Title: Zero-Variance Control Variates
Description: Stein control variates can be used to improve Monte Carlo estimates of expectations when the derivatives of the log target are available. This package implements a variety of such methods, including zero-variance control variates (ZV-CV, Mira et al. (2013) <doi:10.1007/s11222-012-9344-6>), regularised ZV-CV (South et al., 2023 <doi:10.1214/22-BA1328>), control functionals (CF, Oates et al. (2017) <doi:10.1111/rssb.12185>) and semi-exact control functionals (SECF, South et al., 2022 <doi:10.1093/biomet/asab036>). ZV-CV is a parametric approach that is exact for (low order) polynomial integrands with Gaussian targets. CF is a non-parametric alternative that offers better than the standard Monte Carlo convergence rates. SECF has both a parametric and a non-parametric component and it offers the advantages of both for an additional computational cost. Functions for applying ZV-CV and CF to two estimators for the normalising constant of the posterior distribution in [...truncated...]
Author: Leah F. South [aut, cre]
Maintainer: Leah F. South <leah.south@hdr.qut.edu.au>
Diff between ZVCV versions 2.1.2 dated 2022-11-02 and 2.1.3 dated 2025-10-20
DESCRIPTION | 15 +++++----- MD5 | 44 +++++++++++++++---------------- NEWS.md | 10 ++++++- R/Expand_Temperatures.R | 2 - R/RcppExports.R | 10 +++---- R/ZVCV_package.R | 14 +++++----- R/evidence_CTI.R | 2 - R/kernel_methods.R | 62 ++++++++++++++++++++++----------------------- R/zvcv.R | 4 +- man/CF.Rd | 16 +++++------ man/CF_crossval.Rd | 16 +++++------ man/Expand_Temperatures.Rd | 2 - man/K0_fn.Rd | 10 +++---- man/Phi_fn.Rd | 4 +- man/SECF.Rd | 20 +++++++------- man/SECF_crossval.Rd | 20 +++++++------- man/ZVCV_package.Rd | 15 +++++----- man/aSECF.Rd | 16 +++++------ man/aSECF_crossval.Rd | 16 +++++------ man/evidence.Rd | 10 +++---- man/zvcv.Rd | 8 ++--- src/fnToExport.cpp | 10 +++---- src/getPoly.cpp | 7 +++-- 23 files changed, 173 insertions(+), 160 deletions(-)
Title: Test Investment Strategies with English-Like Code
Description: Design, backtest, and analyze portfolio strategies using simple,
English-like function chains. Includes technical indicators, flexible stock
selection, portfolio construction methods (equal weighting, signal weighting,
inverse volatility, hierarchical risk parity), and a compact backtesting
engine for portfolio returns, drawdowns, and summary metrics.
Author: Alberto Pallotta [aut, cre]
Maintainer: Alberto Pallotta <pallottaalberto@gmail.com>
Diff between PortfolioTesteR versions 0.1.2 dated 2025-09-29 and 0.1.3 dated 2025-10-20
PortfolioTesteR-0.1.2/PortfolioTesteR/man/figures |only PortfolioTesteR-0.1.3/PortfolioTesteR/DESCRIPTION | 14 PortfolioTesteR-0.1.3/PortfolioTesteR/MD5 | 114 +- PortfolioTesteR-0.1.3/PortfolioTesteR/NAMESPACE | 17 PortfolioTesteR-0.1.3/PortfolioTesteR/NEWS.md | 102 +- PortfolioTesteR-0.1.3/PortfolioTesteR/R/filters.R | 111 -- PortfolioTesteR-0.1.3/PortfolioTesteR/R/globals.R | 4 PortfolioTesteR-0.1.3/PortfolioTesteR/R/ml.R | 433 ++++++---- PortfolioTesteR-0.1.3/PortfolioTesteR/R/ml_helper.R |only PortfolioTesteR-0.1.3/PortfolioTesteR/R/performance_analytics.R | 429 ++++++--- PortfolioTesteR-0.1.3/PortfolioTesteR/R/utils.R | 406 +++++++++ PortfolioTesteR-0.1.3/PortfolioTesteR/R/weighting.R | 48 - PortfolioTesteR-0.1.3/PortfolioTesteR/README.md | 4 PortfolioTesteR-0.1.3/PortfolioTesteR/build/vignette.rds |binary PortfolioTesteR-0.1.3/PortfolioTesteR/inst/doc/Getting_Started_Advanced.R |only PortfolioTesteR-0.1.3/PortfolioTesteR/inst/doc/Getting_Started_Advanced.Rmd |only PortfolioTesteR-0.1.3/PortfolioTesteR/inst/doc/Getting_Started_Advanced.html |only PortfolioTesteR-0.1.3/PortfolioTesteR/inst/doc/getting-started.R | 2 PortfolioTesteR-0.1.3/PortfolioTesteR/inst/doc/getting-started.Rmd | 11 PortfolioTesteR-0.1.3/PortfolioTesteR/inst/doc/getting-started.html | 13 PortfolioTesteR-0.1.3/PortfolioTesteR/inst/doc/optimization-walkforward.Rmd | 3 PortfolioTesteR-0.1.3/PortfolioTesteR/inst/doc/optimization-walkforward.html | 22 PortfolioTesteR-0.1.3/PortfolioTesteR/inst/examples/cap_exposure_caps.R |only PortfolioTesteR-0.1.3/PortfolioTesteR/inst/examples/demo_quality_momentum_inverse_vol.R | 2 PortfolioTesteR-0.1.3/PortfolioTesteR/inst/examples/demo_regime_hrp_momentum.R | 1 PortfolioTesteR-0.1.3/PortfolioTesteR/inst/examples/demo_wf_full_diagnostics.R | 2 PortfolioTesteR-0.1.3/PortfolioTesteR/inst/examples/limit_positions_selection_basic.R |only PortfolioTesteR-0.1.3/PortfolioTesteR/inst/examples/ml_sequence_gru_pooled.R |only PortfolioTesteR-0.1.3/PortfolioTesteR/inst/examples/ml_tabular_ensemble.R |only PortfolioTesteR-0.1.3/PortfolioTesteR/inst/examples/ml_tabular_xgb_sector_neutral.R |only PortfolioTesteR-0.1.3/PortfolioTesteR/inst/examples/vol_target_momentum_top10_eq.R |only PortfolioTesteR-0.1.3/PortfolioTesteR/man/PortfolioTesteR-package.Rd | 6 PortfolioTesteR-0.1.3/PortfolioTesteR/man/analyze_by_period.Rd |only PortfolioTesteR-0.1.3/PortfolioTesteR/man/analyze_vs_benchmark.Rd | 42 PortfolioTesteR-0.1.3/PortfolioTesteR/man/calculate_daily_values.Rd |only PortfolioTesteR-0.1.3/PortfolioTesteR/man/cap_exposure.Rd | 74 + PortfolioTesteR-0.1.3/PortfolioTesteR/man/combine_scores.Rd | 24 PortfolioTesteR-0.1.3/PortfolioTesteR/man/demo_sector_map.Rd | 35 PortfolioTesteR-0.1.3/PortfolioTesteR/man/download_sp500_sectors.Rd | 2 PortfolioTesteR-0.1.3/PortfolioTesteR/man/join_panels.Rd | 13 PortfolioTesteR-0.1.3/PortfolioTesteR/man/limit_positions.Rd | 52 - PortfolioTesteR-0.1.3/PortfolioTesteR/man/load_mixed_symbols.Rd | 2 PortfolioTesteR-0.1.3/PortfolioTesteR/man/make_labels.Rd | 22 PortfolioTesteR-0.1.3/PortfolioTesteR/man/ml_add_interactions.Rd |only PortfolioTesteR-0.1.3/PortfolioTesteR/man/ml_ic_series_on_scores.Rd |only PortfolioTesteR-0.1.3/PortfolioTesteR/man/ml_make_ensemble.Rd |only PortfolioTesteR-0.1.3/PortfolioTesteR/man/ml_make_model.Rd |only PortfolioTesteR-0.1.3/PortfolioTesteR/man/ml_make_seq_model.Rd |only PortfolioTesteR-0.1.3/PortfolioTesteR/man/ml_panel_op.Rd |only PortfolioTesteR-0.1.3/PortfolioTesteR/man/ml_panel_reduce.Rd |only PortfolioTesteR-0.1.3/PortfolioTesteR/man/ml_plot_ic_roll.Rd |only PortfolioTesteR-0.1.3/PortfolioTesteR/man/ml_prepare_features.Rd |only PortfolioTesteR-0.1.3/PortfolioTesteR/man/panel_lag.Rd | 17 PortfolioTesteR-0.1.3/PortfolioTesteR/man/panel_returns_simple.Rd |only PortfolioTesteR-0.1.3/PortfolioTesteR/man/perf_metrics.Rd |only PortfolioTesteR-0.1.3/PortfolioTesteR/man/portfolio_returns.Rd |only PortfolioTesteR-0.1.3/PortfolioTesteR/man/roll_ic_stats.Rd | 16 PortfolioTesteR-0.1.3/PortfolioTesteR/man/run_example.Rd | 2 PortfolioTesteR-0.1.3/PortfolioTesteR/man/select_top_k_scores_by_group.Rd | 38 PortfolioTesteR-0.1.3/PortfolioTesteR/man/sql_adapter.Rd | 2 PortfolioTesteR-0.1.3/PortfolioTesteR/man/sql_adapter_adjusted.Rd | 2 PortfolioTesteR-0.1.3/PortfolioTesteR/man/tune_ml_backtest.Rd | 114 +- PortfolioTesteR-0.1.3/PortfolioTesteR/man/validate_group_map.Rd | 22 PortfolioTesteR-0.1.3/PortfolioTesteR/man/vol_target.Rd |only PortfolioTesteR-0.1.3/PortfolioTesteR/man/weight_by_risk_parity.Rd | 46 - PortfolioTesteR-0.1.3/PortfolioTesteR/man/wf_sweep_tabular.Rd | 108 +- PortfolioTesteR-0.1.3/PortfolioTesteR/man/yahoo_adapter.Rd | 2 PortfolioTesteR-0.1.3/PortfolioTesteR/tests/testthat/test-ml-helpers.R |only PortfolioTesteR-0.1.3/PortfolioTesteR/vignettes/Getting_Started_Advanced.Rmd |only PortfolioTesteR-0.1.3/PortfolioTesteR/vignettes/getting-started.Rmd | 11 PortfolioTesteR-0.1.3/PortfolioTesteR/vignettes/optimization-walkforward.Rmd | 3 71 files changed, 1610 insertions(+), 783 deletions(-)
More information about PortfolioTesteR at CRAN
Permanent link
Title: Fast Algorithms for Fitting Topic Models and Non-Negative Matrix
Factorizations to Count Data
Description: Implements fast, scalable optimization algorithms for
fitting topic models ("grade of membership" models) and
non-negative matrix factorizations to count data. The methods
exploit the special relationship between the multinomial topic
model (also, "probabilistic latent semantic indexing") and Poisson
non-negative matrix factorization. The package provides tools to
compare, annotate and visualize model fits, including functions to
efficiently create "structure plots" and identify key features in
topics. The 'fastTopics' package is a successor to the
'CountClust' package. For more information, see
<doi:10.48550/arXiv.2105.13440> and
<doi:10.1186/s13059-023-03067-9>. Please also see the GitHub
repository for additional vignettes not included in the package on
CRAN.
Author: Peter Carbonetto [aut, cre],
Kevin Luo [aut],
Kushal Dey [aut],
Joyce Hsiao [ctb],
Abhishek Sarkar [ctb],
Anthony Hung [ctb],
Xihui Lin [ctb],
Paul C. Boutros [ctb],
Minzhe Wang [ctb],
Tracy Ke [ctb],
Eric Weine [ctb],
Matthew Stephens [aut]
Maintainer: Peter Carbonetto <peter.carbonetto@gmail.com>
Diff between fastTopics versions 0.6-192 dated 2024-07-09 and 0.7-30 dated 2025-10-20
DESCRIPTION | 11 +++++----- LICENSE | 2 - MD5 | 35 ++++++++++++++++++++------------- NAMESPACE | 6 +++++ R/annotation_heatmap.R |only R/fit_poisson_nmf.R | 16 ++++++++++----- R/newsgroups.R |only R/structure_plot.R | 28 ++++++++++++++++---------- README.md | 2 - build/vignette.rds |binary data/newsgroups.RData |only inst/doc/relationship.html | 11 +++++----- inst/doc/single_cell_rnaseq_basic.R |only inst/doc/single_cell_rnaseq_basic.Rmd |only inst/doc/single_cell_rnaseq_basic.html |only inst/doc/topics_vs_clusters.html | 6 ++--- man/annotation_heatmap.Rd |only man/fit_poisson_nmf.Rd | 14 +++++++++---- man/newsgroups.Rd |only man/structure_plot.Rd | 19 ++++++++++++++++- src/Makevars | 2 - src/Makevars.win | 2 - vignettes/single_cell_rnaseq_basic.Rmd |only 23 files changed, 103 insertions(+), 51 deletions(-)
Title: Group Sequential Design for Historical Control Trial with
Survival Outcome
Description: It provides functions to design historical controlled trials with survival outcome by group sequential method. The options for interim look boundaries are efficacy only, efficacy & futility or futility only. It also provides the function to monitor the trial for any unplanned look. The package is based on Jianrong Wu, Xiaoping Xiong (2016) <doi:10.1002/pst.1756> and Jianrong Wu, Yimei Li (2020) <doi:10.1080/10543406.2019.1684305>.
Author: Tushar Patni [aut, cre],
Yimei Li [aut],
Jianrong Wu [aut]
Maintainer: Tushar Patni <tushar.patni006@gmail.com>
Diff between HCTDesign versions 0.7.3 dated 2025-08-29 and 0.7.4 dated 2025-10-20
DESCRIPTION | 8 +- MD5 | 40 ++++++------ NAMESPACE | 2 R/EffIM.R | 2 R/FuttIM.R | 2 R/HCT.R | 12 ++- R/IM.R | 2 R/SM.R | 163 ++++++++++++++++++++++++++++----------------------- R/alpha.R | 11 ++- R/beta.R | 11 ++- R/calendar_time.R |only R/sf.R | 2 build/partial.rdb |binary man/EffDesign.Rd | 2 man/EffIM.Rd | 2 man/FutDesign.Rd | 2 man/FutIM.Rd | 2 man/HCTSurvDesign.Rd | 2 man/IM.Rd | 2 man/SM.Rd | 6 - man/calendar_time.Rd |only man/sf.Rd | 2 22 files changed, 156 insertions(+), 119 deletions(-)
More information about SimplicialComplex at CRAN
Permanent link
Title: Extract Data from Professional Volleyball Leagues in North
America
Description: Gather boxscore, play-by-play, and auxiliary data from Major League Volleyball (MLV) <https://provolleyball.com>, League One Volleyball Pro (LOVB Pro) <https://www.lovb.com/pro-league>, and Athletes Unlimited Pro Volleyball <https://auprosports.com/volleyball/> to create a repository of basic and advanced statistics for teams and players.
Author: David Awosoga [aut, cre, cph] ,
Matthew Chow [aut] ,
Ryan Du [aut]
Maintainer: David Awosoga <odo.awosoga@gmail.com>
Diff between rvolleydata versions 1.0.0 dated 2025-09-02 and 1.1.0 dated 2025-10-20
DESCRIPTION | 6 - MD5 | 31 +++++--- NAMESPACE | 4 + NEWS.md | 11 ++- R/lovb.R | 119 +++++++++++++++++++++++++++++++++ R/mlv.R | 123 ++++++++++++++++++++++++++++++++++- README.md | 10 ++ inst/doc/rvolleydata-how-to-use.R | 12 ++- inst/doc/rvolleydata-how-to-use.Rmd | 32 +++++++-- inst/doc/rvolleydata-how-to-use.html | 98 ++++++++++++++++++++++++--- man/figures/logo.svg |only man/load_lovb_player_boxscore.Rd | 58 +++++++++------- man/load_lovb_player_info.Rd |only man/load_lovb_team_boxscore.Rd |only man/load_mlv_player_boxscore.Rd | 59 +++++++++------- man/load_mlv_player_info.Rd |only man/load_mlv_team_boxscore.Rd |only tests/testthat/test_get_data.R | 16 ++-- vignettes/rvolleydata-how-to-use.Rmd | 32 +++++++-- 19 files changed, 501 insertions(+), 110 deletions(-)
Title: Feature Selection
Description: Feature subset selection algorithms modularized in search algorithms and measure utilities.
Author: Alfonso Jimenez-Vilchez [aut, cre],
Francisco Aragon-Royon [aut],
Adan M. Rodriguez [aut],
Antonio Arauzo-Azofra [aut],
Jose Manuel Benitez [aut]
Maintainer: Alfonso Jimenez-Vilchez <i52jivia@uco.es>
This is a re-admission after prior archival of version 2.0.5 dated 2020-11-23
Diff between FSinR versions 2.0.5 dated 2020-11-23 and 2.0.8 dated 2025-10-20
DESCRIPTION | 20 MD5 | 167 ++- NAMESPACE | 1 NEWS |only NEWS.md |only R/Jd.R | 50 - R/LCC.R | 2 R/RFSM.R | 4 R/chi2.R | 4 R/consistency.R | 40 R/determinationCoefficient.R | 2 R/directFeatureSelection.R | 2 R/directSearchGenerator.R | 4 R/discrete.R | 11 R/entropy.R | 28 R/exhaustiveSearch.R | 8 R/fScore.R | 6 R/featureSelection.R | 2 R/filterGenerator.R | 5 R/gini.R | 11 R/hybridFeatureSelection.R | 2 R/hybridSearchGenerator.R | 2 R/localSearch.R | 8 R/mdlc.R | 9 R/metaheuristic.R | 16 R/probabilistic.R | 11 R/relief.R | 389 +++------ R/searchGenerator.R | 4 R/selectIndividualFeatures.R | 24 R/sequentialSelection.R | 33 R/wrapperGenerator.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/FSinR.R | 34 inst/doc/FSinR.html | 601 ++++++++------ inst/doc/methods.R | 12 inst/doc/methods.Rmd | 2 inst/doc/methods.html | 1219 ++++++++++++----------------- man/IEConsistency.Rd | 11 man/IEPConsistency.Rd | 11 man/Jd.Rd | 4 man/LCC.Rd | 2 man/LasVegas.Rd | 9 man/MDLC.Rd | 9 man/ReliefFeatureSetMeasure.Rd | 2 man/antColony.Rd | 4 man/binaryConsistency.Rd | 9 man/breadthFirst.Rd | 4 man/chiSquared.Rd | 2 man/cramer.Rd | 2 man/deepFirst.Rd | 4 man/determinationCoefficient.Rd | 2 man/directFeatureSelection.Rd | 2 man/directSearchAlgorithm.Rd | 4 man/featureSelection.Rd | 2 man/filterEvaluator.Rd | 2 man/fscore.Rd | 2 man/gainRatio.Rd | 10 man/geneticAlgorithm.Rd | 4 man/giniIndex.Rd | 11 man/hillClimbing.Rd | 4 man/hybridFeatureSelection.Rd | 2 man/hybridSearchAlgorithm.Rd | 2 man/is.discrete.Rd |only man/mutualInformation.Rd | 10 man/normalizedRelief.Rd | 2 man/normalizedReliefFeatureSetMeasure.Rd | 2 man/relief.Rd | 2 man/roughsetConsistency.Rd | 9 man/searchAlgorithm.Rd | 4 man/selectDifference.Rd | 4 man/selectKBest.Rd | 4 man/selectPercentile.Rd | 4 man/selectSlope.Rd | 4 man/selectThreshold.Rd | 4 man/selectThresholdRange.Rd | 4 man/sequentialBackwardSelection.Rd | 4 man/sequentialFloatingBackwardSelection.Rd | 4 man/sequentialFloatingForwardSelection.Rd | 6 man/sequentialForwardSelection.Rd | 4 man/simulatedAnnealing.Rd | 4 man/symmetricalUncertain.Rd | 8 man/tabu.Rd | 4 man/whaleOptimization.Rd | 4 man/wrapperEvaluator.Rd | 2 vignettes/methods.Rmd | 2 86 files changed, 1445 insertions(+), 1505 deletions(-)
More information about compIndexBuilder at CRAN
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Title: Design and Analyze Choice-Based Conjoint Experiments
Description: Design and evaluate choice-based conjoint survey experiments. Generate a variety of survey designs, including random designs, frequency-based designs, and D-optimal designs, as well as "labeled" designs (also known as "alternative-specific designs"), designs with "no choice" options, and designs with dominant alternatives removed. Conveniently inspect and compare designs using a variety of metrics, including design balance, overlap, and D-error, and simulate choice data for a survey design either randomly or according to a utility model defined by user-provided prior parameters. Conduct a power analysis for a given survey design by estimating the same model on different subsets of the data to simulate different sample sizes. Bayesian D-efficient designs using the 'cea' and 'modfed' methods are obtained using the 'idefix' package by Traets et al (2020) <doi:10.18637/jss.v096.i03>. Choice simulation and model estimation in power analyses are handled using the 'logitr' package by He [...truncated...]
Author: John Helveston [cre, aut, cph]
Maintainer: John Helveston <john.helveston@gmail.com>
Diff between cbcTools versions 0.6.4 dated 2025-09-23 and 0.7.1 dated 2025-10-20
cbcTools-0.6.4/cbcTools/R/decode.R |only cbcTools-0.6.4/cbcTools/tests/testthat/test_decode.R |only cbcTools-0.7.1/cbcTools/DESCRIPTION | 6 cbcTools-0.7.1/cbcTools/MD5 | 89 - cbcTools-0.7.1/cbcTools/NAMESPACE | 10 cbcTools-0.7.1/cbcTools/NEWS.md | 11 cbcTools-0.7.1/cbcTools/R/choices.R | 69 - cbcTools-0.7.1/cbcTools/R/compare.R | 17 cbcTools-0.7.1/cbcTools/R/depreciated.R |only cbcTools-0.7.1/cbcTools/R/design.R | 165 +- cbcTools-0.7.1/cbcTools/R/design_optim.R | 6 cbcTools-0.7.1/cbcTools/R/encode.R |only cbcTools-0.7.1/cbcTools/R/input_checks.R | 41 cbcTools-0.7.1/cbcTools/R/inspect.R | 288 +++- cbcTools-0.7.1/cbcTools/R/methods.R | 447 +++++- cbcTools-0.7.1/cbcTools/R/power.R | 3 cbcTools-0.7.1/cbcTools/R/util.R | 1 cbcTools-0.7.1/cbcTools/R/validate_design.R |only cbcTools-0.7.1/cbcTools/README.md | 18 cbcTools-0.7.1/cbcTools/build/vignette.rds |binary cbcTools-0.7.1/cbcTools/inst/doc/choices.R | 10 cbcTools-0.7.1/cbcTools/inst/doc/choices.Rmd | 10 cbcTools-0.7.1/cbcTools/inst/doc/choices.html | 264 +-- cbcTools-0.7.1/cbcTools/inst/doc/design.R | 20 cbcTools-0.7.1/cbcTools/inst/doc/design.Rmd | 51 cbcTools-0.7.1/cbcTools/inst/doc/design.html | 727 +++++------ cbcTools-0.7.1/cbcTools/inst/doc/encoding.R |only cbcTools-0.7.1/cbcTools/inst/doc/encoding.Rmd |only cbcTools-0.7.1/cbcTools/inst/doc/encoding.html |only cbcTools-0.7.1/cbcTools/inst/doc/getting-started.R | 2 cbcTools-0.7.1/cbcTools/inst/doc/getting-started.Rmd | 6 cbcTools-0.7.1/cbcTools/inst/doc/getting-started.html | 293 +--- cbcTools-0.7.1/cbcTools/inst/doc/power.R | 26 cbcTools-0.7.1/cbcTools/inst/doc/power.Rmd | 32 cbcTools-0.7.1/cbcTools/inst/doc/power.html | 666 +++++----- cbcTools-0.7.1/cbcTools/man/cbc_decode.Rd | 34 cbcTools-0.7.1/cbcTools/man/cbc_encode.Rd |only cbcTools-0.7.1/cbcTools/man/cbc_inspect.Rd | 2 cbcTools-0.7.1/cbcTools/man/infer_categorical_structure.Rd |only cbcTools-0.7.1/cbcTools/man/infer_encoding.Rd |only cbcTools-0.7.1/cbcTools/man/infer_from_coded_columns.Rd |only cbcTools-0.7.1/cbcTools/man/reconstruct_design_attributes.Rd |only cbcTools-0.7.1/cbcTools/man/validate_design_object.Rd |only cbcTools-0.7.1/cbcTools/man/validate_or_reconstruct.Rd |only cbcTools-0.7.1/cbcTools/tests/testthat/test_choices.R | 31 cbcTools-0.7.1/cbcTools/tests/testthat/test_design.R | 12 cbcTools-0.7.1/cbcTools/tests/testthat/test_encode.R |only cbcTools-0.7.1/cbcTools/tests/testthat/test_inspection.R | 153 -- cbcTools-0.7.1/cbcTools/tests/testthat/test_power.R | 187 -- cbcTools-0.7.1/cbcTools/vignettes/choices.Rmd | 10 cbcTools-0.7.1/cbcTools/vignettes/design.Rmd | 51 cbcTools-0.7.1/cbcTools/vignettes/encoding.Rmd |only cbcTools-0.7.1/cbcTools/vignettes/getting-started.Rmd | 6 cbcTools-0.7.1/cbcTools/vignettes/power.Rmd | 32 54 files changed, 2042 insertions(+), 1754 deletions(-)
Title: Calculation of the Water Deficit Index (WDI) and the Evaporative
Fraction (EF) on Rasters
Description: Provides functions to calculate the Water Deficit Index (WDI) and
the Evaporative Fraction (EF) using geospatial raster data such as fractional
vegetation cover (FVC) and surface-air temperature difference (TS-TA).
The package automates regression-based edge fitting and produces continuous
spatial maps of surface moisture and evaporative dynamics.
Author: Gaelle Hamelin [aut, cre]
Maintainer: Gaelle Hamelin <gaelle.hamelin@institut-agro.fr>
Diff between wdiEF versions 1.0.3 dated 2025-02-19 and 1.0.4 dated 2025-10-20
DESCRIPTION | 29 +++++++++---- MD5 | 10 ++-- NAMESPACE | 1 NEWS.md | 5 -- R/calculate_EF.R | 115 +++++++++++++++++++++--------------------------------- R/calculate_WDI.R | 101 ++++++++++++++++++++--------------------------- 6 files changed, 117 insertions(+), 144 deletions(-)
Title: Immunoglobulin Somatic Hypermutation Analysis
Description: Provides a computational framework for analyzing mutations in
immunoglobulin (Ig) sequences. Includes methods for Bayesian estimation of
antigen-driven selection pressure, mutational load quantification, building of
somatic hypermutation (SHM) models, and model-dependent distance calculations.
Also includes empirically derived models of SHM for both mice and humans.
Citations:
Gupta and Vander Heiden, et al (2015) <doi:10.1093/bioinformatics/btv359>,
Yaari, et al (2012) <doi:10.1093/nar/gks457>,
Yaari, et al (2013) <doi:10.3389/fimmu.2013.00358>,
Cui, et al (2016) <doi:10.4049/jimmunol.1502263>.
Author: Mohamed Uduman [aut],
Namita Gupta [aut],
Susanna Marquez [aut, cre],
Julian Zhou [aut],
Nima Nouri [aut],
Noah Yann Lee [aut],
Ang Cui [ctb],
Jason Vander Heiden [aut],
Gur Yaari [aut],
Steven Kleinstein [aut, cph]
Maintainer: Susanna Marquez <susanna.marquez@yale.edu>
Diff between shazam versions 1.2.0 dated 2023-10-02 and 1.3.0 dated 2025-10-20
shazam-1.2.0/shazam/vignettes/Baseline-Vignette.md |only shazam-1.3.0/shazam/DESCRIPTION | 16 - shazam-1.3.0/shazam/MD5 | 111 ++++----- shazam-1.3.0/shazam/NAMESPACE | 1 shazam-1.3.0/shazam/NEWS.md | 56 ++++- shazam-1.3.0/shazam/R/Baseline.R | 56 ++--- shazam-1.3.0/shazam/R/Core.R | 10 shazam-1.3.0/shazam/R/Deprecated.R | 2 shazam-1.3.0/shazam/R/DistToNearest.R | 167 ++++++++++----- shazam-1.3.0/shazam/R/MutationProfiling.R | 83 +++---- shazam-1.3.0/shazam/R/RegionDefinitions.R | 6 shazam-1.3.0/shazam/R/RegionsExtend.R | 12 - shazam-1.3.0/shazam/R/Shazam.R | 9 shazam-1.3.0/shazam/R/Shmulate.R | 12 - shazam-1.3.0/shazam/R/TargetingModels.R | 44 +-- shazam-1.3.0/shazam/README.md | 10 shazam-1.3.0/shazam/build/partial.rdb |binary shazam-1.3.0/shazam/build/vignette.rds |binary shazam-1.3.0/shazam/inst/CITATION | 11 shazam-1.3.0/shazam/inst/doc/Baseline-Vignette.R | 100 ++++---- shazam-1.3.0/shazam/inst/doc/Baseline-Vignette.Rmd | 4 shazam-1.3.0/shazam/inst/doc/Baseline-Vignette.pdf |binary shazam-1.3.0/shazam/inst/doc/DistToNearest-Vignette.R | 14 - shazam-1.3.0/shazam/inst/doc/DistToNearest-Vignette.Rmd | 2 shazam-1.3.0/shazam/inst/doc/DistToNearest-Vignette.pdf |binary shazam-1.3.0/shazam/inst/doc/Mutation-Vignette.R | 38 +-- shazam-1.3.0/shazam/inst/doc/Mutation-Vignette.Rmd | 42 +-- shazam-1.3.0/shazam/inst/doc/Mutation-Vignette.pdf |binary shazam-1.3.0/shazam/inst/doc/Shmulate-Vignette.Rmd | 2 shazam-1.3.0/shazam/inst/doc/Shmulate-Vignette.pdf |binary shazam-1.3.0/shazam/inst/doc/Targeting-Vignette.R | 42 +-- shazam-1.3.0/shazam/inst/doc/Targeting-Vignette.Rmd | 2 shazam-1.3.0/shazam/inst/doc/Targeting-Vignette.pdf |binary shazam-1.3.0/shazam/man/Baseline-class.Rd | 2 shazam-1.3.0/shazam/man/IMGT_SCHEMES.Rd | 6 shazam-1.3.0/shazam/man/TargetingModel-class.Rd | 2 shazam-1.3.0/shazam/man/calcObservedMutations.Rd | 4 shazam-1.3.0/shazam/man/collapseClones.Rd | 8 shazam-1.3.0/shazam/man/createBaseline.Rd | 2 shazam-1.3.0/shazam/man/createMutabilityMatrix.Rd | 6 shazam-1.3.0/shazam/man/createSubstitutionMatrix.Rd | 6 shazam-1.3.0/shazam/man/createTargetingModel.Rd | 6 shazam-1.3.0/shazam/man/distToNearest.Rd | 17 - shazam-1.3.0/shazam/man/expectedMutations.Rd | 2 shazam-1.3.0/shazam/man/observedMutations.Rd | 4 shazam-1.3.0/shazam/man/plotBaselineDensity.Rd | 2 shazam-1.3.0/shazam/man/plotBaselineSummary.Rd | 2 shazam-1.3.0/shazam/man/shazam-package.Rd | 3 shazam-1.3.0/shazam/man/shazam.Rd | 3 shazam-1.3.0/shazam/man/shmulateSeq.Rd | 9 shazam-1.3.0/shazam/man/slideWindowTunePlot.Rd | 2 shazam-1.3.0/shazam/man/testBaseline.Rd | 6 shazam-1.3.0/shazam/vignettes/Baseline-Vignette.Rmd | 4 shazam-1.3.0/shazam/vignettes/DistToNearest-Vignette.Rmd | 2 shazam-1.3.0/shazam/vignettes/Mutation-Vignette.Rmd | 42 +-- shazam-1.3.0/shazam/vignettes/Shmulate-Vignette.Rmd | 2 shazam-1.3.0/shazam/vignettes/Targeting-Vignette.Rmd | 2 57 files changed, 558 insertions(+), 438 deletions(-)
Title: Viral Quasispecies Comparison from Long-Read Sequencing Data
Description: Performs variety of viral quasispecies diversity analyses [see Pamornchainavakul et al. (2024) <doi:10.21203/rs.3.rs-4637890/v1>] based on long-read sequence alignment. Main functions include 1) sequencing error and other noise minimization and read sampling, 2) Single nucleotide variant (SNV) profiles comparison, and 3) viral quasispecies profiles comparison and visualization.
Author: Nakarin Pamornchainavakul [aut, cre]
Maintainer: Nakarin Pamornchainavakul <pamornakarin@gmail.com>
Diff between longreadvqs versions 0.1.3 dated 2024-08-26 and 0.1.4 dated 2025-10-20
DESCRIPTION | 20 ++++++++++---------- MD5 | 30 +++++++++++++++--------------- NAMESPACE | 2 +- NEWS.md | 7 +++++++ R/AAcompare.R | 9 +++++++-- R/otucompare.R | 7 ++++++- R/pctopt.R | 1 - R/vqsassess.R | 6 +++--- R/vqscompare.R | 11 ++++++++--- R/vqscustompct.R | 6 +++--- R/vqsresub.R | 4 ++-- R/vqssub.R | 6 +++--- README.md | 2 +- build/partial.rdb |binary build/vignette.rds |binary inst/doc/longreadvqs-vignette.html | 22 +++++++++++----------- 16 files changed, 77 insertions(+), 56 deletions(-)
Title: Fast Data Summary Reports
Description: Generates an RMarkdown data report with two components:
a summary of an input dataset and a diff of the dataset relative to an old version.
Author: Bryant Cong [aut, cre]
Maintainer: Bryant Cong <bryant.bcp@gmail.com>
Diff between datareportR versions 0.1 dated 2025-10-16 and 0.1.1 dated 2025-10-20
datareportR-0.1.1/datareportR/DESCRIPTION | 6 +++--- datareportR-0.1.1/datareportR/MD5 | 10 +++------- datareportR-0.1.1/datareportR/R/render_data_report.R | 2 +- datareportR-0.1.1/datareportR/README.md | 8 +++++++- datareportR-0.1/datareportR/inst |only datareportR-0.1/datareportR/tests |only 6 files changed, 14 insertions(+), 12 deletions(-)
Title: Hierarchical Heatmaps
Description: Allows users to create high-quality heatmaps from labelled, hierarchical data. Specifically, for data with a two-level hierarchical structure, it will produce a heatmap where each row and column represents a category at the lower level. These rows and columns are then grouped by the higher-level group each category belongs to, with the names for each category and groups shown in the margins. While other packages (e.g. 'dendextend') allow heatmap rows and columns to be arranged by groups only, 'hhmR' also allows the labelling of the data at both the category and group level.
Author: Michael Mahony [cre, aut, cph] ,
Francisco Rowe [aut] ,
Carmen Cabrera-Arnau [aut]
Maintainer: Michael Mahony <michael.mahony@cantab.net>
Diff between hhmR versions 0.0.1 dated 2025-01-14 and 0.0.1.1 dated 2025-10-20
DESCRIPTION | 17 MD5 | 12 build/vignette.rds |binary data/example_migration.RData |binary data/example_time_series.RData |binary inst/doc/hhmR_overview.R | 2136 ++++++++++++++++++++--------------------- inst/doc/hhmR_overview.html | 1743 ++++++++++++++++----------------- 7 files changed, 1955 insertions(+), 1953 deletions(-)
Title: Scale Invariant Probabilistic Neural Networks
Description: Scale invariant version of the original PNN proposed by Specht (1990) <doi:10.1016/0893-6080(90)90049-q> with the added functionality of allowing for smoothing along multiple dimensions while accounting for covariances within the data set. It is written in the R statistical programming language. Given a data set with categorical variables, we use this algorithm to estimate the probabilities of a new observation vector belonging to a specific category. This type of neural network provides the benefits of fast training time relative to backpropagation and statistical generalization with only a small set of known observations.
Author: Romin Ebrahimi [aut, cre]
Maintainer: Romin Ebrahimi <romin.ebrahimi@utexas.edu>
Diff between spnn versions 1.2.1 dated 2020-01-08 and 1.3.0 dated 2025-10-20
DESCRIPTION | 14 +++++++++----- MD5 | 15 ++++++++------- NEWS | 9 ++++++++- README.md |only build/partial.rdb |binary man/spnn-package.Rd | 8 ++++---- src/Makevars | 13 +++---------- src/Makevars.win | 13 +++---------- src/cpp-internal.cpp | 2 +- 9 files changed, 36 insertions(+), 38 deletions(-)
Title: Time Series and Econometric Modeling
Description: Time series analysis, (dis)aggregation and manipulation, e.g. time series extension, merge, projection, lag, lead, delta, moving and cumulative average and product, selection by index, date and year-period, conversion to daily, monthly, quarterly, (semi)annually. Simultaneous equation models definition, estimation, simulation and forecasting with coefficient restrictions, error autocorrelation, exogenization, add-factors, impact and interim multipliers analysis, conditional equation evaluation, rational expectations, endogenous targeting and model renormalization, structural stability, stochastic simulation and forecast, optimal control.
Author: Andrea Luciani [aut, cre] ,
Roberto Stok [aut],
Bank of Italy [cph]
Maintainer: Andrea Luciani <andrea.luciani@bancaditalia.it>
Diff between bimets versions 4.0.4 dated 2025-05-28 and 4.1.0 dated 2025-10-20
DESCRIPTION | 8 MD5 | 42 +-- NEWS.md | 8 R/bimets_ts_functions.R | 581 +++++++++++++++++++++++++++++++++++++++++- R/sysdata.rda |binary README.md | 15 + build/vignette.rds |binary data/FRB__MCAP__WP__MODEL.rda |binary data/FRB__MODEL.rda |binary data/LONGBASE.rda |binary inst/doc/bimets.R | 164 ++++++----- inst/doc/bimets.Rnw | 32 ++ inst/doc/bimets.pdf |binary inst/doc/frb2bimets.pdf |binary man/BIMETS2CSV.Rd |only man/CSV2BIMETS.Rd |only man/as.bimets.Rd | 2 man/bimets-package.Rd | 34 ++ man/bimetsConf.Rd | 2 man/fromBIMETStoTS.Rd | 2 man/fromBIMETStoXTS.Rd | 2 man/idxOver.Rd | 2 vignettes/bimets.Rnw | 32 ++ 23 files changed, 824 insertions(+), 102 deletions(-)
Title: Numerical Methods and Optimization in Finance
Description: Functions, examples and data from the first and
the second edition of "Numerical Methods and Optimization in
Finance" by M. Gilli, D. Maringer and E. Schumann (2019,
ISBN:978-0128150658). The package provides implementations
of optimisation heuristics (Differential Evolution, Genetic
Algorithms, Particle Swarm Optimisation, Simulated Annealing
and Threshold Accepting), and other optimisation tools, such
as grid search and greedy search. There are also functions
for the valuation of financial instruments such as bonds and
options, for portfolio selection and functions that help
with stochastic simulations.
Author: Enrico Schumann [aut, cre]
Maintainer: Enrico Schumann <es@enricoschumann.net>
Diff between NMOF versions 2.10-1 dated 2024-11-03 and 2.11-0 dated 2025-10-20
DESCRIPTION | 11 +++++----- MD5 | 44 ++++++++++++++++++++-------------------- NAMESPACE | 14 ++++++++++-- NEWS | 43 +++++++++++++++++++++++++++------------ R/market_data.R | 37 ++++++++++++++++++++++++++------- R/portfolio.R | 2 + R/probBO.R |only README.md | 3 ++ build/partial.rdb |binary build/vignette.rds |binary inst/doc/An_overview.pdf |binary inst/doc/DEnss.pdf |binary inst/doc/LSqueens.pdf |binary inst/doc/LSselect.pdf |binary inst/doc/PSlms.pdf |binary inst/doc/TAportfolio.pdf |binary inst/doc/portfolio.pdf |binary inst/doc/qTableEx.pdf |binary inst/doc/repair.pdf |binary inst/doc/vectorise.pdf |binary inst/unitTests/test_results.txt | 30 +++++++++++++-------------- man/French.Rd | 5 ++++ man/PBO.Rd |only man/Ritter.Rd | 22 +++++++------------- 24 files changed, 132 insertions(+), 79 deletions(-)
Title: Many Data on State and State-Like Actors in the International
System
Description: Comprehensively identifying states and state-like actors is difficult.
This package provides data on states and state-like entities in the international system across time.
The package combines and cross-references several existing datasets consistent with the aims and functions of the manydata package.
It also includes functions for identifying state references in text, and for generating fictional state names.
Author: James Hollway [cre, aut, ctb] ,
Bernhard Bieri [ctb] ,
Mylan Evrard [ctb] ,
Esther Peev [ctb] ,
Henrique Sposito [ctb] ,
Jael Tan [ctb]
Maintainer: James Hollway <james.hollway@graduateinstitute.ch>
Diff between manystates versions 1.0.2 dated 2025-10-14 and 1.0.3 dated 2025-10-20
DESCRIPTION | 8 - MD5 | 12 +- NEWS.md | 13 ++ R/generate_states.R | 162 ++++++++++++---------------------- README.md | 20 +++- man/generate_states.Rd | 25 +---- tests/testthat/test-generate_states.R | 2 7 files changed, 106 insertions(+), 136 deletions(-)
Title: Enhanced R Package for 'GEMPACK' .har and .sl4 Files
Description: Provides tools for processing and analyzing .har and .sl4 files, making it easier
for 'GEMPACK' users and 'GTAP' researchers to handle large economic datasets.
It simplifies the management of multiple experiment results, enabling faster
and more efficient comparisons without complexity. Users can extract, restructure,
and merge data seamlessly, ensuring compatibility across different tools.
The processed data can be exported and used in 'R', 'Stata', 'Python', 'Julia', or
any software that supports Text, CSV, or 'Excel' formats.
Author: Pattawee Puangchit [aut, cre]
Maintainer: Pattawee Puangchit <ppuangch@purdue.edu>
Diff between HARplus versions 1.1.0 dated 2025-10-19 and 1.1.2 dated 2025-10-20
HARplus-1.1.0/HARplus/inst/docs/HARplus_1.1.0.pdf |only HARplus-1.1.2/HARplus/DESCRIPTION | 6 - HARplus-1.1.2/HARplus/MD5 | 27 ++++-- HARplus-1.1.2/HARplus/NAMESPACE | 5 + HARplus-1.1.2/HARplus/R/save_har.R | 79 +++++++++++++++++-- HARplus-1.1.2/HARplus/R/shock_cal.R |only HARplus-1.1.2/HARplus/README.md | 50 +++++++++++- HARplus-1.1.2/HARplus/inst/doc/introduction.R | 6 - HARplus-1.1.2/HARplus/inst/doc/introduction.Rmd | 13 +-- HARplus-1.1.2/HARplus/inst/doc/introduction.html | 25 ++---- HARplus-1.1.2/HARplus/inst/docs/HARplus_1.1.2.pdf |only HARplus-1.1.2/HARplus/inst/extdata/baserate.har |only HARplus-1.1.2/HARplus/man/create_calc_config.Rd |only HARplus-1.1.2/HARplus/man/create_initial_config.Rd |only HARplus-1.1.2/HARplus/man/create_target_config.Rd |only HARplus-1.1.2/HARplus/man/save_har.Rd | 37 ++++++++ HARplus-1.1.2/HARplus/man/shock_calculate.Rd |only HARplus-1.1.2/HARplus/man/shock_calculate_uniform.Rd |only HARplus-1.1.2/HARplus/vignettes/introduction.Rmd | 13 +-- 19 files changed, 208 insertions(+), 53 deletions(-)
Title: A Combined Interaction Test for Unreplicated Two-Way Tables
Description: There are several non-functional-form-based interaction tests for testing interaction in unreplicated two-way layouts. However, no single test can detect all patterns of possible interaction and the tests are sensitive to a particular pattern of interaction. This package combines six non-functional-form-based interaction tests for testing additivity. These six tests were proposed by Boik (1993) <doi:10.1080/02664769300000004>, Piepho (1994), Kharrati-Kopaei and Sadooghi-Alvandi (2007) <doi:10.1080/03610920701386851>, Franck et al. (2013) <doi:10.1016/j.csda.2013.05.002>, Malik et al. (2016) <doi:10.1080/03610918.2013.870196> and Kharrati-Kopaei and Miller (2016) <doi:10.1080/00949655.2015.1057821>. The p-values of these six tests are combined by Bonferroni, Sidak, Jacobi polynomial expansion, and the Gaussian copula methods to provide researchers with a testing approach which leverages many existing methods to detect disparate forms of non-additivity. This [...truncated...]
Author: Zahra Shenavari [aut],
Hossein Haghbin [aut, cre] ,
Mahmood Kharrati-Kopaei [aut] ,
Seyed Morteza Najibi [aut]
Maintainer: Hossein Haghbin <haghbin@pgu.ac.ir>
Diff between combinIT versions 2.0.0 dated 2022-10-21 and 2.0.1 dated 2025-10-20
DESCRIPTION | 14 ++++++++------ MD5 | 9 +++++---- NEWS.md | 34 ++++++++++++++++++++++++++++++++++ README.md |only src/Makevars | 15 +++------------ src/Makevars.win | 6 +++++- 6 files changed, 55 insertions(+), 23 deletions(-)
Title: Arbitrary Dimensional Clifford Algebras
Description: A suite of routines for Clifford algebras, using the
'Map' class of the Standard Template Library. Canonical
reference: Hestenes (1987, ISBN 90-277-1673-0, "Clifford algebra
to geometric calculus"). Special cases including Lorentz transforms,
quaternion multiplication, and Grassmann algebra, are discussed.
Vignettes presenting conformal geometric algebra, quaternions and
split quaternions, dual numbers, and Lorentz transforms are
included. The package follows 'disordR' discipline.
Author: Robin K. S. Hankin [aut, cre]
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between clifford versions 1.1-1 dated 2025-05-07 and 1.1-2 dated 2025-10-20
DESCRIPTION | 6 - MD5 | 112 ++++++++++++------- NEWS.md | 13 ++ R/clifford.R | 177 +++++++++++++++---------------- R/print.R | 2 build/partial.rdb |binary build/vignette.rds |binary data/dot.rda |binary inst/CITATION | 11 - inst/doc/clifford.R | 14 +- inst/doc/clifford.Rnw | 6 - inst/doc/clifford.pdf |binary inst/doc/complex_clifford.R |only inst/doc/complex_clifford.Rmd |only inst/doc/complex_clifford.html |only inst/doc/conformal_algebra_clifford.R |only inst/doc/conformal_algebra_clifford.Rmd |only inst/doc/conformal_algebra_clifford.html |only inst/doc/cramer_clifford.R |only inst/doc/cramer_clifford.Rmd |only inst/doc/cramer_clifford.html |only inst/doc/determinants_clifford.R |only inst/doc/determinants_clifford.Rmd |only inst/doc/determinants_clifford.html |only inst/doc/getcoeffs.R |only inst/doc/getcoeffs.Rmd |only inst/doc/getcoeffs.html |only inst/doc/lorentz_clifford.Rmd | 4 inst/doc/lorentz_clifford.html | 26 ++-- inst/doc/pauli_clifford.R |only inst/doc/pauli_clifford.Rmd |only inst/doc/pauli_clifford.html |only inst/doc/pseudoscalar.R |only inst/doc/pseudoscalar.Rmd |only inst/doc/pseudoscalar.html |only inst/doc/quaternion_clifford.R |only inst/doc/quaternion_clifford.Rmd |only inst/doc/quaternion_clifford.html |only inst/doc/signature.Rmd | 8 - inst/doc/signature.html | 24 ++-- inst/dot.Rmd | 2 inst/hankin_aaca_revision3.tex |only inst/nectarines.Rmd | 2 man/Ops.clifford.Rd | 32 ++--- man/cartan.Rd | 4 man/clifford-package.Rd | 10 + man/const.Rd | 14 +- man/dot.Rd | 2 man/grade.Rd | 4 man/horner.Rd | 4 man/lowlevel.Rd | 4 man/magnitude.Rd | 3 man/numeric_to_clifford.Rd | 4 man/print.Rd | 7 - man/rcliff.Rd | 10 - man/signature.Rd | 14 +- man/term.Rd | 1 man/vector.Rd | 4 man/zap.Rd | 4 src/clifford.cpp | 64 ++++++++--- src/clifford.h | 48 ++++---- tests/testthat/test_aak.R |only vignettes/clifford.Rnw | 6 - vignettes/clifford.bib | 48 ++++++++ vignettes/complex_clifford.Rmd |only vignettes/conformal_algebra_clifford.Rmd |only vignettes/cramer_clifford.Rmd |only vignettes/determinants_clifford.Rmd |only vignettes/getcoeffs.Rmd |only vignettes/lorentz_clifford.Rmd | 4 vignettes/pauli_clifford.Rmd |only vignettes/pseudoscalar.Rmd |only vignettes/quaternion_clifford.Rmd |only vignettes/signature.Rmd | 8 - 74 files changed, 420 insertions(+), 286 deletions(-)
Title: Maximum Likelihood Estimation of Various Univariate and
Multivariate Distributions
Description: Several functions for maximum likelihood estimation of various univariate and multivariate distributions. The list includes more than 100 functions for univariate continuous and discrete distributions, distributions that lie on the real line, the positive line, interval restricted, circular distributions. Further, multivariate continuous and discrete distributions, distributions for compositional and directional data, etc. Some references include Johnson N. L., Kotz S. and Balakrishnan N. (1994). "Continuous Univariate Distributions, Volume 1" <ISBN:978-0-471-58495-7>, Johnson, Norman L. Kemp, Adrianne W. Kotz, Samuel (2005). "Univariate Discrete Distributions". <ISBN:978-0-471-71580-1> and Mardia, K. V. and Jupp, P. E. (2000). "Directional Statistics". <ISBN:978-0-471-95333-3>.
Author: Michail Tsagris [aut, cre],
Sofia Piperaki [aut],
Muhammad Imran [ctb],
Rafail Vargiakakis [aut],
Nikolaos Kontemeniotis [aut]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between MLE versions 1.5 dated 2025-04-03 and 1.6 dated 2025-10-20
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- R/colprop.mle.R | 10 ++++++---- R/colreal.mle.R | 14 +++++++++++++- R/prop.mle.R | 3 +++ R/real.mle.R | 14 ++++++++++++-- man/MLE-package.Rd | 4 ++-- man/colprop.mle.Rd | 2 +- man/prop.mle.Rd | 3 ++- 9 files changed, 51 insertions(+), 23 deletions(-)
Title: A Toolbox for CM SAF NetCDF Data
Description: The Satellite Application Facility on Climate Monitoring (CM SAF)
is a ground segment of the European Organization for the Exploitation of
Meteorological Satellites (EUMETSAT) and one of EUMETSATs Satellite Application
Facilities. The CM SAF contributes to the sustainable monitoring of the climate
system by providing essential climate variables related to the energy and water
cycle of the atmosphere (<https://www.cmsaf.eu>). It is a joint cooperation of eight
National Meteorological and Hydrological Services.
The 'cmsaf' R-package includes a 'shiny' based interface for an easy application of
the 'cmsafops' and 'cmsafvis' packages - the CM SAF R Toolbox. The Toolbox offers an
easy way to prepare, manipulate, analyse and visualize CM SAF NetCDF formatted data.
Other CF conform NetCDF data with time, longitude and latitude dimension should be
applicable, but there is no guarantee for an error-free application.
CM SAF climate data records are provided for free via (<https://wui.cm [...truncated...]
Author: Steffen Kothe [aut, cre],
Danny Parsons [ctb]
Maintainer: Steffen Kothe <Steffen.Kothe@dwd.de>
Diff between cmsaf versions 3.5.2 dated 2024-09-27 and 3.6.0 dated 2025-10-20
DESCRIPTION | 16 +- MD5 | 10 - NEWS.md | 4 inst/toolbox/global.R | 31 ++++ inst/toolbox/server.R | 337 ++++++++++++++++++++++++++++++++++++-------------- inst/toolbox/ui.R | 56 +++++++- 6 files changed, 339 insertions(+), 115 deletions(-)
Title: Strategy Estimation
Description: Variants of strategy estimation (Dal Bo & Frechette, 2011, <doi:10.1257/aer.101.1.411>), including the model with parameters for the choice probabilities of the strategies (Breitmoser, 2015, <doi:10.1257/aer.20130675>), and the model with individual level covariates for the selection of strategies by individuals (Dvorak & Fehrler, 2018, <doi:10.2139/ssrn.2986445>).
Author: Fabian Dvorak [aut, cre]
Maintainer: Fabian Dvorak <fabian.dvorak@uni.kn>
Diff between stratEst versions 1.1.7 dated 2025-04-01 and 1.1.8 dated 2025-10-20
DESCRIPTION | 11 ++++++----- MD5 | 4 ++-- src/stratEst.cpp | 24 ++++++++++++------------ 3 files changed, 20 insertions(+), 19 deletions(-)
Title: Ready-to-Use Omics Formatting, Analysis, and Visualization
Pipeline
Description: Provides a flexible and streamlined pipeline for formatting, analyzing, and
visualizing omics data, regardless of omics type (e.g. transcriptomics, proteomics,
metabolomics). The package includes tools for shaping input data into analysis-ready
structures, fitting linear or mixed-effect models, extracting key contrasts, and
generating a rich variety of ready-to-use publication-quality plots.
Designed for transparency and reproducibility across a wide range of study designs,
with customizable components for statistical modeling.
Author: Laura Martinez-Gili [cre, aut, cph]
Maintainer: Laura Martinez-Gili <martinez.gili.laura@gmail.com>
Diff between readyomics versions 0.1.2 dated 2025-09-18 and 0.2.0 dated 2025-10-20
DESCRIPTION | 6 +- MD5 | 10 +-- NEWS.md | 6 +- R/utils_analysis.R | 106 ++++++++++++++++++++++++++++---------- man/adjust_pval.Rd | 31 +++++++---- tests/testthat/test-adjust_pval.R | 58 ++++++++++++++++++++ 6 files changed, 168 insertions(+), 49 deletions(-)
Title: Approximate Algorithm for Horseshoe Prior
Description: Provides exact and approximate algorithms for the horseshoe prior
in linear regression models, which were proposed by Johndrow et al. (2020)
<https://www.jmlr.org/papers/v21/19-536.html>.
Author: Kang Mingi [aut, cre],
Lee Kyoungjae [aut]
Maintainer: Kang Mingi <leehuimin115@g.skku.edu>
Diff between Mhorseshoe versions 0.1.4 dated 2025-03-16 and 0.1.5 dated 2025-10-20
DESCRIPTION | 10 MD5 | 18 - NEWS.md | 56 ++-- R/approximate_algorithm.R | 506 ++++++++++++++++++++++----------------------- R/exact_algorithm.R | 388 +++++++++++++++++----------------- build/vignette.rds |binary inst/doc/Mhorseshoe.R | 21 - inst/doc/Mhorseshoe.Rmd | 517 ++++++++++++++++++++++------------------------ inst/doc/Mhorseshoe.html | 188 +++++++--------- vignettes/Mhorseshoe.Rmd | 517 ++++++++++++++++++++++------------------------ 10 files changed, 1071 insertions(+), 1150 deletions(-)
Title: Storing, Manipulating and Analysis Spectroscopy and Associated
Data
Description: Stores and eases the manipulation of spectra and associated data,
with dedicated classes for spatial and soil-related data.
Author: Pierre Roudier [aut, cre],
Max Kuhn [ctb],
Kristian Hovde Liland [ctb],
Bjorn-Helge Mevik [ctb],
Hadley Wickham [ctb],
Raphael Viscarra Rossel [dtc]
Maintainer: Pierre Roudier <roudierp@landcareresearch.co.nz>
This is a re-admission after prior archival of version 0.5-4 dated 2023-07-07
Diff between spectacles versions 0.5-4 dated 2023-07-07 and 0.5-5 dated 2025-10-20
DESCRIPTION | 10 MD5 | 30 R/Spectra-methods.R | 2530 +++++++++++++++++------------------ R/SpectraDataFrame-methods.R | 1032 +++++++------- R/australia.R | 10 R/preprocessing.R | 560 +++---- R/spectacles-package.R | 3 build/vignette.rds |binary inst/doc/interfacing-with-caret.R | 220 +-- inst/doc/interfacing-with-caret.html | 1269 ++++++++--------- inst/doc/quickstart.R | 130 - inst/doc/quickstart.html | 1003 ++++++------- man/australia.Rd | 10 man/base_line.Rd | 2 man/continuum_removal.Rd | 2 man/spectacles-package.Rd | 1 16 files changed, 3411 insertions(+), 3401 deletions(-)
Title: Radix Tree and Trie-Based String Distances
Description: A collection of Radix Tree and Trie algorithms for finding similar sequences and calculating sequence distances (Levenshtein and other distance metrics). This work was inspired by a trie implementation in Python: "Fast and Easy Levenshtein distance using a Trie." Hanov (2011) <https://stevehanov.ca/blog/index.php?id=114>.
Author: Travers Ching [aut, cre, cph],
Martin Moene [ctb, cph] ,
Steve Hanov [ctb] ,
Martin Leitner-Ankerl [ctb]
Maintainer: Travers Ching <traversc@gmail.com>
Diff between seqtrie versions 0.2.9 dated 2025-03-02 and 0.3.5 dated 2025-10-20
seqtrie-0.2.9/seqtrie/R/covid_cdr3.r |only seqtrie-0.3.5/seqtrie/ChangeLog | 14 seqtrie-0.3.5/seqtrie/DESCRIPTION | 11 seqtrie-0.3.5/seqtrie/MD5 | 68 seqtrie-0.3.5/seqtrie/R/RadixForest.R | 4 seqtrie-0.3.5/seqtrie/R/RadixTree.R | 38 seqtrie-0.3.5/seqtrie/R/RadixTree_search_helpers.R | 8 seqtrie-0.3.5/seqtrie/R/RcppExports.R | 16 seqtrie-0.3.5/seqtrie/R/covid_cdr3.R |only seqtrie-0.3.5/seqtrie/R/pairwise.R | 19 seqtrie-0.3.5/seqtrie/R/utils.R | 210 - seqtrie-0.3.5/seqtrie/README.md | 159 - seqtrie-0.3.5/seqtrie/build/vignette.rds |binary seqtrie-0.3.5/seqtrie/inst/doc/vignette.R | 56 seqtrie-0.3.5/seqtrie/inst/doc/vignette.html | 481 ++-- seqtrie-0.3.5/seqtrie/inst/doc/vignette.rmd | 47 seqtrie-0.3.5/seqtrie/inst/fix_rd_subsections.R |only seqtrie-0.3.5/seqtrie/inst/include/seqtrie/pairwise.h | 73 seqtrie-0.3.5/seqtrie/inst/include/seqtrie/radixmap.h | 1139 +++++++--- seqtrie-0.3.5/seqtrie/inst/include/seqtrie/utility.h | 15 seqtrie-0.3.5/seqtrie/inst/include/simple_progress/simple_progress.h | 1 seqtrie-0.3.5/seqtrie/man/RadixForest.Rd | 56 seqtrie-0.3.5/seqtrie/man/RadixTree.Rd | 106 seqtrie-0.3.5/seqtrie/man/covid_cdr3.Rd | 2 seqtrie-0.3.5/seqtrie/man/dist_matrix.Rd | 13 seqtrie-0.3.5/seqtrie/man/dist_pairwise.Rd | 13 seqtrie-0.3.5/seqtrie/man/dist_search.Rd | 13 seqtrie-0.3.5/seqtrie/man/generate_cost_matrix.Rd | 23 seqtrie-0.3.5/seqtrie/src/RadixForest.cpp | 13 seqtrie-0.3.5/seqtrie/src/RadixTree.cpp | 82 seqtrie-0.3.5/seqtrie/src/RcppExports.cpp | 49 seqtrie-0.3.5/seqtrie/src/pairwise.cpp | 86 seqtrie-0.3.5/seqtrie/src/seqtrie_types.h | 278 +- seqtrie-0.3.5/seqtrie/tests/test_RadixTree.R | 2 seqtrie-0.3.5/seqtrie/tests/test_pairwise.R | 36 seqtrie-0.3.5/seqtrie/tests/test_single_gap_search.R |only seqtrie-0.3.5/seqtrie/vignettes/vignette.rmd | 47 37 files changed, 1970 insertions(+), 1208 deletions(-)
Title: Joint Inference for Competing Risks Data Using Multiple
Endpoints
Description: Tools for competing risks trials that allow simultaneous inference on
recovery and mortality endpoints. Provides data preparation helpers, standard
cumulative incidence estimators (restricted mean time gained/lost), and severity
weighted extensions that integrate longitudinal ordinal outcomes to summarise
treatment benefit. Methods follow Wen, Hu, and Wang (2023) Biometrics 79(3):1635-1645
<doi:10.1111/biom.13752>.
Author: Wenqing Zhang [aut, cre],
Jiyang Wen [aut],
Chen Hu [aut],
Meicheng Wang [aut]
Maintainer: Wenqing Zhang <wzhan115@jhu.edu>
Diff between jointCompRisk versions 0.1.0 dated 2025-10-14 and 0.1.1 dated 2025-10-20
DESCRIPTION | 9 +++++---- MD5 | 15 ++++++++------- NEWS.md |only R/cif_inference.R | 2 +- R/weighted_cif.R | 2 +- inst/doc/Example_analysis.html | 12 ++++++------ inst/doc/Vignette.Rmd | 6 +++++- inst/doc/Vignette.html | 40 ++++++++++++++++++++++------------------ vignettes/Vignette.Rmd | 6 +++++- 9 files changed, 53 insertions(+), 39 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-05-22 0.3.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-10-20 0.3.0
2020-10-29 0.2.0
2020-09-18 0.1.0
Title: 'WhiteboxTools' R Frontend
Description: An R frontend for the 'WhiteboxTools' library, which is an advanced geospatial data analysis platform developed by Prof. John Lindsay at the University of Guelph's Geomorphometry and Hydrogeomatics Research Group. 'WhiteboxTools' can be used to perform common geographical information systems (GIS) analysis operations, such as cost-distance analysis, distance buffering, and raster reclassification. Remote sensing and image processing tasks include image enhancement (e.g. panchromatic sharpening, contrast adjustments), image mosaicing, numerous filtering operations, simple classification (k-means), and common image transformations. 'WhiteboxTools' also contains advanced tooling for spatial hydrological analysis (e.g. flow-accumulation, watershed delineation, stream network analysis, sink removal), terrain analysis (e.g. common terrain indices such as slope, curvatures, wetness index, hillshading; hypsometric analysis; multi-scale topographic position analysis), and LiDAR data processing. [...truncated...]
Author: Qiusheng Wu [aut],
Andrew Brown [aut, cre]
Maintainer: Andrew Brown <brown.andrewg@gmail.com>
Diff between whitebox versions 2.4.2 dated 2025-10-14 and 2.4.3 dated 2025-10-20
DESCRIPTION | 6 +-- MD5 | 25 ++++++------ NEWS.md | 16 ++++++++ R/wbt.R | 1 R/whitebox-package.R | 55 ++++++++++++++++----------- README.md | 26 ++++++------- inst/CITATION | 4 +- inst/doc/datasets.html | 3 - inst/doc/demo.html | 33 ++++++++-------- inst/doc/wbt-method.html | 59 ++++++++++++++---------------- inst/extdata/DEM.tif |only man/extdata-gis.Rd | 9 +--- man/figures/README-terra-plot-facc-1.jpeg |binary tests/testthat/test-wbt_source.R | 6 +++ 14 files changed, 135 insertions(+), 108 deletions(-)
Title: Simultaneous Inference in General Parametric Models
Description: Simultaneous tests and confidence intervals
for general linear hypotheses in parametric models, including
linear, generalized linear, linear mixed effects, and survival models.
The package includes demos reproducing analyzes presented
in the book "Multiple Comparisons Using R" (Bretz, Hothorn,
Westfall, 2010, CRC Press).
Author: Torsten Hothorn [aut, cre] ,
Frank Bretz [aut],
Peter Westfall [aut],
Richard M. Heiberger [ctb],
Andre Schuetzenmeister [ctb],
Susan Scheibe [ctb]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between multcomp versions 1.4-28 dated 2025-01-29 and 1.4-29 dated 2025-10-20
multcomp-1.4-28/multcomp/inst/doc/multcomp-examples.R |only multcomp-1.4-28/multcomp/inst/doc/multcomp-examples.Rnw |only multcomp-1.4-28/multcomp/inst/doc/multcomp-examples.pdf |only multcomp-1.4-28/multcomp/tests/Examples |only multcomp-1.4-28/multcomp/vignettes/multcomp-examples.Rnw |only multcomp-1.4-29/multcomp/DESCRIPTION | 11 ++--- multcomp-1.4-29/multcomp/MD5 | 32 +++++++-------- multcomp-1.4-29/multcomp/R/print.R | 6 +- multcomp-1.4-29/multcomp/build/vignette.rds |binary multcomp-1.4-29/multcomp/data/cholesterol.rda |binary multcomp-1.4-29/multcomp/data/litter.rda |binary multcomp-1.4-29/multcomp/demo/Ch_Appl.Rout.save |only multcomp-1.4-29/multcomp/demo/Ch_GLM.Rout.save |only multcomp-1.4-29/multcomp/demo/Ch_Intro.Rout.save |only multcomp-1.4-29/multcomp/demo/Ch_Misc.Rout.save |only multcomp-1.4-29/multcomp/demo/Ch_Theory.Rout.save |only multcomp-1.4-29/multcomp/inst/NEWS | 4 + multcomp-1.4-29/multcomp/inst/doc/chfls1.pdf |binary multcomp-1.4-29/multcomp/inst/doc/generalsiminf.pdf |binary multcomp-1.4-29/multcomp/man/fattyacid.Rd | 2 multcomp-1.4-29/multcomp/man/methods.Rd | 2 multcomp-1.4-29/multcomp/man/mmm.Rd | 4 - 22 files changed, 33 insertions(+), 28 deletions(-)
Title: Conditioned Latin Hypercube Sampling
Description: Conditioned Latin hypercube sampling, as published by Minasny and McBratney (2006) <DOI:10.1016/j.cageo.2005.12.009>. This method proposes to stratify sampling in presence of ancillary data. An extension of this method, which propose to associate a cost to each individual and take it into account during the optimisation process, is also proposed (Roudier et al., 2012, <DOI:10.1201/b12728>).
Author: Pierre Roudier [aut, cre],
Colby Brugnard [ctb],
Dylan Beaudette [ctb],
Benjamin Louis [ctb],
Kiri Daust [ctb],
David Clifford [ctb],
Andrew Brown [ctb]
Maintainer: Pierre Roudier <roudierp@landcareresearch.co.nz>
Diff between clhs versions 0.9.0 dated 2021-10-14 and 0.9.2 dated 2025-10-20
DESCRIPTION | 22 + MD5 | 34 +- NAMESPACE | 2 NEWS.md | 40 +-- R/clhs-data.frame.R | 61 +++-- R/clhs-package.R | 2 R/clhs-sf.R | 2 R/clhs-terra.R |only R/similarity.R | 6 README.md | 2 build/vignette.rds |binary inst/CITATION | 20 - inst/doc/intro-clhs.html | 443 +++++++++++++++++++++++++++++---------- man/similarity_buffer.Rd | 5 src/Makevars | 2 src/Makevars.win | 2 tests/testthat/test-clhs-gower.R | 4 tests/testthat/test-spdf.R | 4 tests/testthat/test-terra.R |only 19 files changed, 453 insertions(+), 198 deletions(-)
Title: Working with Audio and Video in R
Description: Bindings to 'FFmpeg' <http://www.ffmpeg.org/> AV library for working with
audio and video in R. Generates high quality video from images or R graphics with
custom audio. Also offers high performance tools for reading raw audio, creating
'spectrograms', and converting between countless audio / video formats. This package
interfaces directly to the C API and does not require any command line utilities.
Author: Jeroen Ooms [aut, cre]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between av versions 0.9.5 dated 2025-08-25 and 0.9.6 dated 2025-10-20
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS | 3 +++ R/fft.R | 4 +++- src/fft.c | 23 ++++++++++++++--------- 5 files changed, 27 insertions(+), 17 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 1.3-5 dated 2025-06-03 and 1.3-6 dated 2025-10-20
CHANGES | 2 ++ DESCRIPTION | 10 +++++----- MD5 | 29 ++++++++++++++++++----------- R/reaster.R | 4 ++-- build/partial.rdb |binary build/vignette.rds |binary data/grey_cloud_2015.rda |only inst/doc/delta.R |only inst/doc/delta.Rnw |only inst/doc/delta.pdf |only inst/doc/linkingTo.pdf |binary inst/doc/re.pdf |binary inst/doc/trunc.pdf |binary inst/doc/tutor.pdf |binary man/aster.Rd | 2 ++ man/grey_cloud_2015.Rd |only man/vcov.Rd | 46 ++++++++++++++++++++++++++++++++++++++++++++++ vignettes/delta.Rnw |only vignettes/rout.rda |only 19 files changed, 75 insertions(+), 18 deletions(-)