Title: Variable Neighborhood Trust Region Search
Description: Implements a variable neighborhood trust region search (VNTRS)
algorithm for nonlinear global optimization, based on Bierlaire et al.
(2009) "A Heuristic for Nonlinear Global Optimization"
<doi:10.1287/ijoc.1090.0343>. The method combines neighborhood
exploration with a trust-region framework to search the solution space
efficiently. It can terminate a local search early when the iterates
converge toward a previously visited local optimum or when further
improvement within the current region is unlikely. The algorithm can also
be used to identify multiple local optima.
Author: Lennart Oelschlaeger [aut, cre]
Maintainer: Lennart Oelschlaeger <oelschlaeger.lennart@gmail.com>
Diff between vntrs versions 0.2.1 dated 2026-05-07 and 0.3.0 dated 2026-09-03
DESCRIPTION | 12 MD5 | 34 - NAMESPACE | 10 NEWS.md | 44 ++ R/RcppExports.R | 22 - R/vntrs.R | 646 +++++++++++++++++++++------------ README.md | 237 ++++-------- build/partial.rdb |binary man/figures/README-camel-contour-1.png |only man/figures/logo.png |binary man/vntrs-package.Rd | 75 ++- man/vntrs.Rd | 382 ++++++++++++++----- src/RcppExports.cpp | 26 - src/objective_validation.h | 407 +++++++++++--------- src/optimization_metrics.h |only src/trust_region.cpp | 644 ++++++++++++++++++++++---------- src/vntrs.cpp | 577 ++++++++++++++++++++--------- tests/testthat.R | 8 tests/testthat/test-vntrs.R | 587 +++++++++++++++++------------ 19 files changed, 2338 insertions(+), 1373 deletions(-)
Title: A Bridge Between 'keras' and 'tidymodels'
Description: Provides a seamless bridge between 'keras' and the 'tidymodels'
frameworks. It allows for the dynamic creation of 'parsnip' model
specifications for 'keras' models.
Author: David Diaz [aut, cph, cre]
Maintainer: David Diaz <daviddrsch@gmail.com>
Diff between kerasnip versions 0.1.2 dated 2026-05-02 and 0.2.0 dated 2026-09-03
DESCRIPTION | 13 LICENSE | 4 MD5 | 268 +- NAMESPACE | 193 - R/axe_methods.R | 352 +- R/build_and_compile_model.R | 871 +++---- R/build_spec_function.R | 210 - R/compile_keras_grid.R | 812 +++--- R/create_keras_functional_spec.R | 341 +- R/create_keras_sequential_spec.R | 292 +- R/create_keras_spec_helpers.R | 526 ++-- R/dials.R | 76 R/generate_roxygen_docs.R | 586 ++-- R/generic_fit_helpers.R | 382 +-- R/generic_functional_fit.R | 239 +- R/generic_sequential_fit.R | 236 -- R/globals.R | 27 R/keras_tools.R | 480 ++-- R/kerasnip_add_tailor.R |only R/kerasnip_spec_methods.R | 458 ++- R/laplace_approx_classification.R |only R/laplace_approx_regression.R |only R/output_view.R |only R/postprocess_intervals_classification.R |only R/postprocess_intervals_regression.R |only R/register_core_model.R | 81 R/register_fit_predict.R | 644 +++-- R/register_model_args.R | 196 - R/register_update_method.R | 200 - R/remove_keras_spec.R | 200 - R/step_collapse.R | 360 +-- R/step_lead.R |only R/step_sequence.R |only R/step_view.R |only R/utils.R | 1014 ++++---- R/zzz.R | 294 +- README.md | 442 +-- build/vignette.rds |binary inst/doc/applications.Rmd | 388 +-- inst/doc/applications.html | 1090 ++++----- inst/doc/autoplot_uniqueness.Rmd | 514 ++-- inst/doc/autoplot_uniqueness.html | 1288 +++++----- inst/doc/conformal_intervals.Rmd | 584 ++-- inst/doc/conformal_intervals.html | 1416 ++++++------ inst/doc/functional_api.Rmd | 847 ++++--- inst/doc/functional_api.html | 1642 +++++++------ inst/doc/getting_started.Rmd | 1188 +++++----- inst/doc/getting_started.html | 1846 ++++++++------- inst/doc/multi_output_postprocessing.Rmd |only inst/doc/multi_output_postprocessing.html |only inst/doc/multistep_forecasting.Rmd |only inst/doc/multistep_forecasting.html |only inst/doc/saving_and_reloading.Rmd | 442 +-- inst/doc/saving_and_reloading.html | 1224 +++++----- inst/doc/sequential_model.Rmd | 421 +-- inst/doc/sequential_model.html | 1123 ++++----- inst/doc/tuning_fit_compile_args.Rmd | 1185 +++++----- inst/doc/tuning_fit_compile_args.html | 1870 ++++++++------- inst/doc/workflows_functional.Rmd | 1351 +++++------ inst/doc/workflows_functional.html | 1997 ++++++++--------- inst/doc/workflows_sequential.Rmd | 1196 +++++----- inst/doc/workflows_sequential.html | 1840 +++++++-------- man/augment.kerasnip_output_view.Rd |only man/augment.kerasnip_step_view.Rd |only man/axe-kerasnip_model_fit.Rd | 84 man/compile_keras_grid.Rd | 234 - man/create_keras_functional_spec.Rd | 353 +-- man/create_keras_sequential_spec.Rd | 300 +- man/extract_keras_history.Rd | 60 man/extract_keras_model.Rd | 56 man/extract_mold.kerasnip_output_view.Rd |only man/extract_valid_grid.Rd | 176 - man/fit.kerasnip_spec.Rd | 60 man/fit.kerasnip_tailored_workflow.Rd |only man/generic_functional_fit.Rd | 164 - man/generic_sequential_fit.Rd | 164 - man/glance.kerasnip_model_fit.Rd | 44 man/inform_errors.Rd | 176 - man/inp_spec.Rd | 162 - man/int_conformal_full.kerasnip_output_view.Rd |only man/int_conformal_full.kerasnip_step_view.Rd |only man/int_conformal_split.kerasnip_output_view.Rd |only man/int_conformal_split.kerasnip_step_view.Rd |only man/keras_evaluate.Rd | 184 - man/keras_objects.Rd | 69 man/kerasnip_add_tailor.Rd |only man/kerasnip_output_view.Rd |only man/kerasnip_step_truth.Rd |only man/kerasnip_step_view.Rd |only man/laplace_conf_int_cls.Rd |only man/laplace_conf_int_reg.Rd |only man/laplace_pred_int_cls.Rd |only man/laplace_pred_int_reg.Rd |only man/loss_function_keras.Rd | 38 man/model_exists.Rd | 66 man/optimizer_function.Rd | 38 man/predict.kerasnip_conformal_full.Rd |only man/predict.kerasnip_conformal_full_step.Rd |only man/predict.kerasnip_model_fit.Rd | 76 man/predict.kerasnip_output_view.Rd |only man/predict.kerasnip_step_view.Rd |only man/predict.kerasnip_tailored_fit.Rd |only man/process_x_functional.Rd | 50 man/process_x_sequential.Rd | 46 man/process_y_functional.Rd | 92 man/process_y_sequential.Rd | 72 man/register_keras_loss.Rd | 56 man/register_keras_metric.Rd | 56 man/register_keras_optimizer.Rd | 86 man/remove_keras_spec.Rd | 148 - man/step_collapse.Rd | 142 - man/step_lead.Rd |only man/step_sequence.Rd |only man/tidy.kerasnip_model_fit.Rd | 44 tests/testthat.R | 28 tests/testthat/_snaps/step_lead.md |only tests/testthat/_snaps/step_sequence.md |only tests/testthat/helper_tests.R | 39 tests/testthat/test_add_tailor.R |only tests/testthat/test_autoplot_uniqueness.R | 138 - tests/testthat/test_bare_fit_args.R |only tests/testthat/test_butcher.R | 308 +- tests/testthat/test_compile_keras_grid.R | 512 ++-- tests/testthat/test_conformal.R | 548 ++-- tests/testthat/test_e2e_features.R | 562 ++-- tests/testthat/test_e2e_fit_compile_tuning.R | 168 - tests/testthat/test_e2e_func_classification.R | 773 +++--- tests/testthat/test_e2e_func_multistep_regression.R |only tests/testthat/test_e2e_func_regression.R | 472 ++-- tests/testthat/test_e2e_multiblock_tuning.R | 192 - tests/testthat/test_e2e_seq_classification.R | 192 - tests/testthat/test_e2e_spec_removal.R | 142 - tests/testthat/test_e2e_tuning.R | 134 - tests/testthat/test_generic_fit_helpers.R | 256 +- tests/testthat/test_inp_spec.R | 116 tests/testthat/test_keras_tools.R | 198 - tests/testthat/test_laplace_intervals_classification.R |only tests/testthat/test_laplace_intervals_regression.R |only tests/testthat/test_output_view.R |only tests/testthat/test_postprocessing_helpers.R | 476 ++-- tests/testthat/test_process_y_functional.R |only tests/testthat/test_save_load.R | 376 +-- tests/testthat/test_stacks.R |only tests/testthat/test_step_collapse.R | 272 +- tests/testthat/test_step_lead.R |only tests/testthat/test_step_sequence.R |only tests/testthat/test_step_view.R |only tests/testthat/test_tailor.R |only tests/testthat/test_tidy_glance.R | 194 - vignettes/applications.Rmd | 388 +-- vignettes/autoplot_uniqueness.Rmd | 514 ++-- vignettes/conformal_intervals.Rmd | 584 ++-- vignettes/functional_api.Rmd | 847 ++++--- vignettes/getting_started.Rmd | 1188 +++++----- vignettes/multi_output_postprocessing.Rmd |only vignettes/multistep_forecasting.Rmd |only vignettes/saving_and_reloading.Rmd | 442 +-- vignettes/sequential_model.Rmd | 421 +-- vignettes/tuning_fit_compile_args.Rmd | 1185 +++++----- vignettes/workflows_functional.Rmd | 1351 +++++------ vignettes/workflows_sequential.Rmd | 1196 +++++----- 161 files changed, 26247 insertions(+), 24510 deletions(-)
Title: Fitting Flexible Smooth-in-Time Hazards and Risk Functions via
Logistic and Multinomial Regression
Description: Fit flexible and fully parametric hazard regression models to survival data with single event type or multiple
competing causes via logistic and multinomial regression. Our formulation allows for arbitrary functional forms
of time and its interactions with other predictors for time-dependent hazards and hazard ratios. From the
fitted hazard model, we provide functions to readily calculate and plot cumulative incidence and survival
curves for a given covariate profile. This approach accommodates any log-linear hazard function of
prognostic time, treatment, and covariates, and readily allows for non-proportionality. We also provide
a plot method for visualizing incidence density via population time plots. Based on the case-base sampling
approach of Hanley and Miettinen (2009) <DOI:10.2202/1557-4679.1125>, Saarela and Arjas (2015) <DOI:10.1111/sjos.12125>,
and Saarela (2015) <DOI:10.1007/s10985-015-9352-x>.
Author: Sahir Bhatnagar [aut, cre] ,
Maxime Turgeon [aut] ,
Jesse Islam [aut] ,
Olli Saarela [aut]
,
James Hanley [aut]
Maintainer: Sahir Bhatnagar <sahir.bhatnagar@gmail.com>
Diff between casebase versions 0.10.6 dated 2024-08-17 and 0.10.7 dated 2026-09-03
DESCRIPTION | 11 MD5 | 44 +- NEWS.md | 9 R/data.R | 2 R/plot_methods.R | 8 build/partial.rdb |binary build/vignette.rds |binary inst/doc/competingRisk.html | 69 +-- inst/doc/customizingpopTime.R | 34 - inst/doc/customizingpopTime.html | 122 +++-- inst/doc/plotabsRisk.html | 19 inst/doc/plotsmoothHazard.R | 401 ++++++++---------- inst/doc/plotsmoothHazard.Rmd | 78 +-- inst/doc/plotsmoothHazard.html | 455 +++++++++++++++------ inst/doc/popTime.R | 2 inst/doc/popTime.html | 413 ++++++++++--------- inst/doc/smoothHazard.R | 284 ++++++------- inst/doc/smoothHazard.html | 691 ++++++++++++++++++++++++++------ inst/doc/time-varying-covariates.pdf |binary man/support.Rd | 2 tests/testthat/test-plotSingleEventCB.R | 3 vignettes/plotsmoothHazard.Rmd | 78 +-- vignettes/time-varying-covariates.html | 18 23 files changed, 1671 insertions(+), 1072 deletions(-)
Title: Standardized Economic Reporting and Automated Dynamic Writing /
Synthèse d'Écrits Avec des Règles Automatisées et Dynamiques
Description: Provides tools for generating dynamic and standardized
economic narratives in R Markdown documents. The package is primarily
designed for French-language statistical and economic publications.
It includes functions to describe changes in levels, percentages,
trends, accelerations and short-term economic developments using
consistent linguistic rules. The package supports automated reporting
workflows and reproducible economic writing.
Fournit des outils permettant de générer des textes économiques
dynamiques et standardisés dans des documents R Markdown. Le package
est principalement conçu pour les publications statistiques et
économiques en français. Il propose des fonctions permettant de
décrire les évolutions de niveaux, de pourcentages, de tendances,
d'accélérations et les évolutions conjoncturelles à l'aide de règles
linguistiques homogènes. Le package facilite l'automatisation de la
rédaction et la reproductibilité des publications économiques.
Author: Alexandre Cazenave-Lacroutz [aut] ,
Jules Lejas [cre],
Direction de l'animation de la recherche, des etudes et des
statistiques [cph]
Maintainer: Jules Lejas <jules.lejas@gmail.com>
Diff between serad versions 0.2.3 dated 2026-07-23 and 0.2.4 dated 2026-09-03
DESCRIPTION | 6 +-- MD5 | 16 ++++----- R/init_serad_en.R | 40 +++++++++++------------ R/init_serad_fr.R | 58 ++++++++++++++++------------------ inst/doc/serad.html | 2 - tests/testthat/test-gETa_nom.R | 4 +- tests/testthat/test-gETa_nom_taux.R | 8 ++-- tests/testthat/test-gETa_verbe.R | 16 ++++----- tests/testthat/test-gETa_verbe_taux.R | 6 +-- 9 files changed, 76 insertions(+), 80 deletions(-)
Title: Printing Floating Point Numbers in a Human-Friendly Format
Description: Print vectors (and data frames) of floating point numbers
using a non-scientific format optimized for human readers. Vectors of
numbers are rounded using significant digits, aligned at the decimal
point, and all zeros trailing the decimal point are dropped. See:
Wright (2016). Lucid: An R Package for Pretty-Printing Floating Point
Numbers. In JSM Proceedings, Statistical Computing Section.
Alexandria, VA: American Statistical Association. 2270-2279.
Author: Kevin Wright [aut, cre, cph]
Maintainer: Kevin Wright <kw.stat@gmail.com>
Diff between lucid versions 1.11 dated 2026-03-03 and 1.12 dated 2026-09-03
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- NEWS.md | 5 +++++ build/vignette.rds |binary inst/doc/lucid_examples.R | 4 ++-- inst/doc/lucid_examples.Rmd | 4 ++-- inst/doc/lucid_examples.html | 13 ++++++------- tests/testthat/test_lucid.r | 40 ++++++++++++++++++++-------------------- tests/testthat/test_vc.r | 6 +++--- vignettes/lucid_examples.Rmd | 4 ++-- 10 files changed, 52 insertions(+), 48 deletions(-)
Title: Laboratory Sieve Test Reporting Functions
Description: Functions for making particle-size analysis. Sieve tests are widely used to obtain particle-size distribution of powders or granular materials.
Author: Petr Matousu [aut, cre]
Maintainer: Petr Matousu <pmatousu@ipmtech.cz>
Diff between sievetest versions 1.2.3 dated 2018-06-07 and 1.2.4 dated 2026-09-03
DESCRIPTION | 19 ++++++++++++------- MD5 | 4 ++-- man/drr.Rd | 6 +++--- 3 files changed, 17 insertions(+), 12 deletions(-)
Title: Symbolic Differentiation
Description: R-based solution for symbolic differentiation. It admits
user-defined function as well as function substitution
in arguments of functions to be differentiated. Some symbolic
simplification is part of the work.
Author: Andrew Clausen [aut],
Serguei Sokol [aut, cre] ,
Andreas Rappold [ctb]
Maintainer: Serguei Sokol <sokol@insa-toulouse.fr>
Diff between Deriv versions 4.3.0 dated 2026-07-23 and 4.3.5 dated 2026-09-03
DESCRIPTION | 10 MD5 | 9 NEWS.md | 402 ++++++++++++++++--------------- R/Simplify.R | 2 src/derive_simplif.cpp | 578 +++++++++++++++++++++++++++++----------------- tests/testthat/test_cpp.R |only 6 files changed, 593 insertions(+), 408 deletions(-)
Title: Network Analysis of Dependencies of CRAN Packages
Description: The dependencies of CRAN packages can be analysed in a network fashion. For each package we can obtain the packages that it depends, imports, suggests, etc. By iterating this procedure over a number of packages, we can build, visualise, and analyse the dependency network, enabling us to have a bird's-eye view of the CRAN ecosystem. One aspect of interest is the number of reverse dependencies of the packages, or equivalently the in-degree distribution of the dependency network. This can be fitted by the power law and/or an extreme value mixture distribution <doi:10.1111/stan.12355>, of which functions are provided.
Author: Clement Lee [aut, cre]
Maintainer: Clement Lee <clement.lee.tm@outlook.com>
Diff between crandep versions 0.3.13 dated 2025-06-16 and 0.3.14 dated 2026-09-03
DESCRIPTION | 9 MD5 | 37 ++- NAMESPACE | 5 NEWS.md | 8 R/graph.R | 57 ++++++ README.md | 121 ++++++------ build/vignette.rds |binary inst/doc/cran.R | 18 - inst/doc/cran.html | 422 ++++++++++++++++++++++++--------------------- inst/doc/degree.R | 24 +- inst/doc/degree.Rmd | 4 inst/doc/degree.html | 328 +++++++++++++++++++--------------- inst/doc/introduction.R | 21 +- inst/doc/introduction.Rmd | 23 ++ inst/doc/introduction.html | 307 ++++++++++++++++++++------------ man/topo_sort_kahn.Rd |only tests |only vignettes/degree.Rmd | 4 vignettes/introduction.Rmd | 23 ++ 19 files changed, 833 insertions(+), 578 deletions(-)
Title: Interface for 'All of Us' Researcher Workbench
Description: Streamline use of the 'All of Us' Researcher Workbench (<https://www.researchallofus.org/data-tools/workbench/>)with tools to extract and manipulate data from the 'All of Us' database. Increase interoperability with the Observational Health Data Science and Informatics ('OHDSI') tool stack by decreasing reliance of 'All of Us' tools and allowing for cohort creation via 'Atlas'. Improve reproducible and transparent research using 'All of Us'.
Author: Louisa Smith [aut, cre, cph] ,
Rob Cavanaugh [aut, cph]
Maintainer: Louisa Smith <l.smith@northeastern.edu>
Diff between allofus versions 1.2.0 dated 2024-11-06 and 1.3.0 dated 2026-09-03
DESCRIPTION | 25 ++-- MD5 | 89 ++++++++------ NAMESPACE | 1 NEWS.md | 15 +- R/aou_atlas_cohort.R | 2 R/aou_concept_set.R | 2 R/aou_connect.R | 218 ++++++++++++++++++++++++++++++++++-- R/aou_create_bucket.R |only R/aou_ls.R | 22 +++ R/aou_obs_period.R | 14 +- R/aou_session_info.R | 6 R/aou_survey.R | 25 ++-- R/aou_temp_tables.R | 55 +++++---- R/zzz.R | 180 +++++++++++++++++++++++++++++ README.md | 40 +++++- build/vignette.rds |binary inst/doc/allofus.R | 102 ++++++++-------- inst/doc/allofus.html | 4 inst/doc/atlas.R | 26 ++-- inst/doc/atlas.html | 1 inst/doc/data.R | 66 +++++----- inst/doc/data.html | 9 - inst/doc/workspace.R | 25 ++-- inst/doc/workspace.Rmd | 22 +++ inst/doc/workspace.html | 37 ++++-- man/allofus-package.Rd | 4 man/aou_bucket_to_workspace.Rd | 2 man/aou_collect.Rd | 2 man/aou_compute.Rd | 2 man/aou_concept_set.Rd | 4 man/aou_connect.Rd | 2 man/aou_create_bucket.Rd |only man/aou_create_temp_table.Rd | 2 man/aou_join.Rd | 2 man/aou_ls_bucket.Rd | 2 man/aou_observation_period.Rd | 2 man/aou_session_info.Rd | 6 man/aou_sql.Rd | 2 man/aou_survey.Rd | 2 man/aou_tables.Rd | 2 man/aou_workspace_to_bucket.Rd | 2 man/read_aou_env.Rd |only man/set_env_vars.Rd |only man/workbench_cdr.Rd |only man/workbench_env_vars.Rd |only man/workbench_google_project.Rd |only man/write_aou_env.Rd |only tests/testthat/test-aou_connect.R | 71 +++++++++++ tests/testthat/test-local-backend.R |only vignettes/workspace.Rmd | 22 +++ 50 files changed, 865 insertions(+), 252 deletions(-)
Title: High-Dimensional Methods via Generalised Singular Decomposition
Description: Construct a Canonical Variate Analysis Biplot via the Generalised Singular Value Decomposition, for cases when the number of samples is less than the number of variables. For more information on these biplots, see Ganey, R., & Gardner-Lubbe, S. (2026) <doi:10.1007/s10260-025-00831-y>.
Author: Raeesa Ganey [aut, cre]
Maintainer: Raeesa Ganey <Raeesa.ganey@wits.ac.za>
Diff between wideRhino versions 1.2.0 dated 2026-07-02 and 1.3.0 dated 2026-09-03
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 4 ++-- R/CVAgsvd.R | 17 +++++++++++++---- R/gsvd.R | 5 +++++ README.md | 9 +++++++++ man/CVAgsvd.Rd | 7 ++++++- 7 files changed, 44 insertions(+), 16 deletions(-)
Title: Non-Parametric Trend Tests and Change-Point Detection
Description: The analysis of environmental data often requires
the detection of trends and change-points.
This package includes tests for trend detection
(Cox-Stuart Trend Test, Mann-Kendall Trend Test,
(correlated) Hirsch-Slack Test,
partial Mann-Kendall Trend Test, multivariate (multisite)
Mann-Kendall Trend Test, (Seasonal) Sen's slope,
partial Pearson and Spearman correlation trend test),
change-point detection (Lanzante's test procedures,
Pettitt's test, Buishand Range Test,
Buishand U Test, Standard Normal Homogeinity Test),
detection of non-randomness (Wallis-Moore Phase Frequency Test,
Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test)
and the two sample Robust Rank-Order Distributional Test.
Author: Thorsten Pohlert [aut, cre]
Maintainer: Thorsten Pohlert <thorsten.pohlert@gmx.de>
Diff between trend versions 1.1.7 dated 2026-07-14 and 1.1.8 dated 2026-09-03
DESCRIPTION | 10 +++++----- MD5 | 11 +++++++---- NAMESPACE | 41 +++++++++++++++++++++++------------------ R/itam.R |only inst/NEWS.Rd | 8 ++++++++ inst/doc/trend.pdf |binary man/itam.Rd |only man/plot.itam.Rd |only 8 files changed, 43 insertions(+), 27 deletions(-)
Title: Examples using 'Rcpp' to Interface R and C++
Description: Examples for Seamless R and C++ integration
The 'Rcpp' package contains a C++ library that facilitates the integration of
R and C++ in various ways. This package provides some usage examples.
Note that the documentation in this package currently does not cover all the
features in the package. The site <https://gallery.rcpp.org> regroups a large
number of examples for 'Rcpp'.
Author: Dirk Eddelbuettel [aut, cre] ,
Romain Francois [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppExamples versions 0.1.10 dated 2025-03-17 and 0.1.11 dated 2026-09-03
ChangeLog | 21 +++++++++++++++++++++ DESCRIPTION | 13 +++++++------ MD5 | 20 ++++++++++---------- inst/NEWS.Rd | 7 +++++++ man/RcppDataFrame.Rd | 12 +++++++++--- man/RcppDateExample.Rd | 23 ++++++++++++++++------- man/RcppListExample.Rd | 5 ++++- man/RcppMatrixExample.Rd | 32 ++++++++++++++++++++------------ man/RcppNumericVectorExample.Rd | 15 ++++++++++++--- man/RcppRNGsExample.Rd | 10 ++++++++++ man/RcppStringVectorExample.Rd | 25 +++++++++++++++++-------- 11 files changed, 133 insertions(+), 50 deletions(-)
Title: Tools for Natural Language Processing in French
Description: Tools for Natural Language Processing in French and texts from Marcel Proust's collection
"A La Recherche Du Temps Perdu". The novels contained in this collection are
"Du cote de chez Swann ", "A l'ombre des jeunes filles en fleurs","Le Cote de Guermantes",
"Sodome et Gomorrhe I et II", "La Prisonniere", "Albertine disparue", and "Le Temps retrouve".
Author: Colin Fay [aut, cre]
Maintainer: Colin Fay <contact@colinfay.me>
Diff between proustr versions 0.4.0 dated 2019-02-05 and 0.4.1 dated 2026-09-03
proustr-0.4.0/proustr/data/datalist |only proustr-0.4.0/proustr/inst/hex-proustr.png |only proustr-0.4.1/proustr/DESCRIPTION | 12 proustr-0.4.1/proustr/MD5 | 48 - proustr-0.4.1/proustr/NEWS.md | 5 proustr-0.4.1/proustr/R/pr_stem.R | 4 proustr-0.4.1/proustr/R/proust_char.R | 2 proustr-0.4.1/proustr/R/proust_datasets.R | 2 proustr-0.4.1/proustr/R/proust_sentiments.R | 2 proustr-0.4.1/proustr/README.md | 10 proustr-0.4.1/proustr/build/vignette.rds |binary proustr-0.4.1/proustr/inst/doc/gettingstarted.R | 68 +- proustr-0.4.1/proustr/inst/doc/gettingstarted.html | 398 +++++++----- proustr-0.4.1/proustr/man/albertinedisparue.Rd | 4 proustr-0.4.1/proustr/man/alombredesjeunesfillesenfleurs.Rd | 4 proustr-0.4.1/proustr/man/ducotedechezswann.Rd | 4 proustr-0.4.1/proustr/man/laprisonniere.Rd | 4 proustr-0.4.1/proustr/man/lecotedeguermantes.Rd | 4 proustr-0.4.1/proustr/man/letempretrouve.Rd | 4 proustr-0.4.1/proustr/man/pr_stem_sentences.Rd | 2 proustr-0.4.1/proustr/man/pr_stem_words.Rd | 2 proustr-0.4.1/proustr/man/proust_char.Rd | 6 proustr-0.4.1/proustr/man/proust_characters.Rd | 2 proustr-0.4.1/proustr/man/proust_sentiments.Rd | 4 proustr-0.4.1/proustr/man/sodomeetgomorrhe.Rd | 4 proustr-0.4.1/proustr/man/stop_words.Rd | 4 26 files changed, 357 insertions(+), 242 deletions(-)
Title: Calculates a Natural Capital Assets Index
Description: Calculates a regional natural capital assets index (NCAI) following the methodology designed by NatureScot for Scotland as described in Albon, Balana, Brooker & Eastwood (2014) <https://www.nature.scot/sites/default/files/2025-06/naturescot-commissioned-report-751.pdf> and McKenna et al. (2019) <doi:10.1016/J.ECOLIND.2019.105645>. Processes habitat extent and condition data alongside metadata and weighting systems to produce a yearly single figure indexed relative to a base-year value of 100.
Author: Kate O'Hara [aut, cre],
Chris Littleboy [aut]
Maintainer: Kate O'Hara <k.a.ohara@stir.ac.uk>
Diff between openNCAI versions 0.1.0 dated 2026-05-13 and 0.2.0 dated 2026-09-03
DESCRIPTION | 24 +- MD5 | 56 ++--- NAMESPACE | 3 NEWS.md | 8 R/calc_wellbeing_potential_base.R | 5 R/check_missing.R |only R/get_ncai.R | 16 + R/import_ns_data.R | 52 ++-- R/import_ns_testing_data.R | 22 +- R/make_and_read_data_template.R | 2 R/missingness_internal.R |only R/show_missing.R |only README.md | 13 - inst/WORDLIST |only inst/doc/openNCAI_in_brief.Rmd | 4 inst/doc/openNCAI_in_brief.html | 57 +++-- inst/doc/replicating_scotlands_ncai.R | 4 inst/doc/replicating_scotlands_ncai.Rmd | 17 - inst/doc/replicating_scotlands_ncai.html | 231 ++++++++++++--------- inst/doc/using_openNCAIs_data_entry_templates.Rmd | 6 inst/doc/using_openNCAIs_data_entry_templates.html | 10 man/check_missing.Rd |only man/create_ncai_template.Rd | 2 man/figures/ncai_calculation_process.png |binary man/get_ncai.Rd | 5 man/openNCAI-package.Rd | 5 man/show_missing.Rd |only tests/testthat/helper.R | 19 + tests/testthat/test-check_missing.R |only tests/testthat/test-show_missing.R |only vignettes/openNCAI_in_brief.Rmd | 4 vignettes/replicating_scotlands_ncai.Rmd | 17 - vignettes/using_openNCAIs_data_entry_templates.Rmd | 6 33 files changed, 363 insertions(+), 225 deletions(-)
Title: Functional Shannon Entropy for Virome Mutational Analysis
Description: Estimates Shannon entropy, per gene and per genomic position,
associated with non-synonymous mutation frequencies in viral populations,
such as wastewater samples. The package uses codon translations for
functional insights. Each amino acid can be treated as an individual state,
resulting in a 20-state entropy computation, or grouped into one of six
physicochemical classes, adding further functional context. Provides
normalized values (0-1 scale) to facilitate the direct comparison of
different genomic positions or total functional entropy across multiple
metagenomes. Designed to analyze mutational data using tabular 'Single
Nucleotide Variant' (SNV) frequency tables generated by variant callers
(e.g., 'iVar' or 'LoFreq'), operating independently of consensus sequence
estimation and multiple sequence alignment.
Author: Leandro Roberto Jones [aut, cre] ,
Julieta Marina Manrique [aut]
Maintainer: Leandro Roberto Jones <lrj000@gmail.com>
Diff between MetaEntropy versions 1.3 dated 2026-03-09 and 1.4 dated 2026-09-03
DESCRIPTION | 16 +++--- MD5 | 72 +++++++++++++++------------ NAMESPACE | 6 +- R/as.data.frame.entropyProfile.R | 3 - R/assessHotSpot.R | 1 R/createPositionSummary.R | 6 +- R/createStorage.R | 3 - R/entropyProfile.R | 104 +++++++++++++++++++++++++++++++++++++-- R/fillPosition.R | 8 +-- R/getEntropySignature.R | 8 +-- R/getPosEntropy.R | 2 R/globals.R | 2 R/heatMap_entropyProfiles.R |only R/intraHostVariants.R |only R/plot.entropyProfile.R | 19 ++----- R/print.profileSummary.R | 8 +-- R/print.tydyMutations.R | 7 +- R/summary.entropyProfile.R | 4 - R/wWater.R | 6 +- build/partial.rdb |binary build/vignette.rds |binary data/intraHostVariants.rda |only data/mn908947.3.rda |binary data/wWater.rda |binary inst/doc/intraHostVariants.R |only inst/doc/intraHostVariants.Rmd |only inst/doc/intraHostVariants.html |only inst/doc/overview.Rmd | 2 inst/doc/overview.html | 42 +++++++-------- man/createPositionSummary.Rd | 1 man/createStorage.Rd | 1 man/fillPosition.Rd | 1 man/getPosEntropy.Rd | 1 man/heatmap_entropyProfiles.Rd |only man/intraHostVariants.Rd |only man/print.profileSummary.Rd | 3 - man/print.tidyMutations.Rd | 2 man/wWater.Rd | 6 +- vignettes/intraHostVariants.Rmd |only vignettes/intraHostVariants.bib |only vignettes/overview.Rmd | 2 vignettes/overview.bib | 27 +++++----- 42 files changed, 233 insertions(+), 130 deletions(-)
Title: Meta Analysis Instrumental Variable Estimator
Description: Meta-analysis traditionally assigns more weight to studies with lower standard errors,
assuming higher precision. However, in observational research, precision must be
estimated and is vulnerable to manipulation, such as p-hacking, to achieve statistical
significance. This can lead to spurious precision, invalidating inverse-variance
weighting and bias-correction methods like funnel plots. Common methods for addressing
publication bias, including selection models, often fail or exacerbate the problem.
This package introduces an instrumental variable approach to limit bias caused by
spurious precision in meta-analysis. Methods are described in 'Irsova et al.' (2025)
<doi:10.1038/s41467-025-63261-0>.
Author: Zuzana Irsova [aut] ,
Pedro R. D. Bom [aut] ,
Tomas Havranek [aut] ,
Heiko Rachinger [aut] ,
Petr Cala [aut, cre]
Maintainer: Petr Cala <cala.p@seznam.cz>
Diff between MAIVE versions 0.2.5 dated 2026-08-20 and 0.3.0 dated 2026-09-03
DESCRIPTION | 13 MD5 | 41 +- NAMESPACE | 1 NEWS.md | 35 ++ R/boot.r | 6 R/maivefunction.r | 45 ++ R/metafor.r |only R/validation.r | 82 +++- README.md | 53 ++- inst/WORDLIST | 113 ++++-- inst/doc/introduction.R | 118 ++++--- inst/doc/introduction.Rmd | 75 +++- inst/doc/introduction.html | 366 ++++++++++++---------- man/maive.Rd | 18 - man/maive_from_metafor.Rd |only man/waive.Rd | 11 tests/testthat/fixtures/education.csv |only tests/testthat/fixtures/euro.csv |only tests/testthat/fixtures/euro_v0.2.5_reference.csv |only tests/testthat/test-bootstrap-seed.R |only tests/testthat/test-column-mapping.R |only tests/testthat/test-maive_build_dummy_matrix.R | 80 ++++ tests/testthat/test-maive_slope_metadata.R | 38 ++ tests/testthat/test-metafor-bridge.R |only tests/testthat/test-standard-pair.R |only vignettes/introduction.Rmd | 75 +++- 26 files changed, 807 insertions(+), 363 deletions(-)
Title: Generalised Additive Extreme Value Models
Description: Methods for fitting various extreme value distributions with parameters of
generalised additive model (GAM) form are provided. For details of distributions
see Coles, S.G. (2001) <doi:10.1007/978-1-4471-3675-0>, GAMs see Wood, S.N. (2017)
<doi:10.1201/9781315370279>, and the fitting approach see Wood, S.N., Pya, N. &
Safken, B. (2016) <doi:10.1080/01621459.2016.1180986>. Details of how evgam works
and various examples are given in Youngman, B.D. (2022) <doi:10.18637/jss.v103.i03>.
Author: Ben Youngman [aut, cre]
Maintainer: Ben Youngman <b.youngman@exeter.ac.uk>
Diff between evgam versions 1.0.1 dated 2025-09-23 and 1.0.2 dated 2026-09-03
evgam-1.0.1/evgam/inst |only evgam-1.0.2/evgam/DESCRIPTION | 13 evgam-1.0.2/evgam/MD5 | 153 + evgam-1.0.2/evgam/NAMESPACE | 28 evgam-1.0.2/evgam/NEWS.md | 54 evgam-1.0.2/evgam/R/RcppExports.R | 458 ++++- evgam-1.0.2/evgam/R/agg.R |only evgam-1.0.2/evgam/R/aggauss.R |only evgam-1.0.2/evgam/R/ald.R | 43 evgam-1.0.2/evgam/R/beta.R |only evgam-1.0.2/evgam/R/bgev.R |only evgam-1.0.2/evgam/R/condex.R |only evgam-1.0.2/evgam/R/condexagg.R |only evgam-1.0.2/evgam/R/data.R | 9 evgam-1.0.2/evgam/R/egpd.R |only evgam-1.0.2/evgam/R/evgam-package.R | 9 evgam-1.0.2/evgam/R/exi.R | 26 evgam-1.0.2/evgam/R/exp.R | 6 evgam-1.0.2/evgam/R/family.R |only evgam-1.0.2/evgam/R/gamma.R |only evgam-1.0.2/evgam/R/gamma3.R |only evgam-1.0.2/evgam/R/gauss.R | 12 evgam-1.0.2/evgam/R/generic.R | 838 +++++---- evgam-1.0.2/evgam/R/geoevgam.R |only evgam-1.0.2/evgam/R/gev.R | 50 evgam-1.0.2/evgam/R/gev2.R |only evgam-1.0.2/evgam/R/gevr.R |only evgam-1.0.2/evgam/R/gpd.R | 68 evgam-1.0.2/evgam/R/gpd2.R |only evgam-1.0.2/evgam/R/gpdab.R |only evgam-1.0.2/evgam/R/gw.R |only evgam-1.0.2/evgam/R/laplace.R |only evgam-1.0.2/evgam/R/logdetH.R | 256 +- evgam-1.0.2/evgam/R/logdetS.R | 206 +- evgam-1.0.2/evgam/R/logitgauss.R |only evgam-1.0.2/evgam/R/ltgamma.R |only evgam-1.0.2/evgam/R/ltgammab.R |only evgam-1.0.2/evgam/R/negbin.R |only evgam-1.0.2/evgam/R/nohelp.R | 382 ---- evgam-1.0.2/evgam/R/optim.R |only evgam-1.0.2/evgam/R/penalty.R | 107 - evgam-1.0.2/evgam/R/poisson.R |only evgam-1.0.2/evgam/R/pp.R | 38 evgam-1.0.2/evgam/R/predict.R | 538 +++-- evgam-1.0.2/evgam/R/reml.R | 382 +++- evgam-1.0.2/evgam/R/retlev.R | 242 ++ evgam-1.0.2/evgam/R/rlarge.R |only evgam-1.0.2/evgam/R/rlargec.R |only evgam-1.0.2/evgam/R/setup_and_fit.R | 2431 ++++++++++++++++++--------- evgam-1.0.2/evgam/R/sparse.R |only evgam-1.0.2/evgam/R/weib.R | 67 evgam-1.0.2/evgam/R/weibull3.R |only evgam-1.0.2/evgam/build/partial.rdb |binary evgam-1.0.2/evgam/man/bgev.Rd |only evgam-1.0.2/evgam/man/bgev2gev.Rd |only evgam-1.0.2/evgam/man/custom.family.evgam.Rd |only evgam-1.0.2/evgam/man/df2matdf.Rd |only evgam-1.0.2/evgam/man/dfbind.Rd | 4 evgam-1.0.2/evgam/man/evgam-package.Rd |only evgam-1.0.2/evgam/man/evgam.Rd | 87 evgam-1.0.2/evgam/man/evgam.control.Rd |only evgam-1.0.2/evgam/man/family.evgam.Rd |only evgam-1.0.2/evgam/man/geoevgam.Rd |only evgam-1.0.2/evgam/man/laplace.Rd |only evgam-1.0.2/evgam/man/plot.geoevgam.Rd |only evgam-1.0.2/evgam/man/polarise.Rd |only evgam-1.0.2/evgam/man/predict.evgam.Rd | 8 evgam-1.0.2/evgam/man/predict.geoevgam.Rd |only evgam-1.0.2/evgam/man/qev.Rd | 44 evgam-1.0.2/evgam/man/rmvnorm.Rd |only evgam-1.0.2/evgam/src/Makevars | 2 evgam-1.0.2/evgam/src/Makevars.win | 2 evgam-1.0.2/evgam/src/RcppExports.cpp | 2154 +++++++++++++++++++++++ evgam-1.0.2/evgam/src/aggaussC.cpp |only evgam-1.0.2/evgam/src/aldC.cpp | 477 ++--- evgam-1.0.2/evgam/src/betaC.cpp |only evgam-1.0.2/evgam/src/bgevC.cpp |only evgam-1.0.2/evgam/src/condexC.cpp |only evgam-1.0.2/evgam/src/condex_aggC.cpp |only evgam-1.0.2/evgam/src/egpd.cpp |only evgam-1.0.2/evgam/src/exiC.cpp | 12 evgam-1.0.2/evgam/src/expC.cpp | 4 evgam-1.0.2/evgam/src/extras.cpp | 13 evgam-1.0.2/evgam/src/gamma3C.cpp |only evgam-1.0.2/evgam/src/gammaC.cpp |only evgam-1.0.2/evgam/src/gaussC.cpp | 4 evgam-1.0.2/evgam/src/gev2C.cpp |only evgam-1.0.2/evgam/src/gevC.cpp | 6 evgam-1.0.2/evgam/src/gevaggC.cpp | 1078 +---------- evgam-1.0.2/evgam/src/gevcC.cpp | 4 evgam-1.0.2/evgam/src/gevrC.cpp |only evgam-1.0.2/evgam/src/gpd2C.cpp |only evgam-1.0.2/evgam/src/gpdC.cpp | 4 evgam-1.0.2/evgam/src/gpdabC.cpp |only evgam-1.0.2/evgam/src/gpdcC.cpp | 4 evgam-1.0.2/evgam/src/gradHess.cpp | 797 ++++++++ evgam-1.0.2/evgam/src/gw.cpp |only evgam-1.0.2/evgam/src/logitgaussC.cpp |only evgam-1.0.2/evgam/src/ltgamma.cpp |only evgam-1.0.2/evgam/src/negbinodC.cpp |only evgam-1.0.2/evgam/src/negbinvarC.cpp |only evgam-1.0.2/evgam/src/poisC.cpp |only evgam-1.0.2/evgam/src/ppC.cpp | 12 evgam-1.0.2/evgam/src/ppexiC.cpp | 8 evgam-1.0.2/evgam/src/rlargeC.cpp |only evgam-1.0.2/evgam/src/rlargecC.cpp |only evgam-1.0.2/evgam/src/shared.h |only evgam-1.0.2/evgam/src/weib3C.cpp |only evgam-1.0.2/evgam/src/weibC.cpp | 249 +- 109 files changed, 7812 insertions(+), 3577 deletions(-)
Title: Marginal Survival Estimation with Covariate Adjustment
Description: Provides an efficient and robust implementation for estimating marginal Hazard Ratio (HR) and
Restricted Mean Survival Time (RMST) with covariate adjustment using Daniel et al. (2021) <doi:10.1002/bimj.201900297> and
Karrison et al. (2018) <doi:10.1177/1740774518759281>.
Author: Xinlei Deng [cre, aut] ,
Mark Baillie [aut] ,
Craig Wang [aut] ,
Dominic Magirr [aut],
Alex Przybylski [aut]
Maintainer: Xinlei Deng <xinlei.deng@novartis.com>
Diff between bunsen versions 0.1.0 dated 2025-05-29 and 0.1.1 dated 2026-09-03
bunsen-0.1.0/bunsen/inst |only bunsen-0.1.1/bunsen/DESCRIPTION | 10 ++++--- bunsen-0.1.1/bunsen/MD5 | 26 ++++++++++-------- bunsen-0.1.1/bunsen/NAMESPACE | 3 ++ bunsen-0.1.1/bunsen/NEWS.md | 6 +++- bunsen-0.1.1/bunsen/R/RcppExports.R | 24 +++++++++++++++++ bunsen-0.1.1/bunsen/R/get_point_estimate.R | 4 +- bunsen-0.1.1/bunsen/R/get_variance_estimation.R | 6 ++-- bunsen-0.1.1/bunsen/R/simulate_counterfactuals.R | 3 -- bunsen-0.1.1/bunsen/README.md | 2 - bunsen-0.1.1/bunsen/build/partial.rdb |binary bunsen-0.1.1/bunsen/man/bunsen-package.Rd | 8 +++++ bunsen-0.1.1/bunsen/man/figures |only bunsen-0.1.1/bunsen/man/firstZeroIndex.Rd |only bunsen-0.1.1/bunsen/man/rbinom_matrix_vec.Rd |only bunsen-0.1.1/bunsen/src/cpp_functions.cpp | 32 +++++++++++++++++++---- 16 files changed, 95 insertions(+), 29 deletions(-)
Title: Native Desktop Application Framework
Description: Build native desktop applications for Windows (with future
support planned for macOS and Linux) using 'R' and embedded 'webviews'.
Provides a robust 'R6'-based event loop, asynchronous background task
management via 'mirai' and 'callr', and a native message bridge for
seamless 'R'-to-user-interface communication without listening ports or
network overhead. Allows 'R' developers to create professional,
standalone desktop tools with modern web-based user interfaces while
maintaining a pure 'R' backend.
Author: Janakiraman G [aut, cre, cph] ,
Serge Zaitsev [cph] ),
Steffen Andre Langnes [cph] ),
Bjoern Hoehrmann [cph] ,
Florian Loitsch [cph] ,
Niels Lohmann [cph] ),
Evan Nemerson [cph] ,
The Abseil Authors [cph] ,
Microsoft Corporation [cph] )
Maintainer: Janakiraman G <janakiraman.bt@gmail.com>
Diff between RDesk versions 1.0.5 dated 2026-04-22 and 1.0.7 dated 2026-09-03
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Title: Distances on Directed Graphs
Description: Distances on dual-weighted directed graphs using
priority-queue shortest paths (Padgham (2019) <doi:10.32866/6945>).
Weighted directed graphs have weights from A to B which may differ
from those from B to A. Dual-weighted directed graphs have two sets
of such weights. A canonical example is a street network to be used
for routing in which routes are calculated by weighting distances
according to the type of way and mode of transport, yet lengths of
routes must be calculated from direct distances.
Author: Mark Padgham [aut, cre],
Andreas Petutschnig [aut],
David Cooley [aut],
Robin Lovelace [ctb],
Andrew Smith [ctb],
Malcolm Morgan [ctb],
Andrea Gilardi [ctb] ,
Eduardo Leoni [ctb] ,
Shane Saunders [cph] ,
Stanislaw Adaszewski [cph] ,
Harry Roberts [ct [...truncated...]
Maintainer: Mark Padgham <mark.padgham@email.com>
Diff between dodgr versions 0.4.3 dated 2025-09-01 and 0.5.0 dated 2026-09-03
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Title: Blocking and Randomization for Experimental Design
Description: Intelligently assign samples to batches in order to reduce batch effects.
Batch effects can have a significant impact on data analysis, especially
when the assignment of samples to batches coincides with the contrast
groups being studied. By defining a batch container and a scoring function
that reflects the contrasts, this package allows users to assign samples in
a way that minimizes the potential impact of batch effects on the
comparison of interest. Among other functionality, we provide an
implementation for OSAT score by Yan et al. (2012,
<doi:10.1186/1471-2164-13-689>).
Author: Iakov I. Davydov [aut, cre, cph] ,
Juliane Siebourg-Polster [aut, cph] ,
Guido Steiner [aut, cph],
Konrad Rudolph [ctb] ,
Jitao David Zhang [aut, cph] ,
Balazs Banfai [aut, cph] ,
F. Hoffman-La Roche [cph, fnd]
Maintainer: Iakov I. Davydov <iakov.davydov@roche.com>
Diff between designit versions 0.5.0 dated 2024-03-21 and 0.5.1 dated 2026-09-03
DESCRIPTION | 22 MD5 | 144 ++-- NEWS.md | 16 R/assignment.R | 4 R/batch_container.R | 7 R/batch_container_dimension.R | 5 R/batch_container_from_table.R | 4 R/optimize.R | 4 R/osat.R | 8 R/plot.R | 4 R/score_plates.R | 15 R/shuffle_samples.R | 8 README.md | 13 build/partial.rdb |binary build/vignette.rds |binary inst/doc/NCS22_talk.R | 22 inst/doc/NCS22_talk.Rmd | 5 inst/doc/NCS22_talk.html | 39 - inst/doc/basic_examples.R | 24 inst/doc/basic_examples.Rmd | 140 +++- inst/doc/basic_examples.html | 657 ++++++++++++---------- inst/doc/custom_shuffle.R | 4 inst/doc/custom_shuffle.Rmd | 5 inst/doc/custom_shuffle.html | 29 inst/doc/false_positives.R |only inst/doc/false_positives.Rmd |only inst/doc/false_positives.html |only inst/doc/invivo_study_design.R | 52 - inst/doc/invivo_study_design.Rmd | 5 inst/doc/invivo_study_design.html | 465 ++++++++------- inst/doc/nested_dimensions_examples.R | 4 inst/doc/nested_dimensions_examples.Rmd | 5 inst/doc/nested_dimensions_examples.html | 23 inst/doc/optimizer_examples.R | 32 - inst/doc/optimizer_examples.Rmd | 5 inst/doc/optimizer_examples.html | 171 +++-- inst/doc/osat.R | 4 inst/doc/osat.Rmd | 5 inst/doc/osat.html | 767 +++++++++++++------------- inst/doc/plate_layouts.html | 26 inst/doc/shuffling_with_constraints.R | 4 inst/doc/shuffling_with_constraints.Rmd | 5 inst/doc/shuffling_with_constraints.html | 33 - man/BatchContainer.Rd | 6 man/BatchContainerDimension.Rd | 4 man/assign_from_table.Rd | 4 man/assign_in_order.Rd | 4 man/assign_random.Rd | 4 man/batch_container_from_table.Rd | 4 man/complete_random_shuffling.Rd | 4 man/examples/assignment.R | 4 man/examples/shuffle_with_constraints.R | 4 man/examples/two_step_optimization.R | 4 man/figures/README-optimized_assignment-1.png |binary man/figures/README-optimized_assignment-2.png |binary man/figures/README-random_assignment-1.png |binary man/mk_plate_scoring_functions.Rd | 4 man/mk_subgroup_shuffling_function.Rd | 4 man/mk_swapping_function.Rd | 4 man/optimize_design.Rd | 4 man/osat_score.Rd | 4 man/osat_score_generator.Rd | 4 man/plot_plate.Rd | 4 man/shuffle_with_constraints.Rd | 4 tests/testthat.R | 3 tests/testthat/test-save-random-seed.R | 8 vignettes/NCS22_talk.Rmd | 5 vignettes/basic_examples.Rmd | 140 +++- vignettes/custom_shuffle.Rmd | 5 vignettes/false_positives.Rmd |only vignettes/invivo_study_design.Rmd | 5 vignettes/nested_dimensions_examples.Rmd | 5 vignettes/optimizer_examples.Rmd | 5 vignettes/osat.Rmd | 5 vignettes/shuffling_with_constraints.Rmd | 5 75 files changed, 1793 insertions(+), 1252 deletions(-)
More information about wishartinference at CRAN
Permanent link
More information about Compositionalasmr at CRAN
Permanent link
Title: Graphics in the Context of Analyzing High-Throughput Data
Description: Additional options for making graphics in the context of analyzing high-throughput data are available here.
This includes automatic segmenting of the current device (eg window) to accommodate multiple new plots,
automatic checking for optimal location of legends in plots, small histograms to insert as legends,
histograms re-transforming axis labels to linear when plotting log2-transformed data,
a violin-plot <doi:10.1080/00031305.1998.10480559> function for a wide variety of input-formats,
principal components analysis (PCA) <doi:10.1080/14786440109462720> with bag-plots <doi:10.1080/00031305.1999.10474494>
to highlight and compare the center areas for groups of samples,
generic MA-plots (differential- versus average-value plots) <doi:10.1093/nar/30.4.e15>,
staggered count plots and generation of mouse-over interactive html pages.
Author: Wolfgang Raffelsberger [aut, cre]
Maintainer: Wolfgang Raffelsberger <w.raffelsberger@gmail.com>
Diff between wrGraph versions 1.3.17 dated 2026-07-29 and 1.3.18 dated 2026-09-03
DESCRIPTION | 8 +++---- MD5 | 13 ++++++------ NEWS.md |only R/plotPCAw.R | 21 +++++++++++++------ R/vioplotW.R | 33 ++++++++++++++++++------------ inst/doc/wrGraphVignette1.html | 44 ++++++++++++++++++++--------------------- man/plotPCAw.Rd | 9 ++++++++ man/vioplotW.Rd | 9 +++++--- 8 files changed, 83 insertions(+), 54 deletions(-)
Title: Item-by-Item Iterative Model Fitting
Description: Models high-dimensional data, such as RNA-seq or proteomic data
using an item-by-item strategy. The package contains functions to wrap
high-dimensional data and iterate over them using established R packages
for regression modelling (e.g., 'glmmTMB' or 'mgcv').
Author: Daniel Hammarstroem [aut, cre, cph] ,
Chidimma Echebiri [ctb]
Maintainer: Daniel Hammarstroem <daniel.hammarstrom@inn.no>
Diff between seqwrap versions 0.7.0 dated 2026-05-19 and 0.8.1 dated 2026-09-03
seqwrap-0.7.0/seqwrap/vignettes/resources |only seqwrap-0.8.1/seqwrap/DESCRIPTION | 19 seqwrap-0.8.1/seqwrap/MD5 | 71 seqwrap-0.8.1/seqwrap/NAMESPACE | 16 seqwrap-0.8.1/seqwrap/NEWS.md | 254 ++ seqwrap-0.8.1/seqwrap/R/data-helper.R | 6 seqwrap-0.8.1/seqwrap/R/data.R | 2 seqwrap-0.8.1/seqwrap/R/generic-summaries.R | 501 ++++- seqwrap-0.8.1/seqwrap/R/seqwrap-chunk.R |only seqwrap-0.8.1/seqwrap/R/seqwrap-global.R | 12 seqwrap-0.8.1/seqwrap/R/seqwrap-priors.R |only seqwrap-0.8.1/seqwrap/R/seqwrap.R | 738 +++++-- seqwrap-0.8.1/seqwrap/R/seqwrap_mtf.R | 112 - seqwrap-0.8.1/seqwrap/build/vignette.rds |binary seqwrap-0.8.1/seqwrap/inst/WORDLIST | 8 seqwrap-0.8.1/seqwrap/inst/doc/fitting-lme4-nlme-models-with-seqwrap.html | 316 +-- seqwrap-0.8.1/seqwrap/inst/doc/fitting-lme4-nlme-models-with-seqwrap.qmd | 4 seqwrap-0.8.1/seqwrap/inst/doc/fitting-models-with-seqwrap.html | 982 ++++------ seqwrap-0.8.1/seqwrap/inst/doc/migrating-from-seqwrap-0-7.R |only seqwrap-0.8.1/seqwrap/inst/doc/migrating-from-seqwrap-0-7.html |only seqwrap-0.8.1/seqwrap/inst/doc/migrating-from-seqwrap-0-7.qmd |only seqwrap-0.8.1/seqwrap/man/dispersion_evaluation.Rd |only seqwrap-0.8.1/seqwrap/man/dungan_counts.Rd | 2 seqwrap-0.8.1/seqwrap/man/generic_evaluation.Rd | 81 seqwrap-0.8.1/seqwrap/man/plot.seqwrap_priors.Rd |only seqwrap-0.8.1/seqwrap/man/print.seqwrapResults.Rd | 12 seqwrap-0.8.1/seqwrap/man/print.seqwrap_priors.Rd |only seqwrap-0.8.1/seqwrap/man/residual_diagnostics.Rd |only seqwrap-0.8.1/seqwrap/man/seqwrap.Rd | 72 seqwrap-0.8.1/seqwrap/man/seqwrapResults.Rd | 26 seqwrap-0.8.1/seqwrap/man/seqwrap_cache_clear.Rd |only seqwrap-0.8.1/seqwrap/man/seqwrap_compose.Rd | 36 seqwrap-0.8.1/seqwrap/man/seqwrap_errors.Rd |only seqwrap-0.8.1/seqwrap/man/seqwrap_priors.Rd |only seqwrap-0.8.1/seqwrap/man/seqwrap_summarise.Rd | 43 seqwrap-0.8.1/seqwrap/man/swcontainer.Rd | 18 seqwrap-0.8.1/seqwrap/tests/testthat/test-conditions.R |only seqwrap-0.8.1/seqwrap/tests/testthat/test-generic-evaluation.R |only seqwrap-0.8.1/seqwrap/tests/testthat/test-seqwrap-cache.R |only seqwrap-0.8.1/seqwrap/tests/testthat/test-seqwrap-contract.R |only seqwrap-0.8.1/seqwrap/tests/testthat/test-seqwrap-inputs.R |only seqwrap-0.8.1/seqwrap/tests/testthat/test-seqwrap-priors.R |only seqwrap-0.8.1/seqwrap/tests/testthat/test-seqwrap-targetdata.R | 99 - seqwrap-0.8.1/seqwrap/tests/testthat/test-seqwrap.R | 499 ++--- seqwrap-0.8.1/seqwrap/tests/testthat/test-summarise-warnings.R |only seqwrap-0.8.1/seqwrap/vignettes/fitting-lme4-nlme-models-with-seqwrap.qmd | 4 seqwrap-0.8.1/seqwrap/vignettes/migrating-from-seqwrap-0-7.qmd |only 47 files changed, 2599 insertions(+), 1334 deletions(-)
Title: Multiple Imputation with 'MIDAS2' Denoising Autoencoders
Description: Fits 'MIDAS' denoising autoencoder models for multiple
imputation of missing data, generates multiply-imputed datasets,
computes imputation means, and runs Rubin's rules regression analysis.
Wraps the 'MIDAS2' 'Python' engine via a local 'FastAPI' server over
'HTTP', so no 'reticulate' dependency is needed at runtime. Methods are
described in Lall and Robinson (2022) <doi:10.1017/pan.2020.49> and
Lall and Robinson (2023) <doi:10.18637/jss.v107.i09>.
Author: Thomas Robinson [aut, cre],
Ranjit Lall [aut]
Maintainer: Thomas Robinson <t.robinson7@lse.ac.uk>
Diff between rMIDAS2 versions 0.1.1 dated 2026-03-12 and 0.2.0 dated 2026-09-03
DESCRIPTION | 8 MD5 | 43 +- NEWS.md | 71 ++++ R/client.R | 561 ++++++++++++++++++++++++++-------- R/zzz.R | 7 build/partial.rdb |binary build/vignette.rds |binary inst/doc/migrating-from-rMIDAS.R |only inst/doc/migrating-from-rMIDAS.Rmd |only inst/doc/migrating-from-rMIDAS.html |only man/capture_col_meta.Rd |only man/check_arrow_available.Rd |only man/get_json.Rd | 4 man/has_categorical.Rd |only man/midas.Rd | 6 man/midas_col_meta_registry.Rd |only man/midas_fit.Rd | 34 +- man/midas_transform.Rd | 26 + man/parse_table.Rd | 14 man/post_json.Rd | 5 man/post_parquet.Rd |only man/prepare_categorical.Rd |only man/rMIDAS2-package.Rd | 1 man/restore_col_types.Rd |only man/restore_observed.Rd |only man/to_nested_list.Rd | 9 man/train_params.Rd |only tests/testthat/test-column-types.R |only tests/testthat/test-observed-values.R |only vignettes/migrating-from-rMIDAS.Rmd |only 30 files changed, 626 insertions(+), 163 deletions(-)
Title: Repair Malformed JSON Strings
Description: Repairs malformed JSON strings, particularly those generated by
Large Language Models. Handles missing quotes, trailing commas, unquoted
keys, and other common JSON syntax errors.
Author: Dyfan Jones [aut, cre]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>
Diff between llmjson versions 0.1.0 dated 2026-03-11 and 0.2.1 dated 2026-09-03
DESCRIPTION | 10 +-- MD5 | 33 +++++------ NEWS.md | 18 ++++++ R/extendr-wrappers.R | 18 ++++-- README.md | 1 configure | 2 src/Makevars.in | 30 ++++++---- src/Makevars.win.in | 58 +++++++++++++------ src/entrypoint.c | 2 src/rust/Cargo.lock | 114 ++++++++++++++++++++++++-------------- src/rust/Cargo.toml | 12 ++-- src/rust/document.rs |only src/rust/src/lib.rs | 31 ++++------ src/rust/src/llm_json.rs | 8 -- src/rust/vendor.tar.xz |binary tests/testthat/test-repair_json.R | 45 ++++++++------- tools/config.R | 59 ++++++++++++++++++- tools/msrv.R | 8 ++ 18 files changed, 292 insertions(+), 157 deletions(-)
Title: Highly Performant String Case Converter
Description: Provides a case conversion between common cases like CamelCase and
snake_case. Using the 'rust crate heck' <https://github.com/withoutboats/heck>
as the backend for a highly performant case conversion for 'R'.
Author: Josiah Parry [aut] ,
Dyfan Jones [cre]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>
Diff between heck versions 0.1.5 dated 2025-04-17 and 0.1.7 dated 2026-09-03
DESCRIPTION | 10 +++--- MD5 | 31 ++++++++++---------- NEWS.md | 11 +++++++ R/extendr-wrappers.R | 6 ---- README.md | 28 ------------------ configure | 2 - src/Makevars.in | 30 ++++++++++++-------- src/Makevars.win.in | 28 +++++++++++++----- src/entrypoint.c | 2 + src/rust/Cargo.lock | 73 +++++++++++++++++++++++++++++++------------------ src/rust/Cargo.toml | 10 ++++-- src/rust/document.rs |only src/rust/src/lib.rs | 4 +- src/rust/vendor.tar.xz |binary tests/spelling.R | 10 ++++-- tools/config.R | 59 ++++++++++++++++++++++++++++++++++++--- tools/msrv.R | 8 ++++- 17 files changed, 198 insertions(+), 114 deletions(-)
Title: Species Range Mapping from GBIF Using Ecoregion Constraints
Description: A user-friendly, end-to-end workflow to generate ecologically
informed species range maps from sparse observations using environmental
clustering and convex hulls. Serves as a standalone framework or
complementary approach to Species Distribution Models (SDMs). By
constraining estimated ranges within authoritative or custom ecoregion
boundaries, the approach prevents spurious range over-prediction common in
geometric hull methods. The package automates data acquisition via 'GBIF'
synonym-aware, tiled downloads; curates records using 13 configurable
filters; and supports multi-scale analysis by integrating global or
user-provided spatial layers. Also includes disk-based batch processing for
large-scale studies and built-in tools for cross-validation and
expert-derived evaluations.
Author: Yohann Chauvier [cre, aut] ,
Oskar Hagen [aut] ,
Stefan Pinkert [aut] ,
Camille Albouy [aut] ,
Fabian Fopp [aut] ,
Philipp Brun [aut] ,
Patrice Descombes [aut] ,
Florian Altermatt [aut] ,
Loic Pellissier [aut] ,
Katalin Csillery [aut]
Maintainer: Yohann Chauvier <yohann.chauvier@wsl.ch>
Diff between gbif.range versions 1.9.1 dated 2026-08-07 and 1.9.2 dated 2026-09-03
DESCRIPTION | 35 ++++----- MD5 | 18 ++--- NEWS.md | 148 +++++++++++++++++++----------------------- R/get_status.R | 22 ++++-- R/helpers.R | 9 ++ README.md | 33 ++++++--- inst/doc/getting-started.Rmd | 2 inst/doc/getting-started.html | 2 man/get_status.Rd | 5 + vignettes/getting-started.Rmd | 2 10 files changed, 147 insertions(+), 129 deletions(-)
Title: Forecasting Using State Space Models
Description: Functions implementing Single Source of Error state space models for purposes of time series analysis and forecasting.
The package includes ADAM (Svetunkov, 2023, <https://openforecast.org/adam/>),
Exponential Smoothing (Hyndman et al., 2008, <doi:10.1007/978-3-540-71918-2>),
SARIMA (Svetunkov & Boylan, 2019 <doi: 10.1080/00207543.2019.1600764>),
Complex Exponential Smoothing (Svetunkov & Kourentzes, 2018, <doi:10.13140/RG.2.2.24986.29123>),
Simple Moving Average (Svetunkov & Petropoulos, 2018 <doi:10.1080/00207543.2017.1380326>)
and several simulation functions. It also allows dealing with intermittent demand based on the
iETS framework (Svetunkov & Boylan, 2019, <doi:10.13140/RG.2.2.35897.06242>).
Author: Ivan Svetunkov [aut, cre]
Maintainer: Ivan Svetunkov <ivan@svetunkov.com>
Diff between smooth versions 4.5.0 dated 2026-06-21 and 4.5.1 dated 2026-09-03
DESCRIPTION | 19 MD5 | 150 ++--- NAMESPACE | 2 NEWS | 178 +++--- R/adam-ces.R | 169 ++++- R/adam-es.R | 14 R/adam-gradient.R |only R/adam-gum.R | 124 ++-- R/adam-msarima.R | 2 R/adam-sma.R | 36 - R/adam-ssarima.R | 80 +- R/adam.R | 438 ++++++++++---- R/adamGeneral.R | 31 - R/auto-om.R | 2 R/autoadam.R | 3 R/autoces.R | 2 R/autogum.R | 2 R/automsarima.R | 2 R/autossarima.R | 2 R/globals.R | 1 R/helper.R | 880 +++++++++++++++++++++++------ R/oesg.R | 10 R/om-oes.R | 10 R/om.R | 196 +++++- R/omg.R | 234 ++++++- R/reapply.R | 65 +- R/simces.R | 2 R/simes.R | 2 R/simgum.R | 2 R/simssarima.R | 2 R/sm.R | 31 - R/smooth-package.R | 2 R/smoothCombine.R | 2 R/sparma.R | 98 ++- R/utils-adam.R | 192 ++++-- R/zzz.R | 2 README.md | 29 build/partial.rdb |binary build/vignette.rds |binary inst/doc/adam.html | 445 +++++++-------- inst/doc/ces.html | 26 inst/doc/es.html | 88 +- inst/doc/gum.html | 42 - inst/doc/oes.html | 88 +- inst/doc/om.html | 74 +- inst/doc/simulate.html | 16 inst/doc/sma.R | 2 inst/doc/sma.Rmd | 2 inst/doc/sma.html | 27 inst/doc/smooth.html | 4 inst/doc/ssarima.html | 75 +- man/adam.Rd | 38 - man/auto.om.Rd | 2 man/ces.Rd | 12 man/es.Rd | 21 man/gum.Rd | 4 man/msarima.Rd | 4 man/oes.Rd | 13 man/oesg.Rd | 15 man/om.Rd | 17 man/omg.Rd | 14 man/reapply.Rd | 23 man/smoothCombine.Rd | 2 man/sparma.Rd | 2 man/ssarima.Rd | 4 src/adamGeneral.cpp | 11 src/headers/adamCore.h | 1213 ++++++++++++++++++++++++++++++++++++++--- src/headers/adamGradient.h |only src/python/adamPython.cpp | 59 + tests/testthat/test_autoadam.R | 28 tests/testthat/test_ces.R | 36 + tests/testthat/test_df.R |only tests/testthat/test_gradient.R |only tests/testthat/test_om.R | 45 + tests/testthat/test_omg.R | 15 tests/testthat/test_simulate.R | 19 tests/testthat/test_sma.R |only tests/testthat/test_vcov_opg.R |only vignettes/sma.Rmd | 2 79 files changed, 4062 insertions(+), 1442 deletions(-)
Title: Prevalence to Incidence Calculations for Point-Prevalence
Studies in a Nosocomial Setting
Description: Functions to simulate point prevalence studies (PPSs) of healthcare-associated infections (HAIs) and to convert prevalence to incidence in steady state setups.
Companion package to the preprint Willrich et al., From prevalence to incidence - a new approach in the hospital setting;
<doi:10.1101/554725> , where methods are explained in detail.
Author: Niklas Willrich [aut, cre]
Maintainer: Niklas Willrich <WillrichN@rki.de>
Diff between prevtoinc versions 0.12.0 dated 2019-06-18 and 0.12.1 dated 2026-09-03
prevtoinc-0.12.0/prevtoinc/man/prevtoinc.Rd |only prevtoinc-0.12.1/prevtoinc/DESCRIPTION | 10 prevtoinc-0.12.1/prevtoinc/MD5 | 34 prevtoinc-0.12.1/prevtoinc/NEWS.md | 6 prevtoinc-0.12.1/prevtoinc/R/CIfunctions.R | 14 prevtoinc-0.12.1/prevtoinc/R/calculateIfunctions.R | 57 prevtoinc-0.12.1/prevtoinc/R/prevtoinc.R | 4 prevtoinc-0.12.1/prevtoinc/R/simulationsfunctions.R | 4 prevtoinc-0.12.1/prevtoinc/build/vignette.rds |binary prevtoinc-0.12.1/prevtoinc/inst/doc/prevtoinc_vignette.R | 32 prevtoinc-0.12.1/prevtoinc/inst/doc/prevtoinc_vignette.html | 868 ++++++++---- prevtoinc-0.12.1/prevtoinc/man/calculate_CI_I_pp.Rd | 17 prevtoinc-0.12.1/prevtoinc/man/calculate_I_mixed.Rd | 22 prevtoinc-0.12.1/prevtoinc/man/calculate_I_rhame.Rd | 19 prevtoinc-0.12.1/prevtoinc/man/calculate_I_smooth.Rd | 27 prevtoinc-0.12.1/prevtoinc/man/generate_I_fast.Rd | 11 prevtoinc-0.12.1/prevtoinc/man/prevtoinc-package.Rd |only prevtoinc-0.12.1/prevtoinc/man/simulate_incidence_stats.Rd | 7 prevtoinc-0.12.1/prevtoinc/man/simulate_pps_fast.Rd | 10 19 files changed, 764 insertions(+), 378 deletions(-)
Title: Run Python, Julia, and Rust Inside 'targets' Pipeline Steps
Description: Adds target constructors that make it easy to use Python, Julia, and
Rust inside a 'targets' pipeline using 'reticulate', 'JuliaCall', and 'rextendr'.
Provides tar_target_py(), tar_target_jl(), and tar_target_rs() (with matching
_raw() variants), each mirroring 'targets::tar_target()' and
'targets::tar_target_raw()'. Python and Julia steps run a script via a live
interpreter with optional R pre- and post-scripts; Rust steps compile
'#[extendr]' functions and call them from an R post-script. Results are
returned either as converted R objects or as files written to disk
(format = "file"). Dynamic branching, environment/version selection, a
'crew' controller for isolation, and the full set of tar_target_raw()
arguments are supported.
Author: Pierre Solomon [aut, cre]
Maintainer: Pierre Solomon <pierre.solomon@laposte.net>
Diff between tarpolyglot versions 0.2.0 dated 2026-08-08 and 0.2.1 dated 2026-09-03
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 7 +++++++ R/crew.R | 36 +++++++++++++++++++++++++++++++----- man/polyglot_controller.Rd | 2 ++ tests/testthat/test-crew.R | 43 +++++++++++++++++++++++++++++++++++++++++++ 6 files changed, 92 insertions(+), 14 deletions(-)
Title: Spherical Geometry Operators Using the S2 Geometry Library
Description: Provides R bindings for Google's s2 library for geometric calculations on
the sphere. High-performance constructors and exporters provide high compatibility
with existing spatial packages, transformers construct new geometries from existing
geometries, predicates provide a means to select geometries based on spatial
relationships, and accessors extract information about geometries.
Author: Dewey Dunnington [aut] ,
Edzer Pebesma [aut, cre] ,
Ege Rubak [aut],
Jeroen Ooms [ctb] ,
Google, Inc. [cph]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between s2 versions 1.1.11 dated 2026-06-01 and 1.1.12 dated 2026-09-03
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- build/partial.rdb |binary configure | 8 ++++++-- tools/vendor/abseil-cpp/absl/container/internal/raw_hash_set.h | 2 +- 5 files changed, 14 insertions(+), 10 deletions(-)
Title: Load Data in SQLite from Tabular Files
Description: A lightweight wrapper around the 'RSQLite' package for streamlined loading of
data from tabular files (i,e. delimited text files like Comma Separated Values and
Tab Separated Values, Microsoft Excel, and Arrow Inter-process Communication files)
in 'SQLite' databases. Includes helper functions for inspecting the structure of
the input files, and some functions to simplify activities on the 'SQLite' tables.
Author: Ludovico G. Beretta [aut, cre, cph]
Maintainer: Ludovico G. Beretta <ludovicogiovanni.beretta@gmail.com>
Diff between RSQLite.toolkit versions 0.1.4 dated 2026-09-02 and 0.1.5 dated 2026-09-03
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 4 ++++ man/dbTableFromXlsx.Rd | 3 ++- 4 files changed, 13 insertions(+), 8 deletions(-)
More information about RSQLite.toolkit at CRAN
Permanent link
Title: Predictions, Comparisons, Slopes, Marginal Means, and Hypothesis
Tests
Description: Compute and plot predictions, slopes, marginal means, and comparisons (contrasts, risk ratios, odds, etc.) for over 100 classes of statistical and machine learning models in R. Conduct linear and non-linear hypothesis tests, or equivalence tests. Calculate uncertainty estimates using the delta method, bootstrapping, or simulation-based inference. Details can be found in Arel-Bundock, Greifer, and Heiss (2024) <doi:10.18637/jss.v111.i09>.
Author: Vincent Arel-Bundock [aut, cre, cph] ,
Noah Greifer [ctb] ,
Etienne Bacher [ctb] ,
Grant McDermott [ctb] ,
Andrew Heiss [ctb]
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Diff between marginaleffects versions 0.32.0 dated 2026-02-14 and 1.0.0 dated 2026-09-03
marginaleffects-0.32.0/marginaleffects/R/autodiff.R |only marginaleffects-0.32.0/marginaleffects/R/get_comparisons.R |only marginaleffects-0.32.0/marginaleffects/R/get_predictions.R |only marginaleffects-0.32.0/marginaleffects/R/github_issue.R |only marginaleffects-0.32.0/marginaleffects/R/sanity_by.R |only marginaleffects-0.32.0/marginaleffects/man/autodiff.Rd |only marginaleffects-0.32.0/marginaleffects/tests |only marginaleffects-1.0.0/marginaleffects/DESCRIPTION | 134 +-- marginaleffects-1.0.0/marginaleffects/MD5 | 278 +++---- marginaleffects-1.0.0/marginaleffects/NAMESPACE | 67 + marginaleffects-1.0.0/marginaleffects/NEWS.md | 83 ++ marginaleffects-1.0.0/marginaleffects/R/add_hypothesis.R | 4 marginaleffects-1.0.0/marginaleffects/R/backtransform.R | 26 marginaleffects-1.0.0/marginaleffects/R/broom.R | 2 marginaleffects-1.0.0/marginaleffects/R/by.R | 89 +- marginaleffects-1.0.0/marginaleffects/R/class.R | 58 + marginaleffects-1.0.0/marginaleffects/R/comparisons.R | 366 ++------- marginaleffects-1.0.0/marginaleffects/R/comparisons_plan.R |only marginaleffects-1.0.0/marginaleffects/R/comparisons_plan_bayesian.R |only marginaleffects-1.0.0/marginaleffects/R/comparisons_plan_frequentist.R |only marginaleffects-1.0.0/marginaleffects/R/datagrid.R | 76 + marginaleffects-1.0.0/marginaleffects/R/equivalence.R | 11 marginaleffects-1.0.0/marginaleffects/R/get_ci.R | 68 + marginaleffects-1.0.0/marginaleffects/R/get_comparisons_data.R | 34 marginaleffects-1.0.0/marginaleffects/R/get_comparisons_data_character.R | 2 marginaleffects-1.0.0/marginaleffects/R/get_comparisons_data_factor.R | 87 -- marginaleffects-1.0.0/marginaleffects/R/get_comparisons_data_logical.R | 19 marginaleffects-1.0.0/marginaleffects/R/get_comparisons_data_numeric.R | 36 marginaleffects-1.0.0/marginaleffects/R/get_dataset.R | 4 marginaleffects-1.0.0/marginaleffects/R/get_degrees_of_freedom.R | 25 marginaleffects-1.0.0/marginaleffects/R/get_draws.R | 42 - 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marginaleffects-1.0.0/marginaleffects/R/methods_lme4.R | 2 marginaleffects-1.0.0/marginaleffects/R/methods_mclogit.R | 6 marginaleffects-1.0.0/marginaleffects/R/methods_mhurdle.R | 27 marginaleffects-1.0.0/marginaleffects/R/methods_mice.R | 5 marginaleffects-1.0.0/marginaleffects/R/methods_mlogit.R | 1 marginaleffects-1.0.0/marginaleffects/R/methods_mmrm.R |only marginaleffects-1.0.0/marginaleffects/R/methods_nestedLogit.R |only marginaleffects-1.0.0/marginaleffects/R/methods_nnet.R | 31 marginaleffects-1.0.0/marginaleffects/R/methods_ordinal.R | 187 ++++ marginaleffects-1.0.0/marginaleffects/R/methods_plm.R | 13 marginaleffects-1.0.0/marginaleffects/R/methods_pscl.R | 2 marginaleffects-1.0.0/marginaleffects/R/methods_quantreg.R | 53 - marginaleffects-1.0.0/marginaleffects/R/methods_rms.R | 138 +-- marginaleffects-1.0.0/marginaleffects/R/methods_robustlmm.R | 2 marginaleffects-1.0.0/marginaleffects/R/methods_stats.R |only marginaleffects-1.0.0/marginaleffects/R/methods_survey.R | 38 marginaleffects-1.0.0/marginaleffects/R/methods_survival.R | 14 marginaleffects-1.0.0/marginaleffects/R/methods_svyVGAM.R |only marginaleffects-1.0.0/marginaleffects/R/methods_systemfit.R | 29 marginaleffects-1.0.0/marginaleffects/R/methods_tobit1.R | 2 marginaleffects-1.0.0/marginaleffects/R/multcomp.R | 40 - marginaleffects-1.0.0/marginaleffects/R/package.R | 9 marginaleffects-1.0.0/marginaleffects/R/pad.R | 4 marginaleffects-1.0.0/marginaleffects/R/plan_replay.R |only marginaleffects-1.0.0/marginaleffects/R/plot_build.R | 34 marginaleffects-1.0.0/marginaleffects/R/plot_comparisons.R | 1 marginaleffects-1.0.0/marginaleffects/R/plot_predictions.R | 6 marginaleffects-1.0.0/marginaleffects/R/plot_slopes.R | 1 marginaleffects-1.0.0/marginaleffects/R/predictions.R | 397 +++------- marginaleffects-1.0.0/marginaleffects/R/predictions_plan.R |only marginaleffects-1.0.0/marginaleffects/R/predictions_plan_bayesian.R |only marginaleffects-1.0.0/marginaleffects/R/predictions_plan_frequentist.R |only marginaleffects-1.0.0/marginaleffects/R/print.R | 25 marginaleffects-1.0.0/marginaleffects/R/refit.R | 27 marginaleffects-1.0.0/marginaleffects/R/sanitize_by.R |only marginaleffects-1.0.0/marginaleffects/R/sanitize_comparison.R | 160 +++- marginaleffects-1.0.0/marginaleffects/R/sanitize_hypothesis_formula.R | 6 marginaleffects-1.0.0/marginaleffects/R/sanitize_interaction.R | 16 marginaleffects-1.0.0/marginaleffects/R/sanitize_newdata.R | 104 -- marginaleffects-1.0.0/marginaleffects/R/sanitize_numderiv.R | 2 marginaleffects-1.0.0/marginaleffects/R/sanitize_reserved.R | 2 marginaleffects-1.0.0/marginaleffects/R/sanitize_variables.R | 190 ++-- marginaleffects-1.0.0/marginaleffects/R/sanitize_vcov.R | 61 + marginaleffects-1.0.0/marginaleffects/R/sanity_dots.R | 8 marginaleffects-1.0.0/marginaleffects/R/sanity_inferences.R | 2 marginaleffects-1.0.0/marginaleffects/R/sanity_model.R | 22 marginaleffects-1.0.0/marginaleffects/R/settings.R | 50 - marginaleffects-1.0.0/marginaleffects/R/slopes.R | 19 marginaleffects-1.0.0/marginaleffects/R/sort.R | 7 marginaleffects-1.0.0/marginaleffects/R/tinytest.R | 13 marginaleffects-1.0.0/marginaleffects/R/type_dictionary.R | 14 marginaleffects-1.0.0/marginaleffects/R/utils.R | 178 +++- marginaleffects-1.0.0/marginaleffects/R/vcov_unconditional.R |only marginaleffects-1.0.0/marginaleffects/R/vcov_unconditional_sanitization.R |only marginaleffects-1.0.0/marginaleffects/R/zzz.R | 10 marginaleffects-1.0.0/marginaleffects/build/partial.rdb |binary marginaleffects-1.0.0/marginaleffects/build/vignette.rds |binary marginaleffects-1.0.0/marginaleffects/inst/WORDLIST | 208 ++--- marginaleffects-1.0.0/marginaleffects/man/comparisons.Rd | 44 - marginaleffects-1.0.0/marginaleffects/man/datagrid.Rd | 6 marginaleffects-1.0.0/marginaleffects/man/get_coef.Rd | 28 marginaleffects-1.0.0/marginaleffects/man/get_dataset.Rd | 4 marginaleffects-1.0.0/marginaleffects/man/get_group_names.Rd | 11 marginaleffects-1.0.0/marginaleffects/man/get_model_matrix.Rd | 42 - 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More information about marginaleffects at CRAN
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Title: File IO for Intracranial Electroencephalography
Description: Integrated toolbox supporting common file formats used for intracranial
Electroencephalography (iEEG) and deep-brain stimulation (DBS) study.
Author: Zhengjia Wang [aut, cre]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>
Diff between ieegio versions 0.1.0 dated 2026-05-31 and 0.1.2 dated 2026-09-03
ieegio-0.1.0/ieegio/tests/testthat/testthat-problems.rds |only ieegio-0.1.2/ieegio/DESCRIPTION | 21 ieegio-0.1.2/ieegio/MD5 | 100 - ieegio-0.1.2/ieegio/NAMESPACE | 53 ieegio-0.1.2/ieegio/NEWS.md | 23 ieegio-0.1.2/ieegio/R/aaa-generics-colormap.R |only ieegio-0.1.2/ieegio/R/aaa-generics-streamlines.R | 41 ieegio-0.1.2/ieegio/R/aaa-generics-surface.R | 56 ieegio-0.1.2/ieegio/R/aaa-generics-volume.R | 2 ieegio-0.1.2/ieegio/R/as_ieegio_roi.R |only ieegio-0.1.2/ieegio/R/as_ieegio_surface.R | 106 + ieegio-0.1.2/ieegio/R/as_ieegio_volume.R | 12 ieegio-0.1.2/ieegio/R/colormap.R |only ieegio-0.1.2/ieegio/R/file_system.R | 7 ieegio-0.1.2/ieegio/R/gifti.R | 4 ieegio-0.1.2/ieegio/R/hdf5-class.R | 1220 ++++++++++----- ieegio-0.1.2/ieegio/R/hdf5.R | 232 +- ieegio-0.1.2/ieegio/R/math-collision.R |only ieegio-0.1.2/ieegio/R/math-curve.R | 12 ieegio-0.1.2/ieegio/R/math-tube.R |only ieegio-0.1.2/ieegio/R/math-volume.R | 42 ieegio-0.1.2/ieegio/R/niml.R |only ieegio-0.1.2/ieegio/R/stl.R | 6 ieegio-0.1.2/ieegio/R/utils-vol2surf_atlas.R |only ieegio-0.1.2/ieegio/R/vtk.R | 446 +++++ ieegio-0.1.2/ieegio/README.md | 248 ++- ieegio-0.1.2/ieegio/build/vignette.rds |binary ieegio-0.1.2/ieegio/inst/doc/read-ephys.R | 31 ieegio-0.1.2/ieegio/inst/doc/read-ephys.Rmd | 45 ieegio-0.1.2/ieegio/inst/doc/read-ephys.html | 42 ieegio-0.1.2/ieegio/inst/doc/read-imaging-data.R | 57 ieegio-0.1.2/ieegio/inst/doc/read-imaging-data.Rmd | 95 + ieegio-0.1.2/ieegio/inst/doc/read-imaging-data.html | 94 + ieegio-0.1.2/ieegio/inst/sample_data_registry.txt | 8 ieegio-0.1.2/ieegio/man/LazyH5.Rd | 3 ieegio-0.1.2/ieegio/man/as_ieegio_colormap.Rd |only ieegio-0.1.2/ieegio/man/as_ieegio_colortable.Rd |only ieegio-0.1.2/ieegio/man/as_ieegio_lookup.Rd |only ieegio-0.1.2/ieegio/man/as_ieegio_roi.Rd |only ieegio-0.1.2/ieegio/man/as_ieegio_surface.Rd | 7 ieegio-0.1.2/ieegio/man/burn_curve.Rd | 2 ieegio-0.1.2/ieegio/man/calculate_color.Rd |only ieegio-0.1.2/ieegio/man/colorspace_from_rgb.Rd |only ieegio-0.1.2/ieegio/man/detect_roi_overlap.Rd |only ieegio-0.1.2/ieegio/man/imaging-streamlines.Rd | 10 ieegio-0.1.2/ieegio/man/imaging-surface.Rd | 19 ieegio-0.1.2/ieegio/man/io-vtk-polys.Rd |only ieegio-0.1.2/ieegio/man/io_h5_valid.Rd | 17 ieegio-0.1.2/ieegio/man/io_read_h5.Rd | 5 ieegio-0.1.2/ieegio/man/io_read_niml.Rd |only ieegio-0.1.2/ieegio/man/io_write_h5.Rd | 3 ieegio-0.1.2/ieegio/man/plot_ieegio_colormap.Rd |only ieegio-0.1.2/ieegio/man/read_colormap.Rd |only ieegio-0.1.2/ieegio/man/resolve_roi_as.Rd |only ieegio-0.1.2/ieegio/man/write_colormap.Rd |only ieegio-0.1.2/ieegio/tests/testthat/setup.R | 27 ieegio-0.1.2/ieegio/tests/testthat/test-colormap.R |only ieegio-0.1.2/ieegio/tests/testthat/test-hdf5.R | 856 ++++++++++ ieegio-0.1.2/ieegio/tests/testthat/test-niml.R |only ieegio-0.1.2/ieegio/tests/testthat/test-roi-overlap.R |only ieegio-0.1.2/ieegio/tests/testthat/test-roi-resolve.R |only ieegio-0.1.2/ieegio/tests/testthat/test-vtk-polys.R |only ieegio-0.1.2/ieegio/vignettes/read-ephys.Rmd | 45 ieegio-0.1.2/ieegio/vignettes/read-imaging-data.Rmd | 95 + 64 files changed, 3545 insertions(+), 547 deletions(-)
Title: Matrix Normal Distribution
Description: Density computation, random matrix generation, maximum likelihood estimation, and regression for the matrix normal distribution. References: Pocuca N., Gallaugher M. P., Clark K. M. & McNicholas P. D. (2019). Assessing and Visualizing Matrix Variate Normality. <doi:10.48550/arXiv.1910.02859> and the relevant wikipedia page.
Author: Michail Tsagris [aut, cre],
Alzeley Omar [ctb]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between MN versions 1.1 dated 2026-03-27 and 1.2 dated 2026-09-03
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++++++----- NAMESPACE | 8 +++----- R/mn.equaltest.R |only R/mn.mle.R | 27 +++++++++++++++------------ R/mn.reg.R |only R/mn.reg2.R |only R/mn.reg_null.R |only R/mn.ttest.R |only man/MN-package.Rd | 4 ++-- man/mn.equaltest.Rd |only man/mn.mle.Rd | 20 +++++++++++++------- man/mn.reg.Rd |only man/mn.ttest.Rd |only 14 files changed, 51 insertions(+), 36 deletions(-)
Title: São Paulo Metro Passenger Demand Data
Description: Provides passenger demand data for the São Paulo metro system,
covering 2012 to 2026. Datasets include monthly passenger entries and
transported counts by line, average weekday station entries, daily
station entries, and spatial geometries for metro and commuter train
lines and stations. The bundled datasets are a fixed snapshot, so
analyses stay reproducible and examples run offline; more recent data is
published separately as the upstream sources are updated.
Author: Vinicius Oike [aut, cre, cph]
Maintainer: Vinicius Oike <viniciusoike@gmail.com>
Diff between metrosp versions 1.0.0 dated 2026-05-05 and 1.2.1 dated 2026-09-03
metrosp-1.0.0/metrosp/data/metro_lines.rda |only metrosp-1.0.0/metrosp/man/metro_lines.Rd |only metrosp-1.2.1/metrosp/DESCRIPTION | 30 metrosp-1.2.1/metrosp/MD5 | 71 + metrosp-1.2.1/metrosp/NEWS.md | 203 +++- metrosp-1.2.1/metrosp/R/cache.R |only metrosp-1.2.1/metrosp/R/data.R | 422 +++++++--- metrosp-1.2.1/metrosp/R/read_metro_demand.R |only metrosp-1.2.1/metrosp/README.md | 127 ++- metrosp-1.2.1/metrosp/build/vignette.rds |binary metrosp-1.2.1/metrosp/data/calendar_spo.rda |only metrosp-1.2.1/metrosp/data/lines.rda |binary metrosp-1.2.1/metrosp/data/passengers_entrance.rda |binary metrosp-1.2.1/metrosp/data/passengers_transported.rda |binary metrosp-1.2.1/metrosp/data/station_averages.rda |binary metrosp-1.2.1/metrosp/data/station_daily.rda |binary metrosp-1.2.1/metrosp/data/station_inauguration.rda |only metrosp-1.2.1/metrosp/data/stations.rda |binary metrosp-1.2.1/metrosp/inst/WORDLIST | 89 +- metrosp-1.2.1/metrosp/inst/doc/data-dictionary.R |only metrosp-1.2.1/metrosp/inst/doc/data-dictionary.html |only metrosp-1.2.1/metrosp/inst/doc/data-dictionary.qmd |only metrosp-1.2.1/metrosp/inst/doc/getting_started.R | 2 metrosp-1.2.1/metrosp/inst/doc/getting_started.html | 96 +- metrosp-1.2.1/metrosp/inst/doc/getting_started.qmd | 34 metrosp-1.2.1/metrosp/man/calendar_spo.Rd |only metrosp-1.2.1/metrosp/man/figures/metro_plot.png |only metrosp-1.2.1/metrosp/man/figures/timespan_passengers_entrance.png |only metrosp-1.2.1/metrosp/man/figures/timespan_passengers_transported.png |only metrosp-1.2.1/metrosp/man/figures/timespan_station_averages.png |only metrosp-1.2.1/metrosp/man/figures/timespan_station_daily.png |only metrosp-1.2.1/metrosp/man/lines.Rd | 12 metrosp-1.2.1/metrosp/man/metro_colors.Rd | 14 metrosp-1.2.1/metrosp/man/passengers_entrance.Rd | 88 +- metrosp-1.2.1/metrosp/man/passengers_transported.Rd | 89 +- metrosp-1.2.1/metrosp/man/station_averages.Rd | 68 + metrosp-1.2.1/metrosp/man/station_daily.Rd | 55 - metrosp-1.2.1/metrosp/man/station_inauguration.Rd |only metrosp-1.2.1/metrosp/man/stations.Rd | 12 metrosp-1.2.1/metrosp/tests/testthat/helper-checks.R |only metrosp-1.2.1/metrosp/tests/testthat/test-cache.R |only metrosp-1.2.1/metrosp/tests/testthat/test-dashboard-helpers.R |only metrosp-1.2.1/metrosp/tests/testthat/test-datasets.R | 155 --- metrosp-1.2.1/metrosp/tests/testthat/test-geo-datasets.R | 5 metrosp-1.2.1/metrosp/tests/testthat/test-read-metro-demand.R |only metrosp-1.2.1/metrosp/vignettes/data-dictionary.qmd |only metrosp-1.2.1/metrosp/vignettes/getting_started.qmd | 34 47 files changed, 1067 insertions(+), 539 deletions(-)
Title: Gene Locus Plot with Gene Annotations
Description: Publication-ready regional gene locus plots similar to those produced by the web interface 'LocusZoom' <https://my.locuszoom.org>, but running locally in R. Genetic or genomic data with gene annotation tracks are plotted via R base graphics, 'ggplot2' or 'plotly', allowing flexibility and easy customisation including laying out multiple locus plots on the same page. It uses the 'LDlink' API <https://ldlink.nih.gov/?tab=apiaccess> to query linkage disequilibrium data from the 1000 Genomes Project and can overlay this on plots <doi:10.1093/bioadv/vbaf006>.
Author: Myles Lewis [aut, cre] ,
Tom Willis [ctb]
Maintainer: Myles Lewis <myles.lewis@qmul.ac.uk>
Diff between locuszoomr versions 0.3.10 dated 2026-07-19 and 1.0.0 dated 2026-09-03
DESCRIPTION | 27 +++++++++----- MD5 | 39 +++++++++++++-------- NAMESPACE | 57 +++++++++++++++++++++++++++++++ NEWS.md | 12 ++++++ R/RcppExports.R |only R/genetrack_ly.R | 82 ++++++++++++++++++++++++++++++++++----------- R/genetracks.R | 41 +++++++++++++--------- R/gg_scatter.R | 2 - R/link_LD.R | 32 +++++++++++++---- R/scatter_plot.R | 2 - R/scatter_plotly.R | 1 R/zoom.R |only README.md | 16 ++++++++ build/vignette.rds |binary inst/doc/locuszoomr.Rmd | 2 - inst/doc/locuszoomr.html | 2 - inst/doc/zoom_browser.R |only inst/doc/zoom_browser.Rmd |only inst/doc/zoom_browser.html |only man/zoom.Rd |only src |only vignettes/locuszoomr.Rmd | 2 - vignettes/zoom1.png |only vignettes/zoom2.png |only vignettes/zoom_browser.Rmd |only 25 files changed, 245 insertions(+), 72 deletions(-)
Title: Interface to 'Python'
Description: Interface to 'Python' modules, classes, and functions. When calling
into 'Python', R data types are automatically converted to their equivalent 'Python'
types. When values are returned from 'Python' to R they are converted back to R
types. Compatible with all versions of 'Python' >= 2.7.
Author: Tomasz Kalinowski [aut, cre],
Kevin Ushey [aut],
JJ Allaire [aut],
RStudio [cph, fnd],
Yuan Tang [aut, cph] ,
Dirk Eddelbuettel [ctb, cph],
Bryan Lewis [ctb, cph],
Sigrid Keydana [ctb],
Ryan Hafen [ctb, cph],
Marcus Geelnard [ctb, cph]
Maintainer: Tomasz Kalinowski <tomasz@posit.co>
Diff between reticulate versions 1.46.0 dated 2026-04-09 and 1.47.0 dated 2026-09-03
DESCRIPTION | 12 MD5 | 86 - NAMESPACE | 2 NEWS.md | 55 R/RcppExports.R | 5 R/conda.R | 6 R/conversion.R | 12 R/generator.R | 3 R/install.R | 2 R/output.R | 9 R/package.R | 2 R/pip.R | 3 R/pipenv.R | 10 R/poetry.R | 2 R/py_require.R | 1279 ++++++---------------- R/utils.R | 27 R/uv.R |only R/virtualenv.R | 4 R/zzz.R | 2 build/vignette.rds |binary inst/doc/r_markdown.Rmd | 2 inst/doc/r_markdown.html | 4 inst/python/rpytools/output.py | 6 man/install_miniconda.Rd | 6 man/miniconda_uninstall.Rd | 6 man/miniconda_update.Rd | 6 man/py_require.Rd | 41 man/reticulate.Rd | 3 man/uv_run_tool.Rd | 13 src/python.cpp | 2 src/r_api.h | 2 tests/testthat/_snaps/py_require.md | 61 - tests/testthat/test-cache-age.R |only tests/testthat/test-exclude-newer.R |only tests/testthat/test-py_require-transactions.R |only tests/testthat/test-py_require.R | 36 tests/testthat/test-python-arrays.R | 4 tests/testthat/test-python-dict.R | 2 tests/testthat/test-python-exceptions.R | 66 + tests/testthat/test-python-initialize.R | 2 tests/testthat/test-python-knitr-engine.R | 4 tests/testthat/test-python-output.R | 95 + tests/testthat/test-python-pandas.R | 28 tests/testthat/test-python-pipenv.R | 78 + tests/testthat/test-python-virtual-environments.R | 40 vignettes/r_markdown.Rmd | 2 46 files changed, 972 insertions(+), 1058 deletions(-)
Title: Quantile G-Computation
Description: G-computation for a set of time-fixed exposures with
quantile-based basis functions, possibly under linearity and
homogeneity assumptions. This approach estimates a regression line
corresponding to the expected change in the outcome (on the link
basis) given a simultaneous increase in the quantile-based category
for all exposures. Works with continuous, binary, and right-censored
time-to-event outcomes. Reference: Alexander P. Keil, Jessie P.
Buckley, Katie M. OBrien, Kelly K. Ferguson, Shanshan Zhao, and
Alexandra J. White (2019) A quantile-based g-computation approach to
addressing the effects of exposure mixtures; <doi:10.1289/EHP5838>.
Author: Alexander Keil [aut, cre]
Maintainer: Alexander Keil <alex.keil@nih.gov>
Diff between qgcomp versions 2.18.10 dated 2026-03-24 and 2.19.5 dated 2026-09-03
DESCRIPTION | 10 +- MD5 | 50 +++++----- NAMESPACE | 2 NEWS.md | 21 ++++ R/base_experimental.R | 158 +++++++++++++++++++++++++++++++++ R/base_multinomial.R | 5 - R/base_surv.R | 2 README.md | 2 build/vignette.rds |binary inst/doc/qgcomp-advanced-vignette.html | 42 +++----- inst/doc/qgcomp-basic-vignette.html | 32 +++--- inst/doc/qgcomp-vignette.html | 4 man/print.qgcomppartialavg.Rd |only man/print.qgcomppartialavg_boot.Rd |only man/qgcomp.cch.noboot.Rd | 26 ++--- man/qgcomp.cox.boot.Rd | 26 ++--- man/qgcomp.cox.noboot.Rd | 26 ++--- man/qgcomp.glm.boot.Rd | 26 ++--- man/qgcomp.glm.ee.Rd | 26 ++--- man/qgcomp.glm.noboot.Rd | 26 ++--- man/qgcomp.hurdle.boot.Rd | 26 ++--- man/qgcomp.hurdle.noboot.Rd | 26 ++--- man/qgcomp.multinomial.boot.Rd | 31 +++--- man/qgcomp.multinomial.noboot.Rd | 26 ++--- man/qgcomp.partials.Rd | 26 ++--- man/qgcomp.zi.boot.Rd | 26 ++--- man/qgcomp.zi.noboot.Rd | 26 ++--- 27 files changed, 428 insertions(+), 243 deletions(-)
Title: Mediterranean Forest Simulation
Description: Simulate Mediterranean forest functioning and dynamics using cohort-based description of vegetation [De Caceres et al. (2015) <doi:10.1016/j.agrformet.2015.06.012>; De Caceres et al. (2021) <doi:10.1016/j.agrformet.2020.108233>].
Author: Miquel De Caceres [aut, cre, cph] ,
Nicolas Martin-StPaul [aut] ,
Victor Granda [aut] ,
Antoine Cabon [aut] ,
Arsene Druel [aut] ,
Julien Ruffault [aut] ,
Jordi Martinez-Vilalta [ctb] ,
Maurizio Mencuccini [ctb] ,
Francois Pimont [ctb] ,
Herve Cochar [...truncated...]
Maintainer: Miquel De Caceres <miquelcaceres@gmail.com>
Diff between medfate versions 5.0.0 dated 2026-05-06 and 5.1.0 dated 2026-09-03
medfate-5.0.0/medfate/src/inner_sperry.h |only medfate-5.0.0/medfate/src/inner_sureau.h |only medfate-5.0.0/medfate/tests/testthat/Rplots.pdf |only medfate-5.1.0/medfate/DESCRIPTION | 8 medfate-5.1.0/medfate/MD5 | 183 +- medfate-5.1.0/medfate/R/RcppExports.R | 89 - medfate-5.1.0/medfate/R/VerticalProfiles.R | 8 medfate-5.1.0/medfate/R/dataset_documentation.R | 17 medfate-5.1.0/medfate/R/defaultControl.R | 37 medfate-5.1.0/medfate/R/emptyforest.R | 8 medfate-5.1.0/medfate/R/forest_mergeTrees.R | 22 medfate-5.1.0/medfate/R/plot.forest.R | 15 medfate-5.1.0/medfate/R/plot.spwb.R | 3 medfate-5.1.0/medfate/R/plot_internals.R | 85 - medfate-5.1.0/medfate/R/summary.forest.R | 8 medfate-5.1.0/medfate/R/sysdata.rda |binary medfate-5.1.0/medfate/R/tree2forest.R | 15 medfate-5.1.0/medfate/build/partial.rdb |binary medfate-5.1.0/medfate/data/SpParamsDefinition.rda |binary medfate-5.1.0/medfate/data/SpParamsMED.rda |binary medfate-5.1.0/medfate/data/exampleforest.rda |binary medfate-5.1.0/medfate/data/exampleobs.rda |binary medfate-5.1.0/medfate/man/biophysics.Rd | 4 medfate-5.1.0/medfate/man/defaultControl.Rd | 28 medfate-5.1.0/medfate/man/emptyforest.Rd | 1 medfate-5.1.0/medfate/man/exampleobs.Rd | 16 medfate-5.1.0/medfate/man/forest.Rd | 1 medfate-5.1.0/medfate/man/forest2aboveground.Rd | 1 medfate-5.1.0/medfate/man/growth.Rd | 1 medfate-5.1.0/medfate/man/growth_day.Rd | 1 medfate-5.1.0/medfate/man/hydraulics_conductancefunctions.Rd | 3 medfate-5.1.0/medfate/man/hydraulics_defoliation.Rd | 16 medfate-5.1.0/medfate/man/hydraulics_scalingconductance.Rd | 4 medfate-5.1.0/medfate/man/light_advanced.Rd | 33 medfate-5.1.0/medfate/man/modelInput.Rd | 4 medfate-5.1.0/medfate/man/plot.forest.Rd | 3 medfate-5.1.0/medfate/man/spwb.Rd | 12 medfate-5.1.0/medfate/man/spwb_day.Rd | 11 medfate-5.1.0/medfate/man/tree2forest.Rd | 8 medfate-5.1.0/medfate/man/vprofile_leafAreaDensity.Rd | 4 medfate-5.1.0/medfate/src/RcppExports.cpp | 127 + medfate-5.1.0/medfate/src/aspwb.cpp | 5 medfate-5.1.0/medfate/src/biophysicsutils_c.cpp | 5 medfate-5.1.0/medfate/src/control_c.cpp | 31 medfate-5.1.0/medfate/src/control_c.h | 29 medfate-5.1.0/medfate/src/decomposition_c.cpp | 1 medfate-5.1.0/medfate/src/firebehaviour_c.cpp | 1 medfate-5.1.0/medfate/src/forestutils.cpp | 19 medfate-5.1.0/medfate/src/forestutils_c.cpp | 2 medfate-5.1.0/medfate/src/fuelstructure_c.cpp | 1 medfate-5.1.0/medfate/src/growth.cpp | 19 medfate-5.1.0/medfate/src/growth_day.cpp | 1 medfate-5.1.0/medfate/src/growth_day_c.cpp | 212 +- medfate-5.1.0/medfate/src/growth_day_c.h | 2 medfate-5.1.0/medfate/src/hydraulics_c.cpp | 53 medfate-5.1.0/medfate/src/hydraulics_c.h | 7 medfate-5.1.0/medfate/src/inner_sperry.cpp | 472 ------ medfate-5.1.0/medfate/src/inner_sperry_c.cpp | 140 + medfate-5.1.0/medfate/src/inner_sureau.cpp | 750 ---------- medfate-5.1.0/medfate/src/inner_sureau_c.cpp | 176 +- medfate-5.1.0/medfate/src/inner_sureau_c.h | 6 medfate-5.1.0/medfate/src/lightextinction_advanced.cpp | 52 medfate-5.1.0/medfate/src/lightextinction_advanced.h | 9 medfate-5.1.0/medfate/src/lightextinction_advanced_c.cpp | 170 +- medfate-5.1.0/medfate/src/lightextinction_advanced_c.h | 22 medfate-5.1.0/medfate/src/lightextinction_basic.cpp | 28 medfate-5.1.0/medfate/src/lightextinction_basic.h | 3 medfate-5.1.0/medfate/src/lightextinction_basic_c.cpp | 34 medfate-5.1.0/medfate/src/lightextinction_basic_c.h | 12 medfate-5.1.0/medfate/src/lowlevel_structures_c.cpp | 2 medfate-5.1.0/medfate/src/lowlevel_structures_c.h | 8 medfate-5.1.0/medfate/src/modelInput.cpp | 151 +- medfate-5.1.0/medfate/src/modelInput_c.cpp | 68 medfate-5.1.0/medfate/src/modelInput_c.h | 16 medfate-5.1.0/medfate/src/numerical_solving_c.cpp | 4 medfate-5.1.0/medfate/src/paramutils.cpp | 151 +- medfate-5.1.0/medfate/src/phenology_c.cpp | 8 medfate-5.1.0/medfate/src/photosynthesis_c.cpp | 1 medfate-5.1.0/medfate/src/root_c.cpp | 1 medfate-5.1.0/medfate/src/spwb.cpp | 42 medfate-5.1.0/medfate/src/spwb_day.cpp | 11 medfate-5.1.0/medfate/src/spwb_day_c.cpp | 31 medfate-5.1.0/medfate/src/transpiration_advanced.cpp | 3 medfate-5.1.0/medfate/src/transpiration_advanced_c.cpp | 68 medfate-5.1.0/medfate/src/transpiration_advanced_c.h | 2 medfate-5.1.0/medfate/src/transpiration_basic_c.cpp | 141 + medfate-5.1.0/medfate/src/transpiration_basic_c.h | 7 medfate-5.1.0/medfate/src/windextinction_c.cpp | 1 medfate-5.1.0/medfate/tests/testthat/initialized_objects/growthInput_5.1.0.rds |only medfate-5.1.0/medfate/tests/testthat/initialized_objects/spwbInput_5.1.0.rds |only medfate-5.1.0/medfate/tests/testthat/test_fordyn.R | 4 medfate-5.1.0/medfate/tests/testthat/test_growth.R | 4 medfate-5.1.0/medfate/tests/testthat/test_post_processing.R | 2 medfate-5.1.0/medfate/tests/testthat/test_spwb.R | 4 medfate-5.1.0/medfate/tests/testthat/test_spwb_day.R | 40 95 files changed, 1868 insertions(+), 1940 deletions(-)
Title: Mediation, Moderation and Moderated-Mediation After Model
Fitting
Description: Computes indirect effects, conditional effects, and conditional
indirect effects in a structural equation model or path model after model
fitting, with no need to define any user parameters or label any paths in
the model syntax, using the approach presented in Cheung and Cheung
(2024) <doi:10.3758/s13428-023-02224-z>. Can also form bootstrap
confidence intervals by doing bootstrapping only once and reusing the
bootstrap estimates in all subsequent computations. Supports bootstrap
confidence intervals for standardized (partially or completely) indirect
effects, conditional effects, and conditional indirect effects as described
in Cheung (2009) <doi:10.3758/BRM.41.2.425> and Cheung, Cheung, Lau, Hui,
and Vong (2022) <doi:10.1037/hea0001188>. Model fitting can be done by
structural equation modeling using lavaan() or regression using lm().
Author: Shu Fai Cheung [aut, cre] ,
Sing-Hang Cheung [aut] ,
Rong Wei Sun [ctb]
Maintainer: Shu Fai Cheung <shufai.cheung@gmail.com>
Diff between manymome versions 0.3.6 dated 2026-06-08 and 0.3.7 dated 2026-09-03
DESCRIPTION | 8 MD5 | 491 +++--- NAMESPACE | 12 NEWS.md | 123 + R/all_indirect_paths.R | 14 R/boot2est_lavaan.R | 28 R/boot2est_lm.R | 65 R/check_path.R | 4 R/coef_cond_indirect_effects.R | 2 R/coef_indirect.R | 6 R/coef_indirect_list.R | 2 R/cond_indirect.R | 82 - R/cond_indirect_diff.R | 66 R/cond_indirect_effects_math.R | 6 R/cond_indirect_effects_subset.R | 6 R/confint_cond_indirect_effects.R | 140 + R/confint_indirect.R | 87 - R/confint_indirect_list.R | 25 R/dat_6.R | 2 R/dat_7_mod.R |only R/dat_7_mod_cat.R |only R/dat_7_mod_cat_num.R |only R/dat_sem.R | 2 R/dat_simple_mediation_latent.R | 6 R/do_boot.R | 10 R/do_mc.R | 10 R/find_product.R | 87 - R/get_b.R | 2 R/get_indirect_effect.R | 8 R/get_intercept.R | 4 R/get_prod.R | 2 R/helpers.R | 20 R/index_mome.R | 251 ++- R/indirect.R | 10 R/indirect_proportion.R | 4 R/lav_helpers_mod.R | 2 R/lavaan2lm_list.R | 2 R/lavaan_helpers.R | 16 R/lm2list.R | 8 R/lm_helpers.R | 2 R/mc2est_lavaan.R | 4 R/merge_mod_levels.R | 2 R/mod_levels.R | 16 R/plot_effect_vs_w.R | 16 R/plotmod.R | 14 R/predict_lm_list.R | 2 R/print_boot_out.R | 4 R/print_cond_indirect_effect.R | 46 R/print_delta_med.R | 4 R/print_indirect.R | 10 R/print_indirect_list.R | 4 R/pseudo_jn.r | 29 R/q_functions_helpers.R | 215 ++ R/q_functions_helpers_lavaan.R | 24 R/q_functions_helpers_lavaan_moderator.R |only R/q_mediation.R | 816 +++++++++- R/q_mediation_plot.R | 11 R/summary_lm_list.R | 4 R/total_indirect_effect_list.R | 4 R/wlevels_subset.R | 2 README.md | 26 build/partial.rdb |binary build/vignette.rds |binary data/data_mod_2w.rda |only data/data_mod_2x1w.rda |only data/data_mod_2x2w.rda |only data/data_mod_cat_2w.rda |only data/data_mod_cat_num_2w.rda |only inst/doc/do_boot.Rmd | 4 inst/doc/do_boot.html | 6 inst/doc/do_mc.Rmd | 8 inst/doc/do_mc.html | 10 inst/doc/do_mc_lavaan_mi.Rmd | 72 inst/doc/do_mc_lavaan_mi.html | 152 + inst/doc/manymome.Rmd | 70 inst/doc/manymome.html | 195 +- inst/doc/med_lav.Rmd | 22 inst/doc/med_lav.html | 27 inst/doc/med_lm.Rmd | 30 inst/doc/med_lm.html | 39 inst/doc/mod_levels.Rmd | 26 inst/doc/mod_levels.html | 105 - inst/doc/mome_lm.Rmd | 43 inst/doc/mome_lm.html | 119 - man/all_indirect_paths.Rd | 12 man/check_path.Rd | 4 man/coef.cond_indirect_diff.Rd | 2 man/coef.cond_indirect_effects.Rd | 2 man/coef.indirect.Rd | 6 man/coef.indirect_list.Rd | 2 man/coef.lm_from_lavaan.Rd | 2 man/cond_indirect.Rd | 49 man/cond_indirect_diff.Rd | 14 man/confint.cond_indirect_diff.Rd | 22 man/confint.cond_indirect_effects.Rd | 32 man/confint.indirect.Rd | 28 man/confint.indirect_list.Rd | 24 man/data_med_mod_b_mod.Rd | 2 man/data_mod_2w.Rd |only man/data_mod_2x1w.Rd |only man/data_mod_2x2w.Rd |only man/data_mod_cat_2w.Rd |only man/data_mod_cat_num_2w.Rd |only man/data_sem.Rd | 2 man/do_boot.Rd | 10 man/do_mc.Rd | 8 man/fit2boot_out.Rd | 10 man/fit2mc_out.Rd | 4 man/get_one_cond_indirect_effect.Rd | 6 man/get_prod.Rd | 2 man/index_of_mome.Rd | 140 + man/indirect_i.Rd | 8 man/indirect_proportion.Rd | 4 man/lm2boot_out.Rd | 8 man/lm2list.Rd | 6 man/math_indirect.Rd | 4 man/merge_mod_levels.Rd | 2 man/mod_levels.Rd | 14 man/plot.cond_indirect_effects.Rd | 14 man/plot.q_mediation.Rd | 4 man/plot_effect_vs_w.Rd | 14 man/predict.lm_list.Rd | 2 man/print.boot_out.Rd | 4 man/print.cond_indirect_diff.Rd | 2 man/print.cond_indirect_effects.Rd | 12 man/print.delta_med.Rd | 2 man/print.indirect.Rd | 10 man/print.indirect_list.Rd | 2 man/pseudo_johnson_neyman.Rd | 26 man/q_mediation.Rd | 213 ++ man/simple_mediation_latent.Rd | 4 man/subsetting_cond_indirect_effects.Rd | 4 man/subsetting_wlevels.Rd | 2 man/summary.lm_list.Rd | 4 man/total_indirect_effect.Rd | 2 tests/testthat/test_all_indirect_paths.R | 13 tests/testthat/test_all_indirect_paths_lv.R | 3 tests/testthat/test_cond_indirect_diff.R | 8 tests/testthat/test_cond_indirect_effects_lavaan_do_boot_missing.R | 2 tests/testthat/test_cond_indirect_effects_lavaan_kway_missing.R | 2 tests/testthat/test_cond_indirect_effects_lavaan_lv_mod.R | 21 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tests/testthat/test_jn.r | 8 tests/testthat/test_jn_se.r | 16 tests/testthat/test_mod_only_not_moderated.R | 2 tests/testthat/test_plot_cond_indirect_effects.R | 16 tests/testthat/test_print_all_cond_indirect_effects.R | 2 tests/testthat/test_q_fct_mediation_lm_indicators.R | 2 tests/testthat/test_q_fct_mediation_sem_betaS.R |only tests/testthat/test_q_fct_mediation_sem_fixedx_FALSE.R | 4 tests/testthat/test_q_fct_mediation_sem_indicators_measurement.R | 90 - tests/testthat/test_q_fct_moderated_mediation.R |only tests/testthat/test_q_fct_moderated_mediation_model.R |only tests/testthat/test_q_fct_moderated_mediation_model_betaS.R |only tests/testthat/test_q_fct_moderated_mediation_sem_betaS.R |only tests/testthat/test_sam.R | 8 tests/testthat/test_sam_mediation_mg.R | 11 tests/testthat/test_sam_q_mediation.R | 29 tests/testthat/test_sam_q_mediation_moderation.R |only tests/testthat/test_sam_q_mediation_std.R | 7 tests/testthat/test_sam_update.R | 6 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Title: Arrows for 'ggplot2'
Description: A 'ggplot2' extension that adds specialised arrow geometry layers.
It offers more arrow options than the standard 'grid' arrows that
are built-in many line-based geom layers.
Author: Teun van den Brand [aut, cre]
Maintainer: Teun van den Brand <tahvdbrand@gmail.com>
Diff between ggarrow versions 0.1.1 dated 2025-09-14 and 0.2.0 dated 2026-09-03
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Title: Check User-Supplied Function Arguments
Description: For developers to check user-supplied function arguments. It
is designed to be simple, fast and customizable. Error messages
follow the tidyverse style guide.
Author: Joe Thorley [aut, cre] ,
Kirill Mueller [aut] ,
Ayla Pearson [aut] ,
Florencia D'Andrea [ctb],
Nadine Hussein [ctb] ,
Evan Amies-Galonski [ctb] ,
Stefano Mezzini [ctb] ,
Poisson Consulting [cph, fnd]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>
Diff between chk versions 0.10.0 dated 2025-01-24 and 0.11.0 dated 2026-09-03
DESCRIPTION | 30 + LICENSE | 2 MD5 | 502 +++++++++++++++--------------- NAMESPACE | 9 NEWS.md | 46 ++ R/cc.R | 11 R/check-data.R | 59 ++- R/check-dim.R | 20 - R/check-dirs.R | 28 + R/check-files.R | 28 + R/check-key.R | 20 + R/check-length.R | 4 R/check-names.R | 36 +- R/check-values.R | 33 + R/chk-all-equal.R | 13 R/chk-all-equivalent.R | 20 - R/chk-all-identical.R | 4 R/chk-all-na.R |only R/chk-all.R | 8 R/chk-array.R | 4 R/chk-atomic.R | 4 R/chk-character-or-factor.R | 6 R/chk-character.R | 4 R/chk-chr.R | 6 R/chk-class.R |only R/chk-complex-number.R | 11 R/chk-complex.R | 4 R/chk-count.R | 10 R/chk-data.R | 4 R/chk-date.R | 4 R/chk-datetime.R | 14 R/chk-dbl.R | 4 R/chk-dir.R | 12 R/chk-double.R | 4 R/chk-environment.R | 4 R/chk-equal.R | 17 - R/chk-equivalent.R | 17 - R/chk-ext.R | 15 R/chk-factor.R | 6 R/chk-false.R | 4 R/chk-file.R | 12 R/chk-flag.R | 4 R/chk-function.R | 21 + R/chk-gt.R | 22 + R/chk-gte.R | 22 + R/chk-identical.R | 9 R/chk-integer.R | 4 R/chk-is.R | 8 R/chk-join.R | 23 + R/chk-length.R | 30 + R/chk-lgl.R | 4 R/chk-list.R | 4 R/chk-logical.R | 4 R/chk-lt.R | 22 + R/chk-lte.R | 21 + R/chk-match.R | 22 + R/chk-matrix.R | 6 R/chk-missing.R | 4 R/chk-named.R | 4 R/chk-not-any-na.R | 4 R/chk-not-empty.R | 4 R/chk-not-null.R | 4 R/chk-not-subset.R | 22 + R/chk-null-or.R | 43 ++ R/chk-null.R | 4 R/chk-number.R | 7 R/chk-numeric.R | 4 R/chk-orderset.R | 14 R/chk-r6-class.R |only R/chk-range.R | 37 +- R/chk-raw.R | 4 R/chk-s3-class-strict.R |only R/chk-s3-class.R | 35 +- R/chk-s4-class.R | 25 + R/chk-scalar.R | 6 R/chk-setequal.R | 4 R/chk-sorted.R | 6 R/chk-string.R | 4 R/chk-subset.R | 22 + R/chk-superset.R | 12 R/chk-true.R | 4 R/chk-tz.R | 13 R/chk-unique.R | 4 R/chk-valid-name.R | 8 R/chk-vector.R | 8 R/chk-whole-number.R | 6 R/chk-whole-numeric.R | 9 R/chk-wnum.R | 8 R/chkor-vld.R | 13 R/deprecated.R | 76 +++- R/err.R | 57 ++- R/expect-chk-error.R | 24 + R/generate-check-data.R |only R/internal.R | 18 - R/new-duplicated.R | 16 R/p.R | 12 R/params.R | 5 R/utils.R | 13 build/vignette.rds |binary inst/WORDLIST | 37 +- inst/doc/chk-families.R | 55 +-- inst/doc/chk-families.Rmd | 76 ++-- inst/doc/chk-families.html | 226 +++++++------ inst/doc/chk.Rmd | 10 inst/doc/chk.html | 16 man/check_data.Rd | 33 + man/check_dim.Rd | 16 man/check_dirs.Rd | 16 man/check_files.Rd | 16 man/check_key.Rd | 16 man/check_length.Rd | 16 man/check_names.Rd | 16 man/check_values.Rd | 26 - man/chk-package.Rd | 4 man/chk_all.Rd | 8 man/chk_all_equal.Rd | 20 - man/chk_all_equivalent.Rd | 20 - man/chk_all_identical.Rd | 20 - man/chk_all_na.Rd |only man/chk_array.Rd | 10 man/chk_atomic.Rd | 10 man/chk_character.Rd | 20 - man/chk_character_or_factor.Rd | 26 - man/chk_chr.Rd | 7 man/chk_class.Rd |only man/chk_compatible_lengths.Rd | 4 man/chk_complex.Rd | 20 - man/chk_complex_number.Rd | 23 - man/chk_count.Rd | 29 - man/chk_data.Rd | 11 man/chk_date.Rd | 27 - man/chk_date_time.Rd | 27 - man/chk_dbl.Rd | 6 man/chk_deprecated.Rd | 28 + man/chk_dir.Rd | 6 man/chk_double.Rd | 20 - man/chk_environment.Rd | 20 - man/chk_equal.Rd | 12 man/chk_equivalent.Rd | 12 man/chk_ext.Rd | 6 man/chk_factor.Rd | 18 - man/chk_false.Rd | 33 + man/chk_file.Rd | 6 man/chk_flag.Rd | 33 + man/chk_function.Rd | 12 man/chk_gt.Rd | 10 man/chk_gte.Rd | 10 man/chk_identical.Rd | 12 man/chk_integer.Rd | 20 - man/chk_is.Rd | 13 man/chk_join.Rd | 9 man/chk_length.Rd | 4 man/chk_lgl.Rd | 33 + man/chk_list.Rd | 10 man/chk_logical.Rd | 30 - man/chk_lt.Rd | 10 man/chk_lte.Rd | 10 man/chk_matrix.Rd | 10 man/chk_missing.Rd | 6 man/chk_named.Rd | 4 man/chk_not_any_na.Rd | 9 man/chk_not_empty.Rd | 9 man/chk_not_missing.Rd | 6 man/chk_not_null.Rd | 4 man/chk_not_subset.Rd | 22 + man/chk_null.Rd | 4 man/chk_number.Rd | 29 + man/chk_numeric.Rd | 20 - man/chk_orderset.Rd | 24 + man/chk_r6_class.Rd |only man/chk_range.Rd | 12 man/chk_raw.Rd | 20 - man/chk_s3_class.Rd | 22 - man/chk_s3_class_strict.Rd |only man/chk_s4_class.Rd | 13 man/chk_scalar.Rd | 25 - man/chk_setequal.Rd | 25 - man/chk_sorted.Rd | 2 man/chk_string.Rd | 23 - man/chk_subset.Rd | 23 - man/chk_superset.Rd | 10 man/chk_true.Rd | 33 + man/chk_tz.Rd | 23 - man/chk_unique.Rd | 9 man/chk_unused.Rd | 5 man/chk_used.Rd | 5 man/chk_valid_name.Rd | 4 man/chk_vector.Rd | 10 man/chk_whole_number.Rd | 23 + man/chk_whole_numeric.Rd | 6 man/chk_wnum.Rd | 6 man/chkor_vld.Rd | 8 man/deparse_backtick_chk.Rd | 4 man/err.Rd | 8 man/generate_check_data.Rd |only man/message_chk.Rd | 10 man/p.Rd | 16 man/params.Rd | 4 tests/testthat.R | 8 tests/testthat/helper.R |only tests/testthat/test-aaa-deprecated.R | 11 tests/testthat/test-cc.R | 2 tests/testthat/test-check-data.R | 136 +++++++- tests/testthat/test-check-dim.R | 18 - tests/testthat/test-check-dirs.R | 10 tests/testthat/test-check-files.R | 10 tests/testthat/test-check-key.R | 11 tests/testthat/test-check-length.R | 8 tests/testthat/test-check-names.R | 4 tests/testthat/test-check-values.R | 103 ++++-- tests/testthat/test-chk-all-na.R |only tests/testthat/test-chk-all.R | 15 tests/testthat/test-chk-atomic.R | 9 tests/testthat/test-chk-chr.R | 5 tests/testthat/test-chk-class.R |only tests/testthat/test-chk-complex-number.R | 10 tests/testthat/test-chk-count.R | 10 tests/testthat/test-chk-date-time.R | 20 - tests/testthat/test-chk-date.R | 10 tests/testthat/test-chk-environment.R | 5 tests/testthat/test-chk-file.R | 21 + tests/testthat/test-chk-identical.R | 5 tests/testthat/test-chk-is.R | 17 - tests/testthat/test-chk-join.R | 60 ++- tests/testthat/test-chk-length.R | 10 tests/testthat/test-chk-lgl.R | 10 tests/testthat/test-chk-matrix.R | 2 tests/testthat/test-chk-not-any-na.R | 10 tests/testthat/test-chk-not-empty.R | 10 tests/testthat/test-chk-not-missing.R | 5 tests/testthat/test-chk-not-subset.R | 10 tests/testthat/test-chk-null-or.R | 40 ++ tests/testthat/test-chk-null.R | 5 tests/testthat/test-chk-number.R | 10 tests/testthat/test-chk-orderset.R | 5 tests/testthat/test-chk-r6-class.R |only tests/testthat/test-chk-range.R | 83 ++++ tests/testthat/test-chk-raw.R | 2 tests/testthat/test-chk-s3-class-strict.R |only tests/testthat/test-chk-s3-class.R |only tests/testthat/test-chk-s4-class.R |only tests/testthat/test-chk-setequal.R | 5 tests/testthat/test-chk-string.R | 15 tests/testthat/test-chk-subset.R | 20 - tests/testthat/test-chk-true.R | 5 tests/testthat/test-chk-type.R | 70 +--- tests/testthat/test-chk-unique.R | 10 tests/testthat/test-chk-valid-name.R | 5 tests/testthat/test-chk-vector.R | 5 tests/testthat/test-chk-whole-number.R | 20 - tests/testthat/test-chk-wnum.R | 5 tests/testthat/test-chkor-vld.R | 49 ++ tests/testthat/test-chkor.R | 20 - tests/testthat/test-err.R | 155 +++++++++ tests/testthat/test-expect-chk-error.R | 9 tests/testthat/test-generate-check-data.R |only tests/testthat/test-internal.R | 22 + tests/testthat/test-p.R | 28 + tests/testthat/test-utils.R | 9 vignettes/chk-families.Rmd | 76 ++-- vignettes/chk.Rmd | 10 261 files changed, 3294 insertions(+), 1522 deletions(-)
Title: R-ArcGIS Bridge Utility Functions
Description: Developer oriented utility functions designed to be used as
the building blocks of R packages that work with ArcGIS Location
Services. It provides functionality for authorization, Esri JSON
construction and parsing, as well as other utilities pertaining to
geometry and Esri type conversions. To support 'ArcGIS Pro' users,
authorization can be done via 'arcgisbinding'. Installation
instructions for 'arcgisbinding' can be found at
<https://developers.arcgis.com/r-bridge/installation/>.
Author: Josiah Parry [aut, cre] ,
Kenneth Vernon [ctb] ,
Martha Bass [ctb] ,
Eli Pousson [ctb] ,
Ryan Zomorrodi [ctb]
Maintainer: Josiah Parry <josiah.parry@gmail.com>
Diff between arcgisutils versions 0.6.0 dated 2026-07-10 and 0.6.1 dated 2026-09-03
DESCRIPTION | 8 MD5 | 108 ++--- NEWS.md | 40 +- R/arc-base-req.R | 2 R/esri-features-list.R | 4 R/esri-features-string.R | 4 R/esri-featureset-list.R | 4 R/esri-featureset-string.R | 4 R/extendr-wrappers.R | 6 R/feature-collection.R | 8 R/geoprocessing-class.R | 2 R/geoprocessing-types.R | 6 R/options.R |only R/portal-group-user-list.R | 3 R/search.R | 30 - R/util-parse-esri-json.R | 2 R/utils-geometry.R | 4 R/utils-url.R | 11 cleanup |only cleanup.win |only configure | 2 man/arc_base_req.Rd | 4 man/arc_form_params.Rd | 12 man/arc_group.Rd | 4 man/arc_item.Rd | 4 man/arc_item_data.Rd | 4 man/arc_job_status.Rd | 6 man/arc_portal_resources.Rd | 6 man/arc_portal_urls.Rd | 6 man/arc_portal_users.Rd | 6 man/arc_user.Rd | 4 man/detect_errors.Rd | 2 man/fetch_layer_metadata.Rd | 2 man/gp_job.Rd | 193 +++++----- man/gp_job_from_url.Rd | 6 man/gp_params.Rd | 8 man/layer_json.Rd | 6 man/opts.Rd |only man/self.Rd | 8 man/utilities.Rd | 2 src/Makevars.in | 47 +- src/Makevars.win.in | 71 ++- src/entrypoint.c | 2 src/rust/Cargo.lock | 558 +++++++++++++++++++++-------- src/rust/Cargo.toml | 3 src/rust/document.c |only src/rust/vendor-config.toml | 5 src/rust/vendor.tar.xz |binary tests/testthat/test-arc-base-req.R | 2 tests/testthat/test-arc_token.R | 4 tests/testthat/test-date-column-order.R |only tests/testthat/test-date-handling.R | 2 tests/testthat/test-date-parsing.R | 1 tests/testthat/test-empty-results.R | 19 tests/testthat/test-fetch_layer_metadata.R | 1 tests/testthat/test-geoprocessing-types.R | 12 tests/testthat/test-null-geometry.R | 1 tools/config.R | 17 58 files changed, 786 insertions(+), 490 deletions(-)