Title: Tidy Analysis Tools for Mortality, Fertility, Migration and
Population Data
Description: Analysing vital statistics based on tools
consistent with the tidyverse. Tools are provided for data visualization,
life table calculations, computing net migration numbers, Lee-Carter
modelling; functional data modelling and forecasting.
Author: Rob Hyndman [aut, cre, cph] ,
Sixian Tang [aut] ,
Miles McBain [ctb] ,
Mitchell O'Hara-Wild [ctb]
Maintainer: Rob Hyndman <Rob.Hyndman@monash.edu>
Diff between vital versions 2.0.3 dated 2026-02-12 and 2.1.0 dated 2026-10-04
vital-2.0.3/vital/man/figures/README-coherent-1.png |only vital-2.0.3/vital/man/figures/README-example-1.png |only vital-2.0.3/vital/man/figures/README-example-2.png |only vital-2.0.3/vital/man/figures/README-example-3.png |only vital-2.0.3/vital/man/figures/README-example-4.png |only vital-2.0.3/vital/man/figures/README-example-5.png |only vital-2.0.3/vital/man/figures/README-lc2-1.png |only vital-2.0.3/vital/man/figures/README-pyramid-1.png |only vital-2.0.3/vital/tests/testthat/test_STMOMO.R |only vital-2.1.0/vital/DESCRIPTION | 13 vital-2.1.0/vital/MD5 | 208 +++-- vital-2.1.0/vital/NAMESPACE | 270 ++++--- vital-2.1.0/vital/NEWS.md | 47 - vital-2.1.0/vital/R/FDM.R | 210 ++---- vital-2.1.0/vital/R/LC.R | 224 ++---- vital-2.1.0/vital/R/STMF.R | 106 +-- vital-2.1.0/vital/R/STMOMO.R | 267 ++++--- vital-2.1.0/vital/R/augment.R | 19 vital-2.1.0/vital/R/autoplot.R | 187 +++-- vital-2.1.0/vital/R/collapse_ages.R | 58 - vital-2.1.0/vital/R/components.R | 67 + vital-2.1.0/vital/R/dplyr-verbs-fable.R | 145 +--- vital-2.1.0/vital/R/dplyr-verbs.R | 178 +---- vital-2.1.0/vital/R/dplyr-verbs_models.R | 65 - vital-2.1.0/vital/R/fable.R | 27 vital-2.1.0/vital/R/fabletools.R | 172 ---- vital-2.1.0/vital/R/find_var.R | 15 vital-2.1.0/vital/R/fmean.R | 206 +++-- vital-2.1.0/vital/R/fnaive.R | 198 ++--- vital-2.1.0/vital/R/forecast.R | 195 +++-- vital-2.1.0/vital/R/generate.R | 21 vital-2.1.0/vital/R/globals.R |only vital-2.1.0/vital/R/hfd.R | 6 vital-2.1.0/vital/R/hmd.R | 18 vital-2.1.0/vital/R/interpolate.R | 83 +- vital-2.1.0/vital/R/ktdb.R | 29 vital-2.1.0/vital/R/life_expectancy.R | 18 vital-2.1.0/vital/R/life_table.R | 147 ++-- vital-2.1.0/vital/R/make_pr.R | 143 +--- vital-2.1.0/vital/R/model.R | 136 ++- vital-2.1.0/vital/R/net_migration.R | 122 +-- vital-2.1.0/vital/R/parse.R | 5 vital-2.1.0/vital/R/popsim.R | 385 +++++++---- vital-2.1.0/vital/R/smooth.R | 61 - vital-2.1.0/vital/R/smooth_mortality_law.R | 59 + vital-2.1.0/vital/R/total_fertility_rate.R | 45 - vital-2.1.0/vital/R/transform.R | 9 vital-2.1.0/vital/R/undo_pr.R | 148 +--- vital-2.1.0/vital/R/vital.R | 177 ++--- vital-2.1.0/vital/R/vital_package.R | 30 vital-2.1.0/vital/R/vital_vars.R | 10 vital-2.1.0/vital/README.md | 174 ++-- vital-2.1.0/vital/build/vignette.rds |binary vital-2.1.0/vital/inst/doc/intro.R | 19 vital-2.1.0/vital/inst/doc/intro.Rmd | 34 vital-2.1.0/vital/inst/doc/intro.html | 50 + vital-2.1.0/vital/inst/doc/population_forecasting.Rmd | 38 - vital-2.1.0/vital/inst/doc/population_forecasting.html | 69 + vital-2.1.0/vital/man/FDM.Rd | 7 vital-2.1.0/vital/man/FMEAN.Rd | 9 vital-2.1.0/vital/man/FNAIVE.Rd | 11 vital-2.1.0/vital/man/GAPC.Rd | 14 vital-2.1.0/vital/man/LC.Rd | 15 vital-2.1.0/vital/man/as_vital.Rd | 7 vital-2.1.0/vital/man/autoplot.vital.Rd | 9 vital-2.1.0/vital/man/figures/README-autoplot-1.png |binary vital-2.1.0/vital/man/figures/README-e0-1.png |binary vital-2.1.0/vital/man/figures/README-lc3-1.png |binary vital-2.1.0/vital/man/figures/README-smoothing-1.png |binary vital-2.1.0/vital/man/forecast.Rd | 2 vital-2.1.0/vital/man/generate.Rd | 2 vital-2.1.0/vital/man/generate_population.Rd | 33 vital-2.1.0/vital/man/life_table.Rd | 10 vital-2.1.0/vital/man/make_pr.Rd | 2 vital-2.1.0/vital/man/net_migration.Rd | 11 vital-2.1.0/vital/man/read_hfd.Rd | 2 vital-2.1.0/vital/man/read_hfd_files.Rd | 4 vital-2.1.0/vital/man/read_ktdb.Rd | 2 vital-2.1.0/vital/man/read_stmf.Rd | 19 vital-2.1.0/vital/man/read_stmf_files.Rd | 9 vital-2.1.0/vital/man/reexports.Rd | 4 vital-2.1.0/vital/man/smooth_mortality_law.Rd | 10 vital-2.1.0/vital/man/total_fertility_rate.Rd | 4 vital-2.1.0/vital/man/undo_pr.Rd | 4 vital-2.1.0/vital/man/undo_sd.Rd | 6 vital-2.1.0/vital/man/vital-package.Rd | 1 vital-2.1.0/vital/man/vital_vars.Rd | 2 vital-2.1.0/vital/tests/testthat/Births.txt |only vital-2.1.0/vital/tests/testthat/NORasfrRR.txt |only vital-2.1.0/vital/tests/testthat/test-FDM.R | 250 ++++++- vital-2.1.0/vital/tests/testthat/test-FMEAN.R | 213 ++++++ vital-2.1.0/vital/tests/testthat/test-FNAIVE.R | 174 ++++ vital-2.1.0/vital/tests/testthat/test-LC.R | 271 +++++++ vital-2.1.0/vital/tests/testthat/test-STMOMO.R |only vital-2.1.0/vital/tests/testthat/test-agegroup.R |only vital-2.1.0/vital/tests/testthat/test-as_vital.R |only vital-2.1.0/vital/tests/testthat/test-autoplot.R |only vital-2.1.0/vital/tests/testthat/test-coherent-forecast.R | 51 - vital-2.1.0/vital/tests/testthat/test-coherent.R | 54 + vital-2.1.0/vital/tests/testthat/test-collapse_ages.R | 155 +++- vital-2.1.0/vital/tests/testthat/test-dplyr.R | 198 +++++ vital-2.1.0/vital/tests/testthat/test-hfd.R |only vital-2.1.0/vital/tests/testthat/test-hmd.R | 47 + vital-2.1.0/vital/tests/testthat/test-interpolate.R |only vital-2.1.0/vital/tests/testthat/test-ktdb.R | 30 vital-2.1.0/vital/tests/testthat/test-lifetable.R | 194 +++++ vital-2.1.0/vital/tests/testthat/test-model-parallel.R |only vital-2.1.0/vital/tests/testthat/test-net_migration.R |only vital-2.1.0/vital/tests/testthat/test-popsim.R |only vital-2.1.0/vital/tests/testthat/test-smooth-mortality-law.R | 50 + vital-2.1.0/vital/tests/testthat/test-smooth.R | 110 ++- vital-2.1.0/vital/tests/testthat/test-stmf.R | 57 + vital-2.1.0/vital/tests/testthat/test-tfr.R |only vital-2.1.0/vital/vignettes/intro.Rmd | 34 vital-2.1.0/vital/vignettes/population_forecasting.Rmd | 38 - vital-2.1.0/vital/vignettes/refs.bib | 11 116 files changed, 4517 insertions(+), 2532 deletions(-)
Title: Safe Anytime-Valid Inference
Description: Functions to design and apply tests that are anytime valid. The
functions can be used to design hypothesis tests in the prospective/randomised
control trial setting or in the observational/retrospective setting. The
resulting tests remain valid under both optional stopping and optional
continuation. The current version includes safe t-tests and safe tests of
two proportions. For details on the theory of safe tests, see Ly, A, Boehm,
Grunwald, Ramdas and van Ravenzwaaij (2024). "Safe Anytime-Valid Inference:
Practical maximally flexible sampling designs for experiments based on e-values"
(<doi:10.31234/osf.io/h5vae>) and Grunwald, de Heide
and Koolen (2024) "Safe Testing" (<doi:10.1093/jrsssb/qkae011>), for details
on safe logrank tests see ter Schure, Perez-Ortiz, Ly and Grunwald (2024)
"The Anytime-Valid Logrank Test: Error Control under Continuous Monitoring with
Unlimited Horizon" (<doi:10.51387/24-NEJSDS65>), and Turner, Ly and
Grunwald (2024) "Generic E-variables [...truncated...]
Author: Alexander Ly [cre, aut],
Rosanne Turner [aut],
Yongqi Wang [aut],
Muriel Felipe Perez-Ortiz [ctb],
Udo Boehm [ctb],
Judith ter Schure [ctb],
Peter Grunwald [ctb]
Maintainer: Alexander Ly <alexander.ly.nl@gmail.com>
Diff between safestats versions 0.8.8 dated 2026-09-05 and 0.8.9 dated 2026-10-04
safestats-0.8.8/safestats/tests/testthat/Rplots.pdf |only safestats-0.8.8/safestats/tests/testthat/test-safeLogrankTest.R |only safestats-0.8.8/safestats/vignettes/safeVignetteData/eValueCorrectRejectsT.RData |only safestats-0.8.8/safestats/vignettes/safeVignetteData/eValueFalseRejects2T.RData |only safestats-0.8.8/safestats/vignettes/safeVignetteData/eValueFalseRejectsT.RData |only safestats-0.8.8/safestats/vignettes/safeVignetteData/eValueFalseRejectsTSimple.RData |only safestats-0.8.8/safestats/vignettes/safeVignetteData/eValuesTSimple.RData |only safestats-0.8.8/safestats/vignettes/safeVignetteData/rep2.RData |only safestats-0.8.8/safestats/vignettes/safeVignetteData/rep3.RData |only safestats-0.8.8/safestats/vignettes/safeVignetteData/rep4.RData |only safestats-0.8.8/safestats/vignettes/safeVignetteData/saviTDesignObj.RData |only safestats-0.8.8/safestats/vignettes/safeVignetteData/saviTDesignObj2.RData |only safestats-0.8.8/safestats/vignettes/safeVignetteData/simDeltaTrueIsDeltaMin.RData |only safestats-0.8.8/safestats/vignettes/safeVignetteData/simDeltaTrueLargerDeltaMin.RData |only safestats-0.8.9/safestats/DESCRIPTION | 10 safestats-0.8.9/safestats/MD5 | 154 - safestats-0.8.9/safestats/NAMESPACE | 4 safestats-0.8.9/safestats/NEWS.md | 10 safestats-0.8.9/safestats/R/anova.R |only safestats-0.8.9/safestats/R/helpers.R | 16 safestats-0.8.9/safestats/R/newsafe2x2Test.R |only safestats-0.8.9/safestats/R/safeS3Methods.R | 106 safestats-0.8.9/safestats/R/tTest.R | 19 safestats-0.8.9/safestats/R/zTest.R | 20 safestats-0.8.9/safestats/inst/doc/safestats-vignetteT.R | 220 - safestats-0.8.9/safestats/inst/doc/safestats-vignetteT.Rmd | 215 - safestats-0.8.9/safestats/inst/doc/safestats-vignetteT.html | 1431 ++++------ safestats-0.8.9/safestats/man/checkAndReturnEsMinParameterSide.Rd | 5 safestats-0.8.9/safestats/man/computeBetaBatchSaviZ.Rd | 5 safestats-0.8.9/safestats/man/computeConfidenceInterval2x2LogOdds.Rd |only safestats-0.8.9/safestats/man/computeConfidenceInterval2x2PropDiff.Rd |only safestats-0.8.9/safestats/man/computeConfidenceIntervalZ.Rd | 5 safestats-0.8.9/safestats/man/computeConfidenceSequence2x2LogOdds.Rd |only safestats-0.8.9/safestats/man/computeConfidenceSequence2x2PropDiff.Rd |only safestats-0.8.9/safestats/man/computeConjugateCredibleIntervalTwoSampleT.Rd | 2 safestats-0.8.9/safestats/man/computeEsMinSavi2x2.Rd |only safestats-0.8.9/safestats/man/computeLogrankBetaFrom.Rd | 5 safestats-0.8.9/safestats/man/computeLogrankNEvents.Rd | 5 safestats-0.8.9/safestats/man/computeLogrankZ.Rd | 8 safestats-0.8.9/safestats/man/computeMinEsBatchSaviT.Rd | 5 safestats-0.8.9/safestats/man/computeMinEsBatchSaviZ.Rd | 5 safestats-0.8.9/safestats/man/computeNPlanBatchSaviT.Rd | 5 safestats-0.8.9/safestats/man/computeNPlanBatchSaviZ.Rd | 5 safestats-0.8.9/safestats/man/computeNPlanSavi2x2.Rd |only safestats-0.8.9/safestats/man/computeNPlanSaviT.Rd | 5 safestats-0.8.9/safestats/man/computeNPlanSaviZ.Rd | 5 safestats-0.8.9/safestats/man/computePowerSavi2x2.Rd |only safestats-0.8.9/safestats/man/computePowerSaviT.Rd | 5 safestats-0.8.9/safestats/man/computePowerSaviZ.Rd | 5 safestats-0.8.9/safestats/man/conjugateBfTStat.Rd | 2 safestats-0.8.9/safestats/man/conjugateBfTStatOld.Rd | 2 safestats-0.8.9/safestats/man/designSavi2x2.Rd |only safestats-0.8.9/safestats/man/designSaviLogrank.Rd | 8 safestats-0.8.9/safestats/man/designSaviLogrank2WantBeta.Rd | 8 safestats-0.8.9/safestats/man/designSaviT.Rd | 5 safestats-0.8.9/safestats/man/designSaviT1aWantNPlan.Rd | 5 safestats-0.8.9/safestats/man/designSaviT2WantPower.Rd | 5 safestats-0.8.9/safestats/man/designSaviT3WantEsMin.Rd | 5 safestats-0.8.9/safestats/man/designSaviT3bWantParameter.Rd | 5 safestats-0.8.9/safestats/man/designSaviZ.Rd | 5 safestats-0.8.9/safestats/man/designSaviZ1aWantNPlan.Rd | 5 safestats-0.8.9/safestats/man/designSaviZ2WantPower.Rd | 5 safestats-0.8.9/safestats/man/designSaviZ3WantEsMin.Rd | 5 safestats-0.8.9/safestats/man/designSaviZ3bWantParameter.Rd | 5 safestats-0.8.9/safestats/man/fnchLogPartition.Rd |only safestats-0.8.9/safestats/man/generateSurvData.Rd | 5 safestats-0.8.9/safestats/man/logEValueVec2x2LogOddsEGauss.Rd |only safestats-0.8.9/safestats/man/logEValueVec2x2LogOddsGrow.Rd |only safestats-0.8.9/safestats/man/logEValueVec2x2PropDiffEBeta.Rd |only safestats-0.8.9/safestats/man/logEValueVec2x2PropDiffGrow.Rd |only safestats-0.8.9/safestats/man/logLikelihoodFNCH.Rd |only safestats-0.8.9/safestats/man/logrankSingleEExact.Rd | 5 safestats-0.8.9/safestats/man/logrankSingleZ.Rd | 5 safestats-0.8.9/safestats/man/plot.saviTest.Rd | 7 safestats-0.8.9/safestats/man/predictiveThetas2x2.Rd |only safestats-0.8.9/safestats/man/print.saviTest.Rd | 12 safestats-0.8.9/safestats/man/rLogrank.Rd | 5 safestats-0.8.9/safestats/man/sampleLogrankStoppingTimes.Rd | 5 safestats-0.8.9/safestats/man/sampleStoppingTimesSavi2x2.Rd |only safestats-0.8.9/safestats/man/sampleStoppingTimesSaviT.Rd | 5 safestats-0.8.9/safestats/man/sampleStoppingTimesSaviZ.Rd | 5 safestats-0.8.9/safestats/man/savi2x2TestStat.Rd |only safestats-0.8.9/safestats/man/savi2x2TestStatUmp.Rd |only safestats-0.8.9/safestats/man/saviAnovaOneB.Rd |only safestats-0.8.9/safestats/man/saviAnovaStat.Rd |only safestats-0.8.9/safestats/man/saviLogrankTest.Rd | 10 safestats-0.8.9/safestats/man/saviTTest.Rd | 11 safestats-0.8.9/safestats/man/saviTTestStat.Rd | 63 safestats-0.8.9/safestats/man/saviZTest.Rd | 5 safestats-0.8.9/safestats/man/saviZTestStat.Rd | 5 safestats-0.8.9/safestats/man/solveRIPr2x2PropDiff.Rd |only safestats-0.8.9/safestats/man/solveUmpLogOdds.Rd |only safestats-0.8.9/safestats/man/solveWorstCaseTheta2x2PropDiff.Rd |only safestats-0.8.9/safestats/man/tTestWidthDerivative.Rd | 2 safestats-0.8.9/safestats/tests/testthat/test-savi2x2Helpers.R |only safestats-0.8.9/safestats/tests/testthat/test-saviLogrankTest.R |only safestats-0.8.9/safestats/tests/testthat/test-saviTTestVignette.R |only safestats-0.8.9/safestats/vignettes/safeVignetteData/confSequence1.png |only safestats-0.8.9/safestats/vignettes/safeVignetteData/eValuePath1.png |only safestats-0.8.9/safestats/vignettes/safestats-vignetteT.Rmd | 215 - 100 files changed, 1456 insertions(+), 1259 deletions(-)
Title: Breeding-Related Mixed-Effects Models
Description: Fit relationship-based and customized mixed-effects models with complex variance-covariance structures using the 'lme4' machinery. The core computational algorithms are implemented using the
'Eigen' 'C++' library for numerical linear algebra and 'RcppEigen' 'glue'.
Author: Giovanny Covarrubias-Pazaran [aut, cre]
Maintainer: Giovanny Covarrubias-Pazaran <cova_ruber@live.com.mx>
Diff between lme4breeding versions 1.1.4 dated 2026-09-11 and 1.1.5 dated 2026-10-04
DESCRIPTION | 8 MD5 | 16 - inst/doc/lmebreed.gxe.R | 90 ++++----- inst/doc/lmebreed.gxe.Rmd | 92 ++++----- inst/doc/lmebreed.gxe.html | 390 ++++++++++++++++++--------------------- inst/doc/lmebreed.qg.html | 4 inst/doc/lmebreed.summaries.html | 4 man/lmeb.Rd | 2 vignettes/lmebreed.gxe.Rmd | 92 ++++----- 9 files changed, 334 insertions(+), 364 deletions(-)
Title: Make Data Based on Different Geographies Comparable
Description: Several functions to allow comparisons of data across different geographies, in particular for Canadian census data from different censuses.
Author: Jens von Bergmann [aut, cre]
Maintainer: Jens von Bergmann <jens@mountainmath.ca>
Diff between tongfen versions 0.3.8 dated 2026-08-28 and 0.3.9 dated 2026-10-04
DESCRIPTION | 14 +- MD5 | 105 ++++++++-------- NAMESPACE | 4 NEWS.md | 60 ++++++++- R/helpers.R | 86 +++++++++++-- R/tonfen_deprecated.R | 2 R/tongfen.R | 142 ++++++++++++++------- R/tongfen_anomalies.R |only R/tongfen_ca.R | 103 ++++----------- R/tongfen_ca_deprecated.R | 10 - R/tongfen_ca_estimate.R | 9 - R/tongfen_estimate.R | 57 +++++--- R/tongfen_us.R | 60 +++------ README.md | 19 +- build/stage23.rdb |binary build/vignette.rds |binary inst/doc/polling_districts.html | 13 +- inst/doc/tongfen-ca-estimate.Rmd | 2 inst/doc/tongfen-ca-estimate.html | 4 inst/doc/tongfen.Rmd | 8 - inst/doc/tongfen.html | 16 +- inst/doc/tongfen_anomalies.R |only inst/doc/tongfen_anomalies.Rmd |only inst/doc/tongfen_anomalies.html |only inst/doc/tongfen_ca.html | 8 - inst/doc/tongfen_us.html | 4 man/add_census_ca_base_variables.Rd | 4 man/check_tongfen_areas.Rd | 4 man/check_tongfen_single_areas.Rd | 2 man/estimate_tongfen_correspondence.Rd | 2 man/estimate_tongfen_single_correspondence.Rd | 2 man/get_correspondence_ca_census_for.Rd | 2 man/get_single_correspondence_ca_census_for.Rd | 5 man/get_tongfen_ca_census.Rd | 8 - man/get_tongfen_correspondence_ca_census.Rd | 4 man/get_tongfen_correspondence_us_census.Rd | 3 man/get_tongfen_us_census.Rd | 7 - man/meta_for_additive_variables.Rd | 4 man/meta_for_ca_census_vectors.Rd | 4 man/proportional_reaggregate.Rd | 2 man/tongfen_aggregate.Rd | 15 +- man/tongfen_anomaly_joins.Rd |only man/tongfen_ca_census_ct.Rd | 8 - man/tongfen_detect_anomalies.Rd |only man/tongfen_estimate.Rd | 4 man/tongfen_estimate_ca_census.Rd | 9 - man/tongfen_join_correspondence.Rd |only man/tongfen_join_regions.Rd |only man/tongfen_tag_largest_overlap.Rd | 12 - tests/testthat/test-aggregate.R | 162 +++++++++++++++++++++++++ tests/testthat/test-anomalies.R |only tests/testthat/test-cached-download.R |only tests/testthat/test-correspondence-estimate.R | 35 +++++ tests/testthat/test-estimate.R | 118 ++++++++++++++++++ tests/testthat/test-helpers.R | 15 ++ tests/testthat/test-proportional-reaggregate.R | 60 +++++++++ vignettes/tongfen-ca-estimate.Rmd | 2 vignettes/tongfen.Rmd | 8 - vignettes/tongfen_anomalies.Rmd |only 59 files changed, 887 insertions(+), 340 deletions(-)
Title: Lab for Developing and Testing Recommender Algorithms
Description: Provides a research infrastructure to develop and evaluate
collaborative filtering recommender algorithms. This includes a sparse
representation for user-item matrices, many popular algorithms, top-N recommendations,
and cross-validation. Hahsler (2022) <doi:10.48550/arXiv.2205.12371>.
Author: Michael Hahsler [aut, cre, cph] ,
Bregt Vereet [ctb]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between recommenderlab versions 1.0.7 dated 2025-05-31 and 1.1.0 dated 2026-10-04
recommenderlab-1.0.7/recommenderlab/inst/README_files |only recommenderlab-1.0.7/recommenderlab/inst/doc/recommenderlab.Rnw |only recommenderlab-1.0.7/recommenderlab/inst/doc/recommenderlab.pdf |only recommenderlab-1.0.7/recommenderlab/vignettes/recommenderlab.Rnw |only recommenderlab-1.1.0/recommenderlab/DESCRIPTION | 20 recommenderlab-1.1.0/recommenderlab/MD5 | 146 +- recommenderlab-1.1.0/recommenderlab/NAMESPACE | 6 recommenderlab-1.1.0/recommenderlab/NEWS.md | 23 recommenderlab-1.1.0/recommenderlab/R/AAAoptional.R |only recommenderlab-1.1.0/recommenderlab/R/AllClasses.R | 590 +++++++++- recommenderlab-1.1.0/recommenderlab/R/AllGenerics.R | 44 recommenderlab-1.1.0/recommenderlab/R/HybridRecommender.R | 78 + recommenderlab-1.1.0/recommenderlab/R/RECOM_ALS.R | 4 recommenderlab-1.1.0/recommenderlab/R/RECOM_AR.R | 2 recommenderlab-1.1.0/recommenderlab/R/RECOM_IBCF.R | 6 recommenderlab-1.1.0/recommenderlab/R/RECOM_LIBMF.R | 10 recommenderlab-1.1.0/recommenderlab/R/RECOM_POPULAR.R | 6 recommenderlab-1.1.0/recommenderlab/R/RECOM_RANDOM.R | 3 recommenderlab-1.1.0/recommenderlab/R/RECOM_RERECOMMEND.R | 5 recommenderlab-1.1.0/recommenderlab/R/RECOM_SVD.R | 3 recommenderlab-1.1.0/recommenderlab/R/RECOM_SVDF.R | 3 recommenderlab-1.1.0/recommenderlab/R/Recommender.R | 55 recommenderlab-1.1.0/recommenderlab/R/calcPredictionAccuracy.R | 103 + recommenderlab-1.1.0/recommenderlab/R/data.R |only recommenderlab-1.1.0/recommenderlab/R/dissimilarity.R | 83 + recommenderlab-1.1.0/recommenderlab/R/error.R | 39 recommenderlab-1.1.0/recommenderlab/R/evaluate.R | 119 +- recommenderlab-1.1.0/recommenderlab/R/evaluationScheme.R | 104 + recommenderlab-1.1.0/recommenderlab/R/funkSVD.R | 71 + recommenderlab-1.1.0/recommenderlab/R/normalize.R | 61 + recommenderlab-1.1.0/recommenderlab/R/plot.R | 48 recommenderlab-1.1.0/recommenderlab/R/predict.R | 102 + recommenderlab-1.1.0/recommenderlab/R/ratingMatrix.R | 4 recommenderlab-1.1.0/recommenderlab/R/realRatingMatrix.R | 25 recommenderlab-1.1.0/recommenderlab/R/sparseNAMatrix.R | 68 + recommenderlab-1.1.0/recommenderlab/README.md | 53 recommenderlab-1.1.0/recommenderlab/build/vignette.rds |binary recommenderlab-1.1.0/recommenderlab/inst/doc/recommenderlab.R | 407 ------ recommenderlab-1.1.0/recommenderlab/inst/doc/recommenderlab.Rmd |only recommenderlab-1.1.0/recommenderlab/inst/doc/recommenderlab.html |only recommenderlab-1.1.0/recommenderlab/inst/doc/recommenderlab_vignette.R |only recommenderlab-1.1.0/recommenderlab/inst/doc/recommenderlab_vignette.Rnw |only recommenderlab-1.1.0/recommenderlab/inst/doc/recommenderlab_vignette.pdf |only recommenderlab-1.1.0/recommenderlab/man/HybridRecommender.Rd | 52 recommenderlab-1.1.0/recommenderlab/man/Jester5k.Rd | 36 recommenderlab-1.1.0/recommenderlab/man/MSWeb.Rd | 52 recommenderlab-1.1.0/recommenderlab/man/MovieLense.Rd | 49 recommenderlab-1.1.0/recommenderlab/man/Recommender-class.Rd | 34 recommenderlab-1.1.0/recommenderlab/man/Recommender.Rd | 55 recommenderlab-1.1.0/recommenderlab/man/binaryRatingMatrix-class.Rd | 93 - recommenderlab-1.1.0/recommenderlab/man/calcPredictionAccuracy.Rd | 85 - recommenderlab-1.1.0/recommenderlab/man/dissimilarity.Rd | 83 - recommenderlab-1.1.0/recommenderlab/man/error.Rd | 44 recommenderlab-1.1.0/recommenderlab/man/evaluate.Rd | 88 - recommenderlab-1.1.0/recommenderlab/man/evaluationResultList-class.Rd | 33 recommenderlab-1.1.0/recommenderlab/man/evaluationResults-class.Rd | 41 recommenderlab-1.1.0/recommenderlab/man/evaluationScheme-class.Rd | 39 recommenderlab-1.1.0/recommenderlab/man/evaluationScheme.Rd | 100 - recommenderlab-1.1.0/recommenderlab/man/figures/README-TNR_vs_TPR-1.png |only recommenderlab-1.1.0/recommenderlab/man/funkSVD.Rd | 66 - recommenderlab-1.1.0/recommenderlab/man/getList.Rd | 51 recommenderlab-1.1.0/recommenderlab/man/internal.Rd | 49 recommenderlab-1.1.0/recommenderlab/man/normalize.Rd | 52 recommenderlab-1.1.0/recommenderlab/man/plot.Rd | 69 - recommenderlab-1.1.0/recommenderlab/man/predict.Rd | 70 - recommenderlab-1.1.0/recommenderlab/man/ratingMatrix-class.Rd | 44 recommenderlab-1.1.0/recommenderlab/man/realRatingMatrix-class.Rd | 119 +- recommenderlab-1.1.0/recommenderlab/man/sparseNAMatrix.Rd | 83 - recommenderlab-1.1.0/recommenderlab/man/topNList-class.Rd | 28 recommenderlab-1.1.0/recommenderlab/tests/testthat/test-RECOM_UBCF.R | 19 recommenderlab-1.1.0/recommenderlab/tests/testthat/test-dissimilarity.R | 13 recommenderlab-1.1.0/recommenderlab/tests/testthat/test-eval.R | 4 recommenderlab-1.1.0/recommenderlab/tests/testthat/test-evaluation-split.R |only recommenderlab-1.1.0/recommenderlab/tests/testthat/test-matrix.R | 2 recommenderlab-1.1.0/recommenderlab/tests/testthat/test-optional-recommenders.R |only recommenderlab-1.1.0/recommenderlab/tests/testthat/test-recom.R | 7 recommenderlab-1.1.0/recommenderlab/vignettes/association_rules.bib | 5 recommenderlab-1.1.0/recommenderlab/vignettes/data.bib | 3 recommenderlab-1.1.0/recommenderlab/vignettes/recom_talk.bib | 7 recommenderlab-1.1.0/recommenderlab/vignettes/recommender.bib | 11 recommenderlab-1.1.0/recommenderlab/vignettes/recommenderlab.Rmd |only recommenderlab-1.1.0/recommenderlab/vignettes/recommenderlab_vignette.Rnw |only 82 files changed, 2650 insertions(+), 1227 deletions(-)
More information about recommenderlab at CRAN
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Title: Threshold Model and Unit Root Tests in Cross-Section and Time
Series Data
Description: Threshold model, panel version of Hylleberg et al. (1990) <DOI:10.1016/0304-4076(90)90080-D> seasonal unit root tests, and panel unit root test of Chang (2002) <DOI:10.1016/S0304-4076(02)00095-7>.
Author: Ho Tsung-wu [aut, cre]
Maintainer: Ho Tsung-wu <tsungwu@ntnu.edu.tw>
Diff between pdR versions 1.9.4 dated 2025-08-19 and 1.9.5 dated 2026-10-04
DESCRIPTION | 11 ++++++----- MD5 | 24 ++++++++++++------------ NAMESPACE | 2 +- R/unitRoot.R | 8 ++++++++ man/SMPLSplit_est.Rd | 4 ++-- man/SMPLSplit_example.Rd | 17 +++++++++++------ man/htest_pglm.Rd | 6 +++--- man/inf_M.Rd | 2 +- man/inf_Q.Rd | 2 +- man/invest.Rd | 4 ++-- man/ipsHEGY.Rd | 2 +- man/lagSelect.Rd | 8 ++++---- man/ptm.Rd | 34 +++++++++++++++++----------------- 13 files changed, 69 insertions(+), 55 deletions(-)
Title: Multiple Grubbs-Beck Low-Outlier Test
Description: Compute the multiple Grubbs-Beck low-outlier test on positively distributed
data and utilities for noninterpretive U.S. Geological Survey annual peak-streamflow
data processing discussed in Cohn et al. (2013) and
England et al. (2017) <doi:10.3133/tm4B5>. Other utilities for working with peak streamflow
are provided.
Author: William H. Asquith [aut, cre] ,
John F. England [aut, ctb] ,
George R. Herrmann [ctb]
Maintainer: William H. Asquith <wasquith@usgs.gov>
Diff between MGBT versions 1.1.6 dated 2026-05-27 and 1.1.8 dated 2026-10-04
MGBT-1.1.6/MGBT/R/zzz.R |only MGBT-1.1.8/MGBT/DESCRIPTION | 8 ++++---- MGBT-1.1.8/MGBT/MD5 | 15 +++++++++------ MGBT-1.1.8/MGBT/NAMESPACE | 1 + MGBT-1.1.8/MGBT/NEWS | 23 +++++++++++++++++++++++ MGBT-1.1.8/MGBT/R/makePeakMatrix.R |only MGBT-1.1.8/MGBT/R/plotPeaks.R | 4 ++-- MGBT-1.1.8/MGBT/inst/CITATION | 10 +++++++--- MGBT-1.1.8/MGBT/inst/helpers/getpks |only MGBT-1.1.8/MGBT/man/makePeakMatrix.Rd |only 10 files changed, 46 insertions(+), 15 deletions(-)
Title: Ecological Analysis and Visualization
Description: Support ecological analyses such as ordination and clustering.
Contains consistent and easy wrapper functions of 'stat', 'vegan', and
'labdsv' packages, and visualisation functions of ordination and clustering.
Author: Toshikazu Matsumura [aut, cre]
Maintainer: Toshikazu Matsumura <matutosi@gmail.com>
Diff between ecan versions 0.2.2 dated 2026-08-22 and 0.3.0 dated 2026-10-04
DESCRIPTION | 7 - MD5 | 66 ++++++++---- NAMESPACE | 13 ++ NEWS.md | 52 +++++++++ R/convert.R | 3 R/diversity.R | 2 R/ind_val.R | 12 +- R/one2multi.R | 14 +- R/ordination.R | 9 + R/read_biss.R | 6 - R/twinspan.R |only R/twinspan_hill.R |only R/utils_pad.R | 2 README.md | 165 +++++++++++++++++++++++++------ build |only inst/doc |only inst/extdata |only man/figures/README-twinspan-1.png |only man/ind_val.Rd | 4 man/is_one2multi.Rd | 9 + man/ordination.Rd | 2 man/pseudospecies.Rd |only man/read_biss.Rd | 4 man/tw_downweight.Rd |only man/tw_hill_const.Rd |only man/tw_inertia.Rd |only man/tw_preference.Rd |only man/tw_ra.Rd |only man/tw_species_data.Rd |only man/tw_two_way.Rd |only man/twinspan.Rd |only tests/testthat/test-cluster.R | 12 ++ tests/testthat/test-convert.R | 12 ++ tests/testthat/test-diversity.R | 25 ++++ tests/testthat/test-gen_example_layer.R |only tests/testthat/test-ind_val.R | 59 +++++++++-- tests/testthat/test-layer_construction.R | 16 +++ tests/testthat/test-one2multi.R | 4 tests/testthat/test-ordination.R | 20 +++ tests/testthat/test-read_biss.R |only tests/testthat/test-twinspan.R |only tests/testthat/test-utils_pad.R |only vignettes |only 43 files changed, 432 insertions(+), 86 deletions(-)
Title: Dunn's Test of Multiple Comparisons Using Rank Sums
Description: Computes Dunn's test (1964) for stochastic superiority and reports the results among multiple pairwise comparisons after a Kruskal-Wallis test for stochastic superiority among k groups (Kruskal and Wallis, 1952). 'dunn.test' makes k(k-1)/2 multiple pairwise comparisons based on Dunn's z-test-statistic approximations to the actual rank statistics. The null hypothesis for each pairwise comparison is that the probability of observing a randomly selected value from the first group that is larger than a randomly selected value from the second group equals one half; this null hypothesis corresponds to that of the Wilcoxon-Mann-Whitney rank-sum test. 'dunn.test' accounts for tied ranks.
Author: Alexis Dinno [aut, cre, cph]
Maintainer: Alexis Dinno <alexis.dinno@pdx.edu>
Diff between dunn.test versions 1.4.1 dated 2026-06-05 and 1.4.2 dated 2026-10-04
dunn.test-1.4.1/dunn.test/R/all.integers.R |only dunn.test-1.4.2/dunn.test/DESCRIPTION | 10 ++-- dunn.test-1.4.2/dunn.test/MD5 | 15 +++--- dunn.test-1.4.2/dunn.test/NAMESPACE | 1 dunn.test-1.4.2/dunn.test/R/all_integers.R |only dunn.test-1.4.2/dunn.test/R/dunn.test.R | 62 +++++++++++++------------- dunn.test-1.4.2/dunn.test/R/is_numeric_like.R |only dunn.test-1.4.2/dunn.test/R/kwallis.test.R | 3 - dunn.test-1.4.2/dunn.test/R/zformat.R | 18 +++---- dunn.test-1.4.2/dunn.test/build/partial.rdb |binary 10 files changed, 56 insertions(+), 53 deletions(-)
Title: General Bivariate Copula Theory and Many Utility Functions
Description: Extensive functions for bivariate copula (bicopula) computations and related operations
for bicopula theory. The lower, upper, product, and select other bicopula are implemented along
with operations including the diagonal, survival copula, dual of a copula, co-copula, and
numerical bicopula density. Level sets, horizontal and vertical sections are supported. Numerical
derivatives and inverses of a bicopula are provided through which simulation is implemented.
Bicopula composition, convex combination, asymmetry extension, and products also are provided.
Support extends to the Kendall Function as well as the Lmoments thereof. Kendall Tau,
Spearman Rho and Footrule, Gini Gamma, Blomqvist Beta, Hoeffding Phi, Schweizer-
Wolff Sigma, tail dependency, tail order, skewness, and bivariate Lmoments are implemented, and
positive/negative quadrant dependency, left (right) increasing (decreasing) are available.
Other features include Kullback-Leibler Divergence, Vuong Procedure, spectral measure, [...truncated...]
Author: William Asquith [aut, cre]
Maintainer: William Asquith <william.asquith@ttu.edu>
Diff between copBasic versions 2.2.16 dated 2026-08-31 and 2.2.17 dated 2026-10-04
DESCRIPTION | 8 +- MD5 | 31 ++++---- NAMESPACE | 9 +- NEWS | 17 ++++ R/RFEcop.R |only R/kfuncCOP.R | 10 ++ R/wolfCOPtest.R | 101 +++++++++++++++++++++------- R/wolfCOPtest_drawsim.R |only man/PLACKETTcop.Rd | 2 man/RAYcop.Rd | 10 +- man/copBasic-package.Rd | 33 ++++++++- man/figures/chck_wolfCOPtestCIRC_plot.jpg |binary man/figures/chck_wolfCOPtestCIRC_plot.pdf |binary man/figures/chck_wolfCOPtestCLCIRC_plot.jpg |only man/figures/chck_wolfCOPtestCLCIRC_plot.pdf |only man/rhoCOP.Rd | 4 - man/wolfCOPtest.Rd | 24 ++++-- man/wolfCOPtest_check.Rd | 45 +++++++----- man/wolfCOPtest_drawsim.Rd |only 19 files changed, 215 insertions(+), 79 deletions(-)
Title: Data Visualization and Statistical Tools for Agroindustrial
Experiments
Description: Set of tools for statistical analysis, visualization, and reporting of
agroindustrial and agricultural experiments. The package provides functions
to perform one-way and two-way ANOVA with post-hoc tests (Tukey HSD and
Duncan MRT), Welch ANOVA for heteroscedastic data, and the Games-Howell
post-hoc test as a robust alternative when variance homogeneity fails.
When residual normality fails, the Kruskal-Wallis test (with 'agricolae'
or Dunn post-hoc letters) or, for blocked designs, the Friedman test is
used, so that letters are always obtained through a defensible route.
Normality of residuals is assessed with the Shapiro-Wilk test and
homoscedasticity with the Fligner-Killeen test; the appropriate statistical
path is selected automatically based on these diagnostics. Coefficients of
variation and statistical power (via one-way ANOVA power analysis) are
reported alongside the post-hoc letter display, and each figure includes
a note describing the statistical route used, its rationale, a [...truncated...]
Author: Joaquin Alejandro Salinas Angeles [aut, cre]
Maintainer: Joaquin Alejandro Salinas Angeles <joaquinsa03@gmail.com>
Diff between agrobox versions 0.3.0 dated 2026-04-13 and 0.4.0 dated 2026-10-04
agrobox-0.3.0/agrobox/INDEX |only agrobox-0.4.0/agrobox/DESCRIPTION | 28 + agrobox-0.4.0/agrobox/MD5 | 16 agrobox-0.4.0/agrobox/NAMESPACE | 4 agrobox-0.4.0/agrobox/NEWS.md | 108 +++++ agrobox-0.4.0/agrobox/R/agrobox.R | 697 +++++++++++++++++++++++++---------- agrobox-0.4.0/agrobox/R/agroppt.R |only agrobox-0.4.0/agrobox/R/globals.R | 3 agrobox-0.4.0/agrobox/README.md |only agrobox-0.4.0/agrobox/man/agrobox.Rd | 92 ++-- agrobox-0.4.0/agrobox/man/agroppt.Rd |only 11 files changed, 710 insertions(+), 238 deletions(-)
Title: A Collection of Tools to Conduct Levins' Loop Analysis
Description: Performs Levins' loop analysis of qualitatively-specified complex causal systems. Loop analysis makes qualitative predictions of variable change in a system of causally interdependent variables, where "qualitative" means direct causal relationships and indirect causal effects are coded as sign only (i.e. increases, decreases, no change, and ambiguous). This implementation includes output support for graphs in .dot file format for use with visualization software such as 'graphviz' (<https://graphviz.org>). 'LoopAnalyst' provides tools for the construction and output of community matrices, computation and output of community effect matrices, tables of correlations, adjoint, absolute feedback, weighted feedback and weighted prediction matrices, change in life expectancy matrices, and feedback, path and loop enumeration tools.
Author: Alexis Dinno [aut, cre, cph]
Maintainer: Alexis Dinno <alexis.dinno@pdx.edu>
Diff between LoopAnalyst versions 1.2-7 dated 2024-04-08 and 1.2-8 dated 2026-10-04
DESCRIPTION | 14 ++++++++------ MD5 | 45 ++++++++++++++++++++++++--------------------- NAMESPACE | 25 ++++++++++++++++++++----- R/cem.corr.R | 14 +++++++++----- R/enumerate.loops.R | 8 +++++--- R/enumerate.paths.R | 20 ++++++++++++-------- R/feedback.R | 17 ++++++++++------- R/graph.cem.R | 13 ++++++++----- R/graph.cm.R | 15 +++++++++------ R/make.T.R | 27 +++++++++++++++------------ R/make.adjoint.R | 21 ++++++++++++--------- R/make.cem.R | 28 ++++++++++++++++------------ R/make.clem.R | 9 ++++++++- R/make.cm.R | 33 ++++++++++++++++++--------------- R/make.wfm.R | 25 ++++++++++++++++--------- R/out.cm.R | 8 +++++--- R/pad.left.R |only R/save.cm.R | 12 ++++++++---- R/supcat.R |only R/supprint.R |only R/validate.cem.R | 18 +++++++++++------- R/validate.cm.R | 28 ++++++++++++++++------------ R/weighted.predictions.R | 24 ++++++++++++++---------- build/partial.rdb |binary man/cm.dambacher.Rd | 4 ++-- 25 files changed, 246 insertions(+), 162 deletions(-)
Title: Functions for Medical Statistics Book with some Demographic Data
Description: Several utility functions for the book entitled
"Practices of Medical and Health Data Analysis using R"
(Pearson Education Japan, 2007) with Japanese demographic
data and some demographic analysis related functions.
Author: Minato Nakazawa [aut, cre]
Maintainer: Minato Nakazawa <minatonakazawa@gmail.com>
Diff between fmsb versions 0.7.6 dated 2024-01-19 and 0.7.8 dated 2026-10-04
DESCRIPTION | 14 ++++++---- MD5 | 22 ++++++++-------- NEWS | 10 +++++++ R/demogjpn.R | 70 +++++++++++++++++++++++++++++++++--------------------- R/fmsb.R | 1 build/partial.rdb |binary man/H27MPJ.Rd | 6 +++- man/Jfert.Rd | 40 ++++++++++++++++-------------- man/Jlife.Rd | 2 - man/Jpop.Rd | 17 ++++++++----- man/Jpopl.Rd | 17 ++++++++----- man/Jvital.Rd | 12 +++++---- 12 files changed, 131 insertions(+), 80 deletions(-)
Title: Generate Braille-Enabled Graphics
Description: Provides tools for rendering and visualizing
Braille patterns in R, using the 'liblouis' translation library.
For more information see <https://github.com/wininger/yaleBraille>.
Author: Mike Wininger [aut, cre] ,
liblouis contributors [ctb, cph] )
Maintainer: Mike Wininger <michael.wininger@yale.edu>
Diff between yaleBraille versions 0.2.2 dated 2026-10-02 and 0.2.3 dated 2026-10-04
DESCRIPTION | 11 ++++++----- MD5 | 4 ++-- R/fn_plotInitializr.R | 4 ++-- 3 files changed, 10 insertions(+), 9 deletions(-)
Title: Threshold-Sweep QCA
Description: Provides threshold sweep methods for Qualitative Comparative
Analysis (QCA). Implements Condition Threshold Sweep (CTS, for one or
several conditions), Outcome Threshold Sweep (OTS), and Dual Threshold
Sweep (DTS) for systematic exploration of threshold calibration effects on
crisp-set QCA results. These methods extend traditional robustness
approaches by treating threshold variation as an explicit analytical
dimension and recording the sufficiency solution obtained at each
threshold setting. Also provides Fiss (2011)
<doi:10.5465/amj.2011.60263120> core/peripheral condition classification
via compute_fiss_core() and generate_fiss_chart(), enabling four-symbol
configuration charts that distinguish core conditions (conditions of the
parsimonious term contained in each configuration) from peripheral
conditions (intermediate only). Built on top of the 'QCA' package by Dusa (2019)
<doi:10.1007/978-3-319-75668-4>, with function arguments following 'QCA'
conventions. Based on set [...truncated...]
Author: Yuki Toyoda [aut, cre],
Japan Society for the Promotion of Science [fnd]
Maintainer: Yuki Toyoda <yuki.toyoda.ds@hosei.ac.jp>
Diff between ThSQCA versions 2.0.8 dated 2026-09-26 and 2.0.9 dated 2026-10-04
DESCRIPTION | 10 MD5 | 42 NEWS.md | 2475 +++++++++++++++--------------- R/tsqca_config_chart.R | 46 R/tsqca_core.R | 1150 +++++++------ R/tsqca_cts.R | 1795 ++++++++++----------- R/tsqca_helpers.R | 16 R/tsqca_ots_dts.R | 1728 ++++++++++---------- R/tsqca_report.R | 2081 +++++++++++++------------ README.md | 11 inst/CITATION | 9 inst/doc/ThSQCA_Reproducible_EN.html | 71 inst/doc/ThSQCA_Tutorial_EN.html | 6 man/ThSQCA-package.Rd | 2 man/get_condition_status.Rd | 7 tests/testthat/helper-audit.R |only tests/testthat/helper-audit2.R |only tests/testthat/test-audit-matrix.R |only tests/testthat/test-audit-necessity.R |only tests/testthat/test-audit-random.R |only tests/testthat/test-audit-static.R |only tests/testthat/test-audit2-chart.R |only tests/testthat/test-audit2-invariants.R |only tests/testthat/test-audit2-methods.R |only tests/testthat/test-audit2-names.R |only tests/testthat/test-audit2-oracle.R |only tests/testthat/test-audit3-multi.R |only tests/testthat/test-nonascii-names.R |only tests/testthat/test-report-simple-noN-A.R |only 29 files changed, 4849 insertions(+), 4600 deletions(-)
Title: Simulation of Pleiotropic, Linked and Epistatic Phenotypes
Description: The number of studies involving correlated traits and the availability of tools to handle this type of data has increased considerably in the last decade. With such a demand, we need tools for testing hypotheses related to single and multi-trait (correlated) phenotypes based on many genetic settings. Thus, we implemented various options for simulation of pleiotropy and Linkage Disequilibrium under additive, dominance and epistatic models. The simulation currently takes a marker data set as an input and then uses it for simulating multiple traits as described in Fernandes and Lipka (2020) <doi:10.1186/s12859-020-03804-y>.
Author: Samuel Fernandes [aut, cre] ,
Alexander Lipka [aut]
Maintainer: Samuel Fernandes <samuelbf@uark.edu>
Diff between simplePHENOTYPES versions 1.3.0 dated 2021-01-20 and 1.3.1 dated 2026-10-04
simplePHENOTYPES-1.3.0/simplePHENOTYPES/R/base_line_multi_traits.R |only simplePHENOTYPES-1.3.0/simplePHENOTYPES/R/base_line_single_trait.R |only simplePHENOTYPES-1.3.0/simplePHENOTYPES/R/genotypes.R |only simplePHENOTYPES-1.3.0/simplePHENOTYPES/R/phenotypes.R |only simplePHENOTYPES-1.3.0/simplePHENOTYPES/R/qtn_linkage.R |only simplePHENOTYPES-1.3.0/simplePHENOTYPES/R/qtn_partially_pleiotropic.R |only simplePHENOTYPES-1.3.0/simplePHENOTYPES/R/qtn_pleiotropic.R |only simplePHENOTYPES-1.3.0/simplePHENOTYPES/man/base_line_multi_traits.Rd |only simplePHENOTYPES-1.3.0/simplePHENOTYPES/man/base_line_single_trait.Rd |only simplePHENOTYPES-1.3.0/simplePHENOTYPES/man/genotypes.Rd |only simplePHENOTYPES-1.3.0/simplePHENOTYPES/man/phenotypes.Rd |only simplePHENOTYPES-1.3.0/simplePHENOTYPES/man/qtn_linkage.Rd |only simplePHENOTYPES-1.3.0/simplePHENOTYPES/man/qtn_partially_pleiotropic.Rd |only simplePHENOTYPES-1.3.0/simplePHENOTYPES/man/qtn_pleiotropic.Rd |only simplePHENOTYPES-1.3.1/simplePHENOTYPES/DESCRIPTION | 17 simplePHENOTYPES-1.3.1/simplePHENOTYPES/LICENSE | 2 simplePHENOTYPES-1.3.1/simplePHENOTYPES/MD5 | 50 simplePHENOTYPES-1.3.1/simplePHENOTYPES/NEWS.md | 6 simplePHENOTYPES-1.3.1/simplePHENOTYPES/R/Base_line_multi_traits.R |only simplePHENOTYPES-1.3.1/simplePHENOTYPES/R/Base_line_single_trait.R |only simplePHENOTYPES-1.3.1/simplePHENOTYPES/R/Genotypes.R |only simplePHENOTYPES-1.3.1/simplePHENOTYPES/R/Phenotypes.R |only simplePHENOTYPES-1.3.1/simplePHENOTYPES/R/QTN_linkage.R |only simplePHENOTYPES-1.3.1/simplePHENOTYPES/R/QTN_partially_pleiotropic.R |only simplePHENOTYPES-1.3.1/simplePHENOTYPES/R/QTN_pleiotropic.R |only simplePHENOTYPES-1.3.1/simplePHENOTYPES/R/create_phenotypes.R | 6 simplePHENOTYPES-1.3.1/simplePHENOTYPES/R/numericalization.R | 2 simplePHENOTYPES-1.3.1/simplePHENOTYPES/README.md | 6 simplePHENOTYPES-1.3.1/simplePHENOTYPES/build/partial.rdb |binary simplePHENOTYPES-1.3.1/simplePHENOTYPES/build/vignette.rds |binary simplePHENOTYPES-1.3.1/simplePHENOTYPES/inst/CITATION | 9 simplePHENOTYPES-1.3.1/simplePHENOTYPES/inst/doc/simplePHENOTYPES.R | 330 ++--- simplePHENOTYPES-1.3.1/simplePHENOTYPES/inst/doc/simplePHENOTYPES.html | 592 +++++++--- simplePHENOTYPES-1.3.1/simplePHENOTYPES/man/Base_line_multi_traits.Rd |only simplePHENOTYPES-1.3.1/simplePHENOTYPES/man/Base_line_single_trait.Rd |only simplePHENOTYPES-1.3.1/simplePHENOTYPES/man/Genotypes.Rd |only simplePHENOTYPES-1.3.1/simplePHENOTYPES/man/Phenotypes.Rd |only simplePHENOTYPES-1.3.1/simplePHENOTYPES/man/QTN_linkage.Rd |only simplePHENOTYPES-1.3.1/simplePHENOTYPES/man/QTN_partially_pleiotropic.Rd |only simplePHENOTYPES-1.3.1/simplePHENOTYPES/man/QTN_pleiotropic.Rd |only 40 files changed, 682 insertions(+), 338 deletions(-)
More information about simplePHENOTYPES at CRAN
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Title: Calculate ANSI/ASA S3.5-1997 (R2024) Speech Intelligibility
Index
Description: Calculates the American National Standards Institute (ANSI) S3.5-1997
Speech Intelligibility Index (SII) (ANSI, 1997), a standard method for
computing the intelligibility of speech from acoustical measurements of
speech, noise, and hearing thresholds. This package includes data frames
corresponding to Tables 1 - 4 in the ANSI standard as well as functions
utilizing these tables and user-provided hearing threshold and noise level
measurements to compute the SII score. The methods implemented here extend
the standard computations to allow calculation of SII when the measured
frequencies do not match those required by the standard by applying
interpolation. The package also includes a native C++ implementation of
the 'AUDMOD' specific loudness model for impaired hearing (Bramslow, 2004),
ported from the 'bramslow2004' implementation in the Auditory Modeling
Toolbox (AMT), to calculate loudness in sones. It provides methods to
predict aided SII under hearing aid prescriptive rationales, in [...truncated...]
Author: Gregory R. Warnes [aut, cph],
Mark Shaver [cre, aut]
Maintainer: Mark Shaver <mark.shaver@posteo.net>
Diff between SII versions 1.2.4 dated 2026-09-12 and 1.3.0 dated 2026-10-04
SII-1.2.4/SII/ChangeLog |only SII-1.2.4/SII/NEWS |only SII-1.2.4/SII/R/moore_glasberg.R |only SII-1.2.4/SII/man/calculate_loudness_bramslow2004.Rd |only SII-1.2.4/SII/man/convert_1_3_octave_to_density.Rd |only SII-1.2.4/SII/vignettes/Open-NL_Algorithm.md |only SII-1.3.0/SII/DESCRIPTION | 67 ++---- SII-1.3.0/SII/MD5 | 100 +++++++-- SII-1.3.0/SII/NAMESPACE | 3 SII-1.3.0/SII/NEWS.md |only SII-1.3.0/SII/R/RcppExports.R | 15 + SII-1.3.0/SII/R/audmod.R |only SII-1.3.0/SII/R/benchmark_targets.R | 13 - SII-1.3.0/SII/R/nalr.R | 33 --- SII-1.3.0/SII/R/normal_loudness.R |only SII-1.3.0/SII/R/open_nl.R | 157 ++++++++------ SII-1.3.0/SII/R/sii.R | 203 +++++++------------ SII-1.3.0/SII/README.md | 194 ++++++++++++------ SII-1.3.0/SII/build/vignette.rds |binary SII-1.3.0/SII/inst/doc/SII.pdf |binary SII-1.3.0/SII/man/calculate_loudness.Rd | 3 SII-1.3.0/SII/man/calculate_loudness_audmod.Rd |only SII-1.3.0/SII/man/calculate_loudness_cpp.Rd | 7 SII-1.3.0/SII/man/open_nl.Rd | 21 + SII-1.3.0/SII/man/prescribe_compression.Rd | 2 SII-1.3.0/SII/man/sii.Rd | 2 SII-1.3.0/SII/src/RcppExports.cpp | 48 +++- SII-1.3.0/SII/src/audmod.cpp |only SII-1.3.0/SII/src/bramslow2004.cpp | 38 +-- SII-1.3.0/SII/tests/test_amt_reference.m |only SII-1.3.0/SII/tests/test_loudness_equivalence.R | 14 - SII-1.3.0/SII/tests/testthat/fixtures |only SII-1.3.0/SII/tests/testthat/test-audmod.R |only SII-1.3.0/SII/tests/testthat/test-open-nl-cap.R |only SII-1.3.0/SII/tests/testthat/test-sii.R | 30 -- 35 files changed, 533 insertions(+), 417 deletions(-)
Title: Interface to the SCIP Optimization Suite
Description: Provides an R interface to SCIP (Solving Constraint Integer Programs), a framework for mixed-integer
programming (MIP), mixed-integer nonlinear programming (MINLP), and constraint integer programming
(2025, <doi:10.48550/arXiv.2511.18580>). Supports linear, quadratic, SOS, indicator, and knapsack
constraints with continuous, binary, and integer variables. Includes a one-shot solver interface
and a model-building API for incremental problem construction.
Author: Balasubramanian Narasimhan [aut, cre] ,
SCIP Optimization Suite Authors [cph]
Maintainer: Balasubramanian Narasimhan <naras@stanford.edu>
Diff between scip versions 1.10.0-4 dated 2026-08-30 and 1.10.1-1 dated 2026-10-04
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Title: Local Randomization Methods for RD Designs
Description: Provides tools to perform randomization inference for RD designs under local randomization: rdrandinf() to perform hypothesis testing using randomization inference, rdwinselect() to select a window around the cutoff in which randomization is likely to hold, rdsensitivity() to assess the sensitivity of the results to different window lengths and null hypotheses and rdrbounds() to construct Rosenbaum bounds for sensitivity to unobserved confounders. See Cattaneo, Titiunik and Vazquez-Bare (2016) <https://rdpackages.github.io/references/Cattaneo-Titiunik-VazquezBare_2016_Stata.pdf> for further methodological details, and references.
Author: Matias D. Cattaneo [aut, cre],
Rocio Titiunik [aut],
Gonzalo Vazquez-Bare [aut]
Maintainer: Matias D. Cattaneo <matias.d.cattaneo@gmail.com>
Diff between rdlocrand versions 2.0 dated 2026-05-14 and 3.0 dated 2026-10-04
DESCRIPTION | 7 +- MD5 | 24 +++---- R/rdlocrand_fun.R | 70 ++++++++++++++++++++ R/rdlocrand_package.R | 2 R/rdrandinf.R | 167 ++++++++++++++++++++++++++++++++------------------ R/rdrbounds.R | 16 ++++ R/rdsensitivity.R | 46 +++++++++++-- R/rdwinselect.R | 57 +++++++++++------ man/rdrandinf.Rd | 25 ++++++- man/rdrbounds.Rd | 7 ++ man/rdsensitivity.Rd | 16 ++++ man/rdwinselect.Rd | 15 ++++ tests |only 13 files changed, 340 insertions(+), 112 deletions(-)
Title: Fast and Efficient Access to MODIS Earth Observation Data
Description: Programmatic interface to several NASA Earth Observation 'OPeNDAP' servers (Open-source Project for a Network Data Access Protocol) (<https://www.opendap.org/>). Allows for easy downloads of MODIS subsets, as well as other Earth Observation datacubes, in a time-saving and efficient way : by sampling it at the very downloading phase (spatially, temporally and dimensionally).
Author: Paul Taconet [aut, cre, cph] ,
Nicolas Moiroux [fnd] ,
French National Research Institute for Sustainable Development, IRD
[fnd]
Maintainer: Paul Taconet <paul.taconet@gmail.com>
Diff between modisfast versions 2.0.0 dated 2026-09-30 and 2.0.1 dated 2026-10-04
DESCRIPTION | 6 ++-- MD5 | 18 +++++++------- NEWS.md | 10 +++++++ R/functions_import_data.R | 59 ++++++++++++++++++++++++++++++++++++++++++++-- R/import_modis_cloud.R | 27 ++++++++++++++++++--- R/mf_download_data.R | 26 ++++++++++++++++---- R/mf_get_url.R | 2 - R/mf_import_data.R | 4 ++- README.md | 53 ++++++++++++++--------------------------- man/mf_import_data.Rd | 3 +- 10 files changed, 149 insertions(+), 59 deletions(-)
Title: Implementation of Logistic Box-Cox Regression
Description: Implements a logistic Box-Cox model that adds a shape parameter
to a routine logistic regression model to flexibly estimate the shape
and strength of the relationship between a binary outcome and a
continuous predictor, adjusting for covariates and survey weights. This
model is fully described in Xing, L. et al. (2021) <doi:10.1002/cjs.11587>.
This version extends the original 'lboxcox' package (1.1) with numerically
stabilized likelihood/gradient calculations, vectorized data preprocessing,
and a bootstrap-ensemble estimator.
Author: Li Xing [cre, aut],
Shiyu Xu [aut],
Jing Wang [aut],
Kohlton Booth [aut],
Xuekui Zhang [aut],
Igor Burstyn [aut],
Paul Gustafson [aut]
Maintainer: Li Xing <jnjfayaa@gmail.com>
Diff between lboxcox versions 1.2 dated 2023-12-15 and 2.0.1 dated 2026-10-04
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Title: Native 'LaTeX' Math Rendering for Grid Graphics
Description: Renders 'LaTeX' math equations as native R grid graphics objects
(grobs) using the 'MicroTeX' 'C++' library as the layout engine. Produces
resolution-independent vector output that works on any R graphics device,
with no external 'LaTeX' installation required. Markdown labels and block
documents that mix prose formatting with math are also rendered, for use
with both 'grid' and 'ggplot2'.
Author: Alim Dayim [aut, cre] ,
Nano Michael [cph] ,
Bundled math font authors [cph]
Maintainer: Alim Dayim <ad938@cam.ac.uk>
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Title: Estimate Functional and Stochastic Parameters of Linear Models
with Correlated Residuals and Missing Data
Description: Implements the Wavelet Moment Regression (WAMORE) inference
framework presented in Voirol, L., Xu, H., Zhang, Y., Insolia, L.,
Molinari, R. and Guerrier, S. (2026) <doi:10.48550/arXiv.2607.16264>.
Provides computationally efficient estimation of functional and stochastic
parameters of linear models with correlated residuals, including settings
with missing data. Includes functions to download and plot Global Navigation
Satellite System (GNSS) position time series from the Nevada Geodetic
Laboratory and estimate tectonic velocities and crustal uplift using
composite stochastic models.
Author: Lionel Voirol [aut, cre] ,
Haotian Xu [aut] ,
Yuming Zhang [aut] ,
Luca Insolia [aut] ,
Roberto Molinari [aut] ,
Stephane Guerrier [aut]
Maintainer: Lionel Voirol <lionelvoirol@hotmail.com>
Diff between gmwmx2 versions 0.0.5 dated 2026-06-10 and 0.0.6 dated 2026-10-04
DESCRIPTION | 24 MD5 | 50 NAMESPACE | 80 NEWS.md | 13 R/get_autocovariance.R | 2 R/get_variance_covariance_matrix.R | 2 R/ngl.R | 46 README.md | 20 build/vignette.rds |binary inst/doc/data_generation.html | 14 inst/doc/estimate_geodetic_time_series_from_ngl.Rmd | 2 inst/doc/estimate_geodetic_time_series_from_ngl.html | 10 inst/doc/estimate_linear_models_with_dependent_errors.Rmd | 4 inst/doc/estimate_linear_models_with_dependent_errors.html | 9 inst/doc/estimate_linear_models_with_dependent_errors_and_missing_observations.Rmd | 3 inst/doc/estimate_linear_models_with_dependent_errors_and_missing_observations.html | 34 inst/doc/load_plot_data_ngl.R | 48 inst/doc/load_plot_data_ngl.Rmd | 56 inst/doc/load_plot_data_ngl.html | 4248 +++++++++- man/gmwmx2_plot_colors.Rd | 1 man/plot.gnss_ts_ngl.Rd | 5 vignettes/REFERENCES.bib | 10 vignettes/estimate_geodetic_time_series_from_ngl.Rmd | 2 vignettes/estimate_linear_models_with_dependent_errors.Rmd | 4 vignettes/estimate_linear_models_with_dependent_errors_and_missing_observations.Rmd | 3 vignettes/load_plot_data_ngl.Rmd | 56 26 files changed, 4530 insertions(+), 216 deletions(-)
Title: A Modern and Flexible Data Pipeline for 'SurveyCTO'
Description: A modern and flexible R client for the 'SurveyCTO', a mobile and
offline data collection platform, providing a modern and consistent interface for
programmatic access to server resources. Built on top of the 'httr2' package,
it enables secure and efficient data retrieval and returns analysis-ready
data through optional tidying. It includes functions to create, upload, and
download server datasets, in addition to fetching form data, files, and
submission attachments. Robust authentication and request handling make the
package suitable for automated survey monitoring and downstream analysis.
Author: Gutama Girja Urago [aut, cre, cph]
Maintainer: Gutama Girja Urago <girjagutama@gmail.com>
Diff between ctoclient versions 0.2.0 dated 2026-09-20 and 0.2.3 dated 2026-10-04
DESCRIPTION | 8 MD5 | 35 NAMESPACE | 3 NEWS.md | 76 + R/cto_form_data.R | 19 R/cto_form_data_attachment.R | 17 R/cto_form_dofile.R | 11 R/zzz.R | 82 + inst/doc/form-data.Rmd | 424 +++++----- inst/doc/managing-connections.Rmd | 392 ++++----- tests/testthat/_datasets/band_members/records/upload-f8492c-POST.json | 26 tests/testthat/fixtures/audittest.xlsx |only tests/testthat/test-ctoclient.R | 298 +++---- tests/testthat/test-docx.R | 10 tests/testthat/test-dofile.R | 67 + tests/testthat/test-form-data.R | 40 tests/testthat/test-utils.R | 132 ++- vignettes/form-data.Rmd | 424 +++++----- vignettes/managing-connections.Rmd | 392 ++++----- 19 files changed, 1408 insertions(+), 1048 deletions(-)
Title: Optimal Pairing and Matching via Linear Assignment
Description: Solves optimal pairing and matching problems using linear assignment
algorithms. Provides implementations of the Hungarian method (Kuhn 1955)
<doi:10.1002/nav.3800020109>, Jonker-Volgenant shortest path algorithm
(Jonker and Volgenant 1987) <doi:10.1007/BF02278710>, Auction algorithm
(Bertsekas 1988) <doi:10.1007/BF02186476>, cost-scaling
(Goldberg and Kennedy 1995) <doi:10.1007/BF01585996>, scaling algorithms
(Gabow and Tarjan 1989) <doi:10.1137/0218069>, push-relabel (Goldberg and
Tarjan 1988) <doi:10.1145/48014.61051>, and Sinkhorn entropy-regularized
transport (Cuturi 2013) <doi:10.48550/arxiv.1306.0895>. Designed for
matching plots, sites, samples, or any pairwise optimization problem.
Supports rectangular matrices, forbidden assignments, data frame inputs,
batch solving, k-best solutions, and pixel-level image morphing for
visualization. Includes automatic preprocessing with variable health
checks, multiple scaling methods (standardized, [...truncated...]
Author: Gilles Colling [aut, cre, cph]
Maintainer: Gilles Colling <gilles.colling051@gmail.com>
Diff between couplr versions 1.8.0 dated 2026-09-30 and 1.8.1 dated 2026-10-04
DESCRIPTION | 6 LICENSE | 4 MD5 | 253 +- NEWS.md | 31 R/RcppExports.R | 630 ++--- R/couplr-package.R | 78 R/data.R | 6 R/lap_certify.R | 2 R/lap_implicit.R | 3 R/lap_solve.R | 6 R/matching_cardinality_exact.R | 2 R/matching_constraints.R | 14 R/matching_core.R | 11 R/matching_full.R | 2 R/matching_interop.R | 87 R/matching_lazy.R | 43 R/matching_path.R | 2 R/matching_plots.R | 466 +-- R/matching_preprocessing.R | 1024 ++++---- R/matching_propensity.R | 304 +- R/morph_pixel.R | 1678 ++++++------- inst/CITATION | 18 inst/NOTICE | 4 inst/WORDLIST | 234 - inst/doc/algorithms.R | 29 inst/doc/algorithms.Rmd | 64 inst/doc/algorithms.html | 1966 ---------------- inst/doc/comparison.html | 4 inst/doc/getting-started.html | 4 inst/doc/matching-workflows.html | 8 inst/doc/pixel-morphing.html | 4 inst/doc/troubleshooting.html | 6 inst/scripts/generate_examples.R | 748 +++--- inst/scripts/speed_comparison.R | 332 +- man/hospital_staff.Rd | 6 man/lazy_cost_spec_calipers.Rd | 9 man/lazy_cost_spec_rows.Rd |only man/transpose_lazy_cost_spec.Rd | 6 src/RcppExports.cpp | 81 src/core/lap_callback_source.h | 10 src/core/lap_certify_rcpp.cpp | 3 src/core/lap_hall_rcpp.cpp | 5 src/core/lap_internal.h | 4 src/core/lap_lazy_types.h | 46 src/core/lap_utils_rcpp.cpp | 56 src/core/lap_utils_rcpp.h | 10 src/flow/flow_balltree.h | 85 src/flow/flow_implicit.h | 38 src/flow/flow_implicit_rcpp.cpp | 13 src/flow/flow_path_rcpp.cpp | 4 src/flow/flow_rcpp.cpp | 4 src/flow/flow_tree_nearest.h | 6 src/flow/flow_tree_pricing.h | 11 src/rcpp_interface.cpp | 52 src/solvers/solve_auction_lazy_rcpp.cpp | 5 src/solvers/solve_jv_duals_lazy_rcpp.cpp | 5 tests/testthat.R | 24 tests/testthat/README.md | 256 +- tests/testthat/gabow-tarjan/test_gabow_tarjan_moduleA.R | 258 +- tests/testthat/gabow-tarjan/test_gabow_tarjan_moduleB.R | 316 +- tests/testthat/gabow-tarjan/test_gabow_tarjan_moduleC.R | 318 +- tests/testthat/gabow-tarjan/test_gabow_tarjan_moduleD.R | 344 +- tests/testthat/gabow-tarjan/test_gabow_tarjan_moduleE.R | 656 ++--- tests/testthat/gabow-tarjan/test_gabow_tarjan_moduleF.R | 652 ++--- tests/testthat/helper-gabow_tarjan.R | 114 tests/testthat/test-additional-coverage.R | 850 +++--- tests/testthat/test-assign.R | 614 ++-- tests/testthat/test-assignment-auction-gs.R | 370 +-- tests/testthat/test-assignment-auto.R | 86 tests/testthat/test-assignment-bottleneck.R | 724 ++--- tests/testthat/test-assignment-csa.R | 488 +-- tests/testthat/test-assignment-csflow.R | 128 - tests/testthat/test-assignment-hk01.R | 56 tests/testthat/test-assignment-hungarian.R | 76 tests/testthat/test-assignment-jv.R | 188 - tests/testthat/test-assignment-network-simplex.R | 206 - tests/testthat/test-assignment-push_relabel.R | 692 ++--- tests/testthat/test-assignment-ramshaw_tarjan.R | 636 ++--- tests/testthat/test-assignment.R | 52 tests/testthat/test-auction-hang.R | 114 tests/testthat/test-batch-coverage-final.R | 202 - tests/testthat/test-batch-kbest-extended.R | 356 +- tests/testthat/test-batch-processing.R | 410 +-- tests/testthat/test-blocks-coverage.R | 510 ++-- tests/testthat/test-constraints-coverage.R | 398 +-- tests/testthat/test-cycle-cancel-coverage-2.R | 288 +- tests/testthat/test-cycle-cancel-coverage.R | 272 +- tests/testthat/test-cycle-cancel.R | 260 +- tests/testthat/test-gabow_tarjan_complexity.R | 416 +-- tests/testthat/test-implicit.R | 22 tests/testthat/test-kbest-coverage-final.R | 132 - tests/testthat/test-kbest-lawler.R | 258 +- tests/testthat/test-kbest-murty.R | 78 tests/testthat/test-lap-solve-batch-coverage-2.R | 386 +-- tests/testthat/test-lap-solve-batch-coverage-3.R | 434 +-- tests/testthat/test-lap-solve-batch-coverage.R | 778 +++--- tests/testthat/test-lap-solve-batch-extended.R | 480 +-- tests/testthat/test-line-metric.R | 514 ++-- tests/testthat/test-match-couples-lazy.R | 30 tests/testthat/test-matching-cem.R | 322 +- tests/testthat/test-matching-diagnostics-extended.R | 768 +++--- tests/testthat/test-matching-full.R | 326 +- tests/testthat/test-matching-id-contract.R | 40 tests/testthat/test-matching-interop.R | 316 +- tests/testthat/test-matching-join-coverage.R | 626 ++--- tests/testthat/test-matching-messages.R | 772 +++--- tests/testthat/test-matching-output.R | 166 - tests/testthat/test-matching-parallel.R | 552 ++-- tests/testthat/test-matching-preprocessing-coverage-2.R | 830 +++--- tests/testthat/test-matching-preprocessing-coverage.R | 640 ++--- tests/testthat/test-matching-subclass.R | 344 +- tests/testthat/test-matching-utils-coverage.R | 704 ++--- tests/testthat/test-matching-utils-extended.R | 798 +++--- tests/testthat/test-messages-coverage.R | 322 +- tests/testthat/test-messages-extended.R | 456 +-- tests/testthat/test-morph-pixel-cpp-coverage.R | 778 +++--- tests/testthat/test-morph-tiling.R | 434 +-- tests/testthat/test-network-simplex-coverage.R | 268 +- tests/testthat/test-prepare-cost-matrix.R | 34 tests/testthat/test-preprocessing-coverage.R | 452 +-- tests/testthat/test-print-methods.R | 570 ++-- tests/testthat/test-sensitivity.R | 248 +- tests/testthat/test-sinkhorn.R | 418 +-- tests/testthat/test-solver-csa.R | 600 ++-- tests/testthat/test-utility-functions.R | 652 ++--- tests/testthat/test-utils-extended-2.R | 396 +-- tests/testthat/test-zzz-onload.R | 74 vignettes/algorithms.Rmd | 64 128 files changed, 17144 insertions(+), 18800 deletions(-)
Title: Conover-Iman Test of Multiple Comparisons Using Rank Sums
Description: Computes the Conover-Iman test (1979) for stochastic superiority and reports the results among multiple pairwise comparisons after a Kruskal-Wallis omnibus test for stochastic superiority among k groups (Kruskal and Wallis, 1952). conover.test makes k(k-1)/2 multiple pairwise comparisons based on Conover-Iman t-test-statistic of the rank differences. The null hypothesis for each pairwise comparison is that the probability of observing a randomly selected value from the first group that is larger than a randomly selected value from the second group equals one half; this null hypothesis corresponds to that of the Wilcoxon-Mann-Whitney rank-sum test. conover.test accounts for tied ranks. The Conover-Iman test is strictly valid if and only if the corresponding Kruskal-Wallis null hypothesis is rejected.
Author: Alexis Dinno [aut, cre, cph]
Maintainer: Alexis Dinno <alexis.dinno@pdx.edu>
Diff between conover.test versions 1.2.0 dated 2026-09-16 and 1.2.1 dated 2026-10-04
conover.test-1.2.0/conover.test/R/all.integers.R |only conover.test-1.2.1/conover.test/DESCRIPTION | 10 +++++----- conover.test-1.2.1/conover.test/MD5 | 9 +++++---- conover.test-1.2.1/conover.test/NAMESPACE | 1 - conover.test-1.2.1/conover.test/R/all_integers.R |only conover.test-1.2.1/conover.test/R/conover.test.R | 6 +++--- conover.test-1.2.1/conover.test/R/is_numeric_like.R |only 7 files changed, 13 insertions(+), 13 deletions(-)
Title: General-to-Specific Modelling of Panel Data
Description: Uses several types of indicator saturation and automated General-to-Specific (GETS) modelling from the 'gets' package and applies it to panel data. This allows the detection of structural breaks in panel data, operationalising a reverse causal approach of causal inference, see Pretis and Schwarz (2022) <doi:10.2139/ssrn.4022745>.
Author: Felix Pretis [aut],
Moritz Schwarz [aut, cre]
Maintainer: Moritz Schwarz <moritz.schwarz@scmo.eu>
Diff between getspanel versions 0.2.1 dated 2025-05-13 and 0.2.2 dated 2026-10-04
DESCRIPTION | 10 MD5 | 66 +++--- NAMESPACE | 82 ++++--- NEWS.md | 9 R/fixest_getspanel.R | 2 R/isatpanel.R | 20 + R/plot_counterfactual.R | 4 R/plot_grid.R | 2 R/print.isatpanel.R | 6 build/vignette.rds |binary data/EUCO2residential.rda |binary data/EU_emissions_road.rda |binary data/pandata_simulated.rda |binary inst/doc/introduction.R | 66 +++--- inst/doc/introduction.html | 45 ++-- man/robust_isatpanel.Rd | 4 tests/testthat/_snaps/9-plotting.md |only tests/testthat/_snaps/9-plotting/Grid_plot_outcome1.png |binary tests/testthat/_snaps/9-plotting/Grid_plot_outcome2.png |binary tests/testthat/_snaps/9-plotting/Grid_plot_outcome3.png |binary tests/testthat/_snaps/9-plotting/Grid_plot_outcome4.png |binary tests/testthat/_snaps/9-plotting/Grid_plot_outcome4_regex.png |binary tests/testthat/_snaps/9-plotting/Grid_plot_outcome5.png |binary tests/testthat/_snaps/9-plotting/counterfactual_plot_outcome2.png |binary tests/testthat/_snaps/9-plotting/counterfactual_plot_outcome2_regex.png |binary tests/testthat/_snaps/9-plotting/counterfactual_plot_outcome3_regex.png |binary tests/testthat/_snaps/9-plotting/plot_counterfactual_outcome2_regex.png |binary tests/testthat/_snaps/9-plotting/plot_grid_cfesis_1.png |only tests/testthat/_snaps/9-plotting/plot_grid_cfesis_2.png |only tests/testthat/_snaps/9-plotting/plot_grid_cfesis_3.png |only tests/testthat/_snaps/9-plotting/plot_grid_cfesis_4.png |only tests/testthat/_snaps/9-plotting/plot_grid_cfesis_5.png |only tests/testthat/_snaps/9-plotting/plot_grid_cfesis_6.png |only tests/testthat/_snaps/9-plotting/plot_grid_cfesis_7.png |only tests/testthat/_snaps/9-plotting/plot_grid_cfesis_8.png |only tests/testthat/_snaps/9-plotting/plot_grid_outcome4_regex.png |binary tests/testthat/test-1-isatpanel-short.R | 32 ++- tests/testthat/test-9-plotting.R | 103 ++++++++++ vignettes/simulations.R |only 39 files changed, 314 insertions(+), 137 deletions(-)
Title: Spectral Clustering-Based Method for Identifying B Cell Clones
Description: Provides a computational framework for identification of B cell clones from
Adaptive Immune Receptor Repertoire sequencing (AIRR-Seq) data. Three main
functions are included (identicalClones, hierarchicalClones, and spectralClones)
that perform clustering among sequences of BCRs/IGs (B cell receptors/immunoglobulins)
which share the same V gene, J gene and junction length.
Nouri N and Kleinstein SH (2018) <doi: 10.1093/bioinformatics/bty235>.
Nouri N and Kleinstein SH (2019) <doi: 10.1101/788620>.
Gupta NT, et al. (2017) <doi: 10.4049/jimmunol.1601850>.
Author: Nima Nouri [aut],
Edel Aron [ctb],
Robert Bjornson [ctb],
Gisela Gabernet [ctb],
Cole Jensen [ctb],
Huimin Lyu [ctb],
Susanna Marquez [ctb, cre],
Jason Vander Heiden [aut],
Steven Kleinstein [aut, cph]
Maintainer: Susanna Marquez <susanna.marquez@yale.edu>
Diff between scoper versions 1.5.0 dated 2026-05-05 and 1.6.0 dated 2026-10-04
scoper-1.5.0/scoper/src/fastDist.cpp |only scoper-1.6.0/scoper/DESCRIPTION | 12 scoper-1.6.0/scoper/MD5 | 35 - scoper-1.6.0/scoper/NAMESPACE | 100 ++- scoper-1.6.0/scoper/NEWS.md | 41 + scoper-1.6.0/scoper/R/Functions.R | 555 ++++++++++++++-------- scoper-1.6.0/scoper/R/RcppExports.R | 8 scoper-1.6.0/scoper/README.md | 4 scoper-1.6.0/scoper/build/partial.rdb |binary scoper-1.6.0/scoper/build/vignette.rds |binary scoper-1.6.0/scoper/inst/doc/Scoper-Vignette.R | 6 scoper-1.6.0/scoper/inst/doc/Scoper-Vignette.Rmd | 6 scoper-1.6.0/scoper/inst/doc/Scoper-Vignette.pdf |binary scoper-1.6.0/scoper/man/ScoperClones-class.Rd | 3 scoper-1.6.0/scoper/man/hierarchicalClones.Rd | 108 ++-- scoper-1.6.0/scoper/man/identicalClones.Rd | 57 +- scoper-1.6.0/scoper/man/spectralClones.Rd | 35 - scoper-1.6.0/scoper/src/RcppExports.cpp | 24 scoper-1.6.0/scoper/vignettes/Scoper-Vignette.Rmd | 6 19 files changed, 632 insertions(+), 368 deletions(-)
Title: Environments Behaving (Almost) as Lists
Description: List environments are environments that have list-like properties. For instance, the elements of a list environment are ordered and can be accessed and iterated over using index subsetting, e.g. 'x <- listenv(a = 1, b = 2); for (i in seq_along(x)) x[[i]] <- x[[i]] ^ 2; y <- as.list(x)'.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between listenv versions 1.0.0 dated 2026-06-22 and 1.1.0 dated 2026-10-04
DESCRIPTION | 8 MD5 | 26 - NEWS.md | 86 +++++ R/listenv.R | 213 ++++++++----- R/parse_env_subset.R | 128 +++----- build/vignette.rds |binary inst/doc/listenv.html | 18 - inst/testme/test-aperm.R | 20 - inst/testme/test-get_variable.R | 42 +- inst/testme/test-listenv,dimensions.R | 276 +++++++++++++++-- inst/testme/test-listenv.R | 400 +++++++++++++++++++++---- inst/testme/test-parse_env_subset,dimensions.R | 153 ++++++++- inst/testme/test-parse_env_subset.R | 262 +++++++++++++--- man/parse_env_subset.Rd | 4 14 files changed, 1286 insertions(+), 350 deletions(-)
Title: Binary Expansion Testing
Description: Nonparametric detection of nonuniformity and dependence with Binary Expansion Testing (BET). See Kai Zhang (2019) BET on Independence, Journal of the American Statistical Association, 114:528, 1620-1637, <DOI:10.1080/01621459.2018.1537921>, Kai Zhang, Wan Zhang, Zhigen Zhao, Wen Zhou. (2023). BEAUTY Powered BEAST, <doi:10.48550/arXiv.2103.00674> and Wan Zhang, Zhigen Zhao, Michael Baiocchi, Yao Li, Kai Zhang. (2023) SorBET: A Fast and Powerful Algorithm to Test Dependence of Variables, Technical report.
Author: Wan Zhang [aut, cre],
Zhigen Zhao [aut],
Michael Baiocchi [aut],
Kai Zhang [aut]
Maintainer: Wan Zhang <wanz63@live.unc.edu>
Diff between BET versions 0.5.4 dated 2024-09-08 and 0.6.0 dated 2026-10-04
DESCRIPTION | 10 +++++----- MD5 | 19 ++++++++++++++----- NAMESPACE | 5 +++++ NEWS.md |only R/asymptotic-basis.R |only R/asymptotic.R |only man/BEAST.asymptotic.Rd |only man/BEAST.asymptotic.calibrate.Rd |only man/Beast.Rd | 6 +++--- man/bet.plot.Rd | 2 +- src/Makevars | 3 --- tests |only 12 files changed, 28 insertions(+), 17 deletions(-)
Title: Descriptive, Reliability, and Inferential Tables for
Psychometric Scales and Demographic Data
Description: Provides functions to format and summarise already computed
outputs from commonly used statistical and psychometric functions into
compact, single-row tables and simple graphs, with utilities to export
results to CSV, Word, and Excel formats. The package does not implement
new statistical methods or estimation procedures; instead, it organises
and presents results obtained from existing packages such as 'psych',
'stats', 'gtsummary', and 'lavaan' to streamline reporting workflows in
clinical and psychological research.
Author: Darshankumar Dharaiya [aut, cre]
Maintainer: Darshankumar Dharaiya <dharaiya.darshan@gmail.com>
Diff between scaledescr versions 0.2.7 dated 2026-06-10 and 0.2.8 dated 2026-10-04
DESCRIPTION | 7 - MD5 | 23 ++- NAMESPACE | 3 NEWS.md | 15 ++ R/data.R |only R/make_independent_t_test_table.R | 235 +++++++++++++++++++---------------- R/make_scale_total.R | 25 +++ R/merge_counterbalanced_columns.R |only R/scaledescr_remove_column.R |only data |only inst/CITATION | 22 ++- man/counterbalance.Rd |only man/make_independent_t_test_table.Rd | 36 +++-- man/make_scale_total.Rd | 26 +++ man/merge_counterbalanced_columns.Rd |only man/scaledescr_remove_column.Rd |only 16 files changed, 263 insertions(+), 129 deletions(-)
Title: Multidimensional Poverty Index (MPI) via the Alkire-Foster
Method
Description: Estimate Multidimensional Poverty Index (MPI) measures from household
survey microdata using the Alkire-Foster dual-cutoff counting method (Alkire
and Foster, 2011). Load indicator
specifications from CSV, Excel, JSON, or plain-text files; compute the
headcount ratio (H), intensity (A), and MPI = H x A across any subgroup;
and export results to formatted Excel reports. Supports complex survey
designs — stratification, clustering, and probability weights — and
optionally appends design-based standard errors and confidence intervals.
Author: Bhas Abdulsamad [aut, cre, cph]
Maintainer: Bhas Abdulsamad <aeabdulsamad@gmail.com>
Diff between mpindex versions 0.3.0 dated 2026-06-15 and 0.3.1 dated 2026-10-04
mpindex-0.3.0/mpindex/inst/doc/migrating-to-0-3-0.R |only mpindex-0.3.0/mpindex/inst/doc/migrating-to-0-3-0.Rmd |only mpindex-0.3.0/mpindex/inst/doc/migrating-to-0-3-0.html |only mpindex-0.3.0/mpindex/vignettes/migrating-to-0-3-0.Rmd |only mpindex-0.3.1/mpindex/DESCRIPTION | 12 mpindex-0.3.1/mpindex/MD5 | 64 mpindex-0.3.1/mpindex/NEWS.md | 5 mpindex-0.3.1/mpindex/R/compute-contribution.R | 13 mpindex-0.3.1/mpindex/R/compute-headcount-ratio-adjusted.R | 51 mpindex-0.3.1/mpindex/R/compute-headcount-ratio.R | 28 mpindex-0.3.1/mpindex/R/compute-mpi-from-profile.R | 153 - mpindex-0.3.1/mpindex/R/compute-mpi.R | 53 mpindex-0.3.1/mpindex/R/create-deprivation-matrix.R | 88 - mpindex-0.3.1/mpindex/R/data-helpers.R | 47 mpindex-0.3.1/mpindex/R/define-deprivation.R | 73 mpindex-0.3.1/mpindex/R/define-mpi-specs.R | 69 mpindex-0.3.1/mpindex/R/save-mpi.R | 44 mpindex-0.3.1/mpindex/R/survey-helpers.R | 59 mpindex-0.3.1/mpindex/R/utils.R | 2 mpindex-0.3.1/mpindex/README.md | 4 mpindex-0.3.1/mpindex/build/vignette.rds |binary mpindex-0.3.1/mpindex/inst/doc/migrating-to-0-3-x.R |only mpindex-0.3.1/mpindex/inst/doc/migrating-to-0-3-x.Rmd |only mpindex-0.3.1/mpindex/inst/doc/migrating-to-0-3-x.html |only mpindex-0.3.1/mpindex/inst/doc/mpindex.R | 70 mpindex-0.3.1/mpindex/inst/doc/mpindex.Rmd | 70 mpindex-0.3.1/mpindex/inst/doc/mpindex.html | 1040 +++++++------ mpindex-0.3.1/mpindex/inst/doc/survey-weights.R | 51 mpindex-0.3.1/mpindex/inst/doc/survey-weights.Rmd | 51 mpindex-0.3.1/mpindex/inst/doc/survey-weights.html | 65 mpindex-0.3.1/mpindex/man/compute_mpi.Rd | 8 mpindex-0.3.1/mpindex/man/compute_mpi_from_profile.Rd | 12 mpindex-0.3.1/mpindex/man/define_deprivation.Rd | 26 mpindex-0.3.1/mpindex/man/define_mpi_specs.Rd | 2 mpindex-0.3.1/mpindex/vignettes/migrating-to-0-3-x.Rmd |only mpindex-0.3.1/mpindex/vignettes/mpindex.Rmd | 70 mpindex-0.3.1/mpindex/vignettes/survey-weights.Rmd | 51 37 files changed, 1220 insertions(+), 1061 deletions(-)
Title: Statistical Methods for Survival Data with Dependent Censoring
Description: Several statistical methods for analyzing survival data under various forms of dependent
censoring are implemented in the package. In addition to accounting for dependent censoring, it
offers tools to adjust for unmeasured confounding factors. The implemented approaches allow
users to estimate the dependency between survival time and dependent censoring time, based
solely on observed survival data. For more details on the methods, refer to Deresa and Van
Keilegom (2021) <doi:10.1093/biomet/asaa095>, Czado and Van Keilegom (2023)
<doi:10.1093/biomet/asac067>, Crommen et al. (2024) <doi:10.1007/s11749-023-00903-9>,
Deresa and Van Keilegom (2024) <doi:10.1080/01621459.2022.2161387>, Willems et al. (2025)
<doi:10.48550/arXiv.2403.11860>, Ding and Van Keilegom (2025) and D'Haen et al. (2025)
<doi:10.1007/s10985-025-09647-0>.
Author: Ilias Willems [aut] ,
Gilles Crommen [aut] ,
Negera Wakgari Deresa [aut, cre] ,
Jie Ding [aut] ,
Claudia Czado [aut] ,
Myrthe D'Haen [aut] ,
Ingrid Van Keilegom [aut]
Maintainer: Negera Wakgari Deresa <negera.deresa@gmail.com>
Diff between depCensoring versions 0.1.10 dated 2026-04-13 and 0.1.11 dated 2026-10-04
DESCRIPTION | 13 +--- MD5 | 38 ++++++------ NAMESPACE | 20 ++++-- NEWS.md | 2 R/BoundingCovariateEffects.R | 29 ++++----- R/CopulaBasedCoxPH_pseudoLikelihoodFunctions.R | 45 +++++++------- R/CopulaCoxPHmodel_BootstrapMethods.R | 46 +++++++------- R/FitCopulaBasedCoxPHmodels.R | 24 ++----- R/FrandsenTest.R |only R/FullyParametricCopulas.R | 78 +++++++++++++++++++------ R/NonparametricTransformation.R | 55 ++++++++++------- R/ParamTransfoCompRisks.R | 65 ++++++++++++-------- R/QRdepcens.R | 27 +++++++- R/SemiParametricCopulawithoutCovariates.R | 8 +- R/dataGeneratingFunction.R | 4 - man/FrandsenTest.Rd |only man/SolveLI.Rd | 1 man/estimate.cmprsk.Rd | 10 ++- man/summary.depFit.Rd | 6 - man/summary.indepFit.Rd | 6 - tests/testthat/helper_ParamCop.R | 1 21 files changed, 284 insertions(+), 194 deletions(-)
Title: Sample Selection Models
Description: Two-step
and maximum likelihood estimation
of Heckman-type sample selection models:
standard sample selection models (Tobit-2),
endogenous switching regression models (Tobit-5),
sample selection models with binary dependent outcome variable,
interval regression with sample selection (only ML estimation),
and endogenous treatment effects models.
These methods are described in the three vignettes
that are included in this package
and in econometric textbooks such as
Greene (2011, Econometric Analysis, 7th edition, Pearson).
Author: Arne Henningsen [aut, cre] ,
Ott Toomet [aut],
Sebastian Petersen [ctb]
Maintainer: Arne Henningsen <arne.henningsen@gmail.com>
Diff between sampleSelection versions 1.2-14 dated 2026-01-20 and 1.2-16 dated 2026-10-04
DESCRIPTION | 25 - MD5 | 57 ++- NAMESPACE | 20 - NEWS | 8 R/zzz.R |only build/vignette.rds |binary inst/doc/intReg.R | 2 inst/doc/intReg.pdf |binary inst/doc/selection.R | 2 inst/doc/selection.pdf |binary inst/doc/treatReg.R | 2 inst/doc/treatReg.pdf |binary man/coef.selection.Rd | 5 man/invMillsRatio.Rd | 2 tests/Mroz87SelectionTest.R | 2 tests/Mroz87SelectionTest.Rout.save | 16 - tests/binarySelectionOutcome.R | 32 +- tests/binarySelectionOutcome.Rout.save | 473 ++------------------------------- tests/fail.R | 2 tests/fail.Rout.save | 16 - tests/heckitIvTest.R | 2 tests/heckitIvTest.Rout.save | 16 - tests/intervalTest.R | 26 - tests/intervalTest.Rout.save | 143 ++------- tests/invMillsRatioTest.R | 7 tests/invMillsRatioTest.Rout.save | 21 - tests/probit.R | 2 tests/probit.Rout.save | 16 - tests/selection.R | 2 tests/selection.Rout.save | 16 - 30 files changed, 208 insertions(+), 707 deletions(-)
More information about sampleSelection at CRAN
Permanent link
Title: HMM Toolkit for Inferring IBD Segments from SNP Data
Description: Implements continuous-time hidden Markov models (HMMs) to
infer identity-by-descent (IBD) segments shared by two individuals.
Supports two- and three-state models using single-nucleotide
polymorphism (SNP) genotypes or genotype likelihoods. Provides
posterior probabilities at each marker (forward-backward algorithm),
prediction of IBD segments (Viterbi algorithm), and functions for
visualising results. Supports both autosomal data and X-chromosomal
data. The methodology and package are described in Vigeland et al.
(2026) <doi:10.1016/j.fsigen.2025.103409>.
Author: Magnus Dehli Vigeland [aut, cre]
Maintainer: Magnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>
Diff between ibdfindr versions 0.4.0 dated 2026-08-31 and 0.5.0 dated 2026-10-04
DESCRIPTION | 19 +- MD5 | 76 +++++----- NAMESPACE | 48 +++--- NEWS.md | 17 ++ R/computePR.R | 161 ++++++++++----------- R/data.R | 31 ++++ R/estimateDropout.R |only R/findIBD.R | 59 ++++++- R/findIBD3.R |only R/findSegments.R | 31 ++-- R/fitHMM.R | 107 +++++++------- R/getSNPdata.R |only R/hmm.R | 75 +++++++++ R/hmm3.R |only R/ibdPosteriors.R | 30 ++- R/plotIBD.R | 46 +++++- R/prepForHMM.R | 228 ++++++++++++++++++++++++++++-- R/problemMarkers.R | 28 ++- R/readGL.R |only R/reportInput.R |only R/totalLoglik.R | 15 + R/utils.R | 30 --- README.md | 136 ++++++++++++++++- build |only data/sibsGL.rda |only inst/CITATION | 24 +-- man/brothersX.Rd | 78 +++++----- man/cousinsDemo.Rd | 78 +++++----- man/estimateDropout.Rd |only man/figures/README-brothersX-plot-1.png |binary man/figures/README-cousinsDemo-plot-1.png |binary man/figures/README-sibsGL-plot-1.png |only man/findIBD.Rd | 30 +++ man/findSegments.Rd | 13 + man/fitHMM.Rd | 15 + man/ibdPosteriors.Rd | 11 - man/ibdfindr-package.Rd | 56 +++---- man/plotIBD.Rd | 106 ++++++------- man/problemMarkers.Rd | 70 +++++---- man/readGL.Rd |only man/sibsGL.Rd |only man/totalLoglik.Rd | 4 tests/testthat/test-dropout.R |only tests/testthat/test-findIBD.R | 34 ++-- tests/testthat/test-gl.R |only tests/testthat/test-hmm.R | 3 46 files changed, 1119 insertions(+), 540 deletions(-)
Title: Model-Agnostic Exposure-Response Plots
Description: Provides a fluent mini-language for building exposure-response
plots (model curves/ribbons, quantile-binned summaries, data strips,
and grouped distribution panels) from observed data and a fitted
exposure-response model. Designed to be model-agnostic: any model
object that implements the er_predict() generic (and, optionally,
er_simulate() and er_summary()) can be visualised.
Author: Danielle Navarro [aut, cre]
Maintainer: Danielle Navarro <djnavarro@protonmail.com>
Diff between erplots versions 0.1.2 dated 2026-09-09 and 0.2.0 dated 2026-10-04
DESCRIPTION | 30 + MD5 | 193 +++++++----- NAMESPACE | 21 + NEWS.md | 224 ++++++++++++++ R/data.R | 2 R/er-generics.R | 59 +++ R/er-plot-add.R | 366 ++++++++++++++++------- R/er-plot-api.R | 66 ++-- R/er-plot-build.R | 69 +++- R/er-plot-compose.R | 22 - R/er-plot-layer.R | 213 ++++++++++--- R/er-plot-style-data.R | 82 +++-- R/er-plot-style-group.R | 140 ++++++--- R/er-plot-style-model.R | 71 ++-- R/er-plot-style-quantile.R | 137 ++++++-- R/er-plot-style-summary.R | 70 ++-- R/er-plot-style.R | 310 +++++++++++++------- R/er-plot-theme.R | 51 ++- R/er-style-registry.R |only R/er-tte-add.R |only R/er-tte-api.R |only R/er-tte-layer.R |only R/er-tte-style-censor.R |only R/er-tte-style-curve.R |only R/er-tte-style-model.R |only R/er-tte-style-risktable.R |only R/er-tte-style-summary.R |only R/er-tte-style.R |only R/er-tte-theme.R |only R/er-vpc-add.R | 93 ++++-- R/er-vpc-api.R | 88 +++-- R/er-vpc-build.R | 103 ++++++ R/er-vpc-layer.R | 80 +++-- R/er-vpc-style-observed.R | 116 ++++++- R/er-vpc-style-simulated.R | 119 ++++++- R/er-vpc-style.R |only R/er-vpc-theme.R | 21 - R/utils-helpers.R | 372 +++++++++++++++++++++--- README.md | 26 + inst/WORDLIST | 12 inst/doc/erplots.R | 3 inst/doc/erplots.Rmd | 31 +- inst/doc/erplots.html | 233 ++++++++------- man/ci_quantile.Rd | 11 man/cut_quantile.Rd | 68 +++- man/er_model_interface.Rd | 50 +++ man/er_plot.Rd | 2 man/er_plot_add_data.Rd | 58 ++- man/er_plot_add_groups.Rd | 77 +++- man/er_plot_add_model.Rd | 66 ++-- man/er_plot_add_quantiles.Rd | 63 +++- man/er_plot_add_summary.Rd | 50 ++- man/er_plot_build.Rd | 2 man/er_plot_theme.Rd | 50 ++- man/er_style.Rd | 29 + man/er_style_data.Rd | 88 ++++- man/er_style_group.Rd | 90 ++++- man/er_style_labels.Rd |only man/er_style_model.Rd | 59 ++- man/er_style_quantile.Rd | 86 ++++- man/er_style_summary.Rd | 64 ++-- man/er_style_tag.Rd | 232 ++++++++++---- man/er_style_tte.Rd |only man/er_style_tte_censor.Rd |only man/er_style_tte_curve.Rd |only man/er_style_tte_model.Rd |only man/er_style_tte_risktable.Rd |only man/er_style_tte_summary.Rd |only man/er_style_vpc.Rd |only man/er_style_vpc_observed.Rd | 103 +++++- man/er_style_vpc_simulated.Rd | 106 ++++++ man/er_tte.Rd |only man/er_tte_add_censor.Rd |only man/er_tte_add_curve.Rd |only man/er_tte_add_model.Rd |only man/er_tte_add_risktable.Rd |only man/er_tte_add_summary.Rd |only man/er_tte_build.Rd |only man/er_tte_theme.Rd |only man/er_vpc.Rd | 68 ++-- man/er_vpc_add_observed.Rd | 33 +- man/er_vpc_add_simulated.Rd | 52 ++- man/er_vpc_build.Rd | 2 man/er_vpc_theme.Rd | 21 - man/erplots_data.Rd | 2 man/figures/README-er-plot-2.png |binary tests/testthat/Rplots.pdf |binary tests/testthat/helper-toy-model.R | 65 +++- tests/testthat/test-documentation-styles-sync.R |only tests/testthat/test-er-plot-api.R | 151 +++++++-- tests/testthat/test-er-plot-build.R |only tests/testthat/test-er-plot-layer.R | 71 ++++ tests/testthat/test-er-plot-style-data.R | 6 tests/testthat/test-er-plot-style-dots.R | 2 tests/testthat/test-er-plot-style-group.R | 8 tests/testthat/test-er-plot-style-quantile.R | 34 +- tests/testthat/test-er-plot-style-tag.R | 4 tests/testthat/test-er-plot-theme.R | 42 ++ tests/testthat/test-er-style-registry.R |only tests/testthat/test-er-tte-add.R |only tests/testthat/test-er-tte-api.R |only tests/testthat/test-er-tte-style-censor.R |only tests/testthat/test-er-tte-style-curve.R |only tests/testthat/test-er-tte-style-model.R |only tests/testthat/test-er-tte-style-risktable.R |only tests/testthat/test-er-tte-style-summary.R |only tests/testthat/test-er-tte-theme.R |only tests/testthat/test-er-vpc-add.R | 17 - tests/testthat/test-er-vpc-api.R | 56 ++- tests/testthat/test-er-vpc-build.R |only tests/testthat/test-er-vpc-layer.R | 51 +++ tests/testthat/test-er-vpc-style-observed.R | 42 ++ tests/testthat/test-er-vpc-style-simulated.R | 35 +- tests/testthat/test-er-vpc-theme.R | 7 tests/testthat/test-toy-model-sync.R | 26 + tests/testthat/test-tte-model-sync.R |only tests/testthat/test-utils-helpers.R | 180 +++++++++++ vignettes/erplots.Rmd | 31 +- 118 files changed, 4373 insertions(+), 1410 deletions(-)
Title: Ecological Indices Calculator for Nematode Communities
Description: Provides a computational toolkit for analyzing nematode communities in ecological studies.
Includes methods to quantify nematode-based ecological indicators such as metabolic footprints,
energy flow metrics, and community structure. These tools support assessments of soil health,
ecosystem functioning, and trophic interactions, standardizing the use of nematodes as
bioindicators.
Author: Yuxuan He [aut, cre] ,
Dong Wang [ths],
Yuan Miao [ths]
Maintainer: Yuxuan He <heyuxuan0525@outlook.com>
Diff between Nematode versions 0.3.1 dated 2026-07-12 and 0.3.2 dated 2026-10-04
DESCRIPTION | 8 +++---- MD5 | 6 ++--- NEWS.md | 7 ++++++ R/ecological_indices.R | 56 +++++++++++++++++++++++++++++++++++++++++++------ 4 files changed, 64 insertions(+), 13 deletions(-)
Title: Knowledge Space Theory
Description: Knowledge space theory by Doignon and Falmagne (1999)
<doi:10.1007/978-3-642-58625-5> is a set- and order-theoretical
framework, which proposes mathematical formalisms to operationalize
knowledge structures in a particular domain. The 'kst' package provides
basic functionalities to generate, handle, and manipulate knowledge
structures and knowledge spaces.
Author: Christina Stahl [aut],
David Meyer [aut],
Cord Hockemeyer [aut, cre]
Maintainer: Cord Hockemeyer <cord.hockemeyer@uni-graz.at>
Diff between kst versions 0.5-5 dated 2026-03-09 and 0.5-6 dated 2026-10-04
Changelog | 4 DESCRIPTION | 8 MD5 | 25 +- R/as.binaryMatrix.R | 11 - R/as.famset.R | 12 - build/vignette.rds |binary inst/doc/kst.R | 395 ++++++++++++++++++++++-------------------- inst/doc/kst.Rnw | 91 ++++++--- inst/doc/kst.pdf |binary man/as.binaryMatrix.Rd | 10 - man/as.famset.Rd | 87 ++++----- vignettes/kst-012.pdf |only vignettes/kst-020.pdf |only vignettes/kst-as.relation.pdf |only vignettes/kst.Rnw | 91 ++++++--- 15 files changed, 421 insertions(+), 313 deletions(-)
Title: Visualizing Hypothesis Tests in Multivariate Linear Models
Description: Provides HE plot and other functions for visualizing hypothesis
tests in multivariate linear models. HE plots represent sums-of-squares-and-products
matrices for linear hypotheses and for error using ellipses (in two
dimensions) and ellipsoids (in three dimensions). It also provides other tools for analysis and graphical display of the models
such as robust methods and homogeneity of variance covariance matrices.
The related 'candisc' package provides visualizations in a reduced-rank canonical discriminant space when
there are more than a few response variables.
Author: Michael Friendly [aut, cre] ,
John Fox [aut] ,
Georges Monette [aut] ,
Phil Chalmers [ctb] ,
Duncan Murdoch [ctb],
Gavin Klorfine [ctb]
Maintainer: Michael Friendly <friendly@yorku.ca>
Diff between heplots versions 1.8.5 dated 2026-09-13 and 1.8.6 dated 2026-10-04
DESCRIPTION | 18 MD5 | 59 - NAMESPACE | 2 NEWS.md | 50 R/covEllipses.R | 12 R/eigstatCI.R | 41 R/heplot.R | 27 R/heplot1d.R | 13 R/heplot3d.R | 8 R/label.ellipse.R | 8 R/pvPlot.R | 5 R/robmlm.R | 78 + R/termMeans.R | 26 inst/doc/HE_manova.Rmd | 1827 ++++++++++++++++----------------- inst/doc/HE_manova.html | 34 inst/doc/HE_mmra.html | 6 inst/doc/Robust.html | 4 inst/doc/datasets.html | 32 man/covEllipses.Rd | 7 man/eigstatCI.Rd | 4 man/figures/README-iris4-1.png |binary man/figures/cheatsheet-thumbs.png |only man/heplot.Rd | 25 man/heplot1d.Rd | 12 man/heplot3d.Rd | 7 man/label.ellipse.Rd | 3 man/pvPlot.Rd | 2 man/robmlm.Rd | 19 man/termMeans.Rd | 3 vignettes/HE_manova.Rmd | 1827 ++++++++++++++++----------------- vignettes/images/manova-plastic1-1.png |binary 31 files changed, 2216 insertions(+), 1943 deletions(-)
Title: Broadcasted Array Operations Like 'NumPy'
Description: Implements efficient 'NumPy'-like broadcasted operations for atomic and recursive arrays.
In the context of operations involving 2 (or more) arrays,
“broadcasting” (AKA singleton expansion) refers to efficiently recycling array dimensions,
without making copies.
Besides linking to 'Rcpp',
'broadcast' does not use any external libraries in any way;
'broadcast' was essentially made from scratch and can be installed out-of-the-box.
The implementations available in 'broadcast' include, but are not limited to, the following.
1) Broadcasted element-wise operations on any 2 arrays;
they support a large set of
relational, arithmetic, Boolean, string, and bit-wise operations.
2) A faster, more memory efficient, and broadcasted abind-like function,
for binding arrays along an arbitrary dimension.
3) Broadcasted ifelse-like and apply-like functions.
4) Casting functions,
that cast subset-groups of an array to a new dimension, cast nested lists to dimensional lists, and vice-versa.
5) A few linear [...truncated...]
Author: Tony Wilkes [aut, cre, cph]
Maintainer: Tony Wilkes <tonywilkes.nl@gmail.com>
Diff between broadcast versions 0.1.9.6 dated 2026-08-21 and 0.1.9.8 dated 2026-10-04
broadcast-0.1.9.6/broadcast/R/internal_opfuns.R |only broadcast-0.1.9.6/broadcast/R/overload_ops_math.R |only broadcast-0.1.9.6/broadcast/R/overload_relops.R |only broadcast-0.1.9.6/broadcast/inst/tinytest/bc_b/test-bc_b_andor.R |only broadcast-0.1.9.8/broadcast/DESCRIPTION | 8 broadcast-0.1.9.8/broadcast/MD5 | 100 +- broadcast-0.1.9.8/broadcast/NAMESPACE | 1 broadcast-0.1.9.8/broadcast/NEWS.md | 12 broadcast-0.1.9.8/broadcast/R/aaa03_broadcast_bind.R | 3 broadcast-0.1.9.8/broadcast/R/aaa05_broadcast_typecast.R | 3 broadcast-0.1.9.8/broadcast/R/bc_b.R | 5 broadcast-0.1.9.8/broadcast/R/bc_bit.R | 16 broadcast-0.1.9.8/broadcast/R/broadcastWrappers.R | 7 broadcast-0.1.9.8/broadcast/R/internal_bind.R | 2 broadcast-0.1.9.8/broadcast/R/internal_functions.R | 33 broadcast-0.1.9.8/broadcast/R/internal_is.R |only broadcast-0.1.9.8/broadcast/R/internal_oplists.R |only broadcast-0.1.9.8/broadcast/R/internal_typefuns.R | 59 - broadcast-0.1.9.8/broadcast/R/overload_ops_arith.R |only broadcast-0.1.9.8/broadcast/R/overload_ops_equneq.R |only broadcast-0.1.9.8/broadcast/R/overload_ops_gs.R |only broadcast-0.1.9.8/broadcast/R/overload_ops_intops.R |only broadcast-0.1.9.8/broadcast/R/typecast.R | 6 broadcast-0.1.9.8/broadcast/inst/examples/bc_b.R | 1 broadcast-0.1.9.8/broadcast/inst/examples/checkmissing.R | 2 broadcast-0.1.9.8/broadcast/inst/examples/typecast.R | 4 broadcast-0.1.9.8/broadcast/inst/tinytest/aaa_binary_prep_part1/test-part1-conformalize.R | 2 broadcast-0.1.9.8/broadcast/inst/tinytest/aaa_binary_prep_part1/test-part1-outdim_orig.R | 4 broadcast-0.1.9.8/broadcast/inst/tinytest/bc_b/test-bc_b.R |only broadcast-0.1.9.8/broadcast/inst/tinytest/bc_b/test-bc_b_rel.R | 81 -- broadcast-0.1.9.8/broadcast/inst/tinytest/bc_b/test-logic.R | 24 broadcast-0.1.9.8/broadcast/inst/tinytest/bc_bytes/test-bc_bit_int.R | 4 broadcast-0.1.9.8/broadcast/inst/tinytest/bc_bytes/test-bc_bit_negate.R |only broadcast-0.1.9.8/broadcast/inst/tinytest/bc_bytes/test-bc_bit_raw.R | 5 broadcast-0.1.9.8/broadcast/inst/tinytest/bc_general/test-bc_ifelse.R | 3 broadcast-0.1.9.8/broadcast/inst/tinytest/bc_general/test-bc_ifelse_raw.R | 2 broadcast-0.1.9.8/broadcast/inst/tinytest/bc_general/test-bc_strrep.R | 12 broadcast-0.1.9.8/broadcast/inst/tinytest/bc_num/test-relop_precision.R | 6 broadcast-0.1.9.8/broadcast/inst/tinytest/bind_array_1_basic/test-bind_array-edgecases.R | 9 broadcast-0.1.9.8/broadcast/inst/tinytest/bind_array_1_basic/test-bind_array-errors.R | 7 broadcast-0.1.9.8/broadcast/inst/tinytest/overload/test-error.R | 384 +++++++++- broadcast-0.1.9.8/broadcast/inst/tinytest/shallow2atomic/test-coercion.R | 6 broadcast-0.1.9.8/broadcast/inst/tinytest/test-binary1d.R | 24 broadcast-0.1.9.8/broadcast/inst/tinytest/typecast/test-PBR.R |only broadcast-0.1.9.8/broadcast/inst/tinytest/typecast/test-atomic_typecast.R | 12 broadcast-0.1.9.8/broadcast/inst/tinytest/typecast/test-broadcasterclass.R | 10 broadcast-0.1.9.8/broadcast/inst/tinytest/typecast/test-edgecases.R | 2 broadcast-0.1.9.8/broadcast/man/bc.b.Rd | 6 broadcast-0.1.9.8/broadcast/man/bc.bit.Rd | 15 broadcast-0.1.9.8/broadcast/man/bind_array.Rd | 3 broadcast-0.1.9.8/broadcast/man/checkmissing.Rd | 2 broadcast-0.1.9.8/broadcast/man/typecast.Rd | 10 broadcast-0.1.9.8/broadcast/src/C_inputOK_relop_gs.c |only broadcast-0.1.9.8/broadcast/src/RcppExports.cpp | 2 broadcast-0.1.9.8/broadcast/src/broadcast.h | 271 +++---- broadcast-0.1.9.8/broadcast/src/rcpp_bcRel_cplx.cpp | 27 broadcast-0.1.9.8/broadcast/src/rcpp_bc_cplx.cpp | 74 - broadcast-0.1.9.8/broadcast/tests/tinytest.R | 3 58 files changed, 728 insertions(+), 544 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-04-26 1.5.3
2024-11-04 1.4.0
2024-09-13 1.2.0
2024-06-13 1.1.0
2024-03-14 1.0.8
2024-03-11 1.0.7
2023-11-25 1.0.6
2023-10-31 1.0.5
2023-10-02 1.0.4
2023-09-13 1.0.3
2023-09-05 1.0.2
2022-07-06 0.9.5
2021-10-13 0.9.3
2021-05-20 0.9.2
2021-04-11 0.9.1
2021-04-09 0.9.0
2021-03-31 0.8.2
Title: Robust Generalized Linear Models (GLM) using Mixtures
Description: Robust generalized linear models (GLM) using a mixture method, as described in Beath (2018) <doi:10.1080/02664763.2017.1414164>. This assumes that the data are a mixture of standard observations, being a generalised linear model, and outlier observations from an overdispersed generalized linear model. The overdispersed linear model is obtained by including a normally distributed random effect in the linear predictor of the generalized linear model.
Author: Ken Beath [aut, cre]
Maintainer: Ken Beath <ken@kjbeath.id.au>
Diff between robmixglm versions 1.2-8 dated 2026-07-02 and 1.2-9 dated 2026-10-04
robmixglm-1.2-8/robmixglm/inst/doc/robmixglm-package.pdf |only robmixglm-1.2-8/robmixglm/inst/doc/robmixglm-package.pdf.asis |only robmixglm-1.2-8/robmixglm/vignettes/robmixglm-package.pdf.asis |only robmixglm-1.2-9/robmixglm/DESCRIPTION | 8 robmixglm-1.2-9/robmixglm/MD5 | 30 - robmixglm-1.2-9/robmixglm/NAMESPACE | 18 robmixglm-1.2-9/robmixglm/R/gamma.fit.robmixglm.R | 2 robmixglm-1.2-9/robmixglm/R/outlierProbs.robmixglm.R | 5 robmixglm-1.2-9/robmixglm/R/outlierProbsMix.robmixglm.R |only robmixglm-1.2-9/robmixglm/R/outlierTest.robmixglm.R | 271 ---------- robmixglm-1.2-9/robmixglm/R/outlierTestMix.robmixglm.R |only robmixglm-1.2-9/robmixglm/R/plot.outlierProbsMix.R |only robmixglm-1.2-9/robmixglm/R/print.outlierTestMix.R |only robmixglm-1.2-9/robmixglm/build/vignette.rds |binary robmixglm-1.2-9/robmixglm/inst/NEWS | 8 robmixglm-1.2-9/robmixglm/inst/doc/robmixglm-package.html |only robmixglm-1.2-9/robmixglm/inst/doc/robmixglm-package.html.asis |only robmixglm-1.2-9/robmixglm/man/outlierProbsMix.robmixglm.Rd |only robmixglm-1.2-9/robmixglm/man/outlierTestMix.robmixglm.Rd |only robmixglm-1.2-9/robmixglm/man/plot.outlierProbsMix.Rd |only robmixglm-1.2-9/robmixglm/man/print.outlierTestMix.Rd |only robmixglm-1.2-9/robmixglm/vignettes/robmixglm-package.Rmd |only robmixglm-1.2-9/robmixglm/vignettes/robmixglm-package.bib |only robmixglm-1.2-9/robmixglm/vignettes/robmixglm-package.html.asis |only 24 files changed, 57 insertions(+), 285 deletions(-)
Title: Robust Meta-Analysis and Meta-Regression
Description: Performs meta-analysis and meta-regression using standard and robust methods with confidence intervals based on the profile likelihood. Robust methods are based on alternative distributions for the random effect, either the t-distribution (Lee and Thompson, 2008 <doi:10.1002/sim.2897> or Baker and Jackson, 2008 <doi:10.1007/s10729-007-9041-8>) or mixtures of normals (Beath, 2014 <doi:10.1002/jrsm.1114>).
Author: Ken Beath [aut, cre],
Ben Bolker [ctb],
R Development Core Team [ctb]
Maintainer: Ken Beath <ken@kjbeath.id.au>
Diff between metaplus versions 1.0-8 dated 2026-02-14 and 1.0-10 dated 2026-10-04
metaplus-1.0-10/metaplus/DESCRIPTION | 12 +- metaplus-1.0-10/metaplus/MD5 | 43 +++++----- metaplus-1.0-10/metaplus/NAMESPACE | 14 +++ metaplus-1.0-10/metaplus/R/makestart.profilemix.metaplus.R | 12 +- metaplus-1.0-10/metaplus/R/metaplus.R | 6 + metaplus-1.0-10/metaplus/R/outlierProbs.metaplus.R | 17 +++ metaplus-1.0-10/metaplus/R/outlierProbsMeta.metaplus.R |only metaplus-1.0-10/metaplus/R/plot.outlierProbs.R | 12 +- metaplus-1.0-10/metaplus/R/plot.outlierProbsMeta.R |only metaplus-1.0-10/metaplus/R/testOutliers.metaplus.R | 9 +- metaplus-1.0-10/metaplus/R/testOutliers.profilet.metaplus.R | 2 metaplus-1.0-10/metaplus/R/testOutliersMeta.metaplus.R |only metaplus-1.0-10/metaplus/build/vignette.rds |binary metaplus-1.0-10/metaplus/inst/NEWS | 12 ++ metaplus-1.0-10/metaplus/inst/doc/metaplus-package.html |only metaplus-1.0-10/metaplus/inst/doc/metaplus-package.html.asis |only metaplus-1.0-10/metaplus/man/metaplus-package.Rd | 2 metaplus-1.0-10/metaplus/man/metaplus.Rd | 21 ++-- metaplus-1.0-10/metaplus/man/outlierProbs.Rd | 2 metaplus-1.0-10/metaplus/man/outlierProbsMeta.Rd |only metaplus-1.0-10/metaplus/man/plot.outlierProbs.Rd | 2 metaplus-1.0-10/metaplus/man/plot.outlierProbsMeta.Rd |only metaplus-1.0-10/metaplus/man/testOutliersMeta.Rd |only metaplus-1.0-10/metaplus/vignettes/metaplus-package.Rmd |only metaplus-1.0-10/metaplus/vignettes/metaplus-package.bib |only metaplus-1.0-10/metaplus/vignettes/metaplus-package.html.asis |only metaplus-1.0-8/metaplus/inst/doc/metaplus-package-code.R |only metaplus-1.0-8/metaplus/inst/doc/metaplus-package.pdf |only metaplus-1.0-8/metaplus/inst/doc/metaplus-package.pdf.asis |only metaplus-1.0-8/metaplus/vignettes/metaplus-package.pdf.asis |only 30 files changed, 112 insertions(+), 54 deletions(-)