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:
2019-09-03 0.1.1
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:
2022-09-30 0.3.0
2022-03-08 0.2.0
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:
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:
2025-11-21 0.1.8.17
2024-03-01 0.1.8.10
2023-12-04 0.1.8.6