Title: Pipeline for Explainable Machine Learning with Functional Data
Description: Implements the Variable importance Explainable Elastic Shape Analysis pipeline for explainable machine learning with functional data inputs. Converts training and testing data functional inputs to elastic shape analysis principal components that account for vertical and/or horizontal variability. Computes feature importance to identify important principal components and visualizes variability captured by functional principal components. See Goode et al. (2025) <doi:10.48550/arXiv.2501.07602> for technical details about the methodology.
Author: Katherine Goode [cre, aut],
J. Derek Tucker [aut],
Sandia National Laboratories [cph, fnd]
Maintainer: Katherine Goode <kjgoode@sandia.gov>
Diff between veesa versions 0.1.7 dated 2025-12-04 and 0.1.8 dated 2026-09-18
veesa-0.1.7/veesa/R/center_pcdirs.R |only veesa-0.1.8/veesa/DESCRIPTION | 13 veesa-0.1.8/veesa/MD5 | 59 +-- veesa-0.1.8/veesa/NAMESPACE | 86 ++-- veesa-0.1.8/veesa/NEWS.md | 29 + veesa-0.1.8/veesa/R/align_pcdirs.R | 5 veesa-0.1.8/veesa/R/center_warping_funs.R | 8 veesa-0.1.8/veesa/R/compute_logloss.R | 12 veesa-0.1.8/veesa/R/compute_nmse.R | 3 veesa-0.1.8/veesa/R/compute_pfi.R | 2 veesa-0.1.8/veesa/R/data_shifted_peaks.R | 2 veesa-0.1.8/veesa/R/plot_pc_diffs.R | 113 ++++-- veesa-0.1.8/veesa/R/plot_pc_directions.R | 60 ++- veesa-0.1.8/veesa/R/prep_testing_data.R | 108 +++++- veesa-0.1.8/veesa/R/prep_training_data.R | 42 +- veesa-0.1.8/veesa/R/simulate_functions.R | 16 veesa-0.1.8/veesa/README.md | 48 ++ veesa-0.1.8/veesa/man/align_pcdirs.Rd | 14 veesa-0.1.8/veesa/man/center_warping_funs.Rd | 4 veesa-0.1.8/veesa/man/compute_pfi.Rd | 3 veesa-0.1.8/veesa/man/plot_pc_diffs.Rd | 6 veesa-0.1.8/veesa/man/plot_pc_directions.Rd | 4 veesa-0.1.8/veesa/man/prep_testing_data.Rd | 48 ++ veesa-0.1.8/veesa/man/prep_training_data.Rd | 34 + veesa-0.1.8/veesa/man/shifted_peaks.Rd | 2 veesa-0.1.8/veesa/man/simulate_functions.Rd | 1 veesa-0.1.8/veesa/tests/testthat/test-align_pcdirs.R |only veesa-0.1.8/veesa/tests/testthat/test-center_warping_funs.R |only veesa-0.1.8/veesa/tests/testthat/test-compute_metrics.R |only veesa-0.1.8/veesa/tests/testthat/test-plot_pc_diffs.R |only veesa-0.1.8/veesa/tests/testthat/test-plot_pc_directions.R | 207 ++++++++---- veesa-0.1.8/veesa/tests/testthat/test-prep_testing_data.R | 104 +++++- veesa-0.1.8/veesa/tests/testthat/test-prep_training_data.R | 35 ++ 33 files changed, 789 insertions(+), 279 deletions(-)
Title: Support Functions for Wrangling and Visualization
Description: Suite of helper functions for data wrangling and visualization.
The only theme for these functions is that they tend towards simple, short, and narrowly-scoped.
These functions are built for tasks that often recur but are not large enough in scope to warrant an ecosystem of interdependent functions.
Author: Nicholas J Lyon [aut, cre, cph]
Maintainer: Nicholas J Lyon <nickjlyon@gmail.com>
Diff between supportR versions 1.6.0 dated 2025-12-21 and 1.6.1 dated 2026-09-18
DESCRIPTION | 16 ++--- MD5 | 17 +++-- NAMESPACE | 7 +- NEWS.md | 94 ++++++++++++++++++------------- R/spellcheck_quarto.r |only README.md | 31 ++-------- build/vignette.rds |binary inst/doc/supportr_03_visualizations.html | 6 - man/spellcheck_quarto.Rd |only man/supportR-package.Rd | 7 +- tests/testthat/test-spellcheck_quarto.r |only 11 files changed, 96 insertions(+), 82 deletions(-)
Title: Analyze Outbreak Models of Multi-Group Populations with
Vaccination
Description: Model infectious disease dynamics in populations
with multiple subgroups having different vaccination rates, transmission
characteristics, and contact patterns. Calculate final and intermediate
outbreak sizes, form age-structured contact models with automatic fetching
of U.S. census data, and explore vaccination scenarios with an interactive
'shiny' dashboard for a model with two subgroups, as described in Nguyen et
al. (2024) <doi:10.1016/j.jval.2024.03.039> and Duong et al. (2026)
<doi:10.1093/ofid/ofaf695.217>.
Author: Damon Toth [aut, cre, cph] ,
Jake Wagoner [aut] ,
Willy Ray [aut],
George Vega Yon [ctb] ,
Centers for Disease Control and Prevention's Center for Forecasting and
Outbreak Analytics [fnd]
Maintainer: Damon Toth <damon.toth@hsc.utah.edu>
Diff between multigroup.vaccine versions 0.1.1 dated 2026-02-09 and 0.1.2 dated 2026-09-18
DESCRIPTION | 8 MD5 | 19 +- NEWS.md | 6 R/contactMatrixPolymod.R | 20 +- build/vignette.rds |binary inst/doc/census_functions_demo.html | 7 inst/doc/contact_matrix_examples.html | 282 ++++++++++++++++---------------- inst/doc/measles_agemodel.html | 48 ++--- inst/doc/run_model_on_command_line.html | 32 +-- inst/extdata/polymod_countries_2005.csv |only man/run_my_app.Rd | 2 11 files changed, 217 insertions(+), 207 deletions(-)
More information about multigroup.vaccine at CRAN
Permanent link
Title: Easy Handling Discrete Time Markov Chains
Description: Functions and S4 methods to create and manage discrete time Markov
chains more easily. In addition functions to perform statistical (fitting
and drawing random variates) and probabilistic (analysis of their structural
proprieties) analysis are provided. See Spedicato (2017) <doi:10.32614/RJ-2017-036>.
Some functions for continuous times Markov chains depend on the suggested ctmcd package.
Author: Giorgio Alfredo Spedicato [aut, cre] ,
Tae Seung Kang [aut],
Sai Bhargav Yalamanchi [aut],
Mildenberger Thoralf [ctb] ,
Deepak Yadav [aut],
Ignacio Cordon [aut] ,
Vandit Jain [ctb],
Toni Giorgino [ctb] ,
Richel J.C. Bilderbeek [ctb] ,
Daniel Ebbert [ [...truncated...]
Maintainer: Giorgio Alfredo Spedicato <spedicato_giorgio@yahoo.it>
Diff between markovchain versions 1.0.0 dated 2026-08-25 and 1.1.1 dated 2026-09-18
DESCRIPTION | 10 MD5 | 60 +- NAMESPACE | 6 NEWS.md | 14 R/RcppExports.R | 10 R/ctmcProbabilistic.R | 32 + R/entropyRate.R |only R/fitHigherOrder.R | 8 R/fittingFunctions.R | 55 +- R/fundamentalMatrix.R |only R/kemeny.R |only R/probabilistic.R | 472 ++++++++++++------- inst/doc/an_introduction_to_markovchain_package.R | 103 ++++ inst/doc/an_introduction_to_markovchain_package.Rmd | 328 +++++++++---- inst/doc/an_introduction_to_markovchain_package.pdf |binary inst/doc/gsoc_2017_additions.html | 13 inst/doc/higher_order_markov_chains.html | 11 man/autoLump.Rd |only man/entropyRate.Rd |only man/fundamentalMatrix.Rd |only man/is.lumpable.Rd |only man/kemenyConstant.Rd |only man/lump.Rd |only src/RcppExports.cpp | 28 + src/ctmcFittingFunctions.cpp | 41 + src/ctmcProbabilistic.cpp | 23 src/fitHigherOrder.cpp | 52 +- src/fittingFunctions.cpp | 19 src/probabilistic.cpp | 364 +++++++++++--- tests/testthat/test-ctmcFittingFunctions.R |only tests/testthat/test-entropyRate.R |only tests/testthat/test-fitHigherOrder.R |only tests/testthat/test-fundamentalMatrix.R |only tests/testthat/test-input-hardening.R |only tests/testthat/test-kemeny.R |only tests/testthat/test-lumpability.R |only tests/testthat/testHittingProbabilities.R | 45 + vignettes/an_introduction_to_markovchain_package.Rmd | 328 +++++++++---- vignettes/markovchainBiblio.bib | 37 + 39 files changed, 1533 insertions(+), 526 deletions(-)
Title: Tools Developed by the Long Term Ecological Research Community
Description: Set of the data science tools created by various members of the Long Term
Ecological Research (LTER) community. These functions were initially written largely
as standalone operations and have later been aggregated into this package.
Author: Nicholas Lyon [aut, cre] ,
Angel Chen [aut] ,
Miguel C. Leon [ctb] ,
National Science Foundation [fnd] ,
University of California, Santa Barbara [cph]
Maintainer: Nicholas Lyon <nickjlyon@gmail.com>
Diff between ltertools versions 2.1.0 dated 2025-09-02 and 2.1.1 dated 2026-09-18
DESCRIPTION | 14 ++--- MD5 | 19 +++--- NEWS.md | 72 ++++++++++++++++--------- R/check_key.R | 8 ++ R/standardize.R | 11 ++- README.md | 111 ++++++++++------------------------------ build/vignette.rds |binary inst/doc/ltertools.html | 9 +-- man/check_key.Rd | 4 - man/ltertools-package.Rd | 3 - tests/testthat/test-check_key.R |only 11 files changed, 113 insertions(+), 138 deletions(-)
Title: Access the 'Finto' API
Description: Access and retrieve vocabulary data 'Finto' API <https://api.finto.fi/>, which is a centralized service for interoperable thesauri, ontology and classification schemes for different subject areas.
Author: Akewak Jeba [aut, cre] ,
Leo Lahti [aut]
Maintainer: Akewak Jeba <akewak84@gmail.com>
Diff between finto versions 0.1.1 dated 2025-11-24 and 0.1.2 dated 2026-09-18
DESCRIPTION | 17 +- MD5 | 138 ++++++++-------- NAMESPACE | 5 R/data.R |only R/fetch_kanto_info.R | 2 R/fetch_profession_hierarchy.R | 2 R/fetch_profession_info.R | 2 R/get_alphabetical_index_letters.R | 2 R/get_broader_concepts.R | 2 R/get_broader_transitive_concepts.R | 2 R/get_children_concepts.R | 2 R/get_concept_data.R | 2 R/get_concept_groups.R | 2 R/get_concept_labels.R | 2 R/get_concept_labels_vocid.R | 2 R/get_concepts_by_letter.R | 2 R/get_group_members.R | 2 R/get_hierarchy.R | 2 R/get_kanto.R | 273 ++++++++++++++++++++++++++++----- R/get_label_statistics.R | 2 R/get_mappings.R | 2 R/get_modified_concepts.R | 2 R/get_narrower_concepts.R | 2 R/get_narrower_transitive.R | 2 R/get_new_concepts.R | 2 R/get_related_concepts.R | 2 R/get_top_concepts.R | 2 R/get_types.R | 2 R/get_vocabularies.R | 2 R/get_vocabulary_info.R | 2 R/get_vocabulary_statistics.R | 2 R/get_vocabulary_types.R | 2 R/lookup_concept_by_label.R | 2 R/search_concepts.R | 2 R/search_vocabulary_concepts.R | 2 R/utils.R | 15 + R/yso_places.R |only build/vignette.rds |binary man/fennica_subset.Rd |only man/fetch_kanto_info.Rd | 2 man/fetch_profession_hierarchy.Rd | 2 man/fetch_profession_info.Rd | 2 man/get_alphabetical_index_letters.Rd | 2 man/get_broader_concepts.Rd | 2 man/get_broader_transitive_concepts.Rd | 2 man/get_children_concepts.Rd | 2 man/get_concept_data.Rd | 2 man/get_concept_groups.Rd | 2 man/get_concept_labels.Rd | 2 man/get_concept_labels_vocid.Rd | 2 man/get_concepts_by_letter.Rd | 2 man/get_group_members.Rd | 2 man/get_hierarchy.Rd | 2 man/get_kanto.Rd | 11 + man/get_label_statistics.Rd | 2 man/get_mappings.Rd | 2 man/get_modified_concepts.Rd | 2 man/get_narrower_concepts.Rd | 2 man/get_narrower_transitive.Rd | 2 man/get_new_concepts.Rd | 2 man/get_related_concepts.Rd | 2 man/get_top_concepts.Rd | 2 man/get_types.Rd | 2 man/get_vocabularies.Rd | 2 man/get_vocabulary_info.Rd | 2 man/get_vocabulary_statistics.Rd | 2 man/get_vocabulary_types.Rd | 2 man/lookup_concept_by_label.Rd | 2 man/search_concepts.Rd | 2 man/search_vocabulary_concepts.Rd | 2 man/yso_place.Rd |only tests/testthat/test_search_concepts.R | 3 72 files changed, 463 insertions(+), 119 deletions(-)
Title: Dungeons & Dragons Functions for Players and Dungeon Masters
Description: The goal of 'dndR' is to provide a suite of Dungeons & Dragons related functions.
This package is meant to be useful both to players and Dungeon Masters (DMs).
Some functions apply to many tabletop role-playing games (e.g., dice rolling), but others are focused on Fifth Edition (a.k.a. "5e") and where possible both the 2014 and 2024 versions are supported.
Author: Nicholas Lyon [aut, cre, cph] ,
Tim Schatto-Eckrodt [aut] ,
Humberto Nappo [aut] ,
Billy Mitchell [aut]
Maintainer: Nicholas Lyon <nickjlyon@gmail.com>
Diff between dndR versions 3.1.0 dated 2025-06-11 and 3.1.1 dated 2026-09-18
DESCRIPTION | 16 ++--- MD5 | 26 ++++---- NAMESPACE | 6 +- NEWS.md | 112 ++++++++++++++++---------------------- README.md | 37 +++--------- build/vignette.rds |binary inst/doc/dndr_00_dice.html | 16 +++-- inst/doc/dndr_01_characters.html | 40 +++++++------ inst/doc/dndr_02_creatures.html | 37 ++++++------ inst/doc/dndr_03_spells.html | 5 + inst/doc/dndr_04_encounters.html | 5 + inst/doc/dndr_05_visuals.html | 11 ++- inst/doc/dndr_99_dmg-vs-dndr.html | 4 - man/dndR-package.Rd | 4 + 14 files changed, 150 insertions(+), 169 deletions(-)
Title: Prais-Winsten Estimator for AR(1) Serial Correlation
Description: The Prais-Winsten estimator (Prais & Winsten, 1954) takes into account AR(1) serial correlation of the errors in a linear regression model. The procedure recursively estimates the coefficients and the error autocorrelation of the specified model until sufficient convergence of the AR(1) coefficient is attained.
Author: Franz X. Mohr [aut, cre] ,
Michael Skvrňak [ctb]
Maintainer: Franz X. Mohr <franz.x.mohr@outlook.com>
Diff between prais versions 1.1.4 dated 2025-06-25 and 1.2.0 dated 2026-09-18
DESCRIPTION | 18 +-- MD5 | 43 ++++--- NEWS.md | 76 +++++++++++++ R/data.R | 42 +++---- R/prais_winsten.R | 210 +++++++++++++++++++++++++++++------- R/predict.prais.R | 67 +++++++---- R/print.summary.prais.R | 9 + R/pw_transform.R | 93 ++++++++++++++++ R/summary.prais.R | 46 ++------ R/vcovHC.R | 39 +----- R/vcovPC.R | 54 +++++---- build/partial.rdb |binary inst |only man/barium.Rd | 42 +++---- man/prais-package.Rd | 10 + man/prais_winsten.Rd | 274 ++++++++++++++++++++++-------------------------- man/predict.prais.Rd |only man/summary.prais.Rd | 6 - tests |only 19 files changed, 668 insertions(+), 361 deletions(-)
Title: Optimal Survival Cut-Point Discovery for Time-to-Event Analysis
with 'OptSurvCutR'
Description: Provides a robust workflow for optimal cut-point analysis in
time-to-event ('survival') data. Functions determine the optimal number
of cut-points via find_cutpoint_number(), find their precise locations
via find_cutpoint() using systematic or genetic algorithms (via the
'rgenoud' package), and validate stability via bootstrapping using
validate_cutpoint(). Features include covariate adjustment, parallel
processing, and an extensible S3 plotting engine for clinical
dashboards and diagnostics.
Author: Payton Yau [aut, cre, cph] ,
Suhirthakumar Puvanendran [aut]
Maintainer: Payton Yau <tungon@gmail.com>
Diff between OptSurvCutR versions 0.10.0 dated 2026-06-30 and 0.11.1 dated 2026-09-18
DESCRIPTION | 27 MD5 | 66 - NAMESPACE | 176 ++-- NEWS.md | 90 ++ R/engine-genetic.R | 651 +++++++-------- R/engine-systematic.R | 22 R/find_cutpoint.R | 112 ++ R/find_cutpoint_number.R | 1220 +++++++++++------------------ R/plotting_functions.R | 216 +++-- R/utils-permutations.R | 14 R/validate_cutpoint.R | 747 +++++++++-------- R/validate_cutpoint_methods.R | 569 +++++++------ README.md | 291 +++--- build/partial.rdb |binary build/vignette.rds |binary inst/doc/bilirubin.R | 188 +--- inst/doc/bilirubin.Rmd | 769 +++++++++--------- inst/doc/bilirubin.html | 1197 +++++++++++++--------------- inst/doc/crc.R |only inst/doc/crc.Rmd |only inst/doc/crc.html |only man/OptSurvCutR-package.Rd | 1 man/find_cutpoint.Rd | 65 - man/find_cutpoint_number.Rd | 41 man/plot.find_cutpoint.Rd | 5 man/plot_optimisation_curve.Rd | 36 man/validate_cutpoint.Rd | 9 tests/testthat/helper-data.R | 198 ++-- tests/testthat/test-find_cutpoint.R | 6 tests/testthat/test-find_cutpoint_number.R | 8 tests/testthat/test-plotting.R | 18 tests/testthat/test-stability-metric.R |only tests/testthat/test-utils.R | 56 - tests/testthat/test-validate_cutpoint.R | 4 tests/testthat/test-workflow-integration.R |only vignettes/bilirubin.Rmd | 769 +++++++++--------- vignettes/crc.Rmd |only 37 files changed, 3764 insertions(+), 3807 deletions(-)
Title: Download Radar Data for Biological Research
Description: Load polar volume and vertical profile data for
aeroecological research directly into R. With 'getRad' you can access
data from several sources in Europe and the US and standardize it to
facilitate further exploration in tools such as 'bioRad'.
Author: Bart Kranstauber [aut, cre] ,
Pieter Huybrechts [aut] ),
Peter Desmet [aut] ),
Cecilia Nilsson [ctb] ,
Alexander Tedeschi [ctb] ,
Hidde Leijnse [ctb] ,
Bart Hoekstra [ctb] ,
University of Amsterdam [cph] ,
Biodiversa+ [fnd]
Maintainer: Bart Kranstauber <b.kranstauber@uva.nl>
Diff between getRad versions 0.3.0 dated 2026-06-11 and 0.4.0 dated 2026-09-18
DESCRIPTION | 14 +++--- MD5 | 84 +++++++++++++++++++------------------ NAMESPACE | 1 NEWS.md | 6 ++ R/get_pvol.R | 63 +++++++++++++++++++++++++-- R/get_pvol_cz.R | 5 +- R/get_pvol_de.R | 36 +++++++++++---- R/get_pvol_ee.R | 12 +++-- R/get_pvol_nl.R | 9 ++- R/get_pvol_ord.R |only R/get_pvol_ro.R | 10 +++- R/get_pvol_sk.R | 5 +- R/get_pvol_uk.R |only R/get_pvol_us.R | 7 ++- R/get_vpts.R | 16 +++---- R/get_vpts_aloft.R | 2 R/get_vpts_birdcast.R | 2 R/get_vpts_coverage_aloft.R | 4 - R/get_vpts_coverage_birdcast.R | 4 - R/get_vpts_coverage_rmi.R | 9 ++- R/get_vpts_local_dark_ecology.R | 3 - R/get_vpts_rmi.R | 8 ++- R/get_weather_radars.R | 12 +++-- R/secrets.R | 4 - R/utils.R | 37 ++++++++-------- R/utils_pvol.R | 7 +-- R/utils_vpts_aloft.R | 4 - R/utils_vpts_rmi.R | 8 +-- R/zzz.R | 1 build/vignette.rds |binary inst/doc/supported_sources.R | 30 ++++++++----- inst/doc/supported_sources.Rmd | 43 ++++++++++++------ inst/doc/supported_sources.html | 42 +++++++++++------- man/get_pvol.Rd | 24 +++++++++- man/get_vpts.Rd | 14 +++--- man/get_weather_radars.Rd | 7 +-- tests/testthat/setup.R |only tests/testthat/test-get_pvol.R | 3 + tests/testthat/test-get_pvol_at.R | 8 ++- tests/testthat/test-get_pvol_fi.R | 8 +++ tests/testthat/test-get_pvol_nl.R | 38 +++++++++++++--- tests/testthat/test-get_pvol_ord.R |only tests/testthat/test-get_pvol_ro.R | 39 +++++++++++++++++ tests/testthat/test-get_pvol_us.R | 17 +++++++ vignettes/supported_sources.Rmd | 43 ++++++++++++------ 45 files changed, 478 insertions(+), 211 deletions(-)
Title: A Collection of Tools for Building Cropping System Models
Description: A collection of tools for designing, implementing,
testing, documenting and visualizing dynamic simulation
cropping system models. Models are specified as a combination of
state variables, parameters, intermediate factors and input data that
define a system of ordinary differential equations. Specified models
can be used to simulate dynamic processes using numerical
integration algorithms.
Author: Phillip D Alderman [aut, cre],
Pratishtha Poudel [aut]
Maintainer: Phillip D Alderman <phillip.alderman@okstate.edu>
Diff between csmbuilder versions 0.1.0 dated 2026-04-03 and 0.1.1 dated 2026-09-18
DESCRIPTION | 10 +- MD5 | 33 ++++---- NAMESPACE | 4 NEWS.md | 14 +++ R/csm_create_data_structure.R | 13 ++- R/csm_render_model.R | 12 +- R/csm_run_sim_group.R |only R/helper_functions.R |only R/utilities.R | 132 -------------------------------- inst/tinytest/test_csm_run_sim_group.R |only inst/tinytest/test_pheno_tt.R | 22 +++-- inst/tinytest/test_pheno_vrn.R | 21 +++-- inst/tinytest/test_simple_wheat.R | 38 ++++++--- inst/tinytest/test_soil_water_balance.R | 66 +++++++++------- man/csm_arr_fr_active.Rd |only man/csm_create_data_structure.Rd | 11 ++ man/csm_get_at_t.Rd | 2 man/csm_hill_down_reg.Rd |only man/csm_hill_up_reg.Rd |only man/csm_mod_arr.Rd | 2 man/csm_run_sim_group.Rd |only 21 files changed, 163 insertions(+), 217 deletions(-)
Title: Tools for the OeNB Data Web Service
Description: Tools to access data from the data web service of the Oesterreichische Nationalbank (OeNB), <https://www.oenb.at/en/Statistics/User-Defined-Tables/webservice.html>.
Author: Franz X. Mohr [aut, cre]
Maintainer: Franz X. Mohr <franz.x.mohr@outlook.com>
Diff between oenb versions 0.0.2 dated 2021-03-22 and 0.1.0 dated 2026-09-18
DESCRIPTION | 22 +-- MD5 | 62 +++++++-- NEWS.md | 51 ++++++++ R/oenb_attributes.R | 116 ++++++++++-------- R/oenb_data.R | 75 +++++++---- R/oenb_dataset.R | 92 ++++++++------ R/oenb_frequency.R | 88 ++++++++------ R/oenb_metadata.R | 95 +++++++++------ R/oenb_toc.R | 63 +++++----- R/utils.R |only README.md | 308 +++++++++++++++++++++++++------------------------ build/vignette.rds |binary inst/CITATION |only inst/doc/oenb.R | 56 ++++---- inst/doc/oenb.html | 216 ++++++++++++++++++++-------------- man/oenb_attributes.Rd | 63 +++++----- man/oenb_data.Rd | 121 +++++++++---------- man/oenb_dataset.Rd | 57 ++++----- man/oenb_frequency.Rd | 63 +++++----- man/oenb_metadata.Rd | 63 +++++----- man/oenb_toc.Rd | 51 ++++---- tests |only 22 files changed, 947 insertions(+), 715 deletions(-)
Title: Download Weather Data from Japan Meteorological Agency Website
Description: Provides features that allow users to download
weather data published by the Japan Meteorological Agency (JMA) website
(<https://www.jma.go.jp/jma/index.html>). The data includes information
dating back to 1976 and aligns with the categories available on the website.
Additionally, users can process the best track data of typhoons and easily
handle earthquake record files.
Author: Shinya Uryu [aut, cph, cre]
Maintainer: Shinya Uryu <suika1127@gmail.com>
Diff between jmastats versions 0.3.0 dated 2025-01-27 and 0.3.1 dated 2026-09-18
DESCRIPTION | 11 MD5 | 63 - NEWS.md | 12 R/appdir.R | 32 R/data.R | 12 R/ggplot2_scales.R | 98 +- R/jma_collect.R | 1241 ++++++++++++++++++---------------- R/kishou_feed.R | 47 - R/nearest_station.R | 164 ++-- R/parse_unit.R | 22 R/pivot_tide_level.R | 44 - R/read_eqdb.R | 127 ++- R/read_jma_weather.R | 56 - R/read_tide_level.R | 268 +++---- R/track.R | 143 ++- R/utils.R | 138 ++- README.md | 8 data/earthquake_station.rda |binary data/stations.rda |binary data/tide_station.rda |binary inst/CITATION |only man/earthquake_station.Rd | 4 man/ggplot2-scales.Rd | 4 man/jmastats-package.Rd | 5 man/nearest_station.Rd | 2 man/stations.Rd | 2 man/tide_station.Rd | 6 man/track.Rd | 2 tests/testthat/test-data.R | 10 tests/testthat/test-internals.R | 48 - tests/testthat/test-nearest_station.R | 51 - tests/testthat/test-palette.R | 4 tests/testthat/test-station.R | 18 33 files changed, 1527 insertions(+), 1115 deletions(-)
Title: Faster K-Medoids Clustering Algorithms: FastPAM, FastCLARA,
FastCLARANS
Description: R wrappers of C++ implementation of Faster K-Medoids clustering algorithms (FastPAM, FastCLARA and FastCLARANS) proposed in Erich Schubert, Peter J. Rousseeuw 2019 <doi:10.1007/978-3-030-32047-8_16>.
Author: Xun Li [aut, cre]
Maintainer: Xun Li <lixun910@gmail.com>
Diff between fastkmedoids versions 1.6 dated 2026-03-26 and 1.7 dated 2026-09-18
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- src/pam.cpp | 1 + src/pam.h | 1 + 4 files changed, 9 insertions(+), 7 deletions(-)
Title: Conditional Inference Trees with Stacked Multiple Imputation
Description: Implements the stacked-imputation workflow for conditional
inference trees ('ctree') described in Sherlock et al. (2026)
<doi:10.1080/00273171.2026.2661244>. When data contain missing values,
multiply imputed datasets (e.g., from 'mice') are stacked vertically
and a single 'ctree' is fit on the combined data. To correct for the
artificially inflated sample size introduced by stacking, every
node-level test statistic is divided by the number of imputations M,
the node-level p-values are recomputed from the chi-squared reference
distribution 'ctree' uses (including its multiplicity adjustment across
candidate splitting variables), and the tree is compressed bottom-up
(the Stack/M correction). Degrees of freedom are derived for each node
and each candidate variable, so univariate, bivariate and
higher-dimensional outcomes are all handled, as are unordered factor
predictors, whose degrees of freedom depend on how many levels remain
in a node. The result is a single interpretable tree [...truncated...]
Author: Phillip Sherlock [aut, cre]
Maintainer: Phillip Sherlock <phillip.sherlock@ufl.edu>
Diff between ctreeMI versions 1.0.1 dated 2026-08-26 and 1.1.0 dated 2026-09-18
DESCRIPTION | 6 - MD5 | 43 +++++---- NAMESPACE | 7 + NEWS.md | 91 ++++++++++++++++++++ R/confirm.R |only R/ctreeMI-package.R | 49 +++++++--- R/ctree_stacked.R | 29 +++--- R/node_table.R | 2 man/check_stackM_extraction.Rd | 4 man/confirm_ctreeMI.Rd |only man/ctreeMI-package.Rd | 78 +++++++++++------ man/ctree_stacked.Rd | 184 +++++++++++++++++++++-------------------- man/discover_confirm.Rd |only man/node_table.Rd | 24 ++--- man/print.ctreeMI.Rd | 8 - man/print.ctreeMI_nodes.Rd | 6 - man/print.ctreeMI_report.Rd | 4 man/prune_stackM.Rd | 57 ++++++------ man/prune_unconfirmed.Rd |only man/report_confirm.Rd |only man/report_ctreeMI.Rd | 8 - man/rescale_statistic.Rd | 34 +++---- man/split_holdout.Rd |only man/stack_imputations.Rd | 20 ++-- man/summary.ctreeMI.Rd | 14 +-- tests/testthat/test-confirm.R |only 26 files changed, 416 insertions(+), 252 deletions(-)
Title: 'Opal' Data Repository Client and 'DataSHIELD' Utils
Description: Data integration Web application for biobanks by 'OBiBa'. 'Opal' is
the core database application for biobanks. Participant data, once
collected from any data source, must be integrated and stored in a central
data repository under a uniform model. 'Opal' is such a central repository.
It can import, process, validate, query, analyze, report, and export data.
'Opal' is typically used in a research center to analyze the data acquired at
assessment centres. Its ultimate purpose is to achieve seamless
data-sharing among biobanks. This 'Opal' client allows to interact with 'Opal'
web services and to perform operations on the R server side. 'DataSHIELD'
administration tools are also provided.
Author: Yannick Marcon [aut, cre] ,
Amadou Gaye [ctb] ,
OBiBa group [cph]
Maintainer: Yannick Marcon <yannick.marcon@obiba.org>
Diff between opalr versions 3.6.1 dated 2026-05-27 and 3.7.0 dated 2026-09-18
DESCRIPTION | 8 ++++---- MD5 | 32 +++++++++++++++++++++----------- NAMESPACE | 8 ++++++++ R/datashield.admin.R | 8 +++++++- R/datashield.quota.R |only R/opal.project.R | 38 ++++++++++++++++++++++++++++---------- R/opal.quota.R |only build/vignette.rds |binary inst/doc/datashield-admin.html | 4 ++-- inst/doc/opal-files.html | 4 ++-- inst/doc/opal-projects.html | 4 ++-- inst/doc/opal-rsession.html | 4 ++-- man/dsadmin.log.Rd | 8 +++++++- man/dsadmin.quota.Rd |only man/dsadmin.quota_delete.Rd |only man/dsadmin.quota_enable.Rd |only man/dsadmin.quota_exists.Rd |only man/dsadmin.quota_save.Rd |only man/dsadmin.quota_usage.Rd |only man/dsadmin.quotas.Rd |only man/opal.project_create.Rd | 11 ++++++++--- man/opal.quotas.Rd |only 22 files changed, 91 insertions(+), 38 deletions(-)
Title: NFL Logo Plots in 'ggplot2' and 'gt'
Description: A set of functions to visualize National Football League
analysis in 'ggplot2' plots and 'gt' tables.
Author: Sebastian Carl [aut, cre]
Maintainer: Sebastian Carl <mrcaseb@gmail.com>
Diff between nflplotR versions 1.6.0 dated 2025-11-14 and 1.7.0 dated 2026-09-18
DESCRIPTION | 8 ++--- MD5 | 34 ++++++++++++------------ NAMESPACE | 12 +++++--- NEWS.md | 5 +++ R/nfl_team_factors.R | 4 ++ R/sysdata.rda |binary man/geom_lines.Rd | 6 ++-- man/nflplotR-package.Rd | 16 ++++------- man/nflverse_sitrep.Rd | 2 - man/reexports.Rd | 2 - tests/testthat/_snaps/geom_nfl_logos/p1.svg | 20 +++++++------- tests/testthat/_snaps/geom_nfl_logos/p2.svg | 22 +++++++-------- tests/testthat/_snaps/geom_nfl_logos/p3.svg | 20 +++++++------- tests/testthat/_snaps/geom_nfl_wordmarks/p1.svg | 2 - tests/testthat/_snaps/geom_nfl_wordmarks/p2.svg | 2 - tests/testthat/_snaps/scale_nfl/p1.svg | 2 - tests/testthat/_snaps/theme-elements/p1.svg | 4 +- tests/testthat/_snaps/theme-elements/p2.svg | 4 +- 18 files changed, 87 insertions(+), 78 deletions(-)
Title: Access 'Hugging Face' Models and Datasets
Description: Access models and datasets hosted on the 'Hugging Face' Hub
through its Inference Application Programming Interface (API). Run text
classification, embeddings, chat, translation, image, audio, and other
tasks from tidy 'R' workflows without installing 'Python' by default.
Results are returned as data frames or simple 'R' objects so they can be
composed with 'dplyr', 'tidyr', and related tooling. Helpers also support
Hub search, file download, provider discovery, and guarded uploads for
authenticated workflows. Optional local embeddings and text classification
use 'Python' through 'reticulate'.
Author: Alex Farach [aut, cre, cph],
Sam Terfa [aut, cph],
Jack Penzer [aut, cph]
Maintainer: Alex Farach <alexfarach@gmail.com>
Diff between huggingfaceR versions 2.2.0 dated 2026-08-29 and 2.3.0 dated 2026-09-18
DESCRIPTION | 16 LICENSE | 4 MD5 | 384 - NAMESPACE | 220 NEWS.md | 460 + R/auth.R | 374 - R/batch.R | 450 - R/chat.R | 1146 ++-- R/classify-batch.R | 812 +-- R/classify.R | 348 - R/datasets_api.R | 882 ++- R/defaults.R | 140 R/embeddings-batch.R | 524 +- R/embeddings.R | 438 - R/extract.R | 572 +- R/ez.R | 4308 +++++++++--------- R/generate.R | 354 - R/globals.R | 8 R/hub.R | 2220 ++++----- R/huggingface_hub.R | 202 R/inference.R | 776 +-- R/local-python.R |only R/local-validation.R |only R/local.R |only R/models_with_downloads.R | 20 R/multimodal.R | 1086 ++-- R/providers.R | 439 + R/request.R | 677 +- R/sentence-transformers.R | 138 R/text-tasks.R | 886 +-- R/tidymodels.R | 400 - R/tidytext.R | 448 - R/transformers.R | 340 - R/utils-pipe.R | 32 R/utils.R | 276 - R/zzz.R | 602 +- README.md | 887 +-- man/batch_vector.Rd | 44 man/chat.Rd | 54 man/figures/logo.svg | 78 man/hf_api_request.Rd | 80 man/hf_build_request.Rd | 76 man/hf_caption_image.Rd | 98 man/hf_chat.Rd | 174 man/hf_check_inference.Rd | 82 man/hf_classify.Rd | 104 man/hf_classify_batch.Rd | 110 man/hf_classify_chunks.Rd | 118 man/hf_classify_image.Rd | 98 man/hf_classify_local.Rd |only man/hf_classify_zero_shot.Rd | 112 man/hf_classify_zero_shot_batch.Rd | 116 man/hf_cluster_texts.Rd | 80 man/hf_conversation.Rd | 78 man/hf_create_repo.Rd | 80 man/hf_dataset_info.Rd | 48 man/hf_default_model.Rd | 80 man/hf_delete_repo.Rd | 58 man/hf_describe_image.Rd | 94 man/hf_detect_config.Rd | 44 man/hf_detect_objects.Rd | 100 man/hf_download_model.Rd |only man/hf_embed.Rd | 92 man/hf_embed_batch.Rd | 110 man/hf_embed_chunks.Rd | 124 man/hf_embed_local.Rd |only man/hf_embed_text.Rd | 104 man/hf_embed_umap.Rd | 102 man/hf_extract.Rd | 126 man/hf_extract_topics.Rd | 66 man/hf_ez_conversational.Rd | 74 man/hf_ez_conversational_api_inference.Rd | 134 man/hf_ez_conversational_local_inference.Rd | 104 man/hf_ez_fill_mask.Rd | 68 man/hf_ez_fill_mask_api_inference.Rd | 86 man/hf_ez_fill_mask_local_inference.Rd | 48 man/hf_ez_question_answering.Rd | 72 man/hf_ez_question_answering_api_inference.Rd | 92 man/hf_ez_question_answering_local_inference.Rd | 52 man/hf_ez_sentence_similarity.Rd | 100 man/hf_ez_sentence_similarity_api_inference.Rd | 92 man/hf_ez_sentence_similarity_local_inference.Rd | 62 man/hf_ez_summarization.Rd | 74 man/hf_ez_summarization_api_inference.Rd | 128 man/hf_ez_summarization_local_inference.Rd | 98 man/hf_ez_table_question_answering.Rd | 86 man/hf_ez_table_question_answering_api_inference.Rd | 92 man/hf_ez_table_question_answering_local_inference.Rd | 52 man/hf_ez_text2text_generation.Rd | 66 man/hf_ez_text2text_generation_api_inference.Rd | 86 man/hf_ez_text2text_generation_local_inference.Rd | 48 man/hf_ez_text_classification.Rd | 72 man/hf_ez_text_classification_api_inference.Rd | 86 man/hf_ez_text_classification_local_inference.Rd | 48 man/hf_ez_text_generation.Rd | 66 man/hf_ez_text_generation_api_inference.Rd | 140 man/hf_ez_text_generation_local_inference.Rd | 110 man/hf_ez_token_classification.Rd | 88 man/hf_ez_token_classification_api_inference.Rd | 102 man/hf_ez_token_classification_local_inference.Rd | 72 man/hf_ez_translation.Rd | 62 man/hf_ez_translation_api_inference.Rd | 86 man/hf_ez_translation_local_inference.Rd | 48 man/hf_ez_zero_shot_classification.Rd | 80 man/hf_ez_zero_shot_classification_api_inference.Rd | 98 man/hf_ez_zero_shot_classification_local_inference.Rd | 68 man/hf_fill_mask.Rd | 104 man/hf_fill_mask_payload.Rd | 46 man/hf_generate.Rd | 102 man/hf_get_existing_chunks.Rd | 40 man/hf_get_token.Rd | 40 man/hf_hub_download.Rd | 86 man/hf_inference.Rd | 100 man/hf_list_authors.Rd | 50 man/hf_list_datasets.Rd | 50 man/hf_list_languages.Rd | 50 man/hf_list_libraries.Rd | 50 man/hf_list_licenses.Rd | 50 man/hf_list_models.Rd | 50 man/hf_list_providers.Rd | 71 man/hf_list_repo_files.Rd | 74 man/hf_list_tasks.Rd | 52 man/hf_load_AutoModel_for_task.Rd | 74 man/hf_load_dataset.Rd | 106 man/hf_load_local_model.Rd |only man/hf_load_model.Rd | 48 man/hf_load_pipeline.Rd | 66 man/hf_load_sentence_model.Rd | 90 man/hf_load_tokenizer.Rd | 56 man/hf_local_setup.Rd |only man/hf_model_info.Rd | 50 man/hf_nearest_neighbors.Rd | 82 man/hf_ner.Rd | 112 man/hf_parse_response.Rd | 40 man/hf_perform_batch.Rd | 56 man/hf_push_dataset.Rd | 108 man/hf_python_depends.Rd | 52 man/hf_question_answer.Rd | 112 man/hf_question_answering_payload.Rd | 56 man/hf_read_chunks.Rd | 50 man/hf_resolve_dataset.Rd | 40 man/hf_rows_to_tibble.Rd |only man/hf_run_tools.Rd | 72 man/hf_search_datasets.Rd | 88 man/hf_search_models.Rd | 118 man/hf_search_papers.Rd | 52 man/hf_search_spaces.Rd | 78 man/hf_sentence_encode.Rd | 82 man/hf_sentence_similarity_payload.Rd | 56 man/hf_set_device.Rd | 44 man/hf_set_token.Rd | 74 man/hf_similarity.Rd | 58 man/hf_summarization_payload.Rd | 94 man/hf_summarize.Rd | 114 man/hf_table_question_answer.Rd | 106 man/hf_table_question_answering_payload.Rd | 56 man/hf_text2text_generation_payload.Rd | 46 man/hf_text_classification_payload.Rd | 46 man/hf_text_generation_payload.Rd | 104 man/hf_text_to_image.Rd | 119 man/hf_text_to_speech.Rd | 109 man/hf_token_classification_payload.Rd | 60 man/hf_tool.Rd | 72 man/hf_transcribe.Rd | 102 man/hf_translate.Rd | 152 man/hf_translation_payload.Rd | 46 man/hf_upload_file.Rd | 100 man/hf_vectorize.Rd | 48 man/hf_whoami.Rd | 52 man/hf_write_chunk.Rd | 48 man/hf_zero_shot_classification_payload.Rd | 68 man/models_with_downloads.Rd | 44 man/null_coalesce.Rd | 36 man/pipe.Rd | 46 man/step_hf_embed.Rd | 138 tests/testthat.R | 24 tests/testthat/_snaps |only tests/testthat/helper-local.R |only tests/testthat/helper.R | 36 tests/testthat/test-auth.R | 244 - tests/testthat/test-batch.R | 282 - tests/testthat/test-chat.R | 310 - tests/testthat/test-classify-batch.R | 178 tests/testthat/test-classify.R | 138 tests/testthat/test-dataset-rows.R |only tests/testthat/test-datasets.R | 127 tests/testthat/test-defaults.R | 94 tests/testthat/test-embeddings-batch.R | 150 tests/testthat/test-embeddings.R | 206 tests/testthat/test-extract.R | 226 tests/testthat/test-hub.R | 324 - tests/testthat/test-huggingface_hub.R | 56 tests/testthat/test-local-compatibility.R |only tests/testthat/test-local-loading.R |only tests/testthat/test-local-snapshot.R |only tests/testthat/test-local.R |only tests/testthat/test-multimodal.R | 242 - tests/testthat/test-providers.R | 356 - tests/testthat/test-request.R | 276 - tests/testthat/test-text-tasks.R | 392 - tests/testthat/test-transformers.R | 204 201 files changed, 17779 insertions(+), 17366 deletions(-)
Title: Multivariate VAM Fitting
Description: Fits a multivariate value-added model (VAM), see Broatch, Green, and Karl (2018) <doi:10.32614/RJ-2018-033> and Broatch and Lohr (2012) <doi:10.3102/1076998610396900>, with normally distributed test scores and a binary outcome indicator. A pseudo-likelihood approach, Wolfinger (1993) <doi:10.1080/00949659308811554>, is used for the estimation of this joint generalized linear mixed model. The inner loop of the pseudo-likelihood routine (estimation of a linear mixed model) occurs in the framework of the EM algorithm presented by Karl, Yang, and Lohr (2013) <DOI:10.1016/j.csda.2012.10.004>. This material is based upon work supported by the National Science Foundation under grants DRL-1336027 and DRL-1336265.
Author: Andrew Karl [cre, aut] ,
Jennifer Broatch [aut],
Jennifer Green [aut]
Maintainer: Andrew Karl <akarl@asu.edu>
Diff between RealVAMS versions 0.4-6 dated 2024-04-05 and 0.5.0 dated 2026-09-18
DESCRIPTION | 14 - MD5 | 58 ++-- NAMESPACE | 55 ++-- R/REML_Rm.R | 63 ++++ R/R_mstep2.R | 59 ++++ R/RealVAMS-package.R |only R/RealVAMS.R | 343 +++++++++++++++++++++----- R/example.outcome.data.R |only R/example.score.data.R |only R/plot.RealVAMS.R | 255 ++++++++----------- R/print.RealVAMS.R | 43 +-- R/print.summary.RealVAMS.R | 133 +++++----- R/summary.RealVAMS.R | 42 ++- R/validate-inputs.R |only R/vp_cp.R | 572 ++++++++++++++++++++++---------------------- inst/NEWS | 34 ++ man/REML_Rm.Rd | 150 ++++++----- man/R_mstep2.Rd | 136 +++++----- man/RealVAMS-package.Rd | 92 +++---- man/RealVAMS.Rd | 461 ++++++++++++++++++++--------------- man/example.outcome.data.Rd | 146 +++++------ man/example.score.data.Rd | 152 ++++++----- man/plot.Rd | 103 ++++--- man/print.Rd | 49 ++- man/summary.Rd | 77 +++-- man/vp_cp.Rd | 48 +-- src/REML_Rm.cpp | 10 src/R_mstep.cpp | 10 src/init.c | 4 tests |only 30 files changed, 1808 insertions(+), 1301 deletions(-)
Title: Multivariate Generalized Linear Mixed Models for Ranking Sports
Teams
Description: Maximum likelihood estimates are obtained via an EM algorithm with either a first-order or a fully exponential Laplace approximation as documented by Broatch and Karl (2018) <doi:10.48550/arXiv.1710.05284>,
Karl, Yang, and Lohr (2014) <doi:10.1016/j.csda.2013.11.019>, and by
Karl (2012) <doi:10.1515/1559-0410.1471>. Karl and Zimmerman <doi:10.1016/j.jspi.2020.06.004> use this package to illustrate how the home field effect estimator from a mixed model can be biased under nonrandom scheduling.
Author: Andrew T. Karl [cre, aut] ,
Jennifer Broatch [aut]
Maintainer: Andrew T. Karl <akarl@asu.edu>
Diff between mvglmmRank versions 1.2-5 dated 2026-06-09 and 1.2-6 dated 2026-09-18
DESCRIPTION | 12 MD5 | 82 +++--- NAMESPACE | 11 NEWS | 72 +++-- NEWS.md | 136 ++++++---- R/NB_cre.R | 249 +++++++------------ R/NB_mov.r | 276 ++++++++------------- R/N_mov.r | 483 -------------------------------------- R/PB_cre.R | 379 ++++++++++-------------------- R/binary_cre.R | 239 +++++++----------- R/f2008-data.R |only R/f2009-data.R |only R/f2010-data.R |only R/f2011-data.R |only R/f2012-data.R |only R/game.pred.R | 236 +++++++----------- R/gaussian-helpers.R |only R/mvglmmRank-package.R | 86 +++--- R/mvglmmRank.R | 423 +++++++++++++++++++-------------- R/nba2013-data.R |only R/ncaab2012-data.R |only R/nfl2012-data.R |only R/normal_cre.R | 592 ----------------------------------------------- R/numerical-helpers.R |only R/poisson_cre.R | 268 +++++++-------------- inst/CITATION | 54 ++-- man/NB_cre.Rd | 57 ++-- man/NB_mov.Rd | 57 ++-- man/N_mov.Rd | 52 +--- man/PB_cre.Rd | 64 ++--- man/binary_cre.Rd | 57 ++-- man/f2008.Rd | 66 ++--- man/f2009.Rd | 66 ++--- man/f2010.Rd | 66 ++--- man/f2011.Rd | 66 ++--- man/f2012.Rd | 66 ++--- man/game.pred.Rd | 3 man/gaussian-helpers.Rd |only man/mvglmmRank.Rd | 48 +++ man/nba2013.Rd | 70 ++--- man/ncaab2012.Rd | 68 ++--- man/nfl2012.Rd | 66 ++--- man/normal_cre.Rd | 52 +--- man/numerical-helpers.Rd |only man/poisson_cre.Rd | 64 ++--- tests/testthat |only tests/testthat.R |only 47 files changed, 1661 insertions(+), 2925 deletions(-)
Title: Maximum Likelihood Estimation of Multiple Membership Mixed
Models Used in Value-Added Modeling
Description: An EM algorithm, Karl et al. (2013) <doi:10.1016/j.csda.2012.10.004>,
estimates generalized, reduced generalized, variable, complete, and zero
persistence models by maximum likelihood or restricted maximum likelihood
(the default). These are multiple-membership linear mixed models with
teachers modeled as "G-side" effects and students modeled with either
"G-side" or "R-side" effects; see Mariano et al. (2010)
<doi:10.3102/1076998609346967>.
Author: Andrew Karl [cre, aut] ,
Yan Yang [aut],
Sharon Lohr [aut]
Maintainer: Andrew Karl <akarl@asu.edu>
Diff between GPvam versions 3.2-0 dated 2024-12-12 and 3.3-0 dated 2026-09-18
GPvam-3.2-0/GPvam/man/plot.Rd |only GPvam-3.2-0/GPvam/man/print.Rd |only GPvam-3.2-0/GPvam/man/summary.Rd |only GPvam-3.3-0/GPvam/DESCRIPTION | 22 GPvam-3.3-0/GPvam/MD5 | 79 ++- GPvam-3.3-0/GPvam/NAMESPACE | 100 ++-- GPvam-3.3-0/GPvam/NEWS | 54 ++ GPvam-3.3-0/GPvam/R/GP.csh.R | 176 +++---- GPvam-3.3-0/GPvam/R/GP.un.R | 175 +++---- GPvam-3.3-0/GPvam/R/GPvam-package.R |only GPvam-3.3-0/GPvam/R/GPvam.R | 328 +++++++++++--- GPvam-3.3-0/GPvam/R/REML_Rm.R | 16 GPvam-3.3-0/GPvam/R/R_mstep2.R | 38 + GPvam-3.3-0/GPvam/R/VP.CP.ZP.un.r | 260 +++-------- GPvam-3.3-0/GPvam/R/bias.test.custom.R | 441 ++++++++++--------- GPvam-3.3-0/GPvam/R/data.R |only GPvam-3.3-0/GPvam/R/estimation-helpers.R |only GPvam-3.3-0/GPvam/R/methods.R |only GPvam-3.3-0/GPvam/R/plot.GPvam.R | 240 ++++------ GPvam-3.3-0/GPvam/R/print.GPvam.R | 27 - GPvam-3.3-0/GPvam/R/print.summary.GPvam.R | 35 - GPvam-3.3-0/GPvam/R/rGP.un.R | 175 +++---- GPvam-3.3-0/GPvam/R/summary.GPvam.R | 47 +- GPvam-3.3-0/GPvam/build |only GPvam-3.3-0/GPvam/man/GP.csh.Rd | 51 +- GPvam-3.3-0/GPvam/man/GP.un.Rd | 50 +- GPvam-3.3-0/GPvam/man/GPvam-methods.Rd |only GPvam-3.3-0/GPvam/man/GPvam-package.Rd | 105 ++-- GPvam-3.3-0/GPvam/man/GPvam.Rd | 382 +++++++++------- GPvam-3.3-0/GPvam/man/GPvam.benchmark.Rd | 63 +- GPvam-3.3-0/GPvam/man/REML_Rm.Rd |only GPvam-3.3-0/GPvam/man/R_mstep2.Rd |only GPvam-3.3-0/GPvam/man/VP.CP.ZP.un.Rd | 52 +- GPvam-3.3-0/GPvam/man/bias.test.custom.Rd | 160 ++++-- GPvam-3.3-0/GPvam/man/dot-gpvam_estep.Rd |only GPvam-3.3-0/GPvam/man/dot-gpvam_information.Rd |only GPvam-3.3-0/GPvam/man/dot-gpvam_residual_diagonal.Rd |only GPvam-3.3-0/GPvam/man/dot-gpvam_update_residual.Rd |only GPvam-3.3-0/GPvam/man/plot.GPvam.Rd |only GPvam-3.3-0/GPvam/man/print.GPvam.Rd |only GPvam-3.3-0/GPvam/man/rGP.un.Rd | 51 +- GPvam-3.3-0/GPvam/man/summary.GPvam.Rd |only GPvam-3.3-0/GPvam/man/vam_data.Rd | 131 +++-- GPvam-3.3-0/GPvam/src/REML_Rm.cpp | 8 GPvam-3.3-0/GPvam/src/R_mstep.cpp | 8 GPvam-3.3-0/GPvam/tests |only 46 files changed, 1873 insertions(+), 1401 deletions(-)
Title: Generalized Linear Mixed Models via Fully Exponential Laplace in
EM
Description: Fit generalized linear mixed models (GLMMs) with normal random
effects using first-order Laplace, fully exponential Laplace (FEL) with
mean-only corrections, and FEL with mean and variance-diagonal corrections in
the E-step of an expectation-maximization (EM) algorithm. The current
development version provides a matrix-based interface (y, X, Z) and
supports binary logit and probit, and Poisson log-link models. An EM
framework is used to update fixed effects, random effects, and a single
variance component tau^2 for G = tau^2 I, with staged approximations
(Laplace -> FEL mean-only -> FEL full) for efficiency and stability. A
pseudo-likelihood engine glmmFEL_pl() implements the working-response /
working-weights linearization approach of Wolfinger and O'Connell (1993)
<doi:10.1080/00949659308811554>, and is adapted from the implementation
used in the 'RealVAMS' package (Broatch, Green, and Karl (2018))
<doi:10.32614/RJ-2018-033>. The FEL implementation follows Karl, Yan [...truncated...]
Author: Andrew T. Karl [cre, aut]
Maintainer: Andrew T. Karl <akarl@asu.edu>
Diff between glmmFEL versions 1.0.5 dated 2026-01-09 and 1.0.6 dated 2026-09-18
DESCRIPTION | 17 MD5 | 46 - NEWS.md |only R/fe_derivatives.R | 475 +++++------ R/fe_trace.R | 14 R/glmmFEL-benchmarks.R |only R/glmmFEL-helpers.R | 585 +++++++------- R/glmmFEL-methods.R | 431 +++++----- R/glmmFEL-package.R | 107 +- R/glmmFEL.R | 1193 ++++++++++++------------------ R/glmmFEL_PL.R | 517 ++++++------- R/numerical_helpers.R |only build/partial.rdb |binary inst/benchmarks |only man/glmmFEL-benchmarks.Rd |only man/glmmFEL-package.Rd | 63 - man/glmmFEL.Rd | 88 +- man/glmmFEL_pl.Rd | 2 man/logLik.glmmFELMod.Rd | 2 tests/testthat/fixtures |only tests/testthat/test-glmmFEL-matrix-only.R | 974 ++++++++++++------------ tests/testthat/test-numerical-audit.R |only 22 files changed, 2125 insertions(+), 2389 deletions(-)
Title: Bayesian Inference of Binary, Count and Continuous Data in
Toxicology
Description: Advanced methods for a valuable quantitative environmental
risk assessment using Bayesian inference of several type of
toxicological data. 'binary' (e.g., survival, mobility), 'count'
(e.g., reproduction) and 'continuous' (e.g., growth as length,
weight). Estimation procedures can be used without a deep knowledge
of their underlying probabilistic model or inference methods. Rather,
they were designed to behave as well as possible without requiring a
user to provide values for some obscure parameters. That said, models
can also be used as a first step to tailor new models for more
specific situations.
Author: Virgile Baudrot [aut, cre],
Sandrine Charles [aut],
Marie Laure Delignette-Muller [aut],
Nils Kehrein [ctb],
Guillaume Kon-Kam-King [ctb],
Christelle Lopes [ctb],
Philippe Veber [aut]
Maintainer: Virgile Baudrot <virgile.baudrot@qonfluens.com>
Diff between morseDR versions 0.1.2 dated 2025-05-29 and 0.1.3 dated 2026-09-18
DESCRIPTION | 10 ++-- MD5 | 13 +++-- NEWS | 8 +++ R/priorPosterior.R | 1 README.md | 49 ++++++++++++++++++++- inst/doc/models.html | 35 +++++++-------- inst/doc/tutorial.html | 104 ++++++++++++++++++++++------------------------ tests/testthat/Rplots.pdf |only 8 files changed, 137 insertions(+), 83 deletions(-)
Title: Bias Diagnostic for Linear Mixed Models
Description: Provides a function to perform bias diagnostics on linear mixed models fitted with lmer() from the 'lme4' package. Implements permutation tests for assessing the bias of fixed effects, as described in Karl and Zimmerman (2021) <doi:10.1016/j.jspi.2020.06.004>. Karl and Zimmerman (2020) <doi:10.17632/tmynggddfm.1> provide R code for implementing the test using 'mvglmmRank' output. Development of this package was assisted by 'GPT o1-preview' for code structure and documentation.
Author: Andrew T. Karl [cre, aut]
Maintainer: Andrew T. Karl <akarl@asu.edu>
Diff between mixedbiastest versions 1.0.2 dated 2025-11-30 and 1.0.3 dated 2026-09-18
mixedbiastest-1.0.2/mixedbiastest/tests/testthat/Rplots.pdf |only mixedbiastest-1.0.3/mixedbiastest/DESCRIPTION | 12 mixedbiastest-1.0.3/mixedbiastest/MD5 | 23 mixedbiastest-1.0.3/mixedbiastest/NEWS.md |only mixedbiastest-1.0.3/mixedbiastest/R/list_fixed.R | 5 mixedbiastest-1.0.3/mixedbiastest/R/mixedbiastest.R | 690 ++++------ mixedbiastest-1.0.3/mixedbiastest/build/partial.rdb |binary mixedbiastest-1.0.3/mixedbiastest/man/list_fixed_effects.Rd | 1 mixedbiastest-1.0.3/mixedbiastest/man/mixedbiastest-package.Rd | 5 mixedbiastest-1.0.3/mixedbiastest/man/mixedbiastest.Rd | 20 mixedbiastest-1.0.3/mixedbiastest/tests/testthat.R | 10 mixedbiastest-1.0.3/mixedbiastest/tests/testthat/helper-reference.R |only mixedbiastest-1.0.3/mixedbiastest/tests/testthat/test-lme4-updates.R |only mixedbiastest-1.0.3/mixedbiastest/tests/testthat/test-mixedbiastest.R | 12 mixedbiastest-1.0.3/mixedbiastest/tests/testthat/test-supported-inputs.R |only 15 files changed, 356 insertions(+), 422 deletions(-)
Title: Data & Functions for Working with US ZIP Codes
Description: Make working with ZIP codes in R painless with an integrated dataset of U.S. ZIP codes and functions for working with them.
Search ZIP codes by multiple geographies, including state, county, city & across time zones. Also included are functions for relating
ZIP codes to Census data, geocoding & distance calculations. New
analyses can select an immutable modern data bundle through the
next-generation API, while the historical interface remains
compatible with version 0.3.5 for reproducible research.
Author: Gavin Rozzi [aut, cre]
Maintainer: Gavin Rozzi <gr@gavinrozzi.com>
Diff between zipcodeR versions 0.4.0 dated 2026-09-07 and 0.4.1 dated 2026-09-18
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 14 ++++++++++++++ inst/doc/geographic.html | 2 +- inst/doc/zipcodeR.html | 2 +- tests/testthat/test-04-data-bundles.R | 8 +++++++- 6 files changed, 31 insertions(+), 11 deletions(-)
Title: Solar Potential Calculation for Point Clouds using 'VOSTOK'
Description: Calculate solar potential for LiDAR point clouds using the 'VOSTOK'
(Voxel Octree Solar Toolkit) algorithm. This R program provides an interface to
the original 'VOSTOK' C++ implementation by Bechtold and Hofle (2020), enabling
efficient ray casting and solar position algorithms to compute solar irradiance
for each point while accounting for shadowing effects. Integrates seamlessly with
the 'lidR' package for LiDAR data processing workflows. The original 'VOSTOK'
toolkit is available at <doi:10.11588/data/QNA02B>.
Author: Andrew J. Sanchez Meador [aut, cre],
Sebastian Bechtold [aut] ,
Bernhard Hofle [aut]
Maintainer: Andrew J. Sanchez Meador <andrew.sanchezmeador@nau.edu>
This is a re-admission after prior archival of version 0.2.1 dated 2026-03-25
Diff between vostokR versions 0.2.1 dated 2026-03-25 and 0.2.2 dated 2026-09-18
DESCRIPTION | 12 ++++++------ MD5 | 6 +++--- NAMESPACE | 14 +++++++++----- man/vostokR-package.Rd | 1 + 4 files changed, 19 insertions(+), 14 deletions(-)
Title: Utilities to Support Lidar Applications at the Landscape,
Forest, and Tree Scale
Description: Implements algorithms for terrestrial, mobile, and airborne lidar processing, tree detection,
segmentation, and attribute estimation (Donager et al., 2021)
<doi:10.3390/rs13122297>, and a hierarchical patch delineation algorithm
'PatchMorph' (Girvetz & Greco, 2007) <doi:10.1007/s10980-007-9104-8>. Tree
detection uses rasterized point cloud metrics (relative neighborhood density and
verticality) combined with RANSAC cylinder fitting to locate tree boles and estimate
diameter at breast height. Tree segmentation applies graph-theory approaches inspired
by Tao et al. (2015) <doi:10.1016/j.isprsjprs.2015.08.007> with cylinder fitting
methods from de Conto et al. (2017) <doi:10.1016/j.compag.2017.07.019>. PatchMorph
delineates habitat patches across spatial scales using organism-specific thresholds.
Built on 'lidR' (Roussel et al., 2020) <doi:10.1016/j.rse.2020.112061>.
Author: Andrew Sanchez Meador [aut, cre, ctb] ,
Jonathon Donager [aut, ctb] ,
Blackburn Ryan [aut, ctb] ,
Cannon Jeffery [ctb] ,
Tiago de Conto [ctb, cph] ,
Keith O'Hara [ctb, cph]
Maintainer: Andrew Sanchez Meador <Andrew.SanchezMeador@nau.edu>
This is a re-admission after prior archival of version 1.0.4 dated 2026-04-01
Diff between spanner versions 1.0.4 dated 2026-04-01 and 1.0.5 dated 2026-09-18
DESCRIPTION | 15 MD5 | 34 - NAMESPACE | 44 +- NEWS.md | 6 R/Patch_Morph.R | 404 +++++++++++------------ R/PostProcess_TreeLocations.R | 492 ++++++++++++++-------------- R/Segment_Graph.R | 630 ++++++++++++++++++------------------ R/spanner-package.R | 38 +- build/stage23.rdb |binary man/colorize_las.Rd | 180 +++++----- man/compute_pcv.Rd | 72 ++-- man/compute_ssao.Rd | 90 ++--- man/download_naip_for_las.Rd | 126 +++---- man/eigen_metrics.Rd | 126 +++---- man/merge_las_colors.Rd | 124 +++---- man/segment_graph.Rd | 304 ++++++++--------- tests/testthat/test-eigen-metrics.R | 120 +++--- tests/testthat/test-segmentation.R | 224 ++++++------ 18 files changed, 1522 insertions(+), 1507 deletions(-)
Title: Fast Simulation of Bayesian Optimal Interval Designs for Phase I
Trials
Description: Design and evaluate phase I dose-finding trials that use the
Bayesian optimal interval (BOIN) design of Liu and Yuan (2015)
<doi:10.1111/rssc.12089>. Functions are provided to tabulate the decision
boundaries, to simulate trials, to estimate the dose-toxicity curve under a
monotonicity constraint and to select the maximum tolerated dose. The
simulation engine is written in C++ and draws one random variate per
patient in enrollment order, which reproduces the reference implementation
in the 'BOIN' package trial by trial for a given seed. The traditional 3+3
design is provided as a comparator, with operating characteristics obtained
in closed form rather than by simulation.
Author: Gosuke Homma [aut, cre]
Maintainer: Gosuke Homma <my.name.is.gosuke@gmail.com>
Diff between simFastBOIN versions 1.3.2 dated 2025-12-17 and 2.0.0 dated 2026-09-18
simFastBOIN-1.3.2/simFastBOIN/R/get_boin_boundary.R |only simFastBOIN-1.3.2/simFastBOIN/R/get_boin_decision.R |only simFastBOIN-1.3.2/simFastBOIN/R/get_boin_stopping_boundaries.R |only simFastBOIN-1.3.2/simFastBOIN/R/get_pts_and_tox.R |only simFastBOIN-1.3.2/simFastBOIN/R/isotonic_regression.R |only simFastBOIN-1.3.2/simFastBOIN/R/print.boin_multi_summary.R |only simFastBOIN-1.3.2/simFastBOIN/R/print.boin_summary.R |only simFastBOIN-1.3.2/simFastBOIN/R/select_mtd.R |only simFastBOIN-1.3.2/simFastBOIN/man/get_boin_boundary.Rd |only simFastBOIN-1.3.2/simFastBOIN/man/get_boin_decision.Rd |only simFastBOIN-1.3.2/simFastBOIN/man/get_boin_stopping_boundaries.Rd |only simFastBOIN-1.3.2/simFastBOIN/man/get_pts_and_tox.Rd |only simFastBOIN-1.3.2/simFastBOIN/man/isotonic_regression.Rd |only simFastBOIN-1.3.2/simFastBOIN/man/print.boin_multi_summary.Rd |only simFastBOIN-1.3.2/simFastBOIN/man/print.boin_summary.Rd |only simFastBOIN-1.3.2/simFastBOIN/man/select_mtd.Rd |only simFastBOIN-1.3.2/simFastBOIN/tests/testthat/test-get_boin_boundary.R |only simFastBOIN-1.3.2/simFastBOIN/tests/testthat/test-get_boin_decision.R |only simFastBOIN-1.3.2/simFastBOIN/tests/testthat/test-get_boin_stopping_boundaries.R |only simFastBOIN-1.3.2/simFastBOIN/tests/testthat/test-get_pts_and_tox.R |only simFastBOIN-1.3.2/simFastBOIN/tests/testthat/test-isotonic_regression.R |only simFastBOIN-1.3.2/simFastBOIN/tests/testthat/test-select_mtd.R |only simFastBOIN-2.0.0/simFastBOIN/DESCRIPTION | 45 simFastBOIN-2.0.0/simFastBOIN/LICENSE | 2 simFastBOIN-2.0.0/simFastBOIN/MD5 | 124 + simFastBOIN-2.0.0/simFastBOIN/NAMESPACE | 32 simFastBOIN-2.0.0/simFastBOIN/NEWS.md | 298 ++++ simFastBOIN-2.0.0/simFastBOIN/R/RcppExports.R |only simFastBOIN-2.0.0/simFastBOIN/R/as.data.frame.boin_boundary.R |only simFastBOIN-2.0.0/simFastBOIN/R/boin_boundary.R |only simFastBOIN-2.0.0/simFastBOIN/R/boin_decision_table.R |only simFastBOIN-2.0.0/simFastBOIN/R/boin_isotonic.R |only simFastBOIN-2.0.0/simFastBOIN/R/boin_lambda.R |only simFastBOIN-2.0.0/simFastBOIN/R/boin_p_tox.R |only simFastBOIN-2.0.0/simFastBOIN/R/boin_select_mtd.R |only simFastBOIN-2.0.0/simFastBOIN/R/boin_simulate.R |only simFastBOIN-2.0.0/simFastBOIN/R/boin_stopping_table.R |only simFastBOIN-2.0.0/simFastBOIN/R/deprecated.R |only simFastBOIN-2.0.0/simFastBOIN/R/oc_3p3.R |only simFastBOIN-2.0.0/simFastBOIN/R/oc_multi_table.R |only simFastBOIN-2.0.0/simFastBOIN/R/plot.boin_decision_table.R |only simFastBOIN-2.0.0/simFastBOIN/R/print.boin_boundary.R |only simFastBOIN-2.0.0/simFastBOIN/R/print.boin_decision_table.R |only simFastBOIN-2.0.0/simFastBOIN/R/print.boin_oc.R |only simFastBOIN-2.0.0/simFastBOIN/R/print.boin_oc_multi.R |only simFastBOIN-2.0.0/simFastBOIN/R/print.boin_trials.R |only simFastBOIN-2.0.0/simFastBOIN/R/print.oc_3p3.R |only simFastBOIN-2.0.0/simFastBOIN/R/simFastBOIN-package.R |only simFastBOIN-2.0.0/simFastBOIN/R/sim_3p3.R |only simFastBOIN-2.0.0/simFastBOIN/R/sim_boin.R | 448 +++--- simFastBOIN-2.0.0/simFastBOIN/R/sim_boin_multi.R | 326 +--- simFastBOIN-2.0.0/simFastBOIN/R/validate.R |only simFastBOIN-2.0.0/simFastBOIN/README.md | 450 +----- simFastBOIN-2.0.0/simFastBOIN/build/vignette.rds |binary simFastBOIN-2.0.0/simFastBOIN/inst/WORDLIST |only simFastBOIN-2.0.0/simFastBOIN/inst/doc/simFastBOIN-introduction.R | 256 +-- simFastBOIN-2.0.0/simFastBOIN/inst/doc/simFastBOIN-introduction.Rmd | 420 ++--- simFastBOIN-2.0.0/simFastBOIN/inst/doc/simFastBOIN-introduction.html | 732 ++++------ simFastBOIN-2.0.0/simFastBOIN/inst/validation |only simFastBOIN-2.0.0/simFastBOIN/man/as.data.frame.boin_boundary.Rd |only simFastBOIN-2.0.0/simFastBOIN/man/boin_boundary.Rd |only simFastBOIN-2.0.0/simFastBOIN/man/boin_decision_table.Rd |only simFastBOIN-2.0.0/simFastBOIN/man/boin_isotonic.Rd |only simFastBOIN-2.0.0/simFastBOIN/man/boin_lambda.Rd |only simFastBOIN-2.0.0/simFastBOIN/man/boin_p_tox.Rd |only simFastBOIN-2.0.0/simFastBOIN/man/boin_select_mtd.Rd |only simFastBOIN-2.0.0/simFastBOIN/man/boin_simulate.Rd |only simFastBOIN-2.0.0/simFastBOIN/man/boin_stopping_table.Rd |only simFastBOIN-2.0.0/simFastBOIN/man/oc_3p3.Rd |only simFastBOIN-2.0.0/simFastBOIN/man/plot.boin_decision_table.Rd |only simFastBOIN-2.0.0/simFastBOIN/man/print.boin_boundary.Rd |only simFastBOIN-2.0.0/simFastBOIN/man/print.boin_decision_table.Rd |only simFastBOIN-2.0.0/simFastBOIN/man/print.boin_oc.Rd |only simFastBOIN-2.0.0/simFastBOIN/man/print.boin_oc_multi.Rd |only simFastBOIN-2.0.0/simFastBOIN/man/print.boin_trials.Rd |only simFastBOIN-2.0.0/simFastBOIN/man/print.oc_3p3.Rd |only simFastBOIN-2.0.0/simFastBOIN/man/simFastBOIN-deprecated.Rd |only simFastBOIN-2.0.0/simFastBOIN/man/simFastBOIN-package.Rd |only simFastBOIN-2.0.0/simFastBOIN/man/sim_3p3.Rd |only simFastBOIN-2.0.0/simFastBOIN/man/sim_boin.Rd | 305 ++-- simFastBOIN-2.0.0/simFastBOIN/man/sim_boin_multi.Rd | 243 +-- simFastBOIN-2.0.0/simFastBOIN/src |only simFastBOIN-2.0.0/simFastBOIN/tests/spelling.R |only simFastBOIN-2.0.0/simFastBOIN/tests/testthat.R | 8 simFastBOIN-2.0.0/simFastBOIN/tests/testthat/helper-reference.R |only simFastBOIN-2.0.0/simFastBOIN/tests/testthat/test-3p3.R |only simFastBOIN-2.0.0/simFastBOIN/tests/testthat/test-boin_boundary.R |only simFastBOIN-2.0.0/simFastBOIN/tests/testthat/test-boin_decision_table.R |only simFastBOIN-2.0.0/simFastBOIN/tests/testthat/test-boin_isotonic.R |only simFastBOIN-2.0.0/simFastBOIN/tests/testthat/test-boin_lambda.R |only simFastBOIN-2.0.0/simFastBOIN/tests/testthat/test-boin_p_tox.R |only simFastBOIN-2.0.0/simFastBOIN/tests/testthat/test-boin_reference.R |only simFastBOIN-2.0.0/simFastBOIN/tests/testthat/test-boin_reference_oc.R |only simFastBOIN-2.0.0/simFastBOIN/tests/testthat/test-boin_select_mtd.R |only simFastBOIN-2.0.0/simFastBOIN/tests/testthat/test-boin_simulate.R |only simFastBOIN-2.0.0/simFastBOIN/tests/testthat/test-boin_stopping_table.R |only simFastBOIN-2.0.0/simFastBOIN/tests/testthat/test-deprecated.R |only simFastBOIN-2.0.0/simFastBOIN/tests/testthat/test-mtd_max_estimate.R |only simFastBOIN-2.0.0/simFastBOIN/tests/testthat/test-overdose.R |only simFastBOIN-2.0.0/simFastBOIN/tests/testthat/test-plot_methods.R |only simFastBOIN-2.0.0/simFastBOIN/tests/testthat/test-print_methods.R | 216 +- simFastBOIN-2.0.0/simFastBOIN/tests/testthat/test-sim_boin.R | 340 +--- simFastBOIN-2.0.0/simFastBOIN/tests/testthat/test-sim_boin_multi.R | 367 +---- simFastBOIN-2.0.0/simFastBOIN/tests/testthat/test-stay_on_1_of_3.R |only simFastBOIN-2.0.0/simFastBOIN/vignettes/simFastBOIN-introduction.Rmd | 420 ++--- 105 files changed, 2295 insertions(+), 2737 deletions(-)
Title: Acesso aos Dados do 'SIDRA' do IBGE
Description: Functions for accessing and manipulating data from Brazilian
Institute of Geography and Statistics (IBGE)'s API 'SIDRA' (acronym for IBGE
System of Automatic Retrieval) from the new endpoints
at <https://servicodados.ibge.gov.br/api/docs/agregados?versao=3>. Ferramentas para acessar
e manipular dados via API do Sistema IBGE De Recuperação Automática 'SIDRA'
do Instituto Brasileiro de Geografia e Estatística (IBGE).
Author: Rodrigo Emmanuel Santana Borges [cre, aut, cph]
Maintainer: Rodrigo Emmanuel Santana Borges <rodrigo@borges.net.br>
This is a re-admission after prior archival of version 0.1.9 dated 2025-09-06
Diff between sidra versions 0.1.9 dated 2025-09-06 and 0.2.0 dated 2026-09-18
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- NEWS.md | 8 ++++++++ R/sidra.R | 2 +- R/tab_agr.R | 2 +- R/tab_meta.R | 2 +- R/tab_niveis.R | 2 +- build/vignette.rds |binary inst/doc/sidra.html | 4 ++-- tests/testthat/test-sidra.R | 22 +++++++--------------- tests/testthat/test-tab_agr.R | 15 +++++---------- 11 files changed, 39 insertions(+), 44 deletions(-)
Title: Prepare Data and Trees for Phylogenetic Comparative Methods
Description: Reconcile species names across datasets and phylogenetic trees
for comparative biology workflows. Identifies mismatches due to formatting
differences, taxonomic synonymy, and spelling errors. Produces detailed
reports documenting how each name was resolved, which taxonomic authority
was used, and what remains unresolved. Supports exact matching, name
normalisation, synonym resolution via local taxonomic databases, and
fuzzy matching for likely typos. Detects taxonomic splits and lumps. For
methodological context, see Nakagawa et al. (2026)
<doi:10.32942/X2468Z>.
Author: Shinichi Nakagawa [aut, cre, cph] ,
Santiago Ortega [aut],
Ayumi Mizuno [aut],
Eduardo S.A. Santos [aut],
Malgorzata Lagisz [aut] ,
Bhavya Jain [aut],
Jimuel Jr Celeste [aut],
Sergio Poo Hernandez [aut]
Maintainer: Shinichi Nakagawa <itchyshin@gmail.com>
Diff between prepR4pcm versions 1.0.2 dated 2026-08-25 and 1.0.3 dated 2026-09-18
DESCRIPTION | 8 ++--- MD5 | 26 ++++++++--------- NEWS.md | 4 ++ R/reconcile_accessors.R | 8 ++--- README.md | 2 + inst/doc/bird-workflow.R | 18 +++++------ inst/doc/bird-workflow.html | 44 ++++++----------------------- inst/doc/comparing-tree-backends.html | 6 +-- inst/doc/db-assembly-workflow_mammals.html | 4 +- inst/doc/getting-started.Rmd | 5 +-- inst/doc/getting-started.html | 9 +++-- man/reconcile_mapping.Rd | 8 ++--- tests/testthat/test-authority-mocked.R | 1 vignettes/getting-started.Rmd | 5 +-- 14 files changed, 67 insertions(+), 81 deletions(-)
Title: Transparent and Assisted Linear Modeling Engine
Description: Unified estimation, diagnostics, and reporting for ordinary least
squares (OLS) regression, ANOVA/t-tests, logistic regression, panel data
(fixed/random effects with Hausman test), instrumental variables (2SLS with
weak instrument diagnostics), and difference-in-differences. Designed for
applied researchers in social sciences with integrated "Methodological Customs"
that audit assumptions and provide literature references. All methods
implemented in pure base R without external dependencies beyond stats and
graphics packages.
Author: Manuel Soto-Perez [aut, cre]
Maintainer: Manuel Soto-Perez <msoto@up.edu.mx>
Diff between OLSengine versions 1.1.1 dated 2026-07-31 and 1.2.0 dated 2026-09-18
DESCRIPTION | 6 ++--- MD5 | 18 ++++++++-------- NAMESPACE | 1 NEWS.md | 18 ++++++++++++++++ R/OLS_engine.R | 44 +++++++++++++++++++++++++++++++--------- README.md | 8 +++---- inst/doc/vignette_tutorial.R | 2 - inst/doc/vignette_tutorial.Rmd | 2 - inst/doc/vignette_tutorial.html | 16 +++++++------- vignettes/vignette_tutorial.Rmd | 2 - 10 files changed, 81 insertions(+), 36 deletions(-)
Title: Multivariate Network Meta-Analysis using Bayesian Methods
Description: Tools to conduct Bayesian multivariate network meta-analysis providing
- the single correlation coefficient model by Efthimiou et al. (2015) <doi:10.1093/biostatistics/kxu030>;
- per-outcome consistency checks using the node-splitting method (Dias et al., 2010) <doi:10.1002/sim.3767>;
- per-outcome treatment hierarchies using the surface under the cumulative ranking curve (SUCRA), the probability of best value, or median (or mean) ranks (Salanti et al., 2011) <doi:10.1016/j.jclinepi.2010.03.016>;
- across-outcomes benefit-risk assessment using the VišeKriterijumska Optimizacija I Kompromisno Rešenje (VIKOR) method (Opricovic & Tzeng, 2004) <doi:10.1016/S0377-2217(03)00020-1>;
- convergence checks using trace plots, density plots, or the R-hat statistic;
- forest plots of treatment estimates and consistency checks, scatter plots of per-outcome rankings, Hasse diagrams (Carlsen & Bruggemann, 2014) <doi:10.1002/cem.2569> to visualize the partial order [...truncated...]
Author: Theodoros Evrenoglou [aut, cre] ,
Guido Schwarzer [aut]
Maintainer: Theodoros Evrenoglou <theodoros.evrenoglou@uniklinik-freiburg.de>
Diff between mvnma versions 0.2-0 dated 2026-07-09 and 0.3-0 dated 2026-09-18
mvnma-0.2-0/mvnma/R/mvdata.R |only mvnma-0.2-0/mvnma/man/vikor.Rd |only mvnma-0.3-0/mvnma/DESCRIPTION | 15 mvnma-0.3-0/mvnma/MD5 | 67 mvnma-0.3-0/mvnma/NAMESPACE | 180 +- mvnma-0.3-0/mvnma/NEWS.md | 70 mvnma-0.3-0/mvnma/R/VIKOR.R | 387 +--- mvnma-0.3-0/mvnma/R/as.mcmc.mvnma.R | 180 +- mvnma-0.3-0/mvnma/R/forest.mvnma.R | 420 ++--- mvnma-0.3-0/mvnma/R/forest.netsplit.R |only mvnma-0.3-0/mvnma/R/hasse.R | 201 +- mvnma-0.3-0/mvnma/R/heatplot.mvrank.R | 393 ++-- mvnma-0.3-0/mvnma/R/linechart.R | 255 +-- mvnma-0.3-0/mvnma/R/mvnma-internal.R | 1780 ++++++++++------------ mvnma-0.3-0/mvnma/R/mvnma-package.R | 321 +-- mvnma-0.3-0/mvnma/R/mvnma.R | 1397 +++++++---------- mvnma-0.3-0/mvnma/R/mvnma_code.R | 1137 +++++++------- mvnma-0.3-0/mvnma/R/mvrank.R | 533 +++--- mvnma-0.3-0/mvnma/R/netsplit-internal.R |only mvnma-0.3-0/mvnma/R/netsplit.mvnma.R |only mvnma-0.3-0/mvnma/R/plot.mvrank.R | 189 +- mvnma-0.3-0/mvnma/R/spiechart-internal.R | 72 mvnma-0.3-0/mvnma/R/spiechart.R | 248 +-- mvnma-0.3-0/mvnma/R/updateversion.R |only mvnma-0.3-0/mvnma/R/vikor-internal.R | 354 ++-- mvnma-0.3-0/mvnma/inst/extdata/mvnma_examples.rda |binary mvnma-0.3-0/mvnma/man/as.mcmc.mvnma.Rd | 122 - mvnma-0.3-0/mvnma/man/forest.mvnma.Rd | 184 +- mvnma-0.3-0/mvnma/man/forest.netsplit.mvnma.Rd |only mvnma-0.3-0/mvnma/man/hasse.mvrank.Rd | 124 - mvnma-0.3-0/mvnma/man/heatplot.mvrank.Rd | 218 +- mvnma-0.3-0/mvnma/man/linechart.Rd | 156 - mvnma-0.3-0/mvnma/man/mvnma-package.Rd | 303 +-- mvnma-0.3-0/mvnma/man/mvnma.Rd | 584 +++---- mvnma-0.3-0/mvnma/man/mvrank.Rd | 166 +- mvnma-0.3-0/mvnma/man/netsplit.mvnma.Rd |only mvnma-0.3-0/mvnma/man/plot.mvrank.Rd | 134 - mvnma-0.3-0/mvnma/man/spiechart.Rd | 132 - mvnma-0.3-0/mvnma/man/vikor.mvrank.Rd |only 39 files changed, 5079 insertions(+), 5243 deletions(-)
Title: Dyadic Network Analysis
Description: Contains functions for the MCMC simulation of (multilevel) dyadic network models j2 (Zijlstra, 2017, <doi:10.1080/0022250X.2017.1387858>) and p2 (Van Duijn, Snijders & Zijlstra, 2004, <doi: 10.1046/j.0039-0402.2003.00258.x>), the multilevel p2 model (Zijlstra, Van Duijn & Snijders (2009) <doi: 10.1348/000711007X255336>), and the bidirectional (multilevel) counterpart of the the multilevel p2 model as described in Zijlstra, Van Duijn & Snijders (2009) <doi: 10.1348/000711007X255336>, the (multilevel) b2 model.
Author: Bonne J.H. Zijlstra [aut, cre]
Maintainer: Bonne J.H. Zijlstra <B.J.H.Zijlstra@uva.nl>
Diff between dyads versions 1.2.1 dated 2022-08-17 and 1.2.22.3 dated 2026-09-18
DESCRIPTION | 18 MD5 | 26 - NAMESPACE | 17 R/b2ML.R | 993 +++++++++++++++++++++------------------------ R/internalFunctionsDyads.R | 389 +++++++++++++++++ R/j2.R | 29 - R/j2ML.R |only R/p2.R | 31 - R/p2ML.R | 333 +++++++-------- build/partial.rdb |binary man/b2ML.Rd | 200 ++++----- man/j2.Rd | 156 +++---- man/j2ML.Rd |only man/p2.Rd | 154 +++--- man/p2ML.Rd | 209 ++++----- 15 files changed, 1468 insertions(+), 1087 deletions(-)
Title: Visualisation, Exploration, and Web Communication of
Archaeological Spatial Data
Description: An R 'Shiny' application for visual and statistical exploration and web communication of archaeological spatial data, either remains or sites. It offers interactive 3D and 2D visualisations (cross sections and maps of remains, timeline of the work made in a site) which can be exported in SVG and HTML formats. It performs simple spatial statistics (convex hull, regression surfaces, 2D kernel density estimation) and allows exporting data to other online applications for more complex methods. 'archeoViz' can be used offline locally or deployed on a server, either with interactive input of data or with a static data set. Example is provided at <https://analytics.huma-num.fr/archeoviz/en>.
Author: Sebastien Plutniak [aut, cre] ,
Renata Araujo [ctb] ,
Laura Coltofean [ctb] ,
Nicolas Delsol [ctb] ,
Sara Giardino [ctb] ,
Julian Laabs [ctb]
Maintainer: Sebastien Plutniak <sebastien.plutniak@posteo.net>
Diff between archeoViz versions 1.4.2 dated 2026-07-30 and 1.4.3 dated 2026-09-18
DESCRIPTION | 8 MD5 | 12 NAMESPACE | 2 NEWS.md | 4 R/app_server.R | 302 ++++++++++++++++-------- R/app_ui.R | 1 R/load_interface_terms.R | 576 ++++++++++++++++++++++++++--------------------- 7 files changed, 538 insertions(+), 367 deletions(-)
Title: Functions to Efficiently Access NFL Play by Play Data
Description: A set of functions to access National Football League
play-by-play data from <https://www.nfl.com/>.
Author: Sebastian Carl [aut],
Ben Baldwin [cre, aut],
Lee Sharpe [ctb],
Maksim Horowitz [ctb],
Ron Yurko [ctb],
Samuel Ventura [ctb],
Tan Ho [ctb],
John Edwards [ctb]
Maintainer: Ben Baldwin <bbaldwin206@gmail.com>
Diff between nflfastR versions 5.2.0 dated 2026-02-07 and 6.0.0 dated 2026-09-18
nflfastR-5.2.0/nflfastR/tests/testthat/1999 |only nflfastR-6.0.0/nflfastR/DESCRIPTION | 12 nflfastR-6.0.0/nflfastR/MD5 | 111 nflfastR-6.0.0/nflfastR/NAMESPACE | 33 nflfastR-6.0.0/nflfastR/NEWS.md | 31 nflfastR-6.0.0/nflfastR/R/aggregate_game_stats.R | 750 ---- nflfastR-6.0.0/nflfastR/R/aggregate_game_stats_def.R | 629 --- nflfastR-6.0.0/nflfastR/R/aggregate_game_stats_kicking.R | 193 - nflfastR-6.0.0/nflfastR/R/build_nflfastR_pbp.R | 47 nflfastR-6.0.0/nflfastR/R/build_playstats.R | 31 nflfastR-6.0.0/nflfastR/R/calculate_series_conversion_rates.R | 47 nflfastR-6.0.0/nflfastR/R/calculate_standings.R | 129 nflfastR-6.0.0/nflfastR/R/calculate_stats.R | 417 +- nflfastR-6.0.0/nflfastR/R/data_documentation.R | 5 nflfastR-6.0.0/nflfastR/R/database.R |only nflfastR-6.0.0/nflfastR/R/ep_wp_calculators.R | 38 nflfastR-6.0.0/nflfastR/R/helper_add_cp_cpoe.R | 67 nflfastR-6.0.0/nflfastR/R/helper_add_ep_wp.R | 1789 ++++++---- nflfastR-6.0.0/nflfastR/R/helper_add_fixed_drives.R | 115 nflfastR-6.0.0/nflfastR/R/helper_add_game_data.R | 38 nflfastR-6.0.0/nflfastR/R/helper_add_nflscrapr_mutations.R | 625 ++- nflfastR-6.0.0/nflfastR/R/helper_add_series_data.R | 49 nflfastR-6.0.0/nflfastR/R/helper_add_xpass.R | 35 nflfastR-6.0.0/nflfastR/R/helper_add_xyac.R | 152 nflfastR-6.0.0/nflfastR/R/helper_additional_functions.R | 404 +- nflfastR-6.0.0/nflfastR/R/helper_database_functions.R | 145 nflfastR-6.0.0/nflfastR/R/helper_decode_player_ids.R | 27 nflfastR-6.0.0/nflfastR/R/helper_get_scheds_and_rosters.R | 11 nflfastR-6.0.0/nflfastR/R/helper_scrape_gc.R | 152 nflfastR-6.0.0/nflfastR/R/helper_scrape_nfl.R | 241 + nflfastR-6.0.0/nflfastR/R/helper_tidy_play_stats.R | 200 - nflfastR-6.0.0/nflfastR/R/helper_variable_selector.R | 477 ++ nflfastR-6.0.0/nflfastR/R/nflfastR-package.R | 4 nflfastR-6.0.0/nflfastR/R/report.R | 2 nflfastR-6.0.0/nflfastR/R/save_raw_pbp.R | 92 nflfastR-6.0.0/nflfastR/R/top-level_scraper.R | 48 nflfastR-6.0.0/nflfastR/R/utils.R | 142 nflfastR-6.0.0/nflfastR/data/nfl_stats_variables.rda |binary nflfastR-6.0.0/nflfastR/data/teams_colors_logos.rda |binary nflfastR-6.0.0/nflfastR/man/calculate_player_stats.Rd | 96 nflfastR-6.0.0/nflfastR/man/calculate_player_stats_def.Rd | 27 nflfastR-6.0.0/nflfastR/man/calculate_player_stats_kicking.Rd | 23 nflfastR-6.0.0/nflfastR/man/fast_scraper_roster.Rd | 2 nflfastR-6.0.0/nflfastR/man/nflfastR-package.Rd | 1 nflfastR-6.0.0/nflfastR/man/reexports.Rd | 3 nflfastR-6.0.0/nflfastR/man/report.Rd | 7 nflfastR-6.0.0/nflfastR/man/stat_ids.Rd | 2 nflfastR-6.0.0/nflfastR/man/teams_colors_logos.Rd | 3 nflfastR-6.0.0/nflfastR/man/update_pbp_db.Rd |only nflfastR-6.0.0/nflfastR/tests/testthat/2025 |only nflfastR-6.0.0/nflfastR/tests/testthat/_snaps/build_nflfastR_pbp.md |only nflfastR-6.0.0/nflfastR/tests/testthat/_snaps/stats/calculate_stats.md | 20 nflfastR-6.0.0/nflfastR/tests/testthat/expected_pbp.rds |binary nflfastR-6.0.0/nflfastR/tests/testthat/expected_sc.rds |binary nflfastR-6.0.0/nflfastR/tests/testthat/expected_sc_weekly.rds |binary nflfastR-6.0.0/nflfastR/tests/testthat/games.rds |binary nflfastR-6.0.0/nflfastR/tests/testthat/helpers.R | 68 nflfastR-6.0.0/nflfastR/tests/testthat/test-build_nflfastR_pbp.R | 15 nflfastR-6.0.0/nflfastR/tests/testthat/test-calculate_stats.R | 31 59 files changed, 4103 insertions(+), 3483 deletions(-)
Title: Estimates and Plots Single-Level and Multilevel Latent Class
Models
Description: Efficiently estimates single- and multilevel latent class models with covariates, allowing for output visualization in all specifications. For more technical details, see Lyrvall et al. (2025) <doi:10.1080/00273171.2025.2473935>.
Author: Roberto Di Mari [aut, cre],
Johan Lyrvall [aut],
Zsuzsa Bakk [ctb],
Jennifer Oser [ctb],
Jouni Kuha [ctb]
Maintainer: Roberto Di Mari <roberto.dimari@unict.it>
Diff between multilevLCA versions 2.1.5 dated 2026-08-26 and 2.1.6 dated 2026-09-18
DESCRIPTION | 8 MD5 | 18 - R/RcppExports.R | 8 build/partial.rdb |binary data/dataIEA.rda |binary data/dataTOY.rda |binary src/RcppExports.cpp | 35 --- src/Utils.cpp | 511 ++++++++++++++------------------------------------ src/Utils.h | 2 src/multilevLC_EM.cpp | 274 ++++++++++++++++---------- 10 files changed, 333 insertions(+), 523 deletions(-)
Title: Simultaneous Prediction and Confidence Bands for Functional Data
Description: Computes simultaneous prediction and confidence bands for densely
sampled functional data on a common grid. The calibration builds on the
functional bootstrap approach of Lenhoff et al. (1999)
<doi:10.1016/S0966-6362(98)00043-5>; hierarchical measurement designs are
motivated by Koska et al. (2023)
<doi:10.1016/j.jbiomech.2023.111506>. Independent curves are resampled
individually. Clustered data use an intact-subject bootstrap with equal
subject weighting, and the clustered prediction target is one future
curve from a new subject. Curves are represented by finite Fourier series,
and an 'Rcpp' backend performs the bootstrap calibration.
Author: Daniel Koska [aut, cre, cph]
Maintainer: Daniel Koska <dkoska@proton.me>
Diff between funbootband versions 0.2.0 dated 2025-10-20 and 0.3.0 dated 2026-09-18
DESCRIPTION | 28 +- MD5 | 33 +- NEWS.md | 22 + R/RcppExports.R | 8 R/band.R | 228 ++++++++++++++++--- README.md | 122 +++++----- build/vignette.rds |binary inst/doc/funbootband-intro.R | 136 +++++++---- inst/doc/funbootband-intro.Rmd | 234 ++++++++++++++------ inst/doc/funbootband-intro.html | 434 ++++++++++++++++++++++---------------- inst/examples/clustered_example.R | 85 ++++--- inst/examples/iid_example.R | 59 ++--- inst/validation |only man/band.Rd | 177 +++++++++------ src/RcppExports.cpp | 35 +-- src/band_kernels.cpp | 181 ++++++++++----- tests/testthat/test-band.R | 178 +++++++++++++++ vignettes/funbootband-intro.Rmd | 234 ++++++++++++++------ 18 files changed, 1452 insertions(+), 742 deletions(-)
Title: Text Analysis for All
Description: An R 'shiny' app designed for diverse text analysis tasks, offering a wide range of methodologies tailored to Natural Language Processing (NLP) needs.
It is a versatile, general-purpose tool for analyzing textual data.
'tall' features a comprehensive workflow, including data cleaning, preprocessing, statistical analysis, and visualization, all integrated for effective text analysis.
Author: Massimo Aria [aut, cre, cph] ,
Maria Spano [aut] ,
Luca D'Aniello [aut] ,
Corrado Cuccurullo [ctb] ,
Michelangelo Misuraca [ctb]
Maintainer: Massimo Aria <aria@unina.it>
Diff between tall versions 1.0.0 dated 2026-04-15 and 1.0.1 dated 2026-09-18
DESCRIPTION | 8 MD5 | 50 - NAMESPACE | 80 +- NEWS.md | 350 +++++++++++ R/reinert.R | 8 R/txt_recode_fast.R | 31 - build/partial.rdb |binary inst/tall/collocation.R | 32 - inst/tall/doc_classification.R | 77 +- inst/tall/documents.R | 15 inst/tall/featureroles.R | 121 ++- inst/tall/helpContent.R | 951 +++++++++++++++---------------- inst/tall/import.R | 16 inst/tall/overview.R | 12 inst/tall/preprocessing.R | 42 + inst/tall/settings.R | 94 ++- inst/tall/tallAI.R | 255 +++++--- inst/tall/tallEmbeddings.R | 69 +- inst/tall/tallNLP.R | 63 +- inst/tall/tallSentiment.R | 21 inst/tall/tallTextIO.R | 28 inst/tall/tallTopicModel.R | 218 +++++-- inst/tall/tallUtils.R | 49 + inst/tall/words.R | 15 man/process_multiwords_fast.Rd | 5 tests/testthat/test-process_multiwords.R | 51 + 26 files changed, 1820 insertions(+), 841 deletions(-)
Title: Rendering Parameterized SQL and Translation to Dialects
Description: A rendering tool for parameterized SQL that also translates into
different SQL dialects. These dialects include 'Microsoft SQL Server', 'Oracle',
'PostgreSql', 'Amazon RedShift', 'Apache Impala', 'IBM Netezza', 'Google BigQuery', 'Microsoft PDW', 'Snowflake',
'Azure Synapse Analytics Dedicated', 'Apache Spark', 'SQLite', and 'InterSystems IRIS'.
Author: Martijn Schuemie [aut, cre],
Marc Suchard [aut]
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>
Diff between SqlRender versions 1.19.6 dated 2026-07-31 and 1.19.7 dated 2026-09-18
DESCRIPTION | 10 +++--- MD5 | 24 +++++++-------- NAMESPACE | 16 ++++++---- NEWS.md | 14 +++++++++ inst/csv/replacementPatterns.csv | 32 +++++++++++--------- inst/doc/UsingSqlRender.pdf |binary tests/testthat/test-translate-duckdb.R | 4 +- tests/testthat/test-translate-impala.R | 6 +-- tests/testthat/test-translate-iris.R | 37 ++++++++++++++++++++++-- tests/testthat/test-translate-oracle.R | 24 +++++++++++++++ tests/testthat/test-translate-postgresql.R | 6 +-- tests/testthat/test-translate-sqlite-extended.R | 8 ++--- tests/testthat/test-translate-sqlite.R | 24 ++++++++++++++- 13 files changed, 151 insertions(+), 54 deletions(-)
Title: Analyse Political Texts
Description: Wrangle and annotate different types of political texts.
It also introduces Urgency Analysis,
a new method for the analysis of urgency in political texts.
Author: Henrique Sposito [cre, aut, ctb],
James Hollway [ctb],
Jael Tan [ctb]
Maintainer: Henrique Sposito <henrique.sposito@graduateinstitute.ch>
Diff between poldis versions 0.1.2 dated 2024-09-04 and 0.2.0 dated 2026-09-18
poldis-0.1.2/poldis/R/US_News_Conferences_1960_1980.R |only poldis-0.1.2/poldis/data/US_News_Conferences_1960_1980.rda |only poldis-0.1.2/poldis/man/US_News_Conferences_1960_1980.Rd |only poldis-0.1.2/poldis/man/extract_date.Rd |only poldis-0.1.2/poldis/man/extract_title.Rd |only poldis-0.1.2/poldis/man/sim_urgency.Rd |only poldis-0.2.0/poldis/DESCRIPTION | 30 poldis-0.2.0/poldis/LICENSE | 4 poldis-0.2.0/poldis/MD5 | 78 - poldis-0.2.0/poldis/NAMESPACE | 85 - poldis-0.2.0/poldis/NEWS.md | 271 ++- poldis-0.2.0/poldis/R/US_inaugural_addresses_1993_2025.R |only poldis-0.2.0/poldis/R/class.R | 60 poldis-0.2.0/poldis/R/priorities.R | 80 - poldis-0.2.0/poldis/R/sysdata.rda |binary poldis-0.2.0/poldis/R/text_tools.R | 708 ++++------ poldis-0.2.0/poldis/R/topic.R | 297 +--- poldis-0.2.0/poldis/R/urgency.R | 425 ++---- poldis-0.2.0/poldis/R/utils.R | 77 - poldis-0.2.0/poldis/README.md | 449 +++--- poldis-0.2.0/poldis/build/partial.rdb |binary poldis-0.2.0/poldis/build/vignette.rds |only poldis-0.2.0/poldis/data/US_inaugural_addresses_1993_2025.rda |only poldis-0.2.0/poldis/inst |only poldis-0.2.0/poldis/man/US_inaugural_addresses_1993_2025.Rd |only poldis-0.2.0/poldis/man/annotate_text.Rd | 49 poldis-0.2.0/poldis/man/extract_context.Rd | 72 - poldis-0.2.0/poldis/man/extract_first_sentence.Rd |only poldis-0.2.0/poldis/man/extract_locations.Rd | 48 poldis-0.2.0/poldis/man/extract_match.Rd | 64 poldis-0.2.0/poldis/man/extract_names.Rd | 46 poldis-0.2.0/poldis/man/extract_text_similarities.Rd | 70 poldis-0.2.0/poldis/man/gather_related_terms.Rd | 87 - poldis-0.2.0/poldis/man/gather_topics.Rd | 75 - poldis-0.2.0/poldis/man/get_urgency.Rd | 124 - poldis-0.2.0/poldis/man/read_pdf.Rd | 34 poldis-0.2.0/poldis/man/select_priorities.Rd | 55 poldis-0.2.0/poldis/man/split_text.Rd | 54 poldis-0.2.0/poldis/tests/testthat.R | 8 poldis-0.2.0/poldis/tests/testthat/helper-spacy.R |only poldis-0.2.0/poldis/tests/testthat/test_priorities.R | 39 poldis-0.2.0/poldis/tests/testthat/test_text_tools.R | 104 - poldis-0.2.0/poldis/tests/testthat/test_topic.R | 26 poldis-0.2.0/poldis/tests/testthat/test_urgency.R | 120 - poldis-0.2.0/poldis/vignettes |only 45 files changed, 1823 insertions(+), 1816 deletions(-)
Title: Time Series Analysis Tool using Linear Layered SDEs
Description: Time series analysis tool using linear layered stochastic
differential equations. The package allows for multiple time
series with correlative and/or causal links between them. Unmeasured causal
processes are allowed to affect the measured processes in a layered structure,
hence the name of the package. In case of causal feedback loops,
the matrix operations (including eigenvalue decompositions) allows for
complex numbers. In this case, cyclic behavior can be expected.
Details can be found in Reitan and Liow (2019)<doi:10.1111/2041-210X.13299>.
Author: Trond Reitan [aut, cre] ,
Lee Hsiang Liow [ctb] ,
Adam T. Kocsis [ctb]
Maintainer: Trond Reitan <trond.reitan@geo.uio.no>
Diff between layeranalyzer versions 0.4.1 dated 2026-08-28 and 0.4.2 dated 2026-09-18
DESCRIPTION | 8 - MD5 | 8 - NEWS.md | 5 build/partial.rdb |binary src/layeranalyzer.cpp | 298 +++++++++++++++++++++++++------------------------- 5 files changed, 166 insertions(+), 153 deletions(-)
Title: Baseline Correction of Spectra
Description: Collection of baseline correction algorithms, along with a framework and a Tcl/Tk enabled GUI for optimising baseline algorithm parameters. Typical use of the package is for removing background effects from spectra originating from various types of spectroscopy and spectrometry, possibly optimizing this with regard to regression or classification results. Correction methods include polynomial fitting, weighted local smoothers and many more.
Author: Kristian Hovde Liland [aut, cre] ,
Bjoern-Helge Mevik [aut],
Roberto Canteri [ctb]
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>
Diff between baseline versions 1.3-7 dated 2025-06-18 and 1.3-8 dated 2026-09-18
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Title: Self-Validated Ensemble Models with Lasso and Relaxed Elastic
Net Regression
Description: Implements the self-validated elastic-net and relaxed elastic-net ensemble modeling and multi-response optimization workflow described in Karl (2026) <doi:10.1016/j.chemolab.2026.105660>. Self-validated ensemble models (SVEM; Lemkus et al. (2021) <doi:10.1016/j.chemolab.2021.104439>) are fitted for small-sample design-of-experiments and related workflows using '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, and a random-search optimizer that respects mixture constraints and combines multiple responses via desirability functions. Also includes a permutation-based whole-model test for Gaussian SVEM fits (Karl (2024) <doi:10.1016/j.chemolab.2024.105122>). Package code was drafte [...truncated...]
Author: Andrew T. Karl [cre, aut]
Maintainer: Andrew T. Karl <akarl@asu.edu>
Diff between SVEMnet versions 3.6.0 dated 2026-09-06 and 3.6.2 dated 2026-09-18
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Title: Facilitate Analysis of Proteomic Data from Olink
Description: A collection of functions to facilitate analysis of proteomic
data from Olink, primarily NPX data that has been exported from Olink
Software. The functions also work on QUANT data from
Olink by log- transforming the QUANT data. The functions are focused
on reading data, facilitating data wrangling and quality control
analysis, performing statistical analysis and generating figures to
visualize the results of the statistical analysis. The goal of this
package is to help users extract biological insights from proteomic
data run on the Olink platform.
Author: Kathleen Nevola [aut, cre] ,
Marianne Sandin [aut] ,
Jamey Guess [aut] ,
Simon Forsberg [aut] ,
Christoffer Cambronero [aut] ,
Pascal Pucholt [aut] ,
Boxi Zhang [aut] ,
Masoumeh Sheikhi [aut] ,
Klev Diamanti [aut] ,
Amrita Kar [aut] ,
Lei Conze [aut] [...truncated...]
Maintainer: Kathleen Nevola <biostattools@olink.com>
Diff between OlinkAnalyze versions 5.0.2 dated 2026-06-23 and 5.1.0 dated 2026-09-18
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Title: Various Methods for the Goodness-of-Fit Problem in D>1
Dimensions
Description: Provides multivariate goodness-of-fit testing with a common
interface for several test statistics. Null models may be simple or include
parameter estimation, with p-values obtained by parametric bootstrap
simulation. The function gof_test_adjusted_pvalue() combines several tests
and computes a p-value adjusted for simultaneous inference. The function
gof_power() estimates test power. The functions hybrid_test() and
hybrid_power() use Monte Carlo samples under the null together with
two-sample procedures. The function run.studies() supports systematic power
comparisons of user-supplied and included methods across case studies. See
the included vignettes for method details and references.
Author: Wolfgang Rolke [aut, cre]
Maintainer: Wolfgang Rolke <wolfgang.rolke@upr.edu>
Diff between MDgof versions 1.1.0 dated 2026-08-03 and 1.2.0 dated 2026-09-18
MDgof-1.1.0/MDgof/R/makeTSextra.R |only MDgof-1.2.0/MDgof/DESCRIPTION | 36 MDgof-1.2.0/MDgof/MD5 | 65 MDgof-1.2.0/MDgof/NAMESPACE | 12 MDgof-1.2.0/MDgof/NEWS.md | 7 MDgof-1.2.0/MDgof/R/check.functions.R | 108 - MDgof-1.2.0/MDgof/R/chi_power.R | 138 +- MDgof-1.2.0/MDgof/R/draw_case.R | 79 - MDgof-1.2.0/MDgof/R/gof_power.R | 651 +++++----- MDgof-1.2.0/MDgof/R/gof_test.R | 640 ++++++--- MDgof-1.2.0/MDgof/R/gof_test_adjusted_pvalue.R | 630 ++++----- MDgof-1.2.0/MDgof/R/helper_functions.R |only MDgof-1.2.0/MDgof/R/hybrid_power.R | 20 MDgof-1.2.0/MDgof/R/hybrid_test.R | 25 MDgof-1.2.0/MDgof/R/power_pvals.R | 92 - MDgof-1.2.0/MDgof/R/run.studies.R | 7 MDgof-1.2.0/MDgof/R/signif_digits.R | 62 MDgof-1.2.0/MDgof/R/timecheck.R | 26 MDgof-1.2.0/MDgof/inst/doc/MDgof-Case-Studies.html | 56 MDgof-1.2.0/MDgof/man/MDgof_test-methods.Rd |only MDgof-1.2.0/MDgof/man/as.data.frame.MDgof_power.Rd |only MDgof-1.2.0/MDgof/man/check.functions.Rd | 17 MDgof-1.2.0/MDgof/man/draw_case.Rd | 4 MDgof-1.2.0/MDgof/man/gof_power.Rd | 15 MDgof-1.2.0/MDgof/man/gof_test.Rd | 20 MDgof-1.2.0/MDgof/man/gof_test_adjusted_pvalue.Rd | 7 MDgof-1.2.0/MDgof/man/hybrid_power.Rd | 3 MDgof-1.2.0/MDgof/man/hybrid_test.Rd | 3 MDgof-1.2.0/MDgof/man/makeTSextra.Rd | 5 MDgof-1.2.0/MDgof/man/makemaxProcessor.Rd |only MDgof-1.2.0/MDgof/man/maketypeTS.Rd |only MDgof-1.2.0/MDgof/man/print.MDgof_power.Rd |only MDgof-1.2.0/MDgof/man/run.studies.Rd | 5 MDgof-1.2.0/MDgof/man/signif_digits.Rd | 1 MDgof-1.2.0/MDgof/man/timecheck.Rd | 1 MDgof-1.2.0/MDgof/tests/testthat/test-discrete-custom-TS-signatures.R |only MDgof-1.2.0/MDgof/tests/testthat/test-discrete-matrix-detection.R |only MDgof-1.2.0/MDgof/tests/testthat/test-gof-power-ci.R |only MDgof-1.2.0/MDgof/tests/testthat/test-input-validation.R |only 39 files changed, 1510 insertions(+), 1225 deletions(-)
Title: Interface to Download Meteorological (and Hydrological) Datasets
Description: Automatize downloading of meteorological and hydrological data from publicly available repositories:
OGIMET (<http://ogimet.com/index.phtml.en>),
University of Wyoming - atmospheric vertical profiling data (<http://weather.uwyo.edu/upperair/>),
Polish Institute of Meteorology and Water Management - National Research Institute (<https://danepubliczne.imgw.pl>),
and National Oceanic & Atmospheric Administration (NOAA).
This package also allows for searching geographical coordinates for each observation and calculate distances to the nearest stations.
Author: Bartosz Czernecki [aut, cre] ,
Arkadiusz Glogowski [aut] ,
Jakub Nowosad [aut] ,
IMGW-PIB [ctb]
Maintainer: Bartosz Czernecki <nwp@amu.edu.pl>
Diff between climate versions 1.4.0 dated 2026-07-10 and 1.4.1 dated 2026-09-18
DESCRIPTION | 6 MD5 | 50 +- NEWS.md | 8 R/hydro_imgw.R | 15 R/hydro_imgw_daily.R | 2 R/hydro_imgw_monthly.R | 2 R/hydro_shortening_imgw.R | 62 +-- R/meteo_imgw.R | 13 R/meteo_imgw_daily.R | 12 R/meteo_imgw_hourly.R | 15 R/meteo_imgw_monthly.R | 15 R/meteo_shortening_imgw.R | 52 +- R/utils.R | 7 README.md | 17 data/imgw_hydro_abbrev.rda |binary data/imgw_meteo_abbrev.rda |binary inst/doc/getstarted.Rmd | 6 inst/doc/getstarted.html | 756 ++++++++++++------------------------------- man/hydro_imgw.Rd | 1 man/hydro_shortening_imgw.Rd | 17 man/meteo_imgw.Rd | 5 man/meteo_imgw_daily.Rd | 6 man/meteo_imgw_hourly.Rd | 5 man/meteo_imgw_monthly.Rd | 11 man/meteo_shortening_imgw.Rd | 12 vignettes/getstarted.Rmd | 6 26 files changed, 378 insertions(+), 723 deletions(-)
Title: Holistic Multimodel Domain Analysis for Exploratory Machine
Learning
Description: Holistic Multimodel Domain Analysis (HMDA) is a robust and transparent framework designed for exploratory machine learning research, aiming to enhance the process of feature assessment and selection. HMDA addresses key limitations of traditional machine learning methods by evaluating the consistency across multiple high-performing models within a fine-tuned modeling grid, thereby improving the interpretability and reliability of feature importance assessments. Specifically, it computes Weighted Mean SHapley Additive exPlanations (WMSHAP), which aggregate feature contributions from multiple models based on weighted performance metrics. HMDA also provides confidence intervals to demonstrate the stability of these feature importance estimates. This framework is particularly beneficial for analyzing complex, multidimensional datasets common in health research, supporting reliable exploration of mental health outcomes such as suicidal ideation, suicide attempts, and other psychological cond [...truncated...]
Author: E. F. Haghish [aut, cre, cph]
Maintainer: E. F. Haghish <haghish@hotmail.com>
Diff between HMDA versions 0.3.0 dated 2026-03-04 and 0.4.1 dated 2026-09-18
DESCRIPTION | 8 ++++---- MD5 | 13 ++++++++++--- NAMESPACE | 5 +++++ R/helpers.R |only R/hmda.fastcompute.globalshap.R |only R/hmda.fastcompute.globalwmshap.R |only R/hmda.init.R | 2 +- R/hmda.rashamon.set.R |only man/hmda.fastcompute.globalshap.Rd |only man/hmda.fastcompute.globalwmshap.Rd |only man/hmda.rashomon.set.Rd |only 11 files changed, 20 insertions(+), 8 deletions(-)
Title: Geometrical Functionality of the 'spatstat' Family
Description: Defines spatial data types and supports geometrical operations
on them. Data types include point patterns, windows (domains),
pixel images, line segment patterns, tessellations and hyperframes.
Capabilities include creation and manipulation of data
(using command line or graphical interaction),
plotting, geometrical operations (rotation, shift, rescale,
affine transformation), convex hull, discretisation and
pixellation, Dirichlet tessellation, Delaunay triangulation,
pairwise distances, nearest-neighbour distances,
distance transform, morphological operations
(erosion, dilation, closing, opening), quadrat counting,
geometrical measurement, geometrical covariance,
colour maps, calculus on spatial domains,
Gaussian blur, level sets of images, transects of images,
intersections between objects, minimum distance matching.
(Excludes spatial data on a network, which are supported by
the package 'spatstat.linnet'.)
Author: Adrian Baddeley [aut, cre, cph] ,
Rolf Turner [aut, cph] ,
Ege Rubak [aut, cph] ,
Warick Brown [ctb],
Tilman Davies [ctb],
Ute Hahn [ctb],
Martin Hazelton [ctb],
Abdollah Jalilian [ctb],
Greg McSwiggan [ctb, cph],
Sebastian Meyer [ctb, cph],
Jens Oeh [...truncated...]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.geom versions 3.8-2 dated 2026-07-24 and 3.8-3 dated 2026-09-18
DESCRIPTION | 10 ++++----- MD5 | 20 +++++++++--------- NAMESPACE | 1 NEWS | 24 ++++++++++++++++++++-- R/marks.R | 24 +++++++++++++++++++++- R/plot.im.R | 45 +++++++++++++++++++++++++++++------------- R/ripras.R | 5 ++-- inst/doc/packagesizes.txt | 2 - inst/info/packagesizes.txt | 2 - man/ripras.Rd | 5 ++-- man/spatstat.geom-internal.Rd | 2 + 11 files changed, 103 insertions(+), 37 deletions(-)
Title: External jars for 'rjdverse' R Packages
Description: It provides external jars required for the 'rjdverse' (as 'rjd3toolkit', 'rjd3x13' and 'rjd3tramoseats').
Author: Tanguy Barthelemy [aut, cre, cph]
Maintainer: Tanguy Barthelemy <timeserieswithjdemetraandr@gmail.com>
Diff between rjd3jars versions 0.0.5 dated 2026-07-07 and 0.0.6 dated 2026-09-18
rjd3jars-0.0.5/rjd3jars/inst/java/jdplus-sa-base-api-3.8.0.jar |only rjd3jars-0.0.5/rjd3jars/inst/java/jdplus-sa-base-core-3.8.0.jar |only rjd3jars-0.0.5/rjd3jars/inst/java/jdplus-toolkit-base-api-3.8.0.jar |only rjd3jars-0.0.5/rjd3jars/inst/java/jdplus-toolkit-base-core-3.8.0.jar |only rjd3jars-0.0.5/rjd3jars/inst/java/protobuf-java-4.35.1.jar |only rjd3jars-0.0.6/rjd3jars/DESCRIPTION | 21 + rjd3jars-0.0.6/rjd3jars/MD5 | 40 +-- rjd3jars-0.0.6/rjd3jars/NAMESPACE | 22 - rjd3jars-0.0.6/rjd3jars/NEWS.md | 130 +++++----- rjd3jars-0.0.6/rjd3jars/R/java.R |only rjd3jars-0.0.6/rjd3jars/R/rjd3jars-package.R | 12 rjd3jars-0.0.6/rjd3jars/R/utils.R | 116 ++++---- rjd3jars-0.0.6/rjd3jars/R/zzz.R | 110 ++------ rjd3jars-0.0.6/rjd3jars/README.md | 82 +++--- rjd3jars-0.0.6/rjd3jars/inst/WORDLIST | 106 -------- rjd3jars-0.0.6/rjd3jars/inst/java/jdplus-sa-base-api-3.9.0.jar |only rjd3jars-0.0.6/rjd3jars/inst/java/jdplus-sa-base-core-3.9.0.jar |only rjd3jars-0.0.6/rjd3jars/inst/java/jdplus-toolkit-base-api-3.9.0.jar |only rjd3jars-0.0.6/rjd3jars/inst/java/jdplus-toolkit-base-core-3.9.0.jar |only rjd3jars-0.0.6/rjd3jars/inst/java/protobuf-java-4.36.1.jar |only rjd3jars-0.0.6/rjd3jars/java/README | 12 rjd3jars-0.0.6/rjd3jars/man/java-version.Rd | 76 ++--- rjd3jars-0.0.6/rjd3jars/man/reload_dictionaries.Rd | 38 +- rjd3jars-0.0.6/rjd3jars/man/reload_safactories.Rd | 35 +- rjd3jars-0.0.6/rjd3jars/man/reload_tsproviders.Rd | 38 +- rjd3jars-0.0.6/rjd3jars/man/rjd3jars-package.Rd | 49 ++- rjd3jars-0.0.6/rjd3jars/tests |only 27 files changed, 384 insertions(+), 503 deletions(-)
Title: 'Rcpp' Meets 'C++' Arrays
Description: Interoperability between 'Rcpp' and the 'C++11' array and tuple
types. Linking to this package allows fixed-length 'std::array' objects to
be converted to and from equivalent R vectors, and 'std::tuple' objects
converted to lists, via the as() and wrap() functions. There is also
experimental support for 'std::span' from 'C++20'.
Author: Jon Clayden [cre, aut] ,
Dirk Eddelbuettel [aut],
Andrew Johnson [ctb]
Maintainer: Jon Clayden <code@clayden.org>
Diff between RcppArray versions 0.3.0 dated 2023-11-08 and 0.3.1 dated 2026-09-18
DESCRIPTION | 12 ++++++------ MD5 | 10 +++++----- NEWS.md | 5 +++++ README.md | 8 ++++---- inst/include/RcppArray.h | 13 +++++++++++-- src/main.cpp | 2 -- 6 files changed, 31 insertions(+), 19 deletions(-)
Title: R Bayesian Evidence Synthesis Tools
Description: Tool-set to support Bayesian evidence synthesis. This
includes meta-analysis, (robust) prior derivation from historical
data, operating characteristics and analysis (1 and 2 sample
cases). Please refer to Weber et al. (2021) <doi:10.18637/jss.v100.i19>
for details on applying this package while Neuenschwander et al. (2010)
<doi:10.1177/1740774509356002> and Schmidli et al. (2014)
<doi:10.1111/biom.12242> explain details on the methodology.
Author: Novartis Pharma AG [cph],
Sebastian Weber [aut, cre],
Beat Neuenschwander [ctb],
Heinz Schmidli [ctb],
Baldur Magnusson [ctb],
Yue Li [ctb],
Satrajit Roychoudhury [ctb],
Lukas A. Widmer [ctb] ,
Daniel Sabanes Bove [ctb] ,
Trustees of Columbia Univers [...truncated...]
Maintainer: Sebastian Weber <sebastian.weber@novartis.com>
Diff between RBesT versions 1.11-0 dated 2026-08-04 and 1.12-0 dated 2026-09-18
DESCRIPTION | 8 MD5 | 126 NAMESPACE | 58 NEWS.md | 66 R/RBesT-package.R | 15 R/asthma.R | 2 R/gMAP-center.R |only R/gMAP.R | 248 R/gMAP_draws.R | 4 R/integrate_gauss_quadrature.R | 16 R/mixjson.R | 68 R/sysdata.rda |binary build/partial.rdb |binary inst/REFERENCES.bib | 77 inst/doc/RBesT.pdf |binary inst/doc/introduction.html | 90 inst/sbc/calibration.md5 | 6 inst/sbc/sbc_report.html | 589 - inst/stan/gMAP.stan | 479 + man/RBesT-package.Rd | 15 man/asthma.Rd | 2 man/mixjson.Rd | 9 src/stanExports_gMAP.cc | 34 src/stanExports_gMAP.h | 3112 +++++++--- tests/testthat/fixtures-compact/gmap_binomial_covariate_mvn_model.json | 40 tests/testthat/fixtures-compact/gmap_binomial_covariate_mvn_theta.json | 176 tests/testthat/fixtures-compact/gmap_binomial_covariate_rows_mvn_model.json | 18 tests/testthat/fixtures-compact/gmap_binomial_covariate_rows_mvn_theta.json | 28 tests/testthat/fixtures-compact/gmap_binomial_covariate_rows_spec.R | 2 tests/testthat/fixtures-compact/gmap_binomial_covariate_spec.R | 2 tests/testthat/fixtures-compact/gmap_binomial_extreme_all_response_mvn_model.json | 18 tests/testthat/fixtures-compact/gmap_binomial_extreme_all_response_mvn_theta.json | 28 tests/testthat/fixtures-compact/gmap_binomial_extreme_all_response_spec.R | 2 tests/testthat/fixtures-compact/gmap_binomial_extreme_no_response_mvn_model.json | 18 tests/testthat/fixtures-compact/gmap_binomial_extreme_no_response_mvn_theta.json | 28 tests/testthat/fixtures-compact/gmap_binomial_extreme_no_response_spec.R | 2 tests/testthat/fixtures-compact/gmap_binomial_extreme_two_studies_mvn_model.json | 18 tests/testthat/fixtures-compact/gmap_binomial_extreme_two_studies_mvn_theta.json | 36 tests/testthat/fixtures-compact/gmap_binomial_extreme_two_studies_spec.R | 2 tests/testthat/fixtures-compact/gmap_binomial_fixed_tau_generated_mvn_model.json | 10 tests/testthat/fixtures-compact/gmap_binomial_fixed_tau_generated_mvn_theta.json | 108 tests/testthat/fixtures-compact/gmap_binomial_fixed_tau_generated_spec.R | 2 tests/testthat/fixtures-compact/gmap_binomial_fixed_tau_mvn_model.json | 10 tests/testthat/fixtures-compact/gmap_binomial_fixed_tau_mvn_theta.json | 108 tests/testthat/fixtures-compact/gmap_binomial_fixed_tau_spec.R | 2 tests/testthat/fixtures-compact/gmap_binomial_noncontinuous_studies_mvn_model.json | 18 tests/testthat/fixtures-compact/gmap_binomial_noncontinuous_studies_mvn_theta.json | 88 tests/testthat/fixtures-compact/gmap_binomial_noncontinuous_studies_spec.R | 2 tests/testthat/fixtures-compact/gmap_binomial_single_trial_mvn_model.json | 20 tests/testthat/fixtures-compact/gmap_binomial_single_trial_mvn_theta.json | 12 tests/testthat/fixtures-compact/gmap_binomial_single_trial_spec.R | 2 tests/testthat/fixtures-compact/gmap_binomial_tau_strata_rows_mvn_model.json | 10 tests/testthat/fixtures-compact/gmap_binomial_tau_strata_rows_mvn_theta.json | 26 tests/testthat/fixtures-compact/gmap_binomial_tau_strata_rows_spec.R | 4 tests/testthat/fixtures-mcmc-src/gmap_s2z_prior_pd_fixture.R |only tests/testthat/fixtures-mcmc-src/gmap_s2z_stepsize_ad95_fixture.R |only tests/testthat/fixtures-mcmc-src/gmap_s2z_stepsize_ad99_fixture.R |only tests/testthat/fixtures-mcmc-src/gmap_s2z_switch_off_fixture.R |only tests/testthat/fixtures-mcmc-src/gmap_s2z_switch_on_fixture.R |only tests/testthat/fixtures-mcmc-src/gmap_s2z_verbose_binomial_ncp_fixture.R |only tests/testthat/fixtures-mcmc-src/gmap_s2z_zeta_binomial_cp_fixture.R |only tests/testthat/fixtures-mcmc-src/gmap_s2z_zeta_binomial_ncp_fixture.R |only tests/testthat/fixtures-mcmc-src/gmap_s2z_zeta_normal_ncp_fixture.R |only tests/testthat/helper-compressed-fixtures.R | 6 tests/testthat/helper-s2z.R |only tests/testthat/test-gMAP-compact-fixtures.R | 4 tests/testthat/test-gMAP-quadrature-approximation.R |only tests/testthat/test-gMAP-s2z-center.R |only tests/testthat/test-gMAP-s2z.R |only tests/testthat/test-mixjson.R | 109 vignettes/REFERENCES.bib | 77 71 files changed, 4350 insertions(+), 1710 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-06-27 1.2-0
Title: Selecting Variable Subsets
Description: A collection of functions which (i) assess the quality of variable subsets as surrogates for a full data set, in either an exploratory data analysis or in the context of a multivariate linear model, and (ii) search for subsets which are optimal under various criteria. Theoretical support for the heuristic search methods and exploratory data analysis criteria is in Cadima, Cerdeira, Minhoto (2003, <doi:10.1016/j.csda.2003.11.001>). Theoretical support for the leap and bounds algorithm and the criteria for the general multivariate linear model is in Duarte Silva (2001, <doi:10.1006/jmva.2000.1920>). There is a package vignette "subselect", which includes additional references.
Author: Jorge Orestes Cerdeira [aut],
Pedro Duarte Silva [aut, cre],
Jorge Cadima [aut],
Manuel Minhoto [aut]
Maintainer: Pedro Duarte Silva <psilva@ucp.pt>
Diff between subselect versions 0.16.1 dated 2026-05-04 and 0.16.2 dated 2026-09-18
DESCRIPTION | 8 ++++---- MD5 | 44 ++++++++++++++++++++++---------------------- R/anneal.R | 2 +- R/ccr12.R | 2 +- R/eleaps.R | 2 +- R/genetic.R | 2 +- R/improve.R | 2 +- R/tau2.R | 2 +- R/wald.R | 2 +- R/xi2.R | 2 +- R/zeta2.R | 2 +- build/vignette.rds |binary inst/doc/subselect.R | 2 -- inst/doc/subselect.pdf |binary man/anneal.Rd | 2 +- man/ccr12.Rd | 2 +- man/eleaps.Rd | 2 +- man/genetic.Rd | 2 +- man/improve.Rd | 2 +- man/tau2.Rd | 2 +- man/wald.Rd | 2 +- man/xi2.Rd | 2 +- man/zeta2.Rd | 2 +- 23 files changed, 44 insertions(+), 46 deletions(-)
Title: An Interface to IBGE's SIDRA API
Description: Provides a flexible interface to discover, inspect, plan, and
retrieve aggregate data from the Brazilian Institute of Geography and
Statistics (IBGE) through its SIDRA application programming interfaces.
SIDRA is IBGE's system for retrieving aggregate statistical data.
Author: Renato Prado Siqueira [aut, cre]
Maintainer: Renato Prado Siqueira <rpradosiqueira@gmail.com>
Diff between sidrar versions 0.5.0 dated 2026-08-25 and 0.5.1 dated 2026-09-18
DESCRIPTION | 6 - MD5 | 35 +++--- NEWS.md | 14 ++ R/collect.R | 21 ++- R/fallback.R |only R/get_sidra.R | 30 ++++- R/utils.R | 51 ++++++++ README.md | 36 ++++++ inst/doc/Introduction_to_sidrar.Rmd | 15 ++ inst/doc/Introduction_to_sidrar.html | 17 ++ man/get_sidra.Rd | 14 ++ man/sidra_collect.Rd | 4 man/sidra_provenance.Rd | 2 tests/testthat/helper-fixtures.R | 8 + tests/testthat/test-collect.R | 47 ++++++++ tests/testthat/test-fallback-integration.R |only tests/testthat/test-fallback.R |only tests/testthat/test-live-api.R | 15 ++ tests/testthat/test-utils.R | 168 +++++++++++++++++++++++++++++ vignettes/Introduction_to_sidrar.Rmd | 15 ++ 20 files changed, 467 insertions(+), 31 deletions(-)
Title: Processing and Analyzing Amplicon Sequence Data
Description: Processing and analysis of targeted sequencing data. The package provides a user-friendly interface for core 'VSEARCH' (Rognes et al. (2016), <doi:10.7717/peerj.2584>) functions, in addition to tools for visualization and parameter tuning.
Author: Cassandra Stamsaas [cre, aut],
Lars Snipen [aut],
Torbjoern Rognes [aut],
Hilde Vinje [aut]
Maintainer: Cassandra Stamsaas <cassandra.stamsaas@nmbu.no>
Diff between Rsearch versions 1.1.0 dated 2026-07-20 and 1.2.0 dated 2026-09-18
DESCRIPTION | 8 ++++---- MD5 | 33 +++++++++++++++++---------------- NAMESPACE | 6 ++++-- NEWS.md | 12 ++++++++++++ R/vs_fastq_join.R | 5 ----- R/vs_fastq_mergepairs.R | 9 ++------- R/vs_fastx_trim_filt.R | 11 +++-------- R/vs_merging_lengths.R | 4 ++-- R/vs_optimize_truncee_rate.R | 2 +- R/vs_optimize_truncqual.R | 2 +- README.md | 4 +++- inst/CITATION |only man/vs_fastq_join.Rd | 5 ----- man/vs_fastq_mergepairs.Rd | 9 ++------- man/vs_fastx_trim_filt.Rd | 11 +++-------- man/vs_merging_lengths.Rd | 4 ++-- man/vs_optimize_truncee_rate.Rd | 2 +- man/vs_optimize_truncqual.Rd | 2 +- 18 files changed, 58 insertions(+), 71 deletions(-)
Title: Model Context Protocol Servers and Clients
Description: Implements the Model Context Protocol (MCP). Users can start
'R'-based servers, serving functions as tools for large language
models to call before responding to the user in MCP-compatible apps
like 'Claude Desktop' and 'Claude Code', with options to run those
tools inside of interactive 'R' sessions. On the other end, when 'R'
is the client via the 'ellmer' package, users can register tools from
third-party MCP servers to integrate additional context into chats.
Author: Simon Couch [aut, cre] ,
Winston Chang [aut] ,
Charlie Gao [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Simon Couch <simon.couch@posit.co>
Diff between mcptools versions 1.0.2 dated 2026-08-22 and 1.0.3 dated 2026-09-18
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ tests/testthat/test-socket-dir.R | 5 ++++- 4 files changed, 14 insertions(+), 7 deletions(-)
Title: Clinical Publication
Description: Accelerate the process from clinical data to medical publication,
including clinical data cleaning, significant result screening, and the
generation of publish-ready tables and figures.
Author: Yue Niu [aut, cre, cph] ,
Keyun Wang [aut]
Maintainer: Yue Niu <niuyuesam@163.com>
Diff between clinpubr versions 1.4.1 dated 2026-07-13 and 1.4.2 dated 2026-09-18
DESCRIPTION | 12 MD5 | 122 ++++++-- NAMESPACE | 1 NEWS.md | 12 R/RcppExports.R | 18 + R/baseline_table.R | 38 +- R/classif_model_compare.R | 124 +++----- R/extract_history.R | 49 +-- R/interactions.R | 24 - R/misc.R | 21 - R/time_roc.R | 13 R/utils.R | 27 + inst/doc/baseline-table.html | 8 inst/doc/data-cleaning.html | 180 ++++++------ inst/doc/model-evaluation.html | 20 + man/extract_history.Rd | 3 man/extract_history_single.Rd | 45 +-- man/get_var_types.Rd | 5 man/mov_sort_cpp.Rd |only man/test_normality.Rd | 10 man/theme_pub.Rd |only src/RcppExports.cpp | 13 src/merge_ordered_vectors.cpp |only tests/testthat/_snaps/baseline_table.md | 372 ++++++++++++------------- tests/testthat/_snaps/classif_model_compare.md | 20 - tests/testthat/test-baseline_table.R | 26 + tests/testthat/test-extract_history.R | 12 tools/build_skill_docs.R |only tools/skill_docs |only 29 files changed, 684 insertions(+), 491 deletions(-)
Title: Spatial Network Analysis
Description: Interface package for 'sala', the spatial network analysis library
from the 'depthmapX' software application. The R parts of the code are based
on the 'rdepthmap' package. Allows for the analysis of urban and
building-scale networks and provides metrics and methods usually found
within the Space Syntax domain. Methods in this package are described by K.
Al-Sayed, A. Turner, B. Hillier, S. Iida and A. Penn (2014) "Space Syntax
methodology", and also by A. Turner (2004)
<https://discovery.ucl.ac.uk/id/eprint/2651> "Depthmap 4: a researcher's
handbook".
Author: Petros Koutsolampros [cre, aut] ,
Fani Kostourou [ctb] ,
Kimon Krenz [ctb] ,
Alasdair Turner [ctb] ,
Tasos Varoudis [ctb] ,
Christian Sailer [ctb] ,
Eva Friedrich [ctb] ,
University College London [fnd, cph] ,
Spacelab UK [fnd]
Maintainer: Petros Koutsolampros <r-devel@pklampros.net>
Diff between alcyon versions 0.9.0 dated 2026-08-29 and 0.10.0 dated 2026-09-18
DESCRIPTION | 6 MD5 | 440 +++++------ NEWS.md | 13 R/agentAnalysis.R | 6 configure | 5 configure.ac | 5 configure.win | 22 inst/WORDLIST | 2 man/agentAnalysis.Rd | 2 src/Makevars.in | 9 src/Makevars.win | 10 src/analysis_agent.cpp | 6 src/analysis_axial.cpp | 16 src/analysis_vgaShortestPath.cpp | 6 src/communicator.hpp | 14 src/helper_attr.hpp | 3 src/libs/CMakeLists.txt | 31 src/libs/salalib/CMakeLists.txt | 37 src/libs/salalib/REUSE.toml | 3 src/libs/salalib/agents/CMakeLists.txt | 4 src/libs/salalib/agents/agent.cpp | 127 +-- src/libs/salalib/agents/agent.hpp | 37 src/libs/salalib/agents/agentanalysis.cpp | 14 src/libs/salalib/agents/agentanalysis.hpp | 12 src/libs/salalib/agents/agentprogram.cpp | 41 - src/libs/salalib/agents/agentprogram.hpp | 5 src/libs/salalib/alllinemap.cpp | 11 src/libs/salalib/alllinemap.hpp | 9 src/libs/salalib/analysisresult.hpp | 29 src/libs/salalib/attributemap.hpp | 6 src/libs/salalib/attributetable.cpp | 53 - src/libs/salalib/attributetable.hpp | 42 - src/libs/salalib/attributetablehelpers.hpp | 5 src/libs/salalib/attributetableindex.cpp | 15 src/libs/salalib/attributetableindex.hpp | 3 src/libs/salalib/attributetableview.cpp | 3 src/libs/salalib/attributetableview.hpp | 1 src/libs/salalib/axialminimiser.cpp | 6 src/libs/salalib/axialminimiser.hpp | 6 src/libs/salalib/axialmodules/CMakeLists.txt | 10 src/libs/salalib/axialmodules/axialintegration.cpp | 24 src/libs/salalib/axialmodules/axialintegration.hpp | 44 - src/libs/salalib/axialmodules/axiallocal.cpp | 3 src/libs/salalib/axialmodules/axiallocal.hpp | 6 src/libs/salalib/axialmodules/axialstepdepth.cpp | 1 src/libs/salalib/axialmodules/axialstepdepth.hpp | 10 src/libs/salalib/axialpolygons.cpp | 15 src/libs/salalib/axialpolygons.hpp | 6 src/libs/salalib/connector.cpp | 1 src/libs/salalib/connector.hpp | 2 src/libs/salalib/displayparams.hpp | 1 src/libs/salalib/entityparsing.cpp | 3 src/libs/salalib/entityparsing.hpp | 2 src/libs/salalib/exportutils.cpp | 1 src/libs/salalib/fileproperties.hpp | 5 src/libs/salalib/genlib/CMakeLists.txt | 2 src/libs/salalib/genlib/bsptree.cpp | 5 src/libs/salalib/genlib/bsptree.hpp | 3 src/libs/salalib/genlib/comm.hpp | 11 src/libs/salalib/genlib/containerutils.hpp | 1 src/libs/salalib/genlib/edgeu.cpp | 1 src/libs/salalib/genlib/edgeu.hpp | 1 src/libs/salalib/genlib/event2f.hpp | 1 src/libs/salalib/genlib/exceptions.hpp | 1 src/libs/salalib/genlib/line4f.cpp | 136 +-- src/libs/salalib/genlib/line4f.hpp | 20 src/libs/salalib/genlib/pafmath.cpp | 3 src/libs/salalib/genlib/pafmath.hpp | 11 src/libs/salalib/genlib/point2f.cpp | 3 src/libs/salalib/genlib/point2f.hpp | 2 src/libs/salalib/genlib/point3f.hpp | 3 src/libs/salalib/genlib/poly.cpp | 2 src/libs/salalib/genlib/poly.hpp | 2 src/libs/salalib/genlib/readwritehelpers.hpp | 1 src/libs/salalib/genlib/region4f.cpp | 1 src/libs/salalib/genlib/region4f.hpp | 3 src/libs/salalib/genlib/regiontree.cpp | 2 src/libs/salalib/genlib/regiontree.hpp | 1 src/libs/salalib/genlib/simplematrix.hpp | 1 src/libs/salalib/genlib/stringutils.cpp | 6 src/libs/salalib/genlib/xmlparse.cpp | 12 src/libs/salalib/genlib/xmlparse.hpp | 4 src/libs/salalib/geometrygenerators.cpp | 43 - src/libs/salalib/geometrygenerators.hpp | 1 src/libs/salalib/ianalysis.hpp | 17 src/libs/salalib/importtypedefs.hpp | 1 src/libs/salalib/importutils.cpp | 4 src/libs/salalib/importutils.hpp | 5 src/libs/salalib/isovist.cpp | 43 - src/libs/salalib/isovist.hpp | 4 src/libs/salalib/isovistdef.hpp | 1 src/libs/salalib/isovistutils.hpp | 6 src/libs/salalib/latticemap.cpp | 24 src/libs/salalib/latticemap.hpp | 14 src/libs/salalib/layermanager.hpp | 3 src/libs/salalib/layermanagerimpl.cpp | 7 src/libs/salalib/layermanagerimpl.hpp | 5 src/libs/salalib/linkutils.cpp | 5 src/libs/salalib/linkutils.hpp | 2 src/libs/salalib/mapconverter.cpp | 10 src/libs/salalib/mapconverter.hpp | 6 src/libs/salalib/metagraph.hpp | 6 src/libs/salalib/metagraphreadwrite.cpp | 12 src/libs/salalib/metagraphreadwrite.hpp | 9 src/libs/salalib/mgraph_consts.hpp | 1 src/libs/salalib/ngraph.cpp | 8 src/libs/salalib/ngraph.hpp | 3 src/libs/salalib/pafcolor.cpp | 38 src/libs/salalib/pafcolor.hpp | 2 src/libs/salalib/parsers/CMakeLists.txt | 12 src/libs/salalib/parsers/dxfp.cpp | 5 src/libs/salalib/parsers/dxfp.hpp | 6 src/libs/salalib/parsers/mapinfodata.cpp | 16 src/libs/salalib/parsers/mapinfodata.hpp | 5 src/libs/salalib/parsers/ntfp.cpp | 3 src/libs/salalib/parsers/ntfp.hpp | 2 src/libs/salalib/parsers/tigerp.cpp | 5 src/libs/salalib/parsers/tigerp.hpp | 1 src/libs/salalib/pixelbase.cpp | 32 src/libs/salalib/pixelbase.hpp | 2 src/libs/salalib/pixelref.hpp | 4 src/libs/salalib/point.cpp | 2 src/libs/salalib/point.hpp | 5 src/libs/salalib/pushvalues.cpp | 102 +- src/libs/salalib/pushvalues.hpp | 66 - src/libs/salalib/salaprogram.cpp | 13 src/libs/salalib/salaprogram.hpp | 5 src/libs/salalib/salashape.cpp | 16 src/libs/salalib/salashape.hpp | 2 src/libs/salalib/segmmodules/CMakeLists.txt | 26 src/libs/salalib/segmmodules/segmangular.cpp | 11 src/libs/salalib/segmmodules/segmangular.hpp | 13 src/libs/salalib/segmmodules/segmhelpers.hpp | 4 src/libs/salalib/segmmodules/segmmetric.cpp | 21 src/libs/salalib/segmmodules/segmmetric.hpp | 14 src/libs/salalib/segmmodules/segmmetricpd.cpp | 24 src/libs/salalib/segmmodules/segmmetricpd.hpp | 9 src/libs/salalib/segmmodules/segmmetricshortestpath.cpp | 22 src/libs/salalib/segmmodules/segmmetricshortestpath.hpp | 7 src/libs/salalib/segmmodules/segmtopological.cpp | 16 src/libs/salalib/segmmodules/segmtopological.hpp | 14 src/libs/salalib/segmmodules/segmtopologicalpd.cpp | 10 src/libs/salalib/segmmodules/segmtopologicalpd.hpp | 9 src/libs/salalib/segmmodules/segmtopologicalshortestpath.cpp | 9 src/libs/salalib/segmmodules/segmtopologicalshortestpath.hpp | 7 src/libs/salalib/segmmodules/segmtulip.cpp | 81 +- src/libs/salalib/segmmodules/segmtulip.hpp | 29 src/libs/salalib/segmmodules/segmtulipdepth.cpp | 15 src/libs/salalib/segmmodules/segmtulipdepth.hpp | 9 src/libs/salalib/segmmodules/segmtulipleafchoice.cpp | 72 + src/libs/salalib/segmmodules/segmtulipleafchoice.hpp | 23 src/libs/salalib/segmmodules/segmtulipshortestpath.cpp | 15 src/libs/salalib/segmmodules/segmtulipshortestpath.hpp | 8 src/libs/salalib/shapegraph.cpp | 14 src/libs/salalib/shapegraph.hpp | 11 src/libs/salalib/shapemap.cpp | 39 src/libs/salalib/shapemap.hpp | 14 src/libs/salalib/shapemapgroupdata.cpp | 5 src/libs/salalib/shapemapgroupdata.hpp | 6 src/libs/salalib/shaperef.hpp | 1 src/libs/salalib/spacepixel.cpp | 13 src/libs/salalib/spacepixel.hpp | 4 src/libs/salalib/sparksieve2.cpp | 1 src/libs/salalib/sparksieve2.hpp | 4 src/libs/salalib/tidylines.cpp | 5 src/libs/salalib/tidylines.hpp | 4 src/libs/salalib/tolerances.hpp | 1 src/libs/salalib/vgamodules/CMakeLists.txt | 44 - src/libs/salalib/vgamodules/extractlinkdata.hpp | 7 src/libs/salalib/vgamodules/ivga.hpp | 9 src/libs/salalib/vgamodules/ivgaangular.hpp | 16 src/libs/salalib/vgamodules/ivgametric.hpp | 39 src/libs/salalib/vgamodules/ivgatraversing.hpp | 4 src/libs/salalib/vgamodules/ivgavisual.hpp | 7 src/libs/salalib/vgamodules/vgaangular.cpp | 12 src/libs/salalib/vgamodules/vgaangular.hpp | 18 src/libs/salalib/vgamodules/vgaangulardepth.cpp | 5 src/libs/salalib/vgamodules/vgaangulardepth.hpp | 9 src/libs/salalib/vgamodules/vgaangularopenmp.cpp | 11 src/libs/salalib/vgamodules/vgaangularopenmp.hpp | 19 src/libs/salalib/vgamodules/vgaangularshortestpath.cpp | 9 src/libs/salalib/vgamodules/vgaangularshortestpath.hpp | 7 src/libs/salalib/vgamodules/vgaisovist.cpp | 26 src/libs/salalib/vgamodules/vgaisovist.hpp | 11 src/libs/salalib/vgamodules/vgaisovistzone.cpp | 9 src/libs/salalib/vgamodules/vgaisovistzone.hpp | 17 src/libs/salalib/vgamodules/vgametric.cpp | 31 src/libs/salalib/vgamodules/vgametric.hpp | 19 src/libs/salalib/vgamodules/vgametricdepth.cpp | 30 src/libs/salalib/vgamodules/vgametricdepth.hpp | 9 src/libs/salalib/vgamodules/vgametricdepthlinkcost.cpp | 7 src/libs/salalib/vgamodules/vgametricdepthlinkcost.hpp | 8 src/libs/salalib/vgamodules/vgametricopenmp.cpp | 11 src/libs/salalib/vgamodules/vgametricopenmp.hpp | 22 src/libs/salalib/vgamodules/vgametricshortestpath.cpp | 34 src/libs/salalib/vgamodules/vgametricshortestpath.hpp | 10 src/libs/salalib/vgamodules/vgametricshortestpathtomany.cpp | 16 src/libs/salalib/vgamodules/vgametricshortestpathtomany.hpp | 14 src/libs/salalib/vgamodules/vgathroughvision.cpp | 13 src/libs/salalib/vgamodules/vgathroughvision.hpp | 8 src/libs/salalib/vgamodules/vgavisualglobal.cpp | 48 - src/libs/salalib/vgamodules/vgavisualglobal.hpp | 16 src/libs/salalib/vgamodules/vgavisualglobaldepth.cpp | 7 src/libs/salalib/vgamodules/vgavisualglobaldepth.hpp | 9 src/libs/salalib/vgamodules/vgavisualglobalopenmp.cpp | 23 src/libs/salalib/vgamodules/vgavisualglobalopenmp.hpp | 15 src/libs/salalib/vgamodules/vgavisuallocal.cpp | 23 src/libs/salalib/vgamodules/vgavisuallocal.hpp | 7 src/libs/salalib/vgamodules/vgavisuallocaladjmatrix.cpp | 7 src/libs/salalib/vgamodules/vgavisuallocaladjmatrix.hpp | 9 src/libs/salalib/vgamodules/vgavisuallocalopenmp.cpp | 11 src/libs/salalib/vgamodules/vgavisuallocalopenmp.hpp | 9 src/libs/salalib/vgamodules/vgavisualshortestpath.cpp | 6 src/libs/salalib/vgamodules/vgavisualshortestpath.hpp | 8 src/process_convertExternal.cpp | 8 src/process_convertInternal.cpp | 8 src/process_isovist.cpp | 2 src/rcpp_AllLineMap.cpp | 2 src/rcpp_LatticeMap.cpp | 34 src/rcpp_ShapeGraph.cpp | 26 src/rcpp_ShapeMap.cpp | 21 221 files changed, 2036 insertions(+), 1386 deletions(-)
Title: User-Friendly Tables with Color Helpers for Data Exploration
Description: Make it easy to deal with multiple cross-tables in data exploration, by
creating them, manipulating them, and adding color helpers to highlight deviations
(differences from totals, comparisons between lines or columns, contributions to
variance, odds ratios, etc.) and significance (confidence intervals, stars, etc.).
Create the same kind of tables for regression models, with a framework to compare
model effects with their crude/observed counterpart systematically.
All functions render data frames which can be easily manipulated.
All tables can be exported with formats and colors to 'Excel', html and markdown.
Author: Brice Nocenti [aut, cre]
Maintainer: Brice Nocenti <brice.nocenti@protonmail.com>
Diff between tabxplor versions 2.0.0 dated 2026-08-29 and 2.0.1 dated 2026-09-18
DESCRIPTION | 8 MD5 | 285 ++-- NAMESPACE | 13 NEWS.md | 75 + R/fmt_class.R | 1613 ++-------------------- R/jmvtab-cache.R | 8 R/jmvtab-export.R | 91 + R/jmvtab.b.R | 7 R/jmvtab.h.R | 64 R/jmvtabreg-cache.R | 4 R/jmvtabreg.b.R | 7 R/jmvtabreg.h.R | 67 R/plots.R | 13 R/reg-assumptions.R | 51 R/reg-cross.R | 2 R/reg-empirical.R | 12 R/reg-estimand.R | 12 R/row-model.R | 77 - R/survey-design.R | 8 R/tab-args.R | 14 R/tab-css.R | 169 ++ R/tab-display.R | 197 ++ R/tab-export-prep.R | 466 ++++-- R/tab-export.R | 5 R/tab-footer.R |only R/tab-leaf.R | 19 R/tab-legend.R |only R/tab-options.R | 57 R/tab-palettes.R | 27 R/tab-render-html.R | 202 +- R/tab-resolve.R | 47 R/tab-steps-legacy.R | 11 R/tab-test-display.R | 10 R/tab-tooltip.R | 2 R/tab-transpose-render.R | 16 R/tab-xl-backend.R | 14 R/tab.R | 39 R/tab_classes.R | 702 ++++++++-- R/tab_md.R | 172 +- R/tab_reg.R | 64 R/tab_xl.R | 189 +- R/utils.R | 144 +- R/zzz-fact-keys.R | 25 README.md | 50 inst/doc/tabxplor-programming.Rmd | 4 inst/doc/tabxplor-programming.html | 147 ++ inst/doc/tabxplor-reading-a-regression.Rmd | 6 inst/doc/tabxplor-reading-a-regression.html | 537 +++++-- inst/doc/tabxplor-reg.R | 2 inst/doc/tabxplor-reg.Rmd | 27 inst/doc/tabxplor-reg.html | 1185 +++++++++------- inst/doc/tabxplor-weights.html | 132 + inst/doc/tabxplor.Rmd | 6 inst/doc/tabxplor.html | 473 ++++-- inst/i18n/fr.json | 267 +-- inst/po/en@quot/LC_MESSAGES/R-tabxplor.mo |binary inst/po/fr/LC_MESSAGES/R-tabxplor.mo |binary inst/tabxplor-1.0/tabxplor.js | 10 man/fct_recode_helper.Rd | 27 man/fmt.Rd | 5 man/fmt_attributes.Rd | 4 man/fmt_fields.Rd | 17 man/new_tab.Rd | 38 man/print.tabxplor_md.Rd |only man/print.tabxplor_tab.Rd | 3 man/set_bars.Rd |only man/set_color_palette.Rd | 4 man/set_footer_tabs.Rd |only man/set_legend_words.Rd |only man/set_subtext.Rd |only man/tab.Rd | 7 man/tab_color_legend.Rd | 2 man/tab_css.Rd | 15 man/tab_footer_text.Rd |only man/tab_html.Rd | 20 man/tab_md.Rd | 22 man/tab_note.Rd |only man/tab_pipe.Rd |only man/tab_reg.Rd | 13 man/tab_xl.Rd | 9 man/tabxplor-display.Rd | 31 man/tabxplor-footer.Rd |only man/tabxplor-options.Rd | 7 po/R-fr.po | 1164 ++++++++-------- po/R-tabxplor.pot | 975 +++++++------ tests/testthat/_golden/f_all_pct.rds |binary tests/testthat/_golden/f_chi2.rds |binary tests/testthat/_golden/f_ci_cell.rds |binary tests/testthat/_golden/f_ci_diff.rds |binary tests/testthat/_golden/f_col_pct.rds |binary tests/testthat/_golden/f_col_ref_ci.rds |binary tests/testthat/_golden/f_col_ref_lvl.rds |binary tests/testthat/_golden/f_col_ref_multi.rds |binary tests/testthat/_golden/f_col_ref_or.rds |binary tests/testthat/_golden/f_col_ref_partial.rds |binary tests/testthat/_golden/f_color_afterci.rds |binary tests/testthat/_golden/f_color_contrib.rds |binary tests/testthat/_golden/f_color_diff.rds |binary tests/testthat/_golden/f_common_base.rds |binary tests/testthat/_golden/f_counts.rds |binary tests/testthat/_golden/f_merge2.rds |binary tests/testthat/_golden/f_or.rds |binary tests/testthat/_golden/f_ref_first.rds |binary tests/testthat/_golden/f_ref_named.rds |binary tests/testthat/_golden/f_row_pct.rds |binary tests/testthat/_golden/f_selfcross.rds |binary tests/testthat/_golden/f_subtab.rds |binary tests/testthat/_golden/f_totcol_each.rds |binary tests/testthat/_golden/m_multi.rds |binary tests/testthat/_golden/n_ci_tabvars.rds |binary tests/testthat/_golden/n_ci_tabvars_all.rds |binary tests/testthat/_golden/n_mean.rds |binary tests/testthat/_golden/n_mean_ci.rds |binary tests/testthat/_golden/n_mean_color.rds |binary tests/testthat/_golden/n_mean_sparse.rds |binary tests/testthat/_golden/n_mean_tottab.rds |binary tests/testthat/_golden/n_mean_w.rds |binary tests/testthat/_golden/totn_drop.rds |binary tests/testthat/_golden/totn_keep.rds |binary tests/testthat/_golden/totn_row_drop.rds |binary tests/testthat/_golden/w_weighted.rds |binary tests/testthat/_snaps/golden.md | 1894 ++++++++++++++++++++++++++- tests/testthat/_snaps/tab-render-html.md | 18 tests/testthat/test-edge-cases.R | 22 tests/testthat/test-fmt.R | 24 tests/testthat/test-i18n.R | 32 tests/testthat/test-jmvtab.R | 26 tests/testthat/test-reg-estimand.R | 10 tests/testthat/test-reg-influence.R | 2 tests/testthat/test-row-model.R | 35 tests/testthat/test-survey-design.R | 30 tests/testthat/test-tab-agg.R | 3 tests/testthat/test-tab-classes.R | 298 ++++ tests/testthat/test-tab-color.R | 80 - tests/testthat/test-tab-display.R | 115 + tests/testthat/test-tab-export-prep.R | 185 ++ tests/testthat/test-tab-footer.R |only tests/testthat/test-tab-legend.R |only tests/testthat/test-tab-md.R | 62 tests/testthat/test-tab-options.R | 28 tests/testthat/test-tab-palettes.R | 34 tests/testthat/test-tab-reg.R | 22 tests/testthat/test-tab-render-html.R | 98 + tests/testthat/test-tab-steps-legacy.R | 19 tests/testthat/test-tab-xl.R | 31 tests/testthat/test-utils.R | 6 vignettes/tabxplor-programming.Rmd | 4 vignettes/tabxplor-reading-a-regression.Rmd | 6 vignettes/tabxplor-reg.Rmd | 27 vignettes/tabxplor.Rmd | 6 150 files changed, 8767 insertions(+), 4567 deletions(-)
Title: Object-Oriented Interface for Offline Change-Point Detection
Description: A collection of efficient implementations of popular offline change-point detection algorithms, featuring a consistent, object-oriented interface for practical use.
Author: Minh Long Nguyen [aut, cre],
Toby Hocking [aut],
Charles Truong [aut]
Maintainer: Minh Long Nguyen <edelweiss611428@gmail.com>
Diff between rupturesRcpp versions 1.0.2 dated 2025-11-23 and 1.0.3 dated 2026-09-18
DESCRIPTION | 7 MD5 | 14 - R/zzz.R | 2 README.md | 11 - src/tmplBinSeg.cpp | 24 --- src/tmplPelt.cpp | 113 +++++--------- src/tmplWindow.cpp | 18 -- tests/testthat/test-segModule_PELT.R | 276 +++-------------------------------- 8 files changed, 91 insertions(+), 374 deletions(-)
Title: Generalized Pareto Distribution and Peaks Over Threshold
Description: Some functions useful to perform a Peak Over Threshold
analysis in univariate and bivariate cases, see Beirlant et al. (2004)
<doi:10.1002/0470012382>. A user guide is available in the vignette.
Author: Christophe Dutang [aut, cre] ,
Mathieu Ribatet [aut]
Maintainer: Christophe Dutang <dutangc@gmail.com>
Diff between POT versions 1.1-11 dated 2024-10-17 and 1.1-12 dated 2026-09-18
POT-1.1-11/POT/inst/ChangeLog |only POT-1.1-12/POT/DESCRIPTION | 15 ++++++--- POT-1.1-12/POT/MD5 | 38 +++++++++++++---------- POT-1.1-12/POT/NAMESPACE | 7 +++- POT-1.1-12/POT/R/graph-qqpareto.R |only POT-1.1-12/POT/R/uvgev-gen-retlev.R |only POT-1.1-12/POT/build/vignette.rds |binary POT-1.1-12/POT/inst/ChangeLog.md |only POT-1.1-12/POT/inst/doc/POT.R | 2 - POT-1.1-12/POT/inst/doc/POT.Rnw | 14 ++++---- POT-1.1-12/POT/inst/doc/POT.pdf |binary POT-1.1-12/POT/man/POT-pkg.Rd | 53 ++++++++++++++++++++++++++++++++- POT-1.1-12/POT/man/fitBvGPD.Rd | 22 +++++++++---- POT-1.1-12/POT/man/fitGPD.Rd | 28 +++++++++++------ POT-1.1-12/POT/man/fitMcGPD.Rd | 23 +++++++++++--- POT-1.1-12/POT/man/fitPP.Rd | 26 ++++++++++++++++ POT-1.1-12/POT/man/qqpareto.Rd |only POT-1.1-12/POT/man/retlev.Rd | 21 +++++++++++-- POT-1.1-12/POT/tests/t-fitbvgpd.R | 4 +- POT-1.1-12/POT/tests/t-fitmcgpd.R | 4 +- POT-1.1-12/POT/tests/t-fituvgpd.R | 16 ++++++++- POT-1.1-12/POT/tests/t-retlev-evdpkg.R |only POT-1.1-12/POT/vignettes/POT.Rnw | 14 ++++---- 23 files changed, 218 insertions(+), 69 deletions(-)
Title: K-Sample Tests for Truncated and/or Censored Data
Description: Nonparametric analysis and comparison of distributions
under left truncation and right censoring. The package includes simulation
routines for truncated and/or censored survival data, nonparametric
distribution comparison methods based on Kolmogorov-Smirnov-type and
Cramér-von Mises-type statistics, and bootstrap routines for p-value
approximation. For methodological details, see Lago, de Uña-Álvarez and
Pardo-Fernández (2025) <doi:10.1007/s11749-024-00948-4>
and Lago, Pardo-Fernández and de Uña-Álvarez (2026)
<doi:10.1007/s10985-026-09713-1>.
Author: Adrian Lago [aut, cre],
Jacobo de Una-Alvarez [aut],
Juan Carlos Pardo-Fernandez [aut]
Maintainer: Adrian Lago <adrian.lago@uvigo.gal>
Diff between ksamplesLTRC versions 0.1.0 dated 2026-07-30 and 0.1.1 dated 2026-09-18
DESCRIPTION | 15 +++++++++------ MD5 | 20 ++++++++++++-------- NAMESPACE | 14 +++++++++----- NEWS.md | 19 +++++++++++++++++++ R/auto_test.R | 9 --------- R/lt_cvm.R | 2 +- R/lt_truncation_estimator.R | 4 ++-- R/ltrc_cvm.R | 2 +- inst/doc/ksamplesLTRC.html | 4 ++-- tests/testthat/test-estimators.R |only tests/testthat/test-simulation.R |only tests/testthat/test-summary-plot.R |only tests/testthat/test-tests.R |only 13 files changed, 55 insertions(+), 34 deletions(-)
Title: Calculate Heat Stress Indices
Description: Calculates heat-stress indices from meteorological observations,
including the physically based wet-bulb globe temperature model described
by Liljegren et al. (2008) <doi:10.1080/15459620802310770>. The package
provides an independently maintained R implementation with row-level
diagnostics, configurable physical controls, and batch processing for the
Liljegren method; it is not a bitwise-compatible port of the original
program, and cross-implementation differences are expected.
Author: Yifei Zheng [aut, cre] ,
Ana Casanueva [aut]
Maintainer: Yifei Zheng <zyf0717@gmail.com>
Diff between HeatStressR versions 2.2.1 dated 2026-08-07 and 2.4.0 dated 2026-09-18
DESCRIPTION | 10 - MD5 | 42 +++--- NEWS | 23 +++ R/HeatStressR.R | 2 R/heat_indices.R | 17 +- R/wbgt-parallel.R | 151 ++++++++++++++----------- R/wbgt.Liljegren.R | 104 +++++++---------- README.md | 22 ++- inst/CITATION | 5 inst/doc/README.md | 4 inst/doc/benchmarking.md | 5 inst/doc/liljegren-inputs.md | 10 + inst/doc/non-liljegren-indices.md | 7 - inst/doc/parallelism.md | 22 +-- man/HeatStressR.Rd | 2 man/heat_indices.Rd | 18 +- man/wbgt.Liljegren.Rd | 19 +-- tests/testthat/test.liljegren-solar-geometry.R |only tests/testthat/test.non-liljegren-kernels.R | 6 tests/testthat/test.wbgt-batch-solvers.R | 4 tests/testthat/test.wbgt-diagnostics.R | 26 ++++ tests/testthat/test.wbgt-parallel.R | 73 +++++++----- tests/testthat/test.wbgt-preprocessing.R |only 23 files changed, 343 insertions(+), 229 deletions(-)
Title: Wearable Accelerometer Data File Readers
Description: Reads data collected from wearable acceleratometers as used in sleep and physical activity research. Currently supports file formats: binary data from 'GENEActiv' <https://activinsights.com/>, .bin-format from GENEA devices (not for sale), and .cwa-format from 'Axivity' <https://axivity.com>. Further, it has functions for reading text files with epoch level aggregates from 'Actical', 'Fitbit', 'Actiwatch', 'ActiGraph', and 'PhilipsHealthBand'. Primarily designed to complement R package GGIR <https://CRAN.R-project.org/package=GGIR>.
Author: Vincent T van Hees [aut, cre],
Patrick Bos [aut] ,
Lena Kushleyeva [ctb],
Jing Hua Zhao [ctb],
Evgeny Mirkes [ctb],
Dan Jackson [ctb],
Jairo H Migueles [ctb],
John Muschelli [ctb],
Jia Ying Chua [ctb],
Medical Research Council UK [cph, fnd],
Acceltin [...truncated...]
Maintainer: Vincent T van Hees <v.vanhees@accelting.com>
Diff between GGIRread versions 1.0.10 dated 2026-08-26 and 1.0.11 dated 2026-09-18
DESCRIPTION | 10 ++++++---- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/readGENEActiv.R | 31 ++++++++++++++++++++++++++----- man/GGIRread-package.Rd | 4 ++-- man/readGENEActiv.Rd | 20 ++++++++++++++------ 6 files changed, 57 insertions(+), 22 deletions(-)
Title: Offline Taxonomic Name Matching Against Darwin Core Backbones
Description: Match taxonomic names against locally stored Darwin Core backbone
databases ('WFO', 'COL', 'GBIF', 'ITIS', 'NCBI Taxonomy', 'Open Tree of Life',
'WoRMS', 'Euro+Med', 'Species Fungorum', 'AlgaeBase', 'FishBase',
'SeaLifeBase', 'Reptile Database', 'LCVP', 'WCVP',
'Mammal Diversity Database', 'AviList', 'LPSN'). Provides offline fuzzy and
exact matching with synonym resolution, hybrid name detection, and a unified
output schema across all sources. All heavy computation runs in the 'vectra'
C11 columnar engine.
Author: Gilles Colling [aut, cre, cph]
Maintainer: Gilles Colling <gilles.colling051@gmail.com>
Diff between taxify versions 0.5.0 dated 2026-09-02 and 0.5.5 dated 2026-09-18
DESCRIPTION | 12 MD5 | 281 NAMESPACE | 6 NEWS.md | 349 R/add-alien-first-records.R | 157 R/add-bet.R | 158 R/add-bien.R | 152 R/add-data.R | 1302 +- R/add-ecoflora.R | 5 R/add-kew-sid.R | 122 R/add-leda.R | 157 R/add-trait.R | 737 - R/backbones.R | 44 R/backend.R | 364 R/backends-registry.R | 3 R/basionym.R |only R/browse.R | 1059 - R/cache.R | 601 - R/cite.R | 71 R/classification-tree.R | 520 R/clean.R | 1365 +- R/comm2sci.R | 593 - R/content-store.R | 104 R/disambiguate-authorship.R | 20 R/download.R | 252 R/downstream.R | 439 R/enrichment-meta.R | 37 R/enrichment-tr8.R | 360 R/enrichment.R | 415 R/id2name.R | 264 R/inspect.R | 1187 +- R/lock.R | 223 R/manifest.R | 127 R/parse-name.R | 35 R/pick.R | 212 R/reconcile.R | 262 R/region.R | 2212 ++-- R/register.R | 462 R/taxify-long.R | 431 R/taxify-package.R | 171 R/taxify-result.R | 104 R/taxify.R | 305 R/trait-provenance.R |only R/trait-registry.R | 196 R/upstream.R | 261 README.md | 12 inst/doc/enrichments.R | 16 inst/doc/enrichments.Rmd | 77 inst/doc/enrichments.html | 533 inst/doc/large-scale.Rmd | 18 inst/doc/large-scale.html | 40 inst/doc/regions.Rmd | 532 inst/doc/regions.html | 13 inst/exampledb/enrichment/alien_first_records/latest/alien_first_records.vtr |binary inst/exampledb/enrichment/alien_first_records/latest/meta.json | 40 inst/exampledb/enrichment/amphibio/latest/amphibio.vtr |binary inst/exampledb/enrichment/austraits/latest/austraits.vtr |binary inst/exampledb/enrichment/austraits/latest/austraits_references.vtr |only inst/exampledb/enrichment/austraits/latest/meta.json | 17 inst/exampledb/enrichment/bien/latest/bien.vtr |binary inst/exampledb/enrichment/brot/latest/brot.vtr |binary inst/exampledb/enrichment/brot/latest/brot_references.vtr |only inst/exampledb/enrichment/brot/latest/meta.json | 17 inst/exampledb/enrichment/elton_traits/latest/elton_traits.vtr |binary inst/exampledb/enrichment/fishbase/latest/fishbase.vtr |binary inst/exampledb/enrichment/gift/latest/gift.vtr |binary inst/exampledb/enrichment/gift/latest/gift_references.vtr |only inst/exampledb/enrichment/gift/latest/meta.json | 37 inst/exampledb/enrichment/leda/latest/leda.vtr |binary inst/exampledb/enrichment/leda/latest/leda_references.vtr |only inst/exampledb/enrichment/leda/latest/meta.json | 41 inst/exampledb/enrichment/sealifebase/latest/sealifebase.vtr |binary inst/manifest.json | 5392 +++++++++- man/add_alien_first_records.Rd | 51 man/add_bet.Rd | 5 man/add_bien.Rd | 16 man/add_data.Rd | 14 man/add_ecoflora.Rd | 5 man/add_leda.Rd | 31 man/add_trait.Rd | 30 man/backbone_fixed_kingdom.Rd |only man/basionym_placement.Rd |only man/children.Rd | 27 man/cite.Rd | 29 man/class2tree.Rd | 14 man/comm2sci.Rd | 37 man/downstream.Rd | 32 man/enrichment_groups.Rd | 2 man/id2name.Rd | 6 man/inspect.Rd | 24 man/install_backbones.Rd | 18 man/lookup_genus.Rd | 3 man/lowest_common.Rd | 5 man/normalize_kingdom_group.Rd |only man/parse_name.Rd | 7 man/reconcile.Rd | 9 man/sci2comm.Rd | 5 man/score_candidates.Rd | 21 man/synonyms.Rd | 8 man/taxify.Rd | 25 man/taxify_long.Rd | 5 man/taxify_pin.Rd |only man/taxify_regions.Rd | 2 man/taxify_restore.Rd | 17 man/upstream.Rd | 5 tests/testthat/test-abbrev.R | 462 tests/testthat/test-add-data.R | 911 - tests/testthat/test-add-trait.R | 1678 +-- tests/testthat/test-algaebase.R | 312 tests/testthat/test-backbone-content-id.R | 29 tests/testthat/test-backbone-refresh.R |only tests/testthat/test-backbones.R | 17 tests/testthat/test-basionym.R |only tests/testthat/test-clean.R | 677 - tests/testthat/test-col.R | 284 tests/testthat/test-cross-backbone-recovery.R | 47 tests/testthat/test-descendants.R |only tests/testthat/test-doors-all.R |only tests/testthat/test-download.R |only tests/testthat/test-empty-input.R |only tests/testthat/test-enrich-by-group-authorship.R | 45 tests/testthat/test-enrichment-content-id.R | 40 tests/testthat/test-enrichment-grain.R | 2 tests/testthat/test-enrichment-side-paths.R |only tests/testthat/test-euromed.R | 308 tests/testthat/test-exports-direct.R |only tests/testthat/test-fungorum.R | 312 tests/testthat/test-fuzzy-boundary.R | 57 tests/testthat/test-gap-verbs.R | 3 tests/testthat/test-gbif.R | 12 tests/testthat/test-infraspecific-match.R |only tests/testthat/test-inspect.R | 1018 + tests/testthat/test-itis.R | 558 - tests/testthat/test-lock-identity.R |only tests/testthat/test-match.R | 45 tests/testthat/test-meta.R | 281 tests/testthat/test-multi-backend.R | 859 - tests/testthat/test-ncbi.R | 310 tests/testthat/test-new-verbs.R | 4 tests/testthat/test-ott.R | 310 tests/testthat/test-pin.R |only tests/testthat/test-pinned-version.R |only tests/testthat/test-region-marine.R | 5 tests/testthat/test-region.R | 498 tests/testthat/test-session-memo.R |only tests/testthat/test-taxify-forwarding.R |only tests/testthat/test-taxify.R | 700 - tests/testthat/test-trait-provenance.R |only tests/testthat/test-untested-verbs.R | 621 - tests/testthat/test-verb-inputs.R |only tests/testthat/test-vtr-indexes.R |only tests/testthat/test-worms.R | 310 vignettes/enrichments.Rmd | 77 vignettes/large-scale.Rmd | 18 vignettes/regions.Rmd | 532 155 files changed, 20995 insertions(+), 13722 deletions(-)
Title: OIDC Authentication and OAuth Authorization for 'shiny'
Applications
Description: Provides a simple, configurable framework for 'OpenID Connect'
(OIDC) authentication and 'OAuth 2.0' authorization in 'shiny' applications
using 'S7' classes. Defines providers, clients, and tokens, as well
as various supporting functions and a 'shiny' module. Features include
cross-site request forgery (CSRF) protection, state encryption,
'Proof Key for Code Exchange' (PKCE) handling, validation of OIDC identity
tokens (nonces, signatures, claims), automatic user info retrieval for OIDC
and supported 'OAuth' providers, asynchronous flows,
and hooks for audit logging.
Author: Luka Koning [aut, cre, cph]
Maintainer: Luka Koning <koningluka@gmail.com>
Diff between shinyOAuth versions 0.6.0 dated 2026-09-17 and 0.6.1 dated 2026-09-18
DESCRIPTION | 6 MD5 | 738 - NEWS.md | 6 R/connection_credential_lifecycle.R | 438 R/connection_owner.R | 1524 +- R/connection_store.R | 680 R/custom_cache.R | 498 R/errors__constructors.R | 1940 +- R/errors__events.R | 840 - R/errors__trace.R | 236 R/methods__login.R | 7004 +++++----- R/methods__print.R | 894 - R/methods__token.R | 3912 ++--- R/oauth_connections_ui.R | 838 - R/oauth_form_post_ui.R | 3120 ++-- R/oauth_ui.R | 590 R/providers__apple.R | 344 R/shinyOAuth-package.R | 48 R/telemetry.R | 4034 ++--- R/use_shinyOAuth.R | 518 R/utils__audit_digest.R | 250 R/utils__base64url.R | 142 R/utils__callback_registry.R | 518 R/utils__client_resources.R | 102 R/utils__connection_credentials.R | 706 - R/utils__connection_router.R | 334 R/utils__crypt_primitives.R | 170 R/utils__crypt_state.R | 1332 - R/utils__diagnostic_text.R | 410 R/utils__dpop.R | 2230 +-- R/utils__endpoint_auth.R | 650 R/utils__expires.R | 708 - R/utils__http_audit.R | 790 - R/utils__http_media_type.R | 26 R/utils__http_requests.R | 1600 +- R/utils__jwks_fetch.R | 1984 +- R/utils__jwks_keys.R | 1554 +- R/utils__jwt_id_token.R | 1514 +- R/utils__jwt_jarm.R | 2176 +-- R/utils__jwt_jwe.R | 2032 +- R/utils__jwt_parse.R | 2016 +- R/utils__jwt_signing.R | 1720 +- R/utils__key_dependencies.R | 110 R/utils__managed_module.R | 132 R/utils__mtls.R | 1982 +- R/utils__oauth21.R | 664 R/utils__oauth_params.R | 1866 +- R/utils__random.R | 530 R/utils__refresh_scopes.R | 280 R/utils__resource_binding.R | 400 R/utils__scopes.R | 646 R/utils__shiny_context.R | 680 R/utils__shiny_dispatch.R | 774 - R/utils__shiny_otel.R | 1026 - R/utils__shiny_request_uri.R | 874 - R/utils__shiny_timers.R | 192 R/utils__tls.R | 282 R/utils__url_helpers.R | 2256 +-- R/utils__validators.R | 702 - R/zzz.R | 54 README.md | 328 build/vignette.rds |binary inst/doc/advanced-security.R | 544 inst/doc/advanced-security.html | 2117 +-- inst/doc/audit-logging.R | 32 inst/doc/audit-logging.Rmd | 978 - inst/doc/audit-logging.html | 2305 +-- inst/doc/authentication-flow.R | 18 inst/doc/authentication-flow.html | 1959 +- inst/doc/example-spotify.R | 108 inst/doc/example-spotify.Rmd | 242 inst/doc/example-spotify.html | 957 - inst/doc/multiple-authorizations.R | 394 inst/doc/multiple-authorizations.html | 1583 +- inst/doc/opentelemetry.R | 36 inst/doc/opentelemetry.Rmd | 1086 - inst/doc/opentelemetry.html | 2275 +-- inst/doc/package-options.R | 6 inst/doc/package-options.Rmd | 468 inst/doc/package-options.html | 1473 +- inst/doc/smart-on-fhir.R | 332 inst/doc/smart-on-fhir.html | 1675 +- inst/doc/usage.R | 396 inst/doc/usage.Rmd | 1270 - inst/doc/usage.html | 2085 +- inst/examples/client_bearer_req.R | 80 inst/examples/error_on_softened.R | 24 inst/examples/is_ok_host.R | 24 inst/examples/oauth_client_jarm.R | 76 inst/examples/oauth_form_post_ui.R | 110 inst/examples/oauth_module_server.R | 458 inst/examples/oauth_provider_microsoft.R | 244 inst/examples/spotify-dashboard.R | 2350 +-- inst/www/shinyOAuth.js | 480 man/OAuthClient.Rd | 1342 - man/OAuthProvider.Rd | 1082 - man/OAuthToken.Rd | 268 man/check_oauth21.Rd | 174 man/client_bearer_req.Rd | 180 man/custom_cache.Rd | 348 man/error_on_softened.Rd | 90 man/get_userinfo.Rd | 174 man/handle_callback.Rd | 202 man/introspect_token.Rd | 198 man/is_ok_host.Rd | 126 man/oauth_browser_owner.Rd | 256 man/oauth_client.Rd | 1218 - man/oauth_client_mtls_registration.Rd | 160 man/oauth_connection.Rd | 140 man/oauth_connection_store_memory.Rd | 158 man/oauth_connections.Rd | 302 man/oauth_connections_server.Rd | 280 man/oauth_connections_ui.Rd | 234 man/oauth_form_post_ui.Rd | 300 man/oauth_module_server.Rd | 938 - man/oauth_provider.Rd | 1066 - man/oauth_provider_apple.Rd | 122 man/oauth_provider_auth0.Rd | 58 man/oauth_provider_github.Rd | 54 man/oauth_provider_google.Rd | 66 man/oauth_provider_keycloak.Rd | 104 man/oauth_provider_microsoft.Rd | 348 man/oauth_provider_oidc.Rd | 258 man/oauth_provider_oidc_discover.Rd | 428 man/oauth_provider_okta.Rd | 62 man/oauth_provider_slack.Rd | 70 man/oauth_provider_spotify.Rd | 80 man/oauth_ui.Rd | 194 man/perform_client_bearer_req.Rd | 218 man/perform_resource_req.Rd | 314 man/prepare_call.Rd | 168 man/refresh_token.Rd | 292 man/resource_req.Rd | 314 man/revoke_token.Rd | 176 man/shinyOAuth-package.Rd | 58 man/smart_client.Rd | 326 man/smart_context.Rd | 152 man/smart_discover.Rd | 214 man/smart_launch_route.Rd | 158 man/use_shinyOAuth.Rd | 96 tests/browser-authorization-post.cjs | 84 tests/browser-cookie-ack.cjs | 84 tests/browser-cookie-tossing.cjs | 76 tests/browser-malformed-cookie.cjs | 126 tests/browser-origin-binding.cjs | 222 tests/testthat.R | 194 tests/testthat/fixtures/cran-0.5.0-arguments.json | 788 - tests/testthat/fixtures/mtls/ca-cert.pem | 44 tests/testthat/fixtures/mtls/client-cert.pem | 46 tests/testthat/fixtures/mtls/client-key.pem | 56 tests/testthat/fixtures/mtls/generate-san-fixtures.py | 50 tests/testthat/fixtures/mtls/numeric-dns-cert.pem | 36 tests/testthat/fixtures/mtls/typed-san-cert.pem | 38 tests/testthat/helper-async-daemon.R | 276 tests/testthat/helper-form-post-candidates.R | 240 tests/testthat/helper-jwk.R | 30 tests/testthat/helper-mtls.R | 168 tests/testthat/helper-otel.R | 388 tests/testthat/helper-shinytest2.R | 288 tests/testthat/helper-smart-client.R | 198 tests/testthat/teardown-chromote.R | 44 tests/testthat/teardown-otel.R | 2 tests/testthat/test-absolute-uri-syntax.R | 68 tests/testthat/test-absolute-url-validation.R | 620 tests/testthat/test-access-token-characters.R | 188 tests/testthat/test-access-token-duplicate-json.R | 56 tests/testthat/test-acr-enforcement.R | 1208 - tests/testthat/test-async-authorization.R | 618 tests/testthat/test-async-serialization.R | 466 tests/testthat/test-audit-async-options.R | 2804 ++-- tests/testthat/test-audit-async-session-context.R | 228 tests/testthat/test-audit-shiny-context.R | 724 - 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tests/testthat/test-client-assertion-alg-eddsa.R | 232 tests/testthat/test-client-bearer-req-headers.R | 84 tests/testthat/test-client-bearer-req-url-validation.R | 426 tests/testthat/test-client-jwt-defaults.R | 286 tests/testthat/test-client-resources.R | 382 tests/testthat/test-client-secret-basic-encoding.R | 122 tests/testthat/test-coerce-expires-in.R | 10 tests/testthat/test-connection-audit.R | 372 tests/testthat/test-connection-credentials.R | 382 tests/testthat/test-connection-identity.R | 328 tests/testthat/test-connection-request-object.R | 182 tests/testthat/test-connection-store.R | 516 tests/testthat/test-constant-time-compare.R | 162 tests/testthat/test-cookie-path.R | 178 tests/testthat/test-cookie-tossing.R | 32 tests/testthat/test-custom-cache.R | 174 tests/testthat/test-defaults-and-validation.R | 834 - tests/testthat/test-diagnostic-exposure.R | 724 - tests/testthat/test-discovery-auth-methods.R | 1804 +- tests/testthat/test-discovery-hardened.R | 1626 +- tests/testthat/test-discovery-issuer-mismatch.R | 464 tests/testthat/test-discovery-jarm-aliases.R | 126 tests/testthat/test-discovery-jose-case.R | 120 tests/testthat/test-endpoint-auth.R | 748 - tests/testthat/test-endpoint-condition-privacy.R | 284 tests/testthat/test-endpoint-event-redaction.R | 62 tests/testthat/test-error-response-state.R | 1022 - tests/testthat/test-errors-and-audit.R | 1948 +- tests/testthat/test-exact-list-access.R | 426 tests/testthat/test-example-callback-handlers.R | 252 tests/testthat/test-extra-headers.R | 58 tests/testthat/test-form-post-candidate-store.R | 510 tests/testthat/test-form-post-identical-candidates.R | 62 tests/testthat/test-form-post-module-transport.R | 366 tests/testthat/test-form-post-namespaces.R | 242 tests/testthat/test-form-post-response-mode.R | 4162 ++--- tests/testthat/test-get-callback-bridge.R | 626 tests/testthat/test-helper-otel.R | 98 tests/testthat/test-host-config-reminder.R | 40 tests/testthat/test-http-metadata-privacy.R | 186 tests/testthat/test-id-token-audience.R | 266 tests/testthat/test-id-token-claims.R | 592 tests/testthat/test-inbound-ed25519.R | 130 tests/testthat/test-input-validation-guards.R | 718 - tests/testthat/test-integration-authorization-assertions.R | 122 tests/testthat/test-integration-browser-startup.R | 144 tests/testthat/test-integration-error-policy.R | 176 tests/testthat/test-integration-runner.R | 322 tests/testthat/test-introspect-fallback.R | 12 tests/testthat/test-introspect-token.R | 56 tests/testthat/test-introspection-expiry.R | 50 tests/testthat/test-is_ok_host-review.R | 216 tests/testthat/test-issued-at-boundary.R | 148 tests/testthat/test-issued-at-independent-of-store-ttl.R | 48 tests/testthat/test-jar-jarm-live.R | 548 tests/testthat/test-jarm-compression.R | 38 tests/testthat/test-jose-header-fields.R | 754 - 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tests/testthat/test-microsoft-tenant-independent-validation.R | 400 tests/testthat/test-mirai-utils.R | 722 - tests/testthat/test-module-acceptance-deadline.R | 318 tests/testthat/test-module-test-exports.R | 94 tests/testthat/test-mtls-backend.R | 48 tests/testthat/test-mtls-fixture-readiness.R | 184 tests/testthat/test-mtls-model.R | 920 - tests/testthat/test-mtls-registration.R | 722 - tests/testthat/test-mtls-roundtrip.R | 106 tests/testthat/test-mtls-thumbprint-cache.R | 54 tests/testthat/test-multiple-vignette.R | 76 tests/testthat/test-numeric-option-shapes.R | 130 tests/testthat/test-oauth-client-shiny-warning.R | 102 tests/testthat/test-oauth-error-body.R | 664 tests/testthat/test-oauth-error-privacy.R | 218 tests/testthat/test-oauth-ui.R | 146 tests/testthat/test-oidc-standard-claim-types.R | 224 tests/testthat/test-optional-jwt-claims.R | 160 tests/testthat/test-otel-authorization-privacy.R | 140 tests/testthat/test-otel-disable.R | 500 tests/testthat/test-otel-fallback-warning.R | 58 tests/testthat/test-otel-token-outcomes.R | 296 tests/testthat/test-otel-token-type-privacy.R | 180 tests/testthat/test-otel-userinfo-alg.R | 134 tests/testthat/test-outbound-eddsa.R | 320 tests/testthat/test-par.R | 2146 +-- tests/testthat/test-parameter-overrides.R | 160 tests/testthat/test-pkce-s256-encoding.R | 20 tests/testthat/test-print-claims-privacy.R | 44 tests/testthat/test-print-redaction.R | 490 tests/testthat/test-proactive-refresh-credentials.R | 80 tests/testthat/test-provider-fingerprint.R | 640 tests/testthat/test-provider-helpers.R | 1430 +- tests/testthat/test-random-and-validators.R | 238 tests/testthat/test-reauth-lifetime.R | 432 tests/testthat/test-refresh-credential-outcome.R | 346 tests/testthat/test-refresh-iss-aud.R | 1974 +- tests/testthat/test-refresh-races.R | 644 tests/testthat/test-refresh-single-flight.R | 170 tests/testthat/test-refresh-token.R | 4322 +++--- tests/testthat/test-resource-binding.R | 336 tests/testthat/test-resource-indicators.R | 362 tests/testthat/test-resource-redirect-policy.R | 72 tests/testthat/test-response-compression-limit.R | 116 tests/testthat/test-response-json-types.R | 228 tests/testthat/test-response-mode-validation.R | 908 - tests/testthat/test-rs384.R | 144 tests/testthat/test-scope-validation.R | 1795 +- tests/testthat/test-security-vignette.R | 42 tests/testthat/test-security.R | 168 tests/testthat/test-shiny-request-uri.R | 636 tests/testthat/test-shiny-timers.R | 254 tests/testthat/test-shinytest2-helper.R | 40 tests/testthat/test-slack-profiles.R | 108 tests/testthat/test-smart-authorization-details.R | 544 tests/testthat/test-smart-context.R | 914 - tests/testthat/test-smart-contracts.R | 304 tests/testthat/test-smart-discovery.R | 1292 - tests/testthat/test-smart-identity-versions.R | 156 tests/testthat/test-smart-online-negotiation.R | 478 tests/testthat/test-smart-tls-assessment.R | 106 tests/testthat/test-softeners.R | 380 tests/testthat/test-state-envelope-roundtrip.R | 100 tests/testthat/test-state-fuzz-wrapper.R | 242 tests/testthat/test-state-json-structure.R | 54 tests/testthat/test-state-race.R | 178 tests/testthat/test-state-record-consistency.R | 94 tests/testthat/test-state-size-caps.R | 140 tests/testthat/test-state-store-atomic-take.R | 774 - 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vignettes/example-spotify.Rmd | 242 vignettes/opentelemetry.Rmd | 1086 - vignettes/package-options.Rmd | 468 vignettes/usage.Rmd | 1270 - 370 files changed, 97974 insertions(+), 97826 deletions(-)
Title: Comprehensive Luminescence Dating Data Analysis
Description: A collection of various R functions for the purpose of Luminescence
dating data analysis. This includes, amongst others, data import, export,
application of age models, curve deconvolution, sequence analysis and
plotting of equivalent dose distributions.
Author: Sebastian Kreutzer [aut, trl, cre, dtc] ,
Christoph Burow [aut, trl, dtc] ,
Michael Dietze [aut] ,
Margret C. Fuchs [aut] ,
Christoph Schmidt [aut] ,
Manfred Fischer [aut, trl],
Johannes Friedrich [aut] ,
Norbert Mercier [aut] ,
Rachel K. Smedley [ct [...truncated...]
Maintainer: Sebastian Kreutzer <maintainer_luminescence@r-luminescence.org>
Diff between Luminescence versions 1.3.0 dated 2026-07-22 and 1.3.1 dated 2026-09-18
Luminescence-1.3.0/Luminescence/man/calc_MaxDose.Rd |only Luminescence-1.3.0/Luminescence/man/merge_RLum.Data.Spectrum.Rd |only Luminescence-1.3.1/Luminescence/DESCRIPTION | 26 Luminescence-1.3.1/Luminescence/MD5 | 563 +-- Luminescence-1.3.1/Luminescence/NAMESPACE | 60 Luminescence-1.3.1/Luminescence/NEWS.md | 1656 ++-------- Luminescence-1.3.1/Luminescence/R/Luminescence-generics.R | 60 Luminescence-1.3.1/Luminescence/R/Luminescence-package.R | 4 Luminescence-1.3.1/Luminescence/R/RLum.Analysis-class.R | 31 Luminescence-1.3.1/Luminescence/R/RLum.Data.Curve-class.R | 27 Luminescence-1.3.1/Luminescence/R/RLum.Data.Image-class.R | 14 Luminescence-1.3.1/Luminescence/R/RLum.Data.Spectrum-class.R | 15 Luminescence-1.3.1/Luminescence/R/RLum.Results-class.R | 15 Luminescence-1.3.1/Luminescence/R/Risoe.BINfileData-class.R | 5 Luminescence-1.3.1/Luminescence/R/Risoe.BINfileData2RLum.Analysis.R | 52 Luminescence-1.3.1/Luminescence/R/analyse_Al2O3C_CrossTalk.R | 19 Luminescence-1.3.1/Luminescence/R/analyse_Al2O3C_ITC.R | 10 Luminescence-1.3.1/Luminescence/R/analyse_Al2O3C_Measurement.R | 6 Luminescence-1.3.1/Luminescence/R/analyse_FadingMeasurement.R | 15 Luminescence-1.3.1/Luminescence/R/analyse_IRSAR.RF.R | 168 - Luminescence-1.3.1/Luminescence/R/analyse_SAR.CWOSL.R | 54 Luminescence-1.3.1/Luminescence/R/analyse_SAR.NCF.R | 4 Luminescence-1.3.1/Luminescence/R/analyse_SAR.TL.R | 11 Luminescence-1.3.1/Luminescence/R/analyse_baSAR.R | 2 Luminescence-1.3.1/Luminescence/R/analyse_pIRIRSequence.R | 14 Luminescence-1.3.1/Luminescence/R/calc_AverageDose.R | 2 Luminescence-1.3.1/Luminescence/R/calc_CentralDose.R | 60 Luminescence-1.3.1/Luminescence/R/calc_FadingCorr.R | 4 Luminescence-1.3.1/Luminescence/R/calc_FastRatio.R | 57 Luminescence-1.3.1/Luminescence/R/calc_FiniteMixture.R | 2 Luminescence-1.3.1/Luminescence/R/calc_FuchsLang2001.R | 87 Luminescence-1.3.1/Luminescence/R/calc_Huntley2006.R | 103 Luminescence-1.3.1/Luminescence/R/calc_IEU.R | 4 Luminescence-1.3.1/Luminescence/R/calc_MaxDose.R | 103 Luminescence-1.3.1/Luminescence/R/calc_MinDose.R | 177 - Luminescence-1.3.1/Luminescence/R/calc_MoransI.R | 2 Luminescence-1.3.1/Luminescence/R/calc_OSLLxTxRatio.R | 20 Luminescence-1.3.1/Luminescence/R/calc_SourceDoseRate.R | 48 Luminescence-1.3.1/Luminescence/R/calc_Statistics.R | 45 Luminescence-1.3.1/Luminescence/R/calc_WodaFuchs2008.R | 2 Luminescence-1.3.1/Luminescence/R/calc_gSGC.R | 7 Luminescence-1.3.1/Luminescence/R/calc_gSGC_feldspar.R | 4 Luminescence-1.3.1/Luminescence/R/convert_CW2pLMi.R | 2 Luminescence-1.3.1/Luminescence/R/fit_CWCurve.R | 8 Luminescence-1.3.1/Luminescence/R/fit_DoseResponseCurve.R | 134 Luminescence-1.3.1/Luminescence/R/fit_EmissionSpectra.R | 9 Luminescence-1.3.1/Luminescence/R/fit_IsothermalHolding.R | 5 Luminescence-1.3.1/Luminescence/R/fit_LMCurve.R | 5 Luminescence-1.3.1/Luminescence/R/fit_OSLLifeTimes.R | 10 Luminescence-1.3.1/Luminescence/R/fit_SurfaceExposure.R | 20 Luminescence-1.3.1/Luminescence/R/get_Layout.R | 8 Luminescence-1.3.1/Luminescence/R/internals_RLum.R | 98 Luminescence-1.3.1/Luminescence/R/merge_RLum.Analysis.R | 23 Luminescence-1.3.1/Luminescence/R/merge_RLum.Data.Curve.R | 83 Luminescence-1.3.1/Luminescence/R/merge_RLum.Data.Spectrum.R | 124 Luminescence-1.3.1/Luminescence/R/merge_RLum.R | 36 Luminescence-1.3.1/Luminescence/R/merge_RLum.Results.R | 145 Luminescence-1.3.1/Luminescence/R/merge_Risoe.BINfileData.R | 40 Luminescence-1.3.1/Luminescence/R/plot_AbanicoPlot.R | 703 ++-- Luminescence-1.3.1/Luminescence/R/plot_DRCSummary.R | 11 Luminescence-1.3.1/Luminescence/R/plot_DRTResults.R | 55 Luminescence-1.3.1/Luminescence/R/plot_DetPlot.R | 28 Luminescence-1.3.1/Luminescence/R/plot_DoseResponseCurve.R | 28 Luminescence-1.3.1/Luminescence/R/plot_Histogram.R | 53 Luminescence-1.3.1/Luminescence/R/plot_KDE.R | 81 Luminescence-1.3.1/Luminescence/R/plot_NRt.R | 2 Luminescence-1.3.1/Luminescence/R/plot_RLum.Data.Curve.R | 15 Luminescence-1.3.1/Luminescence/R/plot_RLum.Data.Spectrum.R | 21 Luminescence-1.3.1/Luminescence/R/plot_RLum.R | 13 Luminescence-1.3.1/Luminescence/R/plot_RLum.Results.R | 43 Luminescence-1.3.1/Luminescence/R/plot_RadialPlot.R | 67 Luminescence-1.3.1/Luminescence/R/plot_ViolinPlot.R | 32 Luminescence-1.3.1/Luminescence/R/read_RF2R.R | 75 Luminescence-1.3.1/Luminescence/R/read_XSYG2R.R | 11 Luminescence-1.3.1/Luminescence/R/scale_GammaDose.R | 77 Luminescence-1.3.1/Luminescence/R/verify_SingleGrainData.R | 12 Luminescence-1.3.1/Luminescence/R/write_R2BIN.R | 12 Luminescence-1.3.1/Luminescence/README.md | 11 Luminescence-1.3.1/Luminescence/inst/doc/crosstalk.html | 62 Luminescence-1.3.1/Luminescence/man/Risoe.BINfileData-class.Rd | 2 Luminescence-1.3.1/Luminescence/man/Risoe.BINfileData2RLum.Analysis.Rd | 32 Luminescence-1.3.1/Luminescence/man/analyse_Al2O3C_CrossTalk.Rd | 7 Luminescence-1.3.1/Luminescence/man/analyse_Al2O3C_ITC.Rd | 8 Luminescence-1.3.1/Luminescence/man/analyse_Al2O3C_Measurement.Rd | 2 Luminescence-1.3.1/Luminescence/man/analyse_FadingMeasurement.Rd | 15 Luminescence-1.3.1/Luminescence/man/analyse_IRSAR.RF.Rd | 29 Luminescence-1.3.1/Luminescence/man/analyse_SAR.CWOSL.Rd | 10 Luminescence-1.3.1/Luminescence/man/analyse_SAR.NCF.Rd | 4 Luminescence-1.3.1/Luminescence/man/analyse_SAR.TL.Rd | 4 Luminescence-1.3.1/Luminescence/man/analyse_baSAR.Rd | 2 Luminescence-1.3.1/Luminescence/man/analyse_pIRIRSequence.Rd | 2 Luminescence-1.3.1/Luminescence/man/analyse_portableOSL.Rd | 2 Luminescence-1.3.1/Luminescence/man/apply_CosmicRayRemoval.Rd | 2 Luminescence-1.3.1/Luminescence/man/apply_Crosstalk.Rd | 2 Luminescence-1.3.1/Luminescence/man/apply_EfficiencyCorrection.Rd | 2 Luminescence-1.3.1/Luminescence/man/as.Rd |only Luminescence-1.3.1/Luminescence/man/bin_RLum.Data.Rd | 4 Luminescence-1.3.1/Luminescence/man/calc_AliquotSize.Rd | 2 Luminescence-1.3.1/Luminescence/man/calc_AverageDose.Rd | 4 Luminescence-1.3.1/Luminescence/man/calc_CentralDose.Rd | 4 Luminescence-1.3.1/Luminescence/man/calc_CobbleDoseRate.Rd | 2 Luminescence-1.3.1/Luminescence/man/calc_CommonDose.Rd | 2 Luminescence-1.3.1/Luminescence/man/calc_CosmicDoseRate.Rd | 2 Luminescence-1.3.1/Luminescence/man/calc_EED_Model.Rd | 2 Luminescence-1.3.1/Luminescence/man/calc_FadingCorr.Rd | 2 Luminescence-1.3.1/Luminescence/man/calc_FastRatio.Rd | 7 Luminescence-1.3.1/Luminescence/man/calc_FiniteMixture.Rd | 2 Luminescence-1.3.1/Luminescence/man/calc_FuchsLang2001.Rd | 2 Luminescence-1.3.1/Luminescence/man/calc_HomogeneityTest.Rd | 2 Luminescence-1.3.1/Luminescence/man/calc_Huntley2006.Rd | 12 Luminescence-1.3.1/Luminescence/man/calc_IEU.Rd | 2 Luminescence-1.3.1/Luminescence/man/calc_Lamothe2003.Rd | 2 Luminescence-1.3.1/Luminescence/man/calc_MinDose.Rd | 106 Luminescence-1.3.1/Luminescence/man/calc_MoransI.Rd | 2 Luminescence-1.3.1/Luminescence/man/calc_OSLLxTxDecomposed.Rd | 2 Luminescence-1.3.1/Luminescence/man/calc_OSLLxTxRatio.Rd | 2 Luminescence-1.3.1/Luminescence/man/calc_SourceDoseRate.Rd | 8 Luminescence-1.3.1/Luminescence/man/calc_Statistics.Rd | 25 Luminescence-1.3.1/Luminescence/man/calc_TLLxTxRatio.Rd | 2 Luminescence-1.3.1/Luminescence/man/calc_ThermalLifetime.Rd | 2 Luminescence-1.3.1/Luminescence/man/calc_WodaFuchs2008.Rd | 2 Luminescence-1.3.1/Luminescence/man/calc_gSGC.Rd | 2 Luminescence-1.3.1/Luminescence/man/calc_gSGC_feldspar.Rd | 2 Luminescence-1.3.1/Luminescence/man/combine_De_Dr.Rd | 2 Luminescence-1.3.1/Luminescence/man/convert_Activity2Concentration.Rd | 2 Luminescence-1.3.1/Luminescence/man/convert_BIN2CSV.Rd | 2 Luminescence-1.3.1/Luminescence/man/convert_CW2pHMi.Rd | 2 Luminescence-1.3.1/Luminescence/man/convert_CW2pLM.Rd | 2 Luminescence-1.3.1/Luminescence/man/convert_CW2pLMi.Rd | 2 Luminescence-1.3.1/Luminescence/man/convert_CW2pPMi.Rd | 2 Luminescence-1.3.1/Luminescence/man/convert_Concentration2DoseRate.Rd | 2 Luminescence-1.3.1/Luminescence/man/convert_Daybreak2CSV.Rd | 2 Luminescence-1.3.1/Luminescence/man/convert_PSL2CSV.Rd | 2 Luminescence-1.3.1/Luminescence/man/convert_PSL2Risoe.BINfileData.Rd | 2 Luminescence-1.3.1/Luminescence/man/convert_RLum2Risoe.BINfileData.Rd | 2 Luminescence-1.3.1/Luminescence/man/convert_SG2MG.Rd | 2 Luminescence-1.3.1/Luminescence/man/convert_Second2Gray.Rd | 2 Luminescence-1.3.1/Luminescence/man/convert_Wavelength2Energy.Rd | 2 Luminescence-1.3.1/Luminescence/man/convert_XSYG2CSV.Rd | 2 Luminescence-1.3.1/Luminescence/man/correct_PMTLinearity.Rd | 2 Luminescence-1.3.1/Luminescence/man/dot-as.latex.table.Rd | 2 Luminescence-1.3.1/Luminescence/man/extract_IrradiationTimes.Rd | 2 Luminescence-1.3.1/Luminescence/man/extract_ROI.Rd | 2 Luminescence-1.3.1/Luminescence/man/fit_CWCurve.Rd | 2 Luminescence-1.3.1/Luminescence/man/fit_DoseResponseCurve.Rd | 11 Luminescence-1.3.1/Luminescence/man/fit_EmissionSpectra.Rd | 2 Luminescence-1.3.1/Luminescence/man/fit_LMCurve.Rd | 2 Luminescence-1.3.1/Luminescence/man/fit_OSLLifeTimes.Rd | 4 Luminescence-1.3.1/Luminescence/man/fit_SurfaceExposure.Rd | 2 Luminescence-1.3.1/Luminescence/man/fit_ThermalQuenching.Rd | 2 Luminescence-1.3.1/Luminescence/man/get_Layout.Rd | 2 Luminescence-1.3.1/Luminescence/man/get_RLum.Rd | 4 Luminescence-1.3.1/Luminescence/man/get_rightAnswer.Rd | 2 Luminescence-1.3.1/Luminescence/man/import_Data.Rd | 2 Luminescence-1.3.1/Luminescence/man/length_RLum.Rd | 4 Luminescence-1.3.1/Luminescence/man/melt_RLum.Rd | 4 Luminescence-1.3.1/Luminescence/man/merge_RLum.Analysis.Rd | 10 Luminescence-1.3.1/Luminescence/man/merge_RLum.Data.Curve.Rd | 94 Luminescence-1.3.1/Luminescence/man/merge_RLum.Rd | 10 Luminescence-1.3.1/Luminescence/man/merge_RLum.Results.Rd | 11 Luminescence-1.3.1/Luminescence/man/merge_Risoe.BINfileData.Rd | 10 Luminescence-1.3.1/Luminescence/man/metadata.Rd | 2 Luminescence-1.3.1/Luminescence/man/names_RLum.Rd | 4 Luminescence-1.3.1/Luminescence/man/normalise_RLum.Rd | 2 Luminescence-1.3.1/Luminescence/man/plot_AbanicoPlot.Rd | 122 Luminescence-1.3.1/Luminescence/man/plot_DRCSummary.Rd | 10 Luminescence-1.3.1/Luminescence/man/plot_DRTResults.Rd | 10 Luminescence-1.3.1/Luminescence/man/plot_DetPlot.Rd | 14 Luminescence-1.3.1/Luminescence/man/plot_DoseResponseCurve.Rd | 17 Luminescence-1.3.1/Luminescence/man/plot_FilterCombinations.Rd | 2 Luminescence-1.3.1/Luminescence/man/plot_GrowthCurve.Rd | 11 Luminescence-1.3.1/Luminescence/man/plot_Histogram.Rd | 31 Luminescence-1.3.1/Luminescence/man/plot_KDE.Rd | 16 Luminescence-1.3.1/Luminescence/man/plot_MoranScatterplot.Rd | 2 Luminescence-1.3.1/Luminescence/man/plot_NRt.Rd | 2 Luminescence-1.3.1/Luminescence/man/plot_OSLAgeSummary.Rd | 2 Luminescence-1.3.1/Luminescence/man/plot_RLum.Analysis.Rd | 2 Luminescence-1.3.1/Luminescence/man/plot_RLum.Data.Curve.Rd | 2 Luminescence-1.3.1/Luminescence/man/plot_RLum.Data.Image.Rd | 2 Luminescence-1.3.1/Luminescence/man/plot_RLum.Data.Spectrum.Rd | 11 Luminescence-1.3.1/Luminescence/man/plot_RLum.Rd | 10 Luminescence-1.3.1/Luminescence/man/plot_RLum.Results.Rd | 2 Luminescence-1.3.1/Luminescence/man/plot_ROI.Rd | 2 Luminescence-1.3.1/Luminescence/man/plot_RadialPlot.Rd | 19 Luminescence-1.3.1/Luminescence/man/plot_Risoe.BINfileData.Rd | 2 Luminescence-1.3.1/Luminescence/man/plot_SingleGrainDisc.Rd | 2 Luminescence-1.3.1/Luminescence/man/plot_ViolinPlot.Rd | 8 Luminescence-1.3.1/Luminescence/man/read_BIN2R.Rd | 2 Luminescence-1.3.1/Luminescence/man/read_BINXLOG2R.Rd | 2 Luminescence-1.3.1/Luminescence/man/read_Daybreak2R.Rd | 2 Luminescence-1.3.1/Luminescence/man/read_HeliosOSL2R.Rd | 2 Luminescence-1.3.1/Luminescence/man/read_PSL2R.Rd | 2 Luminescence-1.3.1/Luminescence/man/read_RF2R.Rd | 16 Luminescence-1.3.1/Luminescence/man/read_SPE2R.Rd | 2 Luminescence-1.3.1/Luminescence/man/read_TIFF2R.Rd | 2 Luminescence-1.3.1/Luminescence/man/read_XSYG2R.Rd | 4 Luminescence-1.3.1/Luminescence/man/remove_RLum.Rd | 4 Luminescence-1.3.1/Luminescence/man/remove_SignalBackground.Rd | 2 Luminescence-1.3.1/Luminescence/man/replicate_RLum.Rd | 4 Luminescence-1.3.1/Luminescence/man/report_RLum.Rd | 2 Luminescence-1.3.1/Luminescence/man/sTeve.Rd | 2 Luminescence-1.3.1/Luminescence/man/scale_GammaDose.Rd | 71 Luminescence-1.3.1/Luminescence/man/set_RLum.Rd | 2 Luminescence-1.3.1/Luminescence/man/set_Risoe.BINfileData.Rd | 2 Luminescence-1.3.1/Luminescence/man/smooth_RLum.Rd | 4 Luminescence-1.3.1/Luminescence/man/sort_RLum.Rd | 4 Luminescence-1.3.1/Luminescence/man/structure_RLum.Rd | 4 Luminescence-1.3.1/Luminescence/man/subset_SingleGrainData.Rd | 2 Luminescence-1.3.1/Luminescence/man/template_DRAC.Rd | 2 Luminescence-1.3.1/Luminescence/man/trim_RLum.Data.Rd | 2 Luminescence-1.3.1/Luminescence/man/tune_Data.Rd | 2 Luminescence-1.3.1/Luminescence/man/use_DRAC.Rd | 2 Luminescence-1.3.1/Luminescence/man/verify_SingleGrainData.Rd | 2 Luminescence-1.3.1/Luminescence/man/view.Rd | 4 Luminescence-1.3.1/Luminescence/man/write_R2BIN.Rd | 4 Luminescence-1.3.1/Luminescence/man/write_R2TIFF.Rd | 2 Luminescence-1.3.1/Luminescence/man/write_RLum2CSV.Rd | 2 Luminescence-1.3.1/Luminescence/tests/testthat/_data/RF_new_header.rf |only Luminescence-1.3.1/Luminescence/tests/testthat/_data/xsyg-tests/XSYG_broken_2.xsyg |only Luminescence-1.3.1/Luminescence/tests/testthat/setup.R | 16 Luminescence-1.3.1/Luminescence/tests/testthat/test_RLum.Analysis-class.R | 4 Luminescence-1.3.1/Luminescence/tests/testthat/test_RLum.Data.Image.R | 8 Luminescence-1.3.1/Luminescence/tests/testthat/test_Risoe.BINfileData-class.R | 2 Luminescence-1.3.1/Luminescence/tests/testthat/test_analyse_Al2O3C_CrossTalk.R | 17 Luminescence-1.3.1/Luminescence/tests/testthat/test_analyse_Al2O3C_ITC.R | 7 Luminescence-1.3.1/Luminescence/tests/testthat/test_analyse_Al2O3C_Measurement.R | 42 Luminescence-1.3.1/Luminescence/tests/testthat/test_analyse_FadingMeasurement.R | 37 Luminescence-1.3.1/Luminescence/tests/testthat/test_analyse_IRSAR.RF.R | 46 Luminescence-1.3.1/Luminescence/tests/testthat/test_analyse_SAR.CWOSL.R | 43 Luminescence-1.3.1/Luminescence/tests/testthat/test_analyse_SAR.NCF.R | 7 Luminescence-1.3.1/Luminescence/tests/testthat/test_analyse_SAR.TL.R | 14 Luminescence-1.3.1/Luminescence/tests/testthat/test_analyse_baSAR.R | 1 Luminescence-1.3.1/Luminescence/tests/testthat/test_analyse_pIRIRSequence.R | 16 Luminescence-1.3.1/Luminescence/tests/testthat/test_calc_AliquotSize.R | 8 Luminescence-1.3.1/Luminescence/tests/testthat/test_calc_AverageDose.R | 13 Luminescence-1.3.1/Luminescence/tests/testthat/test_calc_CentralDose.R | 16 Luminescence-1.3.1/Luminescence/tests/testthat/test_calc_CommonDose.R | 9 Luminescence-1.3.1/Luminescence/tests/testthat/test_calc_CosmicDoseRate.R | 4 Luminescence-1.3.1/Luminescence/tests/testthat/test_calc_EED_Model.R | 2 Luminescence-1.3.1/Luminescence/tests/testthat/test_calc_FadingCorr.R | 10 Luminescence-1.3.1/Luminescence/tests/testthat/test_calc_FastRatio.R | 67 Luminescence-1.3.1/Luminescence/tests/testthat/test_calc_FiniteMixture.R | 1 Luminescence-1.3.1/Luminescence/tests/testthat/test_calc_FuchsLang2001.R | 12 Luminescence-1.3.1/Luminescence/tests/testthat/test_calc_HomogeneityTest.R | 4 Luminescence-1.3.1/Luminescence/tests/testthat/test_calc_Huntley2006.R | 74 Luminescence-1.3.1/Luminescence/tests/testthat/test_calc_IEU.R | 13 Luminescence-1.3.1/Luminescence/tests/testthat/test_calc_Lamothe2003.R | 3 Luminescence-1.3.1/Luminescence/tests/testthat/test_calc_MinDose.R | 56 Luminescence-1.3.1/Luminescence/tests/testthat/test_calc_MoransI.R | 2 Luminescence-1.3.1/Luminescence/tests/testthat/test_calc_SourceDoseRate.R | 5 Luminescence-1.3.1/Luminescence/tests/testthat/test_calc_Statistics.R | 18 Luminescence-1.3.1/Luminescence/tests/testthat/test_calc_ThermalLifetime.R | 9 Luminescence-1.3.1/Luminescence/tests/testthat/test_calc_gSGC.R | 11 Luminescence-1.3.1/Luminescence/tests/testthat/test_convert_Activity2Concentration.R | 2 Luminescence-1.3.1/Luminescence/tests/testthat/test_fit_CWCurve.R | 3 Luminescence-1.3.1/Luminescence/tests/testthat/test_fit_DoseResponseCurve.R | 36 Luminescence-1.3.1/Luminescence/tests/testthat/test_fit_EmissionSpectra.R | 11 Luminescence-1.3.1/Luminescence/tests/testthat/test_fit_LMCurve.R | 5 Luminescence-1.3.1/Luminescence/tests/testthat/test_fit_OSLLifeTimes.R | 9 Luminescence-1.3.1/Luminescence/tests/testthat/test_fit_SurfaceExposure.R | 57 Luminescence-1.3.1/Luminescence/tests/testthat/test_fit_ThermalQuenching.R | 6 Luminescence-1.3.1/Luminescence/tests/testthat/test_internals.R | 64 Luminescence-1.3.1/Luminescence/tests/testthat/test_merge_RLum.Analysis.R | 17 Luminescence-1.3.1/Luminescence/tests/testthat/test_merge_RLum.Data.Curve.R | 6 Luminescence-1.3.1/Luminescence/tests/testthat/test_merge_RLum.Data.Spectrum.R | 3 Luminescence-1.3.1/Luminescence/tests/testthat/test_merge_RLum.R | 8 Luminescence-1.3.1/Luminescence/tests/testthat/test_merge_RLum.Results.R | 30 Luminescence-1.3.1/Luminescence/tests/testthat/test_merge_Risoe.BINfileData.R | 10 Luminescence-1.3.1/Luminescence/tests/testthat/test_plot_AbanicoPlot.R | 62 Luminescence-1.3.1/Luminescence/tests/testthat/test_plot_DRCSummary.R | 1 Luminescence-1.3.1/Luminescence/tests/testthat/test_plot_DRTResults.R | 8 Luminescence-1.3.1/Luminescence/tests/testthat/test_plot_DetPlot.R | 20 Luminescence-1.3.1/Luminescence/tests/testthat/test_plot_DoseResponseCurve.R | 3 Luminescence-1.3.1/Luminescence/tests/testthat/test_plot_Histogram.R | 5 Luminescence-1.3.1/Luminescence/tests/testthat/test_plot_KDE.R | 16 Luminescence-1.3.1/Luminescence/tests/testthat/test_plot_RLum.Data.Curve.R | 8 Luminescence-1.3.1/Luminescence/tests/testthat/test_plot_RLum.Data.Spectrum.R | 22 Luminescence-1.3.1/Luminescence/tests/testthat/test_plot_RLum.R | 6 Luminescence-1.3.1/Luminescence/tests/testthat/test_plot_RLum.Results.R | 7 Luminescence-1.3.1/Luminescence/tests/testthat/test_plot_RadialPlot.R | 16 Luminescence-1.3.1/Luminescence/tests/testthat/test_read_RF2R.R | 43 Luminescence-1.3.1/Luminescence/tests/testthat/test_read_XSYG2R.R | 9 Luminescence-1.3.1/Luminescence/tests/testthat/test_scale_GammaDose.R | 10 Luminescence-1.3.1/Luminescence/tests/testthat/test_verify_SingleGrainData.R | 25 Luminescence-1.3.1/Luminescence/tests/testthat/test_write_R2BIN.R | 20 285 files changed, 3874 insertions(+), 4010 deletions(-)
Title: ICESat-2 Data Analysis for Land and Vegetation
Description: Provides tools for downloading, reading, processing, visualizing,
and exporting NASA's ICESat-2 ATL03 (Global Geolocated Photon
Data) and ATL08 (Land and Vegetation Height) products. Supports
photon- and segment-level analysis, spatial sampling, gridding,
statistical and machine-learning modeling, and integration with
'Google Earth Engine' (<https://earthengine.google.com/>) for
wall-to-wall mapping of vegetation structure and other land
attributes.
Author: Carlos Alberto Silva [aut, cph, cre],
Caio Hamamura [aut, cph],
Cesar Alvites [aut, ctb],
Alexander J. Gaskins [aut, ctb],
Sunil Arya [ctb, cph] ),
David Mount [ctb, cph] ),
University of Maryland [cph] ),
Chuck Gantz [ctb] ,
Cole Krehbiel [ctb]
Maintainer: Carlos Alberto Silva <c.silva@ufl.edu>
Diff between ICESat2VegR versions 0.0.1 dated 2026-09-11 and 0.0.2 dated 2026-09-18
DESCRIPTION | 6 ++--- MD5 | 32 ++++++++++++++++++++++++------- R/ATLAS_dataDownload.R | 13 +++++------- R/class.icesat2.h5_local.R | 31 ++++++++++-------------------- R/class.icesat2.h5ds_local.R | 14 +++---------- R/zzz.R | 33 ++++++++------------------------ inst/proj |only man/earthdata_login.Rd | 8 +++---- src/Makevars.ucrt |only src/Makevars.ucrt.in |only tests/testthat/test-integration-local.R | 26 +++++++++++++++++++++++-- 11 files changed, 86 insertions(+), 77 deletions(-)
Title: Biodiversity Data from the GBIF Node Network
Description: The Global Biodiversity Information Facility
('GBIF', <https://www.gbif.org>) sources data from an international network
of data providers, known as 'nodes'. Several of these nodes - the "living
atlases" (<https://living-atlases.gbif.org>) - maintain their own web
services using software originally developed by the Atlas of Living
Australia ('ALA', <https://www.ala.org.au>). 'galah' enables the R community
to directly access data and resources hosted by 'GBIF' and its partner nodes.
Author: Martin Westgate [aut, cre],
Dax Kellie [aut],
Shandiya Balasubramaniam [ctb],
Matilda Stevenson [ctb]
Maintainer: Martin Westgate <martin.westgate@csiro.au>
Diff between galah versions 2.2.0 dated 2026-02-11 and 2.3.0 dated 2026-09-18
galah-2.2.0/galah/R/galah_apply_profile.R |only galah-2.2.0/galah/R/galah_bbox.R |only galah-2.2.0/galah/R/galah_filter.R |only galah-2.2.0/galah/R/galah_geolocate.R |only galah-2.2.0/galah/R/galah_group_by.R |only galah-2.2.0/galah/R/galah_identify.R |only galah-2.2.0/galah/R/galah_polygon.R |only galah-2.2.0/galah/R/galah_radius.R |only galah-2.2.0/galah/R/galah_select.R |only galah-2.2.0/galah/tests/testthat/test-galah_apply_profile.R |only galah-2.2.0/galah/tests/testthat/test-galah_bbox.R |only galah-2.2.0/galah/tests/testthat/test-galah_geolocate.R |only galah-2.2.0/galah/tests/testthat/test-galah_group_by.R |only galah-2.2.0/galah/tests/testthat/test-galah_identify.R |only galah-2.2.0/galah/tests/testthat/test-galah_polygon.R |only galah-2.2.0/galah/tests/testthat/test-galah_radius.R |only galah-2.3.0/galah/DESCRIPTION | 6 galah-2.3.0/galah/MD5 | 245 +++--- galah-2.3.0/galah/NAMESPACE | 5 galah-2.3.0/galah/NEWS.md | 28 galah-2.3.0/galah/R/apply_profile.R |only galah-2.3.0/galah/R/atlas_counts.R | 2 galah-2.3.0/galah/R/atlas_distributions.R | 4 galah-2.3.0/galah/R/atlas_media.R | 39 - galah-2.3.0/galah/R/atlas_occurrences.R | 12 galah-2.3.0/galah/R/atlas_species.R | 2 galah-2.3.0/galah/R/atlas_taxonomy.R | 6 galah-2.3.0/galah/R/authenticate.R | 143 +++ galah-2.3.0/galah/R/build_query.R | 69 + galah-2.3.0/galah/R/capture.R | 86 +- galah-2.3.0/galah/R/capture_events.R |only galah-2.3.0/galah/R/capture_files.R | 13 galah-2.3.0/galah/R/capture_metadata.R | 184 ++-- galah-2.3.0/galah/R/capture_metadata_unnest.R | 39 - galah-2.3.0/galah/R/capture_occurrences.R | 86 +- galah-2.3.0/galah/R/capture_occurrences_count.R | 88 -- galah-2.3.0/galah/R/capture_species.R | 22 galah-2.3.0/galah/R/capture_species_count.R | 47 - galah-2.3.0/galah/R/capture_taxa.R | 50 - galah-2.3.0/galah/R/check.R | 389 ++++------ galah-2.3.0/galah/R/check_queue.R | 4 galah-2.3.0/galah/R/collapse_checks.R | 47 - galah-2.3.0/galah/R/collapse_events.R |only galah-2.3.0/galah/R/collapse_metadata.R | 75 + galah-2.3.0/galah/R/collapse_occurrences.R | 6 galah-2.3.0/galah/R/collapse_occurrences_count_atlas.R | 23 galah-2.3.0/galah/R/collapse_query_set.R | 10 galah-2.3.0/galah/R/collect_events.R |only galah-2.3.0/galah/R/collect_metadata.R | 99 +- galah-2.3.0/galah/R/collect_metadata_unnest.R | 198 ++++- galah-2.3.0/galah/R/collect_occurrences.R | 115 +- galah-2.3.0/galah/R/collect_occurrences_count.R | 55 - 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Title: Local Influence Diagnostics for the Extreme-Value
Birnbaum-Saunders Regression Model
Description: Implements local influence diagnostics for the Extreme-Value
Birnbaum-Saunders (EVBS) regression model: joint maximum likelihood
estimation, conformal normal curvature diagnostics under three
perturbation schemes (case-weight, response variable, and explanatory
variable), randomized quantile residuals with simulation envelope,
Monte Carlo simulation utilities, and publication-quality density and
diagnostic plots. Version 1.1.0 adds the density, distribution and
quantile functions, the finite upper endpoint, return levels and
expected shortfall, block bootstrap standard errors for serially
dependent series, local influence diagnostics for the generalized
extreme-value regression model, and a GAMLSS family allowing the
tail-shape parameter to depend on covariates. Version 1.2.0 adds a
prospective control chart for endpoint identifiability. The methods
are described in Ospina, Lima, Barros, and Macedo (2026, submitted)
and are applied to monthly maximum wind gust data from Itajai, Brazil.
Author: Raydonal Ospina [aut, cre]
Maintainer: Raydonal Ospina <raydonal@de.ufpe.br>
Diff between evbsreg versions 1.0.0 dated 2026-06-30 and 1.2.0 dated 2026-09-18
DESCRIPTION | 22 ++++++++----- MD5 | 38 ++++++++++++++++++----- NAMESPACE | 15 +++++++++ NEWS.md | 61 +++++++++++++++++++++++++++++++++++-- R/blockboot.R |only R/distribution.R |only R/evbsreg_diagnostics.R | 37 +++++++++++++++++++++- R/evbsreg_residuals.R | 2 - R/gamlss_family.R |only R/gev.R |only R/monitor.R |only README.md | 23 +++++++++++-- build/vignette.rds |binary inst/doc/evbsreg.html | 32 +++++++++---------- man/cnc_diagnostics_gev.Rd |only man/devbs.Rd |only man/evbs_block_boot.Rd |only man/evbs_endpoint.Rd |only man/evbs_monitor.Rd |only man/evbs_return_level.Rd |only man/gev_scores.Rd |only man/gevreg.fit.Rd |only man/logEVBS-dist.Rd |only man/logEVBS.Rd |only man/pevbs.Rd |only man/plot.evbs_monitor.Rd |only man/qevbs.Rd |only tests/testthat/test-distribution.R |only tests/testthat/test-gamlss.R |only tests/testthat/test-gev.R |only tests/testthat/test-monitor.R |only 31 files changed, 190 insertions(+), 40 deletions(-)
Title: Fitting Exact Conditional Logistic Regression with Lasso and
Elastic Net Penalties
Description: Tools for the fitting and cross validation of exact conditional logistic regression models with lasso and elastic net penalties. Uses cyclic coordinate descent and warm starts to compute the entire path efficiently.
Author: Stephen Reid [aut, cre],
Robert Tibshirani [aut]
Maintainer: Stephen Reid <sreid1652@gmail.com>
Diff between clogitL1 versions 1.5 dated 2019-02-02 and 1.6 dated 2026-09-18
DESCRIPTION | 18 ++++++++---- MD5 | 30 ++++++++++---------- R/RcppExports.R | 22 +++++++-------- R/cv.clogitL1.R | 3 -- inst/CITATION | 33 +++++++++------------- man/clogitL1-package.Rd | 2 - man/clogitL1.Rd | 2 - man/cv.clogitL1.Rd | 2 - man/plot.clogitL1.Rd | 2 - man/plot.cv.clogitL1.Rd | 2 - man/print.clogitL1.Rd | 10 +++--- man/summary.clogitL1.Rd | 2 - man/summary.cv.clogitL1.Rd | 2 - src/Makevars | 2 - src/Makevars.win | 1 src/RcppExports.cpp | 66 ++++++++++++++++++++++++++++----------------- 16 files changed, 107 insertions(+), 92 deletions(-)
Title: Fast and Memory-Efficient Base R Table Manipulation
Description: A tabular data manipulation, exploration and validation toolkit
with a base R-style interface (subset, transform, aggregate, merge, split)
and no external computation dependency. Grouping, joins, ordering,
filtering, reshaping and delimited-file reading run in a bundled 'C++'
engine that uses multiple threads for the heavier operations. Grouped
reducers accumulate in compiled code without materialising intermediate
columns, so grouped aggregation and counting allocate close to nothing.
Results are returned as an ordinary data frame with a light 'basetable'
class.
Author: Imad El Badisy [aut, cre]
Maintainer: Imad El Badisy <elbadisyimad@gmail.com>
Diff between basetable versions 1.4.1 dated 2026-09-13 and 1.4.2 dated 2026-09-18
DESCRIPTION | 6 +- MD5 | 25 +++++----- NEWS.md | 12 +++++ R/split.R | 3 + README.md | 8 +++ inst/benchmarks/benchmark-results.md | 28 ++++++------ inst/benchmarks/make-readme-figures.R | 15 +++--- inst/doc/benchmarking.html | 78 +++++++++++++++++----------------- inst/doc/functions-reference.pdf |binary man/figures/benchmark-combined.png |only man/figures/benchmark-memory.png |binary man/figures/benchmark-time.png |binary man/split.Rd | 16 ++++-- tests/testthat/test-split.R | 9 +++ 14 files changed, 120 insertions(+), 80 deletions(-)
Title: Inference on Prototypes from Clusters of Features
Description: Procedures for testing for group-wide signal in clusters of variables. Tests can be performed for single groups in isolation (univariate) or multiple groups together (multivariate). Specific tests include the exact and approximate (un)selective likelihood ratio tests described in Reid et al (2015), the selective F test and marginal screening prototype test of Reid and Tibshirani (2015). User may pre-specify columns to be included in prototype formation, or allow the function to select them itself. A mixture of these two is also possible. Any variable selection is accounted for using the selective inference framework. Options for non-sampling and hit-and-run null reference distributions.
Author: Stephen Reid [aut, cre]
Maintainer: Stephen Reid <sreid1652@gmail.com>
Diff between prototest versions 1.2 dated 2019-02-03 and 1.3 dated 2026-09-18
DESCRIPTION | 19 ++++++++----- MD5 | 14 ++++----- R/RcppExports.R | 10 +++--- build/partial.rdb |binary man/prototest-package.Rd | 10 +++--- man/prototest.multivariate.Rd | 6 ++-- man/prototest.univariate.Rd | 8 ++--- src/RcppExports.cpp | 61 +++++++++++++++++++++++++++--------------- 8 files changed, 76 insertions(+), 52 deletions(-)
Title: Within-Subject Mediation Analysis Using Structural Equation
Modeling
Description: Within-subject mediation analysis using structural equation modeling.
Examine how changes in an outcome variable between two conditions are mediated
through one or more variables. Supports within-subject mediation analysis using
the 'lavaan' package by Rosseel (2012) <doi:10.18637/jss.v048.i02>,
and extends Monte Carlo confidence interval estimation to missing data scenarios
using the 'semmcci' package by Pesigan and Cheung (2023) <doi:10.3758/s13428-023-02114-4>.
Author: Wendie Yang [aut, cre] ,
Shu Fai Cheung [aut]
Maintainer: Wendie Yang <1581075494q@gmail.com>
Diff between wsMed versions 1.0.2 dated 2025-12-11 and 1.1.0 dated 2026-09-18
DESCRIPTION | 6 MD5 | 164 - NAMESPACE | 5 NEWS.md | 34 R/GenerateModelCN.R | 4 R/GenerateModelCP.R | 113 R/GenerateModelCustom.R |only R/GenerateModelP.R | 4 R/GenerateModelPC.R | 102 R/MCMI2.R | 18 R/MClav_MCStd2.R | 81 R/MClav_RAM2Lav2.R | 16 R/MClav_StdLav2.R | 8 R/MClav_StdRAM2.R | 27 R/RunMCMIAnalysis.R | 69 R/WSMed.R | 128 R/analyze_mm_categorical.R | 19 R/analyze_mm_continuous.R | 230 - R/calc_basic_contrasts.R | 13 R/plot-effects.R |only R/plot_moderation_curve.R | 259 - R/print-wsMed.R | 43 R/standardization-internal.R |only R/standardize_moderation.R |only R/wsMed-helper.R | 100 build/vignette.rds |binary inst/doc/GenerateModelCN.Rmd | 55 inst/doc/GenerateModelCN.html | 56 inst/doc/GenerateModelCP.Rmd | 53 inst/doc/GenerateModelCP.html | 54 inst/doc/GenerateModelCustom.Rmd |only inst/doc/GenerateModelCustom.html |only inst/doc/GenerateModelP.Rmd | 45 inst/doc/GenerateModelP.html | 47 inst/doc/GenerateModelPC.Rmd | 53 inst/doc/GenerateModelPC.html | 54 inst/doc/MEMORE_vs_wsMed.Rmd | 264 - inst/doc/MEMORE_vs_wsMed.html | 267 - inst/doc/PlottingEffects.Rmd |only inst/doc/PlottingEffects.html |only inst/doc/StandardizedModeratedMediation.Rmd |only inst/doc/StandardizedModeratedMediation.html |only inst/doc/WsMed.Rmd | 2558 +++++++++------ inst/doc/WsMed.html | 2902 ++++++++++-------- inst/doc/printGM.Rmd | 45 inst/doc/printGM.html | 38 man/GenerateModelCustom.Rd |only man/MCMI2.Rd | 51 man/MCStd2.Rd | 20 man/RAM2Lav2.Rd | 8 man/RunMCMIAnalysis.Rd | 33 man/StdLav2.Rd | 6 man/StdRAM2.Rd | 14 man/analyze_mm_continuous.Rd | 106 man/calc_basic_contrasts.Rd | 57 man/dot-fit_and_mc.Rd | 3 man/dot-make_moderation.Rd | 3 man/plot_conditional_effects.Rd |only man/plot_contrasts.Rd |only man/plot_effects.Rd |only man/plot_moderation_curve.Rd | 75 man/standardize_moderation.Rd |only man/validate_wsMed_inputs.Rd | 3 man/wsMed.Rd | 98 tests/testthat/test-GenerateModelCustom.R |only tests/testthat/test-GenerateModelP.R | 6 tests/testthat/test-ImputeData.R | 2 tests/testthat/test-WsMed.R | 579 +++ tests/testthat/test-analyze-mm-continuous.R | 2 tests/testthat/test-choice-case.R |only tests/testthat/test-effect-plots.R |only tests/testthat/test-print.WsMed.R | 244 + tests/testthat/test-standardization-phase1.R |only tests/testthat/test-standardization-phase2.R |only vignettes/GenerateModelCN.Rmd | 55 vignettes/GenerateModelCN.Rmd.original | 55 vignettes/GenerateModelCP.Rmd | 53 vignettes/GenerateModelCP.Rmd.original | 53 vignettes/GenerateModelCustom.Rmd |only vignettes/GenerateModelCustom.Rmd.original |only vignettes/GenerateModelP.Rmd | 45 vignettes/GenerateModelP.Rmd.original | 45 vignettes/GenerateModelPC.Rmd | 53 vignettes/GenerateModelPC.Rmd.original | 53 vignettes/MEMORE_vs_wsMed.Rmd | 264 - vignettes/MEMORE_vs_wsMed.Rmd.original | 15 vignettes/PlottingEffects.Rmd |only vignettes/PlottingEffects.Rmd.original |only vignettes/StandardizedModeratedMediation.Rmd |only vignettes/StandardizedModeratedMediation.Rmd.original |only vignettes/Wa.png |only vignettes/Wb.png |only vignettes/Wc.png |only vignettes/Wd.png |only vignettes/WsMed.Rmd | 2558 +++++++++------ vignettes/WsMed.Rmd.original | 1411 +++++--- vignettes/printGM.Rmd | 45 vignettes/printGM.Rmd.original | 24 98 files changed, 8526 insertions(+), 5447 deletions(-)