Title: Statistical Framework for in Vivo Drug Combination Studies
Description: A framework for evaluating drug combination effects in preclinical in vivo studies.
'SynergyLMM' provides functions to analyze longitudinal tumor growth experiments using mixed-effects models,
perform time-resolved analyses of synergy and antagonism, evaluate model diagnostics and performance,
and assess both post-hoc and a priori statistical power.
The calculation of drug combination synergy follows the statistical framework provided by Demidenko and Miller (2019, <doi:10.1371/journal.pone.0224137>).
The implementation and analysis of linear mixed-effect models is based on the methods described by Pinheiro and Bates (2000, <doi:10.1007/b98882>),
and Gałecki and Burzykowski (2013, <doi:10.1007/978-1-4614-3900-4>).
Author: Rafael Romero-Becerra [aut, cre] ,
Zhi Zhao [ctb],
Tero Aittokallio [ctb]
Maintainer: Rafael Romero-Becerra <rafrombec@gmail.com>
Diff between SynergyLMM versions 1.1.3 dated 2026-05-12 and 1.1.4 dated 2026-08-20
DESCRIPTION | 8 +- MD5 | 32 ++++----- NEWS.md | 19 +++++ R/getRTV.R | 10 +- R/lmmModel.R | 8 +- R/lmmSynergy.R | 16 ---- R/plot_lmmSynergy.R | 67 +++++++++--------- R/utils.R | 42 +++++++++++ build/partial.rdb |binary build/vignette.rds |binary inst/doc/SynergyLMM.html | 7 - tests/testthat/test-lmmDiagnostics.R | 39 +++++++---- tests/testthat/test-lmmModel.R | 20 +++-- tests/testthat/test-lmmPower.R | 67 +++++++++++------- tests/testthat/test-lmmSynergy.R | 120 ++++++++++++++++++++-------------- tests/testthat/test-plot_SynergyLMM.R | 21 ++++- tests/testthat/test-utils.R | 59 ++++++++++++++++ 17 files changed, 353 insertions(+), 182 deletions(-)
Title: Survey Instrument Workflows
Description: Supports survey research workflows built around a typed
instrument object (the sframe). Features include visual instrument
design via a browser-based builder or 'Shiny' studio, export to a
self-contained static HTML survey, an embeddable 'Shiny' module, SHA-256
integrity-checked serialisation to the '.sframe' format, multi-page survey
rendering, branching logic, response quality checking, scale scoring,
psychometric diagnostics, analysis-plan execution, model syntax planning,
an interactive response dashboard, codebook generation, and reproducible
HTML reporting. This release adds three capability themes: multi-criteria
decision analysis (AHP, ANP, DEMATEL, TOPSIS, VIKOR, MOORA, SMART,
WASPAS, PROMETHEE II, ELECTRE I), small-sample survey helpers, and
text and open-ended response analysis (term and n-gram frequency,
keyword in context, co-occurrence and co-occurrence networks, sentiment,
document-feature matrices, and topic modelling via LDA or structural
topic models).
Author: Mohammed Ali Sharafuddin [aut, cre]
Maintainer: Mohammed Ali Sharafuddin <mohammedali.page@gmail.com>
Diff between surveyframe versions 0.3.4 dated 2026-07-24 and 0.4.0 dated 2026-08-20
DESCRIPTION | 26 MD5 | 265 +++++-- NAMESPACE | 139 +++ NEWS.md | 339 +++++++++ R/accessors.R |only R/amendments.R |only R/analysis_plan.R | 182 ++++- R/as_data_frame.R |only R/conditions.R | 57 + R/conjoint_design.R |only R/dashboard.R | 2 R/decision_data.R |only R/decision_dematel.R |only R/decision_methods.R |only R/decision_preference.R |only R/decision_ranking.R |only R/decision_sensitivity.R |only R/demo_helpers.R | 4 R/git_link.R |only R/google_sheets.R | 31 R/model_layer.R | 128 ++- R/plots.R | 819 ++++++++++++++++++++++- R/psychometrics.R | 13 R/quality_report.R | 12 R/read_responses.R | 55 - R/read_write_sframe.R | 145 +++- R/render_survey.R | 210 +++++ R/reporting.R | 150 +--- R/rstudio_addins.R |only R/sf_instrument.R | 7 R/sf_item.R | 109 +++ R/sf_scale.R | 4 R/sframe_methods.R | 21 R/statistics_reports.R | 239 ++++++ R/surveyframe-package.R | 17 R/text_analysis.R |only R/utils.R | 16 R/validate_sframe.R | 237 +++++- R/validation_result.R |only README.md | 57 + build/vignette.rds |binary inst/CITATION | 30 inst/WORDLIST |only inst/builder/survey_builder.html | 573 +++++++++++++++- inst/doc/analysing-survey-responses.R | 10 inst/doc/analysing-survey-responses.Rmd | 10 inst/doc/analysing-survey-responses.html | 154 ---- inst/doc/building-survey-instrument.R | 15 inst/doc/building-survey-instrument.Rmd | 24 inst/doc/building-survey-instrument.html | 56 - inst/doc/efa-cfa-sem-pls-syntax.Rmd | 4 inst/doc/efa-cfa-sem-pls-syntax.html | 66 - inst/doc/mcdm-analysis.R |only inst/doc/mcdm-analysis.Rmd |only inst/doc/mcdm-analysis.html |only inst/doc/scale-reliability-validity.R | 20 inst/doc/scale-reliability-validity.Rmd | 20 inst/doc/scale-reliability-validity.html | 34 inst/doc/small-sample.R |only inst/doc/small-sample.Rmd |only inst/doc/small-sample.html |only inst/doc/surveybuilder-gui-overview.Rmd | 9 inst/doc/surveybuilder-gui-overview.html | 10 inst/doc/surveyframe.R | 73 +- inst/doc/surveyframe.Rmd | 179 ++++- inst/doc/surveyframe.html | 818 +++++++++++++--------- inst/doc/text-analysis.R |only inst/doc/text-analysis.Rmd |only inst/doc/text-analysis.html |only inst/extdata/hotel_supplier_mcdm.sframe |only inst/extdata/hotel_supplier_mcdm_responses.csv |only inst/extdata/surveyframe_input_types_demo.sframe | 35 inst/extdata/tourism_services_demo.sframe | 62 + inst/rstudio |only inst/schema |only inst/shiny/app.R | 372 ++++++++++ inst/static_survey/template.html | 253 +++++++ man/amend_sframe.Rd |only man/amendment_log.Rd |only man/as_sframe.Rd |only man/cfa_syntax.Rd | 4 man/clean_text_responses.Rd |only man/codebook_report.Rd | 4 man/extract_quotes.Rd |only man/launch_builder_demo.Rd | 4 man/launch_dashboard.Rd | 2 man/link_git_commit.Rd |only man/ngram_frequency.Rd |only man/outlier_report.Rd | 2 man/read_responses.Rd | 4 man/render_report.Rd | 2 man/sensitivity_analysis.Rd |only man/sf_accessors.Rd |only man/sf_component_list.Rd |only man/sf_conjoint_design.Rd |only man/sf_identity.Rd |only man/sf_instrument.Rd | 2 man/sf_item.Rd | 21 man/sf_plan-set.Rd |only man/sf_report_accessors.Rd |only man/sf_scale.Rd | 4 man/sf_validation_accessors.Rd |only man/sframe_aggregate_judgements.Rd |only man/sframe_as_data_frame.Rd |only man/sframe_assemble_pairwise.Rd |only man/sframe_codebook_items_display.Rd | 10 man/sframe_collected_weights.Rd |only man/sframe_decision_options.Rd |only man/sframe_dematel_compute.Rd |only man/sframe_draw_likert_diverging.Rd | 4 man/sframe_draw_mosaic.Rd | 4 man/sframe_plot_cooccurrence.Rd |only man/sframe_plot_cooccurrence_network.Rd |only man/sframe_plot_decision_ranking.Rd |only man/sframe_plot_dematel_influence.Rd |only man/sframe_plot_descriptives.Rd | 2 man/sframe_plot_efa_loadings.Rd | 4 man/sframe_plot_group_comparison.Rd | 2 man/sframe_plot_likert_scale.Rd | 2 man/sframe_plot_ngram_frequency.Rd |only man/sframe_plot_sentiment.Rd |only man/sframe_plot_term_frequency.Rd |only man/sframe_plot_topics.Rd |only man/sframe_rated_matrix.Rd |only man/sframe_run_stm_topics.Rd |only man/sframe_run_topic_model_lda.Rd |only man/sframe_small_sample_advisory.Rd |only man/sframe_subset.Rd |only man/sframe_validation.Rd |only man/sframe_warn_design.Rd |only man/surveyframe-package.Rd | 17 man/term_context.Rd |only man/term_frequency.Rd |only man/validate_model.Rd | 18 man/validate_sframe.Rd | 46 - man/validity_report.Rd | 2 tests/testthat/test-accessors.R |only tests/testthat/test-amendments.R |only tests/testthat/test-builder-analysis.R | 8 tests/testthat/test-builder-text-options.R |only tests/testthat/test-chrome-detritus.R |only tests/testthat/test-conjoint-design.R |only tests/testthat/test-core.R | 49 + tests/testthat/test-decision-ahp-anp.R |only tests/testthat/test-decision-data.R |only tests/testthat/test-decision-dematel.R |only tests/testthat/test-decision-item-types.R |only tests/testthat/test-decision-preference.R |only tests/testthat/test-decision-ranking.R |only tests/testthat/test-decision-scale-guards.R |only tests/testthat/test-decision-sensitivity.R |only tests/testthat/test-decision-topsis.R |only tests/testthat/test-git-link.R |only tests/testthat/test-item-rest-correlation.R |only tests/testthat/test-known-vars-expansion.R |only tests/testthat/test-mcdm-fixture.R |only tests/testthat/test-model-type-guards.R |only tests/testthat/test-quality-decision-columns.R |only tests/testthat/test-read-responses-name-repair.R |only tests/testthat/test-repeated-anova-strata.R |only tests/testthat/test-rstudio-addins.R |only tests/testthat/test-serialisation-fixed-point.R |only tests/testthat/test-sframe-schema.R |only tests/testthat/test-shiny-decision-render.R |only tests/testthat/test-shiny-export-shape.R |only tests/testthat/test-studio-decision-roles.R |only tests/testthat/test-text-analysis.R |only tests/testthat/test-text-cooccurrence-network.R |only tests/testthat/test-text-cooccurrence.R |only tests/testthat/test-text-ngram-context.R |only tests/testthat/test-text-sentiment.R |only tests/testthat/test-text-topics.R |only tests/testthat/test-v03-analysis-models.R | 76 ++ tests/testthat/test-v034-effect-cis.R | 36 + tests/testthat/test-v034-family-plots.R | 41 + tests/testthat/test-v034-stats-reporting.R | 2 vignettes/analysing-survey-responses.Rmd | 10 vignettes/building-survey-instrument.Rmd | 24 vignettes/efa-cfa-sem-pls-syntax.Rmd | 4 vignettes/mcdm-analysis.Rmd |only vignettes/scale-reliability-validity.Rmd | 20 vignettes/small-sample.Rmd |only vignettes/surveybuilder-gui-overview.Rmd | 9 vignettes/surveyframe.Rmd | 179 ++++- vignettes/text-analysis.Rmd |only 185 files changed, 5548 insertions(+), 1181 deletions(-)
Title: Robust Latent Profile Analysis
Description: Provides a comprehensive toolset for estimating Latent Profile
Analysis (LPA) models that are robust to multivariate outliers and missing
data. By integrating a high-performance 'C++' engine via 'RcppArmadillo',
it reliably extracts latent profiles using both Expectation-Maximization (EM)
and Markov Chain Monte Carlo (MCMC) Bayesian estimation. The EM engine
implements a Full Information Maximum Likelihood (FIML) approach, Huber
weighting, and LASSO regularization with k-fold cross-validation for optimal
penalty tuning. The MCMC engine utilizes a Bayesian Lasso approach with
Laplace priors, the same Huber down-weighting available in the EM engine,
multiple chains (4 by default), and classic Gelman-Rubin/effective sample
size convergence diagnostics. It supports multiple geometric variance-covariance
models, along with functions for bootstrapped likelihood ratio tests (BLRT), BCH
auxiliary variable analysis, and plotting.
For methodological details on the Bootstrapped Likelihood Ratio T [...truncated...]
Author: Valerio Riccardo Aquila [aut, cre]
Maintainer: Valerio Riccardo Aquila <valerio_aquila@hotmail.it>
Diff between RobustLPA versions 0.1.0 dated 2026-07-05 and 1.0.0 dated 2026-08-20
DESCRIPTION | 29 - MD5 | 59 +- NAMESPACE | 7 NEWS.md | 111 ++++ R/RcppExports.R | 12 R/RobustLPA-package.R | 1 R/bch_robust.R |only R/blrt_robust.R | 179 +++++-- R/data.R |only R/estimate_profiles_robust.R | 188 ++++++- R/label_utils.R |only R/mcmc_diagnostics.R |only R/parallel_utils.R |only R/plot_mcmc_chains.R |only R/plot_robust_lpa.R | 104 +++- R/print_summary_robust_lpa.R |only R/robust_lpa.R | 958 +++++++++++++++++++++++++++++++------ R/robust_m_step.R | 164 ++++-- R/robust_mean.R | 48 + build/vignette.rds |only data |only inst |only man/RobustLPA-package.Rd | 2 man/bch_robust.Rd |only man/blrt_robust.Rd | 81 ++- man/estimate_profiles_robust.Rd | 53 +- man/neuro_data.Rd |only man/plot_mcmc_chains.Rd |only man/plot_robust_lpa.Rd | 22 man/print.robust_lpa.Rd |only man/print.summary.robust_lpa.Rd |only man/robust_lpa.Rd | 243 ++++++++- man/robust_m_step.Rd | 61 +- man/robust_mean.Rd | 32 + man/summary.robust_lpa.Rd |only src/RcppExports.cpp | 36 + src/robust_engine.cpp | 1019 ++++++++++++++++++++++++++++++---------- vignettes |only 38 files changed, 2732 insertions(+), 677 deletions(-)
Title: Fast R and C++ Access to NIfTI Images
Description: Provides very fast read and write access to images stored in the
NIfTI-1, NIfTI-2 and ANALYZE-7.5 formats, with seamless synchronisation
of in-memory image objects between compiled C and interpreted R code. Also
provides a simple image viewer, and a C/C++ API that can be used by other
packages. Not to be confused with 'RNiftyReg', which performs image
registration and applies spatial transformations.
Author: Jon Clayden [cre, aut] ,
Bob Cox [aut],
Mark Jenkinson [aut],
Matt Hall [ctb],
Rick Reynolds [ctb],
Kate Fissell [ctb],
Jean-loup Gailly [cph],
Mark Adler [cph]
Maintainer: Jon Clayden <code@clayden.org>
Diff between RNifti versions 1.9.0 dated 2026-01-13 and 1.10.0 dated 2026-08-20
DESCRIPTION | 10 - MD5 | 113 ++++++++++--- NAMESPACE | 2 NEWS | 57 +++++++ R/attribs.R | 17 +- R/extensions.R | 8 R/foreign.R |only R/image.R | 4 R/nifti.R | 74 +++++---- R/viewer.R | 72 ++++++++ R/xform.R | 22 -- build/partial.rdb |binary inst/doxygen |only inst/include/RNifti.h | 2 inst/include/RNifti/NiftiImage.h | 42 ++--- inst/include/RNifti/NiftiImage_impl.h | 276 ++++++++-------------------------- inst/tinytest/test-35-viewer.R | 40 ++++ inst/tinytest/test-40-foreign.R | 57 ++++++- inst/tinytest/test-55-fuzz.R | 9 + man/ExtensionCodes.Rd | 5 man/asNifti.Rd | 61 ++++--- man/extensions.Rd | 9 - man/readNifti.Rd | 8 man/view.Rd | 49 +++++- man/writeNifti.Rd | 14 + src/main.cpp | 138 +++++++++++------ tools/figures/unnamed-chunk-12-1.png |binary tools/figures/unnamed-chunk-15-1.png |binary tools/figures/unnamed-chunk-5-1.png |binary 29 files changed, 663 insertions(+), 426 deletions(-)
Title: Reality Check and Predictive Ability Tests for Forecast
Evaluation
Description: Implements a comprehensive suite of statistical tests for
evaluating the accuracy of forecasting models against a benchmark.
The package is grounded in the reality check framework of White
(2000) <doi:10.1111/1468-0262.00152>, extended by Hansen (2005)
<doi:10.1198/073500105000000063> for Superior Predictive Ability
(SPA), Giacomini & White (2006) <doi:10.1111/j.1468-0262.2006.00718.x>
for Conditional Predictive Ability (CPA), and Corradi & Swanson
(2006) <doi:10.1016/j.jeconom.2005.07.026> for predictive density
evaluation via the Kullback-Leibler Information Criterion (KLIC) and
ZP Quantile Loss test, the Continuous Ranked Probability
Score (CRPS) (Gneiting & Raftery, 2007)
<doi:10.1198/016214506000001437>, coverage tests (Kupiec, 1995)
<doi:10.3905/jod.1995.407942>, HAC covariance estimation (Newey &
West, 1987) <doi:10.2307/1913610>, and Moving Block Bootstrap
resampling (Kunsch, 1989) <doi:10.1214/aos/1176347265>.
Author: Joanna Jedrzejewska [aut, cre] ,
Krzysztof Drachal [ctb]
Maintainer: Joanna Jedrzejewska <j.jedrzejewska3@uw.edu.pl>
Diff between RCtest versions 1.0 dated 2026-06-02 and 1.1 dated 2026-08-20
DESCRIPTION | 23 ++-- MD5 | 26 ++--- NEWS.md | 16 ++- R/analysis_helpers.R | 93 ++++++++++++++---- R/statistical_tests.R | 175 ++++++++++++++++++++++------------ R/workflow_functions.R | 12 +- man/compute_klic.Rd | 3 man/compute_kupiec.Rd | 3 man/compute_zp.Rd | 3 man/estimate_forecast_variance.Rd | 58 +++++++++-- man/kullback_leibler_test.Rd | 5 man/reality_check_zp_test.Rd | 5 man/run_comprehensive_erc_analysis.Rd | 22 ++++ man/white_reality_check_cdf_approx.Rd | 120 ++++++++++++++++------- 14 files changed, 401 insertions(+), 163 deletions(-)
Title: Nonparametric Probabilistic-Statistical Variate Analysis
Description: Calculate posterior joint and conditional probabilities, probability distributions of population frequencies, information-theoretic measures, and expected utilities, by means of Bayesian nonparametrics. Data can be any combination of nominal, ordinal, continuous, censored, rounded types. Data imputation is automatic and done in a principled way. Markov-chain Monte Carlo calculations are automatically handled and do not require user supervision. Applications range from statistical estimation and probabilistic hypothesis testing to evidence-based inference and decision making, in a wide range of disciplines from astrophysics to medicine. For more details and examples see for instance Porta Mana & al. (2026) <doi:10.31219/osf.io/8nr56>, Dunson & Bhattacharya (2011) <doi:10.1093/acprof:oso/9780199694587.003.0005>, Lindley & Novick (1981) <doi:10.1214/aos/1176345331>, Bernardo & Smith (2000) <doi:10.1002/9780470316870>, Müller et al. (2015) <doi:10 [...truncated...]
Author: PierGianLuca Porta Mana [aut, cre, cph] ,
Aurora Grefsrud [ctb] ,
Hakon Mydland [ctb] ,
Maksim Ohvrill [ctb],
Simen Hesthamar Hauge [ctb]
Maintainer: PierGianLuca Porta Mana <pgl@portamana.org>
Diff between prova versions 1.0.0 dated 2026-07-16 and 2.3.0 dated 2026-08-20
prova-1.0.0/prova/R/util_buildauxmetadata.R |only prova-1.0.0/prova/R/util_checkpoints.R |only prova-1.0.0/prova/R/util_cleanup.R |only prova-1.0.0/prova/R/util_createQfunction.R |only prova-1.0.0/prova/R/util_datacheck.R |only prova-1.0.0/prova/R/util_lprobs.R |only prova-1.0.0/prova/R/util_mcmcstop.R |only prova-1.0.0/prova/R/util_mcsamples.R |only prova-1.0.0/prova/R/util_plotFsamples.R |only prova-1.0.0/prova/R/util_plotfunctions.R |only prova-1.0.0/prova/R/util_prsubset.R |only prova-1.0.0/prova/R/util_vtransform.R |only prova-1.0.0/prova/data/learntExample.rda |only prova-1.0.0/prova/man/buildauxmetadata.Rd |only prova-1.0.0/prova/man/createQfunction.Rd |only prova-1.0.0/prova/man/fftNGS.Rd |only prova-1.0.0/prova/man/figures/prova_symbol.jpg |only prova-1.0.0/prova/man/flexiplot.Rd |only prova-1.0.0/prova/man/funAC.Rd |only prova-1.0.0/prova/man/funESS3.Rd |only prova-1.0.0/prova/man/funMCEQ.Rd |only prova-1.0.0/prova/man/funMCSELD.Rd |only prova-1.0.0/prova/man/hist.probability.Rd |only prova-1.0.0/prova/man/learnbind.Rd |only prova-1.0.0/prova/man/learntExample.Rd |only prova-1.0.0/prova/man/mcjoin.Rd |only prova-1.0.0/prova/man/mcsubset.Rd |only prova-1.0.0/prova/man/metadatatemplate.Rd |only prova-1.0.0/prova/man/plot.probability.Rd |only prova-1.0.0/prova/man/plotFsamples.Rd |only prova-1.0.0/prova/man/plotquantiles.Rd |only prova-1.0.0/prova/man/print.probability.Rd |only prova-1.0.0/prova/man/prova.data.Rd |only prova-1.0.0/prova/man/prsubset.Rd |only prova-1.0.0/prova/man/rowcumsum.Rd |only prova-1.0.0/prova/man/rowinvcumsum.Rd |only prova-1.0.0/prova/man/util_Pcheckpoints.Rd |only prova-1.0.0/prova/man/util_cleanup.Rd |only prova-1.0.0/prova/man/util_combineYX.Rd |only prova-1.0.0/prova/man/util_denorm.Rd |only prova-1.0.0/prova/man/util_joinPtraces.Rd |only prova-1.0.0/prova/man/util_lprobsargsyx.Rd |only prova-1.0.0/prova/man/util_lprobsbase.Rd |only prova-1.0.0/prova/man/util_lprobsmi.Rd |only prova-1.0.0/prova/man/util_prepPcheckpoints.Rd |only prova-1.0.0/prova/man/util_qYXcont.Rd |only prova-1.0.0/prova/man/util_qYXdiscr.Rd |only prova-1.0.0/prova/man/vtransform.Rd |only prova-1.0.0/prova/man/workerfun.Rd |only prova-2.3.0/prova/DESCRIPTION | 14 prova-2.3.0/prova/MD5 | 167 +-- prova-2.3.0/prova/NAMESPACE | 18 prova-2.3.0/prova/NEWS.md | 125 +- prova-2.3.0/prova/R/Pr.R | 595 ++++++----- prova-2.3.0/prova/R/data.R | 37 prova-2.3.0/prova/R/datafiles.R |only prova-2.3.0/prova/R/display.R |only prova-2.3.0/prova/R/exputility.R |only prova-2.3.0/prova/R/internal_buildauxmetadata.R |only prova-2.3.0/prova/R/internal_checkpoints.R |only prova-2.3.0/prova/R/internal_cleanup.R |only prova-2.3.0/prova/R/internal_createQfunction.R |only prova-2.3.0/prova/R/internal_lprobs.R |only prova-2.3.0/prova/R/internal_mcmc.R |only prova-2.3.0/prova/R/internal_plotFsamples.R |only prova-2.3.0/prova/R/internal_retrieveK.R |only prova-2.3.0/prova/R/internal_testPr.R |only prova-2.3.0/prova/R/internal_vtransform.R |only prova-2.3.0/prova/R/learn.R | 404 +++---- prova-2.3.0/prova/R/metadatatemplate.R | 63 - prova-2.3.0/prova/R/mutualinfo.R | 944 +++++++++++++---- prova-2.3.0/prova/R/qPr.R | 662 ++++++++---- prova-2.3.0/prova/R/rPr.R | 214 ++- prova-2.3.0/prova/R/vrtgrid.R | 149 +- prova-2.3.0/prova/README.md | 110 +- prova-2.3.0/prova/data/Kexample.rda |only prova-2.3.0/prova/data/meta_penguins.rda |only prova-2.3.0/prova/inst/doc/intro.Rmd | 761 ++++++-------- prova-2.3.0/prova/inst/doc/intro.html | 1272 +++++++++++------------ prova-2.3.0/prova/inst/doc/mutualinfo.Rmd | 397 +++---- prova-2.3.0/prova/inst/doc/mutualinfo.html | 666 ++++++------ prova-2.3.0/prova/man/Kexample.Rd |only prova-2.3.0/prova/man/Pr.Rd | 134 +- prova-2.3.0/prova/man/data.Rd |only prova-2.3.0/prova/man/dot-Pcheckpoints.Rd |only prova-2.3.0/prova/man/dot-buildauxmetadata.Rd |only prova-2.3.0/prova/man/dot-cleanup.Rd |only prova-2.3.0/prova/man/dot-combineYX.Rd |only prova-2.3.0/prova/man/dot-createQfunction.Rd |only prova-2.3.0/prova/man/dot-denorm.Rd |only prova-2.3.0/prova/man/dot-fftNGS.Rd |only prova-2.3.0/prova/man/dot-funAC.Rd |only prova-2.3.0/prova/man/dot-funESS3.Rd |only prova-2.3.0/prova/man/dot-funMCEQ.Rd |only prova-2.3.0/prova/man/dot-funMCSELD.Rd |only prova-2.3.0/prova/man/dot-joinPtraces.Rd |only prova-2.3.0/prova/man/dot-learnbind.Rd |only prova-2.3.0/prova/man/dot-lprobsargsyx.Rd |only prova-2.3.0/prova/man/dot-lprobsbase.Rd |only prova-2.3.0/prova/man/dot-lprobsmi.Rd |only prova-2.3.0/prova/man/dot-mcjoin.Rd |only prova-2.3.0/prova/man/dot-mcsubset.Rd |only prova-2.3.0/prova/man/dot-plotFsamples.Rd |only prova-2.3.0/prova/man/dot-prepPcheckpoints.Rd |only prova-2.3.0/prova/man/dot-prsubset.Rd |only prova-2.3.0/prova/man/dot-qYXcont.Rd |only prova-2.3.0/prova/man/dot-qYXdiscr.Rd |only prova-2.3.0/prova/man/dot-retrieveK.Rd |only prova-2.3.0/prova/man/dot-rowcumsum.Rd |only prova-2.3.0/prova/man/dot-rowinvcumsum.Rd |only prova-2.3.0/prova/man/dot-signifC.Rd |only prova-2.3.0/prova/man/dot-testPr.Rd |only prova-2.3.0/prova/man/dot-vtransform.Rd |only prova-2.3.0/prova/man/dot-workerfun.Rd |only prova-2.3.0/prova/man/exputility.Rd |only prova-2.3.0/prova/man/figures/README-hist-1.svg |only prova-2.3.0/prova/man/figures/README-plot-1.svg |only prova-2.3.0/prova/man/figures/prova_logo.jpg |only prova-2.3.0/prova/man/hist.prova_mi.Rd |only prova-2.3.0/prova/man/hist.prova_pr.Rd |only prova-2.3.0/prova/man/learn.Rd | 70 - prova-2.3.0/prova/man/meta_penguins.Rd |only prova-2.3.0/prova/man/metadata.Rd |only prova-2.3.0/prova/man/metadataExample.Rd | 1 prova-2.3.0/prova/man/mutualinfo.Rd | 162 +-- prova-2.3.0/prova/man/plot.prova_eu.Rd |only prova-2.3.0/prova/man/plot.prova_pr.Rd |only prova-2.3.0/prova/man/pplot.Rd |only prova-2.3.0/prova/man/print.prova_K.Rd |only prova-2.3.0/prova/man/print.prova_eu.Rd |only prova-2.3.0/prova/man/print.prova_mi.Rd |only prova-2.3.0/prova/man/print.prova_pr.Rd |only prova-2.3.0/prova/man/prova-package.Rd | 4 prova-2.3.0/prova/man/qPr.Rd | 106 - prova-2.3.0/prova/man/rPr.Rd | 40 prova-2.3.0/prova/man/vrtgrid.Rd | 69 - prova-2.3.0/prova/vignettes/intro.Rmd | 761 ++++++-------- prova-2.3.0/prova/vignettes/intro.htm | 1293 +++++++++++------------- prova-2.3.0/prova/vignettes/mutualinfo.Rmd | 397 +++---- prova-2.3.0/prova/vignettes/mutualinfo.htm | 669 ++++++------ 140 files changed, 5533 insertions(+), 4771 deletions(-)
Title: Generalized Linear Models Adjusting for Misrepresentation
Description: Fit Generalized Linear Models to continuous and count outcomes, as well as estimate the prevalence of misrepresentation of an important binary predictor. Misrepresentation typically arises when there is an incentive for the binary factor to be misclassified in one direction (e.g., in insurance settings where policy holders may purposely deny a risk status in order to lower the insurance premium). This is accomplished by treating a subset of the response variable as resulting from a mixture distribution. Model parameters are estimated via the Expectation Maximization algorithm and standard errors of the estimates are obtained from closed forms of the Observed Fisher Information. For an introduction to the models and the misrepresentation framework, see Xia et. al., (2023) <https://variancejournal.org/article/73151-maximum-likelihood-approaches-to-misrepresentation-models-in-glm-ratemaking-model-comparisons>.
Author: Patrick Rafael [cre, aut],
Xia Michelle [aut],
Rexford Akakpo [aut]
Maintainer: Patrick Rafael <pbr2608@vt.edu>
Diff between glmMisrep versions 0.1.1 dated 2024-04-18 and 0.1.2 dated 2026-08-20
DESCRIPTION | 6 +++--- MD5 | 28 ++++++++++++++-------------- NEWS | 6 ++++++ man/LnRegMisrepEM.Rd | 4 ++-- man/MEPS14.Rd | 2 +- man/NormRegMisrepEM.Rd | 4 ++-- man/gammaRegMisrepEM.Rd | 4 ++-- man/nbRegMisrepEM.Rd | 4 ++-- man/poisRegMisrepEM.Rd | 4 ++-- man/predict.misrepEM.Rd | 3 ++- tests/LN-testing.R | 6 +++--- tests/NB-testing.R | 6 +++--- tests/Norm-testing.R | 2 +- tests/Pois-testing.R | 35 +++++++++++++++++++---------------- tests/gamma-testing.R | 6 +++--- 15 files changed, 65 insertions(+), 55 deletions(-)
Title: Bioinformatic Distances
Description: Provides a unified interface for computing, comparing, and
examining distances, dissimilarities, divergences, and selected
similarities for bioinformatics data. The core installation exposes 60
canonical named routes for numerical data and more than 90 when the
suggested 'philentropy' backend is installed; aliases, user-defined
functions, and mixed-data combinations are not included in these counts.
Weighted Minkowski distances can be computed through 'parallelDist', an
internal multicore implementation, or optional 'OpenCL' kernels, while the
established weighted Euclidean GPU implementation is retained as the
optimized p = 2 route. The package also supports theory-guided comparison
of distance distributions for clustering, explicit mathematical property
classifications, mixed-data constructions through 'manydist', and a
specialized Gene Ontology-derived TF-IDF distance.
Author: Quirin Stier [aut, rev, ctb] ,
Michael Thrun [aut, cre] ,
Luca Brinkmann [ctb]
Maintainer: Michael Thrun <m.thrun@gmx.net>
Diff between BIDistances versions 1.0.0 dated 2026-08-19 and 1.0.1 dated 2026-08-20
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- README.md | 2 +- tests/testthat/test-fast-dip-pvalues.R | 17 ++++++++++++----- 4 files changed, 20 insertions(+), 13 deletions(-)
Title: Access Argentine WFS and WMS Geospatial Web Services
Description: Discovers and reads geospatial layers published by Argentine
public organizations through the Open Geospatial Consortium standards
Web Feature Service (WFS) and Web Map Service (WMS). Provides a cached
catalogue of endpoints, capability parsing with version negotiation,
paginated vector downloads returned as 'sf' objects, and raster map
retrieval returned as 'terra' objects. For the underlying standards see
<https://www.ogc.org/standards/wfs/> and <https://www.ogc.org/standards/wms/>.
Author: Thomas Artopoulos [aut, cre]
Maintainer: Thomas Artopoulos <thomas.artopoulos@gmail.com>
Diff between Argentum versions 1.0.0 dated 2025-02-12 and 2.1.0 dated 2026-08-20
Argentum-1.0.0/Argentum/R/clean_url.R |only Argentum-1.0.0/Argentum/R/download_layers.R |only Argentum-1.0.0/Argentum/R/get_capabilities.R |only Argentum-1.0.0/Argentum/R/import_wfs.R |only Argentum-1.0.0/Argentum/R/interactive_download.R |only Argentum-1.0.0/Argentum/R/interactive_import.R |only Argentum-1.0.0/Argentum/R/list_layers.R |only Argentum-1.0.0/Argentum/R/list_organizations.R |only Argentum-1.0.0/Argentum/R/select_organization.R |only Argentum-1.0.0/Argentum/inst/doc/argentum.R |only Argentum-1.0.0/Argentum/inst/doc/argentum.html |only Argentum-1.0.0/Argentum/inst/doc/argentum.rmd |only Argentum-1.0.0/Argentum/man/argentum_download_layers.Rd |only Argentum-1.0.0/Argentum/man/argentum_get_capabilities.Rd |only Argentum-1.0.0/Argentum/man/argentum_import_wfs_layer.Rd |only Argentum-1.0.0/Argentum/man/argentum_interactive_download.Rd |only Argentum-1.0.0/Argentum/man/argentum_interactive_import.Rd |only Argentum-1.0.0/Argentum/man/argentum_list_layers.Rd |only Argentum-1.0.0/Argentum/man/argentum_list_organizations.Rd |only Argentum-1.0.0/Argentum/man/argentum_select_organization.Rd |only Argentum-1.0.0/Argentum/man/clean_url.Rd |only Argentum-1.0.0/Argentum/tests/testthat/test-argentum.R |only Argentum-1.0.0/Argentum/tests/testthat/test-interactive-download.r |only Argentum-1.0.0/Argentum/vignettes/argentum.rmd |only Argentum-2.1.0/Argentum/DESCRIPTION | 34 - Argentum-2.1.0/Argentum/LICENSE | 4 Argentum-2.1.0/Argentum/MD5 | 94 +- Argentum-2.1.0/Argentum/NAMESPACE | 37 - Argentum-2.1.0/Argentum/NEWS.md |only Argentum-2.1.0/Argentum/R/argentum-package.R |only Argentum-2.1.0/Argentum/R/cache.R |only Argentum-2.1.0/Argentum/R/capabilities.R |only Argentum-2.1.0/Argentum/R/catalog.R |only Argentum-2.1.0/Argentum/R/deprecated.R |only Argentum-2.1.0/Argentum/R/download.R |only Argentum-2.1.0/Argentum/R/help.R |only Argentum-2.1.0/Argentum/R/http.R |only Argentum-2.1.0/Argentum/R/interactive.R |only Argentum-2.1.0/Argentum/R/url.R |only Argentum-2.1.0/Argentum/R/wfs.R |only Argentum-2.1.0/Argentum/R/wms.R |only Argentum-2.1.0/Argentum/R/xmlsafe.R |only Argentum-2.1.0/Argentum/README.md | 315 +++++++++- Argentum-2.1.0/Argentum/build/vignette.rds |binary Argentum-2.1.0/Argentum/inst/doc/getting-started.R | 106 +-- Argentum-2.1.0/Argentum/inst/doc/getting-started.Rmd | 198 ++++-- Argentum-2.1.0/Argentum/inst/doc/getting-started.html | 198 +++--- Argentum-2.1.0/Argentum/inst/doc/migrating-to-2-0.R |only Argentum-2.1.0/Argentum/inst/doc/migrating-to-2-0.Rmd |only Argentum-2.1.0/Argentum/inst/doc/migrating-to-2-0.html |only Argentum-2.1.0/Argentum/inst/doc/wms-rasters.R |only Argentum-2.1.0/Argentum/inst/doc/wms-rasters.Rmd |only Argentum-2.1.0/Argentum/inst/doc/wms-rasters.html |only Argentum-2.1.0/Argentum/inst/extdata |only Argentum-2.1.0/Argentum/man/Argentum-package.Rd |only Argentum-2.1.0/Argentum/man/argentum-deprecated.Rd |only Argentum-2.1.0/Argentum/man/argentum_browse.Rd |only Argentum-2.1.0/Argentum/man/argentum_cache_clear.Rd |only Argentum-2.1.0/Argentum/man/argentum_cache_path.Rd |only Argentum-2.1.0/Argentum/man/argentum_capabilities.Rd |only Argentum-2.1.0/Argentum/man/argentum_download.Rd |only Argentum-2.1.0/Argentum/man/argentum_help.Rd |only Argentum-2.1.0/Argentum/man/argentum_layers.Rd |only Argentum-2.1.0/Argentum/man/argentum_options.Rd |only Argentum-2.1.0/Argentum/man/argentum_organizations.Rd |only Argentum-2.1.0/Argentum/man/argentum_read_wfs.Rd |only Argentum-2.1.0/Argentum/man/argentum_read_wms.Rd |only Argentum-2.1.0/Argentum/man/argentum_search_organizations.Rd |only Argentum-2.1.0/Argentum/man/argentum_wms_legend.Rd |only Argentum-2.1.0/Argentum/man/figures |only Argentum-2.1.0/Argentum/tests/testthat.R | 8 Argentum-2.1.0/Argentum/tests/testthat/helper-argentum.R |only Argentum-2.1.0/Argentum/tests/testthat/test-cache.R |only Argentum-2.1.0/Argentum/tests/testthat/test-capabilities.R |only Argentum-2.1.0/Argentum/tests/testthat/test-catalog.R |only Argentum-2.1.0/Argentum/tests/testthat/test-deprecated.R |only Argentum-2.1.0/Argentum/tests/testthat/test-download.R |only Argentum-2.1.0/Argentum/tests/testthat/test-help.R |only Argentum-2.1.0/Argentum/tests/testthat/test-url.R |only Argentum-2.1.0/Argentum/tests/testthat/test-wfs.R |only Argentum-2.1.0/Argentum/tests/testthat/test-wms.R |only Argentum-2.1.0/Argentum/tests/testthat/test-xmlsafe.R |only Argentum-2.1.0/Argentum/vignettes/getting-started.Rmd | 198 ++++-- Argentum-2.1.0/Argentum/vignettes/migrating-to-2-0.Rmd |only Argentum-2.1.0/Argentum/vignettes/wms-rasters.Rmd |only 85 files changed, 865 insertions(+), 327 deletions(-)
Title: A Comprehensive Collection of Agricultural and Agronomic
Datasets
Description: Offers a rich and diverse collection of datasets focused on agriculture, agronomy, animal science,
and related fields. The package includes experimental, observational, and field-trial data on crops such as rice,
wheat, corn, soybean, cotton, coffee, avocado, and orange, as well as forestry species including bamboo, eucalyptus,
and timber. Datasets cover plant breeding and genetics, factorial and randomized block experiments, herbicide and
insecticide efficacy trials, pest and disease infestation, soil characteristics and land suitability, plant growth
regulators, seed germination, and crop yield modeling. Additional datasets address animal science topics such as
cattle insemination and conception, pig and broiler growth, lamb births, and toxicology studies on aquatic and
non-target species. Data sources include peer-reviewed agronomic studies, uniformity and Latin square field trials,
glasshouse experiments, and international agricultural surveys.
Designed for agronomists, researchers [...truncated...]
Author: Renzo Caceres Rossi [aut, cre] ,
Prabhanjan Tattar [ctb] ,
A.P. Gore [ctb] ,
S.A. Paranjape [ctb] ,
M.B. Kulkarni [ctb] ,
Gabriel Danilo Shimizu [ctb] ,
Rodrigo Yudi Palhaci Marubayashi [ctb] ,
Leandro Simoes Azeredo Goncalves [ctb] ,
Al-Ahmadgaid B. [...truncated...]
Maintainer: Renzo Caceres Rossi <arenzocaceresrossi@gmail.com>
Diff between agridatasets versions 0.1.0 dated 2026-08-08 and 0.1.1 dated 2026-08-20
DESCRIPTION | 643 ++++++++++++++++++++++- MD5 | 161 ++--- NEWS.md |only R/agridatasets-package.R | 2 R/data-documentation.R | 2 R/view_datasets_agridatasets.R | 2 README.md | 11 inst/CITATION | 6 inst/licenses/LICENSE.md | 27 inst/licenses/LICENSES_DETAILS.md | 10 tests/testthat/test-alfalfa_soil.R | 2 tests/testthat/test-apple_canker.R | 2 tests/testthat/test-apple_uniformity.R | 2 tests/testthat/test-arabica_soil.R | 2 tests/testthat/test-arabica_temp.R | 2 tests/testthat/test-arabica_terrain.R | 2 tests/testthat/test-arabica_water.R | 2 tests/testthat/test-avocado_us_sale.R | 2 tests/testthat/test-bamboo_growth.R | 2 tests/testthat/test-biological_control.R | 2 tests/testthat/test-bird_grazing.R | 2 tests/testthat/test-black_duck_survival.R | 2 tests/testthat/test-blackgrass_herbicide.R | 2 tests/testthat/test-broiler_growth.R | 2 tests/testthat/test-budworm_pyrethroid.R | 2 tests/testthat/test-carrot_fly_infestation.R | 2 tests/testthat/test-carrot_insecticide.R | 2 tests/testthat/test-cattle_butterfat.R | 2 tests/testthat/test-cauliflower_growth.R | 2 tests/testthat/test-coffee_composition.R | 2 tests/testthat/test-coffee_production.R | 2 tests/testthat/test-cork_tree_direction.R | 2 tests/testthat/test-corn_hybrid_density.R | 2 tests/testthat/test-cotton_pesticide.R | 2 tests/testthat/test-cowpea_maize_yield.R | 2 tests/testthat/test-cows_insemination.R | 2 tests/testthat/test-earthworm_crop_soils.R | 2 tests/testthat/test-earthworm_population.R | 2 tests/testthat/test-eelworm_fumigation.R | 2 tests/testthat/test-egg_weight_daily.R | 2 tests/testthat/test-eucalyptus_progenies.R | 2 tests/testthat/test-fish_feeding.R | 2 tests/testthat/test-fungicide_latin_square.R | 2 tests/testthat/test-grape_uniformity.R | 2 tests/testthat/test-guinea_pig_sleep.R | 2 tests/testthat/test-hawaii_plant_size.R | 2 tests/testthat/test-hawaii_tree_growth.R | 2 tests/testthat/test-idn_rice_farms.R | 2 tests/testthat/test-kiwi_crop_design.R | 2 tests/testthat/test-ladybird_fungus.R | 2 tests/testthat/test-lamb_births.R | 2 tests/testthat/test-nitrofen_toxicity.R | 2 tests/testthat/test-orange_rootstocks.R | 2 tests/testthat/test-peach_uniformity.R | 2 tests/testthat/test-pig_weight_gain.R | 2 tests/testthat/test-plant_growth_regulator.R | 2 tests/testthat/test-pollen_removal.R | 2 tests/testthat/test-potato_scab_sulfur.R | 2 tests/testthat/test-rabbit_body_mass.R | 2 tests/testthat/test-red_wine_quality.R | 2 tests/testthat/test-rice_wheat_production.R | 2 tests/testthat/test-river_deforestation.R | 2 tests/testthat/test-robusta_soil.R | 2 tests/testthat/test-robusta_temp.R | 2 tests/testthat/test-robusta_terrain.R | 2 tests/testthat/test-robusta_water.R | 2 tests/testthat/test-seed_germination.R | 2 tests/testthat/test-soil_munsell_colors.R | 2 tests/testthat/test-soil_munsell_minerals.R | 2 tests/testthat/test-soybean_cultivars.R | 2 tests/testthat/test-strawberry_cross_disease.R | 2 tests/testthat/test-strawberry_yield.R | 2 tests/testthat/test-timber_genetics.R | 2 tests/testthat/test-tomato_insecticides.R | 2 tests/testthat/test-tomato_uniformity.R | 2 tests/testthat/test-toxin_lethal_dose.R | 2 tests/testthat/test-turnip_density.R | 2 tests/testthat/test-us_state_soils.R | 2 tests/testthat/test-view_datasets_agridatasets.R | 2 tests/testthat/test-wheat_bunt.R | 2 tests/testthat/test-wheat_splitsplit.R | 2 tests/testthat/test-willow_cutting_yield.R | 2 82 files changed, 824 insertions(+), 184 deletions(-)
Title: High-Dimensional Mediation Analysis via Transfer Learning
Description: Provides a framework for high-dimensional mediation analysis using transfer learning. The main function TransHDM() integrates large-scale source data to improve the detection power of potential mediators in small-sample target studies. It addresses data heterogeneity via transfer regularization and debiased estimation while controlling the false discovery rate. The package also includes utilities for data generation (gen_simData_homo(), gen_simData_hetero()), baseline methods such as lasso() and dblasso(), sure independence screening via SIS(), and model diagnostics through source_detection(). The methodology is described in Pan et al. (2025) <doi:10.1093/bib/bbaf460>.
Author: Huer Gao [aut, cre, cph],
Lulu Pan [aut, cph],
Yongfu Yu [ctb, cph],
Guoyou Qin [ctb, cph]
Maintainer: Huer Gao <26111020050@m.fudan.edu.cn>
Diff between TransHDM versions 1.0.1 dated 2026-03-17 and 1.1.3 dated 2026-08-20
TransHDM-1.0.1/TransHDM/vignettes/dblasso.png |only TransHDM-1.0.1/TransHDM/vignettes/model.png |only TransHDM-1.1.3/TransHDM/DESCRIPTION | 19 TransHDM-1.1.3/TransHDM/MD5 | 85 TransHDM-1.1.3/TransHDM/NAMESPACE | 14 TransHDM-1.1.3/TransHDM/R/10_mediation_inference.R |only TransHDM-1.1.3/TransHDM/R/11_joint_test.R |only TransHDM-1.1.3/TransHDM/R/1_generate_simulationData_homogeneous_design.R | 20 TransHDM-1.1.3/TransHDM/R/2_generate_simulationData_heterogeneous_design.R | 22 TransHDM-1.1.3/TransHDM/R/4_lasso.R | 21 TransHDM-1.1.3/TransHDM/R/5_dblasso.R | 19 TransHDM-1.1.3/TransHDM/R/7_source_detect.R | 8 TransHDM-1.1.3/TransHDM/R/8_SIS.R | 26 TransHDM-1.1.3/TransHDM/R/9_TransHDM.R | 781 ++-- TransHDM-1.1.3/TransHDM/R/data_inflam.R |only TransHDM-1.1.3/TransHDM/R/plot_TransHDM.R |only TransHDM-1.1.3/TransHDM/R/plot_source_detect.R |only TransHDM-1.1.3/TransHDM/R/summary_10.R |only TransHDM-1.1.3/TransHDM/R/summary_4.R | 16 TransHDM-1.1.3/TransHDM/R/summary_5.R | 152 TransHDM-1.1.3/TransHDM/R/summary_7.R | 17 TransHDM-1.1.3/TransHDM/R/summary_8.R | 33 TransHDM-1.1.3/TransHDM/R/summary_9.R | 23 TransHDM-1.1.3/TransHDM/build/partial.rdb |binary TransHDM-1.1.3/TransHDM/build/vignette.rds |binary TransHDM-1.1.3/TransHDM/data |only TransHDM-1.1.3/TransHDM/inst/WORDLIST | 63 TransHDM-1.1.3/TransHDM/inst/doc/tutorial.R | 326 -- TransHDM-1.1.3/TransHDM/inst/doc/tutorial.Rmd | 361 -- TransHDM-1.1.3/TransHDM/inst/doc/tutorial.html | 1577 ++++------ TransHDM-1.1.3/TransHDM/man/SIS.Rd | 23 TransHDM-1.1.3/TransHDM/man/TransHDM.Rd | 35 TransHDM-1.1.3/TransHDM/man/dblasso.Rd | 16 TransHDM-1.1.3/TransHDM/man/gen_simData_hetero.Rd | 2 TransHDM-1.1.3/TransHDM/man/gen_simData_homo.Rd | 2 TransHDM-1.1.3/TransHDM/man/inflam_effect.Rd |only TransHDM-1.1.3/TransHDM/man/inflam_external1.Rd |only TransHDM-1.1.3/TransHDM/man/inflam_external2.Rd |only TransHDM-1.1.3/TransHDM/man/inflam_target.Rd |only TransHDM-1.1.3/TransHDM/man/joint_test.Rd |only TransHDM-1.1.3/TransHDM/man/lasso.Rd | 17 TransHDM-1.1.3/TransHDM/man/mediation_inference.Rd |only TransHDM-1.1.3/TransHDM/man/plot.TransHDM.Rd |only TransHDM-1.1.3/TransHDM/man/plot.source_detection.Rd |only TransHDM-1.1.3/TransHDM/man/print.SIS.Rd |only TransHDM-1.1.3/TransHDM/man/print.TransHDM.Rd |only TransHDM-1.1.3/TransHDM/man/print.dblasso.Rd |only TransHDM-1.1.3/TransHDM/man/print.lasso.Rd |only TransHDM-1.1.3/TransHDM/man/print.mediation_inference.Rd |only TransHDM-1.1.3/TransHDM/man/print.source_detection.Rd |only TransHDM-1.1.3/TransHDM/man/print.summary.dblasso.Rd |only TransHDM-1.1.3/TransHDM/man/source_detection.Rd | 6 TransHDM-1.1.3/TransHDM/man/summary.mediation_inference.Rd |only TransHDM-1.1.3/TransHDM/tests/test_pipeline.R |only TransHDM-1.1.3/TransHDM/vignettes/tutorial.Rmd | 361 -- 55 files changed, 1857 insertions(+), 2188 deletions(-)
Title: Interface to 'JDemetra+ 3.x' Time Series Analysis Software
Description: R Interface to 'JDemetra+ 3.x'
(<https://github.com/jdemetra>) time series analysis software. It
provides functions allowing to decompose a time series, including
high-frequency data with multiple periodicities.
Author: Jean Palate [aut],
Tanguy Barthelemy [aut, cre, cph]
Maintainer: Tanguy Barthelemy <timeserieswithjdemetraandr@gmail.com>
Diff between rjd3xjars versions 0.1.1 dated 2026-07-08 and 0.1.2 dated 2026-08-20
rjd3xjars-0.1.1/rjd3xjars/inst/java/jdplus-advancedsa-base-api-2.4.1.jar |only rjd3xjars-0.1.1/rjd3xjars/inst/java/jdplus-advancedsa-base-core-2.4.1.jar |only rjd3xjars-0.1.1/rjd3xjars/inst/java/jdplus-highfreq-base-api-2.4.1.jar |only rjd3xjars-0.1.1/rjd3xjars/inst/java/jdplus-highfreq-base-core-2.4.1.jar |only rjd3xjars-0.1.1/rjd3xjars/inst/java/jdplus-sts-base-api-2.4.1.jar |only rjd3xjars-0.1.1/rjd3xjars/inst/java/jdplus-sts-base-core-2.4.1.jar |only rjd3xjars-0.1.2/rjd3xjars/DESCRIPTION | 14 +++--- rjd3xjars-0.1.2/rjd3xjars/MD5 | 22 +++++----- rjd3xjars-0.1.2/rjd3xjars/NEWS.md | 19 ++++++++ rjd3xjars-0.1.2/rjd3xjars/R/zzz.R | 6 +- rjd3xjars-0.1.2/rjd3xjars/README.md | 4 - rjd3xjars-0.1.2/rjd3xjars/inst/WORDLIST |only rjd3xjars-0.1.2/rjd3xjars/inst/java/jdplus-advancedsa-base-api-2.5.2.jar |only rjd3xjars-0.1.2/rjd3xjars/inst/java/jdplus-advancedsa-base-core-2.5.2.jar |only rjd3xjars-0.1.2/rjd3xjars/inst/java/jdplus-highfreq-base-api-2.5.2.jar |only rjd3xjars-0.1.2/rjd3xjars/inst/java/jdplus-highfreq-base-core-2.5.2.jar |only rjd3xjars-0.1.2/rjd3xjars/inst/java/jdplus-sts-base-api-2.5.2.jar |only rjd3xjars-0.1.2/rjd3xjars/inst/java/jdplus-sts-base-core-2.5.2.jar |only rjd3xjars-0.1.2/rjd3xjars/tests |only 19 files changed, 44 insertions(+), 21 deletions(-)
Title: Neuroscience Extension Package for ADaM in 'R' Asset Library
Description: Programming neuroscience specific Clinical Data Standards
Interchange Consortium (CDISC) compliant Analysis Data Model (ADaM)
datasets in 'R'. ADaM datasets are a mandatory part of any New Drug
or Biologics License Application submitted to the United States Food
and Drug Administration (FDA). Analysis derivations are implemented in
accordance with the "Analysis Data Model Implementation Guide" (CDISC
Analysis Data Model Team, 2021,
<https://www.cdisc.org/standards/foundational/adam>). This package
extends the 'admiral' package.
Author: Jian Wang [aut] ,
Meilin Jiang [aut, cre] ,
Miles Almond [aut] ,
Xiao Chen [aut] ,
Fanny Gautier [aut] ,
Gayatri G. [aut],
Leena Khatri [aut] ,
Edoardo Mancini [aut] ,
Eric Nantz [aut],
Lina Patil [aut],
Chris Pelentrides [aut],
Katie Withycombe [aut [...truncated...]
Maintainer: Meilin Jiang <meilin.jiang@lilly.com>
Diff between admiralneuro versions 0.2.0 dated 2026-02-04 and 0.3.0 dated 2026-08-20
DESCRIPTION | 34 +-- MD5 | 54 ++--- NAMESPACE | 310 +++++++++++++++-------------- NEWS.md | 31 ++ R/admiralneuro-package.R | 39 +-- build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST | 7 inst/doc/adlb.R |only inst/doc/adlb.Rmd |only inst/doc/adlb.html |only inst/doc/admiralneuro.Rmd | 6 inst/doc/admiralneuro.html | 11 - inst/doc/adnv.Rmd | 8 inst/doc/adnv.html | 12 - inst/doc/adpet.Rmd | 10 inst/doc/adpet.html | 10 inst/templates/ad_adlb.R |only man/admiralneuro-package.Rd | 6 man/admiralneuro_adapet.Rd | 2 man/admiralneuro_adtpet.Rd | 2 man/adsl_neuro.Rd | 2 man/compute_centiloid.Rd | 4 man/compute_upsit_percentile.Rd | 4 man/figures/eli_lilly_and_company_logo.png |binary man/figures/roche_logo.png |binary vignettes/adlb.Rmd |only vignettes/admiralneuro.Rmd | 6 vignettes/adnv.Rmd | 8 vignettes/adpet.Rmd | 10 vignettes/articles |only 31 files changed, 330 insertions(+), 246 deletions(-)
Title: Solvers for Boundary Value Problems of Differential Equations
Description: Functions that solve boundary value problems ('BVP') of systems of ordinary
differential equations ('ODE') and differential algebraic equations ('DAE').
The functions provide an interface to the FORTRAN functions
'twpbvpC', 'colnew/colsys', and an R-implementation of the shooting method.
Mazzia, F., J.R. Cash and K. Soetaert (2014),
"Solving Boundary Value Problems in the Open Source Software R:
Package bvpSolve" <doi:10.7494/OpMath.2014.34.2.387>.
Author: Karline Soetaert [aut] ,
Jeff Cash [aut],
Francesca Mazzia [aut],
Uri M. Ascher [ctb] ,
G. Bader [ctb] ,
J. Christiansen [ctb] ,
Robert R. Russell [ctb] ,
George Helffrich [cre, ctb]
Maintainer: George Helffrich <ghfbsd@gmail.com>
This is a re-admission after prior archival of version 1.4.4.1 dated 2023-09-21
Diff between bvpSolve versions 1.4.4.1 dated 2023-09-21 and 1.4.4.2 dated 2026-08-20
DESCRIPTION | 37 MD5 | 50 R/Utilities.R | 4 R/bvpsolver.R | 14 build/vignette.rds |binary inst/doc/bvpSolve.R | 1596 ++++++++++++------------- inst/doc/bvpSolve.Rnw | 56 inst/doc/bvpSolve.pdf |binary inst/doc/bvpTests.R | 3114 ++++++++++++++++++++++++------------------------- inst/doc/bvpTests.Rnw | 57 inst/doc/bvpTests.pdf |binary man/bvpSolve.Rd | 8 man/bvpcol.Rd | 12 man/bvptwp.Rd | 6 man/diagnostics.Rd | 12 man/plot.bvpSolve.Rd | 5 src/acdcR.f | 4 src/colnewR.f | 6 src/errmsg.f | 4 src/forcings.c | 2 src/rprintf.c | 36 src/twpbvpa.f | 2 src/twpbvplc.f | 2 vignettes/bvpSolve.Rnw | 56 vignettes/bvpTests.Rnw | 57 vignettes/docs.bib | 4 26 files changed, 2586 insertions(+), 2558 deletions(-)
Title: Gene Operations for Real-Coded Genes
Description: Representation-dependent gene-level operations
for genetic and evolutionary algorithms with real-coded genes
used in the R-package 'xega' <https://CRAN.R-project.org/package=xega>
are collected in this package. The common feature of the gene
operations is that all of them are useful for derivation-free
optimization algorithms. At the moment the package
implements initialization, mutation, crossover, and replication
operations for differential evolution as described in
Price, Kenneth V., Storn, Rainer M. and Lampinen, Jouni A. (2005)
<doi:10.1007/3-540-31306-0>. In addition, several (more recent)
methods for determining the scale factor are provided.
For 'xega''s architecture,
see Geyer-Schulz, A. (2025) <doi:10.5445/IR/1000187255>.
Author: Andreas Geyer-Schulz [aut, cre]
Maintainer: Andreas Geyer-Schulz <Andreas.Geyer-Schulz@kit.edu>
Diff between xegaDfGene versions 1.0.0.9 dated 2026-02-16 and 1.0.0.10 dated 2026-08-20
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS | 4 ++++ R/xegaDfReplicate.R | 2 +- 4 files changed, 11 insertions(+), 7 deletions(-)
Title: Construct Mixed Type Data Structures with Vectors of Vectors
Description: Mixed type vectors are useful for combining semantically similar
classes. Some examples of semantically related classes include time across
different granularities (e.g. daily, monthly, annual) and probability
distributions (e.g. Normal, Uniform, Poisson). These groups of vector types
typically share common statistical operations which vary in results with the
attributes of each vector. The 'vecvec' data structure facilitates efficient
storage and computation across multiple vectors within the same object.
Author: Mitchell O'Hara-Wild [aut, cre]
Maintainer: Mitchell O'Hara-Wild <mail@mitchelloharawild.com>
Diff between vecvec versions 1.2.0 dated 2026-06-23 and 1.3.0 dated 2026-08-20
DESCRIPTION | 10 +- MD5 | 54 ++++++++------ NAMESPACE | 2 NEWS.md | 42 +++++++++++ R/apply.R | 121 +++++++++++++++++++++++++++++++++ R/coercion.R | 13 +++ R/compare.R | 59 +++++++++++++++- R/group-methods.R | 54 ++++++++------ R/hook.R | 24 ++++-- R/predicates.R | 41 +++++++++-- R/replacement.R | 87 +++++++++++++++++++++-- R/utils.R | 97 ++++++++++++++++++++++++-- R/vctrs.R | 102 +++++++++++++++++++++++---- R/vecvec-package.R | 1 R/vecvec.R | 105 ++++++++++++++++------------ README.md | 6 - man/vecvec_mapply.Rd |only src |only tests/testthat/_snaps/format.md | 54 ++++++++++++++ tests/testthat/test-apply.R |only tests/testthat/test-arith.R | 13 +++ tests/testthat/test-coercion.R |only tests/testthat/test-compare.R | 42 +++++++++++ tests/testthat/test-format.R | 21 +++++ tests/testthat/test-math.R | 22 ++++++ tests/testthat/test-predicates.R | 77 +++++++++++++++++++++ tests/testthat/test-replacement.R | 44 ++++++++++++ tests/testthat/test-utils.R |only tests/testthat/test-vctrs.R | 139 ++++++++++++++++++++++++++++++++++++++ tests/testthat/test-vecvec.R | 19 +++++ 30 files changed, 1095 insertions(+), 154 deletions(-)
Title: Manipulating Labelled Data
Description: Work with labelled data imported from 'SPSS'
or 'Stata' with 'haven' or 'foreign'. This package
provides useful functions to deal with "haven_labelled" and
"haven_labelled_spss" classes introduced by 'haven' package.
Author: Joseph Larmarange [aut, cre] ,
Daniel Ludecke [ctb],
Hadley Wickham [ctb],
Michal Bojanowski [ctb],
Francois Briatte [ctb]
Maintainer: Joseph Larmarange <joseph@larmarange.net>
Diff between labelled versions 2.16.0 dated 2025-10-22 and 2.16.1 dated 2026-08-20
DESCRIPTION | 8 - MD5 | 46 +++--- NAMESPACE | 28 ++- NEWS.md | 12 + R/dictionary_to_labels.R | 14 + R/lookfor.R | 11 - R/na_values.R | 4 R/recode.R | 15 + R/retrocompatibility.R | 2 R/to_character.R | 58 ++++--- R/to_factor.R | 104 +++++++------ R/val_labels.R | 193 +++++++++++++++---------- R/var_label.R | 11 - README.md | 3 build/vignette.rds |binary inst/doc/look_for.html | 220 ++++++++++++++--------------- inst/doc/missing_values.html | 3 man/dictionary_to_variable_labels.Rd | 6 man/na_values.Rd | 4 man/reexports.Rd | 4 man/to_character.Rd | 2 man/to_factor.Rd | 6 tests/testthat/test-dictionary_to_labels.R | 15 + tests/testthat/test-labelled.r | 70 ++++++++- 24 files changed, 497 insertions(+), 342 deletions(-)
Title: Miscellaneous Statistical Functions Used in 'guide-R'
Description: Companion package for the manual
'guide-R : Guide pour l’analyse de données d’enquêtes avec R' available at
<https://larmarange.github.io/guide-R/>. 'guideR' implements miscellaneous
functions introduced in 'guide-R' to facilitate statistical analysis and
manipulation of survey data.
Author: Joseph Larmarange [aut, cre]
Maintainer: Joseph Larmarange <joseph@larmarange.net>
Diff between guideR versions 0.11.0 dated 2026-08-03 and 0.12.0 dated 2026-08-20
DESCRIPTION | 16 MD5 | 41 - NAMESPACE | 19 NEWS.md | 26 R/contributions.R | 4 R/deprecated.R |only R/plot_categorical.R | 63 ++ R/plot_continuous.R | 42 + R/plot_means.R | 29 + R/tbl_maihda.R | 874 +++++++++++++++++++++++++++------ README.md | 2 inst/extdata |only man/contributions.Rd | 4 man/da.svyglm.fit.Rd | 40 - man/deprecated.Rd |only man/plot_categorical.Rd | 11 man/plot_continuous.Rd | 19 man/plot_means.Rd | 8 man/tbl_maihda.Rd | 216 ++++++-- tests/testthat/test-maihda.R | 48 + tests/testthat/test-plot_categorical.R | 13 tests/testthat/test-plot_continuous.R | 22 tests/testthat/test-plot_means.R | 7 23 files changed, 1253 insertions(+), 251 deletions(-)
Title: Quiver Plots for 'ggplot2'
Description: An extension of 'ggplot2' to provide quiver plots to visualise vector fields.
This functionality is implemented using a geom to produce a new graphical layer, which
allows aesthetic options. This layer can be overlaid on a map to improve visualisation
of mapped data.
Author: Mitchell O'Hara-Wild [aut, cre]
Maintainer: Mitchell O'Hara-Wild <mail@mitchelloharawild.com>
Diff between ggquiver versions 0.4.0 dated 2025-12-18 and 0.5.0 dated 2026-08-20
ggquiver-0.4.0/ggquiver/R/ggquiver.R |only ggquiver-0.5.0/ggquiver/DESCRIPTION | 8 ggquiver-0.5.0/ggquiver/MD5 | 36 - ggquiver-0.5.0/ggquiver/NAMESPACE | 5 ggquiver-0.5.0/ggquiver/NEWS.md | 10 ggquiver-0.5.0/ggquiver/R/geom-quiver.r | 64 + ggquiver-0.5.0/ggquiver/R/ggquiver-package.R |only ggquiver-0.5.0/ggquiver/R/stat-quiver.r | 37 - ggquiver-0.5.0/ggquiver/README.md | 13 ggquiver-0.5.0/ggquiver/man/figures/README-sealplot-custom-1.png |binary ggquiver-0.5.0/ggquiver/man/geom_quiver.Rd | 14 ggquiver-0.5.0/ggquiver/man/ggquiver-package.Rd | 2 ggquiver-0.5.0/ggquiver/tests/testthat/_snaps/geom_quiver/basic-quiver-plot.svg | 334 ++++----- ggquiver-0.5.0/ggquiver/tests/testthat/_snaps/geom_quiver/quiver-plot-with-center.svg | 334 ++++----- ggquiver-0.5.0/ggquiver/tests/testthat/_snaps/geom_quiver/quiver-plot-with-closed-arrow.svg | 334 ++++----- ggquiver-0.5.0/ggquiver/tests/testthat/_snaps/geom_quiver/quiver-plot-with-legend-arrowhead.svg |only ggquiver-0.5.0/ggquiver/tests/testthat/_snaps/geom_quiver/quiver-plot-with-random-data.svg | 20 ggquiver-0.5.0/ggquiver/tests/testthat/_snaps/geom_quiver/quiver-plot-with-rescale.svg | 338 +++++----- ggquiver-0.5.0/ggquiver/tests/testthat/_snaps/geom_quiver/quiver-plot-with-vecsize-0.svg | 334 ++++----- ggquiver-0.5.0/ggquiver/tests/testthat/test-geom_quiver.R | 43 + ggquiver-0.5.0/ggquiver/tests/testthat/test-stat_quiver.R |only 21 files changed, 1038 insertions(+), 888 deletions(-)
Title: Schema-Based Validation of 'R' Objects with User-Defined Rules
Description: A schema-based validation framework for 'R' objects using user-defined rules. Provides three 'S7' classes 'Registry', 'Schema', and 'Validator' to manage rules, define list-based schemas, and validate data in a flexible and extensible manner.
Author: Luke Jenkins [aut, cre, cph]
Maintainer: Luke Jenkins <luke-jenkins-dev@outlook.com>
Diff between fluffy versions 1.0.0 dated 2026-06-10 and 1.0.1 dated 2026-08-20
DESCRIPTION | 6 MD5 | 52 - NEWS.md | 16 R/aaa_Schema.r | 7 R/abb_add_rule_generics.r | 5 R/registry_defaults.r | 404 ++++++---- R/utils.r | 2 README.md | 11 inst/doc/custom-rules.Rmd | 2 inst/doc/custom-rules.html | 17 inst/doc/validating-data.R | 4 inst/doc/validating-data.Rmd | 4 inst/doc/validating-data.html | 16 inst/doc/validation-rules.Rmd | 2 inst/doc/validation-rules.html | 47 - man/Schema.Rd | 8 man/add_rule.Rd | 5 man/show_builtins.Rd | 2 tests/testthat/test-cross_rule_allowed_forbidden_type_mismatch.r | 44 + tests/testthat/test-cross_rule_length_min_max_length.r |only tests/testthat/test-rule_coerce.r | 5 tests/testthat/test-rule_coerce_last.r | 134 +-- tests/testthat/test-rule_length.r |only tests/testthat/test-rule_min_max_length.r | 2 tests/testthat/test-rule_type.r | 3 vignettes/custom-rules.Rmd | 2 vignettes/validating-data.Rmd | 4 vignettes/validation-rules.Rmd | 2 28 files changed, 539 insertions(+), 267 deletions(-)
Title: Function Argument Validation
Description: Validate function arguments succinctly with informative error messages.
Author: Luke Jenkins [aut, cre, cph]
Maintainer: Luke Jenkins <luke-jenkins-dev@outlook.com>
Diff between favr versions 1.0.0 dated 2025-12-15 and 2.0.0 dated 2026-08-20
favr-1.0.0/favr/R/abort_if_not.r |only favr-1.0.0/favr/R/are_attr.r |only favr-1.0.0/favr/R/are_types.r |only favr-1.0.0/favr/R/are_utils.r |only favr-1.0.0/favr/R/args.r |only favr-1.0.0/favr/R/cast_if_not.r |only favr-1.0.0/favr/R/casting_recycling_helpers.r |only favr-1.0.0/favr/R/checks.r |only favr-1.0.0/favr/R/clean_up.r |only favr-1.0.0/favr/R/enforce.r |only favr-1.0.0/favr/R/errors.r |only favr-1.0.0/favr/R/recycle_if_not.r |only favr-1.0.0/favr/R/schema.r |only favr-1.0.0/favr/tests/testthat/test-abort_if_not.r |only favr-1.0.0/favr/tests/testthat/test-are.r |only favr-1.0.0/favr/tests/testthat/test-cast_if_not.r |only favr-1.0.0/favr/tests/testthat/test-recycle_if_not.r |only favr-2.0.0/favr/DESCRIPTION | 14 favr-2.0.0/favr/MD5 | 171 ++- favr-2.0.0/favr/NAMESPACE | 277 +++-- favr-2.0.0/favr/NEWS.md | 84 + favr-2.0.0/favr/R/abortifnot.r |only favr-2.0.0/favr/R/array_type_checks.r |only favr-2.0.0/favr/R/check.r |only favr-2.0.0/favr/R/deprecate-are.r |only favr-2.0.0/favr/R/deprecate-if_not.r |only favr-2.0.0/favr/R/favr-package.r | 27 favr-2.0.0/favr/R/file_system_checks.r |only favr-2.0.0/favr/R/forbidden_value_checks.r |only favr-2.0.0/favr/R/inheritance_checks.r |only favr-2.0.0/favr/R/modifiers.r |only favr-2.0.0/favr/R/n_length_checks.r |only favr-2.0.0/favr/R/n_size_checks.r |only favr-2.0.0/favr/R/obj_type_friendly.r |only favr-2.0.0/favr/R/oop_checks.r |only favr-2.0.0/favr/R/property_checks.r |only favr-2.0.0/favr/R/questioning-casting_recycling_helpers.r |only favr-2.0.0/favr/R/questioning-clean_up.r |only favr-2.0.0/favr/R/questioning-enforce.r |only favr-2.0.0/favr/R/questioning-errors.r |only favr-2.0.0/favr/R/questioning-helpers.r |only favr-2.0.0/favr/R/questioning-schema.r |only favr-2.0.0/favr/R/s3_check_builders.r |only favr-2.0.0/favr/R/s3_type_checks.r |only favr-2.0.0/favr/R/scalar_type_checks.r |only favr-2.0.0/favr/R/scalar_value_checks.r |only favr-2.0.0/favr/R/type_checks.r |only favr-2.0.0/favr/R/utils.r | 141 +- favr-2.0.0/favr/R/walk_check.r |only favr-2.0.0/favr/README.md | 540 +++++----- favr-2.0.0/favr/man/abort_if_not.Rd | 172 +-- favr-2.0.0/favr/man/abortifnot.Rd |only favr-2.0.0/favr/man/are-bare-type-predicates.Rd | 217 ++-- favr-2.0.0/favr/man/are-scalar-type-predicates.Rd | 185 +-- favr-2.0.0/favr/man/are-type-predicates.Rd | 227 ++-- favr-2.0.0/favr/man/are_empty.Rd | 69 - favr-2.0.0/favr/man/are_integerish.Rd | 181 +-- favr-2.0.0/favr/man/are_named.Rd | 159 +- favr-2.0.0/favr/man/are_true.Rd | 83 - favr-2.0.0/favr/man/array-type-checks.Rd |only favr-2.0.0/favr/man/cast_if_not.Rd | 248 ++-- favr-2.0.0/favr/man/check.Rd |only favr-2.0.0/favr/man/enforce.Rd | 231 ++-- favr-2.0.0/favr/man/favr-package.Rd |only favr-2.0.0/favr/man/favr_casting_recycling_helpers.Rd | 136 +- favr-2.0.0/favr/man/figures/lifecycle-deprecated.svg |only favr-2.0.0/favr/man/figures/lifecycle-experimental.svg |only favr-2.0.0/favr/man/figures/lifecycle-stable.svg |only favr-2.0.0/favr/man/figures/lifecycle-superseded.svg |only favr-2.0.0/favr/man/figures/logo.png |binary favr-2.0.0/favr/man/forbidden-value-checks.Rd |only favr-2.0.0/favr/man/inheritance-checks.Rd |only favr-2.0.0/favr/man/modifiers.Rd |only favr-2.0.0/favr/man/oop-checks.Rd |only favr-2.0.0/favr/man/path-checks.Rd |only favr-2.0.0/favr/man/property-checks.Rd |only favr-2.0.0/favr/man/recycle_if_not.Rd | 244 ++-- favr-2.0.0/favr/man/s3-check-builders.Rd |only favr-2.0.0/favr/man/s3-type-checks.Rd |only favr-2.0.0/favr/man/scalar-type-checks.Rd |only favr-2.0.0/favr/man/scalar-value-checks.Rd |only favr-2.0.0/favr/man/schema.Rd | 365 +++--- favr-2.0.0/favr/man/type-checks.Rd |only favr-2.0.0/favr/man/walk-check.Rd |only favr-2.0.0/favr/tests/testthat/_snaps |only favr-2.0.0/favr/tests/testthat/helper-lifecycle.r |only favr-2.0.0/favr/tests/testthat/helper-types.r |only favr-2.0.0/favr/tests/testthat/test-abortif.r |only favr-2.0.0/favr/tests/testthat/test-abortifnot.r |only favr-2.0.0/favr/tests/testthat/test-check.r |only favr-2.0.0/favr/tests/testthat/test-check_array_matrix.r |only favr-2.0.0/favr/tests/testthat/test-check_atomic.r |only favr-2.0.0/favr/tests/testthat/test-check_bool.r |only favr-2.0.0/favr/tests/testthat/test-check_bytes.r |only favr-2.0.0/favr/tests/testthat/test-check_character.r |only favr-2.0.0/favr/tests/testthat/test-check_complex.r |only favr-2.0.0/favr/tests/testthat/test-check_double.r |only favr-2.0.0/favr/tests/testthat/test-check_integer.r |only favr-2.0.0/favr/tests/testthat/test-check_integerish.r |only favr-2.0.0/favr/tests/testthat/test-check_list.r |only favr-2.0.0/favr/tests/testthat/test-check_logical.r |only favr-2.0.0/favr/tests/testthat/test-check_null.r |only favr-2.0.0/favr/tests/testthat/test-check_numeric.r |only favr-2.0.0/favr/tests/testthat/test-check_raw.r |only favr-2.0.0/favr/tests/testthat/test-check_string.r |only favr-2.0.0/favr/tests/testthat/test-check_true_false.r |only favr-2.0.0/favr/tests/testthat/test-check_vector.r |only favr-2.0.0/favr/tests/testthat/test-check_with.r |only favr-2.0.0/favr/tests/testthat/test-deprecate-abort_if_not.r |only favr-2.0.0/favr/tests/testthat/test-deprecate-are.r |only favr-2.0.0/favr/tests/testthat/test-deprecate-cast_if_not.r |only favr-2.0.0/favr/tests/testthat/test-deprecate-recycle_if_not.r |only favr-2.0.0/favr/tests/testthat/test-forbidden_value_checks.r |only favr-2.0.0/favr/tests/testthat/test-inheritance_checks.r |only favr-2.0.0/favr/tests/testthat/test-misc.r | 2 favr-2.0.0/favr/tests/testthat/test-modifiers.r |only favr-2.0.0/favr/tests/testthat/test-oop_checks.r |only favr-2.0.0/favr/tests/testthat/test-paths.r |only favr-2.0.0/favr/tests/testthat/test-property_checks.r |only favr-2.0.0/favr/tests/testthat/test-s3_df_check.r |only favr-2.0.0/favr/tests/testthat/test-s3_vec_check.r |only favr-2.0.0/favr/tests/testthat/test-walk_check.r |only 122 files changed, 2089 insertions(+), 1684 deletions(-)
Title: Analysis and Visualisation of Ecological Communities
Description: Provides a flexible, extendable representation of an ecological community and a range of functions for analysis and visualisation, focusing on food web, body mass and numerical abundance data. Allows inter-web comparisons such as examining changes in community structure over environmental, temporal or spatial gradients.
Author: Lawrence Hudson [aut, cre],
Dan Reuman [aut],
Rob Emerson [ctb]
Maintainer: Lawrence Hudson <quicklizard@googlemail.com>
Diff between cheddar versions 0.1-639 dated 2024-07-24 and 0.1-640 dated 2026-08-20
DESCRIPTION | 24 ++++++++++++++++++------ MD5 | 28 ++++++++++++++-------------- inst/doc/CheddarQuickstart.R | 2 -- inst/doc/CheddarQuickstart.pdf |binary inst/doc/Collections.R | 2 -- inst/doc/Collections.pdf |binary inst/doc/Community.R | 2 -- inst/doc/Community.pdf |binary inst/doc/ImportExport.R | 2 -- inst/doc/ImportExport.pdf |binary inst/doc/PlotsAndStats.R | 2 -- inst/doc/PlotsAndStats.pdf |binary man/cheddar.Rd | 4 ++-- tests/util_test.R | 21 ++++++++++----------- vignettes/cheddar.bib | 16 +++++++++++++++- 15 files changed, 59 insertions(+), 44 deletions(-)
Title: Helpers for Model Coefficients Tibbles
Description: Provides suite of functions to work with regression model
'broom::tidy()' tibbles. The suite includes functions to group
regression model terms by variable, insert reference and header rows
for categorical variables, add variable labels, and more.
Author: Joseph Larmarange [aut, cre] ,
Daniel D. Sjoberg [aut]
Maintainer: Joseph Larmarange <joseph@larmarange.net>
Diff between broom.helpers versions 1.22.0 dated 2025-09-17 and 1.23.0 dated 2026-08-20
DESCRIPTION | 8 MD5 | 163 ++++++------- NAMESPACE | 46 ++- NEWS.md | 18 + R/assert_package.R | 14 - R/custom_tidiers.R | 123 ++++++++-- R/helpers.R | 7 R/model_get_coefficients_type.R | 86 +++++++ R/model_get_pairwise_contrasts.R | 39 +-- R/model_list_terms_levels.R | 16 - R/model_list_variables.R | 4 R/tidy_add_coefficients_type.R | 6 R/tidy_add_estimate_to_reference_rows.R | 11 R/tidy_add_pairwise_contrasts.R | 19 - R/tidy_add_reference_rows.R | 8 R/tidy_and_attach.R | 11 R/tidy_disambiguate_terms.R | 3 R/tidy_group_by.R | 9 R/tidy_select_variables.R | 5 README.md | 6 build/vignette.rds |binary data/supported_models.rda |binary inst/doc/broom-helpers.html | 353 ++++++++++++++--------------- man/dot-clean_backticks.Rd | 4 man/dot-escape_regex.Rd | 4 man/model_compute_terms_contributions.Rd | 42 +-- man/model_get_assign.Rd | 42 +-- man/model_get_coefficients_type.Rd | 45 +-- man/model_get_contrasts.Rd | 42 +-- man/model_get_model.Rd | 42 +-- man/model_get_model_frame.Rd | 42 +-- man/model_get_model_matrix.Rd | 44 +-- man/model_get_n.Rd | 42 +-- man/model_get_nlevels.Rd | 42 +-- man/model_get_offset.Rd | 42 +-- man/model_get_pairwise_contrasts.Rd | 42 +-- man/model_get_response.Rd | 42 +-- man/model_get_response_variable.Rd | 42 +-- man/model_get_terms.Rd | 42 +-- man/model_get_weights.Rd | 42 +-- man/model_get_xlevels.Rd | 42 +-- man/model_identify_variables.Rd | 44 +-- man/model_list_contrasts.Rd | 42 +-- man/model_list_higher_order_variables.Rd | 42 +-- man/model_list_terms_levels.Rd | 42 +-- man/model_list_variables.Rd | 44 +-- man/reexports.Rd | 2 man/select_helpers.Rd | 2 man/supported_models.Rd | 1 man/tidy_add_coefficients_type.Rd | 34 +- man/tidy_add_contrasts.Rd | 32 +- man/tidy_add_estimate_to_reference_rows.Rd | 38 +-- man/tidy_add_header_rows.Rd | 32 +- man/tidy_add_n.Rd | 34 +- man/tidy_add_pairwise_contrasts.Rd | 32 +- man/tidy_add_reference_rows.Rd | 36 +- man/tidy_add_term_labels.Rd | 32 +- man/tidy_add_variable_labels.Rd | 32 +- man/tidy_all_effects.Rd | 14 - man/tidy_attach_model.Rd | 34 +- man/tidy_avg_comparisons.Rd | 14 - man/tidy_avg_slopes.Rd | 14 - man/tidy_broom.Rd | 15 - man/tidy_coxphms.Rd |only man/tidy_disambiguate_terms.Rd | 32 +- man/tidy_ggpredict.Rd | 14 - man/tidy_group_by.Rd | 32 +- man/tidy_identify_variables.Rd | 32 +- man/tidy_marginal_contrasts.Rd | 14 - man/tidy_marginal_predictions.Rd | 14 - man/tidy_margins.Rd | 14 - man/tidy_multgee.Rd | 15 - man/tidy_parameters.Rd | 17 - man/tidy_plus_plus.Rd | 34 +- man/tidy_remove_intercept.Rd | 32 +- man/tidy_select_variables.Rd | 32 +- man/tidy_svy_vglm.Rd | 15 - man/tidy_vgam.Rd | 15 - man/tidy_with_broom_or_parameters.Rd | 15 - man/tidy_zeroinfl.Rd | 15 - tests/testthat/test-disambiguate_terms.R | 14 - tests/testthat/test-select_helpers.R | 9 tests/testthat/test-tidy_plus_plus.R | 42 +++ 83 files changed, 1468 insertions(+), 1191 deletions(-)
Title: Bayesian Estimation of Mixtures of Multivariate Bernoulli
Distributions
Description: Fully Bayesian inference for estimating the number of clusters and related parameters to heterogeneous binary data.
Author: Panagiotis Papastamoulis [aut, cre]
Maintainer: Panagiotis Papastamoulis <papapast@yahoo.gr>
Diff between BayesBinMix versions 1.4.1 dated 2017-07-04 and 1.4.2 dated 2026-08-20
DESCRIPTION | 18 +++++++++++++----- MD5 | 6 +++--- inst/CITATION | 2 +- man/coupledMetropolis.Rd | 2 +- 4 files changed, 18 insertions(+), 10 deletions(-)
Title: Operations on Permutation Genes
Description: An implementation of
representation-dependent gene level operations for
genetic algorithms with genes representing permutations:
Initialization of genes, mutation, and crossover.
The crossover operation provided is position-based crossover
(Syswerda, G., Chap. 21 in Davis, L. (1991, ISBN:0-442-00173-8).
For mutation, several variants are included: Order-based mutation
(Syswerda, G., Chap. 21 in Davis, L. (1991, ISBN:0-442-00173-8),
randomized Lin-Kernighan heuristics
(Croes, G. A. (1958) <doi:10.1287/opre.6.6.791> and
Lin, S. and Kernighan. B. W. (1973)
<doi:10.1287/opre.21.2.498>),
and randomized greedy operators.
A random mix operator for mutation selects a mutation variant
randomly.
Author: Andreas Geyer-Schulz [aut, cre]
Maintainer: Andreas Geyer-Schulz <Andreas.Geyer-Schulz@kit.edu>
Diff between xegaPermGene versions 1.0.0.1 dated 2025-04-16 and 1.0.0.2 dated 2026-08-20
DESCRIPTION | 12 ++++++------ MD5 | 6 +++--- NEWS | 6 ++++++ R/xegaPermMutate.R | 8 ++++---- 4 files changed, 19 insertions(+), 13 deletions(-)
Title: Binary Gene Operations for Genetic Algorithms
Description: Representation-dependent gene level operations of a
genetic algorithm with binary coded genes
for the R-package 'xega' <https://CRAN.R-project.org/package=xega>:
Initialization of random binary genes, several gene maps for
binary genes, several mutation operators, several crossover
operators with 1 and 2 kids, replication
pipelines for 1 and 2 kids, and, last but not least, function
factories for configuration.
See Goldberg, D. E. (1989, ISBN:0-201-15767-5).
For crossover operators, see
Syswerda, G. (1989, ISBN:1-55860-066-3),
Spears, W. and De Jong, K. (1991, ISBN:1-55860-208-9).
For mutation operators, see
Stanhope, S. A. and Daida, J. M. (1996, ISBN:0-18-201-031-7).
For 'xega''s architecture,
see Geyer-Schulz, A. (2025) <doi:10.5445/IR/1000187255>.
Author: Andreas Geyer-Schulz [aut, cre]
Maintainer: Andreas Geyer-Schulz <Andreas.Geyer-Schulz@kit.edu>
Diff between xegaGaGene versions 1.0.0.6 dated 2026-02-16 and 1.0.0.7 dated 2026-08-20
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS | 4 ++++ R/xegaOperatorPipelinesInGene.R | 4 ++-- 4 files changed, 12 insertions(+), 8 deletions(-)
Title: Extended Evolutionary and Genetic Algorithms
Description: Implementation of a scalable, highly configurable, and
e(x)tended architecture for (e)volutionary and (g)enetic (a)lgorithms.
Multiple representations (binary, real-coded, permutation, and
derivation-tree), a rich collection of genetic operators,
as well as an extended processing pipeline are provided
for genetic algorithms (Goldberg, D. E. (1989, ISBN:0-201-15767-5)),
differential evolution (Price, Kenneth V., Storn, Rainer M. and Lampinen, Jouni A. (2005)
<doi:10.1007/3-540-31306-0>), simulated annealing (Aarts, E., and Korst, J.
(1989, ISBN:0-471-92146-7)), grammar-based genetic programming
(Geyer-Schulz (1997, ISBN:978-3-7908-0830-X)), grammatical evolution
(Ryan, C., O'Neill, M., and Collins, J. J. (2018) <doi:10.1007/978-3-319-78717-6>),
and grammatical differential evolution (O'Neill, M. and Brabazon, A. (2006) in
Arabinia, H. (2006, ISBN:978-193-241596-3).
All algorithms reuse basic adaptive mechanisms for performance optimization.
For the architecture, see Geyer-Sc [...truncated...]
Author: Andreas Geyer-Schulz [aut, cre]
Maintainer: Andreas Geyer-Schulz <Andreas.Geyer-Schulz@kit.edu>
Diff between xega versions 0.9.0.23 dated 2026-02-17 and 0.9.1.0 dated 2026-08-20
DESCRIPTION | 20 +- MD5 | 24 +- NAMESPACE | 8 NEWS | 52 +++++ R/xega-package.R | 47 ++++- R/xegaImproved.R |only R/xegaRerun.R | 42 +++- R/xegaResult.R | 5 R/xegaRun.R | 473 ++++++++++++++++++++++++++++++++++++++++++++++++---- R/xegaVersion.R | 4 man/xega.Rd | 49 +++++ man/xegaImproved.Rd |only man/xegaReRun.Rd | 9 man/xegaRun.Rd | 262 ++++++++++++++++++++++++++-- 14 files changed, 901 insertions(+), 94 deletions(-)
Title: Tailored Knowledge Catalog
Description: Facilitate the management of data from knowledge
resources that are frequently used alone or together
in research environments.
In 'TKCat', knowledge resources are manipulated as modeled database (MDB)
objects. These objects provide access to the data tables along with a general
description of the resource and a detailed data model documenting the
tables, their fields and their relationships.
These MDBs are then gathered in catalogs that can be easily
explored and shared.
Finally, 'TKCat' provides tools to easily subset, filter and combine MDBs and
create new catalogs suited for specific needs.
Author: Patrice Godard [aut, cre, cph]
Maintainer: Patrice Godard <patrice.godard@gmail.com>
Diff between TKCat versions 1.2.2 dated 2026-06-29 and 1.2.3 dated 2026-08-20
DESCRIPTION | 8 - MD5 | 24 ++--- NAMESPACE | 80 ++++++++++------- R/ClickHouse.R | 2 R/chMDB.R | 12 ++ R/chTKCat.R | 10 +- R/fileMDB.R | 18 +-- R/shiny-helpers.R | 4 build/vignette.rds |binary inst/ClickHouse/Data-Model/chTKCat-MDB-data-model.json | 61 ++++++++---- inst/doc/TKCat-KMR-POK.html | 6 - inst/doc/TKCat.html | 64 ++++++------- inst/pkgdown.yml | 6 - 13 files changed, 175 insertions(+), 120 deletions(-)
Title: Tidy Structural Equation Modeling
Description: A tidy workflow for generating, estimating, reporting,
and plotting structural equation models using 'lavaan', 'OpenMx', or
'Mplus'. Throughout this workflow, elements of syntax, results, and graphs
are represented as 'tidy' data, making them easy to customize.
Includes functionality to estimate latent class analyses, and to plot
'dagitty' and 'igraph' objects.
Author: Caspar J. van Lissa [aut, cre] ,
Mauricio Garnier-Villarreal [ctb] ,
Frank C Gootjes [ctb]
Maintainer: Caspar J. van Lissa <c.j.vanlissa@tilburguniversity.edu>
Diff between tidySEM versions 0.2.10 dated 2026-01-11 and 0.2.11 dated 2026-08-20
tidySEM-0.2.10/tidySEM/man/pmc_srmr.Rd |only tidySEM-0.2.11/tidySEM/DESCRIPTION | 8 tidySEM-0.2.11/tidySEM/MD5 | 210 - tidySEM-0.2.11/tidySEM/NAMESPACE | 14 tidySEM-0.2.11/tidySEM/R/descriptives.R | 130 tidySEM-0.2.11/tidySEM/R/deviances_to_thresholds.R |only tidySEM-0.2.11/tidySEM/R/fruchterman-reingold.R |only tidySEM-0.2.11/tidySEM/R/igraph.R | 20 tidySEM-0.2.11/tidySEM/R/lazy_bootstrap.R | 250 - tidySEM-0.2.11/tidySEM/R/mixture-3step.R | 2 tidySEM-0.2.11/tidySEM/R/mixture-pseudo_class.R | 2 tidySEM-0.2.11/tidySEM/R/mx_mixture.R | 6 tidySEM-0.2.11/tidySEM/R/mx_simple_thresholds.R | 276 + tidySEM-0.2.11/tidySEM/R/openmx_functions.R | 108 tidySEM-0.2.11/tidySEM/R/plot-generate_layout.R | 62 tidySEM-0.2.11/tidySEM/R/plot-plot_sem.R | 11 tidySEM-0.2.11/tidySEM/R/plot_growth.R | 77 tidySEM-0.2.11/tidySEM/R/results-table_results.R | 10 tidySEM-0.2.11/tidySEM/R/syntax-create_scales.R | 1 tidySEM-0.2.11/tidySEM/R/syntax-get_data.R | 2 tidySEM-0.2.11/tidySEM/R/wald_test.R | 56 tidySEM-0.2.11/tidySEM/build/partial.rdb |binary tidySEM-0.2.11/tidySEM/build/vignette.rds |binary tidySEM-0.2.11/tidySEM/inst/doc/Generating_syntax.html | 229 - tidySEM-0.2.11/tidySEM/inst/doc/Plotting_graphs.R | 8 tidySEM-0.2.11/tidySEM/inst/doc/Plotting_graphs.Rmd | 8 tidySEM-0.2.11/tidySEM/inst/doc/Plotting_graphs.html | 1156 +++---- tidySEM-0.2.11/tidySEM/inst/doc/SMART_LCA_checklist.R | 2 tidySEM-0.2.11/tidySEM/inst/doc/SMART_LCA_checklist.Rmd | 2 tidySEM-0.2.11/tidySEM/inst/doc/SMART_LCA_checklist.html | 2 tidySEM-0.2.11/tidySEM/inst/doc/Tabulating_results.html | 19 tidySEM-0.2.11/tidySEM/inst/doc/lca_confirmatory.R | 4 tidySEM-0.2.11/tidySEM/inst/doc/lca_confirmatory.Rmd | 4 tidySEM-0.2.11/tidySEM/inst/doc/lca_confirmatory.html | 5 tidySEM-0.2.11/tidySEM/inst/doc/lca_exploratory.R | 2 tidySEM-0.2.11/tidySEM/inst/doc/lca_exploratory.Rmd | 2 tidySEM-0.2.11/tidySEM/inst/doc/lca_exploratory.html | 5 tidySEM-0.2.11/tidySEM/inst/doc/lca_lcga.R | 33 tidySEM-0.2.11/tidySEM/inst/doc/lca_lcga.Rmd | 33 tidySEM-0.2.11/tidySEM/inst/doc/lca_lcga.html | 30 tidySEM-0.2.11/tidySEM/inst/doc/lca_ordinal.R | 3 tidySEM-0.2.11/tidySEM/inst/doc/lca_ordinal.Rmd | 3 tidySEM-0.2.11/tidySEM/inst/doc/lca_ordinal.html | 5 tidySEM-0.2.11/tidySEM/inst/doc/mixed_lca.R | 14 tidySEM-0.2.11/tidySEM/inst/doc/mixed_lca.Rmd | 14 tidySEM-0.2.11/tidySEM/inst/doc/mixed_lca.html | 41 tidySEM-0.2.11/tidySEM/inst/doc/openmx_ordinal.R |only tidySEM-0.2.11/tidySEM/inst/doc/openmx_ordinal.Rmd |only tidySEM-0.2.11/tidySEM/inst/doc/openmx_ordinal.html |only tidySEM-0.2.11/tidySEM/inst/doc/pmc_tutorial.R |only tidySEM-0.2.11/tidySEM/inst/doc/pmc_tutorial.Rmd |only tidySEM-0.2.11/tidySEM/inst/doc/pmc_tutorial.html |only tidySEM-0.2.11/tidySEM/inst/doc/sem_graph.html | 11 tidySEM-0.2.11/tidySEM/man/as_ram.Rd | 23 tidySEM-0.2.11/tidySEM/man/chi_sq.Rd |only tidySEM-0.2.11/tidySEM/man/conf_int.Rd | 10 tidySEM-0.2.11/tidySEM/man/deviances_to_thresholds.Rd |only tidySEM-0.2.11/tidySEM/man/est_sig.Rd | 10 tidySEM-0.2.11/tidySEM/man/get_layout.Rd | 2 tidySEM-0.2.11/tidySEM/man/mx_deviances.Rd |only tidySEM-0.2.11/tidySEM/man/pmc.Rd |only tidySEM-0.2.11/tidySEM/man/skew_kurtosis.Rd | 22 tidySEM-0.2.11/tidySEM/man/srmr.Rd |only tidySEM-0.2.11/tidySEM/man/table_fit.Rd | 10 tidySEM-0.2.11/tidySEM/man/table_prob.Rd | 10 tidySEM-0.2.11/tidySEM/man/table_results.Rd | 10 tidySEM-0.2.11/tidySEM/tests/testthat/Rplots.pdf |binary tidySEM-0.2.11/tidySEM/tests/testthat/_problems/test-graph_sem_label-21.R |only tidySEM-0.2.11/tidySEM/tests/testthat/_problems/test-graph_sem_label-27.R |only tidySEM-0.2.11/tidySEM/tests/testthat/_problems/test-graph_sem_label-33.R |only tidySEM-0.2.11/tidySEM/tests/testthat/_problems/test-graph_sem_label-39.R |only tidySEM-0.2.11/tidySEM/tests/testthat/_problems/test-plot_digits-21.R |only tidySEM-0.2.11/tidySEM/tests/testthat/_problems/test-plot_digits-6.R |only tidySEM-0.2.11/tidySEM/tests/testthat/_problems/test-plot_if_edit-6.R |only tidySEM-0.2.11/tidySEM/tests/testthat/_problems/test-plot_if_edit_overwrite_aes-14.R |only tidySEM-0.2.11/tidySEM/tests/testthat/_problems/test-plot_if_edit_overwrite_aes-3.R |only tidySEM-0.2.11/tidySEM/tests/testthat/test-lavaan_handles_defined_multigroup.R |only tidySEM-0.2.11/tidySEM/tests/testthat/test-new_mx_threshold.R | 30 tidySEM-0.2.11/tidySEM/tests/testthat/test-openmx_binary.R | 290 - tidySEM-0.2.11/tidySEM/tests/testthat/test-openmx_binary_df.rds |only tidySEM-0.2.11/tidySEM/tests/testthat/test-openmx_ordinal.R | 1323 -------- tidySEM-0.2.11/tidySEM/tests/testthat/test-openmx_ordinal_and_cont.R | 670 ++-- tidySEM-0.2.11/tidySEM/tests/testthat/test-openmx_ordinal_and_cont_df.rds |only tidySEM-0.2.11/tidySEM/tests/testthat/test-openmx_ordinal_df.rds |only tidySEM-0.2.11/tidySEM/tests/testthat/test-openmx_ordinal_methods.R | 18 tidySEM-0.2.11/tidySEM/vignettes/Plotting_graphs.Rmd | 8 tidySEM-0.2.11/tidySEM/vignettes/SMART_LCA_checklist.Rmd | 2 tidySEM-0.2.11/tidySEM/vignettes/gmm_bivariate_bic.png |binary tidySEM-0.2.11/tidySEM/vignettes/gmm_plotfit.png |binary tidySEM-0.2.11/tidySEM/vignettes/lca_aux_dep.RData |only tidySEM-0.2.11/tidySEM/vignettes/lca_confirmatory.Rmd | 4 tidySEM-0.2.11/tidySEM/vignettes/lca_exploratory.Rmd | 2 tidySEM-0.2.11/tidySEM/vignettes/lca_lcga.Rmd | 33 tidySEM-0.2.11/tidySEM/vignettes/lca_ordinal.Rmd | 3 tidySEM-0.2.11/tidySEM/vignettes/lca_plot_desc.png |binary tidySEM-0.2.11/tidySEM/vignettes/lca_prob.png |binary tidySEM-0.2.11/tidySEM/vignettes/lca_res.RData |binary tidySEM-0.2.11/tidySEM/vignettes/lcga_plot_fit.png |binary tidySEM-0.2.11/tidySEM/vignettes/lpa_bivariate.png |binary tidySEM-0.2.11/tidySEM/vignettes/lpa_fit_compare.csv | 2 tidySEM-0.2.11/tidySEM/vignettes/lpatablmr.csv | 6 tidySEM-0.2.11/tidySEM/vignettes/mixed_lca.Rmd | 14 tidySEM-0.2.11/tidySEM/vignettes/mixed_lca_bivariate.png |binary tidySEM-0.2.11/tidySEM/vignettes/mixed_lca_fit2.csv | 4 tidySEM-0.2.11/tidySEM/vignettes/mixed_lca_prob.png |binary tidySEM-0.2.11/tidySEM/vignettes/mixed_lca_profiles.png |binary tidySEM-0.2.11/tidySEM/vignettes/mixed_lca_res_blrt.csv | 4 tidySEM-0.2.11/tidySEM/vignettes/mixed_lca_res_pmc.csv |only tidySEM-0.2.11/tidySEM/vignettes/mixed_lca_res_pmc_srmr.csv | 2 tidySEM-0.2.11/tidySEM/vignettes/mplusfit.R | 1538 +++++----- tidySEM-0.2.11/tidySEM/vignettes/openmx_ordinal.Rmd |only tidySEM-0.2.11/tidySEM/vignettes/plot_dist.png |binary tidySEM-0.2.11/tidySEM/vignettes/plot_gmm_desc.png |binary tidySEM-0.2.11/tidySEM/vignettes/plot_gmm_desc_log.png |binary tidySEM-0.2.11/tidySEM/vignettes/plot_gmm_scatter.png |binary tidySEM-0.2.11/tidySEM/vignettes/plot_lpa_desc.png |binary tidySEM-0.2.11/tidySEM/vignettes/plot_traj.png |binary tidySEM-0.2.11/tidySEM/vignettes/plot_trans.png |binary tidySEM-0.2.11/tidySEM/vignettes/pmc_res_blrt.csv |only tidySEM-0.2.11/tidySEM/vignettes/pmc_res_chi2.csv |only tidySEM-0.2.11/tidySEM/vignettes/pmc_res_pmc.csv |only tidySEM-0.2.11/tidySEM/vignettes/pmc_tutorial.Rmd |only tidySEM-0.2.11/tidySEM/vignettes/res_step.RData |binary 123 files changed, 3005 insertions(+), 3925 deletions(-)
Title: Outlier Robust Two-Stage Least Squares Inference and Testing
Description: An implementation of easy tools for outlier robust inference in
two-stage least squares (2SLS) models. The user specifies a reference
distribution against which observations are classified as outliers or not.
After removing the outliers, adjusted standard errors are automatically
provided. Furthermore, several statistical tests for the false outlier
detection rate can be calculated. The outlier removing algorithm can be
iterated a fixed number of times or until the procedure converges. The
algorithms and robust inference are described in more detail in Jiao (2019)
<https://drive.google.com/file/d/1qPxDJnLlzLqdk94X9wwVASptf1MPpI2w/view>.
Author: Jonas Kurle [aut, cre]
Maintainer: Jonas Kurle <mail@jonaskurle.com>
Diff between robust2sls versions 0.2.3 dated 2025-05-20 and 0.2.4 dated 2026-08-20
robust2sls-0.2.3/robust2sls/tests/testthat/_snaps/monte_carlo |only robust2sls-0.2.3/robust2sls/tests/testthat/_snaps/monte_carlo.md |only robust2sls-0.2.3/robust2sls/tests/testthat/test-monte_carlo.R |only robust2sls-0.2.4/robust2sls/DESCRIPTION | 12 robust2sls-0.2.4/robust2sls/MD5 | 111 robust2sls-0.2.4/robust2sls/NEWS.md | 29 robust2sls-0.2.4/robust2sls/R/class.R | 6 robust2sls-0.2.4/robust2sls/README.md | 32 robust2sls-0.2.4/robust2sls/build/robust2sls.pdf |only robust2sls-0.2.4/robust2sls/build/stage23.rdb |binary robust2sls-0.2.4/robust2sls/build/vignette.rds |binary robust2sls-0.2.4/robust2sls/inst/doc/monte-carlo.R | 54 robust2sls-0.2.4/robust2sls/inst/doc/monte-carlo.Rmd | 249 - robust2sls-0.2.4/robust2sls/inst/doc/monte-carlo.html | 498 -- robust2sls-0.2.4/robust2sls/inst/doc/outlier-testing.R | 5 robust2sls-0.2.4/robust2sls/inst/doc/outlier-testing.Rmd | 5 robust2sls-0.2.4/robust2sls/inst/doc/outlier-testing.html | 61 robust2sls-0.2.4/robust2sls/inst/doc/overview.Rmd | 4 robust2sls-0.2.4/robust2sls/inst/doc/overview.html | 31 robust2sls-0.2.4/robust2sls/man/beta_hausman.Rd | 76 robust2sls-0.2.4/robust2sls/man/beta_inf.Rd | 88 robust2sls-0.2.4/robust2sls/man/beta_inf_correction.Rd | 92 robust2sls-0.2.4/robust2sls/man/beta_t.Rd | 68 robust2sls-0.2.4/robust2sls/man/beta_test_avar.Rd | 64 robust2sls-0.2.4/robust2sls/man/conv_diff.Rd | 48 robust2sls-0.2.4/robust2sls/man/new_robust2sls.Rd | 54 robust2sls-0.2.4/robust2sls/man/outliers.Rd | 44 robust2sls-0.2.4/robust2sls/man/outliers_prop.Rd | 46 robust2sls-0.2.4/robust2sls/man/plot.robust2sls.Rd | 52 robust2sls-0.2.4/robust2sls/man/print.robust2sls.Rd | 68 robust2sls-0.2.4/robust2sls/man/validate_robust2sls.Rd | 38 robust2sls-0.2.4/robust2sls/tests/testthat/_snaps/beta_inf_test.md | 518 +-- robust2sls-0.2.4/robust2sls/tests/testthat/_snaps/bootstrap.md | 290 - robust2sls-0.2.4/robust2sls/tests/testthat/_snaps/class/test1_default.png |binary robust2sls-0.2.4/robust2sls/tests/testthat/_snaps/class/test1_m0.png |binary robust2sls-0.2.4/robust2sls/tests/testthat/_snaps/class/test1_m4.png |binary robust2sls-0.2.4/robust2sls/tests/testthat/_snaps/class/test2_default.png |binary robust2sls-0.2.4/robust2sls/tests/testthat/_snaps/class/test3_default.png |binary robust2sls-0.2.4/robust2sls/tests/testthat/_snaps/initial_estimators.md | 1240 +++---- robust2sls-0.2.4/robust2sls/tests/testthat/_snaps/monte_carlo_fixtures |only robust2sls-0.2.4/robust2sls/tests/testthat/_snaps/monte_carlo_fixtures.md |only robust2sls-0.2.4/robust2sls/tests/testthat/_snaps/outlier_tests.md | 1708 +++++----- robust2sls-0.2.4/robust2sls/tests/testthat/create-testdata.R |only robust2sls-0.2.4/robust2sls/tests/testthat/helper-normalise-for-snapshot.R |only robust2sls-0.2.4/robust2sls/tests/testthat/test-beta_inf_test.R | 16 robust2sls-0.2.4/robust2sls/tests/testthat/test-bootstrap.R | 71 robust2sls-0.2.4/robust2sls/tests/testthat/test-initial_estimators.R | 21 robust2sls-0.2.4/robust2sls/tests/testthat/test-iterative_estimators2.R | 9 robust2sls-0.2.4/robust2sls/tests/testthat/test-monte_carlo_fixtures.R |only robust2sls-0.2.4/robust2sls/tests/testthat/test-outlier_tests.R | 115 robust2sls-0.2.4/robust2sls/tests/testthat/test-utility.R | 6 robust2sls-0.2.4/robust2sls/tests/testthat/testdata |only robust2sls-0.2.4/robust2sls/vignettes/monte-carlo.Rmd | 249 - robust2sls-0.2.4/robust2sls/vignettes/outlier-testing.Rmd | 5 robust2sls-0.2.4/robust2sls/vignettes/overview.Rmd | 4 55 files changed, 2884 insertions(+), 3203 deletions(-)
Title: Finite Mixture Modeling, Clustering & Classification
Description: Random univariate and multivariate finite mixture model generation, estimation, clustering, latent class analysis and classification. Variables can be continuous, discrete, independent or dependent and may follow normal, lognormal, Weibull, gamma, Gumbel, binomial, Poisson, Dirac, uniform or circular von Mises parametric families.
Author: Marko Nagode [aut, cre] ,
Branislav Panic [ctb] ,
Jernej Klemenc [ctb] ,
Simon Oman [ctb]
Maintainer: Marko Nagode <marko.nagode@fs.uni-lj.si>
Diff between rebmix versions 2.17.1 dated 2025-11-10 and 2.17.2 dated 2026-08-20
DESCRIPTION | 6 +++--- MD5 | 34 +++++++++++++++++----------------- R/EMMIX.R | 4 ++-- R/RCLRMIX.R | 2 +- R/RCLSMIX.R | 4 ++-- R/REBMIX.R | 2 +- R/RNGMIX.R | 2 +- R/defaults.R | 31 ++++++++++++------------------- build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 5 +++++ inst/doc/rebmix.R | 2 -- inst/doc/rebmix.Rnw | 12 +++++++----- inst/doc/rebmix.pdf |binary src/emf.cpp | 2 +- src/rebmixf.cpp | 2 +- src/rngmixf.cpp | 2 +- vignettes/rebmix.Rnw | 12 +++++++----- 18 files changed, 61 insertions(+), 61 deletions(-)
Title: Read, Write and Edit 'xlsx' Files
Description: Simplifies the creation of 'xlsx' files by
providing a high level interface to writing, styling and editing
worksheets.
Author: Jordan Mark Barbone [aut] ,
Jan Marvin Garbuszus [aut, cre],
Olivier Roy [ctb],
openxlsx authors [cph] ,
Arseny Kapoulkine [ctb, cph]
Maintainer: Jan Marvin Garbuszus <jan.garbuszus@ruhr-uni-bochum.de>
Diff between openxlsx2 versions 1.28 dated 2026-07-02 and 1.29 dated 2026-08-20
DESCRIPTION | 8 - MD5 | 48 +++++------ NAMESPACE | 70 +++++++++-------- NEWS.md | 21 +++++ R/class-workbook.R | 29 ++++++- R/converters.R | 19 ++-- R/read.R | 74 +++++++++++++++--- R/wb_load.R | 34 +++++--- R/wb_styles.R | 4 inst/AUTHORS | 1 inst/WORDLIST | 2 man/col2int.Rd | 17 ++-- man/create_font.Rd | 4 man/wb_to_df.Rd | 7 + src/load_workbook.cpp | 46 +++++++---- src/xlsb.cpp | 8 + src/xlsb_funs.h | 117 +++++++++++++++++++++-------- tests/testthat/test-base_font.R | 2 tests/testthat/test-class-workbook.R | 21 ++++- tests/testthat/test-converters.R | 4 tests/testthat/test-loading_workbook.R | 39 +++++++++ tests/testthat/test-read_from_created_wb.R | 12 ++ tests/testthat/test-read_xlsb.R | 2 tests/testthat/test-wb_functions.R | 2 tests/testthat/test-wb_styles.R | 3 25 files changed, 439 insertions(+), 155 deletions(-)
Title: Fast and Extensible Pattern Discovery in Tabular Data
Description: Fast and extensible framework for discovering interesting patterns
in tabular data. The package searches combinations of fuzzy or Boolean
predicates and evaluates the resulting subgroups using statistical, logical,
or structural measures. It supports a broad range of pattern-discovery
tasks, including
association rules (Agrawal et al., 1994, <https://www.vldb.org/conf/1994/P487.PDF>),
contrast patterns (Chen, 2022, <doi:10.48550/arXiv.2209.13556>),
emerging patterns (Dong et al., 1999, <doi:10.1145/312129.312191>),
subgroup discovery (Atzmueller, 2015, <doi:10.1002/widm.1144>),
and conditional correlations (Hájek, 1978, <doi:10.1007/978-3-642-66943-9>).
User-defined functions may be supplied to guide custom pattern searches,
making the framework applicable beyond traditional association-rule mining.
Efficient implementation enables pattern discovery on large and dense data
sets. Package includes methods for visualization and supports interactive
explo [...truncated...]
Author: Michal Burda [aut, cre]
Maintainer: Michal Burda <michal.burda@osu.cz>
Diff between nuggets versions 2.2.2 dated 2026-07-22 and 2.2.3 dated 2026-08-20
DESCRIPTION | 37 +- MD5 | 148 +++++----- NAMESPACE | 181 ++++++------ NEWS.md | 9 R/dig.R | 15 - R/dig_associations.R | 8 R/dig_baseline_contrasts.R | 3 R/dig_complement_contrasts.R | 3 R/dig_correlations.R | 3 R/dig_grid.R | 3 R/dig_paired_baseline_contrasts.R | 3 R/dig_tautologies.R | 4 R/is_almost_constant.R | 2 R/permute.R |only R/ui-aboutTable.R | 6 R/ui-exploreApp.R | 3 R/ui-searchStatsTable.R |only README.md | 125 +++++--- build/vignette.rds |binary inst/doc/association-rules.Rmd | 5 inst/doc/association-rules.html | 6 inst/doc/comparison-with-arules.R |only inst/doc/comparison-with-arules.Rmd |only inst/doc/comparison-with-arules.html |only inst/doc/conditional-correlations.R |only inst/doc/conditional-correlations.Rmd |only inst/doc/conditional-correlations.html |only inst/doc/contrast-patterns.R |only inst/doc/contrast-patterns.Rmd |only inst/doc/contrast-patterns.html |only inst/doc/custom-patterns.R |only inst/doc/custom-patterns.Rmd |only inst/doc/custom-patterns.html |only inst/doc/data-preparation.Rmd | 16 - inst/doc/data-preparation.html | 41 +- inst/doc/nuggets.Rmd | 12 inst/doc/nuggets.html | 17 + man/dig.Rd | 13 man/dig_associations.Rd | 6 man/dig_baseline_contrasts.Rd | 3 man/dig_complement_contrasts.Rd | 3 man/dig_correlations.Rd | 3 man/dig_grid.Rd | 3 man/dig_paired_baseline_contrasts.Rd | 3 man/dig_tautologies.Rd | 4 man/is_almost_constant.Rd | 2 man/nuggets-package.Rd | 4 man/permute.Rd |only src/dig.cpp | 4 src/dig/AssocStorage.h | 157 +++++++--- src/dig/BaseChain.h | 171 +++++++++-- src/dig/BinomialCoefficients.h | 54 +++ src/dig/BitChain.h | 89 ++++++ src/dig/Bitset.h | 165 +++++++++-- src/dig/Cache.h | 209 +++++--------- src/dig/CallbackCaller.h | 209 +++++++++++++- src/dig/ChainCollection.h | 103 ++++++- src/dig/Clause.h | 49 +++ src/dig/CombinatorialProgress.h | 80 +++++ src/dig/Config.h | 285 +++++++++++++++++++ src/dig/DeductionEngine.h | 228 ++++++++++----- src/dig/Digger.h | 484 +++++++++++++++++++++++++++++---- src/dig/FloatChain.h | 114 ++++++- src/dig/FubitChain.h | 169 ++++++++++- src/dig/SearchStats.h |only src/dig/Selector.h | 52 +++ src/dig/SimdChain.h | 90 ++++++ src/dig/SparseBitChain.h | 118 +++++++- src/test-dig-BaseChain.cpp | 16 - src/test-dig-BitChain.cpp | 20 - src/test-dig-Cache.cpp | 71 ++-- src/test-dig-ChainCollection.cpp | 24 - src/test-dig-DeductionEngine.cpp | 10 src/test-dig-FloatChain.cpp | 24 - src/test-dig-FubitChain.cpp | 24 - src/test-dig-SparseBitChain.cpp | 20 - tests/testthat/test-dig.R | 213 +++++++++++++- tests/testthat/test-permute.R |only vignettes/association-rules.Rmd | 5 vignettes/comparison-with-arules.Rmd |only vignettes/comparison-with-arules.rds |only vignettes/conditional-correlations.Rmd |only vignettes/contrast-patterns.Rmd |only vignettes/custom-patterns.Rmd |only vignettes/data-preparation.Rmd | 16 - vignettes/nuggets.Rmd | 12 86 files changed, 3183 insertions(+), 796 deletions(-)
Title: Fractional Response Regressions
Description: Provides routines for the estimation and specification analysis of fractional response models. Includes univariate one-part, two-part, and double-inflated three-part fractional models. Further incorporates estimators for panel data settings and addresses unobserved heterogeneity and endogeneity via correlated random effects and control function approaches. Extends fractional methodology to multivariate data via fractional multinomial logit models and handles high-dimensional multicollinear data via fractional ridge regression. Calculates analytical partial effects across all model types and includes generalised goodness-of-functional-form (GGOFF) and Regression Equation Specification Error Test (RESET) hypothesis tests. Methods are described in Papke and Wooldridge (1996) <doi:10.1002/(SICI)1099-1255(199611)11:6%3C619::AID-JAE418%3E3.0.CO;2-1>, Papke and Wooldridge (2008) <doi:10.1016/j.jeconom.2008.05.009>, Buis (2008) <http://maartenbuis.nl/software/likelihoodFmlogit.p [...truncated...]
Author: Sulman Olieko Owili [aut, cre]
Maintainer: Sulman Olieko Owili <oliekosulman@gmail.com>
Diff between fracreg versions 1.0.1 dated 2026-08-05 and 1.1.0 dated 2026-08-20
DESCRIPTION | 12 MD5 | 66 - NAMESPACE | 63 + NEWS.md | 24 R/fracreg-package.R | 4 R/fracreg.R | 8 R/fracreg.pe.R | 18 R/fracreg.pe.table.R | 61 - R/fracreg.table.R | 43 R/fracreg.tests.table.R | 28 R/fracreghet.R | 8 R/fracreghet.extractors.R | 2 R/fracreghet.pe.table.R | 41 R/fracreghet.table.R | 42 R/fracreghet.tests.table.R | 26 R/fracregmlogit.R | 23 R/fracregmlogit.pe.R | 169 ++- R/fracregmlogit.plot.R | 4 R/fracregmlogit.wtp.R | 27 R/fracregpd.R | 3 R/fracregpd.pe.R | 28 R/fracregpd.table.R | 53 R/fracregridge.R | 1 R/fracregridge.pe.R | 3 R/utils.R | 1074 ++++++++++++++++--- R/zzz.R | 6 README.md | 1365 +++++++++++------------- inst/doc/fracreg_tutorial.html | 1595 +++++++++++++++-------------- man/figures/README-fracregmlogit_wtp-1.png |binary man/fracreg-package.Rd | 4 man/fracreghet.Rd | 2 man/fracregmlogit.pe.Rd | 8 man/fracregpd.pe.Rd | 24 man/summary.fracregmlogit.Rd | 7 34 files changed, 2979 insertions(+), 1863 deletions(-)
Title: Calculate AZTI’s Marine Biotic Index
Description: Calculate AZTI’s Marine Biotic Index - AMBI. The included list of
benthic fauna species according to their sensitivity
to pollution. Matching species in sample data to the list allows the
calculation of fractions of individuals in the different sensitivity
categories and thereafter the AMBI index. The Shannon Diversity Index H'
and the Danish benthic fauna quality index DKI (Dansk Kvalitetsindeks) can
also be calculated, as well as the multivariate M-AMBI index.
Borja, A., Franco, J. ,Pérez, V. (2000) "A marine biotic index to
establish the ecological quality of soft bottom benthos within European
estuarine and coastal environments" <doi:10.1016/S0025-326X(00)00061-8>.
Author: Ciaran J. Murray [aut, cre, cph] ,
Angel Borja [aut] ,
Sarai Pouso [aut] ,
Inigo Muxika [aut] ,
Joxe Mikel Garmendia [aut] ,
Steen Knudsen [ctb] ,
GES4SEAS [fnd]
Maintainer: Ciaran J. Murray <cjm@niva-dk.dk>
Diff between ambiR versions 0.1.1 dated 2025-12-19 and 0.2.0 dated 2026-08-20
DESCRIPTION | 12 ++++----- MD5 | 40 ++++++++++++++++++--------------- NAMESPACE | 13 ++++++---- NEWS.md | 24 ++++++++++++++----- R/AMBI.R | 17 ++++++++------ R/AMBIr-package.R | 1 R/MAMBI.R | 2 - R/test_data.R | 2 - R/utils-pipe.R | 2 - README.md | 2 + inst/doc/ambi-figures.html | 26 +++++++++++---------- inst/doc/ambiR.html | 7 ++--- inst/doc/background.Rmd | 2 - inst/doc/background.html | 10 ++++---- man/ambiR-package.Rd | 1 man/figures/lifecycle-deprecated.svg |only man/figures/lifecycle-experimental.svg |only man/figures/lifecycle-stable.svg |only man/figures/lifecycle-superseded.svg |only man/pipe.Rd | 2 - man/test_data.Rd | 2 - tests/testthat/test-calc_ambi.R | 12 +++++++++ vignettes/background.Rmd | 2 - 23 files changed, 108 insertions(+), 71 deletions(-)
Title: Semi-Supervised Learning with Mixed Missingness in Finite
Mixture Models
Description: Semi-supervised Gaussian finite mixture models for partially labelled data
under complete-case, missing completely at random (MCAR), entropy-dependent missing
at random (MAR), and mixed MCAR/MAR label-missingness formulations. For the mixed
formulation, the source of a missing label may be observed or latent. The package
supports equal and component-specific covariance matrices, model fitting, simulation,
initialization, prediction, classification performance assessment, and entropy-based
diagnostics. A semi-synthetic Blood Transfusion data set is included to illustrate the
applied workflow.
Author: Geoffrey J. McLachlan [aut] ,
Jinran Wu [aut, cre]
Maintainer: Jinran Wu <jinran.wu@uq.edu.au>
Diff between SSLfmm versions 0.1.0 dated 2025-12-09 and 0.2.0 dated 2026-08-20
SSLfmm-0.1.0/SSLfmm/R/EM_FMM_SemiSupervised.R |only SSLfmm-0.1.0/SSLfmm/R/EM_FMM_SemiSupervised_Complete_Initial.R |only SSLfmm-0.1.0/SSLfmm/R/EM_FMM_SemiSupervised_Initial.R |only SSLfmm-0.1.0/SSLfmm/R/bayesclassifier.R |only SSLfmm-0.1.0/SSLfmm/R/compute_d2.R |only SSLfmm-0.1.0/SSLfmm/R/error_beta_classification.R |only SSLfmm-0.1.0/SSLfmm/R/get_clusterprobs.R |only SSLfmm-0.1.0/SSLfmm/R/get_entropy.R |only SSLfmm-0.1.0/SSLfmm/R/initialestimate.R |only SSLfmm-0.1.0/SSLfmm/R/logsumexp.R |only SSLfmm-0.1.0/SSLfmm/R/neg_loglik.R |only SSLfmm-0.1.0/SSLfmm/R/normalise_logprob.R |only SSLfmm-0.1.0/SSLfmm/R/pack_theta.R |only SSLfmm-0.1.0/SSLfmm/R/rmix.R |only SSLfmm-0.1.0/SSLfmm/R/simulate_mixed_missingness.R |only SSLfmm-0.1.0/SSLfmm/R/unpack_theta.R |only SSLfmm-0.1.0/SSLfmm/R/zzz_imports.R |only SSLfmm-0.1.0/SSLfmm/man/EM_FMM_SemiSupervised.Rd |only SSLfmm-0.1.0/SSLfmm/man/EM_FMM_SemiSupervised_Complete_Initial.Rd |only SSLfmm-0.1.0/SSLfmm/man/EM_FMM_SemiSupervised_Initial.Rd |only SSLfmm-0.1.0/SSLfmm/man/bayesclassifier.Rd |only SSLfmm-0.1.0/SSLfmm/man/compute_d2.Rd |only SSLfmm-0.1.0/SSLfmm/man/error_beta_classification.Rd |only SSLfmm-0.1.0/SSLfmm/man/get_clusterprobs.Rd |only SSLfmm-0.1.0/SSLfmm/man/get_entropy.Rd |only SSLfmm-0.1.0/SSLfmm/man/initialestimate.Rd |only SSLfmm-0.1.0/SSLfmm/man/logsumexp.Rd |only SSLfmm-0.1.0/SSLfmm/man/neg_loglik.Rd |only SSLfmm-0.1.0/SSLfmm/man/normalise_logprob.Rd |only SSLfmm-0.1.0/SSLfmm/man/pack_theta.Rd |only SSLfmm-0.1.0/SSLfmm/man/unpack_theta.Rd |only SSLfmm-0.2.0/SSLfmm/DESCRIPTION | 56 +++--- SSLfmm-0.2.0/SSLfmm/MD5 | 62 +++---- SSLfmm-0.2.0/SSLfmm/NAMESPACE | 36 +--- SSLfmm-0.2.0/SSLfmm/R/00_utils.R |only SSLfmm-0.2.0/SSLfmm/R/01_model.R |only SSLfmm-0.2.0/SSLfmm/R/02_initialization.R |only SSLfmm-0.2.0/SSLfmm/R/03_likelihoods.R |only SSLfmm-0.2.0/SSLfmm/R/04_fit.R |only SSLfmm-0.2.0/SSLfmm/R/05_simulation.R |only SSLfmm-0.2.0/SSLfmm/R/06_metrics_plot.R |only SSLfmm-0.2.0/SSLfmm/README.md |only SSLfmm-0.2.0/SSLfmm/data |only SSLfmm-0.2.0/SSLfmm/man/SSLfmm-package.Rd |only SSLfmm-0.2.0/SSLfmm/man/blood_transfusion.Rd |only SSLfmm-0.2.0/SSLfmm/man/classification_performance.Rd |only SSLfmm-0.2.0/SSLfmm/man/fit_sslfmm.Rd |only SSLfmm-0.2.0/SSLfmm/man/initialize_sslfmm.Rd |only SSLfmm-0.2.0/SSLfmm/man/plot_entropy_labels.Rd |only SSLfmm-0.2.0/SSLfmm/man/predict.SSLfmm.Rd |only SSLfmm-0.2.0/SSLfmm/man/rmix.Rd | 50 ++--- SSLfmm-0.2.0/SSLfmm/man/simulate_mixed_missingness.Rd | 84 ++++------ SSLfmm-0.2.0/SSLfmm/man/simulate_sslfmm.Rd |only SSLfmm-0.2.0/SSLfmm/tests |only 54 files changed, 122 insertions(+), 166 deletions(-)
Title: Fishing Effort Standardization
Description: Marine fisheries governance and management rely heavily on reliable
indicators of stock abundance and fishing pressure to ensure the sustainable
utilization of marine resources. Catch Per Unit Effort (CPUE) is widely used
as an index of relative abundance, but direct comparison of catch rates is
often affected by differences in fishing effort, vessel characteristics,
gear efficiency, and operational practices. The FESta package provides
methods for fishing effort and CPUE standardization, including vessel-based,
gear-based, relative effort, derived effort, generalized linear models,
generalized additive models, generalized linear mixed models, ordered
quantile transformation models, and multi-gear standardization techniques
for fisheries stock assessment and monitoring.
To cite our package run this command, citation("FESta").
Author: Eldho Varghese [aut, cre],
Jayasankar J [aut],
Ashutosh Dalal [aut, ctb],
Sathianandan T V [aut],
Sreepriya V [aut, ctb],
Reshma Gills [ctb],
Grinson George [ctb]
Maintainer: Eldho Varghese <eldhoiasri@gmail.com>
Diff between FESta versions 1.0.1 dated 2026-08-03 and 1.0.2 dated 2026-08-20
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/MGMSstd.R | 40 ++++++++++++++++++++++++++++++++++++++-- R/StdEffort.R | 14 +++++++++----- 4 files changed, 53 insertions(+), 13 deletions(-)
Title: Bayesian Inference Using 'RTMB'
Description: Provides tools for Markov chain Monte Carlo (MCMC) and Maximum A Posteriori (MAP) estimation utilizing the 'RTMB' package. It supports various statistical models including generalized linear mixed models, factor analysis, item response theory, and multidimensional unfolding. The package allows users to easily transition between frequentist and Bayesian paradigms using a unified interface. Automatic differentiation and Laplace approximation follow Kristensen et al. (2016) <doi:10.18637/jss.v070.i05>, and MCMC sampling uses the No-U-Turn Sampler described by Hoffman and Gelman (2014) <https://jmlr.org/papers/v15/hoffman14a.html>.
Author: Hiroshi Shimizu [aut, cre]
Maintainer: Hiroshi Shimizu <simizu706@gmail.com>
Diff between BayesRTMB versions 0.2.4 dated 2026-07-24 and 0.3.0 dated 2026-08-20
DESCRIPTION | 6 MD5 | 164 - NAMESPACE | 8 NEWS.md | 51 R/Base_Fit.R | 81 R/RTMB_Model.R | 7 R/RTMB_Model_impl_classic.R | 31 R/RTMB_Model_impl_optimize.R | 7 R/RTMB_Model_impl_sampling.R | 4 R/centering.R |only R/classic.R | 20 R/model.R | 32 R/parameters.R | 62 R/posterior_predict.R |only R/summary_mcmc.R |only R/wrapper_corr.R | 163 - R/wrapper_fa.R | 66 R/wrapper_glmer.R | 319 +- R/wrapper_irt.R | 34 R/wrapper_lm_glm_lmer.R | 12 R/wrapper_lrt.R | 66 R/wrapper_mdu.R | 198 - R/wrapper_mediation.R | 495 ++- R/wrapper_mixture.R | 70 R/wrapper_table.R | 90 R/wrapper_ttest.R | 42 build/vignette.rds |binary inst/doc/analysis_reference.R | 10 inst/doc/analysis_reference.Rmd | 42 inst/doc/analysis_reference.html | 440 +- inst/doc/introduction.Rmd | 9 inst/doc/introduction.html | 9 inst/doc/ja-analysis_reference.R | 16 inst/doc/ja-analysis_reference.Rmd | 3413 +++++++++++----------- inst/doc/ja-analysis_reference.html | 1048 +++--- inst/doc/ja-introduction.Rmd | 9 inst/doc/ja-introduction.html | 9 inst/doc/ja-rtmb_internals.Rmd | 6 inst/doc/ja-rtmb_internals.html | 26 inst/doc/ja-wrapper_functions.R | 23 inst/doc/ja-wrapper_functions.Rmd | 52 inst/doc/ja-wrapper_functions.html | 146 inst/doc/ja-writing_models.R | 37 inst/doc/ja-writing_models.Rmd | 52 inst/doc/ja-writing_models.html | 785 ++--- inst/doc/rtmb_internals.Rmd | 6 inst/doc/rtmb_internals.html | 23 inst/doc/wrapper_functions.R | 25 inst/doc/wrapper_functions.Rmd | 85 inst/doc/wrapper_functions.html | 310 + inst/doc/writing_models.R | 41 inst/doc/writing_models.Rmd | 61 inst/doc/writing_models.html | 258 - man/Classic_Fit.Rd | 2 man/MAP_Fit.Rd | 4 man/MCMC_Fit.Rd | 4 man/RTMB_Fit_Base.Rd | 112 man/VB_Fit.Rd | 2 man/center_grand_mean.Rd |only man/center_within_cluster.Rd |only man/make_glmer_re_terms.Rd | 11 man/posterior_predict.Rd |only man/pp_check.Rd |only man/rtmb_corr.Rd | 6 man/rtmb_glm.Rd | 4 man/rtmb_glmer.Rd | 8 man/rtmb_lm.Rd | 4 man/rtmb_lmer.Rd | 4 man/rtmb_mediation.Rd | 33 man/rtmb_model.Rd | 10 man/rtmb_table.Rd | 1 man/summary_mcmc.Rd |only tests/testthat/test-centering.R |only tests/testthat/test-fixed-jacobian.R |only tests/testthat/test-formula-data-environment.R | 6 tests/testthat/test-mediation-random-intercepts.R |only tests/testthat/test-posterior-predict.R |only tests/testthat/test-setup-data.R |only tests/testthat/test-summary-mcmc.R |only tests/testthat/test-wrappers.R | 502 +++ vignettes/analysis_reference.Rmd | 42 vignettes/introduction.Rmd | 9 vignettes/ja-analysis_reference.Rmd | 3413 +++++++++++----------- vignettes/ja-introduction.Rmd | 9 vignettes/ja-rtmb_internals.Rmd | 6 vignettes/ja-wrapper_functions.Rmd | 52 vignettes/ja-writing_models.Rmd | 52 vignettes/rtmb_internals.Rmd | 6 vignettes/wrapper_functions.Rmd | 85 vignettes/writing_models.Rmd | 61 90 files changed, 8005 insertions(+), 5412 deletions(-)
Title: R Client for the 'VirusTotal' API
Description: Provides a comprehensive R interface to the 'VirusTotal' API v3.0
<https://docs.virustotal.com/>, a Google service that analyzes files and
URLs for viruses, worms, trojans and other malware. Features include
file/URL scanning, domain categorization, passive DNS information, IP
reputation analysis, IoC relationships, sandbox analysis, and
comment/voting systems. Implements rate limiting, error handling, and
response validation for robust security analysis workflows.
Author: Gaurav Sood [aut, cre]
Maintainer: Gaurav Sood <gsood07@gmail.com>
Diff between virustotal versions 0.6.0 dated 2026-04-13 and 0.7.0 dated 2026-08-20
virustotal-0.6.0/virustotal/man/rate_limit.Rd |only virustotal-0.6.0/virustotal/tests/README.html |only virustotal-0.6.0/virustotal/tests/README.md |only virustotal-0.6.0/virustotal/tests/_covrpage.Rmd |only virustotal-0.6.0/virustotal/tests/testthat/test-data-structures.R |only virustotal-0.6.0/virustotal/tests/testthat/test-pkg-style.R |only virustotal-0.7.0/virustotal/DESCRIPTION | 16 virustotal-0.7.0/virustotal/MD5 | 301 +++++---- virustotal-0.7.0/virustotal/NAMESPACE | 41 - virustotal-0.7.0/virustotal/NEWS.md | 81 ++ virustotal-0.7.0/virustotal/R/domain_report.R | 57 - virustotal-0.7.0/virustotal/R/download_file.R | 23 virustotal-0.7.0/virustotal/R/errors.R | 18 virustotal-0.7.0/virustotal/R/file_report.R | 90 +- virustotal-0.7.0/virustotal/R/get_analysis.R | 4 virustotal-0.7.0/virustotal/R/get_behaviour_evtx.R | 25 virustotal-0.7.0/virustotal/R/get_behaviour_html.R | 25 virustotal-0.7.0/virustotal/R/get_behaviour_memdump.R | 25 virustotal-0.7.0/virustotal/R/get_behaviour_pcap.R | 25 virustotal-0.7.0/virustotal/R/get_behaviour_report.R | 4 virustotal-0.7.0/virustotal/R/get_domain_comments.R | 16 virustotal-0.7.0/virustotal/R/get_domain_info.R | 40 - virustotal-0.7.0/virustotal/R/get_domain_relationship.R | 39 - virustotal-0.7.0/virustotal/R/get_domain_votes.R | 36 - virustotal-0.7.0/virustotal/R/get_file_behaviour_mitre_trees.R | 4 virustotal-0.7.0/virustotal/R/get_file_behaviour_summary.R | 4 virustotal-0.7.0/virustotal/R/get_file_behaviours.R | 6 virustotal-0.7.0/virustotal/R/get_file_comments.R | 22 virustotal-0.7.0/virustotal/R/get_file_download_url.R | 16 virustotal-0.7.0/virustotal/R/get_file_relationships.R | 48 - virustotal-0.7.0/virustotal/R/get_file_upload_url.R | 19 virustotal-0.7.0/virustotal/R/get_file_votes.R | 22 virustotal-0.7.0/virustotal/R/get_ip_comments.R | 12 virustotal-0.7.0/virustotal/R/get_ip_info.R | 12 virustotal-0.7.0/virustotal/R/get_ip_votes.R | 12 virustotal-0.7.0/virustotal/R/get_url_comments.R | 13 virustotal-0.7.0/virustotal/R/get_url_relationships.R | 25 virustotal-0.7.0/virustotal/R/get_url_votes.R | 13 virustotal-0.7.0/virustotal/R/ip_report.R | 21 virustotal-0.7.0/virustotal/R/post_domain_comments.R | 26 virustotal-0.7.0/virustotal/R/post_domain_votes.R | 26 virustotal-0.7.0/virustotal/R/post_file_comments.R | 20 virustotal-0.7.0/virustotal/R/post_file_votes.R | 16 virustotal-0.7.0/virustotal/R/post_ip_comments.R | 24 virustotal-0.7.0/virustotal/R/post_ip_votes.R | 24 virustotal-0.7.0/virustotal/R/post_url_comments.R | 23 virustotal-0.7.0/virustotal/R/post_url_votes.R | 19 virustotal-0.7.0/virustotal/R/rate_limiting.R | 99 --- virustotal-0.7.0/virustotal/R/rescan_domain.R | 4 virustotal-0.7.0/virustotal/R/rescan_file.R | 10 virustotal-0.7.0/virustotal/R/rescan_ip.R | 4 virustotal-0.7.0/virustotal/R/rescan_url.R | 11 virustotal-0.7.0/virustotal/R/s3_classes.R | 26 virustotal-0.7.0/virustotal/R/scan_file.R | 37 - virustotal-0.7.0/virustotal/R/scan_url.R | 7 virustotal-0.7.0/virustotal/R/security.R | 26 virustotal-0.7.0/virustotal/R/set_key.R | 31 virustotal-0.7.0/virustotal/R/url_report.R | 5 virustotal-0.7.0/virustotal/R/utils.R | 78 +- virustotal-0.7.0/virustotal/R/virustotal.R | 314 +++++++--- virustotal-0.7.0/virustotal/R/vt_key.R |only virustotal-0.7.0/virustotal/R/zzz.R | 8 virustotal-0.7.0/virustotal/README.md | 92 ++ virustotal-0.7.0/virustotal/build/vignette.rds |binary virustotal-0.7.0/virustotal/inst/CITATION | 30 virustotal-0.7.0/virustotal/inst/WORDLIST |only virustotal-0.7.0/virustotal/inst/doc/using_virustotal.R | 71 +- virustotal-0.7.0/virustotal/inst/doc/using_virustotal.Rmd | 122 ++- virustotal-0.7.0/virustotal/inst/doc/using_virustotal.html | 105 +-- virustotal-0.7.0/virustotal/man/cleanup_temp_files.Rd | 14 virustotal-0.7.0/virustotal/man/create_safe_temp_dir.Rd | 14 virustotal-0.7.0/virustotal/man/download_file.Rd | 9 virustotal-0.7.0/virustotal/man/file_report.Rd | 3 virustotal-0.7.0/virustotal/man/format_file_size.Rd | 14 virustotal-0.7.0/virustotal/man/get_analysis.Rd | 2 virustotal-0.7.0/virustotal/man/get_behaviour_evtx.Rd | 11 virustotal-0.7.0/virustotal/man/get_behaviour_html.Rd | 11 virustotal-0.7.0/virustotal/man/get_behaviour_memdump.Rd | 11 virustotal-0.7.0/virustotal/man/get_behaviour_pcap.Rd | 11 virustotal-0.7.0/virustotal/man/get_behaviour_report.Rd | 2 virustotal-0.7.0/virustotal/man/get_domain_comments.Rd | 2 virustotal-0.7.0/virustotal/man/get_domain_info.Rd | 4 virustotal-0.7.0/virustotal/man/get_domain_relationship.Rd | 4 virustotal-0.7.0/virustotal/man/get_domain_votes.Rd | 4 virustotal-0.7.0/virustotal/man/get_file_behaviour_mitre_trees.Rd | 2 virustotal-0.7.0/virustotal/man/get_file_behaviour_summary.Rd | 2 virustotal-0.7.0/virustotal/man/get_file_behaviours.Rd | 4 virustotal-0.7.0/virustotal/man/get_file_comments.Rd | 2 virustotal-0.7.0/virustotal/man/get_file_download_url.Rd | 2 virustotal-0.7.0/virustotal/man/get_file_relationships.Rd | 12 virustotal-0.7.0/virustotal/man/get_file_upload_url.Rd | 3 virustotal-0.7.0/virustotal/man/get_file_votes.Rd | 2 virustotal-0.7.0/virustotal/man/get_rate_limit_status.Rd | 6 virustotal-0.7.0/virustotal/man/get_url_comments.Rd | 2 virustotal-0.7.0/virustotal/man/get_url_relationships.Rd | 6 virustotal-0.7.0/virustotal/man/get_url_votes.Rd | 2 virustotal-0.7.0/virustotal/man/has_vt_key.Rd |only virustotal-0.7.0/virustotal/man/init_rate_limit.Rd | 4 virustotal-0.7.0/virustotal/man/ip_report.Rd | 4 virustotal-0.7.0/virustotal/man/is_api_key_configured.Rd | 12 virustotal-0.7.0/virustotal/man/is_rate_limit_initialized.Rd | 4 virustotal-0.7.0/virustotal/man/is_safe_environment.Rd | 14 virustotal-0.7.0/virustotal/man/post_file_comments.Rd | 6 virustotal-0.7.0/virustotal/man/post_file_votes.Rd | 2 virustotal-0.7.0/virustotal/man/post_url_comments.Rd | 6 virustotal-0.7.0/virustotal/man/post_url_votes.Rd | 2 virustotal-0.7.0/virustotal/man/print.virustotal_domain_report.Rd | 4 virustotal-0.7.0/virustotal/man/print.virustotal_error.Rd | 3 virustotal-0.7.0/virustotal/man/print.virustotal_file_report.Rd | 4 virustotal-0.7.0/virustotal/man/print.virustotal_response.Rd | 4 virustotal-0.7.0/virustotal/man/rate-limiting.Rd | 16 virustotal-0.7.0/virustotal/man/record_request.Rd |only virustotal-0.7.0/virustotal/man/rescan_file.Rd | 2 virustotal-0.7.0/virustotal/man/reset_rate_limit.Rd | 10 virustotal-0.7.0/virustotal/man/sanitize_domain.Rd | 12 virustotal-0.7.0/virustotal/man/sanitize_file_path.Rd | 12 virustotal-0.7.0/virustotal/man/sanitize_hash.Rd | 12 virustotal-0.7.0/virustotal/man/sanitize_ip.Rd | 12 virustotal-0.7.0/virustotal/man/sanitize_url.Rd | 12 virustotal-0.7.0/virustotal/man/security-utilities.Rd | 14 virustotal-0.7.0/virustotal/man/set_key.Rd | 13 virustotal-0.7.0/virustotal/man/summary.virustotal_response.Rd | 4 virustotal-0.7.0/virustotal/man/utilities.Rd | 16 virustotal-0.7.0/virustotal/man/validate_vt_response.Rd | 14 virustotal-0.7.0/virustotal/man/virustotal-classes.Rd | 12 virustotal-0.7.0/virustotal/man/virustotal-errors.Rd | 12 virustotal-0.7.0/virustotal/man/virustotal-package.Rd | 13 virustotal-0.7.0/virustotal/man/virustotal_GET.Rd | 13 virustotal-0.7.0/virustotal/man/virustotal_GET_raw.Rd |only virustotal-0.7.0/virustotal/man/virustotal_POST.Rd | 15 virustotal-0.7.0/virustotal/man/virustotal_auth_error.Rd | 10 virustotal-0.7.0/virustotal/man/virustotal_check.Rd | 14 virustotal-0.7.0/virustotal/man/virustotal_domain_report.Rd | 10 virustotal-0.7.0/virustotal/man/virustotal_error.Rd | 10 virustotal-0.7.0/virustotal/man/virustotal_file_report.Rd | 10 virustotal-0.7.0/virustotal/man/virustotal_file_scan.Rd | 10 virustotal-0.7.0/virustotal/man/virustotal_info.Rd | 14 virustotal-0.7.0/virustotal/man/virustotal_ip_report.Rd | 10 virustotal-0.7.0/virustotal/man/virustotal_rate_limit_error.Rd | 10 virustotal-0.7.0/virustotal/man/virustotal_url_scan.Rd | 10 virustotal-0.7.0/virustotal/man/virustotal_validation_error.Rd | 10 virustotal-0.7.0/virustotal/man/virustotal_version.Rd | 14 virustotal-0.7.0/virustotal/man/vt_key.Rd |only virustotal-0.7.0/virustotal/man/vt_request.Rd |only virustotal-0.7.0/virustotal/man/vt_url_id.Rd |only virustotal-0.7.0/virustotal/tests/spelling.R |only virustotal-0.7.0/virustotal/tests/testthat/_snaps |only virustotal-0.7.0/virustotal/tests/testthat/helper-capture.R |only virustotal-0.7.0/virustotal/tests/testthat/helper-fixtures.R |only virustotal-0.7.0/virustotal/tests/testthat/setup.R |only virustotal-0.7.0/virustotal/tests/testthat/test-audit-v3-conformance.R |only virustotal-0.7.0/virustotal/tests/testthat/test-auth.R | 46 - virustotal-0.7.0/virustotal/tests/testthat/test-domain-operations.R | 74 +- virustotal-0.7.0/virustotal/tests/testthat/test-error-handling.R | 89 ++ virustotal-0.7.0/virustotal/tests/testthat/test-file-operations.R | 116 ++- virustotal-0.7.0/virustotal/tests/testthat/test-fixture-hygiene.R |only virustotal-0.7.0/virustotal/tests/testthat/test-fixtures.R |only virustotal-0.7.0/virustotal/tests/testthat/test-integration.R |only virustotal-0.7.0/virustotal/tests/testthat/test-ip-operations.R | 33 - virustotal-0.7.0/virustotal/tests/testthat/test-rate-limiting.R | 138 +++- virustotal-0.7.0/virustotal/tests/testthat/test-s3-print.R |only virustotal-0.7.0/virustotal/tests/testthat/test-url-operations.R | 28 virustotal-0.7.0/virustotal/tests/testthat/test-utils.R |only virustotal-0.7.0/virustotal/vignettes/using_virustotal.Rmd | 122 ++- 164 files changed, 2164 insertions(+), 1431 deletions(-)
Title: Client for the YouTube Data API
Description: Search public YouTube data and retrieve channels, videos,
playlists, comments, captions, live broadcasts, and reference data.
Authenticated methods support common uploads, playlist changes, comment
moderation, and media updates. See the YouTube Data API documentation at
<https://developers.google.com/youtube/v3/>.
Author: Gaurav Sood [aut, cre],
Kate Lyons [ctb],
John Muschelli [ctb]
Maintainer: Gaurav Sood <gsood07@gmail.com>
Diff between tuber versions 1.4.1 dated 2026-08-02 and 2.0.0 dated 2026-08-20
tuber-1.4.1/tuber/R/delete_captions.R |only tuber-1.4.1/tuber/R/delete_channel_sections.R |only tuber-1.4.1/tuber/R/delete_comments.R |only tuber-1.4.1/tuber/R/delete_playlist_items.R |only tuber-1.4.1/tuber/R/delete_playlists.R |only tuber-1.4.1/tuber/R/delete_videos.R |only tuber-1.4.1/tuber/R/get_captions.R |only tuber-1.4.1/tuber/R/get_channel_stats.R |only tuber-1.4.1/tuber/R/get_comment_threads.R |only tuber-1.4.1/tuber/R/get_comments.R |only tuber-1.4.1/tuber/R/get_live_chat_messages.R |only tuber-1.4.1/tuber/R/get_playlist_item_videoids.R |only tuber-1.4.1/tuber/R/get_playlist_items.R |only tuber-1.4.1/tuber/R/get_playlists.R |only tuber-1.4.1/tuber/R/get_related_videos.R |only tuber-1.4.1/tuber/R/get_subscriptions.R |only tuber-1.4.1/tuber/R/get_super_chat_events.R |only tuber-1.4.1/tuber/R/list_caption_tracks.R |only tuber-1.4.1/tuber/R/list_channel_resources.R |only tuber-1.4.1/tuber/R/list_guidecats.R |only tuber-1.4.1/tuber/R/list_langs.R |only tuber-1.4.1/tuber/R/list_videocats.R |only tuber-1.4.1/tuber/R/list_videos.R |only tuber-1.4.1/tuber/R/yt_topic_search.R |only tuber-1.4.1/tuber/man/delete_captions.Rd |only tuber-1.4.1/tuber/man/delete_channel_sections.Rd |only tuber-1.4.1/tuber/man/delete_comments.Rd |only tuber-1.4.1/tuber/man/delete_playlist_items.Rd |only tuber-1.4.1/tuber/man/delete_playlists.Rd |only tuber-1.4.1/tuber/man/delete_videos.Rd |only tuber-1.4.1/tuber/man/get_captions.Rd |only tuber-1.4.1/tuber/man/get_channel_info_cached.Rd |only tuber-1.4.1/tuber/man/get_channel_sections.Rd |only tuber-1.4.1/tuber/man/get_channel_stats.Rd |only tuber-1.4.1/tuber/man/get_comment_threads.Rd |only tuber-1.4.1/tuber/man/get_comments.Rd |only tuber-1.4.1/tuber/man/get_live_chat_messages.Rd |only tuber-1.4.1/tuber/man/get_live_streams.Rd |only tuber-1.4.1/tuber/man/get_playlist_item_videoids.Rd |only tuber-1.4.1/tuber/man/get_playlist_items.Rd |only tuber-1.4.1/tuber/man/get_playlists.Rd |only tuber-1.4.1/tuber/man/get_premiere_info.Rd |only tuber-1.4.1/tuber/man/get_related_videos.Rd |only tuber-1.4.1/tuber/man/get_stats.Rd |only tuber-1.4.1/tuber/man/get_subscriptions.Rd |only tuber-1.4.1/tuber/man/get_super_chat_events.Rd |only tuber-1.4.1/tuber/man/list_caption_tracks.Rd |only tuber-1.4.1/tuber/man/list_channel_resources.Rd |only tuber-1.4.1/tuber/man/list_guidecats.Rd |only tuber-1.4.1/tuber/man/list_langs.Rd |only tuber-1.4.1/tuber/man/list_langs_cached.Rd |only tuber-1.4.1/tuber/man/list_regions_cached.Rd |only tuber-1.4.1/tuber/man/list_videocats.Rd |only tuber-1.4.1/tuber/man/list_videocats_cached.Rd |only tuber-1.4.1/tuber/man/list_videos.Rd |only tuber-1.4.1/tuber/man/search_shorts.Rd |only tuber-1.4.1/tuber/man/track_quota_usage.Rd |only tuber-1.4.1/tuber/man/tuber_GET_cached.Rd |only tuber-1.4.1/tuber/man/yt_topic_search.Rd |only tuber-1.4.1/tuber/tests/testthat/_problems |only tuber-1.4.1/tuber/tests/testthat/test-get-related-videos.R |only tuber-2.0.0/tuber/DESCRIPTION | 18 tuber-2.0.0/tuber/MD5 | 359 +++--- tuber-2.0.0/tuber/NAMESPACE | 63 - tuber-2.0.0/tuber/NEWS.md | 47 tuber-2.0.0/tuber/R/caching.R | 309 ++--- tuber-2.0.0/tuber/R/change_playlist_title.R | 88 + tuber-2.0.0/tuber/R/delete_caption.R |only tuber-2.0.0/tuber/R/delete_channel_section.R |only tuber-2.0.0/tuber/R/delete_comment.R |only tuber-2.0.0/tuber/R/delete_playlist.R |only tuber-2.0.0/tuber/R/delete_playlist_item.R |only tuber-2.0.0/tuber/R/delete_video.R |only tuber-2.0.0/tuber/R/download_caption.R |only tuber-2.0.0/tuber/R/error_handling.R | 42 tuber-2.0.0/tuber/R/extended_endpoints.R | 561 +++------- tuber-2.0.0/tuber/R/get_all_channel_video_stats.R | 39 tuber-2.0.0/tuber/R/get_all_comments.R | 243 +--- tuber-2.0.0/tuber/R/get_channel_details.R |only tuber-2.0.0/tuber/R/get_playlist_item_ids.R | 99 - tuber-2.0.0/tuber/R/get_playlist_video_ids.R |only tuber-2.0.0/tuber/R/get_stats.R | 148 +- tuber-2.0.0/tuber/R/get_video_details.R | 30 tuber-2.0.0/tuber/R/helper_functions.R | 133 +- tuber-2.0.0/tuber/R/insert_channel_banner.R | 34 tuber-2.0.0/tuber/R/list_abuse_report_reasons.R | 100 - tuber-2.0.0/tuber/R/list_captions.R | 104 + tuber-2.0.0/tuber/R/list_channel_activities.R | 201 +-- tuber-2.0.0/tuber/R/list_channel_members.R | 79 - tuber-2.0.0/tuber/R/list_channel_sections.R | 125 +- tuber-2.0.0/tuber/R/list_channel_videos.R | 33 tuber-2.0.0/tuber/R/list_comment_threads.R |only tuber-2.0.0/tuber/R/list_comments.R |only tuber-2.0.0/tuber/R/list_languages.R |only tuber-2.0.0/tuber/R/list_live_chat_messages.R |only tuber-2.0.0/tuber/R/list_my_videos.R | 41 tuber-2.0.0/tuber/R/list_playlist_items.R |only tuber-2.0.0/tuber/R/list_playlists.R |only tuber-2.0.0/tuber/R/list_popular_videos.R |only tuber-2.0.0/tuber/R/list_regions.R | 72 - tuber-2.0.0/tuber/R/list_subscriptions.R |only tuber-2.0.0/tuber/R/list_super_chat_events.R |only tuber-2.0.0/tuber/R/list_video_categories.R |only tuber-2.0.0/tuber/R/quota_management.R | 193 +-- tuber-2.0.0/tuber/R/read_sbv.R | 4 tuber-2.0.0/tuber/R/set_video_thumbnail.R | 14 tuber-2.0.0/tuber/R/tuber.R | 232 ++-- tuber-2.0.0/tuber/R/unicode_utils.R | 1 tuber-2.0.0/tuber/R/update_video_metadata.R | 205 ++- tuber-2.0.0/tuber/R/upload_caption.R | 206 ++- tuber-2.0.0/tuber/R/upload_video.R | 136 +- tuber-2.0.0/tuber/R/utils.R | 42 tuber-2.0.0/tuber/R/yt_oauth.R | 44 tuber-2.0.0/tuber/R/yt_search.R | 218 ++- tuber-2.0.0/tuber/README.md | 140 +- tuber-2.0.0/tuber/build/vignette.rds |binary tuber-2.0.0/tuber/inst/doc/api-conventions.R |only tuber-2.0.0/tuber/inst/doc/api-conventions.Rmd |only tuber-2.0.0/tuber/inst/doc/api-conventions.html |only tuber-2.0.0/tuber/inst/doc/batch-processing-quota.R | 49 tuber-2.0.0/tuber/inst/doc/batch-processing-quota.Rmd | 74 - tuber-2.0.0/tuber/inst/doc/batch-processing-quota.html | 166 +- tuber-2.0.0/tuber/inst/doc/emoji-analysis.R | 24 tuber-2.0.0/tuber/inst/doc/emoji-analysis.Rmd | 24 tuber-2.0.0/tuber/inst/doc/emoji-analysis.html | 24 tuber-2.0.0/tuber/inst/doc/emoji-handling.R | 10 tuber-2.0.0/tuber/inst/doc/emoji-handling.Rmd | 10 tuber-2.0.0/tuber/inst/doc/emoji-handling.html | 10 tuber-2.0.0/tuber/inst/doc/troubleshooting.Rmd | 56 tuber-2.0.0/tuber/inst/doc/troubleshooting.html | 96 - tuber-2.0.0/tuber/inst/doc/tuber-ex.R | 33 tuber-2.0.0/tuber/inst/doc/tuber-ex.Rmd | 35 tuber-2.0.0/tuber/inst/doc/tuber-ex.html | 60 - tuber-2.0.0/tuber/man/add_tuber_attributes.Rd | 3 tuber-2.0.0/tuber/man/change_playlist_title.Rd | 32 tuber-2.0.0/tuber/man/delete_caption.Rd |only tuber-2.0.0/tuber/man/delete_channel_section.Rd |only tuber-2.0.0/tuber/man/delete_comment.Rd |only tuber-2.0.0/tuber/man/delete_playlist.Rd |only tuber-2.0.0/tuber/man/delete_playlist_item.Rd |only tuber-2.0.0/tuber/man/delete_video.Rd |only tuber-2.0.0/tuber/man/download_caption.Rd |only tuber-2.0.0/tuber/man/get_all_channel_video_stats.Rd | 10 tuber-2.0.0/tuber/man/get_all_comments.Rd | 34 tuber-2.0.0/tuber/man/get_cached_response.Rd | 1 tuber-2.0.0/tuber/man/get_channel_details.Rd |only tuber-2.0.0/tuber/man/get_playlist_item_ids.Rd | 51 tuber-2.0.0/tuber/man/get_playlist_video_ids.Rd |only tuber-2.0.0/tuber/man/get_video_broadcast_timing.Rd |only tuber-2.0.0/tuber/man/get_video_details.Rd | 14 tuber-2.0.0/tuber/man/get_video_stats.Rd |only tuber-2.0.0/tuber/man/get_video_thumbnails.Rd | 13 tuber-2.0.0/tuber/man/handle_api_error.Rd | 1 tuber-2.0.0/tuber/man/handle_network_error.Rd | 1 tuber-2.0.0/tuber/man/insert_channel_banner.Rd | 7 tuber-2.0.0/tuber/man/is_cacheable_endpoint.Rd | 1 tuber-2.0.0/tuber/man/is_static_query.Rd | 1 tuber-2.0.0/tuber/man/list_abuse_report_reasons.Rd | 33 tuber-2.0.0/tuber/man/list_captions.Rd | 34 tuber-2.0.0/tuber/man/list_channel_activities.Rd | 62 - tuber-2.0.0/tuber/man/list_channel_members.Rd | 11 tuber-2.0.0/tuber/man/list_channel_sections.Rd | 50 tuber-2.0.0/tuber/man/list_channel_videos.Rd | 21 tuber-2.0.0/tuber/man/list_comment_threads.Rd |only tuber-2.0.0/tuber/man/list_comments.Rd |only tuber-2.0.0/tuber/man/list_languages.Rd |only tuber-2.0.0/tuber/man/list_live_broadcasts.Rd |only tuber-2.0.0/tuber/man/list_live_chat_messages.Rd |only tuber-2.0.0/tuber/man/list_my_videos.Rd | 22 tuber-2.0.0/tuber/man/list_playlist_items.Rd |only tuber-2.0.0/tuber/man/list_playlists.Rd |only tuber-2.0.0/tuber/man/list_popular_videos.Rd |only tuber-2.0.0/tuber/man/list_regions.Rd | 19 tuber-2.0.0/tuber/man/list_subscriptions.Rd |only tuber-2.0.0/tuber/man/list_super_chat_events.Rd |only tuber-2.0.0/tuber/man/list_video_categories.Rd |only tuber-2.0.0/tuber/man/print.tuber_result.Rd | 1 tuber-2.0.0/tuber/man/quota_cost.Rd |only tuber-2.0.0/tuber/man/read_sbv.Rd | 4 tuber-2.0.0/tuber/man/search_short_videos.Rd |only tuber-2.0.0/tuber/man/store_cached_response.Rd | 1 tuber-2.0.0/tuber/man/sub-.tuber_result.Rd | 1 tuber-2.0.0/tuber/man/suggest_solution.Rd | 1 tuber-2.0.0/tuber/man/summary.tuber_result.Rd | 1 tuber-2.0.0/tuber/man/tuber-package.Rd | 4 tuber-2.0.0/tuber/man/tuber_DELETE.Rd | 5 tuber-2.0.0/tuber/man/tuber_GET.Rd | 18 tuber-2.0.0/tuber/man/tuber_POST.Rd | 5 tuber-2.0.0/tuber/man/tuber_POST_json.Rd | 1 tuber-2.0.0/tuber/man/tuber_PUT.Rd | 5 tuber-2.0.0/tuber/man/tuber_check.Rd | 1 tuber-2.0.0/tuber/man/unicode_utils.Rd | 1 tuber-2.0.0/tuber/man/update_video_metadata.Rd | 76 - tuber-2.0.0/tuber/man/upload_caption.Rd | 51 tuber-2.0.0/tuber/man/upload_video.Rd | 13 tuber-2.0.0/tuber/man/validate_channel_id.Rd | 1 tuber-2.0.0/tuber/man/validate_language_code.Rd | 1 tuber-2.0.0/tuber/man/validate_part_parameter.Rd | 1 tuber-2.0.0/tuber/man/validate_playlist_id.Rd | 1 tuber-2.0.0/tuber/man/validate_region_code.Rd | 1 tuber-2.0.0/tuber/man/validate_rfc3339_date.Rd | 1 tuber-2.0.0/tuber/man/validate_video_id.Rd | 1 tuber-2.0.0/tuber/man/warn_deprecated.Rd | 1 tuber-2.0.0/tuber/man/yt_get_quota_usage.Rd | 8 tuber-2.0.0/tuber/man/yt_key.Rd | 15 tuber-2.0.0/tuber/man/yt_oauth.Rd | 30 tuber-2.0.0/tuber/man/yt_reset_quota.Rd | 3 tuber-2.0.0/tuber/man/yt_search.Rd | 24 tuber-2.0.0/tuber/man/yt_set_quota_limit.Rd | 8 tuber-2.0.0/tuber/tests/testthat/test-auth.R | 33 tuber-2.0.0/tuber/tests/testthat/test-basic-functionality.R | 18 tuber-2.0.0/tuber/tests/testthat/test-captions.R | 2 tuber-2.0.0/tuber/tests/testthat/test-channel-members.R | 4 tuber-2.0.0/tuber/tests/testthat/test-channels.R | 24 tuber-2.0.0/tuber/tests/testthat/test-comment-threads.R | 8 tuber-2.0.0/tuber/tests/testthat/test-comments.R | 15 tuber-2.0.0/tuber/tests/testthat/test-integration-ready.R | 73 - tuber-2.0.0/tuber/tests/testthat/test-list-channel-activities.R | 5 tuber-2.0.0/tuber/tests/testthat/test-list-channel-sections.R | 4 tuber-2.0.0/tuber/tests/testthat/test-live-chat.R | 12 tuber-2.0.0/tuber/tests/testthat/test-pagination-mocks.R | 36 tuber-2.0.0/tuber/tests/testthat/test-playlist-items.R | 9 tuber-2.0.0/tuber/tests/testthat/test-playlists.R | 8 tuber-2.0.0/tuber/tests/testthat/test-release-correctness.R |only tuber-2.0.0/tuber/tests/testthat/test-request-assembly.R | 93 - tuber-2.0.0/tuber/tests/testthat/test-super-chat.R | 12 tuber-2.0.0/tuber/tests/testthat/test-thumbnails.R | 10 tuber-2.0.0/tuber/tests/testthat/test-videos.R | 2 tuber-2.0.0/tuber/tests/testthat/test-write-operations.R | 128 +- tuber-2.0.0/tuber/vignettes/api-conventions.Rmd |only tuber-2.0.0/tuber/vignettes/batch-processing-quota.Rmd | 74 - tuber-2.0.0/tuber/vignettes/emoji-analysis.Rmd | 24 tuber-2.0.0/tuber/vignettes/emoji-handling.Rmd | 10 tuber-2.0.0/tuber/vignettes/troubleshooting.Rmd | 56 tuber-2.0.0/tuber/vignettes/tuber-ex.Rmd | 35 235 files changed, 3451 insertions(+), 3024 deletions(-)
Title: Partially Replicated Test-Control Designs for Early Generation
Varietal Trials
Description: Provides functions for generating partially replicated (p-rep)
test-control designs for early generation varietal trials conducted
across multiple environments. The package implements three
construction methods for obtaining p-rep test-control designs with
one or more control treatments. The package extends the partially
replicated design framework of Vinaykumar et al. (2026)
<doi:10.1007/s12355-025-01684-1> to accommodate test-control
comparisons in breeding trials. Functions are provided for
generating randomized and non-randomized layouts and for displaying
the design parameters and treatment allocations for each
environment. The proposed designs are useful for large-scale
varietal evaluation trials where a large number of test lines are
assessed under limited experimental resources.
Author: Vinaykumar L.N. [aut, cre],
Cini Varghese [aut, ctb],
Mohd Harun [aut, ctb],
Sayantani Karmakar [aut, ctb],
Vinayaka [aut, ctb]
Maintainer: Vinaykumar L.N. <vinaymandya123@gmail.com>
Diff between TCpRepDesigns versions 0.0.1 dated 2026-06-25 and 0.0.2 dated 2026-08-20
DESCRIPTION | 41 +-- MD5 | 24 - R/TCpRep1.R | 625 +++++++++++++++++++++++++---------------------- R/TCpRep2.R | 633 +++++++++++++++++++++++++----------------------- R/TCpRep3.R | 633 +++++++++++++++++++++++++----------------------- R/TCpRepEfficiency.R | 355 ++++++++++++++++---------- man/TCpRep1.Rd | 22 - man/TCpRep2.Rd | 20 - man/TCpRep3.Rd | 21 - man/TCpRepEfficiency.Rd | 70 +++-- man/print.TCpRep.Rd | 3 man/print.TCpRep2.Rd | 4 man/print.pRep3.Rd | 4 13 files changed, 1328 insertions(+), 1127 deletions(-)
Title: Simplified Statistical Analysis with Plain-English
Interpretation
Description: A toolkit for common statistical analyses including descriptive statistics, Student's t-tests (one-sample, independent, and paired), one-way and two-way Analysis of Variance (ANOVA), Multivariate Analysis of Variance (MANOVA), chi-square tests, Fisher's Exact Test, McNemar's Test, correlation analysis, simple and multiple linear regression, logistic regression, Friedman Test, and non-parametric tests (Mann-Whitney U, Wilcoxon Signed Rank, and Kruskal-Wallis). Each function automatically interprets results in plain English, reporting effect sizes, confidence intervals, and p-value interpretations, and prints relevant assumption checks by default. A context argument allows users to describe their study design, echoed back alongside the interpretation as a reminder to read results in that context. Post-hoc tests are automatically applied following significant results. A master function automatically detects the appropriate test based on the structure of the input data. Methods are based o [...truncated...]
Author: Uwakmfon Paul [aut, cre, cph]
Maintainer: Uwakmfon Paul <uwakmfon31@gmail.com>
Diff between statease versions 1.3.0 dated 2026-07-02 and 1.4.0 dated 2026-08-20
DESCRIPTION | 8 MD5 | 73 - NEWS.md | 2 R/analyze.R | 50 R/anova2_interpret.R | 55 R/anova_interpret.R | 47 R/check_assumptions.R | 55 R/chisq_interpret.R | 47 R/cor_interpret.R | 47 R/fisher_interpret.R | 39 R/friedman_interpret.R | 39 R/logistic_interpret.R | 53 R/mcnemar_interpret.R | 40 R/mlr_interpret.R | 67 + R/nonparam_interpret.R | 106 + R/power_interpret.R | 4 R/reg_interpret.R | 55 R/ttest_interpret.R | 63 - R/utils-assumptions.R |only README.md | 111 + inst/doc/statease.html | 730 ++++++++----- inst/shiny/app.R | 565 ++++++++++ inst/shiny/rsconnect/shinyapps.io/devwebwacky/statease.dcf | 4 man/analyze.Rd | 6 man/anova2_interpret.Rd | 5 man/anova_interpret.Rd | 5 man/chisq_interpret.Rd | 5 man/cor_interpret.Rd | 6 man/fisher_interpret.Rd | 11 man/friedman_interpret.Rd | 5 man/kruskal_interpret.Rd | 5 man/logistic_interpret.Rd | 5 man/mannwhitney_interpret.Rd | 11 man/mcnemar_interpret.Rd | 5 man/mlr_interpret.Rd | 5 man/reg_interpret.Rd | 5 man/ttest_interpret.Rd | 6 man/wilcoxon_interpret.Rd | 11 38 files changed, 1884 insertions(+), 472 deletions(-)
Title: Hash Table and Hash Set
Description: It provides three implementations of hash tables and hash maps: 1. using
'std::unordered_map' and 'std::unordered_set' C++ libraries, 2. wrapping around
the 'fastmatch' package, 3. using R environment.
Author: Zuguang Gu [aut, cre]
Maintainer: Zuguang Gu <guzuguang@suat-sz.edu.cn>
Diff between hashtable versions 1.0.0 dated 2026-07-27 and 1.0.1 dated 2026-08-20
DESCRIPTION | 8 MD5 | 45 +-- NEWS |only R/RcppExports.R | 168 ++++++++++++ R/hash_env.R | 17 + R/hash_fm.R | 7 R/hash_set.R | 1 R/hash_table.R | 33 ++ build/vignette.rds |binary inst/doc/benchmark2.html | 4 inst/doc/hashtable.R | 8 inst/doc/hashtable.html | 72 ++--- man/hash_env.Rd | 2 man/hash_fm.Rd | 4 man/hash_set.Rd | 2 man/hash_table.Rd | 2 src/RcppExports.cpp | 522 +++++++++++++++++++++++++++++++++++++++ src/hash.h | 3 src/hash_env.cpp | 275 +++++++++++++++++++- src/hash_fm.cpp | 12 src/hash_table.cpp | 161 ++++++++++++ tests/testthat/test_hash_env.R | 21 + tests/testthat/test_hash_fm.R | 19 + tests/testthat/test_hash_table.R | 20 + 24 files changed, 1321 insertions(+), 85 deletions(-)
Title: B Cell Receptor Phylogenetics Toolkit
Description: Provides a set of functions for inferring, visualizing, and analyzing B cell phylogenetic trees.
Provides methods to 1) reconstruct unmutated ancestral sequences,
2) build B cell phylogenetic trees using multiple methods,
3) visualize trees with metadata at the tips,
4) reconstruct intermediate sequences,
5) detect biased ancestor-descendant relationships among metadata types
Workflow examples available at documentation site (see URL).
Citations:
Hoehn et al (2022) <doi:10.1371/journal.pcbi.1009885>,
Hoehn et al (2021) <doi:10.1101/2021.01.06.425648>.
Author: Kenneth Hoehn [aut, cre],
Cole Jensen [aut],
Jessie Fielding [aut],
Hunter Melton [aut],
Susanna Marquez [ctb],
Jason Vander Heiden [ctb],
Erick Matsen [ctb],
Steven Kleinstein [aut, cph]
Maintainer: Kenneth Hoehn <kenneth.b.hoehn@dartmouth.edu>
Diff between dowser versions 2.4.1 dated 2026-03-26 and 2.5.1 dated 2026-08-20
dowser-2.4.1/dowser/inst/doc/Discrete-Trait-Vignette.R |only dowser-2.4.1/dowser/inst/doc/Discrete-Trait-Vignette.Rmd |only dowser-2.4.1/dowser/inst/doc/Discrete-Trait-Vignette.pdf |only dowser-2.4.1/dowser/inst/doc/Germlines-Vignette.R |only dowser-2.4.1/dowser/inst/doc/Germlines-Vignette.Rmd |only dowser-2.4.1/dowser/inst/doc/Germlines-Vignette.pdf |only dowser-2.4.1/dowser/inst/doc/Measurable-Evolution.R |only dowser-2.4.1/dowser/inst/doc/Measurable-Evolution.Rmd |only dowser-2.4.1/dowser/inst/doc/Measurable-Evolution.pdf |only dowser-2.4.1/dowser/inst/doc/NonB-Cell-Data.R |only dowser-2.4.1/dowser/inst/doc/NonB-Cell-Data.Rmd |only dowser-2.4.1/dowser/inst/doc/NonB-Cell-Data.html |only dowser-2.4.1/dowser/inst/doc/Resolve-Light-Chains-Vignette.R |only dowser-2.4.1/dowser/inst/doc/Resolve-Light-Chains-Vignette.Rmd |only dowser-2.4.1/dowser/inst/doc/Resolve-Light-Chains-Vignette.pdf |only dowser-2.4.1/dowser/inst/doc/Sequences-Vignette.R |only dowser-2.4.1/dowser/inst/doc/Sequences-Vignette.Rmd |only dowser-2.4.1/dowser/inst/doc/Sequences-Vignette.pdf |only dowser-2.4.1/dowser/vignettes/Building-Time-Trees-gc-trees.png |only dowser-2.4.1/dowser/vignettes/Building-Time-Trees-mixed-trees.png |only dowser-2.4.1/dowser/vignettes/Discrete-Trait-Vignette.Rmd |only dowser-2.4.1/dowser/vignettes/Germlines-Vignette.Rmd |only dowser-2.4.1/dowser/vignettes/Measurable-Evolution.Rmd |only dowser-2.4.1/dowser/vignettes/NonB-Cell-Data.Rmd |only dowser-2.4.1/dowser/vignettes/Resolve-Light-Chains-Vignette.Rmd |only dowser-2.4.1/dowser/vignettes/Sequences-Vignette.Rmd |only dowser-2.4.1/dowser/vignettes/isotype_model.txt |only dowser-2.5.1/dowser/DESCRIPTION | 19 dowser-2.5.1/dowser/MD5 | 154 dowser-2.5.1/dowser/NAMESPACE | 20 dowser-2.5.1/dowser/NEWS.md | 11 dowser-2.5.1/dowser/R/Clones.R | 104 dowser-2.5.1/dowser/R/Dowser.R | 25 dowser-2.5.1/dowser/R/Germlines.R | 2536 +++++++++- dowser-2.5.1/dowser/R/IO.R |only dowser-2.5.1/dowser/R/Plotting.R | 149 dowser-2.5.1/dowser/R/Statistics.R | 44 dowser-2.5.1/dowser/R/TimeTreesFunctions.R | 605 ++ dowser-2.5.1/dowser/R/TreeFunctions.R | 907 +-- dowser-2.5.1/dowser/README.md | 30 dowser-2.5.1/dowser/build/partial.rdb |binary dowser-2.5.1/dowser/build/vignette.rds |binary dowser-2.5.1/dowser/data/BiopsyTrees.rda |binary dowser-2.5.1/dowser/data/ExampleClones.rda |binary dowser-2.5.1/dowser/data/ExampleMixedClones.rda |binary dowser-2.5.1/dowser/data/IsotypeTrees.rda |binary dowser-2.5.1/dowser/data/TimeTrees.rda |binary dowser-2.5.1/dowser/inst/doc/Building-Time-Trees-Vignette.R | 30 dowser-2.5.1/dowser/inst/doc/Building-Time-Trees-Vignette.Rmd | 6 dowser-2.5.1/dowser/inst/doc/Building-Time-Trees-Vignette.pdf |binary dowser-2.5.1/dowser/inst/doc/Building-Trees-Vignette.pdf |binary dowser-2.5.1/dowser/inst/doc/Input-Output-Vignette.R |only dowser-2.5.1/dowser/inst/doc/Input-Output-Vignette.Rmd |only dowser-2.5.1/dowser/inst/doc/Input-Output-Vignette.pdf |only dowser-2.5.1/dowser/inst/doc/Plotting-Trees-Vignette.R | 26 dowser-2.5.1/dowser/inst/doc/Plotting-Trees-Vignette.Rmd | 26 dowser-2.5.1/dowser/inst/doc/Plotting-Trees-Vignette.pdf |binary dowser-2.5.1/dowser/inst/doc/Quickstart-Vignette.R | 5 dowser-2.5.1/dowser/inst/doc/Quickstart-Vignette.Rmd | 7 dowser-2.5.1/dowser/inst/doc/Quickstart-Vignette.pdf |binary dowser-2.5.1/dowser/inst/get_UCA.py |only dowser-2.5.1/dowser/man/buildAllClonalGermlines.Rd |only dowser-2.5.1/dowser/man/buildBeast.Rd | 6 dowser-2.5.1/dowser/man/buildIgphyml.Rd | 6 dowser-2.5.1/dowser/man/calcRF.Rd | 8 dowser-2.5.1/dowser/man/checkNodeDivergences.Rd |only dowser-2.5.1/dowser/man/createAllGermlines.Rd |only dowser-2.5.1/dowser/man/createGermlines.Rd | 2 dowser-2.5.1/dowser/man/dfToFasta.Rd | 2 dowser-2.5.1/dowser/man/dowser-package.Rd | 2 dowser-2.5.1/dowser/man/dowserObjectEquivalent.Rd |only dowser-2.5.1/dowser/man/exportTrees.Rd | 4 dowser-2.5.1/dowser/man/filterCombs.Rd |only dowser-2.5.1/dowser/man/filterPartialSeqs.Rd |only dowser-2.5.1/dowser/man/getDiffPoint.Rd |only dowser-2.5.1/dowser/man/getDiffPoints.Rd |only dowser-2.5.1/dowser/man/getHeightsAndLengths.Rd |only dowser-2.5.1/dowser/man/getNodeSeq.Rd | 4 dowser-2.5.1/dowser/man/getSeqPath.Rd |only dowser-2.5.1/dowser/man/getSkylines.Rd | 17 dowser-2.5.1/dowser/man/getSubTaxa.Rd | 3 dowser-2.5.1/dowser/man/getTimeTreesIterate.Rd | 43 dowser-2.5.1/dowser/man/getTrees.Rd | 3 dowser-2.5.1/dowser/man/getTreesAndUCAs.Rd |only dowser-2.5.1/dowser/man/installPythonDependencies.Rd |only dowser-2.5.1/dowser/man/makeAirrClone.Rd | 2 dowser-2.5.1/dowser/man/makeSkyline.Rd | 15 dowser-2.5.1/dowser/man/mapSubtrees.Rd |only dowser-2.5.1/dowser/man/plotMSA.Rd |only dowser-2.5.1/dowser/man/plotTrees.Rd | 11 dowser-2.5.1/dowser/man/readBEAST.Rd | 13 dowser-2.5.1/dowser/man/readFasta.Rd | 2 dowser-2.5.1/dowser/man/readIMGT.Rd | 2 dowser-2.5.1/dowser/man/readTreesJSON.Rd |only dowser-2.5.1/dowser/man/setNodeDivergences.Rd |only dowser-2.5.1/dowser/man/treesEquivalent.Rd |only dowser-2.5.1/dowser/man/writeCloneSequences.Rd | 2 dowser-2.5.1/dowser/man/writeFasta.Rd |only dowser-2.5.1/dowser/man/writeTreesJSON.Rd |only dowser-2.5.1/dowser/man/write_clone_to_xml.Rd | 3 dowser-2.5.1/dowser/vignettes/Building-Time-Trees-Vignette.Rmd | 6 dowser-2.5.1/dowser/vignettes/Input-Output-Vignette.Rmd |only dowser-2.5.1/dowser/vignettes/Plotting-Trees-Vignette.Rmd | 26 dowser-2.5.1/dowser/vignettes/Quickstart-Vignette.Rmd | 7 104 files changed, 4122 insertions(+), 771 deletions(-)
Title: Datasets and Basic Statistics for Symbolic Data Analysis
Description: Provides benchmark datasets and foundational tools for Symbolic Data Analysis (SDA). The package includes functions for constructing symbolic data objects from classical data, converting among different interval-valued data formats, managing interval-valued, histogram-valued, modal-valued, and multi-valued data, and performing basic descriptive statistics. It is designed to support teaching, methodological research, and the development of SDA techniques.
Author: Po-Wei Chen [aut],
Chun-houh Chen [aut],
Han-Ming Wu [cre]
Maintainer: Han-Ming Wu <wuhm@g.nccu.edu.tw>
Diff between dataSDA versions 0.2.6 dated 2026-06-12 and 0.2.7 dated 2026-08-20
DESCRIPTION | 8 MD5 | 197 ++++---- NEWS.md | 17 R/data.R | 904 ++++++++++++++++++++------------------ README.md | 8 build/partial.rdb |only inst/doc/dataSDA_intro.Rmd | 4 inst/doc/dataSDA_intro.html | 4 man/abalone.iGAP.Rd | 7 man/abalone.int.Rd | 7 man/acid_rain.int.Rd | 3 man/age_cholesterol_weight.int.Rd | 3 man/age_pyramids.hist.Rd | 10 man/airline_flights.hist.Rd | 3 man/airline_flights2.modal.Rd | 3 man/bank_rates.Rd | 3 man/baseball.int.Rd | 3 man/bats.int.Rd | 10 man/bird.mix.Rd | 3 man/bird_color_taxonomy.hist.Rd | 6 man/bird_species.mix.Rd | 3 man/bird_species_extended.mix.Rd | 3 man/blood.hist.Rd | 6 man/blood_pressure.int.Rd | 3 man/car.int.Rd | 3 man/car_models.int.Rd | 5 man/cardiological.int.Rd | 7 man/cars.int.Rd | 8 man/china_climate_month.hist.Rd | 11 man/china_climate_season.hist.Rd | 11 man/china_temp.int.Rd | 8 man/credit_card.int.Rd | 3 man/crime.modal.Rd | 3 man/crime2.modal.Rd | 3 man/crude_oil_wti.its.Rd | 12 man/djia.its.Rd | 19 man/employment.int.Rd | 3 man/energy_consumption.distr.Rd | 3 man/environment.mix.Rd | 9 man/euro_usd.its.Rd | 7 man/exchange_rate_returns.hist.Rd | 15 man/face.iGAP.Rd | 4 man/finance.int.Rd | 3 man/french_agriculture.hist.Rd | 11 man/freshwater_fish.int.Rd | 5 man/fuel_consumption.modal.Rd | 3 man/fungi.int.Rd | 5 man/hardwood.hist.Rd | 9 man/hdi_gender.int.Rd | 7 man/health_insurance.mix.Rd | 3 man/health_insurance2.modal.Rd | 3 man/hierarchy.Rd | 3 man/hierarchy.hist.Rd | 6 man/hierarchy.int.Rd | 3 man/horses.int.Rd | 3 man/ibovespa.its.Rd | 13 man/iris.int.Rd | 5 man/irish_wind.its.Rd | 3 man/judge1.int.Rd | 15 man/judge2.int.Rd | 15 man/judge3.int.Rd | 15 man/lackinfo.int.Rd | 9 man/lisbon_air_quality.int.Rd | 16 man/loans_by_purpose.int.Rd | 14 man/loans_by_risk.int.Rd | 12 man/loans_by_risk_quantile.int.Rd | 13 man/lung_cancer.hist.Rd | 3 man/lynne1.int.Rd | 4 man/merval.its.Rd | 7 man/mushroom.int.Rd | 3 man/mushroom_fuzzy.mix.Rd | 3 man/nycflights.int.Rd | 9 man/occupations.modal.Rd | 3 man/occupations2.modal.Rd | 3 man/ohtemp.int.Rd | 8 man/oils.int.Rd | 4 man/ozone.hist.Rd | 20 man/petrobras.its.Rd | 13 man/polish_cars.mix.Rd | 9 man/polish_voivodships.int.Rd | 13 man/profession.int.Rd | 3 man/shanghai_stock.its.Rd | 18 man/soccer_bivar.int.Rd | 6 man/sp500.its.Rd | 12 man/synthetic_clusters.int.Rd | 7 man/teams.int.Rd | 3 man/temperature_city.int.Rd | 7 man/tennis.int.Rd | 3 man/town_services.mix.Rd | 3 man/trivial_intervals.int.Rd | 3 man/uscrime.int.Rd | 8 man/utsnow.int.Rd | 15 man/veterinary.int.Rd | 4 man/video1.int.Rd | 12 man/video2.int.Rd | 12 man/video3.int.Rd | 12 man/water_flow.int.Rd | 5 man/wine.int.Rd | 5 man/world_cup.int.Rd | 3 vignettes/dataSDA_intro.Rmd | 4 100 files changed, 1029 insertions(+), 764 deletions(-)
Title: Spatial and Environmental Blocking for Cross-Validation
Description: Creates spatially or environmentally separated, or
group-preserving, training and testing folds for k-fold,
leave-group-out, and leave-one-out cross-validation. Provides spatial
blocking, clustering, buffering, and nearest-neighbour distance-matching
methods, together with tools to visualise folds, summarise fold sizes and class balance,
and assess train–test separation and environmental novelty. Also estimates spatial
autocorrelation ranges in point samples and continuous raster covariates
to provide an initial distance scale for designing spatial folds. Methods
are described in Valavi, R. et al. (2019)
<doi:10.1111/2041-210X.13107>.
Author: Roozbeh Valavi [aut, cre] ,
Jane Elith [aut],
Jose Lahoz-Monfort [aut],
Ian Flint [aut],
Gurutzeta Guillera-Arroita [aut]
Maintainer: Roozbeh Valavi <valavi.r@gmail.com>
Diff between blockCV versions 3.2-0 dated 2025-08-21 and 4.0-0 dated 2026-08-20
blockCV-3.2-0/blockCV/R/v2_buffering.R |only blockCV-3.2-0/blockCV/R/v2_environBlock.R |only blockCV-3.2-0/blockCV/R/v2_explorer.R |only blockCV-3.2-0/blockCV/R/v2_spatialAutoRange.R |only blockCV-3.2-0/blockCV/R/v2_spatialBlock.R |only blockCV-3.2-0/blockCV/man/buffering.Rd |only blockCV-3.2-0/blockCV/man/envBlock.Rd |only blockCV-3.2-0/blockCV/man/foldExplorer.Rd |only blockCV-3.2-0/blockCV/man/rangeExplorer.Rd |only blockCV-3.2-0/blockCV/man/spatialAutoRange.Rd |only blockCV-3.2-0/blockCV/man/spatialBlock.Rd |only blockCV-3.2-0/blockCV/tests/testthat/test-v2-functions.R |only blockCV-4.0-0/blockCV/DESCRIPTION | 30 blockCV-4.0-0/blockCV/MD5 | 123 blockCV-4.0-0/blockCV/NAMESPACE | 31 blockCV-4.0-0/blockCV/NEWS.md |only blockCV-4.0-0/blockCV/R/RcppExports.R | 22 blockCV-4.0-0/blockCV/R/blockCV.R | 37 blockCV-4.0-0/blockCV/R/checks.R | 350 + blockCV-4.0-0/blockCV/R/cv_block_size.R | 6 blockCV-4.0-0/blockCV/R/cv_buffer.R | 89 blockCV-4.0-0/blockCV/R/cv_cluster.R | 285 + blockCV-4.0-0/blockCV/R/cv_distance.R |only blockCV-4.0-0/blockCV/R/cv_group.R |only blockCV-4.0-0/blockCV/R/cv_knndm.R |only blockCV-4.0-0/blockCV/R/cv_nndm.R | 532 +- blockCV-4.0-0/blockCV/R/cv_plot.R | 186 - blockCV-4.0-0/blockCV/R/cv_similarity.R | 364 + blockCV-4.0-0/blockCV/R/cv_spatial.R | 247 - blockCV-4.0-0/blockCV/R/cv_spatial_autocor.R | 97 blockCV-4.0-0/blockCV/R/cv_summary.R |only blockCV-4.0-0/blockCV/R/utils.R | 332 + blockCV-4.0-0/blockCV/README.md |only blockCV-4.0-0/blockCV/build/vignette.rds |binary blockCV-4.0-0/blockCV/inst/doc/tutorial_1.R | 481 +- blockCV-4.0-0/blockCV/inst/doc/tutorial_1.Rmd | 868 ++-- blockCV-4.0-0/blockCV/inst/doc/tutorial_1.html | 1822 +++++----- blockCV-4.0-0/blockCV/inst/doc/tutorial_2.R | 387 +- blockCV-4.0-0/blockCV/inst/doc/tutorial_2.Rmd | 593 +-- blockCV-4.0-0/blockCV/inst/doc/tutorial_2.html | 1437 ++++--- blockCV-4.0-0/blockCV/inst/doc/tutorial_3.R |only blockCV-4.0-0/blockCV/inst/doc/tutorial_3.Rmd |only blockCV-4.0-0/blockCV/inst/doc/tutorial_3.html |only blockCV-4.0-0/blockCV/inst/doc/tutorial_4.R |only blockCV-4.0-0/blockCV/inst/doc/tutorial_4.Rmd |only blockCV-4.0-0/blockCV/inst/doc/tutorial_4.html |only blockCV-4.0-0/blockCV/inst/extdata/species_pb.csv |only blockCV-4.0-0/blockCV/man/blockCV.Rd | 33 blockCV-4.0-0/blockCV/man/cv_block_size.Rd | 4 blockCV-4.0-0/blockCV/man/cv_buffer.Rd | 45 blockCV-4.0-0/blockCV/man/cv_cluster.Rd | 115 blockCV-4.0-0/blockCV/man/cv_distance.Rd |only blockCV-4.0-0/blockCV/man/cv_group.Rd |only blockCV-4.0-0/blockCV/man/cv_knndm.Rd |only blockCV-4.0-0/blockCV/man/cv_nndm.Rd | 56 blockCV-4.0-0/blockCV/man/cv_plot.Rd | 42 blockCV-4.0-0/blockCV/man/cv_similarity.Rd | 72 blockCV-4.0-0/blockCV/man/cv_spatial.Rd | 62 blockCV-4.0-0/blockCV/man/cv_spatial_autocor.Rd | 23 blockCV-4.0-0/blockCV/man/cv_summary.Rd |only blockCV-4.0-0/blockCV/man/figures/cv_clust.jpg |only blockCV-4.0-0/blockCV/man/figures/cv_sim.jpg |only blockCV-4.0-0/blockCV/man/figures/cv_spat.jpg |only blockCV-4.0-0/blockCV/man/figures/cv_spat_folds.jpg |only blockCV-4.0-0/blockCV/tests/testthat/test-balance-folds.R |only blockCV-4.0-0/blockCV/tests/testthat/test-cv_buffer.R | 45 blockCV-4.0-0/blockCV/tests/testthat/test-cv_cluster.R | 185 - blockCV-4.0-0/blockCV/tests/testthat/test-cv_distance.R |only blockCV-4.0-0/blockCV/tests/testthat/test-cv_group.R |only blockCV-4.0-0/blockCV/tests/testthat/test-cv_knndm.R |only blockCV-4.0-0/blockCV/tests/testthat/test-cv_nndm-leakage.R |only blockCV-4.0-0/blockCV/tests/testthat/test-cv_nndm.R | 87 blockCV-4.0-0/blockCV/tests/testthat/test-cv_plot.R | 122 blockCV-4.0-0/blockCV/tests/testthat/test-cv_similarity.R | 158 blockCV-4.0-0/blockCV/tests/testthat/test-cv_spatial.R | 153 blockCV-4.0-0/blockCV/tests/testthat/test-cv_spatial_autocor.R | 24 blockCV-4.0-0/blockCV/tests/testthat/test-cv_summary.R |only blockCV-4.0-0/blockCV/tests/testthat/test-data.R | 6 blockCV-4.0-0/blockCV/tests/testthat/test-interactive-defaults.R |only blockCV-4.0-0/blockCV/tests/testthat/test-presence-bg-validation.R |only blockCV-4.0-0/blockCV/vignettes/tutorial_1.Rmd | 868 ++-- blockCV-4.0-0/blockCV/vignettes/tutorial_2.Rmd | 593 +-- blockCV-4.0-0/blockCV/vignettes/tutorial_3.Rmd |only blockCV-4.0-0/blockCV/vignettes/tutorial_4.Rmd |only 84 files changed, 6685 insertions(+), 4327 deletions(-)
Title: Blinded Sample Size Re-Estimation for Binary Endpoints
Description: Tools for blinded sample size re-estimation (BSSR) in two-arm clinical
trials with binary endpoints, together with the exact power and sample size
calculations that the re-estimation relies on. Five exact statistical tests are
implemented: Pearson chi-squared, Fisher exact, Fisher mid-p, Z-pooled exact
unconditional, and Boschloo exact unconditional. Each test is available with a
one-sided or a two-sided alternative, and the exact unconditional tests can be
combined with the Berger-Boos procedure. Sample sizes can be re-estimated either at
the planning stage, to study the operating characteristics of a design, or from the
blinded data of a trial that is under way. Statistical methods based on Mehrotra et
al. (2003) <doi:10.1111/1541-0420.00051>, Berger and Boos (1994)
<doi:10.1080/01621459.1994.10476836> and Kieser (2020)
<doi:10.1007/978-3-030-49528-2_21>.
Author: Gosuke Homma [aut, cre]
Maintainer: Gosuke Homma <my.name.is.gosuke@gmail.com>
Diff between bbssr versions 1.0.2 dated 2025-06-18 and 2.0.0 dated 2026-08-20
DESCRIPTION | 40 - LICENSE | 2 MD5 | 103 +- NAMESPACE | 55 + NEWS.md | 221 +++-- R/BinaryBSSR.R |only R/BinaryPower.R | 146 ++- R/BinaryPowerBSSR.R | 356 +++++---- R/BinaryRR.R | 239 +++--- R/BinarySampleSize.R | 225 +++-- R/RcppExports.R |only R/bbssr-package.R |only R/cp_bounds.R |only R/fisher_pvalue.R |only R/integer_breaks.R |only R/plot.bbssr_power.R |only R/plot.bbssr_powerbssr.R |only R/plot.bbssr_rr.R |only R/plot.bbssr_samplesize.R |only R/print.bbssr_bssr.R |only R/print.bbssr_power.R |only R/print.bbssr_powerbssr.R |only R/print.bbssr_rr.R |only R/print.bbssr_samplesize.R |only R/resolve_label.R |only R/tie_groups.R |only R/unconditional_pvalue.R |only R/zstat.R |only build/vignette.rds |binary inst/WORDLIST | 82 +- inst/doc/bbssr-interim-reestimation.R |only inst/doc/bbssr-interim-reestimation.Rmd |only inst/doc/bbssr-interim-reestimation.html |only inst/doc/bbssr-introduction.R | 209 ++--- inst/doc/bbssr-introduction.Rmd | 445 ++++------- inst/doc/bbssr-introduction.html | 669 ++++++++--------- inst/doc/bbssr-statistical-methods.R | 337 ++------ inst/doc/bbssr-statistical-methods.Rmd | 779 ++++++-------------- inst/doc/bbssr-statistical-methods.html | 1007 ++++++++----------------- inst/doc/bbssr-validation.R | 587 +++++---------- inst/doc/bbssr-validation.Rmd | 811 +++++++------------- inst/doc/bbssr-validation.html | 1203 ++++++++----------------------- man/BinaryBSSR.Rd |only man/BinaryPower.Rd | 92 +- man/BinaryPowerBSSR.Rd | 127 +-- man/BinaryRR.Rd | 80 +- man/BinarySampleSize.Rd | 85 +- man/bbssr-package.Rd |only man/figures/bssr_comparison.png |binary man/plot.bbssr_power.Rd |only man/plot.bbssr_powerbssr.Rd |only man/plot.bbssr_rr.Rd |only man/plot.bbssr_samplesize.Rd |only man/print.bbssr_bssr.Rd |only man/print.bbssr_power.Rd |only man/print.bbssr_powerbssr.Rd |only man/print.bbssr_rr.Rd |only man/print.bbssr_samplesize.Rd |only src |only tests/testthat/helper-reference.R |only tests/testthat/test-binary-bssr.R |only tests/testthat/test-binary-power-bssr.R | 280 +++---- tests/testthat/test-binary-power.R | 159 +--- tests/testthat/test-binary-rr.R | 249 ++++-- tests/testthat/test-binary-sample-size.R | 99 +- tests/testthat/test-external-reference.R |only tests/testthat/test-internal.R |only tests/testthat/test-s3-methods.R |only vignettes/bbssr-interim-reestimation.Rmd |only vignettes/bbssr-introduction.Rmd | 445 ++++------- vignettes/bbssr-statistical-methods.Rmd | 779 ++++++-------------- vignettes/bbssr-validation.Rmd | 811 +++++++------------- 72 files changed, 4396 insertions(+), 6326 deletions(-)
Title: Analysis the Weather Data for Agriculture
Description: Functions are collected to analyse weather data for agriculture
purposes including to read weather records in multiple formats,
calculate extreme climate index. Demonstration data are included the
SILO daily climate data (licensed under CC BY 4.0, <https://www.longpaddock.qld.gov.au/silo/>).
Author: Bangou Zheng [aut, cre]
Maintainer: Bangou Zheng <zheng.bangyou@gmail.com>
Diff between tidyweather versions 0.2.0 dated 2026-02-19 and 0.3.0 dated 2026-08-20
DESCRIPTION | 10 +- MD5 | 16 ++- NAMESPACE | 10 +- R/spherical_distance.R |only R/thermal_time.R | 137 +++++++++++++++++++++++++++++- man/interpolate_hourly_sin_pp_adjusted.Rd |only man/spherical_distance.Rd |only man/thermal_time.Rd | 12 ++ man/weather_options.Rd | 5 - tests/testthat/test-spherical_distance.R |only tests/testthat/test-thermal_time.R | 77 ++++++++++++++++ 11 files changed, 242 insertions(+), 25 deletions(-)
Title: Management Strategy Evaluation for Salmon Species
Description: Simulation tools to evaluate the long-term effects of salmon management strategies, including a combination of habitat, harvest, and
habitat actions. The stochastic age-structured operating model accommodates complex life histories, including freshwater survival across
early life stages, juvenile survival and fishery exploitation in the marine life stage, partial maturity by age class, and fitness impacts of
hatchery programs on natural spawning populations. 'salmonMSE' also provides an age-structured conditioning model to develop operating models
fitted to data.
Author: Quang Huynh [aut, cre]
Maintainer: Quang Huynh <quang@bluematterscience.com>
Diff between salmonMSE versions 2.1.0 dated 2026-04-25 and 3.0.0 dated 2026-08-20
salmonMSE-2.1.0/salmonMSE/R/Harvest_MMP.R |only salmonMSE-2.1.0/salmonMSE/R/MMSE2SMSE.R |only salmonMSE-2.1.0/salmonMSE/R/Rel.R |only salmonMSE-2.1.0/salmonMSE/R/SOM2MOM.R |only salmonMSE-2.1.0/salmonMSE/R/SOM2MOM_int.R |only salmonMSE-2.1.0/salmonMSE/R/multiHist2SHist.R |only salmonMSE-2.1.0/salmonMSE/man/Harvest_MMP.Rd |only salmonMSE-2.1.0/salmonMSE/man/PNI50.Rd |only salmonMSE-2.1.0/salmonMSE/man/SAR_fitness.Rd |only salmonMSE-2.1.0/salmonMSE/man/SHist-class.Rd |only salmonMSE-2.1.0/salmonMSE/man/salmonMSE-int.Rd |only salmonMSE-2.1.0/salmonMSE/man/smolt_func.Rd |only salmonMSE-3.0.0/salmonMSE/DESCRIPTION | 18 salmonMSE-3.0.0/salmonMSE/MD5 | 107 - salmonMSE-3.0.0/salmonMSE/NAMESPACE | 34 salmonMSE-3.0.0/salmonMSE/NEWS.md | 20 salmonMSE-3.0.0/salmonMSE/R/AHA.R | 61 salmonMSE-3.0.0/salmonMSE/R/CM.R | 6 salmonMSE-3.0.0/salmonMSE/R/CM_int.R | 47 salmonMSE-3.0.0/salmonMSE/R/CMfun.R | 672 ++++++---- salmonMSE-3.0.0/salmonMSE/R/brood_func.R |only salmonMSE-3.0.0/salmonMSE/R/catch_func.R |only salmonMSE-3.0.0/salmonMSE/R/check_SOM.R |only salmonMSE-3.0.0/salmonMSE/R/data_obj.R | 8 salmonMSE-3.0.0/salmonMSE/R/define-SOM.R | 1182 ++++++++---------- salmonMSE-3.0.0/salmonMSE/R/fitness.R | 85 + salmonMSE-3.0.0/salmonMSE/R/hatchery.R | 421 ++++-- salmonMSE-3.0.0/salmonMSE/R/plot-LHG.R | 36 salmonMSE-3.0.0/salmonMSE/R/plot-SOM.R | 391 ++--- salmonMSE-3.0.0/salmonMSE/R/plot-statevar.R | 32 salmonMSE-3.0.0/salmonMSE/R/pm.R | 169 +- salmonMSE-3.0.0/salmonMSE/R/ref.R | 707 +++++----- salmonMSE-3.0.0/salmonMSE/R/salmonMSE.R | 1041 +++++++++++---- salmonMSE-3.0.0/salmonMSE/R/simpleSOM.R |only salmonMSE-3.0.0/salmonMSE/R/zzz.R | 15 salmonMSE-3.0.0/salmonMSE/README.md | 4 salmonMSE-3.0.0/salmonMSE/build/partial.rdb |binary salmonMSE-3.0.0/salmonMSE/data/glossary.rda |binary salmonMSE-3.0.0/salmonMSE/data/multi_SOM.rda |binary salmonMSE-3.0.0/salmonMSE/data/simple_SOM.rda |binary salmonMSE-3.0.0/salmonMSE/inst/include/CMreport.Rmd | 594 ++++----- salmonMSE-3.0.0/salmonMSE/man/CM_MSY.Rd |only salmonMSE-3.0.0/salmonMSE/man/CMfigures.Rd | 49 salmonMSE-3.0.0/salmonMSE/man/Deprecated.Rd |only salmonMSE-3.0.0/salmonMSE/man/Effort_solver.Rd |only salmonMSE-3.0.0/salmonMSE/man/Harvest-class.Rd | 21 salmonMSE-3.0.0/salmonMSE/man/Hatchery-class.Rd | 4 salmonMSE-3.0.0/salmonMSE/man/P_PNI50.Rd |only salmonMSE-3.0.0/salmonMSE/man/SMSE-class.Rd | 27 salmonMSE-3.0.0/salmonMSE/man/brood_func.Rd |only salmonMSE-3.0.0/salmonMSE/man/calc_broodtake.Rd |only salmonMSE-3.0.0/salmonMSE/man/calc_phi.Rd | 2 salmonMSE-3.0.0/salmonMSE/man/calc_pwild_age.Rd | 2 salmonMSE-3.0.0/salmonMSE/man/calc_ref.Rd | 5 salmonMSE-3.0.0/salmonMSE/man/calc_spawners.Rd |only salmonMSE-3.0.0/salmonMSE/man/calc_yearling.Rd |only salmonMSE-3.0.0/salmonMSE/man/catch_func.Rd |only salmonMSE-3.0.0/salmonMSE/man/check_SOM.Rd | 2 salmonMSE-3.0.0/salmonMSE/man/define_hatchery_args.Rd |only salmonMSE-3.0.0/salmonMSE/man/dot-CM_ER.Rd |only salmonMSE-3.0.0/salmonMSE/man/dot-CM_prod.Rd |only salmonMSE-3.0.0/salmonMSE/man/dot-egg_func.Rd |only salmonMSE-3.0.0/salmonMSE/man/fit_CM.Rd | 3 salmonMSE-3.0.0/salmonMSE/man/fitness_func.Rd |only salmonMSE-3.0.0/salmonMSE/man/get_F.Rd | 4 salmonMSE-3.0.0/salmonMSE/man/glossary.Rd | 2 salmonMSE-3.0.0/salmonMSE/man/nextgen_SRR_func.Rd |only salmonMSE-3.0.0/salmonMSE/man/salmonMSE.Rd | 40 salmonMSE-3.0.0/salmonMSE/man/salmonMSE_env.Rd | 2 salmonMSE-3.0.0/salmonMSE/man/simpleSOM-class.Rd |only salmonMSE-3.0.0/salmonMSE/man/stray_func.Rd |only 71 files changed, 3426 insertions(+), 2387 deletions(-)
Title: Univariate and Multivariate Damped Random Walk Processes
Description: Provides tools for fitting and simulating univariate and multivariate damped random walk processes, also known as Ornstein-Uhlenbeck processes or first-order continuous-time autoregressive models, CAR(1) or CARMA(1, 0). The package supports irregularly spaced observation times, heteroscedastic measurement errors, missing measurements across multivariate time series, and polynomial mean trends in normalized time. The current implementation models up to ten time series jointly. Kalman filtering is used to evaluate the likelihood efficiently. Polynomial mean coefficients are handled conditionally within the Kalman recursion, reducing the dimension of numerical maximum likelihood optimization and permitting exact Gaussian conditional updates during Bayesian posterior sampling. Maximum likelihood estimation is computationally efficient and suitable for large-scale data analysis, while Bayesian posterior sampling is better suited to small-scale analyses requiring more careful uncertainty qua [...truncated...]
Author: Zhirui Hu [aut],
Hyungsuk Tak [aut, cre]
Maintainer: Hyungsuk Tak <hyungsuk.tak@gmail.com>
Diff between Rdrw versions 1.0.3 dated 2026-07-02 and 1.0.4 dated 2026-08-20
DESCRIPTION | 10 MD5 | 14 NAMESPACE | 4 R/drw.R | 729 +++++++++++++++++++++++++++++---------------------- man/Rdrw-internal.Rd | 6 man/Rdrw-package.Rd | 8 man/drw.Rd | 10 man/drw.sim.Rd | 2 8 files changed, 457 insertions(+), 326 deletions(-)
Title: An R Interface to the California Academy of Sciences Eschmeyer's
Catalog of Fishes
Description: Accesses the California Academy of Sciences Eschmeyer's Catalog of Fishes in R using web requests. The Catalog of fishes is the leading authority in fish taxonomy. Functions in the package allow users to search for fish taxa and valid names, retrieve taxonomic references, retrieve monthly taxonomic changes, obtain natural history collection information, and see the number of species by taxonomic group. For more information on the Catalog: Fricke, R., Eschmeyer, W. N. & R. van der Laan (eds) 2025. ESCHMEYER'S CATALOG OF FISHES <https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp>.
Author: Samuel R. Borstein [aut, cre],
Brandon Dominy [aut],
Brian O'Meara [aut]
Maintainer: Samuel R. Borstein <sam@borstein.com>
Diff between rcatfish versions 1.0.4 dated 2026-07-07 and 1.0.5 dated 2026-08-20
DESCRIPTION | 10 +- MD5 | 14 +-- NEWS.md | 2 inst/doc/rcatfish-vignette.html | 2 man/rcatfish_classification.Rd | 62 +++++++-------- man/rcatfish_glossary.Rd | 62 +++++++-------- man/rcatfish_updates.Rd | 130 ++++++++++++++++----------------- tests/testthat/test_rcatfish_updates.R | 6 + 8 files changed, 146 insertions(+), 142 deletions(-)
Title: Macros Generating 'nimble' Code
Description: Macros to generate 'nimble' code from a concise syntax. Included are macros for generating linear modeling code using a formula-based syntax and for building for() loops. For more details review the 'nimble' manual: <https://r-nimble.org/manual/cha-user-defined.html#sec:user-macros>.
Author: Ken Kellner [cre, aut],
Perry de Valpine [aut],
Christopher Paciorek [aut],
Daniel Turek [aut]
Maintainer: Ken Kellner <contact@kenkellner.com>
Diff between nimbleMacros versions 0.1.1 dated 2025-03-11 and 0.1.3 dated 2026-08-20
DESCRIPTION | 12 +- MD5 | 37 ++++---- NAMESPACE | 1 NEWS.md |only R/FORLOOP.R | 52 ++++++++--- R/LINPRED.R | 92 ++++++++++++-------- R/LM.R | 39 ++++---- R/utilities.R | 151 +++++++++++++++++++++++++++++++++ R/zzz.R | 1 build/vignette.rds |binary inst/doc/nimbleMacros.Rmd | 4 inst/doc/nimbleMacros.html | 4 man/FORLOOP.Rd | 30 ++++-- man/LINPRED.Rd | 80 +++++++++-------- man/LINPRED_PRIORS.Rd | 74 ++++++++-------- man/LM.Rd | 56 ++++++------ man/simplifyForLoops.Rd |only tests/testthat/test_FORLOOP.R | 84 ++++++++++++++++++ tests/testthat/test_formulaHandlers.R | 2 tests/testthat/test_simplifyForLoops.R |only vignettes/nimbleMacros.Rmd | 4 21 files changed, 519 insertions(+), 204 deletions(-)
Title: Tools and Statistical Procedures in Plant Science
Description: The 'inti' package is part of the 'inkaverse' project for developing
different procedures and tools used in plant science and experimental designs.
The mean aim of the package is to support researchers during the planning of
experiments and data collection (tarpuy()), data analysis and graphics (yupana())
, and scientific writing.
Learn more about the 'inkaverse' project at <https://inkaverse.com/>.
Author: Flavio Lozano-Isla [aut, cre] ,
Yoel Diaz-Saucedo [aut] ,
Maria Belen Kistner [ctb] ,
QuipoLab [ctb],
Inkaverse [cph]
Maintainer: Flavio Lozano-Isla <flozanoisla@gmail.com>
Diff between inti versions 0.7.2 dated 2026-07-28 and 0.7.3 dated 2026-08-20
inti-0.7.2/inti/R/outliers_remove.R |only inti-0.7.2/inti/R/plot_diag.R |only inti-0.7.2/inti/inst/doc/heritability.Rmd |only inti-0.7.2/inti/inst/doc/yupana.Rmd |only inti-0.7.2/inti/man/outliers_remove.Rd |only inti-0.7.2/inti/man/plot_diag.Rd |only inti-0.7.2/inti/vignettes/heritability.Rmd |only inti-0.7.2/inti/vignettes/yupana.Rmd |only inti-0.7.3/inti/DESCRIPTION | 12 inti-0.7.3/inti/MD5 | 117 inti-0.7.3/inti/NAMESPACE | 172 inti-0.7.3/inti/NEWS.md | 4 inti-0.7.3/inti/R/H2cal.R | 50 inti-0.7.3/inti/R/design_augmented.R | 839 ++-- inti-0.7.3/inti/R/design_repblock.R | 656 +++ inti-0.7.3/inti/R/design_split_rcbd.R | 843 +++- inti-0.7.3/inti/R/plot_augmented_design.R | 801 ++-- inti-0.7.3/inti/R/plot_split_rcbd_design.R | 668 ++- inti-0.7.3/inti/R/plot_standard_design.R | 475 +- inti-0.7.3/inti/R/remove_outliers.R | 31 inti-0.7.3/inti/R/rticle.R | 29 inti-0.7.3/inti/R/tarpuy.R | 77 inti-0.7.3/inti/R/tarpuy_design.R | 651 ++- inti-0.7.3/inti/R/tarpuy_plex.R | 796 ++-- inti-0.7.3/inti/R/tarpuy_plotdesign.R | 622 ++- inti-0.7.3/inti/R/tarpuy_traits.R | 684 ++- inti-0.7.3/inti/README.md | 12 inti-0.7.3/inti/build/vignette.rds |binary inti-0.7.3/inti/inst/doc/apps.html | 2 inti-0.7.3/inti/inst/doc/apps.qmd | 7 inti-0.7.3/inti/inst/doc/heritability.R | 15 inti-0.7.3/inti/inst/doc/heritability.html | 1096 ++---- inti-0.7.3/inti/inst/doc/heritability.qmd |only inti-0.7.3/inti/inst/doc/policy.qmd | 7 inti-0.7.3/inti/inst/doc/rticles.qmd | 9 inti-0.7.3/inti/inst/doc/tarpuy.html | 2 inti-0.7.3/inti/inst/doc/tarpuy.qmd | 11 inti-0.7.3/inti/inst/doc/yupana.R | 16 inti-0.7.3/inti/inst/doc/yupana.html | 408 -- inti-0.7.3/inti/inst/doc/yupana.qmd |only inti-0.7.3/inti/inst/tarpuy/helpers.R |only inti-0.7.3/inti/inst/tarpuy/pkgs.R | 94 inti-0.7.3/inti/inst/tarpuy/server.R | 4500 +++++++++++++++++--------- inti-0.7.3/inti/inst/tarpuy/ui.R | 341 - inti-0.7.3/inti/inst/tarpuy/www/msgs.R | 33 inti-0.7.3/inti/inst/tarpuy/www/tarpuy.css |only inti-0.7.3/inti/inst/tarpuy/www/tarpuy.js |only inti-0.7.3/inti/man/H2cal.Rd | 2 inti-0.7.3/inti/man/design_augmented.Rd | 32 inti-0.7.3/inti/man/design_repblock.Rd | 163 inti-0.7.3/inti/man/design_split_rcbd.Rd | 134 inti-0.7.3/inti/man/plot_augmented_design.Rd | 66 inti-0.7.3/inti/man/plot_split_rcbd_design.Rd | 65 inti-0.7.3/inti/man/plot_standard_design.Rd | 68 inti-0.7.3/inti/man/remove_outliers.Rd | 13 inti-0.7.3/inti/man/rticle.Rd | 2 inti-0.7.3/inti/man/tarpuy.Rd | 59 inti-0.7.3/inti/man/tarpuy_design.Rd | 165 inti-0.7.3/inti/man/tarpuy_plex.Rd | 5 inti-0.7.3/inti/man/tarpuy_plotdesign.Rd | 79 inti-0.7.3/inti/man/tarpuy_traits.Rd | 212 - inti-0.7.3/inti/vignettes/apps.qmd | 7 inti-0.7.3/inti/vignettes/heritability.qmd |only inti-0.7.3/inti/vignettes/policy.qmd | 7 inti-0.7.3/inti/vignettes/rticles.qmd | 9 inti-0.7.3/inti/vignettes/tarpuy.qmd | 11 inti-0.7.3/inti/vignettes/yupana.qmd |only 67 files changed, 9296 insertions(+), 5883 deletions(-)
Title: Test Data Engineering
Description: Implements comprehensive test data engineering methods as described in
Shojima (2022, ISBN:978-9811699856). Provides statistical techniques for
engineering and processing test data: Classical Test Theory (CTT) with
reliability coefficients for continuous ability assessment; Item Response
Theory (IRT) including Rasch, 2PL, and 3PL models with item/test information
functions; Latent Class Analysis (LCA) for nominal clustering; Latent Rank
Analysis (LRA) for ordinal clustering with automatic determination of cluster
numbers; Biclustering methods including infinite relational models for
simultaneous clustering of examinees and items without predefined cluster
numbers; and Bayesian Network Models (BNM) for visualizing inter-item
dependencies. Features local dependence analysis through LRA and biclustering,
parameter estimation, dimensionality assessment, and network structure
visualization for educational, psychological, and social science research.
Author: Koji Kosugi [aut, cre]
Maintainer: Koji Kosugi <kosugitti@gmail.com>
Diff between exametrika versions 1.15.0 dated 2026-07-15 and 2.0.0 dated 2026-08-20
exametrika-1.15.0/exametrika/man/IRM.Rd |only exametrika-1.15.0/exametrika/man/StrLearningGA_BNM.Rd |only exametrika-1.15.0/exametrika/man/StrLearningPBIL_BNM.Rd |only exametrika-1.15.0/exametrika/man/StrLearningPBIL_LDLRA.Rd |only exametrika-2.0.0/exametrika/DESCRIPTION | 11 exametrika-2.0.0/exametrika/MD5 | 255 +- exametrika-2.0.0/exametrika/NAMESPACE | 22 exametrika-2.0.0/exametrika/NEWS.md | 642 ++++++ exametrika-2.0.0/exametrika/R/00_EMclus.R | 46 exametrika-2.0.0/exametrika/R/00_EMclus_nominal.R |only exametrika-2.0.0/exametrika/R/00_ModelFitModule.R | 74 exametrika-2.0.0/exametrika/R/00_exametrikaPlot.R | 12 exametrika-2.0.0/exametrika/R/00_exametrikaPrint.R | 30 exametrika-2.0.0/exametrika/R/00_isotonic_CORE.R |only exametrika-2.0.0/exametrika/R/00_plot_irt.R | 2 exametrika-2.0.0/exametrika/R/00_plot_lca_lra.R | 76 exametrika-2.0.0/exametrika/R/00_print_biclustering.R | 88 exametrika-2.0.0/exametrika/R/00_print_lca_lra.R | 136 + exametrika-2.0.0/exametrika/R/00_print_network.R | 14 exametrika-2.0.0/exametrika/R/04C_ParameterEstimation.R | 73 exametrika-2.0.0/exametrika/R/05_LCA.R | 293 ++ exametrika-2.0.0/exametrika/R/06_LRA.R | 53 exametrika-2.0.0/exametrika/R/07_Biclustering.R | 93 exametrika-2.0.0/exametrika/R/07_IRM.R | 18 exametrika-2.0.0/exametrika/R/08A_BNM.R | 179 + exametrika-2.0.0/exametrika/R/08C_BNM_GA.R | 56 exametrika-2.0.0/exametrika/R/09B_LDLRA_GA.R | 30 exametrika-2.0.0/exametrika/R/09_LDLRA.R | 56 exametrika-2.0.0/exametrika/R/10_LDB.R | 19 exametrika-2.0.0/exametrika/R/11_BINET.R | 6 exametrika-2.0.0/exametrika/R/12_LRA_ordinal.R | 180 - exametrika-2.0.0/exametrika/R/13_LRA_rated.R | 45 exametrika-2.0.0/exametrika/R/14_grm.R | 78 exametrika-2.0.0/exametrika/R/15_Biclustering_nominal.R | 33 exametrika-2.0.0/exametrika/R/16_Biclustering_ordinal.R | 162 + exametrika-2.0.0/exametrika/R/17_Biclustering_nominal_IRM.R | 7 exametrika-2.0.0/exametrika/R/18_Biclustering_ordinal_IRM.R | 19 exametrika-2.0.0/exametrika/R/19_Biclustering_rated.R | 7 exametrika-2.0.0/exametrika/R/20_Biclustering_rated_IRM.R | 7 exametrika-2.0.0/exametrika/R/24_M2.R |only exametrika-2.0.0/exametrika/R/RcppExports.R | 12 exametrika-2.0.0/exametrika/inst/doc/biclustering.html | 48 exametrika-2.0.0/exametrika/inst/doc/irt.html | 178 - exametrika-2.0.0/exametrika/inst/doc/latent-class-rank.html | 400 +-- exametrika-2.0.0/exametrika/inst/doc/network-models.html | 4 exametrika-2.0.0/exametrika/man/BINET.Rd | 4 exametrika-2.0.0/exametrika/man/Biclustering.Rd | 29 exametrika-2.0.0/exametrika/man/Biclustering_IRM.Rd | 16 exametrika-2.0.0/exametrika/man/LCA.Rd | 85 exametrika-2.0.0/exametrika/man/LDB.Rd | 4 exametrika-2.0.0/exametrika/man/LD_param_est.Rd | 14 exametrika-2.0.0/exametrika/man/LRA.Rd | 24 exametrika-2.0.0/exametrika/man/M2.Rd |only exametrika-2.0.0/exametrika/man/add_M2.Rd |only exametrika-2.0.0/exametrika/man/grm_iif.Rd | 12 exametrika-2.0.0/exametrika/man/plot.exametrika.Rd | 2 exametrika-2.0.0/exametrika/man/print.exametrika.Rd | 8 exametrika-2.0.0/exametrika/src/RcppExports.cpp | 41 exametrika-2.0.0/exametrika/src/isotonic_core.cpp |only exametrika-2.0.0/exametrika/tests/testthat/_problems |only exametrika-2.0.0/exametrika/tests/testthat/fixtures/mathematica_reference/Chapter04IRT2pl_Item.csv | 30 exametrika-2.0.0/exametrika/tests/testthat/fixtures/mathematica_reference/Chapter04IRT2pl_Q3.csv | 30 exametrika-2.0.0/exametrika/tests/testthat/fixtures/mathematica_reference/Chapter04IRT2pl_Student.csv | 1000 ++++----- exametrika-2.0.0/exametrika/tests/testthat/fixtures/mathematica_reference/Chapter04IRT2pl_Test.csv | 26 exametrika-2.0.0/exametrika/tests/testthat/fixtures/mathematica_reference/Chapter04IRT3pl_Item.csv | 30 exametrika-2.0.0/exametrika/tests/testthat/fixtures/mathematica_reference/Chapter04IRT3pl_Q3.csv | 30 exametrika-2.0.0/exametrika/tests/testthat/fixtures/mathematica_reference/Chapter04IRT3pl_Student.csv | 1000 ++++----- exametrika-2.0.0/exametrika/tests/testthat/fixtures/mathematica_reference/Chapter04IRT3pl_Test.csv | 26 exametrika-2.0.0/exametrika/tests/testthat/fixtures/mathematica_reference/Chapter04IRT4pl_Item.csv | 30 exametrika-2.0.0/exametrika/tests/testthat/fixtures/mathematica_reference/Chapter04IRT4pl_Q3.csv | 30 exametrika-2.0.0/exametrika/tests/testthat/fixtures/mathematica_reference/Chapter04IRT4pl_Student.csv | 1000 ++++----- exametrika-2.0.0/exametrika/tests/testthat/fixtures/mathematica_reference/Chapter04IRT4pl_Test.csv | 26 exametrika-2.0.0/exametrika/tests/testthat/fixtures/mathematica_reference/Chapter05LCA_Class.csv | 6 exametrika-2.0.0/exametrika/tests/testthat/fixtures/mathematica_reference/Chapter05LCA_Item.csv | 30 exametrika-2.0.0/exametrika/tests/testthat/fixtures/mathematica_reference/Chapter05LCA_Student.csv | 1000 ++++----- exametrika-2.0.0/exametrika/tests/testthat/fixtures/mathematica_reference/Chapter05LCA_Test.csv | 26 exametrika-2.0.0/exametrika/tests/testthat/fixtures/mathematica_reference/Chapter06LRA_GTMmic0_Item.csv | 30 exametrika-2.0.0/exametrika/tests/testthat/fixtures/mathematica_reference/Chapter06LRA_GTMmic0_Rank.csv | 6 exametrika-2.0.0/exametrika/tests/testthat/fixtures/mathematica_reference/Chapter06LRA_GTMmic0_Student.csv | 1000 ++++----- exametrika-2.0.0/exametrika/tests/testthat/fixtures/mathematica_reference/Chapter06LRA_GTMmic0_Test.csv | 26 exametrika-2.0.0/exametrika/tests/testthat/fixtures/mathematica_reference/Chapter06LRA_GTMmic1_Item.csv | 30 exametrika-2.0.0/exametrika/tests/testthat/fixtures/mathematica_reference/Chapter06LRA_GTMmic1_Rank.csv | 6 exametrika-2.0.0/exametrika/tests/testthat/fixtures/mathematica_reference/Chapter06LRA_GTMmic1_Student.csv | 1000 ++++----- exametrika-2.0.0/exametrika/tests/testthat/fixtures/mathematica_reference/Chapter06LRA_GTMmic1_Test.csv | 26 exametrika-2.0.0/exametrika/tests/testthat/fixtures/mathematica_reference/Chapter11BINET_CCRR.csv | 236 +- exametrika-2.0.0/exametrika/tests/testthat/fixtures/mathematica_reference/Chapter11BINET_LDPSR.csv | 32 exametrika-2.0.0/exametrika/tests/testthat/fixtures/mathematica_reference/Chapter11BINET_Marginal_Bicluster.csv | 30 exametrika-2.0.0/exametrika/tests/testthat/fixtures/mathematica_reference/Chapter11BINET_Student.csv | 1030 +++++----- exametrika-2.0.0/exametrika/tests/testthat/fixtures/mathematica_reference/Chapter11BINET_Test.csv | 18 exametrika-2.0.0/exametrika/tests/testthat/fixtures/mathematica_reference/TinyBicl_Bicluster.csv |only exametrika-2.0.0/exametrika/tests/testthat/fixtures/mathematica_reference/TinyBicl_Test.csv |only exametrika-2.0.0/exametrika/tests/testthat/fixtures/mathematica_reference/TinyCTT_Item.csv |only exametrika-2.0.0/exametrika/tests/testthat/fixtures/mathematica_reference/TinyCTT_Mutual_Information.csv |only exametrika-2.0.0/exametrika/tests/testthat/fixtures/mathematica_reference/TinyCTT_Phi_Coefficient.csv |only exametrika-2.0.0/exametrika/tests/testthat/fixtures/mathematica_reference/TinyCTT_Test.csv |only exametrika-2.0.0/exametrika/tests/testthat/fixtures/mathematica_reference/TinyCTT_Tetrachoric_Correlation.csv |only exametrika-2.0.0/exametrika/tests/testthat/fixtures/mathematica_reference/TinyIRT2pl_Item.csv |only exametrika-2.0.0/exametrika/tests/testthat/fixtures/mathematica_reference/TinyIRT2pl_Test.csv |only exametrika-2.0.0/exametrika/tests/testthat/fixtures/mathematica_reference/TinyIRT3pl_Item.csv |only exametrika-2.0.0/exametrika/tests/testthat/fixtures/mathematica_reference/TinyIRT3pl_Test.csv |only exametrika-2.0.0/exametrika/tests/testthat/fixtures/mathematica_reference/TinyIRT4pl_Item.csv |only exametrika-2.0.0/exametrika/tests/testthat/fixtures/mathematica_reference/TinyIRT4pl_Test.csv |only exametrika-2.0.0/exametrika/tests/testthat/fixtures/mathematica_reference/TinyLCA_Class.csv |only exametrika-2.0.0/exametrika/tests/testthat/fixtures/mathematica_reference/TinyLCA_Item.csv |only exametrika-2.0.0/exametrika/tests/testthat/fixtures/mathematica_reference/TinyLCA_Test.csv |only exametrika-2.0.0/exametrika/tests/testthat/fixtures/mathematica_reference/TinyLRAmic0_Item.csv |only exametrika-2.0.0/exametrika/tests/testthat/fixtures/mathematica_reference/TinyLRAmic0_Rank.csv |only exametrika-2.0.0/exametrika/tests/testthat/fixtures/mathematica_reference/TinyLRAmic0_Test.csv |only exametrika-2.0.0/exametrika/tests/testthat/fixtures/mathematica_reference/TinyLRAmic1_Item.csv |only exametrika-2.0.0/exametrika/tests/testthat/fixtures/mathematica_reference/TinyLRAmic1_Rank.csv |only exametrika-2.0.0/exametrika/tests/testthat/fixtures/mathematica_reference/TinyLRAmic1_Test.csv |only exametrika-2.0.0/exametrika/tests/testthat/fixtures/mathematica_reference/TinyMissing_Item.csv |only exametrika-2.0.0/exametrika/tests/testthat/fixtures/mathematica_reference/TinyMissing_Test.csv |only exametrika-2.0.0/exametrika/tests/testthat/fixtures/mathematica_reference/TinyRankl_Rankluster.csv |only exametrika-2.0.0/exametrika/tests/testthat/fixtures/mathematica_reference/TinyRankl_Test.csv |only exametrika-2.0.0/exametrika/tests/testthat/fixtures/tiny_data |only exametrika-2.0.0/exametrika/tests/testthat/helper-comparison.R | 13 exametrika-2.0.0/exametrika/tests/testthat/test-biclustering.R | 68 exametrika-2.0.0/exametrika/tests/testthat/test-binet.R | 95 exametrika-2.0.0/exametrika/tests/testthat/test-chatterjee.R | 1 exametrika-2.0.0/exametrika/tests/testthat/test-distractor.R | 7 exametrika-2.0.0/exametrika/tests/testthat/test-glasso.R | 46 exametrika-2.0.0/exametrika/tests/testthat/test-grm.R | 76 exametrika-2.0.0/exametrika/tests/testthat/test-irm-gibbs-cpp.R | 42 exametrika-2.0.0/exametrika/tests/testthat/test-irm-nominal.R | 50 exametrika-2.0.0/exametrika/tests/testthat/test-irm-ordinal.R | 56 exametrika-2.0.0/exametrika/tests/testthat/test-irm-rated.R | 48 exametrika-2.0.0/exametrika/tests/testthat/test-irm.R | 12 exametrika-2.0.0/exametrika/tests/testthat/test-irt.R | 46 exametrika-2.0.0/exametrika/tests/testthat/test-isotonic-core.R |only exametrika-2.0.0/exametrika/tests/testthat/test-lca.R | 511 ++++ exametrika-2.0.0/exametrika/tests/testthat/test-lra-mic.R | 3 exametrika-2.0.0/exametrika/tests/testthat/test-lra-nominal.R | 34 exametrika-2.0.0/exametrika/tests/testthat/test-lra-ordinal.R | 164 + exametrika-2.0.0/exametrika/tests/testthat/test-lra.R | 36 exametrika-2.0.0/exametrika/tests/testthat/test-m2-whitener.R |only exametrika-2.0.0/exametrika/tests/testthat/test-polytomous-biclustering.R | 113 - exametrika-2.0.0/exametrika/tests/testthat/test-regression-1150.R | 8 exametrika-2.0.0/exametrika/tests/testthat/test-regression-softmax.R |only exametrika-2.0.0/exametrika/tests/testthat/test-test-analysis.R | 20 exametrika-2.0.0/exametrika/tests/testthat/test-tiny-biclustering.R |only exametrika-2.0.0/exametrika/tests/testthat/test-tiny-ctt.R |only exametrika-2.0.0/exametrika/tests/testthat/test-tiny-irt.R |only exametrika-2.0.0/exametrika/tests/testthat/test-tiny-lca.R |only exametrika-2.0.0/exametrika/tests/testthat/test-tiny-lra.R |only 145 files changed, 7914 insertions(+), 5028 deletions(-)
Title: Differential Evolution Optimization in Pure R
Description: Differential Evolution (DE) stochastic heuristic algorithms for
global optimization of problems with and without general constraints.
The aim is to curate a collection of its variants that
(1) do not sacrifice simplicity of design,
(2) are essentially tuning-free, and
(3) can be efficiently implemented directly in the R language.
Currently, it provides implementations of the algorithms 'jDE' by
Brest et al. (2006) <doi:10.1109/TEVC.2006.872133> for single-objective
optimization and 'NCDE' by Qu et al. (2012) <doi:10.1109/TEVC.2011.2161873>
for multimodal optimization (single-objective problems with
multiple solutions).
Author: Eduardo L. T. Conceicao [aut, cre],
Martin Maechler [ctb]
Maintainer: Eduardo L. T. Conceicao <mail@eduardoconceicao.org>
Diff between DEoptimR versions 1.2-0 dated 2026-06-07 and 1.2-1 dated 2026-08-20
DESCRIPTION | 12 ++++++------ MD5 | 14 +++++++------- R/JDEoptim.R | 11 +++++++---- R/NCDEoptim.R | 15 +++++++++------ R/SPJDEoptim.R | 4 ++-- build/partial.rdb |binary inst/NEWS.Rd | 7 +++++++ man/SPJDEoptim.Rd | 2 +- 8 files changed, 39 insertions(+), 26 deletions(-)
Title: 'Constrained Quantile Regression with B-Splines'
Description: Quantile regression with B-splines under shape constraints.
The initial version with cubic splines is now augmented with splines
of degree 1 to 4. Constraints for degrees 3 (monotone) and 4
(monotone and convex) use the Karlin-Studden SOCP characterization
for the sign of the polynomial, while other constraints applied
at the knots are added as linear problems. The method for cubic
splines is described in 'Abbes (2026)' <doi:10.5281/zenodo.17427913>.
Other formulations are simple consequences of the other given
references. All B-spline and polynomial functions have been
rewritten for consistency. This package provides an original
B-spline library for conversion between PP-form and B-spline
representation, evaluation, differentiation, callable and
non-callable objects, print human readable pp forms, view basis,
all based on "De Boor\'s" theory. It also
extends to multiple knots to catch up singularities. This feature is
robust in the package including for constrained regression.
T [...truncated...]
Author: Alexandre Abbes [aut, cre]
Maintainer: Alexandre Abbes <alexandre.abbes@proton.me>
Diff between BsplineQuantReg versions 0.2.2 dated 2026-07-28 and 0.2.5 dated 2026-08-20
BsplineQuantReg-0.2.2/BsplineQuantReg/R/bspline_deriv.R |only BsplineQuantReg-0.2.5/BsplineQuantReg/DESCRIPTION | 28 BsplineQuantReg-0.2.5/BsplineQuantReg/MD5 | 93 + BsplineQuantReg-0.2.5/BsplineQuantReg/NAMESPACE | 31 BsplineQuantReg-0.2.5/BsplineQuantReg/NEWS | 30 BsplineQuantReg-0.2.5/BsplineQuantReg/R/bspline-base.R | 392 +++---- BsplineQuantReg-0.2.5/BsplineQuantReg/R/bspline-deriv.R |only BsplineQuantReg-0.2.5/BsplineQuantReg/R/bspline-eval.R | 541 ++++----- BsplineQuantReg-0.2.5/BsplineQuantReg/R/constraints.R | 16 BsplineQuantReg-0.2.5/BsplineQuantReg/R/cubic-regression.R | 212 ++- BsplineQuantReg-0.2.5/BsplineQuantReg/R/deriv-coeffs.R | 148 +- BsplineQuantReg-0.2.5/BsplineQuantReg/R/linear-regression.R | 78 + BsplineQuantReg-0.2.5/BsplineQuantReg/R/onLoad.R | 4 BsplineQuantReg-0.2.5/BsplineQuantReg/R/polynomial-utils.R | 548 +++++++++- BsplineQuantReg-0.2.5/BsplineQuantReg/R/quadratic-regression.R | 110 +- BsplineQuantReg-0.2.5/BsplineQuantReg/R/quantile-regression.R | 92 + BsplineQuantReg-0.2.5/BsplineQuantReg/R/quartic-regression.R | 126 +- BsplineQuantReg-0.2.5/BsplineQuantReg/R/test_bsqr.R | 210 ++- BsplineQuantReg-0.2.5/BsplineQuantReg/R/zzz.R |only BsplineQuantReg-0.2.5/BsplineQuantReg/README.md | 114 +- BsplineQuantReg-0.2.5/BsplineQuantReg/build/vignette.rds |only BsplineQuantReg-0.2.5/BsplineQuantReg/inst/doc |only BsplineQuantReg-0.2.5/BsplineQuantReg/man/Bspline_deriv.Rd | 2 BsplineQuantReg-0.2.5/BsplineQuantReg/man/Bsplinetopp.Rd | 3 BsplineQuantReg-0.2.5/BsplineQuantReg/man/SplineCubicQuant.Rd | 16 BsplineQuantReg-0.2.5/BsplineQuantReg/man/SplineLinearQuant.Rd | 10 BsplineQuantReg-0.2.5/BsplineQuantReg/man/SplineQuadraticQuant.Rd | 9 BsplineQuantReg-0.2.5/BsplineQuantReg/man/SplineQuarticQuant.Rd | 9 BsplineQuantReg-0.2.5/BsplineQuantReg/man/Spline_der_knot.Rd | 2 BsplineQuantReg-0.2.5/BsplineQuantReg/man/bspline_to_deriv_coeffs_cubic.Rd | 13 BsplineQuantReg-0.2.5/BsplineQuantReg/man/bspline_to_deriv_coeffs_lin.Rd | 4 BsplineQuantReg-0.2.5/BsplineQuantReg/man/bspline_to_deriv_coeffs_quart.Rd | 3 BsplineQuantReg-0.2.5/BsplineQuantReg/man/evalpp.Rd | 2 BsplineQuantReg-0.2.5/BsplineQuantReg/man/makpp.Rd | 8 BsplineQuantReg-0.2.5/BsplineQuantReg/man/print.callable_pp.Rd | 2 BsplineQuantReg-0.2.5/BsplineQuantReg/man/print.non_callable_pp.Rd | 2 BsplineQuantReg-0.2.5/BsplineQuantReg/man/quantile_spline.Rd | 8 BsplineQuantReg-0.2.5/BsplineQuantReg/man/setup_solver.Rd |only BsplineQuantReg-0.2.5/BsplineQuantReg/man/show_poly.Rd |only BsplineQuantReg-0.2.5/BsplineQuantReg/man/show_pp.Rd |only BsplineQuantReg-0.2.5/BsplineQuantReg/man/spline_eval.Rd | 2 BsplineQuantReg-0.2.5/BsplineQuantReg/man/view_basis.Rd | 19 BsplineQuantReg-0.2.5/BsplineQuantReg/vignettes |only 43 files changed, 1896 insertions(+), 991 deletions(-)
More information about BsplineQuantReg at CRAN
Permanent link
Title: Add Bio Tooltips to HTML Reports
Description: Provides lightweight helpers for adding gene and chemical
tooltips to 'R Markdown', 'Quarto', 'shiny', 'pkgdown', and other HTML outputs.
The package emits small HTML spans with module-specific data attributes
and attaches the browser-side 'bio-tooltips' JavaScript and CSS assets
through 'htmltools'. Entity lookup and rendering are handled in the
browser by 'bio-tooltips'; this package does not query biological
databases from R during package checks.
Author: Matthew J. Meier [aut, cre]
Maintainer: Matthew J. Meier <matthew.meier@hc-sc.gc.ca>
Diff between BioTooltipR versions 0.1.0 dated 2026-06-30 and 0.1.1 dated 2026-08-20
DESCRIPTION | 11 LICENSE | 4 MD5 | 108 +- NAMESPACE | 36 NEWS.md | 35 R/auto.R | 188 +-- R/columns.R | 244 ++-- R/dependencies.R | 530 +++++----- R/package.R | 16 R/plotly.R | 428 ++++---- R/spans.R | 228 ++-- R/tables.R | 266 ++--- R/utils.R | 226 ++-- README.md | 180 +-- build/vignette.rds |binary inst/WORDLIST | 60 - inst/doc/BioTooltipR.R | 58 - inst/doc/BioTooltipR.Rmd | 426 ++++---- inst/doc/BioTooltipR.html | 417 ++++--- inst/htmltools/bio-tooltips/LICENSE | 12 inst/htmltools/bio-tooltips/README.md | 34 inst/htmltools/bio-tooltips/SOURCE | 44 inst/htmltools/bio-tooltips/bio-tooltips.css | 2 inst/htmltools/bio-tooltips/bio-tooltips.global.js | 478 ++++----- inst/htmltools/d3/LICENSE | 26 inst/htmltools/d3/README.md | 8 inst/htmltools/d3/SOURCE | 34 inst/htmltools/d3/d3.min.js | 4 inst/htmltools/ideogram/LICENSE | 274 ++--- inst/htmltools/ideogram/README.md | 8 inst/htmltools/ideogram/SOURCE | 34 inst/htmltools/ideogram/ideogram.min.js | 4 inst/rmarkdown/templates/biotooltipr-report/skeleton/skeleton.Rmd | 54 - inst/rmarkdown/templates/biotooltipr-report/template.yaml | 4 man/BioTooltipR-package.Rd | 55 - man/auto_gene_tooltips.Rd | 80 - man/bio_tooltip_span.Rd | 92 - man/bio_tooltips_dependency.Rd | 50 man/bt_datatable.Rd | 66 - man/bt_deg_table.Rd | 76 - man/bt_kable.Rd | 82 - man/bt_plotly_gene_hover.Rd | 110 +- man/chem_column.Rd | 82 - man/chem_tt.Rd | 76 - man/gene_column.Rd | 54 - man/gene_tt.Rd | 60 - man/tooltip_column.Rd | 98 - man/use_bio_tooltips.Rd | 142 +- tests/testthat.R | 8 tests/testthat/test-columns.R | 36 tests/testthat/test-dependencies.R | 202 +-- tests/testthat/test-plotly.R | 145 +- tests/testthat/test-spans.R | 50 tests/testthat/test-tables.R | 24 vignettes/BioTooltipR.Rmd | 426 ++++---- 55 files changed, 3316 insertions(+), 3179 deletions(-)
Title: Bayesian Q Methodology: Exact Rank-Order Likelihood for Forced Q
Sorts
Description: A Bayesian analysis for Q methodology, alongside the classical
one. Models the forced Q sort as an ordered partition of the statements
through an exact rank-order likelihood (the design quotas fix the
partition margins, so the likelihood of the observed sorting event is
exact), fits it by a parameter-expanded Gibbs sampler in R with no
compiled code and a
convergence gate on rotation-invariant functionals, resolves
rotational ambiguity via the MatchAlign post-processing of Poworoznek
et al. (2025) <doi:10.1214/25-BA1544>, and returns the familiar Q
tables as posterior summaries: credible intervals for bounded
participant loadings, flag probabilities with an explicit unclassified
state, quota-respecting factor arrays, distinguishing and consensus
statements judged against a posterior critical difference and a
grid-width equivalence region, one posterior false-discovery rule for
all published claims, and a two-signal posterior-predictive workflow
for the number of factors.
Author: Raymond Dacosta Azadda [aut, cre] ,
Henry Ofoe Agbi-Kaiser [aut] ,
Hannah D. Robinson [aut] ,
AK-ACE Team [aut],
Karsten Hueffer [aut],
Taa'aii Peter [aut],
Stacy Rasmus [aut]
Maintainer: Raymond Dacosta Azadda <rdazadda@alaska.edu>
Diff between bayesqm versions 0.1.0 dated 2026-06-17 and 0.2.0 dated 2026-08-20
bayesqm-0.1.0/bayesqm/R/estimation.R |only bayesqm-0.1.0/bayesqm/R/factor_array.R |only bayesqm-0.1.0/bayesqm/R/hyperparameters.R |only bayesqm-0.1.0/bayesqm/R/loadings.R |only bayesqm-0.1.0/bayesqm/R/membership.R |only bayesqm-0.1.0/bayesqm/R/model_selection.R |only bayesqm-0.1.0/bayesqm/R/rename_factors.R |only bayesqm-0.1.0/bayesqm/R/zscores.R |only bayesqm-0.1.0/bayesqm/inst/stan |only bayesqm-0.1.0/bayesqm/man/autoplot.bayesqm_fit.Rd |only bayesqm-0.1.0/bayesqm/man/autoplot.bayesqm_run.Rd |only bayesqm-0.1.0/bayesqm/man/bayesqm-fit-accessors.Rd |only bayesqm-0.1.0/bayesqm/man/bayesqm-fit-methods.Rd |only bayesqm-0.1.0/bayesqm/man/bayesqm-membership.Rd |only bayesqm-0.1.0/bayesqm/man/compute_posterior_scalars.Rd |only bayesqm-0.1.0/bayesqm/man/critical_delta.Rd |only bayesqm-0.1.0/bayesqm/man/demo_run.Rd |only bayesqm-0.1.0/bayesqm/man/make_dominant_panel.Rd |only bayesqm-0.1.0/bayesqm/man/make_elpd_diff.Rd |only bayesqm-0.1.0/bayesqm/man/make_ppc_ridge.Rd |only bayesqm-0.1.0/bayesqm/man/plot.bayesqm_fit.Rd |only bayesqm-0.1.0/bayesqm/man/plot_dist_cons.Rd |only bayesqm-0.1.0/bayesqm/man/plot_elpd.Rd |only bayesqm-0.1.0/bayesqm/man/plot_hyper.Rd |only bayesqm-0.1.0/bayesqm/man/plot_membership.Rd |only bayesqm-0.1.0/bayesqm/man/plot_tucker.Rd |only bayesqm-0.1.0/bayesqm/man/plot_zscore_posterior.Rd |only bayesqm-0.1.0/bayesqm/man/run_bayes.Rd |only bayesqm-0.1.0/bayesqm/man/suggest_delta.Rd |only bayesqm-0.1.0/bayesqm/tests/testthat/_snaps |only bayesqm-0.1.0/bayesqm/tests/testthat/helper-stan.R |only bayesqm-0.1.0/bayesqm/tests/testthat/test-autoplot.R |only bayesqm-0.1.0/bayesqm/tests/testthat/test-factor-array.R |only bayesqm-0.1.0/bayesqm/tests/testthat/test-flagged-rename-plot.R |only bayesqm-0.1.0/bayesqm/tests/testthat/test-model-selection.R |only bayesqm-0.1.0/bayesqm/tests/testthat/test-numerical-pins.R |only bayesqm-0.1.0/bayesqm/tests/testthat/test-plots-snap.R |only bayesqm-0.1.0/bayesqm/tests/testthat/test-print-methods.R |only bayesqm-0.1.0/bayesqm/tests/testthat/test-stan-sampling.R |only bayesqm-0.2.0/bayesqm/DESCRIPTION | 65 bayesqm-0.2.0/bayesqm/MD5 | 222 +- bayesqm-0.2.0/bayesqm/NAMESPACE | 97 bayesqm-0.2.0/bayesqm/NEWS.md |only bayesqm-0.2.0/bayesqm/R/accessors.R | 330 +-- bayesqm-0.2.0/bayesqm/R/align.R |only bayesqm-0.2.0/bayesqm/R/autoplot.R | 629 ----- bayesqm-0.2.0/bayesqm/R/bayesqm-package.R | 121 - bayesqm-0.2.0/bayesqm/R/caption.R | 84 bayesqm-0.2.0/bayesqm/R/checks.R |only bayesqm-0.2.0/bayesqm/R/claims.R |only bayesqm-0.2.0/bayesqm/R/colors.R | 93 bayesqm-0.2.0/bayesqm/R/data.R |only bayesqm-0.2.0/bayesqm/R/demo_fit.R | 218 - bayesqm-0.2.0/bayesqm/R/deprecated.R |only bayesqm-0.2.0/bayesqm/R/fit_bayesian.R |only bayesqm-0.2.0/bayesqm/R/fit_object.R | 448 ---- bayesqm-0.2.0/bayesqm/R/ghk.R |only bayesqm-0.2.0/bayesqm/R/gibbs.R |only bayesqm-0.2.0/bayesqm/R/helpers.R | 5 bayesqm-0.2.0/bayesqm/R/import.R | 2 bayesqm-0.2.0/bayesqm/R/ladder.R |only bayesqm-0.2.0/bayesqm/R/plot_sorts.R |only bayesqm-0.2.0/bayesqm/R/plot_zscores.R |only bayesqm-0.2.0/bayesqm/R/plots.R | 1095 +++------- bayesqm-0.2.0/bayesqm/R/qsort_data.R | 25 bayesqm-0.2.0/bayesqm/R/rotation.R |only bayesqm-0.2.0/bayesqm/R/save_plot.R | 5 bayesqm-0.2.0/bayesqm/R/summaries.R |only bayesqm-0.2.0/bayesqm/R/utils.R | 8 bayesqm-0.2.0/bayesqm/R/zzz.R | 54 bayesqm-0.2.0/bayesqm/README.md | 416 +-- bayesqm-0.2.0/bayesqm/build/partial.rdb |binary bayesqm-0.2.0/bayesqm/build/vignette.rds |binary bayesqm-0.2.0/bayesqm/data |only bayesqm-0.2.0/bayesqm/inst/CITATION | 5 bayesqm-0.2.0/bayesqm/inst/WORDLIST | 145 - bayesqm-0.2.0/bayesqm/inst/doc/bayesqm-intro.R | 99 bayesqm-0.2.0/bayesqm/inst/doc/bayesqm-intro.Rmd | 354 +-- bayesqm-0.2.0/bayesqm/inst/doc/bayesqm-intro.html | 621 ++--- bayesqm-0.2.0/bayesqm/inst/doc/output-codebook.R |only bayesqm-0.2.0/bayesqm/inst/doc/output-codebook.Rmd |only bayesqm-0.2.0/bayesqm/inst/doc/output-codebook.html |only bayesqm-0.2.0/bayesqm/man/bayesqm-colors.Rd | 16 bayesqm-0.2.0/bayesqm/man/bayesqm-defunct.Rd |only bayesqm-0.2.0/bayesqm/man/bayesqm-package.Rd | 136 - bayesqm-0.2.0/bayesqm/man/caption_bayesqm.Rd | 19 bayesqm-0.2.0/bayesqm/man/check_fit.Rd |only bayesqm-0.2.0/bayesqm/man/check_persons.Rd |only bayesqm-0.2.0/bayesqm/man/claims.Rd |only bayesqm-0.2.0/bayesqm/man/coef.bayesqm_fit.Rd |only bayesqm-0.2.0/bayesqm/man/compute_factor_array.Rd | 30 bayesqm-0.2.0/bayesqm/man/compute_flags.Rd |only bayesqm-0.2.0/bayesqm/man/compute_loadings.Rd | 28 bayesqm-0.2.0/bayesqm/man/compute_qdc.Rd |only bayesqm-0.2.0/bayesqm/man/compute_zscores.Rd | 24 bayesqm-0.2.0/bayesqm/man/crib_sheet.Rd |only bayesqm-0.2.0/bayesqm/man/delta_grid.Rd |only bayesqm-0.2.0/bayesqm/man/demo_fit.Rd | 30 bayesqm-0.2.0/bayesqm/man/extend.Rd |only bayesqm-0.2.0/bayesqm/man/factor_characteristics.Rd |only bayesqm-0.2.0/bayesqm/man/figures |only bayesqm-0.2.0/bayesqm/man/fit_bayesian.Rd | 113 - bayesqm-0.2.0/bayesqm/man/fit_ladder.Rd |only bayesqm-0.2.0/bayesqm/man/fitted.bayesqm_fit.Rd |only bayesqm-0.2.0/bayesqm/man/flip_factor.Rd |only bayesqm-0.2.0/bayesqm/man/grizzly_sorts.Rd |only bayesqm-0.2.0/bayesqm/man/loglik_person.Rd |only bayesqm-0.2.0/bayesqm/man/loo_ladder.Rd |only bayesqm-0.2.0/bayesqm/man/matchalign.Rd | 36 bayesqm-0.2.0/bayesqm/man/obesity_sorts.Rd |only bayesqm-0.2.0/bayesqm/man/plot_choice_k.Rd |only bayesqm-0.2.0/bayesqm/man/plot_contrasts.Rd |only bayesqm-0.2.0/bayesqm/man/plot_convergence.Rd |only bayesqm-0.2.0/bayesqm/man/plot_factor_array.Rd |only bayesqm-0.2.0/bayesqm/man/plot_flags.Rd |only bayesqm-0.2.0/bayesqm/man/plot_loading_posterior.Rd | 25 bayesqm-0.2.0/bayesqm/man/plot_person_check.Rd |only bayesqm-0.2.0/bayesqm/man/plot_ppc.Rd | 20 bayesqm-0.2.0/bayesqm/man/plot_sorts.Rd |only bayesqm-0.2.0/bayesqm/man/plot_statement.Rd |only bayesqm-0.2.0/bayesqm/man/plot_zscores.Rd |only bayesqm-0.2.0/bayesqm/man/posterior_interval.Rd |only bayesqm-0.2.0/bayesqm/man/posterior_interval.bayesqm_fit.Rd | 4 bayesqm-0.2.0/bayesqm/man/prior_summary.Rd |only bayesqm-0.2.0/bayesqm/man/prior_summary.bayesqm_fit.Rd | 10 bayesqm-0.2.0/bayesqm/man/read_qsort.Rd | 2 bayesqm-0.2.0/bayesqm/man/rename_factors.Rd | 26 bayesqm-0.2.0/bayesqm/man/rotate_factors.Rd |only bayesqm-0.2.0/bayesqm/man/save_bayesqm_plot.Rd | 5 bayesqm-0.2.0/bayesqm/man/select_k.Rd |only bayesqm-0.2.0/bayesqm/man/sigma.bayesqm_fit.Rd |only bayesqm-0.2.0/bayesqm/tests/testthat/helper-fake-fit.R | 104 bayesqm-0.2.0/bayesqm/tests/testthat/test-accessors.R | 152 - bayesqm-0.2.0/bayesqm/tests/testthat/test-checks-ladder.R |only bayesqm-0.2.0/bayesqm/tests/testthat/test-colors.R | 29 bayesqm-0.2.0/bayesqm/tests/testthat/test-demo-and-data.R | 77 bayesqm-0.2.0/bayesqm/tests/testthat/test-deprecated.R |only bayesqm-0.2.0/bayesqm/tests/testthat/test-edge-cases.R | 106 bayesqm-0.2.0/bayesqm/tests/testthat/test-fit-bayesian.R |only bayesqm-0.2.0/bayesqm/tests/testthat/test-fit-object.R | 132 - bayesqm-0.2.0/bayesqm/tests/testthat/test-gibbs.R |only bayesqm-0.2.0/bayesqm/tests/testthat/test-matchalign.R | 141 - bayesqm-0.2.0/bayesqm/tests/testthat/test-plots.R | 360 --- bayesqm-0.2.0/bayesqm/tests/testthat/test-polish-utils.R | 100 bayesqm-0.2.0/bayesqm/tests/testthat/test-posterior-compat.R | 75 bayesqm-0.2.0/bayesqm/tests/testthat/test-rotation.R |only bayesqm-0.2.0/bayesqm/tests/testthat/test-summaries.R | 204 + bayesqm-0.2.0/bayesqm/vignettes/REFERENCES.bib | 71 bayesqm-0.2.0/bayesqm/vignettes/apa.csl |only bayesqm-0.2.0/bayesqm/vignettes/articles |only bayesqm-0.2.0/bayesqm/vignettes/bayesqm-intro.Rmd | 354 +-- bayesqm-0.2.0/bayesqm/vignettes/output-codebook.Rmd |only 152 files changed, 2846 insertions(+), 4724 deletions(-)
Title: Treatment Effect Estimation for Time-to-Event Data with
Intercurrent Events
Description: Analysis of treatment effects in clinical trials with time-to-event outcomes is complicated by intercurrent events. This package implements methods for estimating and inferring the cumulative incidence functions for time-to-event (TTE) outcomes with intercurrent events (ICE) under the five strategies outlined in the ICH E9 (R1) addendum, see Deng (2025) <doi:10.1002/sim.70091>. This package can be used for analyzing data from both randomized controlled trials and observational studies. In general, the data involve a primary outcome event and, potentially, an intercurrent event. Two data structures are allowed: competing risks, where only the time to the first event is recorded, and semicompeting risks, where the times to both the primary outcome event and intercurrent event (or censoring) are recorded. For estimation methods, users can choose nonparametric estimation (which does not use covariates) and semiparametrically efficient estimation.
Author: Yuhao Deng [aut],
Yi Zhou [cre]
Maintainer: Yi Zhou <yzhou@pku.edu.cn>
Diff between tteICE versions 1.1.4 dated 2026-03-16 and 1.1.5 dated 2026-08-20
DESCRIPTION | 12 - MD5 | 102 ++++++------ NAMESPACE | 61 ++++--- R/basic.R | 2 R/bshaz_tteICE.R | 2 R/coef_tteICE.R | 2 R/plot_ate.R | 2 R/plot_tteICE.R | 3 R/predict_tteICE.R | 2 R/print_tteICE.R | 2 R/scr_composite.R | 2 R/scr_natural_eff.R | 67 +++++--- R/scr_principal.R | 2 R/scr_removed.R | 2 R/scr_tteICE.R | 4 R/scr_whileon.R | 2 R/summary_tteICE.R | 2 R/surv_boot.R | 11 - R/surv_composite_eff.R | 33 ++-- R/surv_natural_eff.R | 49 ++++-- R/surv_principal_eff.R | 48 ++++-- R/surv_removed_eff.R | 48 ++++-- R/surv_treatment_eff.R | 33 ++-- R/surv_tteICE.R | 8 - R/surv_whileon_eff.R | 48 ++++-- R/tteICE.R | 5 R/zph_tteICE.R | 4 build/partial.rdb |binary inst/shiny/server_s1.R | 32 +++- inst/shiny/server_s2.R | 19 +- inst/shiny/server_s3.R | 18 +- inst/shiny/server_s4.R | 14 + inst/shiny/server_s5.R | 18 +- inst/shiny/server_s6.R | 17 +- inst/shiny/ui_data.R | 241 ++++++++++++++++++++++++++---- inst/shiny/www/style_cn_causal.css | 29 +-- inst/tteICE.pdf |binary man/bshaz.Rd | 36 ++-- man/bshaz.tteICE.Rd | 64 ++++---- man/coef.tteICE.Rd | 82 +++++----- man/plot.tteICE.Rd | 3 man/predict.tteICE.Rd | 124 +++++++-------- man/print.summary.tteICE.Rd | 42 ++--- man/print.tteICE.Rd | 2 man/scr.tteICE.Rd | 2 man/summary.tteICE.Rd | 100 ++++++------ man/surv.boot.Rd | 2 man/surv.tteICE.Rd | 6 man/tteICE-package.Rd | 116 +++++++------- man/tteICE.Rd | 295 ++++++++++++++++++------------------- man/zph.Rd | 40 ++--- man/zph.tteICE.Rd | 90 +++++------ 52 files changed, 1164 insertions(+), 786 deletions(-)
Title: Interaction Between R and REDCap
Description: Encapsulates functions to streamline calls from R to the REDCap
API. REDCap (Research Electronic Data CAPture) is a web application for
building and managing online surveys and databases developed at Vanderbilt
University. The Application Programming Interface (API) offers an avenue
to access and modify data programmatically, improving the capacity for
literate and reproducible programming.
Author: Will Beasley [aut, cre] ,
David Bard [ctb] ,
Thomas Wilson [ctb],
John J Aponte [ctb],
Rollie Parrish [ctb] ,
Benjamin Nutter [ctb],
Andrew Peters [ctb] ,
Hao Zhu [ctb] ,
Janosch Linkersdoerfer [ctb] ,
Jonathan Mang [ctb] ,
Felix Torres [ctb],
Philip [...truncated...]
Maintainer: Will Beasley <wibeasley@hotmail.com>
Diff between REDCapR versions 1.6.0 dated 2025-10-08 and 1.7.0 dated 2026-08-20
REDCapR-1.6.0/REDCapR/inst/misc/coph.credentials |only REDCapR-1.6.0/REDCapR/inst/misc/dev-2.credentials |only REDCapR-1.7.0/REDCapR/DESCRIPTION | 8 REDCapR-1.7.0/REDCapR/LICENSE | 4 REDCapR-1.7.0/REDCapR/MD5 | 775 +- REDCapR-1.7.0/REDCapR/NAMESPACE | 113 REDCapR-1.7.0/REDCapR/NEWS.md | 28 REDCapR-1.7.0/REDCapR/R/REDCapR-package.R | 132 REDCapR-1.7.0/REDCapR/R/constant.R | 461 - REDCapR-1.7.0/REDCapR/R/create-batch-glossary.R | 208 REDCapR-1.7.0/REDCapR/R/helpers-testing.R | 266 REDCapR-1.7.0/REDCapR/R/kernel-api.R | 241 REDCapR-1.7.0/REDCapR/R/metadata-utilities.R | 270 REDCapR-1.7.0/REDCapR/R/project-dag-write.R | 359 - REDCapR-1.7.0/REDCapR/R/project-delete-multiple-arm.R | 215 REDCapR-1.7.0/REDCapR/R/project-delete-single-arm.R | 219 REDCapR-1.7.0/REDCapR/R/project-simple.R | 327 - REDCapR-1.7.0/REDCapR/R/redcap-arm-export.R | 372 - REDCapR-1.7.0/REDCapR/R/redcap-column-sanitize.R | 128 REDCapR-1.7.0/REDCapR/R/redcap-dag-read.R | 335 - REDCapR-1.7.0/REDCapR/R/redcap-delete.R | 476 - REDCapR-1.7.0/REDCapR/R/redcap-event-instruments.R | 377 - REDCapR-1.7.0/REDCapR/R/redcap-event-read.R | 379 - REDCapR-1.7.0/REDCapR/R/redcap-file-download-oneshot.R | 522 - REDCapR-1.7.0/REDCapR/R/redcap-file-repo-list.R | 387 - REDCapR-1.7.0/REDCapR/R/redcap-file-upload-oneshot.R | 402 - REDCapR-1.7.0/REDCapR/R/redcap-instrument-download.R | 466 - REDCapR-1.7.0/REDCapR/R/redcap-instrument-repeating.R |only REDCapR-1.7.0/REDCapR/R/redcap-instruments.R | 345 - REDCapR-1.7.0/REDCapR/R/redcap-log-read.R | 445 - REDCapR-1.7.0/REDCapR/R/redcap-metadata-coltypes.R | 1014 +-- REDCapR-1.7.0/REDCapR/R/redcap-metadata-read.R | 439 - REDCapR-1.7.0/REDCapR/R/redcap-metadata-write.R | 315 - REDCapR-1.7.0/REDCapR/R/redcap-next-free-record-name.R | 286 REDCapR-1.7.0/REDCapR/R/redcap-project-info-read.R | 618 +- REDCapR-1.7.0/REDCapR/R/redcap-project.R | 266 REDCapR-1.7.0/REDCapR/R/redcap-read-eav-oneshot.R | 708 +- REDCapR-1.7.0/REDCapR/R/redcap-read-oneshot-eav.R | 815 +- REDCapR-1.7.0/REDCapR/R/redcap-read-oneshot.R | 823 +- REDCapR-1.7.0/REDCapR/R/redcap-read.R | 1244 ++-- REDCapR-1.7.0/REDCapR/R/redcap-report.R | 504 - REDCapR-1.7.0/REDCapR/R/redcap-survey-link-export-oneshot.R | 343 - REDCapR-1.7.0/REDCapR/R/redcap-users-export.R | 451 - REDCapR-1.7.0/REDCapR/R/redcap-variables.R | 359 - REDCapR-1.7.0/REDCapR/R/redcap-version.R | 223 REDCapR-1.7.0/REDCapR/R/redcap-write-oneshot.R | 400 - REDCapR-1.7.0/REDCapR/R/redcap-write.R | 426 - REDCapR-1.7.0/REDCapR/R/retrieve-credential.R | 796 +- REDCapR-1.7.0/REDCapR/R/sanitize-token.R | 196 REDCapR-1.7.0/REDCapR/R/skippers.R | 38 REDCapR-1.7.0/REDCapR/R/utilities.R | 235 REDCapR-1.7.0/REDCapR/R/validate.R | 822 +- REDCapR-1.7.0/REDCapR/README.md | 190 REDCapR-1.7.0/REDCapR/build/vignette.rds |binary REDCapR-1.7.0/REDCapR/inst/WORDLIST | 324 - REDCapR-1.7.0/REDCapR/inst/doc/BasicREDCapROperations.R | 186 REDCapR-1.7.0/REDCapR/inst/doc/BasicREDCapROperations.Rmd | 344 - REDCapR-1.7.0/REDCapR/inst/doc/BasicREDCapROperations.html | 1044 +-- REDCapR-1.7.0/REDCapR/inst/doc/SecurityDatabase.Rmd | 694 +- REDCapR-1.7.0/REDCapR/inst/doc/SecurityDatabase.html | 1438 ++-- REDCapR-1.7.0/REDCapR/inst/doc/TroubleshootingApiCalls.R | 38 REDCapR-1.7.0/REDCapR/inst/doc/TroubleshootingApiCalls.Rmd | 1068 +-- REDCapR-1.7.0/REDCapR/inst/doc/TroubleshootingApiCalls.html | 2112 +++--- REDCapR-1.7.0/REDCapR/inst/doc/advanced-redcapr-operations.R | 282 REDCapR-1.7.0/REDCapR/inst/doc/advanced-redcapr-operations.Rmd | 540 - REDCapR-1.7.0/REDCapR/inst/doc/advanced-redcapr-operations.html | 1192 +-- REDCapR-1.7.0/REDCapR/inst/doc/longitudinal-and-repeating.R | 254 REDCapR-1.7.0/REDCapR/inst/doc/longitudinal-and-repeating.Rmd | 852 +- REDCapR-1.7.0/REDCapR/inst/doc/longitudinal-and-repeating.html | 3080 +++++----- REDCapR-1.7.0/REDCapR/inst/doc/workflow-read.R | 212 REDCapR-1.7.0/REDCapR/inst/doc/workflow-read.Rmd | 866 +- REDCapR-1.7.0/REDCapR/inst/doc/workflow-read.html | 1421 ++-- REDCapR-1.7.0/REDCapR/inst/doc/workflow-write.R | 34 REDCapR-1.7.0/REDCapR/inst/doc/workflow-write.Rmd | 838 +- REDCapR-1.7.0/REDCapR/inst/doc/workflow-write.html | 1512 ++-- REDCapR-1.7.0/REDCapR/inst/misc/bad.credentials | 16 REDCapR-1.7.0/REDCapR/inst/misc/conflicting-rows.credentials | 16 REDCapR-1.7.0/REDCapR/inst/misc/example.credentials | 79 REDCapR-1.7.0/REDCapR/inst/misc/out-of-order.credentials | 16 REDCapR-1.7.0/REDCapR/inst/misc/plugin-redirection.yml | 46 REDCapR-1.7.0/REDCapR/inst/misc/project-redirection.yml | 209 REDCapR-1.7.0/REDCapR/inst/misc/skeleton.credentials | 38 REDCapR-1.7.0/REDCapR/inst/misc/validation-transformation.yml | 280 REDCapR-1.7.0/REDCapR/inst/misc/vignette.css | 72 REDCapR-1.7.0/REDCapR/inst/misc/zero-rows.credentials | 12 REDCapR-1.7.0/REDCapR/inst/test-data/project-color-boxes/Readme.md | 106 REDCapR-1.7.0/REDCapR/inst/test-data/project-color-boxes/data.csv | 8 REDCapR-1.7.0/REDCapR/inst/test-data/project-color-boxes/dictionary.csv | 6 REDCapR-1.7.0/REDCapR/inst/test-data/projects/README.md | 53 REDCapR-1.7.0/REDCapR/inst/test-data/projects/arm-multiple-delete/README.md | 14 REDCapR-1.7.0/REDCapR/inst/test-data/projects/arm-multiple-delete/arm.csv | 8 REDCapR-1.7.0/REDCapR/inst/test-data/projects/arm-multiple-delete/data-old.csv | 114 REDCapR-1.7.0/REDCapR/inst/test-data/projects/arm-multiple-delete/data.csv | 122 REDCapR-1.7.0/REDCapR/inst/test-data/projects/arm-multiple-delete/dictionary.csv | 8 REDCapR-1.7.0/REDCapR/inst/test-data/projects/arm-multiple-delete/event.csv | 6 REDCapR-1.7.0/REDCapR/inst/test-data/projects/arm-single-delete/README.md | 14 REDCapR-1.7.0/REDCapR/inst/test-data/projects/arm-single-delete/data-old.csv | 34 REDCapR-1.7.0/REDCapR/inst/test-data/projects/arm-single-delete/data.csv | 42 REDCapR-1.7.0/REDCapR/inst/test-data/projects/arm-single-delete/dictionary.csv | 8 REDCapR-1.7.0/REDCapR/inst/test-data/projects/arm-single-longitudinal/arm.csv | 2 REDCapR-1.7.0/REDCapR/inst/test-data/projects/arm-single-longitudinal/data.csv | 20 REDCapR-1.7.0/REDCapR/inst/test-data/projects/arm-single-longitudinal/dictionary.csv | 10 REDCapR-1.7.0/REDCapR/inst/test-data/projects/arm-single-longitudinal/event.csv | 6 REDCapR-1.7.0/REDCapR/inst/test-data/projects/blank-for-gray-status/README.md | 48 REDCapR-1.7.0/REDCapR/inst/test-data/projects/blank-for-gray-status/data.csv | 14 REDCapR-1.7.0/REDCapR/inst/test-data/projects/blank-for-gray-status/dictionary.csv | 36 REDCapR-1.7.0/REDCapR/inst/test-data/projects/checkboxes-1/data.csv | 10 REDCapR-1.7.0/REDCapR/inst/test-data/projects/checkboxes-1/dictionary.csv | 10 REDCapR-1.7.0/REDCapR/inst/test-data/projects/clinical-trial-1/README.md | 12 REDCapR-1.7.0/REDCapR/inst/test-data/projects/dag-write/README.md | 24 REDCapR-1.7.0/REDCapR/inst/test-data/projects/dag-write/data.csv | 8 REDCapR-1.7.0/REDCapR/inst/test-data/projects/dag-write/dictionary.csv | 32 REDCapR-1.7.0/REDCapR/inst/test-data/projects/dag/README.md | 16 REDCapR-1.7.0/REDCapR/inst/test-data/projects/decimal-comma-and-dot/data.csv | 10 REDCapR-1.7.0/REDCapR/inst/test-data/projects/decimal-comma-and-dot/dictionary.csv | 18 REDCapR-1.7.0/REDCapR/inst/test-data/projects/decimal-comma-and-dot/metadata.csv | 18 REDCapR-1.7.0/REDCapR/inst/test-data/projects/decimal-comma-and-dot/redcapr-specific/default-mismatched.R | 12 REDCapR-1.7.0/REDCapR/inst/test-data/projects/decimal-comma/data.csv | 10 REDCapR-1.7.0/REDCapR/inst/test-data/projects/decimal-comma/dictionay.csv | 12 REDCapR-1.7.0/REDCapR/inst/test-data/projects/decimal-comma/redcapr-specific/default-mismatched.R | 12 REDCapR-1.7.0/REDCapR/inst/test-data/projects/decimal-comma/redcapr-specific/set-locale.R | 10 REDCapR-1.7.0/REDCapR/inst/test-data/projects/decimal-dot/data.csv | 10 REDCapR-1.7.0/REDCapR/inst/test-data/projects/decimal-dot/dictionary.csv | 12 REDCapR-1.7.0/REDCapR/inst/test-data/projects/decimal-dot/redcapr-specific/set-locale.R | 10 REDCapR-1.7.0/REDCapR/inst/test-data/projects/file-repo/README.md | 32 REDCapR-1.7.0/REDCapR/inst/test-data/projects/file-repo/data.csv | 6 REDCapR-1.7.0/REDCapR/inst/test-data/projects/file-repo/dictionary.csv | 12 REDCapR-1.7.0/REDCapR/inst/test-data/projects/longitudinal-with-repeating-instrument |only REDCapR-1.7.0/REDCapR/inst/test-data/projects/longitudinal/arm.csv | 4 REDCapR-1.7.0/REDCapR/inst/test-data/projects/longitudinal/data.csv | 38 REDCapR-1.7.0/REDCapR/inst/test-data/projects/longitudinal/dictionary.csv | 192 REDCapR-1.7.0/REDCapR/inst/test-data/projects/longitudinal/event.csv | 26 REDCapR-1.7.0/REDCapR/inst/test-data/projects/longitudinal/expected/default.R | 398 - REDCapR-1.7.0/REDCapR/inst/test-data/projects/longitudinal/expected/dummy.R | 4 REDCapR-1.7.0/REDCapR/inst/test-data/projects/longitudinal/expected/filter-character.R | 68 REDCapR-1.7.0/REDCapR/inst/test-data/projects/longitudinal/expected/filter-numeric.R | 98 REDCapR-1.7.0/REDCapR/inst/test-data/projects/longitudinal/expected/so-example-data-frame-retrieval.R | 4 REDCapR-1.7.0/REDCapR/inst/test-data/projects/metadata-write/data.csv | 12 REDCapR-1.7.0/REDCapR/inst/test-data/projects/metadata-write/dictionary.csv | 34 REDCapR-1.7.0/REDCapR/inst/test-data/projects/repeating-instruments-sparse/data.csv | 20 REDCapR-1.7.0/REDCapR/inst/test-data/projects/repeating-instruments-sparse/dictionary.csv | 24 REDCapR-1.7.0/REDCapR/inst/test-data/projects/russian/data.csv | 8 REDCapR-1.7.0/REDCapR/inst/test-data/projects/simple-write/README.md | 10 REDCapR-1.7.0/REDCapR/inst/test-data/projects/simple/README.md | 64 REDCapR-1.7.0/REDCapR/inst/test-data/projects/simple/data.csv | 32 REDCapR-1.7.0/REDCapR/inst/test-data/projects/simple/dictionary.csv | 34 REDCapR-1.7.0/REDCapR/inst/test-data/projects/simple/metadata.csv | 34 REDCapR-1.7.0/REDCapR/inst/test-data/projects/simple/project-old.xml | 1082 +-- REDCapR-1.7.0/REDCapR/inst/test-data/projects/super-wide-3/README.md | 44 REDCapR-1.7.0/REDCapR/inst/test-data/projects/super-wide-3/generate-project.R | 212 REDCapR-1.7.0/REDCapR/inst/test-data/projects/survey/README.md | 42 REDCapR-1.7.0/REDCapR/inst/test-data/projects/survey/expected/default.R | 30 REDCapR-1.7.0/REDCapR/inst/test-data/projects/survey/expected/so-example-data-frame-retrieval.R | 4 REDCapR-1.7.0/REDCapR/inst/test-data/projects/validation-types-1/data.csv | 4 REDCapR-1.7.0/REDCapR/inst/test-data/projects/validation-types-1/dictionary.csv | 102 REDCapR-1.7.0/REDCapR/inst/test-data/projects/vignette-repeating/data.csv | 36 REDCapR-1.7.0/REDCapR/inst/test-data/projects/vignette-repeating/dictionary.csv | 20 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/delete/multiple-arm-four-records.R | 70 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/delete/single-arm-four-records.R | 14 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/event-instruments/1-arm.R | 16 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/event-instruments/2-arms-retrieve-both-arms.R | 48 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/event-instruments/2-arms-retrieve-only-arm-1.R | 34 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/event-instruments/2-arms-retrieve-only-arm-2.R | 28 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/event-instruments/no-arms.R | 2 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/file-repo-list-oneshot/bad-folder-id.R | 2 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/file-repo-list-oneshot/default.R | 23 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/file-repo-list-oneshot/first-subdirectory.R | 17 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/instrument-repeating |only REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/instruments/default.R | 12 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/log-read/2024-10-11.R | 62 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/metadata-coltypes/longitudinal.R | 254 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/metadata-coltypes/problematic-dictionary.R | 18 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/metadata-coltypes/repeating-instruments.R | 34 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/metadata-coltypes/simple.R | 54 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/metadata-coltypes/validation-types.R | 108 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/metadata-read/normal-filter-form-all-three.R | 96 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/metadata-read/normal-filter-form-demographics.R | 64 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/metadata-read/normal-filter-form-health.R | 50 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/metadata-read/normal-filter-form-race_and_ethnicity.R | 42 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/metadata-read/normal.R | 120 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/metadata-read/super-wide-3-subset.R | 96 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/project-info-read/all-test-projects.R | 303 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/project-info-read/chicago.R | 87 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/project-info-read/simple.R | 85 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-batch-plumbing/longitudinal.R | 72 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-batch-plumbing/repeated.R | 50 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-batch-plumbing/simple.R | 14 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-batch-repeating-sparse/default.R | 28 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-batch-simple/blank-for-gray-false.R | 50 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-batch-simple/blank-for-gray-true.R | 52 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-batch-simple/col_types.R | 48 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-batch-simple/default.R | 46 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-batch-simple/error-bad-token.R | 104 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-batch-simple/export_checkbox_label.R | 62 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-batch-simple/filter-character.R | 18 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-batch-simple/filter-numeric.R | 26 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-batch-simple/label-and-dag-one-single-batch.R | 64 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-batch-simple/label-and-dag-three-tiny-batches.R | 64 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-batch-simple/label-header.R | 54 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-batch-simple/label.R | 62 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-batch-simple/na.R | 104 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-batch-simple/raw-and-dag.R | 48 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-batch-simple/raw.R | 46 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-batch-simple/specify-fields-without-record-id.R | 12 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-batch-simple/specify-fields-zero-length.R | 46 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-batch-simple/specify-fields.R | 8 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-batch-simple/specify-forms-only-1st.R | 24 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-batch-simple/specify-forms-without-record-id.R | 18 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-batch-simple/specify-forms.R | 32 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-batch-simple/specify-records-zero-length.R | 46 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-batch-simple/specify-records.R | 34 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-clinical-trial/default.R | 1998 +++--- REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-dag/assigned-to-dag-a.R | 22 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-dag/no-assignment.R | 22 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-eav-oneshot/blank-for-gray-false.R | 94 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-eav-oneshot/blank-for-gray-true.R | 94 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-eav-oneshot/default.R | 90 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-eav-oneshot/filter-character.R | 22 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-eav-oneshot/filter-numeric.R | 38 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-eav-oneshot/specify-fields-zero-length.R | 90 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-eav-oneshot/specify-fields.R | 20 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-eav-oneshot/specify-forms.R | 66 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-eav-oneshot/specify-records-zero-length.R | 90 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-eav-oneshot/specify-records.R | 56 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot-eav/blank-for-gray-false.R | 44 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot-eav/blank-for-gray-true.R | 44 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot-eav/default.R | 42 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot-eav/filter-character.R | 14 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot-eav/filter-numeric.R | 24 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot-eav/label-and-dag.R | 56 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot-eav/label-header.R | 42 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot-eav/raw-and-dag.R | 50 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot-eav/raw.R | 42 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot-eav/specify-forms.R | 30 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot/blank-for-gray-false.R | 50 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot/blank-for-gray-true.R | 106 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot/col_types.R | 102 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot/default.R | 100 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot/export_checkbox_label.R | 114 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot/filter-character.R | 70 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot/filter-numeric.R | 80 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot/force-character-type.R | 102 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot/label-and-dag.R | 118 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot/label-header.R | 106 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot/label.R | 114 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot/na.R | 104 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot/raw-and-dag.R | 104 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot/raw.R | 100 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot/specify-fields-without-record-id.R | 22 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot/specify-fields-zero-length.R | 46 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot/specify-fields.R | 8 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot/specify-forms-only-1st.R | 48 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot/specify-forms-only-2nd.R | 34 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot/specify-forms-without-record-id.R | 32 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot/specify-forms.R | 74 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot/specify-records-zero-length.R | 46 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/read-oneshot/specify-records.R | 34 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/report/col_types.R | 24 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/report/default.R | 26 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/report/export_checkbox_label.R | 30 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/report/force-character-type.R | 26 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/report/label-header.R | 106 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/report/raw.R | 24 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/test-project/read-insert-and-update.R | 40 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/users-export/with-dags--user.R | 27 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/users-export/with-dags--user_form.R | 8 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/users-export/without-dags--user.R | 29 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/users-export/without-dags--user_form.R | 12 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/variables/default.R | 36 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/write-batch/default.R | 96 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/write-batch/update-one-field.R | 92 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/write-batch/update-two-fields.R | 92 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/write-dag/after.R | 16 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/write-dag/before.R | 14 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/write-oneshot/default.R | 96 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/write-oneshot/one-field.R | 92 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/write-oneshot/overwrite-true.R | 90 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/write-oneshot/two-fields.R | 92 REDCapR-1.7.0/REDCapR/man/REDCapR-package.Rd | 217 REDCapR-1.7.0/REDCapR/man/collapse_vector.Rd | 60 REDCapR-1.7.0/REDCapR/man/constant.Rd | 234 REDCapR-1.7.0/REDCapR/man/create_batch_glossary.Rd | 122 REDCapR-1.7.0/REDCapR/man/figures/logo.svg | 278 REDCapR-1.7.0/REDCapR/man/kernel_api.Rd | 152 REDCapR-1.7.0/REDCapR/man/metadata_utilities.Rd | 188 REDCapR-1.7.0/REDCapR/man/redcap_arm_export.Rd | 178 REDCapR-1.7.0/REDCapR/man/redcap_column_sanitize.Rd | 112 REDCapR-1.7.0/REDCapR/man/redcap_dag_read.Rd | 169 REDCapR-1.7.0/REDCapR/man/redcap_delete.Rd | 271 REDCapR-1.7.0/REDCapR/man/redcap_event_instruments.Rd | 216 REDCapR-1.7.0/REDCapR/man/redcap_event_read.Rd | 194 REDCapR-1.7.0/REDCapR/man/redcap_file_download_oneshot.Rd | 292 REDCapR-1.7.0/REDCapR/man/redcap_file_repo_list_oneshot.Rd | 212 REDCapR-1.7.0/REDCapR/man/redcap_file_upload_oneshot.Rd | 266 REDCapR-1.7.0/REDCapR/man/redcap_instrument_download.Rd | 276 REDCapR-1.7.0/REDCapR/man/redcap_instrument_repeating.Rd |only REDCapR-1.7.0/REDCapR/man/redcap_instruments.Rd | 186 REDCapR-1.7.0/REDCapR/man/redcap_log_read.Rd | 259 REDCapR-1.7.0/REDCapR/man/redcap_metadata_coltypes.Rd | 346 - REDCapR-1.7.0/REDCapR/man/redcap_metadata_read.Rd | 194 REDCapR-1.7.0/REDCapR/man/redcap_metadata_write.Rd | 200 REDCapR-1.7.0/REDCapR/man/redcap_next_free_record_name.Rd | 172 REDCapR-1.7.0/REDCapR/man/redcap_project.Rd | 170 REDCapR-1.7.0/REDCapR/man/redcap_project_info_read.Rd | 329 - REDCapR-1.7.0/REDCapR/man/redcap_read.Rd | 651 +- REDCapR-1.7.0/REDCapR/man/redcap_read_eav_oneshot.Rd | 350 - REDCapR-1.7.0/REDCapR/man/redcap_read_oneshot.Rd | 514 - REDCapR-1.7.0/REDCapR/man/redcap_read_oneshot_eav.Rd | 360 - REDCapR-1.7.0/REDCapR/man/redcap_report.Rd | 308 - REDCapR-1.7.0/REDCapR/man/redcap_survey_link_export_oneshot.Rd | 220 REDCapR-1.7.0/REDCapR/man/redcap_users_export.Rd | 157 REDCapR-1.7.0/REDCapR/man/redcap_variables.Rd | 178 REDCapR-1.7.0/REDCapR/man/redcap_version.Rd | 116 REDCapR-1.7.0/REDCapR/man/redcap_write.Rd | 290 REDCapR-1.7.0/REDCapR/man/redcap_write_oneshot.Rd | 250 REDCapR-1.7.0/REDCapR/man/replace_nas_with_explicit.Rd | 98 REDCapR-1.7.0/REDCapR/man/retrieve_credential.Rd | 288 REDCapR-1.7.0/REDCapR/man/sanitize_token.Rd | 146 REDCapR-1.7.0/REDCapR/man/to_api_array.Rd | 52 REDCapR-1.7.0/REDCapR/man/validate.Rd | 310 - REDCapR-1.7.0/REDCapR/tests/manual/README.md | 8 REDCapR-1.7.0/REDCapR/tests/manual/test-could-not-connect-rate.R | 114 REDCapR-1.7.0/REDCapR/tests/manual/test-stress-test-serial.R | 271 REDCapR-1.7.0/REDCapR/tests/spelling.R | 14 REDCapR-1.7.0/REDCapR/tests/test-all.R | 32 REDCapR-1.7.0/REDCapR/tests/testthat/test-arm-export.R | 260 REDCapR-1.7.0/REDCapR/tests/testthat/test-column-sanitize.R | 70 REDCapR-1.7.0/REDCapR/tests/testthat/test-constant.R | 196 REDCapR-1.7.0/REDCapR/tests/testthat/test-create-batch-glossary.R | 198 REDCapR-1.7.0/REDCapR/tests/testthat/test-create-credential-local.R | 74 REDCapR-1.7.0/REDCapR/tests/testthat/test-dag-read.R | 162 REDCapR-1.7.0/REDCapR/tests/testthat/test-delete.R | 406 - REDCapR-1.7.0/REDCapR/tests/testthat/test-event-instruments.R | 372 - REDCapR-1.7.0/REDCapR/tests/testthat/test-event-read.R | 356 - REDCapR-1.7.0/REDCapR/tests/testthat/test-file-oneshot.R | 1166 +-- REDCapR-1.7.0/REDCapR/tests/testthat/test-file-repo-list-oneshot.R | 328 - REDCapR-1.7.0/REDCapR/tests/testthat/test-instrument-repeating.R |only REDCapR-1.7.0/REDCapR/tests/testthat/test-instruments-metadata.R | 164 REDCapR-1.7.0/REDCapR/tests/testthat/test-instruments.R | 188 REDCapR-1.7.0/REDCapR/tests/testthat/test-log-read.R | 100 REDCapR-1.7.0/REDCapR/tests/testthat/test-metadata-coltypes.R | 460 - REDCapR-1.7.0/REDCapR/tests/testthat/test-metadata-read.R | 642 +- REDCapR-1.7.0/REDCapR/tests/testthat/test-metadata-utilities.R | 380 - REDCapR-1.7.0/REDCapR/tests/testthat/test-metadata-write.R | 110 REDCapR-1.7.0/REDCapR/tests/testthat/test-next-free-record-name.R | 188 REDCapR-1.7.0/REDCapR/tests/testthat/test-project-info-read.R | 236 REDCapR-1.7.0/REDCapR/tests/testthat/test-project.R | 158 REDCapR-1.7.0/REDCapR/tests/testthat/test-read-batch-longitudinal.R | 390 - REDCapR-1.7.0/REDCapR/tests/testthat/test-read-batch-plumbing.R | 190 REDCapR-1.7.0/REDCapR/tests/testthat/test-read-batch-repeating-sparse.R | 246 REDCapR-1.7.0/REDCapR/tests/testthat/test-read-batch-simple.R | 1800 ++--- REDCapR-1.7.0/REDCapR/tests/testthat/test-read-batch-survey.R | 228 REDCapR-1.7.0/REDCapR/tests/testthat/test-read-clinical-trial.R | 86 REDCapR-1.7.0/REDCapR/tests/testthat/test-read-dag.R | 90 REDCapR-1.7.0/REDCapR/tests/testthat/test-read-decimal-comma.R | 232 REDCapR-1.7.0/REDCapR/tests/testthat/test-read-decimal-dot.R | 176 REDCapR-1.7.0/REDCapR/tests/testthat/test-read-eav-oneshot.R | 706 +- REDCapR-1.7.0/REDCapR/tests/testthat/test-read-errors.R | 184 REDCapR-1.7.0/REDCapR/tests/testthat/test-read-oneshot-eav.R | 698 +- REDCapR-1.7.0/REDCapR/tests/testthat/test-read-oneshot.R | 1542 ++--- REDCapR-1.7.0/REDCapR/tests/testthat/test-read-russian.R | 88 REDCapR-1.7.0/REDCapR/tests/testthat/test-read-superwide.R | 294 REDCapR-1.7.0/REDCapR/tests/testthat/test-report.R | 346 - REDCapR-1.7.0/REDCapR/tests/testthat/test-retrieve-credential-local.R | 346 - REDCapR-1.7.0/REDCapR/tests/testthat/test-retrieve-credential-mssql.R | 332 - REDCapR-1.7.0/REDCapR/tests/testthat/test-sanitize.R | 146 REDCapR-1.7.0/REDCapR/tests/testthat/test-skippers.R | 22 REDCapR-1.7.0/REDCapR/tests/testthat/test-survey-link-export-oneshot.R | 134 REDCapR-1.7.0/REDCapR/tests/testthat/test-users-export.R | 286 REDCapR-1.7.0/REDCapR/tests/testthat/test-utilities-collapse_vector.R | 40 REDCapR-1.7.0/REDCapR/tests/testthat/test-utilities-replace_nas_with_explicit.R | 160 REDCapR-1.7.0/REDCapR/tests/testthat/test-validate-field-names.R | 105 REDCapR-1.7.0/REDCapR/tests/testthat/test-validate-no-logical.R | 160 REDCapR-1.7.0/REDCapR/tests/testthat/test-validate-record-id-name.R | 78 REDCapR-1.7.0/REDCapR/tests/testthat/test-validate-repeat.R | 66 REDCapR-1.7.0/REDCapR/tests/testthat/test-validate-uniqueness.R | 220 REDCapR-1.7.0/REDCapR/tests/testthat/test-validate.R | 192 REDCapR-1.7.0/REDCapR/tests/testthat/test-variables.R | 186 REDCapR-1.7.0/REDCapR/tests/testthat/test-version.R | 90 REDCapR-1.7.0/REDCapR/tests/testthat/test-write-batch.R | 416 - REDCapR-1.7.0/REDCapR/tests/testthat/test-write-dag.R | 428 - REDCapR-1.7.0/REDCapR/tests/testthat/test-write-error.R | 298 REDCapR-1.7.0/REDCapR/tests/testthat/test-write-oneshot.R | 564 - REDCapR-1.7.0/REDCapR/tests/testthat/test-write-serialization.R |only REDCapR-1.7.0/REDCapR/vignettes/BasicREDCapROperations.Rmd | 344 - REDCapR-1.7.0/REDCapR/vignettes/SecurityDatabase.Rmd | 694 +- REDCapR-1.7.0/REDCapR/vignettes/TroubleshootingApiCalls.Rmd | 1068 +-- REDCapR-1.7.0/REDCapR/vignettes/advanced-redcapr-operations.Rmd | 540 - REDCapR-1.7.0/REDCapR/vignettes/longitudinal-and-repeating.Rmd | 852 +- REDCapR-1.7.0/REDCapR/vignettes/workflow-read.Rmd | 866 +- REDCapR-1.7.0/REDCapR/vignettes/workflow-write.Rmd | 838 +- 391 files changed, 42356 insertions(+), 42029 deletions(-)
Title: Perform Phylogenetic Path Analysis
Description: A comprehensive and easy to use R implementation of confirmatory
phylogenetic path analysis as described by Von Hardenberg and Gonzalez-Voyer
(2012) <doi:10.1111/j.1558-5646.2012.01790.x>. Note that the required
package 'ggm' depends on 'graph' from Bioconductor, which is not installed
automatically; the simplest route is install.packages("BiocManager");
BiocManager::install("phylopath").
Author: Wouter van der Bijl [aut, cre]
Maintainer: Wouter van der Bijl <wouter@zoology.ubc.ca>
Diff between phylopath versions 1.3.1 dated 2025-09-06 and 1.4.0 dated 2026-08-20
DESCRIPTION | 20 - MD5 | 74 +++-- NAMESPACE | 5 NEWS.md | 235 +++++++++++++---- R/DAG.R | 205 ++++++++++++++ R/internal.R | 373 +++++++++++++++++++++++---- R/phylopath.R | 99 ++++--- R/print_and_plot.R | 219 ++++++++++----- build/vignette.rds |binary inst/doc/binary_models.R | 8 inst/doc/binary_models.Rmd | 29 +- inst/doc/binary_models.html | 120 +++++--- inst/doc/intro_to_phylopath.R | 24 - inst/doc/intro_to_phylopath.Rmd | 30 +- inst/doc/intro_to_phylopath.html | 79 ++--- man/as.data.frame.fitted_DAG.Rd |only man/average.Rd | 3 man/average_DAGs.Rd | 3 man/best.Rd | 3 man/choice.Rd | 3 man/coef.fitted_DAG.Rd |only man/est_DAG.Rd | 52 +++ man/figures/unnamed-chunk-2-1.png |binary man/figures/unnamed-chunk-3-1.png |binary man/plot.DAG.Rd | 2 man/plot.fitted_DAG.Rd | 2 man/plot.phylopath_summary.Rd |only man/plot_model_set.Rd | 2 tests/testthat/helper-fixtures.R |only tests/testthat/test-as_data_frame.R |only tests/testthat/test-average_DAGs.R |only tests/testthat/test-basis_set.R |only tests/testthat/test-check_models_data_tree.R | 286 ++++++++++++-------- tests/testthat/test-consensus_order.R |only tests/testthat/test-dag.R | 76 +++-- tests/testthat/test-define_model_set.R | 69 +++- tests/testthat/test-est_DAG.R |only tests/testthat/test-extractors.R |only tests/testthat/test-internals.R |only tests/testthat/test-phylo_path.R |only tests/testthat/test-plots.R |only tests/testthat/test-print_fitted_DAG.R |only tests/testthat/test-statistics.R |only tests/testthat/test-summary.R |only vignettes/binary_models.Rmd | 29 +- vignettes/intro_to_phylopath.Rmd | 30 +- 46 files changed, 1498 insertions(+), 582 deletions(-)
Title: Explainable Outlier Detection Through Decision Tree Conditioning
Description: Outlier detection method that flags suspicious values within observations,
constrasting them against the normal values in a user-readable format, potentially
describing conditions within the data that make a given outlier more rare.
Full procedure is described in Cortes (2020) <doi:10.48550/arXiv.2001.00636>.
Loosely based on the 'GritBot' <https://www.rulequest.com/gritbot-info.html> software.
Author: David Cortes [aut, cre]
Maintainer: David Cortes <david.cortes.rivera@gmail.com>
Diff between outliertree versions 1.10.0-1 dated 2026-03-05 and 1.10.0-2 dated 2026-08-20
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- configure | 26 +++++++++++++------------- configure.ac | 2 +- inst/doc/Introducing_OutlierTree.html | 4 ++-- src/fit_model.cpp | 4 ++-- 6 files changed, 26 insertions(+), 26 deletions(-)
Title: Unified Algorithm for Non-Convex Penalized Estimation for
Generalized Linear Models
Description: An efficient unified nonconvex penalized estimation algorithm for
Gaussian (linear), binomial Logit (logistic), Poisson, multinomial Logit,
and Cox proportional hazard regression models.
The unified algorithm is implemented based on the convex concave procedure and
the algorithm can be applied to most of the existing nonconvex penalties.
The algorithm also supports convex penalty:
least absolute shrinkage and selection operator (LASSO).
Supported nonconvex penalties include
smoothly clipped absolute deviation (SCAD),
minimax concave penalty (MCP), truncated LASSO penalty (TLP),
clipped LASSO (CLASSO), sparse ridge (SRIDGE),
modified bridge (MBRIDGE) and modified log (MLOG).
For high-dimensional data (data set with many variables),
the algorithm selects relevant variables producing a parsimonious regression model.
Kim, D., Lee, S. and Kwon, S. (2021) <doi:10.32614/RJ-2021-003>,
Lee, S., Kwon, S. and Kim, Y. (2016) <doi:10.1016/j.csda.2015.08.019>,
Kwon, S., Lee, S. and Kim, [...truncated...]
Author: Dongshin Kim [aut, cre, cph],
Sunghoon Kwon [aut, cph],
Sangin Lee [aut, cph]
Maintainer: Dongshin Kim <dongshin.kim@outlook.com>
This is a re-admission after prior archival of version 1.0.0 dated 2018-11-17
Diff between ncpen versions 1.0.0 dated 2018-11-17 and 1.0.1 dated 2026-08-20
DESCRIPTION | 20 +- MD5 | 79 ++++---- NAMESPACE | 30 +-- NEWS.md | 23 -- R/ncpen_cpp_wrap.R | 7 R/ncpen_package.R | 5 R/ncpen_util.R | 5 R/ncpen_ux.R | 2 README.md | 8 build |only man/coef.cv.ncpen.Rd | 104 +++++------ man/coef.ncpen.Rd | 82 ++++---- man/control.ncpen.Rd | 282 ++++++++++++++++-------------- man/cv.ncpen.Rd | 323 ++++++++++++++++++----------------- man/cv.ncpen.reg.Rd | 333 +++++++++++++++++++----------------- man/excluded.Rd | 42 ++-- man/fold.cv.ncpen.Rd | 131 +++++++------- man/gic.ncpen.Rd | 134 +++++++------- man/interact.data.Rd | 74 ++++---- man/make.ncpen.data.Rd | 60 +++--- man/native_cpp_ncpen_fun_.Rd | 143 ++++++++------- man/native_cpp_nr_fun_.Rd | 50 ++--- man/native_cpp_obj_fun_.Rd | 46 ++--- man/native_cpp_obj_grad_fun_.Rd | 46 ++--- man/native_cpp_obj_hess_fun_.Rd | 46 ++--- man/native_cpp_p_ncpen_fun_.Rd | 123 +++++++------ man/native_cpp_pen_fun_.Rd | 50 ++--- man/native_cpp_pen_grad_fun_.Rd | 50 ++--- man/native_cpp_qlasso_fun_.Rd | 97 +++++----- man/native_cpp_set_dev_mode_.Rd | 34 +-- man/ncpen-package.Rd | 99 +++++----- man/ncpen.Rd | 367 +++++++++++++++++++++------------------- man/ncpen.reg.Rd | 356 ++++++++++++++++++++------------------ man/plot.cv.ncpen.Rd | 81 ++++---- man/plot.ncpen.Rd | 89 ++++----- man/power.data.Rd | 56 +++--- man/predict.ncpen.Rd | 138 +++++++-------- man/sam.gen.ncpen.Rd | 135 +++++++------- man/same.base.Rd | 42 ++-- man/to.indicators.Rd | 86 ++++----- man/to.ncpen.x.mat.Rd | 105 +++++------ 41 files changed, 2077 insertions(+), 1906 deletions(-)
Title: Multidimensional Item Response Theory
Description: Analysis of discrete response data using
unidimensional and multidimensional item analysis models under the Item
Response Theory paradigm (Chalmers (2012) <doi:10.18637/jss.v048.i06>).
Exploratory and confirmatory item factor analysis models
are estimated with quadrature (EM) or stochastic (MHRM) methods. Confirmatory
bi-factor and two-tier models are available for modeling item testlets using
dimension reduction EM algorithms, while multiple group analyses and
mixed effects designs are included for detecting differential item, bundle,
and test functioning, and for modeling item and person covariates.
Finally, latent class models such as the DINA, DINO, multidimensional latent class,
mixture IRT models, and zero-inflated response models are supported, as well
as a wide family of probabilistic unfolding models.
Author: Phil Chalmers [aut, cre] ,
Joshua Pritikin [ctb],
Alexander Robitzsch [ctb],
Mateusz Zoltak [ctb],
KwonHyun Kim [ctb],
Carl F. Falk [ctb],
Adam Meade [ctb],
Lennart Schneider [ctb],
David King [ctb],
Chen-Wei Liu [ctb],
Ogreden Oguzhan [ctb],
Samuel [...truncated...]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between mirt versions 1.46.1 dated 2026-03-07 and 1.47 dated 2026-08-20
DESCRIPTION | 8 MD5 | 317 ++++++++++++++++++------------------- NAMESPACE | 25 +- NEWS.md | 28 +++ R/00-classes.R | 10 - R/02b-item_methods.R | 238 ++++++++++++++++++++++++++- R/03-estimation.R | 29 +-- R/04-PrepData.R | 2 R/05-model.elements.R | 6 R/06-LoadPars.R | 72 ++++++-- R/DIF.R | 41 +++- R/DTF.R | 2 R/EMstep.group.R | 9 - R/EMstep.utils.R | 7 R/M2.R | 2 R/MDIFF.R | 2 R/MDISC.R | 2 R/Mixture-methods.R | 2 R/PLCI.mirt.R | 2 R/RCI.R | 92 ++++++++++ R/SIBTEST.R | 2 R/SingleGroup-methods.R | 54 +++--- R/areainfo.R | 2 R/averageMI.R | 2 R/bfactor.R | 120 ++++++++++++-- R/boot.LR.R | 2 R/boot.mirt.R | 2 R/createGroup.R | 2 R/createItem.R | 2 R/empirical_ES.R | 2 R/empirical_plot.R | 2 R/empirical_rxx.R | 2 R/estfun.R | 2 R/expand.table.R | 2 R/expected.item.R | 2 R/expected.test.R | 2 R/extract.group.R | 2 R/extract.item.R | 2 R/extract.mirt.R | 3 R/fixef.R | 2 R/fscores.R | 36 +++- R/fscores.internal.R | 305 ++++++++++++++++++++++++++++------- R/gen.difficulty.R | 2 R/imputeMissing.R | 2 R/itemGAM.R | 2 R/itemfit.R | 2 R/iteminfo.R | 2 R/itemplot.R | 19 +- R/itemplot.internal.R | 29 ++- R/itemstats.R | 28 ++- R/key2binary.R | 2 R/lagrange.R | 50 +++++ R/likert2int.R | 2 R/marginal_moments.R | 2 R/marginal_rxx.R | 2 R/mdirt.R | 2 R/mirt-package.R | 25 ++ R/mirt.R | 14 + R/mirt.model.R | 2 R/mirtCluster.R | 4 R/mixedmirt.R | 2 R/mod2values.R | 2 R/multipleGroup.R | 14 + R/personfit.R | 2 R/pirt.R |only R/poly2dich.R | 2 R/probtrace.R | 2 R/randef.R | 2 R/remap.distance.R | 2 R/reverse.score.R | 2 R/simdata.R | 2 R/testinfo.R | 2 R/utils.R | 23 +- R/wald.R | 2 build/partial.rdb |binary build/vignette.rds |binary data/pirt_DIF.RData |only inst/doc/mirt-vignettes.html | 18 +- man/DIF.Rd | 5 man/DTF.Rd | 2 man/DiscreteClass-class.Rd | 2 man/M2.Rd | 2 man/MDIFF.Rd | 2 man/MDISC.Rd | 2 man/MixedClass-class.Rd | 2 man/MixtureClass-class.Rd | 2 man/MultipleGroupClass-class.Rd | 2 man/PLCI.mirt.Rd | 2 man/RCI.Rd | 92 ++++++++++ man/SIBTEST.Rd | 2 man/SingleGroupClass-class.Rd | 2 man/anova-method.Rd | 2 man/areainfo.Rd | 2 man/averageMI.Rd | 2 man/bfactor.Rd | 119 ++++++++++++- man/boot.LR.Rd | 2 man/boot.mirt.Rd | 2 man/coef-method.Rd | 2 man/createGroup.Rd | 2 man/createItem.Rd | 2 man/empirical_ES.Rd | 2 man/empirical_plot.Rd | 2 man/empirical_rxx.Rd | 2 man/expand.table.Rd | 2 man/expected.item.Rd | 2 man/expected.test.Rd | 2 man/extract.group.Rd | 2 man/extract.item.Rd | 2 man/extract.mirt.Rd | 2 man/fixef.Rd | 2 man/fscores.Rd | 27 ++- man/gen.difficulty.Rd | 2 man/imputeMissing.Rd | 2 man/itemGAM.Rd | 2 man/itemfit.Rd | 2 man/iteminfo.Rd | 2 man/itemplot.Rd | 14 + man/itemstats.Rd | 2 man/key2binary.Rd | 2 man/lagrange.Rd | 48 +++++ man/likert2int.Rd | 2 man/logLik-method.Rd | 2 man/marginal_moments.Rd | 2 man/marginal_rxx.Rd | 2 man/mdirt.Rd | 2 man/mirt-package.Rd | 2 man/mirt.Rd | 14 + man/mirt.model.Rd | 2 man/mirtCluster.Rd | 4 man/mixedmirt.Rd | 2 man/mod2values.Rd | 2 man/multipleGroup.Rd | 14 + man/personfit.Rd | 2 man/pirt.Rd |only man/pirt_DIF.Rd |only man/plot-method.Rd | 2 man/poly2dich.Rd | 2 man/print-method.Rd | 2 man/probtrace.Rd | 2 man/randef.Rd | 2 man/remap.distance.Rd | 2 man/residuals-method.Rd | 2 man/reverse.score.Rd | 2 man/secondOrderTest.Rd | 2 man/show-method.Rd | 2 man/simdata.Rd | 2 man/summary-method.Rd | 2 man/testinfo.Rd | 2 man/thetaComb.Rd | 2 man/vcov-method.Rd | 2 man/wald.Rd | 2 src/Estep.cpp | 6 src/Misc.cpp | 10 + src/Misc.h | 2 src/traceLinePts.cpp | 169 ++++++++++++++++--- src/traceLinePts.h | 21 ++ tests/testthat/test-02-mirtTwo.R | 8 tests/testthat/test-07-mixedmirt.R | 13 - tests/testthat/test-10-extras.R | 7 tests/testthat/test-13-grsmIRT.R | 4 tests/testthat/test-14-unfolding.R | 2 tests/testthat/test-19-PIRT.R |only 162 files changed, 1822 insertions(+), 597 deletions(-)
Title: Latent Variable Models
Description: A general implementation of Structural Equation Models
with latent variables (MLE, 2SLS, and composite likelihood
estimators) with both continuous, censored, and ordinal
outcomes (Holst and Budtz-Joergensen (2013) <doi:10.1007/s00180-012-0344-y>).
Mixture latent variable models and non-linear latent variable models
(Holst and Budtz-Joergensen (2020) <doi:10.1093/biostatistics/kxy082>).
The package also provides methods for graph exploration (d-separation,
back-door criterion), simulation of general non-linear latent variable
models, and estimation of influence functions for a broad range of
statistical models.
Author: Klaus K. Holst [aut, cre],
Benedikt Sommer [ctb],
Brice Ozenne [ctb],
Thomas Gerds [ctb]
Maintainer: Klaus K. Holst <klaus@holst.it>
Diff between lava versions 1.9.2 dated 2026-06-30 and 1.9.3 dated 2026-08-20
lava-1.9.2/lava/R/measurement.error.R |only lava-1.9.2/lava/R/zcolorbar.R |only lava-1.9.2/lava/inst/doc/correlation.Rmd |only lava-1.9.2/lava/inst/doc/influencefunction.Rmd |only lava-1.9.2/lava/inst/doc/nonlinear.Rmd |only lava-1.9.2/lava/man/measurement.error.Rd |only lava-1.9.2/lava/vignettes/correlation.Rmd |only lava-1.9.2/lava/vignettes/influencefunction.Rmd |only lava-1.9.2/lava/vignettes/nonlinear.Rmd |only lava-1.9.3/lava/DESCRIPTION | 16 lava-1.9.3/lava/INDEX | 86 lava-1.9.3/lava/MD5 | 153 lava-1.9.3/lava/NAMESPACE | 263 - lava-1.9.3/lava/NEWS.md | 11 lava-1.9.3/lava/R/IC.R | 2 lava-1.9.3/lava/R/Missing.R | 4 lava-1.9.3/lava/R/binomial.rrw.R | 16 lava-1.9.3/lava/R/bootstrap.R | 2 lava-1.9.3/lava/R/colorbar.R |only lava-1.9.3/lava/R/confint.R | 2 lava-1.9.3/lava/R/constrain.R | 2 lava-1.9.3/lava/R/contr.R | 18 lava-1.9.3/lava/R/distribution.R | 87 lava-1.9.3/lava/R/effects.R | 7 lava-1.9.3/lava/R/estimate.array.R | 27 lava-1.9.3/lava/R/estimate.default.R | 18 lava-1.9.3/lava/R/estimate_calculus.R | 91 lava-1.9.3/lava/R/eventTime.R | 99 lava-1.9.3/lava/R/intervention.R | 6 lava-1.9.3/lava/R/measurement_error.R |only lava-1.9.3/lava/R/mixture.R | 4 lava-1.9.3/lava/R/napass0.R | 90 lava-1.9.3/lava/R/sim.default.R | 2 lava-1.9.3/lava/R/sim.lvm.R | 98 lava-1.9.3/lava/R/stack.R |binary lava-1.9.3/lava/R/summary.estimate.R | 5 lava-1.9.3/lava/R/timedep.R | 8 lava-1.9.3/lava/R/twostage.R | 8 lava-1.9.3/lava/R/z_dist_old.R |only lava-1.9.3/lava/README.md | 27 lava-1.9.3/lava/build/vignette.rds |binary lava-1.9.3/lava/inst/doc/correlation.R | 51 lava-1.9.3/lava/inst/doc/correlation.html | 1161 +++---- lava-1.9.3/lava/inst/doc/correlation.qmd |only lava-1.9.3/lava/inst/doc/influencefunction.R | 116 lava-1.9.3/lava/inst/doc/influencefunction.html | 3106 ++++++++----------- lava-1.9.3/lava/inst/doc/influencefunction.qmd |only lava-1.9.3/lava/inst/doc/nonlinear.R | 72 lava-1.9.3/lava/inst/doc/nonlinear.html | 1267 +++---- lava-1.9.3/lava/inst/doc/nonlinear.qmd |only lava-1.9.3/lava/man/IC.default.Rd | 2 lava-1.9.3/lava/man/Missing.Rd | 2 lava-1.9.3/lava/man/binomial.rd.Rd | 10 lava-1.9.3/lava/man/bootstrap.lvm.Rd | 2 lava-1.9.3/lava/man/colorbar.Rd | 2 lava-1.9.3/lava/man/confint.lvmfit.Rd | 2 lava-1.9.3/lava/man/constrain-set.Rd | 2 lava-1.9.3/lava/man/contr.Rd | 1 lava-1.9.3/lava/man/estimate.array.Rd | 4 lava-1.9.3/lava/man/estimate.default.Rd | 4 lava-1.9.3/lava/man/eventTime.Rd | 55 lava-1.9.3/lava/man/figures/estimate-contrast-1.svg | 216 - lava-1.9.3/lava/man/figures/gof1-1.svg | 235 - lava-1.9.3/lava/man/figures/lvm1-1.svg | 48 lava-1.9.3/lava/man/figures/mediation1-1.svg | 42 lava-1.9.3/lava/man/figures/nlin1-1.svg | 108 lava-1.9.3/lava/man/figures/simres1-1.svg | 470 +- lava-1.9.3/lava/man/intervention.lvm.Rd | 4 lava-1.9.3/lava/man/measurement_error.Rd |only lava-1.9.3/lava/man/merge.estimate.Rd | 6 lava-1.9.3/lava/man/mixture.Rd | 4 lava-1.9.3/lava/man/na.pass0.Rd | 7 lava-1.9.3/lava/man/sim.default.Rd | 2 lava-1.9.3/lava/man/sim.lvm.Rd | 83 lava-1.9.3/lava/man/stack.estimate.Rd | 2 lava-1.9.3/lava/man/timedep.Rd | 8 lava-1.9.3/lava/man/twostage.lvmfit.Rd | 2 lava-1.9.3/lava/man/twostageCV.Rd | 6 lava-1.9.3/lava/tests/testthat/test-estimate-array.R | 44 lava-1.9.3/lava/tests/testthat/test-estimate-id.R | 58 lava-1.9.3/lava/tests/testthat/test-merge-estimate.R | 45 lava-1.9.3/lava/tests/testthat/test-misc.R | 27 lava-1.9.3/lava/tests/testthat/test-sim.R | 8 lava-1.9.3/lava/vignettes/correlation.qmd |only lava-1.9.3/lava/vignettes/influencefunction.qmd |only lava-1.9.3/lava/vignettes/nonlinear.qmd |only lava-1.9.3/lava/vignettes/ref.bib | 2 87 files changed, 4285 insertions(+), 4153 deletions(-)
Title: Testlet Item Response Theory
Description: Implementation of Testlet and Item Response Theory.
A light-version yet comprehensive and streamlined framework for psychometric analysis using
unidimensional and multidimensional Item Response Theory
(IRT; Baker & Kim (2004) <doi:10.1201/9781482276725>) and Testlet Response Theory
(TRT; Wainer et al., (2007) <doi:10.1017/CBO9780511618765>).
Designed for researchers, this package supports the estimation of item and person
parameters for a wide variety of models, including binary (i.e., Rasch, 2-Parameter Logistic, 3-Parameter Logistic)
and polytomous (Partial Credit Model, Generalized Partial Credit Model, Graded Response Model) formats. It also supports the estimation of Testlet models (Rasch Testlet, 2-Parameter Logistic Testlet, 3-Parameter Logistic Testlet, Bifactor, Partial Credit Model Testlet, Graded Response), allowing users to account for local item dependence in bundled items. A key feature is the specialized support for combination use and joint estimation of [...truncated...]
Author: Jiawei Xiong [aut, cre],
Cheng Tang [ctb],
Qidi Liu [ctb]
Maintainer: Jiawei Xiong <jiawei.xiong@uga.edu>
Diff between tirt versions 0.3.1 dated 2026-03-24 and 0.4.0 dated 2026-08-20
DESCRIPTION | 22 +++++++++------- MD5 | 52 ++++++++++++++++++++++++++++++--------- NAMESPACE | 12 +++++++++ R/dif.R |only R/information.R |only R/irt_engine.R |only R/irt_trt.R | 25 ++++++++++++++++++ R/item_fit.R |only R/ld_stats.R |only R/mixture_irt.R |only R/person_fit.R |only R/polytomousirt.R | 15 +++++++++-- R/reliability.R |only R/score_table.R |only R/sim_mirt.R |only R/sim_tirt.R |only R/tcc.R |only R/trt_binary.R | 26 ++++++++++++++++++- build/vignette.rds |binary inst/doc/intro_tirt.Rmd | 2 + inst/doc/intro_tirt.html | 6 ++++ inst/doc/psychometric_tools.R |only inst/doc/psychometric_tools.Rmd |only inst/doc/psychometric_tools.html |only man/dif.Rd |only man/irt_trt.Rd | 25 ++++++++++++++++++ man/item_fit.Rd |only man/item_info.Rd |only man/ld_stats.Rd |only man/mixture_irt.Rd |only man/person_fit.Rd |only man/polytomous_irt.Rd | 15 +++++++++-- man/reliability.Rd |only man/score_table.Rd |only man/sim_mirt.Rd |only man/sim_tirt.Rd |only man/tcc.Rd |only man/test_info.Rd |only man/trt_binary.Rd | 26 ++++++++++++++++++- vignettes/intro_tirt.Rmd | 2 + vignettes/psychometric_tools.Rmd |only 41 files changed, 199 insertions(+), 29 deletions(-)
Title: Self-Validated Ensemble Models with Lasso and Relaxed Elastic
Net Regression
Description: Tools for fitting self-validated ensemble models (SVEM; Lemkus et al. (2021) <doi:10.1016/j.chemolab.2021.104439>) in small-sample design-of-experiments and related workflows, using elastic net and relaxed elastic net regression via 'glmnet' (Friedman et al. (2010) <doi:10.18637/jss.v033.i01>). Fractional random-weight bootstraps with anti-correlated validation copies are used to tune penalty paths by validation-weighted AIC/BIC. Supports Gaussian and binomial responses, deterministic expansion helpers for shared factor spaces, prediction with bootstrap uncertainty, a random-search optimizer that respects mixture constraints and combines multiple responses via desirability functions, and a batch sequential-design proposer based on Thompson sampling from the bootstrap ensemble (Thompson (1933) <doi:10.1093/biomet/25.3-4.285>; Kandasamy et al. (2018) <doi:10.48550/arXiv.1705.09236>). Also includes a permutation-based whole-model test for Gaussian SVEM fits (Karl ( [...truncated...]
Author: Andrew T. Karl [cre, aut]
Maintainer: Andrew T. Karl <akarl@asu.edu>
Diff between SVEMnet versions 3.2.3 dated 2026-07-02 and 3.5.0 dated 2026-08-20
DESCRIPTION | 17 MD5 | 98 - NAMESPACE | 12 NEWS | 198 +- R/SVEMnet-package.R | 16 R/SVEMnet.R | 572 +++++-- R/bigexp.R | 172 +- R/coef.R | 111 - R/export_candidates_csv.R | 173 -- R/forward_selection.R |only R/glmnet_compat.R | 230 ++ R/glmnet_with_cv.R | 826 ++++++---- R/ij_diagnostic.R |only R/lipid_screen.R | 29 R/plot.svemnet.R | 174 +- R/predict.cv.R | 37 R/predict.svem_lasso.R | 88 - R/select_candidates.R | 83 - R/spec_limit_utility.R | 65 R/svem_random_table_multi.R | 34 R/svem_score_random.R | 456 +++-- R/svem_select_score_from_table.R | 59 R/svem_significance_test_parallel.R | 2064 +++++++++++++++----------- R/svem_thompson_batch.R |only R/svem_wmt_multi.R | 51 R/validation.R |only inst/CITATION | 2 man/SVEMnet-package.Rd | 16 man/SVEMnet.Rd | 62 man/bigexp_terms.Rd | 37 man/coef.svem_model.Rd | 24 man/forward_aicc.Rd |only man/glmnet_with_cv.Rd | 72 man/lipid_screen.Rd | 15 man/plot.svem_binomial.Rd | 10 man/plot.svem_model.Rd | 10 man/predict.svem_model.Rd | 14 man/predict_cv.Rd | 8 man/print.bigexp_formula.Rd |only man/print.svem_thompson_batch.Rd |only man/svem_export_candidates_csv.Rd | 149 - man/svem_forward.Rd |only man/svem_ij_variance.Rd |only man/svem_nonzero.Rd | 29 man/svem_score_random.Rd | 73 man/svem_significance_test_parallel.Rd | 79 man/svem_thompson_batch.Rd |only man/svem_wmt_multi.Rd | 52 tests/testthat/test-audit-fixes.R | 8 tests/testthat/test-bugfixes-3.3.1.R |only tests/testthat/test-complexity-edf.R | 5 tests/testthat/test-fitter-hardening-3.4.0.R |only tests/testthat/test-forward-selection.R |only tests/testthat/test-member-diagnostics-ij.R |only tests/testthat/test-release-hardening-3.4.0.R |only tests/testthat/test-scoring-hardening-3.4.0.R |only tests/testthat/test-thompson-batch.R |only tests/testthat/test-wmt-hardening-3.4.0.R |only tests/testthat/test_extras.R | 18 59 files changed, 3787 insertions(+), 2461 deletions(-)
Title: Relative Importance Factor Analysis
Description: Tools for estimating, comparing, and visualizing Relative
Importance Factor (RIF) indices based on rank-frequency distributions
and discrete power-law models. The package provides reproducible
workflows for data preparation, model fitting, goodness-of-fit
assessment, bootstrap inference, and publication-ready outputs.
The implemented methodology is described in Llinas et al. (2026)
<doi:10.3390/math14060966>.
Author: Humberto J. Llinas M. [aut, cre],
Humberto J. Llinas S. [aut],
Javier A. De la Hoz M. [aut],
Brian J. Llinas M. [aut],
Jose J. Padilla [aut]
Maintainer: Humberto J. Llinas M. <lhumberto@uninorte.edu.co>
Diff between RIFanalysis versions 0.9.1 dated 2026-08-08 and 0.9.2 dated 2026-08-20
DESCRIPTION | 6 MD5 | 75 +-- NEWS.md |only R/export_rif_excel.R | 65 ++ R/export_rif_plots.R | 2 R/export_rif_visuals.R | 2 R/rif_analysis.R | 6 R/rif_fit_bootstrap.R | 225 +++++++-- R/rif_fit_powerlaw.R | 6 R/rif_workflow_z1.R | 29 + R/rif_workflow_z2.R | 7 R/rif_workflow_z3.R | 55 +- build/partial.rdb |only data/data_by_type.rda |binary inst/doc/Vignette1.R | 13 inst/doc/Vignette1.Rmd | 1057 ++++++++++++++++++++++----------------------- inst/doc/Vignette1.html | 69 +- inst/doc/Vignette2.R | 11 inst/doc/Vignette2.Rmd | 710 +++++++++++++++--------------- inst/doc/Vignette2.html | 65 +- inst/doc/Vignette3.R | 12 inst/doc/Vignette3.Rmd | 757 ++++++++++++++++---------------- inst/doc/Vignette3.html | 59 +- man/RIFanalysis-package.Rd | 2 man/export_rif_excel.Rd | 10 man/export_rif_plots.Rd | 2 man/export_rif_visuals.Rd | 2 man/rif_analysis.Rd | 6 man/rif_fit_bootstrap.Rd | 6 man/rif_fit_powerlaw.Rd | 6 man/rif_workflow_z1.Rd | 11 man/rif_workflow_z2.Rd | 7 man/rif_workflow_z3.Rd | 22 tests |only vignettes/Vignette1.Rmd | 1057 ++++++++++++++++++++++----------------------- vignettes/Vignette2.Rmd | 710 +++++++++++++++--------------- vignettes/Vignette3.Rmd | 757 ++++++++++++++++---------------- 37 files changed, 3055 insertions(+), 2774 deletions(-)
Title: Tools for Information-Based Feature Selection and Scoring
Description: A toolbox of fast, native and parallel implementations of various information-based importance criteria estimators and feature selection filters based on them, inspired by the overview by Brown, Pocock, Zhao and Lujan (2012) <https://www.jmlr.org/papers/v13/brown12a.html>.
Contains, among other, minimum redundancy maximal relevancy ('mRMR') method by Peng, Long and Ding (2005) <doi:10.1109/TPAMI.2005.159>; joint mutual information ('JMI') method by Yang and Moody (1999) <https://papers.nips.cc/paper/1779-data-visualization-and-feature-selection-new-algorithms-for-nongaussian-data>; double input symmetrical relevance ('DISR') method by Meyer and Bontempi (2006) <doi:10.1007/11732242_9> as well as joint mutual information maximisation ('JMIM') method by Bennasar, Hicks and Setchi (2015) <doi:10.1016/j.eswa.2015.07.007>.
Author: Miron B. Kursa [aut, cre]
Maintainer: Miron B. Kursa <m@mbq.me>
Diff between praznik versions 12.0.0 dated 2025-11-11 and 13.0.0 dated 2026-08-20
praznik-12.0.0/praznik/inst/tinytest |only praznik-12.0.0/praznik/tests/tinytest.R |only praznik-13.0.0/praznik/DESCRIPTION | 10 +-- praznik-13.0.0/praznik/MD5 | 84 +++++++++++--------------- praznik-13.0.0/praznik/NAMESPACE | 2 praznik-13.0.0/praznik/R/algorithms.R | 50 ++++++++++++--- praznik-13.0.0/praznik/R/scorers.R | 38 +++++++++++ praznik-13.0.0/praznik/inst/NEWS | 3 praznik-13.0.0/praznik/man/CMI.Rd | 2 praznik-13.0.0/praznik/man/CMIM.Rd | 2 praznik-13.0.0/praznik/man/DISR.Rd | 2 praznik-13.0.0/praznik/man/JIM.Rd | 2 praznik-13.0.0/praznik/man/JMI.Rd | 2 praznik-13.0.0/praznik/man/JMI3.Rd | 2 praznik-13.0.0/praznik/man/JMIM.Rd | 2 praznik-13.0.0/praznik/man/MIM.Rd | 2 praznik-13.0.0/praznik/man/MRMR.Rd | 2 praznik-13.0.0/praznik/man/NJMIM.Rd | 2 praznik-13.0.0/praznik/man/cmiMatrix.Rd | 2 praznik-13.0.0/praznik/man/cmiScores.Rd | 2 praznik-13.0.0/praznik/man/dnmiMatrix.Rd | 2 praznik-13.0.0/praznik/man/hScores.Rd | 2 praznik-13.0.0/praznik/man/icmiMatrix.Rd | 2 praznik-13.0.0/praznik/man/impScores.Rd | 2 praznik-13.0.0/praznik/man/jhScores.Rd | 2 praznik-13.0.0/praznik/man/jmiMatrix.Rd | 2 praznik-13.0.0/praznik/man/jmiScores.Rd | 2 praznik-13.0.0/praznik/man/maxCmiScores.Rd | 2 praznik-13.0.0/praznik/man/maxJmiScores.Rd | 2 praznik-13.0.0/praznik/man/miMatrix.Rd | 2 praznik-13.0.0/praznik/man/miScores.Rd | 2 praznik-13.0.0/praznik/man/minCmiScores.Rd | 2 praznik-13.0.0/praznik/man/minMaxCmiScores.Rd | 2 praznik-13.0.0/praznik/man/njmiMatrix.Rd | 2 praznik-13.0.0/praznik/man/njmiScores.Rd | 2 praznik-13.0.0/praznik/man/nmiMatrix.Rd | 2 praznik-13.0.0/praznik/man/praznik-package.Rd | 6 + praznik-13.0.0/praznik/man/triScores.Rd | 2 praznik-13.0.0/praznik/src/jmi3.h | 2 praznik-13.0.0/praznik/src/trips.h | 2 praznik-13.0.0/praznik/tests/cran.R |only 41 files changed, 188 insertions(+), 67 deletions(-)
Title: Isotonic Distributional Regression (IDR)
Description: Distributional regression under stochastic order restrictions for
numeric and binary response variables and partially ordered covariates,
including right-censored responses via Survival-IDR. See Henzi, Ziegel,
Gneiting (2021) <doi:10.1111/rssb.12450> and Bladt, Henzi, van den Heuvel,
Ziegel (2026) <doi:10.48550/arXiv.2608.02914>.
Author: Bram van den Heuvel [aut, cre],
Alexander Henzi [aut],
Martin Bladt [aut],
Johanna Ziegel [ths]
Maintainer: Bram van den Heuvel <bram.vandenheuvel@stat.math.ethz.ch>
Diff between isodistrreg versions 0.1.0 dated 2021-03-22 and 0.5.2 dated 2026-08-20
isodistrreg-0.1.0/isodistrreg/R/RcppExports.R |only isodistrreg-0.1.0/isodistrreg/R/multivHazardLoop.R |only isodistrreg-0.1.0/isodistrreg/R/partialOrders.R |only isodistrreg-0.1.0/isodistrreg/man/compOrd.Rd |only isodistrreg-0.1.0/isodistrreg/man/multivHazardLoop.Rd |only isodistrreg-0.1.0/isodistrreg/man/neighborPoints.Rd |only isodistrreg-0.1.0/isodistrreg/man/prepareData.Rd |only isodistrreg-0.1.0/isodistrreg/man/reexports.Rd |only isodistrreg-0.1.0/isodistrreg/man/trReduc.Rd |only isodistrreg-0.1.0/isodistrreg/src/RcppExports.cpp |only isodistrreg-0.1.0/isodistrreg/src/idrHazard.cpp |only isodistrreg-0.1.0/isodistrreg/src/isoCdf_sequential.cpp |only isodistrreg-0.1.0/isodistrreg/src/pavaMatrix.cpp |only isodistrreg-0.5.2/isodistrreg/DESCRIPTION | 57 isodistrreg-0.5.2/isodistrreg/MD5 | 156 - isodistrreg-0.5.2/isodistrreg/NAMESPACE | 78 isodistrreg-0.5.2/isodistrreg/R/bagging.R | 304 +- isodistrreg-0.5.2/isodistrreg/R/data.R | 66 isodistrreg-0.5.2/isodistrreg/R/dindexm.R | 303 +- isodistrreg-0.5.2/isodistrreg/R/evaluation.R | 1373 +++++----- isodistrreg-0.5.2/isodistrreg/R/extendr-wrappers.R |only isodistrreg-0.5.2/isodistrreg/R/modeling.R | 1340 +++++---- isodistrreg-0.5.2/isodistrreg/R/package.R | 271 + isodistrreg-0.5.2/isodistrreg/build/partial.rdb |only isodistrreg-0.5.2/isodistrreg/build/vignette.rds |binary isodistrreg-0.5.2/isodistrreg/cleanup |only isodistrreg-0.5.2/isodistrreg/cleanup.win |only isodistrreg-0.5.2/isodistrreg/configure |only isodistrreg-0.5.2/isodistrreg/configure.win |only isodistrreg-0.5.2/isodistrreg/inst/CITATION | 68 isodistrreg-0.5.2/isodistrreg/inst/doc/IDR_arXiv_preprint.Rnw | 14 isodistrreg-0.5.2/isodistrreg/inst/doc/IDR_arXiv_preprint.pdf |binary isodistrreg-0.5.2/isodistrreg/man/bscore.Rd | 6 isodistrreg-0.5.2/isodistrreg/man/crps.Rd | 10 isodistrreg-0.5.2/isodistrreg/man/dindexm.Rd | 29 isodistrreg-0.5.2/isodistrreg/man/dot-onUnload.Rd | 30 isodistrreg-0.5.2/isodistrreg/man/idr.Rd | 111 isodistrreg-0.5.2/isodistrreg/man/idrbag.Rd | 56 isodistrreg-0.5.2/isodistrreg/man/isodistrreg-package.Rd | 60 isodistrreg-0.5.2/isodistrreg/man/isotonic_regression.Rd |only isodistrreg-0.5.2/isodistrreg/man/isotonic_regression_impl.Rd |only isodistrreg-0.5.2/isodistrreg/man/pit.Rd | 20 isodistrreg-0.5.2/isodistrreg/man/plain_survival_isotonic_distributional_regression.Rd |only isodistrreg-0.5.2/isodistrreg/man/plain_survival_isotonic_distributional_regression_threshold.Rd |only isodistrreg-0.5.2/isodistrreg/man/plot.idr.Rd | 15 isodistrreg-0.5.2/isodistrreg/man/predict.dindexfit.Rd | 21 isodistrreg-0.5.2/isodistrreg/man/predict.idrfit.Rd | 31 isodistrreg-0.5.2/isodistrreg/man/qpred.Rd | 9 isodistrreg-0.5.2/isodistrreg/man/qscore.Rd | 6 isodistrreg-0.5.2/isodistrreg/man/rain.Rd | 4 isodistrreg-0.5.2/isodistrreg/man/survival_isotonic_distributional_regression_threshold.Rd |only isodistrreg-0.5.2/isodistrreg/man/warn_once.Rd |only isodistrreg-0.5.2/isodistrreg/src/Makevars.in |only isodistrreg-0.5.2/isodistrreg/src/Makevars.win.in |only isodistrreg-0.5.2/isodistrreg/src/entrypoint.c |only isodistrreg-0.5.2/isodistrreg/src/isodistrreg-win.def |only isodistrreg-0.5.2/isodistrreg/src/rust |only isodistrreg-0.5.2/isodistrreg/tests |only isodistrreg-0.5.2/isodistrreg/tools |only isodistrreg-0.5.2/isodistrreg/vignettes/IDR_arXiv_preprint.Rnw | 14 isodistrreg-0.5.2/isodistrreg/vignettes/arXiv_preprint.pdf |binary 61 files changed, 2504 insertions(+), 1948 deletions(-)
Title: A Blazing Fast Implementation of Random Forest
Description: Yet another implementation of the Random Forest method by Breiman (2001) <doi:10.1023/A:1010933404324>, written in Rust and tailored towards stability, correctness, efficiency and scalability on modern multi-core machines.
Handles both classification and regression, as well as provides permutation feature importance via a novel, highly optimised algorithm.
Author: Miron Bartosz Kursa [aut, cre] ,
Krzysztof Piotr Piwonski [aut]
Maintainer: Miron Bartosz Kursa <m@mbq.me>
Diff between fru versions 0.0.7 dated 2026-05-07 and 1.0.0 dated 2026-08-20
DESCRIPTION | 8 ++++---- MD5 | 19 ++++++++++--------- R/a.R | 4 +++- inst/CITATION |only inst/NEWS | 4 ++++ man/fru.Rd | 4 +++- src/fru/Cargo.lock | 6 +++--- src/fru/Cargo.toml | 2 +- src/xrf/Cargo.lock | 2 +- src/xrf/Cargo.toml | 2 +- src/xrf/src/lib.rs | 9 +++++++++ 11 files changed, 39 insertions(+), 21 deletions(-)
Title: Fundamental Clustering Problems Suite
Description: Over sixty clustering algorithms are provided in this package with consistent input and output, which enables the user to try out algorithms swiftly. Additionally, 26 statistical approaches for the estimation of the number of clusters as well as the mirrored density plot (MD-plot) of clusterability are implemented. The packages is published in Thrun, M.C., Stier Q.: "Fundamental Clustering Algorithms Suite" (2021), SoftwareX, <DOI:10.1016/j.softx.2020.100642>. Moreover, the fundamental clustering problems suite (FCPS) offers a variety of clustering challenges any algorithm should handle when facing real world data, see Thrun, M.C., Ultsch A.: "Clustering Benchmark Datasets Exploiting the Fundamental Clustering Problems" (2020), Data in Brief, <DOI:10.1016/j.dib.2020.105501>.
Author: Michael Thrun [aut, cre, cph] ,
Peter Nahrgang [ctr, ctb],
Felix Pape [ctr, ctb],
Vasyl Pihur [ctb],
Guy Brock [ctb],
Susmita Datta [ctb],
Somnath Datta [ctb],
Luis Winckelmann [com],
Alfred Ultsch [dtc, ctb],
Quirin Stier [ctb, rev]
Maintainer: Michael Thrun <m.thrun@gmx.net>
Diff between FCPS versions 1.4.0 dated 2026-07-15 and 1.4.1 dated 2026-08-20
DESCRIPTION | 10 MD5 | 88 ++--- NAMESPACE | 208 ++++++------ R/APclustering.R | 2 R/AgglomerativeNestingClustering.R | 2 R/AutomaticProjectionBasedClustering.R | 2 R/ClusterAccuracy.R | 219 +++++++------ R/ClusterAlignLabels.R |only R/ClusterApply.R | 2 R/ClusterDendrogram.R | 17 - R/ClusterDistances.R | 2 R/ClusterDunnIndex.R | 4 R/ClusterNoEstimation.R | 2 R/ClusterPlotMDS.R | 2 R/ClusterabilityMDplot.R | 10 R/DatabionicSwarmClustering.R | 4 R/DensityPeakClustering.R | 2 R/DivisiveAnalysisClustering.R | 2 R/FannyClustering.R | 2 R/GenieClustering.R | 137 ++++---- R/HierarchicalClusterData.R | 86 +++-- R/HierarchicalClusterDists.R | 535 ++++++++++++++++++++++++++++++--- R/HierarchicalClustering.R | 286 +++++++++++++---- R/HierarchicalDBSCAN.R | 2 R/IsDissimilarity.R |only R/MSTclustering.R | 2 R/MarkovClustering.R | 2 R/MinimalEnergyClustering.R | 149 ++++----- R/MinimaxLinkageClustering.R | 140 ++++---- R/NetworkClustering.R | 2 R/PAMclustering.R | 2 R/SparseClustering.R | 189 ++++++----- R/kmeansClustering.R | 2 build/partial.rdb |binary inst/doc/FCPS.html | 16 man/ClusterAccuracy.Rd | 10 man/ClusterAlignLabels.Rd |only man/ClusterDendrogram.Rd | 7 man/GenieClustering.Rd | 11 man/HierarchicalClusterData.Rd | 20 - man/HierarchicalClusterDists.Rd | 293 ++++++++++++++++-- man/HierarchicalClustering.Rd | 256 +++++++++++++-- man/IsDissimilarity.Rd |only man/MinimalEnergyClustering.Rd | 106 +++--- man/MinimaxLinkageClustering.Rd | 106 +++--- man/ProjectionPursuitClustering.Rd | 151 ++++----- man/SparseClustering.Rd | 165 +++++----- 47 files changed, 2248 insertions(+), 1007 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 dated 2026-05-29 and 0.1.9.5 dated 2026-08-20
broadcast-0.1.9.5/broadcast/DESCRIPTION | 12 broadcast-0.1.9.5/broadcast/MD5 | 212 ++++--- broadcast-0.1.9.5/broadcast/NAMESPACE | 2 broadcast-0.1.9.5/broadcast/NEWS.md | 35 + broadcast-0.1.9.5/broadcast/R/RcppExports.R | 102 +++ broadcast-0.1.9.5/broadcast/R/aaa00_broadcast_help.R | 6 broadcast-0.1.9.5/broadcast/R/aaa01_broadcast_operators.R | 14 broadcast-0.1.9.5/broadcast/R/aaa02_broadcast_casting.R | 5 broadcast-0.1.9.5/broadcast/R/aaa04_broadcast_linearalgebra.R | 3 broadcast-0.1.9.5/broadcast/R/bc_b.R | 22 broadcast-0.1.9.5/broadcast/R/bc_bit.R | 14 broadcast-0.1.9.5/broadcast/R/bc_cplx.R | 4 broadcast-0.1.9.5/broadcast/R/bc_d.R | 6 broadcast-0.1.9.5/broadcast/R/bc_dim.R | 2 broadcast-0.1.9.5/broadcast/R/bc_i.R | 6 broadcast-0.1.9.5/broadcast/R/bc_ifelse.R | 5 broadcast-0.1.9.5/broadcast/R/bc_list.R | 2 broadcast-0.1.9.5/broadcast/R/bc_raw.R | 2 broadcast-0.1.9.5/broadcast/R/bc_rel.R | 2 broadcast-0.1.9.5/broadcast/R/bc_str.R | 12 broadcast-0.1.9.5/broadcast/R/bc_strrep.R | 2 broadcast-0.1.9.5/broadcast/R/bcapply.R | 2 broadcast-0.1.9.5/broadcast/R/bind_array.R | 3 broadcast-0.1.9.5/broadcast/R/broadcastWrappers.R | 49 - broadcast-0.1.9.5/broadcast/R/broadcaster.R | 46 + broadcast-0.1.9.5/broadcast/R/cast_shallow2atomic.R | 17 broadcast-0.1.9.5/broadcast/R/class_methods.R | 4 broadcast-0.1.9.5/broadcast/R/internal_binary.R | 158 ----- broadcast-0.1.9.5/broadcast/R/internal_bind.R | 9 broadcast-0.1.9.5/broadcast/R/internal_functions.R | 23 broadcast-0.1.9.5/broadcast/R/internal_typefuns.R | 11 broadcast-0.1.9.5/broadcast/R/meta_functions.R | 90 +++ broadcast-0.1.9.5/broadcast/R/reorient_vector.R |only broadcast-0.1.9.5/broadcast/R/vector2array.R | 27 broadcast-0.1.9.5/broadcast/build/partial.rdb |binary broadcast-0.1.9.5/broadcast/inst/examples/bind_array.R | 2 broadcast-0.1.9.5/broadcast/inst/examples/reorient_vector.R |only broadcast-0.1.9.5/broadcast/inst/tinytest/aaa_binary_prep_part1 |only broadcast-0.1.9.5/broadcast/inst/tinytest/aaa_binary_prep_part2 |only broadcast-0.1.9.5/broadcast/inst/tinytest/aaa_binary_prep_part3 |only broadcast-0.1.9.5/broadcast/inst/tinytest/bc_b/logic_gates.csv |only broadcast-0.1.9.5/broadcast/inst/tinytest/bc_b/test-logic.R |only broadcast-0.1.9.5/broadcast/inst/tinytest/bc_bytes/test-bc_bit_int.R | 45 + broadcast-0.1.9.5/broadcast/inst/tinytest/bc_general/test-binaryerrors.R | 4 broadcast-0.1.9.5/broadcast/inst/tinytest/bc_str/test-bc_str_dist.R | 17 broadcast-0.1.9.5/broadcast/inst/tinytest/bind_array_1_basic/test-bind_array-broadcaster.R | 114 ++-- broadcast-0.1.9.5/broadcast/inst/tinytest/cast_lists |only broadcast-0.1.9.5/broadcast/inst/tinytest/class/test-eval.R |only broadcast-0.1.9.5/broadcast/inst/tinytest/class/test-mbroadcasters.R | 21 broadcast-0.1.9.5/broadcast/inst/tinytest/helper/test-vector2array.R | 11 broadcast-0.1.9.5/broadcast/inst/tinytest/internal/test-return_missing.R |only broadcast-0.1.9.5/broadcast/inst/tinytest/overload/test-method_dispatch.R |only broadcast-0.1.9.5/broadcast/inst/tinytest/reorient_vector |only broadcast-0.1.9.5/broadcast/inst/tinytest/shallow2atomic/test-coercion-special.R |only broadcast-0.1.9.5/broadcast/inst/tinytest/shallow2atomic/test-coercion-zerolen.R |only broadcast-0.1.9.5/broadcast/inst/tinytest/shallow2atomic/test-names-1dnames.R |only broadcast-0.1.9.5/broadcast/inst/tinytest/shallow2atomic/test-names-dimnames.R |only broadcast-0.1.9.5/broadcast/inst/tinytest/test-binary1d.R | 4 broadcast-0.1.9.5/broadcast/inst/tinytest/test-binary_errors.R | 4 broadcast-0.1.9.5/broadcast/man/aaa00_broadcast_help.Rd | 8 broadcast-0.1.9.5/broadcast/man/aaa01_broadcast_operators.Rd | 10 broadcast-0.1.9.5/broadcast/man/aaa02_broadcast_casting.Rd | 5 broadcast-0.1.9.5/broadcast/man/bc.b.Rd | 19 broadcast-0.1.9.5/broadcast/man/bc.bit.Rd | 10 broadcast-0.1.9.5/broadcast/man/bc.str.Rd | 6 broadcast-0.1.9.5/broadcast/man/bind_array.Rd | 2 broadcast-0.1.9.5/broadcast/man/broadcaster.Rd | 6 broadcast-0.1.9.5/broadcast/man/cast_shallow2atomic.Rd | 17 broadcast-0.1.9.5/broadcast/man/linear_algebra_stats.Rd | 3 broadcast-0.1.9.5/broadcast/man/reorient_vector.Rd |only broadcast-0.1.9.5/broadcast/man/vector2array.Rd | 14 broadcast-0.1.9.5/broadcast/src/C_arraysize_overflow.c | 2 broadcast-0.1.9.5/broadcast/src/C_max_type.c |only broadcast-0.1.9.5/broadcast/src/RcppExports.cpp | 282 +++++++--- broadcast-0.1.9.5/broadcast/src/broadcast.h | 185 ++++-- broadcast-0.1.9.5/broadcast/src/rcpp_bcRel_bit.cpp | 21 broadcast-0.1.9.5/broadcast/src/rcpp_bc_b.cpp | 17 broadcast-0.1.9.5/broadcast/src/rcpp_bc_bind.cpp | 26 broadcast-0.1.9.5/broadcast/src/rcpp_bindhelpers.cpp | 80 ++ broadcast-0.1.9.5/broadcast/src/rcpp_virt_binary_prep.cpp |only broadcast-0.1.9.5/broadcast/tests/tinytest.R | 17 broadcast-0.1.9/broadcast/inst/examples/recast_dirvector.R |only broadcast-0.1.9/broadcast/inst/tinytest/bc_b/test-bc_b_equivalences.R |only broadcast-0.1.9/broadcast/inst/tinytest/binary_prep |only broadcast-0.1.9/broadcast/inst/tinytest/cast |only broadcast-0.1.9/broadcast/inst/tinytest/shallow2atomic/test-1dnames.R |only broadcast-0.1.9/broadcast/inst/tinytest/shallow2atomic/test-dimnames.R |only broadcast-0.1.9/broadcast/inst/tinytest/shallow2atomic/test-specialcoercion.R |only broadcast-0.1.9/broadcast/inst/tinytest/test-S4error-callerenv.R |only broadcast-0.1.9/broadcast/src/C_bindhelper_get_alongdims.c |only broadcast-0.1.9/broadcast/src/C_bindhelper_max_type.c |only broadcast-0.1.9/broadcast/src/C_bindhelper_sum_along.c |only broadcast-0.1.9/broadcast/src/C_check_conf_dim.c |only broadcast-0.1.9/broadcast/src/C_chunkify_dims.c |only broadcast-0.1.9/broadcast/src/C_determine_dimmode.c |only broadcast-0.1.9/broadcast/src/C_make_outdim.c |only broadcast-0.1.9/broadcast/src/C_pmax.c |only broadcast-0.1.9/broadcast/src/rcpp_classes.cpp |only broadcast-0.1.9/broadcast/src/rcpp_mergedims.cpp |only 99 files changed, 1056 insertions(+), 805 deletions(-)
Title: Content Analysis in R: Integrated Qualitative (LLMs) and
Quantitative Pipeline
Description: Provides an integrated pipeline for content analysis
combining qualitative coding assisted by large language models (LLMs)
with classical quantitative text analysis. Includes modules for
pre-processing (tokenization, stopwords for Brazilian Portuguese),
descriptive statistics, keyness, co-occurrence networks, word clouds
(including comparative and X-ray variants), sentiment analysis via
OpLexicon, Latent Dirichlet Allocation (LDA), inter-coder
reliability metrics (Krippendorff, Gwet), and modern visualizations
based on ggplot2. Special focus on Brazilian corpora and
political-institutional codebooks. Inspired by Maerz and Benoit (2025)
<https://quallmer.github.io/quallmer/>.
Author: Anderson Henrique [aut, cre]
Maintainer: Anderson Henrique <anderson.henrique@usp.br>
Diff between acR versions 0.3.2 dated 2026-08-07 and 0.3.3 dated 2026-08-20
DESCRIPTION | 6 MD5 | 59 ++--- NAMESPACE | 1 NEWS.md | 92 ++++++++ R/ac_ellmer_chat.R | 2 R/ac_qual_code.R | 96 ++++++++ R/ac_qual_codebook.R | 9 R/ac_qual_live.R | 12 - R/ac_qual_models.R | 8 R/ac_qual_report.R | 259 +++++++++++++++++++++++- R/ac_qual_search_literature.R | 4 README.md | 30 ++ inst/doc/analise-proposicoes.R | 4 inst/doc/analise-proposicoes.Rmd | 6 inst/doc/analise-proposicoes.html | 8 inst/doc/qualitativo-llm.R | 4 inst/doc/qualitativo-llm.Rmd | 12 - inst/doc/qualitativo-llm.html | 62 +++-- inst/doc/replicabilidade.html | 14 - man/ac_qual_code.Rd | 9 man/ac_qual_codebook.Rd | 5 man/ac_qual_report_full.Rd |only man/ac_qual_search_literature.Rd | 2 tests/testthat/test-ac_qual_code.R | 134 ++++++++++++ tests/testthat/test-ac_qual_codebook.R | 6 tests/testthat/test-ac_qual_live.R | 28 ++ tests/testthat/test-ac_qual_report.R | 86 +++++++ tests/testthat/test-ac_qual_search_literature.R | 4 tests/testthat/test-plots-snapshot.R | 5 vignettes/analise-proposicoes.Rmd | 6 vignettes/qualitativo-llm.Rmd | 12 - 31 files changed, 862 insertions(+), 123 deletions(-)
Title: Regression Modeling Using Vasicek Distribution
Description: Provides density, cumulative distribution, quantile, and
random generation functions for Vasicek distributions with standard
normal and standard logistic kernels. The normal-kernel distribution is
parameterized by either its mean or a fixed quantile, whereas the
logistic-kernel distribution uses a fixed-quantile parameterization.
Zero-adjusted, one-adjusted, and zero-and-one-adjusted extensions of the
normal-kernel mean parameterization are also provided for responses that
include boundary values. The corresponding 'NVASIM', 'NVASIQ', 'LVASIQ',
'ZANVASIM', 'OANVASIM', and 'ZOANVASIM' families are available for fitting
Generalized Additive Models for Location, Scale and Shape,
as introduced by Rigby and Stasinopoulos (2005,
<doi:10.1111/j.1467-9876.2005.00510.x>). Some functions are written in
'C++' using 'Rcpp', developed by Eddelbuettel and Francois (2011,
<doi:10.18637/jss.v040.i08>).
Author: Josmar Mazucheli [aut, cre],
Bruna Alves [ctb]
Maintainer: Josmar Mazucheli <jmazucheli@gmail.com>
Diff between vasicekreg versions 1.0.2 dated 2026-01-12 and 1.1.0 dated 2026-08-20
vasicekreg-1.0.2/vasicekreg/R/dpqr-vasicekmean.R |only vasicekreg-1.0.2/vasicekreg/R/dpqr-vasicekquant.R |only vasicekreg-1.0.2/vasicekreg/man/VASIM.Rd |only vasicekreg-1.0.2/vasicekreg/man/VASIQ.Rd |only vasicekreg-1.0.2/vasicekreg/src/vasicekmean.cpp |only vasicekreg-1.0.2/vasicekreg/src/vasicekquant.cpp |only vasicekreg-1.1.0/vasicekreg/DESCRIPTION | 29 vasicekreg-1.1.0/vasicekreg/MD5 | 47 vasicekreg-1.1.0/vasicekreg/NAMESPACE | 64 + vasicekreg-1.1.0/vasicekreg/NEWS.md | 94 + vasicekreg-1.1.0/vasicekreg/R/RcppExports.R | 60 - vasicekreg-1.1.0/vasicekreg/R/bodyfat.R | 34 vasicekreg-1.1.0/vasicekreg/R/dpqr-01NvasicekM.R |only vasicekreg-1.1.0/vasicekreg/R/dpqr-0NvasicekM.R |only vasicekreg-1.1.0/vasicekreg/R/dpqr-1NvasicekM.R |only vasicekreg-1.1.0/vasicekreg/R/dpqr-LvasicekQ.R |only vasicekreg-1.1.0/vasicekreg/R/dpqr-NvasicekM.R |only vasicekreg-1.1.0/vasicekreg/R/dpqr-NvasicekQ.R |only vasicekreg-1.1.0/vasicekreg/R/utils.R |only vasicekreg-1.1.0/vasicekreg/R/vasicekreg-package.R | 143 ++ vasicekreg-1.1.0/vasicekreg/README.md |only vasicekreg-1.1.0/vasicekreg/man/LVASIQ.Rd |only vasicekreg-1.1.0/vasicekreg/man/NVASIM.Rd |only vasicekreg-1.1.0/vasicekreg/man/NVASIQ.Rd |only vasicekreg-1.1.0/vasicekreg/man/OANVASIM.Rd |only vasicekreg-1.1.0/vasicekreg/man/ZANVASIM.Rd |only vasicekreg-1.1.0/vasicekreg/man/ZOANVASIM.Rd |only vasicekreg-1.1.0/vasicekreg/man/bodyfat.Rd | 34 vasicekreg-1.1.0/vasicekreg/man/vasicekreg-package.Rd | 144 ++ vasicekreg-1.1.0/vasicekreg/src/LvasicekQ.cpp |only vasicekreg-1.1.0/vasicekreg/src/NvasicekM.cpp |only vasicekreg-1.1.0/vasicekreg/src/NvasicekQ.cpp |only vasicekreg-1.1.0/vasicekreg/src/RcppExports.cpp | 200 +++- vasicekreg-1.1.0/vasicekreg/tests/testthat/helper-global-tau.R |only vasicekreg-1.1.0/vasicekreg/tests/testthat/test-derivatives.R | 481 ++++++++-- vasicekreg-1.1.0/vasicekreg/tests/testthat/test-dpqr.R |only vasicekreg-1.1.0/vasicekreg/tests/testthat/test-families.R |only vasicekreg-1.1.0/vasicekreg/tests/testthat/test-rqres-augmented.R |only 38 files changed, 1148 insertions(+), 182 deletions(-)
Title: Model Cumulative Growing Degree-Days for Pest Monitoring
Description: Pest monitoring is crucial, especially during the early season, to understand the distribution and the proliferation of the target pest. Raw count data from pest monitoring/traps can be coupled with derived environmental variables such as growing degree-day ('GDD') to get useful insights about the pest phenology. This package pulls temperature data from the 'Daymet' application programming interface ('API', <https://daymet.ornl.gov>), or 'Open-Meteo' ('API', <https://open-meteo.com/>) or manual user-supplied CSV file from the California Irrigation Management Information System ('CIMIS', <https://cimis.water.ca.gov>), for a user-specified time period and calculates cumulative growing degree-days. Users provide intended date range, pest of concern, and the geographic coordinates of the trap location to track pest emergence and phenology throughout the growing season.
Author: Santosh Bhandari [aut, cre],
Lalit Kharel [aut],
Mahesh Ghimire [aut]
Maintainer: Santosh Bhandari <santoshbhandari4556@gmail.com>
Diff between TrackTrap versions 1.0.0 dated 2026-06-13 and 1.0.1 dated 2026-08-20
TrackTrap-1.0.0/TrackTrap/data/pest_thresholds.R |only TrackTrap-1.0.0/TrackTrap/tests/testthat/test-phenology.R |only TrackTrap-1.0.1/TrackTrap/DESCRIPTION | 17 TrackTrap-1.0.1/TrackTrap/LICENSE | 2 TrackTrap-1.0.1/TrackTrap/MD5 | 33 TrackTrap-1.0.1/TrackTrap/NEWS.md | 26 TrackTrap-1.0.1/TrackTrap/R/TrackTrap-package.R | 1 TrackTrap-1.0.1/TrackTrap/R/data.R | 25 TrackTrap-1.0.1/TrackTrap/R/phenology.R | 428 +++++----- TrackTrap-1.0.1/TrackTrap/build |only TrackTrap-1.0.1/TrackTrap/data/pest_thresholds.rda |binary TrackTrap-1.0.1/TrackTrap/inst |only TrackTrap-1.0.1/TrackTrap/man/TrackTrap-package.Rd |only TrackTrap-1.0.1/TrackTrap/man/calc_pest_phenology.Rd | 31 TrackTrap-1.0.1/TrackTrap/man/fetch_open_meteo.Rd | 12 TrackTrap-1.0.1/TrackTrap/man/pest_thresholds.Rd | 22 TrackTrap-1.0.1/TrackTrap/man/plot_trap_phenology.Rd | 31 TrackTrap-1.0.1/TrackTrap/tests/testthat/test-calc_pest_phenology.R |only TrackTrap-1.0.1/TrackTrap/tests/testthat/test-pest_thresholds.R |only TrackTrap-1.0.1/TrackTrap/vignettes |only 20 files changed, 375 insertions(+), 253 deletions(-)
Title: World Development Indicators and Other World Bank Data
Description: Search and download data from over 40 databases hosted by the World Bank, including the World Development Indicators ('WDI'), International Debt Statistics, Doing Business, Human Capital Index, and Sub-national Poverty indicators.
Author: Vincent Arel-Bundock [aut, cre] ,
Etienne Bacher [ctb]
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Diff between WDI versions 2.7.10 dated 2026-04-05 and 2.8.0 dated 2026-08-20
DESCRIPTION | 7 ++--- MD5 | 14 +++++----- NEWS.md | 12 ++++++-- R/WDI.R | 51 ++++++++++++++++++++++++++++--------- README.md | 16 +++++++---- data/WDI_data.RData |binary man/WDIcache.Rd | 7 ++--- tests/testthat/helper-pagination.R |only tests/testthat/test-pagination.R |only 9 files changed, 74 insertions(+), 33 deletions(-)
Title: Models for Data from Unmarked Animals
Description: Fits hierarchical models of animal abundance and occurrence to data collected using survey methods such as point counts, site occupancy sampling, distance sampling, removal sampling, and double observer sampling. Parameters governing the state and observation processes can be modeled as functions of covariates. References: Kellner et al. (2023) <doi:10.1111/2041-210X.14123>, Fiske and Chandler (2011) <doi:10.18637/jss.v043.i10>.
Author: Richard Chandler [aut],
Ken Kellner [cre, aut],
Ian Fiske [aut],
David Miller [aut],
Andy Royle [aut],
Jeff Hostetler [aut],
Rebecca Hutchinson [aut],
Adam Smith [aut],
Lea Pautrel [aut],
Marc Kery [ctb],
Mike Meredith [ctb],
Auriel Fournier [ctb],
A [...truncated...]
Maintainer: Ken Kellner <contact@kenkellner.com>
Diff between unmarked versions 1.5.1 dated 2025-09-26 and 1.5.2 dated 2026-08-20
DESCRIPTION | 8 +- MD5 | 81 ++++++++++---------- NAMESPACE | 2 NEWS.md | 6 + R/gdistremoval.R | 4 + R/occuComm.R | 1 R/occuPEN.R | 8 +- R/plotEffects.R | 2 R/ranef.R | 4 - R/simulate.R | 4 - R/square_brackets.R | 1 R/unmarkedFit.R | 25 ++++-- R/unmarkedFrame.R | 17 ++++ R/utils.R | 17 ++++ build/partial.rdb |binary build/vignette.rds |binary inst/doc/cap-recap.html | 2 inst/doc/distsamp.html | 10 +- inst/doc/occuMulti.html | 58 +++++++-------- inst/doc/spp-dist.html | 10 +- inst/doc/unmarked.html | 16 ++-- man/detFuns.Rd | 5 + man/getStarts.Rd |only man/modSel.Rd | 5 + man/pcountOpen.Rd | 139 ++++++++++++++++++------------------ man/predict.Rd | 5 - man/unmarkedFitList-class.rd | 1 man/unmarkedMultFrame.Rd | 1 src/Makevars | 2 src/Makevars.win | 2 tests/testthat/test_distsamp.R | 4 - tests/testthat/test_formatInputs.R | 22 ++--- tests/testthat/test_makePiFun.R | 6 - tests/testthat/test_occu.R | 6 - tests/testthat/test_occuFP.R | 14 +++ tests/testthat/test_occuPEN.R | 27 ++++++ tests/testthat/test_pcount.R | 2 tests/testthat/test_pcount.spHDS.R | 2 tests/testthat/test_pcountOpen.R | 2 tests/testthat/test_plotEffects.R | 32 ++++++++ tests/testthat/test_unmarkedFrame.R | 28 +++++++ tests/testthat/test_utils.R | 27 ++++++ 42 files changed, 401 insertions(+), 207 deletions(-)
Title: Tweedie Distribution
Description: Provides density, distribution function, quantile function, and random
generation for the Tweedie distribution under the compound Poisson-Gamma
parameterisation with power parameter in (1, 2). The density is evaluated
using the series expansion of Dunn and Smyth (2005) <doi:10.1007/s11222-005-4070-y>,
implemented in C++ via 'Rcpp' and 'RcppArmadillo' for performance. A constructor
compatible with the 'distributional' package is also provided for use in tidy
modelling workflows.
Author: Stefano Damato [aut, cre]
Maintainer: Stefano Damato <stefanodamato128@gmail.com>
Diff between tweedieDistr versions 0.1.1 dated 2026-07-23 and 0.2.0 dated 2026-08-20
DESCRIPTION | 6 +- MD5 | 14 ++--- NEWS.md | 4 + src/dtweedie.cpp | 142 +++++++++++++++++++++++++++++++++++-------------------- src/ptweedie.cpp | 10 ++- src/qtweedie.cpp | 42 ++++++++++------ src/utils.cpp | 14 ++++- src/utils.h | 2 8 files changed, 150 insertions(+), 84 deletions(-)
Title: Simple and Configurable Tables in 'HTML', 'LaTeX', 'Markdown',
'Word', 'PNG', 'PDF', and 'Typst' Formats
Description: Create highly customized tables with this simple and dependency-free package. Data frames can be converted to 'HTML', 'LaTeX', 'Markdown', 'Word', 'PNG', 'PDF', or 'Typst' tables. The user interface is minimalist and easy to learn. The syntax is concise. 'HTML' tables can be customized using the flexible 'Bootstrap' framework, and 'LaTeX' code with the 'tabularray' package.
Author: Vincent Arel-Bundock [aut, cre]
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Diff between tinytable versions 0.17.0 dated 2026-06-26 and 0.18.0 dated 2026-08-20
tinytable-0.17.0/tinytable/R/last_style.R |only tinytable-0.18.0/tinytable/DESCRIPTION | 7 tinytable-0.18.0/tinytable/MD5 | 385 +++--- tinytable-0.18.0/tinytable/NEWS.md | 26 tinytable-0.18.0/tinytable/R/aaa_class.R | 73 - tinytable-0.18.0/tinytable/R/ansi.R | 16 tinytable-0.18.0/tinytable/R/build_tt.R | 82 - tinytable-0.18.0/tinytable/R/colors.R | 71 + tinytable-0.18.0/tinytable/R/expand_style.R | 169 ++ tinytable-0.18.0/tinytable/R/format_apply.R | 118 -- tinytable-0.18.0/tinytable/R/format_tt.R | 193 +-- tinytable-0.18.0/tinytable/R/format_vector_escape.R | 7 tinytable-0.18.0/tinytable/R/format_vector_numeric.R | 176 +-- tinytable-0.18.0/tinytable/R/format_vector_replace.R | 47 tinytable-0.18.0/tinytable/R/grid_build.R | 234 +--- tinytable-0.18.0/tinytable/R/grid_finalize.R | 77 - tinytable-0.18.0/tinytable/R/grid_group.R | 56 tinytable-0.18.0/tinytable/R/grid_style.R | 172 -- tinytable-0.18.0/tinytable/R/group_tt.R | 261 +--- tinytable-0.18.0/tinytable/R/group_tt_i.R | 28 tinytable-0.18.0/tinytable/R/group_tt_j.R | 24 tinytable-0.18.0/tinytable/R/html_build.R | 29 tinytable-0.18.0/tinytable/R/html_finalize.R | 67 - tinytable-0.18.0/tinytable/R/html_group.R | 97 - tinytable-0.18.0/tinytable/R/html_style.R | 354 +++--- tinytable-0.18.0/tinytable/R/json.R | 215 ++- tinytable-0.18.0/tinytable/R/nse.R | 40 tinytable-0.18.0/tinytable/R/plot_tt.R | 230 ++- tinytable-0.18.0/tinytable/R/print.R | 98 - tinytable-0.18.0/tinytable/R/rbind2.R | 6 tinytable-0.18.0/tinytable/R/sanity.R | 444 +++---- tinytable-0.18.0/tinytable/R/save_tt.R | 17 tinytable-0.18.0/tinytable/R/style_maps.R |only tinytable-0.18.0/tinytable/R/style_tt.R | 290 ++-- tinytable-0.18.0/tinytable/R/subset.R | 156 ++ tinytable-0.18.0/tinytable/R/tabularray_build.R | 1 tinytable-0.18.0/tinytable/R/tabularray_group.R | 13 tinytable-0.18.0/tinytable/R/tabularray_helpers.R | 101 - tinytable-0.18.0/tinytable/R/tabularray_style.R | 582 +++------- tinytable-0.18.0/tinytable/R/tabulator_build.R | 19 tinytable-0.18.0/tinytable/R/tabulator_columns.R | 111 + tinytable-0.18.0/tinytable/R/tabulator_data.R | 43 tinytable-0.18.0/tinytable/R/tabulator_finalize.R | 42 tinytable-0.18.0/tinytable/R/tabulator_group.R | 6 tinytable-0.18.0/tinytable/R/tabulator_options.R | 34 tinytable-0.18.0/tinytable/R/tabulator_plot.R | 5 tinytable-0.18.0/tinytable/R/tabulator_search.R | 25 tinytable-0.18.0/tinytable/R/tabulator_style.R | 40 tinytable-0.18.0/tinytable/R/tabulator_stylesheet.R | 13 tinytable-0.18.0/tinytable/R/theme_empty.R | 7 tinytable-0.18.0/tinytable/R/theme_html_tabulator.R | 33 tinytable-0.18.0/tinytable/R/theme_latex.R | 40 tinytable-0.18.0/tinytable/R/theme_markdown.R | 10 tinytable-0.18.0/tinytable/R/theme_revealjs.R | 68 - tinytable-0.18.0/tinytable/R/theme_rotate.R | 24 tinytable-0.18.0/tinytable/R/theme_striped.R | 27 tinytable-0.18.0/tinytable/R/theme_tt.R | 47 tinytable-0.18.0/tinytable/R/theme_typst.R | 20 tinytable-0.18.0/tinytable/R/tt.R | 10 tinytable-0.18.0/tinytable/R/typst_style.R | 513 ++++---- tinytable-0.18.0/tinytable/R/typst_tt.R | 298 +++-- tinytable-0.18.0/tinytable/R/utils.R | 160 ++ tinytable-0.18.0/tinytable/README.md | 2 tinytable-0.18.0/tinytable/build/partial.rdb |binary tinytable-0.18.0/tinytable/inst/templates/typst.typ | 4 tinytable-0.18.0/tinytable/inst/tinytable.css | 16 tinytable-0.18.0/tinytable/inst/tinytable_dark.css | 16 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/ansi-styles_01.md | 12 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/ansi-styles_01.txt | 8 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/escape-issue150_caption.html | 16 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/escape-issue150_caption_02.html | 28 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/escape-issue150_caption_02.typ | 15 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/escape-issue150_caption_03.html | 28 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/escape-issue150_caption_03.typ | 31 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/escape-latex.html | 16 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/escape-latex_colnames.html | 16 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/escape-latex_colnames.typ | 11 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/escape-simple.html | 16 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/escape-simple.typ | 11 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/format_tt-conditional_output.html | 16 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/format_tt-vignette_html_markdown.html | 20 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/group-3level.typ | 21 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/group-html_tutorial_01.html | 36 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/group-issue165_extra_row.html | 46 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/group-issue165_extra_row.typ | 15 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/group-issue165_html_centering_style.html | 54 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/group-issue258_01_html.html | 18 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/group-issue258_01_typst.typ | 11 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/group-issue258_02_html.html | 20 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/group-issue258_02_typst.typ | 11 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/group-issue362_duplicate_colum_labels.tex | 3 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/group-multilevel-basic.html | 28 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/group-multilevel-basic.typ | 17 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/group-multilevel-empty.html | 40 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/group-multilevel-empty.typ | 18 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/group-nse.html | 20 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/group-nse.typ | 11 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/group-subset_j-638.html | 30 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/group-subset_j-638.typ | 15 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/group_matrix-multiple_positions_multiple_rows.html | 16 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/group_matrix-multiple_positions_multiple_rows.typ | 11 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/group_matrix-row_duplication.html | 16 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/group_matrix-row_duplication.typ | 11 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/group_matrix-single_column_with_styling.html | 20 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/group_matrix-single_column_with_styling.typ | 11 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/group_matrix-single_position_single_row.html | 16 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/group_matrix-single_position_single_row.typ | 11 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/html-alignment.html | 44 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/html-bootstrap_css.html | 16 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/html-borders.html | 12 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/html-caption.html | 16 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/html-conditional_styling.html | 20 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/html-font_size.html | 28 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/html-footnote.html | 16 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/html-formatting.html | 16 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/html-images.html | 4 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/html-individual_cells.html | 20 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/html-issue297.html | 50 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/html-issue355a.html | 72 - tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/html-issue355b.html | 42 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/html-issue575.html | 54 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/html-issue58.html | 36 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/html-issue88.html | 20 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/html-issue92.html | 28 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/html-line_break.html | 16 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/html-merge_cells.html | 22 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/html-missing_value.html | 16 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/html-omit_headers.html | 16 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/html-spanning_cells.html | 26 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/html-vectorized_color_j.html | 40 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/latex-align_d.tex | 2 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/latex-align_d_02.tex | 2 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/latex-align_d_03.tex | 2 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/latex-align_d_comparator.tex |only tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/latex-borders.tex | 5 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/latex-group_style_order.tex | 2 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/latex-row_color.tex | 2 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/latex-theme_striped.tex | 1 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/line_type-mixed.html |only tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/line_type-mixed.tex |only tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/line_type-mixed.typ |only tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/markdown-long_column_group.txt | 22 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/style-align_partial.html | 40 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/style-align_partial.typ | 11 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/style-issue507_markdown_styles.html | 44 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/style-issue507_markdown_styles.typ | 15 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/style-issue514_white_blue.html | 12 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/style-issue514_white_blue.tex | 7 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/style-issue514_white_blue.typ | 5 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/style-output_conditional.html | 20 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/style-output_conditional.typ | 11 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/style-smallcap.html | 20 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/style-smallcap.typ | 30 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/tibble-pillar_num.typ | 11 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/typst-complicated.typ | 14 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/typst-figure_false.typ |only tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/typst-font_size.typ | 11 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/typst-formatting.typ | 11 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/typst-grid.typ | 5 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/typst-group_columns.typ | 15 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/typst-group_rows.typ | 11 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/typst-issue-139_misaligned_rule_with_group_tt.typ | 14 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/typst-issue323_group_tt_style_tt.typ | 14 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/typst-issue456.typ | 28 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/typst-issue592.typ | 75 - tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/typst-italic_markdown.typ | 11 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/typst-missing_value_replacement.typ | 11 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/typst-more_formatting.typ | 11 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/typst-no_headers.typ | 9 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/typst-significant_cell.typ | 11 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/typst-striped.typ | 5 tinytable-0.18.0/tinytable/inst/tinytest/_tinysnapshot/typst-tblr.typ | 11 tinytable-0.18.0/tinytable/inst/tinytest/helpers.R | 21 tinytable-0.18.0/tinytable/inst/tinytest/test-bugfix.R | 33 tinytable-0.18.0/tinytable/inst/tinytest/test-format.R | 47 tinytable-0.18.0/tinytable/inst/tinytest/test-group.R | 88 + tinytable-0.18.0/tinytable/inst/tinytest/test-group_matrix.R | 31 tinytable-0.18.0/tinytable/inst/tinytest/test-html.R | 46 tinytable-0.18.0/tinytable/inst/tinytest/test-json.R |only tinytable-0.18.0/tinytable/inst/tinytest/test-latex.R | 31 tinytable-0.18.0/tinytable/inst/tinytest/test-line_type.R |only tinytable-0.18.0/tinytable/inst/tinytest/test-markdown.R | 9 tinytable-0.18.0/tinytable/inst/tinytest/test-nse.R |only tinytable-0.18.0/tinytable/inst/tinytest/test-pdf.R | 16 tinytable-0.18.0/tinytable/inst/tinytest/test-plot_tt.R | 27 tinytable-0.18.0/tinytable/inst/tinytest/test-rbind2.R | 12 tinytable-0.18.0/tinytable/inst/tinytest/test-style-resolution.R |only tinytable-0.18.0/tinytable/inst/tinytest/test-style.R | 116 + tinytable-0.18.0/tinytable/inst/tinytest/test-subset.R |only tinytable-0.18.0/tinytable/inst/tinytest/test-tabulator.R | 14 tinytable-0.18.0/tinytable/inst/tinytest/test-tt.R | 35 tinytable-0.18.0/tinytable/inst/tinytest/test-typst.R | 92 + tinytable-0.18.0/tinytable/inst/tinytest/test-utils.R |only tinytable-0.18.0/tinytable/man/print.tinytable.Rd | 1 tinytable-0.18.0/tinytable/man/rbind2-tinytable-tinytable-method.Rd | 2 tinytable-0.18.0/tinytable/man/save_tt.Rd | 3 tinytable-0.18.0/tinytable/man/style_tt.Rd | 11 tinytable-0.18.0/tinytable/man/theme_empty.Rd | 5 tinytable-0.18.0/tinytable/man/theme_markdown.Rd | 4 tinytable-0.18.0/tinytable/man/tt.Rd | 3 200 files changed, 4888 insertions(+), 4285 deletions(-)
Title: Statistical Methods for Regional Counts
Description: Implements statistical methods for analyzing the counts of areal data, with a focus on the detection of spatial clusters and clustering. The package has a heavy emphasis on spatial scan methods, which were first introduced by Kulldorff and Nagarwalla (1995) <doi:10.1002/sim.4780140809> and Kulldorff (1997) <doi:10.1080/03610929708831995>.
Author: Joshua French [aut, cre] ,
Mohammad Meysami [ctb]
Maintainer: Joshua French <joshua.french@ucdenver.edu>
Diff between smerc versions 1.8.4 dated 2024-10-24 and 1.8.6 dated 2026-08-20
DESCRIPTION | 13 +++++++------ MD5 | 20 ++++++++++---------- NEWS.md | 2 ++ R/arg_check_functions.R | 25 +++++++++++++++++++++++++ R/precog.test.R | 4 ++-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/smerc_demo.html | 23 ++++++++++++----------- man/precog.test.Rd | 4 ++-- man/smerc.Rd | 5 +++++ tests/testthat/_snaps |only tests/testthat/test-precog.test.R | 1 + 12 files changed, 66 insertions(+), 31 deletions(-)
Title: Manage 'RStudio' Preferences and Addin Shortcuts
Description: Provides an interface for working with 'RStudio' preference files
to modify settings and addin shortcuts without using point-and-click option
menus. Useful for ensuring a unified experience across devices and for
enforcing best practices. Also exposes some settings not available in the
Global Options dialog.
Author: S.A. van der Wulp [aut, cre, cph],
Daniel D. Sjoberg [aut, cph]
Maintainer: S.A. van der Wulp <vdwulp@gmail.com>
Diff between rstudio.prefs versions 0.1.9 dated 2022-07-16 and 0.2.0 dated 2026-08-20
DESCRIPTION | 52 +- MD5 | 34 - NEWS.md | 176 +++++--- R/fetch_rstudio_prefs.R | 4 R/rstudio.prefs-package.R | 3 R/sysdata.rda |binary R/use_rstudio_keyboard_shortcut.R | 256 ++++++------ R/use_rstudio_prefs.R | 6 R/use_rstudio_secondary_repo.R | 250 ++++++------ README.md | 193 +++++---- inst/WORDLIST | 14 man/fetch_rstudio_prefs.Rd | 2 man/make_path_norm.Rd | 4 man/rstudio.prefs-package.Rd | 18 man/use_rstudio_keyboard_shortcut.Rd | 21 - man/use_rstudio_prefs.Rd | 7 man/use_rstudio_secondary_repo.Rd | 8 tests/testthat/test-use_rstudio_keyboard_shortcut.R | 408 +++++++++++++++++++- 18 files changed, 973 insertions(+), 483 deletions(-)
Title: 'Rcpp' Bindings for the 'Corpus Workbench' ('CWB')
Description: 'Rcpp' Bindings for the C code of the 'Corpus Workbench' ('CWB'), an indexing and query
engine to efficiently analyze large corpora (<https://cwb.sourceforge.io>). 'RcppCWB' is licensed
under the GNU GPL-3, in line with the GPL-3 license of the 'CWB' (<https://www.r-project.org/Licenses/GPL-3>).
The 'CWB' relies on 'pcre2' (BSD license, see <https://github.com/PCRE2Project/pcre2/blob/master/LICENCE.md>)
and 'GLib' (LGPL license, see <https://www.gnu.org/licenses/lgpl-3.0.en.html>).
See the file LICENSE.note for further information. The package includes modified code of the
'rcqp' package (GPL-2, see <https://cran.r-project.org/package=rcqp>). The original work of the authors
of the 'rcqp' package is acknowledged with great respect, and they are listed as authors of this
package. To achieve cross-platform portability (including Windows), using 'Rcpp' for wrapper code
is the approach used by 'RcppCWB'.
Author: Andreas Blaette [aut, cre],
Bernard Desgraupes [aut],
Sylvain Loiseau [aut],
Oliver Christ [ctb],
Bruno Maximilian Schulze [ctb],
Stephanie Evert [ctb],
Arne Fitschen [ctb],
Jeroen Ooms [ctb],
Marius Bertram [ctb],
Tomas Kalibera [ctb]
Maintainer: Andreas Blaette <andreas.blaette@uni-due.de>
Diff between RcppCWB versions 0.6.10 dated 2025-09-30 and 0.6.11 dated 2026-08-20
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 5 +++++ build/vignette.rds |binary inst/doc/vignette.html | 4 ++-- src/cwb/cl/registry.tab.c | 8 ++++---- src/cwb/cqp/macro.c | 2 +- src/cwb/cqp/parser.tab.c | 8 ++++---- 8 files changed, 27 insertions(+), 22 deletions(-)
Title: Functions to Support Extension Education Program Evaluation
Description: Functions and datasets to support Summary and Analysis of
Extension Program Evaluation in R, and An R
Companion for the Handbook of Biological Statistics.
Vignettes are available at <https://rcompanion.org>.
Author: Salvatore Mangiafico [aut, cre]
Maintainer: Salvatore Mangiafico <mangiafico@njaes.rutgers.edu>
Diff between rcompanion versions 2.5.2 dated 2026-01-11 and 2.5.4 dated 2026-08-20
DESCRIPTION | 10 +- MD5 | 14 ++- NAMESPACE | 159 ++++++++++++++++++++++++--------------------- NEWS.md | 13 +++ R/efronRSquared.r | 59 ++++++++++++++-- R/groupwiseFiveNumber.r |only inst/CITATION | 4 - man/efronRSquared.Rd | 29 +++++++- man/groupwiseFiveNumber.Rd |only 9 files changed, 192 insertions(+), 96 deletions(-)
Title: Mechanistic Simulation of Species Range Dynamics
Description: Integrates population dynamics and dispersal into a
mechanistic virtual species simulator. The package can be used to
study the effects of environmental change on population growth and
range shifts. It allows for simple and straightforward definition of
population dynamics (including positive density dependence), extensive
possibilities for defining dispersal kernels, and the ability to
generate virtual ecologist data. Learn more about the 'rangr' at
<https://docs.ropensci.org/rangr/>.
Author: Katarzyna Markowska [aut, cre],
Lechoslaw Kuczynski [aut],
Tad Dallas [rev],
Joanne Potts [rev]
Maintainer: Katarzyna Markowska <katarzyna.markowska@amu.edu.pl>
Diff between rangr versions 1.0.9 dated 2026-01-23 and 1.0.10 dated 2026-08-20
DESCRIPTION | 12 +- MD5 | 30 +++--- NEWS.md | 6 + R/update.sim_data.R | 4 README.md | 62 +++++++------ build/partial.rdb |binary build/vignette.rds |binary inst/doc/rangr.R | 66 +++++++------- inst/doc/rangr.html | 142 ++++++++++++++++---------------- man/figures/README-vis_input_maps-1.png |binary man/figures/README-vis_sim_res_01-1.png |binary man/figures/README-vis_sim_res_02-1.png |binary man/figures/README-vis_sim_res_04-1.png |binary man/get_observations.Rd | 12 +- man/rangr-package.Rd | 3 man/sim.Rd | 4 16 files changed, 177 insertions(+), 164 deletions(-)
Title: Fitting Point Process Models via the Palm Likelihood
Description: Functions to fit point process models using the Palm likelihood. First proposed by Tanaka, Ogata, and Stoyan (2008) <DOI:10.1002/bimj.200610339>, maximisation of the Palm likelihood can provide computationally efficient parameter estimation for point process models in situations where the full likelihood is intractable. This package is chiefly focused on Neyman-Scott point processes, but can also fit the void processes proposed by Jones-Todd et al. (2019) <DOI:10.1002/sim.8046>. The development of this package was motivated by the analysis of capture-recapture surveys on which individuals cannot be identified---the data from which can conceptually be seen as a clustered point process (Stevenson, Borchers, and Fewster, 2019 <DOI:10.1111/biom.12983>). As such, some of the functions in this package are specifically for the estimation of cetacean density from two-camera aerial surveys.
Author: Ben C. Stevenson [aut, cre]
Maintainer: Ben C. Stevenson <ben.stevenson@st-andrews.ac.uk>
Diff between palm versions 1.1.6 dated 2025-07-25 and 1.1.7 dated 2026-08-20
palm-1.1.6/palm/src/Makevars |only palm-1.1.6/palm/src/Makevars.win |only palm-1.1.7/palm/DESCRIPTION | 16 ++++++++-------- palm-1.1.7/palm/MD5 | 6 ++---- palm-1.1.7/palm/data/examples.r | 8 ++++---- 5 files changed, 14 insertions(+), 16 deletions(-)
Title: MSigDB Gene Sets for Multiple Organisms in a Tidy Data Format
Description: Provides the 'Molecular Signatures Database' (MSigDB) gene
sets typically used with the 'Gene Set Enrichment Analysis' (GSEA)
software (Subramanian et al. 2005 <doi:10.1073/pnas.0506580102>,
Liberzon et al. 2015 <doi:10.1016/j.cels.2015.12.004>, Castanza et al.
2023 <doi:10.1038/s41592-023-02014-7>) as an R data frame. The package
includes the human genes as listed in MSigDB as well as the
corresponding symbols and IDs for frequently studied model organisms
such as mouse, rat, pig, fly, and yeast.
Author: Igor Dolgalev [aut, cre, cph]
Maintainer: Igor Dolgalev <igor.dolgalev@nyumc.org>
Diff between msigdbr versions 26.1.0 dated 2026-03-12 and 26.1.1 dated 2026-08-20
DESCRIPTION | 16 ++--- LICENSE | 2 MD5 | 32 +++++----- NAMESPACE | 34 ++-------- NEWS.md | 5 + R/msigdbr-collections.R | 6 - R/msigdbr-package.R | 6 - R/msigdbr-species.R | 3 R/msigdbr.R | 96 ++++++++++++++++++++++-------- R/utils.R | 66 ++++++++++++++------ README.md | 2 build/partial.rdb |binary man/msigdbr-package.Rd | 7 +- man/msigdbr.Rd | 2 tests/testthat/test-msigdbr-collections.R | 16 ++++- tests/testthat/test-msigdbr-species.R | 7 +- tests/testthat/test-msigdbr.R | 76 ++++++++++++++++++++--- 17 files changed, 254 insertions(+), 122 deletions(-)
Title: MRI Tissue Classification
Description: Implements various methods for tissue classification in magnetic
resonance (MR) images of the brain, including normal mixture models
and hidden Markov normal mixture models, as outlined in Feng &
Tierney (2011) <doi:10.18637/jss.v044.i07>. These methods allow a
structural MR image to be classified into gray matter, white matter
and cerebrospinal fluid tissue types.
Author: Dai Feng [aut],
Luke Tierney [aut],
Jon Clayden [cre, aut]
Maintainer: Jon Clayden <code@clayden.org>
Diff between mritc versions 0.6.1 dated 2026-08-04 and 0.6.2 dated 2026-08-20
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 4 ++++ src/updateDistanceUnit_omp.c | 2 ++ 4 files changed, 13 insertions(+), 7 deletions(-)
Title: Meta Analysis Instrumental Variable Estimator
Description: Meta-analysis traditionally assigns more weight to studies with lower standard errors,
assuming higher precision. However, in observational research, precision must be
estimated and is vulnerable to manipulation, such as p-hacking, to achieve statistical
significance. This can lead to spurious precision, invalidating inverse-variance
weighting and bias-correction methods like funnel plots. Common methods for addressing
publication bias, including selection models, often fail or exacerbate the problem.
This package introduces an instrumental variable approach to limit bias caused by
spurious precision in meta-analysis. Methods are described in 'Irsova et al.' (2025)
<doi:10.1038/s41467-025-63261-0>.
Author: Zuzana Irsova [aut] ,
Pedro R. D. Bom [aut] ,
Tomas Havranek [aut] ,
Heiko Rachinger [aut] ,
Petr Cala [aut, cre]
Maintainer: Petr Cala <cala.p@seznam.cz>
Diff between MAIVE versions 0.2.4 dated 2026-02-04 and 0.2.5 dated 2026-08-20
DESCRIPTION | 6 ++-- MD5 | 18 ++++++------ NEWS.md | 11 +++++++ R/ar.r | 6 ++-- R/maivefunction.r | 46 ++++++++++++++++---------------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/funnel-plot.html | 3 +- inst/doc/introduction.html | 3 +- tests/testthat/test-maive_first_stage.R | 6 ++-- 10 files changed, 56 insertions(+), 43 deletions(-)
Title: Probability Distributions as S3 Objects
Description: Tools to create and manipulate probability distributions
using S3. Generics pdf(), cdf(), quantile(), and random() provide
replacements for base R's d/p/q/r style functions. Functions and
arguments have been named carefully to minimize confusion for students
in intro stats courses. The documentation for each distribution
contains detailed mathematical notes.
Author: Alex Hayes [aut] ,
Ralph Moller-Trane [aut] ,
Daniel Jordan [aut],
Paul Northrop [aut] ,
Moritz N. Lang [aut] ,
Reto Stauffer [aut] ,
Achim Zeileis [aut, cre] ,
Emil Hvitfeldt [ctb] ,
Bruna Wundervald [ctb] ,
Alessandro Gasparini [ctb]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between distributions3 versions 0.2.4 dated 2026-07-22 and 0.3.0 dated 2026-08-20
DESCRIPTION | 18 - MD5 | 289 ++++++++++------- NAMESPACE | 94 +++++ NEWS.md | 56 +++ R/Bernoulli.R | 53 ++- R/Beta.R | 12 R/Binomial.R | 58 +++ R/Categorical.R | 35 -- R/Cauchy.R | 12 R/ChiSquare.R | 14 R/Empirical.R |only R/Erlang.R | 10 R/Exponential.R | 12 R/FisherF.R | 17 - R/Frechet.R | 12 R/Gamma.R | 15 R/GeneralisedExtremeValue.R | 14 R/GeneralisedPareto.R | 12 R/Geometric.R | 12 R/Gumbel.R | 12 R/HurdleNegativeBinomial.R | 25 - R/HurdlePoisson.R | 27 - R/HyperGeometric.R | 21 - R/LogNormal.R | 12 R/Logistic.R | 12 R/Multinomial.R | 13 R/NegativeBinomial.R | 18 - R/Normal.R | 91 +++++ R/Poisson.R | 64 +++ R/PoissonBinomial.R | 44 +- R/ReversedWeibull.R | 12 R/SinhArcsinh.R |only R/StudentsT.R | 17 - R/Tukey.R | 10 R/Uniform.R | 84 ++++ R/Weibull.R | 14 R/ZINegativeBinomial.R | 13 R/ZIPoisson.R | 13 R/ZTNegativeBinomial.R | 23 - R/ZTPoisson.R | 25 - R/crps.distribution.R |only R/distribution.R |only R/distributions3-package.R | 1 R/is_discrete.R | 7 R/methods.R | 48 ++ R/plot.R | 208 ++++++------ R/prodist.R | 6 R/score-hessian.R |only R/utils.R | 74 ++-- R/zzz.R |only README.md | 153 ++++++--- man/Beta.Rd | 1 man/Binomial.Rd | 2 man/Categorical.Rd | 2 man/Cauchy.Rd | 1 man/ChiSquare.Rd | 3 man/Empirical.Rd |only man/Erlang.Rd | 3 man/Exponential.Rd | 1 man/FisherF.Rd | 3 man/Frechet.Rd | 1 man/GEV.Rd | 3 man/GP.Rd | 1 man/Gamma.Rd | 3 man/Gumbel.Rd | 1 man/HurdleNegativeBinomial.Rd | 2 man/HurdlePoisson.Rd | 2 man/HyperGeometric.Rd | 2 man/LogNormal.Rd | 1 man/Logistic.Rd | 1 man/Multinomial.Rd | 2 man/NegativeBinomial.Rd | 2 man/Normal.Rd | 1 man/Poisson.Rd | 2 man/RevWeibull.Rd | 1 man/SinhArcsinh.Rd |only man/StudentsT.Rd | 3 man/Tukey.Rd | 3 man/Uniform.Rd | 1 man/Weibull.Rd | 3 man/ZTNegativeBinomial.Rd | 2 man/ZTPoisson.Rd | 2 man/cdf.Empirical.Rd |only man/cdf.Rd | 1 man/cdf.SinhArcsinh.Rd |only man/crps.distribution.Rd |only man/dempirical.Rd |only man/distribution_calculate_moments.Rd |only man/distributions3-package.Rd | 9 man/dsinharcsinh.Rd |only man/fit_mle.Rd | 1 man/geom_auc.Rd | 6 man/hasS3method.Rd |only man/is_discrete.Rd | 1 man/log_likelihood.Rd | 1 man/mean.distribution.Rd |only man/pdf.Empirical.Rd |only man/pdf.Rd | 1 man/pdf.SinhArcsinh.Rd |only man/pdf.distribution.Rd |only man/plot_cdf.Rd | 6 man/plot_pdf.Rd | 6 man/quantile.Empirical.Rd |only man/quantile.SinhArcsinh.Rd |only man/random.Empirical.Rd |only man/random.Rd | 1 man/random.SinhArcsinh.Rd |only man/random.distribution.Rd |only man/score-hessian.Rd |only man/suff_stat.Rd | 1 man/support.Empirical.Rd |only man/support.Rd | 1 man/support.SinhArcsinh.Rd |only src |only tests/testthat/test-Bernoulli.R | 69 ++++ tests/testthat/test-Beta.R | 16 tests/testthat/test-Binomial.R | 91 +++++ tests/testthat/test-Categorical.R | 6 tests/testthat/test-Cauchy.R | 6 tests/testthat/test-ChiSquare.R | 6 tests/testthat/test-Empirical.R |only tests/testthat/test-Erlang.R | 15 tests/testthat/test-Exponential.R | 15 tests/testthat/test-FisherF.R | 6 tests/testthat/test-Frechet.R | 6 tests/testthat/test-Gamma.R | 15 tests/testthat/test-GeneralisedExtremeValue.R | 6 tests/testthat/test-GeneralisedPareto.R | 6 tests/testthat/test-Geometric.R | 16 tests/testthat/test-Gumbel.R | 15 tests/testthat/test-HurdleNegativeBinomial.R | 6 tests/testthat/test-HurdlePoisson.R | 6 tests/testthat/test-HyperGeometric.R | 15 tests/testthat/test-LogNormal.R | 15 tests/testthat/test-Logistic.R | 17 - tests/testthat/test-Multinomial.R | 6 tests/testthat/test-NegativeBinomial.R | 6 tests/testthat/test-Normal.R | 111 ++++++ tests/testthat/test-Poisson.R | 67 +++ tests/testthat/test-PoissonBinomial.R | 6 tests/testthat/test-RevWeibull.R | 6 tests/testthat/test-SinhArcsinh.R |only tests/testthat/test-StudentsT.R | 15 tests/testthat/test-Tukey.R | 6 tests/testthat/test-Uniform.R | 113 ++++++ tests/testthat/test-Weibull.R | 6 tests/testthat/test-ZTNegativeBinomial.R | 6 tests/testthat/test-ZTPoisson.R | 6 tests/testthat/test-check_dots_used.R |only tests/testthat/test-crps-0-usage.R |only tests/testthat/test-crps-CensoredNormal.R |only tests/testthat/test-crps-Empirical.R |only tests/testthat/test-crps-Normal.R |only tests/testthat/test-crps-Poisson.R |only tests/testthat/test-distribution-0-usage.R |only tests/testthat/test-distribution-Normal-cdf.R |only tests/testthat/test-distribution-Normal-pdf.R |only tests/testthat/test-distribution-Normal-quantilecdf.R |only tests/testthat/test-distribution-Poisson-cdf.R |only tests/testthat/test-distribution-Poisson-pdf.R |only tests/testthat/test-distribution-Poisson-quantile.R |only tests/testthat/test-distribution-Poisson-quantilecdf.R |only tests/testthat/test-distribution-Poisson-quantilepdf.R |only tests/testthat/test-distribution-length-zero.R |only tests/testthat/test-hasS3method.R |only tests/testthat/test-score-hessian.R |only tests/testthat/test-utils.R | 1 167 files changed, 1994 insertions(+), 596 deletions(-)
More information about distributions3 at CRAN
Permanent link
Title: Convert Country Names and Country Codes
Description: Standardize country names, convert them into one of 40
different coding schemes, convert between coding schemes, and assign
region descriptors.
Author: Vincent Arel-Bundock [aut, cre] ,
CJ Yetman [ctb] ,
Nils Enevoldsen [ctb] ,
Etienne Bacher [ctb] ,
Samuel Meichtry [ctb]
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Diff between countrycode versions 1.8.0 dated 2026-04-16 and 1.9.0 dated 2026-08-20
countrycode-1.8.0/countrycode/tests/testthat/data-known-name-variations.R |only countrycode-1.8.0/countrycode/tests/testthat/test-known-name-variations.R |only countrycode-1.8.0/countrycode/tests/testthat/test-regex-external.R |only countrycode-1.8.0/countrycode/tests/testthat/test-regex-sentence.R |only countrycode-1.8.0/countrycode/tests/testthat/test-regex-special.R |only countrycode-1.9.0/countrycode/DESCRIPTION | 10 countrycode-1.9.0/countrycode/MD5 | 54 countrycode-1.9.0/countrycode/NEWS.md | 9 countrycode-1.9.0/countrycode/R/codelist.R | 2 countrycode-1.9.0/countrycode/R/countrycode.R | 684 +++++----- countrycode-1.9.0/countrycode/R/countryname.R | 63 countrycode-1.9.0/countrycode/R/get_dictionary.R | 53 countrycode-1.9.0/countrycode/R/guess_field.R | 14 countrycode-1.9.0/countrycode/data/codelist.rda |binary countrycode-1.9.0/countrycode/data/codelist_panel.rda |binary countrycode-1.9.0/countrycode/inst/extdata |only countrycode-1.9.0/countrycode/man/codelist.Rd | 6 countrycode-1.9.0/countrycode/tests/testthat/helper-shared-fixtures.R |only countrycode-1.9.0/countrycode/tests/testthat/test-basic.R | 61 countrycode-1.9.0/countrycode/tests/testthat/test-codelist.R | 188 +- countrycode-1.9.0/countrycode/tests/testthat/test-corner-cases.R | 271 +-- countrycode-1.9.0/countrycode/tests/testthat/test-countryname.R | 78 - countrycode-1.9.0/countrycode/tests/testthat/test-custom-dictionary.R | 76 - countrycode-1.9.0/countrycode/tests/testthat/test-destination-only.R | 24 countrycode-1.9.0/countrycode/tests/testthat/test-destination.R | 11 countrycode-1.9.0/countrycode/tests/testthat/test-dictionary_attributes.R | 34 countrycode-1.9.0/countrycode/tests/testthat/test-nomatch.R | 106 + countrycode-1.9.0/countrycode/tests/testthat/test-regex-internal.R | 20 countrycode-1.9.0/countrycode/tests/testthat/test-shared-fixtures.R |only countrycode-1.9.0/countrycode/tests/testthat/test-unicode-symbols.R | 25 30 files changed, 1016 insertions(+), 773 deletions(-)
Title: Write Reusable, Composable and Modular R Code
Description: A modern module system for R. Organise code into hierarchical,
composable, reusable modules, and use it effortlessly across projects via a
flexible, declarative dependency loading syntax.
Author: Konrad Rudolph [aut, cre] ,
Michael Schubert [ctb]
Maintainer: Konrad Rudolph <konrad.rudolph@gmail.com>
Diff between box versions 1.2.2 dated 2026-04-10 and 1.2.3 dated 2026-08-20
DESCRIPTION | 8 ++--- MD5 | 53 +++++++++++++++++------------------ NEWS.md | 7 ++++ R/box-package.r | 18 +++++++++-- R/paths.r | 4 +- inst/doc/box.html | 9 +++-- inst/doc/box.rmd | 2 - inst/doc/compiled-code.html | 7 ++-- inst/doc/contributing.html | 28 ++++++++++++++++-- inst/doc/contributing.rmd | 21 +++++++++++++ inst/doc/faq.html | 7 ++-- inst/doc/migration.html | 13 ++++---- inst/doc/migration.rmd | 4 +- inst/doc/mod-envs.html | 9 +++-- inst/doc/related.html | 6 +-- inst/doc/related.rmd | 2 - inst/doc/testing.html | 7 ++-- man/box.Rd | 5 +++ man/loaded.Rd | 1 man/parse_export_specs.Rd | 8 ----- tests/testthat/helper-callr.r | 6 --- tests/testthat/support/rprofile.r | 3 - tests/testthat/test-file.r | 4 +- vignettes/box.rmd | 2 - vignettes/contributing.rmd | 21 +++++++++++++ vignettes/extract-benchmark.rmd.skip |only vignettes/migration.rmd | 4 +- vignettes/related.rmd | 2 - 28 files changed, 171 insertions(+), 90 deletions(-)
Title: A S3 Class for Vectors of 64bit Integers
Description: Package 'bit64' provides serializable S3 atomic 64bit (signed) integers.
These are useful for handling database keys and exact counting in +-2^63.
WARNING: do not use them as replacement for 32bit integers, integer64 are not
supported for subscripting by R-core and they have different semantics when
combined with double, e.g. integer64 + double => integer64.
Class integer64 can be used in vectors, matrices, arrays and data.frames.
Methods are available for coercion from and to logicals, integers, doubles,
characters and factors as well as many elementwise and summary functions.
Many fast algorithmic operations such as 'match' and 'order' support inter-
active data exploration and manipulation and optionally leverage caching.
Author: Michael Chirico [aut, cre],
Jens Oehlschlaegel [aut],
Leonardo Silvestri [ctb],
Ofek Shilon [ctb],
Christian Ullerich [ctb]
Maintainer: Michael Chirico <michaelchirico4@gmail.com>
Diff between bit64 versions 4.8.2 dated 2026-05-19 and 4.8.4 dated 2026-08-20
DESCRIPTION | 8 MD5 | 72 +- NAMESPACE | 1 NEWS.md | 17 R/bit64-package.R | 36 - R/hash64.R | 8 R/highlevel64.R | 79 +- R/integer64.R | 239 +++++--- R/matrix64.R | 55 + R/ops64.R | 79 +- R/patch64.R | 22 R/setops64.R | 72 +- R/zzz.R | 57 +- man/as.integer64.character.Rd | 5 man/bit64-package.Rd | 3 man/c.integer64.Rd | 4 man/cache.Rd | 4 man/hashcache.Rd | 4 man/ops64.Rd | 18 man/ramsort.integer64.Rd | 4 man/rep.integer64.Rd | 3 man/runif64.Rd | 4 man/sets.Rd | 6 src/bsearch.c | 241 -------- src/integer64.c | 214 +++---- src/integer64.h | 202 +++++-- src/sortuse64.c | 3 tests/testthat/test-bit64-package.R | 6 tests/testthat/test-cache.R | 124 ++++ tests/testthat/test-hash64.R | 65 ++ tests/testthat/test-highlevel64.R | 374 ++++++++++++- tests/testthat/test-integer64.R | 1006 +++++++++++++++++++++++++----------- tests/testthat/test-matrix64.R | 194 ++++-- tests/testthat/test-ops64.R | 204 ++++++- tests/testthat/test-setops64.R | 48 - tests/testthat/test-sort64.R | 288 +++++++++- tests/testthat/test-sortuse64.R | 46 + 37 files changed, 2605 insertions(+), 1210 deletions(-)
Title: Deal with Dependencies
Description: Manage dependencies during package development. This can
retrieve all dependencies that are used in ".R" files in the "R/"
directory, in ".Rmd" files in "vignettes/" directory and in 'roxygen2'
documentation of functions. There is a function to update the
"DESCRIPTION" file of your package with 'CRAN' packages or any other
remote package. All functions to retrieve dependencies of ".R"
scripts and ".Rmd" or ".qmd" files can be used independently of a
package development.
Author: Vincent Guyader [cre, aut] ,
Sebastien Rochette [aut] ,
Murielle Delmotte [aut] ,
Swann Floc'hlay [aut] ,
ThinkR [cph, fnd]
Maintainer: Vincent Guyader <vincent@thinkr.fr>
Diff between attachment versions 1.0.0 dated 2026-04-25 and 1.1.0 dated 2026-08-20
DESCRIPTION | 6 MD5 | 51 NAMESPACE | 2 NEWS.md | 29 R/add_from_examples.R | 74 + R/att_to_description.R | 24 R/create_renv.R | 2 build/vignette.rds |binary inst/doc/a-fill-pkg-description.R | 195 +-- inst/doc/a-fill-pkg-description.Rmd | 10 inst/doc/a-fill-pkg-description.html | 1178 +++++++++++----------- inst/doc/b-bookdown-and-scripts.R | 102 - inst/doc/b-bookdown-and-scripts.html | 955 ++++++++--------- inst/doc/create-dependencies-file.R | 68 - inst/doc/create-dependencies-file.html | 825 +++++++-------- inst/doc/use_renv.R | 40 inst/doc/use_renv.html | 785 +++++++------- man/att_amend_desc.Rd | 7 man/att_from_examples.Rd | 6 man/attachment-deprecated.Rd | 7 tests/testthat/f1Rmd | 174 +-- tests/testthat/f2R | 96 - tests/testthat/fake_namespace | 12 tests/testthat/test-att_amend_desc_version_pins.R |only tests/testthat/test-att_from_namespace.R | 113 ++ tests/testthat/test-renv_create.R | 42 vignettes/a-fill-pkg-description.Rmd | 10 27 files changed, 2539 insertions(+), 2274 deletions(-)
Title: Automatic Replication Tools for Meta-Analysis
Description: Provides a unified and straightforward interface for
performing a variety of meta-analysis methods directly from user data.
Users can input a data frame, specify key parameters, and effortlessly
execute and compare multiple common meta-analytic models. Designed for
immediate usability, the package facilitates transparent, reproducible
research without manual implementation of each analytical method.
Ideal for researchers aiming for efficiency and reproducibility, it
streamlines workflows from data preparation to results interpretation.
Author: Petr Čala [aut, cre]
Maintainer: Petr Čala <61505008@fsv.cuni.cz>
Diff between artma versions 0.3.3 dated 2026-02-11 and 0.4.1 dated 2026-08-20
artma-0.3.3/artma/R/dummy_functions.R |only artma-0.3.3/artma/R/globals.R |only artma-0.3.3/artma/R/linters.R |only artma-0.3.3/artma/R/transformations.R |only artma-0.3.3/artma/inst/artma/calc/dof.R |only artma-0.3.3/artma/inst/artma/calc/pcc.R |only artma-0.3.3/artma/inst/artma/data/fill.R |only artma-0.3.3/artma/inst/artma/data_config/index.R |only artma-0.3.3/artma/inst/artma/libs/core/number.R |only artma-0.3.3/artma/inst/artma/libs/infrastructure/debug.R |only artma-0.3.3/artma/inst/artma/libs/infrastructure/polyfills.R |only artma-0.3.3/artma/inst/artma/testing |only artma-0.3.3/artma/man/autonomy.describe.Rd |only artma-0.3.3/artma/man/autonomy.get.Rd |only artma-0.3.3/artma/man/autonomy.is_full.Rd |only artma-0.3.3/artma/man/autonomy.is_set.Rd |only artma-0.3.3/artma/man/autonomy.levels.Rd |only artma-0.3.3/artma/man/autonomy.set.Rd |only artma-0.3.3/artma/man/config.fix.Rd |only artma-0.3.3/artma/man/config.get.Rd |only artma-0.3.3/artma/man/config.overrides.Rd |only artma-0.3.3/artma/man/config.reset.Rd |only artma-0.3.3/artma/man/config.set.Rd |only artma-0.3.3/artma/man/data.preview.Rd |only artma-0.3.3/artma/man/dir_create_linter.Rd |only artma-0.3.3/artma/man/indentation_guard_clause_linter.Rd |only artma-0.3.3/artma/man/is_devtools_load.Rd |only artma-0.3.3/artma/man/methods.list.Rd |only artma-0.3.3/artma/man/options.copy.Rd |only artma-0.3.3/artma/man/options.create.Rd |only artma-0.3.3/artma/man/options.delete.Rd |only artma-0.3.3/artma/man/options.fix.Rd |only artma-0.3.3/artma/man/options.help.Rd |only artma-0.3.3/artma/man/options.list.Rd |only artma-0.3.3/artma/man/options.load.Rd |only artma-0.3.3/artma/man/options.modify.Rd |only artma-0.3.3/artma/man/options.open.Rd |only artma-0.3.3/artma/man/options.print_default_dir.Rd |only artma-0.3.3/artma/man/options.remove.Rd |only artma-0.3.3/artma/man/options.validate.Rd |only artma-0.3.3/artma/man/results.dir.Rd |only artma-0.3.3/artma/man/results.open.Rd |only artma-0.3.3/artma/man/viz.get.Rd |only artma-0.3.3/artma/man/viz.set.Rd |only artma-0.3.3/artma/man/viz.themes.Rd |only artma-0.3.3/artma/tests/testthat/test-dir_create_linter.R |only artma-0.3.3/artma/tests/testthat/test-options-significance-marks.R |only artma-0.3.3/artma/tests/testthat/test-polyfills.R |only artma-0.4.1/artma/DESCRIPTION | 46 artma-0.4.1/artma/MD5 | 494 +++-- artma-0.4.1/artma/NAMESPACE | 41 artma-0.4.1/artma/NEWS.md | 409 ++++ artma-0.4.1/artma/R/aaa.R | 75 artma-0.4.1/artma/R/artma.R | 521 +++++ artma-0.4.1/artma/R/autonomy.R | 109 - artma-0.4.1/artma/R/cli.R |only artma-0.4.1/artma/R/data_config.R | 64 artma-0.4.1/artma/R/data_preview.R | 53 artma-0.4.1/artma/R/deprecated.R |only artma-0.4.1/artma/R/generated_check_manifest.R |only artma-0.4.1/artma/R/methods.R | 46 artma-0.4.1/artma/R/options.R | 660 ++++--- artma-0.4.1/artma/R/print.R | 16 artma-0.4.1/artma/R/report.R |only artma-0.4.1/artma/R/results.R | 30 artma-0.4.1/artma/R/viz.R | 53 artma-0.4.1/artma/R/zzz.R | 34 artma-0.4.1/artma/build/vignette.rds |binary artma-0.4.1/artma/inst/artma/calc/index.R | 4 artma-0.4.1/artma/inst/artma/calc/meta.R | 29 artma-0.4.1/artma/inst/artma/calc/methods/elliott.R | 459 ++-- artma-0.4.1/artma/inst/artma/calc/methods/elliott_cache.R |only artma-0.4.1/artma/inst/artma/calc/methods/endo_kink.R | 14 artma-0.4.1/artma/inst/artma/calc/methods/maive.R | 55 artma-0.4.1/artma/inst/artma/calc/methods/selection_model.R | 59 artma-0.4.1/artma/inst/artma/calc/methods/stem.R | 46 artma-0.4.1/artma/inst/artma/cli |only artma-0.4.1/artma/inst/artma/const.R | 70 artma-0.4.1/artma/inst/artma/data/cache_signatures.R | 136 + artma-0.4.1/artma/inst/artma/data/column_recognition.R | 138 - artma-0.4.1/artma/inst/artma/data/compute.R | 198 +- artma-0.4.1/artma/inst/artma/data/configure.R |only artma-0.4.1/artma/inst/artma/data/index.R | 177 + artma-0.4.1/artma/inst/artma/data/interactive_mapping.R | 67 artma-0.4.1/artma/inst/artma/data/method_requirements.R |only artma-0.4.1/artma/inst/artma/data/mock.R |only artma-0.4.1/artma/inst/artma/data/na_handling.R | 307 ++- artma-0.4.1/artma/inst/artma/data/normalize.R |only artma-0.4.1/artma/inst/artma/data/preprocess.R | 547 ++--- artma-0.4.1/artma/inst/artma/data/profile.R |only artma-0.4.1/artma/inst/artma/data/read.R | 380 +--- artma-0.4.1/artma/inst/artma/data/schema_detect.R |only artma-0.4.1/artma/inst/artma/data/schema_persist.R |only artma-0.4.1/artma/inst/artma/data/schema_reconcile.R |only artma-0.4.1/artma/inst/artma/data/schema_ui.R |only artma-0.4.1/artma/inst/artma/data/smart_detection.R | 45 artma-0.4.1/artma/inst/artma/data/utils.R | 225 +- artma-0.4.1/artma/inst/artma/data_config/column_mapping.R |only artma-0.4.1/artma/inst/artma/data_config/defaults.R | 51 artma-0.4.1/artma/inst/artma/data_config/read.R | 9 artma-0.4.1/artma/inst/artma/data_config/resolve.R | 121 + artma-0.4.1/artma/inst/artma/data_config/utils.R | 5 artma-0.4.1/artma/inst/artma/data_config/write.R | 156 + artma-0.4.1/artma/inst/artma/econometric/best_practice_estimate.R |only artma-0.4.1/artma/inst/artma/econometric/bma.R | 457 +++- artma-0.4.1/artma/inst/artma/econometric/exogeneity.R | 618 ++++-- artma-0.4.1/artma/inst/artma/econometric/fma.R | 52 artma-0.4.1/artma/inst/artma/econometric/linear.R | 571 +++++- artma-0.4.1/artma/inst/artma/econometric/maive.R |only artma-0.4.1/artma/inst/artma/econometric/nonlinear.R | 479 ++++- artma-0.4.1/artma/inst/artma/econometric/p_hacking.R | 790 ++++---- artma-0.4.1/artma/inst/artma/econometric/vcov.R |only artma-0.4.1/artma/inst/artma/interactive/ask.R | 2 artma-0.4.1/artma/inst/artma/interactive/box_plot.R | 4 artma-0.4.1/artma/inst/artma/interactive/effect_summary_stats.R | 76 artma-0.4.1/artma/inst/artma/interactive/prima_facie_graphs.R | 2 artma-0.4.1/artma/inst/artma/interactive/save_preference.R | 33 artma-0.4.1/artma/inst/artma/interactive/welcome.R | 4 artma-0.4.1/artma/inst/artma/libs/core/autonomy.R | 197 -- artma-0.4.1/artma/inst/artma/libs/core/file.R | 41 artma-0.4.1/artma/inst/artma/libs/core/grouping.R |only artma-0.4.1/artma/inst/artma/libs/core/log.R |only artma-0.4.1/artma/inst/artma/libs/core/string.R | 82 artma-0.4.1/artma/inst/artma/libs/core/utils.R | 107 - artma-0.4.1/artma/inst/artma/libs/core/validation.R | 48 artma-0.4.1/artma/inst/artma/libs/formatting/results.R | 228 ++ artma-0.4.1/artma/inst/artma/libs/formatting/summary_table.R |only artma-0.4.1/artma/inst/artma/libs/infrastructure/cache.R | 720 ++----- artma-0.4.1/artma/inst/artma/libs/infrastructure/output_files.R |only artma-0.4.1/artma/inst/artma/libs/infrastructure/source_fingerprint.R |only artma-0.4.1/artma/inst/artma/methods/best_practice_estimate.R |only artma-0.4.1/artma/inst/artma/methods/bma.R | 384 +++- artma-0.4.1/artma/inst/artma/methods/box_plot.R | 154 - artma-0.4.1/artma/inst/artma/methods/effect_summary_stats.R | 232 +- artma-0.4.1/artma/inst/artma/methods/exogeneity_tests.R | 139 + artma-0.4.1/artma/inst/artma/methods/fma.R | 249 +- artma-0.4.1/artma/inst/artma/methods/funnel_plot.R | 276 +-- artma-0.4.1/artma/inst/artma/methods/linear_tests.R | 192 +- artma-0.4.1/artma/inst/artma/methods/maive.R |only artma-0.4.1/artma/inst/artma/methods/nonlinear_tests.R | 139 - artma-0.4.1/artma/inst/artma/methods/p_hacking_tests.R | 357 ++- artma-0.4.1/artma/inst/artma/methods/prima_facie_graphs.R | 121 - artma-0.4.1/artma/inst/artma/methods/robma.R |only artma-0.4.1/artma/inst/artma/methods/t_stat_histogram.R | 286 --- artma-0.4.1/artma/inst/artma/methods/variable_summary_stats.R | 114 + artma-0.4.1/artma/inst/artma/modules/index.R | 3 artma-0.4.1/artma/inst/artma/modules/method_execution.R |only artma-0.4.1/artma/inst/artma/modules/methods_table.R |only artma-0.4.1/artma/inst/artma/modules/runtime_methods.R | 406 ++++ artma-0.4.1/artma/inst/artma/modules/utils.R | 17 artma-0.4.1/artma/inst/artma/options/ask.R | 20 artma-0.4.1/artma/inst/artma/options/column_preprocessing.R | 105 - artma-0.4.1/artma/inst/artma/options/files.R | 8 artma-0.4.1/artma/inst/artma/options/index.R | 6 artma-0.4.1/artma/inst/artma/options/inspect.R |only artma-0.4.1/artma/inst/artma/options/migrate.R |only artma-0.4.1/artma/inst/artma/options/prompts.R | 92 - artma-0.4.1/artma/inst/artma/options/resolver.R |only artma-0.4.1/artma/inst/artma/options/significance_marks.R | 52 artma-0.4.1/artma/inst/artma/options/template.R | 255 +- artma-0.4.1/artma/inst/artma/options/templates/options_template.yaml | 786 ++++++-- artma-0.4.1/artma/inst/artma/options/type_registry.R |only artma-0.4.1/artma/inst/artma/options/typed_accessors.R |only artma-0.4.1/artma/inst/artma/options/utils.R | 109 - artma-0.4.1/artma/inst/artma/output/export.R | 277 ++- artma-0.4.1/artma/inst/artma/output/latex.R |only artma-0.4.1/artma/inst/artma/output/ma_table.R |only artma-0.4.1/artma/inst/artma/output/run_manifest.R |only artma-0.4.1/artma/inst/artma/output/run_summary.R |only artma-0.4.1/artma/inst/artma/paths.R | 28 artma-0.4.1/artma/inst/artma/report |only artma-0.4.1/artma/inst/artma/variable/bma.R | 235 ++ artma-0.4.1/artma/inst/artma/variable/detection.R | 221 -- artma-0.4.1/artma/inst/artma/variable/suggestion.R | 154 - artma-0.4.1/artma/inst/artma/visualization/best_practice_estimate.R |only artma-0.4.1/artma/inst/artma/visualization/export.R | 299 +++ artma-0.4.1/artma/inst/artma/visualization/fork_safety.R |only artma-0.4.1/artma/inst/artma/visualization/index.R | 4 artma-0.4.1/artma/inst/artma/visualization/options.R | 29 artma-0.4.1/artma/inst/artma/visualization/theme.R | 7 artma-0.4.1/artma/inst/artma/visualization/ticks.R |only artma-0.4.1/artma/inst/cli |only artma-0.4.1/artma/inst/doc/getting-started.Rmd | 70 artma-0.4.1/artma/inst/doc/getting-started.html | 95 - artma-0.4.1/artma/inst/doc/methods-overview.Rmd |only artma-0.4.1/artma/inst/doc/methods-overview.html |only artma-0.4.1/artma/inst/doc/options-files.Rmd | 179 + artma-0.4.1/artma/inst/doc/options-files.html | 303 ++- artma-0.4.1/artma/inst/doc/release-cycle.html | 3 artma-0.4.1/artma/man/artma-deprecated.Rd |only artma-0.4.1/artma/man/artma-package.Rd | 6 artma-0.4.1/artma/man/artma.Rd | 58 artma-0.4.1/artma/man/autonomy_get.Rd |only artma-0.4.1/artma/man/autonomy_is_full.Rd |only artma-0.4.1/artma/man/autonomy_is_set.Rd |only artma-0.4.1/artma/man/autonomy_set.Rd |only artma-0.4.1/artma/man/cli_build_run_manifest.Rd |only artma-0.4.1/artma/man/cli_dispatch.Rd |only artma-0.4.1/artma/man/cli_dispatch_options.Rd |only artma-0.4.1/artma/man/cli_dispatch_run.Rd |only artma-0.4.1/artma/man/cli_emit_to_stderr.Rd |only artma-0.4.1/artma/man/cli_install.Rd |only artma-0.4.1/artma/man/cli_run.Rd |only artma-0.4.1/artma/man/config_fix.Rd |only artma-0.4.1/artma/man/config_get.Rd |only artma-0.4.1/artma/man/config_overrides.Rd |only artma-0.4.1/artma/man/config_reset.Rd |only artma-0.4.1/artma/man/config_set.Rd |only artma-0.4.1/artma/man/data_preview.Rd |only artma-0.4.1/artma/man/invoke_runtime_methods.Rd | 23 artma-0.4.1/artma/man/methods_list.Rd |only artma-0.4.1/artma/man/offer_options_fix.Rd |only artma-0.4.1/artma/man/options_copy.Rd |only artma-0.4.1/artma/man/options_create.Rd |only artma-0.4.1/artma/man/options_delete.Rd |only artma-0.4.1/artma/man/options_diff.Rd |only artma-0.4.1/artma/man/options_fix.Rd |only artma-0.4.1/artma/man/options_help.Rd |only artma-0.4.1/artma/man/options_list.Rd |only artma-0.4.1/artma/man/options_load.Rd |only artma-0.4.1/artma/man/options_modify.Rd |only artma-0.4.1/artma/man/options_open.Rd |only artma-0.4.1/artma/man/options_print_default_dir.Rd |only artma-0.4.1/artma/man/options_validate.Rd |only artma-0.4.1/artma/man/prompt_install_missing_packages.Rd |only artma-0.4.1/artma/man/report_render.Rd |only artma-0.4.1/artma/man/results_dir.Rd |only artma-0.4.1/artma/man/results_open.Rd |only artma-0.4.1/artma/man/viz_get.Rd |only artma-0.4.1/artma/man/viz_set.Rd |only artma-0.4.1/artma/man/viz_themes.Rd |only artma-0.4.1/artma/tests/E2E/fixtures |only artma-0.4.1/artma/tests/E2E/test-cli.R |only artma-0.4.1/artma/tests/E2E/test-smoke.R |only artma-0.4.1/artma/tests/testthat/helper-linters.R |only artma-0.4.1/artma/tests/testthat/helper-mocking.R |only artma-0.4.1/artma/tests/testthat/modules |only artma-0.4.1/artma/tests/testthat/setup.R | 80 artma-0.4.1/artma/tests/testthat/test-autonomy.R | 297 +-- artma-0.4.1/artma/tests/testthat/test-best-practice-estimate.R |only artma-0.4.1/artma/tests/testthat/test-bma-auto-select.R | 7 artma-0.4.1/artma/tests/testthat/test-bma-collinearity.R | 16 artma-0.4.1/artma/tests/testthat/test-bma-derived-encodings.R |only artma-0.4.1/artma/tests/testthat/test-bma-result-unwrap.R |only artma-0.4.1/artma/tests/testthat/test-bma.R | 523 +++++ artma-0.4.1/artma/tests/testthat/test-bms-reproducibility.R |only artma-0.4.1/artma/tests/testthat/test-box-plot-study-label.R | 63 artma-0.4.1/artma/tests/testthat/test-box-testthat-imports.R |only artma-0.4.1/artma/tests/testthat/test-cache-signature-components.R |only artma-0.4.1/artma/tests/testthat/test-calc-endo-kink.R |only artma-0.4.1/artma/tests/testthat/test-calc-maive.R |only artma-0.4.1/artma/tests/testthat/test-calc-meta.R |only artma-0.4.1/artma/tests/testthat/test-calc-selection-model.R |only artma-0.4.1/artma/tests/testthat/test-calc-stem.R |only artma-0.4.1/artma/tests/testthat/test-cli.R |only artma-0.4.1/artma/tests/testthat/test-data-auto-detection-confirmation.R | 32 artma-0.4.1/artma/tests/testthat/test-data-cache-signature.R |only artma-0.4.1/artma/tests/testthat/test-data-column-recognition.R | 18 artma-0.4.1/artma/tests/testthat/test-data-column-resolution.R | 20 artma-0.4.1/artma/tests/testthat/test-data-compute.R | 193 +- artma-0.4.1/artma/tests/testthat/test-data-config-defaults.R | 137 - artma-0.4.1/artma/tests/testthat/test-data-config-fix.R |only artma-0.4.1/artma/tests/testthat/test-data-config-resolve.R | 147 + artma-0.4.1/artma/tests/testthat/test-data-configure.R |only artma-0.4.1/artma/tests/testthat/test-data-index.R | 15 artma-0.4.1/artma/tests/testthat/test-data-interactive-mapping.R | 165 + artma-0.4.1/artma/tests/testthat/test-data-method-requirements.R |only artma-0.4.1/artma/tests/testthat/test-data-mock.R |only artma-0.4.1/artma/tests/testthat/test-data-na-handling.R |only artma-0.4.1/artma/tests/testthat/test-data-prepare-phases.R |only artma-0.4.1/artma/tests/testthat/test-data-preprocess.R | 419 +--- artma-0.4.1/artma/tests/testthat/test-data-preview.R | 83 artma-0.4.1/artma/tests/testthat/test-data-profile.R |only artma-0.4.1/artma/tests/testthat/test-data-read.R |only artma-0.4.1/artma/tests/testthat/test-data-schema-detect.R |only artma-0.4.1/artma/tests/testthat/test-data-schema-reconcile.R |only artma-0.4.1/artma/tests/testthat/test-data-smart-detection.R | 27 artma-0.4.1/artma/tests/testthat/test-data-utils.R | 339 +++ artma-0.4.1/artma/tests/testthat/test-deprecated-aliases.R |only artma-0.4.1/artma/tests/testthat/test-econometric-exogeneity.R |only artma-0.4.1/artma/tests/testthat/test-econometric-maive.R |only artma-0.4.1/artma/tests/testthat/test-econometric-p-hacking.R |only artma-0.4.1/artma/tests/testthat/test-econometric-vcov.R |only artma-0.4.1/artma/tests/testthat/test-effect-summary-stats-integration.R | 237 +- artma-0.4.1/artma/tests/testthat/test-effect-summary-stats-interactive.R | 117 - artma-0.4.1/artma/tests/testthat/test-effect-summary-stats.R | 21 artma-0.4.1/artma/tests/testthat/test-elliott-cdfs-cache.R |only artma-0.4.1/artma/tests/testthat/test-elliott-simulate-cdfs.R | 85 artma-0.4.1/artma/tests/testthat/test-fma.R | 247 ++ artma-0.4.1/artma/tests/testthat/test-funnel-plot.R | 166 + artma-0.4.1/artma/tests/testthat/test-generated-check-manifest.R |only artma-0.4.1/artma/tests/testthat/test-grouping.R |only artma-0.4.1/artma/tests/testthat/test-indentation_guard_clause_linter.R | 30 artma-0.4.1/artma/tests/testthat/test-interactive.R |only artma-0.4.1/artma/tests/testthat/test-libs-cache.R | 263 +- artma-0.4.1/artma/tests/testthat/test-libs-editor.R | 10 artma-0.4.1/artma/tests/testthat/test-libs-string.R |only artma-0.4.1/artma/tests/testthat/test-linear-tests.R | 920 +++++++++- artma-0.4.1/artma/tests/testthat/test-log.R |only artma-0.4.1/artma/tests/testthat/test-ma-table.R |only artma-0.4.1/artma/tests/testthat/test-method-estimates-contract.R |only artma-0.4.1/artma/tests/testthat/test-method-execution.R |only artma-0.4.1/artma/tests/testthat/test-methods-p-hacking-exogeneity.R |only artma-0.4.1/artma/tests/testthat/test-methods-table.R |only artma-0.4.1/artma/tests/testthat/test-methods-vignette-parity.R |only artma-0.4.1/artma/tests/testthat/test-nonlinear-tests.R | 336 +++ artma-0.4.1/artma/tests/testthat/test-nonlinear-waap-top10.R |only artma-0.4.1/artma/tests/testthat/test-options-column-preprocessing.R | 189 -- artma-0.4.1/artma/tests/testthat/test-options-inspect.R |only artma-0.4.1/artma/tests/testthat/test-options-migration.R |only artma-0.4.1/artma/tests/testthat/test-options-prompt-input.R |only artma-0.4.1/artma/tests/testthat/test-options-resolver.R |only artma-0.4.1/artma/tests/testthat/test-options-roundtrip.R |only artma-0.4.1/artma/tests/testthat/test-options-strict.R |only artma-0.4.1/artma/tests/testthat/test-options-template-parity.R |only artma-0.4.1/artma/tests/testthat/test-options-type-registry.R |only artma-0.4.1/artma/tests/testthat/test-options-typed-accessors.R |only artma-0.4.1/artma/tests/testthat/test-options.R | 605 ++++++ artma-0.4.1/artma/tests/testthat/test-output-export.R |only artma-0.4.1/artma/tests/testthat/test-output-latex.R |only artma-0.4.1/artma/tests/testthat/test-paths.R |only artma-0.4.1/artma/tests/testthat/test-prima-facie-graphs.R |only artma-0.4.1/artma/tests/testthat/test-release-notes.R |only artma-0.4.1/artma/tests/testthat/test-report-integration.R |only artma-0.4.1/artma/tests/testthat/test-report-render.R |only artma-0.4.1/artma/tests/testthat/test-result-formatters.R | 121 + artma-0.4.1/artma/tests/testthat/test-robma.R |only artma-0.4.1/artma/tests/testthat/test-run-manifest.R |only artma-0.4.1/artma/tests/testthat/test-run-summary.R |only artma-0.4.1/artma/tests/testthat/test-run.R | 538 +++++ artma-0.4.1/artma/tests/testthat/test-runtime-methods.R | 279 +++ artma-0.4.1/artma/tests/testthat/test-save-preference.R |only artma-0.4.1/artma/tests/testthat/test-schema-reconcile-integration.R |only artma-0.4.1/artma/tests/testthat/test-summary-table-characterization.R |only artma-0.4.1/artma/tests/testthat/test-t-stat-histogram.R | 181 + artma-0.4.1/artma/tests/testthat/test-variable-suggestion.R | 101 - artma-0.4.1/artma/tests/testthat/test-variable-summary-stats.R |only artma-0.4.1/artma/tests/testthat/test-visualization-fork-safety.R |only artma-0.4.1/artma/tests/testthat/test-visualization.R |only artma-0.4.1/artma/vignettes/getting-started.Rmd | 70 artma-0.4.1/artma/vignettes/methods-overview.Rmd |only artma-0.4.1/artma/vignettes/options-files.Rmd | 179 + 342 files changed, 16390 insertions(+), 7839 deletions(-)
Title: Joint N-Mixture Models for Site-Associated Species
Description: Fits univariate and joint N-mixture models for data on two unmarked site-associated species. Includes functions to estimate latent abundances through empirical Bayes methods.
Author: Rafael de Andrade Moral [aut, cre],
Clarice Garcia Borges Demetrio [aut],
John Hinde [aut]
Maintainer: Rafael de Andrade Moral <rafael_moral@yahoo.com.br>
Diff between jointNmix versions 1.0 dated 2016-11-11 and 1.0-1 dated 2026-08-20
DESCRIPTION | 12 +++++++----- MD5 | 10 +++++----- R/Nmix.R | 2 +- R/jointNmix.R | 2 +- build/partial.rdb |binary man/jointNmix.Rd | 4 ++-- 6 files changed, 16 insertions(+), 14 deletions(-)