More information about MultinomFourier at CRAN
Permanent link
Title: Calculation of Slope-Dependant Accumulated Cost Surface,
Least-Cost Paths, Least-Cost Corridors, Least-Cost Networks
Related to Human Movement Across the Landscape
Description: Provides the facility to calculate non-isotropic accumulated cost surfaces, least-cost paths, least-cost corridors, least-cost networks, ranked alternative paths, cost allocation and cost boundaries, using a number of human-movement-related cost functions that can be selected by the user. The terrain factor can be set as a single value or vary across the landscape via a raster of terrain factors or terrain classes. The package is built around a compute-once design: a single cost surface object is created first and then reused by every analysis function, avoiding redundant computation. Visualisation is fully decoupled from computation and is provided through 'ggplot2' methods that can be invoked, customised, and re-invoked at any time without re-running any analysis. It just requires a Digital Terrain Model, a start location and (optionally) destination locations. See Alberti (2019) <doi:10.1016/j.softx.2019.100331>.
Author: Gianmarco Alberti [aut, cre]
Maintainer: Gianmarco Alberti <gianmarcoalberti@gmail.com>
Diff between movecost versions 3.0.0 dated 2026-06-15 and 3.1.0 dated 2026-10-29
DESCRIPTION | 8 MD5 | 49 ++--- NAMESPACE | 1 NEWS.md | 98 ++++++++++ R/cost_functions.R | 123 ++++++++++-- R/data.R | 2 R/mc_comp.R | 12 + R/mc_export.R | 5 R/mc_surface.R | 171 ++++++++++++++++- R/mc_terrain.R |only R/plot_methods.R | 30 ++- R/utils.R | 12 + README.md | 17 + build/vignette.rds |binary inst/CITATION | 9 inst/doc/movecost.R | 80 ++++++-- inst/doc/movecost.Rmd | 179 +++++++++++++----- inst/doc/movecost.html | 410 ++++++++++++++++++++++++------------------ man/mc_comp.Rd | 6 man/mc_cost_functions.Rd | 90 +++++++-- man/mc_export.Rd | 4 man/mc_surface.Rd | 91 ++++++++- man/mc_terrain_factors.Rd |only man/movecost-package.Rd | 2 man/plot.movecost_surface.Rd | 12 + tests/testthat/test-terrain.R |only vignettes/movecost.Rmd | 179 +++++++++++++----- 27 files changed, 1203 insertions(+), 387 deletions(-)
Title: Manage 'CDISC' 'ADaM' Dataset Specifications in 'YAML' Format
Description: Load, validate, and manipulate Clinical Data Interchange
Standards Consortium ('CDISC') Analysis Data Model ('ADaM') dataset
metadata stored as 'YAML' files. Metadata files are validated against
a JSON schema. Provides functions to inspect and modify columns,
parameters, and row-level operations within and across 'ADaM' domains.
Designed for use with the 'mighty' framework.
Author: Aksel Thomsen [aut, cre],
Ari Siggaard Knoph [aut],
Matthew Phelps [aut],
Giulia Pais [aut],
Katarzyna Graczyk [aut],
Michael Hedegaard Thomsen [aut],
Novo Nordisk A/S [cph]
Maintainer: Aksel Thomsen <oath@novonordisk.com>
Diff between mighty.metadata versions 0.1.0 dated 2026-05-15 and 0.2.0 dated 2026-10-29
mighty.metadata-0.1.0/mighty.metadata/R/z_resolve.R |only mighty.metadata-0.1.0/mighty.metadata/tests/testthat/test-z_resolve.R |only mighty.metadata-0.2.0/mighty.metadata/DESCRIPTION | 18 mighty.metadata-0.2.0/mighty.metadata/MD5 | 160 ++++-- mighty.metadata-0.2.0/mighty.metadata/NAMESPACE | 29 + mighty.metadata-0.2.0/mighty.metadata/NEWS.md | 29 + mighty.metadata-0.2.0/mighty.metadata/R/a_mighty_config.R |only mighty.metadata-0.2.0/mighty.metadata/R/a_study_config.R |only mighty.metadata-0.2.0/mighty.metadata/R/documents.R |only mighty.metadata-0.2.0/mighty.metadata/R/mighty_codelists.R |only mighty.metadata-0.2.0/mighty.metadata/R/mighty_domain.R | 39 + mighty.metadata-0.2.0/mighty.metadata/R/mighty_study.R | 165 ++++-- mighty.metadata-0.2.0/mighty.metadata/R/reexports.R | 4 mighty.metadata-0.2.0/mighty.metadata/R/utils-create-md.R |only mighty.metadata-0.2.0/mighty.metadata/R/utils-schema.R |only mighty.metadata-0.2.0/mighty.metadata/R/utils-vector.R | 74 ++- mighty.metadata-0.2.0/mighty.metadata/R/utils-yml.R | 23 mighty.metadata-0.2.0/mighty.metadata/R/y_codelists.R |only mighty.metadata-0.2.0/mighty.metadata/R/y_create_md.R |only mighty.metadata-0.2.0/mighty.metadata/R/y_create_md_col.R | 40 - mighty.metadata-0.2.0/mighty.metadata/R/y_create_md_param.R |only mighty.metadata-0.2.0/mighty.metadata/R/y_create_md_table.R |only mighty.metadata-0.2.0/mighty.metadata/R/y_create_md_values.R |only mighty.metadata-0.2.0/mighty.metadata/R/y_documents.R |only mighty.metadata-0.2.0/mighty.metadata/R/y_filter_domains.R |only mighty.metadata-0.2.0/mighty.metadata/R/y_populate_core.R | 24 - mighty.metadata-0.2.0/mighty.metadata/R/y_populate_sparse.R | 29 - mighty.metadata-0.2.0/mighty.metadata/R/y_write_config.R | 55 +- mighty.metadata-0.2.0/mighty.metadata/R/z_resolve_includes.R |only mighty.metadata-0.2.0/mighty.metadata/R/z_resolve_subsets.R |only mighty.metadata-0.2.0/mighty.metadata/R/zzz.R | 18 mighty.metadata-0.2.0/mighty.metadata/README.md | 31 - mighty.metadata-0.2.0/mighty.metadata/build/vignette.rds |binary mighty.metadata-0.2.0/mighty.metadata/inst/WORDLIST | 143 ++++-- mighty.metadata-0.2.0/mighty.metadata/inst/doc/adam-schema.html | 118 ++++- mighty.metadata-0.2.0/mighty.metadata/inst/doc/codelists-schema.R |only mighty.metadata-0.2.0/mighty.metadata/inst/doc/codelists-schema.Rmd |only mighty.metadata-0.2.0/mighty.metadata/inst/doc/codelists-schema.html |only mighty.metadata-0.2.0/mighty.metadata/inst/doc/mighty-metadata.R | 9 mighty.metadata-0.2.0/mighty.metadata/inst/doc/mighty-metadata.Rmd | 41 + mighty.metadata-0.2.0/mighty.metadata/inst/doc/mighty-metadata.html | 236 ++++++---- mighty.metadata-0.2.0/mighty.metadata/inst/doc/mighty-schema.html | 25 - mighty.metadata-0.2.0/mighty.metadata/inst/doc/study-schema.Rmd | 35 + mighty.metadata-0.2.0/mighty.metadata/inst/doc/study-schema.html | 112 ++++ mighty.metadata-0.2.0/mighty.metadata/inst/examples/_mighty.yml | 3 mighty.metadata-0.2.0/mighty.metadata/inst/examples/_study.yml | 14 mighty.metadata-0.2.0/mighty.metadata/inst/schema/adam.json | 51 ++ mighty.metadata-0.2.0/mighty.metadata/inst/schema/codelists.json |only mighty.metadata-0.2.0/mighty.metadata/inst/schema/documents.json |only mighty.metadata-0.2.0/mighty.metadata/inst/schema/mighty.json | 20 mighty.metadata-0.2.0/mighty.metadata/inst/schema/study.json | 29 + mighty.metadata-0.2.0/mighty.metadata/man/codelists.Rd |only mighty.metadata-0.2.0/mighty.metadata/man/create_md.Rd |only mighty.metadata-0.2.0/mighty.metadata/man/create_md_col.Rd | 6 mighty.metadata-0.2.0/mighty.metadata/man/create_md_param.Rd |only mighty.metadata-0.2.0/mighty.metadata/man/create_md_table.Rd |only mighty.metadata-0.2.0/mighty.metadata/man/create_md_values.Rd |only mighty.metadata-0.2.0/mighty.metadata/man/documents.Rd |only mighty.metadata-0.2.0/mighty.metadata/man/filter_domains.Rd |only mighty.metadata-0.2.0/mighty.metadata/man/mighty.metadata-options-params.Rd | 2 mighty.metadata-0.2.0/mighty.metadata/man/mighty.metadata-package.Rd | 3 mighty.metadata-0.2.0/mighty.metadata/man/mighty_config.Rd |only mighty.metadata-0.2.0/mighty.metadata/man/mighty_domain.Rd | 32 + mighty.metadata-0.2.0/mighty.metadata/man/mighty_study.Rd | 52 +- mighty.metadata-0.2.0/mighty.metadata/man/reexports.Rd | 5 mighty.metadata-0.2.0/mighty.metadata/man/resolve_includes.Rd | 5 mighty.metadata-0.2.0/mighty.metadata/man/resolve_subsets.Rd |only mighty.metadata-0.2.0/mighty.metadata/man/study_config.Rd |only mighty.metadata-0.2.0/mighty.metadata/man/write_config.Rd |only mighty.metadata-0.2.0/mighty.metadata/tests/testthat/_snaps/a_mighty_config.md |only mighty.metadata-0.2.0/mighty.metadata/tests/testthat/_snaps/a_study_config.md |only mighty.metadata-0.2.0/mighty.metadata/tests/testthat/_snaps/mighty_codelists.md |only mighty.metadata-0.2.0/mighty.metadata/tests/testthat/_snaps/mighty_study.md | 23 mighty.metadata-0.2.0/mighty.metadata/tests/testthat/_snaps/y_codelists.md |only mighty.metadata-0.2.0/mighty.metadata/tests/testthat/_snaps/y_create_md_param.md |only mighty.metadata-0.2.0/mighty.metadata/tests/testthat/_snaps/y_create_md_table.md |only mighty.metadata-0.2.0/mighty.metadata/tests/testthat/_snaps/y_create_md_values.md |only mighty.metadata-0.2.0/mighty.metadata/tests/testthat/_snaps/y_documents.md |only mighty.metadata-0.2.0/mighty.metadata/tests/testthat/_snaps/y_write_config.md | 3 mighty.metadata-0.2.0/mighty.metadata/tests/testthat/_snaps/z_resolve_subsets.md |only mighty.metadata-0.2.0/mighty.metadata/tests/testthat/helper-codelists.R |only mighty.metadata-0.2.0/mighty.metadata/tests/testthat/helper-validations.R |only mighty.metadata-0.2.0/mighty.metadata/tests/testthat/test-a_mighty_config.R |only mighty.metadata-0.2.0/mighty.metadata/tests/testthat/test-a_study_config.R |only mighty.metadata-0.2.0/mighty.metadata/tests/testthat/test-documents.R |only mighty.metadata-0.2.0/mighty.metadata/tests/testthat/test-mighty_codelists.R |only mighty.metadata-0.2.0/mighty.metadata/tests/testthat/test-mighty_domain.R | 29 + mighty.metadata-0.2.0/mighty.metadata/tests/testthat/test-mighty_study.R | 88 +++ mighty.metadata-0.2.0/mighty.metadata/tests/testthat/test-utils-create-md.R |only mighty.metadata-0.2.0/mighty.metadata/tests/testthat/test-utils-schema.R |only mighty.metadata-0.2.0/mighty.metadata/tests/testthat/test-utils-vector.R | 67 ++ mighty.metadata-0.2.0/mighty.metadata/tests/testthat/test-utils-yml.R | 48 -- mighty.metadata-0.2.0/mighty.metadata/tests/testthat/test-y_codelists.R |only mighty.metadata-0.2.0/mighty.metadata/tests/testthat/test-y_create_md.R |only mighty.metadata-0.2.0/mighty.metadata/tests/testthat/test-y_create_md_param.R |only mighty.metadata-0.2.0/mighty.metadata/tests/testthat/test-y_create_md_table.R |only mighty.metadata-0.2.0/mighty.metadata/tests/testthat/test-y_create_md_values.R |only mighty.metadata-0.2.0/mighty.metadata/tests/testthat/test-y_documents.R |only mighty.metadata-0.2.0/mighty.metadata/tests/testthat/test-y_filter_domains.R |only mighty.metadata-0.2.0/mighty.metadata/tests/testthat/test-y_populate_core.R | 42 + mighty.metadata-0.2.0/mighty.metadata/tests/testthat/test-y_populate_sparse.R | 28 + mighty.metadata-0.2.0/mighty.metadata/tests/testthat/test-y_write_config.R | 67 ++ mighty.metadata-0.2.0/mighty.metadata/tests/testthat/test-z_resolve_includes.R |only mighty.metadata-0.2.0/mighty.metadata/tests/testthat/test-z_resolve_subsets.R |only mighty.metadata-0.2.0/mighty.metadata/tests/testthat/test_study/_codelists.yml |only mighty.metadata-0.2.0/mighty.metadata/tests/testthat/test_study/_documents.yml |only mighty.metadata-0.2.0/mighty.metadata/tests/testthat/test_study/_mighty.yml | 2 mighty.metadata-0.2.0/mighty.metadata/tests/testthat/test_study/adae.yml | 3 mighty.metadata-0.2.0/mighty.metadata/tests/testthat/test_study/advs.yml | 10 mighty.metadata-0.2.0/mighty.metadata/vignettes/codelists-schema.Rmd |only mighty.metadata-0.2.0/mighty.metadata/vignettes/mighty-metadata.Rmd | 41 + mighty.metadata-0.2.0/mighty.metadata/vignettes/study-schema.Rmd | 35 + 112 files changed, 1690 insertions(+), 475 deletions(-)
More information about mighty.metadata at CRAN
Permanent link
More information about MixedDiversityAnalysis at CRAN
Permanent link
Title: Iterated Racing for Automatic Algorithm Configuration
Description: Iterated race is an extension of the Iterated F-race method for
the automatic configuration of optimization algorithms, that is,
(offline) tuning their parameters by finding the most appropriate
settings given a set of instances of an optimization problem.
M. López-Ibáñez, J. Dubois-Lacoste, L. Pérez Cáceres, T. Stützle,
and M. Birattari (2016) <doi:10.1016/j.orp.2016.09.002>.
Author: Manuel Lopez-Ibanez [aut, cre] ,
Jeremie Dubois-Lacoste [aut],
Leslie Perez Caceres [aut],
Thomas Stuetzle [aut],
Mauro Birattari [aut],
Eric Yuan [ctb],
Prasanna Balaprakash [ctb],
Nguyen Dang [ctb]
Maintainer: Manuel Lopez-Ibanez <manuel.lopez-ibanez@manchester.ac.uk>
Diff between irace versions 4.5 dated 2026-09-15 and 4.5.1 dated 2026-10-29
DESCRIPTION | 8 +++--- MD5 | 22 +++++++++-------- NAMESPACE | 20 ++++++++------- NEWS.md | 12 +++++++++ R/generation.R | 20 ++++++++++----- R/irace.R | 9 ++++--- R/utils.R | 4 --- R/version.R | 2 - build/partial.rdb |binary inst/doc/irace-package.pdf |binary tests/testthat/test-bug-102.R |only tests/testthat/test-bug-103.R |only vignettes/irace-package.bib | 54 ++++++++++++++++++++++++++++++++---------- 13 files changed, 103 insertions(+), 48 deletions(-)
Title: Offline Credit Risk Modelling, Calibration and Validation
Description: Native credit risk calculations, statistical
estimation, calibration, validation and cash flow simulation using local
structured data. Methods cover consumer and business lending with
explicit modelling assumptions, diagnostics and reproducible reference data.
Author: RiskDataScience GmbH [aut, cph],
Dimitrios Geromichalos [cre]
Maintainer: Dimitrios Geromichalos <riskdatascience@web.de>
Diff between creditratingsystem versions 0.1.0 dated 2026-10-28 and 0.1.1 dated 2026-10-29
DESCRIPTION | 6 ++-- MD5 | 14 +++++----- R/links.R | 8 +++--- README.md | 5 +++ inst/examples/wholesale_sector_journey_review.R | 9 ++++++ tests/test-links.R | 15 +++++++++++ tests/test-retail-pools.R | 2 - tests/test-wholesale-sector-journey-review.R | 31 ++++++++++++++++++++++++ 8 files changed, 74 insertions(+), 16 deletions(-)
More information about creditratingsystem at CRAN
Permanent link
Title: VITA, IG, PLSIM and VM Simulation for Given Covariance and
Marginals
Description: Random sampling from distributions with user-specified population covariance matrix. Marginal information may be fully
specified, for which the package implements the VITA (VIne-To-Anything) algorithm
Grønneberg and Foldnes (2017) <doi:10.1007/s11336-017-9569-6>. See also Grønneberg, Foldnes and Marcoulides (2022) <doi:10.18637/jss.v102.i03>.
Alternatively, marginal skewness and kurtosis may be specified, for which the package
implements the IG (independent generator), PLSIM (piecewise linear) and VM (Vale-Maurelli) algorithms, see Foldnes and Olsson (2016) <doi:10.1080/00273171.2015.1133274>,
Foldnes and Grønneberg (2021) <doi:10.1080/10705511.2021.1949323> and Vale and Maurelli (1983) <doi:10.1007/BF02293687>, respectively.
Author: Njaal Foldnes [aut, cre],
Steffen Groenneberg [aut]
Maintainer: Njaal Foldnes <njal.foldnes@gmail.com>
Diff between covsim versions 1.1.0 dated 2024-05-31 and 1.2.0 dated 2026-10-29
covsim-1.1.0/covsim/vignettes/IG_PL-1.png |only covsim-1.1.0/covsim/vignettes/IG_PL-2.png |only covsim-1.1.0/covsim/vignettes/vignette.Rmd.orig |only covsim-1.1.0/covsim/vignettes/vita-1.png |only covsim-1.2.0/covsim/DESCRIPTION | 21 covsim-1.2.0/covsim/MD5 | 60 covsim-1.2.0/covsim/NAMESPACE | 11 covsim-1.2.0/covsim/NEWS.md | 62 covsim-1.2.0/covsim/R/IG.R | 175 +- covsim-1.2.0/covsim/R/PLSIM.R | 280 ++- covsim-1.2.0/covsim/R/VM.R |only covsim-1.2.0/covsim/R/auxiliary.R | 123 + covsim-1.2.0/covsim/R/simulate_estimate.R |only covsim-1.2.0/covsim/R/vita.R | 69 covsim-1.2.0/covsim/README.md | 54 covsim-1.2.0/covsim/build/vignette.rds |binary covsim-1.2.0/covsim/inst/doc/calibrate-simulate.R |only covsim-1.2.0/covsim/inst/doc/calibrate-simulate.Rmd |only covsim-1.2.0/covsim/inst/doc/calibrate-simulate.html |only covsim-1.2.0/covsim/inst/doc/simulation-study.R |only covsim-1.2.0/covsim/inst/doc/simulation-study.Rmd |only covsim-1.2.0/covsim/inst/doc/simulation-study.html |only covsim-1.2.0/covsim/inst/doc/vignette.R |only covsim-1.2.0/covsim/inst/doc/vignette.Rmd | 402 ----- covsim-1.2.0/covsim/inst/doc/vignette.html | 1117 +++++--------- covsim-1.2.0/covsim/man/calibrate_ig.Rd |only covsim-1.2.0/covsim/man/calibrate_plsim.Rd |only covsim-1.2.0/covsim/man/calibrate_vita.Rd |only covsim-1.2.0/covsim/man/calibrate_vm.Rd |only covsim-1.2.0/covsim/man/rIG.Rd | 17 covsim-1.2.0/covsim/man/rPLSIM.Rd | 25 covsim-1.2.0/covsim/man/rVM.Rd |only covsim-1.2.0/covsim/man/simulate.covsim_calib_ig.Rd |only covsim-1.2.0/covsim/man/simulate.covsim_calib_plsim.Rd |only covsim-1.2.0/covsim/man/simulate.covsim_calib_vita.Rd |only covsim-1.2.0/covsim/man/simulate.covsim_calib_vm.Rd |only covsim-1.2.0/covsim/man/simulate_estimate.Rd |only covsim-1.2.0/covsim/tests/testthat/testCalibrate.R |only covsim-1.2.0/covsim/tests/testthat/testIG.R | 19 covsim-1.2.0/covsim/tests/testthat/testPL.R | 69 covsim-1.2.0/covsim/tests/testthat/testSimulateEstimate.R |only covsim-1.2.0/covsim/tests/testthat/testVM.R |only covsim-1.2.0/covsim/vignettes/calibrate-simulate.Rmd |only covsim-1.2.0/covsim/vignettes/simulation-study.Rmd |only covsim-1.2.0/covsim/vignettes/vignette.Rmd | 402 ----- 45 files changed, 1339 insertions(+), 1567 deletions(-)
Title: Regression Modeling Strategies
Description: Regression modeling, testing, estimation, validation,
graphics, prediction, and typesetting by storing enhanced model design
attributes in the fit. 'rms' is a collection of functions that
assist with and streamline modeling. It also contains functions for
binary and ordinal logistic regression models, ordinal models for
continuous Y with a variety of distribution families and types of censoring
with optional random effects, and the Buckley-James
multiple regression model for right-censored responses, and implements
penalized maximum likelihood estimation for logistic and ordinary
linear models. 'rms' works with almost any regression model, but it
was especially written to work with binary or ordinal regression
models, Cox regression, accelerated failure time models,
ordinary linear models, the Buckley-James model, generalized least
squares for serially or spatially correlated observations, generalized
linear models, and quantile regression.
Author: Frank E Harrell Jr [aut, cre]
Maintainer: Frank E Harrell Jr <fh@fharrell.com>
Diff between rms versions 8.1-1 dated 2026-02-18 and 8.2-0 dated 2026-10-29
rms-8.1-1/rms/R/orm.fit.s |only rms-8.2-0/rms/DESCRIPTION | 17 rms-8.2-0/rms/MD5 | 207 ++- rms-8.2-0/rms/NAMESPACE | 13 rms-8.2-0/rms/NEWS | 35 rms-8.2-0/rms/R/Glm.r | 57 - rms-8.2-0/rms/R/Gls.s | 76 - rms-8.2-0/rms/R/Ocens.r | 944 +++++++++++------ rms-8.2-0/rms/R/Olinks.r | 22 rms-8.2-0/rms/R/Rq.s | 133 ++ rms-8.2-0/rms/R/Survival.orm.r | 309 +++-- rms-8.2-0/rms/R/adapt_orm.r | 28 rms-8.2-0/rms/R/anova.rms.s | 353 ++++++ rms-8.2-0/rms/R/bj.s | 36 rms-8.2-0/rms/R/calibrate.cph.s | 4 rms-8.2-0/rms/R/calibrate.default.s | 2 rms-8.2-0/rms/R/calibrate.orm.r | 2 rms-8.2-0/rms/R/calibrate.psm.s | 4 rms-8.2-0/rms/R/cluster.r |only rms-8.2-0/rms/R/contrast.s | 49 rms-8.2-0/rms/R/corFloorExp.r |only rms-8.2-0/rms/R/cph.s | 134 +- rms-8.2-0/rms/R/hazard.ratio.plot.s | 2 rms-8.2-0/rms/R/impactPO.r | 14 rms-8.2-0/rms/R/infoMxop.r | 243 +++- rms-8.2-0/rms/R/latex.cph.s | 158 ++ rms-8.2-0/rms/R/latex.lrm.s | 80 + rms-8.2-0/rms/R/latex.ols.s | 10 rms-8.2-0/rms/R/latex.pphsm.s | 27 rms-8.2-0/rms/R/latex.psm.s | 27 rms-8.2-0/rms/R/latex.rms.s | 211 +++ rms-8.2-0/rms/R/lrm.fit.r | 1226 ++++++++++++----------- rms-8.2-0/rms/R/lrm.s | 115 +- rms-8.2-0/rms/R/nomogram.s | 2 rms-8.2-0/rms/R/ols.s | 117 +- rms-8.2-0/rms/R/ordParallel.r | 2 rms-8.2-0/rms/R/orm.fit.r |only rms-8.2-0/rms/R/orm.rfit.r |only rms-8.2-0/rms/R/orm.s | 151 ++ rms-8.2-0/rms/R/plot.Predict.s | 2 rms-8.2-0/rms/R/plot.nomogram.s | 2 rms-8.2-0/rms/R/print.psm.s | 51 rms-8.2-0/rms/R/processMI.r | 158 ++ rms-8.2-0/rms/R/psm.s | 2 rms-8.2-0/rms/R/quickRefit.r | 16 rms-8.2-0/rms/R/recode2integer.r | 63 - rms-8.2-0/rms/R/residuals.lrm.s | 2 rms-8.2-0/rms/R/rms.s | 107 +- rms-8.2-0/rms/R/rms.trans.s | 53 rms-8.2-0/rms/R/rmsMisc.s | 689 ++++++++++-- rms-8.2-0/rms/R/summary.rms.s | 211 ++- rms-8.2-0/rms/R/survest.psm.s | 2 rms-8.2-0/rms/R/survplot.npsurv.s | 60 - rms-8.2-0/rms/R/survplot.rms.s | 2 rms-8.2-0/rms/R/val.prob.s | 6 rms-8.2-0/rms/R/val.surv.s | 2 rms-8.2-0/rms/R/validate.cph.s | 31 rms-8.2-0/rms/R/validate.ols.s | 291 +++-- rms-8.2-0/rms/inst/tests/Survival-orm-km.r | 90 + rms-8.2-0/rms/inst/tests/corFloorExp.r |only rms-8.2-0/rms/inst/tests/orm-censor-likelihood.r | 34 rms-8.2-0/rms/inst/tests/orm-censor3.r | 10 rms-8.2-0/rms/inst/tests/orm-re-exact-opt.rds |only rms-8.2-0/rms/inst/tests/orm-re-exact.r |only rms-8.2-0/rms/inst/tests/orm-re.r |only rms-8.2-0/rms/inst/tests/orm7.r | 15 rms-8.2-0/rms/inst/tests/typst.qmd |only rms-8.2-0/rms/inst/tests/yu.rds |only rms-8.2-0/rms/man/ExProb.Rd | 13 rms-8.2-0/rms/man/Glm.Rd | 4 rms-8.2-0/rms/man/Gls.Rd | 4 rms-8.2-0/rms/man/Ocens.Rd | 2 rms-8.2-0/rms/man/Ocens2ord.Rd | 14 rms-8.2-0/rms/man/Olinks.Rd | 5 rms-8.2-0/rms/man/Rq.Rd | 10 rms-8.2-0/rms/man/anova.rms.Rd | 30 rms-8.2-0/rms/man/bj.Rd | 4 rms-8.2-0/rms/man/cluster.Rd |only rms-8.2-0/rms/man/corFloorExp.Rd |only rms-8.2-0/rms/man/impactPO.Rd | 4 rms-8.2-0/rms/man/infoMxop.Rd | 21 rms-8.2-0/rms/man/latex.cph.Rd | 9 rms-8.2-0/rms/man/latexrms.Rd | 19 rms-8.2-0/rms/man/lrm.Rd | 4 rms-8.2-0/rms/man/lrm.fit.Rd | 6 rms-8.2-0/rms/man/mix_re.Rd |only rms-8.2-0/rms/man/nomogram.Rd | 4 rms-8.2-0/rms/man/orm.Rd | 16 rms-8.2-0/rms/man/orm.fit.Rd | 741 +++++++++++-- rms-8.2-0/rms/man/plot.Predict.Rd | 20 rms-8.2-0/rms/man/predict.lrm.Rd | 10 rms-8.2-0/rms/man/print.Glm.Rd | 2 rms-8.2-0/rms/man/print.cph.Rd | 4 rms-8.2-0/rms/man/print.ols.Rd | 4 rms-8.2-0/rms/man/prmiInfo.Rd | 2 rms-8.2-0/rms/man/processMI.Rd | 2 rms-8.2-0/rms/man/processMI.fit.mult.impute.Rd | 2 rms-8.2-0/rms/man/psm.Rd | 4 rms-8.2-0/rms/man/recode2integer.Rd | 10 rms-8.2-0/rms/man/rexVar.Rd | 2 rms-8.2-0/rms/man/rms.Rd | 14 rms-8.2-0/rms/man/rms.trans.Rd | 8 rms-8.2-0/rms/man/rmsMisc.Rd | 65 - rms-8.2-0/rms/man/summary.rms.Rd | 28 rms-8.2-0/rms/man/survplot.Rd | 46 rms-8.2-0/rms/man/validate.Rd | 33 rms-8.2-0/rms/man/validate.Rq.Rd | 3 rms-8.2-0/rms/man/validate.ols.Rd | 2 rms-8.2-0/rms/src/init.c | 22 rms-8.2-0/rms/src/orm_links.f90 |only rms-8.2-0/rms/src/ormeta.f90 |only rms-8.2-0/rms/src/ormidx.f90 |only rms-8.2-0/rms/src/ormll.f90 | 443 +++----- 113 files changed, 5582 insertions(+), 2763 deletions(-)
Title: Histogram-Valued Data Analysis
Description: In the framework of Symbolic Data Analysis, a relatively new
approach to the statistical analysis of multi-valued data, we consider
histogram-valued data, i.e., data described by univariate histograms. The
methods and the basic statistics for histogram-valued data are mainly based
on the L2 Wasserstein metric between distributions, i.e., the Euclidean metric
between quantile functions. The package contains unsupervised classification
techniques, least square regression and tools for histogram-valued data and for
histogram time series. An introducing paper is Irpino A. Verde R. (2015) <doi: 10.1007/s11634-014-0176-4>.
Author: Antonio Irpino [aut, cre]
Maintainer: Antonio Irpino <antonio.irpino@unicampania.it>
Diff between HistDAWass versions 1.0.9 dated 2026-10-18 and 1.0.10 dated 2026-10-29
DESCRIPTION | 11 MD5 | 210 ++++---- NAMESPACE | 238 +++++----- NEWS.md | 197 ++++++++ R/For_Rccp_int.R | 6 R/Fuzzy_cmeans.R | 12 R/H_time_series.R | 17 R/Kohonen_maps.R | 9 R/Met_MatH.R | 37 - R/Met_distributionH.R | 35 + R/Plotting_with_ggplot.R | 21 R/RcppExports.R | 362 +++++++-------- R/Utility.R | 24 + R/principal_components.R | 91 ++- R/regression.R | 12 R/unsuperv_classification.R | 6 README.md | 666 ++++++++++++++-------------- build/partial.rdb |binary build/vignette.rds |only inst |only man/Age_Pyramids_2014.Rd | 44 - man/Agronomique.Rd | 46 - man/Arith-distributionH.Rd | 4 man/BLOOD.Rd | 44 - man/BloodBRITO.Rd | 40 - man/Center.cell.MatH-methods.Rd | 44 - man/China_Month.Rd | 60 +- man/China_Seas.Rd | 60 +- man/DouglasPeucker.Rd | 58 +- man/HTS-class.Rd | 68 +- man/HTS.exponential.smoothing.Rd | 56 +- man/HTS.moving.averages.Rd | 62 +- man/HTS.predict.knn.Rd | 66 +- man/HistDAWass-package.Rd | 176 +++---- man/MatH-class.Rd | 164 +++--- man/OzoneFull.Rd | 42 - man/OzoneH.Rd | 42 - man/RetHTS.Rd | 34 - man/ShortestDistance.Rd | 52 +- man/TMatH-class.Rd | 60 +- man/TdistributionH-class.Rd | 86 +-- man/WH.1d.PCA.Rd | 132 ++--- man/WH.MultiplePCA.Rd | 80 +-- man/WH.bind-methods.Rd | 80 +-- man/WH.mat.prod-methods.Rd | 54 +- man/WH.mat.sum-methods.Rd | 48 +- man/WH.plot_multiple_Spanish.funs.Rd | 92 +-- man/WH.plot_multiple_indivs.Rd | 139 +++-- man/WH.regression.GOF.Rd | 76 +-- man/WH.regression.two.components.Rd | 96 ++-- man/WH.regression.two.components.predict.Rd | 64 +- man/WH.var.covar-methods.Rd | 134 ++--- man/WH.vec.mean-methods.Rd | 72 +-- man/WH_2d_Adaptive_Kohonen_maps.Rd | 242 +++++----- man/WH_2d_Kohonen_maps.Rd | 186 +++---- man/WH_MAT_DIST.Rd | 82 +-- man/WH_adaptive.kmeans.Rd | 170 +++---- man/WH_adaptive_fcmeans.Rd | 170 +++---- man/WH_fcmeans.Rd | 104 ++-- man/WH_hclust.Rd | 114 ++-- man/WH_kmeans.Rd | 136 ++--- man/WassSqDistH-methods.Rd | 90 +-- man/checkEmptyBins-methods.Rd | 66 +- man/compP-methods.Rd | 56 +- man/compQ-methods.Rd | 62 +- man/crwtransform-methods.Rd | 64 +- man/data2hist.Rd | 108 ++-- man/distributionH-class.Rd | 144 +++--- man/dotpW-methods.Rd | 72 +-- man/extract-methods.Rd | 60 +- man/get.MatH.main.info-methods.Rd | 90 +-- man/get.MatH.stats-methods.Rd | 68 +- man/get.cell.MatH-methods.Rd | 68 +- man/get.distr-methods.Rd | 54 +- man/get.histo-methods.Rd | 54 +- man/get.m-methods.Rd | 52 +- man/get.s-methods.Rd | 54 +- man/kurtH-methods.Rd | 52 +- man/meanH-methods.Rd | 50 +- man/plot-HTS.Rd | 72 +-- man/plot-MatH.Rd | 72 +-- man/plot-TdistributionH.Rd | 66 +- man/plot-distributionH.Rd | 80 +-- man/plotPredVsObs.Rd | 82 +-- man/plot_errors.Rd | 78 +-- man/rQQ-methods.Rd | 60 +- man/register-methods.Rd | 70 +- man/registerMH-methods.Rd | 84 +-- man/show-MatH-methods.Rd | 44 - man/show-distributionH-methods.Rd | 46 - man/skewH-methods.Rd | 52 +- man/stations_coordinates.Rd | 48 +- man/stdH-methods.Rd | 52 +- man/subsetHTS-methods.Rd | 46 - src/RcppExports.cpp | 12 src/Utility_fun.cpp | 193 +++++--- tests/testthat/test-hts-arith.R |only tests/testthat/test-plots.R | 30 + vignettes |only 99 files changed, 4205 insertions(+), 3779 deletions(-)
Title: Test for Differences in Diversification Rates over Time
Description: Employ time-calibrated phylogenies and trait/range data to test for
differences in diversification rates over evolutionary time. Extend
the STRAPP test from BAMMtools::traitDependentBAMM() to any time step
along phylogenies. See inst/COPYRIGHTS for details on third-party code.
Author: Mael Dore [aut, cre, cph] ,
Dan Rabosky [ctb],
Mike Grundler [ctb],
Huateng Huang [ctb],
Pascal Title [ctb],
Liam Revell [ctb],
Nicholas J. Matzke [ctb]
Maintainer: Mael Dore <mael.dore@gmail.com>
Diff between deepSTRAPP versions 1.1.0 dated 2026-09-27 and 1.1.1 dated 2026-10-29
DESCRIPTION | 6 MD5 | 85 - NEWS.md | 8 R/build_BAMM_object.R | 10 R/convert_BSMs_to_simmaps.R | 110 + R/convert_contsimmap_to_contMaps.R | 10 README.md | 32 data/eel_biogeo_data.rda |binary inst/CITATION | 2 inst/doc/cut_phylogenies.R | 16 inst/doc/cut_phylogenies.Rmd | 1398 +++++++++++----------- inst/doc/cut_phylogenies.html | 10 inst/doc/deepSTRAPP.html | 4 inst/doc/deepSTRAPP_biogeographic_data.R | 4 inst/doc/deepSTRAPP_biogeographic_data.Rmd | 4 inst/doc/deepSTRAPP_biogeographic_data.html | 6 inst/doc/deepSTRAPP_categorical_data.R | 4 inst/doc/deepSTRAPP_categorical_data.Rmd | 4 inst/doc/deepSTRAPP_categorical_data.html | 6 inst/doc/deepSTRAPP_continuous_data.R | 2 inst/doc/deepSTRAPP_continuous_data.Rmd | 2 inst/doc/deepSTRAPP_continuous_data.html | 4 inst/doc/handle_uncertainty.html | 4 inst/doc/import_external_analyses.R | 23 inst/doc/import_external_analyses.Rmd | 23 inst/doc/import_external_analyses.html | 409 +++--- inst/doc/main_tutorial.R | 4 inst/doc/main_tutorial.Rmd | 4 inst/doc/main_tutorial.html | 8 inst/doc/model_biogeographic_range_evolution.html | 4 inst/doc/model_categorical_trait_evolution.html | 4 inst/doc/model_continuous_trait_evolution.html | 4 inst/doc/model_diversification_dynamics.html | 4 inst/extdata |only man/build_BAMM_object.Rd | 10 man/convert_BSM_to_simmap.Rd | 7 man/convert_contsimmap_to_contMaps.Rd | 10 vignettes/cut_phylogenies.Rmd | 1398 +++++++++++----------- vignettes/deepSTRAPP_biogeographic_data.Rmd | 4 vignettes/deepSTRAPP_categorical_data.Rmd | 4 vignettes/deepSTRAPP_continuous_data.Rmd | 2 vignettes/import_external_analyses.Rmd | 23 vignettes/main_tutorial.Rmd | 4 43 files changed, 1938 insertions(+), 1742 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-08-29 2.1.12
2024-07-17 2.1.11
2024-07-09 2.1.10
2024-06-01 2.1.9
2023-12-01 2.1.6
2023-11-04 2.1.4
2023-11-02 2.1.3
2023-07-10 2.1.0
2023-07-09 2.0.0
2023-06-27 1.4.2
2023-03-06 1.4.1
2022-12-16 1.4.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-11-22 1.0.7
2025-09-03 1.0.3
Title: Zstandard Compression
Description: Compress and decompress data with the 'Zstandard'
algorithm <https://meta.github.io/zstd/>, a fast lossless
compression format. Works on raw vectors in memory and on files, and
can create and extract 'zstd' compressed 'tar' archives. Supports
compression levels, multithreaded compression, long distance
matching, content checksums, and training dictionaries for better
compression of small, similar inputs.
Author: Gabor Csardi [aut, cre],
Posit Software, PBC [cph, fnd] ,
Yann Collet [aut] ,
Meta Platforms, Inc. and affiliates. [cph] ,
rxi [aut, cph]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between zstd versions 0.1.0 dated 2026-10-20 and 0.1.1 dated 2026-10-29
zstd-0.1.0/zstd/src/Makevars |only zstd-0.1.0/zstd/src/zdict.h |only zstd-0.1.0/zstd/src/zstd.c |only zstd-0.1.0/zstd/src/zstd.h |only zstd-0.1.0/zstd/src/zstd_errors.h |only zstd-0.1.1/zstd/DESCRIPTION | 13 +++--- zstd-0.1.1/zstd/MD5 | 43 ++++++++++++--------- zstd-0.1.1/zstd/NAMESPACE | 3 + zstd-0.1.1/zstd/NEWS.md | 5 ++ zstd-0.1.1/zstd/R/zstd-tar.R | 2 zstd-0.1.1/zstd/R/zstd-version.R |only zstd-0.1.1/zstd/cleanup |only zstd-0.1.1/zstd/configure |only zstd-0.1.1/zstd/configure.win |only zstd-0.1.1/zstd/man/zstd_tar_decompress.Rd | 2 zstd-0.1.1/zstd/man/zstd_version.Rd |only zstd-0.1.1/zstd/src/Makevars.in |only zstd-0.1.1/zstd/src/glue.c | 10 ++-- zstd-0.1.1/zstd/src/init.c | 2 zstd-0.1.1/zstd/src/libzstd |only zstd-0.1.1/zstd/src/microtar.c | 6 +- zstd-0.1.1/zstd/src/zstd_r.c | 7 +-- zstd-0.1.1/zstd/src/zstd_r.h | 2 zstd-0.1.1/zstd/src/zstd_stream.c | 3 - zstd-0.1.1/zstd/src/zstd_tar.c | 3 - zstd-0.1.1/zstd/src/zstd_version.c |only zstd-0.1.1/zstd/tests/testthat/test-zstd-version.R |only zstd-0.1.1/zstd/tools/zstd.patch | 12 ++--- 28 files changed, 68 insertions(+), 45 deletions(-)
Title: Multi-State Markov and Hidden Markov Models in Continuous Time
Description: Functions for fitting continuous-time Markov and hidden
Markov multi-state models to longitudinal data. Designed for
processes observed at arbitrary times in continuous time (panel data)
but some other observation schemes are supported. Both Markov
transition rates and the hidden Markov output process can be modelled
in terms of covariates, which may be constant or piecewise-constant
in time.
Author: Christopher Jackson [aut, cre]
Maintainer: Christopher Jackson <chris.jackson@mrc-bsu.cam.ac.uk>
Diff between msm versions 1.8.2 dated 2024-11-07 and 1.9 dated 2026-10-29
DESCRIPTION | 10 MD5 | 70 ++-- NAMESPACE | 112 ++++--- NEWS.md | 15 + R/hmm-dists.R | 6 R/internals_doc.R | 8 R/medists.R | 3 R/msm.R | 31 +- R/optim.R | 500 +++++++++++++++++----------------- R/outputs.R | 3 R/pearson.R | 44 ++ R/prevalence.R | 2 R/simul.R | 289 ++++++++++--------- R/simul_legacy.R |only R/tidy.R | 1 build/vignette.rds |binary inst/doc/msm-manual.R | 2 inst/doc/msm-manual.pdf |binary man/hmmMV.Rd | 2 man/msm-package.Rd | 5 man/msm.object.Rd | 8 man/pearson.msm.Rd | 2 man/plot.prevalence.msm.Rd | 2 man/sim.msm.Rd | 21 + man/simmulti.msm.Rd | 27 + src/lik.c | 3 src/msm-init.c | 4 src/pijt.c | 65 +--- src/simul.c |only tests/testthat/test_datasumm.r | 20 + tests/testthat/test_deriv.r | 63 +++- tests/testthat/test_models.r | 3 tests/testthat/test_models_hmmmulti.r | 8 tests/testthat/test_models_misc.r | 8 tests/testthat/test_pearson.R | 18 + tests/testthat/test_phase.R | 2 tests/testthat/test_simul.R | 108 +++++++ 37 files changed, 878 insertions(+), 587 deletions(-)
Title: Core 'hubverse' Utilities
Description: Core set of low-level utilities common across the
'hubverse'. Used to interact with 'hubverse' schema, Hub configuration files
and model outputs and designed to be primarily used internally by other
'hubverse' packages. See Reich et al. (2022) <doi:10.2105/AJPH.2022.306831>
for an overview of Collaborative Hubs.
Author: Anna Krystalli [aut, cre] ,
Li Shandross [aut],
Nicholas G. Reich [ctb] ,
Evan L. Ray [ctb],
Zhian N. Kamvar [ctb] ,
Consortium of Infectious Disease Modeling Hubs [cph]
Maintainer: Anna Krystalli <annakrystalli@googlemail.com>
Diff between hubUtils versions 1.2.1 dated 2026-07-15 and 1.3.0 dated 2026-10-29
DESCRIPTION | 13 +-- MD5 | 77 +++++++++++------- NAMESPACE | 9 ++ NEWS.md | 20 ++++ R/as_model_out_tbl.R | 5 - R/get_round_value_sets_config.R |only R/get_task_id_type.R |only R/read_model_metadata.R |only R/utils-checks.R |only R/utils-config.R | 54 ++++++++++-- R/utils-get_hub.R | 34 +++---- R/utils-output_type_ids.R |only R/utils-round-config.R | 81 +++++++++++++++---- R/utils-round_ids.R | 34 +++++-- man/create_s3_url.Rd | 2 man/get_config_tid.Rd | 2 man/get_derived_task_ids_config.Rd |only man/get_hub_timezone.Rd | 21 +++- man/get_round_config.Rd |only man/get_round_idx.Rd | 13 ++- man/get_round_model_tasks.Rd | 10 +- man/get_round_output_type_names.Rd |only man/get_round_task_id_names.Rd | 10 +- man/get_round_value_sets_config.Rd |only man/get_schema.Rd | 2 man/get_schema_url.Rd | 2 man/get_schema_valid_versions.Rd | 2 man/get_schema_version_latest.Rd | 2 man/get_task_id_names.Rd | 13 ++- man/get_task_id_type.Rd |only man/get_task_id_values.Rd |only man/get_version_config.Rd | 4 man/is_s3_base_fs.Rd | 2 man/read_config.Rd | 2 man/read_config_file.Rd | 2 man/read_model_metadata.Rd |only tests/testthat/_snaps/get_round_value_sets_config.md |only tests/testthat/_snaps/get_task_id_type.md |only tests/testthat/_snaps/read_model_metadata.md |only tests/testthat/_snaps/utils-config.md |only tests/testthat/_snaps/utils-round-config.md | 57 +++++++++++-- tests/testthat/_snaps/utils-round_ids.md | 15 +-- tests/testthat/helper-expectations.R |only tests/testthat/test-get_round_value_sets_config.R |only tests/testthat/test-get_task_id_type.R |only tests/testthat/test-read_model_metadata.R |only tests/testthat/test-utils-config.R |only tests/testthat/test-utils-get_hub.R | 19 ++++ tests/testthat/test-utils-round-config.R | 80 ++++++++++++++++++ tests/testthat/test-utils-round_ids.R | 61 ++++++++++++++ 50 files changed, 514 insertions(+), 134 deletions(-)
Title: Heteroscedasticity Diagnostics for Linear Models
Description: Provides a unified set of heteroscedasticity diagnostics for
linear-model workflows. It implements classical auxiliary-regression
tests, including those of White (1980) <doi:10.2307/1912934>, Breusch
and Pagan (1979) <doi:10.2307/1911963>, Koenker (1981)
<doi:10.1016/0304-4076(81)90062-2>, Goldfeld and Quandt (1965)
<doi:10.1080/01621459.1965.10480811> and Harvey (1976)
<doi:10.2307/1913974>; the score test of Cook and Weisberg (1983)
<doi:10.1093/biomet/70.1.1>; the ARCH test of Engle (1982)
<doi:10.2307/1912773>; and group-wise tests of equal variance, including
those of Bartlett (1937) <doi:10.1098/rspa.1937.0109>, Brown and Forsythe
(1974) <doi:10.1080/01621459.1974.10482955> and Hartley (1950)
<doi:10.2307/2332383>. Resampling and scalable variants, simulation
utilities, diagnostic visualisation and remediation helpers share a
consistent interface designed for reproducible statistical workflows and
integration with common [...truncated...]
Author: Diogo Ribeiro [aut, cre]
Maintainer: Diogo Ribeiro <dfr@esmad.ipp.pt>
Diff between heteroTests versions 0.11.2 dated 2026-09-26 and 0.16.0 dated 2026-10-29
heteroTests-0.11.2/heteroTests/R/zz_profile_diagnostic_selection.R |only heteroTests-0.11.2/heteroTests/man/rrunAdvancedDiagnostics.Rd |only heteroTests-0.16.0/heteroTests/DESCRIPTION | 14 heteroTests-0.16.0/heteroTests/MD5 | 530 - heteroTests-0.16.0/heteroTests/NAMESPACE | 16 heteroTests-0.16.0/heteroTests/NEWS.md | 4176 ++++++++++ heteroTests-0.16.0/heteroTests/R/HeteroDiagnostic.R | 23 heteroTests-0.16.0/heteroTests/R/additional_tests.R | 763 + heteroTests-0.16.0/heteroTests/R/advancedDiagnostics.R | 22 heteroTests-0.16.0/heteroTests/R/advancedRemediation.R | 4 heteroTests-0.16.0/heteroTests/R/autoTransform.R | 15 heteroTests-0.16.0/heteroTests/R/benchmarking_system.R | 2 heteroTests-0.16.0/heteroTests/R/bootstrap_methods.R | 515 + heteroTests-0.16.0/heteroTests/R/cache.R |only heteroTests-0.16.0/heteroTests/R/dashboard.R | 4 heteroTests-0.16.0/heteroTests/R/diagnosticsRegistry.R | 171 heteroTests-0.16.0/heteroTests/R/ecosystem_integration.R | 245 heteroTests-0.16.0/heteroTests/R/effect_sizes.R | 16 heteroTests-0.16.0/heteroTests/R/error_handling.R | 74 heteroTests-0.16.0/heteroTests/R/fitWLS.R | 810 + heteroTests-0.16.0/heteroTests/R/ggplot_extensions.R | 171 heteroTests-0.16.0/heteroTests/R/intelligent_recommendations.R | 123 heteroTests-0.16.0/heteroTests/R/interface.R |only heteroTests-0.16.0/heteroTests/R/messages.R | 36 heteroTests-0.16.0/heteroTests/R/model_context.R |only heteroTests-0.16.0/heteroTests/R/modern_diagnostics.R | 380 heteroTests-0.16.0/heteroTests/R/parallel_streams.R |only heteroTests-0.16.0/heteroTests/R/performArchLMTest.R | 32 heteroTests-0.16.0/heteroTests/R/performBPRandomEffectsTest.R | 64 heteroTests-0.16.0/heteroTests/R/performBPTest.R | 222 heteroTests-0.16.0/heteroTests/R/performBartlettTest.R | 108 heteroTests-0.16.0/heteroTests/R/performBoxMTest.R | 325 heteroTests-0.16.0/heteroTests/R/performBrownForsytheTest.R | 110 heteroTests-0.16.0/heteroTests/R/performCookWeisbergTest.R | 59 heteroTests-0.16.0/heteroTests/R/performDavidianCarrollTest.R | 30 heteroTests-0.16.0/heteroTests/R/performFlignerKilleenTest.R | 390 heteroTests-0.16.0/heteroTests/R/performGQTest.R | 166 heteroTests-0.16.0/heteroTests/R/performGlejserTest.R | 217 heteroTests-0.16.0/heteroTests/R/performHarrisonMcCabeTest.R |only heteroTests-0.16.0/heteroTests/R/performHartleyFmaxTest.R | 67 heteroTests-0.16.0/heteroTests/R/performHarveyTest.R | 60 heteroTests-0.16.0/heteroTests/R/performKoenkerTest.R | 198 heteroTests-0.16.0/heteroTests/R/performLeveneTest.R | 111 heteroTests-0.16.0/heteroTests/R/performMcLeodLiTest.R | 33 heteroTests-0.16.0/heteroTests/R/performNCVTest.R | 97 heteroTests-0.16.0/heteroTests/R/performOBrienTest.R | 100 heteroTests-0.16.0/heteroTests/R/performParkTest.R | 70 heteroTests-0.16.0/heteroTests/R/performPesaranTest.R | 262 heteroTests-0.16.0/heteroTests/R/performRESETTest.R | 75 heteroTests-0.16.0/heteroTests/R/performScatterDiagnostic.R | 44 heteroTests-0.16.0/heteroTests/R/performSpearmanTest.R | 29 heteroTests-0.16.0/heteroTests/R/performSpreadLevelTest.R | 19 heteroTests-0.16.0/heteroTests/R/performVarianceFormTest.R |only heteroTests-0.16.0/heteroTests/R/performWhiteTest.R | 706 + heteroTests-0.16.0/heteroTests/R/performance.R | 601 + heteroTests-0.16.0/heteroTests/R/plotDiagnostics.R | 133 heteroTests-0.16.0/heteroTests/R/quantile_regression_joint.R | 138 heteroTests-0.16.0/heteroTests/R/remediation.R | 10 heteroTests-0.16.0/heteroTests/R/reporting.R | 6 heteroTests-0.16.0/heteroTests/R/robust_implementations.R | 244 heteroTests-0.16.0/heteroTests/R/runDiagnostics.R | 39 heteroTests-0.16.0/heteroTests/R/runHeteroTests.R | 281 heteroTests-0.16.0/heteroTests/R/runPanelTests.R | 18 heteroTests-0.16.0/heteroTests/R/runTimeSeriesTests.R | 2 heteroTests-0.16.0/heteroTests/R/simulation_framework.R | 51 heteroTests-0.16.0/heteroTests/R/suite_summary.R |only heteroTests-0.16.0/heteroTests/R/test_factory.R | 109 heteroTests-0.16.0/heteroTests/R/test_requirements.R | 8 heteroTests-0.16.0/heteroTests/R/utils.R | 333 heteroTests-0.16.0/heteroTests/R/validation.R | 217 heteroTests-0.16.0/heteroTests/R/zzz.R | 4 heteroTests-0.16.0/heteroTests/inst/CITATION | 18 heteroTests-0.16.0/heteroTests/inst/WORDLIST | 42 heteroTests-0.16.0/heteroTests/inst/doc/bibliography.html | 7 heteroTests-0.16.0/heteroTests/inst/doc/comprehensive_guide.R | 2 heteroTests-0.16.0/heteroTests/inst/doc/comprehensive_guide.Rmd | 2 heteroTests-0.16.0/heteroTests/inst/doc/comprehensive_guide.html | 46 heteroTests-0.16.0/heteroTests/inst/doc/performance_comparison_guide.R | 2 heteroTests-0.16.0/heteroTests/inst/doc/performance_comparison_guide.Rmd | 2 heteroTests-0.16.0/heteroTests/inst/doc/performance_comparison_guide.html | 3266 ------- heteroTests-0.16.0/heteroTests/inst/doc/real_world_case_studies.R | 4 heteroTests-0.16.0/heteroTests/inst/doc/real_world_case_studies.Rmd | 13 heteroTests-0.16.0/heteroTests/inst/doc/real_world_case_studies.html | 351 heteroTests-0.16.0/heteroTests/inst/doc/statistical_theory_and_implementation.R | 2 heteroTests-0.16.0/heteroTests/inst/doc/statistical_theory_and_implementation.Rmd | 31 heteroTests-0.16.0/heteroTests/inst/doc/statistical_theory_and_implementation.html | 102 heteroTests-0.16.0/heteroTests/inst/doc/troubleshooting.Rmd | 6 heteroTests-0.16.0/heteroTests/inst/doc/troubleshooting.html | 10 heteroTests-0.16.0/heteroTests/inst/doc/tutorial.R | 7 heteroTests-0.16.0/heteroTests/inst/doc/tutorial.Rmd | 30 heteroTests-0.16.0/heteroTests/inst/doc/tutorial.html | 58 heteroTests-0.16.0/heteroTests/inst/doc/using_heteroTests.R | 10 heteroTests-0.16.0/heteroTests/inst/doc/using_heteroTests.Rmd | 10 heteroTests-0.16.0/heteroTests/inst/doc/using_heteroTests.html | 1773 ++-- heteroTests-0.16.0/heteroTests/inst/tutorials/03-modern-and-scalable.ipynb | 13 heteroTests-0.16.0/heteroTests/inst/validation/README.md | 2052 ++++ heteroTests-0.16.0/heteroTests/inst/validation/analyse-fixed-effects-size.R |only heteroTests-0.16.0/heteroTests/inst/validation/box-m-approximations-size.R |only heteroTests-0.16.0/heteroTests/inst/validation/box-m-approximations-size.csv |only heteroTests-0.16.0/heteroTests/inst/validation/fixed-effects-dummies.R |only heteroTests-0.16.0/heteroTests/inst/validation/fixed-effects-dummies.csv |only heteroTests-0.16.0/heteroTests/inst/validation/fixed-effects-size-10000.csv |only heteroTests-0.16.0/heteroTests/inst/validation/fixed-effects-size.R |only heteroTests-0.16.0/heteroTests/inst/validation/fixed-effects-size.csv |only heteroTests-0.16.0/heteroTests/inst/validation/fixed-effects-variants-size.R |only heteroTests-0.16.0/heteroTests/inst/validation/fixed-effects-variants-size.csv |only heteroTests-0.16.0/heteroTests/inst/validation/full-sweep-size-power.R | 37 heteroTests-0.16.0/heteroTests/inst/validation/full-sweep-size-power.csv | 5 heteroTests-0.16.0/heteroTests/inst/validation/glejser-skewed-errors.R |only heteroTests-0.16.0/heteroTests/inst/validation/glejser-skewed-errors.csv |only heteroTests-0.16.0/heteroTests/inst/validation/harrison-mccabe-size-power.R |only heteroTests-0.16.0/heteroTests/inst/validation/harrison-mccabe-size-power.csv |only heteroTests-0.16.0/heteroTests/inst/validation/make-table.R | 1404 +++ heteroTests-0.16.0/heteroTests/inst/validation/modified-wald-size-power.R |only heteroTests-0.16.0/heteroTests/inst/validation/modified-wald-size-power.csv |only heteroTests-0.16.0/heteroTests/inst/validation/offset-refits-size.R |only heteroTests-0.16.0/heteroTests/inst/validation/offset-refits-size.csv |only heteroTests-0.16.0/heteroTests/inst/validation/pass-a-size-power.R | 8 heteroTests-0.16.0/heteroTests/inst/validation/survey-designs-size.R |only heteroTests-0.16.0/heteroTests/inst/validation/survey-designs-size.csv |only heteroTests-0.16.0/heteroTests/inst/validation/szroeter-design-null-size.R |only heteroTests-0.16.0/heteroTests/inst/validation/szroeter-design-null-size.csv |only heteroTests-0.16.0/heteroTests/inst/validation/variance-form-dnvk-bootstrap-check.R |only heteroTests-0.16.0/heteroTests/inst/validation/variance-form-dnvk-bootstrap-check.csv |only heteroTests-0.16.0/heteroTests/inst/validation/variance-form-dnvk-design.md |only heteroTests-0.16.0/heteroTests/inst/validation/variance-form-dnvk-prototype.R |only heteroTests-0.16.0/heteroTests/inst/validation/variance-form-dnvk-reproduction.R |only heteroTests-0.16.0/heteroTests/inst/validation/variance-form-dnvk-reproduction.csv |only heteroTests-0.16.0/heteroTests/inst/validation/variance-form-dnvk-size-power.R |only heteroTests-0.16.0/heteroTests/inst/validation/variance-form-dnvk-size-power.csv |only heteroTests-0.16.0/heteroTests/inst/validation/variance-form-size-power.R |only heteroTests-0.16.0/heteroTests/inst/validation/variance-form-size-power.csv |only heteroTests-0.16.0/heteroTests/inst/validation/weighted-fits-refit-reproduction.R |only heteroTests-0.16.0/heteroTests/inst/validation/weighted-fits-refit-reproduction.csv |only heteroTests-0.16.0/heteroTests/inst/validation/weighted-fits-size.R |only heteroTests-0.16.0/heteroTests/inst/validation/weighted-fits-size.csv |only heteroTests-0.16.0/heteroTests/inst/validation/white-bootstrap-transformed-size.R |only heteroTests-0.16.0/heteroTests/inst/validation/white-bootstrap-transformed-size.csv |only heteroTests-0.16.0/heteroTests/inst/validation/wild-multiplier-size.R |only heteroTests-0.16.0/heteroTests/inst/validation/wild-multiplier-size.csv |only heteroTests-0.16.0/heteroTests/inst/validation/wild-no-multiplier-size.R |only heteroTests-0.16.0/heteroTests/inst/validation/wild-no-multiplier-size.csv |only heteroTests-0.16.0/heteroTests/man/HeteroDiagnostic.Rd | 5 heteroTests-0.16.0/heteroTests/man/TestFactory.Rd | 9 heteroTests-0.16.0/heteroTests/man/autoplot.hetero_test_suite.Rd | 42 heteroTests-0.16.0/heteroTests/man/cachedTest.Rd | 104 heteroTests-0.16.0/heteroTests/man/checkData.Rd | 6 heteroTests-0.16.0/heteroTests/man/checkModel.Rd | 30 heteroTests-0.16.0/heteroTests/man/checkModelEnhanced.Rd | 11 heteroTests-0.16.0/heteroTests/man/clearAnalysisCache.Rd | 17 heteroTests-0.16.0/heteroTests/man/clearTestCache.Rd | 17 heteroTests-0.16.0/heteroTests/man/clearValidationCache.Rd | 6 heteroTests-0.16.0/heteroTests/man/compareModelDiagnostics.Rd | 5 heteroTests-0.16.0/heteroTests/man/compareTestResults.Rd | 6 heteroTests-0.16.0/heteroTests/man/figures |only heteroTests-0.16.0/heteroTests/man/fitWLS.Rd | 147 heteroTests-0.16.0/heteroTests/man/generateHeteroRecommendations.Rd | 3 heteroTests-0.16.0/heteroTests/man/hetero_test_suite.Rd | 14 heteroTests-0.16.0/heteroTests/man/ht_logging.Rd | 6 heteroTests-0.16.0/heteroTests/man/listDiagnostics.Rd |only heteroTests-0.16.0/heteroTests/man/messages.Rd | 5 heteroTests-0.16.0/heteroTests/man/performArchLMTest.Rd | 22 heteroTests-0.16.0/heteroTests/man/performBPRandomEffectsTest.Rd | 17 heteroTests-0.16.0/heteroTests/man/performBPTest.Rd | 44 heteroTests-0.16.0/heteroTests/man/performBPTestRobust.Rd | 67 heteroTests-0.16.0/heteroTests/man/performBPTestStreaming.Rd | 25 heteroTests-0.16.0/heteroTests/man/performBartlettTest.Rd | 15 heteroTests-0.16.0/heteroTests/man/performBoxMTest.Rd | 57 heteroTests-0.16.0/heteroTests/man/performBrownForsytheTest.Rd | 15 heteroTests-0.16.0/heteroTests/man/performCookWeisbergTest.Rd | 30 heteroTests-0.16.0/heteroTests/man/performDavidianCarrollTest.Rd | 24 heteroTests-0.16.0/heteroTests/man/performFlignerKilleenTest.Rd | 27 heteroTests-0.16.0/heteroTests/man/performGQTest.Rd | 25 heteroTests-0.16.0/heteroTests/man/performGlejserTest.Rd | 64 heteroTests-0.16.0/heteroTests/man/performHarrisonMcCabeTest.Rd |only heteroTests-0.16.0/heteroTests/man/performHartleyFmaxTest.Rd | 15 heteroTests-0.16.0/heteroTests/man/performHarveyTest.Rd | 22 heteroTests-0.16.0/heteroTests/man/performHighDimensionalTest.Rd | 26 heteroTests-0.16.0/heteroTests/man/performKoenkerTest.Rd | 47 heteroTests-0.16.0/heteroTests/man/performKoenkerTestStreaming.Rd | 28 heteroTests-0.16.0/heteroTests/man/performLeveneTest.Rd | 15 heteroTests-0.16.0/heteroTests/man/performMcLeodLiTest.Rd | 22 heteroTests-0.16.0/heteroTests/man/performNCVTest.Rd | 32 heteroTests-0.16.0/heteroTests/man/performOBrienTest.Rd | 15 heteroTests-0.16.0/heteroTests/man/performParkTest.Rd | 17 heteroTests-0.16.0/heteroTests/man/performPesaranTest.Rd | 43 heteroTests-0.16.0/heteroTests/man/performQuantileRegressionTest.Rd | 50 heteroTests-0.16.0/heteroTests/man/performRESETTest.Rd | 32 heteroTests-0.16.0/heteroTests/man/performRankPermutationTest.Rd | 32 heteroTests-0.16.0/heteroTests/man/performScatterDiagnostic.Rd | 10 heteroTests-0.16.0/heteroTests/man/performSpatialHeteroTest.Rd | 44 heteroTests-0.16.0/heteroTests/man/performSpearmanTest.Rd | 22 heteroTests-0.16.0/heteroTests/man/performSpreadLevelTest.Rd | 22 heteroTests-0.16.0/heteroTests/man/performStudentizedBPTest.Rd | 110 heteroTests-0.16.0/heteroTests/man/performSzroeterTest.Rd | 137 heteroTests-0.16.0/heteroTests/man/performVarianceFormTest.Rd |only heteroTests-0.16.0/heteroTests/man/performWhiteTest.Rd | 53 heteroTests-0.16.0/heteroTests/man/performWhiteTestBootstrap.Rd | 136 heteroTests-0.16.0/heteroTests/man/performWhiteTestRobust.Rd | 37 heteroTests-0.16.0/heteroTests/man/performWhiteTestStreaming.Rd | 50 heteroTests-0.16.0/heteroTests/man/performWildBootstrapTest.Rd | 138 heteroTests-0.16.0/heteroTests/man/plot.power_analysis.Rd | 2 heteroTests-0.16.0/heteroTests/man/plotBeforeAfter.Rd | 26 heteroTests-0.16.0/heteroTests/man/plotDiagnosticSuite.Rd | 5 heteroTests-0.16.0/heteroTests/man/plotDiagnosticSuiteEnhanced.Rd | 5 heteroTests-0.16.0/heteroTests/man/plotResidualsFitted.Rd | 16 heteroTests-0.16.0/heteroTests/man/plotResidualsFittedEnhanced.Rd | 6 heteroTests-0.16.0/heteroTests/man/rbootstrap_test_statistic.Rd | 155 heteroTests-0.16.0/heteroTests/man/rcalculateEffectSize.Rd | 6 heteroTests-0.16.0/heteroTests/man/registerDiagnostic.Rd | 4 heteroTests-0.16.0/heteroTests/man/restimate_test_power.Rd | 6 heteroTests-0.16.0/heteroTests/man/runAdvancedDiagnostics.Rd |only heteroTests-0.16.0/heteroTests/man/runDiagnostics.Rd | 6 heteroTests-0.16.0/heteroTests/man/runHeteroTests.Rd | 100 heteroTests-0.16.0/heteroTests/man/runHeteroTestsParallel.Rd | 17 heteroTests-0.16.0/heteroTests/man/runPanelTests.Rd | 4 heteroTests-0.16.0/heteroTests/man/runSurveyHeteroTests.Rd | 55 heteroTests-0.16.0/heteroTests/man/rvalidateModelInputs.Rd | 8 heteroTests-0.16.0/heteroTests/man/rvalidate_against_reference.Rd | 6 heteroTests-0.16.0/heteroTests/man/simulate_hetero.Rd | 1 heteroTests-0.16.0/heteroTests/man/simulation_framework.Rd | 24 heteroTests-0.16.0/heteroTests/man/std_error.Rd | 5 heteroTests-0.16.0/heteroTests/man/std_warning.Rd | 5 heteroTests-0.16.0/heteroTests/man/suggestRemediation.Rd | 6 heteroTests-0.16.0/heteroTests/man/summary.HeteroDiagnostic.Rd | 5 heteroTests-0.16.0/heteroTests/man/summary.hetero_test_suite.Rd |only heteroTests-0.16.0/heteroTests/man/test.HeteroDiagnostic.Rd | 1 heteroTests-0.16.0/heteroTests/man/test_factory.Rd | 11 heteroTests-0.16.0/heteroTests/man/test_results.Rd |only heteroTests-0.16.0/heteroTests/man/tidy.hetero_test.Rd | 7 heteroTests-0.16.0/heteroTests/man/validateTestInputs.Rd | 11 heteroTests-0.16.0/heteroTests/tests/testthat/_snaps |only heteroTests-0.16.0/heteroTests/tests/testthat/helper-deprecation.R |only heteroTests-0.16.0/heteroTests/tests/testthat/helper-fligner.R |only heteroTests-0.16.0/heteroTests/tests/testthat/helper-model-context.R |only heteroTests-0.16.0/heteroTests/tests/testthat/helper-test-recipes.R |only heteroTests-0.16.0/heteroTests/tests/testthat/test-HeteroDiagnostic.R | 2 heteroTests-0.16.0/heteroTests/tests/testthat/test-additional-tests.R | 2 heteroTests-0.16.0/heteroTests/tests/testthat/test-autoplot.R |only heteroTests-0.16.0/heteroTests/tests/testthat/test-benchmarking-system.R | 8 heteroTests-0.16.0/heteroTests/tests/testthat/test-bootstrap-pvalue-convention.R | 48 heteroTests-0.16.0/heteroTests/tests/testthat/test-boxm.R | 193 heteroTests-0.16.0/heteroTests/tests/testthat/test-cache-contract.R |only heteroTests-0.16.0/heteroTests/tests/testthat/test-cook-weisberg-entry.R |only heteroTests-0.16.0/heteroTests/tests/testthat/test-core-functions.R | 70 heteroTests-0.16.0/heteroTests/tests/testthat/test-data-alignment-guard.R |only heteroTests-0.16.0/heteroTests/tests/testthat/test-deprecated-names.R |only heteroTests-0.16.0/heteroTests/tests/testthat/test-downloadTeachingData.R | 2 heteroTests-0.16.0/heteroTests/tests/testthat/test-ecosystem-integration.R | 21 heteroTests-0.16.0/heteroTests/tests/testthat/test-enhanced-merge.R |only heteroTests-0.16.0/heteroTests/tests/testthat/test-exported-internals.R |only heteroTests-0.16.0/heteroTests/tests/testthat/test-fitwls-offset.R |only heteroTests-0.16.0/heteroTests/tests/testthat/test-fitwls-reestimation.R |only heteroTests-0.16.0/heteroTests/tests/testthat/test-fixed-effects-warning.R |only heteroTests-0.16.0/heteroTests/tests/testthat/test-fligner-killeen-ties.R |only heteroTests-0.16.0/heteroTests/tests/testthat/test-glejser-robust.R |only heteroTests-0.16.0/heteroTests/tests/testthat/test-grouped-fits.R |only heteroTests-0.16.0/heteroTests/tests/testthat/test-harrison-mccabe.R |only heteroTests-0.16.0/heteroTests/tests/testthat/test-hdiag-formula.R | 2 heteroTests-0.16.0/heteroTests/tests/testthat/test-individual-tests.R | 8 heteroTests-0.16.0/heteroTests/tests/testthat/test-input-validation.R |only heteroTests-0.16.0/heteroTests/tests/testthat/test-integration.R | 5 heteroTests-0.16.0/heteroTests/tests/testthat/test-intelligent-recommendations.R | 95 heteroTests-0.16.0/heteroTests/tests/testthat/test-invalid-inputs.R | 2 heteroTests-0.16.0/heteroTests/tests/testthat/test-koenker-studentized.R |only heteroTests-0.16.0/heteroTests/tests/testthat/test-memory-usage.R | 2 heteroTests-0.16.0/heteroTests/tests/testthat/test-model-context.R |only heteroTests-0.16.0/heteroTests/tests/testthat/test-model-data-convention.R |only heteroTests-0.16.0/heteroTests/tests/testthat/test-model-eligibility.R |only heteroTests-0.16.0/heteroTests/tests/testthat/test-network-handling.R | 2 heteroTests-0.16.0/heteroTests/tests/testthat/test-otherTests.R | 2 heteroTests-0.16.0/heteroTests/tests/testthat/test-panel-reference.R | 70 heteroTests-0.16.0/heteroTests/tests/testthat/test-parallel-reproducibility.R |only heteroTests-0.16.0/heteroTests/tests/testthat/test-pass-a-reference.R | 148 heteroTests-0.16.0/heteroTests/tests/testthat/test-pass-b-reference.R | 17 heteroTests-0.16.0/heteroTests/tests/testthat/test-pass-c-reference.R | 11 heteroTests-0.16.0/heteroTests/tests/testthat/test-perform-error-handling.R | 4 heteroTests-0.16.0/heteroTests/tests/testthat/test-performRemainingTests.R | 4 heteroTests-0.16.0/heteroTests/tests/testthat/test-performWhiteTest.R | 636 + heteroTests-0.16.0/heteroTests/tests/testthat/test-plots.R | 10 heteroTests-0.16.0/heteroTests/tests/testthat/test-plotting.R | 21 heteroTests-0.16.0/heteroTests/tests/testthat/test-public-api.R | 235 heteroTests-0.16.0/heteroTests/tests/testthat/test-quantile-joint-reference.R | 43 heteroTests-0.16.0/heteroTests/tests/testthat/test-r-prefixed-and-test.R |only heteroTests-0.16.0/heteroTests/tests/testthat/test-reference-comparisons.R | 110 heteroTests-0.16.0/heteroTests/tests/testthat/test-reference-index.R |only heteroTests-0.16.0/heteroTests/tests/testthat/test-registry-systems.R | 73 heteroTests-0.16.0/heteroTests/tests/testthat/test-remediation.R | 23 heteroTests-0.16.0/heteroTests/tests/testthat/test-resampling-refits.R |only heteroTests-0.16.0/heteroTests/tests/testthat/test-return-contract.R |only heteroTests-0.16.0/heteroTests/tests/testthat/test-robust-methods.R | 124 heteroTests-0.16.0/heteroTests/tests/testthat/test-runHeteroTests.R | 50 heteroTests-0.16.0/heteroTests/tests/testthat/test-s3-classes.R | 61 heteroTests-0.16.0/heteroTests/tests/testthat/test-simulation-names.R |only heteroTests-0.16.0/heteroTests/tests/testthat/test-simulation_framework.R | 10 heteroTests-0.16.0/heteroTests/tests/testthat/test-statistical-accuracy.R | 2 heteroTests-0.16.0/heteroTests/tests/testthat/test-statistical_properties.R | 2 heteroTests-0.16.0/heteroTests/tests/testthat/test-streaming.R | 153 heteroTests-0.16.0/heteroTests/tests/testthat/test-suite-summary.R |only heteroTests-0.16.0/heteroTests/tests/testthat/test-survey-designs.R |only heteroTests-0.16.0/heteroTests/tests/testthat/test-szroeter-registry.R |only heteroTests-0.16.0/heteroTests/tests/testthat/test-utils.R | 8 heteroTests-0.16.0/heteroTests/tests/testthat/test-validation.R | 49 heteroTests-0.16.0/heteroTests/tests/testthat/test-variance-form.R |only heteroTests-0.16.0/heteroTests/tests/testthat/test-weighted-fits.R |only heteroTests-0.16.0/heteroTests/tests/testthat/test-weighted-resampling.R |only heteroTests-0.16.0/heteroTests/vignettes/comprehensive_guide.Rmd | 2 heteroTests-0.16.0/heteroTests/vignettes/performance_comparison_guide.Rmd | 2 heteroTests-0.16.0/heteroTests/vignettes/real_world_case_studies.Rmd | 13 heteroTests-0.16.0/heteroTests/vignettes/statistical_theory_and_implementation.Rmd | 31 heteroTests-0.16.0/heteroTests/vignettes/troubleshooting.Rmd | 6 heteroTests-0.16.0/heteroTests/vignettes/tutorial.Rmd | 30 heteroTests-0.16.0/heteroTests/vignettes/using_heteroTests.Rmd | 10 313 files changed, 21216 insertions(+), 6940 deletions(-)
Title: Read and Write Frictionless Data Packages
Description: Read and write Frictionless Data Packages. A 'Data Package'
(<https://datapackage.org/>) is a simple container format and standard to
describe and package a collection of (tabular) data. It is typically used to
publish FAIR (<https://www.gofair.foundation/fair-principles>) and open
datasets.
Author: Peter Desmet [aut, cre] ),
Damiano Oldoni [aut] ),
Pieter Huybrechts [aut] ),
Sanne Govaert [aut] ),
Kyle Husmann [ctb] ,
Research Institute for Nature and Forest [cph] ,
Research Foundation - Flanders [fnd] ,
NLnet foundation [fnd] ,
Beatriz Milz [ [...truncated...]
Maintainer: Peter Desmet <peter.desmet@inbo.be>
Diff between frictionless versions 1.3.0 dated 2026-07-31 and 2.0.1 dated 2026-10-29
frictionless-1.3.0/frictionless/tests/testthat/data/mark_decimal.csv |only frictionless-1.3.0/frictionless/tests/testthat/data/mark_decimal_group.csv |only frictionless-1.3.0/frictionless/tests/testthat/data/mark_default.csv |only frictionless-2.0.1/frictionless/DESCRIPTION | 21 frictionless-2.0.1/frictionless/MD5 | 180 +-- frictionless-2.0.1/frictionless/NAMESPACE | 2 frictionless-2.0.1/frictionless/NEWS.md | 37 frictionless-2.0.1/frictionless/R/add_properties.R |only frictionless-2.0.1/frictionless/R/add_resource.R | 70 - frictionless-2.0.1/frictionless/R/check_path.R | 18 frictionless-2.0.1/frictionless/R/check_schema.R | 6 frictionless-2.0.1/frictionless/R/col_types.R | 3 frictionless-2.0.1/frictionless/R/collectors.R | 4 frictionless-2.0.1/frictionless/R/create_package.R | 9 frictionless-2.0.1/frictionless/R/create_schema.R | 5 frictionless-2.0.1/frictionless/R/deprecated.R | 4 frictionless-2.0.1/frictionless/R/example_package.R | 20 frictionless-2.0.1/frictionless/R/locale.R | 21 frictionless-2.0.1/frictionless/R/read_from_path.R | 13 frictionless-2.0.1/frictionless/R/read_package.R | 12 frictionless-2.0.1/frictionless/R/read_resource.R | 2 frictionless-2.0.1/frictionless/R/resource.R | 2 frictionless-2.0.1/frictionless/R/schema.R | 11 frictionless-2.0.1/frictionless/R/upgrade_descriptor.R |only frictionless-2.0.1/frictionless/R/upgrade_package.R |only frictionless-2.0.1/frictionless/R/upgrade_resource.R |only frictionless-2.0.1/frictionless/R/upgrade_schema.R |only frictionless-2.0.1/frictionless/R/utils.R | 46 frictionless-2.0.1/frictionless/R/version.R | 49 frictionless-2.0.1/frictionless/R/write_package.R | 4 frictionless-2.0.1/frictionless/README.md | 14 frictionless-2.0.1/frictionless/inst/doc/data-package.R | 22 frictionless-2.0.1/frictionless/inst/doc/data-package.Rmd | 77 - frictionless-2.0.1/frictionless/inst/doc/data-package.html | 167 +-- frictionless-2.0.1/frictionless/inst/doc/data-resource.R | 46 frictionless-2.0.1/frictionless/inst/doc/data-resource.Rmd | 113 +- frictionless-2.0.1/frictionless/inst/doc/data-resource.html | 504 +++++---- frictionless-2.0.1/frictionless/inst/doc/frictionless.Rmd | 95 + frictionless-2.0.1/frictionless/inst/doc/frictionless.html | 258 ++-- frictionless-2.0.1/frictionless/inst/doc/table-dialect.R | 4 frictionless-2.0.1/frictionless/inst/doc/table-dialect.Rmd | 72 - frictionless-2.0.1/frictionless/inst/doc/table-dialect.html | 137 +- frictionless-2.0.1/frictionless/inst/doc/table-schema.R | 7 frictionless-2.0.1/frictionless/inst/doc/table-schema.Rmd | 127 +- frictionless-2.0.1/frictionless/inst/doc/table-schema.html | 431 +++++--- frictionless-2.0.1/frictionless/inst/extdata/v2/datapackage.json | 21 frictionless-2.0.1/frictionless/man/add_properties.Rd |only frictionless-2.0.1/frictionless/man/add_resource.Rd | 15 frictionless-2.0.1/frictionless/man/create_schema.Rd | 2 frictionless-2.0.1/frictionless/man/example_package.Rd | 15 frictionless-2.0.1/frictionless/man/frictionless-package.Rd | 3 frictionless-2.0.1/frictionless/man/read_package.Rd | 2 frictionless-2.0.1/frictionless/man/read_resource.Rd | 2 frictionless-2.0.1/frictionless/man/remove_resource.Rd | 1 frictionless-2.0.1/frictionless/man/schema.Rd | 2 frictionless-2.0.1/frictionless/man/upgrade_package.Rd |only frictionless-2.0.1/frictionless/man/version.Rd | 42 frictionless-2.0.1/frictionless/man/write_package.Rd | 4 frictionless-2.0.1/frictionless/tests/testthat/data/deployments_schema.json | 20 frictionless-2.0.1/frictionless/tests/testthat/data/deployments_schema.yaml | 59 - frictionless-2.0.1/frictionless/tests/testthat/data/deployments_schema_v1.json |only frictionless-2.0.1/frictionless/tests/testthat/data/mark.json | 87 + frictionless-2.0.1/frictionless/tests/testthat/data/mark_int_group.csv |only frictionless-2.0.1/frictionless/tests/testthat/data/mark_int_group_invalid.csv |only frictionless-2.0.1/frictionless/tests/testthat/data/mark_int_group_num_decimal.csv |only frictionless-2.0.1/frictionless/tests/testthat/data/mark_num_decimal.csv |only frictionless-2.0.1/frictionless/tests/testthat/data/mark_num_decimal_group.csv |only frictionless-2.0.1/frictionless/tests/testthat/data/mark_num_default.csv |only frictionless-2.0.1/frictionless/tests/testthat/data/schema_custom.json | 1 frictionless-2.0.1/frictionless/tests/testthat/data/type_datetime.csv | 4 frictionless-2.0.1/frictionless/tests/testthat/data/type_other.csv | 4 frictionless-2.0.1/frictionless/tests/testthat/data/types.json | 46 frictionless-2.0.1/frictionless/tests/testthat/data/valid_minimal.yml | 6 frictionless-2.0.1/frictionless/tests/testthat/test-add_properties.R |only frictionless-2.0.1/frictionless/tests/testthat/test-add_resource.R | 155 +- frictionless-2.0.1/frictionless/tests/testthat/test-check_data.R | 2 frictionless-2.0.1/frictionless/tests/testthat/test-check_package.R | 34 frictionless-2.0.1/frictionless/tests/testthat/test-check_path.R | 23 frictionless-2.0.1/frictionless/tests/testthat/test-check_schema.R | 48 frictionless-2.0.1/frictionless/tests/testthat/test-create_package.R | 46 frictionless-2.0.1/frictionless/tests/testthat/test-create_schema.R | 7 frictionless-2.0.1/frictionless/tests/testthat/test-deprecated.R | 2 frictionless-2.0.1/frictionless/tests/testthat/test-example_package.R | 14 frictionless-2.0.1/frictionless/tests/testthat/test-print.datapackage.R | 18 frictionless-2.0.1/frictionless/tests/testthat/test-read_package.R | 45 frictionless-2.0.1/frictionless/tests/testthat/test-read_resource.R | 517 +++++----- frictionless-2.0.1/frictionless/tests/testthat/test-remove_resource.R | 15 frictionless-2.0.1/frictionless/tests/testthat/test-resource.R | 33 frictionless-2.0.1/frictionless/tests/testthat/test-resource_names.R | 10 frictionless-2.0.1/frictionless/tests/testthat/test-upgrade_descriptor.R |only frictionless-2.0.1/frictionless/tests/testthat/test-upgrade_package.R |only frictionless-2.0.1/frictionless/tests/testthat/test-upgrade_resource.R |only frictionless-2.0.1/frictionless/tests/testthat/test-upgrade_schema.R |only frictionless-2.0.1/frictionless/tests/testthat/test-utils.R | 42 frictionless-2.0.1/frictionless/tests/testthat/test-version.R | 188 +++ frictionless-2.0.1/frictionless/tests/testthat/test-write_package.R | 198 ++- frictionless-2.0.1/frictionless/vignettes/data-package.Rmd | 77 - frictionless-2.0.1/frictionless/vignettes/data-resource.Rmd | 113 +- frictionless-2.0.1/frictionless/vignettes/frictionless.Rmd | 95 + frictionless-2.0.1/frictionless/vignettes/frictionless.Rmd.orig | 34 frictionless-2.0.1/frictionless/vignettes/table-dialect.Rmd | 72 - frictionless-2.0.1/frictionless/vignettes/table-schema.Rmd | 127 +- 102 files changed, 3008 insertions(+), 1856 deletions(-)
Title: Kernel Ridge Regression using 'RcppArmadillo'
Description: Provides core computational operations in C++ via 'RcppArmadillo', enabling faster performance than pure R, improved numerical stability, and parallel execution with OpenMP where available. On systems without OpenMP support, the package automatically falls back to single-threaded execution with no user configuration required. For efficient model selection, it integrates with 'CVST' to provide sequential-testing cross-validation and additionally supports restricted maximum likelihood (REML) for continuous optimization of the regularization parameter. The package offers a unified interface for exact kernel ridge regression and three scalable approximations—Nyström, Pivoted Cholesky, and Random Fourier Features—allowing analyses with substantially larger sample sizes than are feasible with exact KRR. It also integrates with the 'tidymodels' ecosystem via the 'parsnip' model specification 'krr_reg', and the S3 method tunable.krr_reg(). To understand the theoretical background, one can refe [...truncated...]
Author: Gyeongmin Kim [aut] ,
Seyoung Lee [aut] ,
Miyoung Jang [aut] ,
Kwan-Young Bak [aut, cre, cph]
Maintainer: Kwan-Young Bak <kybak@sungshin.ac.kr>
Diff between FastKRR versions 0.2.1 dated 2026-07-21 and 0.2.2 dated 2026-10-29
DESCRIPTION | 10 +- MD5 | 54 ++++++++-------- R/CVST_linkfunction.R | 107 +++++++++++++++++++++++++++----- R/RcppExports.R | 10 +- R/approx_kernel.R | 13 ++- R/error.R | 59 +++++++++++++---- R/link2tidymodels.R | 6 - R/make_kernel.R | 10 +- R/param.R | 2 R/print.R | 2 R/rff_random.R | 2 README.md | 6 - man/approx_kernel.Rd | 11 +-- man/error.krr.Rd | 20 ++++- man/fastkrr.Rd | 42 +++++++++--- man/fastkrr_fit_wrapper.Rd | 2 man/krr_reg.Rd | 4 - man/make_kernel.Rd | 10 +- man/param.krr.Rd | 2 man/predict.krr.Rd | 4 + man/print.approx_kernel.Rd | 2 src/Makevars | 2 src/Makevars.win | 2 src/kernel.cpp | 4 - src/nystorm.cpp | 4 - src/rff.cpp | 4 - tests/testthat/test-CVST_linkfunction.R | 82 ++++++++++++++++++++++++ tests/testthat/test-error.R | 34 ++++++++++ 28 files changed, 385 insertions(+), 125 deletions(-)
Title: Calculate and Visualize Degree-Days for Pest Monitoring
Description: Combines pest trap observations with daily temperatures to
calculate and visualize cumulative degree-days. Temperature inputs
include 'Daymet' <https://daymet.ornl.gov>,
'Open-Meteo' <https://open-meteo.com/>, reports from the California
Irrigation Management Information System ('CIMIS')
<https://cimis.water.ca.gov>, and user-supplied daily weather data.
Degree-days are calculated using the simple-average method with
either an upper threshold applied to the daily mean or an explicitly
selected calculation without an upper cutoff. The first positive
trap count defines the biofix for every pest, with accumulation
beginning on the following day. Negative daily degree-day values
are set to zero. Users can provide temperature thresholds and
optional thermal reference values. Thermal reference
markers and their multiples do not independently establish flight
or generation identities. Complete daily calculations and weather
provenance are retained with the output to support [...truncated...]
Author: Santosh Bhandari [aut, cre],
Lalit Kharel [aut],
Mahesh Ghimire [aut]
Maintainer: Santosh Bhandari <santoshbhandari4556@gmail.com>
Diff between TrackTrap versions 1.0.1 dated 2026-08-20 and 1.1.0 dated 2026-10-29
DESCRIPTION | 44 +- MD5 | 39 + NAMESPACE | 1 NEWS.md | 136 ++++++ R/TrackTrap-package.R | 1 R/data.R | 32 + R/phenology.R | 592 ++++++++++++++++-------------- data/pest_thresholds.rda |binary inst/doc/cimis-manual-workflow.R | 90 +++- inst/doc/cimis-manual-workflow.html | 265 +++++++++++-- inst/doc/cimis-manual-workflow.rmd | 192 ++++++++- inst/extdata |only man/TrackTrap-package.Rd | 4 man/calc_pest_phenology.Rd | 112 +++-- man/fetch_open_meteo.Rd | 50 +- man/pest_thresholds.Rd | 33 + man/plot_trap_phenology.Rd | 80 ++-- tests/testthat/helper-cimis.R |only tests/testthat/test-calc_pest_phenology.R | 162 ++++++-- tests/testthat/test-pest_thresholds.R | 56 ++ tests/testthat/test-phenology.R |only vignettes/cimis-manual-workflow.rmd | 192 ++++++++- 22 files changed, 1488 insertions(+), 593 deletions(-)
Title: Access the 'Open Data API' of Pernambuco Court of Accounts
Description: An R interface to the 'Open Data API' of the Tribunal de Contas do
Estado de Pernambuco (TCE-PE), the Court of Accounts of the State of
Pernambuco, Brazil. Provides tidy, ready-to-use functions to query public
data on revenues, expenditures, commitments, procurement, contracts,
agreements, public works, legal processes, personnel and reference tables
for all state and municipal government entities in Pernambuco. All results
are returned as tibbles with column names converted to 'snake_case' by
default. Uses 'httr2' for HTTP requests and 'cli' for user-friendly
messages. See <https://sistemas.tcepe.tc.br/DadosAbertos/> for the API
documentation.
Author: Andre Leite [aut, cre] ,
Marcos Wasiliew [aut] ,
Hugo Vasconcelos [aut] ,
Carlos Amorim [aut] ,
Diogo Bezerra [aut] ,
Julia Nascimento Barreto [aut]
Maintainer: Andre Leite <leite@castlab.org>
Diff between tceper versions 0.1.4 dated 2026-06-01 and 0.1.5 dated 2026-10-29
DESCRIPTION | 37 - MD5 | 57 +- NAMESPACE | 1 NEWS.md | 31 + R/introspection.R | 11 R/remessa.R | 14 README.md | 6 inst/doc/endpoints-reference.html | 4 inst/extdata/tcepe_dados_abertos_catalogo.json | 595 ++++++++++++++++--------- man/figures/logo.svg | 4 man/tce_benefit_types.Rd | 1 man/tce_budget_statuses.Rd | 1 man/tce_catalog.Rd | 2 man/tce_legal_instrument_documents.Rd | 1 man/tce_legal_instrument_items.Rd | 1 man/tce_legal_instrument_participants.Rd | 1 man/tce_legal_instrument_terms.Rd |only man/tce_legal_instruments.Rd | 1 man/tce_procurement_process_budget.Rd | 1 man/tce_procurement_process_documents.Rd | 1 man/tce_procurement_process_participants.Rd | 1 man/tce_procurement_processes.Rd | 1 man/tce_reference_codes.Rd | 1 man/tce_reference_dates.Rd | 1 man/tce_reference_sources.Rd | 1 man/tce_remessa_works.Rd | 1 man/tce_remessa_works_execution.Rd | 1 man/tce_remessa_works_geometry.Rd | 1 man/tce_update_indices.Rd | 1 man/tceper-package.Rd | 13 30 files changed, 529 insertions(+), 263 deletions(-)
Title: Connecting Stream Mining Components Using Sockets and Web
Services
Description: Adds functionality to connect stream mining components from the stream package using sockets and Web services. The package can be used to create distributed workflows and plumber-based Web services that can be deployed on most common cloud services.
Author: Michael Hahsler [aut, cre, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
This is a re-admission after prior archival of version 0.1.0 dated 2026-10-23
Diff between streamConnect versions 0.1.0 dated 2026-10-23 and 0.1.1 dated 2026-10-29
DESCRIPTION | 8 +- MD5 | 44 +++++++-------- NAMESPACE | 1 NEWS.md | 4 + R/DSC_WebService.R | 44 ++++++++------- R/DSD_ReadSocket.R | 50 +++++++++-------- R/DSD_ReadWebService.R | 52 +++++++++-------- R/has_localhost_server.R |only R/publish_DSC_via_WebService.R | 90 ++++++++++++++++--------------- R/publish_DSD_via_Socket.R | 50 +++++++++-------- R/publish_DSD_via_WebService.R | 110 +++++++++++++++++++------------------- README.md | 11 ++- inst/doc/streamConnect.R | 23 +++++-- inst/doc/streamConnect.Rmd | 24 +++++--- inst/doc/streamConnect.html | 76 +++++++++++++------------- man/DSC_WebService.Rd | 42 +++++++------- man/DSD_ReadSocket.Rd | 50 +++++++++-------- man/DSD_ReadWebService.Rd | 52 +++++++++-------- man/has_localhost_server.Rd |only man/publish_DSC_via_WebService.Rd | 90 ++++++++++++++++--------------- man/publish_DSD_via_Socket.Rd | 50 +++++++++-------- man/publish_DSD_via_WebService.Rd | 110 +++++++++++++++++++------------------- man/streamConnect-package.Rd | 4 - vignettes/streamConnect.Rmd | 24 +++++--- 24 files changed, 544 insertions(+), 465 deletions(-)
Title: Robust Test Statistics for Structural Equation Models
Description: Computes robust p-values for overall fit and nested comparisons of
structural equation models fitted with 'lavaan'. Implements penalized
eigenvalue block averaging and penalized regression (Foldnes, Moss,
Grønneberg, 2025) <doi:10.1080/10705511.2024.2372028>, including their
extension to nested models (Foldnes, Grønneberg, Moss, 2026)
<doi:10.3758/s13428-026-02968-4>, alongside familiar corrections such as
Satorra-Bentler. Supported settings include complete-data ML, GLS, and ULS,
categorical DWLS and ULS, and full-information maximum likelihood with one
or several groups. Score and criterion-difference tests of parameter
restrictions are also available, including restrictions in misspecified
models.
Author: Jonas Moss [aut, cre] ,
Njal Foldnes [ctb] ,
Steffen Groenneberg [ctb]
Maintainer: Jonas Moss <jonas.moss.statistics@gmail.com>
Diff between semTests versions 1.0.0 dated 2026-07-19 and 2.0.0 dated 2026-10-29
semTests-1.0.0/semTests/inst/doc/continuous-data.R |only semTests-1.0.0/semTests/inst/doc/continuous-data.Rmd |only semTests-1.0.0/semTests/inst/doc/continuous-data.html |only semTests-1.0.0/semTests/inst/doc/latent-growth.R |only semTests-1.0.0/semTests/inst/doc/latent-growth.Rmd |only semTests-1.0.0/semTests/inst/doc/latent-growth.html |only semTests-1.0.0/semTests/inst/doc/measurement-invariance.R |only semTests-1.0.0/semTests/inst/doc/measurement-invariance.Rmd |only semTests-1.0.0/semTests/inst/doc/measurement-invariance.html |only semTests-1.0.0/semTests/man/figures/README-plot_eval-1.png |only semTests-1.0.0/semTests/man/figures/README-unnamed-chunk-2-1.png |only semTests-1.0.0/semTests/man/fiml_align_parameter_basis.Rd |only semTests-1.0.0/semTests/man/fiml_parameter_keys.Rd |only semTests-1.0.0/semTests/tools |only semTests-1.0.0/semTests/vignettes/continuous-data.Rmd |only semTests-1.0.0/semTests/vignettes/latent-growth.Rmd |only semTests-1.0.0/semTests/vignettes/measurement-invariance.Rmd |only semTests-2.0.0/semTests/DESCRIPTION | 12 semTests-2.0.0/semTests/MD5 | 144 +- semTests-2.0.0/semTests/NAMESPACE | 8 semTests-2.0.0/semTests/NEWS.md | 60 + semTests-2.0.0/semTests/R/checks.R | 16 semTests-2.0.0/semTests/R/fiml_fmg.R | 105 -- semTests-2.0.0/semTests/R/gamma.R | 69 + semTests-2.0.0/semTests/R/get_a_matrix.R | 114 ++ semTests-2.0.0/semTests/R/inference_control.R |only semTests-2.0.0/semTests/R/inference_geometry.R |only semTests-2.0.0/semTests/R/inference_lavaan.R |only semTests-2.0.0/semTests/R/inference_nested.R |only semTests-2.0.0/semTests/R/inference_tests.R |only semTests-2.0.0/semTests/R/inference_weights.R |only semTests-2.0.0/semTests/R/lavaan_helper.R | 30 semTests-2.0.0/semTests/R/moment_influence.R |only semTests-2.0.0/semTests/R/polychoric_influence.R |only semTests-2.0.0/semTests/R/pvalues.R | 221 +++- semTests-2.0.0/semTests/R/quadratic.R |only semTests-2.0.0/semTests/R/semtest.R |only semTests-2.0.0/semTests/R/support.R | 67 + semTests-2.0.0/semTests/README.md | 167 +-- semTests-2.0.0/semTests/build/partial.rdb |binary semTests-2.0.0/semTests/build/vignette.rds |binary semTests-2.0.0/semTests/inst/doc/categorical-data.R | 106 -- semTests-2.0.0/semTests/inst/doc/categorical-data.Rmd | 235 ++-- semTests-2.0.0/semTests/inst/doc/categorical-data.html | 317 ++---- semTests-2.0.0/semTests/inst/doc/fiml-missing-data.R | 203 +--- semTests-2.0.0/semTests/inst/doc/fiml-missing-data.Rmd | 399 ++------ semTests-2.0.0/semTests/inst/doc/fiml-missing-data.html | 493 +++------- semTests-2.0.0/semTests/inst/doc/score-criterion.R |only semTests-2.0.0/semTests/inst/doc/score-criterion.Rmd |only semTests-2.0.0/semTests/inst/doc/score-criterion.html |only semTests-2.0.0/semTests/inst/doc/semTests.R | 73 - semTests-2.0.0/semTests/inst/doc/semTests.Rmd | 321 +++--- semTests-2.0.0/semTests/inst/doc/semTests.html | 411 ++++---- semTests-2.0.0/semTests/man/align_parameter_basis.Rd |only semTests-2.0.0/semTests/man/check_supported_nested.Rd | 9 semTests-2.0.0/semTests/man/compute_pvalues.Rd | 5 semTests-2.0.0/semTests/man/criterion_test_nested.Rd |only semTests-2.0.0/semTests/man/equilibrated_inverse.Rd |only semTests-2.0.0/semTests/man/figures/logo.png |binary semTests-2.0.0/semTests/man/figures/logo.svg |only semTests-2.0.0/semTests/man/fiml_h1_information_observed.Rd | 2 semTests-2.0.0/semTests/man/fiml_lambdas_nested.Rd | 2 semTests-2.0.0/semTests/man/fiml_restriction.Rd |only semTests-2.0.0/semTests/man/full_parameter_keys.Rd |only semTests-2.0.0/semTests/man/get_a_matrix.Rd |only semTests-2.0.0/semTests/man/inference_control.Rd |only semTests-2.0.0/semTests/man/lambdas_nested.Rd | 4 semTests-2.0.0/semTests/man/lav_ugamma_nested_2000.Rd | 8 semTests-2.0.0/semTests/man/nested_factor_2000.Rd | 2 semTests-2.0.0/semTests/man/ordinal_moment_influence.Rd |only semTests-2.0.0/semTests/man/positive_scale.Rd |only semTests-2.0.0/semTests/man/profile_score_test_matrices.Rd |only semTests-2.0.0/semTests/man/pvalues.Rd | 69 + semTests-2.0.0/semTests/man/restriction_weight.Rd |only semTests-2.0.0/semTests/man/score_test.Rd |only semTests-2.0.0/semTests/man/score_test_matrices.Rd |only semTests-2.0.0/semTests/man/score_test_nested.Rd |only semTests-2.0.0/semTests/man/semTests-support.Rd | 68 + semTests-2.0.0/semTests/man/semtest.Rd |only semTests-2.0.0/semTests/man/ugamma_nested_reference.Rd | 2 semTests-2.0.0/semTests/tests/testthat/test-categorical.R | 10 semTests-2.0.0/semTests/tests/testthat/test-criterion-inference.R |only semTests-2.0.0/semTests/tests/testthat/test-estimators.R | 7 semTests-2.0.0/semTests/tests/testthat/test-fiml-conventions.R | 41 semTests-2.0.0/semTests/tests/testthat/test-guards.R |only semTests-2.0.0/semTests/tests/testthat/test-inference-tests.R |only semTests-2.0.0/semTests/tests/testthat/test-internals.R | 54 + semTests-2.0.0/semTests/tests/testthat/test-lavaan-inference.R |only semTests-2.0.0/semTests/tests/testthat/test-moment-projection.R |only semTests-2.0.0/semTests/tests/testthat/test-residual-spectrum.R |only semTests-2.0.0/semTests/tests/testthat/test-restriction-matrix.R |only semTests-2.0.0/semTests/tests/testthat/test-semtest.R |only semTests-2.0.0/semTests/tests/testthat/test-shared-inference.R |only semTests-2.0.0/semTests/tests/testthat/test-support.R | 30 semTests-2.0.0/semTests/vignettes/categorical-data.Rmd | 235 ++-- semTests-2.0.0/semTests/vignettes/figures |only semTests-2.0.0/semTests/vignettes/fiml-missing-data.Rmd | 399 ++------ semTests-2.0.0/semTests/vignettes/score-criterion.Rmd |only semTests-2.0.0/semTests/vignettes/semTests.Rmd | 321 +++--- 99 files changed, 2349 insertions(+), 2490 deletions(-)
Title: Analyse Citation Data from Google Scholar
Description: Provides tools to retrieve, analyse, and format publication and
citation data from Google Scholar profiles. It supports profile lookup,
publication records, citation histories, scholar comparison, coauthor
networks, journal ranking queries, CV-ready publication lists, and citation
metric summaries.
Author: Guangchuang Yu [aut, cre] ,
James Keirstead [aut],
Gregory Jefferis [aut] ,
Gordon Getzinger [ctb],
Jorge Cimentada [ctb],
Max Czapanskiy [ctb],
Dominique Makowski [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between scholar versions 1.0.0 dated 2026-07-07 and 1.0.1 dated 2026-10-29
DESCRIPTION | 14 LICENSE | 4 MD5 | 132 ++- NAMESPACE | 126 ++- NEWS | 152 ++-- NEWS.md | 125 +-- R/citing.R |only R/coauthors.R | 187 ++--- R/compare.r | 234 +++--- R/data.R | 90 +- R/format_publications.R | 94 +- R/getCompleteAuthors.R | 158 ++-- R/h_index_history.R |only R/openalex.R |only R/predict.r | 134 +-- R/publications.r | 1111 ++++++++++++++------------------ R/scholar-package.r | 159 +++- R/scholar.r | 751 +++++++++++---------- R/utils.R | 778 +++++++++++++++++++--- R/zzz.r | 8 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 30 inst/WORDLIST | 14 inst/doc/scholar.R | 261 ++++--- inst/doc/scholar.html | 949 ++++++++++++++------------- inst/doc/scholar.qmd | 114 +++ man/author_position.Rd | 70 +- man/compare_scholar_careers.Rd | 62 - man/compare_scholars.Rd | 62 - man/format_authors.Rd | 28 man/format_publications.Rd | 56 - man/get_article_cite_history.Rd | 40 - man/get_article_scholar_url.Rd | 38 - man/get_citation_history.Rd | 52 - man/get_citing_articles.Rd |only man/get_coauthors.Rd | 92 +- man/get_complete_authors.Rd | 60 - man/get_h_index_history.Rd |only man/get_journalrank.Rd | 35 - man/get_num_articles.Rd | 34 man/get_num_distinct_journals.Rd | 46 - man/get_num_top_journals.Rd | 54 - man/get_oldest_article.Rd | 34 man/get_profile.Rd | 86 +- man/get_publication_data_extended.Rd | 42 - man/get_publication_date.Rd | 42 - man/get_publication_url.Rd | 42 - man/get_publications.Rd | 114 +-- man/get_scholar_id.Rd | 66 + man/get_scholar_resp.Rd | 46 - man/plot_coauthors.Rd | 58 - man/predict_h_index.Rd | 106 +-- man/scholar-package.Rd | 219 ++++-- man/search_openalex_authors.Rd |only man/search_scholar_ids.Rd | 5 man/set_scholar_cookie.Rd |only man/set_scholar_mirror.Rd | 40 - man/tidy_id.Rd | 34 tests/spelling.R | 6 tests/testthat.R | 8 tests/testthat/_problems |only tests/testthat/fixtures |only tests/testthat/test-citing-articles.R |only tests/testthat/test-coauthors.R | 88 ++ tests/testthat/test-h-index-history.R |only tests/testthat/test-openalex.R |only tests/testthat/test-scholar-id-search.R | 42 + tests/testthat/test-scholar-response.R | 400 +++++++++++ tests/testthat/test-scholar-session.R |only tests/testthat/test-scholar.R | 89 +- tests/testthat/testthat-problems.rds |only vignettes/scholar.qmd | 114 +++ 73 files changed, 4838 insertions(+), 3197 deletions(-)
Title: Get the Category of Content Hosted by a Domain
Description: Fetch website content and classify it through the Python 'piedomains'
text model. Look up domains in 'UT-Capitole', Steven Black, university, archived
'Shallalist' and 'DMOZ' lists, or use 'VirusTotal' <https://www.virustotal.com/>,
'OpenAI' and 'Anthropic' APIs. Report collection outcomes and source provenance.
Includes a historical domain-name classifier trained on 'Shallalist' data.
Author: Gaurav Sood [aut, cre]
Maintainer: Gaurav Sood <gsood07@gmail.com>
Diff between rdomains versions 0.6.0 dated 2026-10-27 and 0.6.1 dated 2026-10-29
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 7 +++++++ tests/testthat/test-audit-http.R | 4 ++++ tests/testthat/test-e2e-fetch.R | 5 ++++- 5 files changed, 23 insertions(+), 9 deletions(-)
Title: Aggregate and Disaggregate Continuous Parameters for
Compartmental Models
Description: A convenient framework for aggregating and disaggregating continuously
varying parameters (for example, case fatality ratio, with age) for proper
parametrization of lower-resolution compartmental models (for example, with
broad age categories) and subsequent upscaling of model outputs to high resolution
(for example, as needed when calculating age-sensitive measures like years-life-lost).
Methods and application to calculating years of life lost are described in
Goodfellow et al. (2025) <doi:10.1371/journal.pcbi.1013420>.
Author: Carl Pearson [aut, cre] ,
Simon Proctor [aut] ,
Lucy Goodfellow [aut]
Maintainer: Carl Pearson <carl.ab.pearson@gmail.com>
Diff between paramix versions 0.0.2 dated 2025-06-10 and 0.0.3 dated 2026-10-29
paramix-0.0.2/paramix/inst/analysis/Rplots.pdf |only paramix-0.0.2/paramix/man/make_partition.Rd |only paramix-0.0.2/paramix/man/make_weight.Rd |only paramix-0.0.2/paramix/man/to_function.Rd |only paramix-0.0.2/paramix/vignettes/intro_cache |only paramix-0.0.2/paramix/vignettes/intro_files |only paramix-0.0.3/paramix/DESCRIPTION | 24 paramix-0.0.3/paramix/LICENSE | 2 paramix-0.0.3/paramix/MD5 | 129 paramix-0.0.3/paramix/NAMESPACE | 34 paramix-0.0.3/paramix/NEWS.md | 31 paramix-0.0.3/paramix/R/aggregate.R | 96 paramix-0.0.3/paramix/R/globals.R |only paramix-0.0.3/paramix/R/helper.R | 51 paramix-0.0.3/paramix/R/internal.R | 234 - paramix-0.0.3/paramix/R/messages.R |only paramix-0.0.3/paramix/R/paramix-package.R | 4 paramix-0.0.3/paramix/R/plotting.R | 101 paramix-0.0.3/paramix/README.md |only paramix-0.0.3/paramix/build/partial.rdb |only paramix-0.0.3/paramix/build/vignette.rds |binary paramix-0.0.3/paramix/inst/CITATION |only paramix-0.0.3/paramix/inst/WORDLIST |only paramix-0.0.3/paramix/inst/analysis/GNUmakefile | 4 paramix-0.0.3/paramix/inst/analysis/README.md |only paramix-0.0.3/paramix/inst/analysis/install.R | 66 paramix-0.0.3/paramix/inst/analysis/renv.lock | 2176 ++++++++-- paramix-0.0.3/paramix/inst/analysis/renv/activate.R | 197 paramix-0.0.3/paramix/inst/analysis/renv/settings.json | 4 paramix-0.0.3/paramix/inst/analysis/scripts/consolidate.R | 13 paramix-0.0.3/paramix/inst/analysis/scripts/disease_pars.R | 24 paramix-0.0.3/paramix/inst/analysis/scripts/distill.R | 40 paramix-0.0.3/paramix/inst/analysis/scripts/fig_averted.R | 213 paramix-0.0.3/paramix/inst/analysis/scripts/fig_fullsummary.R | 174 paramix-0.0.3/paramix/inst/analysis/scripts/fig_incidence.R | 61 paramix-0.0.3/paramix/inst/analysis/scripts/fig_utilities.R | 185 paramix-0.0.3/paramix/inst/analysis/scripts/fig_yll.R | 294 + paramix-0.0.3/paramix/inst/analysis/scripts/incidence.R | 13 paramix-0.0.3/paramix/inst/analysis/scripts/lex.R | 37 paramix-0.0.3/paramix/inst/analysis/scripts/odin.R | 47 paramix-0.0.3/paramix/inst/analysis/scripts/param.R | 77 paramix-0.0.3/paramix/inst/analysis/scripts/population.R | 17 paramix-0.0.3/paramix/inst/analysis/scripts/r0.R | 56 paramix-0.0.3/paramix/inst/analysis/scripts/run_numbers.R | 274 + paramix-0.0.3/paramix/inst/analysis/scripts/simulate.R | 157 paramix-0.0.3/paramix/inst/analysis/scripts/yll.R | 50 paramix-0.0.3/paramix/inst/doc/intro.R | 148 paramix-0.0.3/paramix/inst/doc/intro.Rmd | 152 paramix-0.0.3/paramix/inst/doc/intro.html | 341 + paramix-0.0.3/paramix/inst/doc/reproducing-paper-analysis.R |only paramix-0.0.3/paramix/inst/doc/reproducing-paper-analysis.Rmd |only paramix-0.0.3/paramix/inst/doc/reproducing-paper-analysis.html |only paramix-0.0.3/paramix/man/distill.Rd | 2 paramix-0.0.3/paramix/man/distill_summary.Rd | 2 paramix-0.0.3/paramix/man/figures |only paramix-0.0.3/paramix/man/parameter_summary.Rd | 6 paramix-0.0.3/paramix/man/paramix-package.Rd | 9 paramix-0.0.3/paramix/tests/spelling.R |only paramix-0.0.3/paramix/tests/testthat/test-alembic.R | 170 paramix-0.0.3/paramix/tests/testthat/test-interpolateopts.R | 8 paramix-0.0.3/paramix/tests/testthat/test-messages.R |only paramix-0.0.3/paramix/tests/testthat/test-partitioning.R | 16 paramix-0.0.3/paramix/tests/testthat/test-tofunction.R | 25 paramix-0.0.3/paramix/vignettes/intro.Rmd | 152 paramix-0.0.3/paramix/vignettes/reproducing-paper-analysis.Rmd |only 65 files changed, 4367 insertions(+), 1549 deletions(-)
Title: Panel Sample Selection Models
Description: Fits sample selection models with continuous, binary, and count outcomes in panel and cross-sectional data. Model details are provided in
Bailey and Peng (2025) <doi:10.2139/ssrn.5475626> and Peng and Van den Bulte
(2024) <doi:10.1287/mnsc.2019.01897>.
Author: Jing Peng [aut, cre]
Maintainer: Jing Peng <jing.peng@uconn.edu>
Diff between PanelSelect versions 1.0.1 dated 2026-08-27 and 2.0.0 dated 2026-10-29
PanelSelect-1.0.1/PanelSelect/R/PanelSelect.R |only PanelSelect-1.0.1/PanelSelect/R/imported.R |only PanelSelect-1.0.1/PanelSelect/R/probitRE_linearRE.R |only PanelSelect-1.0.1/PanelSelect/R/probitRE_probitRE.R |only PanelSelect-1.0.1/PanelSelect/R/utilities.R |only PanelSelect-1.0.1/PanelSelect/man/PanelSelect.Rd |only PanelSelect-1.0.1/PanelSelect/man/predict_probitRE_linearRE.Rd |only PanelSelect-1.0.1/PanelSelect/man/predict_probitRE_probitRE.Rd |only PanelSelect-1.0.1/PanelSelect/man/probitRE_PLNRE.Rd |only PanelSelect-1.0.1/PanelSelect/man/probitRE_PoissonRE.Rd |only PanelSelect-1.0.1/PanelSelect/man/probitRE_linearRE.Rd |only PanelSelect-1.0.1/PanelSelect/man/probitRE_probitRE.Rd |only PanelSelect-2.0.0/PanelSelect/DESCRIPTION | 19 PanelSelect-2.0.0/PanelSelect/MD5 | 211 ++ PanelSelect-2.0.0/PanelSelect/NAMESPACE | 95 - PanelSelect-2.0.0/PanelSelect/R/PLNRE.R |only PanelSelect-2.0.0/PanelSelect/R/PanelSelect-package.R |only PanelSelect-2.0.0/PanelSelect/R/PoissonRE.R |only PanelSelect-2.0.0/PanelSelect/R/ProbitRE.R |only PanelSelect-2.0.0/PanelSelect/R/ProbitRE_LinearRE.R |only PanelSelect-2.0.0/PanelSelect/R/ProbitRE_PLNRE.R |only PanelSelect-2.0.0/PanelSelect/R/ProbitRE_PoissonRE.R |only PanelSelect-2.0.0/PanelSelect/R/ProbitRE_ProbitRE.R |only PanelSelect-2.0.0/PanelSelect/R/Probit_Linear.R |only PanelSelect-2.0.0/PanelSelect/R/Probit_PLN.R |only PanelSelect-2.0.0/PanelSelect/R/Probit_Probit.R |only PanelSelect-2.0.0/PanelSelect/R/RcppExports.R | 32 PanelSelect-2.0.0/PanelSelect/R/data_preparation.R |only PanelSelect-2.0.0/PanelSelect/R/diagnostics.R |only PanelSelect-2.0.0/PanelSelect/R/fit_staging.R |only PanelSelect-2.0.0/PanelSelect/R/inference.R |only PanelSelect-2.0.0/PanelSelect/R/initialization_linear.R |only PanelSelect-2.0.0/PanelSelect/R/likelihood.R |only PanelSelect-2.0.0/PanelSelect/R/model_assembly.R |only PanelSelect-2.0.0/PanelSelect/R/model_context.R |only PanelSelect-2.0.0/PanelSelect/R/model_methods.R |only PanelSelect-2.0.0/PanelSelect/R/numerics.R |only PanelSelect-2.0.0/PanelSelect/R/optimizer.R |only PanelSelect-2.0.0/PanelSelect/R/panel_control.R |only PanelSelect-2.0.0/PanelSelect/R/panel_select.R |only PanelSelect-2.0.0/PanelSelect/R/parameters.R |only PanelSelect-2.0.0/PanelSelect/R/predict.R |only PanelSelect-2.0.0/PanelSelect/R/probability.R |only PanelSelect-2.0.0/PanelSelect/R/quadrature.R |only PanelSelect-2.0.0/PanelSelect/R/quadrature_inner.R |only PanelSelect-2.0.0/PanelSelect/R/quadrature_inner_adaptive.R |only PanelSelect-2.0.0/PanelSelect/R/quadrature_split.R |only PanelSelect-2.0.0/PanelSelect/R/quadrature_staged.R |only PanelSelect-2.0.0/PanelSelect/R/quadrature_staged_inner.R |only PanelSelect-2.0.0/PanelSelect/R/quadrature_staged_pln.R |only PanelSelect-2.0.0/PanelSelect/R/quadrature_staged_prepare.R |only PanelSelect-2.0.0/PanelSelect/R/summary.R |only PanelSelect-2.0.0/PanelSelect/build/partial.rdb |only PanelSelect-2.0.0/PanelSelect/build/vignette.rds |binary PanelSelect-2.0.0/PanelSelect/inst/doc/migration.R |only PanelSelect-2.0.0/PanelSelect/inst/doc/migration.Rmd |only PanelSelect-2.0.0/PanelSelect/inst/doc/migration.html |only PanelSelect-2.0.0/PanelSelect/inst/doc/vignette.R | 82 PanelSelect-2.0.0/PanelSelect/inst/doc/vignette.Rmd | 676 ++++--- PanelSelect-2.0.0/PanelSelect/inst/doc/vignette.html | 871 ++++++---- PanelSelect-2.0.0/PanelSelect/man/PanelSelect-package.Rd |only PanelSelect-2.0.0/PanelSelect/man/add_information.Rd |only PanelSelect-2.0.0/PanelSelect/man/check_quadrature.Rd |only PanelSelect-2.0.0/PanelSelect/man/check_stationarity.Rd |only PanelSelect-2.0.0/PanelSelect/man/panel_control.Rd |only PanelSelect-2.0.0/PanelSelect/man/panel_select.Rd |only PanelSelect-2.0.0/PanelSelect/man/panelselect-comparison.Rd |only PanelSelect-2.0.0/PanelSelect/man/panelselect-design.Rd |only PanelSelect-2.0.0/PanelSelect/man/panelselect-inference.Rd |only PanelSelect-2.0.0/PanelSelect/man/panelselect-methods.Rd |only PanelSelect-2.0.0/PanelSelect/man/predict.panelselect.Rd |only PanelSelect-2.0.0/PanelSelect/man/random_effects.Rd |only PanelSelect-2.0.0/PanelSelect/man/residuals.panelselect.Rd |only PanelSelect-2.0.0/PanelSelect/man/summary.panelselect.Rd |only PanelSelect-2.0.0/PanelSelect/man/update.panelselect.Rd |only PanelSelect-2.0.0/PanelSelect/src/Makevars |only PanelSelect-2.0.0/PanelSelect/src/Makevars.win |only PanelSelect-2.0.0/PanelSelect/src/RcppExports.cpp | 142 + PanelSelect-2.0.0/PanelSelect/src/matrix.cpp | 399 +++- PanelSelect-2.0.0/PanelSelect/tests |only PanelSelect-2.0.0/PanelSelect/vignettes/guide.css |only PanelSelect-2.0.0/PanelSelect/vignettes/migration.Rmd |only PanelSelect-2.0.0/PanelSelect/vignettes/vignette.Rmd | 676 ++++--- 83 files changed, 2000 insertions(+), 1203 deletions(-)
Title: More Miscellaneous Steps for the 'recipes' Package
Description: Contains additional miscellaneous steps for the 'recipes' package.
These steps are useful, but doesn't have a good home in other 'recipes'
packages or its extensions.
Author: Emil Hvitfeldt [aut, cre]
Maintainer: Emil Hvitfeldt <emilhhvitfeldt@gmail.com>
This is a re-admission after prior archival of version 0.3.0 dated 2025-09-05
Diff between extrasteps versions 0.3.0 dated 2025-09-05 and 0.3.1 dated 2026-10-29
DESCRIPTION | 6 ++-- MD5 | 46 +++++++++++++++++------------------ NEWS.md | 4 +++ R/date_after.R | 6 +++- R/date_before.R | 6 +++- R/date_nearest.R | 6 +++- R/encoding_binary.R | 2 - R/encoding_frequency.R | 2 - R/time_event.R | 4 ++- README.md | 2 - man/step_date_after.Rd | 12 +++++++-- man/step_date_before.Rd | 12 +++++++-- man/step_date_nearest.Rd | 12 +++++++-- man/step_encoding_binary.Rd | 2 + man/step_encoding_frequency.Rd | 2 + man/step_time_event.Rd | 4 ++- tests/testthat/test-date_after.R | 1 tests/testthat/test-date_before.R | 1 tests/testthat/test-date_nearest.R | 1 tests/testthat/test-maxabs.R | 1 tests/testthat/test-minmax.R | 1 tests/testthat/test-robust.R | 1 tests/testthat/test-time_event.R | 1 tests/testthat/test-unit_normalize.R | 1 24 files changed, 93 insertions(+), 43 deletions(-)
Title: Information-Theoretic Measurement Mapping and Rank Estimation
Description: Maps relationships among measurements using a double-centered,
joint-entropy-normalized mutual information matrix. Provides informational-axis
loadings, primary and extended spectral-boundary diagnostics, and spectral-volume
and informational-gravity summaries for discrete and discretized tabular data.
The selected Primary Informational Rank is a candidate information-spectrum
boundary, not an identified generating dimension. Optional, explicitly
recorded missing-data preparation supports categorical missing states and
numeric median fills with protected missingness indicators.
For methodological details, see Lee-St. John (2026)
<doi:10.5281/zenodo.22028086>.
Author: Terrence J. Lee-St. John [aut, cre]
Maintainer: Terrence J. Lee-St. John <terry@enli.com.au>
Diff between Entropic.Scree versions 1.0.1 dated 2026-09-15 and 1.0.2 dated 2026-10-29
DESCRIPTION | 25 - MD5 | 16 NEWS |only R/Diagnostics.R |only R/EntropicScree.R | 742 +++++++++++++++++++++++++------------------ R/Preparation.R |only build |only man/Entropic.Scree.Rd | 253 +++++++++++--- man/Update.Entropic.Scree.Rd | 54 ++- src/entropic_mi.cpp | 10 tests |only 11 files changed, 728 insertions(+), 372 deletions(-)
More information about Entropic.Scree at CRAN
Permanent link
Title: Multilevel Modeling of Dendroclimatical Fluctuations
Description: Processes multilevel ecological data series (MEDS)
arranged in temporal or spatial hierarchies defined by sampling
designs. The package recursively applies one-level stage functions to
long-format tree-ring and climate data, then optionally fits a
terminal model to the processed series. Terminal fits currently
include mixed-effects detrending through 'nlme' and Friedman
supersmoother detrending through supsmu() of 'stats'. The package also
supports post-detrending comparison and inference tools for
multilevel dendroclimatic analyses. The method is described in
Lara et al. (2018) <doi:10.1371/journal.pone.0196923>.
Author: Wilson Lara-Henao [aut, cre] ,
Felipe Bravo [aut]
Maintainer: Wilson Lara-Henao <wilarhen@gmail.com>
Diff between BIOdry versions 0.9.1 dated 2025-04-03 and 0.9.5 dated 2026-10-29
BIOdry-0.9.1/BIOdry/NEWS |only BIOdry-0.9.1/BIOdry/R/anova.modelFrame.R |only BIOdry-0.9.1/BIOdry/R/frametoLme.R |only BIOdry-0.9.1/BIOdry/R/lmeForm.R |only BIOdry-0.9.1/BIOdry/R/modelFrame.R |only BIOdry-0.9.1/BIOdry/R/plot.modelFrame.R |only BIOdry-0.9.1/BIOdry/R/ringApply.R |only BIOdry-0.9.1/BIOdry/R/summary.modelFrame.R |only BIOdry-0.9.1/BIOdry/R/tdForm.R |only BIOdry-0.9.5/BIOdry/DESCRIPTION | 33 BIOdry-0.9.5/BIOdry/MD5 | 157 +- BIOdry-0.9.5/BIOdry/NAMESPACE | 16 BIOdry-0.9.5/BIOdry/NEWS.md |only BIOdry-0.9.5/BIOdry/R/FriedmanForm_patched_inlinedocs_v3.R |only BIOdry-0.9.5/BIOdry/R/amod.R | 347 ++++- BIOdry-0.9.5/BIOdry/R/anova.frametoLme_patched_inlinedocs.R |only BIOdry-0.9.5/BIOdry/R/arguSelect.R | 101 + BIOdry-0.9.5/BIOdry/R/cClass.R | 75 - BIOdry-0.9.5/BIOdry/R/defineDataRoles_patched_inlinedocs_v2.R |only BIOdry-0.9.5/BIOdry/R/frametoFriedman_patched_inlinedocs_v4.R |only BIOdry-0.9.5/BIOdry/R/frametoLme_patched_inlinedocs_v3.R |only BIOdry-0.9.5/BIOdry/R/levexp.R | 192 ++- BIOdry-0.9.5/BIOdry/R/lmeForm_patched_inlinedocs_v2.R |only BIOdry-0.9.5/BIOdry/R/mUnits.R | 4 BIOdry-0.9.5/BIOdry/R/modelFrame_formNULL_trellis_inlinedocs.R |only BIOdry-0.9.5/BIOdry/R/modelFrame_methods_trellis_inlinedocs.R |only BIOdry-0.9.5/BIOdry/R/moveYr.R | 311 +++-- BIOdry-0.9.5/BIOdry/R/muleMan.R | 92 - BIOdry-0.9.5/BIOdry/R/normalizeGroupLevels_patched_inlinedocs.R |only BIOdry-0.9.5/BIOdry/R/plot.frametoFriedman_patched_inlinedocs_v3.R |only BIOdry-0.9.5/BIOdry/R/plot.frametoLme_patched_inlinedocs.R |only BIOdry-0.9.5/BIOdry/R/plot.modelFrame_trellis_inlinedocs.R |only BIOdry-0.9.5/BIOdry/R/plot.muleMan.R | 101 - BIOdry-0.9.5/BIOdry/R/plot.wlai.R | 279 +++- BIOdry-0.9.5/BIOdry/R/ringApply_patched_inlinedocs_v5.R |only BIOdry-0.9.5/BIOdry/R/roles_types.R |only BIOdry-0.9.5/BIOdry/R/rtimes.R | 283 ++++ BIOdry-0.9.5/BIOdry/R/scacum.R | 278 +++- BIOdry-0.9.5/BIOdry/R/shiftFrame.R | 603 +++++++-- BIOdry-0.9.5/BIOdry/R/slitFrame.R | 154 +- BIOdry-0.9.5/BIOdry/R/tdForm_patched_inlinedocs_docfix2.R |only BIOdry-0.9.5/BIOdry/R/update.frametoLme_patched_inlinedocs_v2.R |only BIOdry-0.9.5/BIOdry/R/wlai.R | 608 +++++++--- BIOdry-0.9.5/BIOdry/build/partial.rdb |binary BIOdry-0.9.5/BIOdry/inst |only BIOdry-0.9.5/BIOdry/man/BIOdry-package.Rd | 2 BIOdry-0.9.5/BIOdry/man/FriedmanForm.Rd |only BIOdry-0.9.5/BIOdry/man/amod.Rd | 96 + BIOdry-0.9.5/BIOdry/man/anova.frametoLme.Rd |only BIOdry-0.9.5/BIOdry/man/anova.modelFrame.Rd | 96 - BIOdry-0.9.5/BIOdry/man/arguSelect.Rd | 11 BIOdry-0.9.5/BIOdry/man/cClass.Rd | 21 BIOdry-0.9.5/BIOdry/man/defineDataRoles.Rd |only BIOdry-0.9.5/BIOdry/man/frametoFriedman.Rd |only BIOdry-0.9.5/BIOdry/man/frametoLme.Rd | 197 +-- BIOdry-0.9.5/BIOdry/man/levexp.Rd | 30 BIOdry-0.9.5/BIOdry/man/lmeForm.Rd | 43 BIOdry-0.9.5/BIOdry/man/mUnits.Rd | 7 BIOdry-0.9.5/BIOdry/man/modelFrame.Rd | 202 ++- BIOdry-0.9.5/BIOdry/man/moveYr.Rd | 104 + BIOdry-0.9.5/BIOdry/man/muleMan.Rd | 57 BIOdry-0.9.5/BIOdry/man/normalizeGroupLevels.Rd |only BIOdry-0.9.5/BIOdry/man/plot.frametoFriedman.Rd |only BIOdry-0.9.5/BIOdry/man/plot.frametoLme.Rd |only BIOdry-0.9.5/BIOdry/man/plot.modelFrame.Rd | 71 - BIOdry-0.9.5/BIOdry/man/plot.muleMan.Rd | 68 - BIOdry-0.9.5/BIOdry/man/plot.wlai.Rd | 112 + BIOdry-0.9.5/BIOdry/man/print.frametoFriedman.Rd |only BIOdry-0.9.5/BIOdry/man/print.frametoLme.Rd |only BIOdry-0.9.5/BIOdry/man/print.modelFrame.Rd |only BIOdry-0.9.5/BIOdry/man/print.summary.frametoFriedman.Rd |only BIOdry-0.9.5/BIOdry/man/print.summary.frametoLme.Rd |only BIOdry-0.9.5/BIOdry/man/print.summary.modelFrame.Rd |only BIOdry-0.9.5/BIOdry/man/ringApply.Rd | 160 ++ BIOdry-0.9.5/BIOdry/man/rtimes.Rd | 32 BIOdry-0.9.5/BIOdry/man/scacum.Rd | 60 BIOdry-0.9.5/BIOdry/man/shiftFrame.Rd | 103 + BIOdry-0.9.5/BIOdry/man/slitFrame.Rd | 34 BIOdry-0.9.5/BIOdry/man/summary.frametoFriedman.Rd |only BIOdry-0.9.5/BIOdry/man/summary.frametoLme.Rd |only BIOdry-0.9.5/BIOdry/man/summary.modelFrame.Rd | 54 BIOdry-0.9.5/BIOdry/man/tdForm.Rd | 38 BIOdry-0.9.5/BIOdry/man/update.frametoLme.Rd |only BIOdry-0.9.5/BIOdry/man/wlai.Rd | 113 + BIOdry-0.9.5/BIOdry/tests |only 85 files changed, 3874 insertions(+), 1471 deletions(-)
Title: Create Metrics of Actigraphy and Activity Analysis
Description: Provides functions for calibrating, counting, and summarizing
actigraphy and activity data into specific metrics and sleep measures.
The metrics include activity counts, step counts, activity index,
Monitor Independent Movement Summary Unit (MIMS), mean amplitude
deviation (MAD), and provides wrappers for sleep estimation from
activity counts using Tudor-Locke (2014) <doi:10.1139/apnm-2013-0173> and
Sadeh (1994) <doi:10.1093/sleep/17.3.201>. Count-intensity thresholds
include Montoye et al. (2020) <doi:10.1080/02640414.2020.1794244> and
Sasaki et al. (2011) <doi:10.1016/j.jsams.2011.04.003>. Raw-acceleration
Euclidean Norm Minus One (ENMO) thresholds include Hildebrand et al. (2014)
<doi:10.1249/MSS.0000000000000289>.
Author: John Muschelli [aut, cre]
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between actimetrics versions 0.9.0 dated 2026-10-20 and 0.10.0 dated 2026-10-29
DESCRIPTION | 30 +++++++----- MD5 | 69 +++++++++++++++++++++-------- NAMESPACE | 27 +++++++++++ NEWS.md | 77 +++++++++++++++++++++++++++++++++ R/ab_calculate_counts.R | 23 +++++++-- R/acti_calculate_stepcount.R | 31 +++++++++++-- R/acti_calculate_walking.R | 1 R/acti_calculate_wear_raw.R |only R/acti_calculate_wear_raw_actipy.R |only R/acti_calculate_wear_raw_ggir.R |only R/acti_count_measures.R | 14 ++++++ R/acti_process.R | 4 + R/acti_sleep_guiders.R |only R/acti_threshold_counts.R |only R/calculate_measures.R | 36 +++++++-------- R/calibrate.R | 6 ++ R/imports.R | 2 R/standardize_for_sleepr.R | 32 +++++-------- man/acti_calculate_ai.Rd | 9 --- man/acti_calculate_counts.Rd | 5 +- man/acti_calculate_measures.Rd | 2 man/acti_calculate_stepcount.Rd | 18 ++++++- man/acti_calculate_wear_raw.Rd |only man/acti_calculate_wear_raw_actipy.Rd |only man/acti_calculate_wear_raw_ggir.Rd |only man/acti_sleep_diary.Rd |only man/acti_sleep_ensemble.Rd |only man/acti_sleep_fuse_labels.Rd |only man/acti_sleep_guider.Rd |only man/acti_sleep_guider_requirements.Rd |only man/acti_sleep_hdcza.Rd |only man/acti_sleep_hlrb.Rd |only man/acti_sleep_horangle.Rd |only man/acti_sleep_l5.Rd |only man/acti_sleep_label.Rd |only man/acti_sleep_labels.Rd |only man/acti_sleep_notworn.Rd |only man/acti_sleep_setwindow.Rd |only man/acti_sleep_sib.Rd |only man/acti_threshold_counts.Rd |only man/acti_threshold_enmo.Rd |only man/acti_threshold_hildebrand.Rd |only man/acti_threshold_montoye.Rd |only man/acti_threshold_romanzini.Rd |only man/acti_threshold_sasaki.Rd |only tests/testthat.R | 4 + tests/testthat/test-coverage-drivers.R | 14 +++--- tests/testthat/test-regressions.R | 61 ++++++++++++++++++++++++++ tests/testthat/test-sleep-guiders.R |only tests/testthat/test-threshold-counts.R |only tests/testthat/test-wear-raw.R |only 51 files changed, 364 insertions(+), 101 deletions(-)
Title: Convert Vietnamese Encodings
Description: Conversion of characters from unsupported Vietnamese character encodings to Unicode characters. These Vietnamese encodings (TCVN3, VISCII, VPS) are not natively supported in R and lead to printing of wrong characters and garbled text (mojibake). This package fixes that problem and provides readable output with the correct Unicode characters (with or without diacritics).
Author: Juergen Niedballa [aut, cre] ,
An The Truong Nguyen [ctb]
Maintainer: Juergen Niedballa <camtrapr@gmail.com>
Diff between vietnameseConverter versions 0.4.0 dated 2021-10-20 and 0.4.1 dated 2026-10-29
DESCRIPTION | 24 MD5 | 28 - NEWS | 30 - R/decodeVN.R | 348 ++++++------- R/loadEncodingTableVN.R | 840 ++++++++++++++++----------------- README.md | 21 build/vignette.rds |binary inst/doc/vietnameseConverter.pdf.asis | 10 man/decodeVN.Rd | 2 man/loadEncodingTableVN.Rd | 2 man/vietnameseConverter-package.Rd | 42 - man/vn_samples.Rd | 96 +-- tests/test-all.R | 4 tests/testthat/test_decodeVN.R | 132 ++--- vignettes/vietnameseConverter.pdf.asis | 10 15 files changed, 807 insertions(+), 782 deletions(-)
More information about vietnameseConverter at CRAN
Permanent link
Title: An Interface to Google Drive
Description: Manage Google Drive files from R.
Author: Lucy D'Agostino McGowan [aut],
Jennifer Bryan [aut, cre] ,
Posit Software, PBC [cph, fnd]
Maintainer: Jennifer Bryan <jenny@posit.co>
Diff between googledrive versions 2.1.2 dated 2025-09-10 and 2.2.0 dated 2026-10-29
googledrive-2.1.2/googledrive/R/deprecated.R |only googledrive-2.1.2/googledrive/R/team_drive.R |only googledrive-2.1.2/googledrive/build |only googledrive-2.1.2/googledrive/inst/doc |only googledrive-2.1.2/googledrive/man/deprecated-team-drive-functions.Rd |only googledrive-2.1.2/googledrive/man/figures/lifecycle-archived.svg |only googledrive-2.1.2/googledrive/man/figures/lifecycle-defunct.svg |only googledrive-2.1.2/googledrive/man/figures/lifecycle-maturing.svg |only googledrive-2.1.2/googledrive/man/figures/lifecycle-questioning.svg |only googledrive-2.1.2/googledrive/man/figures/lifecycle-soft-deprecated.svg |only googledrive-2.1.2/googledrive/man/googledrive-deprecated.Rd |only googledrive-2.1.2/googledrive/tests/testthat/_snaps/deprecated.md |only googledrive-2.1.2/googledrive/tests/testthat/_snaps/utils-ui.md |only googledrive-2.1.2/googledrive/tests/testthat/driver.R |only googledrive-2.1.2/googledrive/tests/testthat/test-deprecated.R |only googledrive-2.1.2/googledrive/tests/testthat/test-utils-ui.R |only googledrive-2.1.2/googledrive/vignettes |only googledrive-2.2.0/googledrive/DESCRIPTION | 22 googledrive-2.2.0/googledrive/MD5 | 222 ++++------ googledrive-2.2.0/googledrive/NAMESPACE | 50 +- googledrive-2.2.0/googledrive/NEWS.md | 43 + googledrive-2.2.0/googledrive/R/dribble.R | 171 ++++--- googledrive-2.2.0/googledrive/R/drive_auth.R | 136 +++++- googledrive-2.2.0/googledrive/R/drive_cp.R | 6 googledrive-2.2.0/googledrive/R/drive_create.R | 8 googledrive-2.2.0/googledrive/R/drive_download.R | 5 googledrive-2.2.0/googledrive/R/drive_endpoints.R | 8 googledrive-2.2.0/googledrive/R/drive_examples.R | 50 +- googledrive-2.2.0/googledrive/R/drive_fields.R | 2 googledrive-2.2.0/googledrive/R/drive_find.R | 88 ++- googledrive-2.2.0/googledrive/R/drive_get.R | 27 - googledrive-2.2.0/googledrive/R/drive_get_path.R | 30 - googledrive-2.2.0/googledrive/R/drive_id-class.R | 20 googledrive-2.2.0/googledrive/R/drive_ls.R | 6 googledrive-2.2.0/googledrive/R/drive_mime_type.R | 6 googledrive-2.2.0/googledrive/R/drive_mkdir.R | 5 googledrive-2.2.0/googledrive/R/drive_mv.R | 6 googledrive-2.2.0/googledrive/R/drive_publish.R | 7 googledrive-2.2.0/googledrive/R/drive_put.R | 4 googledrive-2.2.0/googledrive/R/drive_read.R | 13 googledrive-2.2.0/googledrive/R/drive_rename.R | 5 googledrive-2.2.0/googledrive/R/drive_reveal.R | 2 googledrive-2.2.0/googledrive/R/drive_rm.R | 6 googledrive-2.2.0/googledrive/R/drive_share.R | 13 googledrive-2.2.0/googledrive/R/drive_trash.R | 12 googledrive-2.2.0/googledrive/R/drive_update.R | 4 googledrive-2.2.0/googledrive/R/drive_upload.R | 7 googledrive-2.2.0/googledrive/R/drive_user.R | 6 googledrive-2.2.0/googledrive/R/request_make.R | 8 googledrive-2.2.0/googledrive/R/shared_drive_create.R | 2 googledrive-2.2.0/googledrive/R/shared_drive_find.R | 13 googledrive-2.2.0/googledrive/R/shared_drive_get.R | 13 googledrive-2.2.0/googledrive/R/shared_drives.R | 50 -- googledrive-2.2.0/googledrive/R/sysdata.rda |binary googledrive-2.2.0/googledrive/R/utils-paths.R | 93 +++- googledrive-2.2.0/googledrive/R/utils-ui.R | 45 -- googledrive-2.2.0/googledrive/R/utils.R | 40 + googledrive-2.2.0/googledrive/R/zzz.R | 6 googledrive-2.2.0/googledrive/README.md | 54 +- googledrive-2.2.0/googledrive/inst/WORDLIST | 6 googledrive-2.2.0/googledrive/man/dribble-checks.Rd | 15 googledrive-2.2.0/googledrive/man/drive_auth.Rd | 8 googledrive-2.2.0/googledrive/man/drive_auth_configure.Rd | 19 googledrive-2.2.0/googledrive/man/drive_cp.Rd | 24 - googledrive-2.2.0/googledrive/man/drive_create.Rd | 24 - googledrive-2.2.0/googledrive/man/drive_deauth.Rd | 8 googledrive-2.2.0/googledrive/man/drive_download.Rd | 15 googledrive-2.2.0/googledrive/man/drive_empty_trash.Rd | 10 googledrive-2.2.0/googledrive/man/drive_find.Rd | 14 googledrive-2.2.0/googledrive/man/drive_get.Rd | 19 googledrive-2.2.0/googledrive/man/drive_has_token.Rd | 8 googledrive-2.2.0/googledrive/man/drive_mkdir.Rd | 17 googledrive-2.2.0/googledrive/man/drive_mv.Rd | 23 - googledrive-2.2.0/googledrive/man/drive_publish.Rd | 11 googledrive-2.2.0/googledrive/man/drive_put.Rd | 16 googledrive-2.2.0/googledrive/man/drive_rename.Rd | 17 googledrive-2.2.0/googledrive/man/drive_rm.Rd | 9 googledrive-2.2.0/googledrive/man/drive_scopes.Rd | 8 googledrive-2.2.0/googledrive/man/drive_share.Rd | 12 googledrive-2.2.0/googledrive/man/drive_token.Rd | 10 googledrive-2.2.0/googledrive/man/drive_token_write.Rd |only googledrive-2.2.0/googledrive/man/drive_trash.Rd | 11 googledrive-2.2.0/googledrive/man/drive_update.Rd | 9 googledrive-2.2.0/googledrive/man/drive_upload.Rd | 27 - googledrive-2.2.0/googledrive/man/drive_user.Rd | 10 googledrive-2.2.0/googledrive/man/googledrive-configuration.Rd | 6 googledrive-2.2.0/googledrive/man/googledrive-package.Rd | 1 googledrive-2.2.0/googledrive/man/request_generate.Rd | 10 googledrive-2.2.0/googledrive/man/request_make.Rd | 27 - googledrive-2.2.0/googledrive/man/shortcut_create.Rd | 8 googledrive-2.2.0/googledrive/tests/testthat/_snaps/dribble.md | 79 +++ googledrive-2.2.0/googledrive/tests/testthat/_snaps/drive_auth.md | 40 + googledrive-2.2.0/googledrive/tests/testthat/_snaps/drive_cp.md | 6 googledrive-2.2.0/googledrive/tests/testthat/_snaps/drive_create.md | 15 googledrive-2.2.0/googledrive/tests/testthat/_snaps/drive_download.md | 2 googledrive-2.2.0/googledrive/tests/testthat/_snaps/drive_endpoints.md |only googledrive-2.2.0/googledrive/tests/testthat/_snaps/drive_examples.md | 22 googledrive-2.2.0/googledrive/tests/testthat/_snaps/drive_fields.md | 8 googledrive-2.2.0/googledrive/tests/testthat/_snaps/drive_find.md | 79 +++ googledrive-2.2.0/googledrive/tests/testthat/_snaps/drive_get.md | 54 ++ googledrive-2.2.0/googledrive/tests/testthat/_snaps/drive_ls.md | 26 + googledrive-2.2.0/googledrive/tests/testthat/_snaps/drive_mime_type.md | 8 googledrive-2.2.0/googledrive/tests/testthat/_snaps/drive_share.md | 8 googledrive-2.2.0/googledrive/tests/testthat/_snaps/drive_update.md | 4 googledrive-2.2.0/googledrive/tests/testthat/_snaps/drive_upload.md | 8 googledrive-2.2.0/googledrive/tests/testthat/_snaps/shared_drives.md | 69 ++- googledrive-2.2.0/googledrive/tests/testthat/_snaps/utils-paths.md | 29 - googledrive-2.2.0/googledrive/tests/testthat/test-dribble.R | 53 +- googledrive-2.2.0/googledrive/tests/testthat/test-drive_auth.R | 56 ++ googledrive-2.2.0/googledrive/tests/testthat/test-drive_create.R | 1 googledrive-2.2.0/googledrive/tests/testthat/test-drive_endpoints.R | 10 googledrive-2.2.0/googledrive/tests/testthat/test-drive_examples.R | 5 googledrive-2.2.0/googledrive/tests/testthat/test-drive_fields.R | 4 googledrive-2.2.0/googledrive/tests/testthat/test-drive_find.R | 27 + googledrive-2.2.0/googledrive/tests/testthat/test-drive_get.R | 12 googledrive-2.2.0/googledrive/tests/testthat/test-drive_id-class.R | 55 ++ googledrive-2.2.0/googledrive/tests/testthat/test-drive_ls.R | 9 googledrive-2.2.0/googledrive/tests/testthat/test-drive_upload.R | 7 googledrive-2.2.0/googledrive/tests/testthat/test-request_generate.R | 11 googledrive-2.2.0/googledrive/tests/testthat/test-shared_drives.R | 15 googledrive-2.2.0/googledrive/tests/testthat/test-utils-paths.R | 3 121 files changed, 1515 insertions(+), 926 deletions(-)
Title: Access Google Sheets using the Sheets API V4
Description: Interact with Google Sheets through the Sheets API v4
<https://developers.google.com/sheets/api>. "API" is an acronym for
"application programming interface"; the Sheets API allows users to
interact with Google Sheets programmatically, instead of via a web
browser. The "v4" refers to the fact that the Sheets API is currently
at version 4. This package can read and write both the metadata and
the cell data in a Sheet.
Author: Jennifer Bryan [cre, aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Jennifer Bryan <jenny@posit.co>
Diff between googlesheets4 versions 1.1.2 dated 2025-09-03 and 1.1.3 dated 2026-10-29
googlesheets4-1.1.2/googlesheets4/man/figures/lifecycle-archived.svg |only googlesheets4-1.1.2/googlesheets4/man/figures/lifecycle-defunct.svg |only googlesheets4-1.1.2/googlesheets4/man/figures/lifecycle-deprecated.svg |only googlesheets4-1.1.2/googlesheets4/man/figures/lifecycle-experimental.svg |only googlesheets4-1.1.2/googlesheets4/man/figures/lifecycle-maturing.svg |only googlesheets4-1.1.2/googlesheets4/man/figures/lifecycle-questioning.svg |only googlesheets4-1.1.2/googlesheets4/man/figures/lifecycle-retired.svg |only googlesheets4-1.1.2/googlesheets4/man/figures/lifecycle-soft-deprecated.svg |only googlesheets4-1.1.2/googlesheets4/man/figures/lifecycle-stable.svg |only googlesheets4-1.1.2/googlesheets4/man/figures/lifecycle-superseded.svg |only googlesheets4-1.1.2/googlesheets4/man/gs4_oauth_app.Rd |only googlesheets4-1.1.3/googlesheets4/DESCRIPTION | 18 - googlesheets4-1.1.3/googlesheets4/MD5 | 109 ++++------ googlesheets4-1.1.3/googlesheets4/NAMESPACE | 60 +++-- googlesheets4-1.1.3/googlesheets4/NEWS.md | 15 + googlesheets4-1.1.3/googlesheets4/R/googlesheets4-package.R | 1 googlesheets4-1.1.3/googlesheets4/R/gs4_auth.R | 32 -- googlesheets4-1.1.3/googlesheets4/R/sysdata.rda |binary googlesheets4-1.1.3/googlesheets4/R/utils-ui.R | 6 googlesheets4-1.1.3/googlesheets4/README.md | 22 +- googlesheets4-1.1.3/googlesheets4/inst/WORDLIST | 8 googlesheets4-1.1.3/googlesheets4/man/cell-specification.Rd | 4 googlesheets4-1.1.3/googlesheets4/man/googlesheets4-configuration.Rd | 6 googlesheets4-1.1.3/googlesheets4/man/googlesheets4-package.Rd | 5 googlesheets4-1.1.3/googlesheets4/man/gs4_auth.Rd | 8 googlesheets4-1.1.3/googlesheets4/man/gs4_auth_configure.Rd | 15 - googlesheets4-1.1.3/googlesheets4/man/gs4_browse.Rd | 2 googlesheets4-1.1.3/googlesheets4/man/gs4_create.Rd | 14 - googlesheets4-1.1.3/googlesheets4/man/gs4_deauth.Rd | 8 googlesheets4-1.1.3/googlesheets4/man/gs4_examples.Rd | 2 googlesheets4-1.1.3/googlesheets4/man/gs4_formula.Rd | 14 - googlesheets4-1.1.3/googlesheets4/man/gs4_get.Rd | 2 googlesheets4-1.1.3/googlesheets4/man/gs4_has_token.Rd | 8 googlesheets4-1.1.3/googlesheets4/man/gs4_scopes.Rd | 8 googlesheets4-1.1.3/googlesheets4/man/gs4_token.Rd | 10 googlesheets4-1.1.3/googlesheets4/man/gs4_user.Rd | 4 googlesheets4-1.1.3/googlesheets4/man/range_autofit.Rd | 2 googlesheets4-1.1.3/googlesheets4/man/range_delete.Rd | 16 - googlesheets4-1.1.3/googlesheets4/man/range_flood.Rd | 16 - googlesheets4-1.1.3/googlesheets4/man/range_read.Rd | 2 googlesheets4-1.1.3/googlesheets4/man/range_read_cells.Rd | 2 googlesheets4-1.1.3/googlesheets4/man/range_speedread.Rd | 2 googlesheets4-1.1.3/googlesheets4/man/range_write.Rd | 16 - googlesheets4-1.1.3/googlesheets4/man/request_generate.Rd | 10 googlesheets4-1.1.3/googlesheets4/man/request_make.Rd | 14 - googlesheets4-1.1.3/googlesheets4/man/sheet_add.Rd | 20 - googlesheets4-1.1.3/googlesheets4/man/sheet_append.Rd | 36 +-- googlesheets4-1.1.3/googlesheets4/man/sheet_copy.Rd | 20 - googlesheets4-1.1.3/googlesheets4/man/sheet_delete.Rd | 20 - googlesheets4-1.1.3/googlesheets4/man/sheet_properties.Rd | 20 - googlesheets4-1.1.3/googlesheets4/man/sheet_relocate.Rd | 20 - googlesheets4-1.1.3/googlesheets4/man/sheet_rename.Rd | 20 - googlesheets4-1.1.3/googlesheets4/man/sheet_resize.Rd | 20 - googlesheets4-1.1.3/googlesheets4/man/sheet_write.Rd | 36 +-- googlesheets4-1.1.3/googlesheets4/man/sheets_id.Rd | 14 - googlesheets4-1.1.3/googlesheets4/tests/testthat/_snaps/gs4_auth.md | 18 - googlesheets4-1.1.3/googlesheets4/tests/testthat/_snaps/sheets_id-class.md | 2 googlesheets4-1.1.3/googlesheets4/tests/testthat/_snaps/utils-ui.md | 22 ++ googlesheets4-1.1.3/googlesheets4/tests/testthat/test-gs4_auth.R | 25 -- googlesheets4-1.1.3/googlesheets4/tests/testthat/test-request_generate.R | 2 googlesheets4-1.1.3/googlesheets4/tests/testthat/test-utils-ui.R | 15 + 61 files changed, 371 insertions(+), 400 deletions(-)
Title: Tools for qPCR
Description: Provides tools for quantitative PCR (qPCR) data analysis,
including standard curve calculation with amplification efficiency,
relative expression calculation by the 2-'dCt', 2-'ddCt',
standard curve and 'RqPCR' methods, and RNA volume calculation for
reverse transcription.
Author: Xiang LI [cre, aut]
Maintainer: Xiang LI <lixiang117423@gmail.com>
Diff between qPCRtools versions 1.0.1 dated 2023-11-02 and 1.0.2 dated 2026-10-29
DESCRIPTION | 15 MD5 | 29 - R/CalCurve.R | 460 ++++++++++++------------- R/CalExp2dCt.R | 255 +++++++------- R/CalExp2ddCt.R | 745 ++++++++++++++++++++++------------------- R/CalExpCurve.R | 569 ++++++++++++++++++------------- R/CalExpRqPCR.R | 954 ++++++++++++++++++++++++++++------------------------- R/CalRTable.R | 93 ++--- inst/WORDLIST |only man/CalCurve.Rd | 10 man/CalExp2dCt.Rd | 3 man/CalExp2ddCt.Rd | 14 man/CalExpCurve.Rd | 20 + man/CalExpRqPCR.Rd | 13 man/CalRTable.Rd | 3 tests |only 16 files changed, 1728 insertions(+), 1455 deletions(-)
Title: Dynamic Bayesian Learning for Spatiotemporal Mechanistic Models
Description: Provides tools for Bayesian learning of spatiotemporal dynamical mechanistic models.
Includes methods for parameter estimation, simulation, and inference using hierarchical and
state-space modeling approaches, following Banerjee, Chen, Frankenburg and Zhou (2025)
<https://jmlr.org/papers/v26/22-0896.html>.
Author: Xiang Chen [aut, cre],
Sudipto Banerjee [aut]
Maintainer: Xiang Chen <xiangchen@ucla.edu>
Diff between spDBL versions 1.0.2 dated 2026-06-09 and 1.1.1 dated 2026-10-29
DESCRIPTION | 14 MD5 | 68 ++- NAMESPACE | 8 NEWS.md |only R/calibration_fit.R |only R/calibration_prepare.R |only R/calibration_recover.R |only R/data-dt_calibration.R |only R/func_BS.R | 2 R/func_FFBS.R | 349 ++++++++----------- R/func_gen_data.R | 31 + R/func_wrapper.R | 438 +++++++++--------------- README.md | 82 ++++ build/vignette.rds |binary data/dt_calibration.rda |only inst/doc/calibration-details.Rmd |only inst/doc/calibration-details.html |only inst/doc/calibration.R |only inst/doc/calibration.Rmd |only inst/doc/calibration.html |only inst/doc/emulation.R | 2 inst/doc/emulation.Rmd | 42 +- inst/doc/emulation.html | 520 ++++++++++++++--------------- inst/examples |only inst/extdata |only inst/stan |only man/FFBS_predict_MC.Rd | 2 man/FFBS_predict_exact.Rd | 18 - man/FFBS_sampling.Rd | 21 + man/FFBS_sampling_sigma2R.Rd | 11 man/calibration_fit.Rd |only man/calibration_predict.Rd |only man/calibration_prepare.Rd |only man/calibration_validate.Rd |only man/dt_calibration.Rd |only man/emulator_learn.Rd | 82 ++-- man/emulator_predict.Rd | 49 -- man/plot.spDBL_calibration.Rd |only man/recover_from_EP_exact.Rd | 4 man/summary.spDBL_calibration.Rd |only tests/testthat/helper-calibration.R |only tests/testthat/test-calibration-gaussian.R |only tests/testthat/test-calibration-prepare.R |only tests/testthat/test-calibration-stan.R |only tests/testthat/test-sampling-methods.R |only vignettes/calibration-details.Rmd |only vignettes/calibration.Rmd |only vignettes/emulation.Rmd | 42 +- vignettes/renderEmulation.sh |only 49 files changed, 918 insertions(+), 867 deletions(-)
Title: Publication-Quality 'ggplot2' Visualisation
Description: Wrapper 'ggplot2' functions for publication-quality visualisation.
Aligned with 'ggplot2' and 'tidyverse'. Covers much of what 'ggplot2' does.
Author: David Hodge [aut, cre, cph]
Maintainer: David Hodge <davidhodge931@gmail.com>
Diff between ggblanket versions 21.0.0 dated 2026-07-06 and 30.0.0 dated 2026-10-29
ggblanket-21.0.0/ggblanket/R/set-blanket.R |only ggblanket-21.0.0/ggblanket/man/modern_drift.Rd |only ggblanket-21.0.0/ggblanket/man/set_blanket.Rd |only ggblanket-21.0.0/ggblanket/man/void_drop.Rd |only ggblanket-30.0.0/ggblanket/DESCRIPTION | 12 ggblanket-30.0.0/ggblanket/MD5 | 163 +-- ggblanket-30.0.0/ggblanket/NAMESPACE | 6 ggblanket-30.0.0/ggblanket/NEWS.md | 6 ggblanket-30.0.0/ggblanket/R/gg-area.R | 4 ggblanket-30.0.0/ggblanket/R/gg-bar.R | 4 ggblanket-30.0.0/ggblanket/R/gg-bin2d.R | 4 ggblanket-30.0.0/ggblanket/R/gg-blanket-utils.R | 72 - ggblanket-30.0.0/ggblanket/R/gg-blanket.R | 494 ++++------ ggblanket-30.0.0/ggblanket/R/gg-boxplot.R | 4 ggblanket-30.0.0/ggblanket/R/gg-col.R | 4 ggblanket-30.0.0/ggblanket/R/gg-contour-filled.R | 4 ggblanket-30.0.0/ggblanket/R/gg-contour.R | 4 ggblanket-30.0.0/ggblanket/R/gg-crossbar.R | 4 ggblanket-30.0.0/ggblanket/R/gg-density.R | 4 ggblanket-30.0.0/ggblanket/R/gg-density2d-filled.R | 4 ggblanket-30.0.0/ggblanket/R/gg-density2d.R | 4 ggblanket-30.0.0/ggblanket/R/gg-errorbar.R | 4 ggblanket-30.0.0/ggblanket/R/gg-freqpoly.R | 4 ggblanket-30.0.0/ggblanket/R/gg-hex.R | 4 ggblanket-30.0.0/ggblanket/R/gg-histogram.R | 4 ggblanket-30.0.0/ggblanket/R/gg-jitter.R | 4 ggblanket-30.0.0/ggblanket/R/gg-line.R | 4 ggblanket-30.0.0/ggblanket/R/gg-linerange.R | 4 ggblanket-30.0.0/ggblanket/R/gg-path.R | 4 ggblanket-30.0.0/ggblanket/R/gg-point.R | 4 ggblanket-30.0.0/ggblanket/R/gg-polygon.R | 4 ggblanket-30.0.0/ggblanket/R/gg-qq.R | 4 ggblanket-30.0.0/ggblanket/R/gg-quantile.R | 4 ggblanket-30.0.0/ggblanket/R/gg-raster.R | 4 ggblanket-30.0.0/ggblanket/R/gg-rect.R | 4 ggblanket-30.0.0/ggblanket/R/gg-ribbon.R | 4 ggblanket-30.0.0/ggblanket/R/gg-segment.R | 4 ggblanket-30.0.0/ggblanket/R/gg-sf.R | 4 ggblanket-30.0.0/ggblanket/R/gg-smooth.R | 4 ggblanket-30.0.0/ggblanket/R/gg-spoke.R | 4 ggblanket-30.0.0/ggblanket/R/gg-step.R | 4 ggblanket-30.0.0/ggblanket/R/gg-tile.R | 4 ggblanket-30.0.0/ggblanket/R/gg-violin.R | 4 ggblanket-30.0.0/ggblanket/R/refine-axis-grid.R |only ggblanket-30.0.0/ggblanket/R/refine-legend.R |only ggblanket-30.0.0/ggblanket/R/refine.R | 144 ++ ggblanket-30.0.0/ggblanket/R/set-options.R |only ggblanket-30.0.0/ggblanket/R/theme.R |only ggblanket-30.0.0/ggblanket/README.md | 22 ggblanket-30.0.0/ggblanket/man/figures/README-unnamed-chunk-2-1.png |binary ggblanket-30.0.0/ggblanket/man/figures/README-unnamed-chunk-3-1.png |binary ggblanket-30.0.0/ggblanket/man/gg_area.Rd | 12 ggblanket-30.0.0/ggblanket/man/gg_bar.Rd | 12 ggblanket-30.0.0/ggblanket/man/gg_bin2d.Rd | 12 ggblanket-30.0.0/ggblanket/man/gg_blanket.Rd | 16 ggblanket-30.0.0/ggblanket/man/gg_boxplot.Rd | 12 ggblanket-30.0.0/ggblanket/man/gg_col.Rd | 12 ggblanket-30.0.0/ggblanket/man/gg_contour.Rd | 12 ggblanket-30.0.0/ggblanket/man/gg_contour_filled.Rd | 12 ggblanket-30.0.0/ggblanket/man/gg_crossbar.Rd | 12 ggblanket-30.0.0/ggblanket/man/gg_density.Rd | 12 ggblanket-30.0.0/ggblanket/man/gg_density2d.Rd | 12 ggblanket-30.0.0/ggblanket/man/gg_density2d_filled.Rd | 12 ggblanket-30.0.0/ggblanket/man/gg_errorbar.Rd | 12 ggblanket-30.0.0/ggblanket/man/gg_freqpoly.Rd | 12 ggblanket-30.0.0/ggblanket/man/gg_hex.Rd | 12 ggblanket-30.0.0/ggblanket/man/gg_histogram.Rd | 12 ggblanket-30.0.0/ggblanket/man/gg_jitter.Rd | 12 ggblanket-30.0.0/ggblanket/man/gg_line.Rd | 12 ggblanket-30.0.0/ggblanket/man/gg_linerange.Rd | 12 ggblanket-30.0.0/ggblanket/man/gg_path.Rd | 12 ggblanket-30.0.0/ggblanket/man/gg_point.Rd | 12 ggblanket-30.0.0/ggblanket/man/gg_polygon.Rd | 12 ggblanket-30.0.0/ggblanket/man/gg_qq.Rd | 12 ggblanket-30.0.0/ggblanket/man/gg_quantile.Rd | 12 ggblanket-30.0.0/ggblanket/man/gg_raster.Rd | 12 ggblanket-30.0.0/ggblanket/man/gg_rect.Rd | 12 ggblanket-30.0.0/ggblanket/man/gg_ribbon.Rd | 12 ggblanket-30.0.0/ggblanket/man/gg_segment.Rd | 12 ggblanket-30.0.0/ggblanket/man/gg_sf.Rd | 12 ggblanket-30.0.0/ggblanket/man/gg_smooth.Rd | 12 ggblanket-30.0.0/ggblanket/man/gg_spoke.Rd | 12 ggblanket-30.0.0/ggblanket/man/gg_step.Rd | 12 ggblanket-30.0.0/ggblanket/man/gg_tile.Rd | 12 ggblanket-30.0.0/ggblanket/man/gg_violin.Rd | 12 ggblanket-30.0.0/ggblanket/man/set_colour_blend.Rd |only ggblanket-30.0.0/ggblanket/man/set_fill_blend.Rd |only ggblanket-30.0.0/ggblanket/man/set_refine.Rd |only 88 files changed, 723 insertions(+), 740 deletions(-)
Title: Elastic Functional Data Analysis
Description: Performs alignment, PCA, and modeling of multidimensional and
unidimensional functions using the square-root velocity framework
(Srivastava et al., 2011 <doi:10.48550/arXiv.1103.3817> and Tucker et al., 2014
<DOI:10.1016/j.csda.2012.12.001>). This framework allows for elastic
analysis of functional data through phase and amplitude separation.
Author: J. Derek Tucker [aut, cre] ,
Aymeric Stamm [ctb]
Maintainer: J. Derek Tucker <jdtuck@sandia.gov>
Diff between fdasrvf versions 2.5.0 dated 2026-09-16 and 2.5.1 dated 2026-10-29
fdasrvf-2.5.0/fdasrvf/src/Makevars |only fdasrvf-2.5.1/fdasrvf/DESCRIPTION | 10 fdasrvf-2.5.1/fdasrvf/MD5 | 131 fdasrvf-2.5.1/fdasrvf/NAMESPACE | 4 fdasrvf-2.5.1/fdasrvf/NEWS.md | 79 fdasrvf-2.5.1/fdasrvf/R/RcppExports.R | 4 fdasrvf-2.5.1/fdasrvf/R/SqrtMean.R | 2 fdasrvf-2.5.1/fdasrvf/R/SqrtMedian.R | 2 fdasrvf-2.5.1/fdasrvf/R/align_new.R |only fdasrvf-2.5.1/fdasrvf/R/boxplot-classify.R |only fdasrvf-2.5.1/fdasrvf/R/boxplot.R | 82 fdasrvf-2.5.1/fdasrvf/R/curve_functions.R | 27 fdasrvf-2.5.1/fdasrvf/R/elastic.distance.R | 13 fdasrvf-2.5.1/fdasrvf/R/f_to_srvf.R | 49 fdasrvf-2.5.1/fdasrvf/R/geometry.R | 87 fdasrvf-2.5.1/fdasrvf/R/jointfPCA.R | 4 fdasrvf-2.5.1/fdasrvf/R/kmeans.R | 5 fdasrvf-2.5.1/fdasrvf/R/multiple_align_functions.R | 2 fdasrvf-2.5.1/fdasrvf/R/optimum.reparam.R | 12 fdasrvf-2.5.1/fdasrvf/R/predict.hfpca.R | 2 fdasrvf-2.5.1/fdasrvf/R/predict.jfpca.R | 2 fdasrvf-2.5.1/fdasrvf/R/predict.lpcr.R | 4 fdasrvf-2.5.1/fdasrvf/R/predict.mlpcr.R | 8 fdasrvf-2.5.1/fdasrvf/R/predict.pcr.R | 4 fdasrvf-2.5.1/fdasrvf/R/refactoring.R | 4 fdasrvf-2.5.1/fdasrvf/R/regression_functions.R | 14 fdasrvf-2.5.1/fdasrvf/R/srvf_to_f.R | 6 fdasrvf-2.5.1/fdasrvf/R/time-warping.R | 125 fdasrvf-2.5.1/fdasrvf/R/utils-pointwise.R | 3 fdasrvf-2.5.1/fdasrvf/R/utils.R | 25 fdasrvf-2.5.1/fdasrvf/R/vertFPCA.R | 2 fdasrvf-2.5.1/fdasrvf/README.md | 2 fdasrvf-2.5.1/fdasrvf/cleanup |only fdasrvf-2.5.1/fdasrvf/configure |only fdasrvf-2.5.1/fdasrvf/data/simu_warp.rda |binary fdasrvf-2.5.1/fdasrvf/data/simu_warp_median.rda |binary fdasrvf-2.5.1/fdasrvf/man/align_new.Rd |only fdasrvf-2.5.1/fdasrvf/man/ampbox_data.Rd | 5 fdasrvf-2.5.1/fdasrvf/man/classify.Rd |only fdasrvf-2.5.1/fdasrvf/man/f_to_srvf.Rd | 8 fdasrvf-2.5.1/fdasrvf/man/figures/README-1d_aligned_plot-2.png |binary fdasrvf-2.5.1/fdasrvf/man/figures/README-1d_aligned_plot-3.png |binary fdasrvf-2.5.1/fdasrvf/man/figures/README-1d_aligned_plot-5.png |binary fdasrvf-2.5.1/fdasrvf/man/figures/README-1d_aligned_plot-6.png |binary fdasrvf-2.5.1/fdasrvf/man/gam_to_h.Rd | 2 fdasrvf-2.5.1/fdasrvf/man/gam_to_psi.Rd | 2 fdasrvf-2.5.1/fdasrvf/man/gam_to_v.Rd | 2 fdasrvf-2.5.1/fdasrvf/man/optimum.reparam.Rd | 11 fdasrvf-2.5.1/fdasrvf/man/phbox_data.Rd | 5 fdasrvf-2.5.1/fdasrvf/man/srvf_to_f.Rd | 2 fdasrvf-2.5.1/fdasrvf/man/time_warping.Rd | 4 fdasrvf-2.5.1/fdasrvf/src/Makevars.in |only fdasrvf-2.5.1/fdasrvf/src/RcppExports.cpp | 9 fdasrvf-2.5.1/fdasrvf/src/fdasrsf/DP.cpp | 27 fdasrvf-2.5.1/fdasrvf/src/fdasrsf/DP.h | 3 fdasrvf-2.5.1/fdasrvf/src/fdasrsf/dp_grid.cpp | 26 fdasrvf-2.5.1/fdasrvf/src/wrapperSRSF.cpp | 14 fdasrvf-2.5.1/fdasrvf/tests/testthat/_snaps/align-fpca.md | 4542 +++++----- fdasrvf-2.5.1/fdasrvf/tests/testthat/_snaps/boxplot.md | 579 - fdasrvf-2.5.1/fdasrvf/tests/testthat/_snaps/kmeans.md | 3145 +++--- fdasrvf-2.5.1/fdasrvf/tests/testthat/_snaps/time-warping.md | 3242 +++---- fdasrvf-2.5.1/fdasrvf/tests/testthat/test-boxplot-classify.R |only fdasrvf-2.5.1/fdasrvf/tests/testthat/test-boxplot.R | 12 fdasrvf-2.5.1/fdasrvf/tests/testthat/test-curve-shape.R |only fdasrvf-2.5.1/fdasrvf/tests/testthat/test-kmeans.R | 3 fdasrvf-2.5.1/fdasrvf/tests/testthat/test-l2-geometry.R |only fdasrvf-2.5.1/fdasrvf/tests/testthat/test-modeling-smoke.R |only fdasrvf-2.5.1/fdasrvf/tests/testthat/test-optimum-reparam.R | 48 fdasrvf-2.5.1/fdasrvf/tests/testthat/test-regressions.R | 4 fdasrvf-2.5.1/fdasrvf/tests/testthat/test-smooth-gradient.R |only fdasrvf-2.5.1/fdasrvf/tests/testthat/test-sqrt-mean.R |only fdasrvf-2.5.1/fdasrvf/tests/testthat/test-srvf-representation.R |only fdasrvf-2.5.1/fdasrvf/tests/testthat/test-time-warping.R | 37 fdasrvf-2.5.1/fdasrvf/tests/testthat/test-warp-fun.R |only fdasrvf-2.5.1/fdasrvf/tests/testthat/test-warping-conversions.R |only 75 files changed, 6356 insertions(+), 6090 deletions(-)
Title: Immune Oncology Biological Research
Description: Provides six modules for tumor microenvironment (TME)
analysis based on multi-omics data. These modules cover data
preprocessing, TME estimation, TME infiltrating patterns, cellular
interactions, genome and TME interaction, and visualization for TME
relevant features, as well as modelling based on key features. It
integrates multiple microenvironmental analysis algorithms and
signature estimation methods, simplifying the analysis and downstream
visualization of the TME. In addition to providing a quick and easy
way to construct gene signatures from single-cell RNA-seq data, it
also provides a way to construct a reference matrix for TME
deconvolution from single-cell RNA-seq data. The analysis pipeline and
feature visualization are user-friendly and provide a comprehensive
description of the complex TME, offering insights into tumour-immune
interactions (Zeng D, et al. (2024)
<doi:10.1016/j.crmeth.2024.100910>. Fang Y, et al. (2025)
<doi:10.1002/mdr2.70001>).
Author: Dongqiang Zeng [aut],
Yiran Fang [aut],
Shixiang Wang [aut, cre] ,
Qingcong Luo [aut],
Hongqian Qian [aut]
Maintainer: Shixiang Wang <w_shixiang@163.com>
Diff between IOBR versions 2.2.3 dated 2026-05-30 and 2.2.4 dated 2026-10-28
DESCRIPTION | 14 -- MD5 | 36 +++---- NAMESPACE | 142 +++++++++++++++-------------- NEWS.md | 16 +++ R/download_data.R | 13 ++ R/format_msigdb.R | 24 ++-- R/iobr_cor_plot.R | 12 +- R/palettes.R | 8 - R/sig_gsea.R | 21 ++-- R/sig_heatmap.R | 16 +-- R/surv_group.R | 2 README.md | 2 inst/doc/IOBR-user-manual.html | 4 man/format_msigdb.Rd | 24 ++-- man/patterns_to_na.Rd | 2 man/sig_gsea.Rd | 18 ++- man/signature_score_calculation_methods.Rd | 2 man/timer_available_cancers.Rd | 5 - man/tme_deconvolution_methods.Rd | 2 19 files changed, 197 insertions(+), 166 deletions(-)
Title: Integrated Interface of Bayesian Single Index Models using
'nimble'
Description: Provides tools for fitting Bayesian single index models with
flexible choices of priors for both the index and the link function.
The package implements model estimation and posterior inference using
efficient MCMC algorithms built on the 'nimble' framework, allowing
users to specify, extend, and simulate models in a unified and
reproducible manner. The following methods are implemented in the
package: Antoniadis et al. (2004)
<https://www.jstor.org/stable/24307224>, Wang (2009)
<doi:10.1016/j.csda.2008.12.010>, Choi et al. (2011)
<doi:10.1080/10485251003768019>, Dhara et al. (2019)
<doi:10.1214/19-BA1170>, McGee et al. (2023) <doi:10.1111/biom.13569>.
Author: Seowoo Jung [aut, cre],
Eun-kyung Lee [aut]
Maintainer: Seowoo Jung <jsw1347@ewha.ac.kr>
Diff between BayesSIM versions 2.0.0 dated 2026-10-14 and 2.0.1 dated 2026-10-28
DESCRIPTION | 6 MD5 | 44 - R/bsFisher.R | 1176 ++++++++++++++++++++++++------------------------- R/bsPolar.R | 6 R/bsSphere-functions.R | 1130 +++++++++++++++++++++++------------------------ R/bsSphere.R | 16 R/bsSpike.R | 62 -- R/generics.R | 27 - R/gpFisher.R | 29 - R/gpPolar.R | 14 R/gpSphere-united.R | 28 - R/gpspike.R | 24 - R/prior-params.R | 2 man/bsFisher.Rd | 12 man/bsPolar.Rd | 6 man/bsSphere.Rd | 16 man/bsSpike.Rd | 14 man/fitted.bsim.Rd | 2 man/gpFisher.Rd | 29 - man/gpPolar.Rd | 14 man/gpSphere.Rd | 28 - man/gpSpike.Rd | 24 - man/predict.bsim.Rd | 25 - 23 files changed, 1355 insertions(+), 1379 deletions(-)
Title: Stepped Wedge Cluster Randomized Trial (SW CRT) Design
Description: A set of tools for examining the design and analysis aspects of
stepped wedge cluster randomized trials (SW CRT) based on a repeated
cross-sectional or cohort sampling scheme (Hussey MA and Hughes JP (2007)
Contemporary Clinical Trials 28:182-191).
Author: Jim Hughes [aut, cre],
Navneet R. Hakhu [aut],
Emily Voldal [aut],
Fan Xia [aut]
Maintainer: Jim Hughes <jphughes@uw.edu>
Diff between swCRTdesign versions 4.1 dated 2025-09-04 and 4.2 dated 2026-10-28
swCRTdesign-4.1/swCRTdesign/README.md |only swCRTdesign-4.2/swCRTdesign/DESCRIPTION | 8 +-- swCRTdesign-4.2/swCRTdesign/MD5 | 11 ++-- swCRTdesign-4.2/swCRTdesign/NAMESPACE | 5 -- swCRTdesign-4.2/swCRTdesign/R/swSim2.R | 37 ++++++++------- swCRTdesign-4.2/swCRTdesign/R/swSimPwr.R | 57 +++++++++++++----------- swCRTdesign-4.2/swCRTdesign/man/ReleaseNotes.Rd | 34 ++++++-------- 7 files changed, 79 insertions(+), 73 deletions(-)
Title: Access the 'ObrasGov' Open Data API
Description: Provides a modern interface to the Brazilian federal
government's 'ObrasGov' open data application programming interface
(<https://api-publica.obrasgov.gestao.gov.br>). Retrieves data about
public infrastructure projects, physical execution, contracts,
commitments, geometries, feasibility studies, and project status
histories. Results are returned as tidy tibbles with typed date columns,
preserved nested relationships, pagination metadata, and optional
multi-page collection.
Author: Andre Leite [aut, cre] ,
Marcos Wasiliew [aut] ,
Hugo Vasconcelos [aut] ,
Carlos Amorim [aut] ,
Diogo Bezerra [aut] ,
Julia Nascimento Barreto [aut]
Maintainer: Andre Leite <leite@castlab.org>
Diff between obrasgovr versions 0.1.0 dated 2026-07-24 and 0.1.1 dated 2026-10-28
DESCRIPTION | 27 ++++++++++++++++----------- MD5 | 18 +++++++++--------- NEWS.md | 12 ++++++++++++ R/client.R | 2 +- R/metadata.R | 20 ++++++++++++++++++++ README.md | 7 +++---- inst/CITATION | 5 +++-- man/obrasgovr-package.Rd | 7 ++++--- tests/testthat/test-client.R | 11 +++++++++++ tests/testthat/test-endpoints.R | 23 +++++++++++++++++++++++ 10 files changed, 102 insertions(+), 30 deletions(-)
Title: Benchmarked Silicon Samples for Survey and Experiment Design
Description: Administers survey and experimental instruments to panels of
language-model personas, with option-order randomization and benchmark
comparison against human data. Conjoint effects are estimated from recorded
respondent-level profile assignments. Samples of language-model personas
follow Argyle et al. (2023) <doi:10.1017/pan.2023.2>; the case for
benchmarking them against human data is set out in Bisbee et al. (2024)
<doi:10.1017/pan.2024.5>; the conjoint estimand is the average marginal
component effect of Hainmueller et al. (2014) <doi:10.1093/pan/mpt024>.
Author: Ali Sanaei [aut, cre, cph]
Maintainer: Ali Sanaei <sanaei@uchicago.edu>
Diff between LLMRpanel versions 0.6.1 dated 2026-09-12 and 0.6.3 dated 2026-10-28
DESCRIPTION | 11 MD5 | 81 +++--- NEWS.md | 201 +++++++++++++++ R/00_package.R | 43 ++- R/administer.R | 127 +++++---- R/batch.R | 3 R/benchmark.R | 202 ++++++++++----- R/data.R |only R/gui.R | 214 ++++++++++++---- R/instrument.R | 259 ++++++++++++++----- R/panel.R | 368 +++++++++++++++++++--------- R/persona_frame.R | 14 - R/render.R |only README.md | 42 +-- data |only inst/ai/LLMRpanel.md | 47 ++- inst/doc/design.R | 8 inst/doc/design.Rmd | 85 +++--- inst/doc/design.html | 145 +++++------ man/LLMRpanel-package.Rd | 26 + man/anes_2024_personas.Rd |only man/as_persona_frame.Rd | 14 - man/conjoint_amce.Rd | 22 + man/conjoint_design.Rd | 24 + man/conjoint_instrument.Rd | 49 +-- man/panel_administer.Rd | 126 +++++---- man/panel_batch_submit.Rd | 3 man/panel_benchmark.Rd | 87 +++--- man/panel_bias_audit.Rd | 9 man/panel_from_data.Rd | 34 ++ man/panel_from_personas.Rd | 136 ++++++++-- man/panel_generics.Rd | 18 + man/panel_instrument.Rd | 43 ++- man/panel_items.Rd | 18 - tests/testthat/fixtures |only tests/testthat/helper-warnings.R |only tests/testthat/test-anes-personas.R |only tests/testthat/test-conjoint-power-panel.R | 87 ++++++ tests/testthat/test-documentation.R |only tests/testthat/test-gui.R | 301 ++++++++++++++++++++++ tests/testthat/test-instrument-validation.R |only tests/testthat/test-panel-sampling.R |only tests/testthat/test-panel.R | 112 ++++++++ tests/testthat/test-rendering.R |only tests/testthat/test-review-fixes.R | 7 tests/testthat/test-scaling.R | 9 vignettes/design.Rmd | 85 +++--- 47 files changed, 2268 insertions(+), 792 deletions(-)
Title: Shared 'Shiny' Components for 'LLMR' Family Applications
Description: Reusable 'Shiny' user interface and server components from
which the graphical applications in the 'LLMR' package family are
assembled.
Author: Ali Sanaei [aut, cre]
Maintainer: Ali Sanaei <sanaei@uchicago.edu>
Diff between LLMR.shiny versions 0.1.2 dated 2026-08-04 and 0.1.3 dated 2026-10-28
DESCRIPTION | 8 - MD5 | 28 ++- NEWS.md | 79 +++++++++++ R/io.R | 47 +++++- R/runners.R | 244 +++++++++++++++++++++++++++++----- R/usage.R | 174 +++++++++++++++++++++--- README.md | 98 ++++++++++--- man/extract_token_counts.Rd | 66 ++++++++- man/read_csv_path.Rd | 8 - man/read_csv_upload.Rd | 15 +- man/usage_add.Rd | 38 ++++- man/usage_empty.Rd | 10 - man/usage_tile.Rd | 21 ++ man/validate_column_mapping.Rd | 5 tests/testthat/test-csv-identifiers.R |only tests/testthat/test-usage-unknown.R |only 16 files changed, 715 insertions(+), 126 deletions(-)
Title: Hierarchical Item Response Theory Models
Description: Implementation of a class of hierarchical item response
theory (IRT) models where both the mean and the variance of latent preferences
(ability parameters) may depend on observed covariates. The current
implementation includes both the two-parameter latent trait model for binary data and the
graded response model for ordinal data. Both are fitted via the Expectation-Maximization (EM)
algorithm. Asymptotic standard errors are derived from the observed information
matrix. See Zhou (2019) <doi:10.1017/pan.2018.63> for details.
Author: Xiang Zhou [aut, cre]
Maintainer: Xiang Zhou <xiang_zhou@fas.harvard.edu>
Diff between hIRT versions 0.4.0 dated 2026-09-28 and 0.5.0 dated 2026-10-28
DESCRIPTION | 14 - MD5 | 32 +- NAMESPACE | 2 NEWS.md | 13 R/RcppExports.R |only R/hgrm.R | 732 ++++++++++++++++++++++++++----------------------------- R/hgrm2.R | 523 ++++++++++++++++++--------------------- R/hgrmDIF.R | 738 ++++++++++++++++++++++++++++---------------------------- R/hltm.R | 629 ++++++++++++++++++++++------------------------- R/hltm2.R | 473 ++++++++++++++++------------------- R/utils.R | 16 - R/utils_cpp.R |only R/utils_grm.R | 178 ------------- R/utils_ltm.R | 59 ---- src |only tests |only 16 files changed, 1529 insertions(+), 1880 deletions(-)
Title: Access Brazilian Central Bank 'PIX' Open Data 'API'
Description: Provides a 'tidyverse'-style interface to the Brazilian Central Bank (<https://www.bcb.gov.br>) 'PIX' Open Data 'API' <https://olinda.bcb.gov.br/olinda/servico/Pix_DadosAbertos/versao/v1/aplicacao#!/recursos>.
Retrieve statistics on 'PIX' keys, transactions by municipality, and monthly
transaction summaries. All functions return 'tibbles' and support 'OData'
query parameters for filtering, selecting, and ordering data.
Author: Andre Leite [aut, cre] ,
Marcos Wasiliew [aut] ,
Hugo Vasconcelos [aut] ,
Carlos Amorim [aut] ,
Diogo Bezerra [aut] ,
Julia Nascimento Barreto [aut]
Maintainer: Andre Leite <leite@castlab.org>
Diff between pixr versions 0.1.0 dated 2026-01-31 and 0.1.1 dated 2026-10-28
DESCRIPTION | 41 +++++++++----- MD5 | 40 +++++++++----- NAMESPACE | 2 NEWS.md |only R/client.R | 50 +++-------------- R/pix_cnae.R |only R/pix_dict_users.R |only R/pix_fraud_stats.R | 7 +- R/pixr-package.R | 7 +- R/utils.R | 82 +++++++++++++++++++++++++++-- README.md | 11 +++ build/vignette.rds |binary inst/doc/receiver-profiles-dict-users.R |only inst/doc/receiver-profiles-dict-users.Rmd |only inst/doc/receiver-profiles-dict-users.html |only man/get_pix_cnae_stats.Rd |only man/get_pix_dict_users.Rd |only man/get_pix_fraud_stats.Rd | 2 man/pix_columns.Rd | 8 ++ man/pix_query.Rd | 2 man/pix_url.Rd | 2 man/pixr-package.Rd | 18 ++++-- tests |only vignettes/receiver-profiles-dict-users.Rmd |only 24 files changed, 188 insertions(+), 84 deletions(-)
Title: Functions for the Nakagami Distribution
Description: Density, distribution function, quantile function and random
generation for the Nakagami distribution of Nakagami (1960)
<doi:10.1016/B978-0-08-009306-2.50005-4>.
Author: Jonas Moss [aut, cre]
Maintainer: Jonas Moss <jonas.gjertsen@gmail.com>
Diff between nakagami versions 1.1.0 dated 2021-09-14 and 1.2.0 dated 2026-10-28
nakagami-1.1.0/nakagami/man/suppress_olw.Rd |only nakagami-1.2.0/nakagami/DESCRIPTION | 13 nakagami-1.2.0/nakagami/LICENSE | 4 nakagami-1.2.0/nakagami/MD5 | 32 - nakagami-1.2.0/nakagami/NAMESPACE | 12 nakagami-1.2.0/nakagami/NEWS.md |only nakagami-1.2.0/nakagami/R/assertions.R | 59 - nakagami-1.2.0/nakagami/R/nakagami.R | 288 +++++---- nakagami-1.2.0/nakagami/R/utility.R | 47 + nakagami-1.2.0/nakagami/README.md | 165 ++--- nakagami-1.2.0/nakagami/man/Nakagami.Rd | 157 ++--- nakagami-1.2.0/nakagami/man/figures/logo.png |binary nakagami-1.2.0/nakagami/man/figures/logo.svg |only nakagami-1.2.0/nakagami/tests/testthat.R | 8 nakagami-1.2.0/nakagami/tests/testthat/setup.R | 16 nakagami-1.2.0/nakagami/tests/testthat/test-assertions.R | 64 +- nakagami-1.2.0/nakagami/tests/testthat/test-nakagami.R | 432 +++++++------- nakagami-1.2.0/nakagami/tests/testthat/test-regressions.R |only nakagami-1.2.0/nakagami/tests/testthat/test-utility.R | 13 19 files changed, 658 insertions(+), 652 deletions(-)
Title: Beautiful Regression Tables for Modern Econometrics Packages
Description: Produces publication-quality LaTeX, ASCII, and HTML regression
tables. Designed as a drop-in replacement for the 'stargazer' package
for 'lm' and 'glm' models, with added native support for 'fixest',
'plm', and 'alpaca' objects including automatic fixed-effect and
random-effect indicator rows and SE-type detection. Standard errors can
be supplied as variance-covariance matrices, numeric vectors, or
auto-extracted from supported model objects. Follows the interface of
Hlavac (2022) <https://CRAN.R-project.org/package=stargazer>.
Author: Tom Zylkin [aut, cre]
Maintainer: Tom Zylkin <tzylkin@richmond.edu>
Diff between stargazer2 versions 0.1.1 dated 2026-10-20 and 0.1.2 dated 2026-10-28
DESCRIPTION | 8 +- MD5 | 16 ++--- NEWS.md | 8 ++ R/stargazer.R | 10 +-- R/summary_table.R | 6 -- inst/doc/getting-started.html | 8 +- inst/doc/modern-estimators.html | 4 - inst/doc/plm-panel-data.R | 60 ++++++++++---------- inst/doc/plm-panel-data.html | 119 +--------------------------------------- 9 files changed, 66 insertions(+), 173 deletions(-)
Title: Plot Scaled 'ggplot' Representations of Sports Playing Surfaces
Description: Create scaled 'ggplot' representations of playing surfaces.
Playing surfaces are drawn pursuant to rule-book specifications.
This package should be used as a baseline plot for displaying any type of
tracking data.
Author: Ross Drucker [aut, cre]
Maintainer: Ross Drucker <ross.a.drucker@gmail.com>
Diff between sportyR versions 2.2.3 dated 2025-07-28 and 2.4.5 dated 2026-10-28
DESCRIPTION | 10 MD5 | 139 ++++---- NAMESPACE | 2 NEWS.md | 149 ++++++++- R/cani-functions.R | 8 R/create-shapes.R | 89 +++++ R/features-football.R | 33 +- R/features-hockey.R | 146 ++++---- R/features-lacrosse.R | 282 +++++++++-------- R/features-softball.R |only R/geom-baseball.R | 33 +- R/geom-basketball.R | 44 +- R/geom-curling.R | 33 +- R/geom-football.R | 42 +- R/geom-hockey.R | 49 +- R/geom-lacrosse.R | 130 +++++-- R/geom-soccer.R | 33 +- R/geom-softball.R |only R/geom-tennis.R | 33 +- R/geom-volleyball.R | 33 +- R/get-surface-dimensions.R |only R/plot-helpers.R | 85 +++++ R/sysdata.rda |binary R/utils.R | 28 + build/vignette.rds |binary inst/CITATION |only inst/doc/animating-tracking-data.Rmd | 210 +++++++----- inst/doc/animating-tracking-data.html | 47 ++ inst/doc/customize-plot.Rmd | 200 +++++++----- inst/doc/customize-plot.html | 49 ++ inst/doc/plotting-tracking-data.Rmd | 330 +++++++++++--------- inst/doc/plotting-tracking-data.html | 53 +++ inst/doc/sportyR.R | 3 inst/doc/sportyR.Rmd | 55 ++- inst/doc/sportyR.html | 66 +++- man/geom_lacrosse.Rd | 5 man/geom_softball.Rd |only man/get_surface_dimensions.Rd |only man/lacrosse_goal_arc.Rd | 21 - man/lacrosse_goal_fan.Rd | 12 man/lacrosse_penalty_box_outline.Rd | 2 man/lacrosse_referee_crease.Rd | 7 man/same_color.Rd |only man/scale_plot_units.Rd |only man/softball_base.Rd |only man/softball_batters_box.Rd |only man/softball_catchers_box.Rd |only man/softball_coaches_box.Rd |only man/softball_features_set_colors.Rd |only man/softball_foul_line.Rd |only man/softball_home_plate.Rd |only man/softball_infield_dirt.Rd |only man/softball_pitchers_circle.Rd |only man/softball_pitchers_lane.Rd |only man/softball_pitchers_plate.Rd |only man/softball_running_lane.Rd |only man/unit_conversion_factor.Rd |only tests/testthat/test-cani-functions.R | 4 tests/testthat/test-coordinate-transforms.R | 2 tests/testthat/test-feature-validity.R |only tests/testthat/test-geometry-quirks.R |only tests/testthat/test-get-surface-dimensions.R |only tests/testthat/test-invalid-league-error.R | 5 tests/testthat/test-is_hex.R | 2 tests/testthat/test-loading-of-default-parameters.R | 2 tests/testthat/test-math-functions.R | 2 tests/testthat/test-no-league-error.R | 5 tests/testthat/test-plots-and-features-baseball.R | 2 tests/testthat/test-plots-and-features-basketball.R | 2 tests/testthat/test-plots-and-features-curling.R | 2 tests/testthat/test-plots-and-features-football.R | 2 tests/testthat/test-plots-and-features-hockey.R | 2 tests/testthat/test-plots-and-features-lacrosse.R | 17 + tests/testthat/test-plots-and-features-soccer.R | 2 tests/testthat/test-plots-and-features-softball.R |only tests/testthat/test-plots-and-features-tennis.R | 2 tests/testthat/test-plots-and-features-volleyball.R | 2 tests/testthat/test-shapes.R | 2 tests/testthat/test-unit-conversions.R | 2 vignettes/animating-tracking-data.Rmd | 210 +++++++----- vignettes/customize-plot.Rmd | 200 +++++++----- vignettes/plotting-tracking-data.Rmd | 330 +++++++++++--------- vignettes/sportyR.Rmd | 55 ++- 83 files changed, 2199 insertions(+), 1116 deletions(-)
Title: Reproducible Code for 'Shiny' Objects
Description: Provides functionality to extract reactive expressions from a 'shiny' application and
convert them into stand-alone R scripts. This enables users to reproduce tables and visualisations
outside the interactive UI, facilitating integration into static reports or automated workflows
without requiring access to the original application source code.
Author: Ashley Baldry [aut, cre]
Maintainer: Ashley Baldry <ashley.baldry@acuityanalytics.com>
This is a re-admission after prior archival of version 0.3.0 dated 2026-09-17
Diff between shinyreprex versions 0.3.0 dated 2026-09-17 and 0.4.0 dated 2026-10-28
DESCRIPTION | 11 + MD5 | 32 +++-- NAMESPACE | 1 NEWS.md | 11 + R/reprex_header.R |only R/reprex_lockfile.R | 55 +++++++-- R/reprex_reactive.R | 30 ++++- README.md | 27 ++++ inst/WORDLIST | 1 inst/doc/shinyreprex.Rmd | 30 ++++- inst/doc/shinyreprex.html | 199 +++++++++++++++++++--------------- inst/examples-shiny/lockfile/app.R | 13 ++ man/header_packages.Rd |only man/header_r_version.Rd |only man/reprex_header.Rd |only man/reprex_reactive.Rd | 21 +++ man/resolve_reprex_packages.Rd |only tests/testthat/test-reprex_header.R |only tests/testthat/test-reprex_reactive.R | 40 ++++++ vignettes/shinyreprex.Rmd | 30 ++++- 20 files changed, 381 insertions(+), 120 deletions(-)
Title: Performance Assessment for Continuous and Survival Outcomes
Description: Evaluates prediction accuracy for continuous outcomes and the
predictive performance of survival models in a unified framework.
Implements the R-squared, L-squared, pseudo R-squared and related explained
variation measures of Li and Wang (2019)
<doi:10.1080/01621459.2018.1515079>, the concordance indices of Harrell
et al. (1982) <doi:10.1001/jama.1982.03320430047030> and Uno et al.
(2011) <doi:10.1002/sim.4154>, the time-dependent area under the receiver
operating characteristic curve (AUC) of Heagerty, Lumley and Pepe (2000)
<doi:10.1111/j.0006-341X.2000.00337.x>, and the Brier score of Graf et
al. (1999)
<doi:10.1002/(SICI)1097-0258(19990915/30)18:17/18%3C2529::AID-SIM274%3E3.0.CO;2-5>.
Supports right-censored data; competing risks, following Wolbers et al.
(2014) <doi:10.1093/biostatistics/kxt059>, Wu and Li (2018)
<doi:10.1002/sim.7806> and Zhuang et al. (2025)
<doi:10.48550/arXiv.2507.15040>; and two-phase sampling designs such as
ca [...truncated...]
Author: Tong Zhu [aut],
Zian Zhuang [aut, cre],
Wen Su [aut],
Xiaowu Dai [aut],
Xiaoyan Wang [aut],
Gang Li [aut]
Maintainer: Zian Zhuang <zianzhuang@ucla.edu>
This is a re-admission after prior archival of version 0.1.0 dated 2018-01-22
Diff between PAmeasures versions 0.1.0 dated 2018-01-22 and 2.0.0 dated 2026-10-28
PAmeasures-0.1.0/PAmeasures/R/pam.coxph.R |only PAmeasures-0.1.0/PAmeasures/R/pam.nlm.R |only PAmeasures-0.1.0/PAmeasures/R/pam.survreg.R |only PAmeasures-0.1.0/PAmeasures/man/pam.censor.Rd |only PAmeasures-0.1.0/PAmeasures/man/pam.coxph.Rd |only PAmeasures-0.1.0/PAmeasures/man/pam.nlm.Rd |only PAmeasures-0.1.0/PAmeasures/man/pam.survreg.Rd |only PAmeasures-2.0.0/PAmeasures/DESCRIPTION | 71 +++- PAmeasures-2.0.0/PAmeasures/MD5 | 110 ++++++- PAmeasures-2.0.0/PAmeasures/NAMESPACE | 72 ++++ PAmeasures-2.0.0/PAmeasures/NEWS.md |only PAmeasures-2.0.0/PAmeasures/R/PAmeasures-package.R |only PAmeasures-2.0.0/PAmeasures/R/moore.R | 28 - PAmeasures-2.0.0/PAmeasures/R/pa_calibration.R |only PAmeasures-2.0.0/PAmeasures/R/pa_case_cohort_weights.R |only PAmeasures-2.0.0/PAmeasures/R/pa_cr_event_ipcw.R |only PAmeasures-2.0.0/PAmeasures/R/pa_evaluate_two_phase.R |only PAmeasures-2.0.0/PAmeasures/R/pa_fit_and_eval.R |only PAmeasures-2.0.0/PAmeasures/R/pa_metric_names.R |only PAmeasures-2.0.0/PAmeasures/R/pa_nested_case_control_weights.R |only PAmeasures-2.0.0/PAmeasures/R/pa_nlm.R |only PAmeasures-2.0.0/PAmeasures/R/pa_predict_cif.R |only PAmeasures-2.0.0/PAmeasures/R/pa_predict_coxph.R |only PAmeasures-2.0.0/PAmeasures/R/pa_predict_survreg.R |only PAmeasures-2.0.0/PAmeasures/R/pa_sim_data.R |only PAmeasures-2.0.0/PAmeasures/R/pa_simulate_fine_gray.R |only PAmeasures-2.0.0/PAmeasures/R/pa_survival_eval.R |only PAmeasures-2.0.0/PAmeasures/R/pa_survival_eval_cr.R |only PAmeasures-2.0.0/PAmeasures/R/pam.Brier.R |only PAmeasures-2.0.0/PAmeasures/R/pam.Ct.R |only PAmeasures-2.0.0/PAmeasures/R/pam.censor.R | 151 +++++----- PAmeasures-2.0.0/PAmeasures/R/pam.concordance.R |only PAmeasures-2.0.0/PAmeasures/R/pam.predictSurvProb2survreg.R |only PAmeasures-2.0.0/PAmeasures/R/pam.r2_metrics.R |only PAmeasures-2.0.0/PAmeasures/R/pam.weighted_param.R |only PAmeasures-2.0.0/PAmeasures/R/plot.R |only PAmeasures-2.0.0/PAmeasures/README.md |only PAmeasures-2.0.0/PAmeasures/build |only PAmeasures-2.0.0/PAmeasures/inst |only PAmeasures-2.0.0/PAmeasures/man/PAmeasures-package.Rd |only PAmeasures-2.0.0/PAmeasures/man/moore.Rd | 46 +-- PAmeasures-2.0.0/PAmeasures/man/pa_calibration.Rd |only PAmeasures-2.0.0/PAmeasures/man/pa_case_cohort_weights.Rd |only PAmeasures-2.0.0/PAmeasures/man/pa_evaluate_two_phase.Rd |only PAmeasures-2.0.0/PAmeasures/man/pa_fit_and_eval.Rd |only PAmeasures-2.0.0/PAmeasures/man/pa_metric_names.Rd |only PAmeasures-2.0.0/PAmeasures/man/pa_nested_case_control_weights.Rd |only PAmeasures-2.0.0/PAmeasures/man/pa_nlm.Rd |only PAmeasures-2.0.0/PAmeasures/man/pa_plot_pred.Rd |only PAmeasures-2.0.0/PAmeasures/man/pa_plot_summary.Rd |only PAmeasures-2.0.0/PAmeasures/man/pa_predict_cif.Rd |only PAmeasures-2.0.0/PAmeasures/man/pa_predict_coxph.Rd |only PAmeasures-2.0.0/PAmeasures/man/pa_predict_survreg.Rd |only PAmeasures-2.0.0/PAmeasures/man/pa_sample_design.Rd |only PAmeasures-2.0.0/PAmeasures/man/pa_sim_cox_weibull.Rd |only PAmeasures-2.0.0/PAmeasures/man/pa_simulate_fine_gray.Rd |only PAmeasures-2.0.0/PAmeasures/man/pa_summarize.Rd |only PAmeasures-2.0.0/PAmeasures/man/pa_summarize_cr.Rd |only PAmeasures-2.0.0/PAmeasures/man/pa_survival_eval.Rd |only PAmeasures-2.0.0/PAmeasures/man/pa_survival_eval_cr.Rd |only PAmeasures-2.0.0/PAmeasures/tests |only 61 files changed, 327 insertions(+), 151 deletions(-)
Title: Code to Access Open Access Species Range Maps
Description: Allows access to a proof-of-concept database containing Open Access species range models and relevant metadata. Access to the database is via both 'PostgreSQL' connection and API <https://github.com/EnquistLab/Biendata-Frontend>, allowing diverse use-cases.
Author: Brian Maitner [aut, cre] ,
Cory Merow [aut],
Brad Boyle [aut],
Xiao Feng [aut],
Rethvick Sriram Yugendra Babu [aut],
Brian Enquist [aut]
Maintainer: Brian Maitner <bmaitner@usf.edu>
Diff between OpenRange versions 0.0.2 dated 2026-08-25 and 0.0.3 dated 2026-10-28
DESCRIPTION | 8 - MD5 | 70 +++++---- NAMESPACE | 2 NEWS | 19 ++ R/OpenRange_api_load_species.R | 97 +++++++------ R/OpenRange_api_species.R | 166 +++++++++++------------ R/OpenRange_get_license.R | 22 ++- R/OpenRange_get_stats.R | 48 +++++- R/OpenRange_list_scenarios.R | 21 +- R/OpenRange_load_species.R | 81 ++++++----- R/OpenRange_sf.R | 59 ++++---- R/OpenRange_species.R | 67 ++++----- R/internals.R | 126 +++++++++++++++++ R/ranges_sql.R | 57 +++++-- README.md | 36 ++-- inst/doc/OpenRange.R | 37 ++++- inst/doc/OpenRange.html | 51 ++++--- inst/doc/OpenRange.rmd | 47 +++++- man/OpenRange_api_load_species.Rd | 29 ++-- man/OpenRange_api_species.Rd | 44 +++--- man/OpenRange_get_license.Rd | 16 ++ man/OpenRange_get_stats.Rd | 16 ++ man/OpenRange_list_scenarios.Rd | 6 man/OpenRange_load_species.Rd | 62 +++++--- man/OpenRange_sf.Rd | 25 ++- man/OpenRange_species.Rd | 35 +++- man/dot-api_query.Rd |only man/dot-as_sf.Rd |only man/dot-resource_unavailable.Rd |only man/ranges_sql.Rd | 3 tests/testthat/setup-OpenRange.R | 15 +- tests/testthat/test-OpenRange_api_load_species.R | 7 tests/testthat/test-OpenRange_get_license.R | 10 - tests/testthat/test-OpenRange_get_stats.R | 5 tests/testthat/test-OpenRange_list_scenarios.R | 8 - tests/testthat/test-OpenRange_load_species.R | 5 tests/testthat/test-graceful_failure.R |only vignettes/OpenRange.rmd | 47 +++++- 38 files changed, 911 insertions(+), 436 deletions(-)
Title: Management Strategy Evaluation Toolkit
Description: Development, simulation testing, and implementation of management procedures for fisheries
(see Carruthers & Hordyk (2018) <doi:10.1111/2041-210X.13081>).
Author: Adrian Hordyk [aut, cre],
Quang Huynh [aut],
Tom Carruthers [aut],
Chris Grandin [ctb]
Maintainer: Adrian Hordyk <adrian@bluematterscience.com>
Diff between MSEtool versions 3.7.5 dated 2025-09-29 and 3.7.6 dated 2026-10-28
DESCRIPTION | 14 - MD5 | 64 +++---- NAMESPACE | 281 ++++++++++++++++--------------- NEWS.md | 20 ++ R/Class_definitions.R | 12 - R/Data_Functions.R | 4 R/Data_make_update.R | 22 +- R/MMSE_Object.r | 1 R/MP_tuning.R | 2 R/Misc_Exported.R | 12 - R/Misc_Internal.R | 7 R/SS2Data.R | 59 ++++-- R/SS2MOM.R | 4 R/SS2OM.R | 28 +-- R/SSinternal.R | 31 ++- R/SampleOM.R | 10 - R/aaImportFrom.R | 18 -- R/applyMMP.R | 2 R/multiMSE.R | 51 ++++- R/popdyn.R | 447 +++++++++++++++++++++++++------------------------- R/runMSE.R | 25 +- build/partial.rdb |binary man/CalcMPDynamics.Rd | 9 - man/Rec-class.Rd | 7 man/SS2Data.Rd | 2 man/SS2DataMOM.Rd | 2 man/SS2MOM.Rd | 2 man/applyMMP.Rd | 2 man/applyMP.Rd | 2 man/multiMSE.Rd | 2 man/runMSE.Rd | 2 man/validcpars.Rd | 4 src/popddynCPP.cpp | 8 33 files changed, 644 insertions(+), 512 deletions(-)
Title: Tree-Style Console Logger for Nested Processes
Description: Render nested process execution as a live, colored tree in the console, with tree connectors, status glyphs, and elapsed time per step. Nesting depth is tracked via frame exit handlers so it never desynchronizes, even when a step errors. Builds on the 'cli' package for console rendering.
Author: Ivan Sortino [aut, cre, cph]
Maintainer: Ivan Sortino <ivan.sortino97@gmail.com>
Diff between logtree versions 0.2.0 dated 2026-09-01 and 0.2.1 dated 2026-10-28
DESCRIPTION | 6 +-- MD5 | 14 +++---- NEWS.md | 11 +++++ R/run.R | 71 +++++++++++++++++++++++++++++++------ R/state.R | 9 +++- inst/doc/logtree.html | 14 +++---- man/with_logging.Rd | 11 ++++- tests/testthat/test-with-logging.R | 67 ++++++++++++++++++++++++++++++---- 8 files changed, 161 insertions(+), 42 deletions(-)
Title: Utilities for Working with Google APIs
Description: Provides utilities for working with Google APIs
<https://developers.google.com/apis-explorer>. This includes
functions and classes for handling common credential types and for
preparing, executing, and processing HTTP requests.
Author: Jennifer Bryan [aut, cre] ,
Craig Citro [aut],
Hadley Wickham [aut] ,
Google Inc [cph],
Posit Software, PBC [cph, fnd]
Maintainer: Jennifer Bryan <jenny@posit.co>
Diff between gargle versions 1.6.1 dated 2026-01-29 and 1.7.0 dated 2026-10-28
DESCRIPTION | 22 LICENSE | 2 MD5 | 191 ++-- NAMESPACE | 8 NEWS.md | 21 R/AuthState-class.R | 2 R/aaa.R | 2 R/cred_funs.R | 2 R/credentials_app_default.R | 66 - R/credentials_external_account.R | 236 ++++- R/credentials_gce.R | 14 R/credentials_service_account.R | 2 R/gargle-package.R | 26 R/oauth-cache.R | 28 R/oauth-init.R | 102 ++ R/request_develop.R | 65 - R/request_make.R | 4 R/request_retry.R | 19 R/response_process.R | 40 R/roxygen-templates.R | 6 R/secret.R | 126 -- R/token_fetch.R | 10 R/utils-ui.R | 17 README.md | 9 build/vignette.rds |binary inst/WORDLIST | 18 inst/discovery-doc-ingest/ingest-functions.R | 7 inst/doc/auth-from-web.Rmd | 9 inst/doc/auth-from-web.html | 12 inst/doc/get-api-credentials.Rmd | 29 inst/doc/get-api-credentials.html | 68 - inst/doc/how-gargle-gets-tokens.R | 8 inst/doc/how-gargle-gets-tokens.Rmd | 29 inst/doc/how-gargle-gets-tokens.html | 49 - inst/doc/non-interactive-auth.Rmd | 78 + inst/doc/non-interactive-auth.html | 274 +++-- inst/doc/oauth-client-not-app.R | 65 - inst/doc/oauth-client-not-app.Rmd | 305 ++---- inst/doc/oauth-client-not-app.html | 457 +++------- inst/doc/request-helper-functions.R | 18 inst/doc/request-helper-functions.Rmd | 36 inst/doc/request-helper-functions.html | 60 - inst/doc/troubleshooting.R | 6 inst/doc/troubleshooting.Rmd | 10 inst/doc/troubleshooting.html | 10 man/AuthState-class.Rd | 326 +++---- man/Gargle-class.Rd | 250 ++--- man/GceToken.Rd | 241 ++--- man/WifToken.Rd | 241 ++--- man/credentials_app_default.Rd | 20 man/credentials_byo_oauth2.Rd | 14 man/credentials_external_account.Rd | 87 + man/credentials_gce.Rd | 20 man/credentials_service_account.Rd | 14 man/credentials_user_oauth2.Rd | 16 man/gargle-package.Rd | 3 man/gargle_client.Rd | 2 man/gargle_oauth_client_from_json.Rd | 2 man/gargle_oauth_sitrep.Rd | 13 man/gargle_options.Rd | 18 man/request_develop.Rd | 53 - man/request_make.Rd | 11 man/request_retry.Rd | 4 man/response_process.Rd | 8 man/token_fetch.Rd | 14 tests/testthat.R | 8 tests/testthat/_snaps/credentials_external_account.md |only tests/testthat/_snaps/gargle_oauth_client.md | 2 tests/testthat/_snaps/oauth-init.md | 52 + tests/testthat/_snaps/response_process.md | 38 tests/testthat/_snaps/roxygen-templates.md | 2 tests/testthat/_snaps/secret.md | 60 - tests/testthat/_snaps/token_fetch.md |only tests/testthat/fixtures/books-volumes-list-api-key_200.R |only tests/testthat/fixtures/books-volumes-list-api-key_200.rds |only tests/testthat/fixtures/drive-files-get-nonexistent-file-id_404.rds |binary tests/testthat/fixtures/sheets-spreadsheets-get-api-key-not-enabled_403.rds |binary tests/testthat/fixtures/sheets-spreadsheets-get-bad-field-mask_400.rds |binary tests/testthat/fixtures/sheets-spreadsheets-get-quota-exceeded-readgroup_429.rds |binary tests/testthat/fixtures/sheets-spreadsheets-get-service-disabled.R | 2 tests/testthat/fixtures/userinfo-service-account_200.R |only tests/testthat/fixtures/userinfo-service-account_200.rds |only tests/testthat/test-credentials_app_default.R | 20 tests/testthat/test-credentials_external_account.R |only tests/testthat/test-oauth-cache.R | 10 tests/testthat/test-oauth-init.R | 111 ++ tests/testthat/test-request_develop.R | 27 tests/testthat/test-request_make.R | 12 tests/testthat/test-request_retry.R | 4 tests/testthat/test-response_process.R | 49 + tests/testthat/test-secret.R | 15 tests/testthat/test-token-info.R | 9 tests/testthat/test-token_fetch.R | 14 vignettes/auth-from-web.Rmd | 9 vignettes/get-api-credentials.Rmd | 29 vignettes/how-gargle-gets-tokens.Rmd | 29 vignettes/non-interactive-auth.Rmd | 78 + vignettes/oauth-client-not-app.Rmd | 305 ++---- vignettes/request-helper-functions.Rmd | 36 vignettes/troubleshooting.Rmd | 10 100 files changed, 2664 insertions(+), 2192 deletions(-)
Title: ExifTool Functionality from R
Description: Reads, writes, and edits EXIF and other file metadata using
ExifTool <https://exiftool.org/>, returning read results as a data
frame. ExifTool supports many different metadata formats including EXIF,
GPS, IPTC, XMP, JFIF, GeoTIFF, ICC Profile, Photoshop IRB, FlashPix, AFCP
and ID3, Lyrics3, as well as the maker notes of many digital cameras by
Apple, Canon, Casio, DJI, FLIR, FujiFilm, GE, Google, GoPro, HP, JVC/Victor,
Kodak, Leaf, Minolta/Konica-Minolta, Motorola, Nikon, Nintendo,
Olympus/Epson, Panasonic/Leica, Pentax/Asahi, Phase One, Reconyx, Ricoh,
Samsung, Sanyo, Sigma/Foveon and Sony.
Author: Joshua O'Brien [aut, cre]
Maintainer: Joshua O'Brien <joshmobrien@gmail.com>
Diff between exiftoolr versions 0.2.8 dated 2025-04-20 and 0.2.10 dated 2026-10-28
DESCRIPTION | 18 +++++++++--------- MD5 | 10 +++++----- NAMESPACE | 6 ++++-- NEWS.md | 10 ++++++++++ R/install.R | 12 ++++++++---- man/install_exiftool.Rd | 2 +- 6 files changed, 37 insertions(+), 21 deletions(-)
Title: Bayesian Error Propagation and Forecast Uncertainty
Decomposition
Description: Provides a full pipeline from regularized or standard regression
models (elastic net, linear models, generalized linear models, random
forests) to informed Bayesian priors, structured forecast uncertainty
decomposition (parameter / environmental / residual, plus a temporal
component when the model carries an autocorrelation term), and forecast
shelf life analysis (the quantification of when a forecast becomes
uninformative). Designed for ecological and genomic forecasting with
climate or environmental covariates. Methods build on Bürkner (2017)
<doi:10.18637/jss.v080.i01> for Bayesian regression via 'Stan',
Friedman, Hastie, and Tibshirani (2010) <doi:10.18637/jss.v033.i01>
for elastic net regularization, Wright and Ziegler (2017)
<doi:10.18637/jss.v077.i01> for random forests, and Vehtari, Gelman,
and Gabry (2017) <doi:10.1007/s11222-016-9696-4> for leave-one-out
cross-validation.
Author: Luis Javier Madrigal-Roca [aut, cre],
John Kelly [aut]
Maintainer: Luis Javier Madrigal-Roca <madrigalrocalj@yahoo.com>
Diff between ErrorTracer versions 1.4.0 dated 2026-10-24 and 1.4.1 dated 2026-10-28
DESCRIPTION | 8 +- MD5 | 28 +++---- NEWS.md | 65 ++++++++++++++++ R/plot.R | 145 +++++++++++++++++++++++++++++++++++-- R/predict.R | 63 +++++++++++++++- README.md | 9 +- inst/doc/introduction.Rmd | 7 + inst/doc/introduction.html | 13 ++- inst/doc/worked_example.html | 4 - man/et_plot_decomposition.Rd | 10 ++ man/et_plot_shelf_life.Rd | 9 ++ man/et_predict.Rd | 12 +++ tests/testthat/test-draw-pairing.R | 39 +++++++++ tests/testthat/test-plot.R | 90 ++++++++++++++++++++++ vignettes/introduction.Rmd | 7 + 15 files changed, 464 insertions(+), 45 deletions(-)
Title: Name-Blind Variable-Role Detection by Data Signature
Description: Deterministic, name-blind detection of variable roles (group,
outcome, survival or duration time and event, coupled binary-continuous
pairs, calendar time index, paired and agreement measurements, repeated
measures and panels, scale and rating items, subject or entity identifier,
covariate) in tabular data from any domain -- clinical, financial, social,
experimental. Roles are assigned from each column's information-theoretic signature
-- Shannon entropy, normalized mutual information, and distributional shape
-- rather than from column names, so renaming columns to 'col_1', 'col_2',
... does not change the result ("Data inspice, non nomen"). An optional,
capped name-based hint and automatic header-row detection are also provided.
No large language models and no external data transmission. Extracted from
the 'MDStatR' biostatistics engine; see Boynukara (2026)
<doi:10.5281/zenodo.20707791>.
Author: Can Boynukara [aut, cre, cph]
Maintainer: Can Boynukara <canboynukara1@gmail.com>
Diff between rolescry versions 0.3.0 dated 2026-10-21 and 0.3.1 dated 2026-10-28
DESCRIPTION | 6 MD5 | 16 NEWS.md | 5 R/detect.R | 2122 ++++++++++++++++++++++---------------------- R/mdl.R | 448 ++++----- R/utils.R | 211 ++-- inst/CITATION | 6 tests/testthat/helper-dgp.R | 106 +- tests/testthat/test-v030.R | 520 +++++----- 9 files changed, 1727 insertions(+), 1713 deletions(-)
Title: A Poor Man's Dependency Free Recreation of 'dplyr'
Description: A replication of key functionality from 'dplyr' and the wider 'tidyverse' using only 'base'.
Author: Nathan Eastwood [aut, cre],
Etienne Bacher [ctb]
Maintainer: Nathan Eastwood <nathan.eastwood@icloud.com>
Diff between poorman versions 0.2.8 dated 2026-07-30 and 0.3.0 dated 2026-10-28
poorman-0.2.8/poorman/R/env.R |only poorman-0.2.8/poorman/inst/tinytest/test_joins_filter.R |only poorman-0.2.8/poorman/inst/tinytest/test_mutate_joins.R |only poorman-0.3.0/poorman/DESCRIPTION | 6 poorman-0.3.0/poorman/MD5 | 157 +- poorman-0.3.0/poorman/NAMESPACE | 13 poorman-0.3.0/poorman/NEWS.md | 147 ++ poorman-0.3.0/poorman/R/across.R | 28 poorman-0.3.0/poorman/R/arrange.R | 79 - poorman-0.3.0/poorman/R/bind.R | 5 poorman-0.3.0/poorman/R/context.R | 40 poorman-0.3.0/poorman/R/count-tally.R | 125 + poorman-0.3.0/poorman/R/distinct.R | 55 poorman-0.3.0/poorman/R/dots.R | 48 poorman-0.3.0/poorman/R/fill.R | 78 - poorman-0.3.0/poorman/R/filter.R | 179 +- poorman-0.3.0/poorman/R/group_by.R | 53 poorman-0.3.0/poorman/R/group_metadata.R | 14 poorman-0.3.0/poorman/R/group_split.R | 47 poorman-0.3.0/poorman/R/group_utils.R | 867 +++++++++++- poorman-0.3.0/poorman/R/joins.R | 140 + poorman-0.3.0/poorman/R/joins_filtering.R | 36 poorman-0.3.0/poorman/R/joins_nest.R |only poorman-0.3.0/poorman/R/joins_utils.R |only poorman-0.3.0/poorman/R/label.R |only poorman-0.3.0/poorman/R/lang.R | 4 poorman-0.3.0/poorman/R/lst.R | 13 poorman-0.3.0/poorman/R/mutate.R | 129 + poorman-0.3.0/poorman/R/nest_by.R | 2 poorman-0.3.0/poorman/R/pivot_longer.R | 262 ++- poorman-0.3.0/poorman/R/pivot_wider.R | 289 ++-- poorman-0.3.0/poorman/R/recode.R | 5 poorman-0.3.0/poorman/R/reconstruct.R | 1 poorman-0.3.0/poorman/R/rename.R | 2 poorman-0.3.0/poorman/R/select_positions.R | 64 poorman-0.3.0/poorman/R/slice.R | 318 ++-- poorman-0.3.0/poorman/R/summarise.R | 127 + poorman-0.3.0/poorman/R/transmute.R | 10 poorman-0.3.0/poorman/R/utils.R | 252 +++ poorman-0.3.0/poorman/README.md | 9 poorman-0.3.0/poorman/inst/doc/faq.Rmd | 1 poorman-0.3.0/poorman/inst/doc/faq.html | 3 poorman-0.3.0/poorman/inst/tinytest/test_across.R | 23 poorman-0.3.0/poorman/inst/tinytest/test_arrange.R | 218 +++ poorman-0.3.0/poorman/inst/tinytest/test_bind.R | 21 poorman-0.3.0/poorman/inst/tinytest/test_context.R | 20 poorman-0.3.0/poorman/inst/tinytest/test_count_tally.R | 329 ++++ poorman-0.3.0/poorman/inst/tinytest/test_distinct.R | 47 poorman-0.3.0/poorman/inst/tinytest/test_empty_groups.R | 88 - poorman-0.3.0/poorman/inst/tinytest/test_fill.R | 34 poorman-0.3.0/poorman/inst/tinytest/test_filter.R | 297 ++++ poorman-0.3.0/poorman/inst/tinytest/test_group_by.R | 169 ++ poorman-0.3.0/poorman/inst/tinytest/test_group_metadata.R | 14 poorman-0.3.0/poorman/inst/tinytest/test_group_split.R | 56 poorman-0.3.0/poorman/inst/tinytest/test_joins.R |only poorman-0.3.0/poorman/inst/tinytest/test_joins_filtering.R |only poorman-0.3.0/poorman/inst/tinytest/test_joins_nest.R |only poorman-0.3.0/poorman/inst/tinytest/test_label.R |only poorman-0.3.0/poorman/inst/tinytest/test_lst.R | 23 poorman-0.3.0/poorman/inst/tinytest/test_mutate.R | 413 +++++ poorman-0.3.0/poorman/inst/tinytest/test_nest_by.R | 18 poorman-0.3.0/poorman/inst/tinytest/test_pivot_longer.R | 187 ++ poorman-0.3.0/poorman/inst/tinytest/test_pivot_wider.R | 167 ++ poorman-0.3.0/poorman/inst/tinytest/test_rename.R | 7 poorman-0.3.0/poorman/inst/tinytest/test_rename_with.R | 26 poorman-0.3.0/poorman/inst/tinytest/test_select.R | 64 poorman-0.3.0/poorman/inst/tinytest/test_select_positions.R | 18 poorman-0.3.0/poorman/inst/tinytest/test_slice.R | 215 ++ poorman-0.3.0/poorman/inst/tinytest/test_summarise.R | 481 ++++++ poorman-0.3.0/poorman/inst/tinytest/test_transmute.R | 48 poorman-0.3.0/poorman/inst/tinytest/test_utils.R | 96 + poorman-0.3.0/poorman/man/across.Rd | 2 poorman-0.3.0/poorman/man/arrange.Rd | 6 poorman-0.3.0/poorman/man/count.Rd | 14 poorman-0.3.0/poorman/man/filter.Rd | 8 poorman-0.3.0/poorman/man/filter_joins.Rd | 26 poorman-0.3.0/poorman/man/group_by.Rd | 10 poorman-0.3.0/poorman/man/mutate.Rd | 29 poorman-0.3.0/poorman/man/mutate_joins.Rd | 20 poorman-0.3.0/poorman/man/nest_join.Rd |only poorman-0.3.0/poorman/man/pivot_longer.Rd | 34 poorman-0.3.0/poorman/man/pivot_wider.Rd | 48 poorman-0.3.0/poorman/man/slice.Rd | 17 poorman-0.3.0/poorman/man/summarise.Rd | 45 poorman-0.3.0/poorman/vignettes/faq.Rmd | 1 85 files changed, 5876 insertions(+), 1071 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-07-05 2.0.0
2024-05-08 1.0.0
Title: Multilevel Analysis of Individual Heterogeneity and
Discriminatory Accuracy
Description: Tools for Multilevel Analysis of Individual Heterogeneity and
Discriminatory Accuracy (MAIHDA) for intersectional inequality research.
Methods are described in Merlo (2018) <doi:10.1016/j.socscimed.2017.12.026>
and Evans et al. (2018) <doi:10.1016/j.socscimed.2017.11.011>. The package
creates intersectional strata, fits multilevel MAIHDA models, estimates
variance partition coefficients, proportional change in variance, stratum
effects, and discriminatory-accuracy summaries, and provides diagnostic and
presentation plots.
Author: Hamid Bulut [aut, cre]
Maintainer: Hamid Bulut <me@hamidbulut.com>
Diff between MAIHDA versions 0.2.1 dated 2026-07-09 and 0.3.0 dated 2026-10-28
MAIHDA-0.2.1/MAIHDA/man/calculate_pvc.Rd |only MAIHDA-0.2.1/MAIHDA/man/plot_comparison.Rd |only MAIHDA-0.2.1/MAIHDA/man/plot_group_comparison.Rd |only MAIHDA-0.3.0/MAIHDA/DESCRIPTION | 12 MAIHDA-0.3.0/MAIHDA/MD5 | 454 MAIHDA-0.3.0/MAIHDA/NAMESPACE | 18 MAIHDA-0.3.0/MAIHDA/NEWS.md | 658 - MAIHDA-0.3.0/MAIHDA/R/calculate_pcv.R | 2957 +++-- MAIHDA-0.3.0/MAIHDA/R/compare_maihda.R | 783 + MAIHDA-0.3.0/MAIHDA/R/decompose_maihda.R | 236 MAIHDA-0.3.0/MAIHDA/R/design_weights.R | 655 + MAIHDA-0.3.0/MAIHDA/R/discriminatory_accuracy.R | 775 + MAIHDA-0.3.0/MAIHDA/R/fit_maihda.R | 1346 ++ MAIHDA-0.3.0/MAIHDA/R/information_criteria.R | 413 MAIHDA-0.3.0/MAIHDA/R/interactions.R | 512 MAIHDA-0.3.0/MAIHDA/R/longitudinal.R | 2797 ++++- MAIHDA-0.3.0/MAIHDA/R/maihda_describe.R |only MAIHDA-0.3.0/MAIHDA/R/maihda_sparse_data.R | 122 MAIHDA-0.3.0/MAIHDA/R/maihda_table.R | 123 MAIHDA-0.3.0/MAIHDA/R/maihda_workflow.R | 565 - MAIHDA-0.3.0/MAIHDA/R/make_strata.R | 57 MAIHDA-0.3.0/MAIHDA/R/ordinal_engine.R | 1277 ++ MAIHDA-0.3.0/MAIHDA/R/pcv_importance.R |only MAIHDA-0.3.0/MAIHDA/R/plot_maihda.R | 665 - MAIHDA-0.3.0/MAIHDA/R/plot_prediction_deviation_panels.R | 1513 ++ MAIHDA-0.3.0/MAIHDA/R/predict_maihda.R | 463 MAIHDA-0.3.0/MAIHDA/R/run_app.R | 52 MAIHDA-0.3.0/MAIHDA/R/summary_maihda.R | 2282 +++- MAIHDA-0.3.0/MAIHDA/R/theme_maihda.R | 163 MAIHDA-0.3.0/MAIHDA/R/tidiers.R | 79 MAIHDA-0.3.0/MAIHDA/R/utils_maihda.R | 5544 +++++++++- MAIHDA-0.3.0/MAIHDA/R/vpc_response.R | 480 MAIHDA-0.3.0/MAIHDA/README.md | 50 MAIHDA-0.3.0/MAIHDA/data/maihda_sparse_data.rda |binary MAIHDA-0.3.0/MAIHDA/inst/CITATION | 4 MAIHDA-0.3.0/MAIHDA/inst/doc/bayesian_sparse_maihda.R | 23 MAIHDA-0.3.0/MAIHDA/inst/doc/bayesian_sparse_maihda.Rmd | 141 MAIHDA-0.3.0/MAIHDA/inst/doc/bayesian_sparse_maihda.html | 193 MAIHDA-0.3.0/MAIHDA/inst/doc/binary_outcomes.R | 30 MAIHDA-0.3.0/MAIHDA/inst/doc/binary_outcomes.Rmd | 171 MAIHDA-0.3.0/MAIHDA/inst/doc/binary_outcomes.html | 362 MAIHDA-0.3.0/MAIHDA/inst/doc/case_study_brfss.html | 4 MAIHDA-0.3.0/MAIHDA/inst/doc/cross_classified.R | 1 MAIHDA-0.3.0/MAIHDA/inst/doc/cross_classified.Rmd | 45 MAIHDA-0.3.0/MAIHDA/inst/doc/cross_classified.html | 279 MAIHDA-0.3.0/MAIHDA/inst/doc/finding_interactions.Rmd | 8 MAIHDA-0.3.0/MAIHDA/inst/doc/finding_interactions.html | 17 MAIHDA-0.3.0/MAIHDA/inst/doc/group_comparison.html | 91 MAIHDA-0.3.0/MAIHDA/inst/doc/interactive_app.html | 4 MAIHDA-0.3.0/MAIHDA/inst/doc/interpreting_plots.html | 10 MAIHDA-0.3.0/MAIHDA/inst/doc/introduction.R | 9 MAIHDA-0.3.0/MAIHDA/inst/doc/introduction.Rmd | 38 MAIHDA-0.3.0/MAIHDA/inst/doc/introduction.html | 327 MAIHDA-0.3.0/MAIHDA/inst/doc/longitudinal.R | 9 MAIHDA-0.3.0/MAIHDA/inst/doc/longitudinal.Rmd | 185 MAIHDA-0.3.0/MAIHDA/inst/doc/longitudinal.html | 314 MAIHDA-0.3.0/MAIHDA/inst/doc/planning_a_study.R | 12 MAIHDA-0.3.0/MAIHDA/inst/doc/planning_a_study.Rmd | 316 MAIHDA-0.3.0/MAIHDA/inst/doc/planning_a_study.html | 172 MAIHDA-0.3.0/MAIHDA/inst/doc/reporting_results.Rmd | 5 MAIHDA-0.3.0/MAIHDA/inst/doc/reporting_results.html | 168 MAIHDA-0.3.0/MAIHDA/inst/shiny/app.R | 30 MAIHDA-0.3.0/MAIHDA/man/bootstrap_cc.Rd | 13 MAIHDA-0.3.0/MAIHDA/man/bootstrap_context.Rd | 12 MAIHDA-0.3.0/MAIHDA/man/bootstrap_vpc.Rd | 12 MAIHDA-0.3.0/MAIHDA/man/calculate_pcv.Rd | 388 MAIHDA-0.3.0/MAIHDA/man/cash-.pcv_result.Rd |only MAIHDA-0.3.0/MAIHDA/man/compare_maihda.Rd | 8 MAIHDA-0.3.0/MAIHDA/man/compare_maihda_groups.Rd | 92 MAIHDA-0.3.0/MAIHDA/man/extract_between_variance.Rd | 3 MAIHDA-0.3.0/MAIHDA/man/fit_maihda.Rd | 383 MAIHDA-0.3.0/MAIHDA/man/maihda.Rd | 238 MAIHDA-0.3.0/MAIHDA/man/maihda_bootstrap_fixef.Rd |only MAIHDA-0.3.0/MAIHDA/man/maihda_brms_complete_rows.Rd |only MAIHDA-0.3.0/MAIHDA/man/maihda_brms_cumulative_family.Rd |only MAIHDA-0.3.0/MAIHDA/man/maihda_brms_ordinal_thresholds.Rd | 11 MAIHDA-0.3.0/MAIHDA/man/maihda_cc_summary_brms.Rd | 10 MAIHDA-0.3.0/MAIHDA/man/maihda_check_longitudinal_ids.Rd |only MAIHDA-0.3.0/MAIHDA/man/maihda_check_longitudinal_times.Rd |only MAIHDA-0.3.0/MAIHDA/man/maihda_clmm_cutpoints.Rd |only MAIHDA-0.3.0/MAIHDA/man/maihda_clmm_linpred.Rd | 8 MAIHDA-0.3.0/MAIHDA/man/maihda_clmm_thresholds.Rd | 12 MAIHDA-0.3.0/MAIHDA/man/maihda_containment_df.Rd |only MAIHDA-0.3.0/MAIHDA/man/maihda_context_summary_brms.Rd | 9 MAIHDA-0.3.0/MAIHDA/man/maihda_cross_classified_formula.Rd | 8 MAIHDA-0.3.0/MAIHDA/man/maihda_describe.Rd |only MAIHDA-0.3.0/MAIHDA/man/maihda_discriminatory_accuracy.Rd | 103 MAIHDA-0.3.0/MAIHDA/man/maihda_drop_fixed_terms.Rd |only MAIHDA-0.3.0/MAIHDA/man/maihda_fit_clmm.Rd | 33 MAIHDA-0.3.0/MAIHDA/man/maihda_fit_wemix.Rd | 11 MAIHDA-0.3.0/MAIHDA/man/maihda_fixed_effects_table.Rd |only MAIHDA-0.3.0/MAIHDA/man/maihda_fixed_spans_intercept.Rd |only MAIHDA-0.3.0/MAIHDA/man/maihda_glance.Rd | 6 MAIHDA-0.3.0/MAIHDA/man/maihda_ic.Rd | 59 MAIHDA-0.3.0/MAIHDA/man/maihda_interactions.Rd | 173 MAIHDA-0.3.0/MAIHDA/man/maihda_longitudinal_formula.Rd | 7 MAIHDA-0.3.0/MAIHDA/man/maihda_longitudinal_pcv.Rd | 61 MAIHDA-0.3.0/MAIHDA/man/maihda_mor.Rd | 42 MAIHDA-0.3.0/MAIHDA/man/maihda_prepare_brms_sampling_weights.Rd | 17 MAIHDA-0.3.0/MAIHDA/man/maihda_prepare_group_strata.Rd | 12 MAIHDA-0.3.0/MAIHDA/man/maihda_proportional_odds_test.Rd |only MAIHDA-0.3.0/MAIHDA/man/maihda_sparse_data.Rd | 148 MAIHDA-0.3.0/MAIHDA/man/maihda_strip_brms_weights_term.Rd |only MAIHDA-0.3.0/MAIHDA/man/maihda_table.Rd | 17 MAIHDA-0.3.0/MAIHDA/man/maihda_tag_role.Rd |only MAIHDA-0.3.0/MAIHDA/man/maihda_tidiers.Rd | 26 MAIHDA-0.3.0/MAIHDA/man/maihda_validate_longitudinal.Rd | 13 MAIHDA-0.3.0/MAIHDA/man/maihda_vpc_response.Rd | 97 MAIHDA-0.3.0/MAIHDA/man/maihda_warn_no_grand_mean.Rd |only MAIHDA-0.3.0/MAIHDA/man/maihda_wemix_linpred.Rd | 16 MAIHDA-0.3.0/MAIHDA/man/make_strata.Rd | 23 MAIHDA-0.3.0/MAIHDA/man/pcv_importance.Rd |only MAIHDA-0.3.0/MAIHDA/man/plot.maihda_analysis.Rd | 20 MAIHDA-0.3.0/MAIHDA/man/plot.maihda_describe.Rd |only MAIHDA-0.3.0/MAIHDA/man/plot.maihda_model.Rd | 81 MAIHDA-0.3.0/MAIHDA/man/plot.maihda_pcv_importance.Rd |only MAIHDA-0.3.0/MAIHDA/man/plot_context_vpc.Rd | 7 MAIHDA-0.3.0/MAIHDA/man/plot_effect_decomposition.Rd | 5 MAIHDA-0.3.0/MAIHDA/man/plot_obs_vs_shrunken.Rd | 5 MAIHDA-0.3.0/MAIHDA/man/plot_predicted_strata.Rd | 8 MAIHDA-0.3.0/MAIHDA/man/plot_prediction_deviation_panels.Rd | 65 MAIHDA-0.3.0/MAIHDA/man/plot_stratum_trajectories.Rd | 19 MAIHDA-0.3.0/MAIHDA/man/plot_upset_strata.Rd | 18 MAIHDA-0.3.0/MAIHDA/man/predict.maihda_model.Rd |only MAIHDA-0.3.0/MAIHDA/man/predict_maihda.Rd | 45 MAIHDA-0.3.0/MAIHDA/man/print.maihda_describe.Rd |only MAIHDA-0.3.0/MAIHDA/man/print.maihda_pcv_importance.Rd |only MAIHDA-0.3.0/MAIHDA/man/stepwise_pcv.Rd | 53 MAIHDA-0.3.0/MAIHDA/man/sub-.maihda_ic.Rd |only MAIHDA-0.3.0/MAIHDA/man/summary.maihda_analysis.Rd | 32 MAIHDA-0.3.0/MAIHDA/man/summary.maihda_model.Rd | 280 MAIHDA-0.3.0/MAIHDA/man/theme_maihda.Rd | 99 MAIHDA-0.3.0/MAIHDA/tests/testthat/helper-slow-tests.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/setup-seed.R | 10 MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-07-13.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-07-14.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-07-15.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-07-16.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-07-17.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-07-18.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-07-19.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-07-20.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-07-21.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-07-22.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-07-22b.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-07-23.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-07-23b.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-07-23c.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-07-24.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-07-25.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-07-26.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-07-27.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-07-28.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-07-29.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-07-30.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-07-31.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-08-01.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-08-02.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-08-03.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-08-25.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-08-29.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-08-30.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-08-30b.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-08-30c.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-08-30d.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-08-31.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-08-31b.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-09-01.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-09-01b.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-09-01c.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-09-02.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-09-03.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-09-04.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-09-04b.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-09-06.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-09-06b.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-09-09.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-09-09b.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-09-09c.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-09-10.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-09-10b.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-09-10c.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-09-10d.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-09-13.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-09-13b.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-09-13c.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-09-13d.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-09-14.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-09-14b.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-09-14c.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-09-15.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-09-15b.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-09-15c.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-09-15d.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-09-15e.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-09-17.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-09-17b.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-09-17c.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-09-20.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-09-20b.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-09-24.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-09-25.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-09-26.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-09-26b.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-09-26c.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-09-26d.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-09-26e.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-09-27.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-09-27b.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-09-27c.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-09-28.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-09-28b.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-09-28c.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-09-28d.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-09-28e.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-09-28f.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-10-05-brms-na-level.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-10-05-lme4-all-na.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-10-06-glmm-pcv-ml-bias.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-10-07-brms-pcv-posterior-mean.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-10-07-wemix-boundary.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-10-12-brms-long-pcv-posterior-mean.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-10-12-brms-mor-variance-table.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-10-12-compare-failure-wording.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-10-12-compare-fit-warning-engine.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-10-12-compare-fit-warning-groups.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-10-12-crossed-brms-few-levels.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-10-12-wemix-nonconformable.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-10-12-wemix-summary-warning.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-10-13-crossed-singular-note.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-10-13-interactions-singular-note.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-10-13-lme4-long-pcv-slope-low.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-10-13-ordinal-clmm-start-value.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-10-13-ordinal-ucminf-convergence.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-10-14-app-diagnostics-card.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-10-14-context-few-levels-brms.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-10-14-lme4-covariate-scale.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-10-14-lme4-growth-optimiser.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-10-14-lme4-growth-time-scale.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-10-14-ordinal-covariate-scale.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-10-14-sparse-strata-brms-claims.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-10-18-glmer-growth-optimum.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-10-18-lme4-growth-quadratic-restarts.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-10-18-long-pcv-print-small-variances.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-10-18-rank-deficient-strata.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-10-19-bootstrap-growth-refits.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-10-19-bootstrap-reduced-refit.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-10-19-brms-seed-mc-cores.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-10-19-glmer-bound-directions.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-10-19-glmer-growth-refit-stall.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-10-19-glmer-slope-boundary-traps.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-10-19-literal-markdown-rd.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-10-19-lmer-slope-optimum.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-10-19-sparse-data-rd.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-10-19-sparse-realised-truth.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-10-19-sparse-vignette-intervals.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-10-19-sparse-vignette-lme4-boundary.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-10-20-glmer-slope-scale.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-10-20-lmer-optimum-messages.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-10-20-lmer-zero-variance-stop.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-10-20-singular-flag-units.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-10-20-trap-record-step.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-10-25-diag-block-scale.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-10-25-glmer-zero-variance-stop.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-10-25-lmer-unchecked-fits.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-10-26-glmer-growth-time-units.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-10-26-glmer-unchecked-fits.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-10-26-refit-default-step.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-10-26-tied-block-order.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-10-27-bootmer-call-control.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-10-27-cold-devfun-users.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-10-27-glmer-search-refusal.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-10-27-growth-refit-default-step.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-10-27-output-F01.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-10-27-output-F02-F03.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-audit-2026-10-28-series-pcv-basis.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-calculate_pcv.R | 239 MAIHDA-0.3.0/MAIHDA/tests/testthat/test-compare_maihda.R | 10 MAIHDA-0.3.0/MAIHDA/tests/testthat/test-compare_maihda_groups.R | 33 MAIHDA-0.3.0/MAIHDA/tests/testthat/test-contextual.R | 113 MAIHDA-0.3.0/MAIHDA/tests/testthat/test-correctness-regressions.R | 114 MAIHDA-0.3.0/MAIHDA/tests/testthat/test-count-vpc-response.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-country_data.R | 11 MAIHDA-0.3.0/MAIHDA/tests/testthat/test-cross-classified.R | 137 MAIHDA-0.3.0/MAIHDA/tests/testthat/test-crossed-realised-strata.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-design-weights.R | 173 MAIHDA-0.3.0/MAIHDA/tests/testthat/test-discriminatory-accuracy.R | 1248 +- MAIHDA-0.3.0/MAIHDA/tests/testthat/test-fit_maihda.R | 18 MAIHDA-0.3.0/MAIHDA/tests/testthat/test-fixed-effect-df.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-information_criteria.R | 27 MAIHDA-0.3.0/MAIHDA/tests/testthat/test-interactions.R | 312 MAIHDA-0.3.0/MAIHDA/tests/testthat/test-lme4-deviation-panel-intervals.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-longitudinal.R | 196 MAIHDA-0.3.0/MAIHDA/tests/testthat/test-maihda-workflow.R | 60 MAIHDA-0.3.0/MAIHDA/tests/testthat/test-maihda_describe.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-maihda_table.R | 63 MAIHDA-0.3.0/MAIHDA/tests/testthat/test-make_strata.R | 78 MAIHDA-0.3.0/MAIHDA/tests/testthat/test-negbinomial.R | 50 MAIHDA-0.3.0/MAIHDA/tests/testthat/test-ordinal-engine.R | 72 MAIHDA-0.3.0/MAIHDA/tests/testthat/test-pcv_importance.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-plot_prediction_deviation_panels.R | 71 MAIHDA-0.3.0/MAIHDA/tests/testthat/test-plot_upset.R | 122 MAIHDA-0.3.0/MAIHDA/tests/testthat/test-realised-contexts.R |only MAIHDA-0.3.0/MAIHDA/tests/testthat/test-run_app.R | 6 MAIHDA-0.3.0/MAIHDA/tests/testthat/test-summary_variance.R | 23 MAIHDA-0.3.0/MAIHDA/tests/testthat/test-tidiers.R | 407 MAIHDA-0.3.0/MAIHDA/tests/testthat/test-vpc-response.R | 200 MAIHDA-0.3.0/MAIHDA/tests/testthat/test-weighted-count-vpc.R | 95 MAIHDA-0.3.0/MAIHDA/vignettes/bayesian_sparse_maihda.Rmd | 141 MAIHDA-0.3.0/MAIHDA/vignettes/binary_outcomes.Rmd | 171 MAIHDA-0.3.0/MAIHDA/vignettes/cross_classified.Rmd | 45 MAIHDA-0.3.0/MAIHDA/vignettes/finding_interactions.Rmd | 8 MAIHDA-0.3.0/MAIHDA/vignettes/introduction.Rmd | 38 MAIHDA-0.3.0/MAIHDA/vignettes/longitudinal.Rmd | 185 MAIHDA-0.3.0/MAIHDA/vignettes/planning_a_study.Rmd | 316 MAIHDA-0.3.0/MAIHDA/vignettes/reporting_results.Rmd | 5 MAIHDA-0.3.0/MAIHDA/vignettes/sparse_precomputed.rds |binary 317 files changed, 29908 insertions(+), 5716 deletions(-)
Title: Variable Selection Using Shrinkage Priors
Description: Select variables from shrinkage-prior posterior coefficient draws
using sequential two-means clustering from Li and Pati (2017)
<doi:10.1016/j.csda.2016.10.008>. Estimate a signal count at each tuning
threshold and rank coefficients by posterior median absolute magnitude.
Accept supplied coefficient draws or fit Gaussian shrinkage regression
through 'bayesreg' or native ridge, horseshoe and spike-and-slab samplers.
Retain chain identities for diagnostics, prediction and posterior plots.
Also provide the signal adaptive variable selector
of Ray and Bhattacharya (2018) <doi:10.48550/arXiv.1810.09004>,
decoupled shrinkage and selection with the adaptive-L1 approximation of
Hahn and Carvalho (2015) <doi:10.1080/01621459.2014.993077>, optional
exact two-cluster fitting, basic two-means selection, exact-zero
spike-and-slab inclusion summaries and tuning sensitivity summaries.
Author: Nilson Chapagain [aut, cre] ,
Debdeep Pati [aut]
Maintainer: Nilson Chapagain <nilson.chapagain@gmail.com>
Diff between VsusP versions 1.0.0 dated 2024-06-25 and 1.1.0 dated 2026-10-28
VsusP-1.0.0/VsusP/man/OptimalHbi.Rd |only VsusP-1.1.0/VsusP/DESCRIPTION | 32 VsusP-1.1.0/VsusP/MD5 | 115 + VsusP-1.1.0/VsusP/NAMESPACE | 33 VsusP-1.1.0/VsusP/NEWS.md |only VsusP-1.1.0/VsusP/R/DSS.R |only VsusP-1.1.0/VsusP/R/GaussianFit.R |only VsusP-1.1.0/VsusP/R/S2MSensitivity.R |only VsusP-1.1.0/VsusP/R/S2MVarSelection.R | 248 +--- VsusP-1.1.0/VsusP/R/SAVS.R |only VsusP-1.1.0/VsusP/R/Sequential2Means.R | 448 ++----- VsusP-1.1.0/VsusP/R/SpikeSlabSelection.R |only VsusP-1.1.0/VsusP/R/TwoMeansBeta.R |only VsusP-1.1.0/VsusP/R/VsusP-package.R |only VsusP-1.1.0/VsusP/R/chain-diagnostics.R |only VsusP-1.1.0/VsusP/R/clustering.R |only VsusP-1.1.0/VsusP/R/posterior-plots.R |only VsusP-1.1.0/VsusP/R/result-methods.R |only VsusP-1.1.0/VsusP/R/validation.R |only VsusP-1.1.0/VsusP/README.md | 175 +- VsusP-1.1.0/VsusP/build/partial.rdb |only VsusP-1.1.0/VsusP/build/vignette.rds |binary VsusP-1.1.0/VsusP/inst/doc-data |only VsusP-1.1.0/VsusP/inst/doc/VsusPVignette.R | 283 ++-- VsusP-1.1.0/VsusP/inst/doc/VsusPVignette.Rmd | 611 +++++----- VsusP-1.1.0/VsusP/inst/doc/VsusPVignette.pdf |binary VsusP-1.1.0/VsusP/inst/validation |only VsusP-1.1.0/VsusP/man/ChainDiagnostics.Rd |only VsusP-1.1.0/VsusP/man/DSS.Rd |only VsusP-1.1.0/VsusP/man/FitGaussian.Rd |only VsusP-1.1.0/VsusP/man/PlotAutocorrelation.Rd |only VsusP-1.1.0/VsusP/man/PlotCoefficients.Rd |only VsusP-1.1.0/VsusP/man/PlotInclusion.Rd |only VsusP-1.1.0/VsusP/man/PlotTrace.Rd |only VsusP-1.1.0/VsusP/man/PosteriorDraws.Rd |only VsusP-1.1.0/VsusP/man/S2MSensitivity.Rd |only VsusP-1.1.0/VsusP/man/S2MVarSelection.Rd | 52 VsusP-1.1.0/VsusP/man/S2MVarSelectionV1.Rd | 30 VsusP-1.1.0/VsusP/man/SAVS.Rd |only VsusP-1.1.0/VsusP/man/Sequential2Means.Rd | 100 - VsusP-1.1.0/VsusP/man/Sequential2MeansBeta.Rd | 133 +- VsusP-1.1.0/VsusP/man/SpikeSlabSelection.Rd |only VsusP-1.1.0/VsusP/man/TwoMeansBeta.Rd |only VsusP-1.1.0/VsusP/man/VsusP.Rd |only VsusP-1.1.0/VsusP/man/coef.vsusp_fit.Rd |only VsusP-1.1.0/VsusP/man/figures |only VsusP-1.1.0/VsusP/man/numNoiseCoeff.Rd | 20 VsusP-1.1.0/VsusP/man/optimalHbi.Rd |only VsusP-1.1.0/VsusP/man/plot.vsusp_fit.Rd |only VsusP-1.1.0/VsusP/man/plot.vsusp_tuning.Rd |only VsusP-1.1.0/VsusP/man/predict.vsusp_fit.Rd |only VsusP-1.1.0/VsusP/man/predict.vsusp_sparse.Rd |only VsusP-1.1.0/VsusP/man/summary.vsusp_fit.Rd |only VsusP-1.1.0/VsusP/man/summary.vsusp_selection.Rd |only VsusP-1.1.0/VsusP/man/summary.vsusp_sparse.Rd |only VsusP-1.1.0/VsusP/man/summary.vsusp_spike.Rd |only VsusP-1.1.0/VsusP/man/summary.vsusp_tuning.Rd |only VsusP-1.1.0/VsusP/tests/testthat/helper-native-gaussian.R |only VsusP-1.1.0/VsusP/tests/testthat/test-S2MVarSelection.R | 2 VsusP-1.1.0/VsusP/tests/testthat/test-Sequential2Means.R | 5 VsusP-1.1.0/VsusP/tests/testthat/test-api-contracts.R |only VsusP-1.1.0/VsusP/tests/testthat/test-dss.R |only VsusP-1.1.0/VsusP/tests/testthat/test-native-diagnostics-plots.R |only VsusP-1.1.0/VsusP/tests/testthat/test-native-gaussian.R |only VsusP-1.1.0/VsusP/tests/testthat/test-numNoiseCoeff.R |only VsusP-1.1.0/VsusP/tests/testthat/test-paper-selection.R |only VsusP-1.1.0/VsusP/tests/testthat/test-selection-extensions.R |only VsusP-1.1.0/VsusP/vignettes/VsusPVignette.Rmd | 611 +++++----- 68 files changed, 1459 insertions(+), 1439 deletions(-)
Title: Reliability Analysis Methods for Structural Engineering
Description: Calculate the failure probability of civil engineering problems with Level I up to Level III Methods. References: Spaethe (1991, ISBN:3-211-82348-4) "Die Sicherheit tragender Baukonstruktionen", Au and Beck (2001) "Estimation of small failure probabilities in high dimensions by subset simulation." <doi:10.1016/S0266-8920(01)00019-4>, Breitung (1989) "Asymptotic approximations for probability integrals." <doi:10.1016/0266-8920(89)90024-6>.
Author: Konstantin Nille-Hauf [aut],
Tania Feiri [aut],
Marcus Ricker [aut],
Jan Phillip Schulze-Ardey [ctb],
Til Lux [aut, cre]
Maintainer: Til Lux <til.lux@tu-dortmund.de>
Diff between TesiproV versions 0.9.6 dated 2026-04-22 and 1.0.0 dated 2026-10-28
TesiproV-0.9.6/TesiproV/R/FORM.R |only TesiproV-0.9.6/TesiproV/R/MCIS_helpers.R |only TesiproV-0.9.6/TesiproV/R/MC_IS.R |only TesiproV-0.9.6/TesiproV/R/MC_SubSam.R |only TesiproV-0.9.6/TesiproV/R/MVFOSM.R |only TesiproV-0.9.6/TesiproV/R/SORM.R |only TesiproV-0.9.6/TesiproV/R/StudentT.R |only TesiproV-0.9.6/TesiproV/R/clsModelContainer.R |only TesiproV-0.9.6/TesiproV/R/clsParam.R |only TesiproV-0.9.6/TesiproV/R/helper_debugPrint.R |only TesiproV-0.9.6/TesiproV/R/logStudentT.R |only TesiproV-0.9.6/TesiproV/tests/testthat/startup.Rs |only TesiproV-1.0.0/TesiproV/DESCRIPTION | 29 TesiproV-1.0.0/TesiproV/LICENSE | 2 TesiproV-1.0.0/TesiproV/MD5 | 207 TesiproV-1.0.0/TesiproV/NAMESPACE | 134 TesiproV-1.0.0/TesiproV/NEWS.md | 243 TesiproV-1.0.0/TesiproV/R/MC_CRUDE.R | 676 -- TesiproV-1.0.0/TesiproV/R/TesiproV.R | 71 TesiproV-1.0.0/TesiproV/R/algo_FORM.R |only TesiproV-1.0.0/TesiproV/R/algo_MVFOSM.R |only TesiproV-1.0.0/TesiproV/R/algo_SORM.R |only TesiproV-1.0.0/TesiproV/R/core_basevar.R |only TesiproV-1.0.0/TesiproV/R/core_basevar_helpers.R |only TesiproV-1.0.0/TesiproV/R/core_system.R |only TesiproV-1.0.0/TesiproV/R/dist_logstudent_t.R |only TesiproV-1.0.0/TesiproV/R/dist_shifted_lognormal.R |only TesiproV-1.0.0/TesiproV/R/dist_student_t.R |only TesiproV-1.0.0/TesiproV/R/mc_is_helpers.R |only TesiproV-1.0.0/TesiproV/R/mc_is_log_helpers.R |only TesiproV-1.0.0/TesiproV/R/mc_is_main.R |only TesiproV-1.0.0/TesiproV/R/mc_is_single.R |only TesiproV-1.0.0/TesiproV/R/mc_is_single_helpers.R |only TesiproV-1.0.0/TesiproV/R/mc_is_system.R |only TesiproV-1.0.0/TesiproV/R/mc_subsam.R |only TesiproV-1.0.0/TesiproV/R/parallel_helpers.R | 402 - TesiproV-1.0.0/TesiproV/R/param_basevar.R |only TesiproV-1.0.0/TesiproV/R/param_system.R |only TesiproV-1.0.0/TesiproV/R/qc_oc_helpers.R |only TesiproV-1.0.0/TesiproV/R/qc_qualcon.R |only TesiproV-1.0.0/TesiproV/R/utils_debug.R |only TesiproV-1.0.0/TesiproV/R/utils_math.R |only TesiproV-1.0.0/TesiproV/R/utils_validation.R |only TesiproV-1.0.0/TesiproV/R/zzz.R | 126 TesiproV-1.0.0/TesiproV/README.md | 519 + TesiproV-1.0.0/TesiproV/build/vignette.rds |binary TesiproV-1.0.0/TesiproV/inst/doc/TesiproV-Vignette.R | 803 +- TesiproV-1.0.0/TesiproV/inst/doc/TesiproV-Vignette.Rmd | 2002 +++--- TesiproV-1.0.0/TesiproV/inst/doc/TesiproV-Vignette.html | 3254 +++++----- TesiproV-1.0.0/TesiproV/inst/extdata/benchmarks/benchmark_MCIS_suite.R | 522 - TesiproV-1.0.0/TesiproV/inst/extdata/benchmarks/benchmark_MC_IS_future_chunking.R |only TesiproV-1.0.0/TesiproV/inst/extdata/benchmarks/benchmark_MC_IS_future_memory.R |only TesiproV-1.0.0/TesiproV/inst/extdata/benchmarks/benchmark_MC_IS_single.R | 309 TesiproV-1.0.0/TesiproV/inst/extdata/benchmarks/benchmark_MC_IS_single_backends.R |only TesiproV-1.0.0/TesiproV/inst/extdata/benchmarks/benchmark_MC_IS_unix_cluster_setup.R |only TesiproV-1.0.0/TesiproV/inst/extdata/benchmarks/benchmark_compare_MC_IS.R |only TesiproV-1.0.0/TesiproV/inst/extdata/benchmarks/diagnose_MC_IS_log_weights.R |only TesiproV-1.0.0/TesiproV/man/FORM.Rd | 171 TesiproV-1.0.0/TesiproV/man/Internal-helper-functions-for-MC_IS-open-paren-close-paren.Rd | 58 TesiproV-1.0.0/TesiproV/man/LogStudentT.Rd | 8 TesiproV-1.0.0/TesiproV/man/MC_CRUDE.Rd | 296 TesiproV-1.0.0/TesiproV/man/MC_IS.Rd | 641 - TesiproV-1.0.0/TesiproV/man/MC_IS_gsys.Rd | 97 TesiproV-1.0.0/TesiproV/man/MC_IS_single.Rd | 244 TesiproV-1.0.0/TesiproV/man/MC_IS_system.Rd | 259 TesiproV-1.0.0/TesiproV/man/MC_SubSam.Rd | 166 TesiproV-1.0.0/TesiproV/man/MVFOSM.Rd | 148 TesiproV-1.0.0/TesiproV/man/PARAM_BASEVAR-class.Rd | 92 TesiproV-1.0.0/TesiproV/man/PARAM_DETVAR-class.Rd | 71 TesiproV-1.0.0/TesiproV/man/PARAM_LSF-class.Rd | 34 TesiproV-1.0.0/TesiproV/man/PROB_BASEVAR-class.Rd | 194 TesiproV-1.0.0/TesiproV/man/PROB_DETVAR-class.Rd | 78 TesiproV-1.0.0/TesiproV/man/PROB_MACHINE-class.Rd | 124 TesiproV-1.0.0/TesiproV/man/PROB_QUALCON-class.Rd |only TesiproV-1.0.0/TesiproV/man/SORM.Rd | 166 TesiproV-1.0.0/TesiproV/man/SYS_LSF-class.Rd | 215 TesiproV-1.0.0/TesiproV/man/SYS_PARAM-class.Rd | 154 TesiproV-1.0.0/TesiproV/man/SYS_PROB-class.Rd | 351 - TesiproV-1.0.0/TesiproV/man/StudentT.Rd | 2 TesiproV-1.0.0/TesiproV/man/TesiproV-package.Rd | 94 TesiproV-1.0.0/TesiproV/man/as_record_df.Rd | 45 TesiproV-1.0.0/TesiproV/man/build_gsys.Rd | 2 TesiproV-1.0.0/TesiproV/man/compute_weight_update.Rd | 62 TesiproV-1.0.0/TesiproV/man/debug.print.Rd | 82 TesiproV-1.0.0/TesiproV/man/dot-is_unset.Rd |only TesiproV-1.0.0/TesiproV/man/dot-oc_fit_posterior_hyper.Rd |only TesiproV-1.0.0/TesiproV/man/dot-onLoad.Rd | 107 TesiproV-1.0.0/TesiproV/man/ensure_pkg.Rd | 44 TesiproV-1.0.0/TesiproV/man/init_rng_master.Rd | 46 TesiproV-1.0.0/TesiproV/man/is_empty.Rd | 80 TesiproV-1.0.0/TesiproV/man/is_missing.Rd | 44 TesiproV-1.0.0/TesiproV/man/make_parallel_cluster.Rd | 6 TesiproV-1.0.0/TesiproV/man/make_ready_cluster.Rd | 62 TesiproV-1.0.0/TesiproV/man/make_recorders.Rd | 36 TesiproV-1.0.0/TesiproV/man/parallel_dispatch.Rd | 2 TesiproV-1.0.0/TesiproV/man/record_step.Rd | 44 TesiproV-1.0.0/TesiproV/man/resolve_future_seed.Rd | 92 TesiproV-1.0.0/TesiproV/man/run_parallel.Rd | 11 TesiproV-1.0.0/TesiproV/man/set_cluster_rng.Rd | 34 TesiproV-1.0.0/TesiproV/man/shifted_lnorm.Rd |only TesiproV-1.0.0/TesiproV/tests/testthat.R |only TesiproV-1.0.0/TesiproV/tests/testthat/helper-future-plan.R |only TesiproV-1.0.0/TesiproV/tests/testthat/long_test_empdist.R | 380 - TesiproV-1.0.0/TesiproV/tests/testthat/setup.R | 2 TesiproV-1.0.0/TesiproV/tests/testthat/test-bug-distributions.R |only TesiproV-1.0.0/TesiproV/tests/testthat/test-bug-form-sorm-mvfosm.R |only TesiproV-1.0.0/TesiproV/tests/testthat/test-bug-mc.R |only TesiproV-1.0.0/TesiproV/tests/testthat/test-bug-misc.R |only TesiproV-1.0.0/TesiproV/tests/testthat/test-bug-print-param.R |only TesiproV-1.0.0/TesiproV/tests/testthat/test-bug-qualcon-dim.R |only TesiproV-1.0.0/TesiproV/tests/testthat/test-bug-qualcon-manual.R |only TesiproV-1.0.0/TesiproV/tests/testthat/test-bug-qualcon.R |only TesiproV-1.0.0/TesiproV/tests/testthat/test-bug-slnorm.R |only TesiproV-1.0.0/TesiproV/tests/testthat/test-bug-subset.R |only TesiproV-1.0.0/TesiproV/tests/testthat/test-bug-system-mcc-mcsus.R |only TesiproV-1.0.0/TesiproV/tests/testthat/test-bug-system-smooth.R |only TesiproV-1.0.0/TesiproV/tests/testthat/test-bug-system.R |only TesiproV-1.0.0/TesiproV/tests/testthat/test-log-space-helpers.R |only TesiproV-1.0.0/TesiproV/tests/testthat/test-u-to-x.R |only TesiproV-1.0.0/TesiproV/tests/testthat/test_FORM_Rackwitz.R |only TesiproV-1.0.0/TesiproV/tests/testthat/test_MCIS_system.R | 2455 ++++--- TesiproV-1.0.0/TesiproV/tests/testthat/test_MC_CRUDE_multi.R |only TesiproV-1.0.0/TesiproV/tests/testthat/test_MC_Crude.R |only TesiproV-1.0.0/TesiproV/tests/testthat/test_MC_IS_backend_contract.R |only TesiproV-1.0.0/TesiproV/tests/testthat/test_MC_IS_chunk_reproducibility.R |only TesiproV-1.0.0/TesiproV/tests/testthat/test_MC_IS_log_weighting.R |only TesiproV-1.0.0/TesiproV/tests/testthat/test_MC_IS_single.R | 585 + TesiproV-1.0.0/TesiproV/tests/testthat/test_MC_IS_system_log_stability.R |only TesiproV-1.0.0/TesiproV/tests/testthat/test_Methods.R | 717 +- TesiproV-1.0.0/TesiproV/tests/testthat/test_Methods_addDist.R | 293 TesiproV-1.0.0/TesiproV/tests/testthat/test_Methods_lnorm_x0.R | 155 TesiproV-1.0.0/TesiproV/tests/testthat/test_Spaethe_System.R |only TesiproV-1.0.0/TesiproV/tests/testthat/test_basevars.R | 1798 ++--- TesiproV-1.0.0/TesiproV/tests/testthat/test_basevars_methods.R |only TesiproV-1.0.0/TesiproV/tests/testthat/test_methods_extra.R | 429 - TesiproV-1.0.0/TesiproV/tests/testthat/test_mvfosm.R |only TesiproV-1.0.0/TesiproV/tests/testthat/test_parallel.R | 102 TesiproV-1.0.0/TesiproV/tests/testthat/test_parallel_system.R |only TesiproV-1.0.0/TesiproV/tests/testthat/test_prob_machine.R |only TesiproV-1.0.0/TesiproV/tests/testthat/test_qualcon.R |only TesiproV-1.0.0/TesiproV/tests/testthat/test_seed.R | 231 TesiproV-1.0.0/TesiproV/vignettes/TesiproV-Vignette.Rmd | 2002 +++--- 142 files changed, 12335 insertions(+), 10575 deletions(-)
Title: Utility Functions Around 'JDemetra+ 3.0'
Description: R Interface to 'JDemetra+ 3.x'
(<https://github.com/jdemetra>) time series analysis software. It
provides functions allowing to model time series (create outlier
regressors, user-defined calendar regressors, Unobserved Components
AutoRegressive Integrated Moving Average (UCARIMA) models...), to test
the presence of trading days or seasonal effects and also to set
specifications in pre-adjustment and benchmarking when using 'rjd3x13'
or 'rjd3tramoseats'.
Author: Jean Palate [aut],
Alain Quartier-la-Tente [aut] ,
Tanguy Barthelemy [aut, cre, art, cph],
Anna Smyk [aut],
Eulalie Delaune [aut]
Maintainer: Tanguy Barthelemy <timeserieswithjdemetraandr@gmail.com>
Diff between rjd3toolkit versions 3.9.0 dated 2026-09-21 and 3.9.1 dated 2026-10-28
DESCRIPTION | 14 +++-- MD5 | 42 ++++++++-------- NAMESPACE | 9 ++- NEWS.md | 26 ++++++++++ R/arima.R | 4 + R/calendars.R | 80 +++++++++++++------------------- R/modelling_context.R | 74 +++++++++++++++++++++++++++++ R/protobuf.R | 3 + R/spec_regarima.R | 33 ++++++++++--- README.md | 2 man/add_usrdefvar.Rd | 30 +++++++++--- man/calendar_td.Rd | 8 +-- man/chained_calendar.Rd | 9 --- man/holidays.Rd | 5 -- man/long_term_mean.Rd | 4 - man/national_calendar.Rd | 3 - man/print_calendars.Rd | 6 -- man/rjd3toolkit-package.Rd | 1 man/set_tradingdays.Rd | 3 + man/special_day.Rd | 5 +- man/weighted_calendar.Rd | 9 --- tests/testthat/test-modelling_context.R | 12 +--- 22 files changed, 244 insertions(+), 138 deletions(-)
Title: Methods and Measures for Brain, Cognitive, and Psychometric
Network Analysis
Description: Implements network analysis and graph theory measures used in neuroscience, cognitive science, and psychology. Methods include various filtering methods and approaches such as threshold, dependency (Kenett, Tumminello, Madi, Gur-Gershgoren, Mantegna, & Ben-Jacob, 2010 <doi:10.1371/journal.pone.0015032>), Information Filtering Networks (Barfuss, Massara, Di Matteo, & Aste, 2016 <doi:10.1103/PhysRevE.94.062306>), and Efficiency-Cost Optimization (Fallani, Latora, & Chavez, 2017 <doi:10.1371/journal.pcbi.1005305>). Several network measures are translated from the Brain Connectivity Toolbox (Rubinov & Sporns, 2010 <doi:10.1016/j.neuroimage.2009.10.003>). Brain methods include the recently developed Connectome Predictive Modeling (see references in package). Also implements several network measures including local network characteristics (e.g., centrality), community-level network characteristics (e.g., community centrality), global network characteri [...truncated...]
Author: Alexander Christensen [aut, cre] ,
Guido Previde Massara [ctb] ,
BCT Contributors [cph] ),
Mika Rubinov [cph, ctb] ),
Olaf Sporns [cph, ctb] ),
Alex Fornito [cph, ctb] ,
Jeff Spielberg [cph, ctb] ,
Jonathan Clayden [cph, ctb] ,
Rick Betzel [cph, ctb] [...truncated...]
Maintainer: Alexander Christensen <alexpaulchristensen@gmail.com>
Diff between NetworkToolbox versions 1.4.4 dated 2025-05-08 and 1.5.0 dated 2026-10-28
DESCRIPTION | 47 ++- MD5 | 123 ++++----- NAMESPACE | 78 +++-- NEWS | 594 ++++++++++++++++++++++++++------------------- R/ECO.R | 19 - R/ECOplusMaST.R | 14 - R/LoGo.R | 7 R/MFCF.R | 10 R/MaST.R | 26 + R/TMFG.R | 12 R/betweenness.R | 20 + R/clustcoeff.R | 5 R/comcat.R | 4 R/comm.str.R | 32 +- R/conn.R | 4 R/convertConnBrainMat.R | 6 R/core.items.R | 12 R/cpm.R | 97 +++---- R/degree.R | 2 R/depend.R | 15 - R/depna.R | 11 R/desc.R | 25 + R/desc.all.R | 23 - R/distance.R | 7 R/diversity.R | 20 - R/edgerep.R | 82 ++---- R/eigenvector.R | 5 R/gain.functions.R | 7 R/gateway.R | 15 - R/is.graphical.R | 35 +- R/lattnet.R | 12 R/louvain.R | 26 + R/network.permutation.R | 10 R/participation.R | 15 - R/pathlengths.R | 6 R/plot.cpm.R | 76 +++-- R/randnet.R | 14 - R/resp.rep.R | 15 - R/rspbc.R | 13 R/sim.chordal.R | 3 R/sim.swn.R | 14 - R/stable.R | 3 R/strength.R | 2 R/threshold.R | 37 +- R/transitivity.R | 13 R/un.direct.R | 2 R/utils-NetworkToolbox.R | 128 +++------ R/zzz.R | 27 -- inst/COPYRIGHTS |only man/betweenness.Rd | 5 man/clustcoeff.Rd | 5 man/conn.Rd | 2 man/distance.Rd | 5 man/diversity.Rd | 3 man/eigenvector.Rd | 5 man/gateway.Rd | 4 man/lattnet.Rd | 4 man/louvain.Rd | 5 man/network.permutation.Rd | 2 man/participation.Rd | 4 man/pathlengths.Rd | 6 man/randnet.Rd | 5 man/transitivity.Rd | 5 63 files changed, 1034 insertions(+), 799 deletions(-)
More information about NetworkToolbox at CRAN
Permanent link
Title: Analysis of Designed High-Dimensional Data using the
Comprehensive MultANOVA Framework
Description: A comprehensive and computationally fast framework to analyze high dimensional data associated with an experimental design based on Multiple ANOVAs (MultANOVA). It includes testing the overall significance of terms in the model, post-hoc analyses of significant terms and variable selection. Details may be found in Mahieu, B., & Cariou, V. (2025). MultANOVA Followed by Post Hoc Analyses for Designed High‐Dimensional Data: A Comprehensive Framework That Outperforms ASCA, rMANOVA, and VASCA. Journal of Chemometrics, 39(7). <doi:10.1002/cem.70039>.
Author: Benjamin Mahieu [aut, cre],
Veronique Cariou [aut]
Maintainer: Benjamin Mahieu <benjamin.mahieu@oniris-nantes.fr>
Diff between MultANOVA versions 1.1.0 dated 2026-03-13 and 1.1.1 dated 2026-10-28
DESCRIPTION | 8 - MD5 | 12 - R/DCDA.R | 352 ++++++++++++++++++++++------------------------- R/MultLSD.R | 272 ++++++++++++++++-------------------- R/plot.DCDA.R | 27 ++- build/partial.rdb |binary man/MultANOVA-package.Rd | 1 7 files changed, 323 insertions(+), 349 deletions(-)
Title: Assessing False Discovery Rate Claims in Proteomics
Description: Provides scope, calibration and stability diagnostics to assess
false discovery rate (FDR) claims in peptide and protein identification
workflows based on target-decoy competition and related confidence
measures. Includes the recomputed decoy ratio of the reported list,
accepted decoy counts and local decoy support, the FDP-CV benchmark,
threshold elasticity, posterior error probability (PEP) concordance with
the decoys, equal-chance checks and p-value calibration, explicit
target/decoy label-propagation rules for grouped units, picked-protein
competition, external validation by entrapment (raw and size-corrected
estimates, scope-discordant-set error rate), a ground-truth simulator of
target-decoy competition, and an HTML report. Methods are described in
Chion et al. (2026) <doi:10.64898/2026.04.16.718468>.
Author: Quentin Giai Gianetto [aut, cre] ,
Marie Chion [ctb] ,
Alexandre Godmer [ctb] ,
Thibaut Douche [ctb] ,
Mariette Matondo [ctb]
Maintainer: Quentin Giai Gianetto <quentin.giaigianetto@pasteur.fr>
Diff between diagFDR versions 0.1.2 dated 2026-10-19 and 0.2.1 dated 2026-10-28
diagFDR-0.1.2/diagFDR/NEWS.md |only diagFDR-0.2.1/diagFDR/DESCRIPTION | 44 +++++++++--- diagFDR-0.2.1/diagFDR/MD5 | 47 +++++++++++-- diagFDR-0.2.1/diagFDR/NAMESPACE | 15 ++++ diagFDR-0.2.1/diagFDR/R/alert_basis.R | 4 - diagFDR-0.2.1/diagFDR/R/data.R |only diagFDR-0.2.1/diagFDR/R/entrapment.R |only diagFDR-0.2.1/diagFDR/R/label_rules.R |only diagFDR-0.2.1/diagFDR/R/picked_protein.R |only diagFDR-0.2.1/diagFDR/R/simulate.R |only diagFDR-0.2.1/diagFDR/build/vignette.rds |binary diagFDR-0.2.1/diagFDR/data |only diagFDR-0.2.1/diagFDR/inst/CITATION |only diagFDR-0.2.1/diagFDR/inst/doc/diann.html | 2 diagFDR-0.2.1/diagFDR/inst/doc/quickstart.R |only diagFDR-0.2.1/diagFDR/inst/doc/quickstart.Rmd |only diagFDR-0.2.1/diagFDR/inst/doc/quickstart.html |only diagFDR-0.2.1/diagFDR/inst/templates/dfdr_report.Rmd | 16 ++-- diagFDR-0.2.1/diagFDR/man/as_decoy_logical.Rd |only diagFDR-0.2.1/diagFDR/man/collapse_universe.Rd |only diagFDR-0.2.1/diagFDR/man/dfdr_accepted.Rd |only diagFDR-0.2.1/diagFDR/man/dfdr_check_cv_benchmark.Rd |only diagFDR-0.2.1/diagFDR/man/dfdr_entrapment.Rd |only diagFDR-0.2.1/diagFDR/man/dfdr_entrapment_discordant.Rd |only diagFDR-0.2.1/diagFDR/man/dfdr_entrapment_size_ratio.Rd |only diagFDR-0.2.1/diagFDR/man/dfdr_is_entrapment_group.Rd |only diagFDR-0.2.1/diagFDR/man/dfdr_label_rule_audit.Rd |only diagFDR-0.2.1/diagFDR/man/dfdr_picked_protein.Rd |only diagFDR-0.2.1/diagFDR/man/dfdr_realised_fdp.Rd |only diagFDR-0.2.1/diagFDR/man/dfdr_simulate_tdc.Rd |only diagFDR-0.2.1/diagFDR/man/diann_entrapment_ids.Rd |only diagFDR-0.2.1/diagFDR/man/diann_global_proteingroup.Rd |only diagFDR-0.2.1/diagFDR/man/dot-digest.Rd |only diagFDR-0.2.1/diagFDR/man/dot-entrapment_flag.Rd |only diagFDR-0.2.1/diagFDR/man/label_is_intrinsic.Rd |only diagFDR-0.2.1/diagFDR/man/read_fasta_accessions.Rd |only diagFDR-0.2.1/diagFDR/man/sim_tdc_example.Rd |only diagFDR-0.2.1/diagFDR/tests/testthat/test-entrapment.R |only diagFDR-0.2.1/diagFDR/tests/testthat/test-label-rules.R |only diagFDR-0.2.1/diagFDR/tests/testthat/test-picked-protein.R |only diagFDR-0.2.1/diagFDR/tests/testthat/test-simulate.R |only diagFDR-0.2.1/diagFDR/vignettes/quickstart.Rmd |only 42 files changed, 101 insertions(+), 27 deletions(-)
Title: Flexible Bayes Factor Testing of Scientific Expectations
Description: Implementation of default Bayes factors
for testing statistical hypotheses under various statistical models. The package is
intended for applied quantitative researchers in the
social and behavioral sciences, medical research,
and related fields. The Bayes factor tests can be
executed for statistical models such as
univariate and multivariate normal linear models,
correlation analysis, generalized linear models, special cases of
linear mixed models, survival models, relational
event models. Parameters that can be tested are
location parameters (e.g., group means, regression coefficients),
variances (e.g., group variances), and measures of
association (e.g,. polychoric/polyserial/biserial/tetrachoric/product
moments correlations), among others.
Relevant references on the methodology The statistical underpinnings are
described in
O'Hagan (1995) <DOI:10.1111/j.2517-6161.1995.tb02017.x>,
Mulder and Xin (2022) <DOI:10.1080/00273171.2021.1904809>,
Mulder and Gelissen (2019) <D [...truncated...]
Author: Joris Mulder [aut, cre],
Caspar van Lissa [aut, ctb],
Donald R. Williams [aut, ctb],
Xin Gu [aut, ctb],
Anton Olsson-Collentine [aut, ctb],
Florian Boeing-Messing [aut, ctb],
Jean-Paul Fox [aut, ctb],
Janosch Menke [ctb],
Robbie van Aert [ctb],
Barry [...truncated...]
Maintainer: Joris Mulder <j.mulder3@tilburguniversity.edu>
Diff between BFpack versions 1.6.1 dated 2026-07-10 and 1.6.2 dated 2026-10-28
BFpack-1.6.1/BFpack/vignettes/vignette_BFpack.html |only BFpack-1.6.2/BFpack/DESCRIPTION | 6 - BFpack-1.6.2/BFpack/MD5 | 28 +++---- BFpack-1.6.2/BFpack/NEWS.md | 11 ++ BFpack-1.6.2/BFpack/R/BF.cortest.R | 13 +-- BFpack-1.6.2/BFpack/R/BF.gaussian.R | 38 +++++++--- BFpack-1.6.2/BFpack/inst/doc/vignette_BFpack_correlation.html | 4 - BFpack-1.6.2/BFpack/inst/doc/vignette_BFpack_ergm.html | 4 - BFpack-1.6.2/BFpack/inst/doc/vignette_BFpack_general.Rmd | 16 ++-- BFpack-1.6.2/BFpack/inst/doc/vignette_BFpack_general.html | 36 ++++----- BFpack-1.6.2/BFpack/inst/doc/vignette_BFpack_regression.html | 4 - BFpack-1.6.2/BFpack/man/cor_test.Rd | 3 BFpack-1.6.2/BFpack/src/bct_mixedordinal.f90 | 4 - BFpack-1.6.2/BFpack/tests/testthat/test_bartlett.R | 2 BFpack-1.6.2/BFpack/tests/testthat/test_cor_test_covariates.R |only BFpack-1.6.2/BFpack/vignettes/vignette_BFpack_general.Rmd | 16 ++-- 16 files changed, 109 insertions(+), 76 deletions(-)
Title: Fast Numerical Maximum Likelihood Estimation for Latent Markov
Models
Description: A variety of latent Markov models, including hidden Markov models, hidden semi-Markov models,
state-space models and continuous-time variants can be formulated and estimated within the same framework via directly maximising the likelihood function using the so-called forward algorithm.
Applied researchers often need custom models that standard software does not easily support.
Writing tailored 'R' code offers flexibility but suffers from slow estimation speeds.
We address these issues by providing easy-to-use functions (written in 'C++' for speed) for common tasks like the forward algorithm.
These functions can be combined into custom models in a Lego-type approach, offering up to 10-20 times faster estimation via standard numerical optimisers.
To aid in building fully custom likelihood functions, several vignettes are included that show how to simulate data from and estimate all the above model classes.
Author: Jan-Ole Fischer [aut, cre]
Maintainer: Jan-Ole Fischer <jan-ole.fischer@mailbox.org>
Diff between LaMa versions 2.1.3 dated 2026-08-25 and 3.0.0 dated 2026-10-28
LaMa-2.1.3/LaMa/R/report.R |only LaMa-2.1.3/LaMa/man/logLik.qremlModel.Rd |only LaMa-2.1.3/LaMa/man/make_matrices.Rd |only LaMa-2.1.3/LaMa/man/make_matrices_old.Rd |only LaMa-2.1.3/LaMa/man/report.Rd |only LaMa-2.1.3/LaMa/vignettes/HSMMs_cache |only LaMa-2.1.3/LaMa/vignettes/Inhomogeneous_HMMs_cache |only LaMa-2.1.3/LaMa/vignettes/LaMa_and_RTMB_cache |only LaMa-2.1.3/LaMa/vignettes/Longitudinal_data_cache |only LaMa-2.1.3/LaMa/vignettes/State_space_models_cache |only LaMa-3.0.0/LaMa/DESCRIPTION | 10 LaMa-3.0.0/LaMa/MD5 | 234 - LaMa-3.0.0/LaMa/NAMESPACE | 26 LaMa-3.0.0/LaMa/NEWS.md | 149 + LaMa-3.0.0/LaMa/R/RcppExports.R | 32 LaMa-3.0.0/LaMa/R/decoding_functions.R | 518 ---- LaMa-3.0.0/LaMa/R/forward_algorithms.R | 1021 ++------ LaMa-3.0.0/LaMa/R/helper_functions.R | 21 LaMa-3.0.0/LaMa/R/hsmm_functions_old.R | 4 LaMa-3.0.0/LaMa/R/lama.R |only LaMa-3.0.0/LaMa/R/mcreport.R | 4 LaMa-3.0.0/LaMa/R/model_matrix_functions.R | 1220 ++++----- LaMa-3.0.0/LaMa/R/multistart.R |only LaMa-3.0.0/LaMa/R/penalty_functions.R |only LaMa-3.0.0/LaMa/R/plot_statedens.R |only LaMa-3.0.0/LaMa/R/qreml_functions.R | 2651 +++++---------------- LaMa-3.0.0/LaMa/R/qreml_old_functions.R |only LaMa-3.0.0/LaMa/R/residual_cdfs.R |only LaMa-3.0.0/LaMa/R/residual_functions.R | 186 - LaMa-3.0.0/LaMa/R/scores.R |only LaMa-3.0.0/LaMa/R/sdreportMC.R | 11 LaMa-3.0.0/LaMa/R/simulate.R |only LaMa-3.0.0/LaMa/R/statedens.R |only LaMa-3.0.0/LaMa/R/stationary_functions.R | 16 LaMa-3.0.0/LaMa/R/summary_functions.R |only LaMa-3.0.0/LaMa/R/tpm_functions.R | 70 LaMa-3.0.0/LaMa/R/zzz.R | 43 LaMa-3.0.0/LaMa/inst/doc/Continuous_time_HMMs.R | 4 LaMa-3.0.0/LaMa/inst/doc/Continuous_time_HMMs.Rmd | 4 LaMa-3.0.0/LaMa/inst/doc/Continuous_time_HMMs.html | 16 LaMa-3.0.0/LaMa/inst/doc/Extensions.R | 37 LaMa-3.0.0/LaMa/inst/doc/Extensions.Rmd | 51 LaMa-3.0.0/LaMa/inst/doc/Extensions.html | 630 ++-- LaMa-3.0.0/LaMa/inst/doc/HSMMs.R | 2 LaMa-3.0.0/LaMa/inst/doc/HSMMs.Rmd | 2 LaMa-3.0.0/LaMa/inst/doc/HSMMs.html | 13 LaMa-3.0.0/LaMa/inst/doc/Intro_to_LaMa.R | 4 LaMa-3.0.0/LaMa/inst/doc/Intro_to_LaMa.Rmd | 6 LaMa-3.0.0/LaMa/inst/doc/Intro_to_LaMa.html | 17 LaMa-3.0.0/LaMa/inst/doc/LaMa_and_RTMB.R | 10 LaMa-3.0.0/LaMa/inst/doc/LaMa_and_RTMB.Rmd | 43 LaMa-3.0.0/LaMa/inst/doc/LaMa_and_RTMB.html | 211 + LaMa-3.0.0/LaMa/inst/doc/Longitudinal_data.R | 10 LaMa-3.0.0/LaMa/inst/doc/Longitudinal_data.Rmd | 10 LaMa-3.0.0/LaMa/inst/doc/Longitudinal_data.html | 12 LaMa-3.0.0/LaMa/inst/doc/MMMPPs.R | 4 LaMa-3.0.0/LaMa/inst/doc/MMMPPs.Rmd | 4 LaMa-3.0.0/LaMa/inst/doc/MMMPPs.html | 20 LaMa-3.0.0/LaMa/inst/doc/Penalised_splines.R | 65 LaMa-3.0.0/LaMa/inst/doc/Penalised_splines.Rmd | 98 LaMa-3.0.0/LaMa/inst/doc/Penalised_splines.html | 350 +- LaMa-3.0.0/LaMa/inst/doc/State_space_models.R | 4 LaMa-3.0.0/LaMa/inst/doc/State_space_models.Rmd | 4 LaMa-3.0.0/LaMa/inst/doc/State_space_models.html | 12 LaMa-3.0.0/LaMa/man/MCreport.Rd | 2 LaMa-3.0.0/LaMa/man/cosinor.Rd | 4 LaMa-3.0.0/LaMa/man/forward.Rd | 42 LaMa-3.0.0/LaMa/man/forward_g.Rd | 11 LaMa-3.0.0/LaMa/man/forward_p.Rd | 5 LaMa-3.0.0/LaMa/man/generator_g.Rd | 3 LaMa-3.0.0/LaMa/man/lama.Rd |only LaMa-3.0.0/LaMa/man/logLik.LaMaModel.Rd | 4 LaMa-3.0.0/LaMa/man/make_matrices_dens.Rd | 17 LaMa-3.0.0/LaMa/man/modmat.Rd |only LaMa-3.0.0/LaMa/man/multistart.Rd |only LaMa-3.0.0/LaMa/man/penalty.Rd | 28 LaMa-3.0.0/LaMa/man/penalty2.Rd | 28 LaMa-3.0.0/LaMa/man/penalty_uni.Rd | 2 LaMa-3.0.0/LaMa/man/plot.LaMaModel.Rd |only LaMa-3.0.0/LaMa/man/plot.LaMaResiduals.Rd | 9 LaMa-3.0.0/LaMa/man/pred_matrix.Rd | 27 LaMa-3.0.0/LaMa/man/predict.LaMa_matrices.Rd | 20 LaMa-3.0.0/LaMa/man/predict.smoothdens.Rd |only LaMa-3.0.0/LaMa/man/print.LaMaModel.Rd |only LaMa-3.0.0/LaMa/man/print.LaMa_matrices.Rd |only LaMa-3.0.0/LaMa/man/pseudo_res.Rd | 33 LaMa-3.0.0/LaMa/man/qreml.Rd | 158 - LaMa-3.0.0/LaMa/man/qreml_old.Rd | 79 LaMa-3.0.0/LaMa/man/rep_sp.Rd |only LaMa-3.0.0/LaMa/man/scores.Rd |only LaMa-3.0.0/LaMa/man/sdreport_outer.Rd | 2 LaMa-3.0.0/LaMa/man/simulate.LaMaModel.Rd |only LaMa-3.0.0/LaMa/man/smooth_dens_construct.Rd | 62 LaMa-3.0.0/LaMa/man/smoothdens.Rd |only LaMa-3.0.0/LaMa/man/statedens.Rd |only LaMa-3.0.0/LaMa/man/stateprobs.Rd | 20 LaMa-3.0.0/LaMa/man/stateprobs_g.Rd | 8 LaMa-3.0.0/LaMa/man/stateprobs_p.Rd | 9 LaMa-3.0.0/LaMa/man/stationary_ct.Rd | 2 LaMa-3.0.0/LaMa/man/stationary_p.Rd | 2 LaMa-3.0.0/LaMa/man/summary.LaMaModel.Rd |only LaMa-3.0.0/LaMa/man/summary.qremlModel.Rd | 24 LaMa-3.0.0/LaMa/man/tpm_g.Rd | 16 LaMa-3.0.0/LaMa/man/viterbi.Rd | 19 LaMa-3.0.0/LaMa/man/viterbi_g.Rd | 8 LaMa-3.0.0/LaMa/man/viterbi_p.Rd | 7 LaMa-3.0.0/LaMa/src/RcppExports.cpp | 111 LaMa-3.0.0/LaMa/src/decoding_functions.cpp |only LaMa-3.0.0/LaMa/src/forward_algorithms.cpp | 201 - LaMa-3.0.0/LaMa/tests/testthat/helper-forward.R |only LaMa-3.0.0/LaMa/tests/testthat/test-decoding.R |only LaMa-3.0.0/LaMa/tests/testthat/test-deprecated.R |only LaMa-3.0.0/LaMa/tests/testthat/test-forward.R |only LaMa-3.0.0/LaMa/tests/testthat/test-lama.R |only LaMa-3.0.0/LaMa/tests/testthat/test-multistart.R |only LaMa-3.0.0/LaMa/tests/testthat/test-residuals.R |only LaMa-3.0.0/LaMa/tests/testthat/test-scores.R |only LaMa-3.0.0/LaMa/tests/testthat/test-simulate.R |only LaMa-3.0.0/LaMa/tests/testthat/test-statedens.R |only LaMa-3.0.0/LaMa/tests/testthat/test-tpm.R | 17 LaMa-3.0.0/LaMa/vignettes/Continuous_time_HMMs.Rmd | 4 LaMa-3.0.0/LaMa/vignettes/Extensions.Rmd | 51 LaMa-3.0.0/LaMa/vignettes/HSMMs.Rmd | 2 LaMa-3.0.0/LaMa/vignettes/Intro_to_LaMa.Rmd | 6 LaMa-3.0.0/LaMa/vignettes/LaMa_and_RTMB.Rmd | 43 LaMa-3.0.0/LaMa/vignettes/Longitudinal_data.Rmd | 10 LaMa-3.0.0/LaMa/vignettes/MMMPPs.Rmd | 4 LaMa-3.0.0/LaMa/vignettes/Penalised_splines.Rmd | 98 LaMa-3.0.0/LaMa/vignettes/State_space_models.Rmd | 4 129 files changed, 3629 insertions(+), 5432 deletions(-)
Title: Kernel Density Estimation with Parametric Starts and Asymmetric
Kernels
Description: Handles univariate non-parametric density estimation with
parametric starts and asymmetric kernels in a simple and flexible way.
Kernel density estimation with parametric starts involves fitting a
parametric density to the data before making a correction with kernel
density estimation, see Hjort & Glad (1995) <doi:10.1214/aos/1176324627>.
Asymmetric kernels make kernel density estimation more efficient on bounded
intervals such as (0, 1) and the positive half-line. Supported asymmetric
kernels are the gamma kernel of Chen (2000) <doi:10.1023/A:1004165218295>,
the beta kernel of Chen (1999) <doi:10.1016/S0167-9473(99)00010-9>, and the
copula kernel of Jones & Henderson (2007) <doi:10.1093/biomet/asm068>.
User-supplied kernels, parametric starts, and bandwidths are supported.
Author: Jonas Moss [aut, cre] ,
Martin Tveten [ctb]
Maintainer: Jonas Moss <jonas.gjertsen@gmail.com>
Diff between kdensity versions 1.2.0 dated 2026-05-04 and 2.0.0 dated 2026-10-28
kdensity-1.2.0/kdensity/tests/testthat/test_bandwidth.r |only kdensity-1.2.0/kdensity/tests/testthat/test_generics.r |only kdensity-1.2.0/kdensity/tests/testthat/test_kernels.r |only kdensity-1.2.0/kdensity/tests/testthat/test_starts.r |only kdensity-2.0.0/kdensity/DESCRIPTION | 14 kdensity-2.0.0/kdensity/MD5 | 82 + kdensity-2.0.0/kdensity/NAMESPACE | 6 kdensity-2.0.0/kdensity/NEWS.md | 128 ++ kdensity-2.0.0/kdensity/R/RcppExports.R |only kdensity-2.0.0/kdensity/R/bandwidths.R | 432 +++++++--- kdensity-2.0.0/kdensity/R/compiled.R |only kdensity-2.0.0/kdensity/R/generics.R | 145 +-- kdensity-2.0.0/kdensity/R/grid.R |only kdensity-2.0.0/kdensity/R/helpers.R | 89 ++ kdensity-2.0.0/kdensity/R/kdensity.R | 185 ++-- kdensity-2.0.0/kdensity/R/kernels.R | 108 +- kdensity-2.0.0/kdensity/R/starts.R | 40 kdensity-2.0.0/kdensity/README.md | 170 +-- kdensity-2.0.0/kdensity/build/vignette.rds |binary kdensity-2.0.0/kdensity/inst/doc/tutorial.R | 10 kdensity-2.0.0/kdensity/inst/doc/tutorial.Rmd | 27 kdensity-2.0.0/kdensity/inst/doc/tutorial.html | 64 + kdensity-2.0.0/kdensity/man/bandwidths.Rd | 89 +- kdensity-2.0.0/kdensity/man/figures/README-example-1.png |binary kdensity-2.0.0/kdensity/man/figures/README-simpleuse-1.png |only kdensity-2.0.0/kdensity/man/figures/logo.png |binary kdensity-2.0.0/kdensity/man/figures/logo.svg |only kdensity-2.0.0/kdensity/man/kdensity.Rd | 32 kdensity-2.0.0/kdensity/man/kdensity_grid.Rd |only kdensity-2.0.0/kdensity/man/kernels.Rd | 30 kdensity-2.0.0/kdensity/man/parametric_starts.Rd | 4 kdensity-2.0.0/kdensity/man/plot.kdensity.Rd | 28 kdensity-2.0.0/kdensity/man/plot_helper.Rd | 3 kdensity-2.0.0/kdensity/src |only kdensity-2.0.0/kdensity/tests/testthat/test_assignments.R | 75 + kdensity-2.0.0/kdensity/tests/testthat/test_bandwidth.R |only kdensity-2.0.0/kdensity/tests/testthat/test_compiled_kernels.R |only kdensity-2.0.0/kdensity/tests/testthat/test_degenerate.R |only kdensity-2.0.0/kdensity/tests/testthat/test_gcopula.R |only kdensity-2.0.0/kdensity/tests/testthat/test_generics.R |only kdensity-2.0.0/kdensity/tests/testthat/test_generics_invisible.R | 29 kdensity-2.0.0/kdensity/tests/testthat/test_grid.R |only kdensity-2.0.0/kdensity/tests/testthat/test_invariants.R |only kdensity-2.0.0/kdensity/tests/testthat/test_kdensity.R | 8 kdensity-2.0.0/kdensity/tests/testthat/test_kdensity_helpers.R | 1 kdensity-2.0.0/kdensity/tests/testthat/test_kernels.R |only kdensity-2.0.0/kdensity/tests/testthat/test_registry.R |only kdensity-2.0.0/kdensity/tests/testthat/test_sorted_kernels.R |only kdensity-2.0.0/kdensity/tests/testthat/test_start_weights.R |only kdensity-2.0.0/kdensity/tests/testthat/test_starts.R |only kdensity-2.0.0/kdensity/tests/testthat/test_utility_functions.R | 2 kdensity-2.0.0/kdensity/vignettes/tutorial.Rmd | 27 52 files changed, 1252 insertions(+), 576 deletions(-)
Title: Bayesian Federated Inference
Description: The Bayesian Federated Inference ('BFI') method combines inference results obtained from local data sets in the separate centers. In this version of the package, the 'BFI' methodology is programmed for linear, logistic and survival regression models. For GLMs, see Jonker, Pazira and Coolen (2024) <doi:10.1002/sim.10072>; for survival models, see Pazira, Massa, Weijers, Coolen and Jonker (2026) <doi:10.1080/02664763.2025.2511932>; and for heterogeneous populations, see Jonker, Pazira and Coolen (2025) <doi:10.1017/rsm.2025.6>.
Author: Hassan Pazira [aut, cre] ,
Emanuele Massa [aut] ,
Marianne A. Jonker [aut]
Maintainer: Hassan Pazira <h.pazira@arq.org>
Diff between BFI versions 3.2.0 dated 2026-09-26 and 3.3.0 dated 2026-10-28
DESCRIPTION | 10 MD5 | 64 NAMESPACE | 3 NEWS.md | 36 R/A.l.maker.R | 16 R/BFI.R | 69 R/MAP.estimation.R | 2080 +++++++++++----------- R/bfi-formula-inputs.R |only R/coef.bfi.R | 4 R/confint.bfi.R |only R/inv.prior.cov.R | 1347 +++++++------- R/negloglik.theta.R | 250 +- R/print.bfi.R | 12 R/print.summary.bfi.R |only R/summary.bfi.R | 88 R/vcov.bfi.R | 2 README.md | 2 build/partial.rdb |binary inst/CITATION | 3 man/BFI-internal.Rd | 2 man/BFI-package.Rd | 5 man/BFI.Rd | 19 man/MAP.estimation.Rd | 105 + man/Nurses.Rd | 44 man/b.diag.Rd | 2 man/bfi-methods.Rd | 10 man/confint.bfi.Rd |only man/inv.prior.cov.Rd | 57 man/n.par.Rd | 2 man/summary.bfi.Rd | 53 man/trauma.Rd | 40 tests/testthat/test-MAP.estimation.R | 26 tests/testthat/test-formula-federated-treatment.R |only tests/testthat/test-formula-interface.R |only tests/testthat/test-formula-survival.R |only tests/testthat/test-gaussian-logvariance.R |only tests/testthat/test-s3-classes.R |only tests/testthat/test-summary-print.R |only 38 files changed, 2344 insertions(+), 2007 deletions(-)
Title: Retrieving, Organizing, and Analyzing Estuary Monitoring Data
Description: Tools for retrieving, organizing, and analyzing environmental
data from the System Wide Monitoring Program of the National Estuarine
Research Reserve System <https://cdmo.baruch.sc.edu/>. These tools
address common challenges associated with continuous time series data
for environmental decision making.
Author: Marcus W. Beck [aut, cre],
Kimberly Cressman [ctb]
Maintainer: Marcus W. Beck <mbeck@tbep.org>
Diff between SWMPr versions 2.5.2 dated 2025-02-03 and 2.5.3 dated 2026-10-28
DESCRIPTION | 12 ++++++------ MD5 | 21 ++++++++++++--------- NAMESPACE | 1 + NEWS.md | 4 ++++ R/metab_day.R | 10 +++++----- R/sun_times.R |only build/vignette.rds |binary inst/doc/Overview.Rmd | 4 ++-- inst/doc/Overview.html | 9 +++++---- man/metab_day.Rd | 4 ++-- man/sun_times.Rd |only tests/testthat/test-sun_times.R |only vignettes/Overview.Rmd | 4 ++-- 13 files changed, 39 insertions(+), 30 deletions(-)
Title: Analysis of Metafrontier Models for Efficiency and Productivity
Description: Implements metafrontier production function models for
estimating technical efficiencies and technology gaps for groups of
firms that face different restrictions of a common underlying
metatechnology (group-specific technologies in the sense of Battese,
Rao, and O'Donnell, 2004). Supports both stochastic frontier
analysis (SFA) and data envelopment analysis (DEA) based
metafrontiers. Includes the deterministic metafrontier of Battese,
Rao, and O'Donnell (2004) <doi:10.1023/B:PROD.0000012454.06094.29>,
the stochastic metafrontier of Huang, Huang, and Liu (2014)
<doi:10.1007/s11123-014-0402-2>, and the metafrontier Malmquist
productivity index of O'Donnell, Rao, and Battese (2008)
<doi:10.1007/s00181-007-0119-4>. The deterministic metafrontier can
be identified by either the minimum sum of absolute deviations (LP)
or the minimum sum of squared deviations (QP) criterion. Group
frontiers can be production or cost frontiers, corrected for sample
selection following Greene [...truncated...]
Author: Erik Enstad [aut, cre]
Maintainer: Erik Enstad <erik.enstad@nhh.no>
Diff between metafrontier versions 0.3.1 dated 2026-08-19 and 0.4.0 dated 2026-10-28
DESCRIPTION | 19 MD5 | 129 +- NAMESPACE | 7 NEWS.md | 194 ++++ R/bootstrap.R | 231 ++++- R/diagnostics.R | 41 R/ggplot.R | 62 + R/hypothesis_tests.R | 413 ++++----- R/latent_class.R | 10 R/malmquist.R | 49 - R/metafrontier-package.R | 2 R/metafrontier.R | 249 ++++- R/metafrontier_sfa.R | 111 +- R/methods.R | 30 R/model_extractors.R | 4 R/sfa_estimation.R | 161 +++ R/sfa_panel.R | 7 R/sfa_selection.R |only R/sfa_spatial.R |only R/simulate.R | 995 ++++++++++++----------- R/tfp_index.R |only R/tgr.R | 15 R/zzz.R | 40 inst/doc/introduction.R | 11 inst/doc/introduction.Rmd | 18 inst/doc/introduction.html | 284 +++--- inst/doc/methods.Rmd | 11 inst/doc/methods.html | 106 +- man/autoplot.boot_tgr.Rd | 68 - man/autoplot.malmquist_meta.Rd | 82 - man/autoplot.metafrontier.Rd | 88 +- man/autoplot.tfp_meta.Rd |only man/boot_tgr.Rd | 201 ++-- man/check_convergence.Rd | 15 man/confint.metafrontier.Rd | 96 +- man/malmquist_meta.Rd | 3 man/metafrontier-package.Rd | 2 man/metafrontier.Rd | 66 + man/poolability_test.Rd | 204 ++-- man/predict.metafrontier.Rd | 74 - man/simulate_metafrontier.Rd | 28 man/technology_gap_ratio.Rd | 15 man/tfp_index.Rd |only tests/stress_collinearity.R | 550 ++++++------ tests/stress_test_reviewer6.R | 1208 ++++++++++++++-------------- tests/testthat/test-bootstrap.R | 361 ++++++-- tests/testthat/test-confint-predict.R | 202 ++-- tests/testthat/test-cost-frontier.R |only tests/testthat/test-cross-validation.R | 120 +- tests/testthat/test-ddf.R | 122 +- tests/testthat/test-dea-performance.R | 110 +- tests/testthat/test-dea.R | 332 +++---- tests/testthat/test-estimation-sfa.R | 21 tests/testthat/test-exponential-stability.R |only tests/testthat/test-formula-z.R | 162 +-- tests/testthat/test-ggplot.R | 168 +-- tests/testthat/test-latent-class.R | 182 ++-- tests/testthat/test-malmquist-sfa.R | 176 ++-- tests/testthat/test-malmquist.R | 380 ++++---- tests/testthat/test-models-arg.R | 186 ++-- tests/testthat/test-monte-carlo.R | 138 +-- tests/testthat/test-murphy-topel.R | 274 +++--- tests/testthat/test-na-rows.R |only tests/testthat/test-panel-sfa.R | 178 ++-- tests/testthat/test-produc.R | 156 +-- tests/testthat/test-selection.R |only tests/testthat/test-snapshot.R | 182 ++-- tests/testthat/test-spatial.R |only tests/testthat/test-tfp-index.R |only vignettes/introduction.Rmd | 18 vignettes/methods.Rmd | 11 71 files changed, 5365 insertions(+), 4013 deletions(-)
Title: Easy Access to Model Information for Various Model Objects
Description: A tool to provide an easy, intuitive and consistent
access to information contained in various R models, like model
formulas, model terms, information about random effects, data that was
used to fit the model or data from response variables. 'insight'
mainly revolves around two types of functions: Functions that find
(the names of) information, starting with 'find_', and functions that
get the underlying data, starting with 'get_'. The package has a
consistent syntax and works with many different model objects, where
otherwise functions to access these information are missing.
Author: Daniel Luedecke [aut, cre] ,
Dominique Makowski [aut, ctb] ,
Indrajeet Patil [aut, ctb] ,
Philip Waggoner [aut, ctb] ,
Mattan S. Ben-Shachar [aut, ctb] ,
Brenton M. Wiernik [aut, ctb] ,
Vincent Arel-Bundock [aut, ctb] ,
Etienne Bacher [aut, ctb] ,
Ale [...truncated...]
Maintainer: Daniel Luedecke <officialeasystats@gmail.com>
Diff between insight versions 1.6.0 dated 2026-10-13 and 1.6.1 dated 2026-10-28
DESCRIPTION | 6 MD5 | 146 ++-- NAMESPACE | 9 NEWS.md | 175 +++++ R/export_table.R | 171 ++++- R/find_formula.R | 162 ++++- R/find_parameters.R | 9 R/find_predictors.R | 71 ++ R/find_statistic.R | 2 R/find_terms.R | 35 - R/find_variables.R | 2 R/get_datagrid.R | 30 R/get_loglikelihood.R | 69 ++ R/get_modelmatrix.R | 123 +++ R/get_parameters.R | 9 R/get_predicted.R | 52 + R/get_predicted_ci.R | 111 +++ R/get_predicted_mixed.R | 34 - R/get_sigma.R | 36 + R/get_variances.R | 12 R/is_converged.R | 441 ++++++++++++-- R/is_model_supported.R | 2 R/link_function.R | 2 R/link_inverse.R | 37 + R/null_model.R | 49 + R/utils_get_data.R | 9 inst/doc/display.html | 380 ++++++------ man/export_table.Rd | 25 man/find_formula.Rd | 15 man/find_interactions.Rd | 9 man/find_parameters.Rd | 14 man/find_parameters.averaging.Rd | 9 man/find_parameters.betamfx.Rd | 9 man/find_parameters.glmmTMB.Rd | 12 man/find_parameters.zeroinfl.Rd | 9 man/find_predictors.Rd | 22 man/find_terms.Rd | 15 man/find_variables.Rd | 19 man/get_data.Rd | 9 man/get_datagrid.Rd | 3 man/get_parameters.BGGM.Rd | 9 man/get_parameters.Rd | 9 man/get_parameters.betamfx.Rd | 9 man/get_parameters.betareg.Rd | 9 man/get_parameters.blavaan.Rd | 3 man/get_parameters.gamm.Rd | 9 man/get_parameters.glmmTMB.Rd | 12 man/get_parameters.zeroinfl.Rd | 9 man/get_predicted_ci.Rd | 12 man/get_statistic.Rd | 9 man/get_varcov.Rd | 9 man/is_converged.Rd | 53 + man/n_parameters.Rd | 3 tests/testthat/test-betareg.R | 27 tests/testthat/test-blavaan.R | 38 + tests/testthat/test-brms.R | 24 tests/testthat/test-export_table.R | 399 ++++++++++++ tests/testthat/test-gamlss.R | 8 tests/testthat/test-get_loglikelihood.R | 102 +++ tests/testthat/test-get_modelmatrix.R | 174 +++++ tests/testthat/test-get_predicted.R | 2 tests/testthat/test-get_variance.R | 3 tests/testthat/test-glmmPQL.R | 37 + tests/testthat/test-gls.R | 125 +++ tests/testthat/test-is_converged.R | 7 tests/testthat/test-is_converged_coxph.R | 970 ++++++++++++++++++++++++++++++- tests/testthat/test-lavaan.R | 40 + tests/testthat/test-lme.R | 232 +++++++ tests/testthat/test-lmrob_base.R | 8 tests/testthat/test-nlme.R |only tests/testthat/test-nlmer.R | 7 tests/testthat/test-nls.R |only tests/testthat/test-panelr.R | 4 tests/testthat/test-sdmTMB.R | 2 tests/testthat/test-vglm.R | 49 + 75 files changed, 4198 insertions(+), 569 deletions(-)
Title: Utilities to Weave Hydrologic Fabrics
Description: A collection of utilities that support creation of network attributes for hydrologic networks. Methods and algorithms implemented are documented in Moore et al. (2019) <doi:10.3133/ofr20191096>, Cormen and Leiserson (2022) <ISBN:9780262046305> and Verdin and Verdin (1999) <doi:10.1016/S0022-1694(99)00011-6>.
Author: David Blodgett [aut, cre] ,
Andrew Psoras [ctb]
Maintainer: David Blodgett <dblodgett@usgs.gov>
Diff between hydroloom versions 1.2.2 dated 2026-09-13 and 1.3.0 dated 2026-10-28
DESCRIPTION | 12 MD5 | 225 +-- NAMESPACE | 188 +- NEWS.md | 45 R/00_hydroloom.R | 476 +++---- R/accumulate_downstream.R | 674 +++++----- R/add_divergence.R | 986 +++++++-------- R/add_levelpaths.R | 664 +++++----- R/add_measures.R | 238 +-- R/add_pathlength.R | 156 +- R/add_streamorder-level.R | 610 ++++----- R/add_toids.R | 310 ++-- R/align_names.R | 278 ++-- R/check_hy_graph.R | 780 +++++------ R/check_valid.R | 518 +++---- R/disambiguate.R | 52 R/dissolve_polygons.R | 712 +++++----- R/get_bridges.R | 444 +++--- R/get_hydro_location.R | 18 R/get_subpath.R |only R/hy.R | 366 ++--- R/hy_classes.R | 1622 ++++++++++++------------ R/hydro_location_distance.R |only R/index_points_to_lines.R | 164 +- R/make_attribute_topology.R | 208 +-- R/make_index_ids.R | 974 +++++++------- R/make_node_topology.R | 539 ++++---- R/navigate_connected_paths.R | 404 +++--- R/navigate_network_dfs.R | 530 ++++---- R/navigation_network.R | 788 ++++++------ R/sort_network.R | 660 +++++----- R/subset_network.R | 254 +-- R/to_flownetwork.R | 270 ++-- R/utils.R | 682 +++++----- build/vignette.rds |binary inst/CITATION | 24 inst/doc/hydroloom.R | 352 ++--- inst/doc/hydroloom.Rmd | 698 +++++----- inst/doc/hydroloom.html | 1635 +++++++++++-------------- inst/extdata/new_hope_mainstems.R |only inst/extdata/new_hope_mainstems.csv |only man/accumulate_downstream.Rd | 236 +-- man/add_divergence.Rd | 262 ++-- man/add_hydro_location_distance.Rd |only man/add_levelpaths.Rd | 234 +-- man/add_measures.Rd | 100 - man/add_pathlength.Rd | 84 - man/add_pfafstetter.Rd | 200 +-- man/add_return_divergence.Rd | 142 +- man/add_streamlevel.Rd | 136 +- man/add_streamorder.Rd | 114 - man/add_toids.Rd | 110 - man/add_topo_sort.Rd | 78 - man/check_hy_graph.Rd | 204 +-- man/check_valid.Rd | 82 - man/disambiguate_indexes.Rd | 134 +- man/dissolve_polygons.Rd | 288 ++-- man/format_index_ids.Rd | 46 man/get_bridge_flowlines.Rd | 114 - man/get_confluences.Rd |only man/get_hydro_location.Rd | 72 - man/get_node.Rd | 72 - man/get_partial_length.Rd | 78 - man/get_subpath.Rd |only man/hy.Rd | 84 - man/hy_capabilities.Rd | 62 man/hy_flownetwork.Rd | 188 +- man/hy_network_type.Rd | 62 man/index_hydro_location_distance.Rd |only man/index_points_to_lines.Rd | 279 ++-- man/index_points_to_waterbodies.Rd | 114 - man/is_dendritic.Rd | 60 man/make_attribute_topology.Rd | 100 - man/make_fromids.Rd | 52 man/make_index_ids.Rd | 156 +- man/make_node_topology.Rd | 132 +- man/navigate_connected_paths.Rd | 86 - man/navigate_hydro_network.Rd | 176 +- man/navigate_network_dfs.Rd | 130 - man/rename_geometry.Rd | 52 man/rescale_measures.Rd | 70 - man/sort_network.Rd | 156 +- man/subset_network.Rd | 128 - man/to_flownetwork.Rd | 122 - tests/testthat.R | 24 tests/testthat/data/diversions.csv | 120 - tests/testthat/data/diversions.geojson | 132 +- tests/testthat/data/simple_diversions.geojson | 78 - tests/testthat/helper-mainstems.R |only tests/testthat/test_accumulate.R | 508 +++---- tests/testthat/test_add_divergence.R | 580 ++++---- tests/testthat/test_add_levelpaths.R | 358 ++--- tests/testthat/test_add_pathlength.R | 27 tests/testthat/test_add_pfafstetter.R | 1 tests/testthat/test_add_toids.R | 92 - tests/testthat/test_check_hy_graph.R | 512 +++---- tests/testthat/test_check_valid.R | 340 ++--- tests/testthat/test_dissolve_polygons.R | 490 +++---- tests/testthat/test_get_bridges.R | 594 ++++----- tests/testthat/test_get_hydro_location.R | 1 tests/testthat/test_get_partial_length.R | 90 - tests/testthat/test_get_subpath.R |only tests/testthat/test_hy_classes.R | 770 ++++++----- tests/testthat/test_hydro_location_distance.R |only tests/testthat/test_hydroloom.R | 114 - tests/testthat/test_index.R | 87 + tests/testthat/test_is_outlet.R | 78 - tests/testthat/test_make_attribute_topology.R | 76 - tests/testthat/test_make_index_ids.R | 408 +++--- tests/testthat/test_make_node_topology.R | 303 ++-- tests/testthat/test_navigate_connected_paths.R | 144 +- tests/testthat/test_navigate_network_dfs.R | 314 ++-- tests/testthat/test_outlet_conventions.R | 306 ++-- tests/testthat/test_sort_network.R | 520 +++---- tests/testthat/test_streamorder-level.R | 204 +-- tests/testthat/test_subset_network.R | 170 +- tests/testthat/test_to_flownetwork.R | 108 - tests/testthat/test_utils.R | 258 +-- vignettes/hydroloom.Rmd | 698 +++++----- 119 files changed, 15628 insertions(+), 15428 deletions(-)
Title: Structured Data Science Project Scaffolding
Description: Project scaffolding and workflow tools for reproducible data science.
Manages packages, tracks data integrity, handles database connections,
generates notebooks, and publishes to S3-compatible storage.
More information at <https://framework.table1.org>.
Author: Erik Westlund [aut, cre, cph]
Maintainer: Erik Westlund <erik@table1.org>
Diff between framework versions 1.0.2 dated 2026-02-17 and 1.1.0 dated 2026-10-28
framework-1.0.2/framework/man/dot-get_example_data_path.Rd |only framework-1.1.0/framework/DESCRIPTION | 14 framework-1.1.0/framework/MD5 | 92 ++- framework-1.1.0/framework/NAMESPACE | 31 - framework-1.1.0/framework/NEWS.md | 20 framework-1.1.0/framework/R/ai_context.R | 168 +------ framework-1.1.0/framework/R/ai_skills.R |only framework-1.1.0/framework/R/configure.R | 3 framework-1.1.0/framework/R/configure_ai.R | 43 - framework-1.1.0/framework/R/gui.R | 12 framework-1.1.0/framework/R/project_create.R | 75 +-- framework-1.1.0/framework/R/scaffold.R | 23 framework-1.1.0/framework/R/security_audit.R | 4 framework-1.1.0/framework/README.md | 16 framework-1.1.0/framework/inst/config_skeleton.yml | 1 framework-1.1.0/framework/inst/docs-export/categories.yml | 3 framework-1.1.0/framework/inst/gui/docs.db |binary framework-1.1.0/framework/inst/plumber.R | 18 framework-1.1.0/framework/inst/settings/global-settings-default.yml | 4 framework-1.1.0/framework/inst/settings/settings-catalog.yml | 12 framework-1.1.0/framework/inst/templates/ai-context.course.md | 204 -------- framework-1.1.0/framework/inst/templates/ai-context.presentation.md | 175 ------- framework-1.1.0/framework/inst/templates/ai-context.project.md | 226 --------- framework-1.1.0/framework/inst/templates/ai-context.project_sensitive.md | 234 +--------- framework-1.1.0/framework/inst/templates/framework-cheatsheet.md | 16 framework-1.1.0/framework/inst/templates/framework_global.yml | 3 framework-1.1.0/framework/inst/templates/gitignore-course | 4 framework-1.1.0/framework/inst/templates/gitignore-presentation | 4 framework-1.1.0/framework/inst/templates/gitignore-project | 4 framework-1.1.0/framework/inst/templates/gitignore-sensitive | 4 framework-1.1.0/framework/inst/templates/settings.project.yml | 1 framework-1.1.0/framework/inst/templates/settings.yml | 1 framework-1.1.0/framework/inst/templates/skills |only framework-1.1.0/framework/man/ai_generate_context.Rd | 6 framework-1.1.0/framework/man/ai_skills.Rd |only framework-1.1.0/framework/man/ai_skills_update.Rd |only framework-1.1.0/framework/man/configure_directories.Rd | 1 framework-1.1.0/framework/man/dot-ai_install_skills.Rd |only framework-1.1.0/framework/man/dot-ai_pointer_stub.Rd |only framework-1.1.0/framework/man/dot-ai_skills_for_type.Rd |only framework-1.1.0/framework/man/dot-create_ai_files.Rd | 13 framework-1.1.0/framework/man/dot-create_ai_instructions.Rd | 6 framework-1.1.0/framework/man/dot-generate_skills_section.Rd |only framework-1.1.0/framework/man/framework-package.Rd | 5 framework-1.1.0/framework/man/gui.Rd | 5 framework-1.1.0/framework/tests/testthat/test-ai-skills.R |only framework-1.1.0/framework/tests/testthat/test-configure-ai.R | 46 + framework-1.1.0/framework/tests/testthat/test-configure.R | 8 framework-1.1.0/framework/tests/testthat/test-doc-regressions.R | 3 framework-1.1.0/framework/tests/testthat/test-scaffold.R | 29 + 50 files changed, 481 insertions(+), 1056 deletions(-)
Title: Bayesian Estimation of DINA Model
Description: Estimate the Deterministic Input, Noisy "And" Gate (DINA)
cognitive diagnostic model parameters using the Gibbs sampler described
by Culpepper (2015) <doi:10.3102/1076998615595403>.
Author: Steven Andrew Culpepper [aut, cph] ,
James Joseph Balamuta [aut, cre]
Maintainer: James Joseph Balamuta <balamut2@illinois.edu>
Diff between dina versions 2.0.2 dated 2025-09-27 and 2.0.3 dated 2026-10-28
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 9 +++++++++ build/partial.rdb |binary src/dina-estimation-routine.cpp | 23 +++++++++++++---------- 5 files changed, 29 insertions(+), 17 deletions(-)
Title: Expand 'connector' Package for 'Databricks' Tables and Volumes
Description: Expands the 'connector' <https://github.com/NovoNordisk-OpenSource/connector> package and provides a convenient
interface for accessing and interacting with 'Databricks' <https://www.databricks.com> volumes and
tables directly from R.
Author: Vladimir Obucina [aut, cre],
Steffen Falgreen Larsen [aut],
Aksel Thomsen [aut],
Cervan Girard [aut],
Oliver Lundsgaard [ctb],
Skander Mulder [ctb],
Novo Nordisk A/S [cph]
Maintainer: Vladimir Obucina <vlob@novonordisk.com>
Diff between connector.databricks versions 0.1.0 dated 2025-09-05 and 0.2.0 dated 2026-10-28
DESCRIPTION | 16 +-- MD5 | 77 ++++++++++-------- NAMESPACE | 47 +++++++---- NEWS.md | 13 +++ R/connector.databricks-package.R |only R/sql.R |only R/sql_methods.R |only R/table.R | 34 ++++++-- R/table_methods.R | 22 +++-- R/volume.R | 18 +++- R/volume_utils.R | 78 +++++++++++++++--- README.md | 108 ++++++++----------------- build/vignette.rds |binary inst/WORDLIST | 10 +- inst/config/example_yaml.yaml | 8 - inst/doc/connector-databricks.R | 14 +-- inst/doc/connector-databricks.Rmd | 48 ++++++----- inst/doc/connector-databricks.html | 50 ++++++----- man/ConnectorDatabricksSQL.Rd |only man/ConnectorDatabricksTable.Rd | 130 ++++++++++++++++-------------- man/ConnectorDatabricksVolume.Rd | 140 ++++++++++++++++----------------- man/connector.databricks-package.Rd |only man/connector_databricks_sql.Rd |only man/connector_databricks_table.Rd | 6 + man/connector_databricks_volume.Rd | 2 man/figures/lifecycle-deprecated.svg |only man/figures/lifecycle-experimental.svg |only man/figures/lifecycle-stable.svg |only man/figures/lifecycle-superseded.svg |only man/list_content_cnt.Rd | 14 ++- man/log_read_connector.Rd | 2 man/log_remove_connector.Rd | 2 man/log_write_connector.Rd | 2 man/read_cnt.Rd | 14 ++- man/remove_cnt.Rd | 14 ++- man/tbl_cnt.Rd | 14 ++- man/write_cnt.Rd | 20 ++++ tests/testthat/helper-table.R | 19 ++++ tests/testthat/setup.R | 13 ++- tests/testthat/test-sql.R |only tests/testthat/test-table-utils.R | 23 ++--- tests/testthat/test-table.R | 36 +++++++- tests/testthat/test-volume.R | 48 ++++++----- tests/testthat/test-volume_utils.R | 27 ++++-- vignettes/connector-databricks.Rmd | 48 ++++++----- 45 files changed, 692 insertions(+), 425 deletions(-)
More information about connector.databricks at CRAN
Permanent link
Title: Bayes Factor Design for Two-Arm Binomial Trials
Description: Design and analysis of one- and two-stage clinical
trials using Bayes factors. Implements methods for binomial and
continuous endpoints, including point-null and directional hypotheses,
power calculations, and sample size calibration. Supports one-arm
trials with a single treatment arm and two-arm trials with treatment
and control arms. Includes methods for equivalence, non-inferiority,
and superiority designs.
Author: Riko Kelter [aut, cre]
Maintainer: Riko Kelter <rkelter@uni-koeln.de>
Diff between bfbin2arm versions 0.1.6 dated 2026-09-15 and 0.1.7 dated 2026-10-28
bfbin2arm-0.1.6/bfbin2arm/tests/testthat/test-powerbinbf01seq.R |only bfbin2arm-0.1.7/bfbin2arm/DESCRIPTION | 27 bfbin2arm-0.1.7/bfbin2arm/MD5 | 82 bfbin2arm-0.1.7/bfbin2arm/NAMESPACE | 27 bfbin2arm-0.1.7/bfbin2arm/R/bf_ttest_numeric.R |only bfbin2arm-0.1.7/bfbin2arm/R/design-twoarm-onestage-rope-directional-wrappers.R |only bfbin2arm-0.1.7/bfbin2arm/R/design_bf_ttest.R |only bfbin2arm-0.1.7/bfbin2arm/R/design_twoarm_onestage_rope_directional.R |only bfbin2arm-0.1.7/bfbin2arm/R/globals.R | 14 bfbin2arm-0.1.7/bfbin2arm/R/oc_bf_ttest.R |only bfbin2arm-0.1.7/bfbin2arm/R/priors_ttest.R |only bfbin2arm-0.1.7/bfbin2arm/R/s3-bf_ttest.R |only bfbin2arm-0.1.7/bfbin2arm/R/s3-twoarm_rope_directional_onestage.R |only bfbin2arm-0.1.7/bfbin2arm/R/utils_rope_twoarm_directional.R |only bfbin2arm-0.1.7/bfbin2arm/build/vignette.rds |binary bfbin2arm-0.1.7/bfbin2arm/inst/doc/bfbin2arm-calibrated-bayesian-t-tests.R |only bfbin2arm-0.1.7/bfbin2arm/inst/doc/bfbin2arm-calibrated-bayesian-t-tests.Rmd |only bfbin2arm-0.1.7/bfbin2arm/inst/doc/bfbin2arm-calibrated-bayesian-t-tests.html |only bfbin2arm-0.1.7/bfbin2arm/inst/doc/bfbin2arm-overview.Rmd | 2 bfbin2arm-0.1.7/bfbin2arm/inst/doc/bfbin2arm-overview.html | 59 bfbin2arm-0.1.7/bfbin2arm/inst/doc/bfbin2arm-singlearm-onestage.html | 4 bfbin2arm-0.1.7/bfbin2arm/inst/doc/bfbin2arm-singlearm-twostage_bayesian.html | 4 bfbin2arm-0.1.7/bfbin2arm/inst/doc/bfbin2arm-singlearm_twostage_frequentist.html | 4 bfbin2arm-0.1.7/bfbin2arm/inst/doc/bfbin2arm-singlearm_twostage_full.html | 30 bfbin2arm-0.1.7/bfbin2arm/inst/doc/bfbin2arm-singlearm_twostage_hybrid.html | 4 bfbin2arm-0.1.7/bfbin2arm/inst/doc/bfbin2arm-twoarm-twostage_Bayesian.html | 8 bfbin2arm-0.1.7/bfbin2arm/inst/doc/bfbin2arm-twoarm_onestage_Bayesian.Rmd | 2 bfbin2arm-0.1.7/bfbin2arm/inst/doc/bfbin2arm-twoarm_onestage_Bayesian.html | 22 bfbin2arm-0.1.7/bfbin2arm/man/bfbin2arm.Rd | 2 bfbin2arm-0.1.7/bfbin2arm/man/calibrate_bf_ttest.Rd |only bfbin2arm-0.1.7/bfbin2arm/man/design_twoarm_onestage_rope_directional.Rd |only bfbin2arm-0.1.7/bfbin2arm/man/design_twoarm_onestage_rope_ni.Rd |only bfbin2arm-0.1.7/bfbin2arm/man/design_twoarm_onestage_rope_nisup.Rd |only bfbin2arm-0.1.7/bfbin2arm/man/design_twoarm_onestage_rope_sup.Rd |only bfbin2arm-0.1.7/bfbin2arm/man/make_analysis_prior_greater.Rd |only bfbin2arm-0.1.7/bfbin2arm/man/make_analysis_prior_less_equal.Rd |only bfbin2arm-0.1.7/bfbin2arm/man/make_analysis_prior_two_sided.Rd |only bfbin2arm-0.1.7/bfbin2arm/man/make_design_prior_normal.Rd |only bfbin2arm-0.1.7/bfbin2arm/man/make_design_prior_point.Rd |only bfbin2arm-0.1.7/bfbin2arm/man/make_point_prior.Rd |only bfbin2arm-0.1.7/bfbin2arm/man/make_prior.Rd |only bfbin2arm-0.1.7/bfbin2arm/man/plot.bf_ttest_design.Rd |only bfbin2arm-0.1.7/bfbin2arm/man/plot.twoarm_rope_directional_onestage_design.Rd |only bfbin2arm-0.1.7/bfbin2arm/tests/testthat/helper-slow-tests.R |only bfbin2arm-0.1.7/bfbin2arm/tests/testthat/test-design-singlearm-twostage-rope-wrappers.R | 2 bfbin2arm-0.1.7/bfbin2arm/tests/testthat/test-design-singlearm-twostage-rope.R | 4 bfbin2arm-0.1.7/bfbin2arm/tests/testthat/test-optimal-twostage-all-tests.R | 1 bfbin2arm-0.1.7/bfbin2arm/tests/testthat/test-twoarm-directional-original.R |only bfbin2arm-0.1.7/bfbin2arm/tests/testthat/test-twoarm-directional-psock.R |only bfbin2arm-0.1.7/bfbin2arm/tests/testthat/test-twoarm-directional-single.R |only bfbin2arm-0.1.7/bfbin2arm/tests/testthat/test-utils-rope-twoarm-directional-freq-boundary.R |only bfbin2arm-0.1.7/bfbin2arm/tests/testthat/test-utils-rope-twoarm-directional-quantile-vs-adaptive.R |only bfbin2arm-0.1.7/bfbin2arm/vignettes/bfbin2arm-calibrated-bayesian-t-tests.Rmd |only bfbin2arm-0.1.7/bfbin2arm/vignettes/bfbin2arm-overview.Rmd | 2 bfbin2arm-0.1.7/bfbin2arm/vignettes/bfbin2arm-twoarm_onestage_Bayesian.Rmd | 2 bfbin2arm-0.1.7/bfbin2arm/vignettes/composite-lci-continuous.rds |only bfbin2arm-0.1.7/bfbin2arm/vignettes/composite_lci_no_pce.rds |only bfbin2arm-0.1.7/bfbin2arm/vignettes/figures/bfbin2am-onesample-t-test-ex3.png |only bfbin2arm-0.1.7/bfbin2arm/vignettes/figures/bfbin2arm-onesample-t-test-bayes.png |only bfbin2arm-0.1.7/bfbin2arm/vignettes/figures/bfbin2arm-onesample-t-test-ex1.png |only bfbin2arm-0.1.7/bfbin2arm/vignettes/figures/bfbin2arm-onesample-t-test-freq.png |only bfbin2arm-0.1.7/bfbin2arm/vignettes/references.bib | 3773 +++++----- 62 files changed, 2276 insertions(+), 1799 deletions(-)
Title: Cosmic Microwave Background Data Analysis
Description: Tools for handling and analysing spherical data on a HEALPix grid,
with applications to cosmic microwave background maps. Supports reading FITS
files, converting between spherical and Cartesian coordinates and HEALPix
ordering schemes, selecting sky regions, sampling pixels, and visualising
maps. Implements empirical covariance, correlation and variogram estimation,
covariance model fitting, angular power spectrum estimation, and
distributional and entropy-based comparisons of spherical data. The package
and its methods are described by Fryer, Li and Olenko (2020)
<doi:10.32614/RJ-2020-012>.
Author: Daniel Fryer [aut, cre] ,
Andriy Olenko [aut] ,
Ming Li [aut] ,
Yuguang Wang [aut]
Maintainer: Daniel Fryer <d.fryer@latrobe.edu.au>
This is a re-admission after prior archival of version 1.1.3 dated 2021-12-01
Diff between rcosmo versions 1.1.3 dated 2021-12-01 and 1.1.5 dated 2026-10-28
rcosmo-1.1.3/rcosmo/LICENSE |only rcosmo-1.1.5/rcosmo/DESCRIPTION | 32 rcosmo-1.1.5/rcosmo/MD5 | 318 rcosmo-1.1.5/rcosmo/NAMESPACE | 264 rcosmo-1.1.5/rcosmo/NEWS.md | 150 rcosmo-1.1.5/rcosmo/R/CMBDat.R | 485 rcosmo-1.1.5/rcosmo/R/CMBDataFrame.R | 1003 - rcosmo-1.1.5/rcosmo/R/CMBDataFrameGenerics.R | 2771 ++--- rcosmo-1.1.5/rcosmo/R/CMBDataFrameHelpers.R | 22 rcosmo-1.1.5/rcosmo/R/CMBWindow.R | 334 rcosmo-1.1.5/rcosmo/R/CMBWindowGenerics.R | 913 - rcosmo-1.1.5/rcosmo/R/CMBWindowHelpers.R | 12 rcosmo-1.1.5/rcosmo/R/Conversion.R | 1193 +- rcosmo-1.1.5/rcosmo/R/DeveloperHelpers.R | 50 rcosmo-1.1.5/rcosmo/R/DisplayHEALPix.R | 642 - rcosmo-1.1.5/rcosmo/R/Downloaders.R | 400 rcosmo-1.1.5/rcosmo/R/Geometry.R | 488 rcosmo-1.1.5/rcosmo/R/HPDataFrame.R | 2173 ++-- rcosmo-1.1.5/rcosmo/R/MathHelpers.R | 346 rcosmo-1.1.5/rcosmo/R/NestSearch.R | 1262 +- rcosmo-1.1.5/rcosmo/R/NewGenerics.R | 354 rcosmo-1.1.5/rcosmo/R/RcppExports.R | 176 rcosmo-1.1.5/rcosmo/R/Statistics.R | 5021 ++++------ rcosmo-1.1.5/rcosmo/R/SubWindow.R | 664 - rcosmo-1.1.5/rcosmo/R/rcosmo.R | 73 rcosmo-1.1.5/rcosmo/R/zzz.R | 6 rcosmo-1.1.5/rcosmo/README.md | 4 rcosmo-1.1.5/rcosmo/inst |only rcosmo-1.1.5/rcosmo/man/CMBDat.Rd | 95 rcosmo-1.1.5/rcosmo/man/CMBDataFrame.Rd | 187 rcosmo-1.1.5/rcosmo/man/CMBWindow.Rd | 115 rcosmo-1.1.5/rcosmo/man/HPDataFrame.Rd | 278 rcosmo-1.1.5/rcosmo/man/ancestor.Rd | 51 rcosmo-1.1.5/rcosmo/man/areCompatibleCMBDFs.Rd | 69 rcosmo-1.1.5/rcosmo/man/as.CMBDataFrame.Rd | 156 rcosmo-1.1.5/rcosmo/man/assumedConvex-set.Rd | 34 rcosmo-1.1.5/rcosmo/man/assumedConvex.Rd | 61 rcosmo-1.1.5/rcosmo/man/assumedUniquePix.Rd | 68 rcosmo-1.1.5/rcosmo/man/baseNeighbours.Rd | 55 rcosmo-1.1.5/rcosmo/man/borderPattern.Rd | 44 rcosmo-1.1.5/rcosmo/man/cbind.CMBDataFrame.Rd | 63 rcosmo-1.1.5/rcosmo/man/chi2CMB.Rd | 84 rcosmo-1.1.5/rcosmo/man/children.Rd | 43 rcosmo-1.1.5/rcosmo/man/coords-set-.CMBDataFrame.Rd | 70 rcosmo-1.1.5/rcosmo/man/coords-set-.CMBWindow.Rd | 34 rcosmo-1.1.5/rcosmo/man/coords-set-.HPDataFrame.Rd | 68 rcosmo-1.1.5/rcosmo/man/coords-set-.data.frame.Rd | 66 rcosmo-1.1.5/rcosmo/man/coords-set.Rd | 38 rcosmo-1.1.5/rcosmo/man/coords.CMBDataFrame.Rd | 100 rcosmo-1.1.5/rcosmo/man/coords.CMBWindow.Rd | 90 rcosmo-1.1.5/rcosmo/man/coords.HPDataFrame.Rd | 124 rcosmo-1.1.5/rcosmo/man/coords.Rd | 51 rcosmo-1.1.5/rcosmo/man/coords.data.frame.Rd | 90 rcosmo-1.1.5/rcosmo/man/corrCMB.Rd | 177 rcosmo-1.1.5/rcosmo/man/covCMB.Rd | 178 rcosmo-1.1.5/rcosmo/man/covPwSp.Rd | 97 rcosmo-1.1.5/rcosmo/man/covmodelCMB.Rd | 174 rcosmo-1.1.5/rcosmo/man/displayPixelBoundaries.Rd | 128 rcosmo-1.1.5/rcosmo/man/displayPixels.Rd | 153 rcosmo-1.1.5/rcosmo/man/downloadCMBMap.Rd | 122 rcosmo-1.1.5/rcosmo/man/downloadCMBPS.Rd | 131 rcosmo-1.1.5/rcosmo/man/entropyCMB.Rd | 76 rcosmo-1.1.5/rcosmo/man/exprob.Rd | 73 rcosmo-1.1.5/rcosmo/man/extrCMB.Rd | 72 rcosmo-1.1.5/rcosmo/man/fRen.Rd | 120 rcosmo-1.1.5/rcosmo/man/fmf.Rd | 82 rcosmo-1.1.5/rcosmo/man/geo2sph.Rd | 58 rcosmo-1.1.5/rcosmo/man/geoAngle.Rd | 74 rcosmo-1.1.5/rcosmo/man/geoArea.CMBDataFrame.Rd | 66 rcosmo-1.1.5/rcosmo/man/geoArea.CMBWindow.Rd | 52 rcosmo-1.1.5/rcosmo/man/geoArea.HPDataFrame.Rd | 64 rcosmo-1.1.5/rcosmo/man/geoArea.Rd | 45 rcosmo-1.1.5/rcosmo/man/geoDist.Rd | 86 rcosmo-1.1.5/rcosmo/man/header.Rd | 50 rcosmo-1.1.5/rcosmo/man/healpixCentered.Rd | 70 rcosmo-1.1.5/rcosmo/man/ibp2p.Rd | 53 rcosmo-1.1.5/rcosmo/man/is.CMBDat.Rd | 48 rcosmo-1.1.5/rcosmo/man/is.CMBDataFrame.Rd | 52 rcosmo-1.1.5/rcosmo/man/is.CMBWindow.Rd | 46 rcosmo-1.1.5/rcosmo/man/is.HPDataFrame.Rd | 52 rcosmo-1.1.5/rcosmo/man/jacobiPol.Rd | 64 rcosmo-1.1.5/rcosmo/man/linesCMB.Rd | 111 rcosmo-1.1.5/rcosmo/man/maxDist.Rd | 116 rcosmo-1.1.5/rcosmo/man/maxWindowDist.Rd | 52 rcosmo-1.1.5/rcosmo/man/minDist.Rd | 118 rcosmo-1.1.5/rcosmo/man/minDist2nside.Rd | 63 rcosmo-1.1.5/rcosmo/man/neighbours.Rd | 79 rcosmo-1.1.5/rcosmo/man/nest2ring.Rd | 64 rcosmo-1.1.5/rcosmo/man/nestSearch.Rd | 142 rcosmo-1.1.5/rcosmo/man/nestSearch_step.Rd | 50 rcosmo-1.1.5/rcosmo/man/nside.CMBDataFrame.Rd | 44 rcosmo-1.1.5/rcosmo/man/nside.HPDataFrame.Rd | 46 rcosmo-1.1.5/rcosmo/man/nside.Rd | 41 rcosmo-1.1.5/rcosmo/man/numeric2col.Rd | 63 rcosmo-1.1.5/rcosmo/man/onBPBoundary.Rd | 41 rcosmo-1.1.5/rcosmo/man/ordering-set-.CMBDataFrame.Rd | 52 rcosmo-1.1.5/rcosmo/man/ordering-set-.HPDataFrame.Rd | 34 rcosmo-1.1.5/rcosmo/man/ordering-set.Rd | 44 rcosmo-1.1.5/rcosmo/man/ordering.CMBDataFrame.Rd | 72 rcosmo-1.1.5/rcosmo/man/ordering.HPDataFrame.Rd | 70 rcosmo-1.1.5/rcosmo/man/ordering.Rd | 45 rcosmo-1.1.5/rcosmo/man/p2bp.Rd | 47 rcosmo-1.1.5/rcosmo/man/p2ibp.Rd | 49 rcosmo-1.1.5/rcosmo/man/parent.Rd | 47 rcosmo-1.1.5/rcosmo/man/pix-set-.CMBDataFrame.Rd | 34 rcosmo-1.1.5/rcosmo/man/pix-set.Rd | 44 rcosmo-1.1.5/rcosmo/man/pix.CMBDataFrame.Rd | 70 rcosmo-1.1.5/rcosmo/man/pix.HPDataFrame.Rd | 66 rcosmo-1.1.5/rcosmo/man/pix.Rd | 45 rcosmo-1.1.5/rcosmo/man/pix2coords.Rd | 60 rcosmo-1.1.5/rcosmo/man/pixelArea.Rd | 60 rcosmo-1.1.5/rcosmo/man/pixelWindow.Rd | 66 rcosmo-1.1.5/rcosmo/man/plot.CMBCorrelation.Rd | 65 rcosmo-1.1.5/rcosmo/man/plot.CMBCovariance.Rd | 63 rcosmo-1.1.5/rcosmo/man/plot.CMBDataFrame.Rd | 183 rcosmo-1.1.5/rcosmo/man/plot.CMBWindow.Rd | 129 rcosmo-1.1.5/rcosmo/man/plot.HPDataFrame.Rd | 200 rcosmo-1.1.5/rcosmo/man/plot.variogram.Rd | 55 rcosmo-1.1.5/rcosmo/man/plotAngDis.Rd | 64 rcosmo-1.1.5/rcosmo/man/plotcovmodelCMB.Rd | 102 rcosmo-1.1.5/rcosmo/man/plotvariogram.Rd | 102 rcosmo-1.1.5/rcosmo/man/practicalRangeCMB.Rd | 92 rcosmo-1.1.5/rcosmo/man/print.CMBDataFrame.Rd | 51 rcosmo-1.1.5/rcosmo/man/print.HPDataFrame.Rd | 50 rcosmo-1.1.5/rcosmo/man/print.summary.CMBDataFrame.Rd | 37 rcosmo-1.1.5/rcosmo/man/print.summary.CMBWindow.Rd | 37 rcosmo-1.1.5/rcosmo/man/print.summary.HPDataFrame.Rd | 37 rcosmo-1.1.5/rcosmo/man/pwSpCorr.Rd | 74 rcosmo-1.1.5/rcosmo/man/qqnormWin.Rd | 79 rcosmo-1.1.5/rcosmo/man/qqplotWin.Rd | 87 rcosmo-1.1.5/rcosmo/man/qstat.Rd | 87 rcosmo-1.1.5/rcosmo/man/rbind.CMBDataFrame.Rd | 107 rcosmo-1.1.5/rcosmo/man/rcosmo.Rd | 92 rcosmo-1.1.5/rcosmo/man/resolution.Rd | 50 rcosmo-1.1.5/rcosmo/man/ring2nest.Rd | 56 rcosmo-1.1.5/rcosmo/man/sampleCMB.Rd | 64 rcosmo-1.1.5/rcosmo/man/separatingNside.Rd | 52 rcosmo-1.1.5/rcosmo/man/siblings.Rd | 45 rcosmo-1.1.5/rcosmo/man/sphericalHarmonics.Rd | 96 rcosmo-1.1.5/rcosmo/man/subWindow.Rd | 120 rcosmo-1.1.5/rcosmo/man/summary.CMBDataFrame.Rd | 75 rcosmo-1.1.5/rcosmo/man/summary.CMBWindow.Rd | 58 rcosmo-1.1.5/rcosmo/man/summary.HPDataFrame.Rd | 66 rcosmo-1.1.5/rcosmo/man/triangulate.Rd | 114 rcosmo-1.1.5/rcosmo/man/variofitCMB.Rd | 224 rcosmo-1.1.5/rcosmo/man/variogramCMB.Rd | 175 rcosmo-1.1.5/rcosmo/man/winType-set.Rd | 56 rcosmo-1.1.5/rcosmo/man/winType.Rd | 100 rcosmo-1.1.5/rcosmo/man/window-set-.CMBDataFrame.Rd | 34 rcosmo-1.1.5/rcosmo/man/window-set.Rd | 48 rcosmo-1.1.5/rcosmo/man/window.CMBDat.Rd | 112 rcosmo-1.1.5/rcosmo/man/window.CMBDataFrame.Rd | 324 rcosmo-1.1.5/rcosmo/man/window.HPDataFrame.Rd | 154 rcosmo-1.1.5/rcosmo/man/window.Rd | 49 rcosmo-1.1.5/rcosmo/man/window.data.frame.Rd | 122 rcosmo-1.1.5/rcosmo/tests/testthat/references/readFITScmb_1204_5cols_10rows.rds |binary rcosmo-1.1.5/rcosmo/tests/testthat/test_CMBDat.R | 14 rcosmo-1.1.5/rcosmo/tests/testthat/test_CMBDataFrame.R | 388 rcosmo-1.1.5/rcosmo/tests/testthat/test_CMBWindow.R | 242 rcosmo-1.1.5/rcosmo/tests/testthat/test_conversions.R | 382 rcosmo-1.1.5/rcosmo/tests/testthat/test_cran_review.R |only 161 files changed, 15332 insertions(+), 15369 deletions(-)
Title: Relative Survival, AER and SMR Based on French Death Rates
Description: It computes Relative survival, AER and SMR based on French death rates.
Author: Hugo Varet [aut, cre],
Jean-Philippe Jais [aut]
Maintainer: Hugo Varet <varethugo@gmail.com>
Diff between survexp.fr versions 1.3 dated 2026-10-27 and 1.4 dated 2026-10-28
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- NEWS | 6 ++++++ 3 files changed, 12 insertions(+), 6 deletions(-)
More information about PortinariColors at CRAN
Permanent link
Title: Exact Derivatives via Automatic Differentiation
Description: Automatic differentiation for R functions written with
supported scalar arithmetic and mathematical operations. Provides a
composable derivative operator D that computes gradients, Hessians,
Jacobians, and arbitrary-order derivative tensors at machine precision.
D(D(f)) gives Hessians, D(D(D(f))) gives third-order tensors for
skewness of maximum likelihood estimators, and so on to higher orders.
Supports loops and executed branches composed of supported operations.
Uses nested dual numbers without finite difference truncation error;
floating-point rounding and conditioning still affect results.
Author: Alexander Towell [aut, cre]
Maintainer: Alexander Towell <queelius@gmail.com>
Diff between nabla versions 0.7.1 dated 2026-02-10 and 0.7.2 dated 2026-10-28
DESCRIPTION | 15 +++++++----- MD5 | 19 ++++++++-------- NEWS.md | 11 +++++++++ R/dual-arithmetic.R | 12 ++++++---- R/dual-math.R | 14 +++++++++--- R/nabla-package.R | 4 ++- README.md | 44 +++++++++++++++++++++++++++----------- man/nabla-package.Rd | 4 ++- tests/testthat/test-coverage.R | 4 +-- tests/testthat/test-math.R | 2 - tests/testthat/test-zero-powers.R |only 11 files changed, 90 insertions(+), 39 deletions(-)
Title: 'grid' Pattern Grobs
Description: Provides 'grid' grobs that fill in a user-defined area with various patterns. Includes enhanced versions of the geometric and image-based patterns originally contained in the 'ggpattern' package as well as original 'pch', 'polygon_tiling', 'regular_polygon', 'rose', 'text', 'wave', and 'weave' patterns plus support for custom user-defined patterns.
Author: Trevor L. Davis [aut, cre] ,
Mike FC [aut] ,
ggplot2 authors [ctb]
Maintainer: Trevor L. Davis <trevor.l.davis@gmail.com>
Diff between gridpattern versions 1.4.2 dated 2026-06-23 and 1.5.1 dated 2026-10-28
gridpattern-1.4.2/gridpattern/tests/testthat/Rplots.pdf |only gridpattern-1.5.1/gridpattern/DESCRIPTION | 8 gridpattern-1.5.1/gridpattern/MD5 | 95 gridpattern-1.5.1/gridpattern/NAMESPACE | 9 gridpattern-1.5.1/gridpattern/NEWS.md | 54 gridpattern-1.5.1/gridpattern/R/grid-pattern.R | 147 - gridpattern-1.5.1/gridpattern/R/gridpattern-package.R | 6 gridpattern-1.5.1/gridpattern/R/pattern-array-ambient.R | 2 gridpattern-1.5.1/gridpattern/R/pattern-array-image.R | 2 gridpattern-1.5.1/gridpattern/R/pattern-array-magick.R | 6 gridpattern-1.5.1/gridpattern/R/pattern-array-placeholder.R | 2 gridpattern-1.5.1/gridpattern/R/pattern-array-plasma.R | 4 gridpattern-1.5.1/gridpattern/R/pattern-both-gradient.R | 2 gridpattern-1.5.1/gridpattern/R/pattern-both-hatch.R | 22 gridpattern-1.5.1/gridpattern/R/pattern-both-line.R | 2 gridpattern-1.5.1/gridpattern/R/pattern-both-rose.R | 2 gridpattern-1.5.1/gridpattern/R/pattern-both-text.R | 2 gridpattern-1.5.1/gridpattern/R/pattern-geometry-circle.R | 2 gridpattern-1.5.1/gridpattern/R/pattern-geometry-crosshatch.R | 2 gridpattern-1.5.1/gridpattern/R/pattern-geometry-fill.R | 2 gridpattern-1.5.1/gridpattern/R/pattern-geometry-none.R | 2 gridpattern-1.5.1/gridpattern/R/pattern-geometry-pch.R | 2 gridpattern-1.5.1/gridpattern/R/pattern-geometry-regular_polygon.R | 2 gridpattern-1.5.1/gridpattern/R/pattern-geometry-stripe.R | 2 gridpattern-1.5.1/gridpattern/R/pattern-geometry-tiling.R | 140 - gridpattern-1.5.1/gridpattern/R/pattern-geometry-wave.R | 12 gridpattern-1.5.1/gridpattern/R/pattern-geometry-weave.R | 2 gridpattern-1.5.1/gridpattern/R/pattern-pattern-aRtsy.R | 2 gridpattern-1.5.1/gridpattern/R/registry.R |only gridpattern-1.5.1/gridpattern/R/utils-magick-pattern.R | 2 gridpattern-1.5.1/gridpattern/R/utils-params.R | 174 - gridpattern-1.5.1/gridpattern/R/zzz.R | 3 gridpattern-1.5.1/gridpattern/README.md | 10 gridpattern-1.5.1/gridpattern/build/vignette.rds |binary gridpattern-1.5.1/gridpattern/inst/doc/developing-patterns.R | 45 gridpattern-1.5.1/gridpattern/inst/doc/developing-patterns.Rmd | 158 - gridpattern-1.5.1/gridpattern/inst/doc/developing-patterns.html | 269 + gridpattern-1.5.1/gridpattern/inst/doc/hatching.html | 169 - gridpattern-1.5.1/gridpattern/inst/doc/tiling.html | 1355 +++++----- gridpattern-1.5.1/gridpattern/man/figures/README-wave-1.png |binary gridpattern-1.5.1/gridpattern/man/grid.pattern.Rd | 9 gridpattern-1.5.1/gridpattern/man/grid.pattern_magick.Rd | 2 gridpattern-1.5.1/gridpattern/man/gridpattern-package.Rd | 6 gridpattern-1.5.1/gridpattern/man/local_pattern.Rd |only gridpattern-1.5.1/gridpattern/man/prefer_pattern.Rd |only gridpattern-1.5.1/gridpattern/man/register_pattern.Rd |only gridpattern-1.5.1/gridpattern/man/registered_patterns.Rd |only gridpattern-1.5.1/gridpattern/tests/testthat/test_array.R | 2 gridpattern-1.5.1/gridpattern/tests/testthat/test_geometry.R | 52 gridpattern-1.5.1/gridpattern/tests/testthat/test_registry.R |only gridpattern-1.5.1/gridpattern/tests/testthat/test_utils.R | 33 gridpattern-1.5.1/gridpattern/vignettes/developing-patterns.Rmd | 158 - 52 files changed, 1584 insertions(+), 1398 deletions(-)
Title: Wearable Accelerometer Data File Readers
Description: Reads data collected from wearable acceleratometers as used in sleep and physical activity research. Currently supports file formats: binary data from 'GENEActiv' <https://activinsights.com/>, .bin-format from GENEA devices (not for sale), and .cwa-format from 'Axivity' <https://axivity.com>. Further, it has functions for reading text files with epoch level aggregates from 'Actical', 'Fitbit', 'Actiwatch', 'ActiGraph', and 'PhilipsHealthBand'. Primarily designed to complement R package GGIR <https://CRAN.R-project.org/package=GGIR>.
Author: Vincent T van Hees [aut, cre],
Patrick Bos [aut] ,
Lena Kushleyeva [ctb],
Jing Hua Zhao [ctb],
Evgeny Mirkes [ctb],
Dan Jackson [ctb],
Jairo H Migueles [ctb],
John Muschelli [ctb],
Jia Ying Chua [ctb],
Medical Research Council UK [cph, fnd],
Acceltin [...truncated...]
Maintainer: Vincent T van Hees <v.vanhees@accelting.com>
Diff between GGIRread versions 1.0.11 dated 2026-09-18 and 1.2.0 dated 2026-10-28
DESCRIPTION | 12 MD5 | 22 - NEWS.md | 25 + R/RcppExports.R | 8 R/readAxivity.R | 473 ++++------------------------- man/GGIRread-package.Rd | 4 man/readAxivity.Rd | 85 +++-- src/RcppExports.cpp | 36 ++ src/decodeAxivityBlock.cpp |only src/init.c | 5 src/processAxivityBlocks.cpp |only tests/testthat/test_decodeAxivityBlock.R |only tests/testthat/test_processAxivityBlocks.R |only tests/testthat/test_readAxivity.R | 255 ++++++++++++++- 14 files changed, 456 insertions(+), 469 deletions(-)
Title: Structured Random Variables for Reliability System Distributions
Description: Extends the 'algebraic.dist' distribution algebra to
random variables with internal structure: coherent reliability
systems decomposed into components arranged by a structure function
(series, parallel, k-out-of-n, bridge, and arbitrary topologies via
minimal path sets). Every 'dist_structure' object is a 'dist', so
the full distribution algebra (mean, vcov, sampler, surv, cdf) works
automatically via default methods that compose component-level
distributions through the topology. Adds structural queries:
structure function evaluation, minimal path and cut sets, system
signature, critical states, dual, Birnbaum structural importance,
and system reliability. Topology shortcut constructors (series_dist,
parallel_dist, kofn_dist, bridge_dist) produce ready-to-use dists
from component dists and a chosen structure.
Author: Alexander Towell [aut, cre]
Maintainer: Alexander Towell <lex@metafunctor.com>
Diff between dist.structure versions 0.5.0 dated 2026-05-12 and 0.5.1 dated 2026-10-28
DESCRIPTION | 6 +++--- MD5 | 17 +++++++++-------- NEWS.md | 8 ++++++++ R/exp_kofn.R | 6 +++--- R/exp_parallel.R | 2 +- R/exp_series.R | 5 +++-- R/wei_homogeneous_series.R | 3 ++- R/wei_kofn.R | 6 ++++-- R/wei_series.R | 1 + tests/testthat/test-support.R |only 10 files changed, 34 insertions(+), 20 deletions(-)
More information about dist.structure at CRAN
Permanent link
Title: A Collection of Functions for Directional Data Analysis
Description: A collection of functions for directional data (including massive data, with millions of observations) analysis.
Hypothesis testing, discriminant and regression analysis, MLE of distributions and more are included.
The standard textbook for such data is the "Directional Statistics" by Mardia, K. V. and Jupp, P. E. (2000).
Other references include:
a) Paine J.P., Preston S.P., Tsagris M. and Wood A.T.A. (2018). "An elliptically symmetric angular Gaussian distribution". Statistics and Computing 28(3): 689-697. <doi:10.1007/s11222-017-9756-4>.
b) Tsagris M. and Alenazi A. (2019). "Comparison of discriminant analysis methods on the sphere". Communications in Statistics: Case Studies, Data Analysis and Applications 5(4):467--491. <doi:10.1080/23737484.2019.1684854>.
c) Paine J.P., Preston S.P., Tsagris M. and Wood A.T.A. (2020). "Spherical regression models with general covariates and anisotropic errors". Statistics and Computing 30(1): 153--165. <doi:10.1007/s11222-019-09872 [...truncated...]
Author: Michail Tsagris [aut, cre],
Giorgos Athineou [aut],
Christos Adam [aut],
Zehao Yu [aut],
Anamul Sajib [ctb],
Eli Amson [ctb],
Micah J. Waldstein [ctb],
Panagiotis Papastamoulis [ctb]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between Directional versions 7.9 dated 2026-10-05 and 8.0 dated 2026-10-28
DESCRIPTION | 8 ++++---- MD5 | 13 +++++++------ R/dirda.R | 2 +- R/esag.nr.R |only R/kent.mle.R | 32 ++++++++++++++++++++++---------- man/Directional-package.Rd | 4 ++-- man/esag.mle.Rd | 20 +++++++++++++++----- man/kent.mle.Rd | 19 ++++++++++++------- 8 files changed, 63 insertions(+), 35 deletions(-)
More information about creditratingsystem at CRAN
Permanent link
More information about actuarialfitdist at CRAN
Permanent link
Title: 'jsTree' Bindings for 'Shiny'
Description: Bindings to 'jsTree' <https://www.jstree.com>, a 'JavaScript'
library for interactive trees, to enable rich, editable trees in 'Shiny'
applications. Trees can be searched, checked, rearranged,
styled and remembered across visits, loaded lazily for very large
hierarchies, and built from data frames, 'data.tree' objects or
ontologies.
Author: Trestle Technology, LLC [aut],
Jeff Allen [aut],
Institut de Radioprotection et de Sûrete Nucleaire [cph],
Ivan Bozhanov [ctb, cph] ,
Orange Hill Development [ctb, cph] theme),
Accademia di Belle Arti di Urbino [cph] ,
Mike Schaffer [ctb],
Timm Dank [...truncated...]
Maintainer: Michael Bell <bell_michael_a@lilly.com>
Diff between shinyTree versions 0.3.1 dated 2023-08-07 and 1.0.0 dated 2026-10-28
shinyTree-0.3.1/shinyTree/NEWS |only shinyTree-0.3.1/shinyTree/inst/examples/21-options/app_setState_refresh.R |only shinyTree-0.3.1/shinyTree/inst/www/jsTree-3.3.7/libs |only shinyTree-0.3.1/shinyTree/tests/testthat/test_tree_interactive.R |only shinyTree-1.0.0/shinyTree/DESCRIPTION | 39 shinyTree-1.0.0/shinyTree/MD5 | 215 +- shinyTree-1.0.0/shinyTree/NAMESPACE | 13 shinyTree-1.0.0/shinyTree/NEWS.md |only shinyTree-1.0.0/shinyTree/R/data.tree-conversion.R | 102 - shinyTree-1.0.0/shinyTree/R/get-checked.R | 98 - shinyTree-1.0.0/shinyTree/R/get-selected.R | 171 +- shinyTree-1.0.0/shinyTree/R/init.R | 90 - shinyTree-1.0.0/shinyTree/R/ontology.R |only shinyTree-1.0.0/shinyTree/R/render-tree-lazy.R |only shinyTree-1.0.0/shinyTree/R/render-tree.R | 277 +++ shinyTree-1.0.0/shinyTree/R/render-tree_async.R | 136 - shinyTree-1.0.0/shinyTree/R/shiny-tree.R | 274 ++- shinyTree-1.0.0/shinyTree/R/tree_traversal.R | 6 shinyTree-1.0.0/shinyTree/R/update-tree.R | 354 +++- shinyTree-1.0.0/shinyTree/README.md | 199 +- shinyTree-1.0.0/shinyTree/inst/COPYRIGHTS |only shinyTree-1.0.0/shinyTree/inst/WORDLIST |only shinyTree-1.0.0/shinyTree/inst/examples/01-simple/ui.R | 2 shinyTree-1.0.0/shinyTree/inst/examples/02-attributes/server.R | 3 shinyTree-1.0.0/shinyTree/inst/examples/02-attributes/ui.R | 2 shinyTree-1.0.0/shinyTree/inst/examples/03-checkbox/ui.R | 2 shinyTree-1.0.0/shinyTree/inst/examples/04-selected/server.R | 89 - shinyTree-1.0.0/shinyTree/inst/examples/04-selected/ui.R | 33 shinyTree-1.0.0/shinyTree/inst/examples/05-structure/ui.R | 2 shinyTree-1.0.0/shinyTree/inst/examples/06-search/ui.R | 2 shinyTree-1.0.0/shinyTree/inst/examples/07-drag-and-drop/ui.R | 2 shinyTree-1.0.0/shinyTree/inst/examples/08-class/server.R | 17 shinyTree-1.0.0/shinyTree/inst/examples/08-class/ui.R | 12 shinyTree-1.0.0/shinyTree/inst/examples/11-tree-update/server.R | 66 shinyTree-1.0.0/shinyTree/inst/examples/11-tree-update/ui.R | 54 shinyTree-1.0.0/shinyTree/inst/examples/12-types/ui.R | 3 shinyTree-1.0.0/shinyTree/inst/examples/13-icons/ui.R | 2 shinyTree-1.0.0/shinyTree/inst/examples/14-files/server.R | 2 shinyTree-1.0.0/shinyTree/inst/examples/14-files/ui.R | 2 shinyTree-1.0.0/shinyTree/inst/examples/15-data/server.R | 2 shinyTree-1.0.0/shinyTree/inst/examples/15-data/ui.R | 4 shinyTree-1.0.0/shinyTree/inst/examples/16-async/server.R | 2 shinyTree-1.0.0/shinyTree/inst/examples/17-contextmenu/ui.R | 2 shinyTree-1.0.0/shinyTree/inst/examples/18-modules/app.R | 2 shinyTree-1.0.0/shinyTree/inst/examples/20-api/ui.R | 10 shinyTree-1.0.0/shinyTree/inst/examples/21-options/app.R |only shinyTree-1.0.0/shinyTree/inst/examples/22-dfToTree/server.R | 5 shinyTree-1.0.0/shinyTree/inst/examples/22-dfToTree/ui.R | 3 shinyTree-1.0.0/shinyTree/inst/examples/23-file-icons/server.R | 2 shinyTree-1.0.0/shinyTree/inst/examples/24-checkbox-options/server.R | 11 shinyTree-1.0.0/shinyTree/inst/examples/24-checkbox-options/ui.R | 11 shinyTree-1.0.0/shinyTree/inst/examples/25-duplicate-names |only shinyTree-1.0.0/shinyTree/inst/examples/26-state |only shinyTree-1.0.0/shinyTree/inst/examples/27-lazy |only shinyTree-1.0.0/shinyTree/inst/examples/28-ontology |only shinyTree-1.0.0/shinyTree/inst/www/shinyTree.css |only shinyTree-1.0.0/shinyTree/inst/www/shinyTree.js | 850 ++++++++-- shinyTree-1.0.0/shinyTree/man/depth.Rd | 1 shinyTree-1.0.0/shinyTree/man/dfToTree.Rd | 16 shinyTree-1.0.0/shinyTree/man/dfrapply.Rd | 1 shinyTree-1.0.0/shinyTree/man/expandTree.Rd |only shinyTree-1.0.0/shinyTree/man/get_checked.Rd | 32 shinyTree-1.0.0/shinyTree/man/get_selected.Rd | 37 shinyTree-1.0.0/shinyTree/man/ontologyToTree.Rd |only shinyTree-1.0.0/shinyTree/man/renderEmptyTree.Rd | 3 shinyTree-1.0.0/shinyTree/man/renderTree.Rd | 190 ++ shinyTree-1.0.0/shinyTree/man/renderTreeAsync.Rd | 46 shinyTree-1.0.0/shinyTree/man/set_node_attrs.Rd | 6 shinyTree-1.0.0/shinyTree/man/shinyTree.Rd | 177 +- shinyTree-1.0.0/shinyTree/man/treeToDf.Rd | 12 shinyTree-1.0.0/shinyTree/man/treeToJSON.Rd | 10 shinyTree-1.0.0/shinyTree/man/updateTree.Rd | 36 shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_attr_whitespace |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_bind_cache |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_bind_cache_modal |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_checkbox |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_checkbox_tied |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_checkbox_untied |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_checkbox_untied_cascade |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_contextmenu |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_css_class |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_dnd |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_duplicates |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_empty_tree |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_events_all |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_events_checkbox |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_expand_collapse |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_js_dotted_id |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_js_robust |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_lazy |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_modal_rerender |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_reject_change |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_rmarkdown |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_search |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_search_default |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_search_default_dark |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_search_proton |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_shared_id |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_shared_id_real |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_slow_render |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_state |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_tooltip |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_treetojson |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_types_nested |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_update_loop |only shinyTree-1.0.0/shinyTree/tests/testthat/apps/test_update_loop_changing |only shinyTree-1.0.0/shinyTree/tests/testthat/helper-app.R |only shinyTree-1.0.0/shinyTree/tests/testthat/helper-examples.R |only shinyTree-1.0.0/shinyTree/tests/testthat/helper-traversal.R |only shinyTree-1.0.0/shinyTree/tests/testthat/ontology |only shinyTree-1.0.0/shinyTree/tests/testthat/test_dfTreeConversion.R | 34 shinyTree-1.0.0/shinyTree/tests/testthat/test_duplicate_names.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_get_checked.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_init.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_large_tree.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_lazy.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_leaves_only.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_ontology.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_partial_state.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_render_tree.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_render_tree_async.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_review_fixes.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_shinytest2.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_shinytest2_attr_whitespace.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_shinytest2_bind_cache.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_shinytest2_checkbox_tied.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_shinytest2_checkbox_untied.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_shinytest2_checkbox_untied_cascade.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_shinytest2_contextmenu.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_shinytest2_css_class.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_shinytest2_dnd.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_shinytest2_duplicates.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_shinytest2_example04.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_shinytest2_example25.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_shinytest2_example27.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_shinytest2_example28.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_shinytest2_examples_01_07.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_shinytest2_examples_08_14.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_shinytest2_examples_15_24.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_shinytest2_expand_collapse.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_shinytest2_rmarkdown.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_shinytest2_search.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_shinytest2_search_themes.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_shinytest2_shared_id.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_shinytest2_tooltip.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_shinytest2_treetojson.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_shinytest2_types_nested.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_shinytest2_update_loop.R |only shinyTree-1.0.0/shinyTree/tests/testthat/test_tree.R | 248 ++ shinyTree-1.0.0/shinyTree/tests/testthat/test_tree_traversal.R | 15 150 files changed, 3174 insertions(+), 863 deletions(-)
Title: 'DuckDB' High Throughput Sequencing File Formats Reader
Extension
Description: Bundles the 'duckhts' 'DuckDB' extension for reading High Throughput
Sequencing file formats with 'DuckDB'. The 'DuckDB' C extension API
<https://duckdb.org/docs/stable/clients/c/api> and its 'htslib' dependency are
compiled from vendored sources during package installation. James K Bonfield and co-authors (2021) <doi:10.1093/gigascience/giab007>. VariantKey / RegionKey support follows Nicola Asuni (2018) <doi:10.1101/473744>.
Author: Sounkou Mahamane Toure [aut, cre],
Ryan Ward [aut] ,
Nurture Bio [cph] ,
James K Bonfield, John Marshall,Petr Danecek ,Heng Li , Valeriu Ohan,
Andrew Whitwham,Thomas Keane , Robert M Davies [ctb] ,
DuckHTS Contributors [cph] ),
RBCFTools Authors [cph [...truncated...]
Maintainer: Sounkou Mahamane Toure <sounkoutoure@gmail.com>
Diff between Rduckhts versions 2.0.1.0.1.0 dated 2026-10-24 and 2.0.2.0.1.1 dated 2026-10-28
DESCRIPTION | 6 MD5 | 36 ++- NEWS.md | 21 ++ inst/duckhts_extension/hts_index_builder.c | 213 ++++++++++++++--------- inst/duckhts_extension/mosdepth_table.c | 41 +++- inst/duckhts_extension/samtools_idxstats_table.c | 52 +++-- inst/duckhts_extension/seq_reader.c | 80 +++++--- inst/extdata/geno_format_case.bcf.csi |only inst/extdata/geno_format_case.vcf.gz.tbi |only inst/function_catalog/functions.yaml | 16 + inst/function_catalog/reference.md | 24 ++ inst/tinytest/bcf_snapshot_query.R | 35 ++- inst/tinytest/test_ancestry.R | 3 inst/tinytest/test_bcf.R | 29 ++- inst/tinytest/test_count_error_fit.R | 3 inst/tinytest/test_depth_state_model.R | 3 inst/tinytest/test_mosdepth.R | 6 inst/tinytest/test_samtools_idxstats.R | 6 inst/tinytest/test_somalier_extraction.R | 7 tests/tinytest.R | 8 20 files changed, 409 insertions(+), 180 deletions(-)
Title: Likelihood Contribution Models for Heterogeneous Observation
Types
Description: Constructs likelihood models from heterogeneous observation types
by composing named contributions. Each observation type (exact, left-censored,
right-censored, interval-censored, or custom) contributes independently to the
total log-likelihood, which is summed under an i.i.d. assumption. Provides
contr_name() for standard R distributions and contr_fn() for user-defined
contributions, composed via likelihood_contr() into objects compatible with
the likelihood.model inference framework.
Author: Alexander Towell [aut, cre]
Maintainer: Alexander Towell <lex@metafunctor.com>
Diff between likelihood.contr versions 0.1.1 dated 2026-04-01 and 0.2.0 dated 2026-10-28
DESCRIPTION | 8 ++++---- MD5 | 26 ++++++++++++++++++-------- NAMESPACE | 1 + NEWS.md | 7 +++++++ R/cache.R | 4 ++++ R/frequency.R |only R/likelihood.contr-package.R | 5 +++++ R/likelihood_contr.R | 5 ++++- build/vignette.rds |binary demo |only inst/doc/timeout-benchmarking.R |only inst/doc/timeout-benchmarking.Rmd |only inst/doc/timeout-benchmarking.html |only man/contr_freq.Rd |only man/loglik.Rd | 7 +++++++ tests/testthat/test-frequency.R |only tests/testthat/test-observation-schema.R |only vignettes/timeout-benchmarking.Rmd |only 18 files changed, 50 insertions(+), 13 deletions(-)
More information about likelihood.contr at CRAN
Permanent link
Title: General Transit Feed Specification (GTFS) Editing and Analysing
Tools
Description: Utility functions to read, manipulate, analyse and write
transit feeds in the General Transit Feed Specification (GTFS) data
format.
Author: Daniel Herszenhut [aut] ,
Rafael H. M. Pereira [aut, cre] ,
Pedro R. Andrade [aut] ,
Joao Bazzo [aut] ,
Mark Padgham [ctb],
Christopher Higgins [ctb],
Goncalo F. Matos [ctb],
Yigit Han Eroglu [ctb],
Arthur Bazolli [ctb],
Marcus Saraiva [ctb] ,
Ipea - [...truncated...]
Maintainer: Rafael H. M. Pereira <rafa.pereira.br@gmail.com>
Diff between gtfstools versions 1.4.0 dated 2025-01-08 and 2.0.0 dated 2026-10-28
gtfstools-1.4.0/gtfstools/inst/doc/validating.R |only gtfstools-2.0.0/gtfstools/DESCRIPTION | 51 gtfstools-2.0.0/gtfstools/MD5 | 425 ++- gtfstools-2.0.0/gtfstools/NAMESPACE | 51 gtfstools-2.0.0/gtfstools/NEWS.md | 140 + gtfstools-2.0.0/gtfstools/R/build_graph.R |only gtfstools-2.0.0/gtfstools/R/calendar_helpers.R |only gtfstools-2.0.0/gtfstools/R/combine_nearby_stops.R |only gtfstools-2.0.0/gtfstools/R/convert_seconds_to_time.R |only gtfstools-2.0.0/gtfstools/R/convert_sf_to_shapes.R | 79 gtfstools-2.0.0/gtfstools/R/convert_shapes_to_sf.R | 125 - gtfstools-2.0.0/gtfstools/R/convert_stops_to_sf.R | 98 gtfstools-2.0.0/gtfstools/R/convert_stops_to_shapes.R |only gtfstools-2.0.0/gtfstools/R/convert_time_to_seconds.R | 11 gtfstools-2.0.0/gtfstools/R/cpp11.R | 24 gtfstools-2.0.0/gtfstools/R/crop_gtfs.R | 735 ++++++ gtfstools-2.0.0/gtfstools/R/download_validator.R | 408 ++- gtfstools-2.0.0/gtfstools/R/dt_gtfs.R | 10 gtfstools-2.0.0/gtfstools/R/dwell_time_helpers.R |only gtfstools-2.0.0/gtfstools/R/filter_by_agency_id.R | 27 gtfstools-2.0.0/gtfstools/R/filter_by_date.R |only gtfstools-2.0.0/gtfstools/R/filter_by_period.R |only gtfstools-2.0.0/gtfstools/R/filter_by_route_id.R | 57 gtfstools-2.0.0/gtfstools/R/filter_by_service_id.R | 54 gtfstools-2.0.0/gtfstools/R/filter_by_sf.R | 81 gtfstools-2.0.0/gtfstools/R/filter_by_shape_id.R | 54 gtfstools-2.0.0/gtfstools/R/filter_by_spatial_extent.R | 113 - gtfstools-2.0.0/gtfstools/R/filter_by_stop_id.R | 131 - gtfstools-2.0.0/gtfstools/R/filter_by_time_of_day.R | 328 +-- gtfstools-2.0.0/gtfstools/R/filter_by_trip_id.R | 54 gtfstools-2.0.0/gtfstools/R/filter_by_weekday.R | 29 gtfstools-2.0.0/gtfstools/R/filter_helpers.R | 427 ++-- gtfstools-2.0.0/gtfstools/R/fix_gtfs.R |only gtfstools-2.0.0/gtfstools/R/frequencies_to_stop_times.R | 492 ++-- gtfstools-2.0.0/gtfstools/R/get_active_services.R |only gtfstools-2.0.0/gtfstools/R/get_calendar_overlap.R |only gtfstools-2.0.0/gtfstools/R/get_children_stops.R | 57 gtfstools-2.0.0/gtfstools/R/get_dates.R |only gtfstools-2.0.0/gtfstools/R/get_dwell_time.R |only gtfstools-2.0.0/gtfstools/R/get_parent_station.R | 15 gtfstools-2.0.0/gtfstools/R/get_route_frequency.R |only gtfstools-2.0.0/gtfstools/R/get_route_geometry.R |only gtfstools-2.0.0/gtfstools/R/get_route_speed.R |only gtfstools-2.0.0/gtfstools/R/get_route_timetable.R |only gtfstools-2.0.0/gtfstools/R/get_shape_length.R |only gtfstools-2.0.0/gtfstools/R/get_shapes_geometry.R |only gtfstools-2.0.0/gtfstools/R/get_start_and_end_times.R |only gtfstools-2.0.0/gtfstools/R/get_stop_distances.R |only gtfstools-2.0.0/gtfstools/R/get_stop_frequency.R |only gtfstools-2.0.0/gtfstools/R/get_stop_times_patterns.R | 163 - gtfstools-2.0.0/gtfstools/R/get_stop_timetable.R |only gtfstools-2.0.0/gtfstools/R/get_stops.R |only gtfstools-2.0.0/gtfstools/R/get_stops_geometry.R |only gtfstools-2.0.0/gtfstools/R/get_summary.R |only gtfstools-2.0.0/gtfstools/R/get_trip_duration.R | 198 + gtfstools-2.0.0/gtfstools/R/get_trip_geometry.R | 363 +-- gtfstools-2.0.0/gtfstools/R/get_trip_length.R | 407 +-- gtfstools-2.0.0/gtfstools/R/get_trip_segment_duration.R | 334 +-- gtfstools-2.0.0/gtfstools/R/get_trip_speed.R | 325 +-- gtfstools-2.0.0/gtfstools/R/get_vkt.R |only gtfstools-2.0.0/gtfstools/R/get_vmt.R |only gtfstools-2.0.0/gtfstools/R/gtfstools.R | 308 +- gtfstools-2.0.0/gtfstools/R/interpolate_shape_dist_traveled.R |only gtfstools-2.0.0/gtfstools/R/interpolate_stop_times.R |only gtfstools-2.0.0/gtfstools/R/merge_gtfs.R | 270 ++ gtfstools-2.0.0/gtfstools/R/read_gtfs.R | 17 gtfstools-2.0.0/gtfstools/R/remove_duplicates.R | 7 gtfstools-2.0.0/gtfstools/R/remove_unused_ids.R |only gtfstools-2.0.0/gtfstools/R/set_dwell_time.R |only gtfstools-2.0.0/gtfstools/R/set_max_speed.R |only gtfstools-2.0.0/gtfstools/R/set_min_dwell_time.R |only gtfstools-2.0.0/gtfstools/R/set_route_frequency.R |only gtfstools-2.0.0/gtfstools/R/set_route_speed.R |only gtfstools-2.0.0/gtfstools/R/set_trip_speed.R | 602 +++-- gtfstools-2.0.0/gtfstools/R/shapes_helpers.R |only gtfstools-2.0.0/gtfstools/R/standards.R | 33 gtfstools-2.0.0/gtfstools/R/stop_times_to_frequencies.R |only gtfstools-2.0.0/gtfstools/R/utils.R | 332 +++ gtfstools-2.0.0/gtfstools/R/validate_gtfs.R | 43 gtfstools-2.0.0/gtfstools/R/write_gtfs.R | 11 gtfstools-2.0.0/gtfstools/README.md | 55 gtfstools-2.0.0/gtfstools/build/vignette.rds |binary gtfstools-2.0.0/gtfstools/inst/doc/calendar_overlap.R |only gtfstools-2.0.0/gtfstools/inst/doc/calendar_overlap.Rmd |only gtfstools-2.0.0/gtfstools/inst/doc/calendar_overlap.html |only gtfstools-2.0.0/gtfstools/inst/doc/editing.R |only gtfstools-2.0.0/gtfstools/inst/doc/editing.Rmd |only gtfstools-2.0.0/gtfstools/inst/doc/editing.html |only gtfstools-2.0.0/gtfstools/inst/doc/filtering.R | 68 gtfstools-2.0.0/gtfstools/inst/doc/filtering.Rmd | 89 gtfstools-2.0.0/gtfstools/inst/doc/filtering.html | 521 ++-- gtfstools-2.0.0/gtfstools/inst/doc/graphs.R |only gtfstools-2.0.0/gtfstools/inst/doc/graphs.Rmd |only gtfstools-2.0.0/gtfstools/inst/doc/graphs.html |only gtfstools-2.0.0/gtfstools/inst/doc/gtfstools.R | 36 gtfstools-2.0.0/gtfstools/inst/doc/gtfstools.Rmd | 48 gtfstools-2.0.0/gtfstools/inst/doc/gtfstools.html | 458 ++-- gtfstools-2.0.0/gtfstools/inst/doc/mapping.R |only gtfstools-2.0.0/gtfstools/inst/doc/mapping.Rmd |only gtfstools-2.0.0/gtfstools/inst/doc/mapping.html |only gtfstools-2.0.0/gtfstools/inst/doc/querying.R |only gtfstools-2.0.0/gtfstools/inst/doc/querying.Rmd |only gtfstools-2.0.0/gtfstools/inst/doc/querying.html |only gtfstools-2.0.0/gtfstools/inst/doc/validating.Rmd | 59 gtfstools-2.0.0/gtfstools/inst/doc/validating.html | 81 gtfstools-2.0.0/gtfstools/man/as_dt_gtfs.Rd | 8 gtfstools-2.0.0/gtfstools/man/assert_shapes_fields.Rd |only gtfstools-2.0.0/gtfstools/man/assert_trip_stops_fields.Rd |only gtfstools-2.0.0/gtfstools/man/build_graph.Rd |only gtfstools-2.0.0/gtfstools/man/build_linestrings.Rd |only gtfstools-2.0.0/gtfstools/man/build_service_network.Rd |only gtfstools-2.0.0/gtfstools/man/build_shape_cuts.Rd |only gtfstools-2.0.0/gtfstools/man/build_timetable.Rd |only gtfstools-2.0.0/gtfstools/man/calculate_vkt.Rd |only gtfstools-2.0.0/gtfstools/man/calendar_service_intervals.Rd |only gtfstools-2.0.0/gtfstools/man/check_deprecated_sort_sequence.Rd |only gtfstools-2.0.0/gtfstools/man/check_stop_pair_count.Rd |only gtfstools-2.0.0/gtfstools/man/cluster_stop_nodes.Rd |only gtfstools-2.0.0/gtfstools/man/combine_nearby_stops.Rd |only gtfstools-2.0.0/gtfstools/man/convert_seconds_to_time.Rd |only gtfstools-2.0.0/gtfstools/man/convert_sf_to_shapes.Rd | 8 gtfstools-2.0.0/gtfstools/man/convert_shapes_to_sf.Rd | 33 gtfstools-2.0.0/gtfstools/man/convert_stops_to_sf.Rd | 23 gtfstools-2.0.0/gtfstools/man/convert_stops_to_shapes.Rd |only gtfstools-2.0.0/gtfstools/man/convert_time_to_seconds.Rd | 7 gtfstools-2.0.0/gtfstools/man/crop_gtfs.Rd |only gtfstools-2.0.0/gtfstools/man/dates_to_periods.Rd |only gtfstools-2.0.0/gtfstools/man/download_validator.Rd | 22 gtfstools-2.0.0/gtfstools/man/empty_service_network.Rd |only gtfstools-2.0.0/gtfstools/man/empty_trip_length.Rd |only gtfstools-2.0.0/gtfstools/man/filter_by_agency_id.Rd | 23 gtfstools-2.0.0/gtfstools/man/filter_by_date.Rd |only gtfstools-2.0.0/gtfstools/man/filter_by_period.Rd |only gtfstools-2.0.0/gtfstools/man/filter_by_route_id.Rd | 23 gtfstools-2.0.0/gtfstools/man/filter_by_route_type.Rd | 23 gtfstools-2.0.0/gtfstools/man/filter_by_service_id.Rd | 23 gtfstools-2.0.0/gtfstools/man/filter_by_sf.Rd | 72 gtfstools-2.0.0/gtfstools/man/filter_by_shape_id.Rd | 23 gtfstools-2.0.0/gtfstools/man/filter_by_spatial_extent.Rd | 39 gtfstools-2.0.0/gtfstools/man/filter_by_stop_id.Rd | 63 gtfstools-2.0.0/gtfstools/man/filter_by_time_of_day.Rd | 125 - gtfstools-2.0.0/gtfstools/man/filter_by_trip_id.Rd | 23 gtfstools-2.0.0/gtfstools/man/filter_by_weekday.Rd | 41 gtfstools-2.0.0/gtfstools/man/find_stop_pairs_within.Rd |only gtfstools-2.0.0/gtfstools/man/first_departure_per_trip.Rd |only gtfstools-2.0.0/gtfstools/man/fix_gtfs.Rd |only gtfstools-2.0.0/gtfstools/man/frequencies_to_stop_times.Rd | 64 gtfstools-2.0.0/gtfstools/man/get_active_services.Rd |only gtfstools-2.0.0/gtfstools/man/get_calendar_overlap.Rd |only gtfstools-2.0.0/gtfstools/man/get_dates.Rd |only gtfstools-2.0.0/gtfstools/man/get_dwell_time.Rd |only gtfstools-2.0.0/gtfstools/man/get_frequencies_departures.Rd |only gtfstools-2.0.0/gtfstools/man/get_route_frequency.Rd |only gtfstools-2.0.0/gtfstools/man/get_route_geometry.Rd |only gtfstools-2.0.0/gtfstools/man/get_route_speed.Rd |only gtfstools-2.0.0/gtfstools/man/get_route_timetable.Rd |only gtfstools-2.0.0/gtfstools/man/get_service_days.Rd |only gtfstools-2.0.0/gtfstools/man/get_service_period.Rd |only gtfstools-2.0.0/gtfstools/man/get_service_weights.Rd |only gtfstools-2.0.0/gtfstools/man/get_services_on_days.Rd |only gtfstools-2.0.0/gtfstools/man/get_shape_length.Rd |only gtfstools-2.0.0/gtfstools/man/get_shapes_geometry.Rd |only gtfstools-2.0.0/gtfstools/man/get_start_and_end_times.Rd |only gtfstools-2.0.0/gtfstools/man/get_stop_distances.Rd |only gtfstools-2.0.0/gtfstools/man/get_stop_frequency.Rd |only gtfstools-2.0.0/gtfstools/man/get_stop_node_keys.Rd |only gtfstools-2.0.0/gtfstools/man/get_stop_times_patterns.Rd | 32 gtfstools-2.0.0/gtfstools/man/get_stop_timetable.Rd |only gtfstools-2.0.0/gtfstools/man/get_stops.Rd |only gtfstools-2.0.0/gtfstools/man/get_stops_geometry.Rd |only gtfstools-2.0.0/gtfstools/man/get_summary.Rd |only gtfstools-2.0.0/gtfstools/man/get_trip_departures.Rd |only gtfstools-2.0.0/gtfstools/man/get_trip_duration.Rd | 25 gtfstools-2.0.0/gtfstools/man/get_trip_geometry.Rd | 81 gtfstools-2.0.0/gtfstools/man/get_trip_length.Rd | 120 - gtfstools-2.0.0/gtfstools/man/get_trip_segment_duration.Rd | 41 gtfstools-2.0.0/gtfstools/man/get_trip_speed.Rd | 95 gtfstools-2.0.0/gtfstools/man/get_usable_shapes.Rd |only gtfstools-2.0.0/gtfstools/man/get_vkt.Rd |only gtfstools-2.0.0/gtfstools/man/get_vmt.Rd |only gtfstools-2.0.0/gtfstools/man/gtfstools.Rd | 20 gtfstools-2.0.0/gtfstools/man/has_shapes.Rd |only gtfstools-2.0.0/gtfstools/man/infer_trip_directions.Rd |only gtfstools-2.0.0/gtfstools/man/interpolate_cropped_trips.Rd |only gtfstools-2.0.0/gtfstools/man/interpolate_shape_dist_traveled.Rd |only gtfstools-2.0.0/gtfstools/man/interpolate_stop_times.Rd |only gtfstools-2.0.0/gtfstools/man/is_blank_time.Rd |only gtfstools-2.0.0/gtfstools/man/list_validator_versions.Rd |only gtfstools-2.0.0/gtfstools/man/locate_cropped_trip_cuts.Rd |only gtfstools-2.0.0/gtfstools/man/locate_stops_along_shapes.Rd |only gtfstools-2.0.0/gtfstools/man/map_deprecated_file.Rd |only gtfstools-2.0.0/gtfstools/man/match_stop_times_rows.Rd |only gtfstools-2.0.0/gtfstools/man/max_stop_pairs_without_warning.Rd |only gtfstools-2.0.0/gtfstools/man/merge_gtfs.Rd | 22 gtfstools-2.0.0/gtfstools/man/merge_service_intervals.Rd |only gtfstools-2.0.0/gtfstools/man/parse_dates.Rd |only gtfstools-2.0.0/gtfstools/man/paste_stop_names.Rd |only gtfstools-2.0.0/gtfstools/man/prepare_shape_points.Rd |only gtfstools-2.0.0/gtfstools/man/prepare_trip_stops.Rd |only gtfstools-2.0.0/gtfstools/man/read_gtfs.Rd | 4 gtfstools-2.0.0/gtfstools/man/refresh_secs_columns.Rd |only gtfstools-2.0.0/gtfstools/man/remove_unused_ids.Rd |only gtfstools-2.0.0/gtfstools/man/replace_cropped_shapes.Rd |only gtfstools-2.0.0/gtfstools/man/replace_stop_ids.Rd |only gtfstools-2.0.0/gtfstools/man/report_deps_available.Rd |only gtfstools-2.0.0/gtfstools/man/resolve_shapes_method.Rd |only gtfstools-2.0.0/gtfstools/man/route_type_ids.Rd |only gtfstools-2.0.0/gtfstools/man/roxygen/templates/method.R |only gtfstools-2.0.0/gtfstools/man/set_dwell_time.Rd |only gtfstools-2.0.0/gtfstools/man/set_max_speed.Rd |only gtfstools-2.0.0/gtfstools/man/set_min_dwell_time.Rd |only gtfstools-2.0.0/gtfstools/man/set_route_frequency.Rd |only gtfstools-2.0.0/gtfstools/man/set_route_speed.Rd |only gtfstools-2.0.0/gtfstools/man/set_trip_speed.Rd | 137 + gtfstools-2.0.0/gtfstools/man/shape_point_distances.Rd |only gtfstools-2.0.0/gtfstools/man/shift_cropped_frequencies.Rd |only gtfstools-2.0.0/gtfstools/man/stop_id_references.Rd |only gtfstools-2.0.0/gtfstools/man/stop_times_to_frequencies.Rd |only gtfstools-2.0.0/gtfstools/man/sum_or_na.Rd |only gtfstools-2.0.0/gtfstools/man/summarise_distribution.Rd |only gtfstools-2.0.0/gtfstools/man/summarise_route_frequency.Rd |only gtfstools-2.0.0/gtfstools/man/summarise_services.Rd |only gtfstools-2.0.0/gtfstools/man/time_of_day_window.Rd |only gtfstools-2.0.0/gtfstools/man/time_secs.Rd |only gtfstools-2.0.0/gtfstools/man/validate_gtfs.Rd | 39 gtfstools-2.0.0/gtfstools/man/warn_invalid_ids.Rd |only gtfstools-2.0.0/gtfstools/man/warn_missing_ids.Rd |only gtfstools-2.0.0/gtfstools/man/warn_times_not_interpolated.Rd |only gtfstools-2.0.0/gtfstools/man/warn_trips_without_shape.Rd |only gtfstools-2.0.0/gtfstools/man/write_gtfs.Rd | 12 gtfstools-2.0.0/gtfstools/man/write_summary_report.Rd |only gtfstools-2.0.0/gtfstools/src/Makevars |only gtfstools-2.0.0/gtfstools/src/Makevars.win |only gtfstools-2.0.0/gtfstools/src/convert-time.cpp | 64 gtfstools-2.0.0/gtfstools/src/convert-time.h | 1 gtfstools-2.0.0/gtfstools/src/cpp11.cpp | 52 gtfstools-2.0.0/gtfstools/src/distance_haversine.cpp |only gtfstools-2.0.0/gtfstools/src/sequence_pattern.cpp |only gtfstools-2.0.0/gtfstools/tests/testthat/_snaps/filter_by_sf.md | 15 gtfstools-2.0.0/gtfstools/tests/testthat/_snaps/filter_by_stop_id.md | 17 gtfstools-2.0.0/gtfstools/tests/testthat/test-as_dt_gtfs.R | 2 gtfstools-2.0.0/gtfstools/tests/testthat/test-build_graph.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-combine_nearby_stops.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-convert_seconds_to_time.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-convert_sf_to_shapes.R | 108 + gtfstools-2.0.0/gtfstools/tests/testthat/test-convert_shapes_to_sf.R | 135 - gtfstools-2.0.0/gtfstools/tests/testthat/test-convert_stops_to_sf.R | 95 gtfstools-2.0.0/gtfstools/tests/testthat/test-convert_stops_to_shapes.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-crop_gtfs.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-download_validator.R | 383 ++- gtfstools-2.0.0/gtfstools/tests/testthat/test-filter_by_agency_id.R | 18 gtfstools-2.0.0/gtfstools/tests/testthat/test-filter_by_date.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-filter_by_period.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-filter_by_service_id.R | 16 gtfstools-2.0.0/gtfstools/tests/testthat/test-filter_by_sf.R | 144 - gtfstools-2.0.0/gtfstools/tests/testthat/test-filter_by_shape_id.R | 19 gtfstools-2.0.0/gtfstools/tests/testthat/test-filter_by_spatial_extent.R | 149 + gtfstools-2.0.0/gtfstools/tests/testthat/test-filter_by_stop_id.R | 662 ++---- gtfstools-2.0.0/gtfstools/tests/testthat/test-filter_by_time_of_day.R | 154 + gtfstools-2.0.0/gtfstools/tests/testthat/test-filter_by_trip_id.R | 16 gtfstools-2.0.0/gtfstools/tests/testthat/test-filter_helpers.R | 123 + gtfstools-2.0.0/gtfstools/tests/testthat/test-fix_gtfs.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-frequencies_to_stop_times.R | 281 ++ gtfstools-2.0.0/gtfstools/tests/testthat/test-get_active_services.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-get_calendar_overlap.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-get_dates.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-get_dwell_time.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-get_route_frequency.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-get_route_geometry.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-get_route_speed.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-get_route_timetable.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-get_shape_length.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-get_shapes_geometry.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-get_start_and_end_times.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-get_stop_distances.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-get_stop_frequency.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-get_stop_times_patterns.R | 169 + gtfstools-2.0.0/gtfstools/tests/testthat/test-get_stop_timetable.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-get_stops.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-get_stops_geometry.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-get_summary.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-get_trip_duration.R | 176 + gtfstools-2.0.0/gtfstools/tests/testthat/test-get_trip_geometry.R | 690 ++++-- gtfstools-2.0.0/gtfstools/tests/testthat/test-get_trip_length.R | 904 ++++++-- gtfstools-2.0.0/gtfstools/tests/testthat/test-get_trip_segment_duration.R | 119 - gtfstools-2.0.0/gtfstools/tests/testthat/test-get_trip_speed.R | 541 ++--- gtfstools-2.0.0/gtfstools/tests/testthat/test-get_vkt.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-get_vmt.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-interpolate_shape_dist_traveled.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-interpolate_stop_times.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-merge_gtfs.R | 762 ++++--- gtfstools-2.0.0/gtfstools/tests/testthat/test-read_gtfs.R | 4 gtfstools-2.0.0/gtfstools/tests/testthat/test-remove_duplicates.R | 22 gtfstools-2.0.0/gtfstools/tests/testthat/test-remove_unused_ids.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-set_dwell_time.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-set_max_speed.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-set_min_dwell_time.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-set_route_frequency.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-set_route_speed.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-set_trip_speed.R | 1063 +++++++--- gtfstools-2.0.0/gtfstools/tests/testthat/test-stop_times_to_frequencies.R |only gtfstools-2.0.0/gtfstools/tests/testthat/test-utils.R | 188 + gtfstools-2.0.0/gtfstools/tests/testthat/test-write_gtfs.R | 16 gtfstools-2.0.0/gtfstools/vignettes/calendar_overlap.Rmd |only gtfstools-2.0.0/gtfstools/vignettes/editing.Rmd |only gtfstools-2.0.0/gtfstools/vignettes/filtering.Rmd | 89 gtfstools-2.0.0/gtfstools/vignettes/graphs.Rmd |only gtfstools-2.0.0/gtfstools/vignettes/gtfstools.Rmd | 48 gtfstools-2.0.0/gtfstools/vignettes/mapping.Rmd |only gtfstools-2.0.0/gtfstools/vignettes/querying.Rmd |only gtfstools-2.0.0/gtfstools/vignettes/validating.Rmd | 59 311 files changed, 11464 insertions(+), 6015 deletions(-)
Title: 'shiny' Application for Population Structure and Ancestry
Assessments
Description: Provides a 'shiny' web application developed by the Breeding Insight team
to support pedigree validation and ancestry assessment of plant and animal
populations. The app integrates Mendelian error analysis, parentage assignment
and genetic composition/ancestry methods to help researchers evaluate genomic
relationships through an accessible, web-based interface without requiring
command-line tools. Pedigree validation, Mendelian error analysis and
parentage assignment build on the 'BIGpopA' package
(<https://CRAN.R-project.org/package=BIGpopA>) and support diploid and
polyploid data. Genotypes can be uploaded as dosage tables, VCF files,
or 'PLINK' .ped files. Ancestry estimation uses
the sparse non-negative matrix
factorization method of Frichot et al. (2014) <doi:10.1534/genetics.113.160572>
as implemented in the 'LEA' package by Frichot and Francois (2015)
<doi:10.1111/2041-210X.12382>. Line and breed composition are
estimated using the breed composition regression [...truncated...]
Author: Josue Chinchilla-Vargas [aut, cre],
Alexander M. Sandercock [aut],
Breeding Insight Team [aut]
Maintainer: Josue Chinchilla-Vargas <josue.chinchilla@ufl.edu>
Diff between Familia versions 2.0.0 dated 2026-08-24 and 2.2.0 dated 2026-10-28
Familia-2.0.0/Familia/inst/app/www/BIG_R_logo.png |only Familia-2.0.0/Familia/inst/app/www/BreedingInsight_Primary_RGBColor_400px.png |only Familia-2.0.0/Familia/inst/app/www/BreedingInsight_Secondary_RGBColor_400px.png |only Familia-2.0.0/Familia/tests/testthat/test-convert_to_dosage.R |only Familia-2.2.0/Familia/DESCRIPTION | 16 Familia-2.2.0/Familia/MD5 | 71 +- Familia-2.2.0/Familia/NAMESPACE | 24 Familia-2.2.0/Familia/NEWS.md | 74 ++ Familia-2.2.0/Familia/R/app_server.R | 48 + Familia-2.2.0/Familia/R/app_ui.R | 6 Familia-2.2.0/Familia/R/globals.R | 6 Familia-2.2.0/Familia/R/help_SNMF.R | 77 ++- Familia-2.2.0/Familia/R/help_find_parentage.R | 81 ++- Familia-2.2.0/Familia/R/help_ped_cleaner.R | 3 Familia-2.2.0/Familia/R/help_polybreedtools.R | 91 +++ Familia-2.2.0/Familia/R/help_validate_ped.R | 49 + Familia-2.2.0/Familia/R/mod_Home.R | 15 Familia-2.2.0/Familia/R/mod_SNMF.R | 184 ++++--- Familia-2.2.0/Familia/R/mod_find_parentage.R | 139 ++++- Familia-2.2.0/Familia/R/mod_ped_cleaner.R | 10 Familia-2.2.0/Familia/R/mod_polybreedtools.R | 234 ++++++--- Familia-2.2.0/Familia/R/mod_validate_ped.R | 85 +-- Familia-2.2.0/Familia/R/utils.R | 249 +++++++++- Familia-2.2.0/Familia/README.md | 37 + Familia-2.2.0/Familia/build |only Familia-2.2.0/Familia/inst/CITATION | 2 Familia-2.2.0/Familia/inst/WORDLIST | 21 Familia-2.2.0/Familia/inst/app/www/custom.css | 11 Familia-2.2.0/Familia/inst/app/www/custom.js | 8 Familia-2.2.0/Familia/inst/doc |only Familia-2.2.0/Familia/inst/extdata |only Familia-2.2.0/Familia/tests/testthat/test-example_files.R |only Familia-2.2.0/Familia/tests/testthat/test-read_genotype_upload.R |only Familia-2.2.0/Familia/vignettes |only 34 files changed, 1125 insertions(+), 416 deletions(-)
Title: Sparse Geometry Rasterization with Exact Coverage Fractions
Description: Rasterize polygon, line, and point geometry without
materializing any pixel values. For polygons it computes exact coverage
fractions for polygon-grid intersections, returning sparse tables:
run-length encoded interior cells and individually weighted boundary
cells. The scanline algorithm is O(perimeter) in both time and memory,
using the scan line fill attributed to Wylie et al. (1967)
<doi:10.1145/1465611.1465619>. Exact coverage fractions use the
exactextract algorithm by Daniel Baston, vendored from the
'exactextractr' package <doi:10.32614/CRAN.package.exactextractr>.
Derived from the 'fasterize' package by Noam Ross.
Author: Michael Sumner [aut, cre] ,
Noam Ross [aut] ,
EcoHealth Alliance [cph] ,
Jim Hester [ctb] ,
Daniel Baston [cph] ),
ISciences, LLC [cph] )
Maintainer: Michael Sumner <mdsumner@gmail.com>
Diff between controlledburn versions 0.3.1 dated 2026-10-24 and 0.3.2 dated 2026-10-28
DESCRIPTION | 12 +-- MD5 | 29 ++++--- NAMESPACE | 4 + NEWS.md | 12 +++ R/plot.R |only R/summary.R |only README.md | 19 ++++- inst/doc/algorithms.Rmd | 10 ++ inst/doc/algorithms.html | 30 ++++---- man/controlledburn-package.Rd | 3 man/overview_burn.Rd |only man/plot.controlledburn.Rd |only man/summary.controlledburn.Rd |only src/analytical_coverage.h | 8 +- src/core_scanline.cpp | 135 +++++++++++++++++++++++++++++-------- tests/testthat/test-holes.R |only tests/testthat/test-lattice-snap.R | 34 +++++++++ tests/testthat/test-summary-plot.R |only vignettes/algorithms.Rmd | 10 ++ 19 files changed, 243 insertions(+), 63 deletions(-)
More information about controlledburn at CRAN
Permanent link
Title: Isolate Functions for Remote Execution
Description: Sending functions to remote processes can be wasteful of
resources because they carry their environments with them. With the
carrier package, it is easy to create functions that are isolated from
their environment. These isolated functions, also called crates, print
at the console with their total size and can be easily tested locally
before being sent to a remote.
Author: Lionel Henry [aut, cre],
Posit Software, PBC [cph, fnd]
Maintainer: Lionel Henry <lionel@posit.co>
Diff between carrier versions 0.3.0.4 dated 2025-09-11 and 0.4.0 dated 2026-10-28
DESCRIPTION | 11 ++-- MD5 | 16 ++--- NEWS.md | 25 ++++++++- R/crate.R | 111 +++++++++++++++++++++++++++++++---------- README.md | 14 ++--- man/carrier-package.Rd | 5 + man/crate.Rd | 59 ++++++++++++++------- tests/testthat/_snaps/crate.md | 33 +++++++++++- tests/testthat/test-crate.R | 88 +++++++++++++++++++++++++++++++- 9 files changed, 289 insertions(+), 73 deletions(-)
Title: Algorithms for Quantitative Pedology
Description: The Algorithms for Quantitative Pedology (AQP) project was started in 2009 to organize a loosely-related set of concepts and source code on the topic of soil profile visualization, aggregation, and classification into this package (aqp). Over the past 8 years, the project has grown into a suite of related R packages that enhance and simplify the quantitative analysis of soil profile data. Central to the AQP project is a new vocabulary of specialized functions and data structures that can accommodate the inherent complexity of soil profile information; freeing the scientist to focus on ideas rather than boilerplate data processing tasks <doi:10.1016/j.cageo.2012.10.020>. These functions and data structures have been extensively tested and documented, applied to projects involving hundreds of thousands of soil profiles, and deeply integrated into widely used tools such as SoilWeb <https://casoilresource.lawr.ucdavis.edu/soilweb-apps>. Components of the AQP project (aqp, soilD [...truncated...]
Author: Dylan Beaudette [aut, cre] ,
Pierre Roudier [aut, ctb],
Andrew Brown [aut, ctb],
Stephen Roecker [aut, ctb],
David Rossiter [ctb]
Maintainer: Dylan Beaudette <dylan.beaudette@usda.gov>
Diff between aqp versions 2.3.2 dated 2026-04-30 and 2.3.3 dated 2026-10-28
DESCRIPTION | 8 MD5 | 56 NAMESPACE | 224 ++- NEWS.md | 6 R/SoilProfileCollection-coercion.R | 27 R/SoilProfileCollection-methods.R | 2 R/allocate.R | 2 R/aqp-label-placement-solvers.R | 72 - R/colorChart.R | 2 R/colorQuantiles.R | 2 R/plotSPC.R | 22 R/slab.R | 12 build/partial.rdb |binary build/vignette.rds |binary inst/doc/Introduction-to-SoilProfileCollection-Objects.html | 129 +- inst/doc/Munsell-color-conversion.html | 9 inst/doc/NCSP.html | 13 inst/doc/label-placement.R | 71 - inst/doc/label-placement.Rmd | 87 + inst/doc/label-placement.html | 675 ++++++------ man/SoilProfileCollection-plotting-methods.Rd | 2 man/allocate.Rd | 2 man/coercion-methods.Rd | 35 man/fixOverlap.Rd | 48 man/overlapMetrics.Rd | 14 man/slab.Rd | 10 tests/testthat/Rplots.pdf |binary tests/testthat/test-genhz.R | 6 vignettes/label-placement.Rmd | 87 + 29 files changed, 955 insertions(+), 668 deletions(-)
Title: Publication Toolkit for Water, Sanitation and Hygiene (WASH)
Data
Description: A toolkit to set up an R data package in a consistent
structure. Automates tasks like tidy data export, data dictionary
documentation, README and website creation, and citation management.
Author: Mian Zhong [aut] ,
Margaux Goetschmann [aut] ,
Colin Walder [aut] ,
Lars Schoebitz [aut, cre] ,
Global Health Engineering, ETH Zurich [cph]
Maintainer: Lars Schoebitz <lschoebitz@ethz.ch>
Diff between washr versions 1.1.0 dated 2026-09-02 and 1.2.0 dated 2026-10-28
DESCRIPTION | 14 - MD5 | 99 +++++---- NAMESPACE | 6 NEWS.md | 180 +++++++++++++++++ R/check_publication_readiness.R |only R/config.R |only R/generate_jsonld.R | 56 +++-- R/setup_ci.R | 27 +- R/setup_dictionary.R | 40 ++- R/setup_rawdata.R | 34 +-- R/setup_readme.R | 75 +++++-- R/setup_roxygen.R | 52 +++- R/setup_website.R | 47 +++- R/source_article.R |only R/ui.R |only R/update_citation.R | 121 +++++++++-- R/update_description.R | 99 ++++++++- R/update_dictionary.R |only R/update_metadata.R | 44 ++-- R/use_brand.R | 230 ++++++++++++++++++---- R/utils.R | 29 ++ R/washr-package.R | 10 R/zenodo_json.R |only README.md | 31 ++ inst/doc/washr.R | 15 + inst/doc/washr.Rmd | 69 +++++- inst/doc/washr.html | 194 +++++++++++++++--- inst/templates/README.Rmd | 42 +++- inst/templates/_pkgdown.yml | 19 + man/check_publication_readiness.Rd |only man/setup_ci.Rd | 3 man/setup_dictionary.Rd | 8 man/setup_rawdata.Rd | 6 man/setup_readme.Rd | 14 + man/setup_roxygen.Rd | 9 man/setup_website.Rd | 13 - man/update_citation.Rd | 44 +++- man/update_description.Rd | 43 +++- man/update_dictionary.Rd |only man/update_metadata.Rd | 7 man/update_zenodo_json.Rd |only man/use_brand.Rd | 37 ++- man/washr-package.Rd | 12 + tests/testthat/_snaps/update_citation.md | 2 tests/testthat/_snaps/update_description.md | 7 tests/testthat/test_check_publication_readiness.R |only tests/testthat/test_config.R |only tests/testthat/test_edge_cases.R |only tests/testthat/test_setup_ci.R | 19 + tests/testthat/test_setup_readme.R | 52 ++++ tests/testthat/test_ui.R |only tests/testthat/test_update_citation.R | 113 ++++++++++ tests/testthat/test_update_description.R | 8 tests/testthat/test_update_dictionary.R |only tests/testthat/test_update_metadata.R | 12 + tests/testthat/test_update_zenodo_json.R |only tests/testthat/test_use_brand.R | 196 ++++++++++++++++++ vignettes/washr.Rmd | 69 +++++- 58 files changed, 1845 insertions(+), 362 deletions(-)
Title: Reliable Utilities for Reusable Research Workflows
Description: Provides reusable building blocks for research packages across
matrix representation, numerical computation, neighborhood evaluation,
controlled execution, and runtime interoperability. Core tools preserve
declared sparse semantics, expose dense-memory and output boundaries,
standardize neighborhood and classification results, and align serial and
parallel result and error behavior. Additional helpers support structured
messages, optional dependency checks, and common statistical workflows.
Author: Meng Xu [aut, cre] ,
Haoliang Zhu [aut]
Maintainer: Meng Xu <mengxu98@qq.com>
Diff between thisutils versions 0.5.0 dated 2026-08-21 and 0.5.3 dated 2026-10-28
thisutils-0.5.0/thisutils/inst/python |only thisutils-0.5.3/thisutils/DESCRIPTION | 15 thisutils-0.5.3/thisutils/MD5 | 85 - thisutils-0.5.3/thisutils/NAMESPACE | 8 thisutils-0.5.3/thisutils/NEWS.md | 91 + thisutils-0.5.3/thisutils/R/RcppExports.R | 12 thisutils-0.5.3/thisutils/R/add_pkg_file.R | 76 - thisutils-0.5.3/thisutils/R/as_matrix.R | 13 thisutils-0.5.3/thisutils/R/computation.R | 80 - thisutils-0.5.3/thisutils/R/figlet.R | 63 - thisutils-0.5.3/thisutils/R/fit_trends.R |only thisutils-0.5.3/thisutils/R/log_message.R | 62 - thisutils-0.5.3/thisutils/R/package_management.R | 36 thisutils-0.5.3/thisutils/R/parallelize_fun.R | 599 ++++++---- thisutils-0.5.3/thisutils/R/sparse_cor.R | 23 thisutils-0.5.3/thisutils/R/sparse_matrix_tools.R | 289 ++++ thisutils-0.5.3/thisutils/R/thisutils-package.R | 3 thisutils-0.5.3/thisutils/R/utils.R | 139 +- thisutils-0.5.3/thisutils/inst/doc/reliable-sparse-workflows.R | 6 thisutils-0.5.3/thisutils/inst/doc/reliable-sparse-workflows.Rmd | 6 thisutils-0.5.3/thisutils/inst/doc/reliable-sparse-workflows.html | 40 thisutils-0.5.3/thisutils/inst/include/thisutils/log_message.h | 19 thisutils-0.5.3/thisutils/inst/scripts |only thisutils-0.5.3/thisutils/man/aggregate_matrix.Rd |only thisutils-0.5.3/thisutils/man/col_maxs.Rd |only thisutils-0.5.3/thisutils/man/detect_cores.Rd |only thisutils-0.5.3/thisutils/man/fast_aggregate.Rd |only thisutils-0.5.3/thisutils/man/fit_trends.Rd |only thisutils-0.5.3/thisutils/man/get_verbose.Rd | 4 thisutils-0.5.3/thisutils/man/grapes-or-or-or-grapes.Rd |only thisutils-0.5.3/thisutils/man/invoke_fun.Rd | 8 thisutils-0.5.3/thisutils/man/local_verbose.Rd |only thisutils-0.5.3/thisutils/man/row_maxs.Rd |only thisutils-0.5.3/thisutils/src/ClassificationMetrics.cpp | 24 thisutils-0.5.3/thisutils/src/RcppExports.cpp | 55 thisutils-0.5.3/thisutils/src/curve_summary.cpp |only thisutils-0.5.3/thisutils/src/lisi.cpp | 165 -- thisutils-0.5.3/thisutils/src/matrix_to_table.cpp | 3 thisutils-0.5.3/thisutils/src/table_to_matrix.cpp | 6 thisutils-0.5.3/thisutils/tests/testthat/test-fit-trends.R |only thisutils-0.5.3/thisutils/tests/testthat/test-invoke-fun.R |only thisutils-0.5.3/thisutils/tests/testthat/test-lisi.R | 46 thisutils-0.5.3/thisutils/tests/testthat/test-log_message.R | 12 thisutils-0.5.3/thisutils/tests/testthat/test-package-github-metadata.R |only thisutils-0.5.3/thisutils/tests/testthat/test-package-management.R | 2 thisutils-0.5.3/thisutils/tests/testthat/test-parallelize_fun.R | 533 +++++++- thisutils-0.5.3/thisutils/tests/testthat/test-sparse_matrix_tools.R | 125 ++ thisutils-0.5.3/thisutils/tests/testthat/test-utils.R | 23 thisutils-0.5.3/thisutils/vignettes/reliable-sparse-workflows.Rmd | 6 49 files changed, 1804 insertions(+), 873 deletions(-)
Title: Investigating New Projection Pursuit Index Functions
Description: Projection pursuit is used to find interesting low-dimensional
projections of high-dimensional data by optimizing an index over all
possible projections. The 'spinebil' package contains methods to evaluate
the performance of projection pursuit index functions using tour methods.
A paper describing the methods can be found at <doi:10.1007/s00180-020-00954-8>.
Author: Ursula Laa [aut] ,
Dianne Cook [aut] ,
Tina Rashid Jafari [aut, cre]
Maintainer: Tina Rashid Jafari <tina.rashidjafari@gmail.com>
Diff between spinebil versions 1.0.5 dated 2025-10-17 and 1.0.6 dated 2026-10-28
DESCRIPTION | 12 +- MD5 | 36 +++--- NAMESPACE | 1 NEWS.md | 11 + R/index_scale.R | 88 +++++++++++---- R/ppi_noise_grid.R |only R/sample_size_effect.R | 114 +++++++++++++------ R/utils_tourr.R | 4 build/vignette.rds |binary inst/doc/more_descriptives.R | 8 + inst/doc/more_descriptives.html | 230 ++++++++++++++++++++++++++++++++-------- inst/doc/more_descriptives.qmd | 8 + inst/doc/ppi_diagnostics.html | 178 +++++++++++++++++++++++++++--- inst/doc/spinebil.html | 146 ++++++++++++++++++++++++- man/geodesic_info.Rd | 4 man/ppi_noise_grid.Rd |only man/ppi_samplesize_effect.Rd | 47 +++++++- man/ppi_scale.Rd | 38 +++++- man/spinebil-package.Rd | 1 vignettes/more_descriptives.qmd | 8 + 20 files changed, 773 insertions(+), 161 deletions(-)
Title: Lasso and Elastic-Net Regularized Generalized Linear Models
Description: Extremely efficient procedures for fitting the entire lasso or elastic-net regularization path for linear regression, logistic and multinomial regression models, Poisson regression, Cox model, multiple-response Gaussian, and the grouped multinomial regression; see <doi:10.18637/jss.v033.i01> and <doi:10.18637/jss.v039.i05>. There are two new and important additions. The family argument can be a GLM family object, which opens the door to any programmed family (<doi:10.18637/jss.v106.i01>). This comes with a modest computational cost, so when the built-in families suffice, they should be used instead. The other novelty is the relax option, which refits each of the active sets in the path unpenalized. The algorithm uses cyclical coordinate descent in a path-wise fashion, as described in the papers cited.
Author: Jerome Friedman [aut],
Trevor Hastie [aut, cre],
Rob Tibshirani [aut],
Balasubramanian Narasimhan [aut],
Kenneth Tay [aut],
Noah Simon [aut],
Junyang Qian [ctb],
James Yang [aut],
Jonathan Taylor [aut]
Maintainer: Trevor Hastie <hastie@stanford.edu>
Diff between glmnet versions 5.1 dated 2026-09-24 and 5.2 dated 2026-10-28
DESCRIPTION | 10 MD5 | 65 NAMESPACE | 74 NEWS.md | 25 R/buildPredmat.coxnetlist.R | 6 R/coxgrad.R | 9 R/cv.glmnet.R | 6 R/cv.glmnet.raw.R | 21 R/cv.relaxed.raw.R | 22 R/getOptcv.relaxed.R | 3 R/getcoef.R | 3 R/glmnet-package.R | 18 R/glmnet.control.R | 36 R/predict.glmnet.R | 4 R/predict.multnet.R | 2 R/predict.relaxed.R | 13 README.md | 72 inst/doc/Coxnet.pdf |binary inst/doc/coxdev.html | 828 +++++---- inst/doc/glmnet-history.pdf |binary inst/doc/glmnet.pdf |binary inst/doc/glmnetFamily.pdf |binary inst/doc/relax.pdf |binary man/coxgrad.Rd | 9 man/glmnet.control.Rd | 4 man/predict.glmnet.Rd | 6 src/glmnet_control.cpp | 6 src/glmnetpp/coxdev/cpp/include/coxdev.h | 150 + src/glmnetpp/coxdev/cpp/src/coxdev.cpp | 908 +++++++++- src/glmnetpp/coxdev/cpp/tests |only src/glmnetpp/include/glmnetpp_bits/elnet_point/internal/cox_base.hpp | 11 tests/testthat/helper-functions.R | 45 tests/testthat/test_predict_relaxed.R |only tests/testthat/test_smoke_families.R | 14 34 files changed, 1866 insertions(+), 504 deletions(-)
Title: Implementation of the DISCO Metric for Internal Clustering
Evaluation
Description: Implementation of the DISCO (Density-based Internal Score for
Clusterings with nOise) metric, a cluster validity index for evaluating
density-based clustering results without ground truth labels. DISCO is the
first index to explicitly assess the quality of noise point assignments in
addition to cluster quality. It uses density-connectivity distance derived
from a minimum spanning tree of the mutual-reachability graph, providing
interpretable, bounded scores in [-1, 1]. Higher scores indicate better
clustering. Based on Beer et al. (2025)
<doi:10.48550/arXiv.2503.00127>.
Author: Amin Entezari [aut, cre] ,
Davide Chicco [ctb] ,
Anna Beer [aut] ),
Lena Krieger [aut] ),
Pascal Weber [aut] )
Maintainer: Amin Entezari <amin_entezari@outlook.com>
Diff between discoCVI versions 0.2.0 dated 2026-10-27 and 0.2.1 dated 2026-10-28
DESCRIPTION | 9 +++++---- MD5 | 9 +++++++-- NEWS.md | 7 +++++++ build |only inst/doc |only vignettes |only 6 files changed, 19 insertions(+), 6 deletions(-)
Title: Within-Subject Mediation Analysis Using Structural Equation
Modeling
Description: Within-subject mediation analysis using structural equation modeling.
Examine how changes in an outcome variable between two conditions are mediated
through one or more variables. Supports within-subject mediation analysis using
the 'lavaan' package by Rosseel (2012) <doi:10.18637/jss.v048.i02>,
and extends Monte Carlo confidence interval estimation to missing data scenarios
using the 'semmcci' package by Pesigan and Cheung (2023) <doi:10.3758/s13428-023-02114-4>.
Author: Wendie Yang [aut, cre] ,
Shu Fai Cheung [aut]
Maintainer: Wendie Yang <1581075494q@gmail.com>
Diff between wsMed versions 1.1.0 dated 2026-09-18 and 1.2.0 dated 2026-10-28
wsMed-1.1.0/wsMed/man/print.wsMed.Rd |only wsMed-1.2.0/wsMed/DESCRIPTION | 14 wsMed-1.2.0/wsMed/MD5 | 438 +- wsMed-1.2.0/wsMed/NAMESPACE | 43 wsMed-1.2.0/wsMed/NEWS.md | 163 wsMed-1.2.0/wsMed/R/ARIVwrapper.R | 2 wsMed-1.2.0/wsMed/R/GenerateModelCN.R | 32 wsMed-1.2.0/wsMed/R/GenerateModelCP.R | 22 wsMed-1.2.0/wsMed/R/GenerateModelCustom.R | 11 wsMed-1.2.0/wsMed/R/GenerateModelP.R | 19 wsMed-1.2.0/wsMed/R/GenerateModelPC.R | 22 wsMed-1.2.0/wsMed/R/ImputeData.R | 28 wsMed-1.2.0/wsMed/R/Locationwrapper.R | 2 wsMed-1.2.0/wsMed/R/MCDefWrapper.R | 2 wsMed-1.2.0/wsMed/R/MCLav_Lav2RAM2.R | 2 wsMed-1.2.0/wsMed/R/MCMI2.R | 84 wsMed-1.2.0/wsMed/R/MC_apply_standardization.R | 2 wsMed-1.2.0/wsMed/R/MC_bootstrap_sd_list.R | 2 wsMed-1.2.0/wsMed/R/MC_build_definitions.R | 2 wsMed-1.2.0/wsMed/R/MC_build_std_map.R | 4 wsMed-1.2.0/wsMed/R/MC_evaluate_definitions.R | 4 wsMed-1.2.0/wsMed/R/MC_extract_all_parameters.R | 2 wsMed-1.2.0/wsMed/R/MC_generate_mc_samples.R | 2 wsMed-1.2.0/wsMed/R/MC_get_sd_target_variables.R | 10 wsMed-1.2.0/wsMed/R/MC_resolve_all_dependencies.R | 2 wsMed-1.2.0/wsMed/R/MC_run_mc_mediation.R | 4 wsMed-1.2.0/wsMed/R/MC_summarize_mc_ci.R | 2 wsMed-1.2.0/wsMed/R/MClav_MCStd2.R | 2 wsMed-1.2.0/wsMed/R/MClav_RAM2Lav2.R | 4 wsMed-1.2.0/wsMed/R/MClav_StdLav2.R | 9 wsMed-1.2.0/wsMed/R/MClav_StdRAM2.R | 11 wsMed-1.2.0/wsMed/R/MClav_ThetaHat2.R | 2 wsMed-1.2.0/wsMed/R/MICombineWrapper.R | 2 wsMed-1.2.0/wsMed/R/PrepareData.R | 20 wsMed-1.2.0/wsMed/R/PrepareMissingData.R | 4 wsMed-1.2.0/wsMed/R/RandomGaussianCholwrapper.R | 3 wsMed-1.2.0/wsMed/R/RandomGaussianEigenwrapper.R | 20 wsMed-1.2.0/wsMed/R/RandomGaussianSVDwrapper.R | 3 wsMed-1.2.0/wsMed/R/RandomGaussianZwrapper.R | 2 wsMed-1.2.0/wsMed/R/RunMCMIAnalysis.R | 8 wsMed-1.2.0/wsMed/R/TestPositiveDefinitewrapper.R | 2 wsMed-1.2.0/wsMed/R/ThetaHatStarWrapper.R | 13 wsMed-1.2.0/wsMed/R/ThetaHatWrapper.R | 2 wsMed-1.2.0/wsMed/R/TransformMidsWithPrepareData.R | 10 wsMed-1.2.0/wsMed/R/WSMed.R | 347 - wsMed-1.2.0/wsMed/R/analyze_mm_categorical.R | 3 wsMed-1.2.0/wsMed/R/analyze_mm_continuous.R | 60 wsMed-1.2.0/wsMed/R/calc_basic_contrasts.R | 8 wsMed-1.2.0/wsMed/R/example_data.R | 46 wsMed-1.2.0/wsMed/R/mi-completed.R |only wsMed-1.2.0/wsMed/R/mi-marginal-moments.R |only wsMed-1.2.0/wsMed/R/model-covariances.R |only wsMed-1.2.0/wsMed/R/plot-effects.R | 45 wsMed-1.2.0/wsMed/R/plot_moderation_curve.R | 1 wsMed-1.2.0/wsMed/R/print-helper.R | 70 wsMed-1.2.0/wsMed/R/print-wsMed.R | 96 wsMed-1.2.0/wsMed/R/printGM.R | 71 wsMed-1.2.0/wsMed/R/sort_parameters.R | 6 wsMed-1.2.0/wsMed/R/standardization-internal.R | 7 wsMed-1.2.0/wsMed/R/standardize_moderation.R | 7 wsMed-1.2.0/wsMed/R/totaladjwrapper.R | 2 wsMed-1.2.0/wsMed/R/utils.R | 2 wsMed-1.2.0/wsMed/R/workflow-api.R |only wsMed-1.2.0/wsMed/R/workflow-assemble.R |only wsMed-1.2.0/wsMed/R/workflow-compatibility.R |only wsMed-1.2.0/wsMed/R/workflow-core.R |only wsMed-1.2.0/wsMed/R/workflow-diagnostics.R |only wsMed-1.2.0/wsMed/R/workflow-methods.R |only wsMed-1.2.0/wsMed/R/workflow-plots.R |only wsMed-1.2.0/wsMed/R/workflow-reproducibility.R |only wsMed-1.2.0/wsMed/R/workflow-results.R |only wsMed-1.2.0/wsMed/R/workflow-summary.R |only wsMed-1.2.0/wsMed/R/workflow-support.R |only wsMed-1.2.0/wsMed/R/wsMed-helper.R | 56 wsMed-1.2.0/wsMed/R/wsmed_categorical.R |only wsMed-1.2.0/wsMed/R/wsmed_examples.R |only wsMed-1.2.0/wsMed/README.md | 136 wsMed-1.2.0/wsMed/build/partial.rdb |only wsMed-1.2.0/wsMed/build/vignette.rds |binary wsMed-1.2.0/wsMed/data/wsmed_examples.rda |only wsMed-1.2.0/wsMed/inst/COPYRIGHTS |only wsMed-1.2.0/wsMed/inst/doc/AnalysisGuide.Rmd |only wsMed-1.2.0/wsMed/inst/doc/AnalysisGuide.html |only wsMed-1.2.0/wsMed/inst/doc/CategoricalPredictors.Rmd |only wsMed-1.2.0/wsMed/inst/doc/CategoricalPredictors.html |only wsMed-1.2.0/wsMed/inst/doc/CompatibleImputation.Rmd |only wsMed-1.2.0/wsMed/inst/doc/CompatibleImputation.html |only wsMed-1.2.0/wsMed/inst/doc/GenerateModelCN.Rmd | 414 - wsMed-1.2.0/wsMed/inst/doc/GenerateModelCN.html | 443 -- wsMed-1.2.0/wsMed/inst/doc/GenerateModelCP.Rmd | 386 - wsMed-1.2.0/wsMed/inst/doc/GenerateModelCP.html | 421 - wsMed-1.2.0/wsMed/inst/doc/GenerateModelCustom.Rmd | 655 ++- wsMed-1.2.0/wsMed/inst/doc/GenerateModelCustom.html | 785 ++- wsMed-1.2.0/wsMed/inst/doc/GenerateModelP.Rmd | 377 - wsMed-1.2.0/wsMed/inst/doc/GenerateModelP.html | 375 - wsMed-1.2.0/wsMed/inst/doc/GenerateModelPC.Rmd | 377 - wsMed-1.2.0/wsMed/inst/doc/GenerateModelPC.html | 426 -- wsMed-1.2.0/wsMed/inst/doc/GetStarted.Rmd |only wsMed-1.2.0/wsMed/inst/doc/GetStarted.html |only wsMed-1.2.0/wsMed/inst/doc/MEMORE_vs_wsMed.Rmd | 1144 +---- wsMed-1.2.0/wsMed/inst/doc/MEMORE_vs_wsMed.html | 1288 ++---- wsMed-1.2.0/wsMed/inst/doc/ModularWorkflow.Rmd |only wsMed-1.2.0/wsMed/inst/doc/ModularWorkflow.html |only wsMed-1.2.0/wsMed/inst/doc/PlottingEffects.Rmd | 379 + wsMed-1.2.0/wsMed/inst/doc/PlottingEffects.html | 397 + wsMed-1.2.0/wsMed/inst/doc/ResultsGuide.Rmd |only wsMed-1.2.0/wsMed/inst/doc/ResultsGuide.html |only wsMed-1.2.0/wsMed/inst/doc/StandardizedModeratedMediation.Rmd | 525 +- wsMed-1.2.0/wsMed/inst/doc/StandardizedModeratedMediation.html | 586 +- wsMed-1.2.0/wsMed/inst/doc/WorkflowReliability.Rmd |only wsMed-1.2.0/wsMed/inst/doc/WorkflowReliability.html |only wsMed-1.2.0/wsMed/inst/doc/WsMed.Rmd | 1928 +-------- wsMed-1.2.0/wsMed/inst/doc/WsMed.html | 2112 ++-------- wsMed-1.2.0/wsMed/inst/doc/printGM.Rmd | 21 wsMed-1.2.0/wsMed/inst/doc/printGM.html | 34 wsMed-1.2.0/wsMed/man/ARIVwrapper.Rd | 4 wsMed-1.2.0/wsMed/man/GenerateModelCN.Rd | 11 wsMed-1.2.0/wsMed/man/GenerateModelCP.Rd | 11 wsMed-1.2.0/wsMed/man/GenerateModelCustom.Rd | 21 wsMed-1.2.0/wsMed/man/GenerateModelP.Rd | 11 wsMed-1.2.0/wsMed/man/GenerateModelPC.Rd | 11 wsMed-1.2.0/wsMed/man/ImputeData.Rd | 2 wsMed-1.2.0/wsMed/man/Lav2RAM2.Rd | 2 wsMed-1.2.0/wsMed/man/MCDefWrapper.Rd | 2 wsMed-1.2.0/wsMed/man/MCMI2.Rd | 54 wsMed-1.2.0/wsMed/man/MCStd2.Rd | 20 wsMed-1.2.0/wsMed/man/MICombineWrapper.Rd | 2 wsMed-1.2.0/wsMed/man/PrepareData.Rd | 10 wsMed-1.2.0/wsMed/man/PrepareMissingData.Rd | 7 wsMed-1.2.0/wsMed/man/RAM2Lav2.Rd | 6 wsMed-1.2.0/wsMed/man/RandomGaussianSVDwrapper.Rd | 6 wsMed-1.2.0/wsMed/man/RunMCMIAnalysis.Rd | 30 wsMed-1.2.0/wsMed/man/StdLav2.Rd | 16 wsMed-1.2.0/wsMed/man/StdRAM2.Rd | 16 wsMed-1.2.0/wsMed/man/TestPositiveDefinitewrapper.Rd | 2 wsMed-1.2.0/wsMed/man/ThetaHatStarWrapper.Rd | 13 wsMed-1.2.0/wsMed/man/ThetaHatWrapper.Rd | 2 wsMed-1.2.0/wsMed/man/TotalAdjwrapper.Rd | 4 wsMed-1.2.0/wsMed/man/TransformMidsWithPrepareData.Rd | 2 wsMed-1.2.0/wsMed/man/analyze_mm_continuous.Rd | 64 wsMed-1.2.0/wsMed/man/apply_standardization.Rd | 2 wsMed-1.2.0/wsMed/man/bootstrap_sd_list.Rd | 2 wsMed-1.2.0/wsMed/man/build_definitions.Rd | 2 wsMed-1.2.0/wsMed/man/build_path_std_map.Rd | 2 wsMed-1.2.0/wsMed/man/build_std_map.Rd | 2 wsMed-1.2.0/wsMed/man/calc_basic_contrasts.Rd | 48 wsMed-1.2.0/wsMed/man/dot-make_ci_names.Rd | 4 wsMed-1.2.0/wsMed/man/evaluate_definitions_unstd_v2.Rd | 2 wsMed-1.2.0/wsMed/man/evaluate_definitions_v3.Rd | 2 wsMed-1.2.0/wsMed/man/example_data.Rd | 47 wsMed-1.2.0/wsMed/man/extract_all_parameters.Rd | 2 wsMed-1.2.0/wsMed/man/fix_pct_names.Rd | 4 wsMed-1.2.0/wsMed/man/generate_mc_samples.Rd | 2 wsMed-1.2.0/wsMed/man/get_all_variables_from_path_map.Rd | 2 wsMed-1.2.0/wsMed/man/get_indirect_paths.Rd | 2 wsMed-1.2.0/wsMed/man/get_sd_target_variables.Rd | 2 wsMed-1.2.0/wsMed/man/make_contrasts.Rd | 4 wsMed-1.2.0/wsMed/man/mc_summary_pct.Rd | 2 wsMed-1.2.0/wsMed/man/plot_effects.Rd | 3 wsMed-1.2.0/wsMed/man/printGM.Rd | 2 wsMed-1.2.0/wsMed/man/resolve_all_dependencies.Rd | 2 wsMed-1.2.0/wsMed/man/run_mc_mediation.Rd | 2 wsMed-1.2.0/wsMed/man/sort_parameters.Rd | 2 wsMed-1.2.0/wsMed/man/standardize_moderation.Rd | 22 wsMed-1.2.0/wsMed/man/summarize_mc_ci.Rd | 2 wsMed-1.2.0/wsMed/man/wsMed.Rd | 131 wsMed-1.2.0/wsMed/man/wsmed_categorical.Rd |only wsMed-1.2.0/wsMed/man/wsmed_contrasts.Rd |only wsMed-1.2.0/wsMed/man/wsmed_effects.Rd |only wsMed-1.2.0/wsMed/man/wsmed_examples.Rd |only wsMed-1.2.0/wsMed/man/wsmed_fit.Rd |only wsMed-1.2.0/wsMed/man/wsmed_infer.Rd |only wsMed-1.2.0/wsMed/man/wsmed_inspect.Rd |only wsMed-1.2.0/wsMed/man/wsmed_methods.Rd |only wsMed-1.2.0/wsMed/man/wsmed_model.Rd |only wsMed-1.2.0/wsMed/man/wsmed_plots.Rd |only wsMed-1.2.0/wsMed/man/wsmed_reproducibility.Rd |only wsMed-1.2.0/wsMed/tests/testthat/test-GenerateModelCN.R | 20 wsMed-1.2.0/wsMed/tests/testthat/test-GenerateModelCP.R | 8 wsMed-1.2.0/wsMed/tests/testthat/test-GenerateModelCustom.R | 10 wsMed-1.2.0/wsMed/tests/testthat/test-GenerateModelP.R | 20 wsMed-1.2.0/wsMed/tests/testthat/test-GenerateModelPC.R | 16 wsMed-1.2.0/wsMed/tests/testthat/test-ImputeData.R | 18 wsMed-1.2.0/wsMed/tests/testthat/test-MCMI2.R | 14 wsMed-1.2.0/wsMed/tests/testthat/test-MCStd2.R | 14 wsMed-1.2.0/wsMed/tests/testthat/test-PrepareData.r | 12 wsMed-1.2.0/wsMed/tests/testthat/test-PrepareMissingData.r | 20 wsMed-1.2.0/wsMed/tests/testthat/test-WsMed.R | 18 wsMed-1.2.0/wsMed/tests/testthat/test-analyze-mm-continuous.R | 32 wsMed-1.2.0/wsMed/tests/testthat/test-analyze_mm_categorical.R | 24 wsMed-1.2.0/wsMed/tests/testthat/test-choice-case.R | 8 wsMed-1.2.0/wsMed/tests/testthat/test-get_indirect_paths.R | 14 wsMed-1.2.0/wsMed/tests/testthat/test-mc-reproducibility.R |only wsMed-1.2.0/wsMed/tests/testthat/test-mi-completed.R |only wsMed-1.2.0/wsMed/tests/testthat/test-modular-workflow.R |only wsMed-1.2.0/wsMed/tests/testthat/test-packaged-data.R |only wsMed-1.2.0/wsMed/tests/testthat/test-print.WsMed.R | 20 wsMed-1.2.0/wsMed/tests/testthat/test-printGM.R | 6 wsMed-1.2.0/wsMed/tests/testthat/test-product-covariances.R |only wsMed-1.2.0/wsMed/tests/testthat/test-standardization-phase1.R | 18 wsMed-1.2.0/wsMed/tests/testthat/test-standardization-phase2.R | 9 wsMed-1.2.0/wsMed/tests/testthat/test-workflow-compatibility.R |only wsMed-1.2.0/wsMed/tests/testthat/test-workflow-presentation.R |only wsMed-1.2.0/wsMed/tests/testthat/test-workflow-reliability.R |only wsMed-1.2.0/wsMed/tests/testthat/test-workflow-summary.R |only wsMed-1.2.0/wsMed/tests/testthat/test-workflow-support.R |only wsMed-1.2.0/wsMed/tools |only wsMed-1.2.0/wsMed/vignettes/AnalysisGuide.Rmd |only wsMed-1.2.0/wsMed/vignettes/AnalysisGuide.Rmd.original |only wsMed-1.2.0/wsMed/vignettes/CategoricalPredictors.Rmd |only wsMed-1.2.0/wsMed/vignettes/CategoricalPredictors.Rmd.original |only wsMed-1.2.0/wsMed/vignettes/CompatibleImputation.Rmd |only wsMed-1.2.0/wsMed/vignettes/CompatibleImputation.Rmd.original |only wsMed-1.2.0/wsMed/vignettes/GenerateModelCN.Rmd | 414 - wsMed-1.2.0/wsMed/vignettes/GenerateModelCN.Rmd.original | 414 - wsMed-1.2.0/wsMed/vignettes/GenerateModelCP.Rmd | 386 - wsMed-1.2.0/wsMed/vignettes/GenerateModelCP.Rmd.original | 386 - wsMed-1.2.0/wsMed/vignettes/GenerateModelCustom.Rmd | 655 ++- wsMed-1.2.0/wsMed/vignettes/GenerateModelCustom.Rmd.original | 483 +- wsMed-1.2.0/wsMed/vignettes/GenerateModelP.Rmd | 377 - wsMed-1.2.0/wsMed/vignettes/GenerateModelP.Rmd.original | 377 - wsMed-1.2.0/wsMed/vignettes/GenerateModelPC.Rmd | 377 - wsMed-1.2.0/wsMed/vignettes/GenerateModelPC.Rmd.original | 377 - wsMed-1.2.0/wsMed/vignettes/GetStarted.Rmd |only wsMed-1.2.0/wsMed/vignettes/GetStarted.Rmd.original |only wsMed-1.2.0/wsMed/vignettes/MEMORE_vs_wsMed.Rmd | 1144 +---- wsMed-1.2.0/wsMed/vignettes/MEMORE_vs_wsMed.Rmd.original | 209 wsMed-1.2.0/wsMed/vignettes/ModularWorkflow.Rmd |only wsMed-1.2.0/wsMed/vignettes/ModularWorkflow.Rmd.original |only wsMed-1.2.0/wsMed/vignettes/PlottingEffects.Rmd | 379 + wsMed-1.2.0/wsMed/vignettes/PlottingEffects.Rmd.original | 313 + wsMed-1.2.0/wsMed/vignettes/ResultsGuide.Rmd |only wsMed-1.2.0/wsMed/vignettes/ResultsGuide.Rmd.original |only wsMed-1.2.0/wsMed/vignettes/StandardizedModeratedMediation.Rmd | 525 +- wsMed-1.2.0/wsMed/vignettes/StandardizedModeratedMediation.Rmd.original | 280 - wsMed-1.2.0/wsMed/vignettes/WorkflowReliability.Rmd |only wsMed-1.2.0/wsMed/vignettes/WorkflowReliability.Rmd.original |only wsMed-1.2.0/wsMed/vignettes/WsMed.Rmd | 1928 +-------- wsMed-1.2.0/wsMed/vignettes/WsMed.Rmd.original | 1118 +---- wsMed-1.2.0/wsMed/vignettes/figures |only wsMed-1.2.0/wsMed/vignettes/printGM.Rmd | 21 wsMed-1.2.0/wsMed/vignettes/printGM.Rmd.original | 21 242 files changed, 10752 insertions(+), 15434 deletions(-)
Title: Utility Functions for Plotting
Description: Provides utility functions for plotting. Includes functions for color manipulation, plot customization, panel size control, data optimization for plots, and layout adjustments.
Author: Meng Xu [aut, cre] ,
Haoliang Zhu [aut]
Maintainer: Meng Xu <mengxu98@qq.com>
Diff between thisplot versions 0.4.3 dated 2026-08-01 and 0.4.6 dated 2026-10-28
thisplot-0.4.3/thisplot/man/normalize_to_sum.Rd |only thisplot-0.4.6/thisplot/DESCRIPTION | 26 thisplot-0.4.6/thisplot/MD5 | 80 thisplot-0.4.6/thisplot/NAMESPACE | 14 thisplot-0.4.6/thisplot/NEWS.md | 73 thisplot-0.4.6/thisplot/R/DimDataPlot.R | 114 - thisplot-0.4.6/thisplot/R/GraphPlot.R | 121 - thisplot-0.4.6/thisplot/R/NetworkPlot.R |only thisplot-0.4.6/thisplot/R/StatPlot.R | 73 thisplot-0.4.6/thisplot/R/compute_velocity_on_grid.R | 2 thisplot-0.4.6/thisplot/R/drop_data.R | 8 thisplot-0.4.6/thisplot/R/get_colors.R | 309 ++ thisplot-0.4.6/thisplot/R/heatmap.R | 81 thisplot-0.4.6/thisplot/R/invert_figures.R |only thisplot-0.4.6/thisplot/R/invert_png.R |only thisplot-0.4.6/thisplot/R/invert_svg.R |only thisplot-0.4.6/thisplot/R/major_grid.R | 3 thisplot-0.4.6/thisplot/R/panel_fix.R | 3 thisplot-0.4.6/thisplot/R/plot_autosize.R |only thisplot-0.4.6/thisplot/R/plot_histogram.R |only thisplot-0.4.6/thisplot/R/plot_scatter.R |only thisplot-0.4.6/thisplot/R/print_colored_table.R |only thisplot-0.4.6/thisplot/R/rasterise_plot.R |only thisplot-0.4.6/thisplot/R/sankey.R | 194 - thisplot-0.4.6/thisplot/R/themes.R | 64 thisplot-0.4.6/thisplot/R/thisplot-package.R | 3 thisplot-0.4.6/thisplot/R/utils.R | 194 + thisplot-0.4.6/thisplot/R/visual_colors.R | 11 thisplot-0.4.6/thisplot/README.md | 1098 +++++----- thisplot-0.4.6/thisplot/man/GraphPlot.Rd | 2 thisplot-0.4.6/thisplot/man/NetworkPlot.Rd |only thisplot-0.4.6/thisplot/man/annotation_block_fill_graphics.Rd | 9 thisplot-0.4.6/thisplot/man/annotation_block_graphics.Rd | 9 thisplot-0.4.6/thisplot/man/build_heatmap_annotation.Rd | 17 thisplot-0.4.6/thisplot/man/cluster_within_group2.Rd | 7 thisplot-0.4.6/thisplot/man/get_colors.Rd | 16 thisplot-0.4.6/thisplot/man/get_legend.Rd | 20 thisplot-0.4.6/thisplot/man/heatmap_fixsize.Rd | 15 thisplot-0.4.6/thisplot/man/heatmap_rendersize.Rd | 16 thisplot-0.4.6/thisplot/man/invert_figures.Rd |only thisplot-0.4.6/thisplot/man/invert_png.Rd |only thisplot-0.4.6/thisplot/man/invert_svg.Rd |only thisplot-0.4.6/thisplot/man/major_grid.Rd | 3 thisplot-0.4.6/thisplot/man/no_legend.Rd |only thisplot-0.4.6/thisplot/man/no_margin.Rd |only thisplot-0.4.6/thisplot/man/no_x_text.Rd |only thisplot-0.4.6/thisplot/man/no_y_text.Rd |only thisplot-0.4.6/thisplot/man/plot_autocompose.Rd |only thisplot-0.4.6/thisplot/man/plot_autosize.Rd |only thisplot-0.4.6/thisplot/man/plot_histogram.Rd |only thisplot-0.4.6/thisplot/man/plot_scatter.Rd |only thisplot-0.4.6/thisplot/man/print_colored_table.Rd |only thisplot-0.4.6/thisplot/man/rasterise_plot.Rd |only 53 files changed, 1498 insertions(+), 1087 deletions(-)
Title: Spatial Regression Models with Compositional Data
Description: Spatial and non-spatial regression models with compositional responses (and compositional predictors) using the alpha--transformation. Relevant papers include: Tsagris M. and Pantazis Y. (2026), <doi:10.48550/arXiv.2510.12663>, Tsagris M. (2015), <https://soche.cl/chjs/volumes/06/02/Tsagris(2015).pdf>, Tsagris M.T., Preston S. and Wood A.T.A. (2011), <doi:10.48550/arXiv.1106.1451>.
Author: Michail Tsagris [aut, cre]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between CompositionalSR versions 1.4 dated 2026-04-14 and 1.5 dated 2026-10-28
DESCRIPTION | 8 +++--- MD5 | 28 +++++++++++---------- NAMESPACE | 2 - R/alfa.betest.R |only R/alfa.esf.R | 53 ++++++++++++++++++++++++++++++++++------- R/alfa.reg.R | 2 - R/alfa.reg2.R | 2 - R/alfa.sar.R | 2 - R/alfa.slx.R | 2 - R/alfa.slx2.R | 2 - R/areg.R | 18 ++++++++----- R/rob.alfareg.R | 2 - man/CompositionalSR-package.Rd | 4 +-- man/alfa.betest.Rd |only man/alfa.esf.Rd | 17 +++++++++---- man/cv.alfaesf.Rd | 3 -- 16 files changed, 97 insertions(+), 48 deletions(-)
More information about CompositionalSR at CRAN
Permanent link
Title: Causal Modeling with Coincidence Analysis
Description: Provides comprehensive functionalities for causal modeling with Coincidence Analysis (CNA), which is a configurational comparative method of causal data analysis that was first introduced in Baumgartner (2009) <doi:10.1177/0049124109339369>, and generalized in Baumgartner & Ambuehl (2020) <doi:10.1017/psrm.2018.45>. CNA is designed to recover INUS-causation from data, which is particularly relevant for analyzing processes featuring conjunctural causation (component causation) and equifinality (alternative causation). CNA is currently the only method for INUS-discovery that allows for multiple effects (outcomes/endogenous factors), meaning it can analyze common-cause and causal chain structures. Moreover, as of version 4.0, it is the only method of its kind that provides measures for model evaluation and selection that are custom-made for the problem of INUS-discovery.
Author: Mathias Ambuehl [aut, cre, cph],
Michael Baumgartner [aut, cph],
Ruedi Epple [ctb],
Veli-Pekka Parkkinen [ctb],
Alrik Thiem [ctb]
Maintainer: Mathias Ambuehl <mathias.ambuehl@consultag.ch>
Diff between cna versions 4.0.3 dated 2025-06-02 and 4.1.0 dated 2026-10-28
cna-4.0.3/cna/R/condition.r |only cna-4.0.3/cna/man/condition.Rd |only cna-4.1.0/cna/DESCRIPTION | 8 cna-4.1.0/cna/MD5 | 143 +++++----- cna-4.1.0/cna/NAMESPACE | 6 cna-4.1.0/cna/R/RcppExports.R | 8 cna-4.1.0/cna/R/auxConfigTable.R | 4 cna-4.1.0/cna/R/cna.r | 26 + cna-4.1.0/cna/R/cnaControl.R | 10 cna-4.1.0/cna/R/cna_aux.r | 43 +++ cna-4.1.0/cna/R/coherence.r | 5 cna-4.1.0/cna/R/condList.r |only cna-4.1.0/cna/R/condTbl.r | 21 - cna-4.1.0/cna/R/condition_aux.R | 2 cna-4.1.0/cna/R/configTable.R | 15 - cna-4.1.0/cna/R/csf.R | 74 ++++- cna-4.1.0/cna/R/ctiList.R | 117 +++++++- cna-4.1.0/cna/R/cyclic.R | 9 cna-4.1.0/cna/R/detailMeasures.R | 144 +++++++--- cna-4.1.0/cna/R/full.ct.R | 7 cna-4.1.0/cna/R/func_minim.R |only cna-4.1.0/cna/R/getCondtype.R | 3 cna-4.1.0/cna/R/is.inus.R | 33 +- cna-4.1.0/cna/R/is.submodel.R | 4 cna-4.1.0/cna/R/measures_definitions.R | 4 cna-4.1.0/cna/R/minimalizeCsf.R | 8 cna-4.1.0/cna/R/print.cna.r | 27 -- cna-4.1.0/cna/R/qcond.R | 12 cna-4.1.0/cna/R/randomConds.R | 8 cna-4.1.0/cna/build/partial.rdb |binary cna-4.1.0/cna/build/vignette.rds |binary cna-4.1.0/cna/inst/NEWS | 10 cna-4.1.0/cna/inst/doc/cna.R | 66 +++-- cna-4.1.0/cna/inst/doc/cna.Rnw | 279 +++++++++++++-------- cna-4.1.0/cna/inst/doc/cna.pdf |binary cna-4.1.0/cna/man/cna-internals.Rd | 4 cna-4.1.0/cna/man/cna-package.Rd | 54 ++-- cna-4.1.0/cna/man/cna-solutions.Rd | 370 ++++++++++++++-------------- cna-4.1.0/cna/man/cna.Rd | 149 ++++++----- cna-4.1.0/cna/man/cnaControl.Rd | 382 +++++++++++++++-------------- cna-4.1.0/cna/man/coherence.Rd | 96 +++---- cna-4.1.0/cna/man/condList-methods.Rd | 2 cna-4.1.0/cna/man/condList.Rd |only cna-4.1.0/cna/man/condTbl.Rd | 229 ++++++++--------- cna-4.1.0/cna/man/configTable.Rd | 2 cna-4.1.0/cna/man/ct2df.Rd | 2 cna-4.1.0/cna/man/cyclic.Rd | 4 cna-4.1.0/cna/man/d.autonomy.Rd | 4 cna-4.1.0/cna/man/d.educate.Rd | 6 cna-4.1.0/cna/man/d.irrigate.Rd | 4 cna-4.1.0/cna/man/d.jobsecurity.Rd | 6 cna-4.1.0/cna/man/d.minaret.Rd | 78 ++--- cna-4.1.0/cna/man/d.pacts.Rd | 74 ++--- cna-4.1.0/cna/man/d.pban.Rd | 68 ++--- cna-4.1.0/cna/man/d.performance.Rd | 4 cna-4.1.0/cna/man/d.volatile.Rd | 4 cna-4.1.0/cna/man/d.women.Rd | 4 cna-4.1.0/cna/man/detailMeasures.Rd | 174 +++++++------ cna-4.1.0/cna/man/fs2cs.Rd | 2 cna-4.1.0/cna/man/full.ct.Rd | 18 - cna-4.1.0/cna/man/func_minim.Rd |only cna-4.1.0/cna/man/is.inus.Rd | 434 +++++++++++++++++---------------- cna-4.1.0/cna/man/is.submodel.Rd | 174 ++++++------- cna-4.1.0/cna/man/minimalize.Rd | 8 cna-4.1.0/cna/man/print.cna.Rd | 169 ++++++------ cna-4.1.0/cna/man/randomConds.Rd | 404 +++++++++++++++--------------- cna-4.1.0/cna/man/selectCases.Rd | 178 ++++++------- cna-4.1.0/cna/man/showMeasures.Rd | 115 +++----- cna-4.1.0/cna/man/some.Rd | 2 cna-4.1.0/cna/src/RcppExports.cpp | 14 - cna-4.1.0/cna/src/cna_init.c | 8 cna-4.1.0/cna/src/headers.h | 3 cna-4.1.0/cna/src/minimal_submodel.cpp | 2 cna-4.1.0/cna/src/utils.cpp | 20 - cna-4.1.0/cna/vignettes/cna.Rnw | 279 +++++++++++++-------- cna-4.1.0/cna/vignettes/stfloats.sty |only 76 files changed, 2579 insertions(+), 2067 deletions(-)
Title: Likelihood-Based Statistical Inference in the Fisherian
Tradition
Description: Facilitates building likelihood models in the Fisherian tradition
following Richard Royall (1997, ISBN:978-0412044113) "Statistical Evidence: A
Likelihood Paradigm". Defines generic methods for working with likelihoods
(loglik(), score(), hess_loglik(), fim()) and provides functions for pure
likelihood-based inference (support(), relative_likelihood(),
likelihood_interval(), profile_loglik()).
Author: Alexander Towell [aut, cre]
Maintainer: Alexander Towell <lex@metafunctor.com>
Diff between likelihood.model versions 1.0.1 dated 2026-05-24 and 1.0.2 dated 2026-10-28
DESCRIPTION | 6 +- MD5 | 15 ++--- NEWS.md | 10 +++ R/core-fisherian.R | 111 +++++++++++++++++++++++++------------ inst/doc/exponential-lifetime.html | 2 inst/doc/getting-started.html | 2 man/likelihood_interval.Rd | 7 ++ man/profile_loglik.Rd | 6 ++ tests/regression-profile-domain.R |only 9 files changed, 113 insertions(+), 46 deletions(-)
More information about likelihood.model at CRAN
Permanent link
Title: Dynamic Failure Rate Distributions for Survival Analysis
Description: Flexible framework for specifying survival distributions through
their hazard (failure rate) functions. Define arbitrary time-varying
hazard functions to model complex failure patterns including bathtub
curves, proportional hazards with covariates, and other non-standard
hazard behaviors. Provides automatic computation of survival, CDF, PDF,
quantiles, and sampling. Implements the likelihood model interface for
maximum likelihood estimation with right-censored and left-censored
survival data.
Author: Alexander Towell [aut, cre]
Maintainer: Alexander Towell <queelius@gmail.com>
Diff between flexhaz versions 0.5.2 dated 2026-05-23 and 0.5.3 dated 2026-10-28
DESCRIPTION | 6 +-- MD5 | 21 ++++++------ NEWS.md | 8 ++++ R/dfr_dist.R | 17 +++++++--- R/utils.R | 25 ++++++++++++++- README.md | 44 ++++++++++++--------------- inst/doc/custom_distributions.html | 6 +-- inst/doc/failure_rate.html | 4 +- inst/doc/flexhaz-package.html | 4 +- man/dfr_dist.Rd | 8 +++- tests/testthat/Rplots.pdf |binary tests/testthat/test-observation-validation.R |only 12 files changed, 92 insertions(+), 51 deletions(-)
Title: Compositional Maximum Likelihood Estimation
Description: Provides composable optimization strategies for maximum likelihood
estimation (MLE). Solvers are first-class functions that combine via
sequential chaining, parallel racing, and random restarts. Implements
gradient ascent, Newton-Raphson, quasi-Newton (BFGS), and derivative-free
methods with support for constrained optimization and tracing. Returns
'mle' objects compatible with 'algebraic.mle' for downstream analysis.
Methods based on Nocedal J, Wright SJ (2006) "Numerical Optimization"
<doi:10.1007/978-0-387-40065-5>.
Author: Alexander Towell [aut, cre]
Maintainer: Alexander Towell <queelius@gmail.com>
Diff between compositional.mle versions 2.0.0 dated 2026-03-19 and 2.0.1 dated 2026-10-28
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- NEWS.md | 7 +++++++ R/compose.R | 8 ++++---- inst/doc/case-studies.html | 4 ++-- inst/doc/getting-started.html | 4 ++-- inst/doc/mle-ecosystem.html | 4 ++-- inst/doc/strategy-design.html | 4 ++-- inst/doc/theory-and-intuition.html | 4 ++-- tests/testthat/test-meta-solvers.R | 37 +++++++++++++++++++++++++++++++++++++ 10 files changed, 70 insertions(+), 26 deletions(-)
More information about compositional.mle at CRAN
Permanent link
Title: Algebraic Maximum Likelihood Estimators
Description: The maximum likelihood estimator (MLE) is a technology: under
regularity conditions, any MLE is asymptotically normal with variance given
by the inverse Fisher information. This package exploits that structure by
defining an algebra over MLEs. Compose independent estimators into joint
MLEs via block-diagonal covariance ('joint'), optimally combine repeated
estimates via inverse-variance weighting ('combine'), propagate
transformations via the delta method ('rmap'), and bridge to distribution
algebra via conversion to normal or multivariate normal objects ('as_dist').
Supports asymptotic ('mle', 'mle_numerical') and bootstrap ('mle_boot')
estimators with a unified interface for inference: confidence intervals,
standard errors, AIC, Fisher information, and predictive intervals.
For background on maximum likelihood estimation, see Casella and Berger
(2002, ISBN:978-0534243128). For the delta method and variance estimation,
see Lehmann and Casella (1998, ISBN:978-0387985022).
Author: Alexander Towell [aut, cre]
Maintainer: Alexander Towell <lex@metafunctor.com>
Diff between algebraic.mle versions 2.0.2 dated 2026-03-19 and 2.0.3 dated 2026-10-28
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 11 +++++++++++ R/combine.R | 37 +++++++++++++++++++++++++++++++++---- R/mle_rmap.R | 2 +- man/combine.Rd | 5 +++++ tests/testthat/test-combine.R | 35 +++++++++++++++++++++++++++++++++++ tests/testthat/test-mle_rmap.R | 13 +++++++++++++ 8 files changed, 108 insertions(+), 15 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-11-26 1.0.1
2024-01-19 1.0.0
Title: Common Functionality for the 'dynverse' Packages
Description: Provides common functionality for the 'dynverse' packages.
'dynverse' is created to support the development, execution, and benchmarking of trajectory inference methods.
For more information, check out <https://dynverse.org>.
Author: Robrecht Cannoodt [aut, cre] ,
Wouter Saelens [aut]
Maintainer: Robrecht Cannoodt <rcannood@gmail.com>
Diff between dynutils versions 1.0.12 dated 2025-09-02 and 1.0.13 dated 2026-10-28
dynutils-1.0.12/dynutils/man/dynutils.Rd |only dynutils-1.0.13/dynutils/DESCRIPTION | 10 dynutils-1.0.13/dynutils/MD5 | 52 ++-- dynutils-1.0.13/dynutils/NAMESPACE | 129 +++++----- dynutils-1.0.13/dynutils/NEWS.md | 6 dynutils-1.0.13/dynutils/R/calculate_distance.R | 43 +-- dynutils-1.0.13/dynutils/R/package.R | 5 dynutils-1.0.13/dynutils/R/spearman_rank_sparse.R | 1 dynutils-1.0.13/dynutils/build/vignette.rds |binary dynutils-1.0.13/dynutils/inst/doc/functionality.html | 82 +++--- dynutils-1.0.13/dynutils/man/dynutils-package.Rd |only dynutils-1.0.13/dynutils/tests/testthat/test-add_class.R | 2 dynutils-1.0.13/dynutils/tests/testthat/test-assertions.R | 2 dynutils-1.0.13/dynutils/tests/testthat/test-calculate_distance.R | 79 +++++- dynutils-1.0.13/dynutils/tests/testthat/test-calculate_mean.R | 2 dynutils-1.0.13/dynutils/tests/testthat/test-check_packages.R | 2 dynutils-1.0.13/dynutils/tests/testthat/test-expand_matrix.R | 2 dynutils-1.0.13/dynutils/tests/testthat/test-extend_with.R | 10 dynutils-1.0.13/dynutils/tests/testthat/test-h5.R | 65 ++--- dynutils-1.0.13/dynutils/tests/testthat/test-inherit_default_params.R | 2 dynutils-1.0.13/dynutils/tests/testthat/test-mapdf.R | 2 dynutils-1.0.13/dynutils/tests/testthat/test-news.R | 4 dynutils-1.0.13/dynutils/tests/testthat/test-project_to_segments.R | 2 dynutils-1.0.13/dynutils/tests/testthat/test-random_time_string.R | 2 dynutils-1.0.13/dynutils/tests/testthat/test-safe_tempdir.R | 2 dynutils-1.0.13/dynutils/tests/testthat/test-scaling.R | 34 +- dynutils-1.0.13/dynutils/tests/testthat/test-spearman_rank_sparse.R | 20 + dynutils-1.0.13/dynutils/tests/testthat/test-tibble.R | 2 28 files changed, 331 insertions(+), 231 deletions(-)
Title: 'C++' Implementations of Functional Enrichment Analysis
Description: Fast implementations of functional enrichment analysis methods using 'C++' via 'Rcpp'.
Currently provides Over-Representation Analysis (ORA), Gene Set Enrichment Analysis (GSEA),
design-aware GSEA on RNA-seq counts with per-sample gene set scoring, Weighted Enrichment
Analysis for ORA and GSEA, Network-based Set Enrichment Analysis (NSEA), multi-layer
network-based enrichment, and multi-omics integration workflows. Additional
features include early fusion at the feature level, late fusion at the pathway level,
multi-omics contribution tracing, topology-aware explanation helpers, Bayesian term
selection, and extremely fast Random Walk with Restart (RWR) using 'RcppEigen'. The
enrichment methods build on GSEA by Subramanian et al. (2005)
<doi:10.1073/pnas.0506580102>, the multilevel strategy derived from 'fgsea'
by Korotkevich et al. (2021) <doi:10.1101/060012>, and network-based
enrichment ideas described by Glaab et al. (2012)
<doi:10.1093/bioinformatics/bts389>.
Author: Guangchuang Yu [aut, cre]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between enrichit versions 0.2.6 dated 2026-10-06 and 0.2.7 dated 2026-10-28
DESCRIPTION | 21 +- MD5 | 51 +++-- NAMESPACE | 10 NEWS.md | 336 +++++++++++++++++++-------------- R/bayes_enrich.R | 41 +++- R/deseq2.R |only R/dsea_pathway.R |only R/gsea.R | 104 +++++++++- R/nsea.R | 38 ++- R/ora_gson.R | 57 ++++- R/utilities.R | 94 ++++++++- README.md | 15 + man/as_genes.Rd |only man/as_ranked.Rd |only man/bayes_enrich.Rd | 9 man/dsea.Rd |only man/enrichit-package.Rd | 2 man/ssgsea_scores.Rd |only src/enrichit.cpp | 30 ++ src/gsea_multilevel.cpp | 20 + tests/testthat/test-accessors.R | 34 +++ tests/testthat/test-bayes-enrich.R | 71 ++++++ tests/testthat/test-converters.R | 25 +- tests/testthat/test-deseq2.R |only tests/testthat/test-dsea-pathway.R |only tests/testthat/test-filter-gene-sets.R |only tests/testthat/test-gsea-edge-guards.R |only tests/testthat/test-gsea.R | 88 +++++--- tests/testthat/test-gson-helpers.R | 5 tests/testthat/test-nsea.R | 60 +++++ tests/testthat/test-ora.R | 176 +++++++++++++++++ tests/testthat/test-qvalue-cutoff.R |only 32 files changed, 1028 insertions(+), 259 deletions(-)
Title: Fast Interpretable Greedy-Tree Sums for Tree Ensembles
Description: Flexible, interpretable machine learning algorithm for additive
tree sums (FIGS). Fits a sum of shallow classification and regression
trees (CART) by greedily minimizing residual impurity, growing a new
tree or deepening an existing one at each step, whichever reduces the
residuals most. Supports regression and two-class classification, variable
importance, 'ggplot2' graphics, bootstrap ensembling and seamless
integration with 'parsnip' and 'tidymodels' workflows. The method is
described in Tan et al. (2023) <doi:10.1073/pnas.2310151122>.
Author: Joao Paulo Assis Bonifacio [aut, cre, cph] ,
Geraldo Magela da Cruz Pereira [aut, cph] ,
Pedro Mambelli Fernandes [aut, cph] ,
Joao Vitor Andrade Alves de Souza [aut, cph]
Maintainer: Joao Paulo Assis Bonifacio <jpab.27@hotmail.com>
Diff between figsr versions 0.1.0 dated 2026-08-31 and 0.2.0 dated 2026-10-27
DESCRIPTION | 26 MD5 | 95 + NAMESPACE | 34 NEWS.md | 190 +++ R/bagging.R | 217 ++-- R/data.R |only R/dials.R | 78 - R/figs_tree.R | 532 +++++----- R/figsr-package.R |only R/fit_engine.R | 1057 ++++++++++++++------- R/ggfigs.R |only R/ggfigs_data.R |only R/ggfigs_rules.R |only R/ggfigs_tree.R |only R/importance.R | 131 +- R/plot.R | 413 +++++--- R/predict.R | 203 ++-- R/summary.R | 211 ++-- README.md | 30 build/partial.rdb |only build/vignette.rds |binary data |only inst/WORDLIST | 22 inst/doc/figsr-intro.R | 66 + inst/doc/figsr-intro.Rmd | 210 +++- inst/doc/figsr-intro.html | 288 ++++- inst/doc/missing-values.R |only inst/doc/missing-values.Rmd |only inst/doc/missing-values.html |only man/bagging_figs.Rd | 92 - man/figs.Rd | 170 ++- man/figs_tree.Rd | 85 - man/figsr-package.Rd |only man/figsr_importance.Rd | 77 - man/fit_figs.Rd | 110 +- man/ggfigs.Rd |only man/max_splits.Rd | 42 man/max_trees.Rd | 42 man/pima_diabetes.Rd |only man/plot.figsr_fit.Rd | 94 + man/predict.bagging_figs_fit.Rd | 52 - man/predict.figsr_fit.Rd | 58 - man/predict_figs.Rd | 53 - man/print.figsr_fit.Rd | 52 - man/summary.figsr_fit.Rd | 52 - man/update.figs_tree.Rd |only tests/testthat/fixtures |only tests/testthat/test-classification-probabilities.R |only tests/testthat/test-deep-node-values.R |only tests/testthat/test-edge-cases.R |only tests/testthat/test-engine-regression.R |only tests/testthat/test-formula-interface.R |only tests/testthat/test-ggfigs.R |only tests/testthat/test-mia-consumers.R |only tests/testthat/test-mia-engine.R |only tests/testthat/test-mia-integration.R |only tests/testthat/test-na-method.R |only tests/testthat/test-parsnip.R | 185 ++- tests/testthat/test-predict-missing.R |only tests/testthat/test-print-plot.R |only tests/testthat/test-split-gain.R |only vignettes/figsr-intro.Rmd | 210 +++- vignettes/missing-values.Rmd |only 63 files changed, 3401 insertions(+), 1776 deletions(-)
Title: Simulate and Estimate Close-Kin Dispersal Kernels
Description: Functions for simulating and estimating kinship-related dispersal. Based
on the methods described in M. Jasper, T.L. Schmidt., N.W. Ahmad, S.P. Sinkins & A.A.
Hoffmann (2019) <doi:10.1111/1755-0998.13043> "A genomic approach to inferring kinship
reveals limited intergenerational dispersal in the yellow fever mosquito".
Assumes an additive variance model of dispersal in two dimensions, compatible with
Wright's neighbourhood area. Simple and composite dispersal simulations are supplied,
as well as the functions needed to estimate parent-offspring dispersal for simulated or
empirical data, and to undertake sampling design for future field studies of dispersal.
For ease of use an integrated Shiny app is also included.
Author: Moshe-Elijah Jasper [aut, cre]
Maintainer: Moshe-Elijah Jasper <moshe.jasper@unimelb.edu.au>
Diff between kindisperse versions 0.10.2 dated 2021-07-28 and 0.10.3 dated 2026-10-27
kindisperse-0.10.2/kindisperse/vignettes/FS_kin.csv |only kindisperse-0.10.3/kindisperse/DESCRIPTION | 18 kindisperse-0.10.3/kindisperse/MD5 | 177 kindisperse-0.10.3/kindisperse/NAMESPACE | 497 - kindisperse-0.10.3/kindisperse/NEWS.md | 204 kindisperse-0.10.3/kindisperse/R/DispersalModel.R | 690 - kindisperse-0.10.3/kindisperse/R/KinPairData.R | 638 - kindisperse-0.10.3/kindisperse/R/KinPairSimulation.R | 1848 ++-- kindisperse-0.10.3/kindisperse/R/app.R | 4294 +++++----- kindisperse-0.10.3/kindisperse/R/app_ports.R | 382 kindisperse-0.10.3/kindisperse/R/axial_helper_functions.R | 862 +- kindisperse-0.10.3/kindisperse/R/axials_standard.R | 1114 +- kindisperse-0.10.3/kindisperse/R/data.R | 70 kindisperse-0.10.3/kindisperse/R/dispersal_model.R | 332 kindisperse-0.10.3/kindisperse/R/export_functions.R | 270 kindisperse-0.10.3/kindisperse/R/import_kinpairs.R | 312 kindisperse-0.10.3/kindisperse/R/kindisperse-package.R | 68 kindisperse-0.10.3/kindisperse/R/sample_kindist.R | 470 - kindisperse-0.10.3/kindisperse/R/simgraph_data.R | 230 kindisperse-0.10.3/kindisperse/R/simgraph_graph.R | 942 +- kindisperse-0.10.3/kindisperse/R/simulate_kindist_composite.R | 518 - kindisperse-0.10.3/kindisperse/R/simulate_kindist_custom.R | 890 +- kindisperse-0.10.3/kindisperse/R/simulate_kindist_simple.R | 480 - kindisperse-0.10.3/kindisperse/README.md | 2563 ++--- kindisperse-0.10.3/kindisperse/build/partial.rdb |binary kindisperse-0.10.3/kindisperse/build/vignette.rds |binary kindisperse-0.10.3/kindisperse/inst/doc/using-kindisperse.R | 356 kindisperse-0.10.3/kindisperse/inst/doc/using-kindisperse.Rmd | 990 +- kindisperse-0.10.3/kindisperse/inst/doc/using-kindisperse.html | 2449 +++-- kindisperse-0.10.3/kindisperse/man/DispersalModel-class.Rd | 6 kindisperse-0.10.3/kindisperse/man/KinPairData-class.Rd | 6 kindisperse-0.10.3/kindisperse/man/KinPairSimulation-class.Rd | 6 kindisperse-0.10.3/kindisperse/man/KinPairSimulation_composite.Rd | 126 kindisperse-0.10.3/kindisperse/man/KinPairSimulation_simple.Rd | 108 kindisperse-0.10.3/kindisperse/man/access_sigmas.Rd | 12 kindisperse-0.10.3/kindisperse/man/axials.Rd | 88 kindisperse-0.10.3/kindisperse/man/axials_add.Rd | 6 kindisperse-0.10.3/kindisperse/man/axials_decompose.Rd | 6 kindisperse-0.10.3/kindisperse/man/axials_standard.Rd | 244 kindisperse-0.10.3/kindisperse/man/axials_subtract.Rd | 6 kindisperse-0.10.3/kindisperse/man/axpermute.Rd | 100 kindisperse-0.10.3/kindisperse/man/axpermute_standard.Rd | 272 kindisperse-0.10.3/kindisperse/man/axpermute_subtract.Rd | 124 kindisperse-0.10.3/kindisperse/man/breeding_cycle.Rd | 6 kindisperse-0.10.3/kindisperse/man/breeding_stage.Rd | 4 kindisperse-0.10.3/kindisperse/man/check_valid_kinship.Rd | 34 kindisperse-0.10.3/kindisperse/man/check_valid_lifestage.Rd | 34 kindisperse-0.10.3/kindisperse/man/csv_to_kinpair.Rd | 74 kindisperse-0.10.3/kindisperse/man/df_to_kinpair.Rd | 84 kindisperse-0.10.3/kindisperse/man/dispersal_vector.Rd | 4 kindisperse-0.10.3/kindisperse/man/display_appdata.Rd | 72 kindisperse-0.10.3/kindisperse/man/distances.Rd | 66 kindisperse-0.10.3/kindisperse/man/figures/README-graphical_simulation-1.png |binary kindisperse-0.10.3/kindisperse/man/figures/README-simgraphhist-1.png |binary kindisperse-0.10.3/kindisperse/man/figures/README-simgraphpin-1.png |binary kindisperse-0.10.3/kindisperse/man/filter_methods.Rd | 22 kindisperse-0.10.3/kindisperse/man/filtertype.Rd | 72 kindisperse-0.10.3/kindisperse/man/fs.Rd | 4 kindisperse-0.10.3/kindisperse/man/get_dispersal_model.Rd | 4 kindisperse-0.10.3/kindisperse/man/hs.Rd | 4 kindisperse-0.10.3/kindisperse/man/is.KinPairData.Rd | 34 kindisperse-0.10.3/kindisperse/man/is.KinPairSimulation.Rd | 34 kindisperse-0.10.3/kindisperse/man/kernelshape.Rd | 4 kindisperse-0.10.3/kindisperse/man/kerneltype.Rd | 88 kindisperse-0.10.3/kindisperse/man/kindisperse-package.Rd | 10 kindisperse-0.10.3/kindisperse/man/kinpair_to_csv.Rd | 60 kindisperse-0.10.3/kindisperse/man/kinpair_to_tibble.Rd | 50 kindisperse-0.10.3/kindisperse/man/kinpair_to_tsv.Rd | 60 kindisperse-0.10.3/kindisperse/man/kinship.Rd | 86 kindisperse-0.10.3/kindisperse/man/lifestage.Rd | 86 kindisperse-0.10.3/kindisperse/man/mentari.Rd | 98 kindisperse-0.10.3/kindisperse/man/mount_appdata.Rd | 82 kindisperse-0.10.3/kindisperse/man/read_kindata.Rd | 58 kindisperse-0.10.3/kindisperse/man/reset_appdata.Rd | 68 kindisperse-0.10.3/kindisperse/man/reset_tempdata.Rd | 68 kindisperse-0.10.3/kindisperse/man/retrieve_appdata.Rd | 84 kindisperse-0.10.3/kindisperse/man/retrieve_tempdata.Rd | 74 kindisperse-0.10.3/kindisperse/man/retrieveall_appdata.Rd | 76 kindisperse-0.10.3/kindisperse/man/sample_kindist.Rd | 190 kindisperse-0.10.3/kindisperse/man/sampling_stage.Rd | 6 kindisperse-0.10.3/kindisperse/man/simdims.Rd | 72 kindisperse-0.10.3/kindisperse/man/simgraph_data.Rd | 62 kindisperse-0.10.3/kindisperse/man/simgraph_graph.Rd | 148 kindisperse-0.10.3/kindisperse/man/simtype.Rd | 88 kindisperse-0.10.3/kindisperse/man/simulate_kindist_composite.Rd | 226 kindisperse-0.10.3/kindisperse/man/simulate_kindist_custom.Rd | 4 kindisperse-0.10.3/kindisperse/man/simulate_kindist_simple.Rd | 188 kindisperse-0.10.3/kindisperse/man/stages.Rd | 4 kindisperse-0.10.3/kindisperse/man/visible_stage.Rd | 4 kindisperse-0.10.3/kindisperse/vignettes/using-kindisperse.Rmd | 990 +- 90 files changed, 13542 insertions(+), 12818 deletions(-)
Title: Tools for Dyadic Multilevel Models
Description: Provides tools for dyadic multilevel modeling with linear and
generalized linear mixed-effects models. It validates and prepares
long-format cross-sectional and intensive longitudinal data, including
ecological momentary assessment designs, for distinguishable and
exchangeable dyads. It also supports datasets containing multiple observed
dyad compositions. It constructs composition-aware,
model-ready variables for Actor-Partner Interdependence Models (APIMs),
Dyad-Individual Models (DIMs), and Dyadic Score Models (DSMs). Prepared data
can be used with model engines such as 'glmmTMB' and 'brms' for Gaussian and
non-Gaussian outcomes, including counts, proportions, and skewed continuous
responses. Post-estimation tools compare compatible fitted models and
back-transform exchangeable sum-and-difference random-effect covariance
structures into member-level quantities. Experimental predictive checks
compare observed and simulated response variances and partner correlations in
Gaussian and s [...truncated...]
Author: Pascal Kueng [aut, cre, cph]
Maintainer: Pascal Kueng <kueng.pascal@gmail.com>
Diff between dyadMLM versions 0.2.0 dated 2026-08-21 and 0.3.0 dated 2026-10-27
dyadMLM-0.2.0/dyadMLM/LICENSE |only dyadMLM-0.2.0/dyadMLM/R/add_actor_partner_columns.R |only dyadMLM-0.2.0/dyadMLM/R/add_dyad_individual_columns.R |only dyadMLM-0.2.0/dyadMLM/R/add_dyadic_score_columns.R |only dyadMLM-0.2.0/dyadMLM/R/add_temporal_lag_columns.R |only dyadMLM-0.2.0/dyadMLM/R/assign_arbitrary_member_roles.R |only dyadMLM-0.2.0/dyadMLM/R/backtransform_residual_covariance.R |only dyadMLM-0.2.0/dyadMLM/R/center_predictors.R |only dyadMLM-0.2.0/dyadMLM/R/compare_nested_models.R |only dyadMLM-0.2.0/dyadMLM/R/dyad-generated-columns.R |only dyadMLM-0.2.0/dyadMLM/R/infer_dyad_compositions.R |only dyadMLM-0.2.0/dyadMLM/R/prepare_dyad_data.R |only dyadMLM-0.2.0/dyadMLM/R/print_dyadMLM_data.R |only dyadMLM-0.2.0/dyadMLM/R/summary_dyadMLM_data.R |only dyadMLM-0.2.0/dyadMLM/R/temporary_dyad_occasion_completion.R |only dyadMLM-0.2.0/dyadMLM/R/utils-args.R |only dyadMLM-0.2.0/dyadMLM/R/utils-compositions.R |only dyadMLM-0.2.0/dyadMLM/R/validate-model-compatibility.R |only dyadMLM-0.2.0/dyadMLM/R/validate_dyad_data.R |only dyadMLM-0.3.0/dyadMLM/DESCRIPTION | 29 dyadMLM-0.3.0/dyadMLM/MD5 | 202 - dyadMLM-0.3.0/dyadMLM/NAMESPACE | 11 dyadMLM-0.3.0/dyadMLM/NEWS.md | 79 dyadMLM-0.3.0/dyadMLM/R/data.R | 12 dyadMLM-0.3.0/dyadMLM/R/data_prep.R |only dyadMLM-0.3.0/dyadMLM/R/data_prep_apim.R |only dyadMLM-0.3.0/dyadMLM/R/data_prep_arbitrary_roles.R |only dyadMLM-0.3.0/dyadMLM/R/data_prep_centering.R |only dyadMLM-0.3.0/dyadMLM/R/data_prep_compositions.R |only dyadMLM-0.3.0/dyadMLM/R/data_prep_dim.R |only dyadMLM-0.3.0/dyadMLM/R/data_prep_dsm.R |only dyadMLM-0.3.0/dyadMLM/R/data_prep_generated_columns.R |only dyadMLM-0.3.0/dyadMLM/R/data_prep_lags.R |only dyadMLM-0.3.0/dyadMLM/R/data_prep_model_compatibility.R |only dyadMLM-0.3.0/dyadMLM/R/data_prep_occasion_completion.R |only dyadMLM-0.3.0/dyadMLM/R/data_prep_print.R |only dyadMLM-0.3.0/dyadMLM/R/data_prep_summary.R |only dyadMLM-0.3.0/dyadMLM/R/data_prep_validation.R |only dyadMLM-0.3.0/dyadMLM/R/dyadMLM-package.R | 10 dyadMLM-0.3.0/dyadMLM/R/model_comparison.R |only dyadMLM-0.3.0/dyadMLM/R/model_exchangeable_covariance.R |only dyadMLM-0.3.0/dyadMLM/R/predictive_checks_dependence.R |only dyadMLM-0.3.0/dyadMLM/R/predictive_checks_envelopes.R |only dyadMLM-0.3.0/dyadMLM/R/predictive_checks_groups.R |only dyadMLM-0.3.0/dyadMLM/R/predictive_checks_outcomes.R |only dyadMLM-0.3.0/dyadMLM/R/predictive_checks_plot.R |only dyadMLM-0.3.0/dyadMLM/R/predictive_checks_residuals.R |only dyadMLM-0.3.0/dyadMLM/R/predictive_checks_simulation.R |only dyadMLM-0.3.0/dyadMLM/R/utils_arguments.R |only dyadMLM-0.3.0/dyadMLM/R/utils_compositions.R |only dyadMLM-0.3.0/dyadMLM/README.md | 482 +++ dyadMLM-0.3.0/dyadMLM/inst/CITATION | 6 dyadMLM-0.3.0/dyadMLM/inst/WORDLIST | 55 dyadMLM-0.3.0/dyadMLM/inst/doc/apim.R | 39 dyadMLM-0.3.0/dyadMLM/inst/doc/apim.Rmd | 168 + dyadMLM-0.3.0/dyadMLM/inst/doc/apim.html | 1213 +++++----- dyadMLM-0.3.0/dyadMLM/inst/doc/dim.R | 18 dyadMLM-0.3.0/dyadMLM/inst/doc/dim.Rmd | 55 dyadMLM-0.3.0/dyadMLM/inst/doc/dim.html | 426 +-- dyadMLM-0.3.0/dyadMLM/inst/doc/dsm.R | 18 dyadMLM-0.3.0/dyadMLM/inst/doc/dsm.Rmd | 58 dyadMLM-0.3.0/dyadMLM/inst/doc/dsm.html | 298 +- dyadMLM-0.3.0/dyadMLM/inst/doc/getting-started.R | 13 dyadMLM-0.3.0/dyadMLM/inst/doc/getting-started.Rmd | 30 dyadMLM-0.3.0/dyadMLM/inst/doc/getting-started.html | 1149 ++++----- dyadMLM-0.3.0/dyadMLM/man/add_actor_partner_columns.Rd | 2 dyadMLM-0.3.0/dyadMLM/man/add_dyad_individual_columns.Rd | 13 dyadMLM-0.3.0/dyadMLM/man/add_dyadic_score_columns.Rd | 2 dyadMLM-0.3.0/dyadMLM/man/add_temporal_lag_columns.Rd | 2 dyadMLM-0.3.0/dyadMLM/man/assign_arbitrary_member_roles.Rd | 2 dyadMLM-0.3.0/dyadMLM/man/canonical_composition.Rd | 2 dyadMLM-0.3.0/dyadMLM/man/center_predictors.Rd | 2 dyadMLM-0.3.0/dyadMLM/man/check_dyad_outcomes.Rd |only dyadMLM-0.3.0/dyadMLM/man/check_dyad_residuals.Rd |only dyadMLM-0.3.0/dyadMLM/man/check_partner_dependence.Rd |only dyadMLM-0.3.0/dyadMLM/man/compare_nested_models.Rd | 22 dyadMLM-0.3.0/dyadMLM/man/dyadMLM-package.Rd | 10 dyadMLM-0.3.0/dyadMLM/man/dyad_generated_columns.Rd | 2 dyadMLM-0.3.0/dyadMLM/man/dyads_cross.Rd | 3 dyadMLM-0.3.0/dyadMLM/man/dyads_ild.Rd | 3 dyadMLM-0.3.0/dyadMLM/man/dyads_nbinom_cross.Rd | 3 dyadMLM-0.3.0/dyadMLM/man/dyads_nbinom_ild.Rd | 3 dyadMLM-0.3.0/dyadMLM/man/extract_exchangeable_residual_blocks.Rd | 2 dyadMLM-0.3.0/dyadMLM/man/figures |only dyadMLM-0.3.0/dyadMLM/man/format_group_count.Rd | 2 dyadMLM-0.3.0/dyadMLM/man/format_group_list.Rd | 2 dyadMLM-0.3.0/dyadMLM/man/infer_dyad_compositions.Rd | 2 dyadMLM-0.3.0/dyadMLM/man/make_dyad_suffixes.Rd | 2 dyadMLM-0.3.0/dyadMLM/man/plot.dyadMLM_outcome_check.Rd |only dyadMLM-0.3.0/dyadMLM/man/plot.dyadMLM_partner_check.Rd |only dyadMLM-0.3.0/dyadMLM/man/plot.dyadMLM_residual_check.Rd |only dyadMLM-0.3.0/dyadMLM/man/prepare_dyad_data.Rd | 14 dyadMLM-0.3.0/dyadMLM/man/print.dyadMLM_partner_check.Rd |only dyadMLM-0.3.0/dyadMLM/man/print.dyadMLM_response_simulations.Rd |only dyadMLM-0.3.0/dyadMLM/man/print.exchangeable_covariance.Rd | 2 dyadMLM-0.3.0/dyadMLM/man/recover_exchangeable_covariance.Rd | 35 dyadMLM-0.3.0/dyadMLM/man/resolve_composition_references.Rd | 2 dyadMLM-0.3.0/dyadMLM/man/resolve_dsm_role_order.Rd | 2 dyadMLM-0.3.0/dyadMLM/man/restore_observed_dyad_rows.Rd | 2 dyadMLM-0.3.0/dyadMLM/man/simulate_dyad_responses.Rd |only dyadMLM-0.3.0/dyadMLM/man/summary.dyadMLM_data.Rd | 3 dyadMLM-0.3.0/dyadMLM/man/temporarily_complete_dyad_occasions.Rd | 2 dyadMLM-0.3.0/dyadMLM/man/validate_dim_compatibility.Rd | 10 dyadMLM-0.3.0/dyadMLM/man/validate_dsm_compatibility.Rd | 2 dyadMLM-0.3.0/dyadMLM/man/validate_dyad_data.Rd | 2 dyadMLM-0.3.0/dyadMLM/tests/testthat/helper-predictive-checks.R |only dyadMLM-0.3.0/dyadMLM/tests/testthat/test-add_actor_partner_columns.R | 51 dyadMLM-0.3.0/dyadMLM/tests/testthat/test-add_temporal_lag_columns.R | 32 dyadMLM-0.3.0/dyadMLM/tests/testthat/test-backtransform-residual-covariance.R | 88 dyadMLM-0.3.0/dyadMLM/tests/testthat/test-compare_nested_models.R | 70 dyadMLM-0.3.0/dyadMLM/tests/testthat/test-predictive-checks-compositions.R |only dyadMLM-0.3.0/dyadMLM/tests/testthat/test-predictive-checks-dependence.R |only dyadMLM-0.3.0/dyadMLM/tests/testthat/test-predictive-checks-envelopes.R |only dyadMLM-0.3.0/dyadMLM/tests/testthat/test-predictive-checks-generalized.R |only dyadMLM-0.3.0/dyadMLM/tests/testthat/test-predictive-checks-occasions.R |only dyadMLM-0.3.0/dyadMLM/tests/testthat/test-predictive-checks-outcomes.R |only dyadMLM-0.3.0/dyadMLM/tests/testthat/test-predictive-checks-panels.R |only dyadMLM-0.3.0/dyadMLM/tests/testthat/test-predictive-checks-plot.R |only dyadMLM-0.3.0/dyadMLM/tests/testthat/test-predictive-checks-residuals.R |only dyadMLM-0.3.0/dyadMLM/tests/testthat/test-prepare_dyad_data.R | 108 dyadMLM-0.3.0/dyadMLM/tests/testthat/test-public-api-cleanup.R | 6 dyadMLM-0.3.0/dyadMLM/tests/testthat/test-residual-check-groups.R |only dyadMLM-0.3.0/dyadMLM/tests/testthat/test-simulate-dyad-responses.R |only dyadMLM-0.3.0/dyadMLM/tests/testthat/test-temporary_dyad_occasion_completion.R | 24 dyadMLM-0.3.0/dyadMLM/tests/testthat/test-validate_dyad_data.R | 63 dyadMLM-0.3.0/dyadMLM/vignettes/apim.Rmd | 168 + dyadMLM-0.3.0/dyadMLM/vignettes/assets/dim-grid/dim-grid.css | 14 dyadMLM-0.3.0/dyadMLM/vignettes/diagram-helpers.Rinc | 8 dyadMLM-0.3.0/dyadMLM/vignettes/dim.Rmd | 55 dyadMLM-0.3.0/dyadMLM/vignettes/dsm.Rmd | 58 dyadMLM-0.3.0/dyadMLM/vignettes/getting-started.Rmd | 30 dyadMLM-0.3.0/dyadMLM/vignettes/references.bib | 23 132 files changed, 3489 insertions(+), 1837 deletions(-)
Title: Document Intelligence via 'Docling'
Description: An interface to 'Docling', a document-understanding library that
converts 'PDF', 'DOCX', 'PPTX', 'HTML' and image documents into structured,
AI-ready data. The package wraps the 'Docling' 'Python' package through
'reticulate' to extract layout-aware text, tables and metadata, export to
'Markdown' or 'JSON', and split documents into context-rich chunks suitable
for retrieval-augmented generation (RAG) and embedding pipelines.
Author: Andre Leite [aut, cre] ,
Marcos Wasiliew [aut] ,
Hugo Vasconcelos [aut] ,
Carlos Amorim [aut] ,
Diogo Bezerra [aut] ,
Julia Nascimento Barreto [aut]
Maintainer: Andre Leite <leite@castlab.org>
Diff between doclingr versions 0.1.0 dated 2026-07-10 and 0.1.1 dated 2026-10-27
DESCRIPTION | 43 +++++++++++++-------- MD5 | 37 ++++++++++-------- NAMESPACE | 1 NEWS.md | 15 +++++++ R/chunk.R | 70 ++++++++++++++++++++++++++++++++++- R/write.R |only README.md | 9 ++++ inst/WORDLIST | 17 ++++++-- inst/doc/options.R | 6 +++ inst/doc/options.Rmd | 26 +++++++++++-- inst/doc/options.html | 75 +++++++++++++++++++++++--------------- inst/doc/rag.R | 4 +- inst/doc/rag.Rmd | 7 ++- inst/doc/rag.html | 8 ++-- man/docling_chunk.Rd | 6 +++ man/docling_write_chunks.Rd |only man/doclingr-package.Rd | 13 +++--- tests/testthat/test-chunk-embed.R | 19 ++++++++- tests/testthat/test-write.R |only vignettes/options.Rmd | 26 +++++++++++-- vignettes/rag.Rmd | 7 ++- 21 files changed, 296 insertions(+), 93 deletions(-)
Title: Simultaneous Selection by Trait and WAASB Index
Description: This tool proposes a new ranking algorithm that utilizes a "Y*WAASB" biplot generated by the 'metan'. The aim of the current package is to effectively distinguish the top-ranked genotypes in MET (Multi-Environmental Trials). For a detailed explanation of the process of obtaining "WAASB", "WAASBY" indices, and a "Y*WAASB" biplot, refer to the manual included in this package as well as the study by Olivoto & Lúcio (2020) <doi:10.1111/2041-210X.13384>. In this context, "WAASB" refers to the "Weighted Average of Absolute Scores" provided by Olivoto et al. (2019) <doi:10.2134/agronj2019.03.0220>, which quantifies the stability of genotypes across different environments using linear mixed-effect models. To run the package, you need to extract the "WAASB" and "WAASBY" coefficients using the 'metan' and apply them. This tool utilizes PCA (Principal Component Analysis) and differentiates the entries which may be genotypes, hybrids, varieties, etc using "WAASB", "WAASBY", and a c [...truncated...]
Author: Ali Arminian [aut, cre, cph]
Maintainer: Ali Arminian <abeyran@gmail.com>
Diff between rYWAASB versions 0.4.1 dated 2026-07-12 and 0.4.2 dated 2026-10-27
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NEWS.md | 5 +++++ R/bar_plot1.R | 13 +++++++------ build/stage23.rdb |binary inst/doc/rYWAASB_manual.Rmd | 2 +- inst/doc/rYWAASB_manual.html | 14 +++++++------- inst/extdata/dm.xls |binary inst/extdata/maize.xls |binary vignettes/rYWAASB_manual.Rmd | 2 +- 10 files changed, 34 insertions(+), 28 deletions(-)
Title: Patient-Level Indices from the OMOP Common Data Model
Description: Provides tools to derive standardised, reproducible patient-level
indices and covariates from Observational Medical Outcomes Partnership
(OMOP) Common Data Model (CDM) databases. Functions calculate comorbidity
and frailty scores, including the Charlson Comorbidity Index, Electronic
Frailty Index, and Hospital Frailty Risk Score, as well as body mass index,
polypharmacy, ethnicity, location, and socioeconomic status measures.
Author: Marti Catala [aut, cre] ,
Marta Alcalde-Herraiz [aut] ,
Maria T Sanchez-Santos [aut]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>
Diff between OmopIndices versions 0.1.0 dated 2026-09-17 and 0.2.0 dated 2026-10-27
DESCRIPTION | 12 - MD5 | 63 +++--- NAMESPACE | 10 NEWS.md |only R/OmopIndices-package.R | 1 R/addCharlsonIndex.R | 12 - R/addElectronicFrailtyIndex.R | 9 R/addElectronicFrailtyIndex2.R | 9 R/addIndex.R | 249 ++++++++++++++++++------ R/addUpdatedCharlsonIndex.R | 12 - R/bmi.R | 82 ++++--- R/documentationHelpers.R | 11 + R/hospitalFrailtyRiskScore.R | 9 R/polypharmacy.R | 125 ++++++++++-- R/sysdata.rda |binary R/validate.R | 48 ++++ README.md | 55 ++--- man/OmopIndices-package.Rd | 2 man/addBMI.Rd | 9 man/addCharlsonIndex.Rd | 6 man/addElectronicFrailtyIndex.Rd | 6 man/addHospitalFrailtyRiskScore.Rd | 6 man/addPolypharmacy.Rd |only man/addPolypharmacyCount.Rd | 34 --- man/addUpdatedCharlsonIndex.Rd | 6 man/figures/lifecycle-deprecated.svg |only man/figures/lifecycle-experimental.svg |only man/figures/lifecycle-stable.svg |only man/figures/lifecycle-superseded.svg |only man/windowDoc.Rd |only tests/testthat/test-addCharlsonIndex.R | 18 + tests/testthat/test-addElectronicFrailtyIndex.R | 12 - tests/testthat/test-bmi.R | 178 ++++++++++++++--- tests/testthat/test-ethnicity.R | 53 +++++ tests/testthat/test-location.R | 25 ++ tests/testthat/test-polypharmacy.R | 192 ++++++++++++++++-- 36 files changed, 961 insertions(+), 293 deletions(-)
Title: Protein Quantification in Mass Spectrometry-Based Proteomics
Description: An implementation of the MaxLFQ algorithm by
Cox et al. (2014) <doi:10.1074/mcp.M113.031591> in a comprehensive
pipeline for processing proteomics data in data-independent acquisition mode
(Pham et al. 2020 <doi:10.1093/bioinformatics/btz961>;
Pham et al. 2026 <doi:10.1021/acs.jproteome.5c01038>).
It offers additional options for protein quantification using
the N most intense fragment ions, using all fragment ions,
the median polish algorithm by Tukey (1977, ISBN:0201076160),
and a robust linear model. In general, the tool can be used to integrate
multiple proportional observations into a single quantitative value.
Author: Thang Pham [aut, cre, cph, ctb] ,
Alex Henneman [ctb]
Maintainer: Thang Pham <t.pham@amsterdamumc.nl>
Diff between iq versions 2.0.1 dated 2026-03-21 and 2.1.0 dated 2026-10-27
DESCRIPTION | 6 - MD5 | 55 +++++++------- R/iq-fast.R | 14 ++- R/iq-format.R | 33 ++++++++ build/vignette.rds |binary man/connected_component.Rd | 3 man/create_protein_list.Rd | 2 man/create_protein_table.Rd | 2 man/extract_annotation.Rd | 2 man/fast_MaxLFQ.Rd | 63 ++++++++-------- man/fast_preprocess.Rd | 81 +++++++++++---------- man/fast_read.Rd | 116 +++++++++++++++---------------- man/huber_weight.Rd |only man/long_format_to_iq_format.Rd | 4 - man/maxLFQ.Rd | 62 ++++++++-------- man/meanInt.Rd | 56 +++++++-------- man/median_polish.Rd | 60 ++++++++-------- man/plot_protein.Rd | 2 man/preprocess.Rd | 2 man/process_iq_format.Rd | 3 man/process_long_format.Rd | 3 man/process_matrix.Rd | 3 man/process_wide_format.Rd | 96 +++++++++++++------------ man/rescale.Rd | 3 man/topN.Rd | 58 ++++++++------- src/coordinate_descent.h | 22 ++++- src/iq.cpp | 149 ++++++++++++++++++++++++++-------------- src/maxlfq_bit.h | 11 +- src/utils.h | 22 ++++- 29 files changed, 533 insertions(+), 400 deletions(-)
Title: Implementation of the DISCO Metric for Internal Clustering
Evaluation
Description: Implementation of the DISCO (Density-based Internal Score for
Clusterings with nOise) metric, a cluster validity index for evaluating
density-based clustering results without ground truth labels. DISCO is the
first index to explicitly assess the quality of noise point assignments in
addition to cluster quality. It uses density-connectivity distance derived
from a minimum spanning tree of the mutual-reachability graph, providing
interpretable, bounded scores in [-1, 1]. Higher scores indicate better
clustering. Based on Beer et al. (2025)
<doi:10.48550/arXiv.2503.00127>.
Author: Amin Entezari [aut, cre] ,
Davide Chicco [ctb] ,
Anna Beer [aut] ),
Lena Krieger [aut] ),
Pascal Weber [aut] )
Maintainer: Amin Entezari <amin_entezari@outlook.com>
Diff between discoCVI versions 0.1.1 dated 2026-05-05 and 0.2.0 dated 2026-10-27
DESCRIPTION | 11 +- MD5 | 27 +++-- NAMESPACE | 2 NEWS.md |only R/RcppExports.R |only R/disco.R | 169 +++++++++++++++----------------- R/disco_tree.R |only README.md | 180 +++++++++++++++++++++++++---------- man/compute_dc_distances.Rd | 12 +- man/discoCVI-package.Rd | 7 + man/disco_samples.Rd | 6 + man/extract_dc_distances_from_mst.Rd | 9 + man/p_cluster.Rd | 4 src |only tests |only 15 files changed, 270 insertions(+), 157 deletions(-)
Title: Additional Tools for Developing Spatially Explicit Discrete
Event Simulation (SpaDES) Models
Description: Provides GIS and map utilities, plus additional modeling
tools for developing cellular automata, dynamic raster models, and
agent based models in 'SpaDES'. Included are various methods for
spatial spreading, spatial agents, GIS operations, random map
generation, and others. See '?SpaDES.tools' for a categorized
overview of these additional tools.
Author: Eliot J B McIntire [aut] ,
Alex M Chubaty [aut, cre] ,
Yong Luo [ctb],
Ceres Barros [ctb] ,
Steve Cumming [ctb],
Jean Marchal [ctb],
His Majesty the King in Right of Canada, as represented by the Minister
of Natural Resources Canada [cph]
Maintainer: Alex M Chubaty <achubaty@for-cast.ca>
Diff between SpaDES.tools versions 2.1.3 dated 2026-08-28 and 2.2.0 dated 2026-10-27
DESCRIPTION | 14 - MD5 | 108 ++++++----- NAMESPACE | 2 NEWS.md | 50 +++++ R/RcppExports.R | 59 ++++++ R/SELES.R | 2 R/distanceFromEachPoint.R | 2 R/helpers.R | 11 - R/initialize.R | 6 R/mapReduce.R | 21 +- R/mergeRaster.R | 2 R/neighbourhood.R | 125 ++++++++++--- R/numerical-comparisons.R | 2 R/release-bullets.R | 2 R/rings.R | 2 R/spades-tools-package.R | 3 R/spread-comparison.R |only R/spread.R | 218 ++++++++++++++++++------ R/spread2.R | 98 +++++++--- R/spreadCpp.R |only R/zzz.R | 3 README.md | 2 inst/WORDLIST | 18 + man/SpaDES.tools-package.Rd | 3 man/adj.Rd | 34 +-- man/adjPairsMatrix.Rd | 7 man/directions.Rd | 2 man/inRange01.Rd |only man/randomPolygons.Rd | 2 man/spread.Rd | 90 +++++++++ man/spread2-internals.Rd | 2 man/spread2.Rd | 110 ++++++++++-- man/spreadCpp.Rd |only man/spreadCppEngine.Rd |only man/spreadVsSpread2.Rd |only src/RcppExports.cpp | 46 ++++- src/adj_spread.cpp | 18 + src/inRange01.cpp |only src/spread_cpp.cpp |only tests/testthat/_spread_snapshots/_generate.R | 15 - tests/testthat/test-SELES.R | 2 tests/testthat/test-adj-helpers.R | 31 +++ tests/testthat/test-adj.R | 131 +++++++++++++- tests/testthat/test-distanceFromEachPoint.R | 10 - tests/testthat/test-inRange01.R |only tests/testthat/test-mapReduce.R | 19 +- tests/testthat/test-misc-helpers.R | 4 tests/testthat/test-neutralLandscapeMap.R | 2 tests/testthat/test-rings.R | 18 - tests/testthat/test-splitRaster.R | 2 tests/testthat/test-spokes.R | 4 tests/testthat/test-spread-allocations.R |only tests/testthat/test-spread-argValidation.R |only tests/testthat/test-spread-lengthCheckHoisted.R |only tests/testthat/test-spread-skipChecks.R |only tests/testthat/test-spread-snapshots.R | 6 tests/testthat/test-spread-spreadProbLater.R |only tests/testthat/test-spread.R | 32 ++- tests/testthat/test-spread2-argCombos.R |only tests/testthat/test-spread2.R | 106 +++++++++-- tests/testthat/test-spread3.R | 2 tests/testthat/test-spreadCpp-option.R |only tests/testthat/test-spreadCpp-stopCells.R |only tests/testthat/test-spreadCpp.R |only 64 files changed, 1135 insertions(+), 313 deletions(-)
Title: Model Selection and Multimodel Inference Made Easy
Description: Automated model selection and model-averaging. Provides a
wrapper for glm and other functions, automatically generating
all possible models (under constraints set by the user) with
the specified response and explanatory variables, and finding
the best models in terms of some Information Criterion (AIC,
AICc or BIC). Can handle very large numbers of candidate
models. Features a Genetic Algorithm to find the best models
when an exhaustive screening of the candidates is not feasible.
Author: Vincent Calcagno [aut, cre]
Maintainer: Vincent Calcagno <vincent.calcagno@inrae.fr>
Diff between glmulti versions 1.0.8 dated 2020-05-26 and 1.0.9 dated 2026-10-27
ChangeLog | 3 +++ DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- R/glmulti.r | 8 ++++---- man/coef.glmulti.Rd | 13 ++++++------- man/consensus.Rd | 2 +- man/getfit.Rd | 4 ++-- man/glmulti-class.Rd | 2 +- man/glmulti-methods.Rd | 8 ++++---- man/glmulti.Rd | 49 +++++++++++++++++++++++++++++++++++-------------- man/summary.glmulti.Rd | 2 +- man/write.Rd | 11 +++++++---- 12 files changed, 79 insertions(+), 53 deletions(-)
Title: (Bifactor) ESEM with Continuous (MLR) or Ordinal (WLSMV) Data
Description: Fits bifactor exploratory structural equation models (B-ESEM),
together with standard exploratory structural equation modeling (ESEM)
and confirmatory factor analysis (CFA), for continuous and
ordinal data. Continuous models use 'lavaan' native efa()
blocks with robust maximum likelihood (MLR) estimation.
Ordinal ESEM defaults to the 'lavaan' weighted least squares
mean- and variance-adjusted (WLSMV) estimator; ordinal B-ESEM uses a
custom diagonally weighted least squares (DWLS) path with polychoric
correlations from 'lavaan', rotation-delta standard errors via 'numDeriv',
and a mean- and variance-adjusted chi-square. Target, geomin, and oblimin
rotations use 'GPArotation'; the bifactor ESEM approach follows Morin,
Arens and Marsh (2016) <doi:10.1080/10705511.2014.961800>. Additional
features include multi-group measurement invariance (configural through
strict, with partial invariance), ESEM-within-CFA conversion, McDonald's
omega reliability suite, and the Mehrvarz and Rouder [...truncated...]
Author: Leon T. De Beer [aut, cre]
Maintainer: Leon T. De Beer <leondb@gmail.com>
Diff between bifactory versions 0.6.0 dated 2026-09-09 and 0.6.1 dated 2026-10-27
DESCRIPTION | 8 MD5 | 24 +- NAMESPACE | 2 NEWS.md | 37 +++ R/bifactor.R | 54 ++-- R/mplus_syntax.R | 65 +++-- R/ordered_esem.R | 362 +++++++++++++++----------------- R/utils.R | 16 - man/besem_ordered.Rd | 6 man/esem_ordered.Rd | 9 man/generate_mplus_besem_syntax.Rd | 17 + man/generate_mplus_syntax.Rd | 16 + tests/testthat/test-mplus_syntax.R |only tests/testthat/test-polychoric_source.R |only 14 files changed, 342 insertions(+), 274 deletions(-)
Title: Temporal Tensor Decomposition, a Dimensionality Reduction Tool
for Longitudinal Multivariate Data
Description: TEMPoral TEnsor Decomposition (TEMPTED), is a dimension reduction method for multivariate longitudinal data with varying temporal sampling. It formats the data into a temporal tensor and decomposes it into a summation of low-dimensional components, each consisting of a subject loading vector, a feature loading vector, and a continuous temporal loading function. These loadings provide a low-dimensional representation of subjects or samples and can be used to identify features associated with clusters of subjects or samples. TEMPTED provides the flexibility of allowing subjects to have different temporal sampling, so time points do not need to be binned, and missing time points do not need to be imputed.
Author: Pixu Shi [aut, cre]
Maintainer: Pixu Shi <pixu.shi@duke.edu>
Diff between tempted versions 0.1.1 dated 2024-05-08 and 0.1.2 dated 2026-10-27
tempted-0.1.1/tempted/man/figures |only tempted-0.1.2/tempted/DESCRIPTION | 13 ++-- tempted-0.1.2/tempted/MD5 | 48 ++++----------- tempted-0.1.2/tempted/NAMESPACE | 3 tempted-0.1.2/tempted/R/TEMPTED.R | 70 ++++++++++++++-------- tempted-0.1.2/tempted/R/TEMPTED_package.R | 5 - tempted-0.1.2/tempted/build |only tempted-0.1.2/tempted/inst/CITATION | 17 ++--- tempted-0.1.2/tempted/man/aggregate_feature.Rd | 2 tempted-0.1.2/tempted/man/est_test_subject.Rd | 2 tempted-0.1.2/tempted/man/plot_feature_summary.Rd | 5 + tempted-0.1.2/tempted/man/plot_metafeature.Rd | 5 + tempted-0.1.2/tempted/man/ratio_feature.Rd | 2 tempted-0.1.2/tempted/man/svd_centralize.Rd | 2 tempted-0.1.2/tempted/man/tempted_all.Rd | 2 15 files changed, 92 insertions(+), 84 deletions(-)
Title: 'Arrow' Database Connectivity ('ADBC') Driver Manager
Description: Provides a developer-facing interface to 'Arrow' Database
Connectivity ('ADBC') for the purposes of driver development, driver
testing, and building high-level database interfaces for users. 'ADBC'
<https://arrow.apache.org/adbc/> is an API standard for database access
libraries that uses 'Arrow' for result sets and query parameters.
Author: Dewey Dunnington [aut, cre] ,
Apache Arrow [aut, cph],
Apache Software Foundation [cph]
Maintainer: Dewey Dunnington <dewey@dunnington.ca>
Diff between adbcdrivermanager versions 0.24.0-3 dated 2026-09-14 and 0.25.0 dated 2026-10-27
DESCRIPTION | 6 MD5 | 126 src/Makevars | 4 src/Makevars.win | 4 src/c/driver/common/AdbcDriverCommonConfig.cmake.in |only src/c/driver/flightsql |only src/c/driver/framework/AdbcDriverFrameworkConfig.cmake.in |only src/c/driver/framework/base_driver.h | 25 src/c/driver/framework/connection.h | 3 src/c/driver/framework/status.h | 42 src/c/driver/postgresql/AdbcDriverPostgreSQLConfig.cmake.in |only src/c/driver/postgresql/adbc-driver-postgresql.pc.in |only src/c/driver/postgresql/codegen |only src/c/driver/postgresql/connection.cc | 30 src/c/driver/postgresql/connection.h | 8 src/c/driver/postgresql/copy/reader.h | 37 src/c/driver/postgresql/copy/writer.h | 92 src/c/driver/postgresql/database.cc | 215 src/c/driver/postgresql/database.h | 5 src/c/driver/postgresql/error.cc | 77 src/c/driver/postgresql/error.h | 30 src/c/driver/postgresql/postgres_type.h | 90 src/c/driver/postgresql/postgres_util.h | 2 src/c/driver/postgresql/result_helper.cc | 8 src/c/driver/postgresql/result_helper.h | 3 src/c/driver/postgresql/result_reader.cc | 4 src/c/driver/postgresql/statement.cc | 41 src/c/driver/postgresql/statement.h | 10 src/c/driver/postgresql/type_resolver_init.cc |only src/c/driver/postgresql/type_resolver_init.h |only src/c/driver/sqlite/AdbcDriverSQLiteConfig.cmake.in |only src/c/driver/sqlite/adbc-driver-sqlite.pc.in |only src/c/driver/sqlite/config.h.in |only src/c/driver/sqlite/sqlite.cc | 110 src/c/driver/sqlite/statement_reader.c | 40 src/c/driver_manager/AdbcDriverManagerConfig.cmake.in |only src/c/driver_manager/adbc-driver-manager.pc.in |only src/c/driver_manager/adbc_driver_manager.cc | 106 src/c/driver_manager/adbc_driver_manager_api.cc | 64 src/c/driver_manager/adbc_driver_manager_driver_loading.cc | 16 src/c/driver_manager/adbc_driver_manager_profiles.cc | 8 src/c/driver_manager/current_arch.h | 101 src/c/validation/adbc_validation.h | 6 src/c/validation/adbc_validation_connection.cc | 12 src/c/validation/adbc_validation_statement.cc | 53 src/c/validation/adbc_validation_util.cc | 14 src/c/validation/adbc_validation_util.h | 4 src/c/vendor/boost |only src/c/vendor/fmt/include/fmt/args.h | 173 src/c/vendor/fmt/include/fmt/base.h | 3814 +++++------- src/c/vendor/fmt/include/fmt/chrono.h | 1356 +--- src/c/vendor/fmt/include/fmt/color.h | 427 - src/c/vendor/fmt/include/fmt/compile.h | 398 - src/c/vendor/fmt/include/fmt/core.h | 17 src/c/vendor/fmt/include/fmt/format-inl.h | 1611 ++--- src/c/vendor/fmt/include/fmt/format.h | 3306 +++++----- src/c/vendor/fmt/include/fmt/os.h | 259 src/c/vendor/fmt/include/fmt/ostream.h | 172 src/c/vendor/fmt/include/fmt/printf.h | 404 - src/c/vendor/fmt/include/fmt/ranges.h | 626 + src/c/vendor/fmt/include/fmt/std.h | 789 +- src/c/vendor/fmt/include/fmt/xchar.h | 270 src/c/vendor/fmt/src/fmt.cc | 109 src/c/vendor/fmt/src/format.cc | 18 src/c/vendor/fmt/src/os.cc | 150 src/c/vendor/fmt/support |only src/c/vendor/nanoarrow/nanoarrow.c | 17 src/c/vendor/nanoarrow/nanoarrow.h | 7 src/c/version.rc.in |only src/radbc.cc | 7 tests/testthat/test-options.R | 32 71 files changed, 7918 insertions(+), 7440 deletions(-)
More information about adbcdrivermanager at CRAN
Permanent link
More information about transformerpalettes at CRAN
Permanent link
Title: A Thin Wrapper of 'litedown' to Render Markdown Documents
Description: Render Markdown to HTML/LaTeX. This package has been superseded by 'litedown'. Please call 'litedown::mark()' directly.
Author: Yihui Xie [aut, cre] ,
JJ Allaire [aut],
Jeffrey Horner [aut],
Henrik Bengtsson [ctb],
Jim Hester [ctb],
Yixuan Qiu [ctb],
Kohske Takahashi [ctb],
Adam November [ctb],
Nacho Caballero [ctb],
Jeroen Ooms [ctb],
Thomas Leeper [ctb],
Joe Cheng [ctb],
An [...truncated...]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between markdown versions 2.0 dated 2025-03-23 and 2.1 dated 2026-10-27
markdown-2.0/markdown/inst/examples |only markdown-2.0/markdown/tests/tests.R |only markdown-2.0/markdown/tests/tests.Rout.save |only markdown-2.1/markdown/DESCRIPTION | 17 ++++++++--------- markdown-2.1/markdown/MD5 | 13 +++++-------- markdown-2.1/markdown/NEWS.md | 4 ++++ markdown-2.1/markdown/R/render.R | 16 +++------------- markdown-2.1/markdown/README.md | 10 ---------- markdown-2.1/markdown/man/markdown-package.Rd | 1 + 9 files changed, 21 insertions(+), 40 deletions(-)
Title: Causal Graph Interface
Description: Create, query, and modify causal graphs. 'caugi' (Causal Graph
Interface) is a causality-first, high performance graph package that
provides a simple interface to build, structure, and examine causal
relationships.
Author: Frederik Fabricius-Bjerre [aut, cre, cph] ,
Johan Larsson [aut] ,
Michael Sachs [aut] ,
Bjarke Hautop Kristensen [aut],
Leonard Henckel [ctb, cph] ; see LICENSE.note),
Theo Wuertzen [ctb, cph] ,
Sebastian Weichwald [ctb, cph] ,
Authors of the bundled [...truncated...]
Maintainer: Frederik Fabricius-Bjerre <frederik@fabriciusbjerre.dk>
Diff between caugi versions 1.3.0 dated 2026-09-09 and 1.4.0 dated 2026-10-27
DESCRIPTION | 6 MD5 | 149 ++++++++++---------- NAMESPACE | 1 NEWS.md | 53 +++++++ R/DSL-parser.R | 29 ++- R/caugi.R | 2 R/extendr-wrappers.R | 14 + R/format-caugi.R | 2 R/format-dot.R | 2 R/format-graphml.R | 3 R/format-mermaid.R | 2 R/methods.R | 47 +++--- R/operations.R | 83 +---------- R/queries.R | 42 +++++ R/verbs.R | 51 ++++-- R/zzz.R | 16 ++ README.md | 10 - inst/doc/caugi.html | 8 - inst/doc/comparisons.Rmd | 2 inst/doc/comparisons.html | 2 inst/doc/package_use.html | 4 inst/doc/performance.Rmd | 2 inst/doc/performance.html | 10 - man/ancestors.Rd | 1 man/anteriors.Rd | 1 man/caugi-equality.Rd | 14 + man/children.Rd | 1 man/components.Rd |only man/descendants.Rd | 1 man/districts.Rd | 1 man/edge_types.Rd | 1 man/edges.Rd | 1 man/exogenous.Rd | 1 man/is_acyclic.Rd | 1 man/is_admg.Rd | 1 man/is_ag.Rd | 1 man/is_caugi.Rd | 1 man/is_cpdag.Rd | 1 man/is_dag.Rd | 1 man/is_empty_caugi.Rd | 1 man/is_mag.Rd | 1 man/is_mpdag.Rd | 1 man/is_pdag.Rd | 1 man/is_simple.Rd | 1 man/is_ug.Rd | 1 man/m_separated.Rd | 1 man/markov_blanket.Rd | 1 man/neighbors.Rd | 1 man/nodes.Rd | 1 man/parents.Rd | 1 man/posteriors.Rd | 1 man/same_nodes.Rd | 1 man/spouses.Rd | 1 man/subgraph.Rd | 1 man/topological_sort.Rd | 1 src/rust/src/graph/admg/msep.rs | 126 ++++++++++++----- src/rust/src/graph/aid.rs | 42 ++++- src/rust/src/graph/alg.rs | 1 src/rust/src/graph/alg/adjustment.rs | 8 - src/rust/src/graph/alg/components.rs |only src/rust/src/graph/graphml.rs | 15 -- src/rust/src/graph/metrics.rs | 124 ++++++++++++---- src/rust/src/graph/pdag/enumerate.rs | 243 +++++++++++++++++++++++++++++++++ src/rust/src/graph/serialization.rs | 13 - src/rust/src/graph/session.rs | 97 +++++++++++++ src/rust/src/graph/view.rs | 15 ++ src/rust/src/lib.rs | 153 +++++++++++++++++++- tests/testthat/test-DSL-parser.R | 24 +++ tests/testthat/test-admg.R | 60 ++++++++ tests/testthat/test-components.R |only tests/testthat/test-methods.R | 38 +++++ tests/testthat/test-operations.R | 48 ++++++ tests/testthat/test-plot-composition.R | 10 - tests/testthat/test-registry.R | 47 ++++++ tests/testthat/test-verbs.R | 79 ++++++++++ vignettes/comparisons.Rmd | 2 vignettes/performance.Rmd | 2 77 files changed, 1384 insertions(+), 347 deletions(-)
Title: Multidimensional Scaling of Asymmetric Proximities
Description: Multidimensional scaling models and methods for the visualization and analysis of asymmetric proximity data. An asymmetric data matrix has the same number of rows and columns, and these rows and columns refer to the same set of objects. At least some elements in the upper-triangle are different from the corresponding elements in the lower triangle. An example of an asymmetric matrix is a student migration table, where the rows correspond to the countries of origin of the students and the columns to the destination countries. This package provides algorithms for three multidimensional scaling models, the slide-vector model, a scaling model with unique dimensions and the asymscal model. Furthermore, some other procedures, such as a heat map for skew-symmetric data, and the decomposition of asymmetry are also provided for the exploratory analysis of asymmetric tables.
Author: Berrie Zielman [aut, cre]
Maintainer: Berrie Zielman <berrie.zielman@gmail.com>
Diff between asymmetry versions 2.0.6 dated 2026-03-05 and 2.0.7 dated 2026-10-27
asymmetry-2.0.6/asymmetry/data/asymscalexample.RData |only asymmetry-2.0.6/asymmetry/data/productsafety.RData |only asymmetry-2.0.6/asymmetry/data/studentmigration.RData |only asymmetry-2.0.7/asymmetry/DESCRIPTION | 11 +- asymmetry-2.0.7/asymmetry/MD5 | 44 ++++----- asymmetry-2.0.7/asymmetry/NAMESPACE | 1 asymmetry-2.0.7/asymmetry/R/asymscal.R | 25 ++--- asymmetry-2.0.7/asymmetry/R/hmap.R | 3 asymmetry-2.0.7/asymmetry/R/mdsunique.R | 18 ++- asymmetry-2.0.7/asymmetry/R/plot.slidevector.R | 2 asymmetry-2.0.7/asymmetry/R/slidevector.R | 21 +++- asymmetry-2.0.7/asymmetry/README.md | 14 ++ asymmetry-2.0.7/asymmetry/data/asymscalexample.rda |only asymmetry-2.0.7/asymmetry/data/carswitching.rda |only asymmetry-2.0.7/asymmetry/data/productsafety.rda |only asymmetry-2.0.7/asymmetry/data/studentmigration.rda |only asymmetry-2.0.7/asymmetry/inst/doc/asymmetry.R | 30 ------ asymmetry-2.0.7/asymmetry/inst/doc/asymmetry.Rmd | 42 +------- asymmetry-2.0.7/asymmetry/inst/doc/asymmetry.html | 88 ++++-------------- asymmetry-2.0.7/asymmetry/man/asymscal.Rd | 7 - asymmetry-2.0.7/asymmetry/man/asymscalexample.rd | 2 asymmetry-2.0.7/asymmetry/man/carswitching.Rd |only asymmetry-2.0.7/asymmetry/man/hmap.Rd | 10 +- asymmetry-2.0.7/asymmetry/man/mdsunique.Rd | 10 -- asymmetry-2.0.7/asymmetry/man/plot.Rd | 2 asymmetry-2.0.7/asymmetry/man/slidevector.Rd | 2 asymmetry-2.0.7/asymmetry/vignettes/asymmetry.Rmd | 42 +------- 27 files changed, 134 insertions(+), 240 deletions(-)
Title: 'Arrow' Database Connectivity ('ADBC') 'SQLite' Driver
Description: Provides a developer-facing interface to the 'Arrow' Database
Connectivity ('ADBC') 'SQLite' driver for the purposes of building high-level
database interfaces for users. 'ADBC' <https://arrow.apache.org/adbc/> is
an API standard for database access libraries that uses 'Arrow' for result
sets and query parameters.
Author: Dewey Dunnington [aut, cre] ,
Apache Arrow [aut, cph],
Apache Software Foundation [cph]
Maintainer: Dewey Dunnington <dewey@dunnington.ca>
Diff between adbcsqlite versions 0.24.0-2 dated 2026-09-15 and 0.25.0 dated 2026-10-27
DESCRIPTION | 6 MD5 | 121 src/Makevars.in | 2 src/c/driver/common/AdbcDriverCommonConfig.cmake.in |only src/c/driver/flightsql |only src/c/driver/framework/AdbcDriverFrameworkConfig.cmake.in |only src/c/driver/framework/base_driver.h | 25 src/c/driver/framework/connection.h | 3 src/c/driver/framework/status.h | 42 src/c/driver/postgresql/AdbcDriverPostgreSQLConfig.cmake.in |only src/c/driver/postgresql/adbc-driver-postgresql.pc.in |only src/c/driver/postgresql/codegen |only src/c/driver/postgresql/connection.cc | 30 src/c/driver/postgresql/connection.h | 8 src/c/driver/postgresql/copy/reader.h | 37 src/c/driver/postgresql/copy/writer.h | 92 src/c/driver/postgresql/database.cc | 215 src/c/driver/postgresql/database.h | 5 src/c/driver/postgresql/error.cc | 77 src/c/driver/postgresql/error.h | 30 src/c/driver/postgresql/postgres_type.h | 90 src/c/driver/postgresql/postgres_util.h | 2 src/c/driver/postgresql/result_helper.cc | 8 src/c/driver/postgresql/result_helper.h | 3 src/c/driver/postgresql/result_reader.cc | 4 src/c/driver/postgresql/statement.cc | 41 src/c/driver/postgresql/statement.h | 10 src/c/driver/postgresql/type_resolver_init.cc |only src/c/driver/postgresql/type_resolver_init.h |only src/c/driver/sqlite/AdbcDriverSQLiteConfig.cmake.in |only src/c/driver/sqlite/adbc-driver-sqlite.pc.in |only src/c/driver/sqlite/config.h |only src/c/driver/sqlite/config.h.in |only src/c/driver/sqlite/sqlite.cc | 110 src/c/driver/sqlite/statement_reader.c | 40 src/c/driver_manager/AdbcDriverManagerConfig.cmake.in |only src/c/driver_manager/adbc-driver-manager.pc.in |only src/c/driver_manager/adbc_driver_manager.cc | 106 src/c/driver_manager/adbc_driver_manager_api.cc | 64 src/c/driver_manager/adbc_driver_manager_driver_loading.cc | 16 src/c/driver_manager/adbc_driver_manager_profiles.cc | 8 src/c/driver_manager/current_arch.h | 101 src/c/validation/adbc_validation.h | 6 src/c/validation/adbc_validation_connection.cc | 12 src/c/validation/adbc_validation_statement.cc | 53 src/c/validation/adbc_validation_util.cc | 14 src/c/validation/adbc_validation_util.h | 4 src/c/vendor/boost |only src/c/vendor/fmt/include/fmt/args.h | 173 src/c/vendor/fmt/include/fmt/base.h | 3814 +++++------- src/c/vendor/fmt/include/fmt/chrono.h | 1356 +--- src/c/vendor/fmt/include/fmt/color.h | 427 - src/c/vendor/fmt/include/fmt/compile.h | 398 - src/c/vendor/fmt/include/fmt/core.h | 17 src/c/vendor/fmt/include/fmt/format-inl.h | 1611 ++--- src/c/vendor/fmt/include/fmt/format.h | 3306 +++++----- src/c/vendor/fmt/include/fmt/os.h | 259 src/c/vendor/fmt/include/fmt/ostream.h | 172 src/c/vendor/fmt/include/fmt/printf.h | 404 - src/c/vendor/fmt/include/fmt/ranges.h | 626 + src/c/vendor/fmt/include/fmt/std.h | 789 +- src/c/vendor/fmt/include/fmt/xchar.h | 270 src/c/vendor/fmt/src/fmt.cc | 109 src/c/vendor/fmt/src/format.cc | 18 src/c/vendor/fmt/src/os.cc | 150 src/c/vendor/fmt/support |only src/c/vendor/nanoarrow/nanoarrow.c | 17 src/c/vendor/nanoarrow/nanoarrow.h | 7 src/c/version.rc.in |only 69 files changed, 7893 insertions(+), 7415 deletions(-)
Title: 'Arrow' Database Connectivity ('ADBC') 'PostgreSQL' Driver
Description: Provides a developer-facing interface to the 'Arrow' Database
Connectivity ('ADBC') 'PostgreSQL' driver for the purposes of building high-level
database interfaces for users. 'ADBC' <https://arrow.apache.org/adbc/> is
an API standard for database access libraries that uses 'Arrow' for result
sets and query parameters.
Author: Dewey Dunnington [aut, cre] ,
Apache Arrow [aut, cph],
Apache Software Foundation [cph]
Maintainer: Dewey Dunnington <dewey@dunnington.ca>
Diff between adbcpostgresql versions 0.24.0-2 dated 2026-09-16 and 0.25.0 dated 2026-10-27
DESCRIPTION | 6 MD5 | 124 src/Makevars.in | 5 src/Makevars.ucrt | 5 src/Makevars.win | 5 src/c/driver/common/AdbcDriverCommonConfig.cmake.in |only src/c/driver/flightsql |only src/c/driver/framework/AdbcDriverFrameworkConfig.cmake.in |only src/c/driver/framework/base_driver.h | 25 src/c/driver/framework/connection.h | 3 src/c/driver/framework/status.h | 42 src/c/driver/postgresql/AdbcDriverPostgreSQLConfig.cmake.in |only src/c/driver/postgresql/adbc-driver-postgresql.pc.in |only src/c/driver/postgresql/codegen |only src/c/driver/postgresql/connection.cc | 30 src/c/driver/postgresql/connection.h | 8 src/c/driver/postgresql/copy/reader.h | 37 src/c/driver/postgresql/copy/writer.h | 92 src/c/driver/postgresql/database.cc | 215 src/c/driver/postgresql/database.h | 5 src/c/driver/postgresql/error.cc | 77 src/c/driver/postgresql/error.h | 30 src/c/driver/postgresql/postgres_type.h | 90 src/c/driver/postgresql/postgres_util.h | 2 src/c/driver/postgresql/result_helper.cc | 8 src/c/driver/postgresql/result_helper.h | 3 src/c/driver/postgresql/result_reader.cc | 4 src/c/driver/postgresql/statement.cc | 41 src/c/driver/postgresql/statement.h | 10 src/c/driver/postgresql/type_resolver_init.cc |only src/c/driver/postgresql/type_resolver_init.h |only src/c/driver/sqlite/AdbcDriverSQLiteConfig.cmake.in |only src/c/driver/sqlite/adbc-driver-sqlite.pc.in |only src/c/driver/sqlite/config.h.in |only src/c/driver/sqlite/sqlite.cc | 110 src/c/driver/sqlite/statement_reader.c | 40 src/c/driver_manager/AdbcDriverManagerConfig.cmake.in |only src/c/driver_manager/adbc-driver-manager.pc.in |only src/c/driver_manager/adbc_driver_manager.cc | 106 src/c/driver_manager/adbc_driver_manager_api.cc | 64 src/c/driver_manager/adbc_driver_manager_driver_loading.cc | 16 src/c/driver_manager/adbc_driver_manager_profiles.cc | 8 src/c/driver_manager/current_arch.h | 101 src/c/validation/adbc_validation.h | 6 src/c/validation/adbc_validation_connection.cc | 12 src/c/validation/adbc_validation_statement.cc | 53 src/c/validation/adbc_validation_util.cc | 14 src/c/validation/adbc_validation_util.h | 4 src/c/vendor/boost |only src/c/vendor/fmt/include/fmt/args.h | 173 src/c/vendor/fmt/include/fmt/base.h | 3814 +++++------- src/c/vendor/fmt/include/fmt/chrono.h | 1356 +--- src/c/vendor/fmt/include/fmt/color.h | 427 - src/c/vendor/fmt/include/fmt/compile.h | 398 - src/c/vendor/fmt/include/fmt/core.h | 17 src/c/vendor/fmt/include/fmt/format-inl.h | 1611 ++--- src/c/vendor/fmt/include/fmt/format.h | 3306 +++++----- src/c/vendor/fmt/include/fmt/os.h | 259 src/c/vendor/fmt/include/fmt/ostream.h | 172 src/c/vendor/fmt/include/fmt/printf.h | 404 - src/c/vendor/fmt/include/fmt/ranges.h | 626 + src/c/vendor/fmt/include/fmt/std.h | 789 +- src/c/vendor/fmt/include/fmt/xchar.h | 270 src/c/vendor/fmt/src/fmt.cc | 109 src/c/vendor/fmt/src/format.cc | 18 src/c/vendor/fmt/src/os.cc | 150 src/c/vendor/fmt/support |only src/c/vendor/nanoarrow/nanoarrow.c | 17 src/c/vendor/nanoarrow/nanoarrow.h | 7 src/c/version.rc.in |only 70 files changed, 7902 insertions(+), 7422 deletions(-)
More information about adbcpostgresql at CRAN
Permanent link
Title: Neural Network for Complex Survey Data
Description: The goal of 'surveynnet' is to extend the functionality of 'nnet',
which already supports survey weights, by enabling it to handle clustered
and stratified data. It achieves this by incorporating design effects
through the use of effective sample sizes as outlined by Chen
and Rust (2017), <doi:10.1093/jssam/smw036>, and performed by
'deffCR' in the package 'PracTools' (Valliant, Dever, and Kreuter (2018),
<doi:10.1007/978-3-319-93632-1>).
Author: Aaron Cohen [aut, cre] ,
Raul Cruz-Cano [aut]
Maintainer: Aaron Cohen <cohenaa@iu.edu>
This is a re-admission after prior archival of version 1.0.0 dated 2024-12-09
Diff between surveynnet versions 1.0.0 dated 2024-12-09 and 1.0.1 dated 2026-10-27
DESCRIPTION | 12 +++---- MD5 | 10 +++--- R/predict_surveynnet.R | 25 +++++++++------ R/surveynnet.R | 74 +++++++++++++++++++++++++++++++++++----------- man/predict.surveynnet.Rd | 18 ++++++++--- man/surveynnet.Rd | 35 ++++++++++++++++++--- 6 files changed, 126 insertions(+), 48 deletions(-)
Title: Rocket-Fast Clinical Research Reporting
Description: Description of the tables, both grouped and not grouped, with some associated data management actions,
such as sorting the terms of the variables and deleting terms with zero numbers.
Author: USMR CHU de Bordeaux [aut, cre],
Valentine Renaudeau [aut],
Marion Kret [aut],
Matisse Decilap [aut],
Sahardid Mohamed Houssein [aut],
Mohamedou Sow [aut],
Thomas Ferte [aut]
Maintainer: USMR CHU de Bordeaux <astreinte.usmr@chu-bordeaux.fr>
Diff between RastaRocket versions 1.1.5 dated 2026-05-18 and 1.1.6 dated 2026-10-27
DESCRIPTION | 11 MD5 | 50 - NAMESPACE | 3 NEWS.md | 37 + R/desc_ei_per_pt.R | 4 R/df_builder_ae.R | 258 +++++++-- R/globals.R | 2 R/plot_butterfly_stacked_barplot.R | 182 ++++-- R/plot_dumbell.R | 101 +++ R/plot_volcano.R | 73 +- R/prepare_table.R | 12 R/remove_labelled_type.R |only build/vignette.rds |binary inst/doc/DescribeAE.Rmd | 2 inst/doc/DescribeAE.html | 894 +++++++++++++++++----------------- inst/doc/RastaRocketVignette.R | 2 inst/doc/RastaRocketVignette.Rmd | 2 inst/doc/RastaRocketVignette.html | 7 inst/doc/SetupProject.html | 5 man/desc_ei_per_pt.Rd | 4 man/df_builder_ae.Rd | 31 - man/plot_butterfly_stacked_barplot.Rd | 28 - man/plot_dumbell.Rd | 25 man/plot_volcano.Rd | 26 man/remove_labelled_type.Rd |only vignettes/DescribeAE.Rmd | 2 vignettes/RastaRocketVignette.Rmd | 2 27 files changed, 1082 insertions(+), 681 deletions(-)
Title: Pedigree Validation Genetic Composition of Diploids & Polyploids
Description: Tools for pedigree quality control and genomic breed/line
composition estimation in diploid and polyploid breeding populations.
'BIGpopA' provides functions to check and correct common pedigree
errors, assign parentage from SNP genotype data using Mendelian error
rates, validate parent-offspring trios, and estimate genome-wide
breed or line composition using quadratic programming. Pedigree
validation and parentage assignment support any ploidy, using a
polysomic Mendelian test for even ploidy and a homozygosity-based
check for odd ploidy. Genotypes can be supplied as dosage tables, VCF
files, or 'PLINK' .ped files. For more details about the included
'breedTools' functions, see Funkhouser et al. (2017)
<doi:10.2527/tas2016.0003>.
Author: Josue Chinchilla-Vargas [cre, aut],
Alexander Sandercock [aut],
University of Florida [cph]
Maintainer: Josue Chinchilla-Vargas <josue.chinchilla@ufl.edu>
Diff between BIGpopA versions 2.2.0 dated 2026-10-12 and 2.2.1 dated 2026-10-27
DESCRIPTION | 8 +- MD5 | 17 ++-- NEWS.md | 5 + R/check_ped.R | 138 +++++++++++++++++++++++------------ R/find_parentage.R | 3 inst/doc/BIGpopA.html | 10 +- man/check_ped.Rd | 5 + tests/testthat/test-check_ped.R | 68 +++++++++++++++++ tests/testthat/test-find_parentage.R | 12 +++ tests/testthat/test-hard-cycles.R |only 10 files changed, 199 insertions(+), 67 deletions(-)
Title: Classification and Regression Trees
Description: Classification and regression trees.
Author: Brian Ripley [aut, cre]
Maintainer: Brian Ripley <Brian.Ripley@R-project.org>
Diff between tree versions 1.0-47 dated 2026-08-03 and 1.0-48 dated 2026-10-27
ChangeLog | 9 +++++++++ DESCRIPTION | 10 +++++----- MD5 | 7 ++++--- src/grow.c | 2 +- tests/gini.R |only 5 files changed, 19 insertions(+), 9 deletions(-)
Title: Filter and Query Data Frames in 'shiny' Using an LLM Chat
Interface
Description: Adds an LLM-powered chatbot to your 'shiny' app, that can
turn your users' natural language questions into 'SQL' queries that
run against your data, and return the result as a reactive data frame.
Use it to drive reactive calculations, visualizations, downloads, and
more.
Author: Garrick Aden-Buie [aut, cre] ,
Joe Cheng [aut, ccp],
Carson Sievert [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Garrick Aden-Buie <garrick@posit.co>
This is a re-admission after prior archival of version 0.4.1 dated 2026-09-30
Diff between querychat versions 0.4.1 dated 2026-09-30 and 0.4.2 dated 2026-10-27
DESCRIPTION | 20 ++-- MD5 | 34 +++---- NEWS.md | 12 ++ R/PinSource.R | 30 ++++-- R/QueryChat.R | 76 ++++++++++++---- R/utils-duckdb.R | 31 ++++++ README.md | 2 inst/doc/build.html | 2 inst/doc/context.html | 16 +-- inst/doc/tools.html | 4 inst/doc/visualize.html | 8 - inst/htmldep/viz.css | 3 inst/prompts/ggsql-syntax.md | 27 ++++- man/PinSource.Rd | 9 + man/QueryChat.Rd | 16 ++- tests/testthat/test-PinSource.R | 149 ++++++++++++++++++++++++++++++-- tests/testthat/test-QueryChat.R | 94 +++++++++++++++++++- tests/testthat/test-QueryExecutor.R | 167 ++++++++++++++++++++++++++++++++++++ 18 files changed, 607 insertions(+), 93 deletions(-)
Title: Bayesian Analysis of the Network Autocorrelation Model
Description: The network autocorrelation model (NAM) can be used for studying the degree of social influence
regarding an outcome variable based on one or more known networks.
The degree of social influence is quantified via the network autocorrelation parameters. In case of a single
network, the Bayesian methods of Dittrich, Leenders, and Mulder
(2017) <DOI:10.1016/j.socnet.2016.09.002> and Dittrich, Leenders, and Mulder (2019)
<DOI:10.1177/0049124117729712> are implemented using a normal, flat, or independence
Jeffreys prior for the network autocorrelation. In the case of multiple
networks, the Bayesian methods of Dittrich, Leenders, and Mulder (2020)
<DOI:10.1177/0081175020913899> are implemented using a multivariate normal prior for
the network autocorrelation parameters. Flat priors are implemented
for estimating the coefficients. For Bayesian testing of equality and order-constrained
hypotheses, the default Bayes factor of Gu, Mulder, and Hoijtink, (2018)
<DOI:10.1111/bms [...truncated...]
Author: Joris Mulder [aut, cre],
Dino Dittrich [aut, ctb],
Roger Leenders [aut, ctb]
Maintainer: Joris Mulder <j.mulder3@tilburguniversity.edu>
Diff between BANAM versions 0.2.2 dated 2024-12-03 and 0.2.3 dated 2026-10-27
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- tests/testthat/test_banam.R | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Offline Taxonomic Name Matching Against Darwin Core Backbones
Description: Matches taxonomic names against local copies of published
backbones ('Catalogue of Life', 'GBIF Backbone Taxonomy', 'ITIS',
'World Flora Online', 'WoRMS', 'NCBI Taxonomy', 'Open Tree of Life',
'Euro+Med', 'Species Fungorum', 'AlgaeBase', 'FishBase', 'SeaLifeBase',
'Reptile Database', 'LCVP', 'WCVP', 'Mammal Diversity Database',
'AviList', 'LPSN') and two vegetation classifications, and resolves each
name to its accepted name. It performs the name-resolution step of
'taxize' and 'WorldFlora', run offline against these files. Names are
cleaned of authors and qualifiers, matched exactly and then by edit
distance within their genus, and followed from synonym to accepted name,
with the backbone version recorded on every row. Published trait, status
and distribution datasets are joined on the accepted name, and so is a
table the user supplies. Matching runs in the 'vectra' column-store
engine.
Author: Gilles Colling [aut, cre, cph]
Maintainer: Gilles Colling <gilles.colling051@gmail.com>
Diff between taxify versions 0.6.0 dated 2026-09-30 and 0.7.0 dated 2026-10-27
taxify-0.6.0/taxify/inst/doc/backbones.R |only taxify-0.6.0/taxify/inst/doc/custom-data.R |only taxify-0.6.0/taxify/inst/doc/enrichments.R |only taxify-0.6.0/taxify/inst/doc/fuzzy-matching.R |only taxify-0.6.0/taxify/inst/doc/gbif-requests.R |only taxify-0.6.0/taxify/inst/doc/hybrids-and-aggregates.R |only taxify-0.6.0/taxify/inst/doc/inspecting-names.R |only taxify-0.6.0/taxify/inst/doc/large-scale.R |only taxify-0.6.0/taxify/inst/doc/migration.R |only taxify-0.6.0/taxify/inst/doc/quickstart.R |only taxify-0.6.0/taxify/inst/doc/quickstart.Rmd |only taxify-0.6.0/taxify/inst/doc/quickstart.html |only taxify-0.6.0/taxify/inst/doc/regions.R |only taxify-0.6.0/taxify/inst/manifest.json |only taxify-0.6.0/taxify/vignettes/quickstart.Rmd |only taxify-0.7.0/taxify/DESCRIPTION | 30 taxify-0.7.0/taxify/MD5 | 446 taxify-0.7.0/taxify/NAMESPACE | 5 taxify-0.7.0/taxify/NEWS.md | 4950 +++++----- taxify-0.7.0/taxify/R/add-animaltraits.R | 2 taxify-0.7.0/taxify/R/add-bryoatt.R | 118 taxify-0.7.0/taxify/R/add-ccdb.R | 120 taxify-0.7.0/taxify/R/add-chowdhury.R | 4 taxify-0.7.0/taxify/R/add-clopla.R | 146 taxify-0.7.0/taxify/R/add-col-info.R | 149 taxify-0.7.0/taxify/R/add-combine.R | 504 - taxify-0.7.0/taxify/R/add-common-names.R | 3 taxify-0.7.0/taxify/R/add-data.R | 45 taxify-0.7.0/taxify/R/add-eberswalde.R | 2 taxify-0.7.0/taxify/R/add-edwards-phyto.R | 136 taxify-0.7.0/taxify/R/add-eive.R | 2 taxify-0.7.0/taxify/R/add-faprotax.R | 4 taxify-0.7.0/taxify/R/add-fishbase.R | 182 taxify-0.7.0/taxify/R/add-fishmorph.R | 148 taxify-0.7.0/taxify/R/add-gbif-info.R | 101 taxify-0.7.0/taxify/R/add-gmpd.R | 122 taxify-0.7.0/taxify/R/add-griis.R | 4 taxify-0.7.0/taxify/R/add-hybrid-info.R | 6 taxify-0.7.0/taxify/R/add-hydraulics.R | 6 taxify-0.7.0/taxify/R/add-iucn.R | 88 taxify-0.7.0/taxify/R/add-noddb.R | 2 taxify-0.7.0/taxify/R/add-plantatt.R | 120 taxify-0.7.0/taxify/R/add-repttraits.R | 4 taxify-0.7.0/taxify/R/add-sealifebase.R | 182 taxify-0.7.0/taxify/R/add-sworm.R | 4 taxify-0.7.0/taxify/R/add-trait.R | 14 taxify-0.7.0/taxify/R/add-wfo-info.R | 91 taxify-0.7.0/taxify/R/add-zanne.R | 4 taxify-0.7.0/taxify/R/backbones.R | 91 taxify-0.7.0/taxify/R/backend.R | 127 taxify-0.7.0/taxify/R/backends-registry.R | 5 taxify-0.7.0/taxify/R/basionym.R | 2 taxify-0.7.0/taxify/R/browse.R | 95 taxify-0.7.0/taxify/R/cache.R | 9 taxify-0.7.0/taxify/R/cite.R | 109 taxify-0.7.0/taxify/R/classification-tree.R | 2 taxify-0.7.0/taxify/R/clean.R | 29 taxify-0.7.0/taxify/R/comm2sci.R | 19 taxify-0.7.0/taxify/R/content-store.R | 215 taxify-0.7.0/taxify/R/disambiguate-authorship.R | 125 taxify-0.7.0/taxify/R/download.R | 103 taxify-0.7.0/taxify/R/downstream.R | 2 taxify-0.7.0/taxify/R/enrichment-gift.R | 266 taxify-0.7.0/taxify/R/enrichment.R | 43 taxify-0.7.0/taxify/R/gbif-request.R | 260 taxify-0.7.0/taxify/R/inspect.R | 52 taxify-0.7.0/taxify/R/lock.R | 12 taxify-0.7.0/taxify/R/manifest.R | 51 taxify-0.7.0/taxify/R/nomenclature-codes.R |only taxify-0.7.0/taxify/R/parse-name.R | 43 taxify-0.7.0/taxify/R/pick.R | 199 taxify-0.7.0/taxify/R/reconcile.R | 6 taxify-0.7.0/taxify/R/syntaxon.R |only taxify-0.7.0/taxify/R/taxify-package.R | 38 taxify-0.7.0/taxify/R/taxify-result.R | 31 taxify-0.7.0/taxify/R/taxify.R | 250 taxify-0.7.0/taxify/R/upstream.R | 6 taxify-0.7.0/taxify/README.md | 532 - taxify-0.7.0/taxify/build/vignette.rds |binary taxify-0.7.0/taxify/inst/CITATION |only taxify-0.7.0/taxify/inst/doc/backbones.Rmd | 1045 -- taxify-0.7.0/taxify/inst/doc/backbones.html | 1245 -- taxify-0.7.0/taxify/inst/doc/custom-data.Rmd | 521 - taxify-0.7.0/taxify/inst/doc/custom-data.html | 610 - taxify-0.7.0/taxify/inst/doc/enrichments.Rmd | 2931 ----- taxify-0.7.0/taxify/inst/doc/enrichments.html | 3137 ------ taxify-0.7.0/taxify/inst/doc/exploring.Rmd |only taxify-0.7.0/taxify/inst/doc/exploring.html |only taxify-0.7.0/taxify/inst/doc/fuzzy-matching.Rmd | 784 - taxify-0.7.0/taxify/inst/doc/fuzzy-matching.html | 956 - taxify-0.7.0/taxify/inst/doc/gbif-requests.Rmd | 377 taxify-0.7.0/taxify/inst/doc/gbif-requests.html | 445 taxify-0.7.0/taxify/inst/doc/hybrids-and-aggregates.Rmd | 519 - taxify-0.7.0/taxify/inst/doc/hybrids-and-aggregates.html | 805 - taxify-0.7.0/taxify/inst/doc/inspecting-names.Rmd | 375 taxify-0.7.0/taxify/inst/doc/inspecting-names.html | 510 - taxify-0.7.0/taxify/inst/doc/large-scale.Rmd | 836 - taxify-0.7.0/taxify/inst/doc/large-scale.html | 1103 -- taxify-0.7.0/taxify/inst/doc/migration.Rmd | 512 - taxify-0.7.0/taxify/inst/doc/migration.html | 987 - taxify-0.7.0/taxify/inst/doc/regions.Rmd | 267 taxify-0.7.0/taxify/inst/doc/regions.html | 358 taxify-0.7.0/taxify/inst/doc/taxify.Rmd |only taxify-0.7.0/taxify/inst/doc/taxify.html |only taxify-0.7.0/taxify/inst/doc/vegetation-units.Rmd |only taxify-0.7.0/taxify/inst/doc/vegetation-units.html |only taxify-0.7.0/taxify/inst/exampledb/enrichment/common_names/latest/common_names.vtr |binary taxify-0.7.0/taxify/inst/exampledb/enrichment/common_names/latest/meta.json | 36 taxify-0.7.0/taxify/inst/exampledb/evc |only taxify-0.7.0/taxify/inst/exampledb/vegcz |only taxify-0.7.0/taxify/inst/exampledb/wfo/latest/meta.json | 12 taxify-0.7.0/taxify/inst/exampledb/wfo/latest/wfo.meta | 10 taxify-0.7.0/taxify/inst/exampledb/wfo/latest/wfo.vtr |binary taxify-0.7.0/taxify/inst/manifest_v3.json |only taxify-0.7.0/taxify/man/add_animaltraits.Rd | 2 taxify-0.7.0/taxify/man/add_bryoatt.Rd | 4 taxify-0.7.0/taxify/man/add_ccdb.Rd | 2 taxify-0.7.0/taxify/man/add_chowdhury.Rd | 4 taxify-0.7.0/taxify/man/add_clopla.Rd | 10 taxify-0.7.0/taxify/man/add_col_info.Rd | 2 taxify-0.7.0/taxify/man/add_combine.Rd | 6 taxify-0.7.0/taxify/man/add_combine_imputed.Rd | 2 taxify-0.7.0/taxify/man/add_data.Rd | 8 taxify-0.7.0/taxify/man/add_eberswalde.Rd | 2 taxify-0.7.0/taxify/man/add_edwards_phyto.Rd | 4 taxify-0.7.0/taxify/man/add_eive.Rd | 2 taxify-0.7.0/taxify/man/add_faprotax.Rd | 4 taxify-0.7.0/taxify/man/add_fishbase.Rd | 2 taxify-0.7.0/taxify/man/add_fishmorph.Rd | 2 taxify-0.7.0/taxify/man/add_gift.Rd | 6 taxify-0.7.0/taxify/man/add_gmpd.Rd | 8 taxify-0.7.0/taxify/man/add_griis.Rd | 4 taxify-0.7.0/taxify/man/add_hydraulics.Rd | 6 taxify-0.7.0/taxify/man/add_iucn.Rd | 2 taxify-0.7.0/taxify/man/add_noddb.Rd | 2 taxify-0.7.0/taxify/man/add_plantatt.Rd | 4 taxify-0.7.0/taxify/man/add_repttraits.Rd | 4 taxify-0.7.0/taxify/man/add_sealifebase.Rd | 2 taxify-0.7.0/taxify/man/add_sworm.Rd | 4 taxify-0.7.0/taxify/man/add_trait.Rd | 12 taxify-0.7.0/taxify/man/add_wfo_info.Rd | 3 taxify-0.7.0/taxify/man/add_zanne.Rd | 4 taxify-0.7.0/taxify/man/backbone_code.Rd |only taxify-0.7.0/taxify/man/children.Rd | 4 taxify-0.7.0/taxify/man/cite.Rd | 4 taxify-0.7.0/taxify/man/comm2sci.Rd | 2 taxify-0.7.0/taxify/man/downstream.Rd | 2 taxify-0.7.0/taxify/man/embed_accepted.Rd | 9 taxify-0.7.0/taxify/man/enrichment_cols.Rd | 6 taxify-0.7.0/taxify/man/enrichment_groups.Rd | 4 taxify-0.7.0/taxify/man/figures |only taxify-0.7.0/taxify/man/gbif_fetch.Rd | 2 taxify-0.7.0/taxify/man/gbif_request.Rd | 20 taxify-0.7.0/taxify/man/gift_traits.Rd | 2 taxify-0.7.0/taxify/man/inspect.Rd | 17 taxify-0.7.0/taxify/man/install_backbones.Rd | 11 taxify-0.7.0/taxify/man/list_backbones.Rd | 9 taxify-0.7.0/taxify/man/list_enrichments.Rd | 2 taxify-0.7.0/taxify/man/lowest_common.Rd | 2 taxify-0.7.0/taxify/man/normalize_syntaxon_name.Rd |only taxify-0.7.0/taxify/man/parse_name.Rd | 42 taxify-0.7.0/taxify/man/precompute_keys.Rd | 22 taxify-0.7.0/taxify/man/print.taxify_gbif_keys.Rd |only taxify-0.7.0/taxify/man/print.taxify_result.Rd | 4 taxify-0.7.0/taxify/man/reconcile.Rd | 4 taxify-0.7.0/taxify/man/sci2comm.Rd | 5 taxify-0.7.0/taxify/man/score_candidates.Rd | 3 taxify-0.7.0/taxify/man/sub-.taxify_inspection.Rd |only taxify-0.7.0/taxify/man/sub-.taxify_result.Rd | 4 taxify-0.7.0/taxify/man/taxify-package.Rd | 41 taxify-0.7.0/taxify/man/taxify.Rd | 25 taxify-0.7.0/taxify/man/taxify_build.Rd | 2 taxify-0.7.0/taxify/man/taxify_clean.Rd |only taxify-0.7.0/taxify/man/taxify_download.Rd | 8 taxify-0.7.0/taxify/man/taxify_download_enrichment.Rd | 2 taxify-0.7.0/taxify/man/taxify_ids.Rd | 16 taxify-0.7.0/taxify/man/taxify_lock.Rd | 4 taxify-0.7.0/taxify/man/taxify_pin.Rd | 2 taxify-0.7.0/taxify/man/taxify_restore.Rd | 6 taxify-0.7.0/taxify/man/taxify_store.Rd | 27 taxify-0.7.0/taxify/man/trait_info.Rd | 2 taxify-0.7.0/taxify/man/upstream.Rd | 6 taxify-0.7.0/taxify/tests/testthat/helper-mock-algaebase-backbone.R | 210 taxify-0.7.0/taxify/tests/testthat/helper-mock-backbone.R | 360 taxify-0.7.0/taxify/tests/testthat/helper-mock-euromed-backbone.R | 276 taxify-0.7.0/taxify/tests/testthat/helper-mock-evc-backbone.R |only taxify-0.7.0/taxify/tests/testthat/helper-mock-fungorum-backbone.R | 208 taxify-0.7.0/taxify/tests/testthat/helper-mock-gbif-backbone.R | 454 taxify-0.7.0/taxify/tests/testthat/helper-mock-itis-backbone.R | 280 taxify-0.7.0/taxify/tests/testthat/helper-mock-ncbi-backbone.R | 220 taxify-0.7.0/taxify/tests/testthat/helper-mock-ott-backbone.R | 222 taxify-0.7.0/taxify/tests/testthat/helper-mock-worms-backbone.R | 222 taxify-0.7.0/taxify/tests/testthat/test-add-data.R | 8 taxify-0.7.0/taxify/tests/testthat/test-add-groot-sealifebase.R | 114 taxify-0.7.0/taxify/tests/testthat/test-aggregates.R | 572 - taxify-0.7.0/taxify/tests/testthat/test-backbones.R | 17 taxify-0.7.0/taxify/tests/testthat/test-backend-fishbase-sealifebase.R | 60 taxify-0.7.0/taxify/tests/testthat/test-backend-lcvp-wcvp.R | 116 taxify-0.7.0/taxify/tests/testthat/test-basionym.R | 6 taxify-0.7.0/taxify/tests/testthat/test-browse.R | 4 taxify-0.7.0/taxify/tests/testthat/test-cite.R | 42 taxify-0.7.0/taxify/tests/testthat/test-combine.R | 404 taxify-0.7.0/taxify/tests/testthat/test-content-store.R | 22 taxify-0.7.0/taxify/tests/testthat/test-doors.R | 212 taxify-0.7.0/taxify/tests/testthat/test-download-consent.R |only taxify-0.7.0/taxify/tests/testthat/test-enrichment-grain.R | 4 taxify-0.7.0/taxify/tests/testthat/test-enrichment-side-paths.R | 12 taxify-0.7.0/taxify/tests/testthat/test-enrichment-simple.R | 264 taxify-0.7.0/taxify/tests/testthat/test-extensions.R | 22 taxify-0.7.0/taxify/tests/testthat/test-fuzzy-boundary.R | 6 taxify-0.7.0/taxify/tests/testthat/test-gap-verbs.R | 9 taxify-0.7.0/taxify/tests/testthat/test-gbif-request.R | 1194 +- taxify-0.7.0/taxify/tests/testthat/test-gidias.R | 2 taxify-0.7.0/taxify/tests/testthat/test-hybrid.R | 256 taxify-0.7.0/taxify/tests/testthat/test-inspect.R | 16 taxify-0.7.0/taxify/tests/testthat/test-invacost.R | 2 taxify-0.7.0/taxify/tests/testthat/test-manifest.R | 384 taxify-0.7.0/taxify/tests/testthat/test-multiple-ids.R | 69 taxify-0.7.0/taxify/tests/testthat/test-new-enrichments.R | 194 taxify-0.7.0/taxify/tests/testthat/test-new-verbs.R | 70 taxify-0.7.0/taxify/tests/testthat/test-register.R | 2 taxify-0.7.0/taxify/tests/testthat/test-reptiledb.R | 144 taxify-0.7.0/taxify/tests/testthat/test-source-date.R | 4 taxify-0.7.0/taxify/tests/testthat/test-store-format.R |only taxify-0.7.0/taxify/tests/testthat/test-syntaxon-eva.R |only taxify-0.7.0/taxify/tests/testthat/test-syntaxon.R |only taxify-0.7.0/taxify/tests/testthat/test-taxify-clean.R |only taxify-0.7.0/taxify/tests/testthat/test-taxify-long.R | 206 taxify-0.7.0/taxify/tests/testthat/test-trait-registry.R | 740 - taxify-0.7.0/taxify/vignettes/articles/databases.Rmd | 168 taxify-0.7.0/taxify/vignettes/backbones.Rmd | 1045 -- taxify-0.7.0/taxify/vignettes/custom-data.Rmd | 521 - taxify-0.7.0/taxify/vignettes/enrichments.Rmd | 2931 ----- taxify-0.7.0/taxify/vignettes/exploring.Rmd |only taxify-0.7.0/taxify/vignettes/fuzzy-matching.Rmd | 784 - taxify-0.7.0/taxify/vignettes/gbif-requests.Rmd | 377 taxify-0.7.0/taxify/vignettes/hybrids-and-aggregates.Rmd | 519 - taxify-0.7.0/taxify/vignettes/inspecting-names.Rmd | 375 taxify-0.7.0/taxify/vignettes/large-scale.Rmd | 836 - taxify-0.7.0/taxify/vignettes/migration.Rmd | 512 - taxify-0.7.0/taxify/vignettes/regions.Rmd | 267 taxify-0.7.0/taxify/vignettes/taxify.Rmd |only taxify-0.7.0/taxify/vignettes/vegetation-units.Rmd |only 243 files changed, 16300 insertions(+), 28949 deletions(-)
Title: Cancer RADAR Project Tool
Description: Cancer RADAR is a project which aim is to develop an
infrastructure that allows quantifying the risk of cancer by migration
background across Europe. This package contains a set of functions
cancer registries partners should use to reshape 5 year-age group
cancer incidence data into a set of summary statistics (see Boyle &
Parkin (1991, ISBN:978-92-832-1195-2)) in lines with Cancer RADAR data
protections rules.
Author: Catharina Alberts [aut, rth, pdr],
Damien Georges [aut, cre] ,
Stefano Rosso [aut],
Iacopo Baussano [aut]
Maintainer: Damien Georges <georgesd@iarc.who.int>
Diff between cancerradarr versions 3.0.0 dated 2026-02-16 and 4.1.0 dated 2026-10-27
DESCRIPTION | 16 MD5 | 124 ++-- NAMESPACE | 4 NEWS.md | 42 + R/age_standardized_incidence_rates.R | 95 ++- R/create_canradar_summary_file.R | 516 +++++++++++++++-- R/create_registry_input_file.R | 34 - R/cumulative_risk.R |only R/cumulative_risk_difference.R |only R/cumulative_risk_ratio.R |only R/custom_ageg_aggregation.R | 93 +-- R/data.R | 6 R/diagnose_input_file.R | 48 + R/incidence_rates.R | 19 R/incidence_rates_difference.R | 11 R/incidence_rates_ratio.R | 12 R/indirect_proportional_incidence_ratio.R | 4 R/indirect_standardized_incidence_ratio.R | 13 R/input_template.R |only R/proportional_rates.R | 32 - R/read_cancerradar_data_info.R |only R/read_cancerradar_output_01.R | 58 - R/read_cancerradar_output_02.R | 15 R/read_cancerradar_output_03.R | 18 R/standardized_incidence_rate_difference.R | 41 + R/standardized_incidence_rate_ratio.R | 69 +- README.md | 2 build/vignette.rds |binary data/globocan.2022.eu.rda |binary inst/doc/getting-started.R | 25 inst/doc/getting-started.html | 229 ++++++- inst/doc/getting-started.qmd | 47 + inst/extdata/dictionary_cancerradarr_output_file.xlsx |binary inst/extdata/dynamic_report.Rmd | 27 inst/extdata/ex_cancerRADAR_input_filled.xlsx |binary inst/extdata/ex_cancerRADAR_output.xlsx |binary inst/extdata/static_report.Rmd | 34 + man/age_standardized_incidence_rates.Rd | 36 + man/create_canradar_summary_file.Rd | 15 man/cumulative_risk.Rd |only man/cumulative_risk_difference.Rd |only man/cumulative_risk_ratio.Rd |only man/custom_ageg_aggregation.Rd | 3 man/diagnose_input_file.Rd | 6 man/globocan.2022.eu.Rd | 6 man/incidence_rates.Rd | 5 man/incidence_rates_difference.Rd | 2 man/incidence_rates_ratio.Rd | 2 man/indirect_proportional_incidence_ratio.Rd | 2 man/indirect_standardized_incidence_ratio.Rd | 2 man/proportional_rates.Rd | 2 man/read_cancerradar_data_info.Rd |only man/read_cancerradar_output_01.Rd | 3 man/read_cancerradar_output_02.Rd | 3 man/read_cancerradar_output_03.Rd | 2 man/standardized_incidence_rate_difference.Rd | 24 man/standardized_incidence_rate_ratio.Rd | 27 tests/testthat/test-asr_ci.R |only tests/testthat/test-censored.R |only tests/testthat/test-check_input_columns.R |only tests/testthat/test-check_input_data.R |only tests/testthat/test-create_static_report.R | 3 tests/testthat/test-cumulative_risk.R |only tests/testthat/test-custom_ageg_aggregation.R |only tests/testthat/test-globocan_2022_eu.R |only tests/testthat/test-incidence_rates.R |only tests/testthat/test-incidence_rates_ratio_difference.R |only tests/testthat/test-read_cancerradar_data_info.R |only tests/testthat/test-read_cancerradar_output_01.R | 14 tests/testthat/test-read_cancerradar_output_02.R | 4 tests/testthat/test-ref_argument.R |only tests/testthat/test_cancerradarr.R | 3 vignettes/getting-started.qmd | 47 + 73 files changed, 1423 insertions(+), 422 deletions(-)
Title: Model Agnostic Prediction Intervals
Description: Provides tools for estimating model-agnostic prediction intervals using conformal prediction, bootstrapping, and parametric prediction intervals. The package is designed for ease of use, offering intuitive functions for both binned and full conformal prediction methods, as well as parametric interval estimation with diagnostic checks. Currently only working for continuous predictions. For details on the conformal and bin-conditional conformal prediction methods, see Randahl, Williams, and Hegre (2026) <DOI:10.1017/pan.2025.10010>.
Author: David Randahl [aut, cre],
Jonathan P. Williams [ctb],
Anders Hjort [ctb]
Maintainer: David Randahl <david.randahl@fhs.se>
Diff between pintervals versions 1.1.1 dated 2026-03-03 and 1.3.3 dated 2026-10-27
DESCRIPTION | 13 MD5 | 42 NAMESPACE | 1 NEWS.md |only R/data.R | 160 R/pinterval_bccp.R | 8 R/pinterval_bootstrap.R | 4 R/pinterval_ccp.R | 22 R/pinterval_conformal.R | 6 R/pinterval_mondrian.R | 6 R/pinterval_parametric.R | 2 R/pintervals-package.R | 1 README.md |only build/vignette.rds |binary data/county_turnout_panel.rda |only inst/doc/pintervals.R | 504 + inst/doc/pintervals.Rmd | 827 +- inst/doc/pintervals.html | 9414 +++++------------------------ inst/extdata |only man/county_turnout.Rd | 28 man/county_turnout_panel.Rd |only man/pintervals-package.Rd | 2 tests/testthat/test-county_turnout_panel.R |only vignettes/pintervals.Rmd | 827 +- vignettes/pintervals.bib | 382 - 25 files changed, 3773 insertions(+), 8476 deletions(-)
Title: Lightweight One-Line Resolving Microbial Ecology Program
Description: Provides a robust collection of functions tailored for microbial ecology analysis, encompassing both data analysis and visualization. It introduces an encapsulation feature that streamlines the process into a summary object. With the initial configuration of this summary object, users can execute a wide range of analyses with a single line of code, requiring only two essential parameters for setup. The package delivers comprehensive outputs including analysis objects, statistical outcomes, and visualization-ready data, enhancing the efficiency of research workflows. Designed with user-friendliness in mind, it caters to both novices and seasoned researchers, offering an intuitive interface coupled with adaptable customization options to meet diverse analytical needs.
Author: Ningqi Wang [aut, cre, cph],
Yaozhong Zhang [aut],
Gaofei Jiang [aut]
Maintainer: Ningqi Wang <2434066068@qq.com>
Diff between LorMe versions 2.0.2 dated 2026-01-12 and 2.0.3 dated 2026-10-27
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NAMESPACE | 2 ++ R/Alpha_diversity_calculator.R | 7 +++++++ R/Module_composition.R | 24 ++++++++++++++++++++++-- R/network_visual_re.R | 3 ++- R/structure_plot.R | 36 +++++++++++++++++++++++++++++++++--- man/Module_composition.Rd | 2 +- man/structure_plot.Rd | 3 +++ 9 files changed, 81 insertions(+), 18 deletions(-)
More information about FrailtyPackPlus at CRAN
Permanent link
Title: Bayesian Exponential Random Graph Models
Description: Bayesian analysis for exponential random graph models using
advanced computational algorithms: the approximate exchange algorithm
with adaptive direction sampling (optionally adaptive, delayed-acceptance
and parallel), calibrated pseudo-posteriors, Bayesian
data augmentation for missing network data, and Bayesian goodness-of-fit
diagnostics. More information can be found at:
<https://acaimo.github.io/Bergm/>.
Author: Alberto Caimo [aut, cre],
Lampros Bouranis [aut],
Robert Krause [aut],
Isabella Gollini [aut],
Nial Friel [ctb]
Maintainer: Alberto Caimo <alberto.caimo1@ucd.ie>
Diff between Bergm versions 5.0.7 dated 2023-12-06 and 6.0.0 dated 2026-10-27
Bergm-5.0.7/Bergm/R/plot.bergm.R |only Bergm-5.0.7/Bergm/R/summary.bergm.R |only Bergm-6.0.0/Bergm/DESCRIPTION | 42 +- Bergm-6.0.0/Bergm/MD5 | 71 ++-- Bergm-6.0.0/Bergm/NAMESPACE | 41 +- Bergm-6.0.0/Bergm/NEWS.md |only Bergm-6.0.0/Bergm/R/Bergm-package.R | 33 -- Bergm-6.0.0/Bergm/R/RcppExports.R |only Bergm-6.0.0/Bergm/R/bergm.R | 467 ++++++++++++++++++----------- Bergm-6.0.0/Bergm/R/bergmC.R | 354 +++++++-------------- Bergm-6.0.0/Bergm/R/bergmM.R | 515 +++++++++++++++++++------------- Bergm-6.0.0/Bergm/R/bgof.R | 472 +++++++++++++++++------------ Bergm-6.0.0/Bergm/R/ergmAPL.R | 413 ++++++++++++------------- Bergm-6.0.0/Bergm/R/evidence.R | 45 +- Bergm-6.0.0/Bergm/R/evidenceCJ.R | 346 ++++++++------------- Bergm-6.0.0/Bergm/R/evidencePP.R | 444 ++++++++++----------------- Bergm-6.0.0/Bergm/R/exchange.R |only Bergm-6.0.0/Bergm/R/lazega.R | 3 Bergm-6.0.0/Bergm/R/methods.R |only Bergm-6.0.0/Bergm/R/pseudo.R |only Bergm-6.0.0/Bergm/R/utils.R |only Bergm-6.0.0/Bergm/README.md | 79 ++++ Bergm-6.0.0/Bergm/build |only Bergm-6.0.0/Bergm/inst/WORDLIST | 35 ++ Bergm-6.0.0/Bergm/man/Bergm-package.Rd | 33 +- Bergm-6.0.0/Bergm/man/bergm-methods.Rd |only Bergm-6.0.0/Bergm/man/bergm.Rd | 182 ++++++++--- Bergm-6.0.0/Bergm/man/bergmC.Rd | 58 ++- Bergm-6.0.0/Bergm/man/bergmM.Rd | 115 +++++-- Bergm-6.0.0/Bergm/man/bgof.Rd | 72 ++-- Bergm-6.0.0/Bergm/man/ergmAPL.Rd | 62 +++ Bergm-6.0.0/Bergm/man/evidence.Rd | 19 - Bergm-6.0.0/Bergm/man/evidenceCJ.Rd | 89 +++-- Bergm-6.0.0/Bergm/man/evidencePP.Rd | 58 ++- Bergm-6.0.0/Bergm/man/lazega.Rd | 2 Bergm-6.0.0/Bergm/man/plot.bergm.Rd | 22 - Bergm-6.0.0/Bergm/man/plot.bgof.Rd |only Bergm-6.0.0/Bergm/man/simulate.bergm.Rd |only Bergm-6.0.0/Bergm/man/summary.bergm.Rd | 13 Bergm-6.0.0/Bergm/src |only Bergm-6.0.0/Bergm/tests/testthat |only Bergm-6.0.0/Bergm/tests/testthat.R |only 42 files changed, 2288 insertions(+), 1797 deletions(-)
Title: Tools for Working with Recurrence Rules
Description: Provides tools for defining recurrence rules and recurrence
sets. Recurrence rules are a programmatic way to define a recurring
event, like the first Monday of December. Multiple recurrence rules
can be combined into larger recurrence sets. A full holiday and
calendar interface is also provided that can generate holidays within
a particular year, can detect if a date is a holiday, can respect
holiday observance rules, and allows for custom holidays.
Author: Davis Vaughan [aut, cre],
Posit Software, PBC [cph, fnd]
Maintainer: Davis Vaughan <davis@posit.co>
This is a re-admission after prior archival of version 1.0.0 dated 2023-04-13
Diff between almanac versions 1.0.0 dated 2023-04-13 and 1.0.1 dated 2026-10-27
DESCRIPTION | 16 +-- MD5 | 126 +++++++++++++-------------- NEWS.md | 34 ++++--- R/aaa.R | 12 ++ R/alma-next.R | 1 R/almanac-deprecated.R | 16 ++- R/cache-radjusted.R | 25 ++++- R/cache-rcalendar.R | 18 ++- R/cache-rintersect.R | 19 +++- R/cache-rrule.R | 18 ++- R/cache-rsetdiff.R | 19 +++- R/cache-runion.R | 31 ++++-- R/conversion.R | 30 ++++-- R/holidays.R | 1 R/radjusted.R | 5 - R/rcalendar.R | 22 ++-- R/recur-on-day-of-week.R | 4 R/recur-on-month-of-year.R | 5 - R/rholiday.R | 34 ++++--- R/rrule-print.R | 12 +- R/rrule.R | 40 ++++---- R/rschedule.R | 27 +++-- R/rset.R | 50 ++++++---- R/stepper.R | 32 ++++++ R/utils.R | 90 ++++++++++--------- README.md | 5 - build/vignette.rds |binary inst/doc/adjust-and-shift.R | 2 inst/doc/adjust-and-shift.html | 3 inst/doc/almanac.R | 2 inst/doc/almanac.html | 3 inst/doc/holidays-calendars.R | 2 inst/doc/holidays-calendars.html | 5 - inst/doc/icalendar.R | 2 inst/doc/icalendar.Rmd | 4 inst/doc/icalendar.html | 7 - inst/doc/quarterly.R | 2 inst/doc/quarterly.Rmd | 2 inst/doc/quarterly.html | 7 - src/alma-search.cc | 2 src/utils.h | 15 +++ tests/testthat/_snaps/rholiday.md | 8 - tests/testthat/_snaps/rrule-print.md | 4 tests/testthat/test-adjustments.R | 125 +++++++++++++++++++++----- tests/testthat/test-alma-in.R | 5 - tests/testthat/test-alma-next.R | 82 +++++++++++++---- tests/testthat/test-alma-search.R | 25 ++++- tests/testthat/test-alma-seq.R | 5 - tests/testthat/test-almanac-deprecated.R | 20 +++- tests/testthat/test-misc-quarterly.R | 41 +++++++- tests/testthat/test-radjusted.R | 1 tests/testthat/test-rcalendar.R | 55 +++++++++-- tests/testthat/test-recur-on-easter.R | 120 +++++++++++++++++++++---- tests/testthat/test-recur-on-month-of-year.R | 6 - tests/testthat/test-recur-on-position.R | 1 tests/testthat/test-recur-on-week-of-year.R | 8 + tests/testthat/test-rholiday.R | 11 +- tests/testthat/test-rrule-print.R | 6 + tests/testthat/test-rschedule.R | 7 - tests/testthat/test-rset.R | 56 +++++++++--- tests/testthat/test-stepper.R | 16 ++- tests/testthat/test-vec-cast-date.R | 5 - vignettes/icalendar.Rmd | 4 vignettes/quarterly.Rmd | 2 64 files changed, 935 insertions(+), 428 deletions(-)
Title: Read, Validate, Analyze, and Map GTFS Feeds
Description: Read General Transit Feed Specification (GTFS) zipfiles into a list of R dataframes. Perform validation of the data structure against the specification. Analyze the headways and frequencies at routes and stops. Create maps and perform spatial analysis on the routes and stops. Please see the GTFS documentation here for more detail: <https://gtfs.org/>.
Author: Flavio Poletti [aut, cre],
Daniel Herszenhut [aut] ,
Mark Padgham [aut],
Tom Buckley [aut],
Danton Noriega-Goodwin [aut],
Angela Li [ctb],
Elaine McVey [ctb],
Charles Hans Thompson [ctb],
Michael Sumner [ctb],
Patrick Hausmann [ctb],
Bob Rudis [ctb], [...truncated...]
Maintainer: Flavio Poletti <flavio.poletti@hotmail.ch>
Diff between tidytransit versions 1.8.0 dated 2026-01-26 and 1.8.1 dated 2026-10-27
tidytransit-1.8.0/tidytransit/R/globals.R |only tidytransit-1.8.0/tidytransit/inst/extdata/locations_feed.zip |only tidytransit-1.8.0/tidytransit/inst/extdata/routing-NA-times.zip |only tidytransit-1.8.0/tidytransit/inst/extdata/routing.zip_gtfstools.rds |only tidytransit-1.8.0/tidytransit/inst/extdata/sample-feed-bom.zip |only tidytransit-1.8.0/tidytransit/inst/extdata/sample-feed-calendar_dates.zip |only tidytransit-1.8.0/tidytransit/inst/extdata/sample-feed-fixed.zip |only tidytransit-1.8.0/tidytransit/inst/extdata/sample-feed-invalid.zip |only tidytransit-1.8.0/tidytransit/inst/extdata/sample-feed-plus.zip |only tidytransit-1.8.1/tidytransit/DESCRIPTION | 14 tidytransit-1.8.1/tidytransit/MD5 | 118 +++---- tidytransit-1.8.1/tidytransit/NAMESPACE | 128 ++++---- tidytransit-1.8.1/tidytransit/NEWS.md | 10 tidytransit-1.8.1/tidytransit/R/convert_types.R | 17 - tidytransit-1.8.1/tidytransit/R/dates.R | 86 +++-- tidytransit-1.8.1/tidytransit/R/filters.R | 157 +++++----- tidytransit-1.8.1/tidytransit/R/frequencies.R | 110 +++---- tidytransit-1.8.1/tidytransit/R/geo.R | 127 ++++---- tidytransit-1.8.1/tidytransit/R/gtfsio.R | 10 tidytransit-1.8.1/tidytransit/R/io.R | 27 - tidytransit-1.8.1/tidytransit/R/plot.R | 4 tidytransit-1.8.1/tidytransit/R/raptor-checks.r | 11 tidytransit-1.8.1/tidytransit/R/raptor.R | 144 ++++----- tidytransit-1.8.1/tidytransit/R/service.R | 30 - tidytransit-1.8.1/tidytransit/R/spatial.R | 78 ++-- tidytransit-1.8.1/tidytransit/R/summary.R | 28 - tidytransit-1.8.1/tidytransit/R/sysdata.rda |binary tidytransit-1.8.1/tidytransit/R/tidygtfs.R | 56 ++- tidytransit-1.8.1/tidytransit/R/time.R | 56 ++- tidytransit-1.8.1/tidytransit/R/travel_times.R | 41 +- tidytransit-1.8.1/tidytransit/R/utils.R | 42 +- tidytransit-1.8.1/tidytransit/R/validate_gtfs.R | 79 ++--- tidytransit-1.8.1/tidytransit/build/vignette.rds |binary tidytransit-1.8.1/tidytransit/inst/doc/introduction.Rmd | 2 tidytransit-1.8.1/tidytransit/inst/doc/introduction.html | 60 +-- tidytransit-1.8.1/tidytransit/inst/doc/servicepatterns.Rmd | 2 tidytransit-1.8.1/tidytransit/inst/doc/servicepatterns.html | 2 tidytransit-1.8.1/tidytransit/man/cluster_stops.Rd | 2 tidytransit-1.8.1/tidytransit/man/empty_strings_to_na.Rd | 2 tidytransit-1.8.1/tidytransit/man/filter_feed_by_area.Rd | 4 tidytransit-1.8.1/tidytransit/man/filter_feed_by_date.Rd | 5 tidytransit-1.8.1/tidytransit/man/filter_feed_by_stops.Rd | 9 tidytransit-1.8.1/tidytransit/man/filter_feed_by_trips.Rd | 4 tidytransit-1.8.1/tidytransit/man/filter_stops.Rd | 6 tidytransit-1.8.1/tidytransit/man/json_to_sf.Rd | 2 tidytransit-1.8.1/tidytransit/man/print.tidygtfs.Rd | 6 tidytransit-1.8.1/tidytransit/man/validate_gtfs.Rd | 4 tidytransit-1.8.1/tidytransit/tests/testthat/data |only tidytransit-1.8.1/tidytransit/tests/testthat/test-as_tidygtfs.R | 22 - tidytransit-1.8.1/tidytransit/tests/testthat/test-raptor-transfers.R | 42 +- tidytransit-1.8.1/tidytransit/tests/testthat/test-raptor.R | 115 +++---- tidytransit-1.8.1/tidytransit/tests/testthat/test-read-gtfs.R | 82 +++-- tidytransit-1.8.1/tidytransit/tests/testthat/test-service.R | 2 tidytransit-1.8.1/tidytransit/tests/testthat/test-spatial.R | 67 ++-- tidytransit-1.8.1/tidytransit/tests/testthat/test-time.R | 63 +--- tidytransit-1.8.1/tidytransit/tests/testthat/test-travel_times.R | 37 +- tidytransit-1.8.1/tidytransit/tests/testthat/test-utils.R | 106 +++++- tidytransit-1.8.1/tidytransit/tests/testthat/test-validate.R | 20 - tidytransit-1.8.1/tidytransit/tests/testthat/test-write-gtfs.R | 6 tidytransit-1.8.1/tidytransit/vignettes/introduction.Rmd | 2 tidytransit-1.8.1/tidytransit/vignettes/servicepatterns.Rmd | 2 61 files changed, 1161 insertions(+), 888 deletions(-)
Title: Help with Preparing a New Version of an R Package
Description: Helps to prepare a release. Before releasing an R package it is important to update the DESCRIPTION file and the changelog. This package prepares these files and also updates the versions according to the branches. It relies heavily on the 'desc' packages.
Author: Tanguy Barthelemy [aut, cre, art, cph]
Maintainer: Tanguy Barthelemy <tanguy.barthelemy@insee.fr>
Diff between releaser versions 1.2.1 dated 2026-07-30 and 1.3.0 dated 2026-10-27
releaser-1.2.1/releaser/man/set_latest_deps_version.Rd |only releaser-1.2.1/releaser/tests/testthat/data/DESCRIPTION |only releaser-1.3.0/releaser/DESCRIPTION | 12 releaser-1.3.0/releaser/MD5 | 43 +- releaser-1.3.0/releaser/NAMESPACE | 30 + releaser-1.3.0/releaser/NEWS.md | 32 + releaser-1.3.0/releaser/R/cran-check.R | 183 +++++++-- releaser-1.3.0/releaser/R/deprecated.R | 5 releaser-1.3.0/releaser/R/get_information.R | 196 ++++++++-- releaser-1.3.0/releaser/R/update_description.R | 113 ++++- releaser-1.3.0/releaser/README.md | 68 ++- releaser-1.3.0/releaser/man/change_remotes_field.Rd | 6 releaser-1.3.0/releaser/man/check.Rd | 55 ++ releaser-1.3.0/releaser/man/check_docs.Rd | 5 releaser-1.3.0/releaser/man/get_github_branches.Rd | 5 releaser-1.3.0/releaser/man/get_latest_version.Rd | 14 releaser-1.3.0/releaser/man/set_latest_rjdverse_version.Rd |only releaser-1.3.0/releaser/man/set_rjdverse_remotes.Rd | 11 releaser-1.3.0/releaser/tests/testthat/data/pkg_test |only releaser-1.3.0/releaser/tests/testthat/helper.R | 10 releaser-1.3.0/releaser/tests/testthat/test-change_remotes_field.R | 65 ++- releaser-1.3.0/releaser/tests/testthat/test-check_docs.R |only releaser-1.3.0/releaser/tests/testthat/test-get_different_future_version.R | 4 releaser-1.3.0/releaser/tests/testthat/test-get_latest_version.R |only releaser-1.3.0/releaser/tests/testthat/test-get_version_from_branch.R |only releaser-1.3.0/releaser/tests/testthat/test-set_rjdverse_remotes.R | 55 ++ 26 files changed, 717 insertions(+), 195 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 5.1.0 dated 2026-09-03 and 5.2.0 dated 2026-10-27
DESCRIPTION | 10 MD5 | 134 +++-- R/RcppExports.R | 74 ++- R/dataset_documentation.R | 2 R/defaultControl.R | 50 +- R/extract.R | 2 R/fordyn.R | 7 R/fordynutils.R | 2 R/plot.spwb.R | 33 + R/plot.spwb_day.R | 12 R/plot_internals.R | 97 ++++ R/plot_lowlevel.R | 17 R/regeneration.R | 6 R/shinyplot.R | 6 R/sysdata.rda |binary data/SpParamsDefinition.rda |binary data/SpParamsMED.rda |binary data/exampleobs.rda |binary inst/include/medfate_RcppExports.h | 32 - man/SpParams.Rd | 2 man/aspwb.Rd | 7 man/defaultControl.Rd | 28 - man/growth.Rd | 7 man/hydrology_soilWaterBalance.Rd | 4 man/modelInput.Rd | 26 - man/pheno_updateLeaves.Rd | 8 man/plot.spwb.Rd | 2 man/plot.spwb_day.Rd | 1 man/spwb.Rd | 11 man/spwb_day.Rd | 2 man/transp_modes.Rd | 2 src/RcppExports.cpp | 90 ++- src/aspwb.cpp | 33 + src/biophysicsutils.cpp | 6 src/biophysicsutils.h | 2 src/control_c.cpp | 25 - src/control_c.h | 14 src/forestutils.cpp | 58 +- src/growth.cpp | 33 + src/growth_day_c.cpp | 341 ++++++++++----- src/hydrology.cpp | 8 src/hydrology.h | 2 src/hydrology_c.cpp | 47 +- src/hydrology_c.h | 3 src/inner_sperry_c.cpp | 10 src/inner_sperry_c.h | 2 src/inner_sureau.cpp | 22 src/inner_sureau_c.cpp | 20 src/inner_sureau_c.h | 4 src/medfate_runners.cpp | 45 + src/modelInput.cpp | 264 ++++++++--- src/modelInput_c.cpp | 152 ++++++ src/modelInput_c.h | 25 - src/paramutils.cpp | 145 ++++++ src/paramutils.h | 6 src/phenology.cpp | 10 src/phenology_c.cpp | 215 ++++++--- src/phenology_c.h | 3 src/spwb.cpp | 96 ++-- src/spwb_day.cpp | 2 src/spwb_day_c.cpp | 17 src/transpiration_advanced_c.cpp | 19 src/transpiration_advanced_c.h | 5 src/transpiration_basic.cpp | 2 src/transpiration_basic_c.cpp | 18 src/transpiration_basic_c.h | 2 tests/testthat/Rplots.pdf |only tests/testthat/_problems |only tests/testthat/initialized_objects/growthInput_5.2.0.rds |only tests/testthat/initialized_objects/spwbInput_5.2.0.rds |only 70 files changed, 1706 insertions(+), 624 deletions(-)