Title: Workflow for Open Reproducible Code in Science
Description: Create reproducible and transparent research projects in 'R'.
This package is based on the Workflow for Open
Reproducible Code in Science (WORCS), a step-by-step procedure based on best
practices for
Open Science. It includes an 'RStudio' project template, several
convenience functions, and all dependencies required to make your project
reproducible and transparent. WORCS is explained in the tutorial paper
by Van Lissa, Brandmaier, Brinkman, Lamprecht, Struiksma, & Vreede (2021).
<doi:10.3233/DS-210031>.
Author: Caspar J. Van Lissa [aut, cre] ,
Aaron Peikert [aut] ,
Andreas M. Brandmaier [aut]
Maintainer: Caspar J. Van Lissa <c.j.vanlissa@tilburguniversity.edu>
Diff between worcs versions 0.1.19 dated 2025-07-13 and 0.1.20 dated 2026-02-22
worcs-0.1.19/worcs/inst/rstudio/templates/project/resources/_targets.rmd |only worcs-0.1.20/worcs/DESCRIPTION | 14 worcs-0.1.20/worcs/MD5 | 125 worcs-0.1.20/worcs/NAMESPACE | 5 worcs-0.1.20/worcs/R/add_synthetic.R | 332 +- worcs-0.1.20/worcs/R/check_installation.R | 741 ++--- worcs-0.1.20/worcs/R/dirnames_filenames.R |only worcs-0.1.20/worcs/R/endpoint.R | 558 ++- worcs-0.1.20/worcs/R/github.R | 1034 +++---- worcs-0.1.20/worcs/R/github_actions.R | 177 - worcs-0.1.20/worcs/R/licenses.R | 128 worcs-0.1.20/worcs/R/load_entrypoint.R | 104 worcs-0.1.20/worcs/R/recipes.R | 272 - worcs-0.1.20/worcs/R/save_load.R | 1415 +++++----- worcs-0.1.20/worcs/R/scoped_tempdir.R |only worcs-0.1.20/worcs/R/targets.R | 295 +- worcs-0.1.20/worcs/R/testthat.R | 124 worcs-0.1.20/worcs/R/worcs_project.R | 1366 ++++----- worcs-0.1.20/worcs/R/zzz.R | 22 worcs-0.1.20/worcs/build/partial.rdb |binary worcs-0.1.20/worcs/build/vignette.rds |binary worcs-0.1.20/worcs/inst/doc/citation.R | 20 worcs-0.1.20/worcs/inst/doc/citation.Rmd | 98 worcs-0.1.20/worcs/inst/doc/citation.html | 615 ++-- worcs-0.1.20/worcs/inst/doc/endpoints.R | 46 worcs-0.1.20/worcs/inst/doc/endpoints.Rmd | 238 + worcs-0.1.20/worcs/inst/doc/endpoints.html | 1034 +++---- worcs-0.1.20/worcs/inst/doc/git_cloud.R | 14 worcs-0.1.20/worcs/inst/doc/git_cloud.html | 790 ++--- worcs-0.1.20/worcs/inst/doc/reproduce.R | 15 worcs-0.1.20/worcs/inst/doc/reproduce.Rmd | 234 - worcs-0.1.20/worcs/inst/doc/reproduce.html | 856 +++--- worcs-0.1.20/worcs/inst/doc/setup-docker.R | 20 worcs-0.1.20/worcs/inst/doc/setup-docker.html | 775 ++--- worcs-0.1.20/worcs/inst/doc/setup.R | 12 worcs-0.1.20/worcs/inst/doc/setup.Rmd | 168 - worcs-0.1.20/worcs/inst/doc/setup.html | 732 ++--- worcs-0.1.20/worcs/inst/doc/synthetic_data.R | 216 - worcs-0.1.20/worcs/inst/doc/synthetic_data.html | 1063 +++---- worcs-0.1.20/worcs/inst/doc/targets.R | 14 worcs-0.1.20/worcs/inst/doc/targets.html | 690 ++-- worcs-0.1.20/worcs/inst/doc/workflow.R | 20 worcs-0.1.20/worcs/inst/doc/workflow.Rmd | 273 - worcs-0.1.20/worcs/inst/doc/workflow.html | 1173 ++++---- worcs-0.1.20/worcs/inst/doc/zenodo.R |only worcs-0.1.20/worcs/inst/doc/zenodo.Rmd |only worcs-0.1.20/worcs/inst/doc/zenodo.html |only worcs-0.1.20/worcs/inst/rstudio/templates/project/resources/README.md | 88 worcs-0.1.20/worcs/inst/rstudio/templates/project/resources/_targets.Rmd |only worcs-0.1.20/worcs/inst/rstudio/templates/project/worcs.dcf | 2 worcs-0.1.20/worcs/man/add_endpoint.Rd | 25 worcs-0.1.20/worcs/man/check_worcs_installation.Rd | 13 worcs-0.1.20/worcs/man/notify_synthetic.Rd | 35 worcs-0.1.20/worcs/man/worcs_path.Rd |only worcs-0.1.20/worcs/man/worcs_project.Rd | 2 worcs-0.1.20/worcs/man/worcs_root.Rd |only worcs-0.1.20/worcs/tests/testthat/test-boilerplate_in_manuscript.R |only worcs-0.1.20/worcs/tests/testthat/test-closed_data.R | 176 - worcs-0.1.20/worcs/tests/testthat/test-save_load_expression.R | 136 worcs-0.1.20/worcs/tests/testthat/test-targets.R | 178 - worcs-0.1.20/worcs/tests/testthat/test-testthat_endpoint.R |only worcs-0.1.20/worcs/tests/testthat/test.yaml | 18 worcs-0.1.20/worcs/tests/testthat/tests |only worcs-0.1.20/worcs/vignettes/citation.Rmd | 98 worcs-0.1.20/worcs/vignettes/endpoints.Rmd | 238 + worcs-0.1.20/worcs/vignettes/reproduce.Rmd | 234 - worcs-0.1.20/worcs/vignettes/setup.Rmd | 168 - worcs-0.1.20/worcs/vignettes/workflow.Rmd | 273 - worcs-0.1.20/worcs/vignettes/zenodo.Rmd |only 69 files changed, 8971 insertions(+), 8541 deletions(-)
Title: Easy Model-Builder Functions for 'OpenMx'
Description: Utilities for building certain kinds of common matrices and models in
the extended structural equation modeling package, 'OpenMx'.
Author: Michael D. Hunter [aut, cre] ,
Joshua N. Pritikin [ctb]
Maintainer: Michael D. Hunter <mhunter.ou@gmail.com>
Diff between EasyMx versions 0.3-2 dated 2023-01-30 and 0.4-2 dated 2026-02-22
DESCRIPTION | 15 +- MD5 | 18 ++- NAMESPACE | 2 R/emxModelBuilders.R | 5 R/emxTimeSeries.R | 189 ++++++++++++++++++++++++++++-------- R/emxVARMA.R |only man/emxLVARModel.Rd |only man/emxMixtureModel.Rd | 18 +++ man/emxModelByID.Rd |only man/emxStateSpaceMixtureClassify.Rd | 2 man/emxVARMAModel.Rd |only man/emxVARModel.Rd | 8 + 12 files changed, 200 insertions(+), 57 deletions(-)
Title: Simulating Triad Genomewide Genotypes
Description: Simulate genotypes for case-parent triads, case-control, and quantitative trait samples with realistic linkage diequilibrium structure and allele frequency distribution. For studies of epistasis one can simulate models that involve specific SNPs at specific sets of loci, which we will refer to as "pathways". TriadSim generates genotype data by resampling triad genotypes from existing data. The details of the method is described in the manuscript under preparation "Simulating Autosomal Genotypes with Realistic Linkage Disequilibrium and a Spiked in Genetic Effect" Shi, M., Umbach, D.M., Wise A.S., Weinberg, C.R.
Author: Min Shi [aut, cre]
Maintainer: Min Shi <shi2@niehs.nih.gov>
Diff between TriadSim versions 0.3.0 dated 2021-09-08 and 0.3.1 dated 2026-02-22
DESCRIPTION | 6 MD5 | 8 NEWS.md | 6 build/vignette.rds |binary inst/doc/TriadSim.html | 396 +++++++++++++++++++++++++++++++------------------ 5 files changed, 262 insertions(+), 154 deletions(-)
Title: Alluvial Plots in 'ggplot2'
Description: Alluvial plots use variable-width ribbons and stacked bar plots to
represent multi-dimensional or repeated-measures data with categorical or
ordinal variables; see Riehmann, Hanfler, and Froehlich (2005)
<doi:10.1109/INFVIS.2005.1532152> and Rosvall and Bergstrom (2010)
<doi:10.1371/journal.pone.0008694>.
Alluvial plots are statistical graphics in the sense of Wilkinson (2006)
<doi:10.1007/0-387-28695-0>; they share elements with Sankey diagrams and
parallel sets plots but are uniquely determined from the data and a small
set of parameters. This package extends Wickham's (2010)
<doi:10.1198/jcgs.2009.07098> layered grammar of graphics to generate
alluvial plots from tidy data.
Author: Jason Cory Brunson [aut, cre],
Quentin D. Read [aut]
Maintainer: Jason Cory Brunson <cornelioid@gmail.com>
Diff between ggalluvial versions 0.12.5 dated 2023-02-22 and 0.12.6 dated 2026-02-22
DESCRIPTION | 6 MD5 | 134 +-- NAMESPACE | 1 NEWS.md | 24 R/alluvial-data.r | 7 R/geom-alluvium.r | 50 + R/geom-flow.r | 50 + R/geom-lode.r | 2 R/geom-stratum.r | 2 R/stat-flow.r | 2 R/stat-utils.r | 1 README.md | 88 +- build/partial.rdb |binary build/vignette.rds |binary inst/doc/ggalluvial.R | 2 inst/doc/ggalluvial.html | 166 ++-- inst/doc/ggalluvial.rmd | 10 inst/doc/labels.html | 158 ++-- inst/doc/order-rectangles.html | 144 +-- inst/doc/shiny.R | 374 +++++----- inst/doc/shiny.html | 8 inst/examples/ex-geom-alluvium.r | 2 inst/examples/ex-geom-flow.r | 11 man/figures/README-unnamed-chunk-6-1.png |binary man/figures/README-unnamed-chunk-7-1.png |binary man/geom_alluvium.Rd | 9 man/geom_flow.Rd | 20 man/geom_lode.Rd | 3 man/geom_stratum.Rd | 3 tests/testthat/_snaps/geom-alluvium/geom-alluvium-arctangent-curve-with-custom-range.svg | 156 +++- tests/testthat/_snaps/geom-alluvium/geom-alluvium-arctangent-curve.svg | 156 +++- tests/testthat/_snaps/geom-alluvium/geom-alluvium-basic.svg | 128 ++- tests/testthat/_snaps/geom-alluvium/geom-alluvium-bump-plot.svg | 40 - tests/testthat/_snaps/geom-alluvium/geom-alluvium-cubic-curve.svg | 156 +++- tests/testthat/_snaps/geom-alluvium/geom-alluvium-facets.svg | 128 ++- tests/testthat/_snaps/geom-alluvium/geom-alluvium-line-plot.svg | 30 tests/testthat/_snaps/geom-alluvium/geom-alluvium-linear-curve.svg | 156 +++- tests/testthat/_snaps/geom-alluvium/geom-alluvium-quintic-curve.svg | 156 +++- tests/testthat/_snaps/geom-alluvium/geom-alluvium-sigmoid-curve-with-custom-range.svg | 156 +++- tests/testthat/_snaps/geom-alluvium/geom-alluvium-sigmoid-curve.svg | 156 +++- tests/testthat/_snaps/geom-alluvium/geom-alluvium-sine-curve.svg | 156 +++- tests/testthat/_snaps/geom-alluvium/geom-alluvium-unscaled-knot-positions.svg | 156 +++- tests/testthat/_snaps/geom-flow/geom-flow-aesthetic.svg | 96 +- tests/testthat/_snaps/geom-flow/geom-flow-arctangent-curve-with-custom-range.svg | 116 ++- tests/testthat/_snaps/geom-flow/geom-flow-arctangent-curve.svg | 116 ++- tests/testthat/_snaps/geom-flow/geom-flow-backward-orientation.svg | 116 ++- tests/testthat/_snaps/geom-flow/geom-flow-basic.svg | 48 - tests/testthat/_snaps/geom-flow/geom-flow-cubic-curve.svg | 116 ++- tests/testthat/_snaps/geom-flow/geom-flow-facets.svg | 128 ++- tests/testthat/_snaps/geom-flow/geom-flow-forward-orientation.svg | 116 ++- tests/testthat/_snaps/geom-flow/geom-flow-linear-curve.svg | 116 ++- tests/testthat/_snaps/geom-flow/geom-flow-quintic-curve.svg | 116 ++- tests/testthat/_snaps/geom-flow/geom-flow-sigmoid-curve-with-custom-range.svg | 116 ++- tests/testthat/_snaps/geom-flow/geom-flow-sigmoid-curve.svg | 116 ++- tests/testthat/_snaps/geom-flow/geom-flow-sine-curve.svg | 116 ++- tests/testthat/_snaps/geom-flow/geom-flow-unscaled-knot-positions.svg | 116 ++- tests/testthat/_snaps/geom-lode/geom-lode-lodes-and-alluvia.svg | 128 ++- tests/testthat/_snaps/geom-lode/geom-lode-lodes-as-strata.svg | 128 ++- tests/testthat/_snaps/geom-lode/geom-lode-one-axis.svg | 36 tests/testthat/test-alluvial-data.r | 2 tests/testthat/test-geom-alluvium.r | 20 tests/testthat/test-geom-flow.r | 2 tests/testthat/test-geom-lode.r | 2 tests/testthat/test-geom-stratum.r | 2 tests/testthat/test-stat-alluvium.r | 16 tests/testthat/test-stat-flow.r | 2 tests/testthat/test-stat-stratum.r | 2 vignettes/ggalluvial.rmd | 10 68 files changed, 3388 insertions(+), 1517 deletions(-)
Title: 'DataSHIELD' Server Side Base Functions
Description: Base 'DataSHIELD' functions for the server side. 'DataSHIELD' is a software package which allows
you to do non-disclosive federated analysis on sensitive data. 'DataSHIELD' analytic functions have
been designed to only share non disclosive summary statistics, with built in automated output
checking based on statistical disclosure control. With data sites setting the threshold values for
the automated output checks. For more details, see 'citation("dsBase")'.
Author: Paul Burton [aut] ,
Rebecca Wilson [aut] ,
Olly Butters [aut] ,
Patricia Ryser-Welch [aut] ,
Alex Westerberg [aut],
Leire Abarrategui [aut],
Roberto Villegas-Diaz [aut] ,
Demetris Avraam [aut] ,
Yannick Marcon [aut] ,
Tom Bishop [aut],
Amadou Gaye [a [...truncated...]
Maintainer: Stuart Wheater <stuart.wheater@arjuna.com>
Diff between dsBase versions 6.3.4 dated 2025-09-18 and 6.3.5 dated 2026-02-22
dsBase-6.3.4/dsBase/tests/testthat/perf_files/azure-pipeline.csv |only dsBase-6.3.4/dsBase/tests/testthat/perf_files/circleci.csv |only dsBase-6.3.4/dsBase/tests/testthat/perf_files/cran_check.cvs |only dsBase-6.3.4/dsBase/tests/testthat/perf_files/default_perf_profile.csv |only dsBase-6.3.4/dsBase/tests/testthat/perf_files/hp-laptop_quay.csv |only dsBase-6.3.5/dsBase/DESCRIPTION | 6 - dsBase-6.3.5/dsBase/MD5 | 25 +++-- dsBase-6.3.5/dsBase/NAMESPACE | 1 dsBase-6.3.5/dsBase/R/glmSLMADS.assign.R | 47 +++------- dsBase-6.3.5/dsBase/R/mdPatternDS.R |only dsBase-6.3.5/dsBase/inst/DATASHIELD | 1 dsBase-6.3.5/dsBase/man/mdPatternDS.Rd |only dsBase-6.3.5/dsBase/tests/testthat/perf_files/azure-pipeline_perf-profile.csv |only dsBase-6.3.5/dsBase/tests/testthat/perf_files/circleci_perf-profile.csv |only dsBase-6.3.5/dsBase/tests/testthat/perf_files/cran-check_perf-profile.cvs |only dsBase-6.3.5/dsBase/tests/testthat/perf_files/default_perf-profile.csv |only dsBase-6.3.5/dsBase/tests/testthat/perf_files/hp-laptop-quay_perf-profile.csv |only dsBase-6.3.5/dsBase/tests/testthat/perf_tests/perf_rate.R | 27 ++++- dsBase-6.3.5/dsBase/tests/testthat/test-arg-mdPatternDS.R |only dsBase-6.3.5/dsBase/tests/testthat/test-disc-mdPatternDS.R |only dsBase-6.3.5/dsBase/tests/testthat/test-smk-mdPatternDS.R |only 21 files changed, 58 insertions(+), 49 deletions(-)
Title: Export Tables to LaTeX or HTML
Description: Coerce data to LaTeX and HTML tables.
Author: David B. Dahl [aut],
David Scott [aut, cre],
Charles Roosen [aut],
Arni Magnusson [aut],
Jonathan Swinton [aut],
Ajay Shah [ctb],
Arne Henningsen [ctb],
Benno Puetz [ctb],
Bernhard Pfaff [ctb],
Claudio Agostinelli [ctb],
Claudius Loehnert [ctb],
Davi [...truncated...]
Maintainer: David Scott <d.scott@auckland.ac.nz>
Diff between xtable versions 1.8-4 dated 2019-04-21 and 1.8-8 dated 2026-02-22
DESCRIPTION | 12 - MD5 | 56 +++--- NAMESPACE | 1 NEWS | 34 +++ R/print.xtable.R | 24 +- R/xtable.R | 18 +- R/xtableList.R | 36 ++-- build/vignette.rds |binary inst/doc/OtherPackagesGallery.R | 2 inst/doc/OtherPackagesGallery.Rnw | 331 +++++++++++++++++++------------------ inst/doc/OtherPackagesGallery.pdf |binary inst/doc/listOfTablesGallery.R | 4 inst/doc/listOfTablesGallery.Rnw | 2 inst/doc/listOfTablesGallery.pdf |binary inst/doc/margintable.R | 6 inst/doc/margintable.pdf |binary inst/doc/xtableGallery.R | 139 ++++++++------- inst/doc/xtableGallery.Rnw | 18 ++ inst/doc/xtableGallery.pdf |binary man/print.xtable.Rd | 5 man/string.Rd | 1 man/tli.Rd | 2 man/xtable.Rd | 60 ------ man/xtableFtable.Rd | 5 man/xtableList.Rd | 4 tests/test.xtable.R | 97 ++++++++++ vignettes/OtherPackagesGallery.Rnw | 331 +++++++++++++++++++------------------ vignettes/listOfTablesGallery.Rnw | 2 vignettes/xtableGallery.Rnw | 18 ++ 29 files changed, 679 insertions(+), 529 deletions(-)
Title: Helper Functions for Working with 'REDCap' Data
Description: Helper functions for processing 'REDCap' data in R. 'REDCap' is a
web-enabled application for building and managing surveys and databases
developed at Vanderbilt University.
Author: Raymond Balise [aut, cre] ,
Gabriel Odom [aut] ,
Kyle Grealis [aut] ,
Anna Calderon [aut] ,
Layla Bouzoubaa [aut] ,
Wayne DeFreitas [aut] ,
Lauren Nahodyl [ctb] ,
Daniel Maya [ctb]
Maintainer: Raymond Balise <balise@miami.edu>
Diff between tidyREDCap versions 1.1.3 dated 2026-01-12 and 2.1.0 dated 2026-02-22
DESCRIPTION | 11 MD5 | 37 +- NAMESPACE | 5 NEWS.md | 25 + R/drop_label.R |only R/drop_labels.R | 8 R/import_instruments.R | 47 ++ R/make_choose_all_table.R | 7 R/make_instrument_auto.R | 96 ++--- README.md | 8 inst/doc/dropLabels.R | 22 - inst/doc/dropLabels.Rmd | 85 ++++ inst/doc/dropLabels.html | 532 ++++--------------------------- man/check_project_exists.Rd |only man/drop_label.Rd | 37 +- man/import_instruments.Rd | 4 tests/testthat/test-drop_label.R |only tests/testthat/test-drop_labels.R | 30 + tests/testthat/test-import_instruments.R | 6 vignettes/dropLabels.Rmd | 85 ++++ vignettes/show_numbers.png |only vignettes/show_numbers_2.png |only 22 files changed, 452 insertions(+), 593 deletions(-)
Title: Visualizations for 'mlr3'
Description: Visualization package of the 'mlr3' ecosystem. It features
plots for mlr3 objects such as tasks, learners, predictions, benchmark
results, tuning instances and filters via the 'autoplot()' generic of
'ggplot2'. The package draws plots with the 'viridis' color palette
and applies the minimal theme. Visualizations include barplots,
boxplots, histograms, ROC curves, and Precision-Recall curves.
Author: Michel Lang [aut] ,
Patrick Schratz [aut] ,
Raphael Sonabend [aut] ,
Marc Becker [cre, aut] ,
Jakob Richter [aut] ,
Damir Pulatov [ctb],
John Zobolas [aut]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3viz versions 0.10.1 dated 2025-01-16 and 0.11.0 dated 2026-02-22
mlr3viz-0.10.1/mlr3viz/R/LearnerSurvCoxPH.R |only mlr3viz-0.10.1/mlr3viz/man/autoplot.LearnerSurvCoxPH.Rd |only mlr3viz-0.10.1/mlr3viz/tests/testthat/_snaps/LearnerClasssifGlmnet |only mlr3viz-0.10.1/mlr3viz/tests/testthat/test_LearnerClasssifGlmnet.R |only mlr3viz-0.11.0/mlr3viz/DESCRIPTION | 45 mlr3viz-0.11.0/mlr3viz/MD5 | 314 ++-- mlr3viz-0.11.0/mlr3viz/NAMESPACE | 3 mlr3viz-0.11.0/mlr3viz/NEWS.md | 99 - mlr3viz-0.11.0/mlr3viz/R/BenchmarkResult.R | 26 mlr3viz-0.11.0/mlr3viz/R/EnsembleFSResult.R | 16 mlr3viz-0.11.0/mlr3viz/R/Filter.R | 19 mlr3viz-0.11.0/mlr3viz/R/LearnerClassif.R | 5 mlr3viz-0.11.0/mlr3viz/R/LearnerClassifGlmnet.R | 6 mlr3viz-0.11.0/mlr3viz/R/LearnerClassifRpart.R | 27 mlr3viz-0.11.0/mlr3viz/R/LearnerClustHierarchical.R | 35 mlr3viz-0.11.0/mlr3viz/R/LearnerRegr.R | 5 mlr3viz-0.11.0/mlr3viz/R/OptimInstanceBatchSingleCrit.R | 80 - mlr3viz-0.11.0/mlr3viz/R/PredictionClassif.R | 31 mlr3viz-0.11.0/mlr3viz/R/PredictionClust.R | 16 mlr3viz-0.11.0/mlr3viz/R/PredictionRegr.R | 47 mlr3viz-0.11.0/mlr3viz/R/ResampleResult.R | 57 mlr3viz-0.11.0/mlr3viz/R/TaskClassif.R | 16 mlr3viz-0.11.0/mlr3viz/R/TaskClust.R | 13 mlr3viz-0.11.0/mlr3viz/R/TaskRegr.R | 15 mlr3viz-0.11.0/mlr3viz/R/TuningInstanceBatchSingleCrit.R | 48 mlr3viz-0.11.0/mlr3viz/R/helper.R | 2 mlr3viz-0.11.0/mlr3viz/R/zzz.R | 1 mlr3viz-0.11.0/mlr3viz/README.md | 5 mlr3viz-0.11.0/mlr3viz/build/partial.rdb |binary mlr3viz-0.11.0/mlr3viz/man/autoplot.BenchmarkResult.Rd | 22 mlr3viz-0.11.0/mlr3viz/man/autoplot.EnsembleFSResult.Rd | 7 mlr3viz-0.11.0/mlr3viz/man/autoplot.Filter.Rd | 16 mlr3viz-0.11.0/mlr3viz/man/autoplot.LearnerClassif.Rd | 5 mlr3viz-0.11.0/mlr3viz/man/autoplot.LearnerClassifGlmnet.Rd | 6 mlr3viz-0.11.0/mlr3viz/man/autoplot.LearnerClassifRpart.Rd | 25 mlr3viz-0.11.0/mlr3viz/man/autoplot.LearnerClustHierarchical.Rd | 32 mlr3viz-0.11.0/mlr3viz/man/autoplot.LearnerRegr.Rd | 5 mlr3viz-0.11.0/mlr3viz/man/autoplot.OptimInstanceBatchSingleCrit.Rd | 75 - mlr3viz-0.11.0/mlr3viz/man/autoplot.PredictionClassif.Rd | 19 mlr3viz-0.11.0/mlr3viz/man/autoplot.PredictionClust.Rd | 16 mlr3viz-0.11.0/mlr3viz/man/autoplot.PredictionRegr.Rd | 32 mlr3viz-0.11.0/mlr3viz/man/autoplot.ResampleResult.Rd | 59 mlr3viz-0.11.0/mlr3viz/man/autoplot.TaskClassif.Rd | 16 mlr3viz-0.11.0/mlr3viz/man/autoplot.TaskClust.Rd | 13 mlr3viz-0.11.0/mlr3viz/man/autoplot.TaskRegr.Rd | 15 mlr3viz-0.11.0/mlr3viz/man/autoplot.TuningInstanceBatchSingleCrit.Rd | 48 mlr3viz-0.11.0/mlr3viz/man/figures/README-demo-1.png |binary mlr3viz-0.11.0/mlr3viz/man/figures/README-demo-2.png |binary mlr3viz-0.11.0/mlr3viz/tests/testthat/_snaps/BenchmarkResult/bmr-boxplot.svg | 1 mlr3viz-0.11.0/mlr3viz/tests/testthat/_snaps/BenchmarkResult/bmr-holdout-ci.svg | 1 mlr3viz-0.11.0/mlr3viz/tests/testthat/_snaps/BenchmarkResult/bmr-holdout-roc.svg | 1 mlr3viz-0.11.0/mlr3viz/tests/testthat/_snaps/BenchmarkResult/bmr-prc.svg | 1 mlr3viz-0.11.0/mlr3viz/tests/testthat/_snaps/BenchmarkResult/bmr-roc.svg | 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mlr3viz-0.11.0/mlr3viz/tests/testthat/test_plot_learner_prediction.R | 16 161 files changed, 1512 insertions(+), 1740 deletions(-)
Title: Missing Data Explorer
Description: Correct identification and handling of missing data is one of the most important steps in any analysis. To aid this process, 'mde' provides a very easy to use yet robust framework to quickly get an idea of where the missing data
lies and therefore find the most appropriate action to take.
Graham WJ (2009) <doi:10.1146/annurev.psych.58.110405.085530>.
Author: Nelson Gonzabato [aut, cre]
Maintainer: Nelson Gonzabato <gonzabato@hotmail.com>
Diff between mde versions 0.3.2 dated 2022-02-10 and 0.3.3 dated 2026-02-22
DESCRIPTION | 6 MD5 | 192 +- NAMESPACE | 148 +- NEWS.md | 282 ++-- R/column_based_recode.R | 86 - R/custom_na_recode.R | 158 +- R/dict_recode.R | 152 +- R/drop_all_na.R | 86 - R/drop_na_at.R | 88 - R/drop_na_if.R | 270 ++-- R/drop_row_if.R | 80 - R/get_na_counts.R | 104 - R/helpers.R | 462 +++--- R/na_summary.R | 318 ++-- R/percent_missing.R | 148 +- R/recode_as_na.R | 92 - R/recode_as_na_for.R | 154 +- R/recode_as_na_if.R | 48 R/recode_as_na_str.R | 86 - R/recode_as_value.R | 172 +- R/recode_na_as.R | 156 +- R/recode_na_if.R | 100 - R/sort_by_missingness.R | 106 - R/zzz.R | 22 build/vignette.rds |binary inst/doc/mde_vignette.R | 620 ++++----- inst/doc/mde_vignette.html | 1796 +++++++++++++++------------ inst/doc/mde_vignette.rmd | 1160 ++++++++--------- inst/doc/missingness.R | 224 +-- inst/doc/missingness.html | 993 ++++++++------ inst/doc/missingness.rmd | 444 +++--- inst/doc/recoding.R | 408 +++--- inst/doc/recoding.html | 1489 ++++++++++++---------- inst/doc/recoding.rmd | 820 ++++++------ man/all_na.Rd | 52 man/column_based_recode.Rd | 94 - man/custom_na_recode.Rd | 74 - man/dict_recode.Rd | 80 - man/drop_all_na.Rd | 52 man/drop_na_at.Rd | 70 - man/drop_na_if.Rd | 126 - man/drop_row_if.Rd | 68 - man/get_na_counts.Rd | 62 man/get_na_means.Rd | 38 man/na_counts.Rd | 34 man/na_summary.Rd | 142 +- man/percent_missing.Rd | 64 man/percent_na.Rd | 34 man/recode_as_na.Rd | 86 - man/recode_as_na_for.Rd | 56 man/recode_as_na_if.Rd | 66 man/recode_as_na_str.Rd | 76 - man/recode_helper.Rd | 68 - man/recode_na_as.Rd | 92 - man/recode_na_if.Rd | 60 man/recode_selectors.Rd | 64 man/sort_by_missingness.Rd | 68 - tests/testthat.R | 8 tests/testthat/_snaps/custom_na_recode.md | 10 tests/testthat/_snaps/dict_recode.md | 12 tests/testthat/_snaps/drop_all_na.md | 10 tests/testthat/_snaps/drop_na_at.md | 14 tests/testthat/_snaps/drop_na_if.md | 18 tests/testthat/_snaps/drop_row_if.md | 12 tests/testthat/_snaps/get_na_counts.md | 12 tests/testthat/_snaps/na_summary.md | 27 tests/testthat/_snaps/percent_missing.md | 14 tests/testthat/_snaps/recode_as_na.md | 26 tests/testthat/_snaps/recode_as_na_for.md | 12 tests/testthat/_snaps/recode_as_na_if.md | 10 tests/testthat/_snaps/recode_as_na_str.md | 12 tests/testthat/_snaps/recode_as_value.md | 10 tests/testthat/_snaps/recode_na_as.md | 18 tests/testthat/_snaps/recode_na_if.md | 14 tests/testthat/_snaps/sorting_missingness.md | 10 tests/testthat/test_column_based_recode.R | 68 - tests/testthat/test_custom_na_recode.R | 54 tests/testthat/test_dict_recode.R | 78 - tests/testthat/test_drop_all_na.R | 40 tests/testthat/test_drop_na_at.R | 44 tests/testthat/test_drop_na_if.R | 202 +-- tests/testthat/test_drop_row_if.R | 50 tests/testthat/test_get_na_counts.R | 50 tests/testthat/test_helpers.R | 16 tests/testthat/test_na_summary.R | 132 - tests/testthat/test_percent_missing.R | 44 tests/testthat/test_recode_as_na.R | 128 - tests/testthat/test_recode_as_na_for.R | 198 +- tests/testthat/test_recode_as_na_if.R | 52 tests/testthat/test_recode_as_na_str.R | 80 - tests/testthat/test_recode_as_value.R | 74 - tests/testthat/test_recode_na_as.R | 96 - tests/testthat/test_recode_na_if.R | 52 tests/testthat/test_sorting_missingness.R | 40 vignettes/mde_vignette.rmd | 1160 ++++++++--------- vignettes/missingness.rmd | 444 +++--- vignettes/recoding.rmd | 820 ++++++------ 97 files changed, 8977 insertions(+), 8290 deletions(-)
Title: 'Imath' Computer Graphics Linear Algebra Static Library
Description: Provides a static library for 'Imath'
(see <https://github.com/AcademySoftwareFoundation/Imath>),
a library for functions and data types common in computer graphics
applications, including a 16-bit floating-point type.
Author: Tyler Morgan-Wall [aut, cre] ,
Andrew Kunz [ctb, cph],
Antonio Rojas [ctb, cph],
Brecht Van Lommel [ctb, cph],
Cary Phillips [ctb, cph],
Christina Tempelaar-Lietz [ctb, cph],
Christopher Kulla [ctb, cph],
Daniel Kaneider [ctb, cph],
Dirk Lemstra [ctb [...truncated...]
Maintainer: Tyler Morgan-Wall <tylermw@gmail.com>
Diff between libimath versions 3.1.9-5 dated 2025-10-17 and 3.2.2-0 dated 2026-02-22
libimath-3.1.9-5/libimath/src/Imath/config/LibraryDefine.cmake |only libimath-3.2.2-0/libimath/DESCRIPTION | 6 libimath-3.2.2-0/libimath/MD5 | 41 libimath-3.2.2-0/libimath/src/Imath/CMakeLists.txt | 38 libimath-3.2.2-0/libimath/src/Imath/config/CMakeLists.txt | 61 libimath-3.2.2-0/libimath/src/Imath/config/ImathConfig.cmake.in | 22 libimath-3.2.2-0/libimath/src/Imath/config/ImathConfig.h.in | 7 libimath-3.2.2-0/libimath/src/Imath/config/ImathSetup.cmake | 3 libimath-3.2.2-0/libimath/src/Imath/src/Imath/CMakeLists.txt | 162 +- libimath-3.2.2-0/libimath/src/Imath/src/Imath/ImathEuler.h | 31 libimath-3.2.2-0/libimath/src/Imath/src/Imath/ImathFrustum.h | 3 libimath-3.2.2-0/libimath/src/Imath/src/Imath/ImathFrustumTest.h | 4 libimath-3.2.2-0/libimath/src/Imath/src/Imath/ImathLine.h | 3 libimath-3.2.2-0/libimath/src/Imath/src/Imath/ImathMatrix.h | 2 libimath-3.2.2-0/libimath/src/Imath/src/Imath/ImathPlane.h | 2 libimath-3.2.2-0/libimath/src/Imath/src/Imath/ImathQuat.h | 2 libimath-3.2.2-0/libimath/src/Imath/src/Imath/ImathRoots.h | 4 libimath-3.2.2-0/libimath/src/Imath/src/Imath/ImathVec.h | 48 libimath-3.2.2-0/libimath/src/Makevars.in | 8 libimath-3.2.2-0/libimath/src/Makevars.win.in | 20 libimath-3.2.2-0/libimath/tools/config.R | 793 ++++------ libimath-3.2.2-0/libimath/tools/config/configure.R | 126 - 22 files changed, 777 insertions(+), 609 deletions(-)
Title: Retrieval-Augmented Generation (RAG) Workflows in R with Local
and Web Search
Description: Enables Retrieval-Augmented Generation (RAG) workflows in R by combining
local vector search using 'DuckDB' with optional web search via the 'Tavily' API.
Supports 'OpenAI'- and 'Ollama'-compatible embedding models, full-text and 'HNSW'
(Hierarchical Navigable Small World) indexing, and modular large language model
(LLM) invocation. Designed for advanced question-answering, chat-based
applications, and production-ready AI pipelines. This package is the R
equivalent of the 'python' package 'RAGFlowChain' available at
<https://pypi.org/project/RAGFlowChain/>.
Author: Kwadwo Daddy Nyame Owusu Boakye [aut, cre]
Maintainer: Kwadwo Daddy Nyame Owusu Boakye <kwadwo.owusuboakye@outlook.com>
Diff between RAGFlowChainR versions 0.1.5 dated 2025-05-26 and 0.1.6 dated 2026-02-22
DESCRIPTION | 9 MD5 | 25 - NAMESPACE | 4 NEWS.md |only R/create_rag_chain.R | 702 ++++++++++++++++++++++++++----- R/create_vectorstore.R | 60 ++ R/data_fetcher.R | 72 +-- README.md | 321 ++++---------- man/create_rag_chain.Rd | 17 man/create_vectorstore.Rd | 93 +++- man/fetch_data.Rd | 96 ++-- tests/testthat/test_create_rag_chain.R | 181 +++++++ tests/testthat/test_create_vectorstore.R | 34 - tests/testthat/test_data_fetcher.R | 191 ++++---- 14 files changed, 1253 insertions(+), 552 deletions(-)
Title: A Unified and Longitudinally Aware Framework for ICD-Based
Comorbidity Assessment
Description: Provides comorbidity classification algorithms such as the
Pediatric Complex Chronic Conditions (PCCC), Charlson, and Elixhauser indices,
supports longitudinal comorbidity flagging across encounters, and includes
utilities for working with medical coding schemas such as the International
Classification of Diseases (ICD).
Author: Peter DeWitt [aut, cre, cov] ,
Tell Bennett [ctb] ,
Seth Russell [ctb] ,
Meg Rebull [ctb] ,
Vincent Rubinetti [cov]
Maintainer: Peter DeWitt <peter.dewitt@cuanschutz.edu>
Diff between medicalcoder versions 0.7.0 dated 2025-11-22 and 0.8.0 dated 2026-02-22
medicalcoder-0.7.0/medicalcoder/tests/test-vs-pccc_1.0.6.R |only medicalcoder-0.7.0/medicalcoder/vignettes/articles |only medicalcoder-0.8.0/medicalcoder/DESCRIPTION | 25 medicalcoder-0.8.0/medicalcoder/LICENSE |only medicalcoder-0.8.0/medicalcoder/MD5 | 137 - medicalcoder-0.8.0/medicalcoder/NAMESPACE | 2 medicalcoder-0.8.0/medicalcoder/NEWS.md | 77 medicalcoder-0.8.0/medicalcoder/R/charlson.R | 4 medicalcoder-0.8.0/medicalcoder/R/comorbidities.R | 147 - medicalcoder-0.8.0/medicalcoder/R/datasets.R | 12 medicalcoder-0.8.0/medicalcoder/R/elixhauser.R | 43 medicalcoder-0.8.0/medicalcoder/R/get_charlson_codes.R | 2 medicalcoder-0.8.0/medicalcoder/R/get_icd_codes.R | 14 medicalcoder-0.8.0/medicalcoder/R/get_pccc_conditions.R | 6 medicalcoder-0.8.0/medicalcoder/R/is_icd.R | 4 medicalcoder-0.8.0/medicalcoder/R/lookup_icd_codes.R | 11 medicalcoder-0.8.0/medicalcoder/R/medicalcoder-pkg.R | 2 medicalcoder-0.8.0/medicalcoder/R/pccc.R | 20 medicalcoder-0.8.0/medicalcoder/R/summary.R | 124 - medicalcoder-0.8.0/medicalcoder/R/sysdata.rda |binary medicalcoder-0.8.0/medicalcoder/R/utilities.R | 242 +- medicalcoder-0.8.0/medicalcoder/README.md | 70 medicalcoder-0.8.0/medicalcoder/data/mdcr.rda |binary medicalcoder-0.8.0/medicalcoder/data/mdcr_longitudinal.rda |binary medicalcoder-0.8.0/medicalcoder/inst/WORDLIST | 29 medicalcoder-0.8.0/medicalcoder/inst/doc/charlson.html | 2 medicalcoder-0.8.0/medicalcoder/inst/doc/comorbidities.R | 2 medicalcoder-0.8.0/medicalcoder/inst/doc/comorbidities.Rmd | 26 medicalcoder-0.8.0/medicalcoder/inst/doc/comorbidities.html | 62 medicalcoder-0.8.0/medicalcoder/inst/doc/elixhauser.Rmd | 4 medicalcoder-0.8.0/medicalcoder/inst/doc/elixhauser.html | 58 medicalcoder-0.8.0/medicalcoder/inst/doc/icd.R | 14 medicalcoder-0.8.0/medicalcoder/inst/doc/icd.Rmd | 28 medicalcoder-0.8.0/medicalcoder/inst/doc/icd.html | 656 +++-- medicalcoder-0.8.0/medicalcoder/inst/doc/pccc.html | 138 - medicalcoder-0.8.0/medicalcoder/inst/mappings/icd-codes-and-mappings.R | 15 medicalcoder-0.8.0/medicalcoder/man/comorbidities.Rd | 18 medicalcoder-0.8.0/medicalcoder/man/get_charlson_codes.Rd | 2 medicalcoder-0.8.0/medicalcoder/man/get_icd_codes.Rd | 14 medicalcoder-0.8.0/medicalcoder/man/get_pccc_conditions.Rd | 6 medicalcoder-0.8.0/medicalcoder/man/is_icd.Rd | 10 medicalcoder-0.8.0/medicalcoder/man/lookup_icd_codes.Rd | 7 medicalcoder-0.8.0/medicalcoder/man/mdcr.Rd | 4 medicalcoder-0.8.0/medicalcoder/man/mdcr_longitudinal.Rd | 6 medicalcoder-0.8.0/medicalcoder/man/medicalcoder-package.Rd | 2 medicalcoder-0.8.0/medicalcoder/man/summary.medicalcoder_comorbidities_with_subconditions.Rd | 2 medicalcoder-0.8.0/medicalcoder/tests/expected-ahrq-results.rds |binary medicalcoder-0.8.0/medicalcoder/tests/results_pccc_1.0.6.rds |binary medicalcoder-0.8.0/medicalcoder/tests/results_pccc_1.0.7.rds |only medicalcoder-0.8.0/medicalcoder/tests/test-comorbidities.R | 92 medicalcoder-0.8.0/medicalcoder/tests/test-data-frame-tools.R | 432 +++ medicalcoder-0.8.0/medicalcoder/tests/test-elixhauser-poa-na.R |only medicalcoder-0.8.0/medicalcoder/tests/test-elixhauser.R | 11 medicalcoder-0.8.0/medicalcoder/tests/test-icd_compact_to_full.R | 8 medicalcoder-0.8.0/medicalcoder/tests/test-internal-data.R | 15 medicalcoder-0.8.0/medicalcoder/tests/test-is_icd.R | 15 medicalcoder-0.8.0/medicalcoder/tests/test-longitudinal-comorbidities.R | 1204 +++++----- medicalcoder-0.8.0/medicalcoder/tests/test-lookup_icd_codes.R | 35 medicalcoder-0.8.0/medicalcoder/tests/test-pccc-deltas.R | 8 medicalcoder-0.8.0/medicalcoder/tests/test-poa-in-cumulative.R |only medicalcoder-0.8.0/medicalcoder/tests/test-primarydx.R |only medicalcoder-0.8.0/medicalcoder/tests/test-summary-charlson.R | 35 medicalcoder-0.8.0/medicalcoder/tests/test-summary-elixhauser.R | 39 medicalcoder-0.8.0/medicalcoder/tests/test-summary-pccc-subconditions.R | 37 medicalcoder-0.8.0/medicalcoder/tests/test-summary-pccc.R | 47 medicalcoder-0.8.0/medicalcoder/tests/test-tibble-datatable.R | 18 medicalcoder-0.8.0/medicalcoder/tests/test-vs-ahrq.R | 26 medicalcoder-0.8.0/medicalcoder/tests/test-vs-pccc_1.0.7.R |only medicalcoder-0.8.0/medicalcoder/vignettes/comorbidities.Rmd | 26 medicalcoder-0.8.0/medicalcoder/vignettes/elixhauser.Rmd | 4 medicalcoder-0.8.0/medicalcoder/vignettes/icd.Rmd | 28 medicalcoder-0.8.0/medicalcoder/vignettes/references.bib | 10 72 files changed, 2883 insertions(+), 1254 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-03-25 0.2.0
2016-09-24 0.1-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-09-29 0.6.1
2025-06-16 0.6.0
2024-10-28 0.5.9
2024-09-05 0.5.8
2024-06-23 0.5.7
2022-08-05 0.5.6
2022-03-21 0.5.4
2022-03-16 0.5.3
2022-03-04 0.5.2
2021-11-01 0.5.1
2021-10-13 0.5.0
2021-07-23 0.4.9
2021-06-11 0.4.8
2021-04-27 0.4.7
2021-02-21 0.4.6
2020-11-28 0.4.5
2020-10-21 0.4.0
2020-10-06 0.3.0
Title: Multivariate Genome Wide Marginal Epistasis Test
Description: Epistasis, commonly defined as the interaction between genetic
loci, is known to play an important role in the phenotypic variation of
complex traits. As a result, many statistical methods have been developed to
identify genetic variants that are involved in epistasis, and nearly all of
these approaches carry out this task by focusing on analyzing one trait at a
time. Previous studies have shown that jointly modeling multiple phenotypes
can often dramatically increase statistical power for association mapping. In
this package, we present the 'multivariate MArginal ePIstasis Test'
('mvMAPIT') – a multi-outcome generalization of a recently proposed epistatic
detection method which seeks to detect marginal epistasis or the combined
pairwise interaction effects between a given variant and all other variants.
By searching for marginal epistatic effects, one can identify genetic variants
that are involved in epistasis without the need to identify the exact
partners with which the variants i [...truncated...]
Author: Julian Stamp [cre, aut] ,
Lorin Crawford [aut]
Maintainer: Julian Stamp <julian.d.stamp@gmail.com>
Diff between mvMAPIT versions 2.0.3 dated 2023-09-26 and 2.0.4 dated 2026-02-22
DESCRIPTION | 20 +- MD5 | 60 ++++--- NAMESPACE | 3 NEWS.md | 10 + R/MAPIT.R | 32 +++ R/binary_to_liability.R |only R/globals.R |only R/simulate_data.R | 4 README.md | 21 +- build/vignette.rds |binary data/mvmapit_data.rda |binary inst/doc/mvMAPIT.R | 60 +++---- inst/doc/mvMAPIT.Rmd | 15 + inst/doc/mvMAPIT.html | 40 ++-- inst/doc/study-compare-p-value-combine-methods.html | 15 + inst/doc/study-phillips-bnabs.R | 72 ++++---- inst/doc/study-phillips-bnabs.html | 7 inst/doc/study-wtccc-mice.R | 166 ++++++++++---------- inst/doc/study-wtccc-mice.Rmd | 16 - inst/doc/study-wtccc-mice.html | 21 +- inst/doc/tutorial-docker-mvmapit.html | 45 +++-- inst/doc/tutorial-lt-mapit.R |only inst/doc/tutorial-lt-mapit.Rmd |only inst/doc/tutorial-lt-mapit.html |only inst/doc/tutorial-simulations.R | 82 ++++----- inst/doc/tutorial-simulations.html | 3 man/binary_to_liability.Rd |only src/MAPIT.cpp | 11 - src/mapit/projection.cpp | 4 src/mapit/projection.h | 3 src/mqs/mqs.cpp | 13 + tests/testthat/test-binary_to_liability.R |only vignettes/mvMAPIT.Rmd | 15 + vignettes/study-wtccc-mice.Rmd | 16 - vignettes/tutorial-lt-mapit.Rmd |only 35 files changed, 434 insertions(+), 320 deletions(-)
Title: Rmetrics - Nonlinear and Chaotic Time Series Modelling
Description: Provides a collection of functions for testing various aspects of
univariate time series including independence and neglected
nonlinearities. Further provides functions to investigate the chaotic
behavior of time series processes and to simulate different types of chaotic
time series maps.
Author: Diethelm Wuertz [aut],
Tobias Setz [aut],
Yohan Chalabi [aut],
Paul Smith [cre]
Maintainer: Paul Smith <paul@waternumbers.co.uk>
Diff between fNonlinear versions 4041.82 dated 2024-09-08 and 4052.83 dated 2026-02-22
ChangeLog | 4 ++++ DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NAMESPACE | 2 +- 4 files changed, 12 insertions(+), 8 deletions(-)
Title: Rmetrics - Bivariate Dependence Structures with Copulae
Description: Provides a collection of functions to
manage, to investigate and to analyze bivariate financial returns by
Copulae. Included are the families of Archemedean, Elliptical,
Extreme Value, and Empirical Copulae.
Author: Diethelm Wuertz [aut],
Tobias Setz [aut],
Yohan Chalabi [ctb],
Paul Smith [cre]
Maintainer: Paul Smith <paul@waternumbers.co.uk>
Diff between fCopulae versions 4022.85 dated 2023-01-07 and 4052.86 dated 2026-02-22
ChangeLog | 3 +++ DESCRIPTION | 27 ++++++++++++++++++++------- MD5 | 4 ++-- 3 files changed, 25 insertions(+), 9 deletions(-)