Title: An MCMC Sampler Using the t-Walk Algorithm
Description: Implements the t-walk algorithm, a general-purpose, self-adjusting
Markov Chain Monte Carlo (MCMC) sampler for continuous distributions as
described by Christen & Fox (2010) <doi:10.1214/10-BA603>. The t-walk requires
no tuning and is robust for a wide range of target distributions, including
high-dimensional and multimodal problems. This implementation includes an
option for running multiple chains in parallel to accelerate sampling and
facilitate convergence diagnostics.
Author: Rodrigo Fonseca Villa [aut, cre]
Maintainer: Rodrigo Fonseca Villa <rodrigo03.villa@gmail.com>
Diff between Rtwalk versions 2.0.2 dated 2026-07-30 and 2.1.0 dated 2026-08-28
DESCRIPTION | 8 MD5 | 40 ++-- NAMESPACE | 1 NEWS.md | 45 +++++ R/diagnostics.R | 91 +++++++++-- R/s3-methods.R | 14 + R/twalk_engine.R | 77 +++++++-- R/twalk_main.R | 298 ++++++++++++++++++++++++++++++------ README.md | 59 ++++++- inst/doc/validation_study.R | 44 +++-- inst/doc/validation_study.Rmd | 60 +++++-- inst/doc/validation_study.html | 79 ++++++--- man/calculate_diagnostics.Rd | 6 man/twalk.Rd | 45 ++++- man/visualize_results.Rd | 2 tests/testthat/test-diagnostics.R | 47 +++++ tests/testthat/test-kernels.R | 37 ++++ tests/testthat/test-methods.R | 51 ++++++ tests/testthat/test-twalk.R | 310 +++++++++++++++++++++++++++++++++++++- tests/testthat/test-visualize.R | 19 ++ vignettes/validation_study.Rmd | 60 +++++-- 21 files changed, 1182 insertions(+), 211 deletions(-)
Title: Taxonomic Hierarchy Distances and Lineage Analysis
Description: Computes distances between taxonomic hierarchy nodes using lineage
data retrieved from The Taxonomicon <http://taxonomicon.taxonomy.nl>. For
distinct nodes, distance is defined as the reciprocal of the depth of their
most recent common ancestor; identical nodes have distance zero. This
definition yields an ultrametric within each connected hierarchy. Functions
are provided for lineage retrieval and comparison, clade membership,
pairwise and matrix distance calculation, hierarchical clustering,
principal coordinates analysis, and cache management. Distance matrices are
returned as base R 'dist' objects. The distances represent classification
depth rather than evolutionary time or phylogenetic branch length.
Author: Rodrigo Fonseca Villa [aut, cre]
Maintainer: Rodrigo Fonseca Villa <rodrigo03.villa@gmail.com>
Diff between taxodist versions 0.6.0 dated 2026-08-19 and 0.7.0 dated 2026-08-28
DESCRIPTION | 6 - MD5 | 18 ++--- NEWS.md | 22 ++++++ R/distance.R | 105 +++++++++++++++++++++++---------- R/fetch.R | 20 +++++- data/taxobase.rda |binary inst/CITATION | 2 inst/doc/introduction.html | 2 inst/doc/statistical-applications.html | 2 tests/testthat/test-distance.R | 97 +++++++++++++++++++++++++++++- 10 files changed, 224 insertions(+), 50 deletions(-)
Title: Extracts Risk Neutral Densities of Prices, Money Market Rates
and Government Bond Yields from Interest Rates Futures Options
Prices
Description: Provides with parametric Risk Neutral Densities (RNDs) and cumulative densities of futures prices on fixed-income products. It relies on options on Short Term Interest Rate futures or options on government bond futures. It models the futures price as a mixture of lognormal densities. Leveraging on this, the package provides with the RNDs and cumulative densities of the money market rate or the government bond yield inferred from the futures price, using the RND of the futures price. The package also extracts from the RND of the government bond futures price simultaneously the RND of the cheapest-to-deliver bond yield at options' maturity and the RND of the ctd bond repo rate from options' maturity to futures' maturity. The package also provides with the probability attached to each bond in the delivery basket of a government bond futures to be the cheapest at maturity, and also the non parametric distribution of the spread between two bond yields, using two RNDs based on options on bon [...truncated...]
Author: William Arrata [aut, cre]
Maintainer: William Arrata <william.arrata@gmail.com>
Diff between yrnd versions 0.1.5 dated 2026-07-21 and 0.1.6 dated 2026-08-28
DESCRIPTION | 12 MD5 | 40 NAMESPACE | 2 R/bond_fut_irr_ytm.R |only R/bond_future_charac_bbg.R | 2 R/bond_future_price.R | 106 R/bond_yield_spread.R | 3 R/ctd_bond_yield.R | 120 R/deliv_bonds_charac_bbg.R | 16 R/globals.R | 3 R/option_prices_bbg.R | 9 R/proba_ctd.R | 261 R/proba_ctd_opt.R | 15 R/stir_future_price.R | 102 R/stir_rate.R | 103 inst/doc/yrnd-functions.R | 53 inst/doc/yrnd-functions.Rmd | 70 inst/doc/yrnd-functions.html |101448 ++++-------------------------------------- man/bond_fut_irr_ytm.Rd |only man/bond_future_charac_bbg.Rd | 1 man/proba_ctd.Rd | 6 vignettes/yrnd-functions.Rmd | 70 22 files changed, 11053 insertions(+), 91389 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>
This is a re-admission after prior archival of version 2.1.1 dated 2026-01-11
Diff between SpaDES.tools versions 2.1.1 dated 2026-01-11 and 2.1.3 dated 2026-08-28
SpaDES.tools-2.1.1/SpaDES.tools/man/wrap.Rd |only SpaDES.tools-2.1.3/SpaDES.tools/DESCRIPTION | 29 SpaDES.tools-2.1.3/SpaDES.tools/MD5 | 210 ++++-- SpaDES.tools-2.1.3/SpaDES.tools/NAMESPACE | 185 ++--- SpaDES.tools-2.1.3/SpaDES.tools/NEWS.md | 106 +++ SpaDES.tools-2.1.3/SpaDES.tools/R/RcppExports.R | 48 + SpaDES.tools-2.1.3/SpaDES.tools/R/SELES.R | 31 SpaDES.tools-2.1.3/SpaDES.tools/R/distanceFromEachPoint.R | 6 SpaDES.tools-2.1.3/SpaDES.tools/R/heading.R | 12 SpaDES.tools-2.1.3/SpaDES.tools/R/helpers.R | 12 SpaDES.tools-2.1.3/SpaDES.tools/R/initialize.R | 238 ++----- SpaDES.tools-2.1.3/SpaDES.tools/R/mapReduce.R | 118 +-- SpaDES.tools-2.1.3/SpaDES.tools/R/movement.R | 90 +- SpaDES.tools-2.1.3/SpaDES.tools/R/neighbourhood.R | 132 +++ SpaDES.tools-2.1.3/SpaDES.tools/R/probability.R | 6 SpaDES.tools-2.1.3/SpaDES.tools/R/rastFromDF.R |only SpaDES.tools-2.1.3/SpaDES.tools/R/release-bullets.R |only SpaDES.tools-2.1.3/SpaDES.tools/R/rings.R | 4 SpaDES.tools-2.1.3/SpaDES.tools/R/spades-tools-deprecated.R | 3 SpaDES.tools-2.1.3/SpaDES.tools/R/spades-tools-package.R | 28 SpaDES.tools-2.1.3/SpaDES.tools/R/splitRaster.R | 2 SpaDES.tools-2.1.3/SpaDES.tools/R/spread.R | 30 SpaDES.tools-2.1.3/SpaDES.tools/R/spread2.R | 31 SpaDES.tools-2.1.3/SpaDES.tools/R/spread3.R | 4 SpaDES.tools-2.1.3/SpaDES.tools/R/studyArea.R | 5 SpaDES.tools-2.1.3/SpaDES.tools/README.md | 181 ++++- SpaDES.tools-2.1.3/SpaDES.tools/inst/WORDLIST | 23 SpaDES.tools-2.1.3/SpaDES.tools/inst/examples/example_spread.R | 2 SpaDES.tools-2.1.3/SpaDES.tools/man/SELEStransitions.Rd | 22 SpaDES.tools-2.1.3/SpaDES.tools/man/SpaDES.tools-package.Rd | 24 SpaDES.tools-2.1.3/SpaDES.tools/man/adjPairsMatrix.Rd |only SpaDES.tools-2.1.3/SpaDES.tools/man/adjPairsWithId.Rd |only SpaDES.tools-2.1.3/SpaDES.tools/man/crw.Rd | 11 SpaDES.tools-2.1.3/SpaDES.tools/man/deprecated.Rd | 4 SpaDES.tools-2.1.3/SpaDES.tools/man/distances.Rd | 7 SpaDES.tools-2.1.3/SpaDES.tools/man/dwrpnorm2.Rd | 5 SpaDES.tools-2.1.3/SpaDES.tools/man/neutralLandscapeMap.Rd | 76 +- SpaDES.tools-2.1.3/SpaDES.tools/man/pkgEnv.Rd | 4 SpaDES.tools-2.1.3/SpaDES.tools/man/rastFromDF.Rd |only SpaDES.tools-2.1.3/SpaDES.tools/man/rings.Rd | 2 SpaDES.tools-2.1.3/SpaDES.tools/man/specnumperpatch-probs.Rd | 8 SpaDES.tools-2.1.3/SpaDES.tools/man/splitRaster.Rd | 2 SpaDES.tools-2.1.3/SpaDES.tools/man/spread.Rd | 4 SpaDES.tools-2.1.3/SpaDES.tools/man/spread2.Rd | 5 SpaDES.tools-2.1.3/SpaDES.tools/man/testEquivalentMetadata.Rd | 5 SpaDES.tools-2.1.3/SpaDES.tools/man/wrapTorus.Rd |only SpaDES.tools-2.1.3/SpaDES.tools/src/RcppExports.cpp | 31 SpaDES.tools-2.1.3/SpaDES.tools/src/adj_spread.cpp |only SpaDES.tools-2.1.3/SpaDES.tools/src/duplicated.cpp | 4 SpaDES.tools-2.1.3/SpaDES.tools/src/runif.cpp | 2 SpaDES.tools-2.1.3/SpaDES.tools/tests/testthat/_spread_snapshots |only SpaDES.tools-2.1.3/SpaDES.tools/tests/testthat/setup.R | 1 SpaDES.tools-2.1.3/SpaDES.tools/tests/testthat/test-SELES.R |only SpaDES.tools-2.1.3/SpaDES.tools/tests/testthat/test-adj-helpers.R |only SpaDES.tools-2.1.3/SpaDES.tools/tests/testthat/test-adj.R | 141 ++++ SpaDES.tools-2.1.3/SpaDES.tools/tests/testthat/test-distanceFromEachPoint.R |only SpaDES.tools-2.1.3/SpaDES.tools/tests/testthat/test-heading.R |only SpaDES.tools-2.1.3/SpaDES.tools/tests/testthat/test-initialize.R |only SpaDES.tools-2.1.3/SpaDES.tools/tests/testthat/test-misc-helpers.R |only SpaDES.tools-2.1.3/SpaDES.tools/tests/testthat/test-movement.R |only SpaDES.tools-2.1.3/SpaDES.tools/tests/testthat/test-neutralLandscapeMap.R | 5 SpaDES.tools-2.1.3/SpaDES.tools/tests/testthat/test-probability.R |only SpaDES.tools-2.1.3/SpaDES.tools/tests/testthat/test-randomPolygon.R | 62 + SpaDES.tools-2.1.3/SpaDES.tools/tests/testthat/test-rastFromDF.R |only SpaDES.tools-2.1.3/SpaDES.tools/tests/testthat/test-rings.R |only SpaDES.tools-2.1.3/SpaDES.tools/tests/testthat/test-spokes.R |only SpaDES.tools-2.1.3/SpaDES.tools/tests/testthat/test-spread-snapshots.R |only SpaDES.tools-2.1.3/SpaDES.tools/tests/testthat/test-spread.R | 335 +++++----- SpaDES.tools-2.1.3/SpaDES.tools/tests/testthat/test-spread2.R | 219 +++++- SpaDES.tools-2.1.3/SpaDES.tools/tests/testthat/test-spread3.R |only SpaDES.tools-2.1.3/SpaDES.tools/tests/testthat/test-studyArea.R |only SpaDES.tools-2.1.3/SpaDES.tools/tests/testthat/test-wrapTorus.R |only 72 files changed, 1778 insertions(+), 737 deletions(-)
Title: Hierarchical Piecewise Regression with Smoothed Change-Points
Description: Fits Bayesian hierarchical piecewise regression models with
multiple logistic-smoothed change-points. Non-linear parameters (change-point
locations and transition sharpness) and linear parameters can each be
conditioned on covariates and factors via flexible design matrices.
A random-intercept structure is supported for any parameter. Spike-and-slab
regularization is supported for selecting the number of breakpoints.
Posterior inference uses a Metropolis-within-Gibbs sampler implemented
in 'Rust' for speed. Methods are based on the smooth transition
piecewise regression model of Bacon and Watts (1971) <doi:10.2307/2334389>
and variable selection spike-and-slab priors of Kuo and Mallick (1998)
<https://www.jstor.org/stable/25053023>. Methods are described in
Bindoff (2026) <doi:10.48550/arXiv.2606.19044>.
Author: Aidan D Bindoff [aut, cre]
Maintainer: Aidan D Bindoff <aidan.bindoff@utas.edu.au>
Diff between smoothbp versions 0.2.7 dated 2026-06-16 and 0.2.8 dated 2026-08-28
smoothbp-0.2.7/smoothbp/tools/test_vignette_params.R |only smoothbp-0.2.7/smoothbp/tools/verify_mixing_changes.R |only smoothbp-0.2.8/smoothbp/DESCRIPTION | 21 smoothbp-0.2.8/smoothbp/MD5 | 30 smoothbp-0.2.8/smoothbp/NAMESPACE | 1 smoothbp-0.2.8/smoothbp/NEWS.md | 128 ++ smoothbp-0.2.8/smoothbp/R/methods_text.R | 6 smoothbp-0.2.8/smoothbp/R/smoothbp.R | 7 smoothbp-0.2.8/smoothbp/R/smoothbp_ss.R | 91 + smoothbp-0.2.8/smoothbp/inst/CITATION |only smoothbp-0.2.8/smoothbp/man/reexports.Rd | 40 smoothbp-0.2.8/smoothbp/man/update.smoothbp_ss_fit.Rd |only smoothbp-0.2.8/smoothbp/src/Makevars.win.in | 4 smoothbp-0.2.8/smoothbp/src/rust/src/model.rs | 113 + smoothbp-0.2.8/smoothbp/src/rust/src/sampler.rs | 640 +++++++++- smoothbp-0.2.8/smoothbp/src/rust/src/sampler_re.rs | 619 ++++++++- smoothbp-0.2.8/smoothbp/tests/testthat/test-collapsed-indicator.R |only smoothbp-0.2.8/smoothbp/tests/testthat/test-reparameterise.R |only smoothbp-0.2.8/smoothbp/tests/testthat/test-update-recovery-hypothesis-bf.R | 44 19 files changed, 1594 insertions(+), 150 deletions(-)
Title: A Fast and Flexible Pipeline for Text Classification
Description: A high-level pipeline that simplifies text classification into three streamlined steps:
preprocessing, model training, and standardized prediction.
It unifies the interface for multiple algorithms (including 'glmnet', 'ranger',
'xgboost', and 'naivebayes') and memory-efficient sparse matrix vectorization
methods (Bag-of-Words, Term Frequency, TF-IDF, and Binary). Users can go from
raw text to a fully evaluated sentiment model, complete with ROC-optimized
thresholds, in just a few function calls. The resulting model artifact
automatically aligns the vocabulary of new datasets during the prediction phase,
safely appending predicted classes and probability matrices directly to the
user's original dataframe to preserve metadata.
Author: Alabhya Dahal [aut, cre]
Maintainer: Alabhya Dahal <alabhya.dahal@gmail.com>
Diff between quickSentiment versions 0.3.5 dated 2026-07-13 and 0.3.6 dated 2026-08-28
DESCRIPTION | 6 MD5 | 14 - NAMESPACE | 1 NEWS.md | 13 - R/pre_process.R | 222 +++++++++++++++++---------- README.md | 3 inst/doc/introduction-to-quickSentiment.html | 61 +++---- man/pre_process.Rd | 38 ++-- 8 files changed, 219 insertions(+), 139 deletions(-)
More information about quickSentiment at CRAN
Permanent link
Title: Access the 'Mobility Database' API to Discover Transit Feeds
Description: Search and access transit feed data from the
'Mobility Database' <https://mobilitydatabase.org>. The package wraps the 'Mobility Database'
API, allowing users to discover 'GTFS' (General Transit Feed Specification) and
'GBFS' (General Bikeshare Feed Specification) feeds from agencies worldwide.
Functions are designed to integrate seamlessly with
packages like 'tidytransit' and 'gtfstools' for subsequent feed analysis.
Author: Jason Adle [aut, cre, cph]
Maintainer: Jason Adle <developer@jasonadle.dev>
Diff between mobdb versions 1.0.1 dated 2026-08-07 and 1.0.3 dated 2026-08-28
DESCRIPTION | 6 LICENSE | 4 MD5 | 162 - NAMESPACE | 88 - NEWS.md | 321 +-- R/api-datasets.R | 232 +- R/api-feeds.R | 874 ++++----- R/api-metadata.R | 34 R/api-search.R | 346 +-- R/cache.R | 744 ++++---- R/geo-feeds.R | 470 ++--- R/integration-tidytransit.R | 2188 ++++++++++++------------- R/mobdb-package.R | 60 R/utils-auth.R | 344 +-- R/utils-conditions.R | 94 - R/utils-convenience.R | 380 ++-- R/utils-gtfs-format.R | 282 +-- R/utils-helpers.R | 1350 +++++++-------- R/utils-request.R | 244 +- README.md | 368 ++-- build/vignette.rds |binary inst/doc/gbfs-and-gtfs-rt.R | 148 - inst/doc/gbfs-and-gtfs-rt.Rmd | 332 +-- inst/doc/gbfs-and-gtfs-rt.html | 1062 ++++++------ inst/doc/mobdb.R | 432 ++-- inst/doc/mobdb.Rmd | 646 +++---- inst/doc/mobdb.html | 1308 +++++++------- man/download_best_feed.Rd | 270 +-- man/download_feed.Rd | 306 +-- man/feeds.Rd | 198 +- man/feeds_bbox.Rd | 188 +- man/figures/lifecycle-deprecated.svg | 42 man/figures/lifecycle-experimental.svg | 42 man/figures/lifecycle-stable.svg | 58 man/figures/lifecycle-superseded.svg | 42 man/filter_by_validation.Rd | 156 - man/get_validation_report.Rd | 138 - man/gtfs_to_spec_format.Rd | 128 - man/mobdb-package.Rd | 62 man/mobdb_browse.Rd | 44 man/mobdb_cache_clear.Rd | 56 man/mobdb_cache_info.Rd | 46 man/mobdb_cache_list.Rd | 46 man/mobdb_cache_path.Rd | 78 man/mobdb_can_run_examples.Rd | 38 man/mobdb_datasets.Rd | 98 - man/mobdb_extract_datasets.Rd | 138 - man/mobdb_extract_locations.Rd | 114 - man/mobdb_extract_urls.Rd | 80 man/mobdb_feed_url.Rd | 60 man/mobdb_get_dataset.Rd | 48 man/mobdb_get_feed.Rd | 46 man/mobdb_has_internet.Rd | 38 man/mobdb_has_key.Rd | 42 man/mobdb_has_tidytransit.Rd | 38 man/mobdb_read_gtfs.Rd | 88 - man/mobdb_search.Rd | 210 +- man/mobdb_set_key.Rd | 70 man/view_validation_report.Rd | 102 - tests/testthat.R | 8 tests/testthat/README.md | 184 +- tests/testthat/setup.R | 64 tests/testthat/test-api-feeds.R | 466 ++--- tests/testthat/test-api-metadata.R | 60 tests/testthat/test-api-parameter-validation.R | 46 tests/testthat/test-api-search.R | 348 +-- tests/testthat/test-auth.R | 296 +-- tests/testthat/test-cache.R | 1260 +++++++------- tests/testthat/test-datasets.R | 332 +-- tests/testthat/test-download-best-feed.R | 300 +-- tests/testthat/test-export-gtfs.R | 392 ++-- tests/testthat/test-feed-quality-scoring.R | 736 ++++---- tests/testthat/test-format-feed-summary.R | 574 +++--- tests/testthat/test-geo-feeds.R | 406 ++-- tests/testthat/test-gtfs-format.R | 574 +++--- tests/testthat/test-helpers.R | 724 ++++---- tests/testthat/test-integration.R | 490 ++--- tests/testthat/test-utils-convenience.R | 94 - tests/testthat/test-utils-request.R | 556 +++--- tests/testthat/test-validation-helpers.R | 396 ++-- vignettes/gbfs-and-gtfs-rt.Rmd | 332 +-- vignettes/mobdb.Rmd | 646 +++---- 82 files changed, 12464 insertions(+), 12449 deletions(-)
Title: Hydrologic Geospatial Fabric Extraction Tool Chain
Description: Traverses and works with National Hydrography Dataset Plus (NHDPlus) data. All methods implemented in 'hydrogeofetch' are available in the NHDPlus documentation available from the US Environmental Protection Agency <https://www.epa.gov/waterdata/basic-information>. Previously published as 'nhdplusTools'.
Author: David Blodgett [aut, cre] ,
Mike Johnson [ctb] ,
Marc Weber [ctb] ,
Josh Erickson [ctb],
Lauren Koenig [ctb]
Maintainer: David Blodgett <dblodgett@usgs.gov>
Diff between hydrogeofetch versions 2.0.2 dated 2026-08-28 and 2.0.3 dated 2026-08-28
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 7 +++++++ R/get_drainage_area_estimates.R | 15 +++++++++++---- man/get_drainage_area_estimates.Rd | 3 ++- 5 files changed, 27 insertions(+), 12 deletions(-)
Title: Fast Kernel Density Estimation with Hexagonal Grid
Description: Kernel density estimation with hexagonal grid for bivariate data.
Hexagonal grid has many beneficial properties like equidistant neighbours
and less edge bias, making it better for spatial analyses than the more
commonly used rectangular grid.
Carr, D. B. et al. (1987) <doi:10.2307/2289444>.
Diggle, P. J. (2010) <doi:10.1201/9781420072884>.
Hill, B. (2017) <https://blog.bruce-hill.com/meandering-triangles>.
Jones, M. C. (1993) <doi:10.1007/BF00147776>.
Author: Quoc Hoang Nguyen [aut, cre] ,
Yunshun Chen [aut] ,
Dan Carr [ctb],
binning routine ported by Nicholas Lewin-Koh [ctb],
Martin Maechler [ctb]
Maintainer: Quoc Hoang Nguyen <nguyen.q@wehi.edu.au>
Diff between hexDensity versions 1.4.10 dated 2025-09-28 and 1.4.11 dated 2026-08-28
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 7 ++++++- src/meanderingTriangleC.cpp | 1 + 4 files changed, 14 insertions(+), 8 deletions(-)
Title: Lindley Approximation for Capability Indices under Progressive
Censoring
Description: Implements Bayesian parameter and Generalized Process Capability
Indices (GPCIs) estimation using the Lindley approximation method (Lindley,
1980 <doi:10.2307/2345271>) under progressive Type-II censored data
(Balakrishnan & Aggarwala, 2000 <doi:10.1007/978-1-4612-1334-5>). Evaluates
point estimates and posterior expectations for classical and non-normal
capability indices, including Cpy (Maiti et al., 2010
<doi:10.1080/16843703.2010.11673233>), Spmk (Dey & Saha, 2019
<doi:10.1007/s41872-019-00081-4>), CpTk (Saha et al., 2019
<doi:10.1007/s13198-019-00789-7>), Cpc (Saha et al.,
2022 <doi:10.1080/02664763.2021.1971632>), CNpmc (Alotaibi et al., 2022
<doi:10.1155/2022/3135264>), CNpmkc (Saha et al., 2024
<doi:10.1142/S021853932450013X>), CNpk (Saha et al., 2018
<doi:10.1080/21681015.2018.1437793>), and Vannman's Cp(u,v) family (Vannman,
1995 <doi:10.1111/j.1467-9574.1995.tb01472.x>). Calculates point estimates,
bias, mea [...truncated...]
Author: Shikhar Tyagi [aut, cre] ,
Sumit Kumar [aut],
Arvind Pandey [aut],
Bhupendra Singh [aut],
Vrijesh Tripathi [aut]
Maintainer: Shikhar Tyagi <shikhar1093tyagi@gmail.com>
Diff between gpciLindApproxProgII versions 0.1.0 dated 2026-08-26 and 0.1.1 dated 2026-08-28
gpciLindApproxProgII-0.1.0/gpciLindApproxProgII/tests/testthat/Rplots.pdf |only gpciLindApproxProgII-0.1.1/gpciLindApproxProgII/DESCRIPTION | 9 gpciLindApproxProgII-0.1.1/gpciLindApproxProgII/MD5 | 9 gpciLindApproxProgII-0.1.1/gpciLindApproxProgII/inst/WORDLIST | 50 +++- gpciLindApproxProgII-0.1.1/gpciLindApproxProgII/inst/doc/GPCILindApproxProgII.html | 114 +++++----- gpciLindApproxProgII-0.1.1/gpciLindApproxProgII/tests/testthat/test-all.R | 19 + 6 files changed, 119 insertions(+), 82 deletions(-)
More information about gpciLindApproxProgII at CRAN
Permanent link
Title: Estimation and Additional Tools for Alternative Shared Frailty
Models
Description: Provide estimation and data generation tools for new multivariate frailty models.
This version includes the gamma, inverse Gaussian, weighted Lindley, Birnbaum-Saunders,
truncated normal, mixture of inverse Gaussian, mixture of Birnbaum-Saunders,
generalized exponential, Jorgensen-Seshadri-Whitmore, weighted Akash, weighted Shanker and
weighted Sujatha as the distribution for frailty terms. For the basal model, it
is considered a parametric approach based on the exponential, Weibull and the
piecewise exponential distributions as well as a semiparametric approach. For
details, see Gallardo et al. (2024) <doi:10.1007/s11222-024-10458-w>,
Gallardo et al. (2025) <doi:10.1002/bimj.70044>, Kiprotich et al. (2025) <doi:10.1177/09622802251338984>,
Gallardo et al. (2025) <doi:10.1038/s41598-025-15903-y>, Kiprotich et al. (2026) <doi:10.1080/00949655.2025.2584734
and Mohammadi et al. (2026).
Author: Diego Gallardo [aut, cre],
Marcelo Bourguignon [aut],
John Santibanez [ctb],
Gilbert Kiprotich [ctb],
Pedro Ramos [ctb],
Thomas Augustin [ctb],
Zohreh Mohammadi [ctb],
Paulo Ferreira [ctb],
Gerson Primo [ctb]
Maintainer: Diego Gallardo <dgallardo@ubiobio.cl>
Diff between extrafrail versions 1.14 dated 2025-08-24 and 1.15 dated 2026-08-28
DESCRIPTION | 34 - MD5 | 16 NAMESPACE | 2 NEWS.md | 10 R/frailty.fit.R | 1574 +++++++++++++++++++++++++++++++++++++++++++++++- R/print.extrafrail.R | 190 ----- R/summary.extrafrail.R | 51 + man/frailty.fit.Rd | 6 man/tools.extrafrail.Rd | 4 9 files changed, 1699 insertions(+), 188 deletions(-)
Title: Methods for Analysing 'EQ-5D' Data and Calculating 'EQ-5D' Index
Scores
Description: EQ-5D is a widely used health-related quality-of-life instrument
developed by the EuroQol Group and used in the clinical and economic
evaluation of health care. Health is described using five dimensions
(mobility, self-care, usual activities, pain/discomfort, and
anxiety/depression) rated on either a three-level (EQ-5D-3L and EQ-5D-Y-3L)
or five-level (EQ-5D-5L) scale. Responses can be reported as EQ-5D health
states or converted to utility index scores using country-specific value
sets. The package provides methods for the valuation, reporting and
analysis of EQ-5D data. Utility index scores can be calculated for
EQ-5D-3L, EQ-5D-5L and EQ-5D-Y-3L data using a wide range of value sets and
mapping approaches. Functionality is also provided for descriptive-system
reporting, severity and distributional summaries, informativity measures,
health-state distribution analysis, longitudinal change analysis,
probability of superiority analysis and Health Profile Grid visualisation.
Methods descr [...truncated...]
Author: Fraser Morton [aut, cre],
Jagtar Singh Nijjar [aut]
Maintainer: Fraser Morton <fraser.morton@glasgow.ac.uk>
Diff between eq5d versions 0.16.3 dated 2026-03-30 and 0.17.0 dated 2026-08-28
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Title: Create (Advanced) Coupled Matrix and Tensor Factorization Models
Description: Creation and selection of (Advanced) Coupled Matrix and Tensor Factorization (ACMTF) and ACMTF-Regression (ACMTF-R) models. Selection of the optimal number of components can be done using 'ACMTF_modelSelection()' and 'ACMTFR_modelSelection()'. The CMTF and ACMTF methods were originally described by Acar et al., 2011 <doi:10.48550/arXiv.1105.3422> and Acar et al., 2014 <doi:10.1186/1471-2105-15-239>, respectively.
Author: Geert Roelof van der Ploeg [aut, cre] ,
Johan Westerhuis [ctb] ,
Anna Heintz-Buschart [ctb] ,
Age Smilde [ctb] ,
University of Amsterdam [cph, fnd]
Maintainer: Geert Roelof van der Ploeg <roel@simula.no>
This is a re-admission after prior archival of version 1.0.1 dated 2025-08-22
Diff between CMTFtoolbox versions 1.0.1 dated 2025-08-22 and 1.1.1 dated 2026-08-28
DESCRIPTION | 13 LICENSE | 4 MD5 | 122 +-- NAMESPACE | 66 - NEWS.md | 8 R/ACMTFR_modelSelection.R | 1008 ++++++++++++++-------------- R/ACMTF_modelSelection.R | 680 +++++++++--------- R/FMS_cv.R | 132 +-- R/FMS_random.R | 120 +-- R/acmtf_fg.R | 264 +++---- R/acmtf_fun.R | 142 +-- R/acmtf_gradient.R | 172 ++-- R/acmtf_opt.R | 174 ++-- R/acmtfr_fg.R | 324 ++++----- R/acmtfr_fun.R | 178 ++-- R/acmtfr_gradient.R | 196 ++--- R/acmtfr_opt.R | 188 ++--- R/cmtf_fg.R | 160 ++-- R/cmtf_fun.R | 96 +- R/cmtf_opt.R | 184 ++--- R/computeFMS.R | 154 ++-- R/data.R | 26 R/initializeCMTF.R | 146 ++-- R/npred.R | 240 +++--- R/reinflateFac.R | 132 +-- R/utils.R | 618 ++++++++--------- README.md | 2 build/vignette.rds |binary inst/doc/Introduction.Rmd | 270 +++---- inst/doc/Introduction.html | 38 - man/ACMTFR_modelSelection.Rd | 214 ++--- man/ACMTF_modelSelection.Rd | 192 ++--- man/FMS_cv.Rd | 76 +- man/FMS_random.Rd | 72 +- man/Georgiou2025.Rd | 54 - man/acmtf_fg.Rd | 86 +- man/acmtfr_fg.Rd | 118 +-- man/cmtf_fg.Rd | 74 +- man/npred.Rd | 94 +- man/reinflateMatrix.Rd | 48 - man/reinflateTensor.Rd | 54 - man/removeTwoNormCol.Rd | 42 - tests/testthat.R | 24 tests/testthat/test-ACMTFR_modelSelection.R | 122 +-- tests/testthat/test-ACMTF_modelSelection.R | 86 +- tests/testthat/test-FMS_cv.R | 182 ++--- tests/testthat/test-FMS_random.R | 182 ++--- tests/testthat/test-acmtf_fg.R | 92 +- tests/testthat/test-acmtf_fun.R | 54 - tests/testthat/test-acmtf_opt.R | 336 ++++----- tests/testthat/test-acmtfr_fg.R | 102 +- tests/testthat/test-acmtfr_fun.R | 88 +- tests/testthat/test-acmtfr_gradient.R | 180 ++--- tests/testthat/test-acmtfr_opt.R | 434 ++++++------ tests/testthat/test-cmtf_fg.R | 114 +-- tests/testthat/test-cmtf_opt.R | 314 ++++---- tests/testthat/test-degenScore.R | 8 tests/testthat/test-initializeCMTF.R | 212 ++--- tests/testthat/test-npred.R | 528 +++++++------- tests/testthat/test-reinflateFac.R | 136 +-- tests/testthat/test-utils.R | 19 vignettes/Introduction.Rmd | 270 +++---- 62 files changed, 5237 insertions(+), 5227 deletions(-)
Title: Bayesian Analyses for One- and Two-Sample Inference and
Regression Methods
Description: Perform fundamental analyses using Bayesian parametric and non-parametric inference (regression, anova, 1 and 2 sample inference, non-parametric tests, etc.). (Practically) no Markov chain Monte Carlo (MCMC) is used; all exact finite sample inference is completed via closed form solutions or else through posterior sampling automated to ensure precision in interval estimate bounds. Diagnostic plots for model assessment, and key inferential quantities (point and interval estimates, probability of direction, region of practical equivalence, and Bayes factors) and model visualizations are provided. Bayes factors are computed either by the Savage Dickey ratio given in Dickey (1971) <doi:10.1214/aoms/1177693507> or by Chib's method as given in <doi:10.1080/01621459.1995.10476635>. Interpretations are from Kass and Raftery (1995) <doi:10.1080/01621459.1995.10476572>. ROPE bounds are based on discussions in Kruschke (2018) <doi:10.1177/2515245918771304>. Methods for d [...truncated...]
Author: Daniel K. Sewell [aut, cre, cph] ,
Alan Arakkal [aut]
Maintainer: Daniel K. Sewell <daniel-sewell@uiowa.edu>
Diff between bayesics versions 3.0.1 dated 2026-08-26 and 3.0.2 dated 2026-08-28
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 6 ++++++ R/mediate_b.R | 15 +++++++++++---- 4 files changed, 23 insertions(+), 10 deletions(-)
Title: Predict Energy Expenditure from Accelerometry Data
Description: Simplifies the application of various energy expenditure models. The
package is intended as a hub that brings together methods from a variety of
other, themed packages such as 'Sojourn' and 'TwoRegression'. Several methods
are supported locally as well, including the linear methods of
Hildebrand et al. (2014) <doi:10.1249/MSS.0000000000000289> and the
non-linear adaptation by Ellingson et al. (2017) <doi:10.1088/1361-6579/aa6d00>.
The package can combine output from different methods and produce standardized
output in a range of units.
Author: Paul R. Hibbing [aut, cre],
Children's Mercy Kansas City [cph]
Maintainer: Paul R. Hibbing <paulhibbing@gmail.com>
This is a re-admission after prior archival of version 0.3.1 dated 2026-05-12
Diff between accelEE versions 0.3.1 dated 2026-05-12 and 0.3.2 dated 2026-08-28
DESCRIPTION | 12 ++++++------ MD5 | 4 ++-- NEWS.md | 5 +++++ 3 files changed, 13 insertions(+), 8 deletions(-)
Title: Flexible, Interactive 'shiny' Modules for Almost Any Plot
Description: Offers a core selection of interactivity-first 'shiny' modules for many
plot types meant to serve as flexible building blocks for applications and
as the base for more complex modules. These modules
allow for the rapid and convenient construction of 'shiny' apps with very few lines
of code and decouple plotting from the underlying data. These modules allow
for full plot aesthetic customization by the end user through UI inputs. Utility
functions for simple UI organization, automated UI tooltips, and additional
plot enhancements are also provided. Includes a multi-panel figure builder app
for arranging multiple modules together in a free-form layout.
Author: Jared Andrews [aut, cre] ,
Jacob Martin [aut]
Maintainer: Jared Andrews <jared.andrews07@gmail.com>
Diff between VizModules versions 0.3.0 dated 2026-07-27 and 0.4.0 dated 2026-08-28
VizModules-0.3.0/VizModules/inst/apps/rnaseq-showcase |only VizModules-0.3.0/VizModules/man/INTERNAL_multi_color_picker_css.Rd |only VizModules-0.4.0/VizModules/DESCRIPTION | 16 VizModules-0.4.0/VizModules/MD5 | 435 +++++--- VizModules-0.4.0/VizModules/NAMESPACE | 245 +++- VizModules-0.4.0/VizModules/NEWS.md | 68 + VizModules-0.4.0/VizModules/R/ComplexHeatmap_Heatmap_helpers.R |only VizModules-0.4.0/VizModules/R/ComplexHeatmap_Heatmap_module_app.R |only VizModules-0.4.0/VizModules/R/ComplexHeatmap_Heatmap_module_server.R |only VizModules-0.4.0/VizModules/R/ComplexHeatmap_Heatmap_module_ui.R |only VizModules-0.4.0/VizModules/R/createModuleApp.R | 25 VizModules-0.4.0/VizModules/R/data.R | 88 + VizModules-0.4.0/VizModules/R/dataFilter_module_server.R | 154 ++- VizModules-0.4.0/VizModules/R/dataFilter_module_ui.R | 36 VizModules-0.4.0/VizModules/R/dittoViz_ScatterPlot_module_app.R | 2 VizModules-0.4.0/VizModules/R/dittoViz_ScatterPlot_module_server.R | 403 +++---- VizModules-0.4.0/VizModules/R/dittoViz_ScatterPlot_module_ui.R | 197 --- VizModules-0.4.0/VizModules/R/dittoViz_freqPlot_module_app.R |only VizModules-0.4.0/VizModules/R/dittoViz_freqPlot_module_server.R |only VizModules-0.4.0/VizModules/R/dittoViz_freqPlot_module_ui.R |only VizModules-0.4.0/VizModules/R/dittoViz_yPlot_module_app.R | 2 VizModules-0.4.0/VizModules/R/dittoViz_yPlot_module_server.R | 510 ++++++++-- VizModules-0.4.0/VizModules/R/dittoViz_yPlot_module_ui.R | 163 ++- VizModules-0.4.0/VizModules/R/dumbbellPlot_module_app.R | 2 VizModules-0.4.0/VizModules/R/dumbbellPlot_module_server.R | 64 - VizModules-0.4.0/VizModules/R/dumbbellPlot_module_ui.R | 31 VizModules-0.4.0/VizModules/R/figureBuilder_module_app.R | 11 VizModules-0.4.0/VizModules/R/figureBuilder_module_server.R | 20 VizModules-0.4.0/VizModules/R/figureBuilder_module_ui.R | 12 VizModules-0.4.0/VizModules/R/globals.R | 5 VizModules-0.4.0/VizModules/R/linePlot_module_app.R | 2 VizModules-0.4.0/VizModules/R/linePlot_module_server.R | 108 +- VizModules-0.4.0/VizModules/R/linePlot_module_ui.R | 43 VizModules-0.4.0/VizModules/R/multiColorPicker.R | 357 ------- VizModules-0.4.0/VizModules/R/parallelCoordinatesPlot.R | 1 VizModules-0.4.0/VizModules/R/parallelCoordinatesPlot_module_app.R | 2 VizModules-0.4.0/VizModules/R/parallelCoordinatesPlot_module_server.R | 60 - VizModules-0.4.0/VizModules/R/parallelCoordinatesPlot_module_ui.R | 31 VizModules-0.4.0/VizModules/R/parse_utils.R | 449 ++++++++ VizModules-0.4.0/VizModules/R/piePlot_module_app.R | 2 VizModules-0.4.0/VizModules/R/piePlot_module_server.R | 98 + VizModules-0.4.0/VizModules/R/piePlot_module_ui.R | 47 VizModules-0.4.0/VizModules/R/plot_facets.R | 13 VizModules-0.4.0/VizModules/R/plot_helpers.R | 181 +++ VizModules-0.4.0/VizModules/R/plot_source_data.R | 202 +++ VizModules-0.4.0/VizModules/R/plotly_annotation_utils.R | 191 +++ VizModules-0.4.0/VizModules/R/plotthis_AreaPlot_module_app.R | 2 VizModules-0.4.0/VizModules/R/plotthis_AreaPlot_module_server.R | 62 - VizModules-0.4.0/VizModules/R/plotthis_AreaPlot_module_ui.R | 27 VizModules-0.4.0/VizModules/R/plotthis_BarPlot_module_app.R | 2 VizModules-0.4.0/VizModules/R/plotthis_BarPlot_module_server.R | 106 +- VizModules-0.4.0/VizModules/R/plotthis_BarPlot_module_ui.R | 36 VizModules-0.4.0/VizModules/R/plotthis_BoxPlot_module_app.R | 2 VizModules-0.4.0/VizModules/R/plotthis_BoxPlot_module_server.R | 117 +- VizModules-0.4.0/VizModules/R/plotthis_BoxPlot_module_ui.R | 31 VizModules-0.4.0/VizModules/R/plotthis_DensityPlot_module_app.R | 2 VizModules-0.4.0/VizModules/R/plotthis_DensityPlot_module_server.R | 64 - VizModules-0.4.0/VizModules/R/plotthis_DensityPlot_module_ui.R | 28 VizModules-0.4.0/VizModules/R/plotthis_DotPlot_module_app.R | 2 VizModules-0.4.0/VizModules/R/plotthis_DotPlot_module_server.R | 41 VizModules-0.4.0/VizModules/R/plotthis_DotPlot_module_ui.R | 38 VizModules-0.4.0/VizModules/R/plotthis_Histogram_module_app.R | 2 VizModules-0.4.0/VizModules/R/plotthis_Histogram_module_server.R | 64 - VizModules-0.4.0/VizModules/R/plotthis_Histogram_module_ui.R | 28 VizModules-0.4.0/VizModules/R/plotthis_SplitBarPlot_module_app.R | 2 VizModules-0.4.0/VizModules/R/plotthis_SplitBarPlot_module_server.R | 81 + VizModules-0.4.0/VizModules/R/plotthis_SplitBarPlot_module_ui.R | 36 VizModules-0.4.0/VizModules/R/plotthis_ViolinPlot_module_app.R | 2 VizModules-0.4.0/VizModules/R/plotthis_ViolinPlot_module_server.R | 111 +- VizModules-0.4.0/VizModules/R/plotthis_ViolinPlot_module_ui.R | 31 VizModules-0.4.0/VizModules/R/radarPlot_module_app.R | 2 VizModules-0.4.0/VizModules/R/radarPlot_module_server.R | 102 +- VizModules-0.4.0/VizModules/R/radarPlot_module_ui.R | 48 VizModules-0.4.0/VizModules/R/reactive_defaults.R |only VizModules-0.4.0/VizModules/R/reset_uniform_ui_inputs.R | 91 + VizModules-0.4.0/VizModules/R/select_inputs.R |only VizModules-0.4.0/VizModules/R/stat_helper.R | 395 ++++++- VizModules-0.4.0/VizModules/R/ui_utils.R | 99 + VizModules-0.4.0/VizModules/R/uniform_ui_inputs.R | 215 +++- VizModules-0.4.0/VizModules/R/use_skills.R |only VizModules-0.4.0/VizModules/README.md | 28 VizModules-0.4.0/VizModules/build/vignette.rds |binary VizModules-0.4.0/VizModules/data/example_bar.rda |binary VizModules-0.4.0/VizModules/data/example_composition.rda |only VizModules-0.4.0/VizModules/data/example_demographics.rda |binary VizModules-0.4.0/VizModules/data/example_heatmap_column_data.rda |only VizModules-0.4.0/VizModules/data/example_heatmap_matrix.rda |only VizModules-0.4.0/VizModules/data/example_iris.rda |binary VizModules-0.4.0/VizModules/data/example_markers.rda |binary VizModules-0.4.0/VizModules/data/example_mtcars.rda |binary VizModules-0.4.0/VizModules/data/example_population.rda |binary VizModules-0.4.0/VizModules/data/example_rnaseq.rda |binary VizModules-0.4.0/VizModules/data/example_sales.rda |binary VizModules-0.4.0/VizModules/data/example_school_earnings.rda |binary VizModules-0.4.0/VizModules/data/example_skills.rda |binary VizModules-0.4.0/VizModules/inst/apps/module-gallery/app.R | 57 + VizModules-0.4.0/VizModules/inst/doc/adding-a-new-module.Rmd | 214 ++++ VizModules-0.4.0/VizModules/inst/doc/adding-a-new-module.html | 288 +++++ VizModules-0.4.0/VizModules/inst/doc/custom-model-lines.Rmd | 2 VizModules-0.4.0/VizModules/inst/doc/custom-model-lines.html | 5 VizModules-0.4.0/VizModules/inst/doc/custom-modules.R | 26 VizModules-0.4.0/VizModules/inst/doc/custom-modules.Rmd | 43 VizModules-0.4.0/VizModules/inst/doc/custom-modules.html | 87 + VizModules-0.4.0/VizModules/inst/doc/data-filtering.R |only VizModules-0.4.0/VizModules/inst/doc/data-filtering.Rmd |only VizModules-0.4.0/VizModules/inst/doc/data-filtering.html |only VizModules-0.4.0/VizModules/inst/doc/defaults-and-hiding.R | 31 VizModules-0.4.0/VizModules/inst/doc/defaults-and-hiding.Rmd | 59 + VizModules-0.4.0/VizModules/inst/doc/defaults-and-hiding.html | 282 +++-- VizModules-0.4.0/VizModules/inst/doc/quick-start.Rmd | 1 VizModules-0.4.0/VizModules/inst/doc/quick-start.html | 6 VizModules-0.4.0/VizModules/inst/skills |only VizModules-0.4.0/VizModules/inst/src/multiColorPicker.css | 84 + VizModules-0.4.0/VizModules/inst/src/multiColorPicker.js | 148 ++ VizModules-0.4.0/VizModules/inst/src/vizSelect.js |only VizModules-0.4.0/VizModules/man/ComplexHeatmap_HeatmapApp.Rd |only VizModules-0.4.0/VizModules/man/ComplexHeatmap_HeatmapInfoOutputUI.Rd |only VizModules-0.4.0/VizModules/man/ComplexHeatmap_HeatmapInputsUI.Rd |only VizModules-0.4.0/VizModules/man/ComplexHeatmap_HeatmapMainOutputUI.Rd |only VizModules-0.4.0/VizModules/man/ComplexHeatmap_HeatmapOutputUI.Rd |only VizModules-0.4.0/VizModules/man/ComplexHeatmap_HeatmapServer.Rd |only VizModules-0.4.0/VizModules/man/ComplexHeatmap_HeatmapSubOutputUI.Rd |only VizModules-0.4.0/VizModules/man/INTERNAL_apply_highlight_styling.Rd |only VizModules-0.4.0/VizModules/man/INTERNAL_axis_limit_clears.Rd |only VizModules-0.4.0/VizModules/man/INTERNAL_blank_to_null.Rd |only VizModules-0.4.0/VizModules/man/INTERNAL_calculate_range.Rd | 12 VizModules-0.4.0/VizModules/man/INTERNAL_create_highlight_annotations.Rd | 6 VizModules-0.4.0/VizModules/man/INTERNAL_create_selected_annotations.Rd | 6 VizModules-0.4.0/VizModules/man/INTERNAL_default_group_colors.Rd |only VizModules-0.4.0/VizModules/man/INTERNAL_facet_check.Rd | 4 VizModules-0.4.0/VizModules/man/INTERNAL_freq_maps_one_per.Rd |only VizModules-0.4.0/VizModules/man/INTERNAL_freq_sample_choices.Rd |only VizModules-0.4.0/VizModules/man/INTERNAL_freq_selected_vars.Rd |only VizModules-0.4.0/VizModules/man/INTERNAL_freq_stats_group_col.Rd |only VizModules-0.4.0/VizModules/man/INTERNAL_freq_summary.Rd |only VizModules-0.4.0/VizModules/man/INTERNAL_freq_y_col.Rd |only VizModules-0.4.0/VizModules/man/INTERNAL_has_group_names.Rd |only VizModules-0.4.0/VizModules/man/INTERNAL_heatmap_annotation_col.Rd |only VizModules-0.4.0/VizModules/man/INTERNAL_heatmap_annotation_spec.Rd |only VizModules-0.4.0/VizModules/man/INTERNAL_heatmap_annotation_widget_id.Rd |only VizModules-0.4.0/VizModules/man/INTERNAL_heatmap_build_annotation.Rd |only VizModules-0.4.0/VizModules/man/INTERNAL_heatmap_default_colors.Rd |only VizModules-0.4.0/VizModules/man/INTERNAL_heatmap_resolve_data.Rd |only VizModules-0.4.0/VizModules/man/INTERNAL_heatmap_resolve_split.Rd |only VizModules-0.4.0/VizModules/man/INTERNAL_heatmap_scale_matrix.Rd |only VizModules-0.4.0/VizModules/man/INTERNAL_merge_annotation_sets.Rd |only VizModules-0.4.0/VizModules/man/INTERNAL_multivar_long_df.Rd |only VizModules-0.4.0/VizModules/man/INTERNAL_pairwise_layout.Rd |only VizModules-0.4.0/VizModules/man/INTERNAL_plotted_vars_from_attrs.Rd |only VizModules-0.4.0/VizModules/man/INTERNAL_plotted_vars_from_inputs.Rd |only VizModules-0.4.0/VizModules/man/INTERNAL_reapply_manual_edits.Rd | 9 VizModules-0.4.0/VizModules/man/INTERNAL_require_data_frame.Rd |only VizModules-0.4.0/VizModules/man/INTERNAL_reset_group_colors.Rd |only VizModules-0.4.0/VizModules/man/INTERNAL_same_axis_range.Rd |only VizModules-0.4.0/VizModules/man/INTERNAL_should_include_trace.Rd | 7 VizModules-0.4.0/VizModules/man/INTERNAL_stat_bracket_headroom.Rd |only VizModules-0.4.0/VizModules/man/INTERNAL_viz_select_dependency.Rd |only VizModules-0.4.0/VizModules/man/INTERNAL_with_stable_seed.Rd |only VizModules-0.4.0/VizModules/man/apply_stat_annotations.Rd | 16 VizModules-0.4.0/VizModules/man/collect_source_data.Rd | 149 +- VizModules-0.4.0/VizModules/man/createModuleApp.Rd | 3 VizModules-0.4.0/VizModules/man/dataFilterServer.Rd | 52 - VizModules-0.4.0/VizModules/man/dittoViz_freqPlotApp.Rd |only VizModules-0.4.0/VizModules/man/dittoViz_freqPlotInputsUI.Rd |only VizModules-0.4.0/VizModules/man/dittoViz_freqPlotOutputUI.Rd |only VizModules-0.4.0/VizModules/man/dittoViz_freqPlotServer.Rd |only VizModules-0.4.0/VizModules/man/dittoViz_scatterPlotApp.Rd | 4 VizModules-0.4.0/VizModules/man/dittoViz_scatterPlotInputsUI.Rd | 12 VizModules-0.4.0/VizModules/man/dittoViz_scatterPlotServer.Rd | 11 VizModules-0.4.0/VizModules/man/dittoViz_yPlotApp.Rd | 4 VizModules-0.4.0/VizModules/man/dittoViz_yPlotInputsUI.Rd | 49 VizModules-0.4.0/VizModules/man/dittoViz_yPlotServer.Rd | 8 VizModules-0.4.0/VizModules/man/dumbbellPlotApp.Rd | 4 VizModules-0.4.0/VizModules/man/dumbbellPlotInputsUI.Rd | 7 VizModules-0.4.0/VizModules/man/dumbbellPlotServer.Rd | 8 VizModules-0.4.0/VizModules/man/example_composition.Rd |only VizModules-0.4.0/VizModules/man/example_heatmap_column_data.Rd |only VizModules-0.4.0/VizModules/man/example_heatmap_matrix.Rd |only VizModules-0.4.0/VizModules/man/figureBuilderServer.Rd | 4 VizModules-0.4.0/VizModules/man/finalize_manual_edits.Rd | 15 VizModules-0.4.0/VizModules/man/get_default.Rd | 13 VizModules-0.4.0/VizModules/man/hide_input.Rd |only VizModules-0.4.0/VizModules/man/linePlotApp.Rd | 4 VizModules-0.4.0/VizModules/man/linePlotInputsUI.Rd | 7 VizModules-0.4.0/VizModules/man/linePlotServer.Rd | 8 VizModules-0.4.0/VizModules/man/multiColorPicker.Rd | 16 VizModules-0.4.0/VizModules/man/parallelCoordinatesPlotApp.Rd | 4 VizModules-0.4.0/VizModules/man/parallelCoordinatesPlotInputsUI.Rd | 7 VizModules-0.4.0/VizModules/man/parallelCoordinatesPlotServer.Rd | 8 VizModules-0.4.0/VizModules/man/piePlotApp.Rd | 4 VizModules-0.4.0/VizModules/man/piePlotInputsUI.Rd | 7 VizModules-0.4.0/VizModules/man/piePlotServer.Rd | 8 VizModules-0.4.0/VizModules/man/plotthis_AreaPlotApp.Rd | 4 VizModules-0.4.0/VizModules/man/plotthis_AreaPlotInputsUI.Rd | 7 VizModules-0.4.0/VizModules/man/plotthis_AreaPlotServer.Rd | 8 VizModules-0.4.0/VizModules/man/plotthis_BarPlotApp.Rd | 4 VizModules-0.4.0/VizModules/man/plotthis_BarPlotInputsUI.Rd | 8 VizModules-0.4.0/VizModules/man/plotthis_BarPlotServer.Rd | 8 VizModules-0.4.0/VizModules/man/plotthis_BoxPlotApp.Rd | 4 VizModules-0.4.0/VizModules/man/plotthis_BoxPlotInputsUI.Rd | 7 VizModules-0.4.0/VizModules/man/plotthis_BoxPlotServer.Rd | 8 VizModules-0.4.0/VizModules/man/plotthis_DensityPlotApp.Rd | 4 VizModules-0.4.0/VizModules/man/plotthis_DensityPlotInputsUI.Rd | 8 VizModules-0.4.0/VizModules/man/plotthis_DensityPlotServer.Rd | 8 VizModules-0.4.0/VizModules/man/plotthis_DotPlotApp.Rd | 4 VizModules-0.4.0/VizModules/man/plotthis_DotPlotInputsUI.Rd | 6 VizModules-0.4.0/VizModules/man/plotthis_DotPlotServer.Rd | 8 VizModules-0.4.0/VizModules/man/plotthis_HistogramApp.Rd | 4 VizModules-0.4.0/VizModules/man/plotthis_HistogramInputsUI.Rd | 8 VizModules-0.4.0/VizModules/man/plotthis_HistogramServer.Rd | 8 VizModules-0.4.0/VizModules/man/plotthis_SplitBarPlotApp.Rd | 4 VizModules-0.4.0/VizModules/man/plotthis_SplitBarPlotInputsUI.Rd | 8 VizModules-0.4.0/VizModules/man/plotthis_SplitBarPlotServer.Rd | 8 VizModules-0.4.0/VizModules/man/plotthis_ViolinPlotApp.Rd | 4 VizModules-0.4.0/VizModules/man/plotthis_ViolinPlotInputsUI.Rd | 7 VizModules-0.4.0/VizModules/man/plotthis_ViolinPlotServer.Rd | 8 VizModules-0.4.0/VizModules/man/radarPlotApp.Rd | 4 VizModules-0.4.0/VizModules/man/radarPlotInputsUI.Rd | 8 VizModules-0.4.0/VizModules/man/radarPlotServer.Rd | 8 VizModules-0.4.0/VizModules/man/reset_annotation_inputs.Rd |only VizModules-0.4.0/VizModules/man/reset_axis_title_text.Rd |only VizModules-0.4.0/VizModules/man/resolve_column_targets.Rd |only VizModules-0.4.0/VizModules/man/resolve_palette.Rd | 25 VizModules-0.4.0/VizModules/man/setup_auto_update_logic.Rd | 22 VizModules-0.4.0/VizModules/man/setup_axis_range.Rd |only VizModules-0.4.0/VizModules/man/setup_group_colors.Rd |only VizModules-0.4.0/VizModules/man/setup_reactive_defaults.Rd |only VizModules-0.4.0/VizModules/man/show_input.Rd |only VizModules-0.4.0/VizModules/man/stat_bracket_y_max.Rd |only VizModules-0.4.0/VizModules/man/toggle_input_cell.Rd |only VizModules-0.4.0/VizModules/man/uniform_annotation_inputs_ui.Rd |only VizModules-0.4.0/VizModules/man/update_viz_select.Rd |only VizModules-0.4.0/VizModules/man/use_vizmodules_skills.Rd |only VizModules-0.4.0/VizModules/man/viz_select_input.Rd |only VizModules-0.4.0/VizModules/tests/testthat/test-dataFilter.R |only VizModules-0.4.0/VizModules/tests/testthat/test-figureBuilder.R | 7 VizModules-0.4.0/VizModules/tests/testthat/test-freqPlot.R |only VizModules-0.4.0/VizModules/tests/testthat/test-group_colors.R |only VizModules-0.4.0/VizModules/tests/testthat/test-heatmap.R |only VizModules-0.4.0/VizModules/tests/testthat/test-multiColorPicker.R | 205 ++-- VizModules-0.4.0/VizModules/tests/testthat/test-plot_mods.R | 149 ++ VizModules-0.4.0/VizModules/tests/testthat/test-plot_source_data.R |only VizModules-0.4.0/VizModules/tests/testthat/test-reactive_defaults.R |only VizModules-0.4.0/VizModules/tests/testthat/test-scatterPlot.R | 60 + VizModules-0.4.0/VizModules/tests/testthat/test-select_inputs.R |only VizModules-0.4.0/VizModules/tests/testthat/test-stat_helper.R | 80 + VizModules-0.4.0/VizModules/tests/testthat/test-yPlot.R |only VizModules-0.4.0/VizModules/vignettes/adding-a-new-module.Rmd | 214 ++++ VizModules-0.4.0/VizModules/vignettes/custom-model-lines.Rmd | 2 VizModules-0.4.0/VizModules/vignettes/custom-modules.Rmd | 43 VizModules-0.4.0/VizModules/vignettes/data-filtering.Rmd |only VizModules-0.4.0/VizModules/vignettes/defaults-and-hiding.Rmd | 59 + VizModules-0.4.0/VizModules/vignettes/quick-start.Rmd | 1 253 files changed, 6749 insertions(+), 2275 deletions(-)
Title: Interface to 'TexTra' from R
Description: A wrapper for the 'TexTra' API <https://mt-auto-minhon-mlt.ucri.jgn-x.jp/>,
a web service for translating texts between different languages.
'TexTra' API account is required to use the service.
Author: Toshikazu Matsumura [aut, cre]
Maintainer: Toshikazu Matsumura <matutosi@gmail.com>
Diff between textrar versions 0.8.0 dated 2024-04-23 and 0.9.0 dated 2026-08-28
textrar-0.8.0/textrar/tools |only textrar-0.9.0/textrar/DESCRIPTION | 20 - textrar-0.9.0/textrar/LICENSE | 4 textrar-0.9.0/textrar/MD5 | 40 +- textrar-0.9.0/textrar/NAMESPACE | 16 textrar-0.9.0/textrar/NEWS.md | 34 + textrar-0.9.0/textrar/R/textra.R | 518 ++++++++++++++++++---------- textrar-0.9.0/textrar/README.md | 27 + textrar-0.9.0/textrar/inst/WORDLIST | 2 textrar-0.9.0/textrar/man/base_url.Rd | 46 +- textrar-0.9.0/textrar/man/extract_result.Rd | 62 ++- textrar-0.9.0/textrar/man/gen_params.Rd | 89 +++- textrar-0.9.0/textrar/man/get_token.Rd | 66 ++- textrar-0.9.0/textrar/man/post_request.Rd | 62 +-- textrar-0.9.0/textrar/man/textra.Rd | 76 ++-- textrar-0.9.0/textrar/tests/testthat |only textrar-0.9.0/textrar/tests/testthat.R |only 17 files changed, 683 insertions(+), 379 deletions(-)
Title: Perpendicular Line Transects for Geosciences
Description: Toolset to create perpendicular profile graphs and swath
profiles. Method are based on coordinate rotation algorithm by
Schaeben et al. (2024) <doi:10.1002/mma.9823>.
Author: Tobias Stephan [aut, cre]
Maintainer: Tobias Stephan <tobias.stephan1@yahoo.com>
Diff between geoprofiler versions 0.0.3 dated 2025-12-11 and 0.0.4 dated 2026-08-28
geoprofiler-0.0.3/geoprofiler/man/geoprofiler.Rd |only geoprofiler-0.0.3/geoprofiler/man/profile_coords.Rd |only geoprofiler-0.0.4/geoprofiler/DESCRIPTION | 8 geoprofiler-0.0.4/geoprofiler/MD5 | 46 geoprofiler-0.0.4/geoprofiler/NAMESPACE | 3 geoprofiler-0.0.4/geoprofiler/NEWS.md | 12 geoprofiler-0.0.4/geoprofiler/R/geoprofiler-package.R | 6 geoprofiler-0.0.4/geoprofiler/R/profile_points.R | 614 +++++----- geoprofiler-0.0.4/geoprofiler/R/project.R | 26 geoprofiler-0.0.4/geoprofiler/R/swath.R | 7 geoprofiler-0.0.4/geoprofiler/README.md | 12 geoprofiler-0.0.4/geoprofiler/inst/doc/A_Distances.R | 2 geoprofiler-0.0.4/geoprofiler/inst/doc/A_Distances.Rmd | 2 geoprofiler-0.0.4/geoprofiler/inst/doc/A_Distances.html | 16 geoprofiler-0.0.4/geoprofiler/inst/doc/B_Swath.html | 4 geoprofiler-0.0.4/geoprofiler/man/figures/README-plot-1.png |binary geoprofiler-0.0.4/geoprofiler/man/figures/lifecycle-deprecated.svg |only geoprofiler-0.0.4/geoprofiler/man/figures/lifecycle-experimental.svg |only geoprofiler-0.0.4/geoprofiler/man/figures/lifecycle-stable.svg |only geoprofiler-0.0.4/geoprofiler/man/figures/lifecycle-superseded.svg |only geoprofiler-0.0.4/geoprofiler/man/geoprofiler-package.Rd |only geoprofiler-0.0.4/geoprofiler/man/profile-coords.Rd |only geoprofiler-0.0.4/geoprofiler/man/profile_azimuth.Rd | 19 geoprofiler-0.0.4/geoprofiler/man/profile_line.Rd | 30 geoprofiler-0.0.4/geoprofiler/man/profile_points.Rd | 7 geoprofiler-0.0.4/geoprofiler/man/swath_profile.Rd | 8 geoprofiler-0.0.4/geoprofiler/tests/testthat/test_projection.R | 6 geoprofiler-0.0.4/geoprofiler/vignettes/A_Distances.Rmd | 2 28 files changed, 495 insertions(+), 335 deletions(-)
Title: Qualification of R Software Installations
Description: Qualify R software installations using R Markdown as the foundation
for the Installation Qualification (IQ) and Operational Qualification (OQ) when
used in environments (such as regulated clinical trials) where such
processes may be required.
Author: Donnie Musgrove [aut, cre],
Graeme L. Hickey [aut] ,
Marc Schwartz [aut] ,
Alan Haynes [ctb],
Bryan Martin [ctb],
Medtronic Inc. [cph]
Maintainer: Donnie Musgrove <donniemusgrove@gmail.com>
Diff between rqualify versions 1.0.2 dated 2026-04-16 and 1.1.0 dated 2026-08-28
DESCRIPTION | 22 MD5 | 53 NAMESPACE | 1 NEWS.md | 25 R/check_validation_results.R |only R/platform.R |only R/render_validation.R |only R/rqualify.R | 175 -- R/setup_pandoc_env.R |only R/setup_tinytex_env.R |only R/setup_validation_dirs.R |only README.md | 14 build/vignette.rds |binary inst/doc/rqualify-cran.Rmd | 2 inst/doc/rqualify-cran.html | 42 inst/qualify_r/R-validation.Rmd | 1606 ++++++++++++------------- inst/qualify_r/R-validation.qmd |only inst/qualify_r/example_success/CMDFile1Out.txt | 186 +- inst/qualify_r/example_success/CMDFile2Out.txt | 90 - inst/qualify_r/example_success/CMDFile3Out.txt | 86 - inst/qualify_r/example_success/CMDFile4Out.txt | 86 - inst/qualify_r/example_success/CMDFile5Out.txt | 100 - inst/qualify_r/example_success/CMDFile6Out.txt | 268 ++-- inst/qualify_r/example_success/CMDFile7Out.txt | 818 ++++++------ man/rqualify.Rd | 20 tests/testthat.R | 24 tests/testthat/test-check_validation_results.R |only tests/testthat/test-render_validation.R |only tests/testthat/test-rqualify-orchestration.R |only tests/testthat/test-rqualify.R | 12 tests/testthat/test-setup_pandoc_env.R |only tests/testthat/test-setup_tinytex_env.R |only tests/testthat/test-setup_validation_dirs.R |only vignettes/rqualify-cran.Rmd | 2 34 files changed, 1789 insertions(+), 1843 deletions(-)
Title: Conjoint Analysis with Reliability Correction and Visualization
Description: Provides tools for analyzing data generated from conjoint survey experiments, a method widely used in the social sciences for studying multidimensional preferences. The package implements estimation of marginal means (MMs) and average marginal component effects (AMCEs), with corrections for measurement error. Methods include profile-level and choice-level estimators, bias correction using intra-respondent reliability (IRR), and visualization utilities. For details on the methodology, see Clayton, Horiuchi, Kaufman, King, and Komisarchik (2025) <https://gking.harvard.edu/conjointE>.
Author: Yusaku Horiuchi [aut, cre] ,
Aaron Kaufman [aut] ,
Gary King [aut]
Maintainer: Yusaku Horiuchi <yusaku.horiuchi@gmail.com>
Diff between projoint versions 1.1.3 dated 2026-07-31 and 1.1.4 dated 2026-08-28
DESCRIPTION | 8 - MD5 | 33 ++-- NEWS.md | 11 + R/predict_tau.R | 2 R/reshape_projoint.R | 22 ++ README.md | 15 + inst/CITATION | 2 inst/doc/analyze.R | 6 inst/doc/analyze.Rmd | 13 + inst/doc/analyze.html | 14 + inst/doc/read.R | 6 inst/doc/read.Rmd | 43 ++++- inst/doc/read.html | 167 ++++++++++++---------- man/reshape_projoint.Rd | 22 ++ tests/testthat/test-predict_tau.R |only tests/testthat/test-reshape-projoint-validation.R | 4 vignettes/analyze.Rmd | 13 + vignettes/read.Rmd | 43 ++++- 18 files changed, 291 insertions(+), 133 deletions(-)
Title: Logic Forest
Description: Logic Forest is an ensemble machine learning method that identifies important and interpretable combinations of binary predictors using logic regression trees to model complex relationships with an outcome. Wolf, B.J., Slate, E.H., Hill, E.G. (2010) <doi:10.1093/bioinformatics/btq354>.
Author: Bethany Wolf [aut],
Melica Nikahd [ctb, cre],
Andrew Gothard [ctb],
Madison Hyer [ctb]
Maintainer: Melica Nikahd <melica.nikahd@osumc.edu>
Diff between LogicForest versions 2.1.4 dated 2026-04-03 and 2.1.5 dated 2026-08-28
DESCRIPTION | 6 MD5 | 18 +- R/a.frame.logreg2.R | 1 R/logforest.R | 12 + R/predict.logforest.R | 326 +++++++++++++++++++++++------------------------ R/predict.logreg2.R | 2 R/print.LFprediction.R | 27 +++ R/print.logforest.R | 8 - man/logforest.Rd | 5 man/predict.logforest.Rd | 6 10 files changed, 225 insertions(+), 186 deletions(-)
Title: Causal Distillation Trees
Description: Causal Distillation Tree (CDT) is a novel machine learning method
for estimating interpretable subgroups with heterogeneous treatment effects.
CDT allows researchers to fit any machine learning model (or metalearner) to
estimate heterogeneous treatment effects for each individual, and then
"distills" these predicted heterogeneous treatment effects into
interpretable subgroups by fitting an ordinary decision tree to predict the
previously-estimated heterogeneous treatment effects. This package
provides tools to estimate causal distillation trees (CDT), as detailed in
Huang, Tang, and Kenney (2025) <doi:10.48550/arXiv.2502.07275>.
Author: Tiffany Tang [aut, cre] ,
Melody Huang [aut],
Ana Kenney [aut]
Maintainer: Tiffany Tang <ttang4@nd.edu>
Diff between causalDT versions 1.0.0 dated 2025-09-03 and 1.0.1 dated 2026-08-28
DESCRIPTION | 8 ++++---- MD5 | 22 ++++++++++++---------- NAMESPACE | 1 + NEWS.md |only R/RcppExports.R | 17 +++++++++++++++++ R/diagnostics-stability.R | 10 ---------- R/plot.R | 4 ++++ R/student.R | 2 +- R/teacher.R | 3 ++- README.md | 9 ++++++++- man/jaccardSSI.Rd |only man/plot_jaccard.Rd | 4 ++++ src/stability.cpp | 11 ++++++++--- 13 files changed, 61 insertions(+), 30 deletions(-)
Title: American Travel Behavior and Access Datasets
Description: Subsets of data from the National Household Travel Survey 2017. It includes personal trips, mobility, demographic, and household information. It is suitable for data visualization, data wrangling, joining datasets, exploratory data analysis, group comparisons, simple linear regression, categorical data analysis, and data ethics discussion in data science and statistics classes.
Author: Shiya Cao [aut, cre],
Amber Zhang [ctb],
Anna Zhao [ctb],
Smith College [cph]
Maintainer: Shiya Cao <scao53@smith.edu>
Diff between tripaccess versions 0.1.0 dated 2026-07-04 and 0.2.0 dated 2026-08-28
DESCRIPTION | 13 +++++---- MD5 | 16 +++++------ NEWS.md | 6 +++- R/tripaccess.R | 3 +- README.md | 49 +++++++++++++++++++++++++----------- data/tripaccess.rda |binary inst/doc/house.html | 2 - man/tripaccess.Rd | 3 +- tests/testthat/_snaps/tripaccess.md | 2 - 9 files changed, 61 insertions(+), 33 deletions(-)
Title: Extended Dynamic Quantile Linear Models
Description: Bayesian quantile-regression routines for dynamic state-space
models and static regression under the extended asymmetric Laplace
(exAL) error distribution. The dynamic state-space models are extended
dynamic quantile linear models (exDQLMs). The package combines dynamic
exDQLM inference via Laplace-delta variational Bayes (LDVB), Markov
chain Monte Carlo (MCMC), and legacy importance-sampling variational Bayes
(ISVB) with static exAL regression via LDVB and MCMC, reduced asymmetric
Laplace/dynamic quantile linear model (AL/DQLM) paths through fixed
skewness, component builders for trend/seasonality/regression blocks,
static shrinkage priors including ridge, regularized horseshoe, and
'rhs_ns', evidence lower bound (ELBO) diagnostics, optional C++
accelerators, and posterior predictive synthesis across separately fitted
quantiles through 'quantileSynthesis()'. Dynamic exDQLM methods are
described in Barata et al. (2020) <doi:10.1214/21-AOAS1497>.
Author: Raquel Barata [aut, cre],
Raquel Prado [ths],
Bruno Sanso [ths],
Antonio Aguirre [aut]
Maintainer: Raquel Barata <raquel.a.barata@gmail.com>
Diff between exdqlm versions 1.1.0 dated 2026-07-09 and 1.1.1 dated 2026-08-28
DESCRIPTION | 6 MD5 | 109 ++++--- NEWS.md | 27 + R/compPlot.R | 9 R/exalStaticDiagnostics.R | 2 R/exalStaticFit_methods.R | 11 R/exalStaticLDVB.R | 289 ++++++++++++++++----- R/exalStaticMCMC.R | 143 ++++++++-- R/exal_inference_config.R | 17 + R/exal_sigmagam_structured.R |only R/exdqlm-package.R | 27 + R/exdqlmFit_methods.R | 27 + R/exdqlmForecast.R | 6 R/exdqlmForecastDiagnostics.R | 2 R/exdqlmForecast_methods.R | 8 R/exdqlmLDVB.R | 157 +++++++++-- R/exdqlmMCMC.R | 187 ++++++++++--- R/exdqlmPlot.R | 6 R/exdqlmTransferLDVB.R | 12 R/exdqlmTransferMCMC.R | 2 R/utils.R | 21 + R/zzz.R | 2 README.md | 20 + man/compPlot.Rd | 9 man/diagnostics.exalStaticFit.Rd | 1 man/diagnostics.exdqlmForecast.Rd | 2 man/exalStaticDiagnostics.Rd | 1 man/exalStaticLDVB.Rd | 35 +- man/exalStaticMCMC.Rd | 25 + man/exal_make_vb_sigmagam_control.Rd | 14 + man/exdqlm-package.Rd | 29 +- man/exdqlmForecast.Rd | 6 man/exdqlmForecastDiagnostics.Rd | 2 man/exdqlmLDVB.Rd | 28 +- man/exdqlmMCMC.Rd | 33 +- man/exdqlmPlot.Rd | 6 man/exdqlmTransferLDVB.Rd | 19 + man/exdqlmTransferMCMC.Rd | 19 - man/plot.exalStaticFit.Rd | 4 man/plot.exalStaticLDVB.Rd | 3 man/plot.exalStaticMCMC.Rd | 3 man/plot.exdqlmFit.Rd | 13 man/plot.exdqlmForecast.Rd | 2 man/plot.exdqlmLDVB.Rd | 2 man/predict.exdqlmFit.Rd | 8 man/print.exdqlmForecast.Rd | 2 man/print.exdqlmLDVB.Rd | 2 man/summary.exdqlmForecast.Rd | 2 man/summary.exdqlmLDVB.Rd | 2 src/sampling_truncnorm.cpp | 51 +-- src/sampling_utils.cpp | 286 ++++---------------- tests/testthat/test-exal-inference-config.R | 13 tests/testthat/test-exal-sigmagam-structured.R |only tests/testthat/test-exdqlm-transfer-mcmc.R | 5 tests/testthat/test-rng-repeatability.R |only tests/testthat/test-static-diagnostics.R | 12 tests/testthat/test-vb-mcmc-convergence-controls.R | 33 ++ 57 files changed, 1155 insertions(+), 607 deletions(-)
Title: Coarse-to-Fine Spatial and Spatio-Temporal Modeling
Description: Provides functions for coarse-to-fine spatial and spatio-temporal modeling, enabling fast prediction, regression, and uncertainty quantification for moderate to large datasets. For methodological details, see Murakami et al. (2026) <doi:10.1111/gean.70034> and related work on generalized linear, downscaling, and dynamic spatio-temporal extensions.
Author: Daisuke Murakami [aut, cre],
Alexis Comber [aut],
Takahiro Yoshida [aut],
Narumasa Tsutsumida [aut],
Chris Brunsdon [aut],
Tomoki Nakaya [aut],
Jose Luis Blanco-Claraco [ctb, cph] ),
Marius Muja [cph] ,
David G. Lowe [cph]
Maintainer: Daisuke Murakami <dmuraka@ism.ac.jp>
Diff between spCF versions 0.2.0 dated 2026-08-04 and 0.2.1 dated 2026-08-28
DESCRIPTION | 8 MD5 | 36 - NAMESPACE | 44 - R/cf_dglm.R | 10 R/cf_glm.R | 15 R/cf_lm.R | 13 R/spCFmap.R | 2 R/sp_map_core.R | 286 +++++++-- inst/doc/spCF_glm.html | 79 ++ inst/doc/spCF_lm.html | 48 + inst/shiny/spCFmap/app.R | 48 + inst/shiny/spCFmap/example_downscale.csv | 714 ++++++++++++------------ inst/shiny/spCFmap/example_downscale.geojson | 434 +++++++------- inst/shiny/spCFmap/example_downscale_ReadMe.txt |only inst/shiny/spCFmap/example_point_ReadMe.txt |only man/cf_dglm.Rd | 9 tests/testthat/test-cf_glm.R | 16 tests/testthat/test-cf_lm.R | 20 tests/testthat/test-mapping.R | 103 +++ tests/testthat/test-spCFmap.R | 24 20 files changed, 1195 insertions(+), 714 deletions(-)
Title: Wavelet Analysis
Description: Perform wavelet analysis (orthogonal,translation invariant, tensorial, 1-2-3d transforms, thresholding, block thresholding, linear,...) with applications to data compression, denoising/regression or clustering. The core of the code is a port of 'MATLAB' Wavelab toolbox written by D. Donoho, A. Maleki and M. Shahram.
Author: Fabien Navarro [aut, cre],
Christophe Chesneau [aut]
Maintainer: Fabien Navarro <fnavarro@math.cnrs.fr>
Diff between rwavelet versions 0.4.1 dated 2020-12-12 and 0.4.2 dated 2026-08-28
DESCRIPTION | 31 +- MD5 | 38 +-- NAMESPACE | 1 NEWS.md | 23 + R/BlockThresh2d.R |only R/HardThresh.R | 3 R/SUREThresh.R | 2 R/SoftThresh.R | 3 R/WaveFEX.R |only R/cameraman.R |only R/lena.R |only build/vignette.rds |binary data/cameraman.rda |only data/lena.rda |only inst/doc/rwaveletvignette.R | 90 +++---- inst/doc/rwaveletvignette.html | 500 ++++++++++++++++++++--------------------- man/BlockThresh2d.Rd |only man/HardThresh.Rd | 3 man/RaphNMR.Rd | 4 man/SLphantom.Rd | 4 man/SUREThresh.Rd | 2 man/SoftThresh.Rd | 3 man/WaveFEX.Rd |only man/cameraman.Rd |only man/lena.Rd |only 25 files changed, 372 insertions(+), 335 deletions(-)
Title: Mappable Vector Library for Handling Large Datasets
Description: Mappable vector library provides convenient way to access large datasets. Use all of your data at once, with few limits. Memory mapped data can be shared between multiple R processes. Access speed depends on storage medium, so solid state drive is recommended, preferably with PCI Express (or M.2 nvme) interface or a fast network file system. The data is memory mapped into R and then accessed using usual R list and array subscription operators. Convenience functions are provided for merging, grouping and indexing large vectors and data.frames. The layout of underlying MVL files is optimized for large datasets. The vectors are stored to guarantee alignment for vector intrinsics after memory map. The package is built on top of libMVL, which can be used as a standalone C library. libMVL has simple C API making it easy to interchange datasets with outside programs. Large MVL datasets are distributed via Academic Torrents <https://academictorrents.com/collection/mvl-datasets>.
Author: Vladimir Dergachev [aut, cre]
Maintainer: Vladimir Dergachev <support@altumrete.com>
Diff between RMVL versions 1.1.0.3 dated 2026-04-13 and 1.1.0.4 dated 2026-08-28
DESCRIPTION | 6 +++--- MD5 | 5 +++-- man/print.MVL_INDEX.Rd |only src/libMVL_sort.cc | 1 + 4 files changed, 7 insertions(+), 5 deletions(-)
Title: User-Friendly R Package for Supervised Machine Learning
Pipelines
Description: An interface to build machine learning models for
classification and regression problems. 'mikropml' implements the ML
pipeline described by Topçuoğlu et al. (2020)
<doi:10.1128/mBio.00434-20> with reasonable default options for data
preprocessing, hyperparameter tuning, cross-validation, testing, model
evaluation, and interpretation steps. See the website
<https://www.schlosslab.org/mikropml/> for more information,
documentation, and examples.
Author: Beguem Topcuoglu [aut] ,
Zena Lapp [aut] ,
Kelly Sovacool [aut, cre] ,
Evan Snitkin [aut] ,
Jenna Wiens [aut] ,
Patrick Schloss [aut] ,
Nick Lesniak [ctb] ,
Courtney Armour [ctb] ,
Sarah Lucas [ctb] ,
Tuomas Borman [ctb]
Maintainer: Kelly Sovacool <sovacool@umich.edu>
Diff between mikropml versions 1.7.0 dated 2025-10-28 and 1.7.1 dated 2026-08-28
DESCRIPTION | 8 MD5 | 104 +- NAMESPACE | 46 - NEWS.md | 7 R/checks.R | 165 +++- R/compare_models.R | 38 - R/corr_feats.R | 49 - R/cross_val.R | 60 + R/feature_importance.R | 95 +- R/hyperparameters.R | 11 R/partition.R | 30 R/performance.R | 207 +++-- R/plot.R | 108 +- R/preprocess.R | 393 ++++++---- R/reexports.R | 4 R/run_ml.R | 129 ++- R/train.R | 21 README.md | 44 + build/partial.rdb |binary build/vignette.rds |binary inst/container |only inst/doc/introduction.Rmd | 26 inst/doc/introduction.html | 5 inst/doc/paper.Rmd | 2 inst/doc/paper.html | 143 +-- man/calc_perf_bootstrap_split.Rd | 2 man/calc_perf_metrics.Rd | 2 man/check_all.Rd | 2 man/define_cv.Rd | 2 man/find_permuted_perf_metric.Rd | 2 man/get_feature_importance.Rd | 2 man/get_performance_tbl.Rd | 2 man/mikropml-package.Rd | 1 man/preprocess_data.Rd | 2 man/reexports.Rd | 6 man/run_ml.Rd | 2 tests/testthat/fixtures/predict.R | 13 tests/testthat/fixtures/train-multi.R | 17 tests/testthat/test-checks.R | 137 ++- tests/testthat/test-compare_models.R | 14 tests/testthat/test-corr_feats.R | 143 ++- tests/testthat/test-cross_val.R | 223 +++++- tests/testthat/test-feature_importance.R | 147 +++ tests/testthat/test-hyperparameters.R | 215 ++++- tests/testthat/test-partition.R | 35 tests/testthat/test-performance.R | 136 ++- tests/testthat/test-plot.R | 337 ++++++--- tests/testthat/test-preprocess.R | 1150 +++++++++++++++++++++---------- tests/testthat/test-run_ml.R | 281 ++++++- tests/testthat/test-train.R | 89 +- vignettes/introduction.Rmd | 26 vignettes/paper.Rmd | 2 vignettes/paper.bib | 2 53 files changed, 3352 insertions(+), 1335 deletions(-)
Title: Download Insee French Institute of Statistics Open Data
Description: A wrapper for the French Institute of Statistics (Insee) API
Melodi <https://catalogue-donnees.insee.fr>. Download, search, filter data
and metadata from open data statistical public datasets,
in french or in english.
Author: Cedric Bobinec [aut, cre],
Christophe Goudeau [aut],
Institut national de la statistique et des etudes economiques [cph]
Maintainer: Cedric Bobinec <cedric.bobinec@insee.fr>
Diff between melodi versions 1.1.0 dated 2026-07-29 and 1.1.2 dated 2026-08-28
DESCRIPTION | 6 ++--- MD5 | 10 ++++----- NEWS.md | 6 +++++ R/get_all_data.R | 6 ++++- README.md | 3 +- tests/testthat/test-get_all_data.R | 39 ++++++++++++++++++++++++++++++++----- 6 files changed, 55 insertions(+), 15 deletions(-)
Title: Flexible Graphs for Analysis of Financial Data and Time Series
Description: Flexible wrappers around R graphics modules 'dygraphs' <https://dygraphs.com/> and 'ggplot2' <https://ggplot2.tidyverse.org/> to visualize data commonly found in Financial Studies, with an emphasis on time series.
Interactive time series plots include multiple options for incorporating external data such as forecasts and events. Other static plots useful for time
series data include an intuitive and generic scatter plotter, a boxplot generator suitable for multiple time series, and event study plotters for time series analysis
around sets of dates.
Author: Derek Holmes [aut, cre, cph]
Maintainer: Derek Holmes <derek@derekholmes.com>
Diff between FinanceGraphs versions 0.9.2 dated 2026-08-21 and 0.9.21 dated 2026-08-28
DESCRIPTION | 17 +++--- MD5 | 28 +++++----- NAMESPACE | 1 NEWS.md | 6 ++ R/event_helpers.R | 7 +- R/seas_ggplot.R | 4 - R/ts_ggplot.R | 12 ++-- data/eqtypx.rda |binary data/eqtypx_melt.rda |binary data/eqtyrtn.rda |binary data/example_fcst_set.rda |binary data/nomfxdta.rda |binary data/yc_CMSUST.rda |binary inst/doc/Time-Series-dygraph.html | 88 +++++++++++++++++----------------- inst/doc/Time-Series-scatterplot.html | 12 +--- 15 files changed, 87 insertions(+), 88 deletions(-)
Title: Guarded Resampling Workflows for Leakage-Aware Machine Learning
in R
Description: Provides a guarded resampling workflow for training and evaluating machine-learning models.
When the guarded resampling path is used, preprocessing and model fitting are re-estimated within
each resampling split to reduce leakage risk. Supports multiple resampling schemes, integrates
with established engines in the 'tidymodels' ecosystem, and aims to improve evaluation reliability by
coordinating preprocessing, fitting, and evaluation within supported workflows. Offers a lightweight
AutoML-style workflow by automating model training, resampling, and tuning across multiple algorithms,
while keeping evaluation design explicit and user-controlled.
Author: Selcuk Korkmaz [aut, cre] ,
Dincer Goksuluk [aut] ,
Eda Karaismailoglu [aut]
Maintainer: Selcuk Korkmaz <selcukorkmaz@gmail.com>
Diff between fastml versions 0.7.9 dated 2026-08-19 and 0.7.10 dated 2026-08-28
DESCRIPTION | 20 - MD5 | 52 +- NAMESPACE | 1 NEWS.md | 54 +++ R/engine_helpers.R | 1 R/evaluate_models.R | 2 R/fastml.R | 163 +++++++-- R/params_helpers.R | 263 ++++++++++++--- R/process_model.R | 23 + R/process_model_helpers.R | 47 ++ R/resampling_utils.R | 70 ++++ R/summary.fastml.R | 69 +++ R/train_models.R | 452 +++++++++++++++++++++----- R/tuning_config.R | 12 README.md | 4 man/fastml.Rd | 78 +++- man/summary.fastml.Rd | 9 man/train_models.Rd | 10 tests/testthat/Rplots.pdf |binary tests/testthat/test-algorithm-registry.R |only tests/testthat/test-bootstrap-ci-default.R |only tests/testthat/test-bugfixes-round2.R | 59 +-- tests/testthat/test-holdout-splitting.R | 73 ++++ tests/testthat/test-interface-hints.R |only tests/testthat/test-leakage-not-expressible.R |only tests/testthat/test-metric-set-prob.R |only tests/testthat/test-nested-cv-tuning.R |only tests/testthat/test-prediction-orientation.R |only tests/testthat/test-sanitize.R | 35 +- tests/testthat/test-survival-registry.R |only tests/testthat/test-tuning-grid-scale.R |only tests/testthat/test-xgboost-aft-bounds.R |only 32 files changed, 1229 insertions(+), 268 deletions(-)
Title: Retrieve and Analyze Clinical Trials Data from Public Registers
Description: A system for querying, retrieving and analyzing
protocol- and results-related information on clinical trials from
four public registers, the 'European Union Clinical Trials Register'
('EUCTR', <https://www.clinicaltrialsregister.eu/>),
'ClinicalTrials.gov' (<https://clinicaltrials.gov/> and also
translating queries the retired classic interface), the
'ISRCTN' (<https://www.isrctn.com/>) and the
'European Union Clinical Trials Information System'
('CTIS', <https://euclinicaltrials.eu/>).
Trial information is downloaded, converted and stored as JSON in a
database ('PostgreSQL', 'SQLite', 'DuckDB', 'MongoDB' or 'MariaDB';
via package 'nodbi'). Protocols, statistical analysis plans, informed
consent sheets and other documents in registers associated with trials
can also be downloaded. Other functions implement trial analysis
concepts canonically across registers, identify deduplicated records
across registers, easily find and extract variables (fields) of interest
e [...truncated...]
Author: Ralf Herold [aut, cre] ,
Marek Kubica [cph] ,
Ivan Bozhanov [cph]
Maintainer: Ralf Herold <ralf.herold@mailbox.org>
Diff between ctrdata versions 1.26.2 dated 2026-07-12 and 1.26.3 dated 2026-08-28
DESCRIPTION | 39 +-- MD5 | 82 +++---- NAMESPACE | 196 ++++++++++-------- NEWS.md | 16 + R/ctrFindActiveSubstanceSynonyms.R | 196 ++++++++++++++---- R/ctrLoadQueryIntoDbEuctr.R | 62 ++--- R/ctrdata-package.R | 5 R/ctrdata-registers.R | 14 - R/dbFindIdsUniqueTrials.R | 11 - R/f_likelyPlatformTrial.R | 4 R/f_primaryEndpointResults.R | 24 +- R/f_sampleSize.R | 21 + R/f_trialObjectives.R | 2 R/util_functions.R | 175 +++++----------- R/zzz.R | 8 README.md | 98 +++++---- inst/WORDLIST | 4 inst/doc/ctrdata_install.R | 4 inst/doc/ctrdata_install.Rmd | 7 inst/doc/ctrdata_install.html | 21 + inst/doc/ctrdata_retrieve.html | 2 inst/doc/ctrdata_summarise.html | 2 inst/extdata/demo.sqlite |binary inst/tinytest/ctrdata_ctgov2.R | 13 - inst/tinytest/ctrdata_euctr.R | 41 --- inst/tinytest/more_test_ctrdata_duckdb_ctis.R | 3 inst/tinytest/more_test_ctrdata_duckdb_euctr.R | 3 inst/tinytest/more_test_ctrdata_duckdb_isrctn.R | 3 inst/tinytest/setup_ctrdata.R | 10 inst/tinytest/test_ctrdata_duckdb_ctgov2.R | 3 inst/tinytest/test_ctrdata_function_activesubstance.R | 4 inst/tinytest/test_ctrdata_function_trial-concepts.R | 21 + inst/tinytest/test_ctrdata_function_various.R | 69 ++++-- inst/tinytest/test_ctrdata_mariadb_ctgov2.R |only inst/tinytest/test_ctrdata_mariadb_remote_ctgov2.R |only man/ctrDb.Rd | 3 man/ctrFindActiveSubstanceSynonyms.Rd | 19 - man/ctrdata-package.Rd | 2 man/ctrdata-registers.Rd | 14 - man/ctrdata.Rd | 5 man/f.likelyPlatformTrial.Rd | 4 man/f.sampleSize.Rd | 6 vignettes/ctrdata_install.Rmd | 7 43 files changed, 689 insertions(+), 534 deletions(-)
Title: Functions for Statistics Classes at Carleton College
Description: Includes commands for bootstrapping and permutation tests, a
command for created grouped bar plots, and a demo of the
quantile-normal plot for data drawn from different distributions.
Author: Laura Chihara [aut],
Adam Loy [aut, cre]
Maintainer: Adam Loy <aloy@carleton.edu>
Diff between CarletonStats versions 2.2 dated 2023-08-22 and 2.3 dated 2026-08-28
DESCRIPTION | 16 MD5 | 111 +++--- NEWS.md | 10 R/Data.R | 20 + R/anovaSummarized.R | 86 ++-- R/boot.R | 33 + R/boot.default.R | 159 +++++--- R/boot.formula.R | 32 - R/bootCor.R | 10 R/bootCor.default.R | 101 ++--- R/bootCor.formula.R | 49 +- R/bootPaired.R | 8 R/bootPaired.default.R | 97 ++--- R/bootPaired.formula.R | 51 +- R/bootSlope.R | 8 R/bootSlope.default.R | 77 ++-- R/bootSlope.formula.R | 49 +- R/confIntDemo.R | 141 ++++--- R/confint.R | 2 R/corDemo.R | 48 +- R/groupedBar.R | 10 R/groupedBar.default.R | 160 ++++---- R/groupedBar.formula.R | 53 +- R/missingLevel.R | 24 - R/permTest.R | 26 - R/permTest.default.R | 131 +++---- R/permTest.formula.R | 24 - R/permTestAnova.R | 13 R/permTestAnova.default.R | 107 ++--- R/permTestAnova.formula.R | 26 - R/permTestCor.R | 8 R/permTestCor.default.R | 123 +++--- R/permTestCor.formula.R | 50 +- R/permTestPaired.R | 8 R/permTestPaired.default.R | 142 +++---- R/permTestPaired.formula.R | 50 +- R/permTestSlope.R | 10 R/permTestSlope.default.R | 115 ++---- R/permTestSlope.formula.R | 50 +- R/plot.R | 94 +++-- R/print.R | 198 +++++++--- R/pvalue.R | 13 R/qqPlotDemo.R | 110 ++++-- R/stemPlot.R | 10 R/stemPlot.default.R | 65 +-- R/stemPlot.formula.R | 50 +- R/summary.R | 43 +- R/utils-formula.R |only README.md | 1 data/penguin_survival.rda |only man/CarletonStats-package.Rd | 1 man/boot.Rd | 27 + man/bootSlope.Rd | 2 man/penguin_survival.Rd |only man/permTest.Rd | 19 - man/permTestSlope.Rd | 2 tests/testthat/Rplots.pdf |only tests/testthat/_snaps |only tests/testthat/test-Carl.R | 785 ++++++++++++++++++++++++++++++++++++++++++- 59 files changed, 2359 insertions(+), 1299 deletions(-)
Title: Create and Install Custom 'RStudio' Themes
Description: Create, convert and install custom 'RStudio' editor themes
from 'Visual Studio Code', 'Positron' and 'TextMate' theme files.
Convert themes between 'TextMate', 'Visual Studio Code' and 'Positron'
formats and install bundled ports of popular themes for use in
'RStudio'. Inspect theme files as tabular data for custom conversion
workflows.
Author: Diego Hernangomez [aut, cre, cph] ,
Garrick Aden-Buie [cph] function)
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>
Diff between rstudiothemes versions 1.1.2 dated 2026-06-19 and 1.2.0 dated 2026-08-28
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rstudiothemes-1.2.0/rstudiothemes/tests/testthat/_snaps/utils.md | 38 rstudiothemes-1.2.0/rstudiothemes/tests/testthat/helper.R |only rstudiothemes-1.2.0/rstudiothemes/tests/testthat/test-convert-tm-to-vs.R | 114 rstudiothemes-1.2.0/rstudiothemes/tests/testthat/test-convert-to-rs.R |only rstudiothemes-1.2.0/rstudiothemes/tests/testthat/test-convert-vs-to-tm.R | 173 rstudiothemes-1.2.0/rstudiothemes/tests/testthat/test-generate-uuid.R |only rstudiothemes-1.2.0/rstudiothemes/tests/testthat/test-on-rstudio.R | 20 rstudiothemes-1.2.0/rstudiothemes/tests/testthat/test-read-tm-theme.R | 65 rstudiothemes-1.2.0/rstudiothemes/tests/testthat/test-read-vs-theme.R | 55 rstudiothemes-1.2.0/rstudiothemes/tests/testthat/test-rstudiothemes-actions.R | 399 - rstudiothemes-1.2.0/rstudiothemes/tests/testthat/test-utils.R | 90 rstudiothemes-1.2.0/rstudiothemes/vignettes/rstudiothemes.qmd | 16 96 files changed, 6061 insertions(+), 6683 deletions(-)
Title: Nonparametric Analysis of Longitudinal Data in Factorial
Experiments
Description: Provides nonparametric procedures for the analysis of longitudinal data in factorial experiments. The package implements hypothesis tests on marginal distribution functions and unweighted relative marginal effects. It supports arbitrary crossed factorial designs with longitudinal or repeated-measures factors, missing observations, dependent replicates, rank- and pseudo-rank-based inference, Wald-type and ANOVA-type statistics, multiple contrast tests, and simultaneous confidence intervals.
Author: Frank Konietschke [aut, cre],
Kimihiro Noguchi [ctb] ,
Mahbub Latif [ctb] ,
Karthinathan Thangavelu [ctb] ,
Yulia R. Gel [ctb] ,
Edgar Brunner [ctb]
Maintainer: Frank Konietschke <frank.konietschke@charite.de>
Diff between nparLD versions 2.3.0 dated 2026-08-22 and 2.3.1 dated 2026-08-28
DESCRIPTION | 6 ++--- MD5 | 12 +++++------ NEWS.md | 10 ++++++++- R/Statistics.R | 4 --- R/Utility.R | 18 ++++++++++++----- inst/doc/nparLD.html | 42 ++++++++++++++++++++--------------------- tests/testthat/test-examples.R | 31 ++++++++++++++++++++++++++++++ 7 files changed, 84 insertions(+), 39 deletions(-)
Title: Bayesian Super Imposition by Translation and Rotation Growth
Curve Analysis
Description: The Super Imposition by Translation and Rotation (SITAR) model
is a shape-invariant nonlinear mixed effect model that fits a natural cubic
spline mean curve to the growth data and aligns individual-specific growth
curves to the underlying mean curve via a set of random effects (see Cole,
2010 <doi:10.1093/ije/dyq115> for details). The non-Bayesian version of the
SITAR model can be fit by using the already available R package 'sitar'. Unlike
the 'sitar' package which allows modelling of a single outcome only, the 'bsitar'
package offers great flexibility in fitting models of varying complexities,
including joint modelling of multiple outcomes such as height and weight
(multivariate model). Additionally, the 'bsitar' package allows for the simultaneous
analysis of an outcome separately for subgroups defined by a factor variable such
as gender. This is achieved by fitting separate models for each subgroup
(for example males and females for gender variable). An advantage of this appr [...truncated...]
Author: Satpal Sandhu [aut, cre, cph]
Maintainer: Satpal Sandhu <satpal.sandhu@bristol.ac.uk>
Diff between bsitar versions 0.3.3 dated 2026-03-25 and 0.4.0 dated 2026-08-28
bsitar-0.3.3/bsitar/R/check_and_get_object.R |only bsitar-0.3.3/bsitar/tests/testthat/test-bsitar-rcs-settings.R |only bsitar-0.4.0/bsitar/DESCRIPTION | 46 bsitar-0.4.0/bsitar/MD5 | 200 bsitar-0.4.0/bsitar/NAMESPACE | 26 bsitar-0.4.0/bsitar/NEWS.md | 439 bsitar-0.4.0/bsitar/R/add_model_criterion.R | 45 bsitar-0.4.0/bsitar/R/bsitar.R | 5308 +++------ bsitar-0.4.0/bsitar/R/compare_models.R |only bsitar-0.4.0/bsitar/R/expose_model_functions.R | 91 bsitar-0.4.0/bsitar/R/fitted_draws.R | 177 bsitar-0.4.0/bsitar/R/getNsObject.R |only bsitar-0.4.0/bsitar/R/get_comparisons.R | 758 - bsitar-0.4.0/bsitar/R/get_growthparameters.R | 783 - bsitar-0.4.0/bsitar/R/get_model_criterion.R |only bsitar-0.4.0/bsitar/R/get_predictions.R | 661 - bsitar-0.4.0/bsitar/R/growthparameters.R | 223 bsitar-0.4.0/bsitar/R/hypothesis_test.R | 274 bsitar-0.4.0/bsitar/R/loo_validation.R | 34 bsitar-0.4.0/bsitar/R/modelbased_growthparameters.R | 441 bsitar-0.4.0/bsitar/R/optimize_model.R | 334 bsitar-0.4.0/bsitar/R/plot_caterpillar.R |only bsitar-0.4.0/bsitar/R/plot_conditional_effects.R | 135 bsitar-0.4.0/bsitar/R/plot_curves.R | 937 + bsitar-0.4.0/bsitar/R/plot_diagnostics.R |only bsitar-0.4.0/bsitar/R/plot_ppc.R | 148 bsitar-0.4.0/bsitar/R/predict_draws.R | 212 bsitar-0.4.0/bsitar/R/prior_conflict.R |only bsitar-0.4.0/bsitar/R/prior_sensitivity.R |only bsitar-0.4.0/bsitar/R/prior_table.R |only bsitar-0.4.0/bsitar/R/update_model.R | 205 bsitar-0.4.0/bsitar/R/utils-helper-1.R | 4933 ++++---- bsitar-0.4.0/bsitar/R/utils-helper-10.R | 750 - 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bsitar-0.4.0/bsitar/R/utils-helper-5.R | 5612 ++++------ bsitar-0.4.0/bsitar/R/utils-helper-6.R | 377 bsitar-0.4.0/bsitar/R/utils-helper-7.R | 1234 -- bsitar-0.4.0/bsitar/R/utils-helper-8.R | 244 bsitar-0.4.0/bsitar/R/utils-helper-9.R | 833 - bsitar-0.4.0/bsitar/R/zzz.R | 4 bsitar-0.4.0/bsitar/build/partial.rdb |binary bsitar-0.4.0/bsitar/build/vignette.rds |binary bsitar-0.4.0/bsitar/data/berkeley_exdata.rda |binary bsitar-0.4.0/bsitar/data/berkeley_exfit.rda |binary bsitar-0.4.0/bsitar/inst/REFERENCES.bib | 10 bsitar-0.4.0/bsitar/inst/WORDLIST | 12 bsitar-0.4.0/bsitar/inst/doc/Bayesian_SITAR_model_An_Introduction.Rmd | 34 bsitar-0.4.0/bsitar/inst/doc/Bayesian_SITAR_model_An_Introduction.html | 52 bsitar-0.4.0/bsitar/inst/doc/Bayesian_SITAR_model_fit.R | 2 bsitar-0.4.0/bsitar/inst/doc/Bayesian_SITAR_model_fit.Rmd | 11 bsitar-0.4.0/bsitar/inst/doc/Bayesian_SITAR_model_fit.html | 162 bsitar-0.4.0/bsitar/man/add_model_criterion.Rd | 27 bsitar-0.4.0/bsitar/man/bsitar.Rd | 2264 ++-- bsitar-0.4.0/bsitar/man/compare_models.Rd |only bsitar-0.4.0/bsitar/man/fitted_draws.Rd | 67 bsitar-0.4.0/bsitar/man/getNsObject.Rd | 2 bsitar-0.4.0/bsitar/man/get_comparisons.Rd | 112 bsitar-0.4.0/bsitar/man/get_growthparameters.Rd | 143 bsitar-0.4.0/bsitar/man/get_model_criterion.Rd |only bsitar-0.4.0/bsitar/man/get_predictions.Rd | 119 bsitar-0.4.0/bsitar/man/growthparameters.Rd | 79 bsitar-0.4.0/bsitar/man/hypothesis_test.Rd | 63 bsitar-0.4.0/bsitar/man/is.bgmfit.Rd | 7 bsitar-0.4.0/bsitar/man/loo_validation.Rd | 14 bsitar-0.4.0/bsitar/man/modelbased_growthparameters.Rd | 108 bsitar-0.4.0/bsitar/man/optimize_model.Rd | 17 bsitar-0.4.0/bsitar/man/plot_caterpillar.Rd |only bsitar-0.4.0/bsitar/man/plot_conditional_effects.Rd | 77 bsitar-0.4.0/bsitar/man/plot_curves.Rd | 203 bsitar-0.4.0/bsitar/man/plot_diagnostics.Rd |only bsitar-0.4.0/bsitar/man/plot_ppc.Rd | 132 bsitar-0.4.0/bsitar/man/predict_draws.Rd | 67 bsitar-0.4.0/bsitar/man/prior_conflict.Rd |only bsitar-0.4.0/bsitar/man/prior_sensitivity.Rd |only bsitar-0.4.0/bsitar/man/prior_table.Rd |only bsitar-0.4.0/bsitar/man/update_model.Rd | 34 bsitar-0.4.0/bsitar/tests/testthat/helper-data.R | 684 + bsitar-0.4.0/bsitar/tests/testthat/test-bsitar-bsp-settings.R |only bsitar-0.4.0/bsitar/tests/testthat/test-bsitar-isp-settings.R |only bsitar-0.4.0/bsitar/tests/testthat/test-bsitar-msp-settings.R |only bsitar-0.4.0/bsitar/tests/testthat/test-bsitar-nsk-settings.R | 6 bsitar-0.4.0/bsitar/tests/testthat/test-bsitar-nsp-settings.R | 11 bsitar-0.4.0/bsitar/tests/testthat/test-bsitar-rcs-settings-autocor_all.R |only bsitar-0.4.0/bsitar/tests/testthat/test-bsitar-rcs-settings-corefuns-uvar.R |only bsitar-0.4.0/bsitar/tests/testthat/test-bsitar-rcs-settings-init_prior.R |only bsitar-0.4.0/bsitar/tests/testthat/test-bsitar-rcs-settings-knots_selection.R |only bsitar-0.4.0/bsitar/tests/testthat/test-bsitar-rcs-settings-parameterization_cp.R |only bsitar-0.4.0/bsitar/tests/testthat/test-bsitar-rcs-settings-plot_curves.R |only bsitar-0.4.0/bsitar/tests/testthat/test-bsitar-rcs-settings-plot_diagnostics.R |only bsitar-0.4.0/bsitar/tests/testthat/test-bsitar-rcs-settings-qr.R |only bsitar-0.4.0/bsitar/tests/testthat/test-bsitar-rcs-settings-vf_all.R |only bsitar-0.4.0/bsitar/tests/testthat/test-bsitar-xyadj-settings.R |only bsitar-0.4.0/bsitar/tests/testthat/test-hypothesis_test.R | 89 bsitar-0.4.0/bsitar/tests/testthat/test-prior_conflict.R |only bsitar-0.4.0/bsitar/tests/testthat/test-prior_sensitivity.R |only bsitar-0.4.0/bsitar/vignettes/Bayesian_SITAR_model_An_Introduction.Rmd | 34 bsitar-0.4.0/bsitar/vignettes/Bayesian_SITAR_model_fit.Rmd | 11 118 files changed, 16178 insertions(+), 25149 deletions(-)
Title: Interface to 'episensr' for Sensitivity Analysis of
Epidemiological Results
Description: API for using 'episensr', Basic sensitivity analysis of the
observed relative risks adjusting for unmeasured confounding and
misclassification of the exposure/outcome, or both. See
<https://cran.r-project.org/package=episensr>.
Author: Denis Haine [aut, cre]
Maintainer: Denis Haine <cheval@zaclys.net>
Diff between apisensr versions 2.0.0 dated 2025-05-16 and 2.0.1 dated 2026-08-28
DESCRIPTION | 12 ++++----- MD5 | 30 +++++++++++------------ NAMESPACE | 60 +++++++++++++++++++++++++++------------------- NEWS.md | 6 +++- R/mod_analysis.R | 8 +++--- R/mod_multi.R | 2 - R/mod_notable.R | 20 +++++++-------- R/mod_prob.R | 4 +-- README.md | 15 +++++------ build/vignette.rds |binary inst/CITATION | 6 ++-- inst/app/www/functions.md | 20 +++++++-------- inst/doc/apisensr.Rmd | 20 +++++++-------- inst/doc/apisensr.html | 20 +++++++-------- man/apisensr-package.Rd | 5 +++ vignettes/apisensr.Rmd | 20 +++++++-------- 16 files changed, 134 insertions(+), 114 deletions(-)
Title: Genome-Wide Nucleic Acid Melting Temperature Profiling and
Multi-Omics Integration
Description: Accurate calculation of nucleic acid melting temperature (Tm) is fundamental to many molecular biology applications, and this software scales Tm analysis from individual sequences to genome‑wide thermodynamic profiling. This package extends Tm analysis from simple sequence level computation to comprehensive genome-wide thermodynamic profiling. It takes multiple input formats including sequence strings, FASTA files, genomic coordinates. The implementation provides three Tm calculation methods: the Wallace rule (Thein & Wallace, 1986), empirical GC‑content formulas (Marmur, 1962; Schildkraut, 2010; Wetmur, 1991; Untergasser, 2012; von Ahsen, 2001), and nearest‑neighbor thermodynamics (Breslauer, 1986; Sugimoto, 1996; Allawi, 1998; SantaLucia, 2004; Freier, 1986; Xia, 1998; Chen, 2012; Bommarito, 2000; Turner, 2010; Sugimoto, 1995; Allawi, 1997; SantaLucia, 2005). Twenty-seven nearest-neighbor parameter sets are provided, covering DNA, RNA and RNA/DNA hybrid duplexes. These include se [...truncated...]
Author: Junhui Li [cre, aut] ,
Lihua Julie Zhu [aut]
Maintainer: Junhui Li <ljh.biostat@gmail.com>
Diff between TmCalculator versions 1.0.8 dated 2026-07-29 and 1.0.9 dated 2026-08-28
DESCRIPTION | 10 - MD5 | 21 +- NEWS.md |only R/sysdata.rda |binary R/tm_calculate.R | 146 +++++++++++++++--- R/tm_nn.R | 209 +++++++++++++++++++++++--- R/zzz.R | 287 ++++++++++++++++++++++++++++++++++++- README.md | 72 +++++++++ inst/doc/genome_wide_tm_ecoli.html | 46 ++--- man/TmCalculator-package.Rd | 2 man/tm_calculate.Rd | 131 +++++++++++++--- man/tm_nn.Rd | 132 +++++++++++++++-- 12 files changed, 921 insertions(+), 135 deletions(-)
Title: Reality Check and Predictive Ability Tests for Forecast
Evaluation
Description: Implements a comprehensive suite of statistical tests for
evaluating the accuracy of forecasting models against a benchmark.
The package is grounded in the reality check framework of White
(2000) <doi:10.1111/1468-0262.00152>, extended by Hansen (2005)
<doi:10.1198/073500105000000063> for Superior Predictive Ability
(SPA), Giacomini & White (2006) <doi:10.1111/j.1468-0262.2006.00718.x>
for Conditional Predictive Ability (CPA), and Corradi & Swanson
(2006) <doi:10.1016/j.jeconom.2005.07.026> for predictive density
evaluation via the Kullback-Leibler Information Criterion (KLIC) and
ZP Quantile Loss test, the Continuous Ranked Probability
Score (CRPS) (Gneiting & Raftery, 2007)
<doi:10.1198/016214506000001437>, coverage tests (Kupiec, 1995)
<doi:10.3905/jod.1995.407942>, HAC covariance estimation (Newey &
West, 1987) <doi:10.2307/1913610>, and Moving Block Bootstrap
resampling (Kunsch, 1989) <doi:10.1214/aos/1176347265>.
Author: Joanna Jedrzejewska [aut, cre] ,
Krzysztof Drachal [ctb]
Maintainer: Joanna Jedrzejewska <j.jedrzejewska3@uw.edu.pl>
Diff between RCtest versions 1.1 dated 2026-08-20 and 1.2 dated 2026-08-28
DESCRIPTION | 7 ++-- MD5 | 19 ++++++++--- NEWS.md | 50 ++++++++++++++++++++++-------- R/analysis_helpers.R | 80 ++++++++++++++++++++++++++++++++++--------------- R/workflow_functions.R | 48 ++++++++++++++++++++--------- man/compute_kupiec.Rd | 70 +++++++++++++++++++++++++++++++----------- tests |only 7 files changed, 197 insertions(+), 77 deletions(-)
Title: Project Risk Analysis
Description: Data analysis for Project Risk Management via the Second Moment Method,
Monte Carlo Simulation, Contingency Analysis, Sensitivity Analysis, Earned Value Management,
Learning Curves, Bayesian Methods, and more.
Author: Paul Govan [aut, cre, cph]
Maintainer: Paul Govan <paul.govan2@gmail.com>
This is a re-admission after prior archival of version 0.4.0 dated 2026-04-08
Diff between PRA versions 0.4.0 dated 2026-04-08 and 0.6.0 dated 2026-08-28
PRA-0.4.0/PRA/R/app.R |only PRA-0.4.0/PRA/R/chat.R |only PRA-0.4.0/PRA/R/rag.R |only PRA-0.4.0/PRA/build/vignette.rds |only PRA-0.4.0/PRA/inst/doc |only PRA-0.4.0/PRA/inst/eval |only PRA-0.4.0/PRA/inst/knowledge |only PRA-0.4.0/PRA/man/add_documents.Rd |only PRA-0.4.0/PRA/man/build_knowledge_base.Rd |only PRA-0.4.0/PRA/man/execute_command.Rd |only PRA-0.4.0/PRA/man/format_command_help.Rd |only PRA-0.4.0/PRA/man/format_help_overview.Rd |only PRA-0.4.0/PRA/man/get_ollama_models.Rd |only PRA-0.4.0/PRA/man/parse_command_args.Rd |only PRA-0.4.0/PRA/man/pra_app.Rd |only PRA-0.4.0/PRA/man/pra_chat.Rd |only PRA-0.4.0/PRA/man/pra_command_registry.Rd |only PRA-0.4.0/PRA/man/pra_shiny_app.Rd |only PRA-0.4.0/PRA/man/pra_system_prompt.Rd |only PRA-0.4.0/PRA/man/retrieve_context.Rd |only PRA-0.4.0/PRA/man/route_input.Rd |only PRA-0.4.0/PRA/tests/testthat/test-app.R |only PRA-0.4.0/PRA/tests/testthat/test-chat.R |only PRA-0.4.0/PRA/tests/testthat/test-rag.R |only PRA-0.4.0/PRA/vignettes |only PRA-0.6.0/PRA/DESCRIPTION | 16 PRA-0.6.0/PRA/LICENSE |only PRA-0.6.0/PRA/MD5 | 145 -- PRA-0.6.0/PRA/NAMESPACE | 15 PRA-0.6.0/PRA/NEWS.md | 41 PRA-0.6.0/PRA/R/cormat.R | 60 - PRA-0.6.0/PRA/R/data.R |only PRA-0.6.0/PRA/R/dsm.R | 27 PRA-0.6.0/PRA/R/inference.R | 32 PRA-0.6.0/PRA/R/learning.R | 97 + PRA-0.6.0/PRA/R/mcp.R |only PRA-0.6.0/PRA/R/mcs.R | 88 - PRA-0.6.0/PRA/R/network.R |only PRA-0.6.0/PRA/R/sensitivity.R | 35 PRA-0.6.0/PRA/R/sigmoidal.R | 11 PRA-0.6.0/PRA/R/smm.R | 13 PRA-0.6.0/PRA/R/tools.R | 975 ----------------- PRA-0.6.0/PRA/README.md | 140 -- PRA-0.6.0/PRA/build/partial.rdb |only PRA-0.6.0/PRA/data |only PRA-0.6.0/PRA/inst/CITATION | 12 PRA-0.6.0/PRA/inst/skills |only PRA-0.6.0/PRA/man/building_project.Rd |only PRA-0.6.0/PRA/man/cor_matrix.Rd | 14 PRA-0.6.0/PRA/man/cost_pdf.Rd | 8 PRA-0.6.0/PRA/man/cost_post_pdf.Rd | 22 PRA-0.6.0/PRA/man/figures/README-unnamed-chunk-5-1.png |binary PRA-0.6.0/PRA/man/grandparent_dsm.Rd | 21 PRA-0.6.0/PRA/man/mcs.Rd | 15 PRA-0.6.0/PRA/man/parent_dsm.Rd | 6 PRA-0.6.0/PRA/man/pra_mcp_server.Rd |only PRA-0.6.0/PRA/man/pra_tools.Rd | 9 PRA-0.6.0/PRA/man/prob_net.Rd |only PRA-0.6.0/PRA/man/prob_net_learn.Rd |only PRA-0.6.0/PRA/man/prob_net_sim.Rd |only PRA-0.6.0/PRA/man/prob_net_update.Rd |only PRA-0.6.0/PRA/man/risk_post_prob.Rd | 7 PRA-0.6.0/PRA/man/risk_prob.Rd | 8 PRA-0.6.0/PRA/man/sensitivity.Rd | 5 PRA-0.6.0/PRA/tests/testthat/Rplots.pdf |binary PRA-0.6.0/PRA/tests/testthat/test-cormat.R | 39 PRA-0.6.0/PRA/tests/testthat/test-data.R |only PRA-0.6.0/PRA/tests/testthat/test-inference.R | 29 PRA-0.6.0/PRA/tests/testthat/test-learning.R | 48 PRA-0.6.0/PRA/tests/testthat/test-mcp.R |only PRA-0.6.0/PRA/tests/testthat/test-mcs.R | 39 PRA-0.6.0/PRA/tests/testthat/test-network.R |only PRA-0.6.0/PRA/tests/testthat/test-sensitivity.R | 13 PRA-0.6.0/PRA/tests/testthat/test-sigmoidal.R | 2 PRA-0.6.0/PRA/tests/testthat/test-tools.R | 561 --------- 75 files changed, 723 insertions(+), 1830 deletions(-)
Title: Many Ways to Make, Manipulate, and Modify Myriad Networks
Description: Many tools for making, manipulating, and modifying many different types of networks.
All functions operate with matrices, edge lists, and 'igraph', 'network', and 'tidygraph' objects,
on directed, multiplex, multimodal, signed, and other networks.
The package includes functions for importing and exporting, creating and generating networks,
modifying networks and node and tie attributes,
and describing networks with sensible defaults.
Author: James Hollway [cre, aut, ctb] ,
Tomas Diviak [ctb],
Henrique Sposito [ctb] ,
Christian Steglich [ctb],
Alvaro Uzaheta [ctb]
Maintainer: James Hollway <james.hollway@graduateinstitute.ch>
Diff between manynet versions 2.2.3 dated 2026-07-30 and 2.3.1 dated 2026-08-28
manynet-2.2.3/manynet/R/manip_global.R |only manynet-2.2.3/manynet/R/modif_correlation.R |only manynet-2.2.3/manynet/man/manip_global.Rd |only manynet-2.2.3/manynet/man/modif_correlation.Rd |only manynet-2.2.3/manynet/tests/testthat/test-manip_correlation.R |only manynet-2.3.1/manynet/DESCRIPTION | 12 manynet-2.3.1/manynet/MD5 | 269 - manynet-2.3.1/manynet/NAMESPACE | 431 +- manynet-2.3.1/manynet/NEWS.md | 292 + manynet-2.3.1/manynet/R/class_describe.R | 131 manynet-2.3.1/manynet/R/class_marks.R | 16 manynet-2.3.1/manynet/R/class_measures.R | 81 manynet-2.3.1/manynet/R/class_missing.R |only manynet-2.3.1/manynet/R/class_networks.R | 10 manynet-2.3.1/manynet/R/class_stocnet.R | 183 - manynet-2.3.1/manynet/R/class_validate.R | 52 manynet-2.3.1/manynet/R/coerce_graph.R | 388 +- manynet-2.3.1/manynet/R/coerce_list.R | 329 + manynet-2.3.1/manynet/R/data_fict.R | 29 manynet-2.3.1/manynet/R/data_irps.R | 390 +- manynet-2.3.1/manynet/R/data_ison.R | 754 +++- manynet-2.3.1/manynet/R/make_collect.R | 10 manynet-2.3.1/manynet/R/make_create.R | 20 manynet-2.3.1/manynet/R/make_read.R | 815 ++++ manynet-2.3.1/manynet/R/manip_changes.R | 58 manynet-2.3.1/manynet/R/manip_globals.R |only manynet-2.3.1/manynet/R/manip_info.R | 284 + manynet-2.3.1/manynet/R/manip_nodes.R | 170 manynet-2.3.1/manynet/R/manip_ties.R | 26 manynet-2.3.1/manynet/R/manynet-data.R | 7 manynet-2.3.1/manynet/R/manynet-defunct.R | 69 manynet-2.3.1/manynet/R/manynet-glossary.R | 14 manynet-2.3.1/manynet/R/manynet-utils.R | 7 manynet-2.3.1/manynet/R/mark_changes.R | 130 manynet-2.3.1/manynet/R/mark_classes.R | 2 manynet-2.3.1/manynet/R/mark_features.R | 2 manynet-2.3.1/manynet/R/mark_format.R | 149 manynet-2.3.1/manynet/R/measure_attributes.R | 163 manynet-2.3.1/manynet/R/measure_properties.R | 193 - manynet-2.3.1/manynet/R/modif_backbone.R |only manynet-2.3.1/manynet/R/modif_direction.R | 137 manynet-2.3.1/manynet/R/modif_from.R | 144 manynet-2.3.1/manynet/R/modif_levels.R | 10 manynet-2.3.1/manynet/R/modif_miss.R | 761 ++++ manynet-2.3.1/manynet/R/modif_motifs.R | 84 manynet-2.3.1/manynet/R/modif_paths.R | 16 manynet-2.3.1/manynet/R/modif_permutation.R |only manynet-2.3.1/manynet/R/modif_plexity.R | 228 + manynet-2.3.1/manynet/R/modif_project.R | 535 ++- manynet-2.3.1/manynet/R/modif_proximity.R |only manynet-2.3.1/manynet/R/modif_scope.R | 490 +- manynet-2.3.1/manynet/R/modif_split.R | 250 + manynet-2.3.1/manynet/R/modif_weight.R | 243 + manynet-2.3.1/manynet/R/reexports_classes.R | 46 manynet-2.3.1/manynet/R/zzz.R | 40 manynet-2.3.1/manynet/README.md | 43 manynet-2.3.1/manynet/data/fict_marvel.rda |binary manynet-2.3.1/manynet/data/fict_potter.rda |binary manynet-2.3.1/manynet/data/fict_starwars.rda |binary manynet-2.3.1/manynet/data/irps_blogs.rda |binary manynet-2.3.1/manynet/data/irps_corruption.rda |only manynet-2.3.1/manynet/data/irps_nuclear.rda |binary manynet-2.3.1/manynet/data/irps_supremecourt.rda |only manynet-2.3.1/manynet/data/irps_tribes.rda |only manynet-2.3.1/manynet/data/ison_bankwiring.rda |only manynet-2.3.1/manynet/data/ison_classmates.rda |only manynet-2.3.1/manynet/data/ison_florentine.rda |only manynet-2.3.1/manynet/data/ison_fraternity.rda |only manynet-2.3.1/manynet/data/ison_koenigsberg.rda |binary manynet-2.3.1/manynet/data/ison_monks.rda |binary manynet-2.3.1/manynet/data/ison_tailorshop.rda |only manynet-2.3.1/manynet/inst/figures/cheatsheet.pdf |binary manynet-2.3.1/manynet/inst/tutorials/manynet1/making.Rmd | 28 manynet-2.3.1/manynet/inst/tutorials/manynet1/making.html | 169 manynet-2.3.1/manynet/inst/tutorials/manynet2/manipulating.Rmd | 704 +++- manynet-2.3.1/manynet/inst/tutorials/manynet2/manipulating.html | 1735 +++++++++- manynet-2.3.1/manynet/man/class_describe.Rd | 16 manynet-2.3.1/manynet/man/coerce_list.Rd | 113 manynet-2.3.1/manynet/man/defunct.Rd | 45 manynet-2.3.1/manynet/man/fict_actually.Rd | 13 manynet-2.3.1/manynet/man/fict_marvel.Rd | 58 manynet-2.3.1/manynet/man/fict_potter.Rd | 16 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manynet-2.3.1/manynet/man/modif_plexity.Rd | 61 manynet-2.3.1/manynet/man/modif_project.Rd | 205 + manynet-2.3.1/manynet/man/modif_proximity.Rd |only manynet-2.3.1/manynet/man/modif_scope.Rd | 132 manynet-2.3.1/manynet/man/modif_split.Rd | 83 manynet-2.3.1/manynet/man/modif_weight.Rd | 79 manynet-2.3.1/manynet/tests/testthat/helper-functional.R | 92 manynet-2.3.1/manynet/tests/testthat/sheets/gephi.gexf |only manynet-2.3.1/manynet/tests/testthat/sheets/gexfdynamic.gexf |only manynet-2.3.1/manynet/tests/testthat/sheets/networkcanvas.graphml |only manynet-2.3.1/manynet/tests/testthat/test-coercion.R | 215 + manynet-2.3.1/manynet/tests/testthat/test-functional_from.R | 72 manynet-2.3.1/manynet/tests/testthat/test-functional_impute.R |only manynet-2.3.1/manynet/tests/testthat/test-functional_manips.R | 20 manynet-2.3.1/manynet/tests/testthat/test-functional_marks.R | 46 manynet-2.3.1/manynet/tests/testthat/test-functional_measures.R | 9 manynet-2.3.1/manynet/tests/testthat/test-functional_prints.R | 124 manynet-2.3.1/manynet/tests/testthat/test-functional_to.R | 70 manynet-2.3.1/manynet/tests/testthat/test-make_read.R | 200 + manynet-2.3.1/manynet/tests/testthat/test-manip_add.R | 11 manynet-2.3.1/manynet/tests/testthat/test-manip_format.R | 176 - manynet-2.3.1/manynet/tests/testthat/test-manip_grab.R | 137 manynet-2.3.1/manynet/tests/testthat/test-manip_info.R |only manynet-2.3.1/manynet/tests/testthat/test-manip_layers.R |only manynet-2.3.1/manynet/tests/testthat/test-manip_miss.R | 314 + manynet-2.3.1/manynet/tests/testthat/test-manip_nodes.R |only manynet-2.3.1/manynet/tests/testthat/test-manip_reformed.R | 14 manynet-2.3.1/manynet/tests/testthat/test-manip_split.R | 228 + manynet-2.3.1/manynet/tests/testthat/test-manip_transform.R | 678 +++ manynet-2.3.1/manynet/tests/testthat/test-manynet-data.R | 83 manynet-2.3.1/manynet/tests/testthat/test-mark_is.R | 133 manynet-2.3.1/manynet/tests/testthat/test-modif_proximity.R |only 154 files changed, 13125 insertions(+), 2385 deletions(-)
Title: Parsing Glycan Structure Text Representations
Description: Provides functions to parse glycan structure text representations
into 'glyrepr' glycan structures. Currently, it supports StrucGP-style,
pGlyco-style, IUPAC-condensed, IUPAC-extended, IUPAC-short, IUPAC-compact,
WURCS, LINUCS, Linear Code, GlycoCT, KCF, and GlycoWorkbench formats. It
also provides an automatic parser to detect the format and parse the
structure string.
Author: Bin Fu [aut, cre, cph]
Maintainer: Bin Fu <23110220018@m.fudan.edu.cn>
Diff between glyparse versions 0.7.1 dated 2026-07-08 and 0.8.1 dated 2026-08-28
DESCRIPTION | 13 MD5 | 103 + NAMESPACE | 1 NEWS.md | 26 R/auto-parse.R | 13 R/furanose.R |only R/parse-glycam-iupac.R | 67 - R/parse-glycoct.R | 1489 ++++++++++++++++++++++++---- R/parse-gwb.R |only R/parse-iupac-compact.R | 129 +- R/parse-iupac-condensed.R | 9 R/parse-iupac-extended.R | 61 - R/parse-iupac-short.R | 31 R/parse-kcf.R | 24 R/parse-linear-code.R | 24 R/parse-linucs.R | 56 - R/parse-pglyco.R | 31 R/parse-strucgp.R | 62 - R/parse-wurcs.R | 725 ++++++++++++- R/struc-parser-wrapper.R | 187 ++- R/utils.R | 25 README.md | 14 build/partial.rdb |binary build/vignette.rds |binary inst/doc/glyparse.R | 51 inst/doc/glyparse.Rmd | 239 ++-- inst/doc/glyparse.html | 415 ++++--- man/auto_parse.Rd | 1 man/parse_glycoct.Rd | 13 man/parse_gwb.Rd |only man/parse_iupac_compact.Rd | 4 man/parse_kcf.Rd | 5 man/parse_linucs.Rd | 6 man/parse_pglyco_struc.Rd | 5 man/parse_strucgp_struc.Rd | 5 man/parse_wurcs.Rd | 15 tests/testthat/_snaps/parse-glycoct.md |only tests/testthat/test-auto-parse.R | 29 tests/testthat/test-furanose.R |only tests/testthat/test-mixed-residue-types.R |only tests/testthat/test-parse-glycam-iupac.R | 43 tests/testthat/test-parse-glycoct.R | 610 +++++++++++ tests/testthat/test-parse-gwb.R |only tests/testthat/test-parse-iupac-compact.R | 41 tests/testthat/test-parse-iupac-condensed.R | 39 tests/testthat/test-parse-iupac-extended.R | 51 tests/testthat/test-parse-iupac-short.R | 12 tests/testthat/test-parse-kcf.R | 53 tests/testthat/test-parse-linear-code.R | 13 tests/testthat/test-parse-linucs.R | 60 + tests/testthat/test-parse-pglyco.R | 51 tests/testthat/test-parse-strucgp.R | 51 tests/testthat/test-parse-wurcs.R | 649 ++++++++++++ tests/testthat/test-performance.R | 171 +++ tests/testthat/test-struc-parser-wrapper.R | 58 + vignettes/glyparse.Rmd | 239 ++-- 56 files changed, 5048 insertions(+), 971 deletions(-)
Title: Client for Delphi's 'Epidata' API
Description: The Delphi 'Epidata' API provides real-time access to
epidemiological surveillance data for influenza, 'COVID-19', and other
diseases for the USA at various geographical resolutions, both from
official government sources such as the Center for Disease Control
(CDC) and Google Trends and private partners such as Facebook and
Change 'Healthcare'. It is built and maintained by the Carnegie Mellon
University Delphi research group. To cite this API: David C. Farrow,
Logan C. Brooks, Aaron 'Rumack', Ryan J. 'Tibshirani', 'Roni'
'Rosenfeld' (2015). Delphi 'Epidata' API.
<https://github.com/cmu-delphi/delphi-epidata>.
Author: Logan Brooks [aut],
Dmitry Shemetov [aut],
Samuel Gratzl [aut],
David Weber [ctb, cre],
Nat DeFries [ctb],
Alex Reinhart [ctb],
Daniel J. McDonald [ctb],
Kean Ming Tan [ctb],
Will Townes [ctb],
George Haff [ctb],
Kathryn Mazaitis [ctb]
Maintainer: David Weber <davidweb@andrew.cmu.edu>
Diff between epidatr versions 1.2.4 dated 2026-06-02 and 1.3.0 dated 2026-08-28
epidatr-1.2.4/epidatr/inst/doc/epidatr.R |only epidatr-1.2.4/epidatr/inst/doc/signal-discovery.R |only epidatr-1.2.4/epidatr/inst/doc/v5-api-demo.R |only epidatr-1.2.4/epidatr/inst/doc/versioned-data.R |only epidatr-1.3.0/epidatr/DESCRIPTION | 12 epidatr-1.3.0/epidatr/MD5 | 124 - epidatr-1.3.0/epidatr/NAMESPACE | 3 epidatr-1.3.0/epidatr/NEWS.md | 39 epidatr-1.3.0/epidatr/R/auth.R | 17 epidatr-1.3.0/epidatr/R/cache.R | 50 epidatr-1.3.0/epidatr/R/check.R | 25 epidatr-1.3.0/epidatr/R/covidcast.R | 68 epidatr-1.3.0/epidatr/R/endpoints.R | 1012 +++++++++-- epidatr-1.3.0/epidatr/R/epidatacall.R | 84 epidatr-1.3.0/epidatr/R/epidatr-package.R | 5 epidatr-1.3.0/epidatr/R/model.R | 95 - epidatr-1.3.0/epidatr/R/request.R | 42 epidatr-1.3.0/epidatr/R/utils.R | 225 ++ epidatr-1.3.0/epidatr/README.md | 75 epidatr-1.3.0/epidatr/build/vignette.rds |binary epidatr-1.3.0/epidatr/inst/doc/epidatr.Rmd | 158 + epidatr-1.3.0/epidatr/inst/doc/epidatr.html | 389 ++++ epidatr-1.3.0/epidatr/inst/doc/migration-guide.Rmd |only epidatr-1.3.0/epidatr/inst/doc/migration-guide.html |only epidatr-1.3.0/epidatr/inst/doc/signal-discovery.Rmd | 372 +++- epidatr-1.3.0/epidatr/inst/doc/signal-discovery.html | 554 +++++- epidatr-1.3.0/epidatr/inst/doc/v5-api-demo.Rmd | 205 ++ epidatr-1.3.0/epidatr/inst/doc/v5-api-demo.html | 275 ++ epidatr-1.3.0/epidatr/inst/doc/versioned-data.Rmd | 87 epidatr-1.3.0/epidatr/inst/doc/versioned-data.html | 533 +++++ epidatr-1.3.0/epidatr/man/cast_api_queries.Rd | 39 epidatr-1.3.0/epidatr/man/covidcast_epidata.Rd | 8 epidatr-1.3.0/epidatr/man/dot-aux_key_columns.Rd |only epidatr-1.3.0/epidatr/man/dot-check_cast_empty.Rd |only epidatr-1.3.0/epidatr/man/dot-serialize_key_filters.Rd |only epidatr-1.3.0/epidatr/man/epidata_aux.Rd |only epidatr-1.3.0/epidatr/man/epidata_meta.Rd | 5 epidatr-1.3.0/epidatr/man/fetch_args_list.Rd | 6 epidatr-1.3.0/epidatr/man/note_frozen_endpoint.Rd |only epidatr-1.3.0/epidatr/man/pub_covidcast.Rd | 7 epidatr-1.3.0/epidatr/man/pub_covidcast_meta.Rd | 7 epidatr-1.3.0/epidatr/man/pub_flusurv.Rd | 7 epidatr-1.3.0/epidatr/man/pub_fluview.Rd | 7 epidatr-1.3.0/epidatr/man/pub_fluview_clinical.Rd | 7 epidatr-1.3.0/epidatr/man/pub_fluview_meta.Rd | 7 epidatr-1.3.0/epidatr/man/pub_meta.Rd | 7 epidatr-1.3.0/epidatr/man/pvt_quidel.Rd | 7 epidatr-1.3.0/epidatr/man/set_cache.Rd | 2 epidatr-1.3.0/epidatr/man/warn_v4_sunset.Rd |only epidatr-1.3.0/epidatr/tests/testthat/_snaps/endpoint-urls.md |only epidatr-1.3.0/epidatr/tests/testthat/_snaps/epidatacall.md | 14 epidatr-1.3.0/epidatr/tests/testthat/_snaps/fixtures.md |only epidatr-1.3.0/epidatr/tests/testthat/fixtures |only epidatr-1.3.0/epidatr/tests/testthat/helper-endpoints.R |only epidatr-1.3.0/epidatr/tests/testthat/helper-fixtures.R |only epidatr-1.3.0/epidatr/tests/testthat/helper-live.R | 29 epidatr-1.3.0/epidatr/tests/testthat/test-cache.R | 39 epidatr-1.3.0/epidatr/tests/testthat/test-endpoint-urls.R |only epidatr-1.3.0/epidatr/tests/testthat/test-endpoints.R | 485 +++++ epidatr-1.3.0/epidatr/tests/testthat/test-epidatacall.R | 78 epidatr-1.3.0/epidatr/tests/testthat/test-fixtures.R |only epidatr-1.3.0/epidatr/tests/testthat/test-live.R | 483 +---- epidatr-1.3.0/epidatr/tests/testthat/test-model.R | 11 epidatr-1.3.0/epidatr/tests/testthat/test-utils.R | 56 epidatr-1.3.0/epidatr/vignettes/epidatr.Rmd | 158 + epidatr-1.3.0/epidatr/vignettes/img |only epidatr-1.3.0/epidatr/vignettes/migration-guide.Rmd |only epidatr-1.3.0/epidatr/vignettes/signal-discovery.Rmd | 372 +++- epidatr-1.3.0/epidatr/vignettes/v5-api-demo.Rmd | 205 ++ epidatr-1.3.0/epidatr/vignettes/versioned-data.Rmd | 87 70 files changed, 5461 insertions(+), 1121 deletions(-)
Title: Data Science Infrastructure for Global Health
Description: Supports global health data analysis, including a
publication-ready 'ggplot2' theme, a 'flextable' defaults helper,
a thin pie chart wrapper, built-in regional country-code datasets
with a WHO region lookup helper, a geometric mean function for
indicator aggregation, an average annual rate of reduction function
for indicator progress tracking, direct age standardization against
the bundled WHO World Standard Population, period life-table
construction, a snapshot helper for reproducible data pulls, and
convenience clients for the World Health Organization Global Health
Observatory (GHO) OData API <https://ghoapi.azureedge.net/api/> and
the United Nations Sustainable Development Goals (SDG) API
<https://unstats.un.org/SDGAPI/swagger/>.
Author: Shanlong Ding [aut, cre]
Maintainer: Shanlong Ding <dings@who.int>
This is a re-admission after prior archival of version 0.8.0 dated 2026-07-02
Diff between DSIR versions 0.8.0 dated 2026-07-02 and 0.9.0 dated 2026-08-28
DESCRIPTION | 22 +++++---- MD5 | 64 +++++++++++++++++------------ NAMESPACE | 3 + NEWS.md | 54 ++++++++++++++++++++++++ R/age_standardize.R |only R/data.R | 75 +++++++++++++++++++++++++++++++++- R/gho.R | 16 ------- R/http.R |only R/life_table.R |only R/sdg.R | 21 ++++----- R/sdg_coverage.R | 18 +++++--- R/snapshot.R |only README.md | 2 build/vignette.rds |binary data/afro_cty.rda |binary data/amro_cty.rda |binary data/emro_cty.rda |binary data/euro_cty.rda |binary data/pic_cty.rda |binary data/searo_cty.rda |binary data/who_countries.rda |binary data/who_std_pop.rda |only data/wpro_cty.rda |binary inst/CITATION |only inst/WORDLIST | 32 ++++++++++++++ inst/doc/DSIR.html | 65 ++++++++++++++--------------- inst/doc/visualizing-indicators.html | 4 - man/age_standardize.Rd |only man/life_table.Rd |only man/snapshot.Rd |only man/who_countries.Rd | 18 +++++++- man/who_std_pop.Rd |only tests/testthat/test-age_standardize.R |only tests/testthat/test-gho-get-mock.R | 20 +++++++++ tests/testthat/test-life_table.R |only tests/testthat/test-sdg-coverage.R | 73 +++++++++++++++++++++++++++++++++ tests/testthat/test-sdg-get-mock.R | 34 +++++++++++++++ tests/testthat/test-snapshot.R |only tests/testthat/test-who_countries.R | 25 ++++++++++- tests/testthat/test-who_std_pop.R |only 40 files changed, 441 insertions(+), 105 deletions(-)
Title: Continuous-Time Subgrouping with GIMME
Description: Estimates group-, subgroup-, and individual-level dynamic
structures from multivariate intensive longitudinal data using
continuous-time state-space models. The subgrouping procedure combines
iterative shared-path searches with recurrent-evidence feature screening
and partitioning around medoids. The continuous-time group iterative
multiple model estimation method is described in Park et al. (2025)
<doi:10.1080/10705511.2024.2429544>.
Author: Jonathan J. Park [aut, cre, cph] ,
Nathan Xin Mills [aut, ctb]
Maintainer: Jonathan J. Park <imJPark@UCDavis.edu>
Diff between ctgimme versions 0.0.12 dated 2026-08-24 and 0.1.0 dated 2026-08-28
DESCRIPTION | 6 MD5 | 42 - NEWS.md | 80 +-- R/cleanup.R | 12 R/context.R | 449 ++++++++++--------- R/ctgimme-package.R | 2 R/ctgimme.R | 240 +++++----- R/data-preparation.R | 20 R/fit-helpers.R | 6 R/individual-models.R | 98 ++-- R/model-building.R | 22 R/shared-search.R | 108 ++-- R/subgroup-legacy.R | 26 - R/subgroup-model.R | 26 - README.md | 139 +++--- demo/quick-subgroups.R | 6 inst/WORDLIST | 38 - man/ctgimme.Rd | 18 tests/testthat/test-api.R | 504 +++++++++++----------- tests/testthat/test-core-helpers.R | 243 ++++++++-- tests/testthat/test-multisubject-subgroup-model.R | 56 +- tests/testthat/test-subgroup-time-and-cleanup.R | 72 +-- 22 files changed, 1223 insertions(+), 990 deletions(-)
Title: Join World Bank Data, Country Codes and Maps on the ISO Spine
Description: A complete toolkit for getting country data onto honest maps.
Country names rarely line up across data sources ("US", "U.S.",
"United States", "United States of America" are one country, but a
naive join treats them as four), so 'countryatlas' makes ISO codes the
universal join key. It generalises a one-call, map-ready table that
stitches together 'ggplot2' map geometry, 'WDI' World Bank indicators
and the 'countrycode' Rosetta stone; exposes the join machinery for the
user's own data; ships curated reference data (metadata, group
memberships, an indicator catalogue, flags and currencies); adds
analysis helpers (per-capita, regional roll-ups, ranking, inequality and
convergence statistics); and turns one hand-drawn choropleth into a full
vocabulary of projected, area-honest maps (binned and quantile
choropleths, proportional-symbol, spike, bivariate, cartogram, tile-grid,
flow, small-multiple, animated, globe and interactive), and can hand its
curated, ISO-reconciled tables to 'ggsql' [...truncated...]
Author: Youzhi Yu [aut, cre]
Maintainer: Youzhi Yu <yuyouzhi666@icloud.com>
Diff between countryatlas versions 2.0.0 dated 2026-08-25 and 2.0.1 dated 2026-08-28
DESCRIPTION | 9 +++---- MD5 | 15 +++++++------ NEWS.md | 43 ++++++++++++++++++++++++++++++++++++++ R/cache.R | 9 +++++-- R/ggsql.R | 20 ++++++++++++++++- inst/doc/countryatlas.html | 2 - man/clear_wdi_cache.Rd | 9 +++++-- tests/testthat/setup-user-dirs.R |only tests/testthat/test-standardize.R | 17 ++++++++++----- 9 files changed, 99 insertions(+), 25 deletions(-)
Title: Tree-Based Scan Statistics
Description: Implementation of unconditional Bernoulli Scan Statistic developed
by Kulldorff et al. (2003) <doi:10.1111/1541-0420.00039>
for hierarchical tree structures. Tree-based Scan Statistics are an
exploratory method to identify event clusters across the space of a
hierarchical tree.
Author: Joshua P. Entrop [aut, cre, cph] ,
Viktor Wintzell [aut]
Maintainer: Joshua P. Entrop <joshuaentrop@posteo.de>
Diff between TreeMineR versions 1.1.0 dated 2026-08-25 and 1.1.1 dated 2026-08-28
DESCRIPTION | 6 ++-- MD5 | 12 ++++----- NEWS.md | 4 +++ inst/doc/Tree-based-scan-statistics.R | 2 - inst/doc/Tree-based-scan-statistics.Rmd | 8 ++++-- inst/doc/Tree-based-scan-statistics.html | 38 ++++++++++++++++++++----------- vignettes/Tree-based-scan-statistics.Rmd | 8 ++++-- 7 files changed, 51 insertions(+), 27 deletions(-)
Title: Single-Cell Decomposition using Hierarchical Autoencoder
Description: Provides a fast and accurate pipeline for single-cell analyses.
The 'scDHA' software package can perform clustering, dimension reduction and visualization, classification, and time-trajectory inference on single-cell data (Tran et.al. (2021) <DOI:10.1038/s41467-021-21312-2>).
Author: Ha Nguyen [cre],
Duc Tran [aut],
Tin Nguyen [fnd],
Hao Chen [ctb]
Maintainer: Ha Nguyen <hvn0006@wayne.edu>
Diff between scDHA versions 1.2.3 dated 2025-09-23 and 1.2.4 dated 2026-08-28
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- inst/doc/Example.html | 2 +- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: Hydrologic Geospatial Fabric Extraction Tool Chain
Description: Traverses and works with National Hydrography Dataset Plus (NHDPlus) data. All methods implemented in 'hydrogeofetch' are available in the NHDPlus documentation available from the US Environmental Protection Agency <https://www.epa.gov/waterdata/basic-information>. Previously published as 'nhdplusTools'.
Author: David Blodgett [aut, cre] ,
Mike Johnson [ctb] ,
Marc Weber [ctb] ,
Josh Erickson [ctb],
Lauren Koenig [ctb]
Maintainer: David Blodgett <dblodgett@usgs.gov>
Diff between hydrogeofetch versions 2.0.1 dated 2026-08-21 and 2.0.2 dated 2026-08-28
DESCRIPTION | 6 ++--- MD5 | 8 +++---- NEWS.md | 5 ++++ tests/testthat/fixtures.tar.gz |binary tests/testthat/helper.R | 46 +++++++++++++++++++++++++++++++++++------ 5 files changed, 52 insertions(+), 13 deletions(-)
Title: Basic Sensitivity Analysis of Epidemiological Results
Description: Basic sensitivity analysis of the observed relative risks
adjusting for unmeasured confounding and misclassification of the
exposure/outcome, or both. It follows the bias analysis methods and
examples from the book by Fox M.P., MacLehose R.F., and Lash T.L. "Applying
Quantitative Bias Analysis to Epidemiologic Data, second ed.", ('Springer', 2021).
Author: Denis Haine [aut, cre]
Maintainer: Denis Haine <cheval@zaclys.net>
Diff between episensr versions 2.1.0 dated 2025-11-04 and 2.2.0 dated 2026-08-28
episensr-2.1.0/episensr/R/pipe.R |only episensr-2.1.0/episensr/R/rename.R |only episensr-2.1.0/episensr/man/rename.Rd |only episensr-2.2.0/episensr/DESCRIPTION | 16 - episensr-2.2.0/episensr/MD5 | 74 +++--- episensr-2.2.0/episensr/NAMESPACE | 89 +++---- episensr-2.2.0/episensr/NEWS.md | 2 episensr-2.2.0/episensr/R/confounding.R | 4 episensr-2.2.0/episensr/R/misclassification.R | 4 episensr-2.2.0/episensr/R/utils-pipe.R |only episensr-2.2.0/episensr/README.md | 24 +- episensr-2.2.0/episensr/build/vignette.rds |binary episensr-2.2.0/episensr/inst/CITATION | 6 episensr-2.2.0/episensr/inst/doc/b_probabilistic.Rmd | 4 episensr-2.2.0/episensr/inst/doc/b_probabilistic.html | 16 - episensr-2.2.0/episensr/inst/doc/c_multiple_bias.html | 4 episensr-2.2.0/episensr/inst/doc/d_other_sens.Rmd | 8 episensr-2.2.0/episensr/inst/doc/d_other_sens.html | 21 - episensr-2.2.0/episensr/inst/doc/episensr.Rmd | 6 episensr-2.2.0/episensr/inst/doc/episensr.html | 40 +-- episensr-2.2.0/episensr/man/confounders.Rd | 16 - episensr-2.2.0/episensr/man/confounders_array.Rd | 12 - episensr-2.2.0/episensr/man/confounders_evalue.Rd | 12 - episensr-2.2.0/episensr/man/confounders_ext.Rd | 12 - episensr-2.2.0/episensr/man/confounders_limit.Rd | 12 - episensr-2.2.0/episensr/man/episensr-package.Rd | 5 episensr-2.2.0/episensr/man/mbias.Rd | 4 episensr-2.2.0/episensr/man/misclass.Rd | 10 episensr-2.2.0/episensr/man/misclass_cov.Rd | 6 episensr-2.2.0/episensr/man/pipe.Rd | 28 +- episensr-2.2.0/episensr/man/plot.episensr_booted.Rd | 6 episensr-2.2.0/episensr/man/plot.episensr_probsens.Rd | 6 episensr-2.2.0/episensr/man/plot.mbias.Rd | 6 episensr-2.2.0/episensr/man/probsens_irr.Rd | 6 episensr-2.2.0/episensr/man/probsens_irr_conf.Rd | 12 - episensr-2.2.0/episensr/man/selection.Rd | 4 episensr-2.2.0/episensr/tests/testthat/test-probsens.R | 200 +++++++++++------ episensr-2.2.0/episensr/vignettes/b_probabilistic.Rmd | 4 episensr-2.2.0/episensr/vignettes/d_other_sens.Rmd | 8 episensr-2.2.0/episensr/vignettes/episensr.Rmd | 6 40 files changed, 382 insertions(+), 311 deletions(-)
Title: Discriminant Adaptive Nearest Neighbor Classification
Description: Discriminant Adaptive Nearest Neighbor Classification is a
variation of k nearest neighbors where the shape of the neighborhood is
data driven. The neighborhood is elongated along class boundaries and
shrunk in the orthogonal direction. This package implements dann and
sub_dann from Hastie (1996)
<https://web.stanford.edu/~hastie/Papers/dann_IEEE.pdf>.
Author: Greg McMahan [aut, cre]
Maintainer: Greg McMahan <gmcmacran@gmail.com>
Diff between dann versions 1.2.0 dated 2026-08-22 and 1.3.0 dated 2026-08-28
DESCRIPTION | 6 +-- MD5 | 29 +++++++++++------- NAMESPACE | 3 + NEWS.md | 6 +++ R/RcppExports.R | 26 ++++++++++++++++ R/dann.R | 2 + R/sub_dann.R | 2 + R/threads.R |only README.md | 2 - man/dann_set_threads.Rd |only man/figures |only man/predict.dann.Rd | 2 + man/predict.sub_dann.Rd | 2 + src/RcppExports.cpp | 45 ++++++++++++++++++++++++++++ src/internal_armadillo_helpers.cpp | 59 ++++++++++++++++++++++++++++++++++++- tests/testthat/setup.R |only tests/testthat/test_G_threads.R |only 17 files changed, 168 insertions(+), 16 deletions(-)
Title: Authoring Books and Technical Documents with R Markdown
Description: Output formats and utilities for authoring books and technical documents with R Markdown.
Author: Yihui Xie [aut, cre] ,
Christophe Dervieux [ctb] ,
JJ Allaire [ctb],
Albert Kim [ctb],
Alessandro Samuel-Rosa [ctb],
Andrzej Oles [ctb],
Atsushi Yasumoto [ctb] ,
Aust Frederik [ctb] ,
Bastiaan Quast [ctb],
Ben Marwick [ctb],
Chester Ismay [ctb],
Clif [...truncated...]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between bookdown versions 0.47 dated 2026-06-16 and 0.48 dated 2026-08-28
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/gitbook.R | 2 +- R/html.R | 2 +- R/utils.R | 2 +- build/vignette.rds |binary inst/rstudio/templates/project/resources/common/book.bib | 2 +- 7 files changed, 14 insertions(+), 14 deletions(-)
Title: Client for Central Bank APIs
Description: A client for retrieving data and metadata from central bank
APIs including 'Banco Central do Brasil' (BCB), 'Banco de España'
(BdE), 'Banco de México' (Banxico), 'Banco de Portugal' (BdP), 'Bank
for International Settlements' (BIS), 'Bank of Canada' (BoC), 'Bank of
England' (BoE), 'Bank of Israel' (BoI), 'Bank of Japan' (BoJ), 'Banque
de France' (BdF), 'Czech National Bank' (CNB), 'Deutsche Bundesbank'
(BBk), 'European Central Bank' (ECB), 'National Bank of Poland' (NBP),
'Norges Bank' (NoB), 'Oesterreichische Nationalbank' (OeNB), 'Sveriges
Riksbank' (SRb), and 'Swiss National Bank' (SNB).
Author: Maximilian Muecke [aut, cre]
Maintainer: Maximilian Muecke <muecke.maximilian@gmail.com>
Diff between bbk versions 0.12.0 dated 2026-07-10 and 0.13.0 dated 2026-08-28
DESCRIPTION | 22 - MD5 | 233 ++++++++++---------- NAMESPACE | 55 ++-- NEWS.md | 46 +++ R/assertions.R | 2 R/banxico.R | 10 R/bbk-package.R | 3 R/bbk.R | 41 ++- R/bcb.R | 4 R/bde.R | 47 +++- R/bdp.R | 119 ++++++++-- R/bis.R | 29 -- R/boc.R | 46 +-- R/boe.R | 12 - R/boi.R |only R/boj.R | 20 + R/cnb.R | 13 - R/ecb.R | 27 +- R/fx-rates.R | 31 ++ R/nbp.R | 32 +- R/nob.R | 90 ++++--- R/onb.R | 24 +- R/sdmx.R | 39 +++ R/snb.R | 14 - R/srb.R | 45 ++- R/utils.R | 34 ++ README.md | 7 man/banxico_data.Rd | 5 man/banxico_metadata.Rd | 6 man/bbk-package.Rd | 2 man/bbk_data.Rd | 1 man/bbk_dimension.Rd | 2 man/bbk_metadata.Rd | 2 man/bbk_series.Rd | 1 man/bcb_currencies.Rd | 2 man/bcb_data.Rd | 1 man/bcb_expectations.Rd | 1 man/bcb_fx_rates.Rd | 1 man/bcb_inflation.Rd | 1 man/bcb_selic.Rd | 1 man/bcb_top5.Rd | 1 man/bde_data.Rd | 1 man/bde_latest.Rd | 1 man/bdf_codelist.Rd | 1 man/bdf_data.Rd | 1 man/bdf_dataset.Rd | 1 man/bdf_dimension.Rd | 2 man/bdp_data.Rd | 7 man/bdp_dataset.Rd | 2 man/bdp_dimension.Rd | 2 man/bdp_domain.Rd | 2 man/bdp_series.Rd | 2 man/bis_data.Rd | 1 man/bis_dimension.Rd | 2 man/bis_metadata.Rd | 2 man/boc_data.Rd | 1 man/boc_metadata.Rd | 4 man/boe_data.Rd | 1 man/boi_data.Rd |only man/boi_dimension.Rd |only man/boi_metadata.Rd |only man/boj_data.Rd | 5 man/boj_metadata.Rd | 2 man/cnb_czeonia.Rd | 1 man/cnb_data.Rd | 1 man/cnb_dimension.Rd | 2 man/cnb_fx_other_rates.Rd | 8 man/cnb_fx_rates.Rd | 1 man/cnb_indicators.Rd | 2 man/cnb_pribor.Rd | 1 man/cnb_snapshots.Rd | 2 man/cnb_tree.Rd | 2 man/ecb_data.Rd | 1 man/ecb_dimension.Rd | 2 man/ecb_metadata.Rd | 2 man/figures/README-plotting-1.png |binary man/nbp_fx_rates.Rd | 6 man/nbp_gold.Rd | 6 man/nob_data.Rd | 1 man/nob_dimension.Rd | 2 man/nob_metadata.Rd | 2 man/onb_data.Rd | 1 man/onb_dimension.Rd | 2 man/onb_frequency.Rd | 2 man/onb_hierarchy.Rd | 2 man/onb_metadata.Rd | 2 man/onb_toc.Rd | 2 man/snb_data.Rd | 1 man/snb_dimension.Rd | 2 man/snb_metadata.Rd | 2 man/snb_toc.Rd | 2 man/srb_calendar.Rd | 2 man/srb_cross_rates.Rd | 1 man/srb_data.Rd | 1 man/srb_series.Rd | 2 tests/testthat/_snaps/banxico.md | 17 + tests/testthat/_snaps/bcb.md |only tests/testthat/_snaps/boi.md |only tests/testthat/fixtures/bbk-series-short-header.rds |only tests/testthat/fixtures/bde-data-es.rds |only tests/testthat/fixtures/bdp-data-multi.rds |only tests/testthat/fixtures/boi-data.xml |only tests/testthat/fixtures/boi-dimension.xml |only tests/testthat/fixtures/boi-metadata.xml |only tests/testthat/fixtures/nob-data.xml | 29 -- tests/testthat/test-banxico.R | 12 + tests/testthat/test-bbk.R | 55 ++++ tests/testthat/test-bcb.R | 4 tests/testthat/test-bde.R | 12 + tests/testthat/test-bdp.R | 134 +++++++++++ tests/testthat/test-bis.R | 65 +++++ tests/testthat/test-boc.R | 47 ++++ tests/testthat/test-boe.R | 20 + tests/testthat/test-boi.R |only tests/testthat/test-boj.R | 7 tests/testthat/test-cnb.R | 4 tests/testthat/test-ecb.R | 52 ++++ tests/testthat/test-exchange-rates.R | 36 +++ tests/testthat/test-nbp.R | 17 + tests/testthat/test-nob.R | 68 +++++ tests/testthat/test-onb.R | 41 +++ tests/testthat/test-sdmx.R | 118 +++++++++- tests/testthat/test-snb.R | 16 + tests/testthat/test-srb.R | 30 ++ 124 files changed, 1536 insertions(+), 426 deletions(-)
Title: Structured Covariances Estimators for Pairwise and Spatial
Covariates
Description: Implements estimators for structured covariance matrices in the
presence of pairwise and spatial covariates.
Metodiev, Perrot-Dockès,
Ouadah, Fosdick, Robin, Latouche & Raftery (2026)
<doi:10.1214/26-AOAS2183>.
Author: Martin Metodiev [aut, cre, cph] ,
Marie Perrot-Dockes [aut],
Stephane Robin [aut]
Maintainer: Martin Metodiev <m.metodiev@tutanota.com>
Diff between scov versions 2.0.0 dated 2026-03-18 and 2.0.2 dated 2026-08-28
DESCRIPTION | 15 ++++--- MD5 | 20 +++++----- NAMESPACE | 48 +++++++++++++++--------- NEWS.md | 12 ++---- R/scov.R | 11 +++-- build/vignette.rds |binary inst/doc/scov_vignette.R | 2 - inst/doc/scov_vignette.Rmd | 2 - inst/doc/scov_vignette.html | 85 +++++++++++++++++++++++++++++++++++++++----- man/scov.Rd | 11 +++-- vignettes/scov_vignette.Rmd | 2 - 11 files changed, 144 insertions(+), 64 deletions(-)
Title: Model Evaluation and Analysis
Description: Analyses species distribution models and evaluates their performance. It includes functions for variation partitioning, extracting variable importance, computing several metrics of model discrimination and calibration performance, optimizing prediction thresholds based on a number of criteria, performing multivariate environmental similarity surface (MESS) analysis, and displaying various analytical plots. Initially described in Barbosa et al. (2013) <doi:10.1111/ddi.12100>.
Author: A. Marcia Barbosa [aut, cre],
Jennifer A. Brown [aut],
Alberto Jimenez-Valverde [aut],
Raimundo Real [aut],
Oswald van Ginkel [ctb],
Jurica Levatic [ctb],
Victoria Formoso-Freire [ctb],
Andres Baselga [ctb],
Carola Gomez-Rodriguez [ctb],
Carlos C. Ra [...truncated...]
Maintainer: A. Marcia Barbosa <ana.marcia.barbosa@gmail.com>
Diff between modEvA versions 3.45 dated 2026-05-21 and 3.46 dated 2026-08-28
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- NEWS.md | 25 +++++++++++++++++++++++++ R/HLfit.R | 2 +- R/plotCoeffs.R | 6 ++++++ R/varImp.R | 39 +++++++++++++++++++++++++++++++-------- man/Miller.Rd | 2 +- man/mod2obspred.Rd | 4 ++-- man/modEvA-package.Rd | 4 ++-- man/plotCoeffs.Rd | 8 ++++---- man/threshMeasures.Rd | 6 ++++++ man/varImp.Rd | 12 +++++++----- 12 files changed, 100 insertions(+), 38 deletions(-)
Title: Perform Logistic Normal Multinomial Clustering for Microbiome
Compositional Data
Description: An implementation of logistic normal multinomial (LNM) clustering. It is an extension of LNM mixture model proposed by Fang and Subedi (2020) <doi:10.1038/s41598-023-41318-8>, and is designed for clustering compositional data. The package includes 3 extended models: LNM Factor Analyzer (LNM-FA), LNM Bicluster Mixture Model (LNM-BMM) and Penalized LNM Factor Analyzer (LNM-FA). There are several advantages of LNM models: 1. LNM provides more flexible covariance structure; 2. Factor analyzer can reduce the number of parameters to estimate; 3. Bicluster can simultaneously cluster subjects and taxa, and provides significant biological insights; 4. Penalty term allows sparse estimation in the covariance matrix. Details for model assumptions and interpretation can be found in papers: Tu and Subedi (2023) <doi:10.1007/s00357-023-09452-0> and Tu and Subedi (2022) <doi:10.3329/jsr.v56i2.67469>. It also include a Biclustering algorithm that applies to multivariate normal data: T [...truncated...]
Author: Wangshu Tu [aut, cre],
Sanjeena Subedi [aut],
Yuan Fang [aut]
Maintainer: Wangshu Tu <wangshu.tu@carleton.ca>
Diff between lnmCluster versions 0.3.1 dated 2022-07-20 and 1.0.0 dated 2026-08-28
DESCRIPTION | 17 +- MD5 | 45 +++--- NAMESPACE | 5 R/Micro_bi_PGMM.R | 8 - R/Micro_bi_jensens.R | 4 R/Micro_bi_lasso.R | 6 R/bmm.R |only R/initial_and_main_bmm.R |only R/lnmbiclust.R | 36 ++-- R/lnmfa.R | 29 ++- R/model_selection_bmm.R |only R/plnmfa.R | 27 +-- README.md |only build/vignette.rds |binary inst/doc/lnm-bicluster.R | 200 +++++++++++++++------------ inst/doc/lnm-bicluster.Rmd | 41 ++++- inst/doc/lnm-bicluster.html | 321 ++++++++++++++++++++++++-------------------- man/Mico_bi_PGMM.Rd | 2 man/Mico_bi_jensens.Rd | 2 man/Mico_bi_lasso.Rd | 2 man/bi_fa_T.Rd |only man/bmm.Rd |only man/lnmbiclust.Rd | 30 ++-- man/lnmfa.Rd | 26 +-- man/model_selection_bmm.Rd |only man/plnmfa.Rd | 28 ++- vignettes/lnm-bicluster.Rmd | 41 ++++- 27 files changed, 506 insertions(+), 364 deletions(-)
Title: Fuzzy Similarity in Species Distributions
Description: Functions to compute fuzzy versions of species occurrence patterns based on presence-absence data (including inverse distance interpolation, trend surface analysis, and prevalence-independent favourability obtained from probability of presence), as well as pair-wise fuzzy similarity (based on fuzzy logic versions of commonly used similarity indices) among those occurrence patterns. Includes also functions for model consensus and comparison (overlap and fuzzy similarity, fuzzy loss, fuzzy gain), and for data preparation, such as obtaining unique abbreviations of species names, defining the background region, cleaning and gridding (thinning) point occurrence data onto raster maps, selecting among (pseudo)absences to address survey bias, converting species lists (long format) to presence-absence tables (wide format), transposing part of a data frame, selecting relevant variables for models, assessing the false discovery rate, or analysing and dealing with multicollinearity. Initially desc [...truncated...]
Author: A. Marcia Barbosa [aut],
Alba Estrada [ctb],
Paul Melloy [ctb],
Jose Carlos Guerrero [fnd],
A. Marcia Barbosa [cre]
Maintainer: A. Marcia Barbosa <ana.marcia.barbosa@gmail.com>
Diff between fuzzySim versions 4.54 dated 2026-05-21 and 4.59 dated 2026-08-28
DESCRIPTION | 8 +- MD5 | 28 +++---- NEWS.md | 93 ++++++++++++++++++++++++ R/clampVars.R |only R/corSelect.R | 7 + R/pairwiseRangemaps.R | 178 +++++++++++++++++++++++++++++------------------ R/rangemapSim.R | 27 +++++-- R/selectAbsences.R | 24 +++--- man/biasLayer.Rd | 3 man/clampVars.Rd |only man/corSelect.Rd | 8 +- man/fuzzySim-package.Rd | 4 - man/pairwiseRangemaps.Rd | 42 ++++++----- man/rangemapSim.Rd | 20 ++--- man/selectAbsences.Rd | 10 ++ man/simMat.Rd | 33 +------- 16 files changed, 321 insertions(+), 164 deletions(-)
Title: Kernelized Stein Discrepancy for Goodness-of-Fit Tests and Stein
Sampling
Description: Provides Stein-discrepancy goodness-of-fit tests and
Stein-method-based sampling tools. The tests include kernel Stein
discrepancy U- and V-statistics following Liu et al. (2016)
<doi:10.48550/arXiv.1602.03253> and Chwialkowski et al. (2016)
<doi:10.48550/arXiv.1602.02964>, plus the finite set Stein discrepancy
test of Jitkrittum et al. (2017) <doi:10.48550/arXiv.1705.07673>. The
sampling tools include Stein thinning, Stein Points, Stein Point Markov
chain Monte Carlo, and Stein variational gradient descent following
Riabiz et al. (2022) <doi:10.48550/arXiv.2005.03952>, Chen et al. (2018)
<doi:10.48550/arXiv.1803.10161>, Chen et al. (2019)
<doi:10.48550/arXiv.1905.03673>, and Liu and Wang (2016)
<doi:10.48550/arXiv.1608.04471>. Gaussian mixture utilities are included
for constructing example targets, simulation, density evaluation, and
score callbacks.
Author: Junhao Gao [aut, cre],
Ery Arias-Castro [aut]
Maintainer: Junhao Gao <jug049@ucsd.edu>
Diff between steinsampling versions 0.1.0 dated 2026-07-21 and 0.1.1 dated 2026-08-28
steinsampling-0.1.0/steinsampling/man/compute_fssd_null_pvalue.Rd |only steinsampling-0.1.0/steinsampling/man/compute_fssd_unbiased_stat.Rd |only steinsampling-0.1.0/steinsampling/man/custom_adjusted_gradient.Rd |only steinsampling-0.1.0/steinsampling/man/grw.Rd |only steinsampling-0.1.0/steinsampling/man/grwmetrop.Rd |only steinsampling-0.1.0/steinsampling/man/kernel_generics.Rd |only steinsampling-0.1.0/steinsampling/man/likelihoodgmm.Rd |only steinsampling-0.1.0/steinsampling/man/perturbgmm.Rd |only steinsampling-0.1.0/steinsampling/man/plotgmm.Rd |only steinsampling-0.1.0/steinsampling/man/posteriorgmm.Rd |only steinsampling-0.1.0/steinsampling/man/scorefunctiongmm.Rd |only steinsampling-0.1.0/steinsampling/man/update_svgd.Rd |only steinsampling-0.1.1/steinsampling/DESCRIPTION | 19 steinsampling-0.1.1/steinsampling/MD5 | 138 steinsampling-0.1.1/steinsampling/NAMESPACE | 50 steinsampling-0.1.1/steinsampling/R/bootstrap.R | 282 - steinsampling-0.1.1/steinsampling/R/fssd_test.R | 1210 +++----- steinsampling-0.1.1/steinsampling/R/gmm_model.R | 745 +--- steinsampling-0.1.1/steinsampling/R/kernel_classes.R | 1499 ++++------ steinsampling-0.1.1/steinsampling/R/ksd_u_test.R | 534 --- steinsampling-0.1.1/steinsampling/R/ksd_v_test.R | 581 +-- steinsampling-0.1.1/steinsampling/R/stein_helpers.R | 341 -- steinsampling-0.1.1/steinsampling/R/stein_point_mcmc.R | 1141 +++---- steinsampling-0.1.1/steinsampling/R/stein_points.R | 1061 +++---- steinsampling-0.1.1/steinsampling/R/stein_thinning.R | 247 - steinsampling-0.1.1/steinsampling/R/steinsampling-package.R | 25 steinsampling-0.1.1/steinsampling/R/svgd.R | 448 +- steinsampling-0.1.1/steinsampling/man/compute_tau.Rd | 70 steinsampling-0.1.1/steinsampling/man/cross_kernel.Rd |only steinsampling-0.1.1/steinsampling/man/custom_stein_kernel.Rd | 123 steinsampling-0.1.1/steinsampling/man/densitygmm.Rd |only steinsampling-0.1.1/steinsampling/man/eval_kernel.Rd |only steinsampling-0.1.1/steinsampling/man/find_median_distance.Rd | 54 steinsampling-0.1.1/steinsampling/man/fmin_grid.Rd | 4 steinsampling-0.1.1/steinsampling/man/fmin_mc.Rd | 4 steinsampling-0.1.1/steinsampling/man/fmin_nm.Rd | 15 steinsampling-0.1.1/steinsampling/man/fssd_null_pvalue.Rd |only steinsampling-0.1.1/steinsampling/man/fssd_opt_test.Rd | 123 steinsampling-0.1.1/steinsampling/man/fssd_rand_test.Rd | 74 steinsampling-0.1.1/steinsampling/man/fssd_statistic.Rd |only steinsampling-0.1.1/steinsampling/man/fssd_test.Rd | 120 steinsampling-0.1.1/steinsampling/man/get_score_evaluator.Rd | 35 steinsampling-0.1.1/steinsampling/man/gmm.Rd | 49 steinsampling-0.1.1/steinsampling/man/grad_theta_v_kernel.Rd |only steinsampling-0.1.1/steinsampling/man/grad_x_kernel.Rd |only steinsampling-0.1.1/steinsampling/man/kernel_scale2.Rd |only steinsampling-0.1.1/steinsampling/man/ksd_u_bootstrap.Rd | 55 steinsampling-0.1.1/steinsampling/man/ksd_u_statistic.Rd | 42 steinsampling-0.1.1/steinsampling/man/ksd_u_test.Rd | 116 steinsampling-0.1.1/steinsampling/man/ksd_uq_matrix.Rd | 54 steinsampling-0.1.1/steinsampling/man/ksd_v_bootstrap.Rd | 71 steinsampling-0.1.1/steinsampling/man/ksd_v_statistic.Rd | 43 steinsampling-0.1.1/steinsampling/man/ksd_v_test.Rd | 150 - steinsampling-0.1.1/steinsampling/man/ksd_vq_matrix.Rd | 50 steinsampling-0.1.1/steinsampling/man/mala.Rd | 47 steinsampling-0.1.1/steinsampling/man/print.SteinKernel.Rd |only steinsampling-0.1.1/steinsampling/man/print.stein_points.Rd |only steinsampling-0.1.1/steinsampling/man/rgmm.Rd | 31 steinsampling-0.1.1/steinsampling/man/rwm.Rd | 51 steinsampling-0.1.1/steinsampling/man/sp_mcmc.Rd | 174 - steinsampling-0.1.1/steinsampling/man/sp_mcmc_criterion.Rd | 36 steinsampling-0.1.1/steinsampling/man/sp_mcmc_eval_candidates.Rd | 17 steinsampling-0.1.1/steinsampling/man/sp_mcmc_select_start.Rd | 17 steinsampling-0.1.1/steinsampling/man/sp_mcmc_state.Rd | 14 steinsampling-0.1.1/steinsampling/man/stein_codescent.Rd | 39 steinsampling-0.1.1/steinsampling/man/stein_kernel.Rd | 69 steinsampling-0.1.1/steinsampling/man/stein_kernel_imq_score.Rd | 29 steinsampling-0.1.1/steinsampling/man/stein_kernel_inverse_log.Rd | 33 steinsampling-0.1.1/steinsampling/man/stein_kernel_matrix.Rd | 69 steinsampling-0.1.1/steinsampling/man/stein_points.Rd | 136 steinsampling-0.1.1/steinsampling/man/stein_thinning.Rd | 177 - steinsampling-0.1.1/steinsampling/man/steinsampling-package.Rd | 23 steinsampling-0.1.1/steinsampling/man/svgd.Rd | 134 steinsampling-0.1.1/steinsampling/man/trace_mixed_kernel.Rd |only steinsampling-0.1.1/steinsampling/tests/testthat/helper-test-utils.R | 52 steinsampling-0.1.1/steinsampling/tests/testthat/test-fssd.R | 80 steinsampling-0.1.1/steinsampling/tests/testthat/test-gmm.R | 72 steinsampling-0.1.1/steinsampling/tests/testthat/test-gof-scale-contract.R |only steinsampling-0.1.1/steinsampling/tests/testthat/test-kernels.R | 79 steinsampling-0.1.1/steinsampling/tests/testthat/test-ksd.R | 50 steinsampling-0.1.1/steinsampling/tests/testthat/test-optimizers-and-sampling.R | 164 + steinsampling-0.1.1/steinsampling/tests/testthat/test-svgd-spmcmc.R | 176 - 82 files changed, 4749 insertions(+), 6593 deletions(-)
Title: Assessment of Regression Models Performance
Description: Utilities for computing measures to assess model quality,
which are not directly provided by R's 'base' or 'stats' packages.
These include e.g. measures like r-squared, intraclass correlation
coefficient (Nakagawa, Johnson & Schielzeth (2017)
<doi:10.1098/rsif.2017.0213>), root mean squared error or functions to
check models for overdispersion, singularity or zero-inflation and
more. Functions apply to a large variety of regression models,
including generalized linear models, mixed effects models and Bayesian
models. References: Lüdecke et al. (2021) <doi:10.21105/joss.03139>.
Author: Daniel Luedecke [aut, cre] ,
Dominique Makowski [aut, ctb] ,
Mattan S. Ben-Shachar [aut, ctb] ,
Indrajeet Patil [aut, ctb] ,
Philip Waggoner [aut, ctb] ,
Brenton M. Wiernik [aut, ctb] ,
Remi Theriault [aut, ctb] ,
Vincent Arel-Bundock [ctb] ,
Martin J [...truncated...]
Maintainer: Daniel Luedecke <officialeasystats@gmail.com>
Diff between performance versions 0.17.1 dated 2026-06-30 and 0.18.0 dated 2026-08-28
DESCRIPTION | 41 + MD5 | 70 +-- NAMESPACE | 25 - NEWS.md | 50 ++ R/binned_residuals.R | 22 - R/check_collinearity.R | 55 +- R/check_group_variation.R | 72 ++- R/check_heteroscedasticity.R | 41 + R/check_model_diagnostics.R | 21 R/compare_performance.R | 8 R/icc.R | 3 R/model_performance.lavaan.R | 16 R/performance_ior.R |only R/performance_mor.R |only R/performance_poor.R |only R/r2.R | 142 +++--- R/r2_mcfadden.R | 5 R/test_performance.R | 2 man/binned_residuals.Rd | 23 - man/check_group_variation.Rd | 9 man/check_heteroscedasticity.Rd | 6 man/icc.Rd | 4 man/performance-package.Rd | 1 man/performance_ior.Rd |only man/performance_mor.Rd |only man/performance_poor.Rd |only man/r2.Rd | 8 man/test_performance.Rd | 2 tests/testthat/test-binned_residuals.R | 426 +++---------------- tests/testthat/test-check_collinearity.R | 20 tests/testthat/test-check_group_variation.R | 222 ++++------ tests/testthat/test-check_heteroskedasticity.R | 30 + tests/testthat/test-compare_performance.R | 56 ++ tests/testthat/test-model_performance.gam.R | 18 tests/testthat/test-performance_mor.R |only tests/testthat/test-performance_poor.R |only tests/testthat/test-performance_roc.R | 103 ---- tests/testthat/test-r2.R | 35 + tests/testthat/test-r2_mcfadden.R | 41 + tests/testthat/test-r2_nakagawa.R | 536 ++----------------------- 40 files changed, 905 insertions(+), 1208 deletions(-)
Title: R Binding for the 'Certifiably Optimal RulE ListS (Corels)'
Learner
Description: The 'Certifiably Optimal RulE ListS (Corels)' learner by
Angelino et al described in <doi:10.48550/arXiv.1704.01701> provides interpretable decision
rules with an optimality guarantee, and is made available to R with this package.
See the file 'AUTHORS' for a list of copyright holders and contributors.
Author: Dirk Eddelbuettel [aut, cre] ,
Nicholas Larus-Stone [aut] ,
Elaine Angelino [aut] ,
Daniel Alabi [ctb] ,
Cynthia Rudin [ctb] ,
Margo Seltzer [ctb]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between corels versions 0.0.5 dated 2024-12-04 and 0.0.6 dated 2026-08-28
ChangeLog | 22 DESCRIPTION | 19 MD5 | 12 README.md | 3 build/partial.rdb |binary configure | 3376 ++++++++++++++++++++++++++++++++---------------------- configure.ac | 4 7 files changed, 2091 insertions(+), 1345 deletions(-)
Title: (Bifactor) ESEM with Continuous (MLR) or Ordered (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
ordered-categorical data. Continuous models use 'lavaan' native efa()
blocks with robust maximum likelihood (MLR) estimation.
Ordered-categorical ESEM defaults to the 'lavaan' weighted least squares
mean- and variance-adjusted (WLSMV) estimator; ordered B-ESEM uses a
custom diagonally weighted least squares (DWLS) path with polychoric
correlations from 'psych', 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 t [...truncated...]
Author: Leon T. De Beer [aut, cre]
Maintainer: Leon T. De Beer <leondb@gmail.com>
Diff between bifactory versions 0.5.1 dated 2026-07-11 and 0.5.2 dated 2026-08-28
DESCRIPTION | 6 +++--- MD5 | 24 ++++++++++++------------ NEWS.md | 29 +++++++++++++++++++++++++++++ R/bifactor.R | 8 ++++++++ R/esem.R | 11 +++++++---- R/factor_scores.R | 44 +++++++++++++++++++++++++++++++++++--------- R/methods.R | 30 +++++++++++++++++++++++------- R/ordered_esem.R | 34 ++++++++++++++++++++++------------ R/pipeline.R | 11 +++++++---- R/reliability.R | 11 +++++++---- R/utils.R | 8 ++++---- man/factor_scores.Rd | 9 +++++++++ man/parameters.Rd | 15 ++++++++++++--- 13 files changed, 178 insertions(+), 62 deletions(-)
Title: Nonparametric Comparison of Multivariate Samples
Description: Performs analysis of one-way multivariate data, for small samples using Nonparametric techniques. Using approximations for ANOVA Type, Wilks' Lambda, Lawley Hotelling, and Bartlett Nanda Pillai Test statics, the package compares the multivariate distributions for a single explanatory variable. The comparison is also performed using a permutation test for each of the four test statistics. The package also performs an all-subsets algorithm regarding variables and regarding factor levels.
Author: Woodrow Burchett [aut],
Amanda Ellis [aut],
Wanda Lauth [aut, cre]
Maintainer: Wanda Lauth <wanda.lauth@pmu.ac.at>
Diff between npmv versions 2.4.1 dated 2025-01-07 and 2.5.0 dated 2026-08-28
DESCRIPTION | 24 +++++++++++++++--------- MD5 | 14 +++++++------- NAMESPACE | 1 + R/basenonpartest.R | 24 +++++++++++++++++------- R/nonpartest.R | 32 ++++++++++++++++++++++++-------- man/nonpartest.Rd | 15 +++++++++------ man/npmv-package.Rd | 4 ++-- man/ssnonpartest.Rd | 6 +++--- 8 files changed, 78 insertions(+), 42 deletions(-)
Title: Estimation of Model-Based Predictions, Contrasts and Means
Description: Implements a general interface for model-based estimations
for a wide variety of models, used in the computation of
marginal means, contrast analysis and predictions. For a list of supported models,
see 'insight::supported_models()'.
Author: Dominique Makowski [aut, cre] ,
Daniel Luedecke [aut] ,
Mattan S. Ben-Shachar [aut] ,
Indrajeet Patil [aut] ,
Remi Theriault [aut]
Maintainer: Dominique Makowski <officialeasystats@gmail.com>
Diff between modelbased versions 0.16.0 dated 2026-06-30 and 0.17.0 dated 2026-08-28
DESCRIPTION | 22 +- MD5 | 97 +++++---- NAMESPACE | 16 + NEWS.md | 63 ++++++ R/estimate_contrasts.R | 38 +++ R/estimate_grouplevel.R | 6 R/estimate_means.R | 60 ++++-- R/estimate_predicted.R | 3 R/estimate_slopes.R | 1 R/format.R | 117 +++++++++++- R/get_contexteffects.R | 8 R/get_emcontrasts.R | 82 +++++--- R/get_emmeans.R | 58 +++++ R/get_inequalitycontrasts.R | 27 +- R/get_marginalcontrasts.R | 20 +- R/get_marginalmeans.R | 122 ++++++++++++ R/get_marginaltrends.R | 17 + R/options.R | 10 + R/p_adjust.R | 4 R/pool.R | 4 R/print.R | 22 +- R/summary.R | 2 R/tinyplot.R | 116 +++++++++++ R/utils.R | 2 R/visualisation_recipe.R | 10 - R/visualisation_recipe_internal.R | 1 inst/doc/overview_of_vignettes.Rmd | 4 inst/doc/overview_of_vignettes.html | 7 man/estimate_contrasts.Rd | 82 +++++--- man/estimate_expectation.Rd | 4 man/estimate_means.Rd | 57 ++++- man/estimate_slopes.Rd | 57 ++++- man/get_emmeans.Rd | 85 ++++++-- man/modelbased-options.Rd | 8 man/print.estimate_contrasts.Rd | 8 man/visualisation_recipe.estimate_predicted.Rd | 73 +++++++ tests/testthat/test-brms.R | 37 +++ tests/testthat/test-estimate_contrasts.R | 156 ++++++++++++++-- tests/testthat/test-estimate_contrasts_context.R | 4 tests/testthat/test-estimate_contrasts_counterfactual.R | 11 + tests/testthat/test-estimate_means.R | 38 +++ tests/testthat/test-estimate_means_ci.R | 126 ++++++++++-- tests/testthat/test-estimate_means_mixed.R | 67 +++++- tests/testthat/test-estimate_slopes.R | 32 +++ tests/testthat/test-glmmTMB.R | 113 ++++++++--- tests/testthat/test-mgcv.R | 20 +- tests/testthat/test-vcov.R | 2 tests/testthat/test-weighted_datagrid.R |only vignettes/bibliography.bib | 85 ++++++++ vignettes/overview_of_vignettes.Rmd | 4 50 files changed, 1668 insertions(+), 340 deletions(-)
Title: Improved Text Rendering Support for 'ggplot2'
Description: A 'ggplot2' extension that enables the rendering of
complex formatted plot labels (titles, subtitles, facet labels,
axis labels, etc.). Text boxes with automatic word wrap are also
supported.
Author: Claus O. Wilke [aut] ,
Brenton M. Wiernik [aut, cre]
Maintainer: Brenton M. Wiernik <brenton@wiernik.org>
Diff between ggtext versions 0.1.2 dated 2022-09-16 and 0.2.0 dated 2026-08-28
DESCRIPTION | 14 MD5 | 60 ++- NAMESPACE | 1 NEWS.md | 4 R/draw-keys.R |only R/element-textbox.R | 17 - R/geom-richtext.R | 2 R/ggtext.R | 3 README.md | 27 - build/vignette.rds |binary inst/doc/plotting_text.R | 2 inst/doc/plotting_text.html | 424 +++++++++++++------------- inst/doc/theme_elements.R | 2 inst/doc/theme_elements.html | 473 +++++++++++++++--------------- man/draw_key_richtext.Rd |only man/element_markdown.Rd | 4 man/element_textbox.Rd | 21 - man/figures/README-unnamed-chunk-10-1.png |binary man/figures/README-unnamed-chunk-4-1.png |binary man/figures/README-unnamed-chunk-5-1.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/figures/README-unnamed-chunk-7-1.png |binary man/figures/README-unnamed-chunk-8-1.png |binary man/figures/README-unnamed-chunk-9-1.png |binary man/geom_richtext.Rd | 94 ++++- man/geom_textbox.Rd | 78 +++- man/ggtext.Rd | 19 + tests/testthat/_snaps |only tests/testthat/test-draw-keys.R |only 29 files changed, 687 insertions(+), 558 deletions(-)
Title: Search Download and Handle Data from Copernicus Marine Service
Information
Description: Subset and download data from EU Copernicus Marine
Service Information: <https://data.marine.copernicus.eu>.
Import data on the oceans physical and biogeochemical state
from Copernicus into R without the need of external software.
Author: Pepijn de Vries [aut, cre, dtc]
Maintainer: Pepijn de Vries <pepijn.devries@outlook.com>
Diff between CopernicusMarine versions 0.4.8 dated 2026-07-20 and 0.4.9 dated 2026-08-28
DESCRIPTION | 12 MD5 | 78 ++--- NAMESPACE | 1 NEWS.md | 11 R/cms_catalogue_entry.R | 2 R/cms_cite_product.r | 2 R/cms_download_native.R | 580 +++++++++++++++++++++---------------------- R/cms_download_subset.r | 89 ++++-- R/cms_glossary.R | 2 R/cms_login.r | 4 R/cms_ncdf.R |only R/cms_product_details.r | 2 R/cms_product_metadata.r | 2 R/cms_product_services.r | 2 R/cms_products_list.r | 2 R/cms_wmts.r | 2 R/init.R | 52 ++- R/translate.R | 2 README.md | 53 ++- inst/doc/glossary.html | 4 inst/doc/product-info.html | 2 inst/doc/proxy.html | 2 man/account.Rd | 2 man/cms_cite_product.Rd | 2 man/cms_download_native.Rd | 4 man/cms_download_subset.Rd | 6 man/cms_get_client_info.Rd | 5 man/cms_glossary.Rd | 5 man/cms_login.Rd | 2 man/cms_native_proxy.Rd | 4 man/cms_native_s3.Rd | 8 man/cms_product_details.Rd | 2 man/cms_product_metadata.Rd | 2 man/cms_product_services.Rd | 2 man/cms_products_list.Rd | 2 man/cms_translate.Rd | 3 man/cms_wmts.Rd | 2 man/cms_write_ncdf.Rd |only man/cms_zarr_proxy.Rd | 2 tests/testthat/test_native.r | 4 tests/testthat/test_subset.r | 52 +++ 41 files changed, 574 insertions(+), 441 deletions(-)
More information about CopernicusMarine at CRAN
Permanent link
Title: Search Download and Handle Data from the Copernicus Data Space
Ecosystem
Description: The Copernicus Data Space Ecosystem, is an open
ecosystem that provides free instant access to a wide range
of data and services from the Copernicus Sentinel missions and
more on our planet’s land, oceans and atmosphere. This package
provides entry points to several APIs allowing users to access
the data directly in R.
Author: Pepijn de Vries [aut, cre] ,
Alicia Hamer [rtm] ,
LVVN
[fnd] ,
WMR [ctr]
Maintainer: Pepijn de Vries <pepijn.devries@outlook.com>
Diff between CopernicusDataspace versions 0.0.4 dated 2026-07-20 and 0.0.5 dated 2026-08-28
DESCRIPTION | 10 +++++----- MD5 | 24 ++++++++++++------------ NEWS.md | 7 +++++++ R/init.R | 7 ++++--- R/login.R | 2 +- R/odata_products.R | 5 +++-- R/s3.R | 2 +- R/sentinelhub.R | 4 +++- R/stac.R | 9 +++++++-- R/tidyverse.R | 2 +- inst/doc/OData.html | 16 ++++++++-------- inst/doc/STAC.html | 24 ++++++++++++------------ inst/doc/SentinelHub.html | 28 ++++++++++++++-------------- 13 files changed, 78 insertions(+), 62 deletions(-)
More information about CopernicusDataspace at CRAN
Permanent link
Title: Descriptive Analysis by Groups
Description: Create data summaries for quality control, extensive reports for exploring data, as well as publication-ready univariate or bivariate tables in several formats (plain text, HTML,LaTeX, PDF, Word or Excel. Create figures to quickly visualise the distribution of your data (boxplots, barplots, normality-plots, etc.). Display statistics (mean, median, frequencies, incidences, etc.). Perform the appropriate tests (t-test, Analysis of variance, Kruskal-Wallis, Fisher, log-rank, ...) depending on the nature of the described variable (normal, non-normal or qualitative). Summarize genetic data (Single Nucleotide Polymorphisms) data displaying Allele Frequencies and performing Hardy-Weinberg Equilibrium tests among other typical statistics and tests for these kind of data.
Author: Isaac Subirana [aut, cre] ,
Joan Salvador [ctb]
Maintainer: Isaac Subirana <isubirana@imim.es>
Diff between compareGroups versions 4.10.2 dated 2026-01-07 and 4.10.3 dated 2026-08-28
DESCRIPTION | 8 - MD5 | 14 +- NEWS.md | 4 R/export2md.R | 14 -- R/prepare.r | 9 - inst/app/server.R | 35 ++--- inst/doc/compareGroups_vignette.html | 237 +++++++++++++++++------------------ man/compareGroups-package.Rd | 4 8 files changed, 162 insertions(+), 163 deletions(-)
Title: ARAchnid KNowledge Online
Description: Allows the user to connect with the World Spider Catalogue (WSC; <https://wsc.nmbe.ch/>) and the World Spider Trait (WST; <https://spidertraits.sci.muni.cz/>) databases. Also performs several basic functions such as checking names validity, retrieving coordinate data from the Global Biodiversity Information Facility (GBIF; <https://www.gbif.org/>), and mapping.
Author: Pedro Cardoso [aut, cre]
Maintainer: Pedro Cardoso <pmcardoso@ciencias.ulisboa.pt>
Diff between arakno versions 1.3.2 dated 2026-04-20 and 1.3.3 dated 2026-08-28
arakno-1.3.2/arakno/data/wscmap.csv |only arakno-1.3.2/arakno/man/buildtree.Rd |only arakno-1.3.2/arakno/man/checknames.Rd |only arakno-1.3.3/arakno/DESCRIPTION | 12 +- arakno-1.3.3/arakno/MD5 | 29 ++-- arakno-1.3.3/arakno/NAMESPACE | 4 arakno-1.3.3/arakno/R/arakno.R | 190 ++++++++++++++------------------ arakno-1.3.3/arakno/R/globals.R |only arakno-1.3.3/arakno/data/wscmap.csv.gz |only arakno-1.3.3/arakno/man/authors.Rd | 4 arakno-1.3.3/arakno/man/buildTree.Rd |only arakno-1.3.3/arakno/man/checkNames.Rd |only arakno-1.3.3/arakno/man/countries.Rd | 4 arakno-1.3.3/arakno/man/distribution.Rd | 4 arakno-1.3.3/arakno/man/endemics.Rd | 6 - arakno-1.3.3/arakno/man/lsid.Rd | 4 arakno-1.3.3/arakno/man/map.Rd | 4 arakno-1.3.3/arakno/man/species.Rd | 4 arakno-1.3.3/arakno/man/taxonomy.Rd | 4 19 files changed, 128 insertions(+), 141 deletions(-)
Title: Programmatic Access to Data and Statistics from the World Bank
API
Description: Search and download data from the World Bank Data API. Includes
support for mutliple languages, access to annual, quarterly, and monthly
data.
Author: Mauricio Vargas Sepulveda [aut, cre] ,
Jesse Piburn [aut] ,
The World Bank [dtc]
Maintainer: Mauricio Vargas Sepulveda <m.vargas.sepulveda@gmail.com>
Diff between wbstats versions 1.1 dated 2025-09-14 and 1.2 dated 2026-08-28
wbstats-1.1/wbstats/R/utils-pipe.R |only wbstats-1.1/wbstats/data/wb_cachelist.RData |only wbstats-1.1/wbstats/man/figures/ggplot2-1.png |only wbstats-1.1/wbstats/man/figures/readme-chart-1.png |only wbstats-1.1/wbstats/man/pipe.Rd |only wbstats-1.1/wbstats/tests/testthat |only wbstats-1.1/wbstats/tests/testthat.R |only wbstats-1.1/wbstats/tools |only wbstats-1.2/wbstats/DESCRIPTION | 25 wbstats-1.2/wbstats/MD5 | 93 +- wbstats-1.2/wbstats/NAMESPACE | 25 wbstats-1.2/wbstats/NEWS.md | 13 wbstats-1.2/wbstats/R/build_urls.R | 133 +-- wbstats-1.2/wbstats/R/end_points.R | 34 wbstats-1.2/wbstats/R/format-data.R | 125 +- wbstats-1.2/wbstats/R/search.R | 51 - wbstats-1.2/wbstats/R/sysdata.rda |binary wbstats-1.2/wbstats/R/update_cache.R | 20 wbstats-1.2/wbstats/R/utils.R | 28 wbstats-1.2/wbstats/R/wb_country_coverage.R |only wbstats-1.2/wbstats/R/wb_data.R | 218 ++--- wbstats-1.2/wbstats/R/wbstats-package.R | 14 wbstats-1.2/wbstats/R/zzz.R | 6 wbstats-1.2/wbstats/README.md | 158 ++- wbstats-1.2/wbstats/build/vignette.rds |binary wbstats-1.2/wbstats/data/wb_cachelist.rda |only wbstats-1.2/wbstats/inst/doc/wbstats.Rmd | 500 +++++++---- wbstats-1.2/wbstats/inst/doc/wbstats.html | 553 ++++++++----- wbstats-1.2/wbstats/inst/tinytest |only wbstats-1.2/wbstats/man/figures/logo.svg | 48 - wbstats-1.2/wbstats/man/figures/readme-gdppc-vs-lifexp.png |only wbstats-1.2/wbstats/man/wb_cache.Rd | 25 wbstats-1.2/wbstats/man/wb_cachelist.Rd | 13 wbstats-1.2/wbstats/man/wb_country_coverage.Rd |only wbstats-1.2/wbstats/man/wb_data.Rd | 183 ++-- wbstats-1.2/wbstats/man/wb_end_point_info.Rd | 28 wbstats-1.2/wbstats/man/wb_indicators.Rd | 40 wbstats-1.2/wbstats/man/wb_search.Rd | 48 - wbstats-1.2/wbstats/man/wbstats.Rd | 35 wbstats-1.2/wbstats/tests/tinytest.R |only wbstats-1.2/wbstats/vignettes/wbstats.Rmd | 500 +++++++---- 41 files changed, 1684 insertions(+), 1232 deletions(-)
More information about VanillaCalendar at CRAN
Permanent link
Title: Parse 'User-Agent' Strings
Description: Parses HTTP user agent strings and returns user agent, device and OS information.
This is a ‘V8’-backed package that uses the UA, device and OS definitions from the ‘ua-parser’
project <https://github.com/ua-parser>.
Author: Bob Rudis [aut, cph],
Greg Hunt [aut, cre, cph],
Lindsey Simon [aut] ,
Tobie Langel [aut] ,
Colman Humphrey [ctb],
Jim Vine [ctb]
Maintainer: Greg Hunt <greg@firmansyah.com>
Diff between uaparserjs versions 0.4.0 dated 2026-07-02 and 0.4.1 dated 2026-08-28
uaparserjs-0.4.0/uaparserjs/README.md |only uaparserjs-0.4.1/uaparserjs/DESCRIPTION | 13 ++-- uaparserjs-0.4.1/uaparserjs/MD5 | 24 +++++--- uaparserjs-0.4.1/uaparserjs/NEWS.md | 5 + uaparserjs-0.4.1/uaparserjs/R/uaparser.R | 15 ++--- uaparserjs-0.4.1/uaparserjs/R/utils.R | 2 uaparserjs-0.4.1/uaparserjs/R/zzz.r | 6 -- uaparserjs-0.4.1/uaparserjs/inst/js/bundle.js | 2 uaparserjs-0.4.1/uaparserjs/inst/tinytest/test_exhaustive.R | 27 ++++------ uaparserjs-0.4.1/uaparserjs/inst/tinytest/test_multirow.R | 21 ++++--- uaparserjs-0.4.1/uaparserjs/inst/tinytest/tests/test_device.yaml | 10 +++ uaparserjs-0.4.1/uaparserjs/man/figures |only uaparserjs-0.4.1/uaparserjs/tests/test_device.yaml |only uaparserjs-0.4.1/uaparserjs/tests/test_os.yaml |only uaparserjs-0.4.1/uaparserjs/tests/test_ua.yaml |only 15 files changed, 73 insertions(+), 52 deletions(-)
Title: Design and Analysis Tools for Target Trial Emulation
Description: Design and analysis tools for target trial emulation using longitudinal observational data. Functions are provided for checking person-period data, expanding longitudinal data into sequentially nested trials, estimating inverse probability weights for intention-to-treat and per-protocol analyses, and assessing weight distributions and covariate balance. Additional functions fit weighted pooled discrete-time outcome models, obtain standardized risks and treatment contrasts, and estimate weighted Kaplan-Meier and Aalen-Johansen curves. Two worked examples based on fully synthetic data illustrate an active-comparator new-user study comparing sodium-glucose cotransporter 2 inhibitors with dipeptidyl peptidase-4 inhibitors and an analysis of sequentially nested trials comparing angiotensin receptor blocker and calcium channel blocker strategies.
Author: Hisashi Noma [aut, cre]
Maintainer: Hisashi Noma <noma@ism.ac.jp>
Diff between TTE versions 1.1.1 dated 2026-08-02 and 1.1.2 dated 2026-08-28
DESCRIPTION | 9 +++++---- MD5 | 8 ++++---- NEWS.md | 6 +++++- man/SGLT2.Rd | 2 +- man/TTE-package.Rd | 2 +- 5 files changed, 16 insertions(+), 11 deletions(-)
Title: Statistical Framework for Co-Mediators of Zero-Inflated
Single-Cell Data
Description: A causal mediation framework for single-cell data that incorporates two key features ('MedZIsc', pronounced Magics): (1) zero-inflation using beta regression and (2) overdispersed expression counts using negative binomial regression. This approach also includes a screening step based on penalized and marginal models to handle high-dimensionality. Full methodological details are available in our recent preprint by Ahn S et al. (2025) <doi:10.48550/arXiv.2507.06113>.
Author: Seungjun Ahn [cre, aut] ,
Zhigang Li [ctb]
Maintainer: Seungjun Ahn <seungjun.ahn@mountsinai.org>
Diff between MedZIsc versions 0.0.4 dated 2025-07-16 and 0.0.5 dated 2026-08-28
DESCRIPTION | 8 ++++---- MD5 | 10 ++++++---- NAMESPACE | 1 + R/Magics.R | 9 +++++---- R/compute_M.R |only man/Magics.Rd | 9 +++++---- man/compute_M.Rd |only 7 files changed, 21 insertions(+), 16 deletions(-)
Title: Download and Visualize Essential Global Heating Data
Description: Provides easy access to essential climate change datasets to non-climate experts. Users can download the latest raw data from authoritative sources and view it via pre-defined 'ggplot2' charts. Datasets include atmospheric CO2, methane, emissions, instrumental and proxy temperature records, CMIP6 projections, sea levels, Arctic/Antarctic sea-ice, Hurricanes, Wildfires, and Paleoclimate data. Sources include: NOAA Mauna Loa Laboratory <https://gml.noaa.gov/ccgg/trends/data.html>, Global Carbon Project <https://www.globalcarbonproject.org/carbonbudget/>, NASA GISTEMP <https://data.giss.nasa.gov/gistemp/>, National Snow and Sea Ice Data Center <https://nsidc.org/home>, CSIRO <https://research.csiro.au/slrwavescoast/sea-level/measurements-and-data/sea-level-data/>, NOAA Laboratory for Satellite Altimetry <https://www.star.nesdis.noaa.gov/socd/lsa/SeaLevelRise/> and HURDAT Atlantic Hurricane Database <https://www.aoml.noaa.gov/hrd/hurdat/Data_Storm.htm [...truncated...]
Author: Hernando Cortina [aut, cre]
Maintainer: Hernando Cortina <hch@alum.mit.edu>
Diff between hockeystick versions 0.9.1 dated 2026-07-08 and 1.0.0 dated 2026-08-28
DESCRIPTION | 16 +++--- MD5 | 79 +++++++++++++++++--------------- NAMESPACE | 76 +++++++++++++++++++------------ NEWS.md | 6 ++ R/2kyears_temp.R | 2 R/carbon.R | 2 R/daily_temp.R | 8 +-- R/data_cache.R | 3 + R/emissions.R | 2 R/fires.R | 16 +++--- R/future_climate.R |only R/hurricanes.R | 5 -- R/icecurves.R | 2 R/instrumental_temp.R | 2 R/methane.R | 2 R/paleo.R | 4 - R/seaice.R | 2 R/sealevel.R | 4 - README.md | 46 ++++++++++++------ inst/WORDLIST | 20 ++++++++ inst/doc/usinghockeystick.R | 14 +++++ inst/doc/usinghockeystick.html | 88 ++++++++++++++++++++++-------------- inst/doc/usinghockeystick.qmd | 17 ++++++ man/figures/README-carbon-1.png |binary man/figures/README-cmip6-1.png |only man/figures/README-cmip6anom-1.png |only man/figures/README-dailytemp-1.png |binary man/figures/README-fires-1.png |binary man/figures/README-fires-2.png |binary man/figures/README-grid-1.png |binary man/figures/README-icecurves-1.png |binary man/figures/README-methane-1.png |binary man/figures/README-si-1.png |binary man/figures/README-stripes-1.png |binary man/figures/README-stripes2-1.png |binary man/figures/README-temp-1.png |binary man/figures/README-tempcarbon-1.png |binary man/get_cmip6.Rd |only man/get_cmip6_anom.Rd |only man/hockeystick-package.Rd | 4 - man/plot_cmip6.Rd |only man/plot_cmip6_anom.Rd |only man/plot_dailytemp.Rd | 2 vignettes/usinghockeystick.qmd | 17 ++++++ 44 files changed, 291 insertions(+), 148 deletions(-)
Title: Numerical Tools for 'Rcpp' and Lambda Functions
Description: Provides a 'C++' API for routinely used numerical tools such as integration,
root-finding, and optimization, where function arguments are given as
lambdas. This facilitates 'Rcpp' programming, enabling the development of
'R'-like code in 'C++' where functions can be defined on the fly and use
variables in the surrounding environment.
Author: Andrew M. Raim [aut, cre]
Maintainer: Andrew M. Raim <andrew.raim@gmail.com>
Diff between fntl versions 0.1.3.1 dated 2026-07-30 and 0.1.3.2 dated 2026-08-28
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- inst/doc/fntl.pdf |binary inst/doc/fntl.qmd | 2 +- inst/include/util.h | 2 ++ vignettes/fntl.qmd | 2 +- 6 files changed, 13 insertions(+), 11 deletions(-)
Title: Goodness-of-Fit and Calibration Tests for Logistic Regression
Description: Provides a unified battery of goodness-of-fit and calibration
tests for binary logistic regression, runnable in a single call via
'run.all.gof()'. Around twenty-five tests spanning five decades of
literature are aggregated and grouped by the departure each is built to
detect: global and standardized statistics, partition tests, directed and
covariate-space tests, smoothing and resampling tests, and calibration
tests. Each is obtained from its own package where installed and
attributed to its authors. The package also implements the author's own
procedures for sparse data, where the Hosmer-Lemeshow test loses power:
the omnibus Ebrahim-Farrington test, the directed 'EDGE' test,
'DeepGOF-1' (a pretrained convolutional statistic whose level comes from the
analyst's own parametric bootstrap rather than from the network), a
Cauchy-combination ensemble, 'legoft()' (a pretrained combination whose
weights are fixed offline and ship frozen, so two analysts obtain the same
p-value), and 'shrink. [...truncated...]
Author: Ebrahim Khaled Ebrahim [aut, cre]
Maintainer: Ebrahim Khaled Ebrahim <ebrahimkhaled@alexu.edu.eg>
Diff between ebrahim.gof versions 2.4.0 dated 2026-07-22 and 2.6.0 dated 2026-08-28
DESCRIPTION | 40 MD5 | 24 NAMESPACE | 88 NEWS.md | 750 +++++--- R/deepgof.R |only R/legoft.R |only R/run_all_gof.R | 2925 ++++++++++++++++++--------------- R/shrink_gof.R |only R/sysdata.rda |only inst/doc/ebrahim-farrington-intro.html | 4 man/deepgof1.Rd |only man/legoft.Rd |only man/legoft.localize.Rd |only man/run.all.gof.Rd | 356 +++- man/shrink.gof.Rd |only tests/testthat/test-deepgof1.R |only tests/testthat/test-lecessie-algebra.R |only tests/testthat/test-run-all-gof.R | 354 ++- 18 files changed, 2636 insertions(+), 1905 deletions(-)
Title: Data from the GLM Book by Dobson and Barnett
Description: Example datasets from the book "An Introduction to Generalised Linear Models" (4th edition) (Year: 2018, <isbn:9781138741515>) by Dobson and Barnett.
Author: Adrian Barnett [aut, cre, cph]
Maintainer: Adrian Barnett <a.barnett@qut.edu.au>
Diff between dobson versions 0.4 dated 2018-11-20 and 0.4.1 dated 2026-08-28
dobson-0.4.1/dobson/DESCRIPTION | 18 +++--- dobson-0.4.1/dobson/MD5 | 92 ++++++++++++++++---------------- dobson-0.4.1/dobson/NAMESPACE | 2 dobson-0.4.1/dobson/NEWS.md |only dobson-0.4.1/dobson/README.md |only dobson-0.4.1/dobson/data/achieve.rda |only dobson-0.4.1/dobson/data/anthers.rda |binary dobson-0.4.1/dobson/data/doctors.rda |binary dobson-0.4.1/dobson/man/Cars.Rd | 56 +++++++++---------- dobson-0.4.1/dobson/man/PLOS.Rd | 2 dobson-0.4.1/dobson/man/achieve.Rd |only dobson-0.4.1/dobson/man/aids.Rd | 54 +++++++++--------- dobson-0.4.1/dobson/man/anthers.Rd | 60 ++++++++++---------- dobson-0.4.1/dobson/man/balanced.Rd | 6 +- dobson-0.4.1/dobson/man/beetle.Rd | 54 +++++++++--------- dobson-0.4.1/dobson/man/birthweight.Rd | 52 +++++++++--------- dobson-0.4.1/dobson/man/carbohydrate.Rd | 58 ++++++++++---------- dobson-0.4.1/dobson/man/cholesterol.Rd | 4 - dobson-0.4.1/dobson/man/chronic.Rd | 52 +++++++++--------- dobson-0.4.1/dobson/man/doctors.Rd | 57 ++++++++++--------- dobson-0.4.1/dobson/man/dogs.Rd | 58 ++++++++++---------- dobson-0.4.1/dobson/man/ear.Rd | 56 +++++++++---------- dobson-0.4.1/dobson/man/failure.Rd | 52 +++++++++--------- dobson-0.4.1/dobson/man/graduates.Rd | 2 dobson-0.4.1/dobson/man/hepatitis.Rd | 60 ++++++++++---------- dobson-0.4.1/dobson/man/hiroshima.Rd | 2 dobson-0.4.1/dobson/man/housing.Rd | 52 +++++++++--------- dobson-0.4.1/dobson/man/insurance.Rd | 54 +++++++++--------- dobson-0.4.1/dobson/man/leukemia.Rd | 54 +++++++++--------- dobson-0.4.1/dobson/man/machine.Rd | 4 - dobson-0.4.1/dobson/man/melanoma.Rd | 54 +++++++++--------- dobson-0.4.1/dobson/man/mortality.Rd | 52 +++++++++--------- dobson-0.4.1/dobson/man/moths.Rd | 62 ++++++++++----------- dobson-0.4.1/dobson/man/plant.dried.Rd | 9 +-- dobson-0.4.1/dobson/man/plants.Rd | 46 ++++++++-------- dobson-0.4.1/dobson/man/plasma.Rd | 6 +- dobson-0.4.1/dobson/man/poisson.Rd | 46 ++++++++-------- dobson-0.4.1/dobson/man/remission.Rd | 52 +++++++++--------- dobson-0.4.1/dobson/man/senility.Rd | 50 ++++++++--------- dobson-0.4.1/dobson/man/stroke.wide.Rd | 30 ++++------ dobson-0.4.1/dobson/man/sugar.Rd | 6 +- dobson-0.4.1/dobson/man/survival.Rd | 52 +++++++++--------- dobson-0.4.1/dobson/man/tumor.Rd | 56 +++++++++---------- dobson-0.4.1/dobson/man/ulcer.Rd | 54 +++++++++--------- dobson-0.4.1/dobson/man/unbalanced.Rd | 4 - dobson-0.4.1/dobson/man/vaccine.Rd | 46 ++++++++-------- dobson-0.4.1/dobson/man/waist.Rd | 60 ++++++++++---------- dobson-0.4/dobson/R |only dobson-0.4/dobson/data/achievement.rda |only dobson-0.4/dobson/man/achievement.Rd |only dobson-0.4/dobson/man/dobson.Rd |only 51 files changed, 826 insertions(+), 820 deletions(-)
Title: Deep Compositional Spatial Models
Description: Deep compositional spatial models are standard spatial covariance
models coupled with an injective warping function of the spatial
domain. The warping function is constructed through a composition
of multiple elemental injective functions in a deep-learning
framework. The package implements two cases for the univariate setting; first,
when these warping functions are known up to some weights that
need to be estimated, and, second, when the weights in each layer are random.
In the multivariate setting only the former case is available.
Estimation and inference is done using `tensorflow`, which makes use of
graphics processing units.
For more details see Zammit-Mangion et al. (2022) <doi:10.1080/01621459.2021.1887741>,
Vu et al. (2022) <doi:10.5705/ss.202020.0156>,
Vu et al. (2023) <doi:10.1016/j.spasta.2023.100742>, and
Shao et al. (2025) <doi:10.48550/arXiv.2505.12548>.
Author: Andrew Zammit-Mangion [aut],
Quan Vu [aut, cre],
Xuanjie Shao [aut]
Maintainer: Quan Vu <quanvustats@gmail.com>
Diff between deepspat versions 0.3.1 dated 2025-11-25 and 0.3.2 dated 2026-08-28
deepspat-0.3.1/deepspat/R/NMLL_nn_ST.R |only deepspat-0.3.1/deepspat/R/summary.deepspat_MSP.R |only deepspat-0.3.1/deepspat/R/summary.deepspat_rPP.R |only deepspat-0.3.1/deepspat/R/tent.R |only deepspat-0.3.1/deepspat/man/summary.deepspat_MSP.Rd |only deepspat-0.3.1/deepspat/man/summary.deepspat_rPP.Rd |only deepspat-0.3.2/deepspat/DESCRIPTION | 12 deepspat-0.3.2/deepspat/MD5 | 111 deepspat-0.3.2/deepspat/NAMESPACE | 29 deepspat-0.3.2/deepspat/NEWS.md | 27 deepspat-0.3.2/deepspat/R/AFF.R | 250 - deepspat-0.3.2/deepspat/R/NMLL.R | 48 deepspat-0.3.2/deepspat/R/RBF.R | 70 deepspat-0.3.2/deepspat/R/bisquare.R | 90 deepspat-0.3.2/deepspat/R/bisquare_basis.R | 198 - deepspat-0.3.2/deepspat/R/cov_fns.R | 235 - deepspat-0.3.2/deepspat/R/cov_fns_nn.R | 156 - deepspat-0.3.2/deepspat/R/deepspat.R | 16 deepspat-0.3.2/deepspat/R/deepspat_main.R | 541 ++-- deepspat-0.3.2/deepspat/R/deepspat_main_GP.R | 721 ++--- deepspat-0.3.2/deepspat/R/deepspat_main_MSP.R | 851 +++--- deepspat-0.3.2/deepspat/R/deepspat_main_bivar_GP.R | 1739 ++++++------- deepspat-0.3.2/deepspat/R/deepspat_main_nn_GP.R | 685 ++--- deepspat-0.3.2/deepspat/R/deepspat_main_nn_ST_GP.R | 1114 ++++---- deepspat-0.3.2/deepspat/R/deepspat_main_rPP.R | 764 ++--- deepspat-0.3.2/deepspat/R/deepspat_main_trivar_GP.R | 1871 +++++++------- deepspat-0.3.2/deepspat/R/init_learn_rates.R | 62 deepspat-0.3.2/deepspat/R/plot.deepspat.R |only deepspat-0.3.2/deepspat/R/predict.deepspat.R | 8 deepspat-0.3.2/deepspat/R/predict.deepspat_GP.R | 229 - deepspat-0.3.2/deepspat/R/predict.deepspat_MSP.R |only deepspat-0.3.2/deepspat/R/predict.deepspat_bivar_GP.R | 545 ++-- deepspat-0.3.2/deepspat/R/predict.deepspat_nn_GP.R | 244 + deepspat-0.3.2/deepspat/R/predict.deepspat_nn_ST_GP.R | 346 +- deepspat-0.3.2/deepspat/R/predict.deepspat_rPP.R |only deepspat-0.3.2/deepspat/R/predict.deepspat_trivar_GP.R | 85 deepspat-0.3.2/deepspat/R/print.deepspat.R |only deepspat-0.3.2/deepspat/R/sigmoid.R | 38 deepspat-0.3.2/deepspat/R/sim_data.R | 328 +- deepspat-0.3.2/deepspat/R/summary.deepspat.R |only deepspat-0.3.2/deepspat/R/train_step.R | 53 deepspat-0.3.2/deepspat/R/utils.R | 626 ++-- deepspat-0.3.2/deepspat/R/utils_error.R |only deepspat-0.3.2/deepspat/R/utils_tf.R | 161 - deepspat-0.3.2/deepspat/R/zzz.R | 142 - deepspat-0.3.2/deepspat/README.md | 108 deepspat-0.3.2/deepspat/man/deepspat.Rd | 30 deepspat-0.3.2/deepspat/man/deepspat_GP.Rd | 6 deepspat-0.3.2/deepspat/man/deepspat_MSP.Rd | 5 deepspat-0.3.2/deepspat/man/deepspat_bivar_GP.Rd | 6 deepspat-0.3.2/deepspat/man/deepspat_nn_GP.Rd | 4 deepspat-0.3.2/deepspat/man/deepspat_nn_ST_GP.Rd | 4 deepspat-0.3.2/deepspat/man/deepspat_rPP.Rd | 2 deepspat-0.3.2/deepspat/man/deepspat_trivar_GP.Rd | 4 deepspat-0.3.2/deepspat/man/plot.deepspat.Rd |only deepspat-0.3.2/deepspat/man/predict.deepspat.Rd | 4 deepspat-0.3.2/deepspat/man/predict.deepspat_GP.Rd | 10 deepspat-0.3.2/deepspat/man/predict.deepspat_MSP.Rd |only deepspat-0.3.2/deepspat/man/predict.deepspat_bivar_GP.Rd | 12 deepspat-0.3.2/deepspat/man/predict.deepspat_nn_GP.Rd | 10 deepspat-0.3.2/deepspat/man/predict.deepspat_nn_ST_GP.Rd | 10 deepspat-0.3.2/deepspat/man/predict.deepspat_rPP.Rd |only deepspat-0.3.2/deepspat/man/predict.deepspat_trivar_GP.Rd | 12 deepspat-0.3.2/deepspat/man/print.deepspat.Rd |only deepspat-0.3.2/deepspat/man/summary.deepspat.Rd |only 65 files changed, 6673 insertions(+), 5949 deletions(-)
Title: Bayesian Essentials with R
Description: Allows the reenactment of the R programs used in
the book Bayesian Essentials with R without further programming.
R code being available as well, they can be modified by the user
to conduct one's own simulations.
Marin J.-M. and Robert C. P. (2014) <doi:10.1007/978-1-4614-8687-9>.
Author: Jean-Michel Marin [aut, cre],
Christian P. Robert [aut]
Maintainer: Jean-Michel Marin <jean-michel.marin@umontpellier.fr>
This is a re-admission after prior archival of version 1.6 dated 2024-03-06
Diff between bayess versions 1.6 dated 2024-03-06 and 1.7 dated 2026-08-28
DESCRIPTION | 23 ++++++++++++++++------- MD5 | 4 ++-- README.md | 2 +- 3 files changed, 19 insertions(+), 10 deletions(-)
Title: Optimal Confidence Intervals for Visual Testing
Description: Identifies the optimal confidence level to represent the results of a set of pairwise tests as suggested by Armstrong and Poirier (2025) <doi:10.1017/pan.2024.24>.
Author: Dave Armstrong [aut, cre] ,
William Poirier [aut]
Maintainer: Dave Armstrong <davearmstrong.ps@gmail.com>
Diff between VizTest versions 0.7 dated 2026-03-03 and 0.8 dated 2026-08-28
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++----------- R/functions.R | 14 +++++++++++++- build/vignette.rds |binary inst/doc/compact_letter_displays.html | 12 ++++++------ inst/doc/creating_forest_plots.html | 18 +++++++++--------- inst/doc/heatmaps.html | 19 +++++++++---------- inst/doc/sig_diffs_explanation.html | 20 ++++++++++---------- inst/doc/significance_brackets.html | 10 +++++----- man/geom_forestpoint.Rd | 5 +++++ man/geom_foreststripe.Rd | 5 +++++ man/geom_foresttable.Rd | 5 +++++ 12 files changed, 81 insertions(+), 55 deletions(-)
Title: Classification with Mixture Modelling
Description: Interface of 'MIXMOD' software for supervised, unsupervised and
semi-supervised classification with mixture modelling <doi: 10.18637/jss.v067.i06>.
Author: Florent Langrognet [aut],
Remi Lebret [aut],
Christian Poli [aut],
Serge Iovleff [aut],
Benjamin Auder [aut],
Parmeet Bhatia [ctb],
Anwuli Echenim [ctb],
Christophe Biernacki [ctb],
Gilles Celeux [ctb],
Gerard Govaert [ctb],
Julien Schueller [ctb],
Q [...truncated...]
Maintainer: Quentin Grimonprez <quentingrim@yahoo.fr>
Diff between Rmixmod versions 2.1.10 dated 2023-12-13 and 2.1.12 dated 2026-08-28
DESCRIPTION | 10 MD5 | 119 +- R/Mixmod.R | 451 +++++----- R/MixmodResults.R | 23 R/Strategy.R | 2 configure | 24 man/Rmixmod-package.Rd | 7 man/extract-methods.Rd | 60 - man/initialize-methods.Rd | 14 man/mixmodStrategy.Rd | 2 src/Makevars.in | 8 src/Makevars.win | 10 src/mixmod/Clustering/ClusteringMain.cpp | 11 src/mixmod/Clustering/ClusteringOutput.cpp | 54 - src/mixmod/Clustering/ClusteringStrategy.cpp | 8 src/mixmod/Clustering/ClusteringStrategyInit.cpp | 24 src/mixmod/DiscriminantAnalysis/Learn/LearnOutput.cpp | 54 - src/mixmod/DiscriminantAnalysis/Predict/PredictOutput.cpp | 50 - src/mixmod/Kernel/Algo/Algo.cpp | 2 src/mixmod/Kernel/Algo/CEMAlgo.cpp | 4 src/mixmod/Kernel/Algo/EMAlgo.cpp | 6 src/mixmod/Kernel/Algo/MAPAlgo.cpp | 2 src/mixmod/Kernel/Algo/MAlgo.cpp | 2 src/mixmod/Kernel/Algo/SEMAlgo.cpp | 8 src/mixmod/Kernel/Criterion/CVCriterion.cpp | 34 src/mixmod/Kernel/Criterion/CriterionOutput.cpp | 2 src/mixmod/Kernel/IO/BinaryData.cpp | 42 src/mixmod/Kernel/IO/GaussianData.cpp | 8 src/mixmod/Kernel/IO/Input.cpp | 2 src/mixmod/Kernel/IO/Label.cpp | 4 src/mixmod/Kernel/IO/Partition.cpp | 8 src/mixmod/Kernel/IO/ProbaOutput.cpp | 2 src/mixmod/Kernel/Model/Model.cpp | 74 - src/mixmod/Kernel/Parameter/BinaryEParameter.cpp | 8 src/mixmod/Kernel/Parameter/BinaryEjParameter.cpp | 6 src/mixmod/Kernel/Parameter/BinaryEkParameter.cpp | 6 src/mixmod/Kernel/Parameter/BinaryEkjParameter.cpp | 18 src/mixmod/Kernel/Parameter/BinaryEkjhParameter.cpp | 4 src/mixmod/Kernel/Parameter/BinaryParameter.cpp | 24 src/mixmod/Kernel/Parameter/CompositeParameter.cpp | 8 src/mixmod/Kernel/Parameter/GaussianEDDAParameter.cpp | 24 src/mixmod/Kernel/Parameter/GaussianGeneralParameter.cpp | 2 src/mixmod/Kernel/Parameter/GaussianHDDAParameter.cpp | 68 - src/mixmod/Kernel/Parameter/GaussianParameter.cpp | 2 src/mixmod/Kernel/Parameter/GaussianSphericalParameter.cpp | 8 src/mixmod/Kernel/Parameter/Parameter.cpp | 4 src/mixmod/Matrix/DiagMatrix.cpp | 2 src/mixmod/Matrix/SymmetricMatrix.cpp | 4 src/mixmod/Utilities/OutputAdapter.h |only src/mixmod/Utilities/Random.cpp | 12 src/mixmod/Utilities/Util.cpp | 14 src/mixmod/Utilities/Util.h | 1 src/mixmod/Utilities/exceptions/DCVException.h | 2 src/mixmod/Utilities/exceptions/DCVonlyInGaussianCaseException.h | 2 src/mixmod/Utilities/exceptions/Exception.h | 4 src/mixmod/Utilities/exceptions/InputException.h | 2 src/mixmod/Utilities/exceptions/NumericException.h | 2 src/mixmod/Utilities/exceptions/OtherException.h | 2 src/mixmod/Utilities/maths/Eigen.h | 8 src/mixmod_iostream/IOStreamUtil.cpp | 35 src/mixmod_iostream/NodeOpInput.cpp | 2 61 files changed, 706 insertions(+), 699 deletions(-)
Title: Lean Analytics and Robust Exploration Sidekick
Description: Auxiliary package for better/faster analytics, visualization, data mining, and machine
learning tasks. With a wide variety of family functions, like Machine Learning, Data Wrangling,
Marketing Mix Modeling (Robyn), Exploratory, API, and Scrapper, it helps the analyst or
data scientist to get quick and robust results, without the need of repetitive coding or
advanced R programming skills.
Author: Bernardo Lares [aut, cre]
Maintainer: Bernardo Lares <laresbernardo@gmail.com>
Diff between lares versions 5.4.0 dated 2026-04-23 and 5.4.1 dated 2026-08-28
DESCRIPTION | 8 MD5 | 368 ++++++++++++------------- NAMESPACE | 592 +++++++++++++++++++++-------------------- R/confidence.R | 8 R/correlations.R | 6 R/google_sheets.R | 74 ++--- R/lares.R | 61 ++-- R/onehotencoding.R | 2 R/stocks.R | 2 R/utils_data.R | 50 ++- R/utils_system.R | 14 R/wrangling.R | 6 inst/doc/api-integrations.html | 4 inst/doc/data-wrangling.html | 22 - inst/doc/games.html | 4 inst/doc/machine-learning.html | 102 +++---- inst/doc/robyn_lares.html | 4 man/ROC.Rd | 38 +- man/autoline.Rd | 74 ++--- man/balance_data.Rd | 46 +-- man/bind_files.Rd | 74 ++--- man/bring_api.Rd | 100 +++--- man/cal_split.Rd | 74 ++--- man/categ_reducer.Rd | 46 +-- man/chr2num.Rd | 74 ++--- man/ci_lower.Rd | 4 man/ci_var.Rd | 4 man/clean_text.Rd | 64 ++-- man/clusterKmeans.Rd | 10 man/clusterOptimalK.Rd | 10 man/clusterVisualK.Rd | 10 man/conf_mat.Rd | 38 +- man/corr.Rd | 16 - man/corr_cross.Rd | 16 - man/corr_var.Rd | 34 +- man/crosstab.Rd | 28 - man/dalex_local.Rd | 8 man/dalex_residuals.Rd | 8 man/dalex_variable.Rd | 8 man/date_cuts.Rd | 46 +-- man/date_feats.Rd | 60 ++-- man/db_download.Rd | 98 +++--- man/db_upload.Rd | 98 +++--- man/df_str.Rd | 28 - man/dfr.Rd | 2 man/dft.Rd | 2 man/dist2d.Rd | 10 man/distr.Rd | 48 +-- man/dont_sleep.Rd | 74 ++--- man/encrypt_file.Rd | 20 - man/errors.Rd | 12 man/etf_sector.Rd | 10 man/export_plot.Rd | 74 ++--- man/export_results.Rd | 100 +++--- man/fb_accounts.Rd | 42 +- man/fb_ads.Rd | 42 +- man/fb_creatives.Rd | 42 +- man/fb_insights.Rd | 42 +- man/fb_process.Rd | 42 +- man/fb_report_check.Rd | 42 +- man/fb_rf.Rd | 42 +- man/fb_token.Rd | 42 +- man/file_name.Rd | 70 +--- man/filesGD.Rd | 24 - man/files_functions.Rd | 74 ++--- man/filterdata.Rd | 94 +----- man/font_exists.Rd | 74 ++--- man/forecast_arima.Rd | 4 man/formatColoured.Rd | 74 ++--- man/format_string.Rd | 120 ++++---- man/freqs.Rd | 56 +-- man/freqs_df.Rd | 56 +-- man/freqs_list.Rd | 56 +-- man/freqs_plot.Rd | 56 +-- man/gain_lift.Rd | 38 +- man/gemini_ask.Rd | 32 +- man/get_credentials.Rd | 20 - man/get_tweets.Rd | 20 - man/gg_fill_customs.Rd | 8 man/glued.Rd | 74 ++--- man/google_sheets.Rd | 24 - man/google_trends.Rd | 24 - man/gpt_ask.Rd | 36 +- man/gpt_prompter.Rd | 10 man/grepm.Rd | 74 ++--- man/h2o_automl.Rd | 26 - man/h2o_explainer.Rd | 8 man/h2o_predict.Rd | 26 - man/h2o_selectmodel.Rd | 100 +++--- man/h2o_shap.Rd | 4 man/haveInternet.Rd | 74 ++--- man/holidays.Rd | 78 ++--- man/image_metadata.Rd | 74 ++--- man/importxlsx.Rd | 74 ++--- man/impute.Rd | 76 ++--- man/ip_data.Rd | 103 +++---- man/iter_seeds.Rd | 26 - man/json2vector.Rd | 74 ++--- man/lares_pal.Rd | 8 man/lasso_vars.Rd | 54 +-- man/left_right.Rd | 46 +-- man/list_cats.Rd | 74 ++--- man/listfiles.Rd | 74 ++--- man/loglossBinary.Rd | 12 man/mail_send.Rd | 94 +++--- man/markdown2df.Rd | 74 ++--- man/maze_solve.Rd | 8 man/missingness.Rd | 32 +- man/model_metrics.Rd | 48 +-- man/model_preprocess.Rd | 26 - man/move_files.Rd | 74 ++--- man/mp3_get.Rd | 22 - man/mp3_trim.Rd | 6 man/mp3_update_tags.Rd | 6 man/mplot_conf.Rd | 26 - man/mplot_cuts.Rd | 26 - man/mplot_cuts_error.Rd | 26 - man/mplot_density.Rd | 26 - man/mplot_full.Rd | 26 - man/mplot_gain.Rd | 26 - man/mplot_importance.Rd | 26 - man/mplot_lineal.Rd | 26 - man/mplot_metrics.Rd | 26 - man/mplot_response.Rd | 26 - man/mplot_roc.Rd | 26 - man/mplot_splits.Rd | 26 - man/mplot_topcats.Rd | 26 - man/msplit.Rd | 100 +++--- man/myip.Rd | 76 ++--- man/ngrams.Rd | 18 - man/noPlot.Rd | 20 - man/normalize.Rd | 46 +-- man/num_abbr.Rd | 46 +-- man/ohe_commas.Rd | 54 +-- man/ohse.Rd | 60 ++-- man/outlier_tukey.Rd | 8 man/outlier_zscore.Rd | 8 man/outlier_zscore_plot.Rd | 8 man/plot_cats.Rd | 28 - man/plot_chord.Rd | 20 - man/plot_df.Rd | 28 - man/plot_nums.Rd | 28 - man/plot_palette.Rd | 8 man/plot_survey.Rd | 20 - man/plot_timeline.Rd | 20 - man/prophesize.Rd | 4 man/quants.Rd | 56 +-- man/queryDB.Rd | 20 - man/queryGA.Rd | 54 +-- man/quiet.Rd | 74 ++--- man/read.file.Rd | 74 ++--- man/reduce_pca.Rd | 14 man/reduce_tsne.Rd | 14 man/remove_stopwords.Rd | 18 - man/replaceall.Rd | 64 ++-- man/replacefactor.Rd | 46 +-- man/robyn_hypsbuilder.Rd | 8 man/robyn_marginal.Rd | 8 man/robyn_modelselector.Rd | 8 man/robyn_performance.Rd | 8 man/scrabble.Rd | 8 man/sentimentBreakdown.Rd | 18 - man/shap_var.Rd | 4 man/slackSend.Rd | 46 +-- man/statusbar.Rd | 74 ++--- man/stocks_hist.Rd | 24 - man/stocks_plots.Rd | 24 - man/stocks_report.Rd | 28 - man/sudoku_solver.Rd | 8 man/textCloud.Rd | 18 - man/textFeats.Rd | 64 ++-- man/textTokenizer.Rd | 64 ++-- man/theme_lares.Rd | 8 man/tic.Rd | 74 ++--- man/topics_rake.Rd | 18 - man/tree_var.Rd | 48 +-- man/try_require.Rd | 74 ++--- man/updateLares.Rd | 74 ++--- man/vector2text.Rd | 46 +-- man/warnifnot.Rd | 74 ++--- man/what_size.Rd | 74 ++--- man/winsorize.Rd | 8 man/wordle.Rd | 8 man/year_month.Rd | 46 +-- man/zerovar.Rd | 46 +-- 185 files changed, 4021 insertions(+), 4009 deletions(-)
Title: Direct Labels for Multicolor Plots
Description: An extensible framework
for automatically placing direct labels onto multicolor 'lattice' or
'ggplot2' plots.
Label positions are described using Positioning Methods
which can be re-used across several different plots.
There are heuristics for examining "trellis" and "ggplot" objects
and inferring an appropriate Positioning Method.
Author: Toby Dylan Hocking [aut, cre]
Maintainer: Toby Dylan Hocking <toby.hocking@r-project.org>
Diff between directlabels versions 2026.4.23 dated 2026-04-23 and 2026.8.27 dated 2026-08-28
DESCRIPTION | 13 ++++----- MD5 | 29 +++++++++++++------- NAMESPACE | 4 ++ NEWS | 4 ++ R/RcppExports.R |only R/isoreg_dp.R |only R/utility.function.R | 48 ++++++--------------------------- build/vignette.rds |binary inst/doc/examples.R | 2 - inst/doc/examples.Rmd | 2 - inst/doc/examples.html | 65 +++++++++++++++++++++++++++++---------------- man/aligned_labels_dp.Rd |only man/isoreg_dp.Rd |only man/qp.labels.Rd | 2 - src |only tests/testthat/test-CRAN.R |only vignettes/examples.Rmd | 2 - 17 files changed, 89 insertions(+), 82 deletions(-)
Title: 'Lifebit' Platform 'API' Client
Description: Interacts with the 'Lifebit' Platform Cohort Browser 'API'
<https://cloudos.lifebit.ai>. Enables schema discovery, table exploration,
and read-only 'SQL' query execution with policy-aware behavior and team-based
access control for cohort data analysis. Requires bastion-enabled workspaces
for 'API' access.
Author: Leila Mansouri [aut, cre]
Maintainer: Leila Mansouri <leila.mansouri@lifebit.ai>
Diff between cloudosR versions 0.2.0 dated 2026-06-01 and 0.2.4 dated 2026-08-28
cloudosR-0.2.0/cloudosR/man/build_query_string.Rd |only cloudosR-0.2.0/cloudosR/man/http_request_with_retry.Rd |only cloudosR-0.2.0/cloudosR/man/paginate_results.Rd |only cloudosR-0.2.4/cloudosR/DESCRIPTION | 11 cloudosR-0.2.4/cloudosR/MD5 | 55 cloudosR-0.2.4/cloudosR/NAMESPACE | 3 cloudosR-0.2.4/cloudosR/NEWS.md | 59 cloudosR-0.2.4/cloudosR/R/config.R | 3 cloudosR-0.2.4/cloudosR/R/http.R | 329 +-- cloudosR-0.2.4/cloudosR/R/query.R | 741 ++++--- cloudosR-0.2.4/cloudosR/R/utils.R | 161 + cloudosR-0.2.4/cloudosR/inst/WORDLIST | 6 cloudosR-0.2.4/cloudosR/inst/doc/getting-started.R | 27 cloudosR-0.2.4/cloudosR/inst/doc/getting-started.Rmd | 33 cloudosR-0.2.4/cloudosR/inst/doc/getting-started.html | 151 - cloudosR-0.2.4/cloudosR/man/cloudos.query.Rd | 21 cloudosR-0.2.4/cloudosR/man/cloudos.query_count.Rd |only cloudosR-0.2.4/cloudosR/man/cloudos.query_count_results.Rd |only cloudosR-0.2.4/cloudosR/man/cloudos.query_results.Rd | 15 cloudosR-0.2.4/cloudosR/man/cloudos.query_submit_async.Rd | 11 cloudosR-0.2.4/cloudosR/man/cloudos.query_submit_count_async.Rd |only cloudosR-0.2.4/cloudosR/man/error_body_text.Rd |only cloudosR-0.2.4/cloudosR/man/extract_error_message.Rd |only cloudosR-0.2.4/cloudosR/man/handle_api_error.Rd | 2 cloudosR-0.2.4/cloudosR/man/http_get_parallel.Rd |only cloudosR-0.2.4/cloudosR/man/parse_json_response.Rd | 5 cloudosR-0.2.4/cloudosR/man/process_response.Rd |only cloudosR-0.2.4/cloudosR/man/resolve_max_parallel.Rd |only cloudosR-0.2.4/cloudosR/man/results_response_to_df.Rd |only cloudosR-0.2.4/cloudosR/man/truncate_error_text.Rd |only cloudosR-0.2.4/cloudosR/tests/testthat/helper-config.R |only cloudosR-0.2.4/cloudosR/tests/testthat/test-config.R | 83 cloudosR-0.2.4/cloudosR/tests/testthat/test-http.R |only cloudosR-0.2.4/cloudosR/tests/testthat/test-query.R | 936 +++++++++- cloudosR-0.2.4/cloudosR/tests/testthat/test-utils.R | 43 cloudosR-0.2.4/cloudosR/vignettes/getting-started.Rmd | 33 36 files changed, 1888 insertions(+), 840 deletions(-)
Title: Climate Exposure Relative to a Species' Climatic Niche
Description: Quantifies projected climatic change relative to the climatic
niche represented by a species' current distribution. A weighted current
reference defines the niche centre and empirical radial boundary. Present
and projected conditions at each location give local climatic displacement,
signed change in niche distance, a derived non-radial reconfiguration term,
and exceedance beyond the niche boundary. Occurrence records, range maps,
and binary or continuous species distribution model outputs can define
reference weights. Matrix and spatial workflows return location-level
values, weighted summaries, maps and climatic-variable contributions.
Author: Bohao He [aut, cre]
Maintainer: Bohao He <bohao.he@polimi.it>
Diff between climniche versions 0.0.1 dated 2026-05-29 and 0.3.8 dated 2026-08-28
climniche-0.0.1/climniche/R/diagram.R |only climniche-0.0.1/climniche/inst/extdata/mediterranean_anchovy/anchovy_clean_obis_records.csv |only climniche-0.0.1/climniche/inst/extdata/mediterranean_anchovy/anchovy_climniche_classes.csv |only climniche-0.0.1/climniche/inst/extdata/mediterranean_anchovy/anchovy_climniche_summary.csv |only climniche-0.0.1/climniche/inst/extdata/mediterranean_anchovy/anchovy_climniche_top_variables.csv |only climniche-0.0.1/climniche/man/climniche_diagram_data.Rd |only climniche-0.0.1/climniche/man/climniche_showcase_data.Rd |only climniche-0.0.1/climniche/man/plot_climniche_class_summary.Rd |only climniche-0.0.1/climniche/man/plot_climniche_classes.Rd |only climniche-0.0.1/climniche/man/plot_climniche_diagram.Rd |only climniche-0.0.1/climniche/man/plot_climniche_showcase.Rd |only climniche-0.0.1/climniche/man/plot_variable_contribution.Rd |only climniche-0.0.1/climniche/vignettes/figures/anchovy-climniche-diagram.png |only climniche-0.0.1/climniche/vignettes/figures/anchovy-climniche-showcase.png |only climniche-0.3.8/climniche/DESCRIPTION | 28 climniche-0.3.8/climniche/LICENSE |only climniche-0.3.8/climniche/MD5 | 175 +- climniche-0.3.8/climniche/NAMESPACE | 70 climniche-0.3.8/climniche/NEWS.md | 162 + climniche-0.3.8/climniche/R/aliases.R | 438 +++-- climniche-0.3.8/climniche/R/classify.R | 139 - climniche-0.3.8/climniche/R/contribution_map.R |only climniche-0.3.8/climniche/R/core.R | 303 ++- climniche-0.3.8/climniche/R/departure.R |only climniche-0.3.8/climniche/R/dynamic_plot.R |only climniche-0.3.8/climniche/R/dynamic_report.R |only climniche-0.3.8/climniche/R/metric.R | 141 + climniche-0.3.8/climniche/R/priority.R |only climniche-0.3.8/climniche/R/range.R |only climniche-0.3.8/climniche/R/raster_workflow.R | 241 +- climniche-0.3.8/climniche/R/reference.R |only climniche-0.3.8/climniche/R/report.R | 495 ++++- climniche-0.3.8/climniche/R/series_fit.R |only climniche-0.3.8/climniche/R/showcase.R | 501 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files changed, 5353 insertions(+), 1549 deletions(-)
Title: Fast, Weighted ROC Curves
Description: Fast computation of
Receiver Operating Characteristic (ROC) curves
and Area Under the Curve (AUC)
for weighted binary classification problems
(weights are example-specific cost values).
Author: Toby Dylan Hocking [cre, aut]
Maintainer: Toby Dylan Hocking <toby.hocking@r-project.org>
Diff between WeightedROC versions 2020.1.31 dated 2020-02-01 and 2026.8.27 dated 2026-08-28
DESCRIPTION | 14 + MD5 | 30 +-- NAMESPACE | 8 NEWS | 128 +++++++------- R/AUC.R | 130 +++++++------- R/ROC.R | 376 +++++++++++++++++++++---------------------- build/vignette.rds |binary inst/doc/Definition.R | 42 ++-- inst/doc/Definition.Rnw | 286 ++++++++++++++++---------------- inst/doc/Definition.pdf |binary man/WeightedAUC.Rd | 122 ++++++------- man/WeightedROC.Rd | 288 ++++++++++++++++---------------- tests/testthat.R | 4 tests/testthat/test-auc.R | 332 ++++++++++++++++++------------------- tests/testthat/test-errors.R | 94 +++++----- vignettes/Definition.Rnw | 286 ++++++++++++++++---------------- 16 files changed, 1074 insertions(+), 1066 deletions(-)
Title: Make Data Based on Different Geographies Comparable
Description: Several functions to allow comparisons of data across different geographies, in particular for Canadian census data from different censuses.
Author: Jens von Bergmann [aut, cre]
Maintainer: Jens von Bergmann <jens@mountainmath.ca>
Diff between tongfen versions 0.3.7 dated 2026-06-05 and 0.3.8 dated 2026-08-28
DESCRIPTION | 6 MD5 | 64 ++-- NAMESPACE | 1 NEWS.md | 63 ++++ R/helpers.R | 262 +++++++++++------ R/tongfen.R | 82 +++-- R/tongfen_ca.R | 104 ++++-- R/tongfen_ca_deprecated.R | 16 - R/tongfen_ca_estimate.R | 4 R/tongfen_estimate.R | 29 - R/tongfen_us.R | 373 +++++++++++++++++++++---- README.md | 4 build/stage23.rdb |binary build/vignette.rds |binary inst/doc/tongfen.html | 6 inst/doc/tongfen_ca.R | 4 inst/doc/tongfen_ca.Rmd | 4 inst/doc/tongfen_ca.html | 12 inst/doc/tongfen_us.R | 21 + inst/doc/tongfen_us.Rmd | 34 ++ inst/doc/tongfen_us.html | 49 +++ man/check_tongfen_areas.Rd | 4 man/get_tongfen_ca_census.Rd | 11 man/get_tongfen_correspondence_ca_census.Rd | 12 man/get_tongfen_correspondence_us_census.Rd |only man/get_tongfen_us_census.Rd | 17 + man/tongfen_aggregate.Rd | 11 tests/testthat/test-aggregate.R | 81 +++++ tests/testthat/test-correspondence-estimate.R |only tests/testthat/test-estimate.R |only tests/testthat/test-helpers.R | 138 +++++++++ tests/testthat/test-proportional-reaggregate.R | 32 ++ tests/testthat/test-us-correspondence.R |only vignettes/tongfen_ca.Rmd | 4 vignettes/tongfen_us.Rmd | 34 ++ 35 files changed, 1167 insertions(+), 315 deletions(-)
Title: Latent Dirichlet Allocation Using 'tidyverse' Conventions
Description: Implements an algorithm for Latent Dirichlet
Allocation (LDA), Blei et al. (2003) <https://www.jmlr.org/papers/volume3/blei03a/blei03a.pdf>,
using style conventions from the 'tidyverse',
Wickham et al. (2019)<doi:10.21105/joss.01686>,
and 'tidymodels', Kuhn et al.<https://tidymodels.github.io/model-implementation-principles/>.
Fitting is done via 'warpLDA', a Metropolis-Hastings sampler,
Chen et al. (2016) <doi:10.48550/arXiv.1510.08628>.
Also implements several novel features for LDA such as guided models and
transfer learning.
Author: Tommy Jones [aut, cre] ,
Brendan Knapp [ctb] ,
Barum Park [ctb]
Maintainer: Tommy Jones <jones.thos.w@gmail.com>
Diff between tidylda versions 0.0.7 dated 2025-11-14 and 0.1.0 dated 2026-08-28
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Title: Stability Assessment of Statistical Learning Methods
Description: Graphical and computational methods that can be used to assess the
stability of results from supervised statistical learning.
Author: Michel Philipp [aut],
Carolin Strobl [aut] ,
Achim Zeileis [aut, cre] ,
Thomas Rusch [aut] ,
Kurt Hornik [aut] ,
Lennart Schneider [aut]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between stablelearner versions 0.1-8 dated 2026-07-30 and 0.1-9 dated 2026-08-28
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NAMESPACE | 10 +++++++++- NEWS.md | 8 ++++++++ R/stabletree-coercion.R | 2 +- R/stabletree.R | 2 +- inst/doc/forests.html | 4 ++-- man/stabletree-coercion.Rd | 2 +- 8 files changed, 33 insertions(+), 17 deletions(-)
Title: Humane Interface to Amazon Web Services
Description: An opinionated interface to Amazon Web Services <https://aws.amazon.com>,
with functions for interacting with 'IAM' (Identity and Access Management),
'S3' (Simple Storage Service), 'RDS' (Relational Data Service), Redshift, and Billing.
Lower level functions ('aws_' prefix) are for do it yourself workflows, while
higher level functions ('six_' prefix) automate common tasks.
Author: Sean Kross [aut],
Scott Chamberlain [aut, cre] ,
Fred Hutchinson Cancer Center [fnd]
Maintainer: Scott Chamberlain <sachamber@fredhutch.org>
Diff between sixtyfour versions 0.2.0 dated 2025-03-31 and 0.2.4 dated 2026-08-28
DESCRIPTION | 28 ++- LICENSE | 2 MD5 | 242 +++++++++++++++++----------------- NAMESPACE | 158 ++++++++++++---------- NEWS.md | 4 R/clients.R | 17 ++ R/configure.R | 3 R/database-misc.R | 4 R/database-rds.R | 13 + R/database-redshift.R | 7 R/internal.R | 2 R/policies.R | 8 - R/s3.R | 9 - R/secrets_manager.R | 16 +- R/sixtyfour-package.R | 1 R/users.R | 4 R/utils.R | 4 R/vpc_security_groups.R | 8 - R/wait.R | 4 README.md | 4 build/vignette.rds |binary inst/doc/contributing.Rmd | 6 inst/doc/contributing.html | 10 - man/as_policy_arn.Rd | 26 +-- man/aws_billing.Rd | 6 man/aws_billing_raw.Rd | 6 man/aws_bucket_create.Rd | 22 +-- man/aws_bucket_delete.Rd | 22 +-- man/aws_bucket_download.Rd | 24 +-- man/aws_bucket_exists.Rd | 22 +-- man/aws_bucket_list_objects.Rd | 22 +-- man/aws_bucket_tree.Rd | 22 +-- man/aws_bucket_upload.Rd | 24 +-- man/aws_buckets.Rd | 22 +-- man/aws_db_cluster_status.Rd | 14 - man/aws_db_instance_status.Rd | 14 - man/aws_db_rds_con.Rd | 14 - man/aws_db_rds_create.Rd | 14 - man/aws_db_rds_list.Rd | 16 +- man/aws_db_redshift_con.Rd | 16 +- man/aws_db_redshift_create.Rd | 14 - man/aws_file_attr.Rd | 20 +- man/aws_file_copy.Rd | 18 +- man/aws_file_delete.Rd | 18 +- man/aws_file_download.Rd | 20 +- man/aws_file_exists.Rd | 18 +- man/aws_file_rename.Rd | 18 +- man/aws_file_upload.Rd | 18 +- man/aws_group.Rd | 14 - man/aws_group_create.Rd | 14 - man/aws_group_delete.Rd | 14 - man/aws_group_exists.Rd | 14 - man/aws_groups.Rd | 14 - man/aws_policies.Rd | 28 +-- man/aws_policy.Rd | 26 +-- man/aws_policy_attach.Rd | 26 +-- man/aws_policy_create.Rd | 26 +-- man/aws_policy_delete.Rd | 26 +-- man/aws_policy_delete_version.Rd | 26 +-- man/aws_policy_detach.Rd | 26 +-- man/aws_policy_document_create.Rd | 2 man/aws_policy_exists.Rd | 26 +-- man/aws_policy_list_entities.Rd | 26 +-- man/aws_policy_list_versions.Rd | 26 +-- man/aws_policy_update.Rd | 26 +-- man/aws_role.Rd | 12 - man/aws_role_create.Rd | 12 - man/aws_role_delete.Rd | 12 - man/aws_role_exists.Rd | 12 - man/aws_roles.Rd | 12 - man/aws_secrets_all.Rd | 2 man/aws_secrets_create.Rd | 2 man/aws_secrets_delete.Rd | 2 man/aws_secrets_get.Rd | 2 man/aws_secrets_list.Rd | 2 man/aws_secrets_pwd.Rd | 2 man/aws_secrets_rotate.Rd | 2 man/aws_secrets_update.Rd | 2 man/aws_user.Rd | 24 +-- man/aws_user_access_key.Rd | 22 +-- man/aws_user_access_key_delete.Rd | 22 +-- man/aws_user_add_to_group.Rd | 24 +-- man/aws_user_create.Rd | 24 +-- man/aws_user_current.Rd | 22 +-- man/aws_user_delete.Rd | 24 +-- man/aws_user_exists.Rd | 24 +-- man/aws_users.Rd | 24 +-- man/aws_vpc_sec_group_rules_mod.Rd | 14 - man/aws_vpc_security_group.Rd | 12 - man/aws_vpc_security_group_create.Rd | 12 - man/aws_vpc_security_group_ingress.Rd | 12 - man/aws_vpc_security_groups.Rd | 14 - man/aws_vpc_sg_with_ingress.Rd | 12 - man/aws_vpcs.Rd | 2 man/con_iam.Rd | 2 man/con_s3fs.Rd | 2 man/figure_out_policy_arn.Rd | 2 man/reexports.Rd | 4 man/six_admin_setup.Rd | 12 - man/six_bucket_add_user.Rd | 2 man/six_bucket_change_user.Rd | 2 man/six_bucket_delete.Rd | 34 ++-- man/six_bucket_permissions.Rd | 2 man/six_bucket_remove_user.Rd | 2 man/six_bucket_upload.Rd | 34 ++-- man/six_file_upload.Rd | 34 ++-- man/six_group_delete.Rd | 14 - man/six_user_create.Rd | 36 ++--- man/six_user_creds.Rd | 2 man/six_user_delete.Rd | 36 ++--- man/sixtyfour-package.Rd | 3 tests/testthat/helper-vcr.R | 1 tests/testthat/test-buckets.R | 12 + tests/testthat/test-db-rds.R | 2 tests/testthat/test-db-redshift.R | 2 tests/testthat/test-files.R | 28 ++- tests/testthat/test-policies.R | 9 - tests/testthat/test-s3.R | 21 -- tests/testthat/test-users.R | 3 tests/testthat/test-utils.R | 16 +- tests/testthat/test-vpc.R | 8 - vignettes/contributing.Rmd | 6 122 files changed, 1083 insertions(+), 976 deletions(-)
Title: Sequential Trial Emulation
Description: Implementation of sequential trial emulation for the analysis of observational databases.
The 'SEQTaRget' software accommodates time-varying treatments and confounders, as well as binary
and failure time outcomes. 'SEQTaRget' allows to compare both static and dynamic strategies,
can be used to estimate observational analogs of intention-to-treat
and per-protocol effects, and can adjust for potential selection bias
induced by losses-to-follow-up. (Paper to come).
Author: Ryan O'Dea [aut, cre] ,
Tom Palmer [aut] ,
Paul Madley-Dowd [aut] ,
Alejandro Szmulewicz [aut] ,
Miguel A. Hernan [aut] ,
The President and Fellows of Harvard College [cph]
Maintainer: Ryan O'Dea <ryan.odea@psi.ch>
Diff between SEQTaRget versions 1.4.3 dated 2026-06-23 and 1.4.4 dated 2026-08-28
DESCRIPTION | 28 ++-- MD5 | 88 ++++++++----- NAMESPACE | 63 +++++---- NEWS.md | 6 R/SEQexpand.R | 10 + R/SEQopts.R | 27 +++- R/SEQuential.R | 94 ++++++++++++-- R/class_definitions.R | 16 ++ R/class_methods.R | 130 +++++++++++++++++--- R/class_setters.R | 48 ++++++- R/internal_analysis.R | 68 ++++++++-- R/internal_endoffup.R |only R/internal_glmHelpers.R | 19 ++ R/internal_misc.R | 10 + R/internal_weights.R | 2 README.md | 2 build/vignette.rds |binary inst/doc/ITT.R | 5 inst/doc/ITT.Rmd | 5 inst/doc/ITT.html | 191 +++++++++++++++--------------- inst/doc/SEQuential.R | 1 inst/doc/SEQuential.Rmd | 1 inst/doc/SEQuential.html | 177 +++++++++++++-------------- inst/doc/doseresponse.R | 5 inst/doc/doseresponse.Rmd | 5 inst/doc/doseresponse.html | 191 +++++++++++++++--------------- inst/doc/endoffollowup.R |only inst/doc/endoffollowup.Rmd |only inst/doc/endoffollowup.html |only inst/doc/seqopts.Rmd | 4 inst/doc/seqopts.html | 35 +++++ man/SEQTaRget-package.Rd | 4 man/SEQopts.Rd | 16 ++ man/SEQoutput-class.Rd | 6 man/SEQuential.Rd | 22 +++ man/cached_cols.Rd |only man/clean_models.Rd |only man/create.endoffup.Rd |only man/diagnostics.Rd | 16 ++ man/end_of_fup.Rd |only man/endoffup.counts.Rd |only man/endoffup.estimate.Rd |only man/endoffup.measure.Rd |only man/endoffup.summary.Rd |only man/prepare.output.Rd | 4 man/select_cached_level.Rd |only tests/testthat/test_armspecific_weights.R |only tests/testthat/test_end_of_fup.R |only vignettes/ITT.Rmd | 5 vignettes/SEQuential.Rmd | 1 vignettes/doseresponse.Rmd | 5 vignettes/endoffollowup.Rmd |only vignettes/seqopts.Rmd | 4 53 files changed, 891 insertions(+), 423 deletions(-)
Title: Wrapper for 'run_example()'
Description: Captures errors or missing examples encountered when iteratively running 'run_examplez()', and archives them.
Author: Barry Zeeberg [aut, cre]
Maintainer: Barry Zeeberg <barryz2013@gmail.com>
Diff between runExamplesWrapper versions 1.1 dated 2026-01-16 and 2.0 dated 2026-08-28
runExamplesWrapper-1.1/runExamplesWrapper/R/runExamplesWrapper.R |only runExamplesWrapper-1.1/runExamplesWrapper/man/RunExamples.Rd |only runExamplesWrapper-1.1/runExamplesWrapper/man/balanceCurly.Rd |only runExamplesWrapper-1.1/runExamplesWrapper/man/parseRunExamples.Rd |only runExamplesWrapper-1.1/runExamplesWrapper/man/retrieveExamplesFromMan.Rd |only runExamplesWrapper-1.1/runExamplesWrapper/man/retrieveMan.Rd |only runExamplesWrapper-1.1/runExamplesWrapper/man/startExample.Rd |only runExamplesWrapper-2.0/runExamplesWrapper/DESCRIPTION | 16 +-- runExamplesWrapper-2.0/runExamplesWrapper/MD5 | 24 ++--- runExamplesWrapper-2.0/runExamplesWrapper/NAMESPACE | 10 -- runExamplesWrapper-2.0/runExamplesWrapper/R/run_example.R |only runExamplesWrapper-2.0/runExamplesWrapper/build/vignette.rds |binary runExamplesWrapper-2.0/runExamplesWrapper/inst/doc/runExamplesWrapper.Rmd | 23 ++--- runExamplesWrapper-2.0/runExamplesWrapper/inst/doc/runExamplesWrapper.html | 45 ++++------ runExamplesWrapper-2.0/runExamplesWrapper/man/runExamplesWrapper.Rd |only runExamplesWrapper-2.0/runExamplesWrapper/man/run_examplez.Rd |only runExamplesWrapper-2.0/runExamplesWrapper/vignettes/Figure1.jpg |binary runExamplesWrapper-2.0/runExamplesWrapper/vignettes/runExamplesWrapper.Rmd | 23 ++--- 18 files changed, 58 insertions(+), 83 deletions(-)
More information about runExamplesWrapper at CRAN
Permanent link
Title: Hypothesis Tests for Quantiles and Quantile-Based Measures
Description: Functions to conduct hypothesis tests and derive confidence intervals
for quantiles, linear combinations of quantiles,
ratios of dependent linear combinations and differences
and ratios of all of the above for comparisons between independent samples.
Additionally, quantile-based measures of inequality are also considered.
Author: Shenal Dedduwakumara [aut, cre],
Luke Prendergast [aut],
Robert Staudte [aut]
Maintainer: Shenal Dedduwakumara <shenal.dedduwakumara@adelaide.edu.au>
Diff between rquest versions 1.0.5 dated 2025-06-11 and 1.1.0 dated 2026-08-28
rquest-1.0.5/rquest/R/R.R |only rquest-1.0.5/rquest/R/qor.ln.R |only rquest-1.1.0/rquest/DESCRIPTION | 8 rquest-1.1.0/rquest/MD5 | 43 - rquest-1.1.0/rquest/NAMESPACE | 9 rquest-1.1.0/rquest/NEWS.md | 20 rquest-1.1.0/rquest/R/get.coefs.R |only rquest-1.1.0/rquest/R/q.test.R | 44 - rquest-1.1.0/rquest/R/qcov.R | 98 +-- rquest-1.1.0/rquest/R/qden.R |only rquest-1.1.0/rquest/R/qineq.R | 175 ++++- rquest-1.1.0/rquest/R/qor.R |only rquest-1.1.0/rquest/R/qrcov.R |only rquest-1.1.0/rquest/R/rcv.test.R |only rquest-1.1.0/rquest/R/rquest-package.R | 14 rquest-1.1.0/rquest/README.md | 488 +++++++++++++-- rquest-1.1.0/rquest/man/q.test.Rd | 18 rquest-1.1.0/rquest/man/qcov.Rd | 55 + rquest-1.1.0/rquest/man/qden.Rd |only rquest-1.1.0/rquest/man/qineq.Rd | 50 + rquest-1.1.0/rquest/man/qor.Rd |only rquest-1.1.0/rquest/man/qrcov.Rd |only rquest-1.1.0/rquest/man/rcv.test.Rd |only rquest-1.1.0/rquest/tests/testthat/test-q.test.R | 643 +++++++++++++++++---- rquest-1.1.0/rquest/tests/testthat/test-qcov.R | 111 +++ rquest-1.1.0/rquest/tests/testthat/test-qden.R |only rquest-1.1.0/rquest/tests/testthat/test-qineq.R | 203 ++++++ rquest-1.1.0/rquest/tests/testthat/test-qor.R |only rquest-1.1.0/rquest/tests/testthat/test-qrcov.R |only rquest-1.1.0/rquest/tests/testthat/test-rcv.test.R |only 30 files changed, 1591 insertions(+), 388 deletions(-)
Title: Random Hazard Forests
Description: Random Hazard Forests (RHF) extend Random Survival
Forests (RSF) by directly estimating the hazard function and by
accommodating time-dependent covariates through counting-process
style inputs. The package fits tree ensembles for dynamic survival
prediction, returning hazard, cumulative hazard, integrated hazard,
and related performance summaries for training and test data. The
methods build on Random Survival Forests described by Ishwaran et
al. (2008) <doi:10.1214/08-AOAS169> and on nonparametric hazard
modeling with time-dependent covariates described by Lee et
al. (2021) <doi:10.1214/20-AOS2028>.
Author: Hemant Ishwaran [aut],
Udaya B. Kogalur [aut, cre]
Maintainer: Udaya B. Kogalur <ubk@kogalur.com>
Diff between randomForestRHF versions 1.0.1 dated 2026-04-28 and 2.0.0 dated 2026-08-28
DESCRIPTION | 8 MD5 | 104 ++-- NAMESPACE | 2 NEWS.md | 11 R/auct.rhf.R | 506 ++++++++++++++++++++-- R/importance.rhf_plot.R | 885 +++++++++++++++++++++++++++++++++------- R/plot.rhf.R | 14 R/predict.rhf.R | 32 + R/predict.rhf.workhorse.R | 244 ++++++++++- R/print.rhf.R | 13 R/rhf.R | 12 R/rhf.workhorse.R | 197 ++++++++ R/tune.treesize.rhf.R | 369 ++++++++++++++-- R/utilities_additional.R | 497 ++++++++++++++++------ R/utilities_hazard_simulation.R | 637 +++++++++++++++++++--------- R/utilities_importance.R | 101 ++++ R/utilities_importance_plot.R | 740 +++++++++++++++++++++++++++------ R/utilities_lot.R | 20 R/utilities_tdc.R | 680 +++++++++++++++++++++++++++--- man/auct.rhf.Rd | 14 man/importance.rhf.Rd | 285 +++++++++--- man/plot.rhf.Rd | 6 man/predict.rhf.Rd | 59 ++ man/rhf.Rd | 219 ++++++--- man/tune.treesize.rhf.Rd | 56 ++ man/utilities_internal.Rd | 10 src/Makevars | 1 src/Makevars.win | 1 src/R_init_randomForestRHF.c | 9 src/entry.c | 55 ++ src/entry.h | 4 src/entryGeneric.c | 3 src/external.h | 21 src/internal.c | 21 src/medianLogStitchedHazard.c | 24 - src/processEnsemble.c | 345 ++++++++++++--- src/processEnsemble.h | 7 src/processEnsembleCOE.c |only src/processEnsembleCOE.h |only src/rhfMain.c | 130 +++++ src/sexpOutgoing.c | 14 src/sexpOutgoing.h | 24 - src/shared/stackForestObjects.c | 2 src/splitTDC.c | 42 - src/stackOutput.c | 112 ++++- src/stackOutputQQ.c | 103 ++++ src/stackOutputQQ.h | 19 src/survivalTDC.c | 163 +++++++ src/survivalTDC.h | 1 src/termOps.c | 33 + src/termOps.h | 2 src/terminal.h | 4 src/treeOps.c | 35 + src/weightedStitchedHazard.c | 26 - 54 files changed, 5662 insertions(+), 1260 deletions(-)
More information about randomForestRHF at CRAN
Permanent link
Title: Proportional Apportionment
Description: Calculate seat apportionment for legislative bodies with
various methods. The algorithms include divisor or highest averages methods
(e.g. Jefferson, Webster or Adams), largest remainder methods and
biproportional apportionment.
Gaffke, N. & Pukelsheim, F. (2008) <doi:10.1016/j.mathsocsci.2008.01.004>
Oelbermann, K. F. (2016) <doi:10.1016/j.mathsocsci.2016.02.003>.
Author: Flavio Poletti [aut, cre, cph]
Maintainer: Flavio Poletti <flavio.poletti@hotmail.ch>
Diff between proporz versions 1.5.2 dated 2025-10-10 and 1.5.3 dated 2026-08-28
proporz-1.5.2/proporz/inst/bazi |only proporz-1.5.2/proporz/man/proporz_methods.Rd |only proporz-1.5.3/proporz/DESCRIPTION | 8 proporz-1.5.3/proporz/MD5 | 150 +-- proporz-1.5.3/proporz/NAMESPACE | 4 proporz-1.5.3/proporz/NEWS.md | 7 proporz-1.5.3/proporz/R/S3.R | 34 proporz-1.5.3/proporz/R/bazi.R |only proporz-1.5.3/proporz/R/biproportional-check.R | 103 +- proporz-1.5.3/proporz/R/biproportional-divisors.R | 8 proporz-1.5.3/proporz/R/biproportional-lower.R | 94 +- proporz-1.5.3/proporz/R/biproportional-upper.R | 49 - proporz-1.5.3/proporz/R/biproportional-wto.R | 17 proporz-1.5.3/proporz/R/biproportional.R | 49 - proporz-1.5.3/proporz/R/data.R | 9 proporz-1.5.3/proporz/R/divisor-check.R | 21 proporz-1.5.3/proporz/R/divisor_methods.R | 34 proporz-1.5.3/proporz/R/matrix.R | 9 proporz-1.5.3/proporz/R/proporz.R | 31 proporz-1.5.3/proporz/R/quorum.R | 116 +- proporz-1.5.3/proporz/R/quota_methods.R | 5 proporz-1.5.3/proporz/R/round.R | 20 proporz-1.5.3/proporz/R/shinyapp.R | 439 ++++++---- proporz-1.5.3/proporz/R/utils.R | 53 + proporz-1.5.3/proporz/README.md | 4 proporz-1.5.3/proporz/build/vignette.rds |binary proporz-1.5.3/proporz/inst/doc/apportionment_scenarios.R | 14 proporz-1.5.3/proporz/inst/doc/apportionment_scenarios.Rmd | 14 proporz-1.5.3/proporz/inst/doc/apportionment_scenarios.html | 25 proporz-1.5.3/proporz/inst/doc/modifying_biproporz.R | 3 proporz-1.5.3/proporz/inst/doc/modifying_biproporz.Rmd | 26 proporz-1.5.3/proporz/inst/doc/modifying_biproporz.html | 93 +- proporz-1.5.3/proporz/inst/run_additional_tests.R |only proporz-1.5.3/proporz/inst/test-bazi |only proporz-1.5.3/proporz/man/apply_quorum.Rd | 15 proporz-1.5.3/proporz/man/biproporz.Rd | 37 proporz-1.5.3/proporz/man/ceil_at.Rd | 8 proporz-1.5.3/proporz/man/district_winner_matrix.Rd | 5 proporz-1.5.3/proporz/man/divide_votes_matrix.Rd | 12 proporz-1.5.3/proporz/man/divisor_methods.Rd | 9 proporz-1.5.3/proporz/man/figures/shinyapp-example.gif |binary proporz-1.5.3/proporz/man/find_divisor.Rd | 15 proporz-1.5.3/proporz/man/find_matrix_divisors.Rd | 9 proporz-1.5.3/proporz/man/get_divisors.Rd | 6 proporz-1.5.3/proporz/man/highest_averages_method.Rd | 9 proporz-1.5.3/proporz/man/largest_remainder_method.Rd | 9 proporz-1.5.3/proporz/man/lower_apportionment.Rd | 6 proporz-1.5.3/proporz/man/pivot_to_matrix.Rd | 9 proporz-1.5.3/proporz/man/proporz.Rd | 9 proporz-1.5.3/proporz/man/pukelsheim.Rd | 19 proporz-1.5.3/proporz/man/quorum_functions.Rd | 22 proporz-1.5.3/proporz/man/reached_quorum_any_district.Rd | 4 proporz-1.5.3/proporz/man/reached_quorum_total.Rd | 4 proporz-1.5.3/proporz/man/reached_quorums.Rd | 21 proporz-1.5.3/proporz/man/read_bazi.Rd |only proporz-1.5.3/proporz/man/run_app.Rd | 11 proporz-1.5.3/proporz/man/upper_apportionment.Rd | 14 proporz-1.5.3/proporz/man/uri2020.Rd | 6 proporz-1.5.3/proporz/man/weight_votes_matrix.Rd | 17 proporz-1.5.3/proporz/man/zug2018.Rd | 4 proporz-1.5.3/proporz/tests/testthat/data |only proporz-1.5.3/proporz/tests/testthat/helper.R |only proporz-1.5.3/proporz/tests/testthat/test-biproportional-data.R | 6 proporz-1.5.3/proporz/tests/testthat/test-biproportional-errors.R | 39 proporz-1.5.3/proporz/tests/testthat/test-biproportional.R | 49 - proporz-1.5.3/proporz/tests/testthat/test-divisor.R | 10 proporz-1.5.3/proporz/tests/testthat/test-fuzzy.R |only proporz-1.5.3/proporz/tests/testthat/test-proporz-parameters.R | 34 proporz-1.5.3/proporz/tests/testthat/test-proporz.R | 18 proporz-1.5.3/proporz/tests/testthat/test-quorum.R | 37 proporz-1.5.3/proporz/tests/testthat/test-read_bazi.R |only proporz-1.5.3/proporz/tests/testthat/test-round.R | 12 proporz-1.5.3/proporz/tests/testthat/test-shiny.R |only proporz-1.5.3/proporz/tests/testthat/test-utils.R | 2 proporz-1.5.3/proporz/vignettes/apportionment_scenarios.Rmd | 14 proporz-1.5.3/proporz/vignettes/modifying_biproporz.Rmd | 26 76 files changed, 1220 insertions(+), 746 deletions(-)
Title: Paginate the HTML Output of R Markdown with CSS for Print
Description: Use the paged media properties in CSS and the JavaScript
library 'paged.js' to split the content of an HTML document into discrete
pages. Each page can have its page size, page numbers, margin boxes, and
running headers, etc. Applications of this package include books, letters,
reports, papers, business cards, resumes, and posters.
Author: Yihui Xie [aut, cre] ,
Romain Lesur [aut, cph] ,
Christophe Dervieux [ctb] ,
Brent Thorne [aut] ,
Xianying Tan [aut] ,
Atsushi Yasumoto [ctb] ,
Posit Software, PBC [cph, fnd],
Adam Hyde [ctb] ,
Min-Zhong Lu [ctb] ,
Zulko [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between pagedown versions 0.24 dated 2026-04-09 and 0.25 dated 2026-08-28
DESCRIPTION | 6 +++--- LICENSE | 2 +- MD5 | 14 +++++++------- NEWS.md | 6 ++++++ R/chrome.R | 10 ++++++++-- README.md | 2 +- inst/resources/lua/loft.lua | 29 ++++++++++++++++++++++++++++- tests/test-ci/test-chrome.R | 19 +++++++++++++++---- 8 files changed, 69 insertions(+), 19 deletions(-)
Title: Information Bottleneck Methods for Clustering Mixed-Type Data
Description: Implements multiple variants of the Information Bottleneck ('IB') method
for clustering datasets containing continuous, categorical (nominal/ordinal) and mixed-type variables.
The package provides deterministic, agglomerative, generalised,
sequential, and standard IB clustering algorithms that preserve relevant information while
forming interpretable clusters. The Deterministic Information Bottleneck is described in
Costa et al. (2026) <doi:10.1016/j.patcog.2026.113580>. The standard IB method
originates from Tishby et al. (2000) <doi:10.48550/arXiv.physics/0004057>,
the agglomerative variant from Slonim and Tishby (1999) <https://papers.nips.cc/paper/1651-agglomerative-information-bottleneck>,
the generalised IB from Strouse and Schwab (2017) <doi:10.1162/NECO_a_00961>,
and the sequential IB from Slonim et al. (2002) <doi:10.1145/564376.564401>. Diagnostic and plotting functions are provided to summarise, visualise, and predict from the resulting clusteri [...truncated...]
Author: Angelos Markos [aut, cre],
Efthymios Costa [aut],
Ioanna Papatsouma [aut]
Maintainer: Angelos Markos <amarkos@gmail.com>
Diff between IBclust versions 1.4 dated 2026-07-14 and 1.5 dated 2026-08-28
DESCRIPTION | 8 +- MD5 | 38 ++++++------ NAMESPACE | 1 R/IBclust-package.R | 2 R/aibclust-methods.R | 2 R/as_hclust.R | 2 R/find_elbow.R | 2 R/gibclust-methods.R | 119 ++++++++++++++++++++++++++++++++++++---- R/info_metrics.R | 2 R/make_dendrogram.R | 12 ++-- R/sibclust-methods.R | 136 +++++++++++++++++++++++++++++++++++++++------- build/partial.rdb |binary man/aibclust-methods.Rd | 2 man/as.hclust.aibclust.Rd | 2 man/find_elbow.Rd | 2 man/gibclust-methods.Rd | 45 ++++++++++++--- man/info_metrics.Rd | 2 man/predict.gibclust.Rd | 2 man/predict.sibclust.Rd | 2 man/sibclust-methods.Rd | 46 ++++++++++++--- 20 files changed, 336 insertions(+), 91 deletions(-)
Title: Interactive Forest Plot
Description: Interactive forest plot for clinical trial safety analysis
using 'metalite', 'reactable', 'plotly', and Analysis Data Model (ADaM)
datasets. Includes functionality for adverse event filtering,
incidence-based group filtering, hover-over reveals, and search and sort
operations. The workflow allows for metadata construction, data preparation,
output formatting, and interactive plot generation.
Author: Yilong Zhang [aut],
Benjamin Wang [aut],
Yujie Zhao [aut, cre],
Nan Xiao [ctb],
Hiroaki Fukuda [aut],
Yulia Sidi [ctb],
Xuan Deng [ctb],
Jeetener Chauhan [ctb],
Li Ma [ctb],
Chen Wang [ctb],
Madhusudhan Ginnaram [ctb],
Merck & Co., Inc., Rahway, NJ, [...truncated...]
Maintainer: Yujie Zhao <yujie.zhao@merck.com>
Diff between forestly versions 0.1.5 dated 2026-06-12 and 0.1.6 dated 2026-08-28
forestly-0.1.5/forestly/R/meta_forestly.R |only forestly-0.1.5/forestly/man/meta_forestly.Rd |only forestly-0.1.5/forestly/tests/testthat/helper-meta_forestly.R |only forestly-0.1.5/forestly/tests/testthat/test-independent-testing-meta_forestly.R |only forestly-0.1.6/forestly/DESCRIPTION | 8 forestly-0.1.6/forestly/MD5 | 73 ++-- forestly-0.1.6/forestly/NAMESPACE | 1 forestly-0.1.6/forestly/NEWS.md | 6 forestly-0.1.6/forestly/R/ae_forestly.R | 62 +++ forestly-0.1.6/forestly/R/ae_listing.R | 114 ++++++ forestly-0.1.6/forestly/R/format_ae_forestly.R | 62 +++ forestly-0.1.6/forestly/R/plot.R | 165 ++++++++-- forestly-0.1.6/forestly/R/prepare_ae_forestly.R | 61 +++ forestly-0.1.6/forestly/R/rtf_static_forestly.R | 51 ++- forestly-0.1.6/forestly/README.md | 82 ++++ forestly-0.1.6/forestly/build/vignette.rds |binary forestly-0.1.6/forestly/inst/doc/customize-ae-specific-columns.html | 16 forestly-0.1.6/forestly/inst/doc/customize-color.html | 16 forestly-0.1.6/forestly/inst/doc/customize-diff-label.html | 16 forestly-0.1.6/forestly/inst/doc/customize-digits.html | 16 forestly-0.1.6/forestly/inst/doc/customize-display-only-soc.html | 16 forestly-0.1.6/forestly/inst/doc/customize-listing-columns.html | 16 forestly-0.1.6/forestly/inst/doc/customize-toggle-buttons.html | 18 - forestly-0.1.6/forestly/inst/doc/customize-width.html | 28 - forestly-0.1.6/forestly/inst/doc/customize-xlimit.html | 12 forestly-0.1.6/forestly/inst/doc/forest-plot-static.R | 54 ++- forestly-0.1.6/forestly/inst/doc/forest-plot-static.Rmd | 54 ++- forestly-0.1.6/forestly/inst/doc/forest-plot-static.html | 66 +++- forestly-0.1.6/forestly/man/ae_forestly.Rd | 62 +++ forestly-0.1.6/forestly/man/format_ae_forestly.Rd | 62 +++ forestly-0.1.6/forestly/man/plot_dot.Rd | 55 ++- forestly-0.1.6/forestly/man/plot_errorbar.Rd | 55 ++- forestly-0.1.6/forestly/man/prepare_ae_forestly.Rd | 61 +++ forestly-0.1.6/forestly/man/rtf_static_forestly.Rd | 51 ++- forestly-0.1.6/forestly/man/table_panel.Rd | 55 ++- forestly-0.1.6/forestly/tests/testthat/helper-ae_forestly.R | 2 forestly-0.1.6/forestly/tests/testthat/helper-format_ae_forestly.R | 2 forestly-0.1.6/forestly/tests/testthat/helper-meta_ae.R |only forestly-0.1.6/forestly/tests/testthat/test-ae_forestly.R | 4 forestly-0.1.6/forestly/vignettes/forest-plot-static.Rmd | 54 ++- 40 files changed, 1200 insertions(+), 276 deletions(-)
Title: Data Mining and R Programming for Beginners
Description: Contains functions to simplify the use of data mining methods (classification, regression, clustering, etc.), for students and beginners in R programming. Various R packages are used and wrappers are built around the main functions, to standardize the use of data mining methods (input/output): it brings a certain loss of flexibility, but also a gain of simplicity. The package name came from the French "Fouille de Données en Master 2 Informatique Décisionnelle".
Author: Alexandre Blansche [aut, cre]
Maintainer: Alexandre Blansche <alexandre.blansche@univ-lorraine.fr>
Diff between fdm2id versions 0.9.9 dated 2023-06-12 and 1.0.0 dated 2026-08-28
DESCRIPTION | 23 MD5 | 428 +++--- NAMESPACE | 38 NEWS.md |only R/association.R | 170 +- R/classification.R | 2475 +++++++++++++++++++++++++++++---------- R/clustering.R | 1558 ++++++++++++++++++------ R/dataset.R | 144 +- R/factorial.R | 279 ++++ R/feature.R | 748 ++++++++--- R/misc.R | 419 +++++- R/regression.R | 387 ++++-- R/text.R | 324 ++--- R/visualization.R | 711 +++++++---- build |only data/accident2014.rda |binary data/alcohol.rda |binary data/autompg.rda |binary data/beetles.rda |binary data/birth.rda |binary data/britpop.rda |binary data/capitals.rda |only data/cookies.desc.test.rda |binary data/cookies.desc.train.rda |binary data/cookies.rda |binary data/cookies.y.test.rda |binary data/cookies.y.train.rda |binary data/credit.rda |binary data/data1.rda |binary data/data2.rda |binary data/data3.rda |binary data/decathlon.rda |binary data/eucalyptus.rda |binary data/ionosphere.rda |binary data/linsep.rda |binary data/movies.rda |binary data/ozone.rda |binary data/reg1.rda |binary data/reg1.test.rda |binary data/reg1.train.rda |binary data/reg2.rda |binary data/reg2.test.rda |binary data/reg2.train.rda |binary data/snore.rda |binary data/spine.rda |binary data/spine.test.rda |binary data/spine.train.rda |binary data/temperature.rda |binary data/titanic.rda |binary data/universite.rda |binary data/vowels.rda |binary data/vowels.test.rda |binary data/vowels.train.rda |binary data/wheat.rda |binary data/wine.rda |binary data/zoo.rda |binary inst |only man/ADABOOST.Rd | 14 man/APRIORI.Rd | 17 man/BAGGING.Rd | 14 man/CA.Rd | 8 man/CART.Rd | 22 man/CDA.Rd | 34 man/DBSCAN.Rd | 13 man/EM.Rd | 6 man/FEATURESELECTION.Rd | 27 man/GBREG.Rd |only man/GRADIENTBOOSTING.Rd | 20 man/HCA.Rd | 26 man/KERREG.Rd | 25 man/KMEANS.Rd | 38 man/KNN.Rd | 31 man/LDA.Rd | 24 man/LINREG.Rd | 42 man/LR.Rd | 55 man/MCA.Rd | 12 man/MEANSHIFT.Rd | 8 man/MLP.Rd | 25 man/MLPREG.Rd | 29 man/NB.Rd | 24 man/NMF.Rd | 4 man/PAM.Rd |only man/PCA.Rd | 5 man/POLYREG.Rd | 25 man/QDA.Rd | 24 man/RANDOMFOREST.Rd | 22 man/SOM.Rd | 3 man/SPECTRAL.Rd | 6 man/STUMP.Rd | 28 man/SVM.Rd | 19 man/SVMl.Rd | 20 man/SVMr.Rd | 20 man/SVR.Rd | 27 man/SVRl.Rd | 24 man/SVRr.Rd | 24 man/TEXTMINING.Rd | 13 man/TSNE.Rd | 14 man/alcohol.Rd | 4 man/apriori-class.Rd | 26 man/augmentation.Rd | 6 man/autompg.Rd | 2 man/average.doc.Rd |only man/beetles.Rd | 2 man/boosting-class.Rd | 22 man/boxclus.Rd | 4 man/capitals.Rd |only man/cartdepth.Rd | 2 man/cda-class.Rd | 43 man/check.classes.Rd |only man/closegraphics.Rd | 9 man/compare.Rd | 11 man/compare.accuracy.Rd | 10 man/compare.jaccard.Rd | 18 man/compare.kappa.Rd | 21 man/confusion.Rd | 18 man/cookplot.Rd | 2 man/cost.curves.Rd | 37 man/data.diag.Rd | 10 man/data.gauss.Rd | 8 man/data.parabol.Rd | 8 man/data.target1.Rd | 8 man/data.target2.Rd | 8 man/data.twomoons.Rd | 8 man/data.xor.Rd | 8 man/dataset-class.Rd | 20 man/dbs-class.Rd | 23 man/em-class.Rd | 38 man/eucalyptus.Rd | 2 man/evaluation.adjr2.Rd | 13 man/evaluation.fmeasure.Rd | 36 man/evaluation.fowlkesmallows.Rd | 35 man/evaluation.goodness.Rd | 36 man/evaluation.jaccard.Rd | 29 man/evaluation.kappa.Rd | 5 man/evaluation.precision.Rd | 31 man/evaluation.recall.Rd | 31 man/exportgraphics.Rd | 19 man/factorial-class.Rd | 11 man/filter.rules.Rd | 5 man/frequentwords.Rd | 21 man/general.rules.Rd | 5 man/getvocab.Rd | 19 man/intern.Rd | 8 man/intern.dunn.Rd | 9 man/intern.interclass.Rd | 2 man/intern.intraclass.Rd | 2 man/ionosphere.Rd | 4 man/kmeans.getk.Rd | 35 man/knn-class.Rd | 17 man/leverageplot.Rd | 2 man/loadtext.Rd | 24 man/meanshift-class.Rd | 35 man/model-class.Rd | 14 man/movies.Rd | 8 man/ozone.Rd | 9 man/params-class.Rd | 23 man/performance.Rd | 61 man/plot.apriori.Rd |only man/plot.cda.Rd | 10 man/plot.factorial.Rd | 29 man/plot.selection.Rd |only man/plotcloud.Rd | 13 man/plotclus.Rd | 2 man/plotdata.Rd | 65 - man/plotzipf.Rd | 8 man/predict.factorial.Rd |only man/predict.hca.Rd |only man/predict.pam.Rd |only man/predict.som.Rd |only man/predict.spectral.Rd |only man/predict.textmining.Rd | 7 man/print.boosting.Rd |only man/print.cda.Rd |only man/print.dataset.Rd |only man/print.dbs.Rd |only man/print.em.Rd |only man/print.knn.Rd |only man/print.meanshift.Rd |only man/print.model.Rd |only man/print.params.Rd |only man/print.selection.Rd |only man/print.som.Rd |only man/print.spectral.Rd |only man/query.docs.Rd | 13 man/query.words.Rd | 9 man/regplot.Rd | 2 man/resplot.Rd | 8 man/roc.curves.Rd | 50 man/scatterplot.Rd | 4 man/selectfeatures.Rd | 6 man/selection-class.Rd | 40 man/snore.Rd | 6 man/som-class.Rd | 20 man/spectral-class.Rd | 20 man/spine.Rd | 2 man/splitdata.Rd | 18 man/summary.model.Rd |only man/textmining-class.Rd | 17 man/titanic.Rd | 2 man/treeplot.Rd | 2 man/tune.doc.Rd |only man/vectorize.docs.Rd | 31 man/vectorize.words.Rd | 20 man/vectorizer-class.Rd | 26 man/vowels.Rd | 2 man/wheat.Rd | 2 man/wine.Rd | 2 man/zoo.Rd | 2 tests |only vignettes |only 210 files changed, 7239 insertions(+), 2622 deletions(-)
Title: Survey Analysis Tools for the Chilean Social Observatory
Description: Provides high-level functions to compute estimates (means,
proportions, totals, ratios and quantiles) for complex survey designs,
with automatic classification of statistical reliability, between-year
significance tests and standardised report generation in 'Excel' format
(via 'openxlsx'). It was developed for the Social Observatory
('Observatorio Social') of the Chilean Ministry of Social Development
and implements its data-quality criteria, but it can be applied to any
complex-survey design (for example the Chilean 'CASEN' household survey,
included as example data). The reliability criteria follow Division
Observatorio Social (2023)
<https://bidat.gob.cl/details/ficha/dato/manual-para-la-investigacion-casen-2022>
and Instituto Nacional de Estadisticas (2020)
<https://www.ine.gob.cl/inicio/documentos-de-trabajo/documento/fundamentos-del-est%C3%A1ndar-para-la-evaluaci%C3%B3n-de-la-calidad-de-las-estimaciones-en-encuestas-de-hogares>;
complex-survey estimation methods follo [...truncated...]
Author: Gabriel Sotomayor [aut, cre]
Maintainer: Gabriel Sotomayor <gabrielsotomayorl@gmail.com>
Diff between dosr versions 0.3.4 dated 2026-07-06 and 0.3.6 dated 2026-08-28
DESCRIPTION | 12 - MD5 | 72 +++--- NEWS.md | 130 ++++++++--- R/api_helpers.R | 60 +++++ R/data.R | 12 - R/engine.R | 97 ++++---- R/globals.R | 1 R/multi_bin.R | 157 ++++++++----- R/public_api.R | 152 ++++++++---- R/reporting.R | 244 ++++++++++++-------- R/significance.R | 4 R/survey_direct.R |only R/utils.R | 93 +++++++ data/casen_2022.rda |binary data/casen_2024.rda |binary inst/CITATION |only inst/doc/introduccion.R | 6 inst/doc/introduccion.Rmd | 15 + inst/doc/introduccion.html | 352 +++++++++++++++--------------- inst/doc/metodologia.R | 2 inst/doc/metodologia.Rmd | 5 inst/doc/metodologia.html | 41 +-- man/casen_2022.Rd | 6 man/casen_2024.Rd | 6 man/multi_bin.Rd | 18 + man/obs_cuantil.Rd | 22 + man/obs_media.Rd | 22 + man/obs_prop.Rd | 26 +- man/obs_ratio.Rd | 22 + man/obs_total.Rd | 22 + tests/testthat/helper-synthetic-designs.R |only tests/testthat/test-engine.R | 43 +++ tests/testthat/test-multi-bin.R | 82 ++++++ tests/testthat/test-public-api.R | 132 +++++++++++ tests/testthat/test-significance.R | 26 ++ tests/testthat/test-survey-direct.R |only tests/testthat/test-utils.R | 46 +++ vignettes/introduccion.Rmd | 15 + vignettes/metodologia.Rmd | 5 39 files changed, 1408 insertions(+), 540 deletions(-)
Title: Models Spatially Continuous and Discrete Population Genetic
Structure
Description: A method for modeling genetic data as a combination of discrete
layers, within each of which relatedness may decay continuously with geographic
distance. This package contains code for running analyses (which are implemented
in the modeling language 'rstan') and visualizing and interpreting output. See the
paper for more details on the model and its utility.
Author: Gideon Bradburd [aut, cre]
Maintainer: Gideon Bradburd <bradburd@umich.edu>
Diff between conStruct versions 1.0.6 dated 2024-01-08 and 1.0.7 dated 2026-08-28
CHANGELOG | 2 DESCRIPTION | 10 MD5 | 54 - NAMESPACE | 2 NEWS.md | 5 R/conStruct-package.R | 3 R/model.comparison.R | 10 R/plot.output.R | 56 - R/run.conStruct.R | 16 build/vignette.rds |binary inst/doc/format-data.R | 46 inst/doc/format-data.html | 7 inst/doc/model-comparison.R | 254 ++--- inst/doc/model-comparison.html | 31 inst/doc/run-conStruct.R | 94 - inst/doc/run-conStruct.html | 11 inst/doc/visualize-results.R | 78 - inst/doc/visualize-results.html | 25 man/compare.two.runs.Rd | 10 man/conStruct-package.Rd | 9 src/stanExports_multiK.cc | 34 src/stanExports_multiK.h | 1368 +++++++++++++--------------- src/stanExports_oneK.cc | 34 src/stanExports_oneK.h | 904 ++++++++---------- src/stanExports_space_multiK.cc | 34 src/stanExports_space_multiK.h | 1907 ++++++++++++++++++---------------------- src/stanExports_space_oneK.cc | 34 src/stanExports_space_oneK.h | 1169 +++++++++++------------- 28 files changed, 2887 insertions(+), 3320 deletions(-)
Title: Scraper for Chess-Results.com
Description: Scrape data from <https://chess-results.com> and get a clean
'tibble'. Currently supports tournament information, starting rank,
playing schedule, pairings/results for rounds, and closing rank.
Author: Sirf Haru [aut, cre, cph]
Maintainer: Sirf Haru <sirfharu@proton.me>
Diff between chessResults versions 2026.07.05 dated 2026-07-11 and 2026.08.27 dated 2026-08-28
chessResults-2026.07.05/chessResults/tests/testthat.R |only chessResults-2026.08.27/chessResults/DESCRIPTION | 31 chessResults-2026.08.27/chessResults/MD5 | 12 chessResults-2026.08.27/chessResults/NEWS.md |only chessResults-2026.08.27/chessResults/R/chess_results.R | 548 ++++++++++---- chessResults-2026.08.27/chessResults/README.md | 87 +- chessResults-2026.08.27/chessResults/inst |only chessResults-2026.08.27/chessResults/man/chess_results.Rd | 29 chessResults-2026.08.27/chessResults/tests/spelling.R |only 9 files changed, 509 insertions(+), 198 deletions(-)
Title: Interactive Training App for Data Science and AI Skills
Description: An interactive 'shiny' training companion for people who are
new to data, developed for World Health Organization data trainings.
Bundles hands-on modules for importing data, missing values, outliers,
text cleaning, merging, visualization, and basic statistics, plus a set
of AI-skills pages (prompting levels, a prompt gallery, AI safety rules,
and a methodology case study) and an interactive quiz with per-session
topic filters. Launch the app with run_cata().
Author: Shanlong Ding [aut, cre]
Maintainer: Shanlong Ding <dings@who.int>
Diff between cataScience versions 2.1.2 dated 2026-07-30 and 2.1.3 dated 2026-08-28
DESCRIPTION | 6 MD5 | 8 NEWS.md | 58 +++-- README.md | 120 ++++++------ inst/app/R/app-function.R | 455 +++++++++++++++++++++++----------------------- 5 files changed, 337 insertions(+), 310 deletions(-)
Title: Bootstrap Methods for Complete Survey Data
Description: Bootstrap resampling methods have been widely studied in the context of survey data. This package implements various bootstrap resampling techniques tailored for survey data, with a focus on stratified simple random sampling and stratified two-stage cluster sampling. It provides tools for precise and consistent bootstrap variance estimation for population totals, means, and quartiles. Additionally, it enables easy generation of bootstrap samples for in-depth analysis.
Author: Zeinab Mashreghi [aut, cre]
Maintainer: Zeinab Mashreghi <z.mashreghi@uwinnipeg.ca>
Diff between bootsurv versions 0.0.1 dated 2024-05-17 and 0.1.0 dated 2026-08-28
DESCRIPTION | 13 MD5 | 25 NAMESPACE | 17 NEWS.md |only R/BootReplicates.R |only R/BootstrapWeightsMethods.R | 150 ++++- R/DirectBootstrapMethods.R | 139 ++++ R/PseudoPopBootstrapMethods.R | 110 +++ R/TwoStageBootsrtrapMethods.R | 1180 +++++++++++++++++++++++------------------- man/All.data.Rd | 7 man/boot.replicates.Rd |only man/boot.twostage.Rd | 102 ++- man/boot.weights.stsrs.Rd | 48 + man/direct.boot.stsrs.Rd | 40 + man/pseudopop.boot.stsrs.Rd | 49 + 15 files changed, 1191 insertions(+), 689 deletions(-)
Title: Class and Methods Definitions for Packages 'aws', 'adimpro',
'fmri', 'dwi'
Description: Defines the method extract and provides 'openMP' support as needed in several packages.
Author: Joerg Polzehl [aut, cre],
Felix Anker [ctb]
Maintainer: Joerg Polzehl <joerg.polzehl@wias-berlin.de>
Diff between awsMethods versions 1.1-1 dated 2019-05-08 and 1.1-2 dated 2026-08-28
DESCRIPTION | 12 ++++++------ MD5 | 4 ++-- src/omp_funcs.c | 2 +- 3 files changed, 9 insertions(+), 9 deletions(-)