1.2.0/pqrBayes/src/Rhorseshoe_reg.cpp |only pqrBayes-1.2.0/pqrBayes/src/horseshoe+.cpp |only pqrBayes-1.2.0/pqrBayes/src/horseshoe.cpp |only pqrBayes-1.2.0/pqrBayes/src/horseshoe_reg.cpp |only 43 files changed, 1320 insertions(+), 874 deletions(-)
Title: Simultaneous Confidence Intervals for Ranks
Description: Algorithms to construct simultaneous confidence intervals for
the ranks of means mu_1,...,mu_n based on an independent Gaussian sample
using multiple testing techniques.
Author: Diaa Al Mohamad [aut, cre],
Erik W. van Zwet [aut],
Jelle J. Goeman [aut]
Maintainer: Diaa Al Mohamad <diaa.almohamad@gmail.com>
Diff between ICRanks versions 3.1 dated 2019-06-21 and 3.2 dated 2025-12-07
DESCRIPTION | 34 +++++++++++++++++++++++++--------- MD5 | 6 +++--- R/ic.ranks.R | 16 ++++++++-------- man/ic.ranks.Rd | 36 ++++++++++++++++++++---------------- 4 files changed, 56 insertions(+), 36 deletions(-)
Title: Kumaraswamy Complementary Weibull Geometric (Kw-CWG) Probability
Distribution
Description: Density, distribution function, quantile function
and random generation for the Kumaraswamy Complementary Weibull
Geometric (Kw-CWG) lifetime probability distribution proposed
in Afify, A.Z. et al (2017) <doi:10.1214/16-BJPS322>.
Author: Matheus H. J. Saldanha [aut, cre],
Adriano K. Suzuki [aut]
Maintainer: Matheus H. J. Saldanha <mhjsaldanha@gmail.com>
Diff between elfDistr versions 1.0.0 dated 2019-10-07 and 1.0.1 dated 2025-12-07
elfDistr-1.0.0/elfDistr/man/elfDistr.Rd |only elfDistr-1.0.1/elfDistr/DESCRIPTION | 10 -- elfDistr-1.0.1/elfDistr/MD5 | 17 ++-- elfDistr-1.0.1/elfDistr/NEWS.md |only elfDistr-1.0.1/elfDistr/R/elfDistr-package.R | 5 - elfDistr-1.0.1/elfDistr/man/Kw-CWG.Rd | 1 elfDistr-1.0.1/elfDistr/man/elfDistr-package.Rd |only elfDistr-1.0.1/elfDistr/src/Makevars | 5 - elfDistr-1.0.1/elfDistr/src/RcppExports.cpp | 5 + elfDistr-1.0.1/elfDistr/src/kwcwg-distribution.cpp | 82 ++++++++++++-------- elfDistr-1.0.1/elfDistr/tests/testthat/test_kwcwg.R | 53 +++++------- 11 files changed, 97 insertions(+), 81 deletions(-)
Title: Export Data from 'R' to 'DataGraph'
Description: Functions to pipe data from 'R' to 'DataGraph', a graphing and analysis application for mac OS. Create a live connection using either '.dtable' or '.dtbin' files that can be read by 'DataGraph'. Can save a data frame, collection of data frames and sequences of data frames and individual vectors. For more information see <https://community.visualdatatools.com/datagraph/knowledge-base/r-package/>.
Author: David Adalsteinsson [aut, cre]
Maintainer: David Adalsteinsson <david@visualdatatools.com>
Diff between DataGraph versions 1.2.14 dated 2023-03-02 and 1.2.15 dated 2025-12-07
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- src/Driver.cpp | 5 +++-- 3 files changed, 9 insertions(+), 8 deletions(-)
Title: Multivariate Conditional Volatility Modelling and Forecasting
Description: Methods and tools for estimating, simulating and forecasting of so-called BEKK-models (named after Baba, Engle, Kraft and Kroner) based on the fast Berndt–Hall–Hall–Hausman (BHHH) algorithm described in Hafner and Herwartz (2008) <doi:10.1007/s00184-007-0130-y>. For an overview, we refer the reader to Fülle et al. (2024) <doi:10.18637/jss.v111.i04>.
Author: Markus J. Fuelle [aut, cre],
Alexander Lange [aut],
Christian M. Hafner [aut],
Helmut Herwartz [aut]
Maintainer: Markus J. Fuelle <markus.fuelle@gmail.com>
Diff between BEKKs versions 1.4.5 dated 2024-11-25 and 1.4.6 dated 2025-12-07
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- NAMESPACE | 4 +++- R/BEKKs.R | 2 -- R/backtest.R | 9 ++++----- R/bekk_functions.R | 4 ++-- R/bekk_mc_eval.R | 3 ++- R/summary.backtest.R | 20 ++++++++++---------- build/stage23.rdb |binary man/BEKKs.Rd | 3 --- 10 files changed, 35 insertions(+), 38 deletions(-)
Title: Multiple Imputation Through 'XGBoost'
Description: Multiple imputation using 'XGBoost', subsampling, and predictive mean
matching as described in Deng and Lumley (2023)
<doi:10.1080/10618600.2023.2252501>. The package supports various types of
variables, offers flexible settings, and enables saving an imputation model to impute
new data. Data processing and memory usage have been optimised to speed up
the imputation process.
Author: Yongshi Deng [aut, cre] ,
Thomas Lumley [ths]
Maintainer: Yongshi Deng <agnes.yongshideng@gmail.com>
Diff between mixgb versions 1.5.3 dated 2025-04-06 and 2.0.3 dated 2025-12-07
mixgb-1.5.3/mixgb/R/mixgb_boot.R |only mixgb-1.5.3/mixgb/R/mixgb_boot_xgb_save.R |only mixgb-1.5.3/mixgb/R/mixgb_bootsave.R |only mixgb-2.0.3/mixgb/DESCRIPTION | 17 - mixgb-2.0.3/mixgb/MD5 | 44 +-- mixgb-2.0.3/mixgb/NEWS.md | 37 +++ mixgb-2.0.3/mixgb/R/impute_each.R |only mixgb-2.0.3/mixgb/R/mixgb.R | 2 mixgb-2.0.3/mixgb/R/mixgb_cv.R | 30 +- mixgb-2.0.3/mixgb/R/mixgb_load_use.R | 2 mixgb-2.0.3/mixgb/R/mixgb_null.R | 278 ++--------------------- mixgb-2.0.3/mixgb/R/mixgb_save.R | 122 ++++++---- mixgb-2.0.3/mixgb/R/mixgb_use.R | 2 mixgb-2.0.3/mixgb/R/mixgb_xgb_save.R | 119 +++++---- mixgb-2.0.3/mixgb/R/save_yhatobs.R | 121 ++++++---- mixgb-2.0.3/mixgb/build/partial.rdb |binary mixgb-2.0.3/mixgb/build/vignette.rds |binary mixgb-2.0.3/mixgb/inst/doc/Imputing-newdata.R | 24 - mixgb-2.0.3/mixgb/inst/doc/Imputing-newdata.html | 9 mixgb-2.0.3/mixgb/inst/doc/Using-mixgb.R | 38 +-- mixgb-2.0.3/mixgb/inst/doc/Using-mixgb.Rmd | 5 mixgb-2.0.3/mixgb/inst/doc/Using-mixgb.html | 91 ++++--- mixgb-2.0.3/mixgb/man/default_params.Rd | 2 mixgb-2.0.3/mixgb/src/Makevars | 2 mixgb-2.0.3/mixgb/vignettes/Using-mixgb.Rmd | 5 25 files changed, 435 insertions(+), 515 deletions(-)
Title: Seamless R and C++ Integration
Description: The 'Rcpp' package provides R functions as well as C++ classes which
offer a seamless integration of R and C++. Many R data types and objects can be
mapped back and forth to C++ equivalents which facilitates both writing of new
code as well as easier integration of third-party libraries. Documentation
about 'Rcpp' is provided by several vignettes included in this package, via the
'Rcpp Gallery' site at <https://gallery.rcpp.org>, the paper by Eddelbuettel and
Francois (2011, <doi:10.18637/jss.v040.i08>), the book by Eddelbuettel (2013,
<doi:10.1007/978-1-4614-6868-4>) and the paper by Eddelbuettel and Balamuta (2018,
<doi:10.1080/00031305.2017.1375990>); see 'citation("Rcpp")' for details.
Author: Dirk Eddelbuettel [aut, cre] ,
Romain Francois [aut] ,
JJ Allaire [aut] ,
Kevin Ushey [aut] ,
Qiang Kou [aut] ,
Nathan Russell [aut],
Inaki Ucar [aut] ,
Doug Bates [aut] ,
John Chambers [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between Rcpp versions 1.1.0 dated 2025-07-02 and 1.1.0.8 dated 2025-12-07
Rcpp-1.1.0.8/Rcpp/ChangeLog | 116 +++++++++++++++ Rcpp-1.1.0.8/Rcpp/DESCRIPTION | 9 - Rcpp-1.1.0.8/Rcpp/MD5 | 123 +++++++--------- Rcpp-1.1.0.8/Rcpp/NAMESPACE | 4 Rcpp-1.1.0.8/Rcpp/R/Attributes.R | 70 ++++++++- Rcpp-1.1.0.8/Rcpp/R/RcppLdpath.R | 6 Rcpp-1.1.0.8/Rcpp/R/asis.R |only Rcpp-1.1.0.8/Rcpp/R/zzz.R | 9 - Rcpp-1.1.0.8/Rcpp/build/partial.rdb |binary Rcpp-1.1.0.8/Rcpp/build/vignette.rds |binary Rcpp-1.1.0.8/Rcpp/inst/NEWS.Rd | 38 ++++ Rcpp-1.1.0.8/Rcpp/inst/bib/Rcpp.bib | 15 + Rcpp-1.1.0.8/Rcpp/inst/doc/Rcpp-FAQ.pdf |binary Rcpp-1.1.0.8/Rcpp/inst/doc/Rcpp-FAQ.pdf.asis |only Rcpp-1.1.0.8/Rcpp/inst/doc/Rcpp-attributes.pdf |binary Rcpp-1.1.0.8/Rcpp/inst/doc/Rcpp-attributes.pdf.asis |only Rcpp-1.1.0.8/Rcpp/inst/doc/Rcpp-extending.pdf |binary Rcpp-1.1.0.8/Rcpp/inst/doc/Rcpp-extending.pdf.asis |only Rcpp-1.1.0.8/Rcpp/inst/doc/Rcpp-introduction.pdf |binary Rcpp-1.1.0.8/Rcpp/inst/doc/Rcpp-introduction.pdf.asis |only Rcpp-1.1.0.8/Rcpp/inst/doc/Rcpp-jss-2011.pdf |binary Rcpp-1.1.0.8/Rcpp/inst/doc/Rcpp-jss-2011.pdf.asis |only Rcpp-1.1.0.8/Rcpp/inst/doc/Rcpp-libraries.pdf |binary Rcpp-1.1.0.8/Rcpp/inst/doc/Rcpp-libraries.pdf.asis |only Rcpp-1.1.0.8/Rcpp/inst/doc/Rcpp-modules.pdf |binary Rcpp-1.1.0.8/Rcpp/inst/doc/Rcpp-modules.pdf.asis |only Rcpp-1.1.0.8/Rcpp/inst/doc/Rcpp-package.pdf |binary Rcpp-1.1.0.8/Rcpp/inst/doc/Rcpp-package.pdf.asis |only Rcpp-1.1.0.8/Rcpp/inst/doc/Rcpp-quickref.pdf |binary Rcpp-1.1.0.8/Rcpp/inst/doc/Rcpp-quickref.pdf.asis |only Rcpp-1.1.0.8/Rcpp/inst/doc/Rcpp-sugar.pdf |binary Rcpp-1.1.0.8/Rcpp/inst/doc/Rcpp-sugar.pdf.asis |only Rcpp-1.1.0.8/Rcpp/inst/include/Rcpp/config.h | 4 Rcpp-1.1.0.8/Rcpp/inst/include/Rcpp/exceptions_impl.h | 29 +-- Rcpp-1.1.0.8/Rcpp/inst/include/Rcpp/hash/IndexHash.h | 22 +- Rcpp-1.1.0.8/Rcpp/inst/include/Rcpp/hash/SelfHash.h | 28 ++- Rcpp-1.1.0.8/Rcpp/inst/include/Rcpp/internal/wrap.h | 2 Rcpp-1.1.0.8/Rcpp/inst/include/Rcpp/r/check_r_headers.h |only Rcpp-1.1.0.8/Rcpp/inst/include/Rcpp/r/headers.h | 2 Rcpp-1.1.0.8/Rcpp/inst/include/RcppCommon.h | 5 Rcpp-1.1.0.8/Rcpp/inst/skeleton/zzz.R | 13 - Rcpp-1.1.0.8/Rcpp/inst/tinytest/testRcppModule/R/zzz.R | 9 - Rcpp-1.1.0.8/Rcpp/inst/tinytest/test_sugar.R | 5 Rcpp-1.1.0.8/Rcpp/man/Rcpp-deprecated.Rd | 3 Rcpp-1.1.0.8/Rcpp/man/asisWeave.Rd |only Rcpp-1.1.0.8/Rcpp/man/loadModule.Rd | 3 Rcpp-1.1.0.8/Rcpp/src/api.cpp | 1 Rcpp-1.1.0.8/Rcpp/vignettes/Rcpp-FAQ.pdf.asis |only Rcpp-1.1.0.8/Rcpp/vignettes/Rcpp-attributes.pdf.asis |only Rcpp-1.1.0.8/Rcpp/vignettes/Rcpp-extending.pdf.asis |only Rcpp-1.1.0.8/Rcpp/vignettes/Rcpp-introduction.pdf.asis |only Rcpp-1.1.0.8/Rcpp/vignettes/Rcpp-jss-2011.pdf.asis |only Rcpp-1.1.0.8/Rcpp/vignettes/Rcpp-libraries.pdf.asis |only Rcpp-1.1.0.8/Rcpp/vignettes/Rcpp-modules.pdf.asis |only Rcpp-1.1.0.8/Rcpp/vignettes/Rcpp-package.pdf.asis |only Rcpp-1.1.0.8/Rcpp/vignettes/Rcpp-quickref.pdf.asis |only Rcpp-1.1.0.8/Rcpp/vignettes/Rcpp-sugar.pdf.asis |only Rcpp-1.1.0/Rcpp/R/compilerCheck.R |only Rcpp-1.1.0/Rcpp/R/loadRcppModules.R |only Rcpp-1.1.0/Rcpp/inst/doc/Rcpp-FAQ.Rnw |only Rcpp-1.1.0/Rcpp/inst/doc/Rcpp-attributes.Rnw |only Rcpp-1.1.0/Rcpp/inst/doc/Rcpp-extending.Rnw |only Rcpp-1.1.0/Rcpp/inst/doc/Rcpp-introduction.Rnw |only Rcpp-1.1.0/Rcpp/inst/doc/Rcpp-jss-2011.Rnw |only Rcpp-1.1.0/Rcpp/inst/doc/Rcpp-libraries.Rnw |only Rcpp-1.1.0/Rcpp/inst/doc/Rcpp-modules.Rnw |only Rcpp-1.1.0/Rcpp/inst/doc/Rcpp-package.Rnw |only Rcpp-1.1.0/Rcpp/inst/doc/Rcpp-quickref.Rnw |only Rcpp-1.1.0/Rcpp/inst/doc/Rcpp-sugar.Rnw |only Rcpp-1.1.0/Rcpp/man/compilerCheck.Rd |only Rcpp-1.1.0/Rcpp/man/loadRcppModules-deprecated.Rd |only Rcpp-1.1.0/Rcpp/vignettes/Rcpp-FAQ.Rnw |only Rcpp-1.1.0/Rcpp/vignettes/Rcpp-attributes.Rnw |only Rcpp-1.1.0/Rcpp/vignettes/Rcpp-extending.Rnw |only Rcpp-1.1.0/Rcpp/vignettes/Rcpp-introduction.Rnw |only Rcpp-1.1.0/Rcpp/vignettes/Rcpp-jss-2011.Rnw |only Rcpp-1.1.0/Rcpp/vignettes/Rcpp-libraries.Rnw |only Rcpp-1.1.0/Rcpp/vignettes/Rcpp-modules.Rnw |only Rcpp-1.1.0/Rcpp/vignettes/Rcpp-package.Rnw |only Rcpp-1.1.0/Rcpp/vignettes/Rcpp-quickref.Rnw |only Rcpp-1.1.0/Rcpp/vignettes/Rcpp-sugar.Rnw |only Rcpp-1.1.0/Rcpp/vignettes/pdf |only 82 files changed, 364 insertions(+), 152 deletions(-)
Title: 'NoSQL' Database Connector
Description: Simplified JSON document database access and manipulation,
providing a common API across supported 'NoSQL' databases
'Elasticsearch', 'CouchDB', 'MongoDB' as well as
'SQLite/JSON1', 'PostgreSQL', and 'DuckDB'.
Author: Ralf Herold [aut, cre] ,
Scott Chamberlain [aut] ,
Rich FitzJohn [aut],
Jeroen Ooms [aut],
Ivan Tarbakou [cph]
Maintainer: Ralf Herold <ralf.herold@mailbox.org>
Diff between nodbi versions 0.13.1 dated 2025-06-26 and 0.14.0 dated 2025-12-07
DESCRIPTION | 11 +++-- MD5 | 28 +++++++------- NEWS.md | 8 ++++ R/query.R | 85 +++++++++++++++---------------------------- R/src_couchdb.R | 2 - R/src_duckdb.R | 2 - R/src_elastic.R | 2 - R/src_mongo.R | 2 - R/src_postgres.R | 3 + R/src_sqlite.R | 4 +- R/update.R | 6 ++- R/zzz.R | 5 +- inst/doc/nodbi-overview.html | 2 - tests/testthat/core-nodbi.R | 27 ++++++++++--- tests/testthat/helper.R | 10 +++++ 15 files changed, 108 insertions(+), 89 deletions(-)
Title: Convert and Impute Dates to ISO Standard ("International
Organization for Standardization")
Description: Provides functions to convert and impute date values to the ISO 8601
standard format. The package automatically recognizes date patterns within a
data frame and transforms them into consistent ISO-formatted dates. It also
supports imputing missing month or day components in partial date strings
using user-defined rules. Only one date format can be applied within a single
data frame column.
Author: Lukasz Andrzejewski [aut, cre]
Maintainer: Lukasz Andrzejewski <lukasz.coding@gmail.com>
Diff between datetoiso versions 1.1.1 dated 2025-11-18 and 1.2.0 dated 2025-12-07
DESCRIPTION | 8 +- MD5 | 20 +++-- NAMESPACE | 4 - NEWS.md | 110 +++++++++++++++------------ R/impute_date.R | 20 +---- R/reconcile.R |only man/compare_rows_with_same_index.Rd |only man/get_same_class.Rd |only man/impute_date.Rd | 144 ++++++++++++++++++------------------ man/impute_date_dmy.Rd | 134 ++++++++++++++++----------------- man/impute_date_ymd.Rd | 134 ++++++++++++++++----------------- man/reconcile.Rd |only man/reconcile_without_index.Rd |only tests/testthat/test-reconcile.R |only 14 files changed, 287 insertions(+), 287 deletions(-)
Title: Analyzing Censored Factor Models
Description: Provides generation and estimation of censored factor models for high-dimensional data with censored errors (normal, t, logistic). Includes Sparse Orthogonal Principal Components (SOPC), and evaluation metrics. Based on Guo G. (2023) <doi:10.1007/s00180-022-01270-z>.
Author: Guangbao Guo [aut, cre],
Tong Meng [aut]
Maintainer: Guangbao Guo <ggb11111111@163.com>
Diff between CFM versions 0.7.0 dated 2025-11-13 and 0.8.0 dated 2025-12-07
DESCRIPTION | 6 +++--- MD5 | 11 ++++++++++- R/Aids2.R |only R/bcdata.R |only R/data_yoghurt.R |only data |only man/Aids2.Rd |only man/bcdata.Rd |only man/yoghurt.Rd |only 9 files changed, 13 insertions(+), 4 deletions(-)
Title: WOFOST Crop Growth Simulation Model
Description: An implementation of the WOFOST ("World Food Studies") crop growth model. WOFOST is a dynamic simulation model that uses daily weather data, and crop, soil and management parameters to simulate crop growth and development. See De Wit et al. (2019) <doi:10.1016/j.agsy.2018.06.018> for a recent review of the history and use of the model.
Author: Robert J. Hijmans [cre, aut],
Huang Fang [ctb],
C.A. van Diepen [ctb],
Allard de Wit [ctb],
Daniel van Kraalingen [ctb],
Tamme van der Wal [ctb],
C. Rappoldt [ctb],
Hendrik Boogard [ctb],
I.G.A.M. Noy [ctb],
Alterra, Wageningen-UR [cph]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Diff between Rwofost versions 0.8-6 dated 2025-12-04 and 0.8-7 dated 2025-12-07
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- build/partial.rdb |binary src/wofost.cpp | 15 ++++++++++----- 4 files changed, 17 insertions(+), 12 deletions(-)
Title: Spectral Modularity Clustering
Description: Implements the network clustering algorithm described in
Newman (2006) <doi:10.1103/PhysRevE.74.036104>. The complete
iterative algorithm comprises of two steps. In the first step, the
network is expressed in terms of its leading eigenvalue and
eigenvector and recursively partition into two communities.
Partitioning occurs if the maximum positive
eigenvalue is greater than the tolerance (10e-5) for the current
partition, and if it results in a positive contribution to the
Modularity.
Given an initial separation using the leading eigen step, 'rSpectral'
then continues to maximise for the change in Modularity using a
fine-tuning step - or variate thereof. The first stage here is to
find the node which, when moved from one community to another,
gives the maximum change in Modularity. This node’s community is
then fixed and we repeat the process until all nodes have been moved.
The whole process is repeated from this new state until the change
in the Modularity, between the new and o [...truncated...]
Author: Colin Mclean [aut] ,
Anatoly Sorokin [aut, cre]
Maintainer: Anatoly Sorokin <lptolik@gmail.com>
This is a re-admission after prior archival of version 1.0.0.10 dated 2023-01-18
Diff between rSpectral versions 1.0.0.10 dated 2023-01-18 and 1.0.0.14 dated 2025-12-07
DESCRIPTION | 8 +++--- MD5 | 26 +++++++++++----------- R/igraph.R | 2 - R/rSpectral-package.R | 2 - README.md | 6 +++++ build/partial.rdb |binary inst/CITATION | 19 ++++++++-------- man/figures/README-karate.example-1.png |binary man/figures/README-plot.rspec.default-1.png |binary man/figures/README-plot.rspec.fixneig-1.png |binary man/figures/README-plot.rspec.fixneig.cnmin-1.png |binary man/rSpectral.Rd | 4 +-- man/spectral_igraph_communities.Rd | 2 - src/Makevars | 1 14 files changed, 38 insertions(+), 32 deletions(-)
Title: Reduced-Rank Regression
Description: Multivariate regression methodologies including
classical reduced-rank regression (RRR)
studied by Anderson (1951) <doi:10.1214/aoms/1177729580> and
Reinsel and Velu (1998) <doi:10.1007/978-1-4757-2853-8>,
reduced-rank regression via adaptive nuclear norm penalization
proposed by Chen et al. (2013) <doi:10.1093/biomet/ast036> and
Mukherjee et al. (2015) <doi:10.1093/biomet/asx080>,
robust reduced-rank regression (R4) proposed by
She and Chen (2017) <doi:10.1093/biomet/asx032>,
generalized/mixed-response reduced-rank regression (mRRR) proposed by
Luo et al. (2018) <doi:10.1016/j.jmva.2018.04.011>,
row-sparse reduced-rank regression (SRRR) proposed by
Chen and Huang (2012) <doi:10.1080/01621459.2012.734178>,
reduced-rank regression with a sparse singular value decomposition (RSSVD)
proposed by Chen et al. (2012) <doi:10.1111/j.1467-9868.2011.01002.x>
and sparse and orthogonal factor regression (SOFAR) proposed by
Uematsu et al. (2019) <d [...truncated...]
Author: Kun Chen [aut, cre] ,
Wenjie Wang [aut] ,
Jun Yan [ctb]
Maintainer: Kun Chen <kun.chen@uconn.edu>
Diff between rrpack versions 0.1-13 dated 2022-06-16 and 0.1-14 dated 2025-12-07
DESCRIPTION | 14 +++++++------- MD5 | 8 ++++---- R/mrrr.R | 16 ++++++++-------- man/mrrr.Rd | 16 ++++++++-------- src/Makevars | 1 - 5 files changed, 27 insertions(+), 28 deletions(-)
Title: Radiocarbon Calibration Curves
Description: The IntCal20 radiocarbon calibration curves (Reimer et al. 2020 <doi:10.1017/RDC.2020.68>) are provided as a data package, together with previous IntCal curves (IntCal13, IntCal09, IntCal04, IntCal98), other curves (e.g., NOTCal04 [van der Plicht et al. 2004], Arnold & Libby 1951, Stuiver & Suess 1966, Pearson & Stuiver 1986) and postbomb curves. Also provided are functions to copy the curves into memory, and to read, query and plot the data underlying the IntCal20 curves.
Author: Maarten Blaauw [aut, cre] ,
Christopher Bronk Ramsey [ctb]
Maintainer: Maarten Blaauw <maarten.blaauw@qub.ac.uk>
Diff between rintcal versions 1.3.0 dated 2025-07-09 and 1.3.1 dated 2025-12-07
rintcal-1.3.0/rintcal/inst/extdata/Arnold_Libby_1951.txt |only rintcal-1.3.1/rintcal/DESCRIPTION | 10 rintcal-1.3.1/rintcal/MD5 | 30 +- rintcal-1.3.1/rintcal/NEWS.md | 4 rintcal-1.3.1/rintcal/R/data.R | 27 +- rintcal-1.3.1/rintcal/R/rintcal.R | 77 ++++--- rintcal-1.3.1/rintcal/build/partial.rdb |binary rintcal-1.3.1/rintcal/build/vignette.rds |binary rintcal-1.3.1/rintcal/inst/doc/rintcal.R | 18 - rintcal-1.3.1/rintcal/inst/doc/rintcal.Rmd | 48 ++-- rintcal-1.3.1/rintcal/inst/doc/rintcal.html | 128 ++++++------ rintcal-1.3.1/rintcal/inst/extdata/Arnold_Libby_1951.14C |only rintcal-1.3.1/rintcal/inst/extdata/Pearson_Stuiver_1986.14C |only rintcal-1.3.1/rintcal/inst/extdata/Stuiver_Suess_1966.14C |only rintcal-1.3.1/rintcal/man/ccurve.Rd | 15 + rintcal-1.3.1/rintcal/man/glue.ccurves.Rd | 4 rintcal-1.3.1/rintcal/man/intcal.data.Rd | 5 rintcal-1.3.1/rintcal/vignettes/rintcal.Rmd | 48 ++-- 18 files changed, 230 insertions(+), 184 deletions(-)
Title: Read, Write and Edit 'xlsx' Files
Description: Simplifies the creation of 'xlsx' files by
providing a high level interface to writing, styling and editing
worksheets.
Author: Jordan Mark Barbone [aut] ,
Jan Marvin Garbuszus [aut, cre],
Olivier Roy [ctb],
openxlsx authors [cph] ,
Arseny Kapoulkine [ctb, cph]
Maintainer: Jan Marvin Garbuszus <jan.garbuszus@ruhr-uni-bochum.de>
Diff between openxlsx2 versions 1.21 dated 2025-10-31 and 1.22 dated 2025-12-07
openxlsx2-1.21/openxlsx2/R/onUnload.R |only openxlsx2-1.21/openxlsx2/man/figures/tableoptions.pdf |only openxlsx2-1.21/openxlsx2/man/figures/tableoptions.png |only openxlsx2-1.22/openxlsx2/DESCRIPTION | 11 openxlsx2-1.22/openxlsx2/MD5 | 214 +-- openxlsx2-1.22/openxlsx2/NAMESPACE | 2 openxlsx2-1.22/openxlsx2/NEWS.md | 41 openxlsx2-1.22/openxlsx2/R/RcppExports.R | 12 openxlsx2-1.22/openxlsx2/R/class-comment.R | 109 + openxlsx2-1.22/openxlsx2/R/class-workbook-utils.R | 3 openxlsx2-1.22/openxlsx2/R/class-workbook-wrappers.R | 164 +- openxlsx2-1.22/openxlsx2/R/class-workbook.R | 110 - openxlsx2-1.22/openxlsx2/R/converters.R | 22 openxlsx2-1.22/openxlsx2/R/dates.R | 13 openxlsx2-1.22/openxlsx2/R/deprecate.R | 103 - openxlsx2-1.22/openxlsx2/R/get-named-regions.R | 2 openxlsx2-1.22/openxlsx2/R/helper-functions.R | 8 openxlsx2-1.22/openxlsx2/R/openxlsx2-package.R | 10 openxlsx2-1.22/openxlsx2/R/read.R | 89 - openxlsx2-1.22/openxlsx2/R/utils.R | 144 ++ openxlsx2-1.22/openxlsx2/R/wb_functions.R | 109 + openxlsx2-1.22/openxlsx2/R/wb_load.R | 13 openxlsx2-1.22/openxlsx2/R/wb_styles.R | 10 openxlsx2-1.22/openxlsx2/R/write.R | 22 openxlsx2-1.22/openxlsx2/R/xl_open.R | 115 +- openxlsx2-1.22/openxlsx2/R/zzz.R |only openxlsx2-1.22/openxlsx2/build/vignette.rds |binary openxlsx2-1.22/openxlsx2/inst/WORDLIST | 2 openxlsx2-1.22/openxlsx2/inst/doc/Update-from-openxlsx.R | 2 openxlsx2-1.22/openxlsx2/inst/doc/Update-from-openxlsx.Rmd | 2 openxlsx2-1.22/openxlsx2/inst/doc/Update-from-openxlsx.html | 2 openxlsx2-1.22/openxlsx2/inst/doc/conditional-formatting.Rmd | 2 openxlsx2-1.22/openxlsx2/inst/doc/conditional-formatting.html | 2 openxlsx2-1.22/openxlsx2/inst/doc/openxlsx2.Rmd | 2 openxlsx2-1.22/openxlsx2/inst/doc/openxlsx2.html | 6 openxlsx2-1.22/openxlsx2/inst/doc/openxlsx2_read_to_df.R | 2 openxlsx2-1.22/openxlsx2/inst/doc/openxlsx2_read_to_df.Rmd | 4 openxlsx2-1.22/openxlsx2/inst/doc/openxlsx2_read_to_df.html | 6 openxlsx2-1.22/openxlsx2/inst/doc/openxlsx2_style_manual.R | 4 openxlsx2-1.22/openxlsx2/inst/doc/openxlsx2_style_manual.Rmd | 4 openxlsx2-1.22/openxlsx2/inst/doc/openxlsx2_style_manual.html | 4 openxlsx2-1.22/openxlsx2/man/col2int.Rd | 5 openxlsx2-1.22/openxlsx2/man/col_widths-wb.Rd | 2 openxlsx2-1.22/openxlsx2/man/convertToExcelDate.Rd | 2 openxlsx2-1.22/openxlsx2/man/convert_date.Rd | 8 openxlsx2-1.22/openxlsx2/man/create_hyperlink.Rd | 6 openxlsx2-1.22/openxlsx2/man/delete_data.Rd | 2 openxlsx2-1.22/openxlsx2/man/dims_to_dataframe.Rd | 4 openxlsx2-1.22/openxlsx2/man/filter-wb.Rd | 2 openxlsx2-1.22/openxlsx2/man/int2col.Rd | 5 openxlsx2-1.22/openxlsx2/man/named_region-wb.Rd | 2 openxlsx2-1.22/openxlsx2/man/openxlsx2-package.Rd | 4 openxlsx2-1.22/openxlsx2/man/openxlsx2_options.Rd | 3 openxlsx2-1.22/openxlsx2/man/row_heights-wb.Rd | 5 openxlsx2-1.22/openxlsx2/man/wbWorkbook.Rd | 15 openxlsx2-1.22/openxlsx2/man/wb_add_conditional_formatting.Rd | 2 openxlsx2-1.22/openxlsx2/man/wb_add_data.Rd | 3 openxlsx2-1.22/openxlsx2/man/wb_add_data_table.Rd | 12 openxlsx2-1.22/openxlsx2/man/wb_add_data_validation.Rd | 2 openxlsx2-1.22/openxlsx2/man/wb_add_page_break.Rd | 2 openxlsx2-1.22/openxlsx2/man/wb_get_tables.Rd | 4 openxlsx2-1.22/openxlsx2/man/wb_open.Rd | 6 openxlsx2-1.22/openxlsx2/man/wb_remove_tables.Rd | 2 openxlsx2-1.22/openxlsx2/man/wb_save.Rd | 31 openxlsx2-1.22/openxlsx2/man/wb_to_df.Rd | 13 openxlsx2-1.22/openxlsx2/man/wb_workbook.Rd | 18 openxlsx2-1.22/openxlsx2/man/write_data.Rd | 2 openxlsx2-1.22/openxlsx2/man/write_datatable.Rd | 14 openxlsx2-1.22/openxlsx2/man/write_formula.Rd | 4 openxlsx2-1.22/openxlsx2/man/xl_open.Rd | 3 openxlsx2-1.22/openxlsx2/src/RcppExports.cpp | 36 openxlsx2-1.22/openxlsx2/src/date.cpp | 14 openxlsx2-1.22/openxlsx2/src/helper_functions.cpp | 406 ++++--- openxlsx2-1.22/openxlsx2/src/load_workbook.cpp | 49 openxlsx2-1.22/openxlsx2/src/openxlsx2.h | 250 +--- openxlsx2-1.22/openxlsx2/src/pugi.cpp | 50 openxlsx2-1.22/openxlsx2/src/styles_xml.cpp | 27 openxlsx2-1.22/openxlsx2/src/write_file.cpp | 41 openxlsx2-1.22/openxlsx2/src/xlsb.cpp | 26 openxlsx2-1.22/openxlsx2/src/xlsb_flags.h | 574 ++++------ openxlsx2-1.22/openxlsx2/src/xlsb_funs.h | 42 openxlsx2-1.22/openxlsx2/tests/testthat/helper.R | 28 openxlsx2-1.22/openxlsx2/tests/testthat/test-Workbook_properties.R | 1 openxlsx2-1.22/openxlsx2/tests/testthat/test-class-comment.R | 77 - 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Title: Negative Binomial Mixed Models Using Large-Sample Approximation
for Differential Expression Analysis of ScRNA-Seq Data
Description: A fast negative binomial mixed model for conducting association analysis of multi-subject single-cell data. It can be used for identifying marker genes, differential expression and co-expression analyses. The model includes subject-level random effects to account for the hierarchical structure in multi-subject single-cell data. See He et al. (2021) <doi:10.1038/s42003-021-02146-6>.
Author: Liang He [aut, cre],
Raghav Sharma [ctb]
Maintainer: Liang He <hyx520101@gmail.com>
Diff between nebula versions 1.5.3 dated 2024-02-15 and 1.5.6 dated 2025-12-07
DESCRIPTION | 8 +- MD5 | 20 +++--- R/nebula.R | 39 +++++++++--- R/utils.R | 29 +++++---- README.md | 116 +++++++++++++++++++++--------------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/nebula_example.Rmd | 8 +- inst/doc/nebula_example.html | 136 +++++++++++++++++++++---------------------- man/nebula.Rd | 2 vignettes/nebula_example.Rmd | 8 +- 11 files changed, 206 insertions(+), 160 deletions(-)
Title: Generate Isolines and Isobands from Regularly Spaced Elevation
Grids
Description: A fast C++ implementation to generate contour lines
(isolines) and contour polygons (isobands) from regularly spaced grids
containing elevation data.
Author: Hadley Wickham [aut] ,
Claus O. Wilke [aut] ,
Thomas Lin Pedersen [aut, cre] ,
Posit, PBC [cph, fnd]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@posit.co>
Diff between isoband versions 0.2.7 dated 2022-12-20 and 0.3.0 dated 2025-12-07
isoband-0.2.7/isoband/R/isoband.R |only isoband-0.2.7/isoband/src/init.cpp |only isoband-0.2.7/isoband/src/utils.h |only isoband-0.3.0/isoband/DESCRIPTION | 38 isoband-0.3.0/isoband/LICENSE | 4 isoband-0.3.0/isoband/MD5 | 89 isoband-0.3.0/isoband/NAMESPACE | 1 isoband-0.3.0/isoband/NEWS.md | 11 isoband-0.3.0/isoband/R/clip-lines.R | 20 isoband-0.3.0/isoband/R/cpp11.R |only isoband-0.3.0/isoband/R/iso-to-sfg.R | 16 isoband-0.3.0/isoband/R/isoband-package.R |only isoband-0.3.0/isoband/R/isobands-grob.R | 28 isoband-0.3.0/isoband/R/isobands.R | 36 isoband-0.3.0/isoband/R/isolines-grob.R | 126 isoband-0.3.0/isoband/R/label-placer.R | 74 isoband-0.3.0/isoband/R/plot-iso.R | 64 isoband-0.3.0/isoband/R/utilities.R | 9 isoband-0.3.0/isoband/README.md | 4 isoband-0.3.0/isoband/build/vignette.rds |binary isoband-0.3.0/isoband/inst/doc/isoband1.R | 4 isoband-0.3.0/isoband/inst/doc/isoband1.Rmd | 6 isoband-0.3.0/isoband/inst/doc/isoband1.html | 216 - isoband-0.3.0/isoband/inst/doc/isoband3.R | 2 isoband-0.3.0/isoband/inst/doc/isoband3.Rmd | 4 isoband-0.3.0/isoband/inst/doc/isoband3.html | 211 - isoband-0.3.0/isoband/man/figures/README-basic-example-plot-1.png |binary isoband-0.3.0/isoband/man/figures/README-volcano-1.png |binary isoband-0.3.0/isoband/man/isoband-package.Rd | 14 isoband-0.3.0/isoband/src/Makevars | 1 isoband-0.3.0/isoband/src/Makevars.win | 1 isoband-0.3.0/isoband/src/clip-lines.cpp | 92 isoband-0.3.0/isoband/src/clip-lines.h | 12 isoband-0.3.0/isoband/src/cpp11.cpp |only isoband-0.3.0/isoband/src/isoband.cpp | 191 - isoband-0.3.0/isoband/src/polygon.h | 6 isoband-0.3.0/isoband/src/separate-polygons.cpp | 69 isoband-0.3.0/isoband/src/separate-polygons.h | 5 isoband-0.3.0/isoband/tests/testthat.R | 8 isoband-0.3.0/isoband/tests/testthat/_snaps |only isoband-0.3.0/isoband/tests/testthat/test-clip-lines.R | 92 isoband-0.3.0/isoband/tests/testthat/test-iso-to-sfg.R | 250 + isoband-0.3.0/isoband/tests/testthat/test-isobands.R | 1503 ++++++++-- isoband-0.3.0/isoband/tests/testthat/test-isolines-grob.R | 61 isoband-0.3.0/isoband/tests/testthat/test-isolines.R | 207 + isoband-0.3.0/isoband/tests/testthat/test-label-placer.R | 39 isoband-0.3.0/isoband/vignettes/isoband1.Rmd | 6 isoband-0.3.0/isoband/vignettes/isoband3.Rmd | 4 48 files changed, 2543 insertions(+), 981 deletions(-)
Title: Visualizing Hypothesis Tests in Multivariate Linear Models
Description: Provides HE plot and other functions for visualizing hypothesis
tests in multivariate linear models. HE plots represent sums-of-squares-and-products
matrices for linear hypotheses and for error using ellipses (in two
dimensions) and ellipsoids (in three dimensions). It also provides other tools for analysis and graphical display of the models
such as robust methods and homogeneity of variance covariance matrices.
The related 'candisc' package provides visualizations in a reduced-rank canonical discriminant space when
there are more than a few response variables.
Author: Michael Friendly [aut, cre] ,
John Fox [aut] ,
Georges Monette [aut] ,
Phil Chalmers [ctb] ,
Duncan Murdoch [ctb]
Maintainer: Michael Friendly <friendly@yorku.ca>
Diff between heplots versions 1.7.8 dated 2025-08-18 and 1.8.1 dated 2025-12-07
DESCRIPTION | 18 MD5 | 270 ++-- NAMESPACE | 5 NEWS.md | 27 R/Ellipsoid.R | 16 R/Mahalanobis.R | 15 R/arrow3d.R | 7 R/bartlettTests.R | 13 R/bbox3d.R | 7 R/boxM.R | 453 +++++--- R/coefplot.mlm.R | 18 R/colDevs.R | 14 R/covEllipses.R | 110 + R/cqplot.R | 56 - R/cross3d.R | 3 R/datasets.R | 896 ++++++++-------- R/distancePlot.R | 29 R/ellipse.axes.R | 32 R/ellipse.box.R | 14 R/ellipse3d.axes.R | 13 R/etasq.R | 26 R/glance.mlm.R | 19 R/gsorth.R | 22 R/heplot.R | 293 ++--- R/heplot1d.R | 99 - R/heplot3d.R | 128 +- R/heplots-package.R | 49 R/interpPlot.R | 18 R/label.ellipse.R | 214 ++- R/leveneTests.R | 25 R/logdetCI.R | 22 R/mark.H0.R | 8 R/noteworthy.R | 32 R/pairs.mlm.R | 37 R/plot.boxM.R | 63 - R/plot.robmlm.R | 59 - R/rel_diff.R | 8 R/robmlm.R | 45 R/schoolsites.R | 24 R/statList.R | 26 R/termMeans.R | 6 R/text_usr.R |only R/trans.colors.R | 4 R/uniStats.R | 4 inst/CITATION | 2 inst/doc/HE_manova.html | 27 inst/doc/HE_mmra.html | 25 inst/doc/Robust.html | 11 inst/doc/datasets.R | 29 inst/doc/datasets.Rmd | 48 inst/doc/datasets.html | 1323 +++++++++++++++++++----- man/AddHealth.Rd | 17 man/Adopted.Rd | 20 man/Bees.Rd | 22 man/Diabetes.Rd | 18 man/Ellipsoid.Rd | 6 man/FootHead.Rd | 16 man/Headache.Rd | 32 man/Hernior.Rd | 30 man/Iwasaki_Big_Five.Rd | 30 man/Mahalanobis.Rd | 14 man/MockJury.Rd | 38 man/NLSY.Rd | 18 man/NeuroCog.Rd | 30 man/Oslo.Rd | 50 man/Overdose.Rd | 148 +- man/Parenting.Rd | 12 man/Plastic.Rd | 12 man/Pottery2.Rd | 44 man/Probe.Rd | 32 man/RatWeight.Rd | 16 man/ReactTime.Rd | 18 man/Rohwer.Rd | 41 man/RootStock.Rd | 12 man/Sake.Rd | 22 man/Skulls.Rd | 28 man/SocGrades.Rd | 24 man/SocialCog.Rd | 16 man/TIPI.Rd | 57 - man/VocabGrowth.Rd | 12 man/WeightLoss.Rd | 16 man/arrow3d.Rd | 9 man/bartlettTests.Rd | 8 man/bbox3d.Rd | 13 man/boxM.Rd | 147 +- man/coefplot.Rd | 9 man/colDevs.Rd | 4 man/covEllipses.Rd | 45 man/cqplot.Rd | 27 man/cross3d.Rd | 9 man/distancePlot.Rd | 250 ++-- man/dogfood.Rd | 18 man/ellipse.axes.Rd | 6 man/ellipse.box.Rd | 141 +- man/ellipse3d.axes.Rd | 17 man/etasq.Rd | 27 man/figures/README-iris4-1.png |binary man/glance.mlm.Rd | 19 man/heplot.Rd | 65 - man/heplot1d.Rd | 41 man/heplot3d.Rd | 38 man/heplots-package.Rd | 31 man/interpPlot.Rd | 6 man/label.ellipse.Rd | 137 +- man/leveneTests.Rd | 16 man/logdetCI.Rd | 11 man/mathscore.Rd | 10 man/noteworthy.Rd | 180 +-- man/oral.Rd | 18 man/pairs.mlm.Rd | 18 man/peng.Rd | 172 +-- man/plot.boxM.Rd | 18 man/plot.robmlm.Rd | 37 man/robmlm.Rd | 30 man/schooldata.Rd | 27 man/schoolsites.Rd | 108 - man/statList.Rd | 8 man/termMeans.Rd | 8 man/text_usr.Rd |only man/trans.colors.Rd | 2 man/uniStats.Rd | 4 vignettes/datasets.Rmd | 48 vignettes/fig/manova-addhealth-means-each-1.png |binary vignettes/fig/manova-addhealth-means-plot-1.png |binary vignettes/fig/manova-jury-mod1-pairs-1.png |binary vignettes/fig/manova-plastic1-1.png |binary vignettes/fig/manova-plastic1a-1.png |binary vignettes/fig/manova-plastic2-1.png |binary vignettes/fig/manova-skulls-HE-pairs-1.png |binary vignettes/fig/mmra-grades-pairs-1.png |binary vignettes/fig/mmra-hern-pairs-1.png |binary vignettes/fig/mmra-rohwer-HE1-1.png |binary vignettes/fig/mmra-rohwer-HE2-1.png |binary vignettes/fig/mmra-rohwer-HE2-2.png |binary vignettes/fig/mmra-rohwer-HE3-1.png |binary vignettes/fig/mmra-rohwer-long-ggplot-1.png |binary vignettes/fig/robust-pottery-pairs-1.png |binary 137 files changed, 4429 insertions(+), 2916 deletions(-)
Title: Rmetrics - Markets and Basic Statistics
Description: Provides a collection of functions to
explore and to investigate basic properties of financial returns
and related quantities.
The covered fields include techniques of explorative data analysis
and the investigation of distributional properties, including
parameter estimation and hypothesis testing. Even more there are
several utility functions for data handling and management.
Author: Diethelm Wuertz [aut] ,
Tobias Setz [aut],
Yohan Chalabi [aut],
Martin Maechler [ctb] ,
CRAN Team [ctb],
Georgi N. Boshnakov [cre, aut]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>
Diff between fBasics versions 4041.97 dated 2024-08-19 and 4052.98 dated 2025-12-07
DESCRIPTION | 17 ++++-- MD5 | 46 +++++++++--------- NEWS.md | 17 ++++++ data/Capitalization.rda |binary data/DowJones30.csv.gz |binary data/HedgeFund.rda |binary data/PensionFund.csv.gz |binary data/SWXLP.csv.gz |binary data/cars2.csv.gz |binary data/msft.dat.rda |binary data/nyse.csv.gz |binary data/swissEconomy.rda |binary data/usdthb.csv.gz |binary inst/pkgdown.yml | 4 - man/plot-acfPlot.Rd | 105 +++++++++++++++++++++++++++---------------- man/plot-boxPlot.Rd | 40 ++++++++++++---- man/plot-histPlot.Rd | 31 +++++++++++- man/plot-qqPlot.Rd | 88 +++++++++++++++++++++++++----------- man/plot-returnSeriesGUI.Rd | 47 ++++++++++++++----- man/plot-scalinglawPlot.Rd | 62 ++++++++++++++++--------- man/plot-seriesPlot.Rd | 57 +++++++++++++++-------- man/stableSlider.Rd | 30 +++++++++++- man/utils-interactivePlot.Rd | 43 ++++++++++++++--- src/nig.c | 14 +---- 24 files changed, 420 insertions(+), 181 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 1.4.3 dated 2025-10-30 and 1.4.5 dated 2025-12-07
Colossus-1.4.3/Colossus/man/Check_Iters.Rd |only Colossus-1.4.3/Colossus/man/RunCaseControlRegression_Omnibus.Rd |only Colossus-1.4.3/Colossus/man/RunCoxRegression_Omnibus.Rd |only Colossus-1.4.3/Colossus/man/RunLogisticRegression_Omnibus.Rd |only Colossus-1.4.3/Colossus/man/RunPoissonRegression_Omnibus.Rd |only Colossus-1.4.3/Colossus/man/apply_norm.Rd |only Colossus-1.4.5/Colossus/DESCRIPTION | 8 Colossus-1.4.5/Colossus/MD5 | 207 +- Colossus-1.4.5/Colossus/NAMESPACE | 5 Colossus-1.4.5/Colossus/NEWS.md | 11 Colossus-1.4.5/Colossus/R/BasicRun.R | 602 +++++++ Colossus-1.4.5/Colossus/R/CaseControl_Regression.R | 26 Colossus-1.4.5/Colossus/R/Cox_Regression.R | 69 Colossus-1.4.5/Colossus/R/LogitRegression.R | 8 Colossus-1.4.5/Colossus/R/ObjValidate.R | 45 Colossus-1.4.5/Colossus/R/Poisson_Regression.R | 109 - Colossus-1.4.5/Colossus/R/RcppExports.R | 34 Colossus-1.4.5/Colossus/R/SurvTypes.R | 138 + Colossus-1.4.5/Colossus/R/Utility.R | 451 ++++- Colossus-1.4.5/Colossus/R/zzz.R | 45 Colossus-1.4.5/Colossus/README.md | 40 Colossus-1.4.5/Colossus/build/vignette.rds |binary Colossus-1.4.5/Colossus/inst/WORDLIST | 8 Colossus-1.4.5/Colossus/inst/doc/Alt_Run_Opt.R | 8 Colossus-1.4.5/Colossus/inst/doc/Alt_Run_Opt.Rmd | 12 Colossus-1.4.5/Colossus/inst/doc/Alt_Run_Opt.html | 533 ++---- Colossus-1.4.5/Colossus/inst/doc/Control_Options.html | 157 -- Colossus-1.4.5/Colossus/inst/doc/Dose_Formula_Inputs.html | 186 +- Colossus-1.4.5/Colossus/inst/doc/Equation_Expression.R | 2 Colossus-1.4.5/Colossus/inst/doc/Equation_Expression.Rmd | 2 Colossus-1.4.5/Colossus/inst/doc/Equation_Expression.html | 365 ++-- Colossus-1.4.5/Colossus/inst/doc/Excess_and_Predicted_Cases.R | 16 Colossus-1.4.5/Colossus/inst/doc/Excess_and_Predicted_Cases.Rmd | 21 Colossus-1.4.5/Colossus/inst/doc/Excess_and_Predicted_Cases.html | 198 +- Colossus-1.4.5/Colossus/inst/doc/Grad_Hess.html | 489 ++---- Colossus-1.4.5/Colossus/inst/doc/Logistic.R | 11 Colossus-1.4.5/Colossus/inst/doc/Logistic.Rmd | 11 Colossus-1.4.5/Colossus/inst/doc/Logistic.html | 433 ++--- Colossus-1.4.5/Colossus/inst/doc/Matched_Case_Control.R | 10 Colossus-1.4.5/Colossus/inst/doc/Matched_Case_Control.Rmd | 10 Colossus-1.4.5/Colossus/inst/doc/Matched_Case_Control.html | 407 ++--- Colossus-1.4.5/Colossus/inst/doc/Multi_Realization.html | 210 +- Colossus-1.4.5/Colossus/inst/doc/Plotting_And_Analysis.html | 492 +++--- Colossus-1.4.5/Colossus/inst/doc/SMR_Analysis.html | 278 +-- Colossus-1.4.5/Colossus/inst/doc/Script_Comparison_Epicure.html | 230 +- Colossus-1.4.5/Colossus/inst/doc/Starting-Description.Rmd | 5 Colossus-1.4.5/Colossus/inst/doc/Starting-Description.html | 634 +++----- Colossus-1.4.5/Colossus/inst/doc/Time_Dep_Cov.html | 398 ++--- Colossus-1.4.5/Colossus/inst/doc/Wald_and_Log_Bound.Rmd | 2 Colossus-1.4.5/Colossus/inst/doc/Wald_and_Log_Bound.html | 783 ++++------ Colossus-1.4.5/Colossus/inst/doc/count_time_tables.html | 600 +++---- Colossus-1.4.5/Colossus/man/CaseControlRun.Rd | 4 Colossus-1.4.5/Colossus/man/CoxRun.Rd | 3 Colossus-1.4.5/Colossus/man/CoxRunMulti.Rd | 3 Colossus-1.4.5/Colossus/man/Date_Shift.Rd | 2 Colossus-1.4.5/Colossus/man/EventAssignment.poisres.Rd | 4 Colossus-1.4.5/Colossus/man/EventAssignment.poisresbound.Rd |only Colossus-1.4.5/Colossus/man/Event_Count_Gen.Rd | 2 Colossus-1.4.5/Colossus/man/Event_Time_Gen.Rd | 2 Colossus-1.4.5/Colossus/man/Joint_Multiple_Events.Rd | 2 Colossus-1.4.5/Colossus/man/LikelihoodBound.coxres.Rd | 3 Colossus-1.4.5/Colossus/man/LikelihoodBound.poisres.Rd | 4 Colossus-1.4.5/Colossus/man/LogisticRun.Rd | 4 Colossus-1.4.5/Colossus/man/PoisRun.Rd | 4 Colossus-1.4.5/Colossus/man/PoisRunJoint.Rd | 4 Colossus-1.4.5/Colossus/man/PoisRunMulti.Rd | 4 Colossus-1.4.5/Colossus/man/Replace_Missing.Rd | 2 Colossus-1.4.5/Colossus/man/Residual.poisres.Rd | 4 Colossus-1.4.5/Colossus/man/Time_Since.Rd | 2 Colossus-1.4.5/Colossus/man/factorize.Rd | 2 Colossus-1.4.5/Colossus/man/gen_time_dep.Rd | 2 Colossus-1.4.5/Colossus/src/Calc_Repeated.cpp | 168 -- Colossus-1.4.5/Colossus/src/Main_Bound.cpp | 145 - Colossus-1.4.5/Colossus/src/Main_Functions.cpp | 145 - Colossus-1.4.5/Colossus/src/Main_Multi.cpp | 57 Colossus-1.4.5/Colossus/src/Omnibus_Pieces.cpp | 137 - Colossus-1.4.5/Colossus/src/Omnibus_Pieces.h | 2 Colossus-1.4.5/Colossus/src/Plot_Extensions.cpp | 21 Colossus-1.4.5/Colossus/src/R_Interface.cpp | 108 - Colossus-1.4.5/Colossus/src/R_Interface.h | 6 Colossus-1.4.5/Colossus/src/RcppExports.cpp | 37 Colossus-1.4.5/Colossus/src/Step_Calc.cpp | 3 Colossus-1.4.5/Colossus/src/Step_Grad.cpp | 4 Colossus-1.4.5/Colossus/src/Step_Newton.cpp | 7 Colossus-1.4.5/Colossus/src/Subterms_Risk.cpp | 247 +-- Colossus-1.4.5/Colossus/src/Subterms_Risk.h | 6 Colossus-1.4.5/Colossus/tests/testthat/test-Assigned.R | 100 - Colossus-1.4.5/Colossus/tests/testthat/test-CaseControl.R | 67 Colossus-1.4.5/Colossus/tests/testthat/test-Cox_Plot.R | 167 -- Colossus-1.4.5/Colossus/tests/testthat/test-Cox_Regression.R | 179 -- Colossus-1.4.5/Colossus/tests/testthat/test-Formula.R | 109 - Colossus-1.4.5/Colossus/tests/testthat/test-Gradient.R | 119 - Colossus-1.4.5/Colossus/tests/testthat/test-Joint.R | 63 Colossus-1.4.5/Colossus/tests/testthat/test-Logbound.R | 118 - Colossus-1.4.5/Colossus/tests/testthat/test-Logit.R | 12 Colossus-1.4.5/Colossus/tests/testthat/test-Multidose.R | 156 - Colossus-1.4.5/Colossus/tests/testthat/test-Norm.R | 59 Colossus-1.4.5/Colossus/tests/testthat/test-Omnibus.R | 58 Colossus-1.4.5/Colossus/tests/testthat/test-Poisson_Regression.R | 77 Colossus-1.4.5/Colossus/tests/testthat/test-Poisson_Residual.R | 27 Colossus-1.4.5/Colossus/tests/testthat/test-Utility.R | 127 + Colossus-1.4.5/Colossus/vignettes/Alt_Run_Opt.Rmd | 12 Colossus-1.4.5/Colossus/vignettes/Equation_Expression.Rmd | 2 Colossus-1.4.5/Colossus/vignettes/Excess_and_Predicted_Cases.Rmd | 21 Colossus-1.4.5/Colossus/vignettes/Logistic.Rmd | 11 Colossus-1.4.5/Colossus/vignettes/Matched_Case_Control.Rmd | 10 Colossus-1.4.5/Colossus/vignettes/Starting-Description.Rmd | 5 Colossus-1.4.5/Colossus/vignettes/Wald_and_Log_Bound.Rmd | 2 108 files changed, 4966 insertions(+), 5994 deletions(-)
Title: Client for World Banks's 'Indicators' and 'Poverty and
Inequality Platform (PIP)' APIs
Description: Download and search data from the 'World Bank Indicators
API', which provides access to nearly 16,000 time series indicators.
See
<https://datahelpdesk.worldbank.org/knowledgebase/articles/889392-about-the-indicators-api-documentation>
for further details about the API.
Author: Maximilian Muecke [aut, cre]
Maintainer: Maximilian Muecke <muecke.maximilian@gmail.com>
This is a re-admission after prior archival of version 0.7.0 dated 2025-11-10
Diff between worldbank versions 0.7.0 dated 2025-11-10 and 0.7.1 dated 2025-12-06
worldbank-0.7.0/worldbank/tests/testthat/setup.R |only worldbank-0.7.1/worldbank/DESCRIPTION | 8 +- worldbank-0.7.1/worldbank/MD5 | 31 ++++----- worldbank-0.7.1/worldbank/NEWS.md | 4 + worldbank-0.7.1/worldbank/R/indicators.R | 18 +++++ worldbank-0.7.1/worldbank/man/wb_country.Rd | 2 worldbank-0.7.1/worldbank/man/wb_data.Rd | 2 worldbank-0.7.1/worldbank/man/wb_income_level.Rd | 2 worldbank-0.7.1/worldbank/man/wb_indicator.Rd | 2 worldbank-0.7.1/worldbank/man/wb_language.Rd | 2 worldbank-0.7.1/worldbank/man/wb_lending_type.Rd | 2 worldbank-0.7.1/worldbank/man/wb_region.Rd | 2 worldbank-0.7.1/worldbank/man/wb_source.Rd | 2 worldbank-0.7.1/worldbank/man/wb_topic.Rd | 2 worldbank-0.7.1/worldbank/tests/testthat/test-fone.R | 4 - worldbank-0.7.1/worldbank/tests/testthat/test-indicators.R | 43 ++++++------- worldbank-0.7.1/worldbank/tests/testthat/test-pip.R | 2 17 files changed, 84 insertions(+), 44 deletions(-)
Title: Collecting 'TikTok' Data
Description: Getting 'TikTok' data (<https://www.tiktok.com/>) through the official
and unofficial APIs—in other words, you can track 'TikTok'.
Author: Johannes B. Gruber [aut, cre]
Maintainer: Johannes B. Gruber <JohannesB.Gruber@gmail.com>
This is a re-admission after prior archival of version 0.1.0 dated 2025-11-24
Diff between traktok versions 0.1.0 dated 2025-11-24 and 0.1.1 dated 2025-12-06
DESCRIPTION | 6 MD5 | 20 - NEWS.md | 2 R/utils.R | 3 README.md | 10 inst/WORDLIST | 5 inst/doc/research-api.Rmd | 2 inst/doc/research-api.html | 3 inst/doc/unofficial-api.Rmd | 492 +++++++++++++++++++++---------------------- vignettes/research-api.Rmd | 2 vignettes/unofficial-api.Rmd | 492 +++++++++++++++++++++---------------------- 11 files changed, 524 insertions(+), 513 deletions(-)
Title: Estimation of the Rasch Model for Multistage Tests
Description: Provides conditional maximum likelihood (CML) item parameter estimation of both sequential and cumulative deterministic multistage designs (Zwitser & Maris, 2015, <doi:10.1007/s11336-013-9369-6>) and probabilistic sequential and cumulative multistage designs (Steinfeld & Robitzsch, 2024, <doi:10.1007/s41237-024-00228-3>). Supports CML item parameter estimation of conventional linear designs and additional functions for the likelihood ratio test (Andersen, 1973, <doi:10.1007/BF02291180>) as well as functions for simulating various types of multistage designs.
Author: Jan Steinfeld [cre, aut] ,
Alexander Robitzsch [aut]
Maintainer: Jan Steinfeld <jan.d.steinfeld@gmail.com>
Diff between tmt versions 0.3.6-0 dated 2025-06-20 and 0.3.6-4 dated 2025-12-06
DESCRIPTION | 14 +- MD5 | 34 ++--- NEWS.md | 3 R/helper_functions.R | 3 R/raschmodel.mst.R | 40 ++++++ R/sim.rm.R | 11 + R/tmt_gmc.R | 6 + R/tmt_mstdesign.R | 115 ++++++++++++++++++- R/tmt_msttemplate.R | 38 +++++- R/tmt_sim.R | 161 +++++++++++++++++++++++++-- README.md | 22 ++- build/partial.rdb |binary build/vignette.rds |binary inst/NEWS | 8 + inst/doc/introduction_to_tmt.html | 8 - src/esf_mst_sum_vector.cpp | 201 ++++++++++++++++++++++++++++++++-- src/esf_mst_sum_vector_s2.h | 151 ++++++++++++++++++++++++- tests/testthat/test-helperfunctions.R | 26 ++-- 18 files changed, 748 insertions(+), 93 deletions(-)
Title: Tidy Methods for Bayesian Treatment Effect Models
Description: Functions for extracting tidy data from Bayesian treatment effect models, in particular BART, but extensions are possible. Functionality includes extracting tidy posterior summaries as in 'tidybayes' <https://github.com/mjskay/tidybayes>, estimating (average) treatment effects, common support calculations, and plotting useful summaries of these.
Author: Joshua J Bon [aut, cre]
Maintainer: Joshua J Bon <joshuajbon@gmail.com>
Diff between tidytreatment versions 0.3.1 dated 2025-01-10 and 0.3.2 dated 2025-12-06
tidytreatment-0.3.1/tidytreatment/man/fitted_draws.bartMachine.Rd |only tidytreatment-0.3.1/tidytreatment/man/fitted_draws.lbart.Rd |only tidytreatment-0.3.1/tidytreatment/man/fitted_draws.mbart.Rd |only tidytreatment-0.3.1/tidytreatment/man/fitted_draws.mbart2.Rd |only tidytreatment-0.3.1/tidytreatment/man/fitted_draws.pbart.Rd |only tidytreatment-0.3.1/tidytreatment/man/fitted_draws.wbart.Rd |only tidytreatment-0.3.1/tidytreatment/man/fitted_draws_BART.Rd |only tidytreatment-0.3.2/tidytreatment/DESCRIPTION | 15 - tidytreatment-0.3.2/tidytreatment/MD5 | 90 +++--- tidytreatment-0.3.2/tidytreatment/NAMESPACE | 16 - tidytreatment-0.3.2/tidytreatment/NEWS.md | 5 tidytreatment-0.3.2/tidytreatment/R/average-treatment-effects-posterior.R | 6 tidytreatment-0.3.2/tidytreatment/R/common-support.R | 12 tidytreatment-0.3.2/tidytreatment/R/helper.R | 2 tidytreatment-0.3.2/tidytreatment/R/tidy-posterior-BART.R | 141 +++++++--- tidytreatment-0.3.2/tidytreatment/R/tidy-posterior-bartMachine.R | 26 - tidytreatment-0.3.2/tidytreatment/R/tidy-posterior-stan4bart.R | 40 -- tidytreatment-0.3.2/tidytreatment/R/tidytreatment-package.R | 2 tidytreatment-0.3.2/tidytreatment/R/treatment-effects-bartCause.R | 2 tidytreatment-0.3.2/tidytreatment/R/treatment-effects-posterior.R | 11 tidytreatment-0.3.2/tidytreatment/R/tree-extract-BART.R | 2 tidytreatment-0.3.2/tidytreatment/build/vignette.rds |binary tidytreatment-0.3.2/tidytreatment/inst/doc/use-tidytreatment-BART-binary-outcome.R |only tidytreatment-0.3.2/tidytreatment/inst/doc/use-tidytreatment-BART-binary-outcome.Rmd |only tidytreatment-0.3.2/tidytreatment/inst/doc/use-tidytreatment-BART-binary-outcome.html |only tidytreatment-0.3.2/tidytreatment/inst/doc/use-tidytreatment-BART.R | 10 tidytreatment-0.3.2/tidytreatment/inst/doc/use-tidytreatment-BART.Rmd | 10 tidytreatment-0.3.2/tidytreatment/inst/doc/use-tidytreatment-BART.html | 85 +++--- tidytreatment-0.3.2/tidytreatment/inst/doc/use-tidytreatment-bartCause.R | 4 tidytreatment-0.3.2/tidytreatment/inst/doc/use-tidytreatment-bartCause.Rmd | 4 tidytreatment-0.3.2/tidytreatment/inst/doc/use-tidytreatment-bartCause.html | 75 ++--- tidytreatment-0.3.2/tidytreatment/man/avg_treatment_effects.Rd | 2 tidytreatment-0.3.2/tidytreatment/man/epred_draws.bartMachine.Rd |only tidytreatment-0.3.2/tidytreatment/man/epred_draws.lbart.Rd |only tidytreatment-0.3.2/tidytreatment/man/epred_draws.mbart.Rd |only tidytreatment-0.3.2/tidytreatment/man/epred_draws.mbart2.Rd |only tidytreatment-0.3.2/tidytreatment/man/epred_draws.pbart.Rd |only tidytreatment-0.3.2/tidytreatment/man/epred_draws.stan4bartFit.Rd | 4 tidytreatment-0.3.2/tidytreatment/man/epred_draws.wbart.Rd |only tidytreatment-0.3.2/tidytreatment/man/epred_draws_BART.Rd |only tidytreatment-0.3.2/tidytreatment/man/has_common_support.Rd | 2 tidytreatment-0.3.2/tidytreatment/man/linpred_draws.stan4bartFit.Rd | 6 tidytreatment-0.3.2/tidytreatment/man/predicted_draws.lbart.Rd |only tidytreatment-0.3.2/tidytreatment/man/predicted_draws.pbart.Rd |only tidytreatment-0.3.2/tidytreatment/man/predicted_draws.stan4bartFit.Rd | 10 tidytreatment-0.3.2/tidytreatment/man/predicted_draws_BART.Rd | 6 tidytreatment-0.3.2/tidytreatment/man/tidy_ate.Rd | 2 tidytreatment-0.3.2/tidytreatment/man/tidy_att.Rd | 2 tidytreatment-0.3.2/tidytreatment/man/tidytreatment.Rd | 4 tidytreatment-0.3.2/tidytreatment/man/treatment_effects.Rd | 2 tidytreatment-0.3.2/tidytreatment/man/treatment_effects.bartcFit.Rd | 2 tidytreatment-0.3.2/tidytreatment/man/treatment_effects.default.Rd | 2 tidytreatment-0.3.2/tidytreatment/tests/testthat/test-fitted.R | 2 tidytreatment-0.3.2/tidytreatment/vignettes/use-tidytreatment-BART-binary-outcome.Rmd |only tidytreatment-0.3.2/tidytreatment/vignettes/use-tidytreatment-BART.Rmd | 10 tidytreatment-0.3.2/tidytreatment/vignettes/use-tidytreatment-bartCause.Rmd | 4 56 files changed, 362 insertions(+), 256 deletions(-)
Title: Robust Exponential Factor Analysis
Description: A robust alternative to the traditional principal component estimator is proposed within the framework of factor models, known as Robust Exponential Factor Analysis, specifically designed for the modeling of high-dimensional datasets with heavy-tailed distributions. The algorithm estimates the latent factors and the loading by minimizing the exponential squared loss function. To determine the appropriate number of factors, we propose a modified rank minimization technique, which has been shown to significantly enhance finite-sample performance. For more detail of Robust Exponential Factor Analysis, please refer to Hu et al. (2026) <doi:10.1016/j.jmva.2025.105567>.
Author: Jiaqi Hu [cre, aut],
Xueqin Wang [aut]
Maintainer: Jiaqi Hu <hujiaqi@mail.ustc.edu.cn>
Diff between REFA versions 0.1.0 dated 2023-11-19 and 0.2.0 dated 2025-12-06
DESCRIPTION | 16 +++---- MD5 | 28 ++++++------- NAMESPACE | 29 +++++++------- NEWS.md | 2 R/FA.R | 37 ++++++++++++++++++ R/REFA.R | 54 ++++++++++++++++++++++++++ R/auxiliary.R | 67 ++++++++++++++++++++++++++++++--- R/gendata.R | 115 ++++++++++++++++++++++++++++++++++++++------------------- man/ECC.Rd | 28 ++++++++----- man/FA.Rd | 35 +++++++++-------- man/REFA.Rd | 47 +++++++++++++---------- man/REFA_FN.Rd | 50 ++++++++++++++---------- man/TR.Rd | 19 ++++++--- man/est_num.Rd | 25 +++++++----- man/gendata.Rd | 41 +++++++++++--------- 15 files changed, 417 insertions(+), 176 deletions(-)
Title: Bindings for 'Open Source Routing Machine'
Description: Install and control 'Open Source Routing Machine' ('OSRM')
backend executables to prepare routing data and run/stop a local
'OSRM' server. For computations with the running server use the 'osrm'
R package (<https://cran.r-project.org/package=osrm>).
Author: Egor Kotov [aut, cre, cph]
Maintainer: Egor Kotov <kotov.egor@gmail.com>
Diff between osrm.backend versions 0.1.0 dated 2025-12-03 and 0.1.1 dated 2025-12-06
osrm.backend-0.1.0/osrm.backend/inst/doc/osrm-backend.qmd |only osrm.backend-0.1.0/osrm.backend/man/print.osrm_job.Rd |only osrm.backend-0.1.0/osrm.backend/vignettes/osrm-backend.qmd |only osrm.backend-0.1.1/osrm.backend/DESCRIPTION | 10 osrm.backend-0.1.1/osrm.backend/MD5 | 26 osrm.backend-0.1.1/osrm.backend/NEWS.md | 4 osrm.backend-0.1.1/osrm.backend/R/utils.R | 29 osrm.backend-0.1.1/osrm.backend/README.md | 11 osrm.backend-0.1.1/osrm.backend/build/vignette.rds |binary osrm.backend-0.1.1/osrm.backend/inst/CITATION | 5 osrm.backend-0.1.1/osrm.backend/inst/doc/osrm-backend.R | 64 - osrm.backend-0.1.1/osrm.backend/inst/doc/osrm-backend.Rmd |only osrm.backend-0.1.1/osrm.backend/inst/doc/osrm-backend.html | 443 ++++++++-- osrm.backend-0.1.1/osrm.backend/tests/testthat/setup-osrm.R | 61 - osrm.backend-0.1.1/osrm.backend/tests/testthat/teardown.R |only osrm.backend-0.1.1/osrm.backend/tests/testthat/test-osrm_server.R | 10 osrm.backend-0.1.1/osrm.backend/vignettes/osrm-backend.Rmd |only 17 files changed, 472 insertions(+), 191 deletions(-)
Title: Model Selection and Tuning Utilities
Description: Provides a lightweight framework for model selection
and hyperparameter tuning in R. The package offers intuitive tools for
grid search, cross-validation, and combined grid search with cross-validation
that work seamlessly with virtually any modeling package. Designed for
flexibility and ease of use, it standardizes tuning workflows while
remaining fully compatible with a wide range of model interfaces and
estimation functions.
Author: Daniel Molitor [aut, cre]
Maintainer: Daniel Molitor <molitdj97@gmail.com>
Diff between modeltuning versions 0.1.2 dated 2025-10-28 and 0.1.3 dated 2025-12-06
DESCRIPTION | 11 ++++++----- MD5 | 13 +++++++------ NEWS.md |only README.md | 20 +++++++++++++------- inst/doc/basic-usage.html | 18 +++++++++--------- inst/doc/data-masking.html | 36 +++++++++++++++++++----------------- inst/doc/scaling-with-aws.html | 16 ++++++++-------- man/modeltuning-package.Rd | 1 + 8 files changed, 63 insertions(+), 52 deletions(-)
Title: Bootstrap Analyses of Sampling Uncertainty in Goodness-of-Fit
Statistics
Description: Uses jackknife and bootstrap methods to quantify the sampling uncertainty in goodness-of-fit statistics. Full details are in Clark et al. (2021), "The abuse of popular performance metrics in hydrologic modeling", Water Resources Research, <doi:10.1029/2020WR029001>.
Author: Martyn Clark [aut],
Kevin Shook [aut, trl, cre]
Maintainer: Kevin Shook <kshook@kshook.ca>
Diff between gumboot versions 1.0.1 dated 2023-10-18 and 1.0.2 dated 2025-12-06
DESCRIPTION | 12 ++++++------ MD5 | 14 +++++++------- R/gumboot-package.R | 3 ++- build/partial.rdb |binary build/vignette.rds |binary inst/doc/using_gumboot.R | 10 +++++----- inst/doc/using_gumboot.html | 21 +++++++++++---------- man/gumboot-package.Rd | 2 ++ 8 files changed, 33 insertions(+), 29 deletions(-)