Title: Token-Authenticated REST API Retrieval Toolkit
Description: A small, dependency-light toolkit for talking to token-authenticated
REST APIs. It manages authentication tokens in process environment variables
(never written to disk), builds requests with configurable authentication and
pagination strategies, and retrieves paginated data either one page at a time
or in chunks combined into a single tibble. The design is API-agnostic: a
single 'apifetch_api' profile describes an endpoint together with how it
authenticates and paginates, so the same verbs work across different services.
Author: Andre Leite [aut, cre] ,
Hugo Vasconcelos [aut] ,
Diogo Bezerra [aut] ,
Marcos Wasiliew [aut] ,
Carlos Amorim [aut] ,
Julia Nascimento Barreto [aut]
Maintainer: Andre Leite <leite@castlab.org>
Diff between apifetch versions 0.1.0 dated 2026-07-02 and 0.2.0 dated 2026-09-28
DESCRIPTION | 40 ++++++++----- MD5 | 28 ++++----- NEWS.md | 31 ++++++++++ R/api.R | 9 +-- R/fetch.R | 47 ++++++++++++--- R/tokens.R | 17 +++-- R/utils.R | 56 +++++++++++------- README.md | 11 +++ man/af_fetch_all.Rd | 6 +- man/af_paginate.Rd | 3 - man/af_store_token.Rd | 7 +- man/apifetch-package.Rd | 13 ++-- man/parse_queries.Rd | 4 + tests/testthat/test-api.R | 127 +++++++++++++++++++++++++++++++++++++++++++ tests/testthat/test-tokens.R | 19 ++++++ 15 files changed, 335 insertions(+), 83 deletions(-)
Title: Immunoglobulin Clonal Lineage and Diversity Analysis
Description: Provides methods for high-throughput adaptive immune
receptor repertoire sequencing (AIRR-Seq; Rep-Seq) analysis. In
particular, immunoglobulin (Ig) sequence lineage reconstruction,
lineage topology analysis, diversity profiling, amino acid property
analysis and gene usage.
Citations:
Gupta and Vander Heiden, et al (2017) <doi:10.1093/bioinformatics/btv359>,
Stern, Yaari and Vander Heiden, et al (2014) <doi:10.1126/scitranslmed.3008879>.
Author: Susanna Marquez [cre, aut],
Namita Gupta [aut],
Nima Nouri [aut],
Ruoyi Jiang [aut],
Julian Zhou [aut],
Kenneth Hoehn [aut],
Daniel Gadala-Maria [ctb],
Edel Aron [ctb],
Cole Jensen [aut],
Gisela Gabernet [ctb],
Caroline Sullivan [ctb],
Hailong Meng [ [...truncated...]
Maintainer: Susanna Marquez <susanna.marquez@yale.edu>
Diff between alakazam versions 1.4.3 dated 2026-04-29 and 1.5.0 dated 2026-09-28
alakazam-1.4.3/alakazam/tests |only alakazam-1.5.0/alakazam/DESCRIPTION | 10 alakazam-1.5.0/alakazam/MD5 | 100 +--- alakazam-1.5.0/alakazam/NAMESPACE | 253 ++++++------ alakazam-1.5.0/alakazam/NEWS.md | 21 + alakazam-1.5.0/alakazam/R/Alakazam.R | 11 alakazam-1.5.0/alakazam/R/AminoAcids.R | 4 alakazam-1.5.0/alakazam/R/Diversity.R | 2 alakazam-1.5.0/alakazam/R/Gene.R | 2 alakazam-1.5.0/alakazam/R/Lineage.R | 4 alakazam-1.5.0/alakazam/R/RcppExports.R | 41 +- alakazam-1.5.0/alakazam/R/Sequence.R | 307 ++++++++++++++- alakazam-1.5.0/alakazam/R/Topology.R | 10 alakazam-1.5.0/alakazam/README.md | 8 alakazam-1.5.0/alakazam/build/partial.rdb |binary alakazam-1.5.0/alakazam/build/vignette.rds |binary alakazam-1.5.0/alakazam/inst/doc/AminoAcids-Vignette.pdf |binary alakazam-1.5.0/alakazam/inst/doc/Diversity-Vignette.pdf |binary alakazam-1.5.0/alakazam/inst/doc/Fastq-Vignette.R | 2 alakazam-1.5.0/alakazam/inst/doc/Fastq-Vignette.Rmd | 2 alakazam-1.5.0/alakazam/inst/doc/Fastq-Vignette.pdf |binary alakazam-1.5.0/alakazam/inst/doc/Files-Vignette.pdf |binary alakazam-1.5.0/alakazam/inst/doc/GeneUsage-Vignette.pdf |binary alakazam-1.5.0/alakazam/man/ABBREV_AA.Rd | 2 alakazam-1.5.0/alakazam/man/DEFAULT_COLORS.Rd | 8 alakazam-1.5.0/alakazam/man/IMGT_REGIONS.Rd | 2 alakazam-1.5.0/alakazam/man/IUPAC_CODES.Rd | 8 alakazam-1.5.0/alakazam/man/alakazam-package.Rd | 1 alakazam-1.5.0/alakazam/man/alakazam.Rd | 5 alakazam-1.5.0/alakazam/man/buildPhylipLineage.Rd | 4 alakazam-1.5.0/alakazam/man/collapseDuplicates.Rd | 47 +- alakazam-1.5.0/alakazam/man/fastDist.Rd |only alakazam-1.5.0/alakazam/man/fastDistAA.Rd |only alakazam-1.5.0/alakazam/man/nonsquareDist.Rd | 2 alakazam-1.5.0/alakazam/man/pairwiseEqual.Rd | 12 alakazam-1.5.0/alakazam/man/seqMismatchCount.Rd |only alakazam-1.5.0/alakazam/src/RcppDistance.cpp | 22 - alakazam-1.5.0/alakazam/src/RcppExports.cpp | 78 +++ alakazam-1.5.0/alakazam/src/RcppSeqMismatch.cpp |only alakazam-1.5.0/alakazam/src/fastDist.cpp |only alakazam-1.5.0/alakazam/src/fastDistAA.cpp |only alakazam-1.5.0/alakazam/vignettes/Fastq-Vignette.Rmd | 2 42 files changed, 703 insertions(+), 267 deletions(-)
Title: Transition Network Analysis (TNA)
Description: Provides tools for performing Transition Network Analysis (TNA) to
study relational dynamics, including functions for building and plotting TNA
models, calculating centrality measures, and identifying dominant events and
patterns. TNA statistical techniques (e.g., bootstrapping and permutation
tests) ensure the reliability of observed insights and confirm that
identified dynamics are meaningful. See (Saqr et al., 2025)
<doi:10.1145/3706468.3706513> for more details on TNA.
Author: Mohammed Saqr [aut],
Santtu Tikka [aut],
Sonsoles Lopez-Pernas [aut, cre, cph]
Maintainer: Sonsoles Lopez-Pernas <sonsoles.lopez@uef.fi>
Diff between tna versions 1.2.3 dated 2026-04-26 and 1.3.1 dated 2026-09-28
DESCRIPTION | 6 MD5 | 60 +-- NEWS.md | 39 ++ R/bootstrap.R | 28 + R/build.R | 2 R/centralities.R | 14 R/check.R | 12 R/data.R | 394 +++++++++++++++++------- R/groups.R | 4 R/plot.R | 157 ++++++++- R/pruning.R | 61 +++ R/utilities.R | 74 ++++ inst/doc/communities_and_cliques.html | 6 inst/doc/complete_tutorial.html | 22 - inst/doc/grouped_sequences.html | 556 +++++++++++++++++----------------- inst/doc/prepare_data.html | 10 inst/doc/tna.html | 4 man/bootstrap.Rd | 11 man/bootstrap_cliques.Rd | 16 man/centralities.Rd | 2 man/plot.tna_permutation.Rd | 13 man/plot.tna_reliability.Rd | 6 man/prepare_data.Rd | 32 + man/prune.Rd | 8 tests/testthat/test-bootstrap.R | 27 + tests/testthat/test-build.R | 22 + tests/testthat/test-centralities.R | 69 ++++ tests/testthat/test-clusters.R | 6 tests/testthat/test-data.R | 267 ++++++++++++++++ tests/testthat/test-groups.R | 13 tests/testthat/test-pruning.R | 33 ++ 31 files changed, 1476 insertions(+), 498 deletions(-)
Title: Client for the Brazilian Foreign Trade Statistics API
('ComexStat')
Description: Interface to the 'ComexStat' API
<https://comexstat.mdic.gov.br/> from the Brazilian Ministry of
Development, Industry, Trade and Services (MDIC). Provides access to
detailed export and import data, including general trade statistics
(1997-present), city-level data, historical data (1989-1996), and
auxiliary tables with product codes (NCM - Nomenclatura Comum do
Mercosul, NBM - Nomenclatura Brasileira de Mercadorias, HS -
Harmonized System), countries, economic classifications (CGCE -
Classificacao por Grandes Categorias Economicas, SITC - Standard
International Trade Classification, ISIC - International Standard
Industrial Classification), and other categories. Uses only 'httr2'
for HTTP requests and 'cli' for console messages.
Author: Andre Leite [aut, cre],
Marcos Wasilew [aut],
Hugo Vasconcelos [aut],
Carlos Amorim [aut],
Diogo Bezerra [aut]
Maintainer: Andre Leite <leite@castlab.org>
Diff between comexr versions 0.3.0 dated 2026-05-21 and 0.4.0 dated 2026-09-28
DESCRIPTION | 12 +- MD5 | 68 ++++++----- NEWS.md | 60 ++++++++++ R/historical.R | 34 ++++- R/query.R | 6 - R/query_city.R | 6 - R/tables.R | 50 ++++---- R/utils.R | 225 ++++++++++++++++++++------------------ README.md | 14 +- inst/doc/city-profile.R | 16 +- inst/doc/city-profile.Rmd | 16 +- inst/doc/city-profile.html | 16 +- inst/doc/querying-trade-data.Rmd | 2 inst/doc/querying-trade-data.html | 2 inst/doc/state-trade-profile.R | 5 inst/doc/state-trade-profile.Rmd | 9 - inst/doc/state-trade-profile.html | 12 -- man/comex_available_years.Rd | 8 + man/comex_details.Rd | 9 + man/comex_export.Rd | 2 man/comex_filter_values.Rd | 10 + man/comex_filters.Rd | 9 + man/comex_historical.Rd | 8 + man/comex_import.Rd | 2 man/comex_last_update.Rd | 5 man/comex_metrics.Rd | 9 + man/comex_query.Rd | 4 man/comex_query_city.Rd | 4 man/comexr-package.Rd | 2 man/figures/logo.png |only man/figures/logo.svg | 172 +++++------------------------ tests |only vignettes/city-profile.Rmd | 16 +- vignettes/querying-trade-data.Rmd | 2 vignettes/state-trade-profile.Rmd | 9 - 35 files changed, 432 insertions(+), 392 deletions(-)
Title: Vehicle Routing Problem Solver Built on 'PyVRP'
Description: A 'tidyverse'-style interface to high-performance vehicle routing
problem (VRP) solving. Vendors the C++ core of the 'PyVRP' solver
(<https://github.com/PyVRP/PyVRP>) and rewires it through 'cpp11', with no
'Python' runtime dependency. Supports the capacitated VRP, time windows,
multiple depots, heterogeneous fleets, prize-collecting and multi-trip
variants, driven by an iterated local search metaheuristic.
Author: Andre Leite [aut, cre],
Marcos Wasilew [aut],
Hugo Vasconcelos [aut],
Carlos Amorim [aut],
Diogo Bezerra [aut],
Niels Wouda [ctb, cph] ,
Thibaut Vidal [cph] ,
ORTEC [cph]
Maintainer: Andre Leite <leite@castlab.org>
Diff between vrpr versions 0.1.1 dated 2026-08-27 and 0.2.0 dated 2026-09-28
vrpr-0.1.1/vrpr/src/vendor/pyvrp/Trip.cpp |only vrpr-0.1.1/vrpr/src/vendor/pyvrp/Trip.h |only vrpr-0.1.1/vrpr/src/vendor/pyvrp/search/Exchange.h |only vrpr-0.1.1/vrpr/src/vendor/pyvrp/search/SwapRoutes.cpp |only vrpr-0.1.1/vrpr/src/vendor/pyvrp/search/SwapRoutes.h |only vrpr-0.1.1/vrpr/src/vendor/pyvrp/search/SwapStar.cpp |only vrpr-0.1.1/vrpr/src/vendor/pyvrp/search/SwapStar.h |only vrpr-0.1.1/vrpr/src/vendor/pyvrp/search/primitives.cpp |only vrpr-0.1.1/vrpr/src/vendor/pyvrp/search/primitives.h |only vrpr-0.2.0/vrpr/DESCRIPTION | 6 vrpr-0.2.0/vrpr/MD5 | 184 +- vrpr-0.2.0/vrpr/NAMESPACE | 4 vrpr-0.2.0/vrpr/NEWS.md | 37 vrpr-0.2.0/vrpr/R/cpp11.R | 16 vrpr-0.2.0/vrpr/R/ils.R | 36 vrpr-0.2.0/vrpr/R/local_search.R | 16 vrpr-0.2.0/vrpr/R/model.R | 48 vrpr-0.2.0/vrpr/R/penalty.R | 114 - vrpr-0.2.0/vrpr/R/plot.R | 57 vrpr-0.2.0/vrpr/R/problem_data.R | 64 vrpr-0.2.0/vrpr/R/result.R | 8 vrpr-0.2.0/vrpr/R/solution.R | 95 - vrpr-0.2.0/vrpr/README.md | 7 vrpr-0.2.0/vrpr/inst/doc/vrpr.R | 15 vrpr-0.2.0/vrpr/inst/doc/vrpr.Rmd | 28 vrpr-0.2.0/vrpr/inst/doc/vrpr.html | 123 - vrpr-0.2.0/vrpr/man/add_shipments.Rd |only vrpr-0.2.0/vrpr/man/ils_params.Rd | 10 vrpr-0.2.0/vrpr/man/routes.Rd | 11 vrpr-0.2.0/vrpr/man/unplanned.Rd |only vrpr-0.2.0/vrpr/man/vrp_problem_data.Rd | 9 vrpr-0.2.0/vrpr/src/Makevars | 40 vrpr-0.2.0/vrpr/src/Makevars.win | 40 vrpr-0.2.0/vrpr/src/cpp11.cpp | 32 vrpr-0.2.0/vrpr/src/local_search.cpp | 132 - vrpr-0.2.0/vrpr/src/problem_data.cpp | 98 - vrpr-0.2.0/vrpr/src/solution.cpp | 141 + vrpr-0.2.0/vrpr/src/vendor/pyvrp/Activity.cpp |only vrpr-0.2.0/vrpr/src/vendor/pyvrp/Activity.h |only vrpr-0.2.0/vrpr/src/vendor/pyvrp/Client.cpp |only vrpr-0.2.0/vrpr/src/vendor/pyvrp/Client.h |only vrpr-0.2.0/vrpr/src/vendor/pyvrp/ClientGroup.cpp |only vrpr-0.2.0/vrpr/src/vendor/pyvrp/ClientGroup.h |only vrpr-0.2.0/vrpr/src/vendor/pyvrp/CostEvaluator.h | 169 - vrpr-0.2.0/vrpr/src/vendor/pyvrp/Depot.cpp |only vrpr-0.2.0/vrpr/src/vendor/pyvrp/Depot.h |only vrpr-0.2.0/vrpr/src/vendor/pyvrp/DurationSegment.cpp | 13 vrpr-0.2.0/vrpr/src/vendor/pyvrp/DurationSegment.h | 15 vrpr-0.2.0/vrpr/src/vendor/pyvrp/DynamicBitset.cpp | 5 vrpr-0.2.0/vrpr/src/vendor/pyvrp/DynamicBitset.h | 7 vrpr-0.2.0/vrpr/src/vendor/pyvrp/LoadSegment.cpp | 39 vrpr-0.2.0/vrpr/src/vendor/pyvrp/LoadSegment.h | 90 - vrpr-0.2.0/vrpr/src/vendor/pyvrp/Location.cpp |only vrpr-0.2.0/vrpr/src/vendor/pyvrp/Location.h |only vrpr-0.2.0/vrpr/src/vendor/pyvrp/Measure.h | 39 vrpr-0.2.0/vrpr/src/vendor/pyvrp/PiecewiseLinearFunction.h |only vrpr-0.2.0/vrpr/src/vendor/pyvrp/ProblemData.cpp | 595 ------ vrpr-0.2.0/vrpr/src/vendor/pyvrp/ProblemData.h | 679 +------ vrpr-0.2.0/vrpr/src/vendor/pyvrp/README.md | 11 vrpr-0.2.0/vrpr/src/vendor/pyvrp/Route.cpp | 683 ++++--- vrpr-0.2.0/vrpr/src/vendor/pyvrp/Route.h | 217 +- vrpr-0.2.0/vrpr/src/vendor/pyvrp/Shipment.cpp |only vrpr-0.2.0/vrpr/src/vendor/pyvrp/Shipment.h |only vrpr-0.2.0/vrpr/src/vendor/pyvrp/Solution.cpp | 280 ++- vrpr-0.2.0/vrpr/src/vendor/pyvrp/Solution.h | 121 - vrpr-0.2.0/vrpr/src/vendor/pyvrp/VehicleType.cpp |only vrpr-0.2.0/vrpr/src/vendor/pyvrp/VehicleType.h |only vrpr-0.2.0/vrpr/src/vendor/pyvrp/bindings.cpp | 900 ++++++---- vrpr-0.2.0/vrpr/src/vendor/pyvrp/bindings.h | 66 vrpr-0.2.0/vrpr/src/vendor/pyvrp/logging.h |only vrpr-0.2.0/vrpr/src/vendor/pyvrp/pyvrp_version.txt | 4 vrpr-0.2.0/vrpr/src/vendor/pyvrp/search/ClientSegment.h |only vrpr-0.2.0/vrpr/src/vendor/pyvrp/search/DeliverySegment.h |only vrpr-0.2.0/vrpr/src/vendor/pyvrp/search/DepotSegment.h |only vrpr-0.2.0/vrpr/src/vendor/pyvrp/search/InsertOptionalClient.cpp |only vrpr-0.2.0/vrpr/src/vendor/pyvrp/search/InsertOptionalClient.h |only vrpr-0.2.0/vrpr/src/vendor/pyvrp/search/InsertOptionalShipment.cpp |only vrpr-0.2.0/vrpr/src/vendor/pyvrp/search/InsertOptionalShipment.h |only vrpr-0.2.0/vrpr/src/vendor/pyvrp/search/LocalSearch.cpp | 571 ++---- vrpr-0.2.0/vrpr/src/vendor/pyvrp/search/LocalSearch.h | 92 - vrpr-0.2.0/vrpr/src/vendor/pyvrp/search/LocalSearchOperator.h | 82 vrpr-0.2.0/vrpr/src/vendor/pyvrp/search/PerturbationManager.cpp | 138 + vrpr-0.2.0/vrpr/src/vendor/pyvrp/search/PerturbationManager.h | 7 vrpr-0.2.0/vrpr/src/vendor/pyvrp/search/PickupSegment.h |only vrpr-0.2.0/vrpr/src/vendor/pyvrp/search/Relocate.h |only vrpr-0.2.0/vrpr/src/vendor/pyvrp/search/RelocateAlternative.cpp |only vrpr-0.2.0/vrpr/src/vendor/pyvrp/search/RelocateAlternative.h |only vrpr-0.2.0/vrpr/src/vendor/pyvrp/search/RelocateDelivery.cpp |only vrpr-0.2.0/vrpr/src/vendor/pyvrp/search/RelocateDelivery.h |only vrpr-0.2.0/vrpr/src/vendor/pyvrp/search/RelocatePickup.cpp |only vrpr-0.2.0/vrpr/src/vendor/pyvrp/search/RelocatePickup.h |only vrpr-0.2.0/vrpr/src/vendor/pyvrp/search/RelocateShipment.cpp |only vrpr-0.2.0/vrpr/src/vendor/pyvrp/search/RelocateShipment.h |only vrpr-0.2.0/vrpr/src/vendor/pyvrp/search/RelocateWithDepot.cpp | 276 +-- vrpr-0.2.0/vrpr/src/vendor/pyvrp/search/RelocateWithDepot.h | 50 vrpr-0.2.0/vrpr/src/vendor/pyvrp/search/RemoveAdjacentDepot.cpp |only vrpr-0.2.0/vrpr/src/vendor/pyvrp/search/RemoveAdjacentDepot.h |only vrpr-0.2.0/vrpr/src/vendor/pyvrp/search/RemoveOptionalClient.cpp |only vrpr-0.2.0/vrpr/src/vendor/pyvrp/search/RemoveOptionalClient.h |only vrpr-0.2.0/vrpr/src/vendor/pyvrp/search/RemoveOptionalShipment.cpp |only vrpr-0.2.0/vrpr/src/vendor/pyvrp/search/RemoveOptionalShipment.h |only vrpr-0.2.0/vrpr/src/vendor/pyvrp/search/ReplaceGroup.cpp |only vrpr-0.2.0/vrpr/src/vendor/pyvrp/search/ReplaceGroup.h |only vrpr-0.2.0/vrpr/src/vendor/pyvrp/search/ReplaceOptionalClient.cpp |only vrpr-0.2.0/vrpr/src/vendor/pyvrp/search/ReplaceOptionalClient.h |only vrpr-0.2.0/vrpr/src/vendor/pyvrp/search/ReplaceOptionalShipment.cpp |only vrpr-0.2.0/vrpr/src/vendor/pyvrp/search/ReplaceOptionalShipment.h |only vrpr-0.2.0/vrpr/src/vendor/pyvrp/search/Route.cpp | 282 +-- vrpr-0.2.0/vrpr/src/vendor/pyvrp/search/Route.h | 510 +++-- vrpr-0.2.0/vrpr/src/vendor/pyvrp/search/SearchSpace.cpp | 91 - vrpr-0.2.0/vrpr/src/vendor/pyvrp/search/SearchSpace.h | 72 vrpr-0.2.0/vrpr/src/vendor/pyvrp/search/Solution.cpp | 349 +++ vrpr-0.2.0/vrpr/src/vendor/pyvrp/search/Solution.h | 63 vrpr-0.2.0/vrpr/src/vendor/pyvrp/search/Swap.h |only vrpr-0.2.0/vrpr/src/vendor/pyvrp/search/SwapTails.cpp | 96 - vrpr-0.2.0/vrpr/src/vendor/pyvrp/search/SwapTails.h | 15 vrpr-0.2.0/vrpr/src/vendor/pyvrp/search/bindings.cpp | 569 ++++-- vrpr-0.2.0/vrpr/src/vendor/pyvrp/search/neighbourhood.cpp |only vrpr-0.2.0/vrpr/src/vendor/pyvrp/search/neighbourhood.h |only vrpr-0.2.0/vrpr/tests/testthat/test-local-search.R | 6 vrpr-0.2.0/vrpr/tests/testthat/test-plot.R | 22 vrpr-0.2.0/vrpr/tests/testthat/test-shipments.R |only vrpr-0.2.0/vrpr/vignettes/vrpr.Rmd | 28 123 files changed, 4666 insertions(+), 3957 deletions(-)
Title: Panel Quantile Autoregressive Distributed Lag Model
Description: Estimation of Panel Quantile Autoregressive Distributed Lag
(PQARDL) models that combine panel ARDL methodology with quantile
regression. Supports Pooled Mean Group (PMG), Mean Group (MG), and
Dynamic Fixed Effects (DFE) estimators across multiple quantiles.
Computes long-run cointegrating parameters, error correction term speed
of adjustment, half-life of adjustment, and performs Wald tests for
parameter equality across quantiles. Based on the econometric frameworks
of Pesaran, Shin, and Smith (1999) <doi:10.1080/01621459.1999.10474156>,
Cho, Kim, and Shin (2015) <doi:10.1016/j.jeconom.2015.05.003>, and
Bildirici and Kayikci (2022).
Author: Muhammad Alkhalaf [aut, cre, cph]
Maintainer: Muhammad Alkhalaf <muhammedalkhalaf@gmail.com>
Diff between xtpqardl versions 1.0.1 dated 2026-03-12 and 1.0.3 dated 2026-09-28
DESCRIPTION | 26 - MD5 | 23 - NAMESPACE | 30 +- NEWS.md | 16 + R/methods.R | 8 R/xtpqardl-package.R | 6 R/xtpqardl.R | 686 ++++++++++++++++++++++-------------------------- README.md | 8 build/partial.rdb |binary inst/CITATION |only man/xtpqardl-package.Rd | 14 man/xtpqardl.Rd | 33 +- tests |only 13 files changed, 430 insertions(+), 420 deletions(-)
Title: Comprehensive Unit Root and Stationarity Tests
Description: A unified framework for unit root and stationarity testing
including quantile ADF tests (Koenker and Xiao, 2004)
<doi:10.1198/016214504000001114>, GARCH-based unit root tests with
endogenous structural breaks (Narayan and Liu, 2015)
<doi:10.1016/j.eneco.2014.11.021>, and comprehensive Dickey-Fuller,
Phillips-Perron, KPSS, ERS/DF-GLS, Zivot-Andrews, and
Kobayashi-McAleer tests with an Elder-Kennedy decision strategy
(Elder and Kennedy, 2001) <doi:10.1080/00220480109595179>.
Author: Muhammad Abdullah Alkhalaf [aut, cre, cph]
Maintainer: Muhammad Abdullah Alkhalaf <muhammedalkhalaf@gmail.com>
Diff between unitrootests versions 1.1.0 dated 2026-04-02 and 1.1.2 dated 2026-09-28
DESCRIPTION | 8 - MD5 | 11 - NAMESPACE | 48 +++--- R/qadf_main.R | 397 +++++++++++++++++++++++------------------------------- build/partial.rdb |binary inst |only man/qadf.Rd | 34 ++-- 7 files changed, 234 insertions(+), 264 deletions(-)
Title: Reapportion Data from One Geography to Another
Description: A port of the 'spReapportion' package, using Simple Features in order to lose the dependencies to the retired 'maptools' and 'rgeos' packages.
Author: Francois Briatte [aut, cre] ,
Joel Gombin [aut]
Maintainer: Francois Briatte <f.briatte@gmail.com>
Diff between sfReapportion versions 0.2.0 dated 2026-04-21 and 0.2.2 dated 2026-09-28
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/sfReapportion.R | 31 +++++++++---------------------- README.md | 11 +++++++++-- man/sfReapportion.Rd | 18 +++++++++--------- tests/testthat/test.sfReapportion.R | 16 ++++++++++------ 6 files changed, 45 insertions(+), 47 deletions(-)
Title: Residual-Based Fully Modified Vector Autoregression
Description: Implements the Residual-Based Fully Modified Vector Autoregression
(RBFM-VAR) estimator of Chang (2000) <doi:10.1017/S0266466600166058>.
The RBFM-VAR procedure extends Phillips (1995) FM-VAR to handle any unknown
mixture of I(0), I(1), and I(2) components without prior knowledge of the
number or location of unit roots. Provides automatic lag selection via
information criteria (AIC, BIC, HQ), long-run variance estimation using
Bartlett, Parzen, or Quadratic Spectral kernels with Andrews (1991)
<doi:10.2307/2938229> automatic bandwidth selection, Granger non-causality
testing with asymptotically chi-squared Wald statistics, impulse response
functions (IRF) with bootstrap confidence intervals, forecast error variance
decomposition (FEVD), and out-of-sample forecasting.
Author: Muhammad Alkhalaf [aut, cre, cph] ,
Yoosoon Chang [ctb]
Maintainer: Muhammad Alkhalaf <muhammedalkhalaf@gmail.com>
Diff between rbfmvar versions 2.0.2 dated 2026-04-09 and 2.1.0 dated 2026-09-28
DESCRIPTION | 8 - MD5 | 42 +++--- NEWS.md | 17 ++ R/forecast.R | 79 ++++------- R/granger.R | 34 ++--- R/irf.R | 184 +++++++++++++-------------- R/lag_selection.R | 28 ++-- R/lrv.R | 65 ++++++--- R/rbfmvar-package.R | 2 R/rbfmvar.R | 241 +++++++++++++----------------------- README.md | 266 ++++++++++++++++++++-------------------- inst |only man/dot-kernel_max_lag.Rd |only man/dot-rbfmvar_irf_array.Rd |only man/dot-rbfmvar_levels.Rd |only man/estimate_cross_lrv.Rd |only man/estimate_onesided_lrv.Rd | 4 man/estimate_var_ols.Rd | 4 man/forecast.rbfmvar.Rd | 12 - man/granger_test.Rd | 8 - man/irf.Rd | 14 +- man/rbfmvar-package.Rd | 168 ++++++++++++------------- man/rbfmvar.Rd | 12 + man/rbfmvar_estimate.Rd | 24 +++ tests/testthat/test-chang2000.R |only 25 files changed, 606 insertions(+), 606 deletions(-)
Title: Forest Plots, Funnel Plots, and Visual Funnel Plot Inference for
Meta-Analysis
Description: A compilation of functions to create visually appealing and information-rich
plots of meta-analytic data using 'ggplot2'. Provides functions to create forest
plots, funnel plots, and many of their variants, including rainforest plots,
thick forest plots, additional evidence contour funnel plots, and sunset funnel
plots. In addition, functionalities for visual inference with funnel plots in
the context of meta-analysis are provided. Further functionalities include
plots for comparing fixed-effect and random-effects models and dedicated
visualizations for three-level meta-analysis.
Author: Michael Kossmeier [cre, aut],
Ulrich S. Tran [aut],
Martin Voracek [aut],
Verena Pilar [aut]
Maintainer: Michael Kossmeier <michael.kossmeier@univie.ac.at>
Diff between metaviz versions 0.3.1 dated 2020-04-09 and 0.4.0 dated 2026-09-28
DESCRIPTION | 36 +- MD5 | 47 +- NAMESPACE | 8 NEWS.md | 72 ++-- R/funnelinf.R | 4 R/metaviz.R | 123 ++++-- R/viz_forest.R | 47 +- R/viz_forest_internal.R | 28 - R/viz_funnel.R | 122 ++++-- R/viz_tlma_forest.R |only R/viz_tlma_studyinfo.R |only R/wineq_baujat.R |only R/wineq_forest.R |only R/wineq_forest_internal.R |only R/wineq_gini.R |only R/wineq_plots.R |only build/vignette.rds |binary inst/doc/funnelinf.R | 40 +- inst/doc/funnelinf.html | 457 +++++++++++++++++-------- inst/doc/metaviz.R | 46 +- inst/doc/metaviz.html | 622 ++++++++++++++++++++++------------- man/internal_wineq_forest_classic.Rd |only man/internal_wineq_forest_rain.Rd |only man/internal_wineq_forest_thick.Rd |only man/metaviz-package.Rd | 147 ++++++-- man/viz_forest.Rd | 32 + man/viz_funnel.Rd | 94 +++-- man/viz_tlma_forest.Rd |only man/viz_tlma_studyinfo.Rd |only man/wineq_baujat.Rd |only man/wineq_forest.Rd |only man/wineq_gini.Rd |only 32 files changed, 1249 insertions(+), 676 deletions(-)
Title: Cointegration Tests with Structural Breaks in Small Samples
Description: Implements cointegration tests with structural breaks designed
for small sample sizes, following the methodology of Trinh (2022)
<https://ideas.repec.org/p/ema/worpap/2022-01.html>. Supports models with no breaks, breaks in
constant only, and breaks in both constant and slope. Provides endogenous
break date detection using ADF or SSR minimization criteria, with
the size-corrected 5% critical values of the response surfaces in
Trinh (2022), for up to three regressors.
Author: Muhammad Alkhalaf [aut, cre, cph]
Maintainer: Muhammad Alkhalaf <muhammedalkhalaf@gmail.com>
Diff between cointsmall versions 1.0.2 dated 2026-03-19 and 1.0.4 dated 2026-09-28
DESCRIPTION | 17 - MD5 | 27 +-- NEWS.md | 11 + R/cointsmall-package.R | 2 R/cointsmall.R | 35 +--- R/combined.R | 11 - R/critical_values.R | 339 +++++++-------------------------------- README.md | 202 +++++++++++------------ build/partial.rdb |binary inst |only man/cointsmall-package.Rd | 118 ++++++------- man/cointsmall.Rd | 13 - man/cointsmall_combined.Rd | 6 man/cointsmall_cv.Rd | 56 ++---- tests/testthat/test-cointsmall.R | 12 + 15 files changed, 317 insertions(+), 532 deletions(-)
Title: Unit Root Tests for Bounded Time Series
Description: Implements unit root tests for bounded time series following
Cavaliere and Xu (2014) <doi:10.1016/j.jeconom.2013.08.026>. Standard
unit root tests (ADF, Phillips-Perron) have non-standard limiting
distributions when the time series is bounded. This package provides
modified ADF and M-type tests (MZ-alpha, MZ-t, MSB) with p-values computed
via Monte Carlo simulation of bounded Brownian motion. Supports one-sided
(lower bound only) and two-sided bounds, with automatic lag selection
using the MAIC criterion of Ng and Perron (2001)
<doi:10.1111/1468-0262.00256>.
Author: Muhammad Alkhalaf [aut, cre, cph] ,
Giuseppe Cavaliere [ctb] ,
Fang Xu [ctb]
Maintainer: Muhammad Alkhalaf <muhammedalkhalaf@gmail.com>
Diff between boundedur versions 1.0.1 dated 2026-03-16 and 1.0.3 dated 2026-09-28
DESCRIPTION | 10 - MD5 | 29 ++-- NEWS.md | 14 ++ R/boundedur-package.R | 2 R/boundedur.R | 149 +++++++++--------------- R/lag_selection.R | 93 +++++---------- R/simulate.R | 147 +++++------------------ R/tests.R | 247 ++++++++-------------------------------- README.md | 214 +++++++++++++++++----------------- build/partial.rdb |binary inst |only man/boundedur-package.Rd | 121 ++++++++++--------- man/boundedur.Rd | 28 +++- man/select_lag_maic.Rd | 20 +-- man/simulate_bounded_bm.Rd | 14 +- tests/testthat/test-boundedur.R | 19 +++ 16 files changed, 440 insertions(+), 667 deletions(-)
Title: Perform a Relative Weights Analysis
Description: Perform a Relative Weights Analysis (RWA) (a.k.a. Key Drivers Analysis) as per the method described
in Tonidandel & LeBreton (2015) <DOI:10.1007/s10869-014-9351-z>, with its original roots in Johnson (2000) <DOI:10.1207/S15327906MBR3501_1>. In essence, RWA decomposes
the total variance predicted in a regression model into weights that accurately reflect the proportional
contribution of the predictor variables, which addresses the issue of multi-collinearity. In typical scenarios,
RWA returns similar results to Shapley regression, but with a significant advantage on computational performance.
Author: Martin Chan [aut, cre]
Maintainer: Martin Chan <martinchan53@gmail.com>
Diff between rwa versions 1.0.0 dated 2026-09-16 and 1.0.1 dated 2026-09-28
DESCRIPTION | 6 MD5 | 14 - NEWS.md | 220 +++++++++++++------------- inst/doc/bootstrap-confidence-intervals.html | 137 ++++++++-------- inst/doc/evaluating-rwa-method-reference.html | 4 inst/doc/introduction-to-rwa.html | 6 inst/doc/regression-methods.html | 4 tests/testthat/test-matrix-contract.R | 22 ++ 8 files changed, 222 insertions(+), 191 deletions(-)
Title: Entropy Based Method for the Detection of Significant Variation
in Gene Expression Data
Description: An implementation of a method based on information theory devised
for the identification of genes showing a significant variation of expression
across multiple conditions. Given expression estimates from any number of
RNA-Seq samples and conditions it identifies genes or transcripts with a
significant variation of expression across all the conditions studied,
together with the samples in which they are over- or under-expressed.
It also detects genes whose relative isoform usage changes across
samples (isoform switching).
Zambelli et al. (2018) <doi:10.1093/nar/gky055>.
Author: Federico Zambelli [aut, cre] ,
Giulio Pavesi [aut]
Maintainer: Federico Zambelli <federico.zambelli@unimi.it>
Diff between RNentropy versions 1.2.3 dated 2022-04-13 and 1.3.3 dated 2026-09-28
DESCRIPTION | 20 +++-- MD5 | 49 +++++++++----- NEWS.md | 49 ++++++++++++++ R/RN_iso_calc.R |only R/RN_iso_select.R |only R/RNentropy-internal.R | 62 ++++++++++++++++++ R/RNentropy_iso_switch.R |only README.md | 131 ++++++++++++++++++++++++++++++++++++++- build/partial.rdb |binary data/RN_IsoSwitch_Example_S7.rda |only data/datalist | 1 inst/CITATION | 29 ++++++-- inst/extdata |only man/RN_BarresLab_FPMK.Rd | 4 - man/RN_BarresLab_design.Rd | 8 +- man/RN_Brain_Example_tpm.Rd | 4 - man/RN_IsoSwitch_Example_S7.Rd |only man/RN_calc.Rd | 28 -------- man/RN_calc_GPV.Rd | 14 ---- man/RN_calc_LPV.Rd | 29 -------- man/RN_iso_calc.Rd |only man/RN_iso_select.Rd |only man/RN_pmi.Rd | 50 -------------- man/RN_select.Rd | 30 -------- man/RNentropy-package.Rd | 37 ++++++++++- man/RNentropy.Rd | 49 +++++++------- man/RNentropy_iso_switch.Rd |only tests |only 28 files changed, 379 insertions(+), 215 deletions(-)
Title: Strict JSON Encoding and Decoding via the 'Jansson' C Library
Description: An R-safe profile of RFC 8259 JSON: parsing and generation
backed by the 'Jansson' C library, linked as a system library where one
is available and compiled from the bundled sources otherwise. The
parser rejects, with classed conditions carrying line, column, and byte
position: malformed or truncated input, trailing content, duplicate
object keys at any depth, invalid UTF-8, escapes encoding a null
character, reals overflowing double,
and integer literals whose magnitude exceeds 2^53, the range within
which a double represents every integer exactly.
Number literals with a fraction or exponent convert by ordinary
correctly rounded IEEE 754 double conversion. Objects decode to named
lists in key order, arrays to unnamed lists, and scalars to length-one
vectors. The encoder maps named lists to objects in insertion order,
unnamed lists to arrays, guarantees that every finite double, signed
zero included, round-trips to the exact same value (whole-number
doubles are written as integers), an [...truncated...]
Author: Troy Hernandez [aut, cre] ,
cornball.ai [cph],
Petri Lehtinen [ctb, cph] ,
Basile Starynkevitch [ctb, cph] ,
Graeme Smecher [ctb, cph] ,
Sean Bright [ctb, cph] ,
David M. Gay [ctb] ,
Lucent Technologies [cph] ,
Bob Jenkins [ctb] , bundled by
Jansson [...truncated...]
Maintainer: Troy Hernandez <troy@cornball.ai>
Diff between janssonr versions 0.1.2 dated 2026-09-12 and 0.1.3 dated 2026-09-28
DESCRIPTION | 8 +++---- MD5 | 12 +++++------ NEWS.md | 28 +++++++++++++++++++++++++++ inst/tinytest/test_roundtrip.R | 18 +++++++++++++++++ src/jansson/PATCHES.md | 42 ++++++++++++++++++++++++++++++++++++++--- src/jansson/dtoa.c | 18 ++++++++++++----- src/jansson/hashtable.h | 8 ++++++- 7 files changed, 115 insertions(+), 19 deletions(-)
Title: Fast Partial Least Squares for High-Dimensional Data
Description: Fast implementations of partial least squares models for
high-dimensional regression and classification. The 'fastPLS' software
provides
compiled implementations of PLS-SVD, a SIMPLS-family estimator, OPLS and
kernel PLS, together
with truncated singular value decomposition backends, discriminant
classifiers, cross-validation utilities and optional 'CUDA' or Apple 'Metal'
acceleration when the required system libraries are available. Compact
latent prediction and memory-aware numerical routes support analyses with
large predictor or multivariate-response matrices.
Author: Stefano Cacciatore [aut, cre] ,
Dupe Ojo [aut] ,
Leonardo Tenori [aut] ,
Alessia Vignoli [aut]
Maintainer: Stefano Cacciatore <tkcaccia@gmail.com>
Diff between fastPLS versions 0.2 dated 2024-12-11 and 0.3 dated 2026-09-28
fastPLS-0.2/fastPLS/R/RcppExports.R |only fastPLS-0.2/fastPLS/inst/include/fastPLS.h |only fastPLS-0.2/fastPLS/man/fastPLS-internal.Rd |only fastPLS-0.2/fastPLS/man/optim.pls.cv.Rd |only fastPLS-0.2/fastPLS/man/transformy.Rd |only fastPLS-0.2/fastPLS/src/Makevars |only fastPLS-0.2/fastPLS/src/Makevars.win |only fastPLS-0.2/fastPLS/src/RcppExports.cpp |only fastPLS-0.2/fastPLS/src/export-inline-header.cpp |only fastPLS-0.2/fastPLS/src/fastPLS.cpp |only fastPLS-0.2/fastPLS/src/irlba.c |only fastPLS-0.2/fastPLS/src/irlba.h |only fastPLS-0.3/fastPLS/DESCRIPTION | 81 fastPLS-0.3/fastPLS/INSTALL |only fastPLS-0.3/fastPLS/LICENSE |only fastPLS-0.3/fastPLS/MD5 | 116 fastPLS-0.3/fastPLS/NAMESPACE | 32 fastPLS-0.3/fastPLS/NEWS.md |only fastPLS-0.3/fastPLS/R/backend.R |only fastPLS-0.3/fastPLS/R/main.R |13946 ++++++++++++++++++- fastPLS-0.3/fastPLS/R/native_api.R |only fastPLS-0.3/fastPLS/R/resident_cuda.R |only fastPLS-0.3/fastPLS/README.md |only fastPLS-0.3/fastPLS/build |only fastPLS-0.3/fastPLS/cleanup |only fastPLS-0.3/fastPLS/configure |only fastPLS-0.3/fastPLS/configure.win |only fastPLS-0.3/fastPLS/inst/DATA_SOURCES.md |only fastPLS-0.3/fastPLS/inst/doc |only fastPLS-0.3/fastPLS/inst/include/fastpls |only fastPLS-0.3/fastPLS/inst/licenses |only fastPLS-0.3/fastPLS/man/ViP.Rd | 55 fastPLS-0.3/fastPLS/man/cuda_info.Rd |only fastPLS-0.3/fastPLS/man/evaluate.Rd |only fastPLS-0.3/fastPLS/man/fastPLS_blas.Rd |only fastPLS-0.3/fastPLS/man/fastcor.Rd | 73 fastPLS-0.3/fastPLS/man/fastsvd.Rd |only fastPLS-0.3/fastPLS/man/has_cuda.Rd |only fastPLS-0.3/fastPLS/man/has_metal.Rd |only fastPLS-0.3/fastPLS/man/plot.fastPLS.Rd |only fastPLS-0.3/fastPLS/man/plot.permutation.Rd |only fastPLS-0.3/fastPLS/man/pls.Rd | 337 fastPLS-0.3/fastPLS/man/pls.double.cv.Rd | 323 fastPLS-0.3/fastPLS/man/pls.single.cv.Rd |only fastPLS-0.3/fastPLS/man/predict.fastPLS.Rd | 112 fastPLS-0.3/fastPLS/src/Makevars.in |only fastPLS-0.3/fastPLS/src/Makevars.win.in |only fastPLS-0.3/fastPLS/src/accelerator_core_backend.h |only fastPLS-0.3/fastPLS/src/core_accelerator_stubs.cpp |only fastPLS-0.3/fastPLS/src/core_cpu_backend.cpp |only fastPLS-0.3/fastPLS/src/core_cpu_backend.h |only fastPLS-0.3/fastPLS/src/core_cpu_lapack.cpp |only fastPLS-0.3/fastPLS/src/core_cpu_lapack_f32.cpp |only fastPLS-0.3/fastPLS/src/core_cuda_backend.cu |only fastPLS-0.3/fastPLS/src/core_init.cpp |only fastPLS-0.3/fastPLS/src/core_metal_backend.mm.in |only fastPLS-0.3/fastPLS/src/cuda_resident_api.cuh |only fastPLS-0.3/fastPLS/src/cuda_resident_api.h |only fastPLS-0.3/fastPLS/src/cuda_resident_component.cuh |only fastPLS-0.3/fastPLS/src/cuda_resident_labels.cuh |only fastPLS-0.3/fastPLS/src/cuda_resident_lda.cuh |only fastPLS-0.3/fastPLS/src/cuda_resident_metrics.cuh |only fastPLS-0.3/fastPLS/src/cuda_resident_plssvd.cuh |only fastPLS-0.3/fastPLS/src/cuda_resident_preprocess.cuh |only fastPLS-0.3/fastPLS/src/cuda_resident_r.cpp |only fastPLS-0.3/fastPLS/src/cuda_resident_rsvd.cuh |only fastPLS-0.3/fastPLS/src/cuda_resident_simpls.cuh |only fastPLS-0.3/fastPLS/src/cuda_resident_special.cuh |only fastPLS-0.3/fastPLS/src/cuda_resident_variance.cuh |only fastPLS-0.3/fastPLS/src/r_api.cpp |only fastPLS-0.3/fastPLS/src/r_api.h |only fastPLS-0.3/fastPLS/src/rsvd_audit.cpp |only fastPLS-0.3/fastPLS/src/rsvd_audit.h |only fastPLS-0.3/fastPLS/tests |only fastPLS-0.3/fastPLS/tools |only fastPLS-0.3/fastPLS/vignettes |only 76 files changed, 14444 insertions(+), 631 deletions(-)
Title: Robust Bayesian Longitudinal Regularized Semiparametric Mixed
Models
Description: Our recently developed fully robust Bayesian semiparametric mixed-effect model for high-dimensional longitudinal studies with heterogeneous observations can be implemented through this package. This model can distinguish between time-varying interactions and constant-effect-only cases to avoid model misspecifications. Facilitated by spike-and-slab priors, this model leads to superior performance in estimation, identification and statistical inference. In particular, robust Bayesian inferences in terms of valid Bayesian credible intervals on both parametric and nonparametric effects can be validated on finite samples. The Markov chain Monte Carlo algorithms of the proposed and alternative models are efficiently implemented in 'C++'.
Author: Kun Fan [aut, cre],
Cen Wu [aut]
Maintainer: Kun Fan <fzt0428@gmail.com>
Diff between Blend versions 0.1.2 dated 2026-02-16 and 0.1.3 dated 2026-09-28
DESCRIPTION | 14 +++++++------- MD5 | 10 +++++----- R/Blend-package.R | 6 ++++-- README.md | 6 +++++- build/partial.rdb |binary man/Blend-package.Rd | 11 +++++++---- 6 files changed, 28 insertions(+), 19 deletions(-)
Title: Parse 'Tableau' Workbooks into Functional Data
Description: High-performance parsing of 'Tableau' workbook files into
tidy data frames and dependency graphs for other visualization tools
like R 'Shiny' or 'Power BI' replication, plus an interactive 'Shiny'
workbook inspector for uploaded .twb and .twbx files.
Author: George Arthur [aut, cre]
Maintainer: George Arthur <prigasgenthian48@gmail.com>
Diff between twbparser versions 0.5.0 dated 2026-06-18 and 0.5.1 dated 2026-09-28
twbparser-0.5.0/twbparser/R/server_api.R |only twbparser-0.5.0/twbparser/man/print_datasource_summary.Rd |only twbparser-0.5.0/twbparser/man/tbs_custom_sql_graphql.Rd |only twbparser-0.5.0/twbparser/man/tbs_publish_info.Rd |only twbparser-0.5.1/twbparser/DESCRIPTION | 8 twbparser-0.5.1/twbparser/MD5 | 84 - twbparser-0.5.1/twbparser/NAMESPACE | 18 twbparser-0.5.1/twbparser/NEWS.md | 307 +++- twbparser-0.5.1/twbparser/R/active-bindings.R | 14 twbparser-0.5.1/twbparser/R/analytics.R | 499 +++---- twbparser-0.5.1/twbparser/R/dashboard_details.R | 14 twbparser-0.5.1/twbparser/R/formatting.R | 630 ++++------ twbparser-0.5.1/twbparser/R/insights.R | 17 twbparser-0.5.1/twbparser/R/migration.R |only twbparser-0.5.1/twbparser/R/parse_twb.R |only twbparser-0.5.1/twbparser/R/rebuild.R |only twbparser-0.5.1/twbparser/R/report.R | 114 - twbparser-0.5.1/twbparser/R/sheet_details.R | 28 twbparser-0.5.1/twbparser/R/twb_parser.R | 283 +++- twbparser-0.5.1/twbparser/R/utils.R | 76 - twbparser-0.5.1/twbparser/R/validators.R | 8 twbparser-0.5.1/twbparser/R/viz_spec.R |only twbparser-0.5.1/twbparser/README.md | 545 ++++---- twbparser-0.5.1/twbparser/inst/WORDLIST | 51 twbparser-0.5.1/twbparser/inst/cheatsheet/twbparser-cheatsheet.tex | 26 twbparser-0.5.1/twbparser/inst/doc/twbparser-intro.R | 35 twbparser-0.5.1/twbparser/inst/doc/twbparser-intro.Rmd | 76 + twbparser-0.5.1/twbparser/inst/doc/twbparser-intro.html | 176 ++ twbparser-0.5.1/twbparser/inst/extdata/rebuild_kit.twb |only twbparser-0.5.1/twbparser/man/TwbParser.Rd | 197 +-- twbparser-0.5.1/twbparser/man/audit_tableau_folder.Rd |only twbparser-0.5.1/twbparser/man/export_migration_bundle.Rd |only twbparser-0.5.1/twbparser/man/parse_twb.Rd |only twbparser-0.5.1/twbparser/man/render_migration_brief.Rd |only twbparser-0.5.1/twbparser/man/scaffold_quarto_dashboard.Rd |only twbparser-0.5.1/twbparser/man/scaffold_shiny_dashboard.Rd |only twbparser-0.5.1/twbparser/man/translate_tableau_calc.Rd |only twbparser-0.5.1/twbparser/man/twb_calc_build_order.Rd |only twbparser-0.5.1/twbparser/man/twb_compatibility.Rd |only twbparser-0.5.1/twbparser/man/twb_dashboard_size.Rd | 84 - twbparser-0.5.1/twbparser/man/twb_formatting.Rd | 96 - twbparser-0.5.1/twbparser/man/twb_lineage.Rd |only twbparser-0.5.1/twbparser/man/twb_migration_assessment.Rd |only twbparser-0.5.1/twbparser/man/twb_parameter_usage.Rd |only twbparser-0.5.1/twbparser/man/twb_sheet_spec.Rd |only twbparser-0.5.1/twbparser/man/twb_tooltips.Rd | 74 - twbparser-0.5.1/twbparser/man/twb_unused_fields.Rd |only twbparser-0.5.1/twbparser/man/validate_relationships.Rd | 4 twbparser-0.5.1/twbparser/tests/testthat/Rplots.pdf |only twbparser-0.5.1/twbparser/tests/testthat/test-active-bindings.R | 18 twbparser-0.5.1/twbparser/tests/testthat/test-formatting.R | 262 ++-- twbparser-0.5.1/twbparser/tests/testthat/test-migration.R |only twbparser-0.5.1/twbparser/tests/testthat/test-parse_twb.R |only twbparser-0.5.1/twbparser/tests/testthat/test-rebuild.R |only twbparser-0.5.1/twbparser/tests/testthat/test-release-integration.R |only twbparser-0.5.1/twbparser/tests/testthat/test-shiny-app.R |only twbparser-0.5.1/twbparser/tests/testthat/test-viz_spec.R |only twbparser-0.5.1/twbparser/vignettes/twbparser-intro.Rmd | 76 + 58 files changed, 2264 insertions(+), 1556 deletions(-)
Title: Diagnostics for OMOP Common Data Model Drug Records
Description: Ingredient specific diagnostics for drug exposure records in the Observational Medical Outcomes Partnership (OMOP) common data model.
Author: Ger Inberg [aut, cre] ,
Edward Burn [aut] ,
Theresa Burkard [aut] ,
Yuchen Guo [ctb] ,
Marti Catala [ctb] ,
Mike Du [ctb] ,
Xintong Li [ctb] ,
Ross Williams [ctb] ,
Erasmus MC [cph]
Maintainer: Ger Inberg <g.inberg@erasmusmc.nl>
Diff between DrugExposureDiagnostics versions 1.1.10 dated 2026-07-26 and 1.2.0 dated 2026-09-28
DrugExposureDiagnostics-1.1.10/DrugExposureDiagnostics/inst/testCases |only DrugExposureDiagnostics-1.2.0/DrugExposureDiagnostics/DESCRIPTION | 14 DrugExposureDiagnostics-1.2.0/DrugExposureDiagnostics/MD5 | 47 +- DrugExposureDiagnostics-1.2.0/DrugExposureDiagnostics/NAMESPACE | 9 DrugExposureDiagnostics-1.2.0/DrugExposureDiagnostics/NEWS.md | 3 DrugExposureDiagnostics-1.2.0/DrugExposureDiagnostics/R/DrugExposureDiagnostics-package.R | 1 DrugExposureDiagnostics-1.2.0/DrugExposureDiagnostics/R/checkTimeBetween.R | 9 DrugExposureDiagnostics-1.2.0/DrugExposureDiagnostics/R/executeChecks.R | 24 + DrugExposureDiagnostics-1.2.0/DrugExposureDiagnostics/build/vignette.rds |binary DrugExposureDiagnostics-1.2.0/DrugExposureDiagnostics/inst/doc/DrugSig.html | 2 DrugExposureDiagnostics-1.2.0/DrugExposureDiagnostics/inst/doc/DrugTimeBetween.R |only DrugExposureDiagnostics-1.2.0/DrugExposureDiagnostics/inst/doc/DrugTimeBetween.Rmd |only DrugExposureDiagnostics-1.2.0/DrugExposureDiagnostics/inst/doc/DrugTimeBetween.html |only DrugExposureDiagnostics-1.2.0/DrugExposureDiagnostics/inst/doc/IntroductionToDrugExposureDiagnostics.Rmd | 4 DrugExposureDiagnostics-1.2.0/DrugExposureDiagnostics/inst/doc/IntroductionToDrugExposureDiagnostics.html | 10 DrugExposureDiagnostics-1.2.0/DrugExposureDiagnostics/man/DrugExposureDiagnostics-package.Rd | 1 DrugExposureDiagnostics-1.2.0/DrugExposureDiagnostics/man/ShinyApp.Rd | 87 ++--- DrugExposureDiagnostics-1.2.0/DrugExposureDiagnostics/man/ShinyModule.Rd | 158 +++++----- DrugExposureDiagnostics-1.2.0/DrugExposureDiagnostics/man/dataPlotPanel.Rd | 146 ++++----- DrugExposureDiagnostics-1.2.0/DrugExposureDiagnostics/man/executeChecks.Rd | 4 DrugExposureDiagnostics-1.2.0/DrugExposureDiagnostics/man/executeChecksSingleIngredient.Rd | 4 DrugExposureDiagnostics-1.2.0/DrugExposureDiagnostics/man/metaDataPanel.Rd | 136 ++++---- DrugExposureDiagnostics-1.2.0/DrugExposureDiagnostics/man/summariseTimeBetween.Rd | 9 DrugExposureDiagnostics-1.2.0/DrugExposureDiagnostics/tests/testthat/test-SyntheaSqlServer.R | 2 DrugExposureDiagnostics-1.2.0/DrugExposureDiagnostics/tests/testthat/test-checkTimeBetween.R | 30 + DrugExposureDiagnostics-1.2.0/DrugExposureDiagnostics/vignettes/DrugTimeBetween.Rmd |only DrugExposureDiagnostics-1.2.0/DrugExposureDiagnostics/vignettes/IntroductionToDrugExposureDiagnostics.Rmd | 4 27 files changed, 377 insertions(+), 327 deletions(-)
More information about DrugExposureDiagnostics at CRAN
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Title: Access the 'TransfereGov' Open Data APIs
Description: Provides a modern interface to the open data application
programming interfaces of the Brazilian federal government's
'TransfereGov' platform
(<https://www.gov.br/transferegov/pt-br/ferramentas-gestao/dados-abertos>).
Covers the special transfers, fund-to-fund transfers, partnership
management, and decentralized credit ('TED') modules, which together
publish seventy-four tables on action plans, programs, proposals,
partnerships, budget commitments, credit notes, financial execution,
management reports, and payment orders. Filters are the
services' own typed query parameters, validated against the published
schema before a request is made, and results are returned as tidy tibbles
with types taken from that schema. Automatic pagination, request
throttling, retries with exponential backoff, and an optional response
cache are included.
Author: Andre Leite [aut, cre] ,
Marcos Wasiliew [aut],
Hugo Vasconcelos [aut] ,
Carlos Amorim [aut] ,
Diogo Bezerra [aut] ,
Julia Nascimento Barreto [aut]
Maintainer: Andre Leite <leite@castlab.org>
Diff between transferegovr versions 0.1.0 dated 2026-08-08 and 0.2.0 dated 2026-09-28
transferegovr-0.1.0/transferegovr/R/filters.R |only transferegovr-0.1.0/transferegovr/man/filters.Rd |only transferegovr-0.1.0/transferegovr/man/tg_operators.Rd |only transferegovr-0.1.0/transferegovr/tests/testthat/test-filters.R |only transferegovr-0.2.0/transferegovr/DESCRIPTION | 26 transferegovr-0.2.0/transferegovr/MD5 | 91 + transferegovr-0.2.0/transferegovr/NAMESPACE | 26 transferegovr-0.2.0/transferegovr/NEWS.md | 149 ++- transferegovr-0.2.0/transferegovr/R/client.R | 235 ++--- transferegovr-0.2.0/transferegovr/R/get.R | 433 +++------ transferegovr-0.2.0/transferegovr/R/metadata.R | 135 +- transferegovr-0.2.0/transferegovr/R/params.R |only transferegovr-0.2.0/transferegovr/R/parse.R | 50 - transferegovr-0.2.0/transferegovr/R/sysdata.rda |binary transferegovr-0.2.0/transferegovr/R/transferegovr-package.R | 3 transferegovr-0.2.0/transferegovr/README.md | 200 ++-- transferegovr-0.2.0/transferegovr/inst/WORDLIST | 8 transferegovr-0.2.0/transferegovr/inst/doc/joining-tables.R | 100 +- transferegovr-0.2.0/transferegovr/inst/doc/joining-tables.Rmd | 340 ++++--- transferegovr-0.2.0/transferegovr/inst/doc/joining-tables.html | 430 +++++---- transferegovr-0.2.0/transferegovr/inst/doc/pagination.R | 133 +- transferegovr-0.2.0/transferegovr/inst/doc/pagination.Rmd | 285 +++--- transferegovr-0.2.0/transferegovr/inst/doc/pagination.html | 311 +++--- transferegovr-0.2.0/transferegovr/inst/doc/transferegovr.R | 197 ++-- transferegovr-0.2.0/transferegovr/inst/doc/transferegovr.Rmd | 341 ++++--- transferegovr-0.2.0/transferegovr/inst/doc/transferegovr.html | 370 ++++--- transferegovr-0.2.0/transferegovr/man/figures/architecture.svg | 171 ++- transferegovr-0.2.0/transferegovr/man/module_shortcuts.Rd | 18 transferegovr-0.2.0/transferegovr/man/tg_count.Rd | 36 transferegovr-0.2.0/transferegovr/man/tg_fields.Rd | 28 transferegovr-0.2.0/transferegovr/man/tg_get.Rd | 106 +- transferegovr-0.2.0/transferegovr/man/tg_metadata.Rd | 4 transferegovr-0.2.0/transferegovr/man/tg_modules.Rd | 7 transferegovr-0.2.0/transferegovr/man/tg_params.Rd |only transferegovr-0.2.0/transferegovr/man/tg_schema_date.Rd | 4 transferegovr-0.2.0/transferegovr/man/tg_tables.Rd | 18 transferegovr-0.2.0/transferegovr/man/tg_updated_at.Rd |only transferegovr-0.2.0/transferegovr/man/transferegovr-package.Rd | 2 transferegovr-0.2.0/transferegovr/tests/testthat/_snaps |only transferegovr-0.2.0/transferegovr/tests/testthat/helper-mocks.R | 72 - transferegovr-0.2.0/transferegovr/tests/testthat/setup.R |only transferegovr-0.2.0/transferegovr/tests/testthat/test-cache.R | 44 transferegovr-0.2.0/transferegovr/tests/testthat/test-client.R | 299 ++---- transferegovr-0.2.0/transferegovr/tests/testthat/test-live.R | 355 ++++++- transferegovr-0.2.0/transferegovr/tests/testthat/test-metadata.R | 184 ++- transferegovr-0.2.0/transferegovr/tests/testthat/test-pagination.R | 465 +++++----- transferegovr-0.2.0/transferegovr/tests/testthat/test-params.R |only transferegovr-0.2.0/transferegovr/tests/testthat/test-parse.R | 84 + transferegovr-0.2.0/transferegovr/vignettes/joining-tables.Rmd | 340 ++++--- transferegovr-0.2.0/transferegovr/vignettes/pagination.Rmd | 285 +++--- transferegovr-0.2.0/transferegovr/vignettes/transferegovr.Rmd | 341 ++++--- 51 files changed, 3765 insertions(+), 2961 deletions(-)
Title: Deploy Docs, Apps, and APIs to 'Posit Connect', 'shinyapps.io',
and 'RPubs'
Description: Programmatic deployment interface for 'RPubs',
'shinyapps.io', and 'Posit Connect'. Supported content types include R
Markdown documents, Shiny applications, Plumber APIs, plots, and
static web content.
Author: Aron Atkins [aut, cre],
Toph Allen [aut],
Hadley Wickham [aut],
Jonathan McPherson [aut],
JJ Allaire [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Aron Atkins <aron@posit.co>
Diff between rsconnect versions 1.11.1 dated 2026-09-21 and 1.11.2 dated 2026-09-28
rsconnect-1.11.1/rsconnect/tests/integration |only rsconnect-1.11.2/rsconnect/DESCRIPTION | 6 rsconnect-1.11.2/rsconnect/MD5 | 66 - rsconnect-1.11.2/rsconnect/NAMESPACE | 1 rsconnect-1.11.2/rsconnect/NEWS.md | 12 rsconnect-1.11.2/rsconnect/R/auth.R | 4 rsconnect-1.11.2/rsconnect/R/client-connect.R | 7 rsconnect-1.11.2/rsconnect/R/client-connectCloud.R | 23 rsconnect-1.11.2/rsconnect/R/client-shinyapps.R | 7 rsconnect-1.11.2/rsconnect/R/deleteContent.R |only rsconnect-1.11.2/rsconnect/R/deployApp.R | 66 + rsconnect-1.11.2/rsconnect/R/servers.R | 6 rsconnect-1.11.2/rsconnect/build/vignette.rds |binary rsconnect-1.11.2/rsconnect/man/deleteContent.Rd |only rsconnect-1.11.2/rsconnect/man/deployApp.Rd | 21 rsconnect-1.11.2/rsconnect/tests/testthat/_snaps/deployApp.md | 23 rsconnect-1.11.2/rsconnect/tests/testthat/helper-http.R | 20 rsconnect-1.11.2/rsconnect/tests/testthat/helper.R | 76 + rsconnect-1.11.2/rsconnect/tests/testthat/test-accounts.R | 18 rsconnect-1.11.2/rsconnect/tests/testthat/test-appMetadata.R | 24 rsconnect-1.11.2/rsconnect/tests/testthat/test-applications.R | 65 + rsconnect-1.11.2/rsconnect/tests/testthat/test-auth.R | 135 ++ rsconnect-1.11.2/rsconnect/tests/testthat/test-bundlePackageRenv.R | 32 rsconnect-1.11.2/rsconnect/tests/testthat/test-client-connectCloud.R | 79 + rsconnect-1.11.2/rsconnect/tests/testthat/test-client.R | 16 rsconnect-1.11.2/rsconnect/tests/testthat/test-configureApp.R |only rsconnect-1.11.2/rsconnect/tests/testthat/test-deleteContent.R |only rsconnect-1.11.2/rsconnect/tests/testthat/test-deployApp.R | 547 +++++++++- rsconnect-1.11.2/rsconnect/tests/testthat/test-deployTFModel.R |only rsconnect-1.11.2/rsconnect/tests/testthat/test-deploymentTarget.R | 3 rsconnect-1.11.2/rsconnect/tests/testthat/test-envvars.R |only rsconnect-1.11.2/rsconnect/tests/testthat/test-identityFederation.R | 8 rsconnect-1.11.2/rsconnect/tests/testthat/test-migrateToConnectCloud.R | 13 rsconnect-1.11.2/rsconnect/tests/testthat/test-purgeApp.R |only rsconnect-1.11.2/rsconnect/tests/testthat/test-restartApp.R |only rsconnect-1.11.2/rsconnect/tests/testthat/test-servers.R | 27 rsconnect-1.11.2/rsconnect/tests/testthat/test-tasks.R |only rsconnect-1.11.2/rsconnect/tests/testthat/test-terminateApp.R |only rsconnect-1.11.2/rsconnect/tests/testthat/test-usage.R |only 39 files changed, 1198 insertions(+), 107 deletions(-)
Title: Diagnostics and Models for Underdispersed Count Data
Description: Tools for detecting and modeling underdispersion in count data
(conditional variance below the conditional mean), the case the Poisson and
negative binomial defaults cannot represent. Provides a screening diagnostic
that benchmarks at-risk dispersion against a zero-truncated Poisson,
regression-adjusted tests of equidispersion, and a dispersion profile that
compares the variance-to-mean curves of competing families against the data;
the continuous parameter binomial (CPB) and generalized event count (Katz)
regressions with zero-truncated, hurdle, and zero-inflated forms and
high-dimensional fixed effects with a split-panel jackknife bias correction;
matched Poisson, negative binomial, COM-Poisson (rate- and mean-parameterized),
generalized Poisson, gamma-count, and double Poisson regressions through the
same interface, with frequency weights, offsets, and analytic, robust, and
cluster-robust standard errors; bootstrap and profile-likelihood inference;
proper scoring rules, rootograms, [...truncated...]
Author: Benjamin E. Bagozzi [aut, cre]
Maintainer: Benjamin E. Bagozzi <bagozzib@udel.edu>
Diff between underdisp versions 0.1.0 dated 2026-08-20 and 0.1.1 dated 2026-09-28
DESCRIPTION | 44 MD5 | 200 ++-- NAMESPACE | 524 ++++++----- NEWS.md | 602 ++++++++++--- R/RcppExports.R | 56 + R/broom.R | 29 R/calibrate_alpha.R |only R/calibration.R | 903 +++++++++++--------- R/compois.R | 38 R/count_families.R |only R/cpb.R | 705 +++++++++++---- R/data.R | 81 - R/dispersion_profile.R |only R/dispersion_test.R |only R/distributions.R | 430 +++++---- R/family.R | 388 ++++---- R/fe.R | 576 +++++++------ R/gec.R | 910 +++++++++++--------- R/gec_variants.R | 656 ++++++++------ R/glm_families.R | 1324 ++++++++++++++++-------------- R/hurdle.R | 441 +++++---- R/jackknife.R | 4 R/methods.R | 266 +++--- R/parity_methods.R | 976 +++++++++++++--------- R/qoi.R | 479 +++++----- R/qoi_count.R | 516 ++++++----- R/qoi_mixture.R | 489 +++++------ R/simulate.R | 25 R/ud_screen.R | 107 +- R/underdisp-package.R | 31 R/utils.R |only R/zi.R | 941 +++++++++++---------- R/zzz.R | 74 + README.md | 221 ++--- inst/CITATION |only inst/doc/underdisp.R | 50 - inst/doc/underdisp.Rmd | 539 ++++++------ inst/doc/underdisp.html | 417 +++++---- man/alpha_confint.Rd | 62 - man/calibrate_alpha.Rd |only man/compare_models.Rd | 78 - man/compois-distribution.Rd | 23 man/confint.cpb.Rd | 54 - man/confint.underdisp.Rd |only man/count_reg.Rd | 123 ++ man/cpb-distribution.Rd | 5 man/cpb.Rd | 234 +++-- man/cpb_fe.Rd | 281 +++--- man/cv_score.Rd | 118 +- man/dispersion_profile.Rd |only man/dispersion_test.Rd |only man/doublepois-distribution.Rd |only man/first_difference.Rd | 115 +- man/first_difference.hurdle_cpb.Rd | 4 man/gammacount-distribution.Rd |only man/gec-distribution.Rd | 15 man/gec.Rd | 19 man/gec_fe.Rd | 18 man/genpois-distribution.Rd |only man/hurdle_count.Rd | 29 man/hurdle_cpb.Rd | 7 man/hurdle_gec.Rd | 7 man/implied_ceiling.Rd | 76 - man/irr.Rd | 72 - man/irr.count.Rd | 15 man/peacekeeping.Rd | 99 +- man/pit_hist.Rd | 83 - man/predict.count_reg.Rd | 7 man/predict.cpb.Rd | 9 man/predict.cpb_fe.Rd | 11 man/rcpb.Rd | 65 - man/rootogram.Rd | 82 - man/score.Rd | 102 +- man/summary.cpb.Rd | 43 man/tidy.cpb.Rd | 5 man/ud_screen.Rd | 229 ++--- man/underdisp-package.Rd | 41 man/zi_count.Rd | 33 man/zi_cpb.Rd | 9 man/zi_gec.Rd | 9 src/RcppExports.cpp | 195 ++++ src/cmp_mean.cpp |only src/cpb_fe.cpp | 367 ++++++-- src/cpb_ll.cpp | 80 - src/cpb_pmf.h |only src/family_norm.cpp |only src/gec_fe.cpp | 276 +++++- src/gec_ll.cpp | 68 + tests/testthat/test-alpha-interval.R |only tests/testthat/test-arguments.R |only tests/testthat/test-calibrate-alpha.R |only tests/testthat/test-calibration-weights.R |only tests/testthat/test-calibration.R | 80 + tests/testthat/test-compois-ridge.R |only tests/testthat/test-dispersion-weights.R |only tests/testthat/test-dispersion.R |only tests/testthat/test-edge-usability.R |only tests/testthat/test-families.R |only tests/testthat/test-fe-inner.R |only tests/testthat/test-fe-mixture.R | 70 - tests/testthat/test-fe.R | 56 - tests/testthat/test-glm-families.R | 4 tests/testthat/test-guard-warning.R |only tests/testthat/test-hurdle.R | 83 + tests/testthat/test-newdata-coding.R |only tests/testthat/test-overconditioning.R | 2 tests/testthat/test-parity2.R |only tests/testthat/test-qoi-mixture.R | 2 tests/testthat/test-qoi-parity.R | 4 tests/testthat/test-review1.R |only tests/testthat/test-review2-numerics.R |only tests/testthat/test-review2.R |only tests/testthat/test-screen-boot.R | 2 tests/testthat/test-screen-nb.R |only tests/testthat/test-tables.R | 8 tests/testthat/test-weights.R |only tests/testthat/test-zi-fe-symmetric.R | 2 vignettes/underdisp.Rmd | 539 ++++++------ 118 files changed, 10052 insertions(+), 7010 deletions(-)
Title: Metabolomics and Spectral Data Analysis and Mining
Description: Provides methods for metabolomics and spectral data analysis,
including data import, preprocessing, visualization, univariate and
multivariate analysis, machine learning, feature selection, and pathway
analysis. The package supports analytical workflows for different data
types used in metabolomics and spectroscopy. Some optional functionality
uses the suggested packages 'cyjShiny' and 'specmine.datasets'. The package
'specmine.datasets' is maintained separately at
<https://github.com/PedroFontao/specmine.datasets>.
Author: Christopher Costa [aut],
Marcelo Maraschin [aut],
Miguel Rocha [aut],
Sara Cardoso [aut],
Telma Afonso [aut],
Bruno Pereira [aut],
Pedro Fontao [aut, cre],
Rafael Moreira [aut],
C. Beleites [cph],
Jie Hao [cph]
Maintainer: Pedro Fontao <pedrofontao812004@gmail.com>
Diff between specmine versions 4.0.0 dated 2026-09-08 and 4.0.1 dated 2026-09-28
DESCRIPTION | 9 ++++++--- MD5 | 2 +- 2 files changed, 7 insertions(+), 4 deletions(-)
Title: Query 'Azure Data Lake Storage Gen2' with 'DuckDB'
Description: Provides convenience utilities for using 'DuckDB' directly over
datasets stored in 'Azure Data Lake Storage Gen2' (ADLS Gen2,
'abfss://'). Opens connections configured for Azure-backed 'Delta Lake'
and 'Parquet' data, registers Azure credentials as 'DuckDB' secrets, and
supports optional repository mirrors for restricted networks. Integrates
well with 'DBI' for SQL workflows and with 'dplyr' and 'dbplyr' for lazy
table queries.
Author: Pedro Baltazar [aut, cre, cph]
Maintainer: Pedro Baltazar <pedrobtz@gmail.com>
Diff between quak versions 0.1.0 dated 2026-06-09 and 0.1.1 dated 2026-09-28
quak-0.1.0/quak/tests/testthat/_problems |only quak-0.1.1/quak/DESCRIPTION | 22 +- quak-0.1.1/quak/MD5 | 90 ++++------ quak-0.1.1/quak/NAMESPACE | 2 quak-0.1.1/quak/NEWS.md | 65 +++++++ quak-0.1.1/quak/R/arrow.R |only quak-0.1.1/quak/R/azure.R | 38 +++- quak-0.1.1/quak/R/datasets.R | 117 +++++++++++-- quak-0.1.1/quak/R/delta.R | 7 quak-0.1.1/quak/R/lake.R | 22 +- quak-0.1.1/quak/R/options.R | 13 + quak-0.1.1/quak/R/repositories.R | 40 +++- quak-0.1.1/quak/R/tables.R | 57 +++--- quak-0.1.1/quak/R/zzz.R | 4 quak-0.1.1/quak/README.md | 120 ++++++++++--- quak-0.1.1/quak/inst |only quak-0.1.1/quak/man/az_account_scopes.Rd |only quak-0.1.1/quak/man/az_set_chain_secret.Rd | 4 quak-0.1.1/quak/man/az_set_sp_secret.Rd | 4 quak-0.1.1/quak/man/az_set_token_secret.Rd | 4 quak-0.1.1/quak/man/check_azure_url.Rd | 9 - quak-0.1.1/quak/man/collect.tbl_az.Rd | 16 + quak-0.1.1/quak/man/collect_arrow.Rd |only quak-0.1.1/quak/man/delta_url.Rd |only quak-0.1.1/quak/man/ext_cache_path.Rd | 2 quak-0.1.1/quak/man/load_delta.Rd | 5 quak-0.1.1/quak/man/normalize_azure_url.Rd |only quak-0.1.1/quak/man/quak-package.Rd | 6 quak-0.1.1/quak/man/stream_arrow.Rd |only quak-0.1.1/quak/man/tbl_delta.Rd | 7 quak-0.1.1/quak/tests/testthat/helper-tables.R |only quak-0.1.1/quak/tests/testthat/test-arrow.R |only quak-0.1.1/quak/tests/testthat/test-azure.R | 68 +++++++ quak-0.1.1/quak/tests/testthat/test-datasets.R | 189 +++++++++++++++++++-- quak-0.1.1/quak/tests/testthat/test-delta.R | 2 quak-0.1.1/quak/tests/testthat/test-lake.R | 51 ++++- quak-0.1.1/quak/tests/testthat/test-options.R | 14 + quak-0.1.1/quak/tests/testthat/test-repositories.R | 35 +++ quak-0.1.1/quak/tests/testthat/test-tables.R | 10 - 39 files changed, 818 insertions(+), 205 deletions(-)
Title: Fitting Latent Space Item Response Models using Joint Maximum
Likelihood Estimation
Description: In Latent Space Item Response Models, subjects and items are embedded in a multidimensional Euclidean latent space.
As such, interactions among persons, items, and person-item combinations can be revealed that are unmodelled in
more conventional item response theory models. This package implements the methods from Molenaar & Jeon (2026)<doi:10.1017/psy.2025.10068> and can be used to fit Latent Space Item Response Models
to data using joint maximum likelihood estimation. The package can handle binary data, ordinal data, and data with mixed scales.
The package incorporates facilities for data simulation, rotation of the latent space, and K-fold cross-validation to select the
number of dimensions of the latent space.
Author: Dylan Molenaar [aut, cre]
Maintainer: Dylan Molenaar <d.molenaar@uva.nl>
Diff between LSMjml versions 0.6.0 dated 2025-12-19 and 0.7.0 dated 2026-09-28
DESCRIPTION | 8 - MD5 | 29 ++--- NAMESPACE | 2 R/LSMboot.R |only R/LSMdist.R |only R/LSMfit.R | 318 +++++++++++++++++++++++++++++++++++++------------------ R/LSMrotate.R | 13 +- R/LSMselect.R | 3 R/LSMsim.R | 8 - R/LSMstartsMDS.R |only R/LSMvecpar.R | 2 man/LSMboot.Rd |only man/LSMdist.Rd |only man/LSMfit.Rd | 38 +++--- man/LSMrotate.Rd | 21 +-- man/LSMselect.Rd | 18 +-- man/LSMsim.Rd | 30 ++--- src/LSMjml.cpp | 8 - 18 files changed, 320 insertions(+), 178 deletions(-)
Title: Measuring Functional Diversity (FD) from Multiple Traits, and
Other Tools for Functional Ecology
Description: Computes different multidimensional FD indices. Implements a distance-based framework to measure FD that allows any number and type of functional traits, and can also consider species relative abundances. Also contains other useful tools for functional ecology.
Author: Etienne Laliberte [aut],
Pierre Legendre [aut],
Bill Shipley [aut],
Marcelino de la Cruz Rot [cre]
Maintainer: Marcelino de la Cruz Rot <marcelino.delacruz@urjc.es>
Diff between FD versions 1.0-12.5 dated 2026-05-04 and 1.0-12.6 dated 2026-09-28
DESCRIPTION | 24 ++++++++++++++---------- MD5 | 4 ++-- inst/NEWS | 7 ++++++- 3 files changed, 22 insertions(+), 13 deletions(-)
Title: Population Fisher Information Matrix
Description: Evaluate or optimize designs for nonlinear mixed effects models
using the Fisher Information matrix. Supports population, individual, and
Bayesian 'FIMs', covariates, inter-occasion variability, and D-optimal search
('Fedorov-Wynn', multiplicative, simplex, 'PSO', 'PGBO').
Author: Romain Leroux [aut] ,
France Mentre [cre] ,
Antoine Croxo [ctb] ,
Jeremy Seurat [ctb]
Maintainer: France Mentre <pfim@inserm.fr>
Diff between PFIM versions 7.0.3 dated 2026-04-09 and 8.0 dated 2026-09-28
PFIM-7.0.3/PFIM/R/ModelODEBolus.R |only PFIM-7.0.3/PFIM/R/ModelODEDoseInEquations.R |only PFIM-7.0.3/PFIM/R/ModelODEDoseNotInEquations.R |only PFIM-7.0.3/PFIM/R/plotMethods.R |only PFIM-7.0.3/PFIM/R/utils.R |only PFIM-7.0.3/PFIM/build/partial.rdb |only PFIM-7.0.3/PFIM/inst/doc/Design_Evaluation_and_Optimization_in_Continuous_Space.R |only PFIM-7.0.3/PFIM/inst/doc/Design_Evaluation_and_Optimization_in_Continuous_Space.Rmd |only PFIM-7.0.3/PFIM/inst/doc/Design_Evaluation_and_Optimization_in_Continuous_Space.html |only PFIM-7.0.3/PFIM/inst/doc/Design_Evaluation_and_Optimization_in_Discrete_Space.R |only PFIM-7.0.3/PFIM/inst/doc/Design_Evaluation_and_Optimization_in_Discrete_Space.Rmd |only PFIM-7.0.3/PFIM/inst/doc/Design_Evaluation_and_Optimization_in_Discrete_Space.html |only PFIM-7.0.3/PFIM/man/Combined.Rd |only PFIM-7.0.3/PFIM/man/computeVMat.Rd |only PFIM-7.0.3/PFIM/man/fisherSimplex.Rd |only PFIM-7.0.3/PFIM/man/fun.amoeba.Rd |only PFIM-7.0.3/PFIM/man/getListLastName.Rd |only PFIM-7.0.3/PFIM/man/plot.Rd |only PFIM-7.0.3/PFIM/man/show.Rd |only PFIM-7.0.3/PFIM/tests/testthat/test-example.R |only PFIM-7.0.3/PFIM/vignettes/Design_Evaluation_and_Optimization_in_Continuous_Space.Rmd |only PFIM-7.0.3/PFIM/vignettes/Design_Evaluation_and_Optimization_in_Discrete_Space.Rmd |only PFIM-7.0.3/PFIM/vignettes/Library_of_Models.html |only PFIM-7.0.3/PFIM/vignettes/figures |only PFIM-7.0.3/PFIM/vignettes/outputs |only PFIM-8.0/PFIM/DESCRIPTION | 119 PFIM-8.0/PFIM/LICENSE |only PFIM-8.0/PFIM/MD5 | 676 ++- PFIM-8.0/PFIM/NAMESPACE | 367 + PFIM-8.0/PFIM/NEWS.md | 166 PFIM-8.0/PFIM/R/Additive.R |only PFIM-8.0/PFIM/R/Administration.R | 143 PFIM-8.0/PFIM/R/AdministrationConstraints.R | 49 PFIM-8.0/PFIM/R/Arm.R | 997 ++--- PFIM-8.0/PFIM/R/BayesianFim.R | 952 ++--- PFIM-8.0/PFIM/R/CategoricalCovariate.R |only PFIM-8.0/PFIM/R/CategoricalCovariateWithIOV.R |only PFIM-8.0/PFIM/R/Combined1.R | 104 PFIM-8.0/PFIM/R/Combined2.R |only PFIM-8.0/PFIM/R/Constant.R | 107 PFIM-8.0/PFIM/R/Covariate.R |only PFIM-8.0/PFIM/R/CovariateModelEquation.R |only PFIM-8.0/PFIM/R/CovariateTest.R |only PFIM-8.0/PFIM/R/Design.R | 582 +-- PFIM-8.0/PFIM/R/Distribution.R | 76 PFIM-8.0/PFIM/R/Evaluation.R | 565 +-- PFIM-8.0/PFIM/R/Exponential.R |only PFIM-8.0/PFIM/R/FedorovWynnAlgorithm.R | 1813 ++------- PFIM-8.0/PFIM/R/Fim.R | 479 ++ PFIM-8.0/PFIM/R/IndividualFim.R | 752 +-- PFIM-8.0/PFIM/R/LibraryOfModels.R | 43 PFIM-8.0/PFIM/R/LibraryOfPDModels.R | 79 PFIM-8.0/PFIM/R/LibraryOfPKModels.R | 419 -- PFIM-8.0/PFIM/R/LogNormal.R | 32 PFIM-8.0/PFIM/R/Model.R | 608 ++- PFIM-8.0/PFIM/R/ModelAnalytic.R | 653 +-- PFIM-8.0/PFIM/R/ModelAnalyticInfusion.R | 680 +-- PFIM-8.0/PFIM/R/ModelAnalyticInfusionSteadyState.R | 537 -- PFIM-8.0/PFIM/R/ModelAnalyticSteadyState.R | 500 +- PFIM-8.0/PFIM/R/ModelError.R | 358 + PFIM-8.0/PFIM/R/ModelInfusion.R | 52 PFIM-8.0/PFIM/R/ModelODE.R | 527 ++ PFIM-8.0/PFIM/R/ModelODEInfusion.R | 71 PFIM-8.0/PFIM/R/ModelODEInfusionDoseInEquation.R | 595 +-- PFIM-8.0/PFIM/R/ModelParameter.R | 339 + PFIM-8.0/PFIM/R/MultiplicativeAlgorithm.R | 652 +-- PFIM-8.0/PFIM/R/Normal.R | 28 PFIM-8.0/PFIM/R/Optimization.R | 1406 ++----- PFIM-8.0/PFIM/R/PFIM-package.R | 184 PFIM-8.0/PFIM/R/PFIMProject.R | 974 ++--- PFIM-8.0/PFIM/R/PGBOAlgorithm.R | 524 -- PFIM-8.0/PFIM/R/PSOAlgorithm.R | 654 --- PFIM-8.0/PFIM/R/PopulationFim.R | 977 +---- PFIM-8.0/PFIM/R/Proportional.R | 100 PFIM-8.0/PFIM/R/RcppExports.R |only PFIM-8.0/PFIM/R/SamplingTimeConstraints.R | 485 +- PFIM-8.0/PFIM/R/SamplingTimes.R | 45 PFIM-8.0/PFIM/R/SimplexAlgorithm.R | 737 +-- PFIM-8.0/PFIM/R/covariate-test-power.R |only PFIM-8.0/PFIM/R/covariates-fim-indbayes.R |only PFIM-8.0/PFIM/R/covariates-fim.R |only PFIM-8.0/PFIM/R/evaluation-accessors.R |only PFIM-8.0/PFIM/R/evaluation-plots.R |only PFIM-8.0/PFIM/R/evaluation-report-kable.R |only PFIM-8.0/PFIM/R/evaluation-report.R |only PFIM-8.0/PFIM/R/model-analytic-eval.R |only PFIM-8.0/PFIM/R/model-covariates.R |only PFIM-8.0/PFIM/R/model-error-variance.R |only PFIM-8.0/PFIM/R/model-gradient.R |only PFIM-8.0/PFIM/R/model-library-remap.R |only PFIM-8.0/PFIM/R/model-ode-bolus-simulate.R |only PFIM-8.0/PFIM/R/model-ode-bolus.R |only PFIM-8.0/PFIM/R/model-type-dispatch.R |only PFIM-8.0/PFIM/R/model-variance.R |only PFIM-8.0/PFIM/R/pfim-arm-constraints.R |only PFIM-8.0/PFIM/R/pfim-constraint-grid.R |only PFIM-8.0/PFIM/R/pfim-constraints-helpers.R |only PFIM-8.0/PFIM/R/pfim-continuous-opt.R |only PFIM-8.0/PFIM/R/pfim-errors.R |only PFIM-8.0/PFIM/R/pfim-extensions.R |only PFIM-8.0/PFIM/R/pfim-fim-cache.R |only PFIM-8.0/PFIM/R/pfim-fim-labels.R |only PFIM-8.0/PFIM/R/pfim-fim-optimal-arms.R |only PFIM-8.0/PFIM/R/pfim-fim-optimizer-wiring.R |only PFIM-8.0/PFIM/R/pfim-fim-report-render.R |only PFIM-8.0/PFIM/R/pfim-flat-sampling-layout.R |only PFIM-8.0/PFIM/R/pfim-gradient-perf.R |only PFIM-8.0/PFIM/R/pfim-linear-algebra.R |only PFIM-8.0/PFIM/R/pfim-model-registry.R |only PFIM-8.0/PFIM/R/pfim-multi-design-opt.R |only PFIM-8.0/PFIM/R/pfim-plot-perf.R |only PFIM-8.0/PFIM/R/pfim-project-access.R |only PFIM-8.0/PFIM/R/pfim-rd-examples.R |only PFIM-8.0/PFIM/R/pfim-registry.R |only PFIM-8.0/PFIM/R/pfim-session.R |only PFIM-8.0/PFIM/R/pfim-subject-fim.R |only PFIM-8.0/PFIM/R/pfim-utils.R |only PFIM-8.0/PFIM/R/population-fim-variance.R |only PFIM-8.0/PFIM/R/s7-reexports.R |only PFIM-8.0/PFIM/R/zzz.R | 38 PFIM-8.0/PFIM/build/vignette.rds |binary PFIM-8.0/PFIM/inst/CITATION | 6 PFIM-8.0/PFIM/inst/doc/Example01.R |only PFIM-8.0/PFIM/inst/doc/Example01.Rmd |only PFIM-8.0/PFIM/inst/doc/Example01.html |only PFIM-8.0/PFIM/inst/doc/Example02.R |only PFIM-8.0/PFIM/inst/doc/Example02.Rmd |only PFIM-8.0/PFIM/inst/doc/Example02.html |only PFIM-8.0/PFIM/inst/doc/Example03.R |only PFIM-8.0/PFIM/inst/doc/Example03.Rmd |only PFIM-8.0/PFIM/inst/doc/Example03.html |only PFIM-8.0/PFIM/inst/doc/Example04.R |only PFIM-8.0/PFIM/inst/doc/Example04.Rmd |only PFIM-8.0/PFIM/inst/doc/Example04.html |only PFIM-8.0/PFIM/inst/doc/LibraryOfModels.R | 147 PFIM-8.0/PFIM/inst/doc/LibraryOfModels.Rmd | 1883 +++++----- PFIM-8.0/PFIM/inst/doc/LibraryOfModels.html | 95 PFIM-8.0/PFIM/inst/doc/index.html |only PFIM-8.0/PFIM/inst/examples |only PFIM-8.0/PFIM/inst/fixtures |only PFIM-8.0/PFIM/inst/include |only PFIM-8.0/PFIM/inst/rmarkdown/pfim-report-tables.css |only PFIM-8.0/PFIM/inst/rmarkdown/templates/skeleton/EvaluationBayesianFIM.Rmd | 206 - PFIM-8.0/PFIM/inst/rmarkdown/templates/skeleton/EvaluationIndividualFIM.Rmd | 212 - PFIM-8.0/PFIM/inst/rmarkdown/templates/skeleton/EvaluationPopulationFIM.Rmd | 214 - PFIM-8.0/PFIM/inst/rmarkdown/templates/skeleton/OptimizationFedorovWynnAlgorithmBayesianFIM.Rmd | 245 - PFIM-8.0/PFIM/inst/rmarkdown/templates/skeleton/OptimizationFedorovWynnAlgorithmIndividualFIM.Rmd | 250 - PFIM-8.0/PFIM/inst/rmarkdown/templates/skeleton/OptimizationFedorovWynnAlgorithmPopulationFIM.Rmd | 251 - PFIM-8.0/PFIM/inst/rmarkdown/templates/skeleton/OptimizationMultiplicativeAlgorithmBayesianFIM.Rmd | 246 - PFIM-8.0/PFIM/inst/rmarkdown/templates/skeleton/OptimizationMultiplicativeAlgorithmIndividualFIM.Rmd | 253 - PFIM-8.0/PFIM/inst/rmarkdown/templates/skeleton/OptimizationMultiplicativeAlgorithmPopulationFIM.Rmd | 252 - PFIM-8.0/PFIM/inst/rmarkdown/templates/skeleton/OptimizationPGBOAlgorithmBayesianFIM.Rmd | 234 - PFIM-8.0/PFIM/inst/rmarkdown/templates/skeleton/OptimizationPGBOAlgorithmIndividualFIM.Rmd | 240 - PFIM-8.0/PFIM/inst/rmarkdown/templates/skeleton/OptimizationPGBOAlgorithmPopulationFIM.Rmd | 241 - PFIM-8.0/PFIM/inst/rmarkdown/templates/skeleton/OptimizationPSOAlgorithmBayesianFIM.Rmd | 234 - PFIM-8.0/PFIM/inst/rmarkdown/templates/skeleton/OptimizationPSOAlgorithmIndividualFIM.Rmd | 240 - PFIM-8.0/PFIM/inst/rmarkdown/templates/skeleton/OptimizationPSOAlgorithmPopulationFIM.Rmd | 241 - PFIM-8.0/PFIM/inst/rmarkdown/templates/skeleton/OptimizationSimplexAlgorithmBayesianFIM.Rmd | 234 - PFIM-8.0/PFIM/inst/rmarkdown/templates/skeleton/OptimizationSimplexAlgorithmIndividualFIM.Rmd | 240 - PFIM-8.0/PFIM/inst/rmarkdown/templates/skeleton/OptimizationSimplexAlgorithmPopulationFIM.Rmd | 241 - PFIM-8.0/PFIM/inst/vignette-data |only PFIM-8.0/PFIM/inst/vignette-scripts |only PFIM-8.0/PFIM/man/Additive.Rd |only PFIM-8.0/PFIM/man/Administration.Rd | 83 PFIM-8.0/PFIM/man/AdministrationConstraints.Rd | 38 PFIM-8.0/PFIM/man/Arm.Rd | 92 PFIM-8.0/PFIM/man/BayesianFim.Rd | 67 PFIM-8.0/PFIM/man/CategoricalCovariate.Rd |only PFIM-8.0/PFIM/man/CategoricalCovariateWithIOV.Rd |only PFIM-8.0/PFIM/man/Combined1.Rd |only PFIM-8.0/PFIM/man/Combined2.Rd |only PFIM-8.0/PFIM/man/Constant.Rd | 48 PFIM-8.0/PFIM/man/Covariate.Rd |only PFIM-8.0/PFIM/man/CovariateModelEquation.Rd |only PFIM-8.0/PFIM/man/CovariateTest-class.Rd |only PFIM-8.0/PFIM/man/Dcriterion.Rd | 20 PFIM-8.0/PFIM/man/Design.Rd | 75 PFIM-8.0/PFIM/man/Distribution.Rd | 35 PFIM-8.0/PFIM/man/Evaluation.Rd | 96 PFIM-8.0/PFIM/man/Exponential.Rd |only PFIM-8.0/PFIM/man/FedorovWynnAlgorithm.Rd | 108 PFIM-8.0/PFIM/man/FedorovWynnAlgorithm_Rcpp.Rd | 51 PFIM-8.0/PFIM/man/Fim.Rd | 40 PFIM-8.0/PFIM/man/IndividualFim.Rd | 64 PFIM-8.0/PFIM/man/LibraryOfModels.Rd | 29 PFIM-8.0/PFIM/man/LibraryOfPDModels.Rd | 40 PFIM-8.0/PFIM/man/LibraryOfPKModels.Rd | 41 PFIM-8.0/PFIM/man/Linear2BolusSingleDose_ClQV1V2.Rd | 12 PFIM-8.0/PFIM/man/Linear2BolusSingleDose_kk12k21V.Rd | 12 PFIM-8.0/PFIM/man/Linear2BolusSteadyState_ClQV1V2tau.Rd | 12 PFIM-8.0/PFIM/man/Linear2BolusSteadyState_kk12k21Vtau.Rd | 12 PFIM-8.0/PFIM/man/Linear2FirstOrderSingleDose_kaClQV1V2.Rd | 12 PFIM-8.0/PFIM/man/Linear2FirstOrderSingleDose_kakk12k21V.Rd | 12 PFIM-8.0/PFIM/man/Linear2FirstOrderSteadyState_kaClQV1V2tau.Rd | 12 PFIM-8.0/PFIM/man/Linear2FirstOrderSteadyState_kakk12k21Vtau.Rd | 12 PFIM-8.0/PFIM/man/Linear2InfusionSingleDose_ClQV1V2.Rd | 12 PFIM-8.0/PFIM/man/Linear2InfusionSingleDose_kk12k21V.Rd | 12 PFIM-8.0/PFIM/man/Linear2InfusionSteadyState_ClQV1V2tau.Rd | 12 PFIM-8.0/PFIM/man/Linear2InfusionSteadyState_kk12k21Vtau.Rd | 12 PFIM-8.0/PFIM/man/LogNormal.Rd | 27 PFIM-8.0/PFIM/man/Model.Rd | 77 PFIM-8.0/PFIM/man/ModelAnalytic.Rd | 82 PFIM-8.0/PFIM/man/ModelAnalyticInfusion.Rd | 85 PFIM-8.0/PFIM/man/ModelAnalyticInfusionSteadyState.Rd | 83 PFIM-8.0/PFIM/man/ModelAnalyticSteadyState.Rd | 84 PFIM-8.0/PFIM/man/ModelError.Rd | 65 PFIM-8.0/PFIM/man/ModelInfusion.Rd | 74 PFIM-8.0/PFIM/man/ModelODE.Rd | 74 PFIM-8.0/PFIM/man/ModelODEBolus.Rd | 80 PFIM-8.0/PFIM/man/ModelODEDoseInEquations.Rd | 83 PFIM-8.0/PFIM/man/ModelODEDoseNotInEquations.Rd | 86 PFIM-8.0/PFIM/man/ModelODEInfusion.Rd | 80 PFIM-8.0/PFIM/man/ModelODEInfusionDoseInEquation.Rd | 86 PFIM-8.0/PFIM/man/ModelParameter.Rd | 69 PFIM-8.0/PFIM/man/MultiplicativeAlgorithm.Rd | 118 PFIM-8.0/PFIM/man/MultiplicativeAlgorithm_Rcpp.Rd | 57 PFIM-8.0/PFIM/man/Normal.Rd | 31 PFIM-8.0/PFIM/man/Optimization.Rd | 219 - PFIM-8.0/PFIM/man/PFIM-package.Rd | 139 PFIM-8.0/PFIM/man/PFIMProject.Rd | 99 PFIM-8.0/PFIM/man/PGBOAlgorithm.Rd | 118 PFIM-8.0/PFIM/man/PSOAlgorithm.Rd | 116 PFIM-8.0/PFIM/man/PopulationFim.Rd | 52 PFIM-8.0/PFIM/man/Proportional.Rd | 57 PFIM-8.0/PFIM/man/Report.Rd | 44 PFIM-8.0/PFIM/man/SamplingTimeConstraints.Rd | 94 PFIM-8.0/PFIM/man/SamplingTimes.Rd | 40 PFIM-8.0/PFIM/man/SimplexAlgorithm.Rd | 106 PFIM-8.0/PFIM/man/adjustGradient.Rd | 30 PFIM-8.0/PFIM/man/aggregateGradientsWithCovariates.Rd |only PFIM-8.0/PFIM/man/aggregateVarianceWithCovariates.Rd |only PFIM-8.0/PFIM/man/armAdministration.Rd | 26 PFIM-8.0/PFIM/man/checkSamplingTimeConstraintsForMetaheuristic.Rd | 46 PFIM-8.0/PFIM/man/checkValiditySamplingConstraint.Rd | 29 PFIM-8.0/PFIM/man/computeCovariateValue.Rd |only PFIM-8.0/PFIM/man/constraintsTableForReport.Rd | 42 PFIM-8.0/PFIM/man/convertPKModelAnalyticToPKModelODE.Rd | 56 PFIM-8.0/PFIM/man/covariateTest.Rd |only PFIM-8.0/PFIM/man/createEffectVector.Rd |only PFIM-8.0/PFIM/man/defineCovariatesData.Rd |only PFIM-8.0/PFIM/man/defineFim.Rd | 32 PFIM-8.0/PFIM/man/defineModelAdministration.Rd | 81 PFIM-8.0/PFIM/man/defineModelEquationsFromLibraryOfModel.Rd | 41 PFIM-8.0/PFIM/man/defineModelType.Rd | 42 PFIM-8.0/PFIM/man/defineModelWrapper.Rd | 54 PFIM-8.0/PFIM/man/defineOptimizationAlgorithm.Rd | 24 PFIM-8.0/PFIM/man/definePKModel.Rd | 84 PFIM-8.0/PFIM/man/definePKPDModel.Rd | 82 PFIM-8.0/PFIM/man/ensureModelOutputNames.Rd |only PFIM-8.0/PFIM/man/evaluateAnalyticCore.Rd |only PFIM-8.0/PFIM/man/evaluateAnalyticInfusionCore.Rd |only PFIM-8.0/PFIM/man/evaluateAnalyticInfusionSteadyStateCore.Rd |only PFIM-8.0/PFIM/man/evaluateAnalyticSteadyStateCore.Rd |only PFIM-8.0/PFIM/man/evaluateArm.Rd | 34 PFIM-8.0/PFIM/man/evaluateCovariatesEffects.Rd |only PFIM-8.0/PFIM/man/evaluateDesign.Rd | 26 PFIM-8.0/PFIM/man/evaluateErrorModelDerivatives.Rd | 24 PFIM-8.0/PFIM/man/evaluateFim.Rd | 59 PFIM-8.0/PFIM/man/evaluateInitialConditions.Rd | 32 PFIM-8.0/PFIM/man/evaluateModel.Rd | 84 PFIM-8.0/PFIM/man/evaluateModelGradient.Rd | 25 PFIM-8.0/PFIM/man/evaluateModelGradientCore.Rd |only PFIM-8.0/PFIM/man/evaluateModelGradientWithCovariates.Rd |only PFIM-8.0/PFIM/man/evaluateModelVariance.Rd | 30 PFIM-8.0/PFIM/man/evaluateModelWithCovariates.Rd |only PFIM-8.0/PFIM/man/evaluateOmegaMatrixFromCovariates.Rd |only PFIM-8.0/PFIM/man/evaluateVarianceFIM.Rd | 39 PFIM-8.0/PFIM/man/finiteDifferenceHessian.Rd | 36 PFIM-8.0/PFIM/man/fun_amoeba_Rcpp.Rd |only PFIM-8.0/PFIM/man/generateCovariatesCombination.Rd |only PFIM-8.0/PFIM/man/generateDosesCombination.Rd | 26 PFIM-8.0/PFIM/man/generateFimsFromConstraints.Rd | 39 PFIM-8.0/PFIM/man/generateReportEvaluation.Rd | 38 PFIM-8.0/PFIM/man/generateReportOptimization.Rd | 33 PFIM-8.0/PFIM/man/generateSamplingTimesCombination.Rd | 26 PFIM-8.0/PFIM/man/generateSamplingsFromSamplingConstraints.Rd | 33 PFIM-8.0/PFIM/man/getArmConstraints.Rd | 26 PFIM-8.0/PFIM/man/getArmData.Rd | 24 PFIM-8.0/PFIM/man/getArmEvaluationGradientsMatrix.Rd |only PFIM-8.0/PFIM/man/getArmEvaluationVarianceFlat.Rd |only PFIM-8.0/PFIM/man/getCategoryOfReference.Rd |only PFIM-8.0/PFIM/man/getCorrelationMatrix.Rd | 35 PFIM-8.0/PFIM/man/getCovariateEffects.Rd |only PFIM-8.0/PFIM/man/getCovariateTestTables.Rd |only PFIM-8.0/PFIM/man/getDcriterion.Rd | 35 PFIM-8.0/PFIM/man/getDeterminant.Rd | 33 PFIM-8.0/PFIM/man/getEvaluationDesign.Rd |only PFIM-8.0/PFIM/man/getFim.Rd |only PFIM-8.0/PFIM/man/getFisherMatrix.Rd | 35 PFIM-8.0/PFIM/man/getMixtureDcriterion.Rd |only PFIM-8.0/PFIM/man/getModelErrorData.Rd | 24 PFIM-8.0/PFIM/man/getModelParametersData.Rd | 34 PFIM-8.0/PFIM/man/getNumberOfOccasionsForModel.Rd |only PFIM-8.0/PFIM/man/getOccasionsFromIOVCovariates.Rd |only PFIM-8.0/PFIM/man/getRSE.Rd | 31 PFIM-8.0/PFIM/man/getRealisedDcriterion.Rd |only PFIM-8.0/PFIM/man/getSE.Rd | 30 PFIM-8.0/PFIM/man/getSamplingData.Rd | 25 PFIM-8.0/PFIM/man/getShrinkage.Rd | 31 PFIM-8.0/PFIM/man/hasCovariates.Rd |only PFIM-8.0/PFIM/man/inferNumberOfOccasions.Rd |only PFIM-8.0/PFIM/man/modelParametersWithCovariates.Rd |only PFIM-8.0/PFIM/man/optimizeDesign.Rd | 53 PFIM-8.0/PFIM/man/parseCombinationName.Rd |only PFIM-8.0/PFIM/man/pdModelLibrary.Rd |only PFIM-8.0/PFIM/man/pfim-arm-constraints.Rd |only PFIM-8.0/PFIM/man/pfim-constraints-helpers.Rd |only PFIM-8.0/PFIM/man/pfim-extensions.Rd |only PFIM-8.0/PFIM/man/pfim-fim-optimizer-wiring.Rd |only PFIM-8.0/PFIM/man/pfim-registry.Rd |only PFIM-8.0/PFIM/man/pfim_cache_stats.Rd |only PFIM-8.0/PFIM/man/pfim_get_option.Rd |only PFIM-8.0/PFIM/man/pfim_list_extensions.Rd |only PFIM-8.0/PFIM/man/pfim_register_fim_type.Rd |only PFIM-8.0/PFIM/man/pfim_register_model_class.Rd |only PFIM-8.0/PFIM/man/pfim_register_optimizer.Rd |only PFIM-8.0/PFIM/man/pfim_registered_model_classes.Rd |only PFIM-8.0/PFIM/man/pfim_reset_session.Rd |only PFIM-8.0/PFIM/man/pfim_resolve_model_class.Rd |only PFIM-8.0/PFIM/man/pfim_set_option.Rd |only PFIM-8.0/PFIM/man/pgbo_optimize_Rcpp.Rd |only PFIM-8.0/PFIM/man/pkModelLibrary.Rd |only PFIM-8.0/PFIM/man/plotEvaluation.Rd | 33 PFIM-8.0/PFIM/man/plotEvaluationResults.Rd | 63 PFIM-8.0/PFIM/man/plotEvaluationSI.Rd | 66 PFIM-8.0/PFIM/man/plotFrequencies.Rd | 30 PFIM-8.0/PFIM/man/plotFrequenciesFedorovWynnAlgorithm.Rd | 20 PFIM-8.0/PFIM/man/plotRSE.Rd | 30 PFIM-8.0/PFIM/man/plotRSEFIM.Rd | 54 PFIM-8.0/PFIM/man/plotSE.Rd | 29 PFIM-8.0/PFIM/man/plotSEFIM.Rd | 57 PFIM-8.0/PFIM/man/plotSensitivityIndices.Rd | 31 PFIM-8.0/PFIM/man/plotShrinkage.Rd | 51 PFIM-8.0/PFIM/man/plotWeights.Rd | 29 PFIM-8.0/PFIM/man/plotWeightsMultiplicativeAlgorithm.Rd | 29 PFIM-8.0/PFIM/man/processArmEvaluationResults.Rd | 29 PFIM-8.0/PFIM/man/processArmEvaluationSI.Rd | 29 PFIM-8.0/PFIM/man/projectOf.Rd |only PFIM-8.0/PFIM/man/projectProp.Rd |only PFIM-8.0/PFIM/man/prop.Rd |only PFIM-8.0/PFIM/man/pso_optimize_Rcpp.Rd |only PFIM-8.0/PFIM/man/rebuildEvalModel.Rd |only PFIM-8.0/PFIM/man/remapOdePkLibraryEquations.Rd |only PFIM-8.0/PFIM/man/remapOdePkLibraryText.Rd |only PFIM-8.0/PFIM/man/remapPkpdLibraryEquations.Rd |only PFIM-8.0/PFIM/man/remapPkpdLibraryText.Rd |only PFIM-8.0/PFIM/man/replaceVariablesLibraryOfModels.Rd | 27 PFIM-8.0/PFIM/man/resolveNumberOfOccasions.Rd |only PFIM-8.0/PFIM/man/run.Rd | 42 PFIM-8.0/PFIM/man/s7-reexports.Rd |only PFIM-8.0/PFIM/man/saveCovariateTest.Rd |only PFIM-8.0/PFIM/man/setEvaluationFim.Rd | 68 PFIM-8.0/PFIM/man/setOptimalArms.Rd | 54 PFIM-8.0/PFIM/man/setSamplingConstraintForOptimization.Rd | 26 PFIM-8.0/PFIM/man/show-methods.Rd |only PFIM-8.0/PFIM/man/showFIM.Rd | 59 PFIM-8.0/PFIM/man/tablesForReport.Rd | 68 PFIM-8.0/PFIM/man/updateSamplingTimes.Rd | 28 PFIM-8.0/PFIM/man/usesCovariateOccasionStructure.Rd |only PFIM-8.0/PFIM/src |only PFIM-8.0/PFIM/tests/testthat.R | 8 PFIM-8.0/PFIM/tests/testthat/helper-assign-in-call.R |only PFIM-8.0/PFIM/tests/testthat/helper-cas10.R |only PFIM-8.0/PFIM/tests/testthat/helper-cov-iov-poster.R |only PFIM-8.0/PFIM/tests/testthat/helper-eval-opt-references.R |only PFIM-8.0/PFIM/tests/testthat/helper-expect-s7.R |only PFIM-8.0/PFIM/tests/testthat/helper-gold-fim.R |only PFIM-8.0/PFIM/tests/testthat/helper-linalg-cpp.R |only PFIM-8.0/PFIM/tests/testthat/helper-ode-opt.R |only PFIM-8.0/PFIM/tests/testthat/helper-opt-access.R |only PFIM-8.0/PFIM/tests/testthat/test-analytic-eval.R |only PFIM-8.0/PFIM/tests/testthat/test-arm-sampling-plots.R |only PFIM-8.0/PFIM/tests/testthat/test-bayesian-fim-branches.R |only PFIM-8.0/PFIM/tests/testthat/test-code-style.R |only PFIM-8.0/PFIM/tests/testthat/test-combined2-fim-types.R |only PFIM-8.0/PFIM/tests/testthat/test-cov-iov-poster.R |only PFIM-8.0/PFIM/tests/testthat/test-covariate-test.R |only PFIM-8.0/PFIM/tests/testthat/test-cpp-kernels.R |only PFIM-8.0/PFIM/tests/testthat/test-cran-review.R |only PFIM-8.0/PFIM/tests/testthat/test-eval-opt-references.R |only PFIM-8.0/PFIM/tests/testthat/test-example-basic.R |only PFIM-8.0/PFIM/tests/testthat/test-example-pk-1cpt.R |only PFIM-8.0/PFIM/tests/testthat/test-example-pk-2cpt.R |only PFIM-8.0/PFIM/tests/testthat/test-example-pk-mm.R |only PFIM-8.0/PFIM/tests/testthat/test-fim-cache.R |only PFIM-8.0/PFIM/tests/testthat/test-fim-covariates-helpers.R |only PFIM-8.0/PFIM/tests/testthat/test-fim-pipeline.R |only PFIM-8.0/PFIM/tests/testthat/test-fim-quality.R |only PFIM-8.0/PFIM/tests/testthat/test-gcsf-poped.R |only PFIM-8.0/PFIM/tests/testthat/test-gold-fim.R |only PFIM-8.0/PFIM/tests/testthat/test-gradient-perf.R |only PFIM-8.0/PFIM/tests/testthat/test-guards.R |only PFIM-8.0/PFIM/tests/testthat/test-infusion-covariates.R |only PFIM-8.0/PFIM/tests/testthat/test-infusion-pkpd-ode.R |only PFIM-8.0/PFIM/tests/testthat/test-infusion-steady-state.R |only PFIM-8.0/PFIM/tests/testthat/test-joint-mult-iov.R |only PFIM-8.0/PFIM/tests/testthat/test-library-catalogue.R |only PFIM-8.0/PFIM/tests/testthat/test-linalg-cpp.R |only PFIM-8.0/PFIM/tests/testthat/test-mfvar-cpp.R |only PFIM-8.0/PFIM/tests/testthat/test-minor-polish.R |only PFIM-8.0/PFIM/tests/testthat/test-model-error.R |only PFIM-8.0/PFIM/tests/testthat/test-model-type-dispatch.R |only PFIM-8.0/PFIM/tests/testthat/test-ode-cache-cpp.R |only PFIM-8.0/PFIM/tests/testthat/test-ode-models.R |only PFIM-8.0/PFIM/tests/testthat/test-ode-report.R |only PFIM-8.0/PFIM/tests/testthat/test-optimization-accessors.R |only PFIM-8.0/PFIM/tests/testthat/test-optimization-algorithms.R |only PFIM-8.0/PFIM/tests/testthat/test-optimization-metaheuristic.R |only PFIM-8.0/PFIM/tests/testthat/test-pfim-architecture.R |only PFIM-8.0/PFIM/tests/testthat/test-pfim-joint-mult-shrink.R |only PFIM-8.0/PFIM/tests/testthat/test-pkpd-covariate.R |only PFIM-8.0/PFIM/tests/testthat/test-pkpd-ode-outputs.R |only PFIM-8.0/PFIM/tests/testthat/test-pop-fim-cov-combo.R |only PFIM-8.0/PFIM/tests/testthat/test-pop-mu-chain.R |only PFIM-8.0/PFIM/tests/testthat/test-reports.R |only PFIM-8.0/PFIM/tests/testthat/test-review-fixes.R |only PFIM-8.0/PFIM/vignettes/Example01.Rmd |only PFIM-8.0/PFIM/vignettes/Example02.Rmd |only PFIM-8.0/PFIM/vignettes/Example03.Rmd |only PFIM-8.0/PFIM/vignettes/Example04.Rmd |only PFIM-8.0/PFIM/vignettes/LibraryOfModels.Rmd | 1883 +++++----- PFIM-8.0/PFIM/vignettes/data |only PFIM-8.0/PFIM/vignettes/references.bib | 93 423 files changed, 16266 insertions(+), 18484 deletions(-)
Title: Panel Data Pre-Testing and Diagnostic Suite
Description: Pre-testing and diagnostic tools for panel data analysis.
Researchers should run these tests before any panel regression to
verify modelling assumptions. The package implements: (1) the Hsiao
(2014, <ISBN:978-1-107-65763-2>) homogeneity F-tests (F1/F2/F3),
Swamy (1970) <doi:10.2307/1913012> parameter heterogeneity test, and
Pesaran (2004) <doi:10.2139/ssrn.572504> cross-sectional dependence
test via xtpretest(); (2) missing-data detection, mechanism testing,
and imputation for unbalanced panels via xtmispanel(); (3)
quantile-regression cross-sectional dependence tests (T_tau and
T-tilde_tau statistics) of Demetrescu, Hosseinkouchack and Rodrigues
(2023) via xtcsdq(); and (4) the
panel quantile-regression slope homogeneity S-hat and D-hat
statistics of Galvao, Juhl, Montes-Rojas and Olmo (2017)
<doi:10.1093/jjfinec/nbx016> via xtqsh(). Together these
tests address three fundamental pre-testing questions: (i) are
slopes homogeneous? (ii) is there cross-sectional d [...truncated...]
Author: Muhammad Abdullah Alkhalaf [aut, cre, cph]
Maintainer: Muhammad Abdullah Alkhalaf <muhammedalkhalaf@gmail.com>
Diff between paneltests versions 1.0.5 dated 2026-05-04 and 1.0.6 dated 2026-09-28
DESCRIPTION | 10 MD5 | 46 - NAMESPACE | 22 NEWS.md | 6 R/xtcsdq.R | 900 ++++++++++++++++---------------- R/xtmispanel.R | 1042 ++++++++++++++++++------------------- R/xtpretest.R | 872 +++++++++++++++---------------- R/xtqsh.R | 1072 +++++++++++++++++++-------------------- build/partial.rdb |binary inst/CITATION | 2 man/print.xtcsdq.Rd | 38 - man/print.xtqsh.Rd | 26 man/qsh_sample.Rd | 40 - man/summary.xtcsdq.Rd | 38 - man/summary.xtqsh.Rd | 26 man/xtcsdq.Rd | 214 +++---- man/xtmispanel.Rd | 162 ++--- man/xtpretest.Rd | 134 ++-- man/xtqsh.Rd | 82 +- tests/testthat.R | 8 tests/testthat/test-xtcsdq.R | 122 ++-- tests/testthat/test-xtmispanel.R | 138 ++--- tests/testthat/test-xtpretest.R | 96 +-- tests/testthat/test-xtqsh.R | 122 ++-- 24 files changed, 2612 insertions(+), 2606 deletions(-)
Title: Hierarchical Item Response Theory Models
Description: Implementation of a class of hierarchical item response
theory (IRT) models where both the mean and the variance of latent preferences
(ability parameters) may depend on observed covariates. The current
implementation includes both the two-parameter latent trait model for binary data and the
graded response model for ordinal data. Both are fitted via the Expectation-Maximization (EM)
algorithm. Asymptotic standard errors are derived from the observed information
matrix. See Zhou (2019) <doi:10.1017/pan.2018.63> for details.
Author: Xiang Zhou [aut, cre]
Maintainer: Xiang Zhou <xiang_zhou@fas.harvard.edu>
This is a re-admission after prior archival of version 0.3.0 dated 2020-03-26
Diff between hIRT versions 0.3.0 dated 2020-03-26 and 0.4.0 dated 2026-09-28
DESCRIPTION | 19 - MD5 | 41 +- NAMESPACE | 5 NEWS.md | 12 R/coef.R | 45 ++- R/hgrm.R | 763 ++++++++++++++++++++++++++-------------------------- R/hgrm2.R | 551 ++++++++++++++++++------------------- R/hgrmDIF.R |only R/hltm.R | 663 ++++++++++++++++++++++----------------------- R/hltm2.R | 505 +++++++++++++++++----------------- R/print.R | 37 +- R/utils.R | 5 R/utils_grm.R | 98 ++++++ README.md | 504 +++++++++++++++++----------------- build |only man/coef_item.Rd | 2 man/hgrm.Rd | 10 man/hgrm2.Rd | 8 man/hgrmDIF.Rd |only man/hltm.Rd | 10 man/hltm2.Rd | 8 man/nes_econ2008.Rd | 6 man/print.hIRT.Rd | 39 +- 23 files changed, 1730 insertions(+), 1601 deletions(-)
Title: Fourier ARDL Methods: Quantile, Nonlinear, Multi-Threshold &
Unit Root Tests
Description: Comprehensive implementation of advanced ARDL methodologies for
cointegration analysis with structural breaks and asymmetric effects.
Includes: (1) Fourier Quantile ARDL (FQARDL) - quantile regression with
Fourier approximation for analyzing relationships across the conditional
distribution; (2) Fourier Nonlinear ARDL (FNARDL) - asymmetric cointegration
with partial sum decomposition following Shin, Yu & Greenwood-Nimmo (2014)
<doi:10.1007/978-1-4899-8008-3_9>; (3) Multi-Threshold NARDL (MTNARDL) -
multiple regime asymmetry analysis; (4) Fourier Unit Root Tests - ADF and
KPSS tests with Fourier terms following Enders & Lee (2012)
<doi:10.1016/j.econlet.2012.04.081> and Becker, Enders & Lee (2006)
<doi:10.1111/j.1467-9892.2006.00478.x>. Features automatic lag and frequency
selection, PSS bounds testing following Pesaran, Shin & Smith (2001)
<doi:10.1002/jae.616>, bootstrap cointegration tests, Wald tests for
asymmetry, dynamic multiplier computati [...truncated...]
Author: Muhammad Alkhalaf [aut, cre, cph]
Maintainer: Muhammad Alkhalaf <muhammedalkhalaf@gmail.com>
Diff between fqardl versions 1.0.4 dated 2026-08-22 and 1.0.5 dated 2026-09-28
DESCRIPTION | 23 MD5 | 42 - NEWS.md | 89 ++ R/bounds_test.R | 22 R/data.R | 58 - R/fnardl.R | 11 R/fourier.R | 472 +++++++------- R/fqardl.R | 12 R/funitroot.R | 1345 ++++++++++++++++++++---------------------- R/mtnardl.R | 11 R/plots.R | 722 +++++++++++----------- R/plots_nardl.R | 612 +++++++++---------- R/qardl.R | 8 R/zzz.R | 34 - README.md | 76 +- man/fourier_adf_test.Rd | 8 man/fqardl-package.Rd | 1 man/generate_fourier_terms.Rd | 6 man/perform_bounds_test.Rd | 7 man/plot.fnardl.Rd | 6 man/plot.fqardl.Rd | 6 man/select_optimal_lags.Rd | 6 22 files changed, 1811 insertions(+), 1766 deletions(-)
Title: Routines for Common fMRI Processing Tasks
Description: Supports fMRI (functional magnetic resonance imaging)
analysis tasks including reading in 'CIFTI', 'GIFTI' and
'NIFTI' data, temporal filtering, nuisance regression, and
aCompCor (anatomical Components Correction) (Muschelli et al.
(2014) <doi:10.1016/j.neuroimage.2014.03.028>).
Author: Amanda Mejia [aut, cre] ,
Damon Pham [aut] ,
Mark Fiecas [ctb]
Maintainer: Amanda Mejia <mandy.mejia@gmail.com>
Diff between fMRItools versions 0.7.2 dated 2025-12-23 and 0.8.3 dated 2026-09-28
fMRItools-0.7.2/fMRItools/R/dice_overlap.R |only fMRItools-0.7.2/fMRItools/man/dice_overlap.Rd |only fMRItools-0.8.3/fMRItools/DESCRIPTION | 14 fMRItools-0.8.3/fMRItools/MD5 | 46 - fMRItools-0.8.3/fMRItools/NAMESPACE | 29 fMRItools-0.8.3/fMRItools/NEWS.md | 5 fMRItools-0.8.3/fMRItools/R/carpetplot.R | 5 fMRItools-0.8.3/fMRItools/R/dice_coef.R |only fMRItools-0.8.3/fMRItools/R/dual_reg.R | 102 +-- fMRItools-0.8.3/fMRItools/R/dual_reg_parc.R | 108 +-- fMRItools-0.8.3/fMRItools/R/flags2spikes.R |only fMRItools-0.8.3/fMRItools/R/fsl_bptf.R | 3 fMRItools-0.8.3/fMRItools/R/mask_BOLD.R |only fMRItools-0.8.3/fMRItools/R/match_nets.R |only fMRItools-0.8.3/fMRItools/R/norm_BOLD.R | 436 ++++++++++---- fMRItools-0.8.3/fMRItools/R/var_decomp.R | 68 +- fMRItools-0.8.3/fMRItools/man/dice_coef.Rd |only fMRItools-0.8.3/fMRItools/man/dual_reg.Rd | 96 ++- fMRItools-0.8.3/fMRItools/man/dual_reg_parc.Rd | 92 ++ fMRItools-0.8.3/fMRItools/man/fMRItools.Rd | 3 fMRItools-0.8.3/fMRItools/man/flags2spikes.Rd |only fMRItools-0.8.3/fMRItools/man/fsl_bptf.Rd | 3 fMRItools-0.8.3/fMRItools/man/mask_BOLD.Rd |only fMRItools-0.8.3/fMRItools/man/match_nets.Rd |only fMRItools-0.8.3/fMRItools/man/norm_BOLD.Rd | 108 ++- fMRItools-0.8.3/fMRItools/man/var_decomp.Rd | 3 fMRItools-0.8.3/fMRItools/tests/run_fMRItools_tests.R | 6 fMRItools-0.8.3/fMRItools/tests/testthat/test-misc.R | 61 + fMRItools-0.8.3/fMRItools/tests/testthat/test-norm_BOLD.R |only fMRItools-0.8.3/fMRItools/tests/testthat/test-varDecomp.R |only 30 files changed, 822 insertions(+), 366 deletions(-)
Title: Bootstrap-Based Methods for the Study of Fish Stocks and Aquatic
Populations
Description: A suite of bootstrap-based models and tools for analyzing fish
stocks and aquatic populations. Designed for ecologists and fisheries
scientists, it supports data from length-frequency distributions,
tag-and-recapture studies, and hard structure readings (e.g., otoliths).
See Schwamborn et al., 2019 for background. The package includes functions for
bootstrapped fitting of growth curves and plotting.
Author: Ralf Schwamborn [aut] ,
Tobias K. Mildenberger [aut],
Marc H. Taylor [aut],
Margit Wilhelm [aut] ,
Wencheng Lau-Medrano [aut, cre]
Maintainer: Wencheng Lau-Medrano <luis.laum@gmail.com>
This is a re-admission after prior archival of version 1.0.2 dated 2025-07-02
Diff between fishboot versions 1.0.2 dated 2025-07-02 and 1.0.3 dated 2026-09-28
fishboot-1.0.2/fishboot/NEWS.md |only fishboot-1.0.2/fishboot/README.md |only fishboot-1.0.3/fishboot/DESCRIPTION | 28 +++---- fishboot-1.0.3/fishboot/MD5 | 20 ++--- fishboot-1.0.3/fishboot/NAMESPACE | 94 ++++++++++++++---------- fishboot-1.0.3/fishboot/R/ELEFAN_GA_boot.R | 23 ----- fishboot-1.0.3/fishboot/R/ELEFAN_SA_boot.R | 20 ----- fishboot-1.0.3/fishboot/R/grotag_boot.R | 26 +++--- fishboot-1.0.3/fishboot/man/ELEFAN_GA_boot.Rd | 23 ----- fishboot-1.0.3/fishboot/man/ELEFAN_SA_boot.Rd | 20 ----- fishboot-1.0.3/fishboot/man/fishboot-package.Rd | 9 -- fishboot-1.0.3/fishboot/man/grotag_boot.Rd | 26 +++--- 12 files changed, 106 insertions(+), 183 deletions(-)
Title: Comprehensive ARDL: Panel, Bootstrap and Fourier Methods
Description: A unified framework for Autoregressive Distributed Lag (ARDL) modeling
and cointegration analysis. Implements Panel ARDL with Pooled Mean Group (PMG),
Mean Group (MG), and Dynamic Fixed Effects (DFE) estimators following
Pesaran, Shin and Smith (1999) <doi:10.1080/01621459.1999.10474156>.
Provides bootstrap-based bounds testing per Pesaran, Shin & Smith (2001)
<doi:10.1002/jae.616>. Includes Quantile Nonlinear ARDL (QNARDL) combining
distributional and asymmetric effects based on Shin, Yu & Greenwood-Nimmo (2014)
<doi:10.1007/978-1-4899-8008-3_9>, and Fourier ARDL for modeling smooth
structural breaks following Enders & Lee (2012) <doi:10.1016/j.econlet.2012.04.081>.
Features include Augmented ARDL (AARDL) with deferred t and F tests,
Multiple-Threshold NARDL for complex asymmetries, Rolling/Recursive ARDL
for time-varying relationships, and Panel NARDL for nonlinear panel cointegration.
All methods include comprehensive diagnostics, publication-read [...truncated...]
Author: Muhammad Abdullah Alkhalaf [aut, cre] ,
Yeleazar Levchenko [ctb] )
Maintainer: Muhammad Abdullah Alkhalaf <muhammedalkhalaf@gmail.com>
Diff between ardlverse versions 2.0.0 dated 2026-06-29 and 2.0.2 dated 2026-09-28
DESCRIPTION | 16 MD5 | 26 NEWS.md | 9 R/augmented_ardl.R | 1204 +++++++++++++++++++++---------------------- R/bootstrap_ardl.R | 1240 ++++++++++++++++++++++---------------------- R/data.R | 468 ++++++++-------- R/diagnostics.R | 1038 ++++++++++++++++++------------------- R/fourier_ardl.R | 1230 ++++++++++++++++++++++---------------------- R/mtnardl.R | 1282 ++++++++++++++++++++++----------------------- R/panel_nardl.R | 1480 ++++++++++++++++++++++++++--------------------------- R/qnardl.R | 1278 ++++++++++++++++++++++----------------------- R/rolling_ardl.R | 1114 +++++++++++++++++++-------------------- R/zzz.R | 92 +-- man/pnardl.Rd | 7 14 files changed, 5247 insertions(+), 5237 deletions(-)
Title: An Interface to IBGE's SIDRA API
Description: Provides a flexible interface to discover, inspect, plan, and
retrieve aggregate data from the Brazilian Institute of Geography and
Statistics (IBGE) through its SIDRA application programming interfaces.
SIDRA is IBGE's system for retrieving aggregate statistical data.
Author: Renato Prado Siqueira [aut, cre]
Maintainer: Renato Prado Siqueira <rpradosiqueira@gmail.com>
Diff between sidrar versions 0.5.1 dated 2026-09-18 and 0.6.0 dated 2026-09-28
DESCRIPTION | 6 MD5 | 64 ++++--- NEWS.md | 44 +++++ R/checkpoint.R |only R/collect.R | 132 +++++++++++++--- R/discovery.R | 41 ++++- R/fallback-format.R |only R/fallback-validation.R |only R/fallback.R | 70 ++++---- R/get_sidra.R | 45 ++++- R/info-fallback.R |only R/info_sidra.R | 30 +++ R/query.R | 80 +++++++++ R/split-url.R |only R/utils.R | 213 ++++++++++++++++++++++---- README.md | 158 ++++++++++++++++--- inst/doc/Introduction_to_sidrar.R | 19 ++ inst/doc/Introduction_to_sidrar.Rmd | 88 +++++++++- inst/doc/Introduction_to_sidrar.html | 166 ++++++++++++++------ man/get_sidra.Rd | 45 ++++- man/info_sidra.Rd | 11 + man/sidra_collect.Rd | 39 ++++ man/sidra_provenance.Rd | 2 man/sidra_split.Rd | 17 -- tests/testthat/test-api-contract.R | 8 tests/testthat/test-checkpoint.R |only tests/testthat/test-classification-fallback.R |only tests/testthat/test-collect.R | 13 - tests/testthat/test-compatibility-060.R |only tests/testthat/test-fallback-format.R |only tests/testthat/test-fallback-integration.R | 103 +++++++++++- tests/testthat/test-fallback-validation.R |only tests/testthat/test-fallback.R | 191 ++++++++++++++++++++++- tests/testthat/test-info-fallback.R |only tests/testthat/test-live-api.R | 47 +++++ tests/testthat/test-retry-after-option.R |only tests/testthat/test-retry-after.R |only tests/testthat/test-split-url.R |only tests/testthat/test-utils.R | 73 ++++++++ vignettes/Introduction_to_sidrar.Rmd | 88 +++++++++- 40 files changed, 1524 insertions(+), 269 deletions(-)
Title: Bindings to the 'libmdbx' Embedded Key-Value Store
Description: Provides low-level bindings to 'libmdbx', a compact and fast
transactional key-value store built on memory-mapped files
(<https://libmdbx.dqdkfa.ru/>). Database environments, transactions,
and byte-oriented read and write operations are exposed directly. The
'libmdbx' sources are bundled and compiled into the package, so no
system library installation is required.
Author: Pedro Baltazar [aut, cre, cph],
Leonid Yuriev [ctb, cph] ,
Howard Chu [ctb, cph] ,
Symas Corporation [cph] ,
Martin Hedenfalk [ctb, cph]
Maintainer: Pedro Baltazar <pedrobtz@gmail.com>
Diff between mdbx versions 0.1.0 dated 2026-09-27 and 0.1.1 dated 2026-09-28
DESCRIPTION | 6 +- MD5 | 14 +++--- NEWS.md | 12 +++++ inst/COPYRIGHTS | 6 ++ src/Makevars | 14 ++++++ src/Makevars.win | 12 +++++ src/vendor/libmdbx/mdbx-internals.h | 6 ++ src/vendor/libmdbx/mdbx.c | 75 ++++++++++++++++++++---------------- 8 files changed, 100 insertions(+), 45 deletions(-)
Title: ICESat-2 Data Analysis for Land and Vegetation
Description: Provides tools for downloading, reading, processing, visualizing,
and exporting NASA's ICESat-2 ATL03 (Global Geolocated Photon
Data) and ATL08 (Land and Vegetation Height) products. Supports
photon- and segment-level analysis, spatial sampling, gridding,
statistical and machine-learning modeling, and integration with
'Google Earth Engine' (<https://earthengine.google.com/>) for
wall-to-wall mapping of vegetation structure and other land
attributes.
Author: Carlos Alberto Silva [aut, cph, cre],
Caio Hamamura [aut, cph],
Cesar Alvites [aut, ctb],
Alexander J. Gaskins [aut, ctb],
Sunil Arya [ctb, cph] ),
David Mount [ctb, cph] ),
University of Maryland [cph] ),
Chuck Gantz [ctb] ,
Cole Krehbiel [ctb]
Maintainer: Carlos Alberto Silva <c.silva@ufl.edu>
Diff between ICESat2VegR versions 0.0.2 dated 2026-09-18 and 0.0.3 dated 2026-09-28
DESCRIPTION | 6 MD5 | 26 +-- R/ATL03_ATL08_photons_attributes_dt_join.R | 8 - R/ATLAS_dataDownload.R | 12 - R/class.icesat2.h5_local.R | 16 -- R/class.icesat2.h5ds_local.R | 8 - R/gdalBindings.R | 12 - R/predict_h5.R | 47 +++--- R/zzz.R | 18 +- man/earthdata_login.Rd | 8 - man/predict_h5-ANY-icesat2.atl03_seg_dt-character-method.Rd | 1 man/predict_h5-ANY-icesat2.atl08_dt-character-method.Rd | 3 man/predict_h5.Rd | 3 tests/testthat/test-integration-local.R | 82 ++++++++++-- 14 files changed, 160 insertions(+), 90 deletions(-)
Title: Calculate and Analyze Blau Statuses for Measuring Social
Distance
Description: Calculate and analyze Blau statuses for quantifying social
distance between individuals belonging to organizations. Relational
(network) data can be incorporated for additional analyses. The methods
build on affiliation ecology and Blau space as described by McPherson
(1983) <doi:10.2307/2117719>, McPherson and Ranger-Moore (1991)
<doi:10.1093/sf/70.1.19>, McPherson, Popielarz and Drobnic (1992)
<doi:10.2307/2096202>, McPherson and Rotolo (1996)
<doi:10.2307/2096330>, and McPherson (2004)
<doi:10.1093/icc/13.1.263>. The implementation of Blau-space analyses
in 'Blaunet' is described by Genkin et al. (2018)
<doi:10.1371/journal.pone.0204990>. This project is supported by the
Defense Threat Reduction Agency (DTRA) Grant HDTRA-10-1-0043.
Author: Cheng Wang [aut, cre],
Michael Genkin [aut],
George Berry [aut],
Liyuan Chen [aut],
Matthew Brashears [aut]
Maintainer: Cheng Wang <chengwang@wayne.edu>
This is a re-admission after prior archival of version 2.2.1 dated 2022-09-27
Diff between Blaunet versions 2.2.1 dated 2022-09-27 and 3.0.0 dated 2026-09-28
Blaunet-2.2.1/Blaunet/inst/scripts/analysis.R |only Blaunet-2.2.1/Blaunet/inst/scripts/blaububbles.R |only Blaunet-2.2.1/Blaunet/inst/scripts/blaunetgui.R |only Blaunet-2.2.1/Blaunet/inst/scripts/browse.R |only Blaunet-2.2.1/Blaunet/inst/scripts/dimensions.R |only Blaunet-2.2.1/Blaunet/inst/scripts/dynamics.R |only Blaunet-2.2.1/Blaunet/inst/scripts/graph.R |only Blaunet-2.2.1/Blaunet/inst/scripts/network.R |only Blaunet-2.2.1/Blaunet/inst/scripts/nicheplot.R |only Blaunet-2.2.1/Blaunet/inst/scripts/open.R |only Blaunet-3.0.0/Blaunet/DESCRIPTION | 27 ++++-- Blaunet-3.0.0/Blaunet/MD5 | 43 ++++++----- Blaunet-3.0.0/Blaunet/R/blaunet.shiny.R |only Blaunet-3.0.0/Blaunet/R/blaunetgui.r | 16 ++-- Blaunet-3.0.0/Blaunet/R/niche.analysis.outputs.R |only Blaunet-3.0.0/Blaunet/R/niche.dynamics.extensions.R |only Blaunet-3.0.0/Blaunet/R/plot.network.graph.R |only Blaunet-3.0.0/Blaunet/R/plot.niche.2d.R |only Blaunet-3.0.0/Blaunet/R/plot.niche.3d.R |only Blaunet-3.0.0/Blaunet/R/plot.niche.dynamics.3d.R |only Blaunet-3.0.0/Blaunet/R/read.blaunet.attribute.file.R |only Blaunet-3.0.0/Blaunet/R/read.blaunet.network.file.R |only Blaunet-3.0.0/Blaunet/R/run.blau.bubble.analysis.R |only Blaunet-3.0.0/Blaunet/R/run.network.statistics.R |only Blaunet-3.0.0/Blaunet/R/run.niche.analysis.R |only Blaunet-3.0.0/Blaunet/R/run.niche.dynamics.cross.sectional.R |only Blaunet-3.0.0/Blaunet/R/run.niche.dynamics.longitudinal.R |only Blaunet-3.0.0/Blaunet/R/run.niche.plot.analysis.R |only Blaunet-3.0.0/Blaunet/R/run.salient.dimension.analysis.R |only Blaunet-3.0.0/Blaunet/R/zzz.R | 2 Blaunet-3.0.0/Blaunet/inst/scripts/command.pdf |binary Blaunet-3.0.0/Blaunet/inst/scripts/graphic.pdf |binary Blaunet-3.0.0/Blaunet/inst/shiny |only Blaunet-3.0.0/Blaunet/man/Blaunet-package.Rd | 9 +- Blaunet-3.0.0/Blaunet/man/blaunetgui.Rd | 4 - Blaunet-3.0.0/Blaunet/man/export.dyadic.Rd | 21 +++-- 36 files changed, 75 insertions(+), 47 deletions(-)
Title: Package Checks for 'rOpenSci'
Description: Check whether a package is ready for submission to the 'rOpenSci'
peer review system ('rOpenSci' authors (2026) <doi:10.5281/zenodo.2553043>
"'rOpenSci' Packages: Development, Maintenance, and Peer Review").
Incorporates the 'goodpractice' package and many additional checks,
including aspects related to maintenance of online public code
repositories.
Author: Mark Padgham [aut, cre] ,
Maelle Salmon [aut],
Jacob Wujciak-Jens [aut] ,
Kelli F. Johnson [ctb] ,
Eunseop Kim [aut] ,
Katrina Brock [ctb] ,
Andy Teucher [aut] ,
Eric R. Scott [aut]
Maintainer: Mark Padgham <mark.padgham@email.com>
Diff between pkgcheck versions 0.3.0 dated 2026-09-27 and 0.3.1 dated 2026-09-28
DESCRIPTION | 6 - MD5 | 34 ++++---- NEWS.md | 1 R/info-ci.R | 3 R/info-git.R | 17 +--- R/info-github.R | 4 R/stats-checks.R | 70 ++++++++++++++++- inst/doc/autotest-pkgcheck-gp.html | 4 inst/doc/environment.html | 4 inst/doc/extending-checks.html | 4 inst/doc/list-checks.html | 4 tests/testthat/_snaps/extra-checks/checks-extra.html | 64 +++++++-------- tests/testthat/_snaps/extra-checks/checks-extra.md | 50 ++++++------ tests/testthat/_snaps/extra-checks/checks-print.md | 4 tests/testthat/_snaps/pkgcheck/checks0.html | 78 +++++++++---------- tests/testthat/_snaps/pkgcheck/checks0.md | 50 ++++++------ tests/testthat/_snaps/pkgcheck/checks1.html | 78 +++++++++---------- tests/testthat/_snaps/pkgcheck/checks1.md | 50 ++++++------ 18 files changed, 299 insertions(+), 226 deletions(-)
Title: J&J Innovative Medicine ADaM Test Data
Description: A set of Analysis Data Model (ADaM) datasets constructed by
modifying the ADaM datasets in the 'pharmaverseadam' package to meet J&J Innovative Medicine's
standard data structure for Clinical and Statistical Programming.
Author: David Munoz Tord [aut, cre],
Nicholas Masel [aut],
Joe Kovach [aut],
Mahesh Divakaran [ctb],
Renfei Mao [ctb],
J&J Innovative Medicine [cph, fnd]
Maintainer: David Munoz Tord <david.munoztord@mailbox.org>
Diff between pharmaverseadamjnj versions 0.0.6 dated 2026-09-24 and 0.0.7 dated 2026-09-28
DESCRIPTION | 6 +-- MD5 | 98 +++++++++++++++++++++++++++--------------------------- NEWS.md | 85 +++++++++++++++++++++++++++++++++++++++++++++- R/adae.R | 65 +++++++++++++++++++---------------- R/adaecomp.R | 22 +++++++++++- R/adaeocmq.R | 65 +++++++++++++++++++---------------- R/adcm.R | 2 - R/addili.R | 8 +++- R/addisp.R | 4 +- R/adex.R | 49 +++++++++++++++++++++++---- R/adexsum.R | 6 ++- R/adishum.R | 60 ++++++++++++++++++++------------- R/adlb.R | 83 +++++++++++---------------------------------- R/adpc.R | 5 +- R/adsl.R | 6 ++- R/adslcomp.R | 8 ++-- R/adttesaf.R | 2 - R/advs.R | 4 +- data/adae.rda |binary data/adaecomp.rda |binary data/adaeocmq.rda |binary data/adcm.rda |binary data/addili.rda |binary data/addisp.rda |binary data/adeg.rda |binary data/adex.rda |binary data/adexsum.rda |binary data/adishum.rda |binary data/adlb.rda |binary data/adpc.rda |binary data/adsl.rda |binary data/adslcomp.rda |binary data/adttesaf.rda |binary data/advs.rda |binary inst/WORDLIST | 73 ++++++++++++++++++++++++++++++++++++++++ man/adae.Rd | 65 +++++++++++++++++++---------------- man/adaecomp.Rd | 22 +++++++++++- man/adaeocmq.Rd | 65 +++++++++++++++++++---------------- man/adcm.Rd | 2 - man/addili.Rd | 8 +++- man/addisp.Rd | 4 +- man/adex.Rd | 49 +++++++++++++++++++++++---- man/adexsum.Rd | 6 ++- man/adishum.Rd | 60 ++++++++++++++++++++------------- man/adlb.Rd | 83 +++++++++++---------------------------------- man/adpc.Rd | 5 +- man/adsl.Rd | 6 ++- man/adslcomp.Rd | 8 ++-- man/adttesaf.Rd | 2 - man/advs.Rd | 4 +- 50 files changed, 644 insertions(+), 396 deletions(-)
More information about pharmaverseadamjnj at CRAN
Permanent link
Title: Multiple Imputation by Chained Equations with Multilevel Data
Description: Addons for the 'mice' package to perform multiple imputation using chained equations with two-level data. Includes imputation methods dedicated to sporadically and systematically missing values. Imputation of continuous, binary or count variables are available. Following the recommendations of Audigier, V. et al (2018) <doi:10.1214/18-STS646>, the choice of the imputation method for each variable can be facilitated by a default choice tuned according to the structure of the incomplete dataset. Allows parallel calculation and overimputation for 'mice'.
Author: Vincent Audigier [aut, cre] ,
Matthieu Resche-Rigon [aut] ,
Johanna Munoz Avila [ctb]
Maintainer: Vincent Audigier <vincent.audigier@cnam.fr>
Diff between micemd versions 1.10.1 dated 2025-08-27 and 1.11.0 dated 2026-09-28
DESCRIPTION | 12 ++-- MD5 | 10 +-- NAMESPACE | 3 - R/copulaIPD.R | 138 ++++++++++++++++++++++------------------------ build/partial.rdb |binary man/find.defaultMethod.Rd | 1 6 files changed, 81 insertions(+), 83 deletions(-)
Title: Spatially Explicit Population Models of Disease Transmission in
Wildlife
Description: This extension of the pattern-oriented modeling framework of the
'poems' package provides a collection of modules and functions customized
for modeling disease transmission on a population scale in a spatiotemporally
explicit manner. This includes seasonal time steps, dispersal functions that
track disease state of dispersers, results objects that store disease states,
and a population simulator that includes disease dynamics.
Author: July Pilowsky [aut, cre] ,
National Science Foundation Biology Integration Institute 2213854 [fnd]
Maintainer: July Pilowsky <pilowskyj@caryinstitute.org>
Diff between epizootic versions 2.0.0 dated 2025-11-12 and 2.1.0 dated 2026-09-28
epizootic-2.0.0/epizootic/tests/testthat/test_results |only epizootic-2.1.0/epizootic/DESCRIPTION | 15 epizootic-2.1.0/epizootic/MD5 | 32 - epizootic-2.1.0/epizootic/NAMESPACE | 47 + epizootic-2.1.0/epizootic/NEWS.md | 8 epizootic-2.1.0/epizootic/R/RcppExports.R | 49 + epizootic-2.1.0/epizootic/R/aspatial_sir_seasons.R |only epizootic-2.1.0/epizootic/R/aspatial_siri_seasons.R | 4 epizootic-2.1.0/epizootic/R/check_aspatial_sir_inputs.R |only epizootic-2.1.0/epizootic/build/vignette.rds |binary epizootic-2.1.0/epizootic/man/DiseaseModel.Rd | 264 +++++----- epizootic-2.1.0/epizootic/man/SimulationHandler.Rd | 228 ++++---- epizootic-2.1.0/epizootic/man/aspatial_sir.Rd |only epizootic-2.1.0/epizootic/man/check_aspatial_sir_inputs.Rd |only epizootic-2.1.0/epizootic/man/epizootic-package.Rd | 5 epizootic-2.1.0/epizootic/man/sir_model_summer.Rd |only epizootic-2.1.0/epizootic/man/sir_model_winter.Rd |only epizootic-2.1.0/epizootic/src/RcppExports.cpp | 20 epizootic-2.1.0/epizootic/src/aspatial_sir.cpp |only epizootic-2.1.0/epizootic/tests/testthat/test-SimulationHandler.R | 5 epizootic-2.1.0/epizootic/tests/testthat/test-aspatial_sir_seasons.R |only 21 files changed, 397 insertions(+), 280 deletions(-)
Title: Spatial and Network Based Individual Level Models for Epidemics
Description: Provides tools for simulating from discrete-time individual level models for infectious disease data analysis. This epidemic model class contains spatial and contact-network based models with two disease types: Susceptible-Infectious (SI) and Susceptible-Infectious-Removed (SIR).
Author: Vineetha Warriyar K. V. [aut],
Waleed Almutiry [aut, cre],
Rob Deardon [aut, ths]
Maintainer: Waleed Almutiry <w.mutiry@etec.gov.sa>
Diff between EpiILM versions 1.5.3 dated 2025-09-26 and 1.5.4 dated 2026-09-28
DESCRIPTION | 12 ++++++------ MD5 | 6 +++--- build/partial.rdb |binary inst/doc/Predict.pdf |binary 4 files changed, 9 insertions(+), 9 deletions(-)
Title: Design and Analysis for Clinical Trials
Description: The applications and evaluation of the operating characteristics of many statistical methodologies require the use of
sophisticated software or extensive simulations. 'DACT' is designed to serve a wide range of innovative statistical designs and analyses.
The primary objective of the 'DACT' software is to promote the understanding and application of cutting-edge statistical solutions in
clinical trials. For this reason, the software is free for non-commercial scientific research, including but not limited to academic
researchers and research/teaching institutions. Computing codes are available upon request.
For more details see P. Gao (2024) <doi:10.1080/10543406.2024.2341673>.
Gao, P., Zhang, W. (2024) <doi:10.1080/10543406.2024.2358796>.
P. Gao & Y. Li (2024) <doi:10.1080/10543406.2023.2233590>.
P. Gao, Y. Li (2024) <doi:10.1080/10543406.2024.2342518>.
Gao, P., L. Liu, and C. Mehta. (2013) <doi:10.1002/sim.5847>.
Author: Ping Gao [aut, cre]
Maintainer: Ping Gao <support@innovatiostat.com>
Diff between DACT versions 0.1.2 dated 2026-09-22 and 1.0.0 dated 2026-09-28
DESCRIPTION | 14 MD5 | 238 +++++++++- NAMESPACE | 199 ++++++++ R/2asd_analysis.R |only R/2asd_common.R |only R/2asd_design.R |only R/2asd_simulation_2.R |only R/ASD_analysis.R |only R/ASD_common.R |only R/ASD_simulations_4.R |only R/GSD_design.R |only R/MASD_Design.R |only R/MASD_analysis.R |only R/MASD_common.R |only R/MASD_simulation_2.R |only R/fixed_power_simulations.R |only R/fixed_sample.R |only R/hybrid_DACT.R |only R/one_arm_analysis.R | 1 R/one_arm_asd_simulations.R | 11 R/parallel.R | 20 R/public_base.R | 6 R/public_common.R | 94 +++ man/MSD_Sample_size_OF_boundary_binary_diff.Rd |only man/MSD_Sample_size_OF_boundary_neg_binomial.Rd |only man/MSD_Sample_size_OF_boundary_normal.Rd |only man/MSD_Sample_size_OF_boundary_poisson.Rd |only man/MSD_Sample_size_OF_boundary_survival_Schoenfeld.Rd |only man/MSD_Sample_size_alsp_boundary_binary_diff.Rd |only man/MSD_Sample_size_alsp_boundary_neg_binomial.Rd |only man/MSD_Sample_size_alsp_boundary_normal.Rd |only man/MSD_Sample_size_alsp_boundary_poisson.Rd |only man/MSD_Sample_size_alsp_boundary_survival_Schoenfeld.Rd |only man/MSD_power_OF_boundary_binary_diff.Rd |only man/MSD_power_OF_boundary_neg_binomial.Rd |only man/MSD_power_OF_boundary_normal.Rd |only man/MSD_power_OF_boundary_poisson.Rd |only man/MSD_power_OF_boundary_survival_Schoenfeld.Rd |only man/MSD_power_alsp_boundary_binary_diff.Rd |only man/MSD_power_alsp_boundary_neg_binomial.Rd |only man/MSD_power_alsp_boundary_normal.Rd |only man/MSD_power_alsp_boundary_poisson.Rd |only man/MSD_power_alsp_boundary_survival_Schoenfeld.Rd |only man/Sample_size_OF_boundary_binary_diff.Rd |only man/Sample_size_OF_boundary_binary_diff_NI.Rd |only man/Sample_size_OF_boundary_neg_binomial.Rd |only man/Sample_size_OF_boundary_neg_binomial_NI.Rd |only man/Sample_size_OF_boundary_normal.Rd |only man/Sample_size_OF_boundary_normal_NI.Rd |only man/Sample_size_OF_boundary_poisson.Rd |only man/Sample_size_OF_boundary_poisson_NI.Rd |only man/Sample_size_OF_boundary_survival_Schoenfeld.Rd |only man/Sample_size_OF_boundary_survival_Schoenfeld_NI.Rd |only man/Sample_size_alsp_boundary_binary_diff.Rd |only man/Sample_size_alsp_boundary_binary_diff_NI.Rd |only man/Sample_size_alsp_boundary_neg_binomial.Rd |only man/Sample_size_alsp_boundary_neg_binomial_NI.Rd |only man/Sample_size_alsp_boundary_normal.Rd |only man/Sample_size_alsp_boundary_normal_NI.Rd |only man/Sample_size_alsp_boundary_poisson.Rd |only man/Sample_size_alsp_boundary_poisson_NI.Rd |only man/Sample_size_alsp_boundary_survival_Schoenfeld.Rd |only man/Sample_size_alsp_boundary_survival_Schoenfeld_NI.Rd |only man/Sample_size_pocock_boundary_binary_diff.Rd |only man/Sample_size_pocock_boundary_binary_diff_NI.Rd |only man/Sample_size_pocock_boundary_neg_binomial.Rd |only man/Sample_size_pocock_boundary_neg_binomial_NI.Rd |only man/Sample_size_pocock_boundary_normal.Rd |only man/Sample_size_pocock_boundary_normal_NI.Rd |only man/Sample_size_pocock_boundary_poisson.Rd |only man/Sample_size_pocock_boundary_poisson_NI.Rd |only man/Sample_size_pocock_boundary_survival_Schoenfeld.Rd |only man/Sample_size_pocock_boundary_survival_Schoenfeld_NI.Rd |only man/Two_stage_asd_simu_OC_binary.Rd |only man/Two_stage_asd_simu_OC_neg_binomial.Rd |only man/Two_stage_asd_simu_OC_normal.Rd |only man/Two_stage_asd_simu_OC_poisson.Rd |only man/Two_stage_asd_simu_OC_survival.Rd |only man/asd_ci_est_back.Rd |only man/asd_new_design.Rd |only man/asd_new_design_survival.Rd |only man/asd_new_design_theta.Rd |only man/asd_new_design_theta_survival.Rd |only man/asd_power_simu_binary.Rd |only man/asd_power_simu_neg_binomial.Rd |only man/asd_power_simu_normal.Rd |only man/asd_power_simu_poisson.Rd |only man/asd_power_simu_survival.Rd |only man/asd_simu_OC_binary.Rd |only man/asd_simu_OC_neg_binomial.Rd |only man/asd_simu_OC_normal.Rd |only man/asd_simu_OC_poisson.Rd |only man/asd_simu_OC_survival.Rd |only man/fixed_rej_nbglm_simu.Rd |only man/fixed_rej_rate_binary.Rd |only man/fixed_rej_rate_normal.Rd |only man/fixed_rej_rate_poisson.Rd |only man/fixed_rej_rate_surv_cox.Rd |only man/gsd_ci_est.Rd |only man/gsd_power_simu_binary.Rd |only man/gsd_power_simu_negbinom.Rd |only man/gsd_power_simu_normal.Rd |only man/gsd_power_simu_poisson.Rd |only man/gsd_power_simu_survival.Rd |only man/hybrid_fixed_prior_rej_binary_simu.Rd |only man/hybrid_fixed_prior_rej_negbinom_simu.Rd |only man/hybrid_fixed_prior_rej_normal_simu.Rd |only man/hybrid_fixed_prior_rej_poisson_simu.Rd |only man/hybrid_fixed_prior_rej_survival_simu.Rd |only man/hybrid_random_prior_rej_binary_simu.Rd |only man/hybrid_random_prior_rej_negbinom_simu.Rd |only man/hybrid_random_prior_rej_normal_simu.Rd |only man/hybrid_random_prior_rej_poisson_simu.Rd |only man/hybrid_random_prior_rej_survival_simu.Rd |only man/interim_analysis.Rd | 1 man/masd_est_back_no_drop.Rd |only man/masd_est_back_with_drop.Rd |only man/masd_est_ci.Rd |only man/masd_new_samsz.Rd |only man/masd_new_samsz_survival.Rd |only man/masd_new_samsz_theta.Rd |only man/masd_new_samsz_theta_survival.Rd |only man/masd_power_simu_adapt_binary.Rd |only man/masd_power_simu_adapt_neg_binomial.Rd |only man/masd_power_simu_adapt_normal.Rd |only man/masd_power_simu_adapt_poisson.Rd |only man/masd_power_simu_adapt_survival.Rd |only man/masd_simu_OC_binary.Rd |only man/masd_simu_OC_neg_binomial.Rd |only man/masd_simu_OC_normal.Rd |only man/masd_simu_OC_poisson.Rd |only man/masd_simu_OC_survival.Rd |only man/msd_power_simu_binary.Rd |only man/msd_power_simu_neg_binomial.Rd |only man/msd_power_simu_normal.Rd |only man/msd_power_simu_poisson.Rd |only man/msd_power_simu_survival.Rd |only man/new_sample_size_hybrid.Rd |only man/one_arm_ad_3_stg_binary.Rd | 2 man/one_arm_ad_two_stg_binary.Rd | 2 man/one_arm_rej_2_stg_binary.Rd | 2 man/one_arm_rej_3_stg_binary.Rd | 2 man/one_arm_rej_simon_binary.Rd | 2 man/power_OF_boundary_binary_diff.Rd |only man/power_OF_boundary_binary_diff_NI.Rd |only man/power_OF_boundary_neg_binomial.Rd |only man/power_OF_boundary_neg_binomial_NI.Rd |only man/power_OF_boundary_normal.Rd |only man/power_OF_boundary_normal_NI.Rd |only man/power_OF_boundary_poisson.Rd |only man/power_OF_boundary_poisson_NI.Rd |only man/power_OF_boundary_survival_Schoenfeld.Rd |only man/power_OF_boundary_survival_Schoenfeld_NI.Rd |only man/power_alsp_boundary_binary_diff.Rd |only man/power_alsp_boundary_binary_diff_NI.Rd |only man/power_alsp_boundary_neg_binomial.Rd |only man/power_alsp_boundary_neg_binomial_NI.Rd |only man/power_alsp_boundary_normal.Rd |only man/power_alsp_boundary_normal_NI.Rd |only man/power_alsp_boundary_poisson.Rd |only man/power_alsp_boundary_poisson_NI.Rd |only man/power_alsp_boundary_survival_Schoenfeld.Rd |only man/power_alsp_boundary_survival_Schoenfeld_NI.Rd |only man/power_binary_diff.Rd |only man/power_binary_diff_NI.Rd |only man/power_pocock_boundary_binary_diff.Rd |only man/power_pocock_boundary_binary_diff_NI.Rd |only man/power_pocock_boundary_neg_binomial.Rd |only man/power_pocock_boundary_neg_binomial_NI.Rd |only man/power_pocock_boundary_normal.Rd |only man/power_pocock_boundary_normal_NI.Rd |only man/power_pocock_boundary_poisson.Rd |only man/power_pocock_boundary_poisson_NI.Rd |only man/power_pocock_boundary_survival_Schoenfeld.Rd |only man/power_pocock_boundary_survival_Schoenfeld_NI.Rd |only man/power_two_sample_Poisson.Rd |only man/power_two_sample_Poisson_NI.Rd |only man/power_two_sample_neg_binomial.Rd |only man/power_two_sample_neg_binomial_NI.Rd |only man/power_two_sample_normal.Rd |only man/power_two_sample_normal_NI.Rd |only man/power_two_sample_surv_Schoenfeld.Rd |only man/power_two_sample_surv_Schoenfeld_NI.Rd |only man/sample_size_binary_diff.Rd |only man/sample_size_binary_diff_NI.Rd |only man/sample_size_neg_binomial.Rd |only man/sample_size_neg_binomial_NI.Rd |only man/sample_size_two_sample_Poisson.Rd |only man/sample_size_two_sample_Poisson_NI.Rd |only man/sample_size_two_sample_normal.Rd |only man/sample_size_two_sample_normal_NI.Rd |only man/sample_size_two_sample_surv_Schoenfeld.Rd |only man/sample_size_two_sample_surv_Schoenfeld_NI.Rd |only man/two_stage_Sample_size_OF_boundary_binary_diff.Rd |only man/two_stage_Sample_size_OF_boundary_neg_binomial.Rd |only man/two_stage_Sample_size_OF_boundary_normal.Rd |only man/two_stage_Sample_size_OF_boundary_poisson.Rd |only man/two_stage_Sample_size_OF_boundary_survival_Schoenfeld.Rd |only man/two_stage_Sample_size_alsp_boundary_binary_diff.Rd |only man/two_stage_Sample_size_alsp_boundary_neg_binomial.Rd |only man/two_stage_Sample_size_alsp_boundary_normal.Rd |only man/two_stage_Sample_size_alsp_boundary_poisson.Rd |only man/two_stage_Sample_size_alsp_boundary_survival_Schoenfeld.Rd |only man/two_stage_ci_0.Rd |only man/two_stage_ci_1.Rd |only man/two_stage_est_back.Rd |only man/two_stage_power_OF_boundary_binary_diff.Rd |only man/two_stage_power_OF_boundary_neg_binomial.Rd |only man/two_stage_power_OF_boundary_normal.Rd |only man/two_stage_power_OF_boundary_poisson.Rd |only man/two_stage_power_OF_boundary_survival_Schoenfeld.Rd |only man/two_stage_power_alsp_boundary_binary_diff.Rd |only man/two_stage_power_alsp_boundary_neg_binomial.Rd |only man/two_stage_power_alsp_boundary_normal.Rd |only man/two_stage_power_alsp_boundary_poisson.Rd |only man/two_stage_power_alsp_boundary_survival_Schoenfeld.Rd |only man/two_stg_adapt_power_simu_binary.Rd |only man/two_stg_adapt_power_simu_neg_binomial.Rd |only man/two_stg_adapt_power_simu_normal.Rd |only man/two_stg_adapt_power_simu_poisson.Rd |only man/two_stg_adapt_power_simu_survival.Rd |only man/two_stg_power_simu_binary.Rd |only man/two_stg_power_simu_neg_binomial.Rd |only man/two_stg_power_simu_normal.Rd |only man/two_stg_power_simu_poisson.Rd |only man/two_stg_power_simu_survival.Rd |only 226 files changed, 560 insertions(+), 34 deletions(-)
Title: 'ONNX Runtime' Integration
Description: Provides high-performance R bindings for 'ONNX Runtime'
<https://onnxruntime.ai/>, enabling efficient machine learning model inference. Written in 'Rust' for memory safety
and speed, the package supports cross-platform model execution with multiple
execution providers. Includes comprehensive error handling and validation,
with bundled MNIST example model for immediate testing and prototyping.
Designed for production use with support for macOS (arm64), Linux (x64/arm64),
and Windows (x64). Runtime libraries are downloaded on explicit request from
<https://github.com/microsoft/onnxruntime/releases>.
Author: Chanyub Park [aut, cre] ,
The authors of the dependency Rust crates [ctb] ,
ONNX Project contributors [ctb, cph] ,
Microsoft Corporation [cph]
Maintainer: Chanyub Park <mrchypark@gmail.com>
Diff between churon versions 0.1.12 dated 2026-09-25 and 0.1.13 dated 2026-09-28
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++----------- R/install_onnx_runtime.R | 14 +++++++++++--- R/zzz.R | 4 +++- src/Makevars | 3 --- src/Makevars.win | 4 +--- tests/testthat/test-end-to-end.R | 16 ++++++++++++---- tests/testthat/test-error-handling.R | 8 ++++++-- tests/testthat/test-inference-execution.R | 8 ++++++-- tests/testthat/test-runtime-configuration.R | 15 +++++++++++++-- tests/testthat/test-session-management.R | 12 +++++++++--- tools/setup-dev.R | 17 +++++++++++++---- 12 files changed, 88 insertions(+), 41 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-09-03 1.0.0
Title: Simulation Framework for Sports Physiology and Analytics
Description: Provides a rule-based simulation environment for modeling
real-world athlete performance, dynamic training sessions, hierarchical
variance, and missing telemetry data.
Author: Mohammad Abbas [aut, cre]
Maintainer: Mohammad Abbas <ma.abbas3107@gmail.com>
Diff between sportsfeatures versions 0.2.0 dated 2026-09-14 and 0.3.0 dated 2026-09-28
sportsfeatures-0.2.0/sportsfeatures/R/sportsfeatures-package.R |only sportsfeatures-0.2.0/sportsfeatures/R/utils.R |only sportsfeatures-0.2.0/sportsfeatures/build/partial.rdb |only sportsfeatures-0.2.0/sportsfeatures/data/sports_features.rda |only sportsfeatures-0.2.0/sportsfeatures/man/get_sportsdata.Rd |only sportsfeatures-0.2.0/sportsfeatures/man/sports_features.Rd |only sportsfeatures-0.2.0/sportsfeatures/man/sportsfeatures-package.Rd |only sportsfeatures-0.3.0/sportsfeatures/DESCRIPTION | 42 ++--- sportsfeatures-0.3.0/sportsfeatures/LICENSE | 2 sportsfeatures-0.3.0/sportsfeatures/MD5 | 25 +-- sportsfeatures-0.3.0/sportsfeatures/NAMESPACE | 5 sportsfeatures-0.3.0/sportsfeatures/R/data.R | 79 +--------- sportsfeatures-0.3.0/sportsfeatures/build/vignette.rds |only sportsfeatures-0.3.0/sportsfeatures/data/sports_features_missing.rda |binary sportsfeatures-0.3.0/sportsfeatures/inst |only sportsfeatures-0.3.0/sportsfeatures/man/sports_features_missing.Rd | 48 +++++- sportsfeatures-0.3.0/sportsfeatures/vignettes |only 17 files changed, 83 insertions(+), 118 deletions(-)
More information about sportsfeatures at CRAN
Permanent link
Title: Bayesian Dynamic Models for Count Time Series
Description: Fits Bayesian state-space models for count time series using a
latent log-rate (Poisson), latent logit (binomial) or latent
additive-log-ratio (multinomial choice counts) formulation. Each latent
trajectory follows a first-order random walk or a stationary AR(1)
process and is sampled by Metropolis-within-Gibbs using the implied
Gaussian Markov random field full conditionals. The latent increments can
be Gaussian, Student-t, a finite scale mixture of normals, or follow a
stochastic volatility process, and the Poisson and binomial families
support zero inflation. It implements and extends the methodology of
Zens and Bijak (2026) <doi:10.1214/26-AOAS2171>.
Author: Gregor Zens [aut, cre]
Maintainer: Gregor Zens <zens@iiasa.ac.at>
Diff between DynCount versions 0.1.0 dated 2026-07-14 and 0.2.0 dated 2026-09-28
DynCount-0.1.0/DynCount/man/forecast.Rd |only DynCount-0.2.0/DynCount/DESCRIPTION | 33 DynCount-0.2.0/DynCount/MD5 | 94 - DynCount-0.2.0/DynCount/NAMESPACE | 3 DynCount-0.2.0/DynCount/NEWS.md |only DynCount-0.2.0/DynCount/R/DynCount-package.R | 94 - DynCount-0.2.0/DynCount/R/data.R | 104 - DynCount-0.2.0/DynCount/R/fit.R | 472 ++++- DynCount-0.2.0/DynCount/R/forecast.R |only DynCount-0.2.0/DynCount/R/innovations.R | 266 +-- DynCount-0.2.0/DynCount/R/plot.R | 253 ++- DynCount-0.2.0/DynCount/R/predict.R | 131 - DynCount-0.2.0/DynCount/R/priors.R | 376 ++-- DynCount-0.2.0/DynCount/R/sampler.R | 656 +++++--- DynCount-0.2.0/DynCount/R/simulate.R | 164 +- DynCount-0.2.0/DynCount/R/summary.R | 199 +- DynCount-0.2.0/DynCount/R/utils.R | 133 + DynCount-0.2.0/DynCount/R/zero-inflation.R | 18 DynCount-0.2.0/DynCount/README.md | 108 - DynCount-0.2.0/DynCount/build/vignette.rds |binary DynCount-0.2.0/DynCount/data/med_weekly.rda |binary DynCount-0.2.0/DynCount/data/uk_weekly.rda |binary DynCount-0.2.0/DynCount/inst/doc/DynCount-intro.R | 90 - DynCount-0.2.0/DynCount/inst/doc/DynCount-intro.Rmd | 400 +++-- DynCount-0.2.0/DynCount/inst/doc/DynCount-intro.html | 800 ++++++---- DynCount-0.2.0/DynCount/man/DynCount-package.Rd | 101 - DynCount-0.2.0/DynCount/man/dynamic_prior.Rd | 66 DynCount-0.2.0/DynCount/man/fit_dynamic_model.Rd | 258 ++- DynCount-0.2.0/DynCount/man/forecast.dynamic_fit.Rd | 76 DynCount-0.2.0/DynCount/man/med_weekly.Rd | 15 DynCount-0.2.0/DynCount/man/plot.dynamic_fit.Rd | 3 DynCount-0.2.0/DynCount/man/plot_fitted.Rd | 15 DynCount-0.2.0/DynCount/man/plot_forecast.Rd | 34 DynCount-0.2.0/DynCount/man/plot_latent.Rd | 18 DynCount-0.2.0/DynCount/man/plot_zero_inflation.Rd | 10 DynCount-0.2.0/DynCount/man/predict.dynamic_fit.Rd | 22 DynCount-0.2.0/DynCount/man/reexports.Rd |only DynCount-0.2.0/DynCount/man/simulate_dynamic_binomial.Rd | 3 DynCount-0.2.0/DynCount/man/simulate_dynamic_multinomial.Rd |only DynCount-0.2.0/DynCount/man/simulate_dynamic_poisson.Rd | 3 DynCount-0.2.0/DynCount/man/structural_zero_prob.Rd | 14 DynCount-0.2.0/DynCount/man/summary.dynamic_fit.Rd | 34 DynCount-0.2.0/DynCount/man/uk_weekly.Rd | 15 DynCount-0.2.0/DynCount/tests/testthat/test-dynamics-horizon.R | 6 DynCount-0.2.0/DynCount/tests/testthat/test-fit-multinomial.R |only DynCount-0.2.0/DynCount/tests/testthat/test-fit-poisson.R | 11 DynCount-0.2.0/DynCount/tests/testthat/test-gmrf-bands.R | 2 DynCount-0.2.0/DynCount/tests/testthat/test-interface.R |only DynCount-0.2.0/DynCount/tests/testthat/test-mu-offset-init.R | 2 DynCount-0.2.0/DynCount/tests/testthat/test-posthoc-forecast.R |only DynCount-0.2.0/DynCount/tests/testthat/test-priors.R | 37 DynCount-0.2.0/DynCount/vignettes/DynCount-intro.Rmd | 400 +++-- 52 files changed, 3690 insertions(+), 1849 deletions(-)
Title: Common String Format Validation
Description: Validates common string formats including financial
identifiers (ISIN, CUSIP, SEDOL, FIGI, IBAN, LEI), publication
identifiers (ISBN, ISSN, DOI, ORCID), and general formats (email,
UUID, URL, semver), with check digit verification where applicable.
Author: Maximilian Muecke [aut, cre]
Maintainer: Maximilian Muecke <muecke.maximilian@gmail.com>
Diff between checkstring versions 0.2.0 dated 2026-06-29 and 0.2.1 dated 2026-09-28
DESCRIPTION | 11 +++----- MD5 | 28 ++++++++++----------- NEWS.md | 12 +++++++++ R/id.R | 41 ++++++++++++------------------- R/string.R | 56 +++++++++++++++++++++++++------------------ README.md | 2 - man/is_base64.Rd | 2 - man/is_base64url.Rd | 6 ++-- man/is_cuid2.Rd | 5 +++ man/is_email.Rd | 4 +-- man/is_figi.Rd | 4 ++- man/is_url.Rd | 4 +-- man/is_uuid.Rd | 4 +-- tests/testthat/test-id.R | 6 ++++ tests/testthat/test-string.R | 23 ++++++++++++++++- 15 files changed, 126 insertions(+), 82 deletions(-)
Title: Scholarly and Academic Identifier Utilities
Description: Detects, normalizes, classifies, and extracts scholarly identifier
strings. Provides lightweight, dependency-free helpers for identifier
types including DOIs, ORCID iDs, ISBNs, ISSNs, arXiv and
PubMed identifiers, ROR and ISNI, OpenAlex and ADS bibcodes, RRID, ARK,
SWHID, and selected life-science accessions (UniProt, RefSeq, SRA, GEO,
BioProject, and genome assemblies). Functions are vectorized, predictable,
and suitable as low-level building blocks for other R packages and data
workflows. Use 'scholid_types()' for the authoritative type list. For
online lookup, conversion, metadata retrieval, and linked identifier
discovery, see 'scholidonline'.
Author: Thomas Rauter [aut, cre, fnd]
Maintainer: Thomas Rauter <rauterthomas0@gmail.com>
Diff between scholid versions 0.2.0 dated 2026-06-04 and 0.2.1 dated 2026-09-28
DESCRIPTION | 10 MD5 | 57 - NEWS.md | 28 R/classify_scholid.R | 7 R/detect_scholid_type.R | 10 R/extract_scholid.R | 287 ++++----- R/input_validation.R | 162 +++++ R/is_idtype_functions.R | 938 ++++++++++++++---------------- R/is_scholid.R | 4 R/normalize_scholid.R | 87 +- R/scholid-package.R | 4 R/scholid_types.R | 7 README.md | 2 inst/WORDLIST | 1 inst/doc/scholid_definitions.Rmd | 19 inst/doc/scholid_definitions.html | 19 man/extract_scholid.Rd | 6 man/is_scholid.Rd | 4 man/normalize_scholid.Rd | 6 man/scholid-package.Rd | 4 man/scholid_types.Rd | 7 tests/testthat/helper-scholid_fixtures.R |only tests/testthat/test-classify_scholid.R | 76 ++ tests/testthat/test-detect_scholid_type.R | 53 + tests/testthat/test-extract_scholid.R | 169 +++++ tests/testthat/test-input_validation.R | 34 + tests/testthat/test-is_scholid.R | 153 ++++ tests/testthat/test-normalize_scholid.R | 153 ++++ tests/testthat/test-scholid_types.R | 10 vignettes/scholid_definitions.Rmd | 19 30 files changed, 1578 insertions(+), 758 deletions(-)
Title: Euclidean and Mutual Reachability Minimum Spanning Trees
Description: Functions to compute Euclidean minimum spanning trees using single-,
sesqui-, and dual-tree Boruvka algorithms. Thanks to K-d trees, they are
fast in spaces of low intrinsic dimensionality. Mutual reachability
distances (used in the definition of the 'HDBSCAN*' algorithm)
are supported too. The package also includes relatively fast fallback
minimum spanning tree and nearest-neighbours algorithms for spaces of
higher dimensionality. The 'Python' version of 'quitefastmst' is available
via 'PyPI'.
Author: Marek Gagolewski [aut, cre, cph]
Maintainer: Marek Gagolewski <marek@gagolewski.com>
Diff between quitefastmst versions 0.9.1 dated 2026-02-11 and 0.9.2 dated 2026-09-28
DESCRIPTION | 10 - MD5 | 24 ++-- NEWS | 16 ++ R/RcppExports.R | 11 -- man/mst_euclid.Rd | 11 -- man/quitefastmst-package.Rd | 5 src/RcppFastmst.cpp | 14 +- src/c_common.h | 5 src/c_disjoint_sets.h | 2 src/c_fastmst.h | 2 src/c_kdtree.h | 3 src/c_kdtree_boruvka.h | 239 ++++++++++++++++++++++++++------------------ src/mst_euclid_kdtree.cpp | 18 --- 13 files changed, 205 insertions(+), 155 deletions(-)
Title: Computations and Approximations for Bessel Functions
Description: Computations for Bessel function for complex, real and partly
'mpfr' (arbitrary precision) numbers; notably interfacing TOMS 644;
approximations for large arguments, experiments, etc.
Author: Martin Maechler [aut, cre]
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between Bessel versions 0.7-0 dated 2026-01-11 and 0.7-1 dated 2026-09-28
DESCRIPTION | 18 MD5 | 33 NAMESPACE | 10 R/incompleteBesselK.R |only R/lsum.R | 23 TODO | 7 build/partial.rdb |only build/vignette.rds |binary inst/NEWS.Rd | 16 inst/doc/other-Bessels.R | 2 inst/doc/other-Bessels.pdf |binary man/Bessel.Rd | 2 man/besselI.nuAsym.Rd | 85 + man/besselIs.Rd | 10 man/incompleteBesselK.Rd |only src/IncompleteBessel.f |only src/init.c | 10 src/zbsubs.c | 2638 ++++++++++++++++++++--------------------- tests/Airy-tsts.R | 126 + tests/incompleteBesselK-tsts.R |only 20 files changed, 1551 insertions(+), 1429 deletions(-)
Title: Bernstein Polynomial Based Semiparametric Survival Analysis
Description: Semiparametric survival analysis based on Bernstein polynomials.
'spsurv' includes proportional hazards, proportional odds and accelerated
failure time frameworks for right-censored data. RV Panaro (2020)
<doi:10.48550/arXiv.2003.10548>.
Author: Renato Panaro [aut, cre, cph] ,
Fabio Demarqui [ths, rev] ,
Vinicius Mayrink [ths]
Maintainer: Renato Panaro <rvpanaro@gmail.com>
This is a re-admission after prior archival of version 1.0.0 dated 2020-03-31
Diff between spsurv versions 1.0.0 dated 2020-03-31 and 1.1.0 dated 2026-09-28
spsurv-1.0.0/spsurv/R/handlers.R |only spsurv-1.0.0/spsurv/R/itsamp.R |only spsurv-1.0.0/spsurv/R/survivor.R |only spsurv-1.0.0/spsurv/R/utils2.R |only spsurv-1.0.0/spsurv/configure |only spsurv-1.0.0/spsurv/configure.win |only spsurv-1.0.0/spsurv/inst/doc/spsurv.R |only spsurv-1.0.0/spsurv/inst/doc/spsurv.Rmd |only spsurv-1.0.0/spsurv/inst/doc/spsurv.html |only spsurv-1.0.0/spsurv/inst/stan/spbp_frailty.stan |only spsurv-1.0.0/spsurv/man/coef-methods.Rd |only spsurv-1.0.0/spsurv/man/coef.Rd |only spsurv-1.0.0/spsurv/man/confint-methods.Rd |only spsurv-1.0.0/spsurv/man/confint.Rd |only spsurv-1.0.0/spsurv/man/extract-methods.Rd |only spsurv-1.0.0/spsurv/man/extract.Rd |only spsurv-1.0.0/spsurv/man/itsamp.Rd |only spsurv-1.0.0/spsurv/man/mode.Rd |only spsurv-1.0.0/spsurv/man/stan_dens-methods.Rd |only spsurv-1.0.0/spsurv/man/stan_dens.Rd |only spsurv-1.0.0/spsurv/man/survivor.Rd |only spsurv-1.0.0/spsurv/man/traceplot-methods.Rd |only spsurv-1.0.0/spsurv/man/traceplot.Rd |only spsurv-1.0.0/spsurv/man/vcov-methods.Rd |only spsurv-1.0.0/spsurv/man/vcov.Rd |only spsurv-1.0.0/spsurv/src/stanExports_spbp_frailty.cc |only spsurv-1.0.0/spsurv/src/stanExports_spbp_frailty.h |only spsurv-1.0.0/spsurv/vignettes/spsurv.Rmd |only spsurv-1.1.0/spsurv/DESCRIPTION | 64 spsurv-1.1.0/spsurv/MD5 | 237 spsurv-1.1.0/spsurv/NAMESPACE | 67 spsurv-1.1.0/spsurv/NEWS.md |only spsurv-1.1.0/spsurv/R/augment.spbp.R |only spsurv-1.1.0/spsurv/R/bernstein.R |only spsurv-1.1.0/spsurv/R/bp.basis.R |only spsurv-1.1.0/spsurv/R/bpfits.R | 154 spsurv-1.1.0/spsurv/R/coef.R |only spsurv-1.1.0/spsurv/R/ggresiduals.R |only spsurv-1.1.0/spsurv/R/glance.spbp.R |only spsurv-1.1.0/spsurv/R/interval.R |only spsurv-1.1.0/spsurv/R/model.matrix.R |only spsurv-1.1.0/spsurv/R/parsnip-spsurv-data.R |only spsurv-1.1.0/spsurv/R/parsnip-spsurv-fit.R |only spsurv-1.1.0/spsurv/R/parsnip-spsurv-pred.R |only spsurv-1.1.0/spsurv/R/print.spbp.R | 240 spsurv-1.1.0/spsurv/R/print.summary.bpaft.bayes.R | 8 spsurv-1.1.0/spsurv/R/print.summary.bpaft.mle.R | 7 spsurv-1.1.0/spsurv/R/print.summary.bpph.bayes.R | 7 spsurv-1.1.0/spsurv/R/print.summary.bpph.mle.R | 7 spsurv-1.1.0/spsurv/R/print.summary.bppo.bayes.R | 7 spsurv-1.1.0/spsurv/R/print.summary.bppo.mle.R | 7 spsurv-1.1.0/spsurv/R/print.summary.spbp.R |only spsurv-1.1.0/spsurv/R/print.summary.spbp.bayes.R | 37 spsurv-1.1.0/spsurv/R/print.summary.spbp.mle.R | 49 spsurv-1.1.0/spsurv/R/pw.basis.R |only spsurv-1.1.0/spsurv/R/spbp-compat-utils.R |only spsurv-1.1.0/spsurv/R/spbp-estimates.R |only spsurv-1.1.0/spsurv/R/spbp-model-comparison.R |only spsurv-1.1.0/spsurv/R/spbp-predict-censored.R |only spsurv-1.1.0/spsurv/R/spbp.R | 884 ++- spsurv-1.1.0/spsurv/R/spsurv-package.R | 34 spsurv-1.1.0/spsurv/R/stanmodels.R | 5 spsurv-1.1.0/spsurv/R/summary.spbp.R | 270 - spsurv-1.1.0/spsurv/R/survfit.R |only spsurv-1.1.0/spsurv/R/tidy.spbp.R |only spsurv-1.1.0/spsurv/R/tidybayes-spbp.R |only spsurv-1.1.0/spsurv/R/utils.R | 686 +- 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spsurv-1.1.0/spsurv/src/stanExports_spbp.cc | 34 spsurv-1.1.0/spsurv/src/stanExports_spbp.h | 2646 +++++----- spsurv-1.1.0/spsurv/tests/testthat.R | 3 spsurv-1.1.0/spsurv/tests/testthat/helper-bayes.R |only spsurv-1.1.0/spsurv/tests/testthat/helper-mle.R |only spsurv-1.1.0/spsurv/tests/testthat/test-aft-cumhaz-gradients-fd.R |only spsurv-1.1.0/spsurv/tests/testthat/test-bp-basis.R |only spsurv-1.1.0/spsurv/tests/testthat/test-bpfits.R |only spsurv-1.1.0/spsurv/tests/testthat/test-cheap-wins.R |only spsurv-1.1.0/spsurv/tests/testthat/test-coef.R |only spsurv-1.1.0/spsurv/tests/testthat/test-coverage-gaps.R |only spsurv-1.1.0/spsurv/tests/testthat/test-coverage.R |only spsurv-1.1.0/spsurv/tests/testthat/test-glance.R |only spsurv-1.1.0/spsurv/tests/testthat/test-handlers.R |only spsurv-1.1.0/spsurv/tests/testthat/test-interval.R |only spsurv-1.1.0/spsurv/tests/testthat/test-model-comparison.R |only spsurv-1.1.0/spsurv/tests/testthat/test-model-matrix.R |only 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spsurv-1.1.0/spsurv/tests/testthat/test-vcov.R |only spsurv-1.1.0/spsurv/tests/testthat/test.R | 152 spsurv-1.1.0/spsurv/vignettes/bayesian-analysis.Rmd |only spsurv-1.1.0/spsurv/vignettes/bayesian-analysis_files |only spsurv-1.1.0/spsurv/vignettes/bp-degree.Rmd |only spsurv-1.1.0/spsurv/vignettes/diagnostics.Rmd |only spsurv-1.1.0/spsurv/vignettes/getting-started.Rmd |only spsurv-1.1.0/spsurv/vignettes/mle-inference.Rmd |only spsurv-1.1.0/spsurv/vignettes/model-families.Rmd |only spsurv-1.1.0/spsurv/vignettes/survival-ggplot.Rmd |only spsurv-1.1.0/spsurv/vignettes/tidymodels.Rmd |only 193 files changed, 4004 insertions(+), 2496 deletions(-)
Title: Spherical Geometry Operators Using the S2 Geometry Library
Description: Provides R bindings for Google's s2 library for geometric calculations on
the sphere. High-performance constructors and exporters provide high compatibility
with existing spatial packages, transformers construct new geometries from existing
geometries, predicates provide a means to select geometries based on spatial
relationships, and accessors extract information about geometries.
Author: Dewey Dunnington [aut] ,
Edzer Pebesma [aut, cre] ,
Ege Rubak [aut],
Jeroen Ooms [ctb] ,
Google, Inc. [cph]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between s2 versions 1.1.12 dated 2026-09-03 and 1.1.13 dated 2026-09-28
DESCRIPTION | 6 ++--- MD5 | 38 ++++++++++++++++---------------- NEWS.md | 16 +++++++++++-- configure | 47 ++++++++++++++++++++++++++++++++++------ src/Makevars.in | 14 ++++++++--- src/s2/mutable_s2shape_index.cc | 4 +-- src/s2/s2cell_iterator.h | 4 +-- src/s2/s2cell_range_iterator.h | 4 +-- src/s2/s2lax_loop_shape.cc | 8 +++--- src/s2/s2lax_polygon_shape.cc | 12 +++++----- src/s2/s2lax_polyline_shape.cc | 4 +-- src/s2/s2loop.cc | 8 +++--- src/s2/s2polygon.cc | 8 +++--- src/s2/s2polyline.cc | 4 +-- src/s2/s2shape_index.h | 2 - src/s2/util/coding/coder.cc | 16 ++++++------- src/s2/util/coding/coder.h | 8 +++--- src/s2/util/gtl/compact_array.h | 9 +++---- src/s2/util/math/vector.h | 15 ++++++------ tools/build_absl.sh | 4 +-- 20 files changed, 140 insertions(+), 91 deletions(-)
More information about ROI.plugin.coinclp at CRAN
Permanent link
Title: Unsupervised Clustering of Multiple Censored Time-to-Event
Endpoints
Description: Provides basic tools and wrapper functions for computing clusters of instances described by multiple time-to-event censored endpoints. From long-format datasets, where one instance is described by one or more dated records, the main function, `make_state_matrices()`, creates state matrices. Based on these matrices, optimised procedures using the Jaccard distance between instances enable the construction of longitudinal typologies. The package is under active development, with additional tools for graphical representation of typologies planned. For methodological details, see our accompanying paper: `Delord M, Douiri A (2025) <doi:10.1186/s12874-025-02476-7>`.
Author: Marc Delord [aut, cre]
Maintainer: Marc Delord <mdelord@gmail.com>
This is a re-admission after prior archival of version 1.2.1 dated 2025-06-13
Diff between MSCA versions 1.2.1 dated 2025-06-13 and 1.4.0 dated 2026-09-28
DESCRIPTION | 6 - MD5 | 22 ++--- NAMESPACE | 2 NEWS.md | 42 +++++++++++ R/fast_clara_jaccard.R | 170 +++++++++++++++++++++++++++++++--------------- R/get_cluster_sequences.R | 2 R/seq_stats.R | 2 README.md | 2 inst/doc/MSCA.Rmd | 8 +- inst/doc/MSCA.html | 126 +++++++++++++++++----------------- man/fast_clara_jaccard.Rd | 39 +++++++--- vignettes/MSCA.Rmd | 8 +- 12 files changed, 280 insertions(+), 149 deletions(-)
Title: Collection of Correlation, Agreement, and Reliability Estimators
Description: Compute correlation, association, agreement, and reliability
measures for small to high-dimensional datasets through a consistent
matrix-oriented interface. Supports classical correlations (Pearson,
Spearman, Kendall, Chatterjee's rank correlation), distance correlation, partial correlation with
regularised estimators, shrinkage correlation for p >= n settings, robust
correlations including biweight mid-correlation, percentage-bend,
Winsorized, and skipped correlation, latent-variable methods for binary
and ordinal data, pairwise and overall intraclass correlation for wide
data, repeated-measures correlation, and agreement/reliability analyses
based on Cohen's kappa, weighted kappa, multi-rater kappa, Gwet's AC1/AC2,
Krippendorff's alpha, Bland-Altman methods, Lin's concordance correlation
coefficient, Poisson GLMM concordance for count data, and
repeated-measures intraclass/concordance correlation, including robust
concordance based on minimum covariance determinant estimates.
Impl [...truncated...]
Author: Thiago de Paula Oliveira [aut, cre]
Maintainer: Thiago de Paula Oliveira <thiago.paula.oliveira@gmail.com>
Diff between matrixCorr versions 0.12.2 dated 2026-05-31 and 0.12.3 dated 2026-09-28
DESCRIPTION | 15 MD5 | 75 - NAMESPACE | 6 NEWS.md |only R/RcppExports.R | 24 R/chatterjee_xi.R | 27 R/concordance_corr.R | 2 R/corr_result_s3.R | 39 R/dcor.R | 667 ++++++++++++---- R/display_utils.R | 4 R/robust_ccc.R |only R/robust_dcor.R | 15 R/view_corr_shiny.R | 2 README.md | 42 - inst/doc/v01-matrixCorr-introduction.Rmd | 2 inst/doc/v01-matrixCorr-introduction.html | 4 inst/doc/v02-wide-correlation-workflows.R | 4 inst/doc/v02-wide-correlation-workflows.Rmd | 12 inst/doc/v02-wide-correlation-workflows.html | 26 inst/doc/v05-agreement-and-icc-wide.R | 19 inst/doc/v05-agreement-and-icc-wide.Rmd | 57 + inst/doc/v05-agreement-and-icc-wide.html | 335 ++++---- man/bcdcor.Rd |only man/ccc.Rd | 2 man/dcor.Rd | 256 +++--- man/matrixCorr-package.Rd | 5 man/robust_ccc.Rd |only man/robust_dcor.Rd | 15 man/view_corr_shiny.Rd | 2 man/xi_corr.Rd | 27 src/RcppExports.cpp | 70 + src/distance_correlation.cpp | 445 +++++++++- tests/testthat/test-na-method-complete.R | 1 tests/testthat/test-robust-ccc.R |only tests/testthat/test_dcor.R | 200 ++++ tests/testthat/test_output_modes_corr_methods.R | 2 tests/testthat/test_refactor_pairwise_summary.R | 6 tests/testthat/test_s3_dispatch_all_corr_combinations.R | 50 - vignettes/v01-matrixCorr-introduction.Rmd | 2 vignettes/v02-wide-correlation-workflows.Rmd | 12 vignettes/v05-agreement-and-icc-wide.Rmd | 57 + 41 files changed, 1893 insertions(+), 636 deletions(-)
Title: PH/MAP Parameter Estimation
Description: Estimation methods for phase-type
distribution (PH) and Markovian arrival process (MAP) from
empirical data (point and grouped data) and density function.
The tool is based on the following researches:
Okamura et al. (2009) <doi:10.1109/TNET.2008.2008750>,
Okamura and Dohi (2009) <doi:10.1109/QEST.2009.28>,
Okamura et al. (2011) <doi:10.1016/j.peva.2011.04.001>,
Okamura et al. (2013) <doi:10.1002/asmb.1919>,
Horvath and Okamura (2013) <doi:10.1007/978-3-642-40725-3_10>,
Okamura and Dohi (2016) <doi:10.15807/jorsj.59.72>.
Author: Hiroyuki Okamura [aut, cre]
Maintainer: Hiroyuki Okamura <okamu@hiroshima-u.ac.jp>
This is a re-admission after prior archival of version 1.0.0 dated 2022-11-22
Diff between mapfit versions 1.0.0 dated 2022-11-22 and 1.0.1 dated 2026-09-28
DESCRIPTION | 11 - MD5 | 46 +++---- NAMESPACE | 1 NEWS.md | 22 +++ R/common.R | 15 ++ R/data_map.R | 18 +- R/data_phase.R | 2 R/mapfit-package.R | 2 R/mapfit.R | 6 R/model_cf1.R | 15 ++ R/model_erhmm.R | 6 R/model_gmmpp.R | 3 R/model_herlang.R | 3 R/model_map.R | 13 -- R/model_ph.R | 3 README.md | 240 ++++++++++++++++--------------------- build/partial.rdb |binary man/figures/README-draw_plot-1.png |binary man/mapfit.group.Rd | 6 src/phase_gen.h | 8 - src/phase_herlang.h | 8 - tests/testthat/test-CF1.R | 33 +++++ tests/testthat/test-mapfit.R | 14 ++ tests/testthat/test-phfit.R | 20 +++ 24 files changed, 304 insertions(+), 191 deletions(-)
Title: Lorenz and Penalized Lorenz Regressions
Description: Inference for the Lorenz and penalized Lorenz regressions. More broadly, the package proposes functions to assess inequality and graphically represent it. The Lorenz Regression procedure is introduced in Heuchenne and Jacquemain (2022) <doi:10.1016/j.csda.2021.107347> and in Jacquemain, A., C. Heuchenne, and E. Pircalabelu (2024) <doi:10.1214/23-EJS2200>. The implementation is described in Jacquemain and Heuchenne (2026) <doi:10.18637/jss.v117.i06>.
Author: Alexandre Jacquemain [aut, cre] ,
Xingjie Shi [ctb]
Maintainer: Alexandre Jacquemain <aljacquemain@gmail.com>
Diff between LorenzRegression versions 2.3.1 dated 2026-02-12 and 2.3.2 dated 2026-09-28
LorenzRegression-2.3.1/LorenzRegression/inst/NEWS.Rd |only LorenzRegression-2.3.2/LorenzRegression/DESCRIPTION | 8 - LorenzRegression-2.3.2/LorenzRegression/MD5 | 47 +++++----- LorenzRegression-2.3.2/LorenzRegression/NEWS.md | 4 LorenzRegression-2.3.2/LorenzRegression/R/FABS-estimation.R | 2 LorenzRegression-2.3.2/LorenzRegression/R/GA-estimation.R | 2 LorenzRegression-2.3.2/LorenzRegression/R/Lorenz-bootstrap-combine.R | 4 LorenzRegression-2.3.2/LorenzRegression/R/Lorenz-bootstrap.R | 6 - LorenzRegression-2.3.2/LorenzRegression/R/Lorenz-regression.R | 4 LorenzRegression-2.3.2/LorenzRegression/R/LorenzRegression-package.R | 9 + LorenzRegression-2.3.2/LorenzRegression/R/PLR-BIC.R | 2 LorenzRegression-2.3.2/LorenzRegression/R/PLR-CV.R | 4 LorenzRegression-2.3.2/LorenzRegression/R/Rearrangement-estimation.R | 2 LorenzRegression-2.3.2/LorenzRegression/R/SCADFABS-estimation.R | 2 LorenzRegression-2.3.2/LorenzRegression/build |only LorenzRegression-2.3.2/LorenzRegression/inst/CITATION |only LorenzRegression-2.3.2/LorenzRegression/man/Lorenz.FABS.Rd | 12 +- LorenzRegression-2.3.2/LorenzRegression/man/Lorenz.GA.Rd | 8 - LorenzRegression-2.3.2/LorenzRegression/man/Lorenz.Reg.Rd | 14 +- LorenzRegression-2.3.2/LorenzRegression/man/Lorenz.SCADFABS.Rd | 8 - LorenzRegression-2.3.2/LorenzRegression/man/Lorenz.boot.Rd | 14 +- LorenzRegression-2.3.2/LorenzRegression/man/Lorenz.boot.combine.Rd | 14 +- LorenzRegression-2.3.2/LorenzRegression/man/LorenzRegression-package.Rd | 11 +- LorenzRegression-2.3.2/LorenzRegression/man/PLR.BIC.Rd | 4 LorenzRegression-2.3.2/LorenzRegression/man/PLR.CV.Rd | 10 +- LorenzRegression-2.3.2/LorenzRegression/man/Rearrangement.estimation.Rd | 8 - 26 files changed, 103 insertions(+), 96 deletions(-)
More information about LorenzRegression at CRAN
Permanent link
Title: Fatigue Crack Growth in Reliability
Description: Fatigue Crack Growth in Reliability estimates the distribution of material
lifetime due to mechanical fatigue efforts. The 'FCGR' package provides
simultaneous crack growth curves fitting to different specimens in materials
under mechanical stress efforts. Linear mixed-effects models with
smoothing B-Splines and the linearized Paris-Erdogan law are applied.
Once defined the fail for a determined crack length, the distribution
function of failure times to fatigue is obtained. The density function is
estimated by applying nonparametric binned kernel density estimate ('bkde')
and the kernel estimator of the distribution function ('kde'). The results
of Pinheiro and Bates method based on nonlinear mixed-effects regression
('nlme') can be also retrieved. The package contains the crack.growth(), PLOT.cg(),
IB.F(), and Alea.A (database) functions.
Author: Antonio Meneses [aut, cre],
Salvador Naya [ctb],
Javier Tarrio-Saavedra [ctb],
Ignacio Lopez-Ullibarri [ctb]
Maintainer: Antonio Meneses <antoniomenesesfreire@hotmail.com>
This is a re-admission after prior archival of version 1.0-0 dated 2015-10-13
Diff between FCGR versions 1.0-0 dated 2015-10-13 and 1.2-0 dated 2026-09-28
FCGR-1.0-0/FCGR/data/Alea.A.txt |only FCGR-1.0-0/FCGR/man/FCGR-package.Rd |only FCGR-1.0-0/FCGR/man/IB.F.rd |only FCGR-1.0-0/FCGR/man/PLOT.cg.rd |only FCGR-1.2-0/FCGR/DESCRIPTION | 56 +-- FCGR-1.2-0/FCGR/MD5 | 22 - FCGR-1.2-0/FCGR/NAMESPACE | 39 +- FCGR-1.2-0/FCGR/R/Alea,A.R |only FCGR-1.2-0/FCGR/R/IB.F.R | 631 ++++++++++++++++------------------- FCGR-1.2-0/FCGR/R/PLOT.cg.R | 178 +++++++-- FCGR-1.2-0/FCGR/R/cracks.growth.R | 548 ++++++++++++++++-------------- FCGR-1.2-0/FCGR/data/Alea.A.rda |only FCGR-1.2-0/FCGR/man/Alea.A.Rd | 64 +-- FCGR-1.2-0/FCGR/man/IB.F.Rd |only FCGR-1.2-0/FCGR/man/PLOT.cg.Rd |only FCGR-1.2-0/FCGR/man/cracks.growth.Rd | 161 ++++---- 16 files changed, 899 insertions(+), 800 deletions(-)
Title: Continuous Time Distance-Based and Network-Based Individual
Level Models for Epidemics
Description: Provides tools for simulating from continuous-time individual level models of disease transmission, and carrying out infectious disease data analyses with the same models. The epidemic models considered are distance-based and/or contact network-based models within Susceptible-Infectious-Removed (SIR) or Susceptible-Infectious-Notified-Removed (SINR) compartmental frameworks. <doi:10.18637/jss.v098.i10>.
Author: Waleed Almutiry [aut, cre],
Rob Deardon [aut, ths],
Vineetha Warriyar K. V. [ctb]
Maintainer: Waleed Almutiry <w.mutiry@etec.gov.sa>
This is a re-admission after prior archival of version 1.1.8 dated 2025-09-23
Diff between EpiILMCT versions 1.1.8 dated 2025-09-23 and 1.1.9 dated 2026-09-28
DESCRIPTION | 12 - MD5 | 4 man/datagen.Rd | 398 ++++++++++++++++++++++++++++----------------------------- 3 files changed, 207 insertions(+), 207 deletions(-)
Title: Generic Implementation of a PK/PD Model
Description: A generic, easy-to-use and expandable implementation of a
pharmacokinetic (PK) / pharmacodynamic (PD) model based on the S4
class system. This package allows the user to read and write
pharmacometric models from and to files, including a JSON-based
interface to import Campsis models defined using a formal JSON schema
distributed with the package. Models can be adapted further on the fly
in the R environment using an intuitive API to add, modify or delete
equations, ordinary differential equations (ODEs), model parameters or
compartment properties (such as infusion duration or rate,
bioavailability and initial values). The package also provides export
facilities for use with the simulation packages 'rxode2' and
'mrgsolve'. The package itself is licensed under the GPL (>= 3); the
JSON schema file shipped in inst/extdata is licensed separately under
the Creative Commons Attribution 4.0 International (CC BY 4.0). This
package is designed and intended to be used with the package
'campsi [...truncated...]
Author: Nicolas Luyckx [aut, cre],
Calvagone [cph]
Maintainer: Nicolas Luyckx <nicolas.luyckx@lynxsoft.be>
Diff between campsismod versions 1.4.1 dated 2026-09-27 and 1.4.2 dated 2026-09-28
DESCRIPTION | 17 ++++++++++------- MD5 | 4 ++-- NEWS.md | 3 +++ 3 files changed, 15 insertions(+), 9 deletions(-)
Title: Tilted and Data-Sharpened Nonparametric Density Estimation
Description: High-order nonparametric density estimators built by perturbing a
conventional kernel estimator, either by re-weighting the observations
("tilting") or by moving them ("data sharpening"). The perturbation is
chosen so that the estimator inherits the fast convergence rate of an
infinite-order kernel estimator, such as the sinc or trapezoidal flat-top
estimator, while remaining a proper non-negative density without the
oscillatory tails those estimators suffer from. Two criteria are provided:
minimising the L2 distance to an infinite-order comparator, following
Doosti and Hall (2016) <doi:10.1111/rssb.12112>, and minimising a
cross-validation criterion that needs no comparator and is much faster,
following Doosti, Hall and Mateu (2018) <doi:10.1016/j.jspi.2017.12.003>.
Author: Hassan Doosti [aut, cre, cph]
Maintainer: Hassan Doosti <hassan.doosti@mq.edu.au>
Diff between tiltdens versions 0.1.1 dated 2026-09-21 and 0.2.0 dated 2026-09-28
DESCRIPTION | 6 - MD5 | 42 +++++++------ NAMESPACE | 3 NEWS.md | 26 ++++++++ R/bandwidth.R | 5 + R/breaks.R | 4 - R/constraints.R | 6 - R/conventional.R |only R/kernel_registry.R | 116 +++++++++++++++++++++++++++++++++++- R/multivariate_fit.R | 2 R/sharpen.R | 131 ++++++++++++++++++++++++++++++++--------- R/solver.R | 40 +++++------- R/tilt.R | 3 R/tilt_cv.R | 8 +- build/partial.rdb |binary build/vignette.rds |binary inst/doc/tiltdens.html | 4 - man/conventional_density.Rd |only man/make_kernel.Rd |only man/sharpen_density.Rd | 63 +++++++++++++------ man/tilt_cv.Rd | 3 man/tilt_density.Rd | 3 man/tilt_density_cv.Rd | 3 tests/testthat/test-revision.R |only 24 files changed, 362 insertions(+), 106 deletions(-)
More information about saebenchmarking at CRAN
Permanent link
Title: Faithful and Scalable MARCXML Parsing
Description: Parses Machine-Readable Cataloging ('MARC 21') XML
<https://www.loc.gov/standards/marcxml/> into a canonical tidy long
representation while preserving leaders, control fields, data fields,
indicators, repeated fields, repeated subfields, and source order.
Provides an in-memory reader for manageable catalogues and a
bounded-memory converter that writes larger collections as 'Parquet'
datasets, with optional local parallel processing.
Author: Lorenzo Isella [aut, cre]
Maintainer: Lorenzo Isella <lorenzo.isella@gmail.com>
Diff between marcxmlr versions 0.2.1 dated 2026-09-19 and 0.3.1 dated 2026-09-28
DESCRIPTION | 16 MD5 | 40 NAMESPACE | 2 NEWS.md | 36 R/arrow-writer.R |only R/canonical-diagnostics.R |only R/marcxml-to-parquet.R | 65 - R/multi-file-parquet.R | 11 R/read-marcxml.R | 33 R/utils.R | 4 R/write-marcxml.R |only README.md | 1404 ++++++++++++---------------- man/diagnose_canonical.Rd |only man/parse_marcxml_record.Rd |only man/read_marcxml.Rd | 51 - man/write_marcxml.Rd |only src/marcxml-native.c | 778 +++++++++++++++ tests/testthat/fixtures |only tests/testthat/helper-writer-fixtures.R |only tests/testthat/test-canonical-diagnostics.R |only tests/testthat/test-gzip-xml.R |only tests/testthat/test-native-writer.R |only tests/testthat/test-parquet-multifile.R | 2 tests/testthat/test-parquet.R | 2 tests/testthat/test-read-marcxml.R | 2 tests/testthat/test-write-marcxml-arrow.R |only tests/testthat/test-write-marcxml.R |only tools/benchmark-writer.R |only 28 files changed, 1543 insertions(+), 903 deletions(-)
Title: Annotation of Mass Spectra
Description: Provides a comprehensive suite of functions to efficiently annotate mass spectra data.
Motivated by the need for rapid and accurate chemical identification in high-resolution mass
spectrometry, it integrates built-in chemical databases and high-performance C++ algorithms.
Users can perform mass-to-charge (m/Z) and retention time searches, determine elemental
compositions of molecules using heuristic rules, including specific isotopes, and annotate MS2
spectra with structural metrics using configurable chemistry rules.
Author: Sylvain Dechaumet [aut, cre],
Etienne Thevenot [ctb],
Eric Venot [rev],
Annelaure Damont [ctb],
Anais Legrand [ctb]
Maintainer: Sylvain Dechaumet <sylvain.dechaumet@cea.fr>
Diff between Spec2Annot versions 1.3.4 dated 2026-09-26 and 1.3.5 dated 2026-09-28
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/search_space.R | 29 ++++++++++++++--------------- tests/testthat/test-brute_force_const.R | 10 +++++----- 4 files changed, 25 insertions(+), 26 deletions(-)
Title: Encapsulated 'REDCap' Projects for Synchronized Data Pipelines
Description: Wraps dozens of 'REDCap' API endpoints into a standardized R6
object. Research Electronic Data Capture ('REDCap') is a survey and
database web application software maintained by Vanderbilt University.
It has a robust application programming interface (API) utilized by
several R packages. 'REDCapSync' uses 'redcapAPI' and 'REDCapR'
behind-the-scenes to retrieve all metadata, data, and log details for
a project. To minimize unnecessary server calls, the interim 'REDCap'
log is analyzed and used to only update necessary records.
Furthermore, the user can define custom datasets that save to a
directory. Those datasets continue to refresh when projects are
synced. Having a secure, standardized, API-efficient,
project-agnostic R object for 'REDCap' projects, streamlines
downstream use in scripts, functions, and shiny applications.
Author: Brandon Rose [cre, aut, cph] ,
Natalie Goulett [ctb]
Maintainer: Brandon Rose <thecodingdocs@gmail.com>
Diff between REDCapSync versions 0.2.0 dated 2026-09-27 and 0.2.1 dated 2026-09-28
DESCRIPTION | 15 ++--- MD5 | 23 ++++---- NAMESPACE | 2 NEWS.md | 13 ++-- R/REDCapSync-package.R | 2 R/datasets.R | 55 ++++++++++++-------- inst/doc/Datasets.R | 3 - inst/doc/Datasets.Rmd | 3 - inst/doc/Datasets.html | 75 ++++++++++++++-------------- inst/doc/Projects.html | 4 - tests/testthat/test-datasets.R | 108 +++++++++++++++++++++++++++++++++++++++++ tests/testthat/test-fields.R |only vignettes/Datasets.Rmd | 3 - 13 files changed, 218 insertions(+), 88 deletions(-)
Title: Print Directory Trees for R Projects and Folders
Description: Quickly visualize 'R' project directory structures with automatic
project detection and clean tree output.
Author: George Arthur [aut, cre, cph]
Maintainer: George Arthur <prigasgenthian48@gmail.com>
Diff between printtree versions 0.2.1 dated 2026-05-16 and 0.2.2 dated 2026-09-28
DESCRIPTION | 6 MD5 | 24 - NEWS.md | 43 +- R/print_rtree.R | 752 +++++++++++++++++++++----------------- R/utils-snapshot.R | 6 inst/WORDLIST | 3 inst/doc/feature-tour.R | 22 - inst/doc/feature-tour.Rmd | 236 ++++++----- inst/doc/feature-tour.html | 25 - man/print_rtree.Rd | 4 man/write_tree.Rd | 93 ++-- tests/testthat/test-print_rtree.R | 378 +++++++++++++------ vignettes/feature-tour.Rmd | 236 ++++++----- 13 files changed, 1061 insertions(+), 767 deletions(-)
Title: Hierarchical Linear Modeling with Visualization and
Decomposition
Description: Provides functions for visualization and decomposition in
hierarchical linear models (HLM) for applications in education, psychology,
and the social sciences. Includes variance decomposition for two-level and
three-level data structures following Snijders and Bosker (2012,
ISBN:9781849202015), intraclass correlation (ICC) estimation and design
effect computation as described in Shrout and Fleiss (1979)
<doi:10.1037/0033-2909.86.2.420>, and contextual effect decomposition via
the Mundlak (1978) <doi:10.2307/1913646> specification distinguishing
within- and between-cluster components, with the uncertainty of the
contextual contrast obtained from the full fixed-effect covariance matrix.
Teaching displays cover simulated intraclass correlations, partial pooling
of cluster means, random-slope heterogeneity, and cross-level interaction
with an observed Level-2 moderator, following Hofmann and Gavin (1998)
<doi:10.1177/014920639802400504> and Hamaker and Muthen (2020)
<do [...truncated...]
Author: Subir Hait [aut, cre]
Maintainer: Subir Hait <haitsubi@msu.edu>
Diff between hlmLab versions 0.1.0 dated 2026-04-16 and 0.2.0 dated 2026-09-28
hlmLab-0.1.0/hlmLab/R/hlm_xint_geom.R |only hlmLab-0.2.0/hlmLab/DESCRIPTION | 22 - hlmLab-0.2.0/hlmLab/MD5 | 60 ++- hlmLab-0.2.0/hlmLab/NAMESPACE | 4 hlmLab-0.2.0/hlmLab/NEWS.md |only hlmLab-0.2.0/hlmLab/R/globals.R | 15 hlmLab-0.2.0/hlmLab/R/hlm_context.R | 221 +++++++++-- hlmLab-0.2.0/hlmLab/R/hlm_cross_level_plot.R |only hlmLab-0.2.0/hlmLab/R/hlm_decompose.R | 8 hlmLab-0.2.0/hlmLab/R/hlm_decompose_long.R | 10 hlmLab-0.2.0/hlmLab/R/hlm_icc.R | 128 +++++- hlmLab-0.2.0/hlmLab/R/hlm_icc_demo.R |only hlmLab-0.2.0/hlmLab/R/hlm_icc_plot.R | 61 ++- hlmLab-0.2.0/hlmLab/R/hlm_random_slope_plot.R |only hlmLab-0.2.0/hlmLab/R/hlm_shrinkage_plot.R |only hlmLab-0.2.0/hlmLab/README.md | 439 ++++++++++++----------- hlmLab-0.2.0/hlmLab/build |only hlmLab-0.2.0/hlmLab/inst/WORDLIST | 52 +- hlmLab-0.2.0/hlmLab/inst/app/app.R | 4 hlmLab-0.2.0/hlmLab/man/hlm_context.Rd | 57 ++ hlmLab-0.2.0/hlmLab/man/hlm_context_plot.Rd | 13 hlmLab-0.2.0/hlmLab/man/hlm_cross_level_plot.Rd |only hlmLab-0.2.0/hlmLab/man/hlm_decompose.Rd | 6 hlmLab-0.2.0/hlmLab/man/hlm_decompose_long.Rd | 10 hlmLab-0.2.0/hlmLab/man/hlm_icc.Rd | 36 + hlmLab-0.2.0/hlmLab/man/hlm_icc_demo.Rd |only hlmLab-0.2.0/hlmLab/man/hlm_icc_plot.Rd | 22 - hlmLab-0.2.0/hlmLab/man/hlm_random_slope_plot.Rd |only hlmLab-0.2.0/hlmLab/man/hlm_shrinkage_plot.Rd |only hlmLab-0.2.0/hlmLab/man/hlm_xint_geom.Rd | 44 +- hlmLab-0.2.0/hlmLab/man/plot.hlm_context.Rd | 4 hlmLab-0.2.0/hlmLab/tests/spelling.R | 6 hlmLab-0.2.0/hlmLab/tests/testthat |only hlmLab-0.2.0/hlmLab/tests/testthat.R |only 34 files changed, 816 insertions(+), 406 deletions(-)