Title: Tools and Statistical Procedures in Plant Science
Description: The 'inti' package is part of the 'inkaverse' project for developing
different procedures and tools used in plant science and experimental designs.
The mean aim of the package is to support researchers during the planning of
experiments and data collection (tarpuy()), data analysis and graphics (yupana())
, and scientific writing.
Learn more about the 'inkaverse' project at <https://inkaverse.com/>.
Author: Flavio Lozano-Isla [aut, cre] ,
Maria Belen Kistner [ctb] ,
QuipoLab [ctb],
Inkaverse [cph]
Maintainer: Flavio Lozano-Isla <flozanoisla@gmail.com>
Diff between inti versions 0.6.9 dated 2025-10-17 and 0.6.91 dated 2026-01-10
DESCRIPTION | 8 - MD5 | 49 ++++----- NEWS.md | 5 R/design_noreps.R | 2 R/design_repblock.R | 2 R/figure2rmd.R | 2 R/plot_raw.R | 48 +++------ R/plot_smr.R | 40 +++---- R/table2rmd.R | 2 R/tarpuy_plex.R | 2 R/utils.R | 31 +++++ build/partial.rdb |binary build/vignette.rds |binary inst/doc/apps.html | 6 - inst/doc/rticles.html | 22 ---- inst/doc/rticles.qmd | 28 ----- inst/extdata/_extensions/scihub/analysis.qmd | 100 +++++++++++++++---- inst/extdata/_extensions/scihub/design/labels.qmd | 23 ++-- inst/extdata/_extensions/scihub/files/authorship.pdf |only inst/tarpuy/ui.R | 2 man/design_noreps.Rd | 2 man/design_repblock.Rd | 2 man/plot_raw.Rd | 7 - man/plot_smr.Rd | 14 ++ man/tarpuy_plex.Rd | 2 vignettes/rticles.qmd | 28 ----- 26 files changed, 237 insertions(+), 190 deletions(-)
Title: Tools for Computational Optimal Transport
Description: Transport theory has seen much success in many fields of statistics and machine learning. We provide a variety of algorithms to compute Wasserstein distance, barycenter, and others. See Peyré and Cuturi (2019) <doi:10.1561/2200000073> for the general exposition to the study of computational optimal transport.
Author: Kisung You [aut, cre]
Maintainer: Kisung You <kisung.you@outlook.com>
Diff between T4transport versions 0.1.7 dated 2025-12-22 and 0.1.8 dated 2026-01-10
T4transport-0.1.7/T4transport/R/dist_hdist.R |only T4transport-0.1.7/T4transport/man/hdist.Rd |only T4transport-0.1.8/T4transport/DESCRIPTION | 7 T4transport-0.1.8/T4transport/MD5 | 34 ++-- T4transport-0.1.8/T4transport/NAMESPACE | 6 T4transport-0.1.8/T4transport/NEWS.md | 8 + T4transport-0.1.8/T4transport/R/RcppExports.R | 4 T4transport-0.1.8/T4transport/R/hist_dist.R |only T4transport-0.1.8/T4transport/R/image_bary.R |only T4transport-0.1.8/T4transport/R/image_dist.R |only T4transport-0.1.8/T4transport/R/image_interp.R |only T4transport-0.1.8/T4transport/R/image_med.R |only T4transport-0.1.8/T4transport/R/test_compare_two.R | 39 ++--- T4transport-0.1.8/T4transport/build/partial.rdb |binary T4transport-0.1.8/T4transport/man/histdist.Rd |only T4transport-0.1.8/T4transport/man/imagebary.Rd |only T4transport-0.1.8/T4transport/man/imagedist.Rd |only T4transport-0.1.8/T4transport/man/imageinterp.Rd |only T4transport-0.1.8/T4transport/man/imagemed.Rd |only T4transport-0.1.8/T4transport/src/Makevars | 3 T4transport-0.1.8/T4transport/src/Makevars.win | 3 T4transport-0.1.8/T4transport/src/RcppExports.cpp | 15 ++ T4transport-0.1.8/T4transport/src/utility_EMD.cpp | 156 +++++++++++++++++++++ T4transport-0.1.8/T4transport/src/utility_EMD.h | 4 24 files changed, 237 insertions(+), 42 deletions(-)
Title: Density Deconvolution Using Bayesian Semiparametric Methods
Description: Estimates the density of a variable in a measurement error setup, potentially with an excess of zero values. For more details see Sarkar (2022) <doi:10.1080/01621459.2020.1782220>.
Author: Blake Moya [aut],
Mainak Manna [cre, aut],
Abhra Sarkar [aut],
The University of Texas at Austin [cph, fnd]
Maintainer: Mainak Manna <mainakmanna29@utexas.edu>
Diff between BayesDecon versions 0.1.3 dated 2026-01-09 and 0.1.4 dated 2026-01-10
DESCRIPTION | 8 ++++---- MD5 | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-)
Title: Estimating Length-Based Indicators for Fish Stock
Description: Provides tools for estimating length-based indicators from length frequency data to assess fish stock status and manage fisheries sustainably. Implements methods from Cope and Punt (2009) <doi:10.1577/C08-025.1> for data-limited stock assessment and Froese (2004) <doi:10.1111/j.1467-2979.2004.00144.x> for detecting overfishing using simple indicators. Key functions include:
FrequencyTable(): Calculate the frequency table from the collected and also the extract the length frequency data from the frequency table with the upper length_range. A numeric value specifying the bin width for class intervals. If not provided, the bin width is automatically calculated using Wang (2020) <doi:10.1016/j.fishres.2019.105474> formula.
FreqTM(): Creates a frequency distribution table for fish length data across multiple months using a consistent length class structure. The bin width is determined by either a custom value or Wang's formula, applied uniformly across all months. The func [...truncated...]
Author: Ataher Ali [aut, cre],
Mohammed Shahidul Alam [aut]
Maintainer: Ataher Ali <ataher.cu.ms@gmail.com>
Diff between aLBI versions 0.1.8 dated 2025-07-14 and 0.1.9 dated 2026-01-10
DESCRIPTION | 14 MD5 | 25 + NAMESPACE | 6 R/DataDescription.R | 39 ++ R/FishPar.R | 6 R/FishSS.R | 95 +++--- R/FreqTM.R |only data/lenfreqM.rda |only inst/doc/Introduction.R | 38 ++ inst/doc/Introduction.Rmd | 121 +++++--- inst/doc/Introduction.html | 645 ++++++++++++++++++++++++++------------------- inst/exdata/lenfreqM.xlsx |only man/FishSS.Rd | 14 man/FreqTM.Rd |only man/lenfreqM.Rd |only vignettes/Introduction.Rmd | 121 +++++--- 16 files changed, 719 insertions(+), 405 deletions(-)
Title: Data Visualization and Statistical Tools for Agroindustrial
Experiments
Description: Set of tools for statistical analysis, visualization, and reporting of
agroindustrial and agricultural experiments. The package provides functions
to perform ANOVA with post-hoc tests (e.g. Tukey HSD and Duncan MRR),
compute coefficients of variation, and generate publication-ready summaries.
High-level wrappers allow automated multi-variable analysis with optional
clustering by experimental factors, as well as direct export of results to
Excel spreadsheets and high-resolution image tables for reporting.
Functions build on 'ggplot2', 'stats', and related packages and follow
methods widely used in agronomy (field trials and plant breeding).
Key references include Tukey (1949) <doi:10.2307/3001913>,
Duncan (1955) <doi:10.2307/3001478>, and Cohen (1988, ISBN:9781138892899);
see also 'agricolae' <https://CRAN.R-project.org/package=agricolae>
and Wickham (2016, ISBN:9783319242750> for 'ggplot2'.
Versión en español: Conjunto de herramientas para el análisis estadístico,
[...truncated...]
Author: Joaquin Alejandro Salinas Angeles [aut, cre]
Maintainer: Joaquin Alejandro Salinas Angeles <joaquinsa03@gmail.com>
Diff between agrobox versions 0.2.0 dated 2026-01-07 and 0.2.1 dated 2026-01-10
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NAMESPACE | 8 -------- NEWS.md | 9 +++++++++ R/agrotabla.R | 28 +++++++++++++++++++++++++--- man/agrotabla.Rd | 1 + 6 files changed, 45 insertions(+), 21 deletions(-)
Title: Guarded Resampling Workflows for Safe and Automated Machine
Learning in R
Description: Provides a guarded resampling workflow for training and evaluating machine‑learning models.
When the guarded resampling path is used, preprocessing and model fitting are re‑estimated within
each resampling split to reduce leakage risk. Supports multiple resampling schemes, integrates
with established engines in the 'tidymodels' ecosystem, and aims to improve evaluation reliability by
coordinating preprocessing, fitting, and evaluation within supported workflows. Offers a lightweight
AutoML‑style workflow by automating model training, resampling, and tuning across multiple algorithms,
while keeping evaluation design explicit and user‑controlled.
Author: Selcuk Korkmaz [aut, cre] ,
Dincer Goksuluk [aut] ,
Eda Karaismailoglu [aut]
Maintainer: Selcuk Korkmaz <selcukorkmaz@gmail.com>
Diff between fastml versions 0.7.5 dated 2025-12-22 and 0.7.6 dated 2026-01-10
fastml-0.7.5/fastml/man/framingham.Rd |only fastml-0.7.6/fastml/DESCRIPTION | 11 fastml-0.7.6/fastml/MD5 | 31 - fastml-0.7.6/fastml/R/evaluate_models.R | 26 + fastml-0.7.6/fastml/R/explainer_helpers.R | 48 +- fastml-0.7.6/fastml/R/fastml.R | 158 ++++++- fastml-0.7.6/fastml/R/plot.fastml.R | 8 fastml-0.7.6/fastml/R/process_model.R | 221 ++++++++-- fastml-0.7.6/fastml/R/resampling_guard.R | 21 fastml-0.7.6/fastml/R/summary.fastml.R | 12 fastml-0.7.6/fastml/R/train_models.R | 21 fastml-0.7.6/fastml/man/fastml.Rd | 6 fastml-0.7.6/fastml/man/fastml_compute_holdout_results.Rd | 6 fastml-0.7.6/fastml/man/process_model.Rd | 6 fastml-0.7.6/fastml/tests/testthat/test-custom-metric-holdout.R |only fastml-0.7.6/fastml/tests/testthat/test-fastml.R | 51 ++ fastml-0.7.6/fastml/tests/testthat/test-holdout-splitting.R |only fastml-0.7.6/fastml/tests/testthat/test-survival.R | 24 + 18 files changed, 539 insertions(+), 111 deletions(-)
Title: High-Level Functions for Tabulating, Charting and Reporting
Survey Data
Description: Craft polished tables and plots in Markdown reports.
Simply choose whether to treat your data as counts or metrics,
and the package will automatically generate well-designed default tables and plots for you.
Boiled down to the basics, with labeling features and simple interactive reports.
All functions are 'tidyverse' compatible.
Author: Jakob Juenger [aut, cre, cph] ,
Henrieke Kotthoff [aut, ctb] ,
Chantal Gaertner [ctb] ,
Sophia Rinne [ctb]
Maintainer: Jakob Juenger <jakob.juenger@uni-muenster.de>
Diff between volker versions 3.2.0 dated 2025-10-10 and 3.3.0 dated 2026-01-10
volker-3.2.0/volker/man/skim_boxplot.Rd |only volker-3.3.0/volker/DESCRIPTION | 24 volker-3.3.0/volker/MD5 | 86 volker-3.3.0/volker/NAMESPACE | 2 volker-3.3.0/volker/NEWS.md | 5 volker-3.3.0/volker/R/cluster.R | 16 volker-3.3.0/volker/R/config.R | 2 volker-3.3.0/volker/R/import-standalone-purrr.R | 488 +- volker-3.3.0/volker/R/labels.R | 2 volker-3.3.0/volker/R/model.R | 138 volker-3.3.0/volker/R/plots.R | 110 volker-3.3.0/volker/R/report.R | 104 volker-3.3.0/volker/R/skim.R | 215 - volker-3.3.0/volker/R/tables.R | 58 volker-3.3.0/volker/README.md | 53 volker-3.3.0/volker/inst/doc/introduction.R | 30 volker-3.3.0/volker/inst/doc/introduction.Rmd | 1272 ++++--- volker-3.3.0/volker/inst/doc/introduction.html | 143 volker-3.3.0/volker/man/add_clusters.Rd | 12 volker-3.3.0/volker/man/add_model.Rd | 14 volker-3.3.0/volker/man/dot-get_numbers_col.Rd |only volker-3.3.0/volker/man/dot-plot_bars.Rd | 6 volker-3.3.0/volker/man/dot-report_mdl.Rd | 12 volker-3.3.0/volker/man/get_angle.Rd | 2 volker-3.3.0/volker/man/model_metrics_plot.Rd | 4 volker-3.3.0/volker/man/model_metrics_tab.Rd | 4 volker-3.3.0/volker/man/plot_counts_items_grouped_items.Rd | 9 volker-3.3.0/volker/man/plot_counts_one_grouped.Rd | 4 volker-3.3.0/volker/man/plot_metrics.Rd | 2 volker-3.3.0/volker/man/plot_metrics_items_cor_items.Rd | 3 volker-3.3.0/volker/man/report_metrics.Rd | 28 volker-3.3.0/volker/man/skim_grouped.Rd | 4 volker-3.3.0/volker/man/skim_metrics.Rd | 24 volker-3.3.0/volker/man/volker-package.Rd | 3 volker-3.3.0/volker/tests/testthat/_snaps/clean.md | 228 - volker-3.3.0/volker/tests/testthat/_snaps/clusters.md | 200 - volker-3.3.0/volker/tests/testthat/_snaps/effects.md | 1440 ++++---- volker-3.3.0/volker/tests/testthat/_snaps/factors.md | 180 - volker-3.3.0/volker/tests/testthat/_snaps/idx.md | 214 - volker-3.3.0/volker/tests/testthat/_snaps/labels.md | 810 ++-- volker-3.3.0/volker/tests/testthat/_snaps/skim.md | 94 volker-3.3.0/volker/tests/testthat/_snaps/tables.md | 2122 ++++++------- volker-3.3.0/volker/tests/testthat/test-plots.R | 83 volker-3.3.0/volker/tests/testthat/test-theme.R | 1 volker-3.3.0/volker/vignettes/introduction.Rmd | 1272 ++++--- 45 files changed, 4961 insertions(+), 4562 deletions(-)
Title: Compute Risk Scores for Cardiovascular Diseases
Description: Calculate various cardiovascular disease risk scores from the
Framingham Heart Study (FHS), the American College of Cardiology (ACC),
and the American Heart Association (AHA) as described in D’agostino, et al
(2008) <doi:10.1161/circulationaha.107.699579>, Goff, et al (2013)
<doi:10.1161/01.cir.0000437741.48606.98>, and Mclelland, et al (2015)
<doi:10.1016/j.jacc.2015.08.035>, and Khan, et al (2024)
<doi:10.1161/CIRCULATIONAHA.123.067626>.
Author: Victor Castro [aut, cre]
Maintainer: Victor Castro <vcastro@mgh.harvard.edu>
Diff between CVrisk versions 1.1.1 dated 2023-08-19 and 1.2.1 dated 2026-01-10
DESCRIPTION | 24 + MD5 | 67 +++- NAMESPACE | 19 - NEWS.md | 55 ++-- R/ascvd_10y_accaha.R | 190 +++++++------- R/ascvd_10y_frs.R | 216 +++++++-------- R/ascvd_10y_frs_simple.R | 200 +++++++------- R/ascvd_prevent.R |only R/chd_10y_mesa.R | 194 +++++++------- R/chd_10y_mesa_cac.R | 200 +++++++------- R/compute_CVrisk.R | 138 +++++----- R/data.R | 225 ++++++++-------- R/make_sample_data.R |only R/mesa_cac_coef.R | 66 ++-- R/mesa_coef.R | 62 ++-- README.md | 143 +++++----- build/partial.rdb |binary build/vignette.rds |only data/sample_data.rda |binary inst |only man/CVrisk-package.Rd | 7 man/ascvd_10y_prevent.Rd |only man/ascvd_30y_prevent.Rd |only man/ascvd_pooled_coef.Rd | 90 +++--- man/compute_CVrisk.Rd | 20 + man/figures |only man/make_sample_data.Rd |only man/sample_data.Rd | 1 tests/testthat.R | 8 tests/testthat/test-ascvd_10y_accaha.R | 392 ++++++++++++++++++++--------- tests/testthat/test-ascvd_10y_frs.R | 208 ++++++++++++++- tests/testthat/test-ascvd_10y_frs_simple.R | 196 +++++++++++++- tests/testthat/test-ascvd_10y_prevent.R |only tests/testthat/test-chd_10y_mesa.R | 203 +++++++++++++-- tests/testthat/test-chd_10y_mesa_cac.R | 215 ++++++++++++++- tests/testthat/test-compute_CVrisk.R | 216 +++++++++++++-- tests/testthat/test-data.R |only tests/testthat/test-make_sample_data.R |only vignettes |only 39 files changed, 2214 insertions(+), 1141 deletions(-)
Title: Efficient Stepwise Selection in Decomposable Models
Description: An implementation of the ESS algorithm following Amol Deshpande, Minos Garofalakis,
Michael I Jordan (2013) <doi:10.48550/arXiv.1301.2267>. The ESS algorithm
is used for model selection in decomposable graphical models.
Author: Mads Lindskou [aut, cre]
Maintainer: Mads Lindskou <mads@math.aau.dk>
Diff between ess versions 1.1.2 dated 2021-05-31 and 1.1.2.1 dated 2026-01-10
DESCRIPTION | 9 ++++----- MD5 | 6 +++--- build/partial.rdb |binary data/derma.rda |binary 4 files changed, 7 insertions(+), 8 deletions(-)
Title: Chat-Based Interactive Artificial Intelligence for R
Description: The Large Language Model (LLM) represents a groundbreaking advancement
in data science and programming, and also allows us to extend the world of R.
A seamless interface for integrating the 'OpenAI' Web APIs into R is provided in this package.
This package leverages LLM-based AI techniques, enabling efficient knowledge discovery and data analysis.
The previous functions such as seamless translation and image generation have been moved
to other packages 'deepRstudio' and 'stableDiffusion4R'.
Author: Satoshi Kume [aut, cre]
Maintainer: Satoshi Kume <satoshi.kume.1984@gmail.com>
Diff between chatAI4R versions 0.3.6 dated 2025-02-11 and 1.3.1 dated 2026-01-10
chatAI4R-0.3.6/chatAI4R/R/chatAI4pdf.R |only chatAI4R-0.3.6/chatAI4R/R/create_eBay_Description.R |only chatAI4R-0.3.6/chatAI4R/R/summaryWebScraping.R |only chatAI4R-0.3.6/chatAI4R/man/chatAI4pdf.Rd |only chatAI4R-0.3.6/chatAI4R/man/summaryWebScrapingText.Rd |only chatAI4R-1.3.1/chatAI4R/DESCRIPTION | 18 chatAI4R-1.3.1/chatAI4R/MD5 | 119 +- chatAI4R-1.3.1/chatAI4R/NAMESPACE | 29 chatAI4R-1.3.1/chatAI4R/R/DifyChat4R.R |only chatAI4R-1.3.1/chatAI4R/R/RevisedText.R | 40 chatAI4R-1.3.1/chatAI4R/R/TextSummary.R | 40 chatAI4R-1.3.1/chatAI4R/R/addCommentCode.R | 75 + chatAI4R-1.3.1/chatAI4R/R/autocreateFunction4R.R | 644 ++++++++++++++-- chatAI4R-1.3.1/chatAI4R/R/chat4R.R | 102 +- chatAI4R-1.3.1/chatAI4R/R/chat4R_history.R | 24 chatAI4R-1.3.1/chatAI4R/R/chat4R_streaming.R | 18 chatAI4R-1.3.1/chatAI4R/R/chat4Rv2.R | 44 - chatAI4R-1.3.1/chatAI4R/R/completions4R.R | 69 + chatAI4R-1.3.1/chatAI4R/R/conversation4R.R | 113 +- chatAI4R-1.3.1/chatAI4R/R/convertRscript2Function.R | 18 chatAI4R-1.3.1/chatAI4R/R/convertScientificLiterature.R | 18 chatAI4R-1.3.1/chatAI4R/R/createEBAYdes.R |only chatAI4R-1.3.1/chatAI4R/R/createImagePrompt_v1.R | 10 chatAI4R-1.3.1/chatAI4R/R/createImagePrompt_v2.R | 106 ++ chatAI4R-1.3.1/chatAI4R/R/createRcode.R | 19 chatAI4R-1.3.1/chatAI4R/R/createRfunction.R | 72 + chatAI4R-1.3.1/chatAI4R/R/createSpecifications4R.R | 80 + chatAI4R-1.3.1/chatAI4R/R/discussion_flow_v1.R | 189 +++- chatAI4R-1.3.1/chatAI4R/R/discussion_flow_v2.R | 204 +++-- chatAI4R-1.3.1/chatAI4R/R/enrichTextContent.R | 19 chatAI4R-1.3.1/chatAI4R/R/gemini4R.R |only chatAI4R-1.3.1/chatAI4R/R/geminiGrounding4R.R |only chatAI4R-1.3.1/chatAI4R/R/internal_state.R |only chatAI4R-1.3.1/chatAI4R/R/interpretResult.R |only chatAI4R-1.3.1/chatAI4R/R/multiLLMviaionet.R |only chatAI4R-1.3.1/chatAI4R/R/replicateAPI4R.R | 137 ++- chatAI4R-1.3.1/chatAI4R/R/slow_print_v2.R | 39 chatAI4R-1.3.1/chatAI4R/R/speakInEN.R |only chatAI4R-1.3.1/chatAI4R/R/textEmbedding.R | 51 - chatAI4R-1.3.1/chatAI4R/R/textFileInput4ai.R | 349 ++++++++ chatAI4R-1.3.1/chatAI4R/inst/rebuild_package.R |only chatAI4R-1.3.1/chatAI4R/inst/rstudio/addins.dcf | 5 chatAI4R-1.3.1/chatAI4R/inst/sh |only chatAI4R-1.3.1/chatAI4R/man/DifyChat4R.Rd |only chatAI4R-1.3.1/chatAI4R/man/addCommentCode.Rd | 20 chatAI4R-1.3.1/chatAI4R/man/autocreateFunction4R.Rd | 35 chatAI4R-1.3.1/chatAI4R/man/chat4R.Rd | 13 chatAI4R-1.3.1/chatAI4R/man/chat4Rv2.Rd | 6 chatAI4R-1.3.1/chatAI4R/man/completions4R.Rd | 28 chatAI4R-1.3.1/chatAI4R/man/createEBAYdes.Rd | 12 chatAI4R-1.3.1/chatAI4R/man/createImagePrompt_v2.Rd | 39 chatAI4R-1.3.1/chatAI4R/man/createSpecifications4R.Rd | 9 chatAI4R-1.3.1/chatAI4R/man/discussion_flow_v1.Rd | 14 chatAI4R-1.3.1/chatAI4R/man/discussion_flow_v2.Rd | 5 chatAI4R-1.3.1/chatAI4R/man/gemini4R.Rd |only chatAI4R-1.3.1/chatAI4R/man/geminiGrounding4R.Rd |only chatAI4R-1.3.1/chatAI4R/man/interpretResult.Rd |only chatAI4R-1.3.1/chatAI4R/man/ionet_models.Rd |only chatAI4R-1.3.1/chatAI4R/man/list_ionet_models.Rd |only chatAI4R-1.3.1/chatAI4R/man/multiLLMviaionet.Rd |only chatAI4R-1.3.1/chatAI4R/man/print.multiLLM_result.Rd |only chatAI4R-1.3.1/chatAI4R/man/print_multiLLM_results.Rd |only chatAI4R-1.3.1/chatAI4R/man/refresh_ionet_models.Rd |only chatAI4R-1.3.1/chatAI4R/man/replicatellmAPI4R.Rd | 38 chatAI4R-1.3.1/chatAI4R/man/revisedText.Rd | 19 chatAI4R-1.3.1/chatAI4R/man/speakInEN.Rd |only chatAI4R-1.3.1/chatAI4R/man/textEmbedding.Rd | 13 chatAI4R-1.3.1/chatAI4R/man/textFileInput4ai.Rd | 34 chatAI4R-1.3.1/chatAI4R/tests/test |only chatAI4R-1.3.1/chatAI4R/tests/testthat.R | 7 chatAI4R-1.3.1/chatAI4R/tests/testthat/test_chatAI4R.R | 32 71 files changed, 2385 insertions(+), 590 deletions(-)
Title: Summarize Data for Scientific Publication
Description: Create and format tables and APA statistics for
scientific publication. This includes making a 'Table 1'
to summarize demographics across groups, correlation tables
with significance indicated by stars, and extracting formatted
statistical summarizes from simple tests for in-text notation.
The package also includes functions for Winsorizing data based
on a Z-statistic cutoff.
Author: David Pagliaccio [aut, cre]
Maintainer: David Pagliaccio <david.pagliaccio@gmail.com>
This is a re-admission after prior archival of version 1.2.3 dated 2024-03-08
Diff between scipub versions 1.2.3 dated 2024-03-08 and 1.3.0 dated 2026-01-10
DESCRIPTION | 23 - MD5 | 39 +- NAMESPACE | 2 R/FullTable1.R | 599 +++++++++++++----------------------------- R/apastat.R | 4 R/correltable.R | 470 ++++++-------------------------- R/gg_groupplot.R | 27 + R/partial_correltable.R | 238 ++++------------ R/utils.R |only R/winsorZ.R | 17 - R/winsorZ_find.R | 9 build/vignette.rds |binary inst/doc/scipub_vignette.R | 8 inst/doc/scipub_vignette.Rmd | 6 inst/doc/scipub_vignette.html | 414 ++++++++++------------------- man/FullTable1.Rd | 19 + man/apastat.Rd | 2 man/correltable.Rd | 16 - man/gg_groupplot.Rd | 6 man/partial_correltable.Rd | 16 - vignettes/scipub_vignette.Rmd | 6 21 files changed, 622 insertions(+), 1299 deletions(-)
Title: Multivariate Menu for Radiant: Business Analytics using R and
Shiny
Description: The Radiant Multivariate menu includes interfaces for perceptual
mapping, factor analysis, cluster analysis, and conjoint analysis. The
application extends the functionality in 'radiant.data'.
Author: Vincent Nijs [aut, cre]
Maintainer: Vincent Nijs <radiant@rady.ucsd.edu>
This is a re-admission after prior archival of version 1.6.7 dated 2025-03-10
Diff between radiant.multivariate versions 1.6.7 dated 2025-03-10 and 1.6.8 dated 2026-01-10
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/mds.R | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
More information about radiant.multivariate at CRAN
Permanent link
Title: Propensity Score Methods for Survival Analysis
Description: Implements propensity score weighting methods for estimating
counterfactual survival functions, marginal hazard ratios, and
weighted Kaplan-Meier and cumulative risk curves in observational
studies with time-to-event outcomes. Supports binary and multiple
treatment groups with inverse probability of treatment weighting (IPW),
overlap weighting (OW), and average treatment effect on the treated
(ATT). Includes symmetric trimming (Crump extension) for extreme
propensity scores. Variance estimation via analytical M-estimation or
bootstrap. Methods based on Li et al. (2018) <doi:10.1080/01621459.2016.1260466>,
Li & Li (2019) <doi:10.1214/19-AOAS1282>, and Cheng et al. (2022)
<doi:10.1093/aje/kwac043>.
Author: Chengxin Yang [aut, cre],
Chao Cheng [aut],
Fan Li [aut],
Fan Li [aut]
Maintainer: Chengxin Yang <chengxin.yang@duke.edu>
Diff between PSsurvival versions 0.1.0 dated 2025-12-09 and 0.2.0 dated 2026-01-10
DESCRIPTION | 33 MD5 | 40 NAMESPACE | 4 NEWS.md | 84 + R/A00-surveff.R | 121 + R/B00-marCoxph.R | 109 - R/C00-weighted-km.R |only R/C01-weighted-km-estimator.R |only README.md | 38 build/vignette.rds |binary inst/doc/PSsurvival-tutorial.R | 148 + inst/doc/PSsurvival-tutorial.Rmd | 307 ++- inst/doc/PSsurvival-tutorial.html | 3049 +++++++++++++++++++++++++++++--------- man/estimate_weighted_km.Rd |only man/marCoxph.Rd | 70 man/plot.weightedKM.Rd |only man/print.weightedKM.Rd |only man/summary.weightedKM.Rd |only man/surveff.Rd | 77 man/weightedKM.Rd |only tests/testthat/test-marCoxph.R | 37 tests/testthat/test-surveff.R | 35 tests/testthat/test-validation.R | 12 tests/testthat/test-weightedKM.R |only vignettes/PSsurvival-tutorial.Rmd | 307 ++- 25 files changed, 3389 insertions(+), 1082 deletions(-)
Title: Semiparametric Bivariate Correlated Frailty Models Fit
Description: Fit semiparametric bivariate correlated frailty models.
Author: Mesfin Haileyesus [aut, cre]
Maintainer: Mesfin Haileyesus <mesfinh1@umbc.edu>
This is a re-admission after prior archival of version 0.1.1 dated 2022-12-10
Diff between bcfrailph versions 0.1.1 dated 2022-12-10 and 0.1.2 dated 2026-01-10
bcfrailph-0.1.1/bcfrailph/R/simbcfrailph.R |only bcfrailph-0.1.1/bcfrailph/man/simbcfrailph.Rd |only bcfrailph-0.1.2/bcfrailph/DESCRIPTION | 25 bcfrailph-0.1.2/bcfrailph/MD5 | 46 - bcfrailph-0.1.2/bcfrailph/NAMESPACE | 2 bcfrailph-0.1.2/bcfrailph/R/bcfrailph.R | 87 +- bcfrailph-0.1.2/bcfrailph/R/bcfrailph.control.R | 14 bcfrailph-0.1.2/bcfrailph/R/fitbccv.gammasp.R | 110 ++- bcfrailph-0.1.2/bcfrailph/R/fitbccv.lognsp.R | 108 +-- bcfrailph-0.1.2/bcfrailph/R/plot.bcfrailph.R | 2 bcfrailph-0.1.2/bcfrailph/R/print.bcfrailph.R | 2 bcfrailph-0.1.2/bcfrailph/R/shrgamsp.R | 36 - bcfrailph-0.1.2/bcfrailph/R/simbcfrail.R |only bcfrailph-0.1.2/bcfrailph/R/simstdybcf.R | 30 bcfrailph-0.1.2/bcfrailph/R/summary.bcfrailph.R | 2 bcfrailph-0.1.2/bcfrailph/R/utilities.R | 754 +++++++++++++-------- bcfrailph-0.1.2/bcfrailph/man/bcfrailph.Rd | 81 +- bcfrailph-0.1.2/bcfrailph/man/bcfrailph.control.Rd | 12 bcfrailph-0.1.2/bcfrailph/man/fitbccv.gammasp.Rd | 30 bcfrailph-0.1.2/bcfrailph/man/fitbccv.lognsp.Rd | 32 bcfrailph-0.1.2/bcfrailph/man/plot.bcfrailph.Rd | 2 bcfrailph-0.1.2/bcfrailph/man/print.bcfrailph.Rd | 2 bcfrailph-0.1.2/bcfrailph/man/shrgamsp.Rd | 32 bcfrailph-0.1.2/bcfrailph/man/simbcfrail.Rd |only bcfrailph-0.1.2/bcfrailph/man/simstdybcf.Rd | 18 bcfrailph-0.1.2/bcfrailph/man/summary.bcfrailph.Rd | 2 26 files changed, 888 insertions(+), 541 deletions(-)
Title: Treatment Switching
Description: Implements rank preserving structural failure time model (RPSFTM), iterative parameter estimation (IPE), inverse probability of censoring weights (IPCW), marginal structural model (MSM), simple two-stage estimation (TSEsimp), and improved two-stage estimation with g-estimation (TSEgest) methods for treatment switching in randomized clinical trials.
Author: Kaifeng Lu [aut, cre]
Maintainer: Kaifeng Lu <kaifenglu@gmail.com>
Diff between trtswitch versions 0.2.2 dated 2025-11-16 and 0.2.3 dated 2026-01-10
trtswitch-0.2.2/trtswitch/R/splines.R |only trtswitch-0.2.2/trtswitch/man/bscpp.Rd |only trtswitch-0.2.2/trtswitch/man/findInterval3.Rd |only trtswitch-0.2.2/trtswitch/man/nscpp.Rd |only trtswitch-0.2.2/trtswitch/man/qrcpp.Rd |only trtswitch-0.2.2/trtswitch/man/splineDesigncpp.Rd |only trtswitch-0.2.2/trtswitch/tests/testthat/test-bscpp.R |only trtswitch-0.2.2/trtswitch/tests/testthat/test-nscpp.R |only trtswitch-0.2.2/trtswitch/tests/testthat/test-qrcpp.R |only trtswitch-0.2.2/trtswitch/tests/testthat/test-splineDesigncpp.R |only trtswitch-0.2.3/trtswitch/DESCRIPTION | 16 trtswitch-0.2.3/trtswitch/MD5 | 242 trtswitch-0.2.3/trtswitch/NAMESPACE | 27 trtswitch-0.2.3/trtswitch/NEWS.md | 15 trtswitch-0.2.3/trtswitch/R/RcppExports.R | 453 trtswitch-0.2.3/trtswitch/R/assess_phregr.R |only trtswitch-0.2.3/trtswitch/R/data.R | 22 trtswitch-0.2.3/trtswitch/R/ipcw.R | 188 trtswitch-0.2.3/trtswitch/R/ipe.R | 154 trtswitch-0.2.3/trtswitch/R/liferegr.R | 209 trtswitch-0.2.3/trtswitch/R/logisregr.R | 204 trtswitch-0.2.3/trtswitch/R/msm.R | 175 trtswitch-0.2.3/trtswitch/R/phregr.R | 227 trtswitch-0.2.3/trtswitch/R/plot.assess_phregr.R |only trtswitch-0.2.3/trtswitch/R/plot.ipcw.R | 365 trtswitch-0.2.3/trtswitch/R/plot.ipe.R | 74 trtswitch-0.2.3/trtswitch/R/plot.msm.R | 367 trtswitch-0.2.3/trtswitch/R/plot.rpsftm.R | 72 trtswitch-0.2.3/trtswitch/R/plot.tsegest.R | 84 trtswitch-0.2.3/trtswitch/R/plot.tsesimp.R | 80 trtswitch-0.2.3/trtswitch/R/preptdc.R | 74 trtswitch-0.2.3/trtswitch/R/print.assess_phregr.R |only trtswitch-0.2.3/trtswitch/R/print.ipcw.R | 27 trtswitch-0.2.3/trtswitch/R/print.ipe.R | 26 trtswitch-0.2.3/trtswitch/R/print.liferegr.R | 135 trtswitch-0.2.3/trtswitch/R/print.logisregr.R | 132 trtswitch-0.2.3/trtswitch/R/print.msm.R | 27 trtswitch-0.2.3/trtswitch/R/print.phregr.R | 129 trtswitch-0.2.3/trtswitch/R/print.rpsftm.R | 36 trtswitch-0.2.3/trtswitch/R/print.tsegest.R | 43 trtswitch-0.2.3/trtswitch/R/print.tsesimp.R | 49 trtswitch-0.2.3/trtswitch/R/residuals_liferegr.R | 163 trtswitch-0.2.3/trtswitch/R/residuals_phregr.R | 176 trtswitch-0.2.3/trtswitch/R/rpsftm.R | 157 trtswitch-0.2.3/trtswitch/R/survfit_phregr.R | 131 trtswitch-0.2.3/trtswitch/R/trtswitch-package.R | 12 trtswitch-0.2.3/trtswitch/R/tsegest.R | 160 trtswitch-0.2.3/trtswitch/R/tsesimp.R | 186 trtswitch-0.2.3/trtswitch/R/utilities.R |only trtswitch-0.2.3/trtswitch/R/zph_phregr.R |only trtswitch-0.2.3/trtswitch/data/liver.rda |only trtswitch-0.2.3/trtswitch/inst/doc/ipcw.html | 36 trtswitch-0.2.3/trtswitch/inst/doc/ipe.R | 2 trtswitch-0.2.3/trtswitch/inst/doc/ipe.Rmd | 2 trtswitch-0.2.3/trtswitch/inst/doc/ipe.html | 4 trtswitch-0.2.3/trtswitch/inst/doc/msm.html | 38 trtswitch-0.2.3/trtswitch/inst/doc/rpsftm.R | 2 trtswitch-0.2.3/trtswitch/inst/doc/rpsftm.Rmd | 2 trtswitch-0.2.3/trtswitch/inst/doc/rpsftm.html | 4 trtswitch-0.2.3/trtswitch/inst/doc/tsegest.R | 2 trtswitch-0.2.3/trtswitch/inst/doc/tsegest.Rmd | 2 trtswitch-0.2.3/trtswitch/inst/doc/tsegest.html | 34 trtswitch-0.2.3/trtswitch/inst/doc/tsesimp.R | 15 trtswitch-0.2.3/trtswitch/inst/doc/tsesimp.Rmd | 4 trtswitch-0.2.3/trtswitch/inst/doc/tsesimp.html | 30 trtswitch-0.2.3/trtswitch/inst/licenses |only trtswitch-0.2.3/trtswitch/inst/vendor |only trtswitch-0.2.3/trtswitch/man/assess_phregr.Rd |only trtswitch-0.2.3/trtswitch/man/ipcw.Rd | 20 trtswitch-0.2.3/trtswitch/man/ipe.Rd | 18 trtswitch-0.2.3/trtswitch/man/kmdiff.Rd | 38 trtswitch-0.2.3/trtswitch/man/kmest.Rd | 5 trtswitch-0.2.3/trtswitch/man/liferegr.Rd | 15 trtswitch-0.2.3/trtswitch/man/liver.Rd |only trtswitch-0.2.3/trtswitch/man/logisregr.Rd | 10 trtswitch-0.2.3/trtswitch/man/lrtest.Rd | 19 trtswitch-0.2.3/trtswitch/man/merge_append.Rd |only trtswitch-0.2.3/trtswitch/man/msm.Rd | 18 trtswitch-0.2.3/trtswitch/man/phregr.Rd | 16 trtswitch-0.2.3/trtswitch/man/plot.assess_phregr.Rd |only trtswitch-0.2.3/trtswitch/man/preptdc.Rd | 16 trtswitch-0.2.3/trtswitch/man/print.assess_phregr.Rd |only trtswitch-0.2.3/trtswitch/man/process_cov.Rd |only trtswitch-0.2.3/trtswitch/man/recensor_sim_rpsftm.Rd | 35 trtswitch-0.2.3/trtswitch/man/rmdiff.Rd | 16 trtswitch-0.2.3/trtswitch/man/rmest.Rd | 7 trtswitch-0.2.3/trtswitch/man/rpsftm.Rd | 18 trtswitch-0.2.3/trtswitch/man/survQuantile.Rd | 6 trtswitch-0.2.3/trtswitch/man/survsplit.Rd | 2 trtswitch-0.2.3/trtswitch/man/tsegest.Rd | 11 trtswitch-0.2.3/trtswitch/man/tsegestsim.Rd | 10 trtswitch-0.2.3/trtswitch/man/tsesimp.Rd | 18 trtswitch-0.2.3/trtswitch/man/tssim.Rd | 56 trtswitch-0.2.3/trtswitch/man/zph_phregr.Rd |only trtswitch-0.2.3/trtswitch/src/Makevars |only trtswitch-0.2.3/trtswitch/src/Makevars.win |only trtswitch-0.2.3/trtswitch/src/RcppExports.cpp | 741 trtswitch-0.2.3/trtswitch/src/dataframe_list.cpp |only trtswitch-0.2.3/trtswitch/src/dataframe_list.h |only trtswitch-0.2.3/trtswitch/src/ipcw.cpp | 2778 +- trtswitch-0.2.3/trtswitch/src/ipe.cpp | 1833 - trtswitch-0.2.3/trtswitch/src/logistic_regression.cpp | 1753 - trtswitch-0.2.3/trtswitch/src/logistic_regression.h | 61 trtswitch-0.2.3/trtswitch/src/msm.cpp | 2385 + trtswitch-0.2.3/trtswitch/src/recensor_sim_rpsftm.cpp | 938 trtswitch-0.2.3/trtswitch/src/rpsftm.cpp | 1893 - trtswitch-0.2.3/trtswitch/src/ska |only trtswitch-0.2.3/trtswitch/src/splines.cpp | 1315 - trtswitch-0.2.3/trtswitch/src/splines.h | 64 trtswitch-0.2.3/trtswitch/src/survival_analysis.cpp |12695 +++++----- trtswitch-0.2.3/trtswitch/src/survival_analysis.h | 394 trtswitch-0.2.3/trtswitch/src/thread_utils.h |only trtswitch-0.2.3/trtswitch/src/tsegest.cpp | 2801 +- trtswitch-0.2.3/trtswitch/src/tsegestsim.cpp | 591 trtswitch-0.2.3/trtswitch/src/tsesimp.cpp | 2020 - trtswitch-0.2.3/trtswitch/src/tssim.cpp | 475 trtswitch-0.2.3/trtswitch/src/utilities.cpp | 1791 - trtswitch-0.2.3/trtswitch/src/utilities.h | 525 trtswitch-0.2.3/trtswitch/tests/testthat/test-ipcw.R | 8 trtswitch-0.2.3/trtswitch/tests/testthat/test-ipe.R | 6 trtswitch-0.2.3/trtswitch/tests/testthat/test-kmest.R | 16 trtswitch-0.2.3/trtswitch/tests/testthat/test-liferegr.R | 36 trtswitch-0.2.3/trtswitch/tests/testthat/test-logisregr.R | 42 trtswitch-0.2.3/trtswitch/tests/testthat/test-lrtest.R | 15 trtswitch-0.2.3/trtswitch/tests/testthat/test-phregr.R | 34 trtswitch-0.2.3/trtswitch/tests/testthat/test-residuals_liferegr.R | 22 trtswitch-0.2.3/trtswitch/tests/testthat/test-residuals_phregr.R | 68 trtswitch-0.2.3/trtswitch/tests/testthat/test-rmdiff.R | 61 trtswitch-0.2.3/trtswitch/tests/testthat/test-rmest.R | 20 trtswitch-0.2.3/trtswitch/tests/testthat/test-rpsftm.R | 8 trtswitch-0.2.3/trtswitch/tests/testthat/test-survfit_phregr.R | 58 trtswitch-0.2.3/trtswitch/tests/testthat/test-tsegest.R | 2 trtswitch-0.2.3/trtswitch/tests/testthat/test-tsesimp.R | 14 trtswitch-0.2.3/trtswitch/tests/testthat/test-zph_phregr.R |only trtswitch-0.2.3/trtswitch/vignettes/ipe.Rmd | 2 trtswitch-0.2.3/trtswitch/vignettes/rpsftm.Rmd | 2 trtswitch-0.2.3/trtswitch/vignettes/tsegest.Rmd | 2 trtswitch-0.2.3/trtswitch/vignettes/tsesimp.Rmd | 4 138 files changed, 21676 insertions(+), 18965 deletions(-)
Title: Download and Tidy IPC and CH Data
Description: Utilities to access Integrated Food Security Phase Classification
(IPC) and Cadre Harmonisé (CH) food security data. Wrapper functions are
available for all of the 'IPC-CH' Public API (<https://docs.api.ipcinfo.org>)
simplified and advanced endpoints to easily download the data in a clean and
tidy format.
Author: Giulia Martini [aut, cre, cph]
Maintainer: Giulia Martini <giulia.martini@un.org>
Diff between ripc versions 0.3.1 dated 2024-06-25 and 0.3.2 dated 2026-01-10
DESCRIPTION | 17 MD5 | 62 +-- NAMESPACE | 26 - NEWS.md | 170 ++++----- R/Ripc-package.R | 18 - R/create_areas_df.R | 172 +++++----- R/create_base_df.R | 200 +++++------ R/create_groups_df.R | 76 ++-- R/extract_dates.R | 78 ++-- R/ipc_get.R | 2 R/ipc_get_analyses.R | 190 +++++------ R/ipc_get_areas.R | 266 +++++++-------- R/ipc_get_country.R | 196 +++++------ R/ipc_get_icons.R | 162 ++++----- R/ipc_get_points.R | 220 ++++++------ R/ipc_get_population.R | 1 R/null_converter.R | 50 +- R/population_utils.R | 238 ++++++------- README.md | 344 ++++++++++---------- build/vignette.rds |binary inst/WORDLIST | 34 - inst/doc/ipc-api.Rmd | 188 +++++----- inst/doc/ipc-api.html | 788 +++++++++++++++++++++++----------------------- man/ipc_get.Rd | 60 +-- man/ipc_get_analyses.Rd | 144 ++++---- man/ipc_get_areas.Rd | 188 +++++----- man/ipc_get_country.Rd | 154 ++++---- man/ipc_get_icons.Rd | 152 ++++---- man/ipc_get_points.Rd | 170 ++++----- man/ipc_get_population.Rd | 218 ++++++------ man/ripc-package.Rd | 4 vignettes/ipc-api.Rmd | 188 +++++----- 32 files changed, 2389 insertions(+), 2387 deletions(-)
Title: Functional-Based Chain Ladder for Claims Reserving
Description: Functional claims reserving methods based on aggregated chain-ladder data, also known as a run-off triangle, implemented in three nonparametric algorithms (PARALLAX, REACT, and MACRAME) proposed in Maciak, Mizera, and Pešta (2022) <doi:10.1017/asb.2022.4>. Additional methods including permutation bootstrap for completed run-off triangles are also provided.
Author: Matus Maciak [aut, cre],
Rastislav Matus [aut, ctb],
Ivan Mizera [aut],
Michal Pesta [aut]
Maintainer: Matus Maciak <maciak@karlin.mff.cuni.cz>
Diff between ProfileLadder versions 0.2.1 dated 2025-10-23 and 0.2.2 dated 2026-01-10
DESCRIPTION | 13 ++++++++----- MD5 | 7 ++++++- build |only inst |only vignettes |only 5 files changed, 14 insertions(+), 6 deletions(-)
Title: Process Improvement using Data
Description: A collection of scripts and data files for the statistics text:
"Process Improvement using Data" <https://learnche.org/pid/> and the online
course "Experimentation for Improvement" found on Coursera. The package
contains code for designed experiments, data sets and other convenience
functions used in the book.
Author: Kevin Dunn [aut, cre]
Maintainer: Kevin Dunn <kgdunn@gmail.com>
Diff between pid versions 0.50 dated 2018-11-23 and 0.65 dated 2026-01-10
DESCRIPTION | 23 +++++------ LICENSE | 4 - MD5 | 44 +++++++++++---------- NAMESPACE | 32 ++++++++------- R/contourPlot.R | 3 - R/grocery.R | 3 - R/manufacture.R | 3 - R/paretoPlot.R | 3 - R/pid-package.R |only R/popcorn.R | 3 - R/tradeOffTable.R | 3 - R/tradeoff.R | 1 build |only man/boilingpot.Rd | 18 ++++---- man/contourPlot.Rd | 70 +++++++++++++--------------------- man/distillateflow.Rd | 8 +-- man/grocery.Rd | 40 ++++++------------- man/manfacture.Rd | 39 ++++++------------- man/paretoPlot.Rd | 101 ++++++++++++++++++++------------------------------ man/pid-package.Rd | 2 man/popcorn.Rd | 40 ++++++------------- man/solar.Rd | 32 +++++++-------- man/tradeOffTable.Rd | 54 +++++++------------------- man/tradeoff.Rd | 21 ++-------- 24 files changed, 231 insertions(+), 316 deletions(-)
Title: Model-Based Sliced Inverse Regression
Description: An R package for dimension reduction based on finite Gaussian mixture modeling of inverse regression.
Author: Luca Scrucca [aut, cre]
Maintainer: Luca Scrucca <luca.scrucca@unibo.it>
Diff between msir versions 1.3.3 dated 2020-12-16 and 1.4 dated 2026-01-10
DESCRIPTION | 22 MD5 | 25 NEWS.md | 5 R/msir.R | 26 R/spinplot.R | 36 build/partial.rdb |only build/vignette.rds |binary inst/CITATION | 28 inst/doc/msir.R | 72 - inst/doc/msir.Rmd | 51 - inst/doc/msir.html | 1814 ++++++++++++++++++++++++++++++++++++++++++------- man/msir-package.Rd | 3 vignettes/msir.Rmd | 51 - vignettes/vignette.css | 39 - 14 files changed, 1736 insertions(+), 436 deletions(-)
Title: Change Point Detection for Non-Stationary and Cross-Correlated
Time Series
Description: Implements methods for multiple change point detection in multivariate
time series with non-stationary dynamics and cross-correlations. The methodology
is based on a model in which each component has a fluctuating mean represented by
a random walk with occasional abrupt shifts, combined with a stationary vector
autoregressive structure to capture temporal and cross-sectional dependence. The
framework is broadly applicable to correlated multivariate sequences in which
large, sudden shifts occur in all or subsets of components and are the primary
targets of interest, whereas small, smooth fluctuations are not. Although random
walks are used as a modeling device, they provide a flexible approximation for a
wide class of slowly varying or locally smooth dynamics, enabling robust
performance beyond the strict random walk setting.
Author: Yuhan Tian [aut, cre],
Abolfazl Safikhani [aut]
Maintainer: Yuhan Tian <yuhan.tian@fau.de>
Diff between FluxPoint versions 0.1.1 dated 2026-01-06 and 0.1.2 dated 2026-01-10
FluxPoint-0.1.1/FluxPoint/R/FluxPoint-package.R |only FluxPoint-0.1.1/FluxPoint/R/RcppExports.R |only FluxPoint-0.1.1/FluxPoint/man/FluxPoint-package.Rd |only FluxPoint-0.1.1/FluxPoint/src |only FluxPoint-0.1.2/FluxPoint/DESCRIPTION | 11 +++++------ FluxPoint-0.1.2/FluxPoint/MD5 | 19 ++++++------------- FluxPoint-0.1.2/FluxPoint/NAMESPACE | 3 +-- FluxPoint-0.1.2/FluxPoint/NEWS.md | 7 +++++++ FluxPoint-0.1.2/FluxPoint/R/Functions.R | 16 ++++++++-------- FluxPoint-0.1.2/FluxPoint/man/inver.Rd | 4 ++-- FluxPoint-0.1.2/FluxPoint/man/sqrtmat.Rd | 4 ++-- 11 files changed, 31 insertions(+), 33 deletions(-)
Title: Extreme Value Statistics and Quantile Estimation
Description: Fit, plot and compare several (extreme value) distribution functions.
Compute (truncated) distribution quantile estimates and plot return periods on a linear scale.
On the fitting method, see Asquith (2011): Distributional Analysis with L-moment Statistics [...] ISBN 1463508417.
Author: Berry Boessenkool [aut, cre]
Maintainer: Berry Boessenkool <berry-b@gmx.de>
Diff between extremeStat versions 1.5.11 dated 2025-07-28 and 1.5.12 dated 2026-01-10
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- R/distLextreme.R | 2 +- inst/doc/extremeStat.html | 9 +++++---- man/distLextreme.Rd | 2 +- 5 files changed, 16 insertions(+), 15 deletions(-)
Title: 'C++' Implementations of Functional Enrichment Analysis
Description: Fast implementations of functional enrichment analysis methods using 'C++' via 'Rcpp'.
Currently provides Over-Representation Analysis (ORA) and Gene Set Enrichment Analysis (GSEA).
The multilevel GSEA algorithm is derived from the 'fgsea' package.
Methods are described in Subramanian et al. (2005) <doi:10.1073/pnas.0506580102> and Korotkevich et al. (2021) <doi:10.1101/060012>.
Author: Guangchuang Yu [aut, cre]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between enrichit versions 0.0.8 dated 2025-12-22 and 0.0.9 dated 2026-01-10
DESCRIPTION | 12 +++---- MD5 | 12 +++---- NEWS.md | 4 ++ R/gsea.R | 25 +++++++++++++-- R/utilities.R | 76 ++++++++++++++++++++++++++++++++++++++++++++++ inst/doc/enrichit.html | 32 ++++++++++++------- tests/testthat/test-ora.R | 16 ++++----- 7 files changed, 142 insertions(+), 35 deletions(-)
Title: R Interface to 'DuckDB' Database with Spatial Extension
Description: Fast & memory-efficient functions to analyze and manipulate large
spatial data data sets. It leverages the fast analytical
capabilities of 'DuckDB' and its spatial extension (see <https://duckdb.org/docs/stable/core_extensions/spatial/overview>)
while maintaining compatibility with R’s spatial data ecosystem to
work with spatial vector data.
Author: Adrian Cidre Gonzalez [aut, cre] ,
Rafael H. M. Pereira [aut] ,
Egor Kotov [aut]
Maintainer: Adrian Cidre Gonzalez <adrian.cidre@gmail.com>
Diff between duckspatial versions 0.2.0 dated 2025-04-29 and 0.9.0 dated 2026-01-10
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Title: An Interactive and Feature-Rich Data Viewer
Description: Provides an interactive viewer for 'data.frame' and 'tibble' objects using 'shiny' <https://shiny.posit.co/> and 'DT' <https://rstudio.github.io/DT/>. It supports complex filtering, column selection, and automatic generation of reproducible 'dplyr' <https://dplyr.tidyverse.org/> code for data manipulation. The package is designed for ease of use in data exploration and reporting workflows.
Author: Madhan Kumar N [aut, cre],
Siddhesh Pujari [aut],
Gomathi S [aut],
Mackenzie Haight [aut]
Maintainer: Madhan Kumar N <madhanmanoj1999@gmail.com>
Diff between dataviewR versions 0.1.1 dated 2025-07-21 and 1.0.0 dated 2026-01-10
dataviewR-0.1.1/dataviewR/inst/doc/dataviewR-intro.R |only dataviewR-0.1.1/dataviewR/inst/doc/dataviewR-intro.Rmd |only dataviewR-0.1.1/dataviewR/inst/doc/dataviewR-intro.html |only dataviewR-0.1.1/dataviewR/man/figures/dataviewR_logo.png |only dataviewR-0.1.1/dataviewR/tests/testthat/test-dataviewer.R |only dataviewR-0.1.1/dataviewR/vignettes/dataviewR-intro.Rmd |only dataviewR-1.0.0/dataviewR/DESCRIPTION | 21 dataviewR-1.0.0/dataviewR/MD5 | 64 dataviewR-1.0.0/dataviewR/NAMESPACE | 14 dataviewR-1.0.0/dataviewR/NEWS.md | 50 dataviewR-1.0.0/dataviewR/R/dataviewer.R | 680 ++++++---- dataviewR-1.0.0/dataviewR/R/dataviewer_tab_server.R |only dataviewR-1.0.0/dataviewR/R/dataviewer_tab_ui.R |only dataviewR-1.0.0/dataviewR/R/dataviewer_ui_head.R |only dataviewR-1.0.0/dataviewR/R/list_dataviewers.R |only dataviewR-1.0.0/dataviewR/R/stop_all_dataviewers.R |only dataviewR-1.0.0/dataviewR/R/stop_dataviewer.R |only dataviewR-1.0.0/dataviewR/README.md | 253 --- dataviewR-1.0.0/dataviewR/build/vignette.rds |binary dataviewR-1.0.0/dataviewR/inst/doc/Exporting-and-Reproducibility.R |only dataviewR-1.0.0/dataviewR/inst/doc/Exporting-and-Reproducibility.Rmd |only dataviewR-1.0.0/dataviewR/inst/doc/Exporting-and-Reproducibility.html |only dataviewR-1.0.0/dataviewR/inst/doc/Filtering-Expressions.Rmd |only dataviewR-1.0.0/dataviewR/inst/doc/Filtering-Expressions.html |only dataviewR-1.0.0/dataviewR/inst/doc/Introduction-to-dataviewR.R |only dataviewR-1.0.0/dataviewR/inst/doc/Introduction-to-dataviewR.Rmd |only dataviewR-1.0.0/dataviewR/inst/doc/Introduction-to-dataviewR.html |only dataviewR-1.0.0/dataviewR/inst/doc/Multiple-Datasets.Rmd |only dataviewR-1.0.0/dataviewR/inst/doc/Multiple-Datasets.html |only dataviewR-1.0.0/dataviewR/inst/doc/adam-clinical-dataset.Rmd |only dataviewR-1.0.0/dataviewR/inst/doc/adam-clinical-dataset.html |only dataviewR-1.0.0/dataviewR/man/dataviewer.Rd | 32 dataviewR-1.0.0/dataviewR/man/figures/logo.png |only dataviewR-1.0.0/dataviewR/man/list_dataviewers.Rd |only dataviewR-1.0.0/dataviewR/man/stop_all_dataviewers.Rd |only dataviewR-1.0.0/dataviewR/man/stop_dataviewer.Rd |only dataviewR-1.0.0/dataviewR/tests/testthat/test-background_process.R |only dataviewR-1.0.0/dataviewR/tests/testthat/test-dataviewer_main.R |only dataviewR-1.0.0/dataviewR/tests/testthat/test-dataviewer_module.R |only dataviewR-1.0.0/dataviewR/tests/testthat/test-error_handling.R |only dataviewR-1.0.0/dataviewR/tests/testthat/test-module_advanced.R |only dataviewR-1.0.0/dataviewR/tests/testthat/test-tab_management.R |only dataviewR-1.0.0/dataviewR/vignettes/Exporting-and-Reproducibility.Rmd |only dataviewR-1.0.0/dataviewR/vignettes/Filtering-Expressions.Rmd |only dataviewR-1.0.0/dataviewR/vignettes/Introduction-to-dataviewR.Rmd |only dataviewR-1.0.0/dataviewR/vignettes/Multiple-Datasets.Rmd |only dataviewR-1.0.0/dataviewR/vignettes/adam-clinical-dataset.Rmd |only dataviewR-1.0.0/dataviewR/vignettes/figures |only 48 files changed, 611 insertions(+), 503 deletions(-)
Title: Import Data from EDC Software
Description: A convenient toolbox to import data exported from Electronic Data Capture (EDC) software 'TrialMaster'.
Author: Dan Chaltiel [aut, cre]
Maintainer: Dan Chaltiel <dan.chaltiel@gmail.com>
Diff between EDCimport versions 0.6.0 dated 2025-06-24 and 0.7.0 dated 2026-01-10
DESCRIPTION | 10 MD5 | 143 NAMESPACE | 521 - NEWS.md | 60 R/EDCimport-package.R | 29 R/assertions.R | 5 R/clean_names.R | 10 R/compare_databases.R |only R/crf_plot.R | 8 R/data.R | 40 R/edc_database.R |only R/edc_join.R |only R/edc_unify_subjid.R | 11 R/find.R | 4 R/helpers.R | 142 R/lastnews_table.R | 2 R/lookup.R | 7 R/patient_gridplot.R | 10 R/population_plot.R | 9 R/read_all_csv.R | 16 R/read_all_sas.R | 12 R/read_all_xpt.R | 8 R/read_trialmaster.R | 23 R/sanity_checks.R | 121 R/sas_format.R | 4 R/split_mixed.R | 9 R/swimmerplot.R | 74 R/utils.R | 245 R/utils_labels.R |only R/utils_read.R | 146 R/viewer.R | 126 R/viewer_server.R | 110 R/viewer_ui.R | 51 README.md | 4 build/vignette.rds |binary inst/IMPORTLIST | 1 inst/WORDLIST | 2 inst/autoimport_cache.rds |binary inst/doc/checking.html | 12 inst/doc/trialmaster_date_error.html |only inst/doc/trialmaster_date_error.qmd |only inst/doc/visualizing.html | 6 inst/edc_viewer/www/edc_viewer.css | 38 man/compare_databases.Rd |only man/edc_database.Rd | 2 man/edc_example_multiple.Rd |only man/edc_left_join.Rd | 2 man/edc_swimmerplot.Rd | 21 man/edc_viewer.Rd | 15 man/get_datasets.Rd | 2 man/read_all_csv.Rd | 3 man/read_all_sas.Rd | 5 man/read_all_xpt.Rd | 3 man/save_edc_data_warnings.Rd | 18 man/save_plotly.Rd | 5 man/set_project_name.Rd | 7 tests/testthat/_snaps/compare_databases.md |only tests/testthat/_snaps/patient_gridplot/edc-patient-gridplot-args.svg | 821 +- tests/testthat/_snaps/patient_gridplot/edc-patient-gridplot-default.svg | 905 +-- tests/testthat/_snaps/patient_gridplot/edc-patient-gridplot-gradient.svg | 901 +-- tests/testthat/_snaps/population_plot/pop-plot.svg | 1796 +++--- tests/testthat/_snaps/read_all_csv.md | 20 tests/testthat/_snaps/sanity.md | 16 tests/testthat/_snaps/swimmerplot/swimmerplot-origin-group.svg | 2874 ++++------ tests/testthat/_snaps/trialmaster-simple.md | 5 tests/testthat/helper-init.R | 41 tests/testthat/test-compare_databases.R |only tests/testthat/test-edc_join.R |only tests/testthat/test-helpers.R | 19 tests/testthat/test-patient_gridplot.R | 30 tests/testthat/test-read_all_csv.R | 44 tests/testthat/test-read_all_sas.R | 49 tests/testthat/test-sanity.R | 2 tests/testthat/test-trialmaster-simple.R | 6 tests/testthat/test-trialmaster.R | 24 tests/testthat/test-utils.R | 5 vignettes/img |only vignettes/trialmaster_date_error.qmd |only 78 files changed, 4968 insertions(+), 4692 deletions(-)
Title: Simple Methods for Calculating and Backtesting Value at Risk and
Expected Shortfall
Description: Enables the user to calculate Value at Risk (VaR)
and Expected Shortfall (ES) by means of various types of historical
simulation. Currently plain-, age-, volatility-weighted- and filtered
historical simulation are implemented in this package. Volatility weighting
can be carried out via an exponentially weighted moving average model
(EWMA) or other GARCH-type models. The performance can be assessed via
Traffic Light Test, Coverage Tests and Loss Functions. The methods of the
package are described in Gurrola-Perez, P. and Murphy, D. (2015)
<https://EconPapers.repec.org/RePEc:boe:boeewp:0525> as well as McNeil, J.,
Frey, R., and Embrechts, P. (2015) <https://ideas.repec.org/b/pup/pbooks/10496.html>.
Author: Sebastian Letmathe [aut, cre]
Maintainer: Sebastian Letmathe <sebastian.let@yahoo.com>
Diff between quarks versions 1.1.5 dated 2025-10-13 and 1.1.6 dated 2026-01-10
DESCRIPTION | 6 +-- MD5 | 6 +-- NEWS.md | 5 ++ R/runFTSdata.R | 96 ++++++++++++++++++++++++++++++++++++++++----------------- 4 files changed, 80 insertions(+), 33 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 3.3.0 dated 2025-12-09 and 3.4.0 dated 2026-01-10
DESCRIPTION | 6 MD5 | 21 NAMESPACE | 29 R/cache_ip_functions.R |only R/get.snowball.R | 5 R/groundhog.library.R | 1452 ++++++++++++++++++++++----------------------- R/install.snowball.R | 25 R/interlibrary.functions.R | 46 + R/localize.R | 38 + R/show_startup.R |only R/utils.R | 55 + R/zzz.R | 5 man/show_startup.Rd |only 13 files changed, 929 insertions(+), 753 deletions(-)
Title: Unified Interface for Machine Learning Models
Description: Provides a unified R6-based interface for various machine learning models with automatic interface detection, consistent cross-validation, model interpretations via numerical derivatives, and visualization. Supports both regression and classification tasks with any model function that follows R's standard modeling conventions (formula or matrix interface).
Author: T. Moudiki [aut, cre]
Maintainer: T. Moudiki <thierry.moudiki@gmail.com>
Diff between unifiedml versions 0.1.0 dated 2025-11-13 and 0.2.0 dated 2026-01-10
DESCRIPTION | 8 +- MD5 | 23 ++++-- NAMESPACE | 7 ++ NEWS.md | 6 + R/matrix-vs-formula-interface.R |only README.md | 29 +++++--- build/partial.rdb |binary build/vignette.rds |binary inst/doc/formula_vs_matrix.R |only inst/doc/formula_vs_matrix.Rmd |only inst/doc/formula_vs_matrix.html |only inst/doc/unifiedml-vignette.html | 133 ++++++++++++++++++--------------------- man/formula_to_matrix.Rd |only man/matrix_to_formula.Rd |only man/print.model_adapter.Rd |only vignettes/booster.html |only vignettes/formula_vs_matrix.Rmd |only 17 files changed, 117 insertions(+), 89 deletions(-)
Title: Tools for Developing R Packages Interfacing with 'Stan'
Description: Provides various tools for developers of R packages interfacing
with 'Stan' <https://mc-stan.org>, including functions to set up the required
package structure, S3 generics and default methods to unify function naming
across 'Stan'-based R packages, and vignettes with recommendations for
developers.
Author: Jonah Gabry [aut, cre],
Ben Goodrich [aut],
Martin Lysy [aut],
Andrew Johnson [aut],
Hamada S. Badr [ctb],
Marco Colombo [ctb],
Stefan Siegert [ctb],
Visruth Srimath Kandali [ctb],
Trustees of Columbia University [cph]
Maintainer: Jonah Gabry <jgabry@gmail.com>
Diff between rstantools versions 2.5.0 dated 2025-09-01 and 2.6.0 dated 2026-01-10
rstantools-2.5.0/rstantools/man/figures/stanlogo.png |only rstantools-2.6.0/rstantools/DESCRIPTION | 20 +- rstantools-2.6.0/rstantools/MD5 | 25 +- rstantools-2.6.0/rstantools/NEWS.md | 7 rstantools-2.6.0/rstantools/R/rstan_create_package.R | 10 - rstantools-2.6.0/rstantools/R/rstantools-package.R | 2 rstantools-2.6.0/rstantools/build/vignette.rds |binary rstantools-2.6.0/rstantools/inst/doc/developer-guidelines.html | 2 rstantools-2.6.0/rstantools/inst/doc/minimal-rstan-package.Rmd | 5 rstantools-2.6.0/rstantools/inst/doc/minimal-rstan-package.html | 66 +++--- rstantools-2.6.0/rstantools/man/figures/logo.svg | 97 ---------- rstantools-2.6.0/rstantools/man/rstan_create_package.Rd | 2 rstantools-2.6.0/rstantools/man/rstantools-package.Rd | 4 rstantools-2.6.0/rstantools/vignettes/minimal-rstan-package.Rmd | 5 14 files changed, 82 insertions(+), 163 deletions(-)
Title: Regression Models for Ordinal Data
Description: Implementation of cumulative link (mixed) models also known
as ordered regression models, proportional odds models, proportional
hazards models for grouped survival times and ordered logit/probit/...
models. Estimation is via maximum likelihood and mixed models are fitted
with the Laplace approximation and adaptive Gauss-Hermite quadrature.
Multiple random effect terms are allowed and they may be nested, crossed or
partially nested/crossed. Restrictions of symmetry and equidistance can be
imposed on the thresholds (cut-points/intercepts). Standard model
methods are available (summary, anova, drop-methods, step,
confint, predict etc.) in addition to profile methods and slice
methods for visualizing the likelihood function and checking
convergence.
Author: Rune Haubo Bojesen Christensen [aut, cre]
Maintainer: Rune Haubo Bojesen Christensen <rune.haubo@gmail.com>
Diff between ordinal versions 2023.12-4.1 dated 2024-08-19 and 2025.12-29 dated 2026-01-10
ordinal-2023.12-4.1/ordinal/vignettes/static_figs |only ordinal-2025.12-29/ordinal/DESCRIPTION | 8 ordinal-2025.12-29/ordinal/LICENCE.note | 2 ordinal-2025.12-29/ordinal/MD5 | 115 ++-- ordinal-2025.12-29/ordinal/NEWS | 11 ordinal-2025.12-29/ordinal/R/AO.R | 2 ordinal-2025.12-29/ordinal/R/clm.R | 2 ordinal-2025.12-29/ordinal/R/clm.Thetamat.R | 2 ordinal-2025.12-29/ordinal/R/clm.anova.R | 2 ordinal-2025.12-29/ordinal/R/clm.fit.R | 2 ordinal-2025.12-29/ordinal/R/clm.fitter.R | 2 ordinal-2025.12-29/ordinal/R/clm.frames.R | 2 ordinal-2025.12-29/ordinal/R/clm.methods.R | 2 ordinal-2025.12-29/ordinal/R/clm.nominal_test.R | 2 ordinal-2025.12-29/ordinal/R/clm.predict.R | 2 ordinal-2025.12-29/ordinal/R/clm.profile.R | 2 ordinal-2025.12-29/ordinal/R/clm.simple.R | 2 ordinal-2025.12-29/ordinal/R/clm.slice.R | 2 ordinal-2025.12-29/ordinal/R/clm.slice2D.R | 2 ordinal-2025.12-29/ordinal/R/clm.start.R | 2 ordinal-2025.12-29/ordinal/R/clm2.R | 2 ordinal-2025.12-29/ordinal/R/clmm.R | 2 ordinal-2025.12-29/ordinal/R/clmm.formula.R | 2 ordinal-2025.12-29/ordinal/R/clmm.methods.R | 2 ordinal-2025.12-29/ordinal/R/clmm.ranef.R | 2 ordinal-2025.12-29/ordinal/R/clmm.ssr.R | 2 ordinal-2025.12-29/ordinal/R/clmm.start.R | 2 ordinal-2025.12-29/ordinal/R/clmm2.R | 2 ordinal-2025.12-29/ordinal/R/clmm2.utils.R | 2 ordinal-2025.12-29/ordinal/R/contrast_utils.R | 6 ordinal-2025.12-29/ordinal/R/control.R | 2 ordinal-2025.12-29/ordinal/R/convergence.R | 4 ordinal-2025.12-29/ordinal/R/derivatives.R | 2 ordinal-2025.12-29/ordinal/R/drop.coef.R | 2 ordinal-2025.12-29/ordinal/R/gdist.R | 2 ordinal-2025.12-29/ordinal/R/gumbel.R | 2 ordinal-2025.12-29/ordinal/R/lgamma.R | 2 ordinal-2025.12-29/ordinal/R/terms_utils.R | 2 ordinal-2025.12-29/ordinal/R/utils.R | 2 ordinal-2025.12-29/ordinal/R/warning_functions.R | 2 ordinal-2025.12-29/ordinal/build/vignette.rds |binary ordinal-2025.12-29/ordinal/data/income.rda |binary ordinal-2025.12-29/ordinal/data/soup.rda |binary ordinal-2025.12-29/ordinal/data/wine.rda |binary ordinal-2025.12-29/ordinal/inst/doc/clm_article.R | 366 +++++++++++--- ordinal-2025.12-29/ordinal/inst/doc/clm_article.Rnw | 243 +++++++++ ordinal-2025.12-29/ordinal/inst/doc/clm_article.pdf |binary ordinal-2025.12-29/ordinal/inst/doc/clmm2_tutorial.pdf |binary ordinal-2025.12-29/ordinal/src/get_fitted.c | 2 ordinal-2025.12-29/ordinal/src/init.c | 2 ordinal-2025.12-29/ordinal/src/links.c | 2 ordinal-2025.12-29/ordinal/src/links.h | 2 ordinal-2025.12-29/ordinal/src/utilityFuns.c | 2 ordinal-2025.12-29/ordinal/tests/testthat/test-clm.R | 11 ordinal-2025.12-29/ordinal/vignettes/clm_article.Rnw | 243 +++++++++ ordinal-2025.12-29/ordinal/vignettes/clm_article_refs.bib | 13 ordinal-2025.12-29/ordinal/vignettes/ordinal.bib | 10 57 files changed, 915 insertions(+), 193 deletions(-)
Title: Visualizing the Elements Within Bio-Sequences
Description: Visualizing the types and distribution of elements within
bio-sequences. At the same time, We have developed a geom layer,
geom_rrect(), that can generate rounded rectangles. No external references
are used in the development of this package.
Author: Shiqi Zhao [aut, cre, cph]
Maintainer: Shiqi Zhao <zhaosq89@163.com>
Diff between BioVizSeq versions 1.0.4 dated 2025-08-22 and 1.0.5 dated 2026-01-10
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ R/smart_plot.R | 10 +++++----- 4 files changed, 15 insertions(+), 11 deletions(-)
Title: Bhavcopy and Live Market Data from National Stock Exchange (NSE)
& Bombay Stock Exchange (BSE) India
Description: Download Current & Historical Bhavcopy. Get Live Market data from NSE India of Equities and Derivatives (F&O) segment. Data source <https://www.nseindia.com/>.
Author: Nandan Patil [cre, aut]
Maintainer: Nandan Patil <tryanother609@gmail.com>
This is a re-admission after prior archival of version 1.5.7 dated 2025-12-12
Diff between nser versions 1.5.7 dated 2025-12-12 and 1.5.8 dated 2026-01-10
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/fobhav1.R | 5 +++-- build/vignette.rds |binary man/fobhav1.Rd | 3 ++- 5 files changed, 13 insertions(+), 11 deletions(-)
Title: Interactive Networks, Timelines, Barplots, Galleries with
'D3.js'
Description: Creates interactive analytic graphs with 'R'. It joins the data analysis power of R and the visualization libraries of JavaScript in one package. The package provides interactive networks, timelines, barplots, image galleries and evolving networks. Graphs are represented as 'D3.js' graphs embedded in a web page ready for its interactive analysis and exploration.
Author: Modesto Escobar [aut, cph, cre] ,
Carlos Prieto [aut] ,
David Barrios [aut]
Maintainer: Modesto Escobar <modesto@usal.es>
Diff between rD3plot versions 1.1.37 dated 2025-07-03 and 1.1.45 dated 2026-01-10
DESCRIPTION | 11 MD5 | 122 NAMESPACE | 1 R/gallery.R | 161 R/layouts.R | 518 R/methods.R | 12 R/multigraph.R | 2 R/pie.R | 310 README.md | 26 build |only data/crannetworkdata.RData |only inst/doc |only inst/extdata/c.Heliobates.png |binary inst/extdata/c.Olivacea.png |binary inst/extdata/c.Pallida.png |binary inst/extdata/c.Parvulus.png |binary inst/extdata/c.Pauper.png |binary inst/extdata/c.Psitticula.png |binary inst/extdata/g.Conirostris.png |binary inst/extdata/g.Difficilis.png |binary inst/extdata/g.Fortis.png |binary inst/extdata/g.Fuliginosa.png |binary inst/extdata/g.Magnirostris.png |binary inst/extdata/g.Scandens.png |binary inst/extdata/p.Crassirostris.png |binary inst/www/barplot.js | 1752 +-- inst/www/bootstrap.scrolling.nav.css |20398 +++++++++++++++++------------------ inst/www/ca.js | 4 inst/www/colorScales.js | 136 inst/www/d3.layout.cloud.js | 998 - inst/www/d3.min.js | 4 inst/www/en.js | 4 inst/www/es.js | 4 inst/www/functions.js | 56 inst/www/gallery.js | 25 inst/www/gallery2.js | 142 inst/www/gallery3.js |only inst/www/help_es.html | 190 inst/www/html2canvas.min.js | 38 inst/www/iro.min.js | 14 inst/www/jspdf.min.js | 570 inst/www/jszip.min.js | 28 inst/www/multigraph.js | 212 inst/www/multipages.css | 264 inst/www/multipages.js | 370 inst/www/network.js | 17 inst/www/pie.js | 1298 +- inst/www/reset.css | 90 inst/www/styles.css | 48 inst/www/styles2.css | 62 inst/www/styles3.css |only inst/www/template.html | 24 inst/www/timeline.js | 2364 ++-- inst/www/tutorial.css | 254 inst/www/tutorial_ca.js | 84 inst/www/tutorial_en.js | 84 inst/www/tutorial_es.js | 84 man/crannetworkdata.Rd |only man/gallery2_rd3.Rd | 32 man/gallery3_rd3.Rd |only man/gallery_rd3.Rd | 5 man/rd3_addDescription.Rd | 64 man/rd3_addImage.Rd | 64 vignettes |only 64 files changed, 15666 insertions(+), 15280 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 1.1.0.8.2 dated 2026-01-07 and 1.1.1 dated 2026-01-10
Rcpp-1.1.0.8.2/Rcpp/man/RcppUnitTests.Rd |only Rcpp-1.1.1/Rcpp/ChangeLog | 136 +++++++++- Rcpp-1.1.1/Rcpp/DESCRIPTION | 9 Rcpp-1.1.1/Rcpp/MD5 | 114 ++++---- Rcpp-1.1.1/Rcpp/R/Attributes.R | 90 ++---- Rcpp-1.1.1/Rcpp/R/Module.R | 2 Rcpp-1.1.1/Rcpp/R/Rcpp.package.skeleton.R | 26 - Rcpp-1.1.1/Rcpp/R/RcppLdpath.R | 12 Rcpp-1.1.1/Rcpp/R/asis.R | 4 Rcpp-1.1.1/Rcpp/R/inline.R | 6 Rcpp-1.1.1/Rcpp/R/loadModule.R | 13 Rcpp-1.1.1/Rcpp/README.md | 24 - Rcpp-1.1.1/Rcpp/build/partial.rdb |binary Rcpp-1.1.1/Rcpp/build/vignette.rds |binary Rcpp-1.1.1/Rcpp/cleanup | 4 Rcpp-1.1.1/Rcpp/inst/NEWS.Rd | 40 ++ Rcpp-1.1.1/Rcpp/inst/bib/Rcpp.bib | 72 ++--- Rcpp-1.1.1/Rcpp/inst/doc/Rcpp-FAQ.pdf |binary Rcpp-1.1.1/Rcpp/inst/doc/Rcpp-attributes.pdf |binary Rcpp-1.1.1/Rcpp/inst/doc/Rcpp-extending.pdf |binary Rcpp-1.1.1/Rcpp/inst/doc/Rcpp-introduction.pdf |binary Rcpp-1.1.1/Rcpp/inst/doc/Rcpp-jss-2011.pdf |binary Rcpp-1.1.1/Rcpp/inst/doc/Rcpp-libraries.pdf |binary Rcpp-1.1.1/Rcpp/inst/doc/Rcpp-modules.pdf |binary Rcpp-1.1.1/Rcpp/inst/doc/Rcpp-package.pdf |binary Rcpp-1.1.1/Rcpp/inst/doc/Rcpp-quickref.pdf |binary Rcpp-1.1.1/Rcpp/inst/doc/Rcpp-sugar.pdf |binary Rcpp-1.1.1/Rcpp/inst/include/Rcpp/DataFrame.h | 17 - Rcpp-1.1.1/Rcpp/inst/include/Rcpp/Environment.h | 29 +- Rcpp-1.1.1/Rcpp/inst/include/Rcpp/Function.h | 13 Rcpp-1.1.1/Rcpp/inst/include/Rcpp/Module.h | 4 Rcpp-1.1.1/Rcpp/inst/include/Rcpp/Rmath.h | 9 Rcpp-1.1.1/Rcpp/inst/include/Rcpp/S4.h | 11 Rcpp-1.1.1/Rcpp/inst/include/Rcpp/Symbol.h | 8 Rcpp-1.1.1/Rcpp/inst/include/Rcpp/api/meat/Rcpp_eval.h | 29 -- Rcpp-1.1.1/Rcpp/inst/include/Rcpp/as.h | 13 Rcpp-1.1.1/Rcpp/inst/include/Rcpp/config.h | 8 Rcpp-1.1.1/Rcpp/inst/include/Rcpp/exceptions.h | 6 Rcpp-1.1.1/Rcpp/inst/include/Rcpp/internal/caster.h | 11 Rcpp-1.1.1/Rcpp/inst/include/Rcpp/internal/export.h | 4 Rcpp-1.1.1/Rcpp/inst/include/Rcpp/macros/mask.h |only Rcpp-1.1.1/Rcpp/inst/include/Rcpp/proxy/AttributeProxy.h | 27 + Rcpp-1.1.1/Rcpp/inst/include/Rcpp/proxy/NamesProxy.h | 4 Rcpp-1.1.1/Rcpp/inst/include/Rcpp/proxy/SlotProxy.h | 2 Rcpp-1.1.1/Rcpp/inst/include/Rcpp/r/headers.h | 6 Rcpp-1.1.1/Rcpp/inst/include/Rcpp/r_cast.h | 9 Rcpp-1.1.1/Rcpp/inst/include/Rcpp/sugar/undoRmath.h | 2 Rcpp-1.1.1/Rcpp/inst/include/Rcpp/vector/Vector.h | 6 Rcpp-1.1.1/Rcpp/inst/include/Rcpp/vector/proxy.h | 7 Rcpp-1.1.1/Rcpp/inst/include/Rcpp/vector/traits.h | 9 Rcpp-1.1.1/Rcpp/inst/include/RcppCommon.h | 9 Rcpp-1.1.1/Rcpp/inst/tinytest/cpp/stack.cpp | 16 - Rcpp-1.1.1/Rcpp/inst/tinytest/testRcppInterfaceExporter/src/RcppExports.cpp | 2 Rcpp-1.1.1/Rcpp/inst/tinytest/testRcppInterfaceUser/tests/tests.R | 10 Rcpp-1.1.1/Rcpp/inst/tinytest/test_interface.R | 16 - Rcpp-1.1.1/Rcpp/inst/tinytest/test_system.R | 8 Rcpp-1.1.1/Rcpp/src/attributes.cpp | 9 Rcpp-1.1.1/Rcpp/src/barrier.cpp | 17 - Rcpp-1.1.1/Rcpp/tests/tinytest.R | 13 59 files changed, 506 insertions(+), 380 deletions(-)
Title: Interactive Analytic Networks
Description: Create interactive analytic networks. It joins the data analysis power of R to obtain coincidences, co-occurrences and correlations, and the visualization libraries of 'JavaScript' in one package.
Author: Modesto Escobar [cre, aut, cph] ,
David Barrios [aut],
Carlos Prieto [aut] ,
Luis Martinez-Uribe [aut] ,
Pablo Cabrera-Alvarez [aut] ,
Cristina Calvo-Lopez [aut]
Maintainer: Modesto Escobar <modesto@usal.es>
Diff between netCoin versions 2.1.9 dated 2025-07-03 and 2.1.19 dated 2026-01-10
DESCRIPTION | 8 MD5 | 176 +++++++++++--------- NAMESPACE | 3 R/caring.R | 2 R/coex.R | 84 ++++----- R/exports.R | 24 +- R/gallery.R | 2 R/get_templates.R | 22 ++ R/multigraph.R | 68 +++---- R/pie.R | 74 ++++---- build/partial.rdb |binary build/vignette.rds |binary inst/doc/galleries.R |only inst/doc/galleries.Rmd |only inst/doc/galleries.html |only inst/doc/netCoin.html | 9 - inst/doc/surCoin.Rmd | 336 +++++++++++++++++++-------------------- inst/doc/surCoin.html | 5 inst/extdata/c.Heliobates.png |binary inst/extdata/c.Olivacea.png |binary inst/extdata/c.Pallida.png |binary inst/extdata/c.Parvulus.png |binary inst/extdata/c.Pauper.png |binary inst/extdata/c.Psitticula.png |binary inst/extdata/circle.svg |only inst/extdata/circle_blue.svg |only inst/extdata/circle_green.svg |only inst/extdata/circle_red.svg |only inst/extdata/g.Conirostris.png |binary inst/extdata/g.Difficilis.png |binary inst/extdata/g.Fortis.png |binary inst/extdata/g.Fuliginosa.png |binary inst/extdata/g.Magnirostris.png |binary inst/extdata/g.Scandens.png |binary inst/extdata/p.Crassirostris.png |binary inst/extdata/square.svg |only inst/extdata/square_blue.svg |only inst/extdata/square_green.svg |only inst/extdata/square_red.svg |only inst/extdata/triangle.svg |only inst/extdata/triangle_blue.svg |only inst/extdata/triangle_green.svg |only inst/extdata/triangle_red.svg |only man/addDescription.Rd | 78 ++++----- man/addImage.Rd | 78 ++++----- man/addNetCoin.Rd | 2 man/allNet.Rd | 2 man/asGallery.Rd | 2 man/asNodes.Rd | 2 man/barCoin.Rd | 2 man/calCentr.Rd | 2 man/cobCoin.Rd | 92 +++++----- man/coexist.Rd | 108 ++++++------ man/coin.Rd | 2 man/coocur.rd | 2 man/d_netCorr.Rd | 114 ++++++------- man/dichotomize.Rd | 2 man/distant.Rd | 2 man/dyncohort.Rd | 106 ++++++------ man/edgeList.Rd | 2 man/exhibit.Rd | 17 + man/expectedList.Rd | 2 man/fromIgraph.Rd | 2 man/gallery.Rd | 7 man/gallery3.Rd |only man/get_panel_template.Rd | 74 ++++---- man/get_template.Rd | 122 +++++++------- man/get_template2.Rd | 2 man/glmCoin.Rd | 2 man/incTime.Rd | 2 man/layoutCircle.Rd | 2 man/layoutGrid.Rd | 2 man/logCoin.Rd | 102 +++++------ man/lower.Rd | 2 man/makeT.Rd | 2 man/makeT2.Rd | 2 man/mobileEdges.Rd | 2 man/multigraphCreate.Rd | 2 man/netCoin-package.Rd | 3 man/netCoin.Rd | 2 man/netCorr.Rd | 2 man/pathCoin.Rd | 4 man/pieCoin.Rd | 2 man/propCoin.Rd | 2 man/renderLinks.Rd | 81 ++++----- man/saveGhml.Rd | 62 +++---- man/savePajek.Rd | 2 man/shinyCoin.Rd | 2 man/sim.Rd | 2 man/surCoin.Rd | 2 man/surScat.Rd | 2 man/timeCoin.Rd | 2 man/toIgraph.Rd | 2 man/works.Rd | 68 +++---- vignettes/exhibit.png |only vignettes/galleries.Rmd |only vignettes/gallery.png |only vignettes/netExhibit.png |only vignettes/surCoin.Rmd | 336 +++++++++++++++++++-------------------- 99 files changed, 1193 insertions(+), 1140 deletions(-)
Title: Visualization and Polytomous Modeling of Survival and Competing
Risks
Description: A publication-ready toolkit for modern survival and competing risks
analysis with a minimal, formula-based interface. Both nonparametric
estimation and direct polytomous regression of cumulative incidence
functions (CIFs) are supported. The main functions 'cifcurve()', 'cifplot()',
and 'cifpanel()' estimate survival and CIF curves and produce high-quality
graphics with risk tables, censoring and competing-risk marks, and
multi-panel or inset layouts built on 'ggplot2' and 'ggsurvfit'. The modeling
function 'polyreg()' performs direct polytomous regression for coherent joint
modeling of all cause-specific CIFs to estimate risk ratios, odds ratios, or
subdistribution hazard ratios at user-specified time points. All core
functions adopt a formula-and-data syntax and return tidy and extensible
outputs that integrate smoothly with 'modelsummary', 'broom', and the broader
'tidyverse' ecosystem. Key numerical routines are implemented in C++ via
'Rcpp'.
Author: Shiro Tanaka [aut, cre, cph] ,
Shigetaka Kobari [ctb],
Chisato Honda [ctb]
Maintainer: Shiro Tanaka <gestimation@gmail.com>
Diff between cifmodeling versions 0.9.6 dated 2025-12-13 and 0.9.8 dated 2026-01-10
DESCRIPTION | 6 MD5 | 81 +- NEWS.md | 209 +++-- R/RcppExports.R | 4 R/cif-stat-arguments.R | 60 - R/cif-visual-arguments.R | 155 ++-- R/cifcurve.R | 87 +- R/cifpanel.R | 93 +- R/cifplot.R | 447 +++++++++--- R/functions-utility.R | 40 - R/functions-warning.R | 18 R/helper-cifpanel.R | 39 - R/helper-cifplot.R | 147 ++++ build/stage23.rdb |binary inst/doc/v4_examples.html | 4 inst/doc/v5_gallery.html | 20 inst/doc/v7_arguments.Rmd | 19 inst/doc/v7_arguments.html | 55 + man/cif-stat-arguments.Rd | 10 man/cif-visual-arguments.Rd | 34 man/cifcurve.Rd | 17 man/cifpanel.Rd | 42 + man/cifplot.Rd | 25 src/RcppExports.cpp | 9 src/calculateAJ_Rcpp.cpp | 175 +++- tests/testthat/test-calculateCI.R | 203 +++++ tests/testthat/test-cifpanel.R | 171 ++++ tests/testthat/test-cifplot.R | 1046 ++++++++++++++++++++++++++++- tests/testthat/test-n-risk-type.R |only vignettes/fig/function-example04-1-3-1.png |binary vignettes/fig/function-example04-2-1-1.png |binary vignettes/fig/function-gallery-1-01-1.png |binary vignettes/fig/function-gallery-1-02-1.png |binary vignettes/fig/function-gallery-2-02-1.png |binary vignettes/fig/function-gallery-2-03-1.png |binary vignettes/fig/function-gallery-2-04-1.png |binary vignettes/fig/function-gallery-3-01-1.png |binary vignettes/fig/function-gallery-5-01-1.png |binary vignettes/fig/function-gallery-7-01-1.png |binary vignettes/fig/function-gallery-7-02-1.png |binary vignettes/fig/function-gallery-8-01-1.png |binary vignettes/v7_arguments.Rmd | 19 42 files changed, 2689 insertions(+), 546 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-02-10 0.0.5
2017-05-02 0.0.3
Title: Versatile Curation of Table Metadata
Description: A YAML-based
mechanism for working with table metadata. Supports
compact syntax for creating, modifying, viewing, exporting,
importing, displaying, and plotting metadata coded as column
attributes. The 'yamlet' dialect is valid 'YAML' with
defaults and conventions chosen to improve readability.
See ?yamlet, ?decorate, ?modify, ?io_csv, and ?ggplot.decorated.
Author: Tim Bergsma [aut, cre]
Maintainer: Tim Bergsma <bergsmat@gmail.com>
Diff between yamlet versions 1.2.5 dated 2025-06-20 and 1.3.1 dated 2026-01-10
yamlet-1.2.5/yamlet/R/vec_cast.R |only yamlet-1.2.5/yamlet/R/vec_ptype2.R |only yamlet-1.2.5/yamlet/man/print.decorated_ggplot.Rd |only yamlet-1.2.5/yamlet/vignettes/scripted-html_files |only yamlet-1.3.1/yamlet/DESCRIPTION | 16 yamlet-1.3.1/yamlet/MD5 | 364 ++--- yamlet-1.3.1/yamlet/NAMESPACE | 18 yamlet-1.3.1/yamlet/R/as_categorical.R |only yamlet-1.3.1/yamlet/R/classified.R | 71 - yamlet-1.3.1/yamlet/R/decorate.R | 35 yamlet-1.3.1/yamlet/R/desolve.R | 11 yamlet-1.3.1/yamlet/R/dvec.R | 4 yamlet-1.3.1/yamlet/R/enscript.R | 4 yamlet-1.3.1/yamlet/R/explicit_guide.R | 1 yamlet-1.3.1/yamlet/R/explicit_guide_factor.R |only yamlet-1.3.1/yamlet/R/ggplot.R | 360 +---- yamlet-1.3.1/yamlet/R/ggplot_build.R | 262 +++ yamlet-1.3.1/yamlet/R/isometric.R | 131 + yamlet-1.3.1/yamlet/R/mapframe.R |only yamlet-1.3.1/yamlet/R/resolve.R | 55 yamlet-1.3.1/yamlet/R/vec_ptype2_dvec.R | 4 yamlet-1.3.1/yamlet/R/yamlet_options.R | 12 yamlet-1.3.1/yamlet/build/vignette.rds |binary yamlet-1.3.1/yamlet/inst/doc/aesthetics.R |only yamlet-1.3.1/yamlet/inst/doc/aesthetics.Rmd |only yamlet-1.3.1/yamlet/inst/doc/aesthetics.html |only yamlet-1.3.1/yamlet/inst/doc/scripted-html.Rmd | 5 yamlet-1.3.1/yamlet/inst/doc/scripted-html.html | 697 ++++------ yamlet-1.3.1/yamlet/inst/doc/scripted-pdf.pdf |binary yamlet-1.3.1/yamlet/inst/doc/yamlet-introduction.html | 117 - yamlet-1.3.1/yamlet/inst/extdata/modeling |only yamlet-1.3.1/yamlet/man/arbitrate.NULL.Rd | 46 yamlet-1.3.1/yamlet/man/arbitrate.Rd | 52 yamlet-1.3.1/yamlet/man/arbitrate.default.Rd | 48 yamlet-1.3.1/yamlet/man/arbitrate.list.Rd | 46 yamlet-1.3.1/yamlet/man/arbitrate.namedList.Rd | 44 yamlet-1.3.1/yamlet/man/as.data.frame.dvec.Rd | 130 - yamlet-1.3.1/yamlet/man/as_categorical.Rd |only yamlet-1.3.1/yamlet/man/as_categorical.decorated.Rd |only yamlet-1.3.1/yamlet/man/as_decorated.Rd | 4 yamlet-1.3.1/yamlet/man/as_decorated.default.Rd | 4 yamlet-1.3.1/yamlet/man/as_dvec.Rd | 110 - yamlet-1.3.1/yamlet/man/as_dvec.character.Rd | 100 - yamlet-1.3.1/yamlet/man/as_dvec.complex.Rd | 100 - yamlet-1.3.1/yamlet/man/as_dvec.dvec.Rd | 104 - yamlet-1.3.1/yamlet/man/as_dvec.integer.Rd | 100 - yamlet-1.3.1/yamlet/man/as_dvec.logical.Rd | 102 - yamlet-1.3.1/yamlet/man/as_dvec.numeric.Rd | 108 - yamlet-1.3.1/yamlet/man/as_dvec.units.Rd | 56 yamlet-1.3.1/yamlet/man/as_units.dvec.Rd | 58 yamlet-1.3.1/yamlet/man/c.classified.Rd | 9 yamlet-1.3.1/yamlet/man/c.dvec.Rd | 138 + yamlet-1.3.1/yamlet/man/classified.classified.Rd | 162 +- yamlet-1.3.1/yamlet/man/classified.dvec.Rd | 182 +- yamlet-1.3.1/yamlet/man/classified.factor.Rd | 130 - yamlet-1.3.1/yamlet/man/data_context.Rd |only yamlet-1.3.1/yamlet/man/data_context.ggplot.Rd |only yamlet-1.3.1/yamlet/man/dd_cast.Rd | 44 yamlet-1.3.1/yamlet/man/dd_ptype2.Rd | 44 yamlet-1.3.1/yamlet/man/decorate.Rd | 4 yamlet-1.3.1/yamlet/man/decorate.character.Rd | 4 yamlet-1.3.1/yamlet/man/decorate.data.frame.Rd | 4 yamlet-1.3.1/yamlet/man/decorate.list.Rd | 4 yamlet-1.3.1/yamlet/man/decorate_groups.Rd | 74 - yamlet-1.3.1/yamlet/man/decorate_groups.data.frame.Rd | 108 - yamlet-1.3.1/yamlet/man/decorations.Rd | 4 yamlet-1.3.1/yamlet/man/decorations.data.frame.Rd | 4 yamlet-1.3.1/yamlet/man/decorations_groups.Rd | 74 - yamlet-1.3.1/yamlet/man/decorations_groups.data.frame.Rd | 116 - yamlet-1.3.1/yamlet/man/desolve.Rd | 5 yamlet-1.3.1/yamlet/man/desolve.classified.Rd | 145 +- yamlet-1.3.1/yamlet/man/desolve.data.frame.Rd | 77 - yamlet-1.3.1/yamlet/man/desolve.decorated.Rd | 5 yamlet-1.3.1/yamlet/man/desolve.default.Rd |only yamlet-1.3.1/yamlet/man/desolve.dvec.Rd | 147 +- yamlet-1.3.1/yamlet/man/drop_title.Rd | 98 - yamlet-1.3.1/yamlet/man/drop_title.decorated.Rd | 96 - yamlet-1.3.1/yamlet/man/drop_title.default.Rd | 82 - yamlet-1.3.1/yamlet/man/drop_title.dvec.Rd | 98 - yamlet-1.3.1/yamlet/man/enscript.Rd | 66 yamlet-1.3.1/yamlet/man/enscript.default.Rd | 230 +-- yamlet-1.3.1/yamlet/man/explicit_guide.Rd | 2 yamlet-1.3.1/yamlet/man/explicit_guide.data.frame.Rd | 4 yamlet-1.3.1/yamlet/man/explicit_guide.dvec.Rd | 134 - yamlet-1.3.1/yamlet/man/explicit_guide.factor.Rd |only yamlet-1.3.1/yamlet/man/explicit_guide.yamlet.Rd | 2 yamlet-1.3.1/yamlet/man/format.dvec.Rd | 94 - yamlet-1.3.1/yamlet/man/get_labs.Rd | 36 yamlet-1.3.1/yamlet/man/gg_new.Rd | 24 yamlet-1.3.1/yamlet/man/ggplot.decorated.Rd | 14 yamlet-1.3.1/yamlet/man/ggplot_build.decorated_ggplot.Rd | 36 yamlet-1.3.1/yamlet/man/group_by_decorations.Rd | 74 - yamlet-1.3.1/yamlet/man/group_by_decorations.data.frame.Rd | 100 - yamlet-1.3.1/yamlet/man/implicit_guide.Rd | 2 yamlet-1.3.1/yamlet/man/implicit_guide.data.frame.Rd | 2 yamlet-1.3.1/yamlet/man/implicit_guide.dvec.Rd | 178 +- yamlet-1.3.1/yamlet/man/implicit_guide.factor.Rd |only yamlet-1.3.1/yamlet/man/infer_guide.Rd | 4 yamlet-1.3.1/yamlet/man/io_res.decorated.Rd | 150 +- yamlet-1.3.1/yamlet/man/is_dvec.Rd | 42 yamlet-1.3.1/yamlet/man/isometric.Rd | 5 yamlet-1.3.1/yamlet/man/length.dvec.Rd | 96 - yamlet-1.3.1/yamlet/man/make_title.Rd | 98 - yamlet-1.3.1/yamlet/man/make_title.decorated.Rd | 94 - yamlet-1.3.1/yamlet/man/make_title.default.Rd | 82 - yamlet-1.3.1/yamlet/man/make_title.dvec.Rd | 96 - yamlet-1.3.1/yamlet/man/mapframe.Rd |only yamlet-1.3.1/yamlet/man/mapframe.default.Rd |only yamlet-1.3.1/yamlet/man/mapframe.ggplot.Rd |only yamlet-1.3.1/yamlet/man/merge.decorated.Rd | 2 yamlet-1.3.1/yamlet/man/names-set-.decorated.Rd | 2 yamlet-1.3.1/yamlet/man/print.dvec.Rd | 94 - yamlet-1.3.1/yamlet/man/reconcile.Rd | 40 yamlet-1.3.1/yamlet/man/reconcile.list.Rd | 60 yamlet-1.3.1/yamlet/man/redecorate.Rd | 4 yamlet-1.3.1/yamlet/man/reexports.Rd | 2 yamlet-1.3.1/yamlet/man/rescale.dvec.Rd | 42 yamlet-1.3.1/yamlet/man/resolve.Rd | 5 yamlet-1.3.1/yamlet/man/resolve.classified.Rd | 145 +- yamlet-1.3.1/yamlet/man/resolve.data.frame.Rd | 77 - yamlet-1.3.1/yamlet/man/resolve.decorated.Rd | 5 yamlet-1.3.1/yamlet/man/resolve.default.Rd |only yamlet-1.3.1/yamlet/man/resolve.dvec.Rd | 149 +- yamlet-1.3.1/yamlet/man/resolve.factor.Rd |only yamlet-1.3.1/yamlet/man/scale_type.dvec.Rd | 30 yamlet-1.3.1/yamlet/man/scripted.Rd | 42 yamlet-1.3.1/yamlet/man/sub-.decorated.Rd | 2 yamlet-1.3.1/yamlet/man/sub-.dvec.Rd | 108 - yamlet-1.3.1/yamlet/man/sub-sub-.decorated.Rd | 2 yamlet-1.3.1/yamlet/man/sub-sub-.dvec.Rd | 104 - yamlet-1.3.1/yamlet/man/sub-subset-.decorated.Rd | 2 yamlet-1.3.1/yamlet/man/sub-subset-.dvec.Rd | 106 - yamlet-1.3.1/yamlet/man/subset-.decorated.Rd | 2 yamlet-1.3.1/yamlet/man/subset-.dvec.Rd | 106 - yamlet-1.3.1/yamlet/man/symmetric.Rd | 5 yamlet-1.3.1/yamlet/man/to_yamlet.numeric.Rd | 92 - yamlet-1.3.1/yamlet/man/type_sum.classified.Rd | 36 yamlet-1.3.1/yamlet/man/unclassified.dvec.Rd | 106 - yamlet-1.3.1/yamlet/man/undecorate.Rd |only yamlet-1.3.1/yamlet/man/undecorate.default.Rd |only yamlet-1.3.1/yamlet/man/vec_cast.character.dvec.Rd | 38 yamlet-1.3.1/yamlet/man/vec_cast.classified.classified.Rd | 38 yamlet-1.3.1/yamlet/man/vec_cast.classified.factor.Rd | 38 yamlet-1.3.1/yamlet/man/vec_cast.complex.dvec.Rd | 38 yamlet-1.3.1/yamlet/man/vec_cast.data.frame.decorated.Rd | 44 yamlet-1.3.1/yamlet/man/vec_cast.decorated.data.frame.Rd | 44 yamlet-1.3.1/yamlet/man/vec_cast.decorated.decorated.Rd | 44 yamlet-1.3.1/yamlet/man/vec_cast.double.dvec.Rd | 38 yamlet-1.3.1/yamlet/man/vec_cast.dvec.character.Rd | 38 yamlet-1.3.1/yamlet/man/vec_cast.dvec.complex.Rd | 38 yamlet-1.3.1/yamlet/man/vec_cast.dvec.double.Rd | 38 yamlet-1.3.1/yamlet/man/vec_cast.dvec.dvec.Rd | 42 yamlet-1.3.1/yamlet/man/vec_cast.dvec.integer.Rd | 38 yamlet-1.3.1/yamlet/man/vec_cast.dvec.logical.Rd | 42 yamlet-1.3.1/yamlet/man/vec_cast.factor.classified.Rd | 38 yamlet-1.3.1/yamlet/man/vec_cast.integer.dvec.Rd | 38 yamlet-1.3.1/yamlet/man/vec_cast.logical.dvec.Rd | 42 yamlet-1.3.1/yamlet/man/vec_ptype2.character.dvec.Rd | 42 yamlet-1.3.1/yamlet/man/vec_ptype2.classified.classified.Rd | 88 - yamlet-1.3.1/yamlet/man/vec_ptype2.classified.factor.Rd | 38 yamlet-1.3.1/yamlet/man/vec_ptype2.complex.dvec.Rd | 42 yamlet-1.3.1/yamlet/man/vec_ptype2.data.frame.decorated.Rd | 44 yamlet-1.3.1/yamlet/man/vec_ptype2.decorated.data.frame.Rd | 44 yamlet-1.3.1/yamlet/man/vec_ptype2.decorated.decorated.Rd | 44 yamlet-1.3.1/yamlet/man/vec_ptype2.double.dvec.Rd | 42 yamlet-1.3.1/yamlet/man/vec_ptype2.dvec.character.Rd | 42 yamlet-1.3.1/yamlet/man/vec_ptype2.dvec.complex.Rd | 42 yamlet-1.3.1/yamlet/man/vec_ptype2.dvec.double.Rd | 67 yamlet-1.3.1/yamlet/man/vec_ptype2.dvec.dvec.Rd | 76 - yamlet-1.3.1/yamlet/man/vec_ptype2.dvec.integer.Rd | 42 yamlet-1.3.1/yamlet/man/vec_ptype2.dvec.logical.Rd | 42 yamlet-1.3.1/yamlet/man/vec_ptype2.factor.classified.Rd | 38 yamlet-1.3.1/yamlet/man/vec_ptype2.integer.dvec.Rd | 42 yamlet-1.3.1/yamlet/man/vec_ptype2.logical.dvec.Rd | 42 yamlet-1.3.1/yamlet/man/vec_ptype_abbr.dvec.Rd | 46 yamlet-1.3.1/yamlet/man/yamlet_options.Rd | 214 +-- yamlet-1.3.1/yamlet/tests/testthat/122.rds |binary yamlet-1.3.1/yamlet/tests/testthat/123.rds |binary yamlet-1.3.1/yamlet/tests/testthat/124.rds |binary yamlet-1.3.1/yamlet/tests/testthat/125.rds |binary yamlet-1.3.1/yamlet/tests/testthat/126.rds |binary yamlet-1.3.1/yamlet/tests/testthat/127.rds |binary yamlet-1.3.1/yamlet/tests/testthat/129.rds |binary yamlet-1.3.1/yamlet/tests/testthat/134.rds |only yamlet-1.3.1/yamlet/tests/testthat/135.rds |only yamlet-1.3.1/yamlet/tests/testthat/136.rds |only yamlet-1.3.1/yamlet/tests/testthat/Rplots.pdf |binary yamlet-1.3.1/yamlet/tests/testthat/graphics-yamlet.R | 139 + yamlet-1.3.1/yamlet/tests/testthat/legends.R |only yamlet-1.3.1/yamlet/tests/testthat/test-classified.R | 44 yamlet-1.3.1/yamlet/tests/testthat/test-yamlet.R | 7 yamlet-1.3.1/yamlet/vignettes/aesthetics.Rmd |only yamlet-1.3.1/yamlet/vignettes/scripted-html.Rmd | 5 yamlet-1.3.1/yamlet/vignettes/scripted-pdf_files/figure-latex/unnamed-chunk-4-1.pdf |binary yamlet-1.3.1/yamlet/vignettes/scripted-pdf_files/figure-latex/unnamed-chunk-5-1.pdf |binary 195 files changed, 5321 insertions(+), 4899 deletions(-)
Title: Visualization and Imputation of Missing Values
Description: Provides methods for imputation and visualization of
missing values. It includes graphical tools to explore the amount, structure
and patterns of missing and/or imputed values, supporting exploratory
data analysis and helping to investigate potential missingness mechanisms
(details in Alfons, Templ and Filzmoser, <doi:10.1007/s11634-011-0102-y>.
The quality of imputations can be assessed visually using a wide range of
univariate, bivariate and multivariate plots.
The package further provides several imputation methods,
including efficient implementations of k-nearest neighbour and hot-deck
imputation (Kowarik and Templ 2013, <doi:10.18637/jss.v074.i07>,
iterative robust model-based multiple
imputation (Templ 2011, <doi:10.1016/j.csda.2011.04.012>;
Templ 2023, <doi:10.3390/math11122729>), and machine learning–based
approaches such as robust GAM-based multiple imputation
(Templ 2024, <doi:10.1007/s11222-024-10429-1>) as well as gradient boosting
(XGBoost) an [...truncated...]
Author: Matthias Templ [aut, cre],
Alexander Kowarik [aut] ,
Andreas Alfons [aut],
Johannes Gussenbauer [aut],
Nina Niederhametner [aut],
Eileen Vattheuer [aut],
Gregor de Cillia [aut],
Bernd Prantner [ctb],
Wolfgang Rannetbauer [aut]
Maintainer: Matthias Templ <matthias.templ@gmail.com>
Diff between VIM versions 6.2.6 dated 2025-09-18 and 7.0.0 dated 2026-01-10
DESCRIPTION | 51 +++- MD5 | 77 ++++-- NAMESPACE | 26 ++ NEWS.md | 6 R/VIM-package.R | 28 +- R/gowerD.R | 1 R/helper_vimpute.R |only R/irmi.R | 16 + R/vimpute.R |only R/xgboostImpute.R | 56 ++--- build/vignette.rds |binary inst/doc/VIM.Rmd | 2 inst/doc/VIM.html | 30 +- inst/doc/VisualImp.R | 112 ++++++++++ inst/doc/VisualImp.Rmd | 198 +++++++++++++++++ inst/doc/VisualImp.html | 412 +++++++++++++++++++++++++++++-------- inst/doc/donorImp.html | 99 +++----- inst/doc/impPCA.R |only inst/doc/impPCA.Rmd |only inst/doc/impPCA.html |only inst/doc/irmi.html | 91 +++----- inst/doc/modelImp.html | 107 ++++----- inst/doc/vimpute.R |only inst/doc/vimpute.Rmd |only inst/doc/vimpute.html |only inst/doc/xgboostImpute.R |only inst/doc/xgboostImpute.Rmd |only inst/doc/xgboostImpute.html |only inst/tinytest/test_vimpute.R |only inst/tinytest/test_xgboostImpute.R | 18 + man/VIM-package.Rd | 22 + man/figures |only man/hotdeck.Rd | 1 man/impPCA.Rd | 1 man/irmi.Rd | 6 man/kNN.Rd | 1 man/matchImpute.Rd | 1 man/medianSamp.Rd | 1 man/rangerImpute.Rd | 1 man/regressionImp.Rd | 1 man/sampleCat.Rd | 1 man/vimpute.Rd |only man/xgboostImpute.Rd | 13 - vignettes/VIM.Rmd | 2 vignettes/VisualImp.Rmd | 198 +++++++++++++++++ vignettes/impPCA.Rmd |only vignettes/vimpute.Rmd |only vignettes/xgboostImpute.Rmd |only 48 files changed, 1207 insertions(+), 372 deletions(-)
Title: Infers Novel Immunoglobulin Alleles from Sequencing Data
Description: Infers the V genotype of an individual from immunoglobulin (Ig)
repertoire sequencing data (AIRR-Seq, Rep-Seq). Includes detection of
any novel alleles. This information is then used to correct existing V
allele calls from among the sample sequences.
Citations:
Gadala-Maria, et al (2015) <doi:10.1073/pnas.1417683112>,
Gadala-Maria, et al (2019) <doi:10.3389/fimmu.2019.00129>.
Author: Daniel Gadala-Maria [aut],
Susanna Marquez [aut, cre],
Moriah Cohen [aut],
Jason Vander Heiden [aut],
Gur Yaari [aut],
Steven Kleinstein [aut, cph]
Maintainer: Susanna Marquez <susanna.marquez@yale.edu>
Diff between tigger versions 1.1.0 dated 2023-10-10 and 1.1.2 dated 2026-01-10
DESCRIPTION | 12 MD5 | 82 +-- NEWS.md | 19 R/bayesian.R | 168 +++---- R/data.R | 72 +-- R/evidence.R | 212 ++++----- R/functions.R | 888 ++++++++++++++++++++--------------------- R/tigger.R | 29 - README.md | 9 build/partial.rdb |binary build/vignette.rds |binary inst/doc/Tigger-Vignette.Rmd | 14 inst/doc/Tigger-Vignette.pdf |binary man/AIRRDb.Rd | 6 man/GermlineIGHV.Rd | 8 man/SampleDb.Rd | 6 man/SampleGenotype.Rd | 6 man/SampleGermlineIGHV.Rd | 6 man/SampleNovel.Rd | 8 man/cleanSeqs.Rd | 2 man/findNovelAlleles.Rd | 72 +-- man/findUnmutatedCalls.Rd | 6 man/generateEvidence.Rd | 70 +-- man/genotypeFasta.Rd | 4 man/getMutCount.Rd | 4 man/getMutatedPositions.Rd | 4 man/getPopularMutationCount.Rd | 4 man/inferGenotype.Rd | 22 - man/inferGenotypeBayesian.Rd | 56 +- man/insertPolymorphisms.Rd | 6 man/plotGenotype.Rd | 4 man/plotNovel.Rd | 30 - man/readIgFasta.Rd | 4 man/reassignAlleles.Rd | 14 man/selectNovel.Rd | 2 man/sortAlleles.Rd | 12 man/subsampleDb.Rd | 24 - man/tigger-package.Rd | 3 man/tigger.Rd | 13 man/updateAlleleNames.Rd | 8 man/writeFasta.Rd | 2 vignettes/Tigger-Vignette.Rmd | 14 42 files changed, 971 insertions(+), 954 deletions(-)
Title: Compact and Flexible Summaries of Data
Description: A simple to use summary function that can be used with pipes
and displays nicely in the console. The default summary statistics may
be modified by the user as can the default formatting. Support for
data frames and vectors is included, and users can implement their own
skim methods for specific object types as described in a vignette.
Default summaries include support for inline spark graphs.
Instructions for managing these on specific operating systems are
given in the "Using skimr" vignette and the README.
Author: Elin Waring [cre, aut],
Michael Quinn [aut],
Amelia McNamara [aut],
Eduardo Arino de la Rubia [aut],
Hao Zhu [aut],
Julia Lowndes [ctb],
Shannon Ellis [aut],
Hope McLeod [ctb],
Hadley Wickham [ctb],
Kirill Mueller [ctb],
RStudio, Inc. [cph] ,
Connor K [...truncated...]
Maintainer: Elin Waring <elin.waring@gmail.com>
Diff between skimr versions 2.2.1 dated 2025-07-26 and 2.2.2 dated 2026-01-10
DESCRIPTION | 10 MD5 | 44 NEWS.md | 5 R/skim_print.R | 2 build/vignette.rds |binary inst/doc/Skimr_defaults.html | 8 inst/doc/extending_skimr.html | 8 inst/doc/using_skimr.Rmd | 2 inst/doc/using_skimr.html | 10 inst/other_docs/blog.Rmd | 3 inst/other_docs/blog.html | 642 +++++++--- inst/other_docs/blog.md | 239 ++- inst/other_docs/blog_v2.Rmd | 44 inst/other_docs/blog_v2.html | 503 +++++-- inst/other_docs/blog_v2.md | 179 +- inst/rmarkdown/templates/fonts-in-skimr/skeleton/skeleton.log |only inst/rmarkdown/templates/fonts-in-skimr/skeleton/skeleton.pdf |only tests/bugreport.Rmd |only tests/bugreport.html |only tests/bugreport.pdf |only tests/testthat/_problems |only tests/testthat/test-skim_print.R | 1 vignettes/skimr.R |only vignettes/skimr.html |only vignettes/using_skimr.Rmd | 2 25 files changed, 1152 insertions(+), 550 deletions(-)
Title: Maximum Entropy Bootstrap for Time Series
Description: Maximum entropy density based dependent data bootstrap.
An algorithm is provided to create a population of time series (ensemble)
without assuming stationarity. The reference paper (Vinod, H.D., 2004
<DOI:10.1016/j.jempfin.2003.06.002>) explains how the algorithm satisfies
the ergodic theorem and the central limit theorem.
Author: Hrishikesh D. Vinod [aut],
Javier Lopez-de-Lacalle [aut],
Fred Viole [aut, cre]
Maintainer: Fred Viole <ovvo.open.source@gmail.com>
Diff between meboot versions 1.4-9.4 dated 2023-08-22 and 1.4-9.5 dated 2026-01-10
DESCRIPTION | 29 ++++++++++++++++++----------- MD5 | 14 +++++++------- inst/doc/Toy_Example_Exposition.pdf |binary inst/doc/meboot.R | 32 ++++++++++++++++---------------- inst/doc/meboot.Rnw | 4 +--- inst/doc/meboot.pdf |binary vignettes/meboot.Rnw | 4 +--- vignettes/meboot.bib | 16 ++++++++-------- 8 files changed, 51 insertions(+), 48 deletions(-)
Title: A Wrapper Around 'rjags' to Streamline 'JAGS' Analyses
Description: A set of wrappers around 'rjags' functions to run Bayesian analyses in 'JAGS' (specifically, via 'libjags'). A single function call can control adaptive, burn-in, and sampling MCMC phases, with MCMC chains run in sequence or in parallel. Posterior distributions are automatically summarized (with the ability to exclude some monitored nodes if desired) and functions are available to generate figures based on the posteriors (e.g., predictive check plots, traceplots). Function inputs, argument syntax, and output format are nearly identical to the 'R2WinBUGS'/'R2OpenBUGS' packages to allow easy switching between MCMC samplers.
Author: Ken Kellner [cre, aut],
Mike Meredith [ctb]
Maintainer: Ken Kellner <contact@kenkellner.com>
Diff between jagsUI versions 1.6.2 dated 2024-01-30 and 1.6.3 dated 2026-01-10
DESCRIPTION | 10 - MD5 | 14 +- R/run_rjags.R | 8 + build/vignette.rds |binary inst/doc/jagsUI.R | 20 +- inst/doc/jagsUI.html | 280 ++++++++++++++++++----------------------- inst/tinytest/test_autojags.R | 17 +- inst/tinytest/test_run_rjags.R | 30 ++-- 8 files changed, 185 insertions(+), 194 deletions(-)
Title: 'GeoNetwork' API R Interface
Description: Provides an R interface to the 'GeoNetwork' API (<https://geonetwork-opensource.org/#api>) allowing to upload and publish metadata in a 'GeoNetwork' web-application and expose it to OGC CSW.
Author: Emmanuel Blondel [aut, cre]
Maintainer: Emmanuel Blondel <emmanuel.blondel1@gmail.com>
Diff between geonapi versions 0.8 dated 2025-01-31 and 0.8-1 dated 2026-01-10
DESCRIPTION | 13 ++-- MD5 | 16 ++--- NEWS.md | 14 ++++ R/GNLegacyAPIManager.R | 20 +++--- R/GNOpenAPIManager.R | 139 ++++++++++++++++++++++++++++++++++++++++++---- R/GNPriv.R | 7 -- README.md | 3 man/GNLegacyAPIManager.Rd | 21 ++++-- man/GNOpenAPIManager.Rd | 87 ++++++++++++++++++++++++---- 9 files changed, 259 insertions(+), 61 deletions(-)
Title: A Partial Clustering Algorithm
Description: Provide the 'CrossClustering' algorithm (Tellaroli et al.
(2016) <doi:10.1371/journal.pone.0152333>), which is a partial
clustering algorithm that combines the Ward's minimum variance and
Complete Linkage algorithms, providing automatic estimation of a
suitable number of clusters and identification of outlier elements.
Author: Paola Tellaroli [cre, aut],
Marco Bazzi [aut],
Michele Donato [aut],
Livio Finos [aut],
Philippe Courcoux [aut],
Corrado Lanera [aut]
Maintainer: Paola Tellaroli <paola.tellaroli@gmail.com>
Diff between CrossClustering versions 4.1.2 dated 2024-05-14 and 4.1.3 dated 2026-01-10
DESCRIPTION | 10 MD5 | 78 +- NAMESPACE | 40 - NEWS.md | 7 R/CrossClustering-package.R | 12 R/ari.R | 484 +++++++++--------- R/cc_crossclustering.R | 698 +++++++++++++------------- R/cc_get_cluster.R | 188 +++---- R/cc_test_ari.R | 190 +++---- R/cc_test_ari_permutation.R | 128 ++-- R/consensus_cluster.R | 212 +++---- R/data.R | 128 ++-- R/dependencies.R | 12 R/reverse_table.R | 62 +- R/utils.R | 126 ++-- build/partial.rdb |binary man/CrossClustering-package.Rd | 64 +- man/ari.Rd | 204 +++---- man/cc_crossclustering.Rd | 486 +++++++++--------- man/cc_get_cluster.Rd | 144 ++--- man/cc_test_ari.Rd | 108 ++-- man/cc_test_ari_permutation.Rd | 104 +-- man/chain_effect.Rd | 44 - man/consensus_cluster.Rd | 134 ++-- man/is_zero.Rd | 42 - man/nb_data.Rd | 54 +- man/prune_zero_tail.Rd | 54 +- man/reverse_table.Rd | 60 +- man/toy.Rd | 32 - man/twomoons.Rd | 50 - man/worms.Rd | 50 - tests/spelling.R | 14 tests/testthat.R | 8 tests/testthat/test-ari.R | 190 +++---- tests/testthat/test-cc_crossclustering.R | 2 tests/testthat/test-cc_get_cluster.R | 76 +- tests/testthat/test-cc_test_ari.R | 100 +-- tests/testthat/test-cc_test_ari_permutation.R | 146 ++--- tests/testthat/test-consensus_cluster.R | 100 +-- tests/testthat/test-utils.R | 36 - 40 files changed, 2342 insertions(+), 2335 deletions(-)
More information about CrossClustering at CRAN
Permanent link
Title: Utility Functions for 'spatstat'
Description: Contains utility functions for the 'spatstat' family of packages
which may also be useful for other purposes.
Author: Adrian Baddeley [aut, cre] ,
Rolf Turner [aut] ,
Ege Rubak [aut]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.utils versions 3.2-0 dated 2025-09-20 and 3.2-1 dated 2026-01-10
DESCRIPTION | 8 ++++---- MD5 | 23 +++++++++++++---------- NAMESPACE | 1 + NEWS | 11 +++++++++++ R/longvec.R |only R/utiltext.R | 2 +- inst/doc/packagesizes.txt | 1 + inst/info/packagesizes.txt | 1 + man/difflong.Rd |only man/macros/defns.Rd | 3 +++ src/init.c | 8 +++++--- src/longvec.c |only src/proto.h | 2 ++ tests/numerical.R | 7 +++++++ 14 files changed, 49 insertions(+), 18 deletions(-)
More information about spatstat.utils at CRAN
Permanent link
Title: Operationalizing Social Determinants of Health Data for
Researchers
Description: Accesses raw data via API and calculates social
determinants of health measures for user-specified locations in the
US, returning them in tidyverse- and sf-compatible data frames.
Author: Nik Krieger [aut, cre],
Jarrod Dalton [aut],
Cindy Wang [aut],
Adam Perzynski [aut],
National Institutes of Health/National Institute on Aging [fnd] . All of its contents
are solely the responsibility of the authors and do not necessarily
represent t [...truncated...]
Maintainer: Nik Krieger <nikkrieger@gmail.com>
Diff between sociome versions 2.2.5 dated 2023-12-06 and 3.0.0 dated 2026-01-10
sociome-2.2.5/sociome/tests/testthat/nmcounties.rda |only sociome-2.2.5/sociome/tests/testthat/test_tidycensus_related.R |only sociome-3.0.0/sociome/DESCRIPTION | 14 sociome-3.0.0/sociome/LICENSE | 2 sociome-3.0.0/sociome/MD5 | 89 sociome-3.0.0/sociome/NEWS.md | 355 +- sociome-3.0.0/sociome/R/calculate_adi.R | 1337 +++++----- sociome-3.0.0/sociome/R/census_api_key.R | 14 sociome-3.0.0/sociome/R/centers.R | 959 +++---- sociome-3.0.0/sociome/R/data_documentation.R | 244 + sociome-3.0.0/sociome/R/dissimilarity.R | 289 +- sociome-3.0.0/sociome/R/get_adi.R | 701 ++--- sociome-3.0.0/sociome/R/get_geoids.R | 231 - sociome-3.0.0/sociome/R/get_tidycensus.R | 692 +++-- sociome-3.0.0/sociome/R/ref_area.R | 598 ++-- sociome-3.0.0/sociome/R/setup.R | 2 sociome-3.0.0/sociome/R/synthetic_population.R | 683 ++--- sociome-3.0.0/sociome/R/utils-pipe.R | 24 sociome-3.0.0/sociome/R/validation.R | 755 +++-- sociome-3.0.0/sociome/data/acs_age_sex_race_ethnicity_vars.rda |binary sociome-3.0.0/sociome/data/acs_vars.rda |binary sociome-3.0.0/sociome/data/dataset_year_geography_availability.rda |only sociome-3.0.0/sociome/data/decennial_age_sex_race_ethnicity_vars.rda |binary sociome-3.0.0/sociome/data/decennial_vars.rda |binary sociome-3.0.0/sociome/data/state_geoids.rda |only sociome-3.0.0/sociome/man/acs_age_sex_race_ethnicity_vars.Rd | 61 sociome-3.0.0/sociome/man/acs_vars.Rd | 92 sociome-3.0.0/sociome/man/append_dissimilarities.Rd | 174 - sociome-3.0.0/sociome/man/calculate_adi.Rd | 147 - sociome-3.0.0/sociome/man/census_api_key.Rd | 16 sociome-3.0.0/sociome/man/dataset_year_geography_availability.Rd |only sociome-3.0.0/sociome/man/decennial_age_sex_race_ethnicity_vars.Rd | 62 sociome-3.0.0/sociome/man/decennial_vars.Rd | 51 sociome-3.0.0/sociome/man/get_adi.Rd | 58 sociome-3.0.0/sociome/man/get_areas_near_coordinates.Rd | 322 +- sociome-3.0.0/sociome/man/get_geoids.Rd | 187 - sociome-3.0.0/sociome/man/lon_lat_from_area.Rd | 122 sociome-3.0.0/sociome/man/pipe.Rd | 24 sociome-3.0.0/sociome/man/state_geoids.Rd |only sociome-3.0.0/sociome/man/synthetic_population.Rd | 354 +- sociome-3.0.0/sociome/tests/testthat.R | 16 sociome-3.0.0/sociome/tests/testthat/_snaps |only sociome-3.0.0/sociome/tests/testthat/helper-setup.R |only sociome-3.0.0/sociome/tests/testthat/test-dissimilarity.R |only sociome-3.0.0/sociome/tests/testthat/test-get_adi.R |only sociome-3.0.0/sociome/tests/testthat/test-get_geoids.R |only sociome-3.0.0/sociome/tests/testthat/test-get_tidycensus.R |only sociome-3.0.0/sociome/tests/testthat/test-ref_area.R |only sociome-3.0.0/sociome/tests/testthat/test-synthetic_population.R |only sociome-3.0.0/sociome/tests/testthat/test-validators.R |only sociome-3.0.0/sociome/tests/testthat/test_area_population.R |only 51 files changed, 4541 insertions(+), 4134 deletions(-)
Title: Simulate Data from State Space Models
Description: Provides a streamlined and user-friendly framework
for simulating data in state space models,
particularly when the number of subjects/units (n) exceeds one,
a scenario commonly encountered in social and behavioral sciences.
This package was designed to generate data for the simulations
performed in Pesigan, Russell, and Chow (2025) <doi:10.1037/met0000779>.
Author: Ivan Jacob Agaloos Pesigan [aut, cre, cph] ,
Michael A. Russell [ctb] ,
Sy-Miin Chow [ctb]
Maintainer: Ivan Jacob Agaloos Pesigan <r.jeksterslab@gmail.com>
Diff between simStateSpace versions 1.2.12 dated 2025-10-10 and 1.2.14 dated 2026-01-10
DESCRIPTION | 14 MD5 | 92 +-- NAMESPACE | 2 NEWS.md | 12 R/RcppExports.R | 138 +++++ R/simStateSpace-lin-sde-mean-y.R | 4 R/simStateSpace-ssm-mean-y.R | 4 build/partial.rdb |binary man/LinSDE2SSM.Rd | 2 man/LinSDECovEta.Rd | 2 man/LinSDECovY.Rd | 2 man/LinSDEMeanEta.Rd | 2 man/LinSDEMeanY.Rd | 6 man/ProjectToHurwitz.Rd | 2 man/ProjectToStability.Rd | 2 man/SSMCovEta.Rd | 2 man/SSMCovY.Rd | 2 man/SSMMeanEta.Rd | 2 man/SSMMeanY.Rd | 6 man/SimAlphaN.Rd | 2 man/SimBetaN.Rd | 2 man/SimBetaN2.Rd | 2 man/SimBetaNCovariate.Rd |only man/SimCovDiagN.Rd | 2 man/SimCovN.Rd | 2 man/SimIotaN.Rd | 2 man/SimNuN.Rd | 2 man/SimPhiN.Rd | 2 man/SimPhiN2.Rd | 2 man/SimPhiNCovariate.Rd |only man/SimSSMFixed.Rd | 2 man/SimSSMIVary.Rd | 2 man/SimSSMLinGrowth.Rd | 2 man/SimSSMLinGrowthIVary.Rd | 4 man/SimSSMLinSDEFixed.Rd | 2 man/SimSSMLinSDEIVary.Rd | 2 man/SimSSMOUFixed.Rd | 2 man/SimSSMOUIVary.Rd | 2 man/SimSSMVARFixed.Rd | 2 man/SimSSMVARIVary.Rd | 2 man/SpectralRadius.Rd | 2 man/TestPhi.Rd | 2 man/TestPhiHurwitz.Rd | 2 man/TestStability.Rd | 2 man/TestStationarity.Rd | 2 src/RcppExports.cpp | 43 + src/source.cpp | 369 ++++++++++++++- tests/testthat/test-simStateSpace-sim-beta-n-covariate.R |only tests/testthat/test-simStateSpace-sim-phi-n-covariate.R |only 49 files changed, 681 insertions(+), 77 deletions(-)
Title: Variance Stabilizing Transformations for Single Cell UMI Data
Description: A normalization method for single-cell UMI count data using a
variance stabilizing transformation. The transformation is based on a
negative binomial regression model with regularized parameters. As part of the
same regression framework, this package also provides functions for
batch correction, and data correction. See Hafemeister and Satija (2019)
<doi:10.1186/s13059-019-1874-1>, and Choudhary and Satija (2022) <doi:10.1186/s13059-021-02584-9>
for more details.
Author: Christoph Hafemeister [aut] ,
Saket Choudhary [aut, cre] ,
Rahul Satija [ctb]
Maintainer: Saket Choudhary <saketc@iitb.ac.in>
Diff between sctransform versions 0.4.2 dated 2025-04-30 and 0.4.3 dated 2026-01-10
DESCRIPTION | 14 +- MD5 | 44 ++++---- NEWS.md | 11 +- R/data.R | 2 R/denoise.R | 82 +++------------- R/differential_expression.R | 42 +------- R/plotting.R | 20 --- R/utils.R | 215 +++++++++++++++++++++--------------------- R/vst.R | 51 ++------- README.md | 6 - build/partial.rdb |binary man/clip_matrix_values.Rd |only man/close_progress_bar.Rd |only man/compare_expression.Rd | 12 -- man/correct.Rd | 10 - man/correct_counts.Rd | 10 - man/get_model_formula.Rd |only man/get_model_var.Rd | 10 - man/get_residual_var.Rd | 10 - man/get_residuals.Rd | 10 - man/pbmc.Rd | 2 man/plot_model_pars.Rd | 10 - man/prepare_regressor_data.Rd |only man/setup_progress_bar.Rd |only man/update_progress_bar.Rd |only man/vst.Rd | 10 - 26 files changed, 217 insertions(+), 354 deletions(-)
Title: Phylogenetic Ridge Regression Methods for Comparative Studies
Description: Functions for phylogenetic analysis (Castiglione et al., 2018 <doi:10.1111/2041-210X.12954>). The functions perform the estimation of phenotypic evolutionary rates, identification of phenotypic evolutionary rate shifts, quantification of direction and size of evolutionary change in multivariate traits, the computation of ontogenetic shape vectors and test for morphological convergence.
Author: Pasquale Raia [aut],
Silvia Castiglione [aut, cre],
Carmela Serio [aut],
Giorgia Girardi [aut],
Alessandro Mondanaro [aut],
Marina Melchionna [aut],
Mirko Di Febbraro [aut],
Antonio Profico [aut],
Francesco Carotenuto [aut]
Maintainer: Silvia Castiglione <silvia.castiglione@unina.it>
Diff between RRphylo versions 3.0.1 dated 2025-07-12 and 3.0.2 dated 2026-01-10
DESCRIPTION | 10 +++--- MD5 | 40 ++++++++++++------------- R/overfitPGLS.R | 2 - R/overfitRR.R | 4 +- R/overfitSS.R | 2 - R/overfitST.R | 2 - R/resampleTree.R | 62 ++++++++++++---------------------------- R/search.shift.R | 4 +- build/vignette.rds |binary inst/doc/Alternative-trees.html | 6 +-- inst/doc/Plotting-tools.html | 50 ++++++++++++++++---------------- inst/doc/RRphylo.html | 16 +++++----- inst/doc/Tree-Manipulation.html | 38 ++++++++++++------------ inst/doc/search.conv.html | 6 +-- inst/doc/search.shift.html | 4 +- inst/doc/search.trend.html | 6 +-- man/overfitPGLS.Rd | 2 - man/overfitRR.Rd | 2 - man/overfitSS.Rd | 2 - man/overfitST.Rd | 2 - man/resampleTree.Rd | 23 +++++++++----- 21 files changed, 135 insertions(+), 148 deletions(-)
Title: Robust Change-Point Tests
Description: Provides robust methods to detect change-points in uni- or multivariate time series. They can cope with corrupted data and heavy tails. Focus is on the detection of abrupt changes in location, but changes in the scale or dependence structure can be detected as well. This package provides tests for change detection in uni- and multivariate time series based on Huberized versions of CUSUM tests proposed in Duerre and Fried (2019) <DOI:10.48550/arXiv.1905.06201>, and tests for change detection in univariate time series based on 2-sample U-statistics or 2-sample U-quantiles as proposed by Dehling et al. (2015) <DOI:10.1007/978-1-4939-3076-0_12> and Dehling, Fried and Wendler (2020) <DOI:10.1093/biomet/asaa004>. Furthermore, the packages provides tests on changes in the scale or the correlation as proposed in Gerstenberger, Vogel and Wendler (2020) <DOI:10.1080/01621459.2019.1629938>, Dehling et al. (2017) <DOI:10.1017/S026646661600044X>, and Wied et al. (2014) [...truncated...]
Author: Sheila Goerz [aut, cre],
Alexander Duerre [aut],
Roland Fried [ctb, ths]
Maintainer: Sheila Goerz <sheila.goerz@tu-dortmund.de>
Diff between robcp versions 0.3.9 dated 2025-06-25 and 0.3.10 dated 2026-01-10
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/modifChol.c | 4 ++-- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Easily Visualize Data from 'ERDDAP™' Servers via the 'rerddap'
Package
Description: Easily visualize and animate 'tabledap' and 'griddap' objects obtained via the 'rerddap' package in a simple one-line command, using either base graphics or 'ggplot2' graphics. 'plotdap' handles extracting and reshaping the data, map projections and continental outlines. Optionally the data can be animated through time using the 'gganmiate' package.
Author: Carson Sievert [aut],
Roy Mendelssohn [aut, ctb, cre]
Maintainer: Roy Mendelssohn <roy.mendelssohn@noaa.gov>
Diff between plotdap versions 1.1.0 dated 2025-06-29 and 1.1.1 dated 2026-01-10
DESCRIPTION | 12 ++-- MD5 | 18 +++--- NEWS.md | 6 ++ R/bbox_set.R | 90 +++++++++++++++++++++++++------- build/vignette.rds |binary inst/doc/using_plotdap.R | 28 ++++++++++ inst/doc/using_plotdap.Rmd | 54 +++++++++++++++++-- inst/doc/using_plotdap.html | 121 ++++++++++++++++++++++++++++++++++---------- man/bbox_set.Rd | 21 +++++-- vignettes/using_plotdap.Rmd | 54 +++++++++++++++++-- 10 files changed, 327 insertions(+), 77 deletions(-)
Title: Tabulate P.L. 94-171 Redistricting Data Summary Files
Description: Tools to process legacy format summary redistricting data files
produced by the United States Census Bureau pursuant to P.L. 94-171. These
files are generally available earlier but are difficult to work with as-is.
Author: Cory McCartan [aut, cre],
Christopher T. Kenny [aut]
Maintainer: Cory McCartan <mccartan@psu.edu>
Diff between PL94171 versions 1.1.3 dated 2025-02-19 and 1.2.1 dated 2026-01-10
DESCRIPTION | 19 +++++++++--------- MD5 | 23 +++++++++++----------- NEWS.md | 7 ++++++ R/pl_read.R | 47 ++++++++++++++++++++++++++++++++++++++++----- R/utils.R | 4 +-- R/utils_1990.R |only build/vignette.rds |binary inst/doc/PL94171.Rmd | 2 - inst/doc/PL94171.html | 13 ++++++------ man/PL94171-package.Rd | 2 - man/pl_url.Rd | 4 +-- tests/testthat/test-urls.R | 6 ++--- vignettes/PL94171.Rmd | 2 - 13 files changed, 88 insertions(+), 41 deletions(-)
Title: Photobiological Calculations
Description: Definitions of classes, methods, operators and functions for use
in photobiology and radiation meteorology and climatology. Calculation of
effective (weighted) and not-weighted irradiances/doses, fluence rates,
transmittance, reflectance, absorptance, absorbance and diverse ratios and
other derived quantities from spectral data. Local maxima and minima: peaks,
valleys and spikes. Conversion between energy-and photon-based units.
Wavelength interpolation. Colours and vision. This package is part of the
'r4photobiology' suite, Aphalo, P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.
Author: Pedro J. Aphalo [aut, cre] ,
Titta K. Kotilainen [ctb] ,
Glenn Davis [ctb],
Agnese Fazio [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between photobiology versions 0.14.0 dated 2025-09-26 and 0.14.1 dated 2026-01-10
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS.md | 7 ++++++- R/zmspct.classes.R | 27 ++++++++++++++++++++------- README.md | 6 +++--- build/partial.rdb |binary build/vignette.rds |binary inst/doc/userguide-0-r4p-introduction.html | 2 +- inst/doc/userguide-1-radiation.html | 6 +++--- 9 files changed, 45 insertions(+), 27 deletions(-)
Title: SDTM Test Data for the 'Pharmaverse' Family of Packages
Description: A set of Study Data Tabulation Model (SDTM) datasets from the
Clinical Data Interchange Standards Consortium (CDISC) pilot project
used for testing and developing Analysis Data Model (ADaM) datasets
inside the pharmaverse family of packages. SDTM dataset specifications
are described in the CDISC SDTM implementation guide, accessible by
creating a free account on <https://www.cdisc.org/>.
Author: Lina Patil [aut, cre],
Stefan Bundfuss [aut] ,
Kristin Dahnert [aut],
Fanny Gautier [aut] ,
Edoardo Mancini [aut] ,
Tomoyuki Namai [aut],
Vinh Nguyen [aut],
Vladyslav Shuliar [aut] ,
Cytel Inc. [cph, fnd],
F. Hoffmann-La Roche AG [cph, fnd],
GlaxoSmi [...truncated...]
Maintainer: Lina Patil <lina.patil@cytel.com>
Diff between pharmaversesdtm versions 1.3.1 dated 2025-08-21 and 1.4.0 dated 2026-01-10
DESCRIPTION | 15 +- MD5 | 259 ++++++++++++++++++++++------------------- NEWS.md | 46 +++++++ R/ae.R | 2 R/ae_ophtha.R | 2 R/ag_neuro.R |only R/ce_vaccine.R | 2 R/cm.R | 2 R/dm.R | 5 R/dm_metabolic.R | 5 R/dm_neuro.R |only R/dm_peds.R | 2 R/dm_vaccine.R | 2 R/ds.R | 2 R/eg.R | 2 R/ex.R | 2 R/ex_ophtha.R | 2 R/ex_vaccine.R | 2 R/face_vaccine.R | 2 R/is_ada.R |only R/is_vaccine.R | 2 R/lb.R | 2 R/lb_metabolic.R | 2 R/lb_neuro.R |only R/lb_onco_pcwg3.R |only R/mh.R | 2 R/nv_neuro.R |only R/oe_ophtha.R | 2 R/pc.R | 5 R/pp.R | 2 R/qs_metabolic.R | 2 R/qs_ophtha.R | 60 ++++----- R/rs_onco.R | 2 R/rs_onco_ca125.R | 2 R/rs_onco_imwg.R | 2 R/rs_onco_irecist.R | 2 R/rs_onco_pcwg3.R | 11 - R/rs_onco_recist.R | 2 R/sc_ophtha.R | 2 R/sdg_db.R | 2 R/smq_db.R | 2 R/suppae.R | 2 R/suppce_vaccine.R | 2 R/suppdm.R | 2 R/suppdm_vaccine.R | 2 R/suppds.R | 2 R/suppex_vaccine.R | 2 R/suppface_vaccine.R | 2 R/suppis_vaccine.R | 2 R/suppnv_neuro.R |only R/supprs_onco_ca125.R | 2 R/supprs_onco_imwg.R | 2 R/supptr_onco.R | 2 R/sv.R | 2 R/tr_onco.R | 2 R/tr_onco_recist.R | 2 R/ts.R | 2 R/tu_onco.R | 2 R/tu_onco_recist.R | 2 R/vs.R | 2 R/vs_metabolic.R | 2 R/vs_peds.R | 2 R/vs_vaccine.R | 2 README.md | 32 ++++- data/ag_neuro.rda |only data/dm.rda |binary data/dm_metabolic.rda |binary data/dm_neuro.rda |only data/dm_vaccine.rda |binary data/is_ada.rda |only data/lb_neuro.rda |only data/lb_onco_pcwg3.rda |only data/nv_neuro.rda |only data/pc.rda |binary data/qs_ophtha.rda |binary data/rs_onco_pcwg3.rda |binary data/suppdm.rda |binary data/suppnv_neuro.rda |only inst/WORDLIST | 32 +++-- inst/extdata/sdtms-specs.json | 210 ++++++++++++++++++++++++--------- man/ae.Rd | 1 man/ae_ophtha.Rd | 1 man/ag_neuro.Rd |only man/ce_vaccine.Rd | 1 man/cm.Rd | 1 man/dm.Rd | 4 man/dm_metabolic.Rd | 4 man/dm_neuro.Rd |only man/dm_peds.Rd | 1 man/dm_vaccine.Rd | 1 man/ds.Rd | 1 man/eg.Rd | 1 man/ex.Rd | 1 man/ex_ophtha.Rd | 1 man/ex_vaccine.Rd | 1 man/face_vaccine.Rd | 1 man/is_ada.Rd |only man/is_vaccine.Rd | 1 man/lb.Rd | 1 man/lb_metabolic.Rd | 1 man/lb_neuro.Rd |only man/lb_onco_pcwg3.Rd |only man/mh.Rd | 1 man/nv_neuro.Rd |only man/oe_ophtha.Rd | 1 man/pc.Rd | 4 man/pharmaversesdtm-package.Rd | 1 man/pp.Rd | 1 man/qs_metabolic.Rd | 1 man/qs_ophtha.Rd | 59 ++++----- man/rs_onco.Rd | 1 man/rs_onco_ca125.Rd | 1 man/rs_onco_imwg.Rd | 1 man/rs_onco_irecist.Rd | 1 man/rs_onco_pcwg3.Rd | 10 - man/rs_onco_recist.Rd | 1 man/sc_ophtha.Rd | 1 man/sdg_db.Rd | 1 man/smq_db.Rd | 1 man/suppae.Rd | 1 man/suppce_vaccine.Rd | 1 man/suppdm.Rd | 1 man/suppdm_vaccine.Rd | 1 man/suppds.Rd | 1 man/suppex_vaccine.Rd | 1 man/suppface_vaccine.Rd | 1 man/suppis_vaccine.Rd | 1 man/suppnv_neuro.Rd |only man/supprs_onco_ca125.Rd | 1 man/supprs_onco_imwg.Rd | 1 man/supptr_onco.Rd | 1 man/sv.Rd | 1 man/tr_onco.Rd | 1 man/tr_onco_recist.Rd | 1 man/ts.Rd | 1 man/tu_onco.Rd | 1 man/tu_onco_recist.Rd | 1 man/vs.Rd | 1 man/vs_metabolic.Rd | 1 man/vs_peds.Rd | 1 man/vs_vaccine.Rd | 1 141 files changed, 591 insertions(+), 315 deletions(-)
More information about pharmaversesdtm at CRAN
Permanent link
Title: Getting Bibliographic Records from 'OpenAlex' Database Using
'DSL' API
Description: A set of tools to extract bibliographic content from
'OpenAlex' database using API <https://docs.openalex.org>.
Author: Massimo Aria [aut, cre, cph] ,
Corrado Cuccurullo [ctb] ,
Trang Le [aut] ,
June Choe [aut]
Maintainer: Massimo Aria <aria@unina.it>
Diff between openalexR versions 2.0.2 dated 2025-10-21 and 3.0.0 dated 2026-01-10
DESCRIPTION | 8 - MD5 | 56 ++++++------ NEWS.md | 12 +- R/oa2bibliometrix.R | 2 R/oa2df.R | 191 ++++++++++++++++++++++++++++++----------- R/oa_fetch.R | 147 ++++++++++++++++++------------- R/oa_ngrams.R | 30 +++--- R/oa_snowball.R | 6 - R/openalexR-internal.R | 14 +-- R/utils.R | 9 - README.md | 93 +++++++++++-------- data/concept_abbrev.rda |binary data/oa2df_coverage.rda |binary man/authors2df.Rd | 9 - man/concepts2df.Rd | 9 - man/funders2df.Rd | 9 - man/institutions2df.Rd | 9 - man/oa2bibliometrix.Rd | 2 man/oa_fetch.Rd | 14 +-- man/oa_query.Rd | 2 man/oa_request.Rd | 7 + man/publishers2df.Rd | 9 - man/sources2df.Rd | 9 - man/topics2df.Rd | 9 - man/works2df.Rd | 10 -- tests/testthat/test-coverage.R | 9 + tests/testthat/test-oa2df.R | 8 - tests/testthat/test-oa_fetch.R | 35 +++++-- tests/testthat/test-oa_query.R | 10 ++ 29 files changed, 418 insertions(+), 310 deletions(-)
Title: Nonlinear Nonparametric Statistics
Description: NNS (Nonlinear Nonparametric Statistics) leverages partial moments – the fundamental elements of variance that asymptotically approximate the area under f(x) – to provide a robust foundation for nonlinear analysis while maintaining linear equivalences. NNS delivers a comprehensive suite of advanced statistical techniques, including: Numerical integration, Numerical differentiation, Clustering, Correlation, Dependence, Causal analysis, ANOVA, Regression, Classification, Seasonality, Autoregressive modeling, Normalization, Stochastic dominance and Advanced Monte Carlo sampling. All routines based on: Viole, F. and Nawrocki, D. (2013), Nonlinear Nonparametric Statistics: Using Partial Moments (ISBN: 1490523995).
Author: Fred Viole [aut, cre],
Roberto Spadim [ctb]
Maintainer: Fred Viole <ovvo.open.source@gmail.com>
Diff between NNS versions 11.6.3 dated 2025-11-28 and 11.6.4 dated 2026-01-10
DESCRIPTION | 12 +-- MD5 | 28 +++---- R/Numerical_Differentiation.R | 2 R/Partial_Moments.R | 15 ++++ R/Partition_Map.R | 2 R/Stack.R | 135 ++++++++++++++++++++----------------- README.md | 6 - inst/doc/NNSvignette_Overview.Rmd | 1 inst/doc/NNSvignette_Overview.html | 12 ++- man/NNS.Rd | 2 man/NNS.part.Rd | 2 src/Makevars | 2 src/Makevars.win | 3 src/internal_functions.cpp | 17 +++- vignettes/NNSvignette_Overview.Rmd | 1 15 files changed, 143 insertions(+), 97 deletions(-)
Title: Thematic Cartography
Description: Create and integrate thematic maps in your workflow. This package
helps to design various cartographic representations such as proportional
symbols, choropleth or typology maps. It also offers several functions to
display layout elements that improve the graphic presentation of maps
(e.g. scale bar, north arrow, title, labels). 'mapsf' maps 'sf' objects on
'base' graphics.
Author: Timothee Giraud [cre, aut] ,
Hugues Pecout [ctb] ,
Ronan Ysebaert [ctb] ,
Elina Marveaux [ctb] ,
Ian Fellows [cph] ,
Jim Lemon [cph]
Maintainer: Timothee Giraud <timothee.giraud@cnrs.fr>
Diff between mapsf versions 1.0.0 dated 2025-07-01 and 1.1.0 dated 2026-01-10
DESCRIPTION | 10 ++-- MD5 | 88 ++++++++++++++++++------------------- NEWS.md | 16 ++++++ R/mf_annotation.R | 8 +++ R/mf_arrow.R | 47 ++++++++++--------- R/mf_choro.R | 6 ++ R/mf_credits.R | 34 ++++++++------ R/mf_doc_utils.R | 2 R/mf_grad.R | 6 ++ R/mf_inset.R | 5 +- R/mf_map.R | 104 ++++++++++++++++++++++++-------------------- R/mf_png.R | 7 +- R/mf_prop.R | 8 +++ R/mf_prop_choro.R | 14 +++++ R/mf_prop_typo.R | 17 +++++-- R/mf_raster.R | 11 ++++ R/mf_raster_utils.R | 4 + R/mf_scale.R | 21 +++----- R/mf_shadow.R | 10 ++-- R/mf_symb.R | 2 R/mf_symb_choro.R | 8 +++ R/mf_theme.R | 16 +++++- R/mf_title.R | 15 +++--- README.md | 35 +++++--------- build/vignette.rds |binary inst/doc/mapsf.R | 2 inst/doc/mapsf.Rmd | 6 +- inst/doc/mapsf.html | 26 +++++------ inst/tinytest/test_export.R | 5 ++ inst/tinytest/test_theme.R | 4 - man/figures/example1-1.png |binary man/mf_annotation.Rd | 3 + man/mf_choro.Rd | 6 ++ man/mf_grad.Rd | 6 ++ man/mf_map.Rd | 104 ++++++++++++++++++++++++-------------------- man/mf_png.Rd | 12 ++++- man/mf_prop.Rd | 6 ++ man/mf_prop_choro.Rd | 6 ++ man/mf_prop_typo.Rd | 8 ++- man/mf_raster.Rd | 6 ++ man/mf_scale.Rd | 3 - man/mf_symb.Rd | 3 - man/mf_symb_choro.Rd | 6 ++ man/mf_theme.Rd | 13 +++++ vignettes/mapsf.Rmd | 6 +- 45 files changed, 463 insertions(+), 262 deletions(-)
Title: Legends for Maps
Description: Create legends for maps and other graphics. Thematic maps need to
be accompanied by legible legends to be fully comprehensible. This package
offers a wide range of legends useful for cartography, some of which may
also be useful for other types of graphics.
Author: Timothee Giraud [cre, aut]
Maintainer: Timothee Giraud <timothee.giraud@cnrs.fr>
Diff between maplegend versions 0.4.0 dated 2025-12-04 and 0.5.0 dated 2026-01-10
DESCRIPTION | 6 ++-- MD5 | 20 +++++++------- NEWS.md | 6 ++++ R/lg_choro.R | 3 ++ R/lg_choro_horiz.R | 3 ++ R/lg_grad_line.R | 3 ++ R/lg_prop.R | 4 +- R/lg_prop_line.R | 6 ++-- R/lg_symb.R | 6 ++-- R/lg_typo.R | 6 ++-- inst/tinytest/tests.R | 70 ++++++++++++++++++++++++++++++++++++++++++++------ 11 files changed, 104 insertions(+), 29 deletions(-)
Title: The Interpolate, Truncate, Project (ITP) Root-Finding Algorithm
Description: Implements the Interpolate, Truncate, Project (ITP) root-finding
algorithm developed by Oliveira and Takahashi (2021) <doi:10.1145/3423597>.
The user provides the function, from the real numbers to the real numbers,
and an interval with the property that the values of the function at its
endpoints have different signs. If the function is continuous over this
interval then the ITP method estimates the value at which the function is
equal to zero. If the function is discontinuous then a point of
discontinuity at which the function changes sign may be found.
The function can be supplied using either an R function or an external
pointer to a C++ function. Tuning parameters of the ITP algorithm can be
set by the user. Default values are set based on arguments in Oliveira and
Takahashi (2021).
Author: Paul J. Northrop [aut, cre, cph]
Maintainer: Paul J. Northrop <p.northrop@ucl.ac.uk>
Diff between itp versions 1.2.1 dated 2023-12-02 and 1.2.2 dated 2026-01-10
DESCRIPTION | 10 +++++----- MD5 | 20 ++++++++++---------- NEWS.md | 8 ++++++++ R/itp.R | 5 +++-- README.md | 12 +++++------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/itp-vignette.html | 24 +++++++++++++----------- man/itp-package.Rd | 1 - man/itp.Rd | 5 +++-- src/RcppExports.cpp | 24 ++++++++++++------------ 11 files changed, 59 insertions(+), 50 deletions(-)
Title: A 'ggplot2' Implement of Venn Diagram
Description: Easy-to-use functions to generate 2-7 sets Venn or upset plot in publication quality.
'ggVennDiagram' plot Venn or upset using well-defined geometry dataset and 'ggplot2'. The shapes of 2-4 sets
Venn use circles and ellipses, while the shapes of 4-7 sets Venn use irregular polygons (4 has both forms), which
are developed and imported from another package 'venn', authored by Adrian Dusa. We provided internal functions to
integrate shape data with user provided sets data, and calculated the geometry of every regions/intersections
of them, then separately plot Venn in four components, set edges/labels, and region edges/labels.
From version 1.0, it is possible to customize these components as you demand in ordinary 'ggplot2' grammar.
From version 1.4.4, it supports unlimited number of sets, as it can draw a plain upset plot automatically when
number of sets is more than 7.
Author: Chun-Hui Gao [aut, cre] ,
Guangchuang Yu [ctb] ,
Adrian Dusa [aut, cph] ,
Turgut Yigit Akyol [ctb]
Maintainer: Chun-Hui Gao <gaospecial@gmail.com>
Diff between ggVennDiagram versions 1.5.4 dated 2025-06-21 and 1.5.7 dated 2026-01-10
DESCRIPTION | 8 ++--- MD5 | 46 ++++++++++++++-------------- NEWS.md | 8 +++++ R/ggVennDiagram.R | 4 +- R/upset_plot.R | 48 +++++++++++++++++++++++++----- README.md | 2 - build/vignette.rds |binary inst/doc/VennCalculator.html | 5 +-- inst/doc/fully-customed.html | 11 +++--- inst/doc/using-ggVennDiagram.R | 2 - inst/doc/using-ggVennDiagram.Rmd | 2 - inst/doc/using-ggVennDiagram.html | 11 +++--- inst/doc/using-new-shapes.html | 5 +-- man/figures/README-unnamed-chunk-11-1.png |binary man/figures/README-unnamed-chunk-12-1.png |binary man/figures/README-unnamed-chunk-13-1.png |binary man/figures/README-unnamed-chunk-14-1.png |binary man/figures/README-unnamed-chunk-4-1.png |binary man/figures/README-unnamed-chunk-4-2.png |binary man/figures/README-unnamed-chunk-5-1.png |binary man/figures/README-unnamed-chunk-5-2.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/upset-plot.Rd | 13 ++++++++ vignettes/using-ggVennDiagram.Rmd | 2 - 24 files changed, 114 insertions(+), 53 deletions(-)
Title: Simple Fisheries Stock Assessment Methods
Description: A variety of simple fish stock assessment methods.
Author: Derek H. Ogle [aut, cre],
Jason C. Doll [aut],
A. Powell Wheeler [aut],
Alexis Dinno [aut] )
Maintainer: Derek H. Ogle <DerekOgle51@gmail.com>
Diff between FSA versions 0.10.0 dated 2025-05-06 and 0.10.1 dated 2026-01-10
DESCRIPTION | 10 MD5 | 57 +- NEWS.md | 16 R/PSDWRtest.R |only R/PSDlit.R | 3 R/WSlit.R | 2 R/chapmanRobson.R | 10 R/metaM.R | 22 R/psdAdd.R | 213 ++++++-- R/psdCalc.R | 52 +- R/psdVal.R | 34 - R/wrAdd.R | 170 ++++-- R/wsVal.R | 88 +-- data/PSDWRtest.rda |only data/PSDlit.rdata |binary data/WSlit.rdata |binary inst/extdata/PSDWR_data4testthat.csv |only inst/extdata/PSDWR_data4testthat.xlsx |only man/PSDWRtest.Rd |only man/PSDlit.Rd | 3 man/WSlit.Rd | 2 man/metaM.Rd | 13 man/psdAdd.Rd | 151 ++++-- man/psdCalc.Rd | 45 - man/psdVal.Rd | 16 man/wrAdd.Rd | 123 +++- man/wsVal.Rd | 61 +- tests/testthat/Rplots.pdf |binary tests/testthat/testthat_PSD.R | 841 +++++++++++++++++----------------- tests/testthat/testthat_WSWR.R | 162 ++++-- tests/testthat/testthat_catchCurve.R | 12 tests/testthat/testthat_metaM.R | 7 32 files changed, 1279 insertions(+), 834 deletions(-)
Title: Padronizador de Endereços Brasileiros (Brazilian Addresses
Standardizer)
Description: Padroniza endereços brasileiros a partir de diferentes
critérios. Os métodos de padronização incluem apenas manipulações
básicas de strings, não oferecendo suporte a correspondências
probabilísticas entre strings. (Standardizes brazilian addresses using
different criteria. Standardization methods include only basic string
manipulation, not supporting probabilistic matches between strings.)
Author: Daniel Herszenhut [aut, cre] ,
Rafael H. M. Pereira [aut] ,
Lucas Mation [aut] ,
Gabriel Garcia de Almeida [aut]
Maintainer: Daniel Herszenhut <dhersz@gmail.com>
Diff between enderecobr versions 0.4.1 dated 2025-02-18 and 0.5.0 dated 2026-01-10
DESCRIPTION | 30 + LICENSE | 4 MD5 | 63 ++-- NAMESPACE | 37 +- NEWS.md | 12 R/extendr-wrappers.R |only R/padronizar_bairros.R | 152 --------- R/padronizar_ceps.R | 39 -- R/padronizar_complementos.R | 241 --------------- R/padronizar_estados.R | 67 ---- R/padronizar_logradouros.R | 260 ---------------- R/padronizar_municipios.R | 102 ------ R/padronizar_numeros.R | 22 - R/padronizar_tipos_de_logradouro.R | 125 -------- build/vignette.rds |binary configure |only configure.win |only inst/doc/enderecobr.html | 5 man/enderecobr.Rd | 63 ++-- man/padronizar_bairros.Rd | 78 ++--- man/padronizar_ceps.Rd | 76 ++-- man/padronizar_complementos.Rd | 78 ++--- man/padronizar_estados.Rd | 98 +++--- man/padronizar_logradouros.Rd | 80 ++--- man/padronizar_numeros.Rd | 90 ++--- man/padronizar_tipos_de_logradouro.Rd | 78 ++--- src |only tests/testes_nao_automaticos/rust-bench.R |only tests/testthat/_snaps/padronizar_enderecos.md | 404 +++++++++++++------------- tests/testthat/_snaps/padronizar_numeros.md | 16 - tools |only 31 files changed, 640 insertions(+), 1580 deletions(-)
Title: Connect to an OMOP Common Data Model
Description: Provides tools for working with observational health data in the
Observational Medical Outcomes Partnership (OMOP) Common Data Model format with a pipe friendly syntax.
Common data model database table references are stored in a single compound object along with metadata.
Author: Adam Black [aut, cre] ,
Artem Gorbachev [aut],
Edward Burn [aut],
Marti Catala Sabate [aut],
Ioanna Nika [aut]
Maintainer: Adam Black <black@ohdsi.org>
Diff between CDMConnector versions 2.2.0 dated 2025-09-16 and 2.3.0 dated 2026-01-10
CDMConnector-2.2.0/CDMConnector/man/figures/logo_small.png |only CDMConnector-2.3.0/CDMConnector/DESCRIPTION | 8 CDMConnector-2.3.0/CDMConnector/MD5 | 57 - CDMConnector-2.3.0/CDMConnector/NAMESPACE | 4 CDMConnector-2.3.0/CDMConnector/NEWS.md | 8 CDMConnector-2.3.0/CDMConnector/R/Eunomia.R | 5 CDMConnector-2.3.0/CDMConnector/R/cdm.R | 20 CDMConnector-2.3.0/CDMConnector/R/cdmSubset.R | 18 CDMConnector-2.3.0/CDMConnector/R/dateadd.R | 64 ++ CDMConnector-2.3.0/CDMConnector/R/dbSource.R | 2 CDMConnector-2.3.0/CDMConnector/R/generateCohortSet.R | 43 - CDMConnector-2.3.0/CDMConnector/R/generateConceptCohortSet.R | 213 +++---- CDMConnector-2.3.0/CDMConnector/R/reexports-omopgenerics.R | 8 CDMConnector-2.3.0/CDMConnector/R/utils.R | 5 CDMConnector-2.3.0/CDMConnector/README.md | 11 CDMConnector-2.3.0/CDMConnector/build/vignette.rds |binary CDMConnector-2.3.0/CDMConnector/inst/doc/a01_getting-started.html | 108 +-- CDMConnector-2.3.0/CDMConnector/inst/doc/a02_cohorts.R | 294 +++++----- CDMConnector-2.3.0/CDMConnector/inst/doc/a02_cohorts.html | 251 +------- CDMConnector-2.3.0/CDMConnector/inst/doc/a03_dbplyr.html | 7 CDMConnector-2.3.0/CDMConnector/inst/doc/a04_DBI_connection_examples.html | 3 CDMConnector-2.3.0/CDMConnector/inst/doc/a06_using_cdm_attributes.html | 7 CDMConnector-2.3.0/CDMConnector/man/cdmFromCon.Rd | 2 CDMConnector-2.3.0/CDMConnector/man/figures/logo.png |binary CDMConnector-2.3.0/CDMConnector/man/reexports.Rd | 4 CDMConnector-2.3.0/CDMConnector/man/tblGroup.Rd | 2 CDMConnector-2.3.0/CDMConnector/tests/testthat/setup.R | 4 CDMConnector-2.3.0/CDMConnector/tests/testthat/test-02-db-cdm.R | 4 CDMConnector-2.3.0/CDMConnector/tests/testthat/test-04-db-generateConceptCohortSet.R | 50 + CDMConnector-2.3.0/CDMConnector/tests/testthat/test-07-db-dateadd.R | 29 30 files changed, 618 insertions(+), 613 deletions(-)
Title: Bayesian Linear Mixed-Effects Models
Description: Maximum a posteriori estimation for linear and generalized linear mixed-effects models in a Bayesian setting, implementing the methods of Chung, et al. (2013) <doi:10.1007/s11336-013-9328-2>. Extends package 'lme4' (Bates, Maechler, Bolker, and Walker (2015) <doi:10.18637/jss.v067.i01>).
Author: Vincent Dorie [aut, cre] ,
Douglas Bates [ctb] ,
Martin Maechler [ctb] ,
Ben Bolker [ctb] ,
Steven Walker [ctb]
Maintainer: Vincent Dorie <vdorie@gmail.com>
Diff between blme versions 1.0-6 dated 2024-09-07 and 1.0-7 dated 2026-01-10
ChangeLog | 8 DESCRIPTION | 19 - MD5 | 25 - NAMESPACE | 5 R/blmer.R | 642 +++++++++++++++++++++++++++++------------ R/control.R | 12 R/devFun.R | 46 +- R/dist_independent_ts.R |only R/optimize.R | 134 ++++++-- R/parameters.R | 94 +++--- inst/common/glmmData.R | 30 - inst/common/lmmData.R | 38 +- man/blmer.Rd | 2 tests/testthat/test-10-refit.R | 23 + 14 files changed, 752 insertions(+), 326 deletions(-)
Title: Tools for Survey Statistics in Educational Assessment
Description: Contains tools for survey statistics (especially in educational
assessment) for datasets with replication designs (jackknife,
bootstrap, replicate weights; see Kolenikov, 2010;
Pfefferman & Rao, 2009a, 2009b, <doi:10.1016/S0169-7161(09)70003-3>,
<doi:10.1016/S0169-7161(09)70037-9>); Shao, 1996,
<doi:10.1080/02331889708802523>).
Descriptive statistics, linear and logistic regression,
path models for manifest variables with measurement error
correction and two-level hierarchical regressions for weighted
samples are included. Statistical inference can be conducted for
multiply imputed datasets and nested multiply imputed datasets
and is in particularly suited for the analysis of plausible values
(for details see George, Oberwimmer & Itzlinger-Bruneforth, 2016;
Bruneforth, Oberwimmer & Robitzsch, 2016; Robitzsch, Pham &
Yanagida, 2016). The package development was supported by BIFIE
(Federal Institute for Educational Research, Innovation and Development
of [...truncated...]
Author: BIFIE [aut],
Alexander Robitzsch [aut],
Konrad Oberwimmer [aut, cre]
Maintainer: Konrad Oberwimmer <konrad.oberwimmer@iqs.gv.at>
Diff between BIFIEsurvey versions 3.6-6 dated 2024-04-25 and 3.8.0 dated 2026-01-10
BIFIEsurvey-3.6-6/BIFIEsurvey/R/BIFIE_NMIcombine_results.R |only BIFIEsurvey-3.6-6/BIFIEsurvey/R/BIFIE_NMIcombine_results_extract_parameters.R |only BIFIEsurvey-3.6-6/BIFIEsurvey/R/BIFIE_data_pv_vars_create_datlist.R |only BIFIEsurvey-3.6-6/BIFIEsurvey/R/BIFIE_lavaan_survey_NMIcombine.R |only BIFIEsurvey-3.6-6/BIFIEsurvey/R/BIFIE_nmi_error_message.R |only BIFIEsurvey-3.8.0/BIFIEsurvey/DESCRIPTION | 28 ++- BIFIEsurvey-3.8.0/BIFIEsurvey/MD5 | 92 +++++----- BIFIEsurvey-3.8.0/BIFIEsurvey/R/BIFIE.by.R | 2 BIFIEsurvey-3.8.0/BIFIEsurvey/R/BIFIE.correl.R | 2 BIFIEsurvey-3.8.0/BIFIEsurvey/R/BIFIE.crosstab.R | 2 BIFIEsurvey-3.8.0/BIFIEsurvey/R/BIFIE.data.R | 14 + BIFIEsurvey-3.8.0/BIFIEsurvey/R/BIFIE.data.jack.R | 10 - BIFIEsurvey-3.8.0/BIFIEsurvey/R/BIFIE.ecdf.R | 28 +-- BIFIEsurvey-3.8.0/BIFIEsurvey/R/BIFIE.freq.R | 2 BIFIEsurvey-3.8.0/BIFIEsurvey/R/BIFIE.hist.R | 2 BIFIEsurvey-3.8.0/BIFIEsurvey/R/BIFIE.linreg.R | 10 - BIFIEsurvey-3.8.0/BIFIEsurvey/R/BIFIE.logistreg.R | 10 - BIFIEsurvey-3.8.0/BIFIEsurvey/R/BIFIE.pathmodel.R | 2 BIFIEsurvey-3.8.0/BIFIEsurvey/R/BIFIE.univar.R | 2 BIFIEsurvey-3.8.0/BIFIEsurvey/R/BIFIE_by_helper_pureR.R | 12 - BIFIEsurvey-3.8.0/BIFIEsurvey/R/RcppExports.R | 50 ++--- BIFIEsurvey-3.8.0/BIFIEsurvey/R/bifie_NMIcombine_results.R |only BIFIEsurvey-3.8.0/BIFIEsurvey/R/bifie_NMIcombine_results_extract_parameters.R |only BIFIEsurvey-3.8.0/BIFIEsurvey/R/bifie_data_pv_vars_create_datlist.R |only BIFIEsurvey-3.8.0/BIFIEsurvey/R/bifie_lavaan_survey_NMIcombine.R |only BIFIEsurvey-3.8.0/BIFIEsurvey/R/bifie_nmi_error_message.R |only BIFIEsurvey-3.8.0/BIFIEsurvey/R/zzz.R | 14 + BIFIEsurvey-3.8.0/BIFIEsurvey/README.md | 26 +- BIFIEsurvey-3.8.0/BIFIEsurvey/build/partial.rdb |binary BIFIEsurvey-3.8.0/BIFIEsurvey/data/data.bifie01.rda |binary BIFIEsurvey-3.8.0/BIFIEsurvey/data/data.pisaNLD.rda |binary BIFIEsurvey-3.8.0/BIFIEsurvey/data/data.test1.rda |binary BIFIEsurvey-3.8.0/BIFIEsurvey/data/data.timss1.ind.rda |binary BIFIEsurvey-3.8.0/BIFIEsurvey/data/data.timss1.rda |binary BIFIEsurvey-3.8.0/BIFIEsurvey/data/data.timss2.rda |binary BIFIEsurvey-3.8.0/BIFIEsurvey/data/data.timss3.rda |binary BIFIEsurvey-3.8.0/BIFIEsurvey/data/data.timss4.rda |binary BIFIEsurvey-3.8.0/BIFIEsurvey/data/data.timssrep.rda |binary BIFIEsurvey-3.8.0/BIFIEsurvey/inst/CITATION | 34 +-- BIFIEsurvey-3.8.0/BIFIEsurvey/inst/NEWS | 61 ++---- BIFIEsurvey-3.8.0/BIFIEsurvey/man/BIFIE.twolevelreg.Rd | 2 BIFIEsurvey-3.8.0/BIFIEsurvey/man/BIFIEsurvey-package.Rd | 36 --- BIFIEsurvey-3.8.0/BIFIEsurvey/src/Makevars | 2 BIFIEsurvey-3.8.0/BIFIEsurvey/src/Makevars.win | 2 BIFIEsurvey-3.8.0/BIFIEsurvey/src/RcppExports.cpp | 5 BIFIEsurvey-3.8.0/BIFIEsurvey/src/bifiesurvey_rcpp_helper.cpp | 23 ++ BIFIEsurvey-3.8.0/BIFIEsurvey/src/bifiesurvey_rcpp_helper.h | 2 BIFIEsurvey-3.8.0/BIFIEsurvey/src/bifiesurvey_rcpp_jack_data_prep.cpp | 3 BIFIEsurvey-3.8.0/BIFIEsurvey/src/bifiesurvey_rcpp_linreg.cpp | 12 - BIFIEsurvey-3.8.0/BIFIEsurvey/src/bifiesurvey_rcpp_logistreg.cpp | 19 +- BIFIEsurvey-3.8.0/BIFIEsurvey/src/bifiesurvey_rcpp_main.cpp | 68 ++++--- BIFIEsurvey-3.8.0/BIFIEsurvey/src/bifiesurvey_rcpp_pathmodel.cpp | 13 + 52 files changed, 323 insertions(+), 267 deletions(-)
Title: Flexible Bayes Factor Testing of Scientific Expectations
Description: Implementation of default Bayes factors
for testing statistical hypotheses under various statistical models. The package is
intended for applied quantitative researchers in the
social and behavioral sciences, medical research,
and related fields. The Bayes factor tests can be
executed for statistical models such as
univariate and multivariate normal linear models,
correlation analysis, generalized linear models, special cases of
linear mixed models, survival models, relational
event models. Parameters that can be tested are
location parameters (e.g., group means, regression coefficients),
variances (e.g., group variances), and measures of
association (e.g,. polychoric/polyserial/biserial/tetrachoric/product
moments correlations), among others.
The statistical underpinnings are
described in
O'Hagan (1995) <DOI:10.1111/j.2517-6161.1995.tb02017.x>,
De Santis and Spezzaferri (2001) <DOI:10.1016/S0378-3758(00)00240-8>,
Mulder and Xin (2022) <DOI:10.1080/00273171.2021.1904809& [...truncated...]
Author: Joris Mulder [aut, cre],
Caspar van Lissa [aut, ctb],
Donald R. Williams [aut, ctb],
Xin Gu [aut, ctb],
Anton Olsson-Collentine [aut, ctb],
Florian Boeing-Messing [aut, ctb],
Jean-Paul Fox [aut, ctb],
Janosch Menke [ctb],
Robbie van Aert [ctb],
Barry [...truncated...]
Maintainer: Joris Mulder <j.mulder3@tilburguniversity.edu>
Diff between BFpack versions 1.5.0 dated 2025-06-08 and 1.5.3 dated 2026-01-10
DESCRIPTION | 10 MD5 | 54 - NAMESPACE | 4 NEWS.md | 15 R/BF.cortest.R | 358 +---------- R/BF.ergm.R | 2 R/BF.gaussian.R | 7 R/BF.lm.R | 4 R/BF.meta.R | 141 ++-- R/BF.mvt_test.R | 8 R/BF.polr.R | 2 R/BF.print.R | 23 R/BF.summary.R | 23 R/BF.ttest.R | 9 R/BF.var.R | 11 R/zzz.R | 8 build/vignette.rds |binary inst/doc/vignette_BFpack.html | 8 man/cor_test.Rd | 19 src/BFpack_init.c | 4 src/Makevars | 6 src/bct_mixedordinal.f90 | 545 +++++++++++++++-- tests/testthat/test_BFcortest.R | 35 - tests/testthat/test_BFmeta.R | 6 tests/testthat/test_application4_BF.mlm_regression.R | 2 tests/testthat/test_application6_BF.mlm_correlations.R | 2 tests/testthat/test_metafor.R | 4 tests/testthat/test_ttest.R | 6 28 files changed, 779 insertions(+), 537 deletions(-)
Title: Distribution of the 'BayesX' C++ Sources
Description: 'BayesX' performs Bayesian inference in structured additive regression (STAR) models.
The R package BayesXsrc provides the 'BayesX' command line tool for easy installation.
A convenient R interface is provided in package R2BayesX.
Author: Nikolaus Umlauf [aut, cre] ,
Daniel Adler [aut],
Thomas Kneib [aut] ,
Stefan Lang [aut],
Achim Zeileis [aut]
Maintainer: Nikolaus Umlauf <Nikolaus.Umlauf@uibk.ac.at>
Diff between BayesXsrc versions 3.0-6 dated 2025-03-10 and 3.0-7 dated 2026-01-10
DESCRIPTION | 19 ++++++++++--------- MD5 | 18 +++++++++--------- src/Makefile | 6 ++---- src/Makefile.inner.win | 6 ++---- src/Makefile.win | 6 ++---- src/dev-Makefile | 6 ++---- src/dev-Makefile.inner.win | 6 ++---- src/dev-Makefile.win | 6 ++---- src/rel-Makefile | 6 ++---- src/rel-Makefile.win | 6 ++---- 10 files changed, 35 insertions(+), 50 deletions(-)
Title: Mining Association Rules and Frequent Itemsets
Description: Provides the infrastructure for representing, manipulating
and analyzing transaction data and patterns (frequent itemsets and
association rules). Also provides C implementations of the
association mining algorithms Apriori and Eclat. Hahsler, Gruen and
Hornik (2005) <doi:10.18637/jss.v014.i15>.
Author: Michael Hahsler [aut, cre, cph] ,
Christian Buchta [aut, cph],
Bettina Gruen [aut, cph],
Kurt Hornik [aut, cph] ,
Christian Borgelt [ctb, cph],
Ian Johnson [ctb],
Makhlouf Ledmi [ctb]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between arules versions 1.7-11 dated 2025-05-29 and 1.7.13 dated 2026-01-10
DESCRIPTION | 10 ++++---- MD5 | 40 ++++++++++++++++----------------- NEWS.md | 9 +++++++ R/confint.R | 3 +- R/dissimilarity.R | 10 ++++---- R/fim4r.R | 22 +++++++++--------- R/inspect.R | 6 ++--- R/itemFrequency.R | 2 - R/random.transactions.R | 2 - README.md | 38 +++++++++++++++---------------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/arules.R | 54 ++++++++++++++++++++++----------------------- inst/doc/arules.Rnw | 15 +++++------- inst/doc/arules.pdf |binary man/c.Rd | 2 - man/fim4r.Rd | 22 +++++++++--------- man/pmml.Rd | 2 - man/random.transactions.Rd | 2 - vignettes/arules.Rnw | 15 +++++------- vignettes/arules.bib | 15 ++++-------- 21 files changed, 135 insertions(+), 134 deletions(-)
Title: Life History Analysis Tools
Description: Estimate aquatic species life history using robust techniques.
This package supports users undertaking two types of analysis: 1) Growth from
length-at-age data, and 2) maturity analyses for length and/or age data.
Maturity analyses are performed using generalised linear model approaches incorporating
either a binomial or quasibinomial distribution.
Growth modelling is performed using the multimodel approach presented by
Smart et al. (2016) "Multimodel approaches in shark and ray growth studies:
strengths, weaknesses and the future" <doi:10.1111/faf.12154>.
Author: Jonathan Smart [aut, cre, ctb]
Maintainer: Jonathan Smart <jonsmartphd@gmail.com>
Diff between AquaticLifeHistory versions 1.0.5 dated 2023-11-17 and 1.0.6 dated 2026-01-10
DESCRIPTION | 15 MD5 | 56 - NAMESPACE | 48 - NEWS.md | 12 R/AquaticLifeHistory.R | 132 +-- R/Growth_functions.R | 1144 +++++++++++++-------------- R/Helper_functions.R | 52 - R/Maturity_functions.R | 788 +++++++++--------- README.md | 212 ++--- build/vignette.rds |binary inst/CITATION | 68 - inst/doc/Growth_estimation.R | 400 ++++----- inst/doc/Growth_estimation.Rmd | 626 +++++++-------- inst/doc/Growth_estimation.html | 1579 +++++++++++++++++++------------------- inst/doc/Maturity_analyses.R | 334 ++++---- inst/doc/Maturity_analyses.Rmd | 574 ++++++------- inst/doc/Maturity_analyses.html | 1265 +++++++++++++++--------------- man/AquaticLifeHistory.Rd | 48 - man/Calculate_MMI.Rd | 60 - man/Estimate_Age_Maturity.Rd | 106 +- man/Estimate_Growth.Rd | 100 +- man/Estimate_Len_Maturity.Rd | 118 +- man/boot_data.Rd | 38 man/figures/unnamed-chunk-2-1.png |binary man/figures/unnamed-chunk-3-1.png |binary man/growth_data.Rd | 60 - man/maturity_data.Rd | 62 - vignettes/Growth_estimation.Rmd | 626 +++++++-------- vignettes/Maturity_analyses.Rmd | 574 ++++++------- 29 files changed, 4562 insertions(+), 4535 deletions(-)
More information about AquaticLifeHistory at CRAN
Permanent link
Title: Random GO Database
Description: The Gene Ontology (GO) Consortium <https://geneontology.org/> organizes genes
into hierarchical categories based on biological process (BP), molecular function (MF) and
cellular component (CC, i.e., subcellular localization). Tools such as 'GoMiner' (see Zeeberg, B.R.,
Feng, W., Wang, G. et al. (2003) <doi:10.1186/gb-2003-4-4-r28>) can leverage GO to perform
ontological analysis of microarray and proteomics studies, typically generating a list of
significant functional categories. The significance is traditionally determined by randomizing
the input gene list to computing the false discovery rate (FDR) of the enrichment p-value for
each category. We explore here the novel alternative of randomizing the GO database rather than
the gene list.
Author: Barry Zeeberg [aut, cre]
Maintainer: Barry Zeeberg <barryz2013@gmail.com>
Diff between randomGODB versions 1.0 dated 2025-05-07 and 1.1 dated 2026-01-10
DESCRIPTION | 14 ++++----- MD5 | 18 +++++------ NAMESPACE | 1 R/randomGODB.R | 71 +++++++++++++++++++++++++++++++++++++++++------ build/vignette.rds |binary inst/doc/randomGODB.html | 4 +- man/characterizeDB.Rd | 16 +++++++++- man/fractAncest.Rd | 16 +++++++++- man/hitters.Rd | 19 +++++++++++- man/leafList.Rd | 10 +++++- 10 files changed, 137 insertions(+), 32 deletions(-)
Title: Plausible Naive Bayes Classifier Using PDE
Description: A nonparametric, multicore-capable plausible naive Bayes classifier based on the Pareto density estimation (PDE) featuring a plausible approach to a pitfall in the Bayesian theorem covering low evidence cases. Stier, Q., Hoffmann, J., and Thrun, M.C.: "Classifying with the Fine Structure of Distributions: Leveraging Distributional Information for Robust and Plausible Naive Bayes" (2026), Machine Learning and Knowledge Extraction (MAKE), <DOI:10.3390/make8010013>.
Author: Michael Thrun [aut, cph, cre] ,
Quirin Stier [aut, rev] ,
Tim Robin Neldner [ctr, ctb]
Maintainer: Michael Thrun <m.thrun@gmx.net>
Diff between PDEnaiveBayes versions 0.2.8 dated 2025-11-17 and 0.2.9 dated 2026-01-10
DESCRIPTION | 13 ++++++----- MD5 | 40 +++++++++++++++++++++-------------- R/RcppExports.R | 14 ++++++------ README.md |only build/partial.rdb |binary build/vignette.rds |only inst |only man/ApplyBayesTheorem4Likelihoods.Rd | 4 +++ man/GetLikelihoods.Rd | 4 +++ man/PDEnaiveBayes-package.Rd | 4 ++- man/PlotBayesianDecision2D.Rd | 5 ++++ man/PlotLikelihoodFuns.Rd | 4 +++ man/PlotLikelihoods.Rd | 4 +++ man/PlotNaiveBayes.Rd | 6 ++++- man/PlotPosteriors.Rd | 6 ++++- man/Predict_naiveBayes.Rd | 7 +++++- man/Train_naiveBayes.Rd | 6 ++++- man/Train_naiveBayes_multicore.Rd | 4 +++ man/defineOrEstimateDistribution.Rd | 4 +++ man/predict.PDEbayes.Rd | 6 ++++- vignettes |only 21 files changed, 96 insertions(+), 35 deletions(-)