Title: Semi-Supervised Algorithm for Document Scaling
Description: A word embeddings-based semi-supervised model for document scaling Watanabe (2020) <doi:10.1080/19312458.2020.1832976>.
LSS allows users to analyze large and complex corpora on arbitrary dimensions with seed words exploiting efficiency of word embeddings (SVD, Glove).
It can generate word vectors on a users-provided corpus or incorporate a pre-trained word vectors.
Author: Kohei Watanabe [aut, cre, cph]
Maintainer: Kohei Watanabe <watanabe.kohei@gmail.com>
Diff between LSX versions 1.5.0 dated 2025-09-12 and 1.5.1 dated 2025-12-08
DESCRIPTION | 12 ++++----- MD5 | 20 +++++++-------- NAMESPACE | 1 NEWS.md | 4 +++ R/as.textmodel.R | 18 +++++++++---- R/textmodel_lss.R | 3 +- build/partial.rdb |binary tests/testthat/Rplots.pdf |binary tests/testthat/test-as.textmodel.R | 4 ++- tests/testthat/test-textplot.R | 48 ++++++++++++++++++------------------- tests/testthat/test-utils.R | 1 11 files changed, 63 insertions(+), 48 deletions(-)
Title: Manage Branding and Accessibility of R Projects
Description: A tool for building projects that are visually consistent,
accessible, and easy to maintain. It provides functions for managing
branding assets, applying organization-wide themes using 'brand.yml',
and setting up new projects with accessibility features and correct
branding. It supports 'quarto', 'shiny', and 'rmarkdown' projects, and
integrates with 'ggplot2'. The accessibility features are based
on the Web Content Accessibility Guidelines
<https://www.w3.org/WAI/WCAG22/quickref/?versions=2.1>
and Accessible Rich Internet Applications (ARIA) specifications
<https://www.w3.org/WAI/ARIA/apg/>. The branding framework implements
the 'brand.yml' specification <https://posit-dev.github.io/brand-yml/>.
Author: Willy Ray [aut, cre],
Andrew Pulsipher [aut, ctb] ,
Centers for Disease Control and Prevention's Center for Forecasting and
Outbreak Analytics [fnd]
Maintainer: Willy Ray <william.ray@hsc.utah.edu>
Diff between rbranding versions 0.1.0 dated 2025-11-21 and 0.1.1 dated 2025-12-08
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- inst/doc/ggplot2-integration.html | 8 ++++---- inst/doc/rbranding.html | 2 +- inst/tinytest/test_ggplot2.R | 18 ++++++++---------- 5 files changed, 20 insertions(+), 22 deletions(-)
Title: Simple TD API Client
Description: Upload R data.frame to Arm Treasure Data, see <https://www.treasuredata.com/>.
You can execute database or table handling for resources on Arm Treasure Data.
Author: Aki Ariga [aut, cre, cph]
Maintainer: Aki Ariga <ariga@treasure-data.com>
Diff between RTD versions 0.4.1 dated 2020-07-26 and 0.4.2 dated 2025-12-08
DESCRIPTION | 11 +--- MD5 | 8 +-- NEWS.md | 4 + README.md | 10 +++ tests/testthat/test-td.R | 118 +++++++++++++++++++++++++++++++++++------------ 5 files changed, 110 insertions(+), 41 deletions(-)
Title: 'Praat Picture' Style Plots of Acoustic Data
Description: Quickly and easily generate plots of acoustic data aligned with transcriptions similar to those made in 'Praat' using either derived signals generated directly in R with 'wrassp' or imported derived signals from 'Praat'. Provides easy and fast out-of-the-box solutions but also a high extent of flexibility. Also provides options for embedding audio in figures and animating figures.
Author: Rasmus Puggaard-Rode [aut, cre, cph]
Maintainer: Rasmus Puggaard-Rode <rasmus.puggaard-rode@ling-phil.ox.ac.uk>
Diff between praatpicture versions 1.6.2 dated 2025-08-25 and 1.7.0 dated 2025-12-08
DESCRIPTION | 12 - MD5 | 22 +- NEWS.md | 16 + R/draw_spectralslice.R | 504 ++++++++++++++++++++++++---------------------- R/formantplot.R | 111 +++++++--- R/praatpicture.R | 58 ++++- R/specplot.R | 200 ++++++++++++------ R/waveplot.R | 51 ++-- man/draw_spectralslice.Rd | 14 - man/praatpicture.Rd | 28 ++ man/specplot.Rd | 20 + man/waveplot.Rd | 8 12 files changed, 651 insertions(+), 393 deletions(-)
Title: Hysteretic and Gatekeeping Depressions Model
Description: Implementation of the Hysteretic and Gatekeeping Depressions Model (HGDM) which calculates variable connected/contributing areas and resulting discharge volumes in prairie basins dominated by depressions ("slough" or "potholes"). The small depressions are combined into a single "meta" depression which explicitly models the hysteresis between the storage of water and the connected/contributing areas of the depressions. The largest (greater than 5% of the total depressional area) depression (if it exists) is represented separately to model its gatekeeping, i.e. the blocking of upstream flows until it is filled. The methodolgy is described in detail in Shook and Pomeroy (2025, <doi:10.1016/j.jhydrol.2025.132821>).
Author: Kevin Shook [cre, aut]
Maintainer: Kevin Shook <kshook@kshook.ca>
Diff between HGDMr versions 1.0.0 dated 2025-02-21 and 1.0.1 dated 2025-12-08
DESCRIPTION | 12 ++++++------ MD5 | 6 +++--- inst/doc/HGDMr_examples.html | 9 +++++---- man/HGDMr-package.Rd | 2 +- 4 files changed, 15 insertions(+), 14 deletions(-)
Title: Distributional Random Forests
Description: An implementation of distributional random forests as introduced in Cevid & Michel & Meinshausen & Buhlmann (2020) <doi:10.48550/arXiv.2005.14458>.
Author: Jeffrey Naf [cre],
Loris Michel [aut],
Domagoj Cevid [aut]
Maintainer: Jeffrey Naf <jeffrey.naf@unige.ch>
Diff between drf versions 1.1.0 dated 2021-03-29 and 1.2.0 dated 2025-12-08
DESCRIPTION | 20 MD5 | 143 +- NAMESPACE | 1 R/analysis_tools.R | 8 R/drf.R | 612 ++-------- R/input_utilities.R | 202 +-- R/mmdVariableImportance.R | 4 R/predict.R |only man/drf.Rd | 136 +- man/predict.drf.Rd | 153 +- src/Makevars | 3 src/RcppExports.cpp | 5 src/src/analysis/SplitFrequencyComputer.cpp | 30 src/src/analysis/SplitFrequencyComputer.h | 30 src/src/commons/Data.cpp | 30 src/src/commons/Data.h | 30 src/src/commons/DefaultData.cpp | 30 src/src/commons/DefaultData.h | 30 src/src/commons/SparseData.cpp | 30 src/src/commons/SparseData.h | 30 src/src/commons/globals.h | 19 src/src/commons/utility.cpp | 30 src/src/commons/utility.h | 30 src/src/forest/Forest.cpp | 30 src/src/forest/Forest.h | 30 src/src/forest/ForestOptions.cpp | 30 src/src/forest/ForestOptions.h | 30 src/src/forest/ForestPredictor.cpp | 30 src/src/forest/ForestPredictor.h | 30 src/src/forest/ForestPredictors.cpp | 30 src/src/forest/ForestPredictors.h | 30 src/src/forest/ForestTrainer.cpp | 30 src/src/forest/ForestTrainer.h | 30 src/src/forest/ForestTrainers.cpp | 30 src/src/forest/ForestTrainers.h | 30 src/src/prediction/DefaultPredictionStrategy.h | 30 src/src/prediction/OptimizedPredictionStrategy.h | 30 src/src/prediction/Prediction.cpp | 30 src/src/prediction/Prediction.h | 30 src/src/prediction/PredictionValues.cpp | 30 src/src/prediction/PredictionValues.h | 30 src/src/prediction/RegressionPredictionStrategy.cpp | 30 src/src/prediction/RegressionPredictionStrategy.h | 30 src/src/prediction/collector/OptimizedPredictionCollector.cpp | 30 src/src/prediction/collector/OptimizedPredictionCollector.h | 30 src/src/prediction/collector/PredictionCollector.h | 30 src/src/prediction/collector/SampleWeightComputer.cpp | 30 src/src/prediction/collector/SampleWeightComputer.h | 30 src/src/prediction/collector/TreeTraverser.cpp | 30 src/src/prediction/collector/TreeTraverser.h | 30 src/src/relabeling/NoopRelabelingStrategy.cpp | 30 src/src/relabeling/NoopRelabelingStrategy.h | 30 src/src/relabeling/RelabelingStrategy.h | 30 src/src/sampling/RandomSampler.cpp | 27 src/src/sampling/RandomSampler.h | 30 src/src/sampling/SamplingOptions.cpp | 30 src/src/sampling/SamplingOptions.h | 30 src/src/splitting/FourierSplittingRule.cpp | 30 src/src/splitting/FourierSplittingRule.h | 30 src/src/splitting/RegressionSplittingRule.cpp | 30 src/src/splitting/RegressionSplittingRule.h | 30 src/src/splitting/SplittingRule.h | 30 src/src/splitting/factory/FourierSplittingRuleFactory.cpp | 30 src/src/splitting/factory/FourierSplittingRuleFactory.h | 30 src/src/splitting/factory/RegressionSplittingRuleFactory.cpp | 30 src/src/splitting/factory/RegressionSplittingRuleFactory.h | 30 src/src/splitting/factory/SplittingRuleFactory.h | 30 src/src/tree/Tree.cpp | 8 src/src/tree/Tree.h | 8 src/src/tree/TreeOptions.cpp | 30 src/src/tree/TreeOptions.h | 30 src/src/tree/TreeTrainer.cpp | 30 src/src/tree/TreeTrainer.h | 30 73 files changed, 1372 insertions(+), 1687 deletions(-)
Title: Fast and Beautiful Interactive Visualization for 'Markdown' and
'Shiny'
Description: Apache licensed alternative to 'Highcharter' which provides
functions for both fast and beautiful interactive visualization for 'Markdown'
and 'Shiny'.
Author: Mauricio Vargas Sepulveda [aut, cre, cph] ,
John Coene [aut],
Ariel Alvarado [ctb],
Sylvain Lesage [ctb],
Curran Kelleher [ctb],
Fernando Becerra [ctb],
Natural Earth [dtc],
R Consortium [fnd]
Maintainer: Mauricio Vargas Sepulveda <m.vargas.sepulveda@gmail.com>
This is a re-admission after prior archival of version 1.0.2 dated 2025-11-25
Diff between d3po versions 1.0.2 dated 2025-11-25 and 1.0.3 dated 2025-12-08
DESCRIPTION | 8 MD5 | 32 +-- R/api.R | 52 ++++-- inst/doc/examples.R | 376 ++++++++++++++++++++++++------------------- inst/doc/examples.Rmd | 98 ++++++++--- inst/doc/examples.html | 422 +++++++++++++++++++++++++------------------------ man/po_area.Rd | 5 man/po_bar.Rd | 5 man/po_box.Rd | 5 man/po_donut.Rd | 5 man/po_geomap.Rd | 5 man/po_line.Rd | 5 man/po_network.Rd | 5 man/po_pie.Rd | 5 man/po_scatter.Rd | 5 man/po_treemap.Rd | 5 vignettes/examples.Rmd | 98 ++++++++--- 17 files changed, 689 insertions(+), 447 deletions(-)
Title: Interface to the arXiv API
Description: An interface to the API for 'arXiv',
a repository of electronic preprints for
computer science, mathematics, physics, quantitative biology,
quantitative finance, and statistics.
Author: Karthik Ram [aut] ,
Karl Broman [aut, cre]
Maintainer: Karl Broman <broman@wisc.edu>
Diff between aRxiv versions 0.14 dated 2025-11-14 and 0.16 dated 2025-12-08
DESCRIPTION | 8 ++--- MD5 | 18 ++++++------ NEWS.md | 14 ++++++++++ R/arxiv_open.R | 7 ++++- R/can_arxiv_connect.R | 3 ++ R/clean.R | 7 ++--- R/parse.R | 8 ++++- inst/doc/aRxiv.html | 30 ++++++++++----------- tests/testthat/test-clean.R | 61 ++++++++++++++++++++++++-------------------- tests/testthat/test-sort.R | 6 +--- 10 files changed, 96 insertions(+), 66 deletions(-)
Title: Seamless R and C++ Integration
Description: The 'Rcpp' package provides R functions as well as C++ classes which
offer a seamless integration of R and C++. Many R data types and objects can be
mapped back and forth to C++ equivalents which facilitates both writing of new
code as well as easier integration of third-party libraries. Documentation
about 'Rcpp' is provided by several vignettes included in this package, via the
'Rcpp Gallery' site at <https://gallery.rcpp.org>, the paper by Eddelbuettel and
Francois (2011, <doi:10.18637/jss.v040.i08>), the book by Eddelbuettel (2013,
<doi:10.1007/978-1-4614-6868-4>) and the paper by Eddelbuettel and Balamuta (2018,
<doi:10.1080/00031305.2017.1375990>); see 'citation("Rcpp")' for details.
Author: Dirk Eddelbuettel [aut, cre] ,
Romain Francois [aut] ,
JJ Allaire [aut] ,
Kevin Ushey [aut] ,
Qiang Kou [aut] ,
Nathan Russell [aut],
Inaki Ucar [aut] ,
Doug Bates [aut] ,
John Chambers [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between Rcpp versions 1.1.0.8 dated 2025-12-07 and 1.1.0.8.1 dated 2025-12-08
ChangeLog | 1 + DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- inst/NEWS.Rd | 2 ++ inst/doc/Rcpp-introduction.pdf |binary tests/tinytest.R | 2 +- 6 files changed, 13 insertions(+), 10 deletions(-)
Title: 'knitr' Bootstrap Framework
Description: A framework to create Bootstrap <https://getbootstrap.com/> HTML reports from 'knitr'
'rmarkdown'.
Author: Jim Hester [aut, cre]
Maintainer: Jim Hester <james.f.hester@gmail.com>
Diff between knitrBootstrap versions 1.0.3 dated 2024-02-06 and 1.0.4 dated 2025-12-08
knitrBootstrap-1.0.3/knitrBootstrap/man/knitrBootstrap.Rd |only knitrBootstrap-1.0.4/knitrBootstrap/DESCRIPTION | 20 +++-- knitrBootstrap-1.0.4/knitrBootstrap/MD5 | 38 +++++----- knitrBootstrap-1.0.4/knitrBootstrap/NEWS.md | 3 knitrBootstrap-1.0.4/knitrBootstrap/R/knit_bootstrap.R | 11 +- knitrBootstrap-1.0.4/knitrBootstrap/README.md | 16 ++-- knitrBootstrap-1.0.4/knitrBootstrap/build/vignette.rds |binary knitrBootstrap-1.0.4/knitrBootstrap/inst/doc/cars.Rmd | 2 knitrBootstrap-1.0.4/knitrBootstrap/inst/doc/cars.html | 10 +- knitrBootstrap-1.0.4/knitrBootstrap/inst/doc/illusions.Rmd | 4 - knitrBootstrap-1.0.4/knitrBootstrap/inst/doc/illusions.html | 4 - knitrBootstrap-1.0.4/knitrBootstrap/inst/doc/maps.html | 8 +- knitrBootstrap-1.0.4/knitrBootstrap/inst/doc/two-D.R | 2 knitrBootstrap-1.0.4/knitrBootstrap/inst/doc/two-D.Rmd | 2 knitrBootstrap-1.0.4/knitrBootstrap/inst/doc/two-D.html | 32 +++++--- knitrBootstrap-1.0.4/knitrBootstrap/man/bootstrap_document.Rd | 14 ++- knitrBootstrap-1.0.4/knitrBootstrap/man/knit_bootstrap_md.Rd | 2 knitrBootstrap-1.0.4/knitrBootstrap/man/knitrBootstrap-package.Rd |only knitrBootstrap-1.0.4/knitrBootstrap/vignettes/cars.Rmd | 2 knitrBootstrap-1.0.4/knitrBootstrap/vignettes/illusions.Rmd | 4 - knitrBootstrap-1.0.4/knitrBootstrap/vignettes/two-D.Rmd | 2 21 files changed, 97 insertions(+), 79 deletions(-)
More information about knitrBootstrap at CRAN
Permanent link
Title: Tools for Analyzing QTL Experiments
Description: Analysis of experimental crosses to identify genes
(called quantitative trait loci, QTLs) contributing to variation in
quantitative traits.
Broman et al. (2003) <doi:10.1093/bioinformatics/btg112>.
Author: Karl W Broman [aut, cre] ,
Hao Wu [aut],
Gary Churchill [ctb] ,
Saunak Sen [ctb] ,
Danny Arends [ctb] ,
Robert Corty [ctb],
Timothee Flutre [ctb],
Ritsert Jansen [ctb],
Pjotr Prins [ctb] ,
Lars Ronnegard [ctb],
Rohan Shah [ctb],
Laura Shannon [ctb],
[...truncated...]
Maintainer: Karl W Broman <broman@wisc.edu>
Diff between qtl versions 1.72 dated 2025-11-19 and 1.74 dated 2025-12-08
DESCRIPTION | 8 +-- MD5 | 110 +++++++++++++++++++++--------------------- NEWS.md | 5 + inst/doc/bcsft.pdf |binary inst/doc/rqtltour.pdf |binary inst/doc/rqtltour2.pdf |binary src/countXO.c | 1 src/discan.c | 1 src/discan_covar.c | 1 src/effectscan.c | 1 src/findDupMarkers_notexact.c | 1 src/fitqtl_hk.c | 1 src/fitqtl_hk_binary.c | 1 src/fitqtl_imp.c | 1 src/fitqtl_imp_binary.c | 1 src/hmm_4way.c | 1 src/hmm_bc.c | 1 src/hmm_bci.c | 1 src/hmm_bcsft.c | 1 src/hmm_bgmagic16.c | 1 src/hmm_f2.c | 1 src/hmm_f2i.c | 1 src/hmm_main.c | 1 src/hmm_ri4self.c | 1 src/hmm_ri4sib.c | 1 src/hmm_ri8self.c | 1 src/hmm_ri8selfIRIP1.c | 1 src/hmm_ri8sib.c | 1 src/hmm_util.c | 1 src/inferFounderHap.c | 1 src/info.c | 1 src/lapackutil.c | 1 src/markerlrt.c | 1 src/pickMarkerSubset.c | 1 src/ril48_reorg.c | 2 src/ripple.c | 1 src/scanone_ehk.c | 1 src/scanone_em.c | 1 src/scanone_em_covar.c | 1 src/scanone_hk.c | 1 src/scanone_hk_binary.c | 1 src/scanone_imp.c | 1 src/scanone_mr.c | 1 src/scanone_np.c | 1 src/scantwo_binary_em.c | 1 src/scantwo_binary_hk.c | 1 src/scantwo_em.c | 1 src/scantwo_hk.c | 1 src/scantwo_imp.c | 1 src/scantwo_mr.c | 1 src/scantwopermhk.c | 1 src/simulate.c | 1 src/simulate_ril.c | 1 src/stahl_mf.c | 1 src/summary_scantwo.c | 1 src/test_bcsft.c | 1 56 files changed, 64 insertions(+), 110 deletions(-)
Title: Detecting Changes in Autocorrelated and Fluctuating Signals
Description: Detect abrupt changes in time series with local fluctuations as a random walk process and autocorrelated noise as an AR(1) process. See Romano, G., Rigaill, G., Runge, V., Fearnhead, P. (2021) <doi:10.1080/01621459.2021.1909598>.
Author: Gaetano Romano [aut, cre],
Guillem Rigaill [aut],
Vincent Runge [aut],
Paul Fearnhead [aut]
Maintainer: Gaetano Romano <g.romano@lancaster.ac.uk>
Diff between DeCAFS versions 3.3.3 dated 2023-01-06 and 3.3.5 dated 2025-12-08
DeCAFS-3.3.3/DeCAFS/src/Makevars |only DeCAFS-3.3.5/DeCAFS/DESCRIPTION | 12 ++++++------ DeCAFS-3.3.5/DeCAFS/MD5 | 7 +++---- DeCAFS-3.3.5/DeCAFS/NEWS.md | 14 ++++++++++++++ DeCAFS-3.3.5/DeCAFS/build/partial.rdb |binary 5 files changed, 23 insertions(+), 10 deletions(-)
Title: Multilevel Latent Time Series Models with 'R' and 'Stan'
Description: Fit multilevel manifest or latent time-series models, including popular Dynamic Structural Equation Models (DSEM).
The models can be set up and modified with user-friendly functions and are fit to the data using 'Stan' for Bayesian inference.
Path models and formulas for user-defined models can be easily created with functions using 'knitr'.
Asparouhov, Hamaker, & Muthen (2018) <doi:10.1080/10705511.2017.1406803>.
Author: Kenneth Koslowski [aut, cre, cph] ,
Fabian Muench [aut] ,
Tobias Koch [aut] ,
Jana Holtmann [aut]
Maintainer: Kenneth Koslowski <kenneth.koslowski@uni-leipzig.de>
Diff between mlts versions 1.0.0 dated 2024-06-27 and 2.0.0 dated 2025-12-08
DESCRIPTION | 19 MD5 | 156 NAMESPACE | 39 NEWS.md | 27 R/VARprepare.R | 701 +- R/ar1_data.R | 26 R/create_missings.R | 309 - R/mlts-package.R | 26 R/mlts_fit.R | 998 ++- R/mlts_model.R | 880 ++- R/mlts_model_betw.R | 362 - R/mlts_model_check.R | 52 R/mlts_model_constraint.R | 325 - R/mlts_model_eval.R | 938 +-- R/mlts_model_formula.R | 1761 +++--- R/mlts_model_measurement.R | 529 +- R/mlts_model_paths.R | 2449 ++++----- R/mlts_param_labels.R | 332 - R/mlts_paths.R |only R/mlts_plot.R | 692 +- R/mlts_posterior_sample.R |only R/mlts_pp_check.R |only R/mlts_sim.R | 965 +-- R/mlts_standardized.R | 4 R/mlts_standardized_btw.R | 616 +- R/mlts_standardized_within.R | 414 - R/model_helper_functions.R | 653 ++ R/prepare_data.R | 417 - R/sim_helper_functions.R |only R/stanmodels.R | 56 R/summary.R | 671 +- R/ts_data.R | 28 README.md | 634 +- build/partial.rdb |binary build/vignette.rds |binary configure.win | 10 inst/CITATION | 36 inst/doc/betw_predictors.R | 170 inst/doc/betw_predictors.html | 1466 ++--- inst/doc/manifest_ar.R | 91 inst/doc/manifest_ar.Rmd | 290 - inst/doc/manifest_ar.html | 1201 ++-- inst/doc/manifest_var.R | 18 inst/doc/manifest_var.Rmd | 44 inst/doc/manifest_var.html | 723 +- inst/rmarkdown/templates/formula/skeleton/skeleton.Rmd | 32 inst/rmarkdown/templates/formula/template.yaml | 8 inst/rmarkdown/templates/pathmodel/skeleton/skeleton.Rmd | 48 inst/rmarkdown/templates/pathmodel/template.yaml | 8 inst/stan/VAR_latent.stan | 782 +-- inst/stan/VAR_latentCovsFix.stan | 731 +- inst/stan/VAR_manifest.stan | 565 +- inst/stan/VAR_manifestCovsFix.stan | 530 +- inst/stan/include/license.stan | 28 man/ar1_data.Rd | 54 man/create_missings.Rd | 90 man/figures/README-ar1_plot-1.png |binary man/figures/README-unnamed-chunk-5-1.png |only man/mlts-package.Rd | 60 man/mlts_fit.Rd | 339 - man/mlts_model.Rd | 400 - man/mlts_model_formula.Rd | 104 man/mlts_model_paths.Rd | 110 man/mlts_paths.Rd |only man/mlts_plot.Rd | 228 man/mlts_posterior_sample.Rd |only man/mlts_pp_check.Rd |only man/mlts_sim.Rd | 177 man/mlts_standardized.Rd | 113 man/summary.mltsfit.Rd | 124 man/ts_data.Rd | 56 tests/local/test-mlts_model_formula.R | 174 tests/local/test-mlts_model_paths.R | 172 tests/testthat.R | 24 tests/testthat/test-create_missings.R | 104 tests/testthat/test-mlts_model.R | 56 tests/testthat/test-prepare_data.R | 36 vignettes/apa.csl | 3828 +++++++-------- vignettes/ar1_fit.rds |binary vignettes/betw_preds_fit1.txt | 90 vignettes/betw_preds_fit2.txt | 110 vignettes/manifest_ar.Rmd | 290 - vignettes/manifest_var.Rmd | 44 83 files changed, 15085 insertions(+), 13558 deletions(-)
Title: Estimation of Model-Based Predictions, Contrasts and Means
Description: Implements a general interface for model-based estimations
for a wide variety of models, used in the computation of
marginal means, contrast analysis and predictions. For a list of supported models,
see 'insight::supported_models()'.
Author: Dominique Makowski [aut, cre] ,
Daniel Luedecke [aut] ,
Mattan S. Ben-Shachar [aut] ,
Indrajeet Patil [aut] ,
Remi Theriault [aut]
Maintainer: Dominique Makowski <officialeasystats@gmail.com>
Diff between modelbased versions 0.13.0 dated 2025-08-30 and 0.13.1 dated 2025-12-08
DESCRIPTION | 24 - MD5 | 107 ++++---- NAMESPACE | 4 NEWS.md | 21 + R/as.data.frame.R |only R/estimate_contrasts.R | 24 + R/estimate_contrasts_effectsize.R | 41 ++- R/estimate_grouplevel.R | 206 +++++++++++----- R/estimate_means.R | 83 ++++-- R/estimate_slopes.R | 1 R/format.R | 54 +++- R/get_inequalitycontrasts.R | 2 R/get_marginalcontrasts.R | 35 +- R/get_marginaleffects_type.R | 36 +- R/get_marginalmeans.R | 108 +++++--- R/get_marginaltrends.R | 3 R/options.R | 10 R/residualize_over_grid.R | 2 R/standardize_methods.R | 12 R/summary.R | 2 R/table_footer.R | 28 ++ R/tinyplot.R | 95 ++++++- R/visualisation_recipe.R | 6 R/visualisation_recipe_internal.R | 2 README.md | 20 + build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST | 100 ++----- inst/doc/overview_of_vignettes.Rmd | 1 inst/doc/overview_of_vignettes.html | 2 man/as.data.frame.estimate_contrasts.Rd |only man/describe_nonlinear.Rd | 2 man/estimate_contrasts.Rd | 8 man/estimate_expectation.Rd | 2 man/estimate_grouplevel.Rd | 35 +- man/estimate_means.Rd | 48 +++ man/estimate_slopes.Rd | 4 man/figures/unnamed-chunk-3-1.png |binary man/get_emmeans.Rd | 10 man/modelbased-options.Rd | 9 man/pool_contrasts.Rd | 2 man/pool_predictions.Rd | 2 man/print.estimate_contrasts.Rd | 13 - man/puppy_love.Rd | 64 ++-- man/residualize_over_grid.Rd | 2 man/visualisation_recipe.estimate_predicted.Rd | 51 ++- tests/testthat/test-as.data.frame.R |only tests/testthat/test-attributes_estimatefun.R | 38 ++ tests/testthat/test-equivalence.R |only tests/testthat/test-estimate_contrasts_counterfactual.R |only tests/testthat/test-estimate_contrasts_effectsize.R | 106 ++++++-- tests/testthat/test-estimate_filter.R | 19 + tests/testthat/test-estimate_grouplevel.R | 145 +++++++++++ tests/testthat/test-keep_iterations.R | 47 ++- tests/testthat/test-ordinal.R | 1 tests/testthat/test-plot-grouplevel.R | 2 vignettes/overview_of_vignettes.Rmd | 1 57 files changed, 1180 insertions(+), 460 deletions(-)
Title: Most Likely Transformations: Documentation and Regression Tests
Description: Additional documentation, a package vignette and
regression tests for package mlt.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mlt.docreg versions 1.1-11 dated 2025-10-08 and 1.1-12 dated 2025-12-08
DESCRIPTION | 8 ++++---- MD5 | 16 +++++++++++----- build/vignette.rds |binary inst/NEWS.Rd | 8 ++++++++ inst/doc/mlt.pdf |binary tests/AFT-Ex.Rout.save |only tests/KM-Ex.Rout.save |only tests/faithful.Rout.save |only tests/orm-Ex.Rout.save |only tests/timedep_covar.Rout.save |only tests/truncreg-Ex.Rout.save |only vignettes/defs.tex | 2 +- 12 files changed, 24 insertions(+), 10 deletions(-)
Title: Dice Plot Visualization for 'ggplot2'
Description: Provides 'ggplot2' extensions for creating dice-based visualizations
where each dot position represents a specific categorical variable. The package
includes geom_dice() for displaying presence/absence of categorical variables
using traditional dice patterns. Each dice position (1-6) represents a different
category, with dots shown only when that category is present. This allows
intuitive visualization of up to 6 categorical variables simultaneously.
Author: Matthias Flotho [aut, cre]
Maintainer: Matthias Flotho <matthias.flotho@ccb.uni-saarland.de>
Diff between ggdiceplot versions 0.1.1 dated 2025-10-14 and 1.0.1 dated 2025-12-08
ggdiceplot-0.1.1/ggdiceplot/R/geom-dice-ggproto.R |only ggdiceplot-0.1.1/ggdiceplot/inst |only ggdiceplot-1.0.1/ggdiceplot/DESCRIPTION | 16 +- ggdiceplot-1.0.1/ggdiceplot/MD5 | 19 +- ggdiceplot-1.0.1/ggdiceplot/R/geom-dice-ggprotto.R | 17 +- ggdiceplot-1.0.1/ggdiceplot/R/sample_datasets.R |only ggdiceplot-1.0.1/ggdiceplot/README.md | 123 +++++++++-------- ggdiceplot-1.0.1/ggdiceplot/data/sample_dice_miRNA.rda |only ggdiceplot-1.0.1/ggdiceplot/man/geom_dice.Rd | 2 ggdiceplot-1.0.1/ggdiceplot/man/sample_dice_data1.Rd | 51 ++----- ggdiceplot-1.0.1/ggdiceplot/man/sample_dice_data2.Rd | 45 +----- ggdiceplot-1.0.1/ggdiceplot/man/sample_dice_large.Rd | 48 +----- ggdiceplot-1.0.1/ggdiceplot/man/sample_dice_miRNA.Rd |only 13 files changed, 137 insertions(+), 184 deletions(-)
Title: Adaptive Lasso Quantile Regression with Fixed Effects
Description: Quantile regression with fixed effects solves longitudinal data, considering the individual intercepts as fixed effects. The parametric set of this type of problem used to be huge. Thus penalized methods such as Lasso are currently applied. Adaptive Lasso presents oracle proprieties, which include Gaussianity and correct model selection. Bayesian information criteria (BIC) estimates the optimal tuning parameter lambda. Plot tools are also available.
Author: Ian Meneghel Danilevicz [aut, cre] ,
Pascal Bondon [aut],
Valderio A. Reisen [aut]
Maintainer: Ian Meneghel Danilevicz <iandanilevicz@gmail.com>
Diff between alqrfe versions 1.2 dated 2025-07-03 and 1.3 dated 2025-12-08
alqrfe-1.2/alqrfe/R/LQRFE_main_v3.R |only alqrfe-1.3/alqrfe/DESCRIPTION | 10 +++-- alqrfe-1.3/alqrfe/MD5 | 21 ++++++----- alqrfe-1.3/alqrfe/R/LQRFE_main.R |only alqrfe-1.3/alqrfe/R/RcppExports.R | 17 ++++++--- alqrfe-1.3/alqrfe/man/clean_data.Rd | 2 - alqrfe-1.3/alqrfe/man/mqr.Rd | 2 - alqrfe-1.3/alqrfe/man/mqr_alpha.Rd | 2 - alqrfe-1.3/alqrfe/man/plot_alpha.Rd | 2 - alqrfe-1.3/alqrfe/man/plot_taus.Rd | 2 - alqrfe-1.3/alqrfe/man/qr.Rd | 19 +++++++++- alqrfe-1.3/alqrfe/src/LQRFE_arma.cpp | 62 +++++++++++++++++------------------ alqrfe-1.3/alqrfe/tests |only 13 files changed, 80 insertions(+), 59 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-08-07 1.10
2015-07-20 1.07
2014-12-05 1.06
2013-12-11 1.05
2009-02-10 1.04
2008-02-16 1.03
2007-09-11 1.02
2006-08-03 1.01
Title: Simulation of Legal Exemption System for European Cartel Law
Description: Monte Carlo simulations of a game-theoretic model for the
legal exemption system of the European cartel law are implemented
in order to estimate the (mean) deterrent effect of this system.
The input and output parameters of the simulated cartel
opportunities can be visualized by three-dimensional projections.
A description of the model is given in Moritz et al. (2018)
<doi:10.1515/bejeap-2017-0235>.
Author: Martin Becker [aut, cre]
Maintainer: Martin Becker <martin.becker@mx.uni-saarland.de>
Diff between SimEUCartelLaw versions 1.0.3 dated 2022-06-13 and 1.0.4 dated 2025-12-08
DESCRIPTION | 11 ++++++----- MD5 | 4 ++-- src/SimEUCartelLaw.c | 1 - 3 files changed, 8 insertions(+), 8 deletions(-)
More information about SimEUCartelLaw at CRAN
Permanent link
Title: Multivariate Synthetic Control Method Using Time Series
Description: Three generalizations of the synthetic control method (which has
already an implementation in package 'Synth') are implemented: first,
'MSCMT' allows for using multiple outcome variables, second, time series
can be supplied as economic predictors, and third, a well-defined
cross-validation approach can be used.
Much effort has been taken to make the implementation as stable as possible
(including edge cases) without losing computational efficiency.
A detailed description of the main algorithms is given in
Becker and Klößner (2018) <doi:10.1016/j.ecosta.2017.08.002>.
Author: Martin Becker [aut, cre] ,
Stefan Kloessner [aut],
Karline Soetaert [com],
Jack Dongarra [cph],
R.J. Hanson [cph],
K.H. Haskell [cph],
Cleve Moler [cph],
LAPACK authors [cph]
Maintainer: Martin Becker <martin.becker@mx.uni-saarland.de>
Diff between MSCMT versions 1.4.0 dated 2024-03-19 and 1.4.1 dated 2025-12-08
DESCRIPTION | 11 ++++++----- MD5 | 20 ++++++++++---------- NEWS | 7 +++++++ build/partial.rdb |binary build/vignette.rds |binary inst/doc/CheckingSynth.R | 2 +- inst/doc/CheckingSynth.html | 6 +++--- inst/doc/UsingTimeSeries.R | 2 +- inst/doc/WorkingWithMSCMT.R | 2 +- inst/doc/WorkingWithMSCMT.html | 32 ++++++++++++++++---------------- src/MSCMT.c | 2 +- 11 files changed, 46 insertions(+), 38 deletions(-)
Title: Extracts the Backbone from Networks
Description: An implementation of methods for extracting a sparse unweighted network (i.e. a backbone)
from an unweighted network (e.g., Hamann et al., 2016 <doi:10.1007/s13278-016-0332-2>), a weighted network
(e.g., Serrano et al., 2009 <doi:10.1073/pnas.0808904106>), or a weighted projection (e.g., Neal et al., 2021
<doi:10.1038/s41598-021-03238-3>).
Author: Zachary Neal [aut, cre] ,
Rachel Domagalski [ctb],
Bruce Sagan [ctb],
Karl Godard [ctb]
Maintainer: Zachary Neal <zpneal@msu.edu>
Diff between backbone versions 3.0.2 dated 2025-10-06 and 3.0.3 dated 2025-12-08
backbone-3.0.2/backbone/R/utils.R |only backbone-3.0.3/backbone/DESCRIPTION | 8 backbone-3.0.3/backbone/MD5 | 37 +- backbone-3.0.3/backbone/NAMESPACE | 3 backbone-3.0.3/backbone/NEWS.md | 5 backbone-3.0.3/backbone/R/backbone.R | 9 backbone-3.0.3/backbone/R/backbone_from_projection.R | 4 backbone-3.0.3/backbone/R/backbone_from_unweighted.R | 26 +- backbone-3.0.3/backbone/R/backbone_from_weighted.R | 8 backbone-3.0.3/backbone/R/functions_s3.R |only backbone-3.0.3/backbone/R/functions_unweighted.R | 3 backbone-3.0.3/backbone/R/functions_util.R |only backbone-3.0.3/backbone/R/functions_weighted.R | 6 backbone-3.0.3/backbone/inst/doc/backbone.R | 24 + backbone-3.0.3/backbone/inst/doc/backbone.Rmd | 37 ++ backbone-3.0.3/backbone/inst/doc/backbone.html | 241 +++++++++---------- backbone-3.0.3/backbone/inst/doc/senate.html | 25 + backbone-3.0.3/backbone/man/backbone.Rd | 4 backbone-3.0.3/backbone/man/bicm.Rd | 2 backbone-3.0.3/backbone/man/fastball.Rd | 2 backbone-3.0.3/backbone/vignettes/backbone.Rmd | 37 ++ 21 files changed, 270 insertions(+), 211 deletions(-)
Title: Penalized Quantile Regression with Fixed Effects
Description: Quantile regression with fixed effects is a general model for longitudinal data. Here we proposed to solve it by several methods. The estimation methods include three loss functions as check, asymmetric least square and asymmetric Huber functions; and three structures as simple regression, fixed effects and fixed effects with penalized intercepts by LASSO.
Author: Ian Meneghel Danilevicz [aut, cre] ,
Valderio A Reisen [aut],
Pascal Bondon [aut]
Maintainer: Ian Meneghel Danilevicz <iandanilevicz@gmail.com>
Diff between pqrfe versions 1.2 dated 2025-11-14 and 1.3 dated 2025-12-08
pqrfe-1.2/pqrfe/build |only pqrfe-1.2/pqrfe/inst |only pqrfe-1.2/pqrfe/man/check_lambda.Rd |only pqrfe-1.2/pqrfe/man/choice_p.Rd |only pqrfe-1.2/pqrfe/man/d_psi_als.Rd |only pqrfe-1.2/pqrfe/man/d_psi_mq.Rd |only pqrfe-1.2/pqrfe/man/f_den.Rd |only pqrfe-1.2/pqrfe/man/f_tab.Rd |only pqrfe-1.2/pqrfe/man/loss_er.Rd |only pqrfe-1.2/pqrfe/man/loss_erfe.Rd |only pqrfe-1.2/pqrfe/man/loss_erlasso.Rd |only pqrfe-1.2/pqrfe/man/loss_mqr.Rd |only pqrfe-1.2/pqrfe/man/loss_mqrfe.Rd |only pqrfe-1.2/pqrfe/man/loss_mqrlasso.Rd |only pqrfe-1.2/pqrfe/man/loss_qr.Rd |only pqrfe-1.2/pqrfe/man/loss_qrfe.Rd |only pqrfe-1.2/pqrfe/man/loss_qrlasso.Rd |only pqrfe-1.2/pqrfe/man/optim_er.Rd |only pqrfe-1.2/pqrfe/man/optim_erfe.Rd |only pqrfe-1.2/pqrfe/man/optim_erlasso.Rd |only pqrfe-1.2/pqrfe/man/optim_mqr.Rd |only pqrfe-1.2/pqrfe/man/optim_mqrfe.Rd |only pqrfe-1.2/pqrfe/man/optim_mqrlasso.Rd |only pqrfe-1.2/pqrfe/man/optim_qr.Rd |only pqrfe-1.2/pqrfe/man/optim_qrfe.Rd |only pqrfe-1.2/pqrfe/man/optim_qrlasso.Rd |only pqrfe-1.2/pqrfe/man/pqrfe-package.Rd |only pqrfe-1.2/pqrfe/man/print.PQR.Rd |only pqrfe-1.2/pqrfe/man/psi_als.Rd |only pqrfe-1.2/pqrfe/man/psi_mq.Rd |only pqrfe-1.2/pqrfe/man/q_cov.Rd |only pqrfe-1.2/pqrfe/man/rho_koenker.Rd |only pqrfe-1.2/pqrfe/man/rho_mq.Rd |only pqrfe-1.2/pqrfe/man/sgf.Rd |only pqrfe-1.2/pqrfe/src/Makevars |only pqrfe-1.2/pqrfe/tests/tinytest.R |only pqrfe-1.3/pqrfe/DESCRIPTION | 14 pqrfe-1.3/pqrfe/MD5 | 53 --- pqrfe-1.3/pqrfe/NAMESPACE | 13 pqrfe-1.3/pqrfe/R/PQRFE_main.R | 219 ++++++++------- pqrfe-1.3/pqrfe/R/RcppExports.R | 487 +++++++++++++++++----------------- pqrfe-1.3/pqrfe/man/pqr.Rd | 17 + pqrfe-1.3/pqrfe/src/Makevars.win | 13 pqrfe-1.3/pqrfe/src/PQRFE_arma.cpp | 296 +++++++++----------- pqrfe-1.3/pqrfe/src/RcppExports.cpp | 77 ----- pqrfe-1.3/pqrfe/tests/testthat |only 46 files changed, 562 insertions(+), 627 deletions(-)
Title: Machine-Readable Data Analysis Results with Function Wrappers
Description: You can use the set of wrappers for analytical schemata
to reduce the effort in writing machine-readable data. The set of all-in-one
wrappers will cover widely used functions from data analysis packages.
Author: Olga Lezhnina [aut] ,
Manuel Prinz [aut] ,
Markus Stocker [aut, cre] ,
Open Research Knowledge Graph Project and Contributors [cph]
Maintainer: Markus Stocker <markus.stocker@tib.eu>
Diff between mrap versions 1.0.0 dated 2025-11-25 and 1.0.1 dated 2025-12-08
DESCRIPTION | 18 +++++++++--------- MD5 | 6 +++--- NEWS.md | 4 ++++ man/mrap-package.Rd | 4 ++-- 4 files changed, 18 insertions(+), 14 deletions(-)
Title: Estimate Inverse Probability Weights
Description: Functions to estimate the probability to receive the observed treatment, based on
individual characteristics. The inverse of these probabilities can be used as weights when
estimating causal effects from observational data via marginal structural models. Both point
treatment situations and longitudinal studies can be analysed. The same functions can be used to
correct for informative censoring.
Author: Hung Thai Tran [aut, cre],
Willem M. van der Wal [aut],
Ronald B. Geskus [aut]
Maintainer: Hung Thai Tran <hungtt@oucru.org>
Diff between ipw versions 1.2.1.1 dated 2025-07-28 and 1.2.2 dated 2025-12-08
DESCRIPTION | 23 +++++++++++++++-------- MD5 | 8 ++++---- R/ipwpoint.R | 43 +++++++++++++++++++++++++++++++++++++++++++ build/partial.rdb |binary man/ipwpoint.Rd | 12 +++++++----- 5 files changed, 69 insertions(+), 17 deletions(-)
Title: Automated Multicollinearity Management
Description: Provides a comprehensive and automated workflow for managing multicollinearity in data frames with numeric and/or categorical variables. The package integrates five robust methods into a single function: (1) target encoding of categorical variables based on response values (Micci-Barreca, 2001 (Micci-Barreca, D. 2001 <doi:10.1145/507533.507538>); (2) automated feature prioritization to preserve key predictors during filtering; (3 and 4) pairwise correlation and VIF filtering across all variable types (numeric–numeric, numeric–categorical, and categorical–categorical); (5) adaptive correlation and VIF thresholds. Together, these methods enable a reliable multicollinearity management in most use cases while maintaining model integrity. The package also supports parallel processing and progress tracking via the packages 'future' and 'progressr', and provides seamless integration with the 'tidymodels' ecosystem through a dedicated recipe step.
Author: Blas M. Benito [aut, cre, cph]
Maintainer: Blas M. Benito <blasbenito@gmail.com>
Diff between collinear versions 2.0.0 dated 2024-11-08 and 3.0.0 dated 2025-12-08
collinear-2.0.0/collinear/R/cor_cramer_v.R |only collinear-2.0.0/collinear/R/identify.R |only collinear-2.0.0/collinear/R/imports.R |only collinear-2.0.0/collinear/R/performance_score_auc.R |only collinear-2.0.0/collinear/R/performance_score_r2.R |only collinear-2.0.0/collinear/R/performance_score_v.R |only collinear-2.0.0/collinear/R/preference_order_collinear.R |only collinear-2.0.0/collinear/R/preference_order_methods.R |only collinear-2.0.0/collinear/R/target_encoding_methods.R |only collinear-2.0.0/collinear/R/validate.R |only collinear-2.0.0/collinear/man/add_white_noise.Rd |only collinear-2.0.0/collinear/man/collinear-package.Rd |only collinear-2.0.0/collinear/man/cor_cramer_v.Rd |only collinear-2.0.0/collinear/man/encoded_predictor_name.Rd |only collinear-2.0.0/collinear/man/f_auc.Rd |only collinear-2.0.0/collinear/man/f_r2.Rd |only collinear-2.0.0/collinear/man/f_r2_counts.Rd |only collinear-2.0.0/collinear/man/f_v.Rd |only collinear-2.0.0/collinear/man/f_v_rf_categorical.Rd |only collinear-2.0.0/collinear/man/identify_predictors.Rd |only collinear-2.0.0/collinear/man/identify_predictors_categorical.Rd |only collinear-2.0.0/collinear/man/identify_predictors_numeric.Rd |only collinear-2.0.0/collinear/man/identify_predictors_type.Rd |only collinear-2.0.0/collinear/man/identify_predictors_zero_variance.Rd |only collinear-2.0.0/collinear/man/performance_score_auc.Rd |only collinear-2.0.0/collinear/man/performance_score_r2.Rd |only collinear-2.0.0/collinear/man/performance_score_v.Rd |only collinear-2.0.0/collinear/man/preference_order_collinear.Rd |only collinear-2.0.0/collinear/man/validate_data_cor.Rd |only collinear-2.0.0/collinear/man/validate_data_vif.Rd |only collinear-2.0.0/collinear/man/validate_df.Rd |only collinear-2.0.0/collinear/man/validate_encoding_arguments.Rd |only collinear-2.0.0/collinear/man/validate_predictors.Rd |only collinear-2.0.0/collinear/man/validate_preference_order.Rd |only collinear-2.0.0/collinear/man/validate_response.Rd |only collinear-2.0.0/collinear/tests/testthat/test-auc.R |only collinear-2.0.0/collinear/tests/testthat/test-cramer_v.R |only collinear-2.0.0/collinear/tests/testthat/test-identify.R |only collinear-2.0.0/collinear/tests/testthat/test-preference_order_methods.R |only collinear-2.0.0/collinear/tests/testthat/test-target_encoding_methods.R |only collinear-2.0.0/collinear/tests/testthat/test-validate.R |only collinear-3.0.0/collinear/DESCRIPTION | 19 collinear-3.0.0/collinear/LICENSE | 4 collinear-3.0.0/collinear/MD5 | 303 ++- collinear-3.0.0/collinear/NAMESPACE | 90 - collinear-3.0.0/collinear/NEWS.md | 208 +- collinear-3.0.0/collinear/R/case_weights.R | 88 - collinear-3.0.0/collinear/R/collinear.R | 819 ++++++---- collinear-3.0.0/collinear/R/collinear_select.R |only collinear-3.0.0/collinear/R/collinear_stats.R |only collinear-3.0.0/collinear/R/cor_clusters.R | 148 + collinear-3.0.0/collinear/R/cor_cramer.R |only collinear-3.0.0/collinear/R/cor_df.R | 622 +++---- collinear-3.0.0/collinear/R/cor_matrix.R | 144 + collinear-3.0.0/collinear/R/cor_select.R | 239 -- collinear-3.0.0/collinear/R/cor_stats.R |only collinear-3.0.0/collinear/R/data.R | 165 +- collinear-3.0.0/collinear/R/drop_geometry_column.R | 58 collinear-3.0.0/collinear/R/f_auto.R |only collinear-3.0.0/collinear/R/f_auto_rules.R |only collinear-3.0.0/collinear/R/f_binomial_gam.R |only collinear-3.0.0/collinear/R/f_binomial_glm.R |only collinear-3.0.0/collinear/R/f_binomial_rf.R |only collinear-3.0.0/collinear/R/f_categorical_rf.R |only collinear-3.0.0/collinear/R/f_count_gam.R |only collinear-3.0.0/collinear/R/f_count_glm.R |only collinear-3.0.0/collinear/R/f_count_rf.R |only collinear-3.0.0/collinear/R/f_functions.R |only collinear-3.0.0/collinear/R/f_numeric_gam.R |only collinear-3.0.0/collinear/R/f_numeric_glm.R |only collinear-3.0.0/collinear/R/f_numeric_rf.R |only collinear-3.0.0/collinear/R/identify_categorical_variables.R |only collinear-3.0.0/collinear/R/identify_logical_variables.R |only collinear-3.0.0/collinear/R/identify_numeric_variables.R |only collinear-3.0.0/collinear/R/identify_response_type.R |only collinear-3.0.0/collinear/R/identify_valid_variables.R |only collinear-3.0.0/collinear/R/identify_zero_variance_variables.R |only collinear-3.0.0/collinear/R/model_formula.R | 341 +--- collinear-3.0.0/collinear/R/preference_order.R | 619 +++++-- collinear-3.0.0/collinear/R/print.collinear_output.R |only collinear-3.0.0/collinear/R/print.collinear_selection.R |only collinear-3.0.0/collinear/R/score_auc.R |only collinear-3.0.0/collinear/R/score_cramer.R |only collinear-3.0.0/collinear/R/score_r2.R |only collinear-3.0.0/collinear/R/step_collinear.R |only collinear-3.0.0/collinear/R/summary.collinear_output.R |only collinear-3.0.0/collinear/R/summary.collinear_selection.R |only collinear-3.0.0/collinear/R/target_encoding_lab.R | 352 ++-- collinear-3.0.0/collinear/R/target_encoding_loo.R |only collinear-3.0.0/collinear/R/target_encoding_mean.R |only collinear-3.0.0/collinear/R/target_encoding_rank.R |only collinear-3.0.0/collinear/R/validate_arg_df.R |only collinear-3.0.0/collinear/R/validate_arg_df_not_null.R |only collinear-3.0.0/collinear/R/validate_arg_encoding_method.R |only collinear-3.0.0/collinear/R/validate_arg_f.R |only collinear-3.0.0/collinear/R/validate_arg_function_name.R |only collinear-3.0.0/collinear/R/validate_arg_max_cor.R |only collinear-3.0.0/collinear/R/validate_arg_max_vif.R |only collinear-3.0.0/collinear/R/validate_arg_predictors.R |only collinear-3.0.0/collinear/R/validate_arg_preference_order.R |only collinear-3.0.0/collinear/R/validate_arg_quiet.R |only collinear-3.0.0/collinear/R/validate_arg_responses.R |only collinear-3.0.0/collinear/R/vif.R |only collinear-3.0.0/collinear/R/vif_df.R | 259 +-- collinear-3.0.0/collinear/R/vif_select.R | 331 ---- collinear-3.0.0/collinear/R/vif_stats.R |only collinear-3.0.0/collinear/README.md | 624 +++++-- collinear-3.0.0/collinear/data/experiment_adaptive_thresholds.rda |only collinear-3.0.0/collinear/data/experiment_cor_vs_vif.rda |only collinear-3.0.0/collinear/data/gam_cor_to_vif.rda |only collinear-3.0.0/collinear/data/prediction_cor_to_vif.rda |only collinear-3.0.0/collinear/data/vi.rda |binary collinear-3.0.0/collinear/data/vi_predictors.rda |binary collinear-3.0.0/collinear/data/vi_predictors_categorical.rda |binary collinear-3.0.0/collinear/data/vi_predictors_numeric.rda |binary collinear-3.0.0/collinear/data/vi_responses.rda |only collinear-3.0.0/collinear/data/vi_smol.rda |only collinear-3.0.0/collinear/inst/WORDLIST | 55 collinear-3.0.0/collinear/inst/experiments |only collinear-3.0.0/collinear/man/case_weights.Rd | 43 collinear-3.0.0/collinear/man/collinear.Rd | 269 +-- collinear-3.0.0/collinear/man/collinear_select.Rd |only collinear-3.0.0/collinear/man/collinear_stats.Rd |only collinear-3.0.0/collinear/man/cor_clusters.Rd | 90 - 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collinear-3.0.0/collinear/man/toy.Rd | 12 collinear-3.0.0/collinear/man/validate_arg_df.Rd |only collinear-3.0.0/collinear/man/validate_arg_df_not_null.Rd |only collinear-3.0.0/collinear/man/validate_arg_encoding_method.Rd |only collinear-3.0.0/collinear/man/validate_arg_f.Rd |only collinear-3.0.0/collinear/man/validate_arg_function_name.Rd |only collinear-3.0.0/collinear/man/validate_arg_max_cor.Rd |only collinear-3.0.0/collinear/man/validate_arg_max_vif.Rd |only collinear-3.0.0/collinear/man/validate_arg_predictors.Rd |only collinear-3.0.0/collinear/man/validate_arg_preference_order.Rd |only collinear-3.0.0/collinear/man/validate_arg_quiet.Rd |only collinear-3.0.0/collinear/man/validate_arg_responses.Rd |only collinear-3.0.0/collinear/man/vi.Rd | 10 collinear-3.0.0/collinear/man/vi_predictors.Rd | 8 collinear-3.0.0/collinear/man/vi_predictors_categorical.Rd | 8 collinear-3.0.0/collinear/man/vi_predictors_numeric.Rd | 8 collinear-3.0.0/collinear/man/vi_responses.Rd |only collinear-3.0.0/collinear/man/vi_smol.Rd |only collinear-3.0.0/collinear/man/vif.Rd |only collinear-3.0.0/collinear/man/vif_df.Rd | 100 - collinear-3.0.0/collinear/man/vif_select.Rd | 200 -- collinear-3.0.0/collinear/man/vif_stats.Rd |only collinear-3.0.0/collinear/tests/testthat/test-case_weights.R | 119 + collinear-3.0.0/collinear/tests/testthat/test-collinear.R | 720 ++++++-- collinear-3.0.0/collinear/tests/testthat/test-collinear_select.R |only collinear-3.0.0/collinear/tests/testthat/test-collinear_stats.R |only collinear-3.0.0/collinear/tests/testthat/test-cor_clusters.R | 31 collinear-3.0.0/collinear/tests/testthat/test-cor_cramer.R |only collinear-3.0.0/collinear/tests/testthat/test-cor_df.R | 113 - collinear-3.0.0/collinear/tests/testthat/test-cor_matrix.R | 135 + collinear-3.0.0/collinear/tests/testthat/test-cor_select.R | 128 - collinear-3.0.0/collinear/tests/testthat/test-cor_stats.R |only collinear-3.0.0/collinear/tests/testthat/test-drop_geometry_column.R |only collinear-3.0.0/collinear/tests/testthat/test-f_auto.R |only collinear-3.0.0/collinear/tests/testthat/test-f_auto_rules.R |only collinear-3.0.0/collinear/tests/testthat/test-f_binomial_gam.R |only collinear-3.0.0/collinear/tests/testthat/test-f_binomial_glm.R |only collinear-3.0.0/collinear/tests/testthat/test-f_binomial_rf.R |only collinear-3.0.0/collinear/tests/testthat/test-f_categorical_rf.R |only collinear-3.0.0/collinear/tests/testthat/test-f_count_gam.R |only collinear-3.0.0/collinear/tests/testthat/test-f_count_glm.R |only collinear-3.0.0/collinear/tests/testthat/test-f_count_rf.R |only collinear-3.0.0/collinear/tests/testthat/test-f_functions.R |only collinear-3.0.0/collinear/tests/testthat/test-f_numeric_gam.R |only collinear-3.0.0/collinear/tests/testthat/test-f_numeric_glm.R |only collinear-3.0.0/collinear/tests/testthat/test-f_numeric_rf.R |only collinear-3.0.0/collinear/tests/testthat/test-identify_categorical_variables.R |only collinear-3.0.0/collinear/tests/testthat/test-identify_logical_variables.R |only collinear-3.0.0/collinear/tests/testthat/test-identify_numeric_variables.R |only collinear-3.0.0/collinear/tests/testthat/test-identify_response_type.R |only collinear-3.0.0/collinear/tests/testthat/test-identify_valid_variables.R |only collinear-3.0.0/collinear/tests/testthat/test-identify_zero_variance_variables.R |only collinear-3.0.0/collinear/tests/testthat/test-model_formula.R |only collinear-3.0.0/collinear/tests/testthat/test-preference_order.R | 334 +++- collinear-3.0.0/collinear/tests/testthat/test-print.collinear_output.R |only collinear-3.0.0/collinear/tests/testthat/test-print.collinear_selection.R |only collinear-3.0.0/collinear/tests/testthat/test-score_auc.R |only collinear-3.0.0/collinear/tests/testthat/test-score_cramer.R |only collinear-3.0.0/collinear/tests/testthat/test-score_r2.R |only collinear-3.0.0/collinear/tests/testthat/test-step_collinear.R |only collinear-3.0.0/collinear/tests/testthat/test-summary.collinear_output.R |only collinear-3.0.0/collinear/tests/testthat/test-summary.collinear_selection.R |only collinear-3.0.0/collinear/tests/testthat/test-target_encoding_lab.R | 144 + collinear-3.0.0/collinear/tests/testthat/test-target_encoding_loo.R |only collinear-3.0.0/collinear/tests/testthat/test-target_encoding_mean.R |only collinear-3.0.0/collinear/tests/testthat/test-target_encoding_rank.R |only collinear-3.0.0/collinear/tests/testthat/test-validate_arg_df.R |only collinear-3.0.0/collinear/tests/testthat/test-validate_arg_df_not_null.R |only collinear-3.0.0/collinear/tests/testthat/test-validate_arg_encoding_method.R |only collinear-3.0.0/collinear/tests/testthat/test-validate_arg_f.R |only collinear-3.0.0/collinear/tests/testthat/test-validate_arg_function_name.R |only collinear-3.0.0/collinear/tests/testthat/test-validate_arg_max_cor.R |only collinear-3.0.0/collinear/tests/testthat/test-validate_arg_max_vif.R |only collinear-3.0.0/collinear/tests/testthat/test-validate_arg_predictors.R |only collinear-3.0.0/collinear/tests/testthat/test-validate_arg_preference_order.R |only collinear-3.0.0/collinear/tests/testthat/test-validate_arg_quiet.R |only collinear-3.0.0/collinear/tests/testthat/test-validate_arg_responses.R |only collinear-3.0.0/collinear/tests/testthat/test-vif.R |only collinear-3.0.0/collinear/tests/testthat/test-vif_df.R | 131 - collinear-3.0.0/collinear/tests/testthat/test-vif_select.R | 141 - collinear-3.0.0/collinear/tests/testthat/test-vif_stats.R |only 247 files changed, 5604 insertions(+), 3741 deletions(-)
Title: Karl Broman's R Code
Description: Miscellaneous R functions, including functions related to
graphics (mostly for base graphics), permutation tests, running
mean/median, and general utilities.
Author: Karl W Broman [aut, cre] ,
Aimee Teo Broman [ctb]
Maintainer: Karl W Broman <broman@wisc.edu>
Diff between broman versions 0.90 dated 2025-10-10 and 0.92 dated 2025-12-08
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 5 +++++ data/numbers-cap.RData |binary data/numbers.RData |binary src/normalize.c | 1 - src/runningmean.c | 1 - src/runningratio2.c | 1 - 8 files changed, 16 insertions(+), 14 deletions(-)
Title: Tools for Analyzing Crossover Interference
Description: Analysis of crossover interference in experimental crosses,
particularly regarding the gamma model. See, for example,
Broman and Weber (2000) <doi:10.1086/302923>.
Author: Karl W Broman [aut, cre] ,
Il-Youp Kwak [ctb]
Maintainer: Karl W Broman <broman@wisc.edu>
Diff between xoi versions 0.72 dated 2023-03-22 and 0.74 dated 2025-12-08
DESCRIPTION | 15 ++++++++------- MD5 | 18 +++++++++--------- NEWS.md | 5 +++++ data/bssbsb.RData |binary src/GammaS.h | 1 - src/kfunc.c | 1 - src/kwak_coincidence.c | 1 - src/kwak_get_n_xo.c | 1 - src/kwak_identify.c | 1 - src/kwak_intensity.c | 1 - 10 files changed, 22 insertions(+), 22 deletions(-)
Title: Clinical Trial Style Data Readout Listings
Description: Listings are often part of the submission of clinical trial
data in regulatory settings. We provide a framework for the specific
formatting features often used when displaying large datasets in that
context.
Author: Gabriel Becker [aut] ,
Adrian Waddell [aut],
Joe Zhu [aut, cre] ,
Davide Garolini [aut] ,
Emily de la Rua [aut] ,
Abinaya Yogasekaram [ctb] ,
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Joe Zhu <joe.zhu@roche.com>
Diff between rlistings versions 0.2.12 dated 2025-06-15 and 0.2.13 dated 2025-12-08
DESCRIPTION | 19 ++-- MD5 | 44 +++++------ NAMESPACE | 2 NEWS.md | 5 + R/rlistings.R | 50 +++++++----- R/rlistings_methods.R | 45 +++++++++-- inst/WORDLIST | 2 inst/doc/col_formatting.html | 91 +++++++++++------------ inst/doc/large_list.R | 20 +++-- inst/doc/large_list.Rmd | 21 +++-- inst/doc/large_list.html | 79 +++++++++++--------- inst/doc/pagination.html | 7 + inst/doc/ref_footnotes.html | 7 + inst/doc/rlistings.html | 33 ++++---- man/listing_methods.Rd | 16 ++-- man/listings.Rd | 7 + man/make_row_df-listing_df-method.Rd | 13 ++- man/matrix_form-listing_df-method.Rd | 13 ++- man/vec_nlines.Rd | 15 +++ tests/testthat/test-listings.R | 129 ++++++++++++++++++++++++++++++--- tests/testthat/test-paginate_listing.R | 37 +++++++++ tests/testthat/test-print.R | 44 ++++++----- vignettes/large_list.Rmd | 21 +++-- 23 files changed, 496 insertions(+), 224 deletions(-)
Title: Estimating the Number of Essential Genes in a Genome
Description: Estimating the number of essential genes in a genome on
the basis of data from a random transposon mutagenesis experiment,
through the use of a Gibbs sampler.
Lamichhane et al. (2003) <doi:10.1073/pnas.1231432100>.
Author: Karl W Broman [aut, cre]
Maintainer: Karl W Broman <broman@wisc.edu>
Diff between negenes versions 1.2 dated 2025-05-11 and 1.4 dated 2025-12-08
DESCRIPTION | 10 ++--- MD5 | 10 ++--- NEWS.md | 5 ++ build/partial.rdb |binary data/Mtb80.RData |binary src/negenes.c | 94 +++++++++++++++++++++++++----------------------------- 6 files changed, 60 insertions(+), 59 deletions(-)
Title: m-Out-of-n Bootstrap Functions
Description: Functions and examples based on the m-out-of-n bootstrap suggested by
Politis, D.N. and Romano, J.P. (1994) <doi:10.1214/aos/1176325770>.
Additionally there are functions to estimate the scaling factor tau
and the subsampling size m. For a detailed description and a full list
of references, see Dalitz, C. and Lögler, F. (2025)
<doi:10.32614/RJ-2025-031>.
Author: Christoph Dalitz [aut, cre],
Felix Loegler [aut]
Maintainer: Christoph Dalitz <christoph.dalitz@hs-niederrhein.de>
Diff between moonboot versions 1.0.1 dated 2025-02-21 and 2.0.1 dated 2025-12-08
Changelog | 19 ++++++++++++ DESCRIPTION | 12 ++++---- MD5 | 26 ++++++++--------- R/distpower.R | 2 - R/moonboot.R | 78 ++++++++++++++++++++++++++++++---------------------- R/sherman.R | 6 ++-- README.md | 6 ++-- build/partial.rdb |binary inst/CITATION | 16 ++++++---- man/distPower.Rd | 2 - man/estimate.m.Rd | 11 ++++--- man/estimate.tau.Rd | 17 ++++++----- man/mboot.Rd | 4 +- man/mboot.ci.Rd | 20 +++++++++---- 14 files changed, 133 insertions(+), 86 deletions(-)
Title: An Accurate kNN Implementation with Multiple Distance Measures
Description: Similarly to the 'FNN' package, this package allows calculation of the k nearest neighbors (kNN) of a data matrix.
The implementation is based on cover trees introduced by
Alina Beygelzimer, Sham Kakade, and John Langford (2006) <doi:10.1145/1143844.1143857>.
Author: Philipp Angerer [cre, aut] ,
David Crane [cph, aut]
Maintainer: Philipp Angerer <philipp.angerer@helmholtz-muenchen.de>
Diff between knn.covertree versions 1.0 dated 2019-10-28 and 1.1 dated 2025-12-08
DESCRIPTION | 14 +++++++------- MD5 | 13 +++++++------ R/knn.covertree-package.r | 3 +-- README.md | 10 ++++++---- build |only man/knn.Rd | 10 ++++++++-- man/knn.covertree-package.Rd | 21 +++++++++++++++++++-- src/RcppExports.cpp | 5 +++++ 8 files changed, 53 insertions(+), 23 deletions(-)
Title: Fair Gated Algorithm for Targeted Equity
Description: Tools for training and analysing fairness-aware gated neural
networks for subgroup-aware prediction and interpretation in clinical datasets.
Methods draw on prior work in mixture-of-experts neural networks by
Jordan and Jacobs (1994) <doi:10.1007/978-1-4471-2097-1_113>,
fairness-aware learning by Hardt, Price, and Srebro (2016) <doi:10.48550/arXiv.1610.02413>,
and personalised treatment prediction for depression by Iniesta, Stahl, and McGuffin (2016)
<doi:10.1016/j.jpsychires.2016.03.016>.
Author: Rhys Holland [aut, cre],
Raquel Iniesta [aut]
Maintainer: Rhys Holland <rhys.holland@icloud.com>
Diff between fairGATE versions 0.1.0 dated 2025-11-19 and 0.1.1 dated 2025-12-08
DESCRIPTION | 17 +++++++++----- MD5 | 4 +-- inst/doc/introduction-to-fairGATE.html | 40 ++++++++++++++++----------------- 3 files changed, 34 insertions(+), 27 deletions(-)
Title: Ecological Inference in 2x2 Tables
Description: Implements the Bayesian and likelihood methods proposed in Imai, Lu, and Strauss (2008 <doi:10.1093/pan/mpm017>) and (2011 <doi:10.18637/jss.v042.i05>) for ecological inference in 2 by 2 tables as well as the method of bounds introduced by Duncan and Davis (1953). The package fits both parametric and nonparametric models using either the Expectation-Maximization algorithms (for likelihood models) or the Markov chain Monte Carlo algorithms (for Bayesian models). For all models, the individual-level data can be directly incorporated into the estimation whenever such data are available. Along with in-sample and out-of-sample predictions, the package also provides a functionality which allows one to quantify the effect of data aggregation on parameter estimation and hypothesis testing under the parametric likelihood models.
Author: Kosuke Imai [aut, cre],
Ying Lu [aut],
Aaron Strauss [aut],
Hubert Jin [ctb]
Maintainer: Kosuke Imai <imai@Harvard.Edu>
Diff between eco versions 4.0-5 dated 2025-10-23 and 4.0-6 dated 2025-12-08
ChangeLog | 1 + DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ src/fintegrate.c | 2 +- src/gibbsEM.c | 2 +- src/rand.c | 2 +- src/vector.c | 2 +- 7 files changed, 15 insertions(+), 14 deletions(-)
Title: Extracting and Visualizing Bayesian Graphical Models
Description: Fit and visualize the results of a Bayesian analysis of networks commonly found in psychology.
The package supports fitting cross-sectional network models fitted using the packages 'BDgraph', 'bgms' and 'BGGM',
as well as network comparison fitted using the 'bgms' and 'BBGM'.
The package provides the parameter estimates, posterior inclusion probabilities, inclusion Bayes factor, and the
posterior density of the parameters. In addition, for 'BDgraph' and 'bgms' it allows to assess the posterior
structure space. Furthermore, the package comes with an extensive suite for visualizing results.
Author: Karoline Huth [aut, cre] ,
Sara Keetelaar [ctb],
Nikola Sekulovski [ctb],
Gali Geller [ctb]
Maintainer: Karoline Huth <k.huth@uva.nl>
Diff between easybgm versions 0.2.1 dated 2024-10-17 and 0.3.1 dated 2025-12-08
easybgm-0.2.1/easybgm/R/sparse_dense.R |only easybgm-0.2.1/easybgm/man/sparse_or_dense.Rd |only easybgm-0.2.1/easybgm/tests/testthat/_snaps |only easybgm-0.3.1/easybgm/DESCRIPTION | 29 - easybgm-0.3.1/easybgm/MD5 | 58 +- easybgm-0.3.1/easybgm/NAMESPACE | 20 easybgm-0.3.1/easybgm/R/AuxiliaryFunctions.R | 319 +++++++------- easybgm-0.3.1/easybgm/R/bgm_plot_class.R | 118 ++--- easybgm-0.3.1/easybgm/R/easybgm.R | 92 ++-- easybgm-0.3.1/easybgm/R/easybgm_compare.R |only easybgm-0.3.1/easybgm/R/functions.bdgraph.R | 43 + easybgm-0.3.1/easybgm/R/functions.bggm.R | 9 easybgm-0.3.1/easybgm/R/functions.bggmcompare.R |only easybgm-0.3.1/easybgm/R/functions.bgms.R | 278 ++++++++---- easybgm-0.3.1/easybgm/R/functions.bgmscompare.R |only easybgm-0.3.1/easybgm/R/plottingfunctions.bgmCompare.R |only easybgm-0.3.1/easybgm/R/plottingfunctions.bgms.R | 99 +++- easybgm-0.3.1/easybgm/R/plottingfunctions.easybgm.R | 249 +++++++++- easybgm-0.3.1/easybgm/R/summary.easybgm.R | 255 ++++++++--- easybgm-0.3.1/easybgm/R/summary.easybgm_compare.R |only easybgm-0.3.1/easybgm/man/HDI.Rd | 4 easybgm-0.3.1/easybgm/man/centrality.Rd | 12 easybgm-0.3.1/easybgm/man/clusterBayesfactor.Rd |only easybgm-0.3.1/easybgm/man/complexity_probs.Rd | 2 easybgm-0.3.1/easybgm/man/easybgm.Rd | 48 +- easybgm-0.3.1/easybgm/man/easybgm_compare.Rd |only easybgm-0.3.1/easybgm/man/edgeevidence.Rd | 11 easybgm-0.3.1/easybgm/man/network.Rd | 2 easybgm-0.3.1/easybgm/man/print.easybgm_compare.Rd |only easybgm-0.3.1/easybgm/man/prior_sensitivity.Rd | 8 easybgm-0.3.1/easybgm/man/structure.Rd | 2 easybgm-0.3.1/easybgm/man/structure_probs.Rd | 2 easybgm-0.3.1/easybgm/man/summary.easybgm.Rd | 6 easybgm-0.3.1/easybgm/man/summary.easybgm_compare.Rd |only easybgm-0.3.1/easybgm/tests/testthat/Rplots.pdf |binary easybgm-0.3.1/easybgm/tests/testthat/test-easybgm.R | 385 +++++++++++------ 36 files changed, 1410 insertions(+), 641 deletions(-)
Title: Create Scale Linkage Scores
Description: Perform a 'probabilistic' linkage of two data files using a scaling procedure using the methods described in Goldstein, H., Harron, K. and Cortina-Borja, M. (2017) <doi:10.1002/sim.7287>.
Author: Chris Charlton [aut, cre],
Harvey Goldstein [aut]
Maintainer: Chris Charlton <c.charlton@bristol.ac.uk>
Diff between Scalelink versions 1.0 dated 2019-02-20 and 1.0-2 dated 2025-12-08
DESCRIPTION | 12 ++++++------ MD5 | 18 +++++++++--------- NEWS | 8 ++++++++ R/pkgname.R | 5 ++--- man/Scalelink.Rd | 6 ++---- man/calcScores.Rd | 10 ++++++++-- src/Makevars | 1 - src/Makevars.win | 1 - src/RcppExports.cpp | 5 +++++ src/rcpp_build_astar.cpp | 5 ++--- 10 files changed, 42 insertions(+), 29 deletions(-)
Title: An Interface to the Nexus Class Library
Description: An interface to the Nexus Class Library which allows parsing
of NEXUS, Newick and other phylogenetic tree file formats. It provides
elements of the file that can be used to build phylogenetic objects
such as ape's 'phylo' or phylobase's 'phylo4(d)'. This functionality
is demonstrated with 'read_newick_phylo()' and 'read_nexus_phylo()'.
Author: Francois Michonneau [aut, cre] ,
Ben Bolker [aut] ,
Mark Holder [aut] ,
Paul Lewis [aut] ,
Brian O'Meara [aut]
Maintainer: Francois Michonneau <francois.michonneau@gmail.com>
Diff between rncl versions 0.8.7 dated 2023-01-08 and 0.8.8 dated 2025-12-08
DESCRIPTION | 20 +++++++++--------- MD5 | 18 ++++++++-------- NAMESPACE | 1 NEWS.md | 4 +++ R/collapse_singles.R | 1 R/rncl-package.R | 3 -- R/rncl.R | 36 ++++++++++++++------------------- README.md | 7 +++--- build/partial.rdb |binary man/rncl.Rd | 55 ++++++++++++++++++++++++++++++++------------------- 10 files changed, 79 insertions(+), 66 deletions(-)
Title: Tools for Highfrequency Data Analysis
Description: Provide functionality to manage, clean and match highfrequency
trades and quotes data, calculate various liquidity measures, estimate and
forecast volatility, detect price jumps and investigate microstructure noise and intraday
periodicity. A detailed vignette can be found in the open-access paper
"Analyzing Intraday Financial Data in R: The highfrequency Package"
by Boudt, Kleen, and Sjoerup (2022, <doi:10.18637/jss.v104.i08>).
Author: Kris Boudt [aut, cre] ,
Jonathan Cornelissen [aut],
Scott Payseur [aut],
Giang Nguyen [ctb],
Onno Kleen [aut] ,
Emil Sjoerup [aut]
Maintainer: Kris Boudt <kris.boudt@ugent.be>
Diff between highfrequency versions 1.0.1 dated 2023-10-04 and 1.0.2 dated 2025-12-08
highfrequency-1.0.1/highfrequency/man/MDtest.Rd |only highfrequency-1.0.1/highfrequency/man/RBPCov_bi.Rd |only highfrequency-1.0.1/highfrequency/man/cholCovrMRCov.Rd |only highfrequency-1.0.2/highfrequency/DESCRIPTION | 14 - highfrequency-1.0.2/highfrequency/MD5 | 75 +++--- highfrequency-1.0.2/highfrequency/NEWS.md | 6 highfrequency-1.0.2/highfrequency/R/HARmodel.R | 4 highfrequency-1.0.2/highfrequency/R/HEAVYmodel.R | 2 highfrequency-1.0.2/highfrequency/R/dataHandling.R | 15 - highfrequency-1.0.2/highfrequency/R/driftBursts.R | 4 highfrequency-1.0.2/highfrequency/R/internalRealizedMeasures.R | 51 +--- highfrequency-1.0.2/highfrequency/R/internalSpotVolAndDrift.R | 24 -- highfrequency-1.0.2/highfrequency/R/liquidityMeasures.R | 2 highfrequency-1.0.2/highfrequency/R/realizedMeasures.R | 13 - highfrequency-1.0.2/highfrequency/R/spotVolAndDrift.R | 114 +++++----- highfrequency-1.0.2/highfrequency/man/AJjumpTest.Rd | 2 highfrequency-1.0.2/highfrequency/man/HARmodel.Rd | 2 highfrequency-1.0.2/highfrequency/man/HEAVYmodel.Rd | 2 highfrequency-1.0.2/highfrequency/man/ReMeDI.Rd | 2 highfrequency-1.0.2/highfrequency/man/ReMeDIAsymptoticVariance.Rd | 2 highfrequency-1.0.2/highfrequency/man/aggregatePrice.Rd | 2 highfrequency-1.0.2/highfrequency/man/businessTimeAggregation.Rd | 2 highfrequency-1.0.2/highfrequency/man/driftBursts.Rd | 2 highfrequency-1.0.2/highfrequency/man/getLiquidityMeasures.Rd | 2 highfrequency-1.0.2/highfrequency/man/getTradeDirection.Rd | 2 highfrequency-1.0.2/highfrequency/man/plot.DBH.Rd | 4 highfrequency-1.0.2/highfrequency/man/plot.HARmodel.Rd | 2 highfrequency-1.0.2/highfrequency/man/plot.HEAVYmodel.Rd | 2 highfrequency-1.0.2/highfrequency/man/predict.HARmodel.Rd | 2 highfrequency-1.0.2/highfrequency/man/print.DBH.Rd | 4 highfrequency-1.0.2/highfrequency/man/quotesCleanup.Rd | 2 highfrequency-1.0.2/highfrequency/man/rQPVar.Rd | 2 highfrequency-1.0.2/highfrequency/man/rSemiCov.Rd | 2 highfrequency-1.0.2/highfrequency/man/rTSCov.Rd | 2 highfrequency-1.0.2/highfrequency/man/rThresholdCov.Rd | 9 highfrequency-1.0.2/highfrequency/man/spotDrift.Rd | 18 - highfrequency-1.0.2/highfrequency/man/spotVol.Rd | 75 +++--- highfrequency-1.0.2/highfrequency/tests/testthat/Rplots.pdf |binary highfrequency-1.0.2/highfrequency/tests/testthat/tests_models.R | 8 highfrequency-1.0.2/highfrequency/tests/testthat/tests_spotvol_and_drift.R | 2 40 files changed, 241 insertions(+), 237 deletions(-)
Title: Circular Visualization
Description: Circular layout is an efficient way for the visualization of huge
amounts of information. Here this package provides an implementation
of circular layout generation in R as well as an enhancement of available
software. The flexibility of the package is based on the usage of low-level
graphics functions such that self-defined high-level graphics can be easily
implemented by users for specific purposes. Together with the seamless
connection between the powerful computational and visual environment in R,
it gives users more convenience and freedom to design figures for
better understanding complex patterns behind multiple dimensional data.
The package is described in Gu et al. 2014 <doi:10.1093/bioinformatics/btu393>.
Author: Zuguang Gu [aut, cre]
Maintainer: Zuguang Gu <z.gu@dkfz.de>
Diff between circlize versions 0.4.16 dated 2024-02-20 and 0.4.17 dated 2025-12-08
DESCRIPTION | 14 - LICENSE | 2 MD5 | 48 +++--- NAMESPACE | 7 NEWS | 20 ++ R/chordDiagram.R | 9 - R/circos.heatmap.R | 36 ++++ R/genomic.R | 15 + R/global.R | 1 R/link.R | 42 ++--- R/low_level.R | 271 ++++++++++++++++++++++++++++++----- R/plot.R | 9 - R/utils.R | 198 +++++++++++++++++++++++++ build/vignette.rds |binary inst/CITATION | 24 +-- inst/doc/circlize.Rmd | 10 - inst/doc/circlize.html | 221 ++++++++++++++++++++++++++-- man/chordDiagram.Rd | 183 +++++++++++++++-------- man/circos.dendrogram.Rd | 3 man/circos.heatmap.get.x.Rd |only man/circos.initializeWithIdeogram.Rd | 2 man/circos.raster.Rd | 3 man/circos.rect.Rd | 3 man/circos.stackedText.Rd |only man/circos.trackPlotRegion.Rd | 2 vignettes/circlize.Rmd | 10 - 26 files changed, 929 insertions(+), 204 deletions(-)
Title: Perform HTTP Requests and Process the Responses
Description: Tools for creating and modifying HTTP requests, then
performing them and processing the results. 'httr2' is a modern
re-imagining of 'httr' that uses a pipe-based interface and solves
more of the problems that API wrapping packages face.
Author: Hadley Wickham [aut, cre],
Posit Software, PBC [cph, fnd],
Maximilian Girlich [ctb]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between httr2 versions 1.2.1 dated 2025-07-22 and 1.2.2 dated 2025-12-08
DESCRIPTION | 14 +-- MD5 | 73 ++++++++--------- NAMESPACE | 1 NEWS.md | 10 ++ R/iterate-responses.R | 15 ++- R/oauth-flow-auth-code.R | 4 R/otel.R |only R/pooled-request.R | 14 +++ R/req-cache.R | 2 R/req-dry-run.R | 2 R/req-error.R | 7 + R/req-perform-connection.R | 36 ++++++-- R/req-perform.R | 53 +++++++++--- R/req-promise.R | 7 - R/req-throttle.R | 22 ++++- R/req-url.R | 8 - R/url.R | 13 +-- R/zzz.R | 1 README.md | 16 +-- inst/doc/httr2.Rmd | 2 inst/doc/httr2.html | 41 +++++---- man/StreamingBody.Rd | 3 man/req_auth_aws_v4.Rd | 2 man/req_cache.Rd | 2 man/req_oauth_auth_code.Rd | 2 man/resps_successes.Rd | 16 ++- tests/testthat/_snaps/req-perform-connection.md | 10 ++ tests/testthat/test-req-body.R | 2 tests/testthat/test-req-dry-run.R | 2 tests/testthat/test-req-perform-connection.R | 99 ++++++++++++++++++++++++ tests/testthat/test-req-perform-parallel.R | 63 +++++++++++++++ tests/testthat/test-req-perform.R | 92 ++++++++++++++++++++++ tests/testthat/test-req-promise.R | 65 +++++++++++++++ tests/testthat/test-req-throttle.R | 53 ++++++++++++ tests/testthat/test-resp-url.R | 2 tests/testthat/test-resp.R | 1 tests/testthat/test-url.R | 18 ++++ vignettes/httr2.Rmd | 2 38 files changed, 627 insertions(+), 148 deletions(-)
Title: ASCII Formatting for Values and Tables
Description: We provide a framework for rendering complex tables to ASCII,
and a set of formatters for transforming values or sets of values into
ASCII-ready display strings.
Author: Gabriel Becker [aut] ,
Adrian Waddell [aut],
Davide Garolini [aut] ,
Emily de la Rua [aut] ,
Abinaya Yogasekaram [ctb] ,
Joe Zhu [aut, cre] ,
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Joe Zhu <joe.zhu@roche.com>
Diff between formatters versions 0.5.11 dated 2025-04-09 and 0.5.12 dated 2025-12-08
DESCRIPTION | 28 ++++++------ MD5 | 61 +++++++++++++-------------- NAMESPACE | 5 ++ NEWS.md | 8 +++ R/format_value.R | 61 +++++++++++++++++++++++---- R/generics.R | 71 ++++++++++++++++++++++++++++++- R/matrix_form.R | 87 +++++++++++++++++++++++++-------------- R/mpf_exporters.R | 13 +++-- R/pagination.R | 76 +++++++++++++++++++++------------- R/tostring.R | 12 ++--- build/vignette.rds |binary inst/WORDLIST | 3 - inst/doc/formatters.html | 9 ++-- man/MatrixPrintForm.Rd | 7 ++- man/export_as_pdf.Rd | 13 ++++- man/export_as_rtf.Rd | 10 ++++ man/export_as_txt.Rd | 13 ++++- man/format_value.Rd | 13 ++++- man/list_formats.Rd | 7 +++ man/make_row_df.Rd | 15 ++++-- man/matrix_form.Rd | 15 ++++-- man/mpf_to_rtf.Rd | 8 +-- man/obj_round_type.Rd |only man/paginate_indices.Rd | 17 ++++--- man/propose_column_widths.Rd | 13 ++++- man/round_fmt.Rd | 26 +++++++++-- man/test_matrix_form.Rd | 12 ++++- man/tostring.Rd | 8 +-- man/vert_pag_indices.Rd | 17 ++++--- tests/testthat/test-formatters.R | 87 ++++++++++++++++++++++++++++++++++++++- tests/testthat/test-listings.R | 2 tests/testthat/test-pagination.R | 53 +++++++++++++++++++++++ 32 files changed, 582 insertions(+), 188 deletions(-)
Title: Tidy and Geospatial Kernel Smoothing
Description: Extensions of the kernel smoothing functions from the 'ks' package for compatibility with the tidyverse and geospatial ecosystems <doi:10.1007/s00180-024-01543-9>.
Author: Tarn Duong [aut, cre]
Maintainer: Tarn Duong <tarn.duong@gmail.com>
Diff between eks versions 1.1.1 dated 2025-07-08 and 1.1.2 dated 2025-12-08
CHANGELOG | 4 ++++ DESCRIPTION | 12 ++++++------ MD5 | 18 +++++++++--------- NAMESPACE | 2 +- R/prelim.R | 14 +++++++++----- R/sf-ks-prelim.R | 11 ++++++----- build/vignette.rds |binary inst/doc/tidysf_kde.html | 22 ++++++++++++---------- man/contour.Rd | 9 +++++++-- man/tidyst_as_kde.Rd | 1 + 10 files changed, 55 insertions(+), 38 deletions(-)
Title: Fast Best Subset Selection
Description: Extremely efficient toolkit for solving the best subset selection problem <https://www.jmlr.org/papers/v23/21-1060.html>. This package is its R interface. The package implements and generalizes algorithms designed in <doi:10.1073/pnas.2014241117> that exploits a novel sequencing-and-splicing technique to guarantee exact support recovery and globally optimal solution in polynomial times for linear model. It also supports best subset selection for logistic regression, Poisson regression, Cox proportional hazard model, Gamma regression, multiple-response regression, multinomial logistic regression, ordinal regression, Ising model reconstruction <doi:10.1080/01621459.2025.2571245>, (sequential) principal component analysis, and robust principal component analysis. The other valuable features such as the best subset of group selection <doi:10.1287/ijoc.2022.1241> and sure independence screening <doi:10.1111/j.1467-9868.2008.00674.x> are also provided.
Author: Jin Zhu [aut, cre] ,
Zezhi Wang [aut],
Liyuan Hu [aut],
Junhao Huang [aut],
Kangkang Jiang [aut],
Yanhang Zhang [aut],
Borui Tang [aut],
Shiyun Lin [aut],
Junxian Zhu [aut],
Canhong Wen [aut],
Heping Zhang [aut] ,
Xueqin Wang [aut] ,
spectra contribu [...truncated...]
Maintainer: Jin Zhu <zhuj1jqx@gmail.com>
Diff between abess versions 0.4.10 dated 2025-04-05 and 0.4.11 dated 2025-12-08
DESCRIPTION | 24 ++++++++++++------------ MD5 | 20 ++++++++++++-------- NAMESPACE | 2 ++ NEWS.md | 4 ++++ R/abess.R | 2 +- R/abessgraph.R |only R/generate.graph.R |only man/abess-package.Rd | 1 - man/abess.Rd | 2 +- man/generate.bmn.data.Rd |only man/slide.Rd |only src/AlgorithmGLM.h | 4 ++-- src/api.cpp | 27 +++++++++++++++++++-------- 13 files changed, 53 insertions(+), 33 deletions(-)
Title: Odds Ratio Tools for Logistic Regression
Description: Produces odds ratio analyses with comprehensive reporting tools. Generates
plots, summary tables, and diagnostic checks for logistic regression models
fitted with 'glm()' using binomial family. Provides visualisation methods,
formatted reporting tables via 'gt', and tools to assess logistic regression
model assumptions.
Author: Craig Parylo [aut, cre, cph]
Maintainer: Craig Parylo <craig.parylo2@nhs.net>
Diff between plotor versions 0.7.0 dated 2025-07-01 and 0.8.0 dated 2025-12-08
plotor-0.7.0/plotor/tests/testthat/test_data/df_correlated.Rds |only plotor-0.7.0/plotor/tests/testthat/test_data/df_diabetes.Rds |only plotor-0.7.0/plotor/tests/testthat/test_data/df_infert.Rds |only plotor-0.7.0/plotor/tests/testthat/test_data/df_separated.Rds |only plotor-0.7.0/plotor/tests/testthat/test_data/df_streptb.Rds |only plotor-0.7.0/plotor/tests/testthat/test_data/df_titanic.Rds |only plotor-0.7.0/plotor/tests/testthat/test_data/df_triple_outcome.Rds |only plotor-0.7.0/plotor/tests/testthat/test_data/lr_correlated_four.Rds |only plotor-0.7.0/plotor/tests/testthat/test_data/lr_correlated_two.Rds |only plotor-0.7.0/plotor/tests/testthat/test_data/lr_diabetes.Rds |only plotor-0.7.0/plotor/tests/testthat/test_data/lr_infert.Rds |only plotor-0.7.0/plotor/tests/testthat/test_data/lr_separated.Rds |only plotor-0.7.0/plotor/tests/testthat/test_data/lr_streptb.Rds |only plotor-0.7.0/plotor/tests/testthat/test_data/lr_titanic.Rds |only plotor-0.7.0/plotor/tests/testthat/test_data/lr_triple_outcome.Rds |only plotor-0.7.0/plotor/tests/testthat/test_data/nonlr_streptb.Rds |only plotor-0.8.0/plotor/DESCRIPTION | 29 plotor-0.8.0/plotor/LICENSE | 4 plotor-0.8.0/plotor/MD5 | 61 plotor-0.8.0/plotor/NAMESPACE | 14 plotor-0.8.0/plotor/NEWS.md | 299 plotor-0.8.0/plotor/R/gt_extras.R | 806 - plotor-0.8.0/plotor/R/plot_or.R | 4550 ++++++---- plotor-0.8.0/plotor/R/plotor-package.R | 16 plotor-0.8.0/plotor/README.md | 481 - plotor-0.8.0/plotor/build/vignette.rds |binary plotor-0.8.0/plotor/inst/doc/using_plotor.R | 334 plotor-0.8.0/plotor/inst/doc/using_plotor.Rmd | 762 - plotor-0.8.0/plotor/inst/doc/using_plotor.html | 3163 +++--- plotor-0.8.0/plotor/man/check_or.Rd | 84 plotor-0.8.0/plotor/man/figures/README-unnamed-chunk-4-1.png |binary plotor-0.8.0/plotor/man/figures/README-unnamed-chunk-4-1.svg | 2370 ++--- plotor-0.8.0/plotor/man/plot_or.Rd | 123 plotor-0.8.0/plotor/man/plotor-package.Rd | 52 plotor-0.8.0/plotor/man/table_or.Rd | 181 plotor-0.8.0/plotor/tests/testthat.R | 24 plotor-0.8.0/plotor/tests/testthat/helper_generate_data.R |only plotor-0.8.0/plotor/tests/testthat/test-plot_or.R | 536 - plotor-0.8.0/plotor/tests/testthat/test_data/make_test_data.R | 1288 +- plotor-0.8.0/plotor/vignettes/using_plotor.Rmd | 762 - 40 files changed, 8824 insertions(+), 7115 deletions(-)
Title: Population and Evolutionary Genetics Analysis System
Description: Functions for reading, writing, plotting, analysing, and manipulating allelic and haplotypic data, including from VCF files, and for the analysis of population nucleotide sequences and micro-satellites including coalescent analyses, linkage disequilibrium, population structure (Fst, Amova) and equilibrium (HWE), haplotype networks, minimum spanning tree and network, and median-joining networks.
Author: Emmanuel Paradis [aut, cre, cph] ,
Thibaut Jombart [aut, cph] ,
Zhian N. Kamvar [aut, cph] ,
Brian Knaus [aut, cph] ,
Klaus Schliep [aut, cph] ,
Alastair Potts [aut, cph] ,
David Winter [aut, cph]
Maintainer: Emmanuel Paradis <Emmanuel.Paradis@ird.fr>
Diff between pegas versions 1.3 dated 2023-12-13 and 1.4 dated 2025-12-08
DESCRIPTION | 29 ++++++----- MD5 | 48 +++++++++---------- NEWS | 38 +++++++++++++++ R/dist.asd.R | 6 +- R/haplotype.R | 111 ++++++++++++++++++++++++++++++++++++++------- R/mjn.R | 52 ++++++++++++--------- R/zzz.R | 5 +- build/partial.rdb |binary build/vignette.rds |binary inst/doc/PlotHaploNet.R | 46 +++++++++--------- inst/doc/PlotHaploNet.Rnw | 3 - inst/doc/PlotHaploNet.pdf |binary inst/doc/ReadingFiles.pdf |binary man/Fst.Rd | 2 man/alleles2loci.Rd | 2 man/amova.Rd | 3 - man/conversion.Rd | 13 ++--- man/hap.div.Rd | 4 + man/haplotype.Rd | 8 ++- man/hw.test.Rd | 4 - man/jaguar.Rd | 2 man/mst.Rd | 45 ++++++++++++------ man/read.gtx.Rd | 3 - man/utilities.Rd | 2 vignettes/PlotHaploNet.Rnw | 3 - 25 files changed, 295 insertions(+), 134 deletions(-)
Title: Tools for Bayesian Analyses
Description: Provides tools for conducting Bayesian analyses and Bayesian model averaging
(Kass and Raftery, 1995, <doi:10.1080/01621459.1995.10476572>,
Hoeting et al., 1999, <doi:10.1214/ss/1009212519>). The package contains
functions for creating a wide range of prior distribution objects, mixing posterior
samples from 'JAGS' and 'Stan' models, plotting posterior distributions, and etc...
The tools for working with prior distribution span from visualization, generating 'JAGS'
and 'bridgesampling' syntax to basic functions such as rng, quantile, and distribution functions.
Author: Frantisek Bartos [aut, cre]
Maintainer: Frantisek Bartos <f.bartos96@gmail.com>
Diff between BayesTools versions 0.2.22 dated 2025-09-14 and 0.2.23 dated 2025-12-08
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 4 ++++ R/JAGS-diagnostics.R | 7 ++++++- R/model-averaging-plots.R | 8 ++++---- build/partial.rdb |binary inst/doc/ComparisonR.html | 6 +++--- inst/doc/SpikeAndSlab.html | 4 ++-- 8 files changed, 29 insertions(+), 20 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-03-06 0.4.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-03-25 0.2.4
Title: Propensity Score Matching of Non-Binary Treatments
Description: Propensity score matching for non-binary treatments.
Author: Jason Bryer [aut, cre]
Maintainer: Jason Bryer <jason@bryer.org>
Diff between TriMatch versions 1.0.0 dated 2025-04-03 and 1.0.1 dated 2025-12-08
DESCRIPTION | 18 +++++++++--------- MD5 | 27 +++++++++++++++------------ NAMESPACE | 5 ++++- NEWS.md | 5 +++++ R/TriMatch-package.R | 1 - R/ezANOVA.R |only R/ezANOVA_main.R |only R/plot.balance.R | 2 +- R/summary.triangle.matches.R | 2 +- build/vignette.rds |binary inst/doc/TriMatch.R | 16 +++++++--------- inst/doc/TriMatch.Rmd | 10 ++++------ inst/doc/TriMatch.pdf |binary man/ezANOVA.Rd |only man/summary.triangle.matches.Rd | 2 +- vignettes/TriMatch.Rmd | 10 ++++------ 16 files changed, 51 insertions(+), 47 deletions(-)
Title: The Plate Plot for Network Meta-Analysis Results
Description: A graphical display of results from network meta-analysis (NMA).
It is suitable for outcomes like odds ratio (OR), risk ratio (RR),
risk difference (RD) and standardized mean difference (SMD).
It also has an option to visually display and compare
the surface under the cumulative ranking (SUCRA) of different treatments.
Author: Zhenxun Wang [aut, cre],
Lifeng Lin [ctb],
Shanshan Zhao [ctb],
Haitao Chu [ctb]
Maintainer: Zhenxun Wang <wang6795@alumni.umn.edu>
Diff between nmaplateplot versions 1.0.2 dated 2024-04-07 and 1.0.3 dated 2025-12-08
DESCRIPTION | 10 MD5 | 22 NEWS.md | 6 R/nmaplateplot.R | 97 R/pe_text_conversion.R | 87 build/vignette.rds |binary inst/doc/nmaplateplot-intro.R | 118 inst/doc/nmaplateplot-intro.Rmd | 135 inst/doc/nmaplateplot-intro.html |20037 +++++++++++++++++++++++++++++++++++++-- man/nmaplateplot-package.Rd | 2 man/plateplot.Rd | 45 vignettes/nmaplateplot-intro.Rmd | 135 12 files changed, 19573 insertions(+), 1121 deletions(-)
Title: Generalized Gamma Probability Distribution
Description: Density, distribution function, quantile function and random generation for the Generalized Gamma proposed in Stacy, E. W. (1962) <doi:10.1214/aoms/1177704481>.
Author: Matheus H. J. Saldanha [aut, cre],
Adriano K. Suzuki [aut]
Maintainer: Matheus H. J. Saldanha <mhjsaldanha@gmail.com>
Diff between ggamma versions 1.0.1 dated 2019-12-15 and 1.0.2 dated 2025-12-08
ggamma-1.0.1/ggamma/man/ggamma.Rd |only ggamma-1.0.2/ggamma/DESCRIPTION | 11 +++++------ ggamma-1.0.2/ggamma/MD5 | 7 ++++--- ggamma-1.0.2/ggamma/NEWS.md |only ggamma-1.0.2/ggamma/R/ggamma-package.R | 5 +---- ggamma-1.0.2/ggamma/man/ggamma-package.Rd |only 6 files changed, 10 insertions(+), 13 deletions(-)
Title: Construct Reproducible Analytic Data Sets as R Packages
Description: A framework to help construct R data packages in a
reproducible manner. Potentially time consuming processing of raw data
sets into analysis ready data sets is done in a reproducible manner
and decoupled from the usual 'R CMD build' process so that data sets
can be processed into R objects in the data package and the data
package can then be shared, built, and installed by others without the
need to repeat computationally costly data processing. The package
maintains data provenance by turning the data processing scripts into
package vignettes, as well as enforcing documentation and version
checking of included data objects. Data packages can be version
controlled on 'GitHub', and used to share data for manuscripts,
collaboration and reproducible research.
Author: Greg Finak [aut, cph] ,
Paul Obrecht [ctb],
Ellis Hughes [ctb] ,
Jimmy Fulp [ctb],
Marie Vendettuoli [ctb] ,
Dave Slager [ctb, cre] ,
Jason Taylor [ctb],
Kara Woo [rev] ,
William Landau [rev]
Maintainer: Dave Slager <dslager@fredhutch.org>
Diff between DataPackageR versions 0.16.1 dated 2024-09-17 and 0.16.2 dated 2025-12-08
DataPackageR-0.16.1/DataPackageR/R/logger.R |only DataPackageR-0.16.1/DataPackageR/tests/testthat/test-logger.R |only DataPackageR-0.16.2/DataPackageR/DESCRIPTION | 19 +- DataPackageR-0.16.2/DataPackageR/MD5 | 48 ++--- DataPackageR-0.16.2/DataPackageR/NAMESPACE | 14 - DataPackageR-0.16.2/DataPackageR/NEWS.md | 17 + DataPackageR-0.16.2/DataPackageR/R/build.R | 44 +---- DataPackageR-0.16.2/DataPackageR/R/digests.R | 21 -- DataPackageR-0.16.2/DataPackageR/R/load_save.R | 1 DataPackageR-0.16.2/DataPackageR/R/processData.R | 87 +--------- DataPackageR-0.16.2/DataPackageR/R/prompt.R | 1 DataPackageR-0.16.2/DataPackageR/R/skeleton.R | 15 - DataPackageR-0.16.2/DataPackageR/R/use.R | 6 DataPackageR-0.16.2/DataPackageR/R/yamlR.R | 17 - DataPackageR-0.16.2/DataPackageR/README.md | 50 ++--- DataPackageR-0.16.2/DataPackageR/build/vignette.rds |binary DataPackageR-0.16.2/DataPackageR/inst/WORDLIST | 2 DataPackageR-0.16.2/DataPackageR/inst/doc/Using_DataPackageR.Rmd | 6 DataPackageR-0.16.2/DataPackageR/inst/doc/Using_DataPackageR.html | 60 +++--- DataPackageR-0.16.2/DataPackageR/inst/doc/YAML_Configuration_Details.R | 12 - DataPackageR-0.16.2/DataPackageR/inst/doc/YAML_Configuration_Details.html | 21 +- DataPackageR-0.16.2/DataPackageR/man/package_build.Rd | 3 DataPackageR-0.16.2/DataPackageR/tests/testthat/test-data-name-change.R | 5 DataPackageR-0.16.2/DataPackageR/tests/testthat/test-edge-cases.R | 2 DataPackageR-0.16.2/DataPackageR/tests/testthat/test-project-path.R | 2 DataPackageR-0.16.2/DataPackageR/vignettes/Using_DataPackageR.Rmd | 6 26 files changed, 166 insertions(+), 293 deletions(-)
Title: Solutions for Common Problems in Base R
Description: Contains functions for solving commonly encountered problems while
programming in R. This package is intended to provide a lightweight
supplement to Base R, and will be useful for almost any R user.
Author: David Bosak [aut, cre],
Duong Tran [ctb]
Maintainer: David Bosak <dbosak01@gmail.com>
Diff between common versions 1.1.3 dated 2024-04-05 and 1.1.4 dated 2025-12-08
DESCRIPTION | 8 MD5 | 35 +- NAMESPACE | 5 NEWS.md | 6 R/common.R | 2 R/operators.R | 541 +++++++++++++++++++++++++++++++++++++++- README.md | 23 + build/vignette.rds |binary inst/doc/common.R | 2 inst/doc/common.Rmd | 33 +- inst/doc/common.html | 47 ++- man/common.Rd | 2 man/grapes-eq-grapes.Rd | 11 man/grapes-ge-grapes.Rd |only man/grapes-gt-grapes.Rd |only man/grapes-le-grapes.Rd |only man/grapes-lt-grapes.Rd |only man/grapes-ne-grapes.Rd |only man/grapes-p-grapes.Rd | 10 tests/testthat/test-operators.R | 224 ++++++++++++++++ vignettes/common.Rmd | 33 +- 21 files changed, 915 insertions(+), 67 deletions(-)
Title: Aster Models
Description: Aster models (Geyer, Wagenius, and Shaw, 2007,
<doi:10.1093/biomet/asm030>; Shaw, Geyer, Wagenius, Hangelbroek, and
Etterson, 2008, <doi:10.1086/588063>; Geyer, Ridley, Latta, Etterson,
and Shaw, 2013, <doi:10.1214/13-AOAS653>) are exponential family
regression models for life
history analysis. They are like generalized linear models except that
elements of the response vector can have different families (e. g.,
some Bernoulli, some Poisson, some zero-truncated Poisson, some normal)
and can be dependent, the dependence indicated by a graphical structure.
Discrete time survival analysis, life table analysis,
zero-inflated Poisson regression, and
generalized linear models that are exponential family (e. g., logistic
regression and Poisson regression with log link) are special cases.
Main use is for data in which there is survival over discrete time periods
and there is additional data about what happens conditional on survival
(e. g., number of offspring). Uses the ex [...truncated...]
Author: Charles J. Geyer [aut, cre]
Maintainer: Charles J. Geyer <geyer@umn.edu>
Diff between aster versions 1.3-6 dated 2025-10-20 and 1.3-7 dated 2025-12-08
CHANGES | 2 ++ DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- R/reaster.R | 2 +- build/partial.rdb |binary build/vignette.rds |binary inst/doc/delta.pdf |binary inst/doc/linkingTo.pdf |binary inst/doc/re.pdf |binary inst/doc/trunc.pdf |binary inst/doc/tutor.pdf |binary 11 files changed, 17 insertions(+), 15 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-05-02 1.1.1
2025-04-09 1.1.0
2025-01-24 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-11-25 1.0.2
2025-11-23 1.0.1
2023-06-19 0.5.5
2023-03-03 0.3.4
2021-09-23 0.3.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-02-08 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-09-03 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-11-21 0.1.8.17
2024-03-01 0.1.8.10
2023-12-04 0.1.8.6
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-09-30 0.3.0
2022-03-08 0.2.0